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Studies (GWAS)"]}" data-trace="false" data-dom-id="Pill-react-component-493d1045-9976-4181-a897-0559da760e43"></div> <div id="Pill-react-component-493d1045-9976-4181-a897-0559da760e43"></div> </a><a data-click-track="profile-user-info-expand-research-interests" data-has-card-for-ri-list="211385129" href="https://www.academia.edu/Documents/in/Human_evolutionary_genetics"><div class="js-react-on-rails-component" style="display:none" data-component-name="Pill" data-props="{"color":"gray","children":["Human evolutionary genetics"]}" data-trace="false" data-dom-id="Pill-react-component-7963cca4-f8ba-4177-98b7-e02fc3b4375b"></div> <div id="Pill-react-component-7963cca4-f8ba-4177-98b7-e02fc3b4375b"></div> </a><a data-click-track="profile-user-info-expand-research-interests" data-has-card-for-ri-list="211385129" href="https://www.academia.edu/Documents/in/Human_Genetics"><div class="js-react-on-rails-component" style="display:none" data-component-name="Pill" data-props="{"color":"gray","children":["Human Genetics"]}" data-trace="false" data-dom-id="Pill-react-component-55efe6f0-c341-48b9-8544-8dbd2d576d38"></div> <div id="Pill-react-component-55efe6f0-c341-48b9-8544-8dbd2d576d38"></div> </a><a data-click-track="profile-user-info-expand-research-interests" data-has-card-for-ri-list="211385129" href="https://www.academia.edu/Documents/in/Infectious_Diseases"><div class="js-react-on-rails-component" style="display:none" data-component-name="Pill" data-props="{"color":"gray","children":["Infectious Diseases"]}" data-trace="false" data-dom-id="Pill-react-component-2397af41-e8f7-4c6f-b050-33148f85869e"></div> <div id="Pill-react-component-2397af41-e8f7-4c6f-b050-33148f85869e"></div> </a></div></div></div></div><div class="right-panel-container"><div class="user-content-wrapper"><div class="uploads-container" id="social-redesign-work-container"><div class="upload-header"><h2 class="ds2-5-heading-sans-serif-xs">Uploads</h2></div><div class="documents-container backbone-social-profile-documents" style="width: 100%;"><div class="u-taCenter"></div><div class="profile--tab_content_container js-tab-pane tab-pane active" id="all"><div class="profile--tab_heading_container js-section-heading" data-section="Papers" id="Papers"><h3 class="profile--tab_heading_container">Papers by Zabrina Brumme</h3></div><div class="js-work-strip profile--work_container" data-work-id="105427229"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/105427229/Measured_creatine_phosphokinase_in_perfusate_from_reperfused_murine_hearts"><img alt="Research paper thumbnail of Measured creatine phosphokinase in perfusate from reperfused murine hearts" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/105427229/Measured_creatine_phosphokinase_in_perfusate_from_reperfused_murine_hearts">Measured creatine phosphokinase in perfusate from reperfused murine hearts</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">&lt;b&gt;Copyright information:&lt;/b&gt;Taken from &quot;Insulin-like growth factor-1 protects i...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">&lt;b&gt;Copyright information:&lt;/b&gt;Taken from &quot;Insulin-like growth factor-1 protects ischemic murine myocardium from ischemia/reperfusion associated injury&quot;Critical Care 2003;7(6):R176-R183.Published online 10 Oct 2003PMCID:PMC374373.Copyright © 2003 Davani et al., licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article&#39;s original URL. Hearts were prepared for Langendorf reperfusion and perfused until the monitored heart rate and pressure were stable (approximately 3–5 min); then they were subjected to 20 min of ischemia followed by reperfusion. Perfusate solution was collected (approximately 1 ml/4 min) around each time point for determination of CPK activity. For all time points, tumour necrosis factor (TNF)-α reperfusion generated a significant elevation in the detectable amount of CPK activity relative to that detected with insulin-like growth factor (IGF)-1 reperfusion (&amp;lt; 0.005, by analysis of variance).</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427229"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427229"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427229; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); 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</script> <div class="js-work-strip profile--work_container" data-work-id="105427227"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/105427227/Myocardium_from_Ischemia_Reperfusion"><img alt="Research paper thumbnail of Myocardium from Ischemia/Reperfusion" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/105427227/Myocardium_from_Ischemia_Reperfusion">Myocardium from Ischemia/Reperfusion</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Insulin-like growth factor-1 protects ischemic murine</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427227"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427227"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427227; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=105427227]").text(description); $(".js-view-count[data-work-id=105427227]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 105427227; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='105427227']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=105427227]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":105427227,"title":"Myocardium from Ischemia/Reperfusion","internal_url":"https://www.academia.edu/105427227/Myocardium_from_Ischemia_Reperfusion","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="105427226"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/105427226/CTN_328_immunogenicity_outcomes_in_people_living_with_HIV_in_Canada_following_vaccination_for_COVID_19_HIV_COV_protocol_for_an_observational_cohort_study"><img alt="Research paper thumbnail of CTN 328: immunogenicity outcomes in people living with HIV in Canada following vaccination for COVID-19 (HIV-COV): protocol for an observational cohort study" class="work-thumbnail" src="https://attachments.academia-assets.com/104885348/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/105427226/CTN_328_immunogenicity_outcomes_in_people_living_with_HIV_in_Canada_following_vaccination_for_COVID_19_HIV_COV_protocol_for_an_observational_cohort_study">CTN 328: immunogenicity outcomes in people living with HIV in Canada following vaccination for COVID-19 (HIV-COV): protocol for an observational cohort study</a></div><div class="wp-workCard_item"><span>BMJ Open</span><span>, 2021</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">IntroductionMost existing vaccines require higher or additional doses or adjuvants to provide sim...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">IntroductionMost existing vaccines require higher or additional doses or adjuvants to provide similar protection for people living with HIV (PLWH) compared with HIV-uninfected individuals. Additional research is necessary to inform COVID-19 vaccine use in PLWH.Methods and analysisThis multicentred observational Canadian cohort study will enrol 400 PLWH aged&gt;16 years from Montreal, Ottawa, Toronto and Vancouver. Subpopulations of PLWH of interest will include individuals: (1) &gt;55 years of age; (2) with CD4 counts &lt;350 cells/mm3; (3) with multimorbidity (&gt;2 comorbidities) and (4) ‘stable’ or ‘reference’ PLWH (CD4 T cells &gt;350 cells/mm3, suppressed viral load for&gt;6 months and&lt;1 comorbidity). Data for 1000 HIV-negative controls will be obtained via a parallel cohort study (Stop the Spread Ottawa), using similar time points and methods. Participants receiving&gt;1 COVID-19 vaccine will attend five visits: prevaccination; 1 month following the first vaccine dose; and ...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="554474690a266723d5d4c5561dc8f174" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":104885348,"asset_id":105427226,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/104885348/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427226"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427226"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427226; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="105427225"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/105427225/OR21_HLA_C_downregulation_by_HIV_adapts_to_host_HLA_genotype"><img alt="Research paper thumbnail of OR21 HLA-C downregulation by HIV adapts to host HLA genotype" class="work-thumbnail" src="https://attachments.academia-assets.com/104885347/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/105427225/OR21_HLA_C_downregulation_by_HIV_adapts_to_host_HLA_genotype">OR21 HLA-C downregulation by HIV adapts to host HLA genotype</a></div><div class="wp-workCard_item"><span>Human Immunology</span><span>, 2018</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="eca024b228575e9e615c3e25bb0ac461" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":104885347,"asset_id":105427225,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/104885347/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427225"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427225"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427225; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=105427225]").text(description); $(".js-view-count[data-work-id=105427225]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 105427225; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='105427225']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "eca024b228575e9e615c3e25bb0ac461" } } $('.js-work-strip[data-work-id=105427225]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":105427225,"title":"OR21 HLA-C downregulation by HIV adapts to host HLA genotype","internal_url":"https://www.academia.edu/105427225/OR21_HLA_C_downregulation_by_HIV_adapts_to_host_HLA_genotype","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[{"id":104885347,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/104885347/thumbnails/1.jpg","file_name":"j.humimm.2018.07.02620230809-1-vlihrr.pdf","download_url":"https://www.academia.edu/attachments/104885347/download_file","bulk_download_file_name":"OR21_HLA_C_downregulation_by_HIV_adapts.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/104885347/j.humimm.2018.07.02620230809-1-vlihrr-libre.pdf?1691609763=\u0026response-content-disposition=attachment%3B+filename%3DOR21_HLA_C_downregulation_by_HIV_adapts.pdf\u0026Expires=1741107188\u0026Signature=awTGcNKrdUyam6p93VkFTphn4ogyj5RJqOSe5POItaQcGx-ci0AnE~--zaGheF-A-BuwBVKpGfyAL-Pb1~~ZvWe2snOJM0RCBuccMhFq-gad4R62c2gybiDJSexgFzCfIFmqCbveLYeJqNp4QPLWRC9I57iQxDM4cE7syX8Bn9KNWrhoGnQ-ZFTag3nmSNPoIKMr~BEAJy49ru~w2zaR1T8oJDK8PrFipMWhI-AIsqY-fAO7qy39E9jnr2A-QyVK8TEUYanerokrR6sx8kkZvZJlUgbd94WWRtvJo-onRvOQCL95m1MGCqSdGab4nWPnlZ92AFHZWxYZaKqwbhzt5A__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="105427224"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/105427224/TCR_clonotypes_modulate_the_protective_effect_of_HLA_class_I_molecules_in_HIV_1_infection"><img alt="Research paper thumbnail of TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection" class="work-thumbnail" src="https://attachments.academia-assets.com/105038468/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/105427224/TCR_clonotypes_modulate_the_protective_effect_of_HLA_class_I_molecules_in_HIV_1_infection">TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection</a></div><div class="wp-workCard_item"><span>Nature Immunology</span><span>, 2012</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Human leukocyte antigen (HLA) B*27 and B*57 are associated with protection against HIV-1 disease ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Human leukocyte antigen (HLA) B*27 and B*57 are associated with protection against HIV-1 disease progression, yet most persons expressing these alleles are unable to control HIV-1. Here we show that HLA-B*27-restricted CD8 + T cells in controllers and progressors differ in their ability to inhibit virus replication through targeting of the immunodominant Gag epitope. This is associated with distinct TCR clonotypes, characterized by superior control of HIV-1 replication in vitro, greater cross-reactivity against epitope variants, and enhanced perforin delivery. Clonotypespecific differences in antiviral efficacy were also observed for an immunodominant HLA-B*57 restricted response in controllers and progressors. Thus, the efficacy of protective alleles is modulated by specific TCR clonotypes selected in natural infection, providing a functional explanation for divergent HIV-1 outcomes. A subset of HIV-1-infected persons, here termed elite controllers, are distinguished by their ability to maintain a state of apparent durable control of HIV-1 replication without the need for antiviral therapy 1,2. Viral control is linked to expression of certain human leukocyte antigen (HLA) class I alleles 3-5 , particularly B*57, B*27, and B*5801, suggesting an immunologic basis related to CD8 + T cell function. Indeed, a recent genome-wide</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="8d2944372f4342ac4282e9ded73380fa" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":105038468,"asset_id":105427224,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/105038468/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427224"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427224"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427224; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=105427224]").text(description); $(".js-view-count[data-work-id=105427224]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 105427224; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='105427224']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "8d2944372f4342ac4282e9ded73380fa" } } $('.js-work-strip[data-work-id=105427224]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":105427224,"title":"TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection","internal_url":"https://www.academia.edu/105427224/TCR_clonotypes_modulate_the_protective_effect_of_HLA_class_I_molecules_in_HIV_1_infection","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[{"id":105038468,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/105038468/thumbnails/1.jpg","file_name":"ptpmcrender.pdf","download_url":"https://www.academia.edu/attachments/105038468/download_file","bulk_download_file_name":"TCR_clonotypes_modulate_the_protective_e.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/105038468/ptpmcrender-libre.pdf?1692169006=\u0026response-content-disposition=attachment%3B+filename%3DTCR_clonotypes_modulate_the_protective_e.pdf\u0026Expires=1741107188\u0026Signature=LlfZwsrIo~5Pnnrq6jsmpvYSvpBrXh0yGeUejZJ4rGtbJx-Gzu443lSMK4gyj0S9BC5zxqaqBjyGgkl~9SbHlzRntP4DF2VMY1sG3cu1ObrgUh1EyPpLYEyV-va15LZQa~vwVHCUMIU4MmHYbD-wk0sEp3Vg1pK6VvMktmWkyRzz-WsUJLd1H6sX4kJxTjIHjxPWwDjfbWyZRkC9ojy66R-2p7gZEggjUY-iDn74yUy3LUOdLq6r-AIJTUquUDsx76~xClMbyvEtyss1eILDm2N04Ho99NZKhIPv21W-HdRGCnYaD6N2cEqf8lXO16QBXek3bqoDWjBL0g~NXMT8Jw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="105427223"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/105427223/Predictors_of_HIV_Drug_Resistance_Mutations_in_a_Large_Antiretroviral_Naive_Cohort_Initiating_Triple_Antiretroviral_Therapy"><img alt="Research paper thumbnail of Predictors of HIV Drug‐Resistance Mutations in a Large Antiretroviral‐Naive Cohort Initiating Triple Antiretroviral Therapy" class="work-thumbnail" src="https://attachments.academia-assets.com/104885329/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/105427223/Predictors_of_HIV_Drug_Resistance_Mutations_in_a_Large_Antiretroviral_Naive_Cohort_Initiating_Triple_Antiretroviral_Therapy">Predictors of HIV Drug‐Resistance Mutations in a Large Antiretroviral‐Naive Cohort Initiating Triple Antiretroviral Therapy</a></div><div class="wp-workCard_item"><span>The Journal of Infectious Diseases</span><span>, 2005</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Objective. The objective of this study was to systematically characterize the incidence and deter...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Objective. The objective of this study was to systematically characterize the incidence and determinants of antiretroviral resistance in the HOMER (Highly Active Antiretroviral Therapy [HAART] Observational Medical Evaluation and Research) cohort of 1191 human immunodeficiency virus-infected, antiretroviral-naive adults initiating HAART in British Columbia, Canada. Methods. All plasma samples with plasma virus loads (pVLs) 11000 copies/mL collected during the first 30 months of follow-up were genotyped for drug resistance. The primary outcome measure was time to the first detection of major drug-resistance mutation(s). Cox proportional hazard regression was used to identify factors significantly associated with the detection of drug-resistance mutations. Results. Drug-resistance mutations were detected in 298 subjects (25%). Factors significantly associated with detection of drug-resistance mutations included high baseline pVL (multivariate hazard ratio [HR], 1.59; P !) and adherence (estimated using prescription-refill data and/or untimed plasma drug-concentration mea-.001 surements). When compared with subjects with low (0%-!20%) prescription-refill percentages, subjects at an elevated risk of harboring drug-resistance mutations were those with relatively high but imperfect prescriptionrefill percentages (80%-!90%; multivariate HR, 4.15;) and those with essentially perfect (у95%) refill P ! .001 percentages but with 2 plasma drug concentrations below the steady-state trough concentration minus 1 standard deviation (multivariate HR, 4.57;). Initial use of nonnucleoside reverse-transcriptase inhibitor-based P ! .001 HAART was significantly associated with multiclass drug resistance (multivariate HR, 1.84;). P p .001 Conclusion. High baseline pVLs and substantial but imperfect levels of adherence were major predictors of antiretroviral resistance.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="0c5b2cad5f330af19347c24e04cfe275" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":104885329,"asset_id":105427223,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/104885329/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427223"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427223"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427223; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=105427223]").text(description); $(".js-view-count[data-work-id=105427223]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 105427223; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='105427223']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="105427186"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/105427186/Insulin_like_growth_factor_1_in_myocardial_tissue_interaction_with_tumor_necrosis_factor"><img alt="Research paper thumbnail of Insulin-like growth factor-1 in myocardial tissue: interaction with tumor necrosis factor" class="work-thumbnail" src="https://attachments.academia-assets.com/104885332/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/105427186/Insulin_like_growth_factor_1_in_myocardial_tissue_interaction_with_tumor_necrosis_factor">Insulin-like growth factor-1 in myocardial tissue: interaction with tumor necrosis factor</a></div><div class="wp-workCard_item"><span>Critical care (London, England)</span><span>, 2003</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Insulin-like growth factor (IGF)-1 is a well characterized growth factor that plays a role in the...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Insulin-like growth factor (IGF)-1 is a well characterized growth factor that plays a role in the regulation of myocardial structure and function. Using an ex vivo murine model, Davani and coworkers, in this issue of Critical Care, demonstrate that IGF-1 confers cardiac protection against ischemia via mitochondria-dependent mechanisms. Those investigators used the ratio of mitochondrial to nuclear DNA to demonstrate that IGF-1, which prevents reduction in this ratio during reperfusion, provides cytoprotection. This commentary also reviews mechanisms of IGF-1 function and provides a graphic representation of IGF-1 signaling mechanisms in potential crosstalk relations with mediators of inflammation in the heart (specifically tumor necrosis factor-alpha).</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="2d67e8acd6ea2e3e6e751576e6a4d9c4" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":104885332,"asset_id":105427186,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/104885332/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427186"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427186"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427186; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=105427186]").text(description); $(".js-view-count[data-work-id=105427186]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 105427186; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='105427186']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862464"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862464/Molecular_Epidemiology_of_HIV_1_in_Ghana_Subtype_Distribution_Drug_Resistance_and_Coreceptor_Usage"><img alt="Research paper thumbnail of Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage" class="work-thumbnail" src="https://attachments.academia-assets.com/101563686/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862464/Molecular_Epidemiology_of_HIV_1_in_Ghana_Subtype_Distribution_Drug_Resistance_and_Coreceptor_Usage">Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage</a></div><div class="wp-workCard_item"><span>Viruses</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origin...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.9%) subtype in the region, with the complex recombinant 06_cpx (4%) present as well. Unique recombinants, most of which were mosaics containing CRF02_AG and/or 06_cpx, made up 37% of sequences, while “pure” subtypes were rare (&lt;6%). Pretreatment resistance to at least one drug class was observed in 17% of the cohort, with NNRTI resistance being the most common (12%) and INSTI resistance being relatively rare (2%). CXCR4-using HIV-1 sequences were identified in 23% of participants. Overall, our findings advance...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="92d2f5029681a26923d48d5e3fc7c7c1" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563686,"asset_id":100862464,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563686/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862464"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862464"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862464; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862463"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862463/Antibody_response_durability_following_three_dose_COVID_19_vaccination_in_people_with_HIV_receiving_suppressive_ART"><img alt="Research paper thumbnail of Antibody response durability following three-dose COVID-19 vaccination in people with HIV receiving suppressive ART" class="work-thumbnail" src="https://attachments.academia-assets.com/101563723/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862463/Antibody_response_durability_following_three_dose_COVID_19_vaccination_in_people_with_HIV_receiving_suppressive_ART">Antibody response durability following three-dose COVID-19 vaccination in people with HIV receiving suppressive ART</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACTBackgroundLimited data exist regarding longer-term antibody responses following three-dos...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACTBackgroundLimited data exist regarding longer-term antibody responses following three-dose COVID-19 vaccination, and the impact of a first SARS-CoV-2 infection during this time, in people living with HIV (PLWH) receiving suppressive antiretroviral therapy (ART). We quantified wild-type-(WT), Omicron BA.1- and Omicron BA.5-specific responses up to six months post-third dose in 64 PLWH and 117 controls who remained COVID-19-naive or experienced their first SARS-CoV-2 infection during this time.DesignLongitudinal observational cohort.MethodsWe quantified WT- and Omicron-specific Anti-Spike receptor-binding domain IgG concentrations, ACE2 displacement activities and live virus neutralization at one, three and six months post-third vaccine dose.ResultsThird doses boosted all antibody measures above two-dose levels, but BA.1-specific responses remained significantly lower than WT-specific ones, with BA.5-specific responses lower still. Serum IgG concentrations declined at similar ...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="c42d72dec88304eebd2fb80a8bde9661" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563723,"asset_id":100862463,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563723/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862463"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862463"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862463; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862462"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/100862462/Reconstructed_ancestral_sequences_at_the_root_of_the_inferred_Gag_and_Nef_phylogenies_representing_the_estimated_most_recent_common_ancestor_MRCA_of_the_North_American_epidemic"><img alt="Research paper thumbnail of Reconstructed ancestral sequences at the root of the inferred Gag and Nef phylogenies, representing the estimated most recent common ancestor (MRCA) of the North American epidemic" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/100862462/Reconstructed_ancestral_sequences_at_the_root_of_the_inferred_Gag_and_Nef_phylogenies_representing_the_estimated_most_recent_common_ancestor_MRCA_of_the_North_American_epidemic">Reconstructed ancestral sequences at the root of the inferred Gag and Nef phylogenies, representing the estimated most recent common ancestor (MRCA) of the North American epidemic</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">&lt;p&gt;A minimum of ≥50,000 reconstructions of the ancestral sequence at the root of the Gag an...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">&lt;p&gt;A minimum of ≥50,000 reconstructions of the ancestral sequence at the root of the Gag and Nef phylogenies were performed, and the inferred MRCA was computed as the “grand consensus” of these replicate reconstructions. For each codon, reconstruction confidence (computed as the frequency of each amino acid observed across all reconstructions) is indicated on the y-axis on a scale from 0 (0%) to 1 (100%). Blue letters represent the highest-confidence residue at each position; green letters represent lower-confidence residues. All amino acids observed at &gt;0.01 (&gt;1%) reconstruction frequency are shown. Yellow boxes highlight positions where the highest-confidence (blue) inferred ancestral residue differs from the North American consensus B sequence (displayed in &lt;b&gt;&lt;a href=&quot;<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004295#pgen.1004295.s003&quot" rel="nofollow">http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004295#pgen.1004295.s003&quot</a>; target=&quot;_blank&quot;&gt;Figure S3&lt;/a&gt;&lt;/b&gt;).&lt;/p</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862462"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862462"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862462; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862461"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862461/HIV_proviral_genetic_diversity_compartmentalization_and_inferred_dynamics_in_lung_and_blood_during_long_term_suppressive_antiretroviral_therapy"><img alt="Research paper thumbnail of HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy" class="work-thumbnail" src="https://attachments.academia-assets.com/101563724/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862461/HIV_proviral_genetic_diversity_compartmentalization_and_inferred_dynamics_in_lung_and_blood_during_long_term_suppressive_antiretroviral_therapy">HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">The lung is an understudied site of HIV persistence. We isolated 882 subgenomic proviral sequence...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">The lung is an understudied site of HIV persistence. We isolated 882 subgenomic proviral sequences by single-genome approaches from blood and lung from nine individuals on long-term suppressive antiretroviral therapy (ART), and characterized genetic diversity and compartmentalization using formal tests. Consistent with clonal expansion as a driver of HIV persistence, identical sequences comprised between 9% to 86% of within-host datasets, though their location (blood vs. lung) followed no consistent pattern. The majority (77%) of participants harbored at least one sequence shared across blood and lung, supporting the migration of clonally-expanded cells between sites. No participant exhibited genetic compartmentalization so obvious that it was visually apparent in a phylogeny. When formal tests were applied however, two (22%) participants showed modest yet significant support for compartmentalization when analysis was restricted to distinct proviruses per site. This increased to fou...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="9dab12c1f006745e1c2288252ebd3352" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563724,"asset_id":100862461,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563724/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862461"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862461"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862461; 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dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "9dab12c1f006745e1c2288252ebd3352" } } $('.js-work-strip[data-work-id=100862461]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":100862461,"title":"HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy","internal_url":"https://www.academia.edu/100862461/HIV_proviral_genetic_diversity_compartmentalization_and_inferred_dynamics_in_lung_and_blood_during_long_term_suppressive_antiretroviral_therapy","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[{"id":101563724,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/101563724/thumbnails/1.jpg","file_name":"2022.05.26.493568.full.pdf","download_url":"https://www.academia.edu/attachments/101563724/download_file","bulk_download_file_name":"HIV_proviral_genetic_diversity_compartme.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/101563724/2022.05.26.493568.full-libre.pdf?1682607840=\u0026response-content-disposition=attachment%3B+filename%3DHIV_proviral_genetic_diversity_compartme.pdf\u0026Expires=1741107188\u0026Signature=SSi9F2wAROKiYFsENyh~10c8ixzcfrLQfN7UoYN-rwD8N9azUf5z58hknDY~FS5KyPNixe14RtBgL5HTWCzyGJWxs1RSts6IVQwTwsph1S2qD~v01jMk9UBgzwWot5g5OZGSFoygksDrvpULR8grdG9h12dc18JbTTGEM5LUPw6fKv60uhid0iD55VCKwly21xfTpsXQf2l2Mg48cSZlxtY32PTuBz43kVLs834FmlhZV7pjrncONwjds2yhDhMNHHOiJTwtMzSXRpRz~PVYYUVzRGFQKs~MtjjhTe8R6viMahmGVmaZAjvCodjR7vmkbWX042yrpnxlpwUMIPbBRQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862460"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/100862460/Gag_residues_exhibiting_significant_diversification_over_time_are_biased_towards_known_HLA_associated_sites"><img alt="Research paper thumbnail of Gag residues exhibiting significant diversification over time are biased towards known HLA-associated sites" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/100862460/Gag_residues_exhibiting_significant_diversification_over_time_are_biased_towards_known_HLA_associated_sites">Gag residues exhibiting significant diversification over time are biased towards known HLA-associated sites</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">&lt;p&gt;&lt;b&gt;Panel A:&lt;/b&gt; Differences in Shannon entropy (Δentropy) between modern and...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">&lt;p&gt;&lt;b&gt;Panel A:&lt;/b&gt; Differences in Shannon entropy (Δentropy) between modern and historic sequences are shown for every Gag codon. Positive y-values indicate higher entropy in modern vs. historic sequences at that codon; negative y-values indicate the opposite. Red bars indicate significant entropy differences (defined as p&lt;0.001, q&lt;0.01); blue colors indicate differences that do not reach this significance threshold. Grey dots designate known HIV sites under selection by HLA (as defined in &lt;a href=&quot;<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004295#pgen.1004295-Carlson1&quot" rel="nofollow">http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004295#pgen.1004295-Carlson1&quot</a>; target=&quot;_blank&quot;&gt;[43]&lt;/a&gt;). Green dots designate sites that display significant evidence of pervasive positive selection (dN/dS&gt;1; posterior probability &gt;0.9). &lt;b&gt;Panel B:&lt;/b&gt; Same as panel A, but sorted by decreasing Δentropy rather than codon order. &lt;b&gt;Panel C:&lt;/b&gt; Graphical depiction of a 2×2 contingency table stratifying variable (&lt;99% conserved) Gag codons based on their status as HLA-associated (yes vs. no), and whether they exhibited significant Δentropy between modern and historic datasets (p&lt;0.001 [red] vs. not [blue]). Ns are indicated above each bar. &lt;b&gt;Panel D:&lt;/b&gt; Graphical depiction of a 2×2 contingency table stratifying variable (&lt;99% conserved) Gag codons based on their status as HLA-associated (yes vs. no) and evidence that they are under significant pervasive positive selection (dN/dS&gt;1; posterior probability &gt;0.9 [green] vs. not [black]). Ns are indicated above each bar.&lt;/p</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862460"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862460"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862460; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=100862460]").text(description); $(".js-view-count[data-work-id=100862460]").attr('title', description).tooltip(); 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</script> <div class="js-work-strip profile--work_container" data-work-id="100862459"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862459/People_with_HIV_receiving_suppressive_antiretroviral_therapy_show_typical_antibody_durability_after_dual_COVID_19_vaccination_and_strong_third_dose_responses"><img alt="Research paper thumbnail of People with HIV receiving suppressive antiretroviral therapy show typical antibody durability after dual COVID-19 vaccination, and strong third dose responses" class="work-thumbnail" src="https://attachments.academia-assets.com/101563722/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862459/People_with_HIV_receiving_suppressive_antiretroviral_therapy_show_typical_antibody_durability_after_dual_COVID_19_vaccination_and_strong_third_dose_responses">People with HIV receiving suppressive antiretroviral therapy show typical antibody durability after dual COVID-19 vaccination, and strong third dose responses</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACTBackgroundLonger-term humoral responses to two-dose COVID-19 vaccines remain incompletely...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACTBackgroundLonger-term humoral responses to two-dose COVID-19 vaccines remain incompletely characterized in people living with HIV (PLWH), as do initial responses to a third dose.MethodsWe measured antibodies against the SARS-CoV-2 spike protein receptor-binding domain, ACE2 displacement and viral neutralization against wild-type and Omicron strains up to six months following two-dose vaccination, and one month following the third dose, in 99 PLWH receiving suppressive antiretroviral therapy, and 152 controls.ResultsThough humoral responses naturally decline following two-dose vaccination, we found no evidence of lower antibody concentrations nor faster rates of antibody decline in PLWH compared to controls after accounting for sociodemographic, health and vaccine-related factors. We also found no evidence of poorer viral neutralization in PLWH after two doses, nor evidence that a low nadir CD4+ T-cell count compromised responses. Post-third-dose humoral responses substantial...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="8b0847cc3dd03b28ccb82e0ee84fd73e" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563722,"asset_id":100862459,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563722/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862459"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862459"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862459; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862458"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862458/Author_Correction_HIV_1_diversity_considerations_in_the_application_of_the_Intact_Proviral_DNA_Assay_IPDA_"><img alt="Research paper thumbnail of Author Correction: HIV-1 diversity considerations in the application of the Intact Proviral DNA Assay (IPDA)" class="work-thumbnail" src="https://attachments.academia-assets.com/101563683/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862458/Author_Correction_HIV_1_diversity_considerations_in_the_application_of_the_Intact_Proviral_DNA_Assay_IPDA_">Author Correction: HIV-1 diversity considerations in the application of the Intact Proviral DNA Assay (IPDA)</a></div><div class="wp-workCard_item"><span>Nature Communications</span><span>, 2021</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">The original version of this Article contained an error for the 'RPP30-Shear Forward Primer seque...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">The original version of this Article contained an error for the 'RPP30-Shear Forward Primer sequence' provided in the 'Intact Proviral DNA Assay (IPDA)' section of the Methods, which incorrectly read 'CCAATTTGCTGCTCCTTGGG'. The correct sequence of the 'RPP30-Shear Forward Primer' is 'CCATTTGCTGCTCCTTGGG'. This has been corrected in both the PDF and HTML versions of the Article.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="b25e415000064d56988c42d749e68687" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563683,"asset_id":100862458,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563683/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862458"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862458"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862458; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862457"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862457/Influence_of_HLA_C_Expression_Level_on_HIV_Control"><img alt="Research paper thumbnail of Influence of HLA-C Expression Level on HIV Control" class="work-thumbnail" src="https://attachments.academia-assets.com/101563719/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862457/Influence_of_HLA_C_Expression_Level_on_HIV_Control">Influence of HLA-C Expression Level on HIV Control</a></div><div class="wp-workCard_item"><span>Science</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Thwarting HIV Multiple genome-wide association studies have revealed that human leukocyte antigen...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Thwarting HIV Multiple genome-wide association studies have revealed that human leukocyte antigen (HLA) genes of the major histocompatibility complex locus have the strongest impact on HIV. In particular, a single-nucleotide polymorphism 35 base pairs upstream of HLA-C shows significant association with viral load and protection against HIV. How HLA-C mediates these effects is unknown. Apps et al. (p. 87 ) now demonstrate that increasing surface expression of HLA-C is associated with reduced viral load and reduced rate of progression to low CD4 + T cell counts in African and European Americans. High HLA-C expression likely promoted improved HIV control through a more effective cytotoxic CD8 + T cell response. In contrast to HIV infection, high HLA-C expression was associated with a higher risk of the inflammatory bowel disease, Crohn&#39;s disease.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="ddac903103316708e0a084b3585562ca" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563719,"asset_id":100862457,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563719/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862457"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862457"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862457; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862456"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862456/A_method_for_Killer_cell_Immunoglobulin_like_Receptor_KIR_3DL1_3DS1_genotyping_using_DNA_recovered_from_frozen_plasma"><img alt="Research paper thumbnail of A method for Killer-cell Immunoglobulin-like Receptor (KIR) 3DL1/3DS1 genotyping using DNA recovered from frozen plasma" class="work-thumbnail" src="https://attachments.academia-assets.com/101563726/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862456/A_method_for_Killer_cell_Immunoglobulin_like_Receptor_KIR_3DL1_3DS1_genotyping_using_DNA_recovered_from_frozen_plasma">A method for Killer-cell Immunoglobulin-like Receptor (KIR) 3DL1/3DS1 genotyping using DNA recovered from frozen plasma</a></div><div class="wp-workCard_item"><span>Journal of Immunological Methods</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">We describe a reliable and semi-automated method for Killer-cell Immunoglobulin-like Receptor (KI...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">We describe a reliable and semi-automated method for Killer-cell Immunoglobulin-like Receptor (KIR) 3DL1/S1 genotyping using DNA recovered from frozen plasma. The primers and protocol were first validated using two independent genomic DNA reference panels. To confirm the approach using plasma-derived DNA, total nucleic acids were extracted from 69 paired frozen PBMC and plasma specimens representing all common KIR3DL1/S1 genotypes (3DS1/3DS1, 3DS1/3DL1 and 3DL1/3DL1, including rare allele 3DL1*054), and analyzed in a blinded fashion. The method involves independent nested PCR amplification of KIR3DL1/S1 Exon 4, and if required Exon 3, using universal sequence-specific primers, followed by bidirectional sequencing. The free basecalling software RECall is recommended for rapid, semi-automated chromatogram analysis. KIR3DL1/S1 type assignment is based on two key nucleotide polymorphisms in Exon 4 and, if required, up to two additional polymorphisms in exon 3. Assignment can be performed manually or using our web-based algorithm, KIR3D. Extractions from plasma yielded median [IQR] nucleic acid concentrations of 0.9 [below the limit of detection-2.45] ng/μl. PCR was successful for 100% of exon 4 (69/69) and exon 3 (29/29) plasma amplifications. Chromatogram quality was high and concordance between PBMC and plasma-derived types was 100%. The estimated lower limit of input DNA required for reliable typing is 0.01 ng/μl. This method provides reliable and accurate KIR3DL1/S1 typing when conventional sources of high-quality genomic DNA are unavailable or limiting.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="03b18cf46a6bb85c0bb1499c169f13df" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563726,"asset_id":100862456,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563726/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862456"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862456"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862456; 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dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "03b18cf46a6bb85c0bb1499c169f13df" } } $('.js-work-strip[data-work-id=100862456]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":100862456,"title":"A method for Killer-cell Immunoglobulin-like Receptor (KIR) 3DL1/3DS1 genotyping using DNA recovered from frozen plasma","internal_url":"https://www.academia.edu/100862456/A_method_for_Killer_cell_Immunoglobulin_like_Receptor_KIR_3DL1_3DS1_genotyping_using_DNA_recovered_from_frozen_plasma","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[{"id":101563726,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/101563726/thumbnails/1.jpg","file_name":"pmc4944815.pdf","download_url":"https://www.academia.edu/attachments/101563726/download_file","bulk_download_file_name":"A_method_for_Killer_cell_Immunoglobulin.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/101563726/pmc4944815-libre.pdf?1682607692=\u0026response-content-disposition=attachment%3B+filename%3DA_method_for_Killer_cell_Immunoglobulin.pdf\u0026Expires=1741107188\u0026Signature=SCVxy7RwBFSMzTZtBqwe5K95zrhUrRV6gGEdCLvm4Uc93A7UGgoqThgDtzAuuSy4twqc~CMPfA0JWu8fDZdSfDw-9IkYsI-9Bq0I9SKRn21aBDH6nuf0bQg2p593tPeFcsP3I28b00WxwQO3m63YlzPkvWGRMUiHOq0iY7dWajv-zlDwhQN4YXP0iBZxn6wH0La7ui8-Ksq3aZOYmJNsrtLbmDxGbd5nFO7gvTgfxmcQuUxtz32tjIKd5NYIW6Xu5XkeoR2U0zMvpTr3tyZ89ay~l8haiTGiisPsqDdLBAdMIYs1UIwwjfgsnKpgLH0laPs-fK1Kr0laH006z4Usxg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100861762"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/100861762/SARS_CoV_2_live_virus_neutralization_after_four_COVID_19_vaccine_doses_in_people_with_HIV_receiving_suppressive_antiretroviral_therapy"><img alt="Research paper thumbnail of SARS-CoV-2 live virus neutralization after four COVID-19 vaccine doses in people with HIV receiving suppressive antiretroviral therapy" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/100861762/SARS_CoV_2_live_virus_neutralization_after_four_COVID_19_vaccine_doses_in_people_with_HIV_receiving_suppressive_antiretroviral_therapy">SARS-CoV-2 live virus neutralization after four COVID-19 vaccine doses in people with HIV receiving suppressive antiretroviral therapy</a></div><div class="wp-workCard_item"><span>AIDS</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100861762"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100861762"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100861762; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=100861762]").text(description); $(".js-view-count[data-work-id=100861762]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 100861762; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='100861762']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=100861762]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":100861762,"title":"SARS-CoV-2 live virus neutralization after four COVID-19 vaccine doses in people with HIV receiving suppressive antiretroviral therapy","internal_url":"https://www.academia.edu/100861762/SARS_CoV_2_live_virus_neutralization_after_four_COVID_19_vaccine_doses_in_people_with_HIV_receiving_suppressive_antiretroviral_therapy","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="86670683"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/86670683/Serial_infection_with_SARS_CoV_2_Omicron_BA_1_and_BA_2_following_three_dose_COVID_19_vaccination"><img alt="Research paper thumbnail of Serial infection with SARS-CoV-2 Omicron BA.1 and BA.2 following three-dose COVID-19 vaccination" class="work-thumbnail" src="https://attachments.academia-assets.com/91069400/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/86670683/Serial_infection_with_SARS_CoV_2_Omicron_BA_1_and_BA_2_following_three_dose_COVID_19_vaccination">Serial infection with SARS-CoV-2 Omicron BA.1 and BA.2 following three-dose COVID-19 vaccination</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACTSARS-CoV-2 Omicron infections are common among individuals who are vaccinated or have rec...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACTSARS-CoV-2 Omicron infections are common among individuals who are vaccinated or have recovered from prior variant infection, but few reports have documented serial Omicron infections. We characterized SARS-CoV-2 humoral responses in a healthy young person who acquired laboratory-confirmed Omicron BA.1.15 ten weeks after a third dose of BNT162b2, and BA.2 thirteen weeks later. Responses were compared to those of 124 COVID-19 naive vaccinees. One month after the second and third vaccine doses, the participant’s wild-type and BA.1-specific IgG, ACE2 competition and virus neutralization activities were average for a COVID-19 naive triple-vaccinated individual. BA.1 infection boosted the participant’s responses to the cohort ≥95th percentile, but even this strong “hybrid” immunity failed to protect against BA.2. Moreover, reinfection increased BA.1 and BA.2-specific responses only modestly. Results illustrate the risk of Omicron infection in fully vaccinated individuals and high...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="d9d0927505a1a893883715a87f04cf7c" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":91069400,"asset_id":86670683,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/91069400/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="86670683"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="86670683"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 86670683; 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</script> </div><div class="profile--tab_content_container js-tab-pane tab-pane" data-section-id="13516083" id="papers"><div class="js-work-strip profile--work_container" data-work-id="105427229"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/105427229/Measured_creatine_phosphokinase_in_perfusate_from_reperfused_murine_hearts"><img alt="Research paper thumbnail of Measured creatine phosphokinase in perfusate from reperfused murine hearts" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/105427229/Measured_creatine_phosphokinase_in_perfusate_from_reperfused_murine_hearts">Measured creatine phosphokinase in perfusate from reperfused murine hearts</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">&lt;b&gt;Copyright information:&lt;/b&gt;Taken from &quot;Insulin-like growth factor-1 protects i...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">&lt;b&gt;Copyright information:&lt;/b&gt;Taken from &quot;Insulin-like growth factor-1 protects ischemic murine myocardium from ischemia/reperfusion associated injury&quot;Critical Care 2003;7(6):R176-R183.Published online 10 Oct 2003PMCID:PMC374373.Copyright © 2003 Davani et al., licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article&#39;s original URL. Hearts were prepared for Langendorf reperfusion and perfused until the monitored heart rate and pressure were stable (approximately 3–5 min); then they were subjected to 20 min of ischemia followed by reperfusion. Perfusate solution was collected (approximately 1 ml/4 min) around each time point for determination of CPK activity. For all time points, tumour necrosis factor (TNF)-α reperfusion generated a significant elevation in the detectable amount of CPK activity relative to that detected with insulin-like growth factor (IGF)-1 reperfusion (&amp;lt; 0.005, by analysis of variance).</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427229"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427229"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427229; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=105427229]").text(description); $(".js-view-count[data-work-id=105427229]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 105427229; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='105427229']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=105427229]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":105427229,"title":"Measured creatine phosphokinase in perfusate from reperfused murine hearts","internal_url":"https://www.academia.edu/105427229/Measured_creatine_phosphokinase_in_perfusate_from_reperfused_murine_hearts","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="105427228"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/105427228/MOESM2_of_Longitudinal_within_host_evolution_of_HIV_Nef_mediated_CD4_HLA_and_SERINC5_downregulation_activity_a_case_study"><img alt="Research paper thumbnail of MOESM2 of Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/105427228/MOESM2_of_Longitudinal_within_host_evolution_of_HIV_Nef_mediated_CD4_HLA_and_SERINC5_downregulation_activity_a_case_study">MOESM2 of Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Additional file 2: Codon-by-codon analysisÂ of Nef sequence with function.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427228"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427228"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427228; 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</script> <div class="js-work-strip profile--work_container" data-work-id="105427227"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/105427227/Myocardium_from_Ischemia_Reperfusion"><img alt="Research paper thumbnail of Myocardium from Ischemia/Reperfusion" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/105427227/Myocardium_from_Ischemia_Reperfusion">Myocardium from Ischemia/Reperfusion</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Insulin-like growth factor-1 protects ischemic murine</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427227"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427227"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427227; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=105427227]").text(description); $(".js-view-count[data-work-id=105427227]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 105427227; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='105427227']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=105427227]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":105427227,"title":"Myocardium from Ischemia/Reperfusion","internal_url":"https://www.academia.edu/105427227/Myocardium_from_Ischemia_Reperfusion","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="105427226"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/105427226/CTN_328_immunogenicity_outcomes_in_people_living_with_HIV_in_Canada_following_vaccination_for_COVID_19_HIV_COV_protocol_for_an_observational_cohort_study"><img alt="Research paper thumbnail of CTN 328: immunogenicity outcomes in people living with HIV in Canada following vaccination for COVID-19 (HIV-COV): protocol for an observational cohort study" class="work-thumbnail" src="https://attachments.academia-assets.com/104885348/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/105427226/CTN_328_immunogenicity_outcomes_in_people_living_with_HIV_in_Canada_following_vaccination_for_COVID_19_HIV_COV_protocol_for_an_observational_cohort_study">CTN 328: immunogenicity outcomes in people living with HIV in Canada following vaccination for COVID-19 (HIV-COV): protocol for an observational cohort study</a></div><div class="wp-workCard_item"><span>BMJ Open</span><span>, 2021</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">IntroductionMost existing vaccines require higher or additional doses or adjuvants to provide sim...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">IntroductionMost existing vaccines require higher or additional doses or adjuvants to provide similar protection for people living with HIV (PLWH) compared with HIV-uninfected individuals. Additional research is necessary to inform COVID-19 vaccine use in PLWH.Methods and analysisThis multicentred observational Canadian cohort study will enrol 400 PLWH aged&gt;16 years from Montreal, Ottawa, Toronto and Vancouver. Subpopulations of PLWH of interest will include individuals: (1) &gt;55 years of age; (2) with CD4 counts &lt;350 cells/mm3; (3) with multimorbidity (&gt;2 comorbidities) and (4) ‘stable’ or ‘reference’ PLWH (CD4 T cells &gt;350 cells/mm3, suppressed viral load for&gt;6 months and&lt;1 comorbidity). Data for 1000 HIV-negative controls will be obtained via a parallel cohort study (Stop the Spread Ottawa), using similar time points and methods. Participants receiving&gt;1 COVID-19 vaccine will attend five visits: prevaccination; 1 month following the first vaccine dose; and ...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="554474690a266723d5d4c5561dc8f174" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":104885348,"asset_id":105427226,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/104885348/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427226"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427226"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427226; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="105427225"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/105427225/OR21_HLA_C_downregulation_by_HIV_adapts_to_host_HLA_genotype"><img alt="Research paper thumbnail of OR21 HLA-C downregulation by HIV adapts to host HLA genotype" class="work-thumbnail" src="https://attachments.academia-assets.com/104885347/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/105427225/OR21_HLA_C_downregulation_by_HIV_adapts_to_host_HLA_genotype">OR21 HLA-C downregulation by HIV adapts to host HLA genotype</a></div><div class="wp-workCard_item"><span>Human Immunology</span><span>, 2018</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="eca024b228575e9e615c3e25bb0ac461" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":104885347,"asset_id":105427225,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/104885347/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427225"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427225"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427225; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=105427225]").text(description); $(".js-view-count[data-work-id=105427225]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 105427225; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='105427225']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "eca024b228575e9e615c3e25bb0ac461" } } $('.js-work-strip[data-work-id=105427225]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":105427225,"title":"OR21 HLA-C downregulation by HIV adapts to host HLA genotype","internal_url":"https://www.academia.edu/105427225/OR21_HLA_C_downregulation_by_HIV_adapts_to_host_HLA_genotype","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[{"id":104885347,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/104885347/thumbnails/1.jpg","file_name":"j.humimm.2018.07.02620230809-1-vlihrr.pdf","download_url":"https://www.academia.edu/attachments/104885347/download_file","bulk_download_file_name":"OR21_HLA_C_downregulation_by_HIV_adapts.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/104885347/j.humimm.2018.07.02620230809-1-vlihrr-libre.pdf?1691609763=\u0026response-content-disposition=attachment%3B+filename%3DOR21_HLA_C_downregulation_by_HIV_adapts.pdf\u0026Expires=1741107188\u0026Signature=awTGcNKrdUyam6p93VkFTphn4ogyj5RJqOSe5POItaQcGx-ci0AnE~--zaGheF-A-BuwBVKpGfyAL-Pb1~~ZvWe2snOJM0RCBuccMhFq-gad4R62c2gybiDJSexgFzCfIFmqCbveLYeJqNp4QPLWRC9I57iQxDM4cE7syX8Bn9KNWrhoGnQ-ZFTag3nmSNPoIKMr~BEAJy49ru~w2zaR1T8oJDK8PrFipMWhI-AIsqY-fAO7qy39E9jnr2A-QyVK8TEUYanerokrR6sx8kkZvZJlUgbd94WWRtvJo-onRvOQCL95m1MGCqSdGab4nWPnlZ92AFHZWxYZaKqwbhzt5A__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="105427224"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/105427224/TCR_clonotypes_modulate_the_protective_effect_of_HLA_class_I_molecules_in_HIV_1_infection"><img alt="Research paper thumbnail of TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection" class="work-thumbnail" src="https://attachments.academia-assets.com/105038468/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/105427224/TCR_clonotypes_modulate_the_protective_effect_of_HLA_class_I_molecules_in_HIV_1_infection">TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection</a></div><div class="wp-workCard_item"><span>Nature Immunology</span><span>, 2012</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Human leukocyte antigen (HLA) B*27 and B*57 are associated with protection against HIV-1 disease ...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Human leukocyte antigen (HLA) B*27 and B*57 are associated with protection against HIV-1 disease progression, yet most persons expressing these alleles are unable to control HIV-1. Here we show that HLA-B*27-restricted CD8 + T cells in controllers and progressors differ in their ability to inhibit virus replication through targeting of the immunodominant Gag epitope. This is associated with distinct TCR clonotypes, characterized by superior control of HIV-1 replication in vitro, greater cross-reactivity against epitope variants, and enhanced perforin delivery. Clonotypespecific differences in antiviral efficacy were also observed for an immunodominant HLA-B*57 restricted response in controllers and progressors. Thus, the efficacy of protective alleles is modulated by specific TCR clonotypes selected in natural infection, providing a functional explanation for divergent HIV-1 outcomes. A subset of HIV-1-infected persons, here termed elite controllers, are distinguished by their ability to maintain a state of apparent durable control of HIV-1 replication without the need for antiviral therapy 1,2. Viral control is linked to expression of certain human leukocyte antigen (HLA) class I alleles 3-5 , particularly B*57, B*27, and B*5801, suggesting an immunologic basis related to CD8 + T cell function. Indeed, a recent genome-wide</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="8d2944372f4342ac4282e9ded73380fa" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":105038468,"asset_id":105427224,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/105038468/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427224"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427224"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427224; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=105427224]").text(description); $(".js-view-count[data-work-id=105427224]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 105427224; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='105427224']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "8d2944372f4342ac4282e9ded73380fa" } } $('.js-work-strip[data-work-id=105427224]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":105427224,"title":"TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection","internal_url":"https://www.academia.edu/105427224/TCR_clonotypes_modulate_the_protective_effect_of_HLA_class_I_molecules_in_HIV_1_infection","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[{"id":105038468,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/105038468/thumbnails/1.jpg","file_name":"ptpmcrender.pdf","download_url":"https://www.academia.edu/attachments/105038468/download_file","bulk_download_file_name":"TCR_clonotypes_modulate_the_protective_e.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/105038468/ptpmcrender-libre.pdf?1692169006=\u0026response-content-disposition=attachment%3B+filename%3DTCR_clonotypes_modulate_the_protective_e.pdf\u0026Expires=1741107188\u0026Signature=LlfZwsrIo~5Pnnrq6jsmpvYSvpBrXh0yGeUejZJ4rGtbJx-Gzu443lSMK4gyj0S9BC5zxqaqBjyGgkl~9SbHlzRntP4DF2VMY1sG3cu1ObrgUh1EyPpLYEyV-va15LZQa~vwVHCUMIU4MmHYbD-wk0sEp3Vg1pK6VvMktmWkyRzz-WsUJLd1H6sX4kJxTjIHjxPWwDjfbWyZRkC9ojy66R-2p7gZEggjUY-iDn74yUy3LUOdLq6r-AIJTUquUDsx76~xClMbyvEtyss1eILDm2N04Ho99NZKhIPv21W-HdRGCnYaD6N2cEqf8lXO16QBXek3bqoDWjBL0g~NXMT8Jw__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="105427223"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/105427223/Predictors_of_HIV_Drug_Resistance_Mutations_in_a_Large_Antiretroviral_Naive_Cohort_Initiating_Triple_Antiretroviral_Therapy"><img alt="Research paper thumbnail of Predictors of HIV Drug‐Resistance Mutations in a Large Antiretroviral‐Naive Cohort Initiating Triple Antiretroviral Therapy" class="work-thumbnail" src="https://attachments.academia-assets.com/104885329/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/105427223/Predictors_of_HIV_Drug_Resistance_Mutations_in_a_Large_Antiretroviral_Naive_Cohort_Initiating_Triple_Antiretroviral_Therapy">Predictors of HIV Drug‐Resistance Mutations in a Large Antiretroviral‐Naive Cohort Initiating Triple Antiretroviral Therapy</a></div><div class="wp-workCard_item"><span>The Journal of Infectious Diseases</span><span>, 2005</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Objective. The objective of this study was to systematically characterize the incidence and deter...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Objective. The objective of this study was to systematically characterize the incidence and determinants of antiretroviral resistance in the HOMER (Highly Active Antiretroviral Therapy [HAART] Observational Medical Evaluation and Research) cohort of 1191 human immunodeficiency virus-infected, antiretroviral-naive adults initiating HAART in British Columbia, Canada. Methods. All plasma samples with plasma virus loads (pVLs) 11000 copies/mL collected during the first 30 months of follow-up were genotyped for drug resistance. The primary outcome measure was time to the first detection of major drug-resistance mutation(s). Cox proportional hazard regression was used to identify factors significantly associated with the detection of drug-resistance mutations. Results. Drug-resistance mutations were detected in 298 subjects (25%). Factors significantly associated with detection of drug-resistance mutations included high baseline pVL (multivariate hazard ratio [HR], 1.59; P !) and adherence (estimated using prescription-refill data and/or untimed plasma drug-concentration mea-.001 surements). When compared with subjects with low (0%-!20%) prescription-refill percentages, subjects at an elevated risk of harboring drug-resistance mutations were those with relatively high but imperfect prescriptionrefill percentages (80%-!90%; multivariate HR, 4.15;) and those with essentially perfect (у95%) refill P ! .001 percentages but with 2 plasma drug concentrations below the steady-state trough concentration minus 1 standard deviation (multivariate HR, 4.57;). Initial use of nonnucleoside reverse-transcriptase inhibitor-based P ! .001 HAART was significantly associated with multiclass drug resistance (multivariate HR, 1.84;). P p .001 Conclusion. High baseline pVLs and substantial but imperfect levels of adherence were major predictors of antiretroviral resistance.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="0c5b2cad5f330af19347c24e04cfe275" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":104885329,"asset_id":105427223,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/104885329/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427223"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427223"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427223; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="105427186"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/105427186/Insulin_like_growth_factor_1_in_myocardial_tissue_interaction_with_tumor_necrosis_factor"><img alt="Research paper thumbnail of Insulin-like growth factor-1 in myocardial tissue: interaction with tumor necrosis factor" class="work-thumbnail" src="https://attachments.academia-assets.com/104885332/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/105427186/Insulin_like_growth_factor_1_in_myocardial_tissue_interaction_with_tumor_necrosis_factor">Insulin-like growth factor-1 in myocardial tissue: interaction with tumor necrosis factor</a></div><div class="wp-workCard_item"><span>Critical care (London, England)</span><span>, 2003</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Insulin-like growth factor (IGF)-1 is a well characterized growth factor that plays a role in the...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Insulin-like growth factor (IGF)-1 is a well characterized growth factor that plays a role in the regulation of myocardial structure and function. Using an ex vivo murine model, Davani and coworkers, in this issue of Critical Care, demonstrate that IGF-1 confers cardiac protection against ischemia via mitochondria-dependent mechanisms. Those investigators used the ratio of mitochondrial to nuclear DNA to demonstrate that IGF-1, which prevents reduction in this ratio during reperfusion, provides cytoprotection. This commentary also reviews mechanisms of IGF-1 function and provides a graphic representation of IGF-1 signaling mechanisms in potential crosstalk relations with mediators of inflammation in the heart (specifically tumor necrosis factor-alpha).</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="2d67e8acd6ea2e3e6e751576e6a4d9c4" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":104885332,"asset_id":105427186,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/104885332/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="105427186"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="105427186"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 105427186; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862464"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862464/Molecular_Epidemiology_of_HIV_1_in_Ghana_Subtype_Distribution_Drug_Resistance_and_Coreceptor_Usage"><img alt="Research paper thumbnail of Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage" class="work-thumbnail" src="https://attachments.academia-assets.com/101563686/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862464/Molecular_Epidemiology_of_HIV_1_in_Ghana_Subtype_Distribution_Drug_Resistance_and_Coreceptor_Usage">Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage</a></div><div class="wp-workCard_item"><span>Viruses</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origin...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.9%) subtype in the region, with the complex recombinant 06_cpx (4%) present as well. Unique recombinants, most of which were mosaics containing CRF02_AG and/or 06_cpx, made up 37% of sequences, while “pure” subtypes were rare (&lt;6%). Pretreatment resistance to at least one drug class was observed in 17% of the cohort, with NNRTI resistance being the most common (12%) and INSTI resistance being relatively rare (2%). CXCR4-using HIV-1 sequences were identified in 23% of participants. Overall, our findings advance...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="92d2f5029681a26923d48d5e3fc7c7c1" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563686,"asset_id":100862464,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563686/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862464"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862464"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862464; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862463"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862463/Antibody_response_durability_following_three_dose_COVID_19_vaccination_in_people_with_HIV_receiving_suppressive_ART"><img alt="Research paper thumbnail of Antibody response durability following three-dose COVID-19 vaccination in people with HIV receiving suppressive ART" class="work-thumbnail" src="https://attachments.academia-assets.com/101563723/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862463/Antibody_response_durability_following_three_dose_COVID_19_vaccination_in_people_with_HIV_receiving_suppressive_ART">Antibody response durability following three-dose COVID-19 vaccination in people with HIV receiving suppressive ART</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACTBackgroundLimited data exist regarding longer-term antibody responses following three-dos...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACTBackgroundLimited data exist regarding longer-term antibody responses following three-dose COVID-19 vaccination, and the impact of a first SARS-CoV-2 infection during this time, in people living with HIV (PLWH) receiving suppressive antiretroviral therapy (ART). We quantified wild-type-(WT), Omicron BA.1- and Omicron BA.5-specific responses up to six months post-third dose in 64 PLWH and 117 controls who remained COVID-19-naive or experienced their first SARS-CoV-2 infection during this time.DesignLongitudinal observational cohort.MethodsWe quantified WT- and Omicron-specific Anti-Spike receptor-binding domain IgG concentrations, ACE2 displacement activities and live virus neutralization at one, three and six months post-third vaccine dose.ResultsThird doses boosted all antibody measures above two-dose levels, but BA.1-specific responses remained significantly lower than WT-specific ones, with BA.5-specific responses lower still. Serum IgG concentrations declined at similar ...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="c42d72dec88304eebd2fb80a8bde9661" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563723,"asset_id":100862463,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563723/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862463"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862463"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862463; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862462"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/100862462/Reconstructed_ancestral_sequences_at_the_root_of_the_inferred_Gag_and_Nef_phylogenies_representing_the_estimated_most_recent_common_ancestor_MRCA_of_the_North_American_epidemic"><img alt="Research paper thumbnail of Reconstructed ancestral sequences at the root of the inferred Gag and Nef phylogenies, representing the estimated most recent common ancestor (MRCA) of the North American epidemic" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/100862462/Reconstructed_ancestral_sequences_at_the_root_of_the_inferred_Gag_and_Nef_phylogenies_representing_the_estimated_most_recent_common_ancestor_MRCA_of_the_North_American_epidemic">Reconstructed ancestral sequences at the root of the inferred Gag and Nef phylogenies, representing the estimated most recent common ancestor (MRCA) of the North American epidemic</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">&lt;p&gt;A minimum of ≥50,000 reconstructions of the ancestral sequence at the root of the Gag an...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">&lt;p&gt;A minimum of ≥50,000 reconstructions of the ancestral sequence at the root of the Gag and Nef phylogenies were performed, and the inferred MRCA was computed as the “grand consensus” of these replicate reconstructions. For each codon, reconstruction confidence (computed as the frequency of each amino acid observed across all reconstructions) is indicated on the y-axis on a scale from 0 (0%) to 1 (100%). Blue letters represent the highest-confidence residue at each position; green letters represent lower-confidence residues. All amino acids observed at &gt;0.01 (&gt;1%) reconstruction frequency are shown. Yellow boxes highlight positions where the highest-confidence (blue) inferred ancestral residue differs from the North American consensus B sequence (displayed in &lt;b&gt;&lt;a href=&quot;<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004295#pgen.1004295.s003&quot" rel="nofollow">http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004295#pgen.1004295.s003&quot</a>; target=&quot;_blank&quot;&gt;Figure S3&lt;/a&gt;&lt;/b&gt;).&lt;/p</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862462"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862462"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862462; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862461"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862461/HIV_proviral_genetic_diversity_compartmentalization_and_inferred_dynamics_in_lung_and_blood_during_long_term_suppressive_antiretroviral_therapy"><img alt="Research paper thumbnail of HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy" class="work-thumbnail" src="https://attachments.academia-assets.com/101563724/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862461/HIV_proviral_genetic_diversity_compartmentalization_and_inferred_dynamics_in_lung_and_blood_during_long_term_suppressive_antiretroviral_therapy">HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">The lung is an understudied site of HIV persistence. We isolated 882 subgenomic proviral sequence...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">The lung is an understudied site of HIV persistence. We isolated 882 subgenomic proviral sequences by single-genome approaches from blood and lung from nine individuals on long-term suppressive antiretroviral therapy (ART), and characterized genetic diversity and compartmentalization using formal tests. Consistent with clonal expansion as a driver of HIV persistence, identical sequences comprised between 9% to 86% of within-host datasets, though their location (blood vs. lung) followed no consistent pattern. The majority (77%) of participants harbored at least one sequence shared across blood and lung, supporting the migration of clonally-expanded cells between sites. No participant exhibited genetic compartmentalization so obvious that it was visually apparent in a phylogeny. When formal tests were applied however, two (22%) participants showed modest yet significant support for compartmentalization when analysis was restricted to distinct proviruses per site. This increased to fou...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="9dab12c1f006745e1c2288252ebd3352" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563724,"asset_id":100862461,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563724/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862461"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862461"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862461; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=100862461]").text(description); $(".js-view-count[data-work-id=100862461]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 100862461; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='100862461']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (true){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "9dab12c1f006745e1c2288252ebd3352" } } $('.js-work-strip[data-work-id=100862461]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":100862461,"title":"HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy","internal_url":"https://www.academia.edu/100862461/HIV_proviral_genetic_diversity_compartmentalization_and_inferred_dynamics_in_lung_and_blood_during_long_term_suppressive_antiretroviral_therapy","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[{"id":101563724,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/101563724/thumbnails/1.jpg","file_name":"2022.05.26.493568.full.pdf","download_url":"https://www.academia.edu/attachments/101563724/download_file","bulk_download_file_name":"HIV_proviral_genetic_diversity_compartme.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/101563724/2022.05.26.493568.full-libre.pdf?1682607840=\u0026response-content-disposition=attachment%3B+filename%3DHIV_proviral_genetic_diversity_compartme.pdf\u0026Expires=1741107188\u0026Signature=SSi9F2wAROKiYFsENyh~10c8ixzcfrLQfN7UoYN-rwD8N9azUf5z58hknDY~FS5KyPNixe14RtBgL5HTWCzyGJWxs1RSts6IVQwTwsph1S2qD~v01jMk9UBgzwWot5g5OZGSFoygksDrvpULR8grdG9h12dc18JbTTGEM5LUPw6fKv60uhid0iD55VCKwly21xfTpsXQf2l2Mg48cSZlxtY32PTuBz43kVLs834FmlhZV7pjrncONwjds2yhDhMNHHOiJTwtMzSXRpRz~PVYYUVzRGFQKs~MtjjhTe8R6viMahmGVmaZAjvCodjR7vmkbWX042yrpnxlpwUMIPbBRQ__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862460"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/100862460/Gag_residues_exhibiting_significant_diversification_over_time_are_biased_towards_known_HLA_associated_sites"><img alt="Research paper thumbnail of Gag residues exhibiting significant diversification over time are biased towards known HLA-associated sites" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/100862460/Gag_residues_exhibiting_significant_diversification_over_time_are_biased_towards_known_HLA_associated_sites">Gag residues exhibiting significant diversification over time are biased towards known HLA-associated sites</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">&lt;p&gt;&lt;b&gt;Panel A:&lt;/b&gt; Differences in Shannon entropy (Δentropy) between modern and...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">&lt;p&gt;&lt;b&gt;Panel A:&lt;/b&gt; Differences in Shannon entropy (Δentropy) between modern and historic sequences are shown for every Gag codon. Positive y-values indicate higher entropy in modern vs. historic sequences at that codon; negative y-values indicate the opposite. Red bars indicate significant entropy differences (defined as p&lt;0.001, q&lt;0.01); blue colors indicate differences that do not reach this significance threshold. Grey dots designate known HIV sites under selection by HLA (as defined in &lt;a href=&quot;<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004295#pgen.1004295-Carlson1&quot" rel="nofollow">http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004295#pgen.1004295-Carlson1&quot</a>; target=&quot;_blank&quot;&gt;[43]&lt;/a&gt;). Green dots designate sites that display significant evidence of pervasive positive selection (dN/dS&gt;1; posterior probability &gt;0.9). &lt;b&gt;Panel B:&lt;/b&gt; Same as panel A, but sorted by decreasing Δentropy rather than codon order. &lt;b&gt;Panel C:&lt;/b&gt; Graphical depiction of a 2×2 contingency table stratifying variable (&lt;99% conserved) Gag codons based on their status as HLA-associated (yes vs. no), and whether they exhibited significant Δentropy between modern and historic datasets (p&lt;0.001 [red] vs. not [blue]). Ns are indicated above each bar. &lt;b&gt;Panel D:&lt;/b&gt; Graphical depiction of a 2×2 contingency table stratifying variable (&lt;99% conserved) Gag codons based on their status as HLA-associated (yes vs. no) and evidence that they are under significant pervasive positive selection (dN/dS&gt;1; posterior probability &gt;0.9 [green] vs. not [black]). Ns are indicated above each bar.&lt;/p</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862460"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862460"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862460; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=100862460]").text(description); $(".js-view-count[data-work-id=100862460]").attr('title', description).tooltip(); 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</script> <div class="js-work-strip profile--work_container" data-work-id="100862459"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862459/People_with_HIV_receiving_suppressive_antiretroviral_therapy_show_typical_antibody_durability_after_dual_COVID_19_vaccination_and_strong_third_dose_responses"><img alt="Research paper thumbnail of People with HIV receiving suppressive antiretroviral therapy show typical antibody durability after dual COVID-19 vaccination, and strong third dose responses" class="work-thumbnail" src="https://attachments.academia-assets.com/101563722/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862459/People_with_HIV_receiving_suppressive_antiretroviral_therapy_show_typical_antibody_durability_after_dual_COVID_19_vaccination_and_strong_third_dose_responses">People with HIV receiving suppressive antiretroviral therapy show typical antibody durability after dual COVID-19 vaccination, and strong third dose responses</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACTBackgroundLonger-term humoral responses to two-dose COVID-19 vaccines remain incompletely...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACTBackgroundLonger-term humoral responses to two-dose COVID-19 vaccines remain incompletely characterized in people living with HIV (PLWH), as do initial responses to a third dose.MethodsWe measured antibodies against the SARS-CoV-2 spike protein receptor-binding domain, ACE2 displacement and viral neutralization against wild-type and Omicron strains up to six months following two-dose vaccination, and one month following the third dose, in 99 PLWH receiving suppressive antiretroviral therapy, and 152 controls.ResultsThough humoral responses naturally decline following two-dose vaccination, we found no evidence of lower antibody concentrations nor faster rates of antibody decline in PLWH compared to controls after accounting for sociodemographic, health and vaccine-related factors. We also found no evidence of poorer viral neutralization in PLWH after two doses, nor evidence that a low nadir CD4+ T-cell count compromised responses. Post-third-dose humoral responses substantial...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="8b0847cc3dd03b28ccb82e0ee84fd73e" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563722,"asset_id":100862459,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563722/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862459"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862459"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862459; 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The correct sequence of the 'RPP30-Shear Forward Primer' is 'CCATTTGCTGCTCCTTGGG'. This has been corrected in both the PDF and HTML versions of the Article.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="b25e415000064d56988c42d749e68687" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563683,"asset_id":100862458,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563683/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862458"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862458"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862458; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862457"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862457/Influence_of_HLA_C_Expression_Level_on_HIV_Control"><img alt="Research paper thumbnail of Influence of HLA-C Expression Level on HIV Control" class="work-thumbnail" src="https://attachments.academia-assets.com/101563719/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862457/Influence_of_HLA_C_Expression_Level_on_HIV_Control">Influence of HLA-C Expression Level on HIV Control</a></div><div class="wp-workCard_item"><span>Science</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">Thwarting HIV Multiple genome-wide association studies have revealed that human leukocyte antigen...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">Thwarting HIV Multiple genome-wide association studies have revealed that human leukocyte antigen (HLA) genes of the major histocompatibility complex locus have the strongest impact on HIV. In particular, a single-nucleotide polymorphism 35 base pairs upstream of HLA-C shows significant association with viral load and protection against HIV. How HLA-C mediates these effects is unknown. Apps et al. (p. 87 ) now demonstrate that increasing surface expression of HLA-C is associated with reduced viral load and reduced rate of progression to low CD4 + T cell counts in African and European Americans. High HLA-C expression likely promoted improved HIV control through a more effective cytotoxic CD8 + T cell response. In contrast to HIV infection, high HLA-C expression was associated with a higher risk of the inflammatory bowel disease, Crohn&#39;s disease.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="ddac903103316708e0a084b3585562ca" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563719,"asset_id":100862457,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563719/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862457"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862457"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862457; 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$(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100862456"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/100862456/A_method_for_Killer_cell_Immunoglobulin_like_Receptor_KIR_3DL1_3DS1_genotyping_using_DNA_recovered_from_frozen_plasma"><img alt="Research paper thumbnail of A method for Killer-cell Immunoglobulin-like Receptor (KIR) 3DL1/3DS1 genotyping using DNA recovered from frozen plasma" class="work-thumbnail" src="https://attachments.academia-assets.com/101563726/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/100862456/A_method_for_Killer_cell_Immunoglobulin_like_Receptor_KIR_3DL1_3DS1_genotyping_using_DNA_recovered_from_frozen_plasma">A method for Killer-cell Immunoglobulin-like Receptor (KIR) 3DL1/3DS1 genotyping using DNA recovered from frozen plasma</a></div><div class="wp-workCard_item"><span>Journal of Immunological Methods</span><span>, 2013</span></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">We describe a reliable and semi-automated method for Killer-cell Immunoglobulin-like Receptor (KI...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">We describe a reliable and semi-automated method for Killer-cell Immunoglobulin-like Receptor (KIR) 3DL1/S1 genotyping using DNA recovered from frozen plasma. The primers and protocol were first validated using two independent genomic DNA reference panels. To confirm the approach using plasma-derived DNA, total nucleic acids were extracted from 69 paired frozen PBMC and plasma specimens representing all common KIR3DL1/S1 genotypes (3DS1/3DS1, 3DS1/3DL1 and 3DL1/3DL1, including rare allele 3DL1*054), and analyzed in a blinded fashion. The method involves independent nested PCR amplification of KIR3DL1/S1 Exon 4, and if required Exon 3, using universal sequence-specific primers, followed by bidirectional sequencing. The free basecalling software RECall is recommended for rapid, semi-automated chromatogram analysis. KIR3DL1/S1 type assignment is based on two key nucleotide polymorphisms in Exon 4 and, if required, up to two additional polymorphisms in exon 3. Assignment can be performed manually or using our web-based algorithm, KIR3D. Extractions from plasma yielded median [IQR] nucleic acid concentrations of 0.9 [below the limit of detection-2.45] ng/μl. PCR was successful for 100% of exon 4 (69/69) and exon 3 (29/29) plasma amplifications. Chromatogram quality was high and concordance between PBMC and plasma-derived types was 100%. The estimated lower limit of input DNA required for reliable typing is 0.01 ng/μl. This method provides reliable and accurate KIR3DL1/S1 typing when conventional sources of high-quality genomic DNA are unavailable or limiting.</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="03b18cf46a6bb85c0bb1499c169f13df" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":101563726,"asset_id":100862456,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/101563726/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100862456"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100862456"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100862456; 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dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "03b18cf46a6bb85c0bb1499c169f13df" } } $('.js-work-strip[data-work-id=100862456]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":100862456,"title":"A method for Killer-cell Immunoglobulin-like Receptor (KIR) 3DL1/3DS1 genotyping using DNA recovered from frozen plasma","internal_url":"https://www.academia.edu/100862456/A_method_for_Killer_cell_Immunoglobulin_like_Receptor_KIR_3DL1_3DS1_genotyping_using_DNA_recovered_from_frozen_plasma","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[{"id":101563726,"title":"","file_type":"pdf","scribd_thumbnail_url":"https://attachments.academia-assets.com/101563726/thumbnails/1.jpg","file_name":"pmc4944815.pdf","download_url":"https://www.academia.edu/attachments/101563726/download_file","bulk_download_file_name":"A_method_for_Killer_cell_Immunoglobulin.pdf","bulk_download_url":"https://d1wqtxts1xzle7.cloudfront.net/101563726/pmc4944815-libre.pdf?1682607692=\u0026response-content-disposition=attachment%3B+filename%3DA_method_for_Killer_cell_Immunoglobulin.pdf\u0026Expires=1741107188\u0026Signature=SCVxy7RwBFSMzTZtBqwe5K95zrhUrRV6gGEdCLvm4Uc93A7UGgoqThgDtzAuuSy4twqc~CMPfA0JWu8fDZdSfDw-9IkYsI-9Bq0I9SKRn21aBDH6nuf0bQg2p593tPeFcsP3I28b00WxwQO3m63YlzPkvWGRMUiHOq0iY7dWajv-zlDwhQN4YXP0iBZxn6wH0La7ui8-Ksq3aZOYmJNsrtLbmDxGbd5nFO7gvTgfxmcQuUxtz32tjIKd5NYIW6Xu5XkeoR2U0zMvpTr3tyZ89ay~l8haiTGiisPsqDdLBAdMIYs1UIwwjfgsnKpgLH0laPs-fK1Kr0laH006z4Usxg__\u0026Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA"}]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="100861762"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" rel="nofollow" href="https://www.academia.edu/100861762/SARS_CoV_2_live_virus_neutralization_after_four_COVID_19_vaccine_doses_in_people_with_HIV_receiving_suppressive_antiretroviral_therapy"><img alt="Research paper thumbnail of SARS-CoV-2 live virus neutralization after four COVID-19 vaccine doses in people with HIV receiving suppressive antiretroviral therapy" class="work-thumbnail" src="https://a.academia-assets.com/images/blank-paper.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" rel="nofollow" href="https://www.academia.edu/100861762/SARS_CoV_2_live_virus_neutralization_after_four_COVID_19_vaccine_doses_in_people_with_HIV_receiving_suppressive_antiretroviral_therapy">SARS-CoV-2 live virus neutralization after four COVID-19 vaccine doses in people with HIV receiving suppressive antiretroviral therapy</a></div><div class="wp-workCard_item"><span>AIDS</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="100861762"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="100861762"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 100861762; window.Academia.workViewCountsFetcher.queue(workId, function (count) { var description = window.$h.commaizeInt(count) + " " + window.$h.pluralize(count, 'View'); $(".js-view-count[data-work-id=100861762]").text(description); $(".js-view-count[data-work-id=100861762]").attr('title', description).tooltip(); }); });</script></span></span><span><span class="percentile-widget hidden"><span class="u-mr2x work-percentile"></span></span><script>$(function () { var workId = 100861762; window.Academia.workPercentilesFetcher.queue(workId, function (percentileText) { var container = $(".js-work-strip[data-work-id='100861762']"); container.find('.work-percentile').text(percentileText.charAt(0).toUpperCase() + percentileText.slice(1)); container.find('.percentile-widget').show(); container.find('.percentile-widget').removeClass('hidden'); }); });</script></span></div><div id="work-strip-premium-row-container"></div></div></div><script> require.config({ waitSeconds: 90 })(["https://a.academia-assets.com/assets/wow_profile-a9bf3a2bc8c89fa2a77156577594264ee8a0f214d74241bc0fcd3f69f8d107ac.js","https://a.academia-assets.com/assets/work_edit-ad038b8c047c1a8d4fa01b402d530ff93c45fee2137a149a4a5398bc8ad67560.js"], function() { // from javascript_helper.rb var dispatcherData = {} if (false){ window.WowProfile.dispatcher = window.WowProfile.dispatcher || _.clone(Backbone.Events); dispatcherData = { dispatcher: window.WowProfile.dispatcher, downloadLinkId: "-1" } } $('.js-work-strip[data-work-id=100861762]').each(function() { if (!$(this).data('initialized')) { new WowProfile.WorkStripView({ el: this, workJSON: {"id":100861762,"title":"SARS-CoV-2 live virus neutralization after four COVID-19 vaccine doses in people with HIV receiving suppressive antiretroviral therapy","internal_url":"https://www.academia.edu/100861762/SARS_CoV_2_live_virus_neutralization_after_four_COVID_19_vaccine_doses_in_people_with_HIV_receiving_suppressive_antiretroviral_therapy","owner_id":211385129,"coauthors_can_edit":true,"owner":{"id":211385129,"first_name":"Zabrina","middle_initials":null,"last_name":"Brumme","page_name":"ZabrinaBrumme","domain_name":"independent","created_at":"2021-12-29T12:19:59.219-08:00","display_name":"Zabrina Brumme","url":"https://independent.academia.edu/ZabrinaBrumme"},"attachments":[]}, dispatcherData: dispatcherData }); $(this).data('initialized', true); } }); $a.trackClickSource(".js-work-strip-work-link", "profile_work_strip") }); </script> <div class="js-work-strip profile--work_container" data-work-id="86670683"><div class="profile--work_thumbnail hidden-xs"><a class="js-work-strip-work-link" data-click-track="profile-work-strip-thumbnail" href="https://www.academia.edu/86670683/Serial_infection_with_SARS_CoV_2_Omicron_BA_1_and_BA_2_following_three_dose_COVID_19_vaccination"><img alt="Research paper thumbnail of Serial infection with SARS-CoV-2 Omicron BA.1 and BA.2 following three-dose COVID-19 vaccination" class="work-thumbnail" src="https://attachments.academia-assets.com/91069400/thumbnails/1.jpg" /></a></div><div class="wp-workCard wp-workCard_itemContainer"><div class="wp-workCard_item wp-workCard--title"><a class="js-work-strip-work-link text-gray-darker" data-click-track="profile-work-strip-title" href="https://www.academia.edu/86670683/Serial_infection_with_SARS_CoV_2_Omicron_BA_1_and_BA_2_following_three_dose_COVID_19_vaccination">Serial infection with SARS-CoV-2 Omicron BA.1 and BA.2 following three-dose COVID-19 vaccination</a></div><div class="wp-workCard_item"><span class="js-work-more-abstract-truncated">ABSTRACTSARS-CoV-2 Omicron infections are common among individuals who are vaccinated or have rec...</span><a class="js-work-more-abstract" data-broccoli-component="work_strip.more_abstract" data-click-track="profile-work-strip-more-abstract" href="javascript:;"><span> more </span><span><i class="fa fa-caret-down"></i></span></a><span class="js-work-more-abstract-untruncated hidden">ABSTRACTSARS-CoV-2 Omicron infections are common among individuals who are vaccinated or have recovered from prior variant infection, but few reports have documented serial Omicron infections. We characterized SARS-CoV-2 humoral responses in a healthy young person who acquired laboratory-confirmed Omicron BA.1.15 ten weeks after a third dose of BNT162b2, and BA.2 thirteen weeks later. Responses were compared to those of 124 COVID-19 naive vaccinees. One month after the second and third vaccine doses, the participant’s wild-type and BA.1-specific IgG, ACE2 competition and virus neutralization activities were average for a COVID-19 naive triple-vaccinated individual. BA.1 infection boosted the participant’s responses to the cohort ≥95th percentile, but even this strong “hybrid” immunity failed to protect against BA.2. Moreover, reinfection increased BA.1 and BA.2-specific responses only modestly. Results illustrate the risk of Omicron infection in fully vaccinated individuals and high...</span></div><div class="wp-workCard_item wp-workCard--actions"><span class="work-strip-bookmark-button-container"></span><a id="d9d0927505a1a893883715a87f04cf7c" class="wp-workCard--action" rel="nofollow" data-click-track="profile-work-strip-download" data-download="{"attachment_id":91069400,"asset_id":86670683,"asset_type":"Work","button_location":"profile"}" href="https://www.academia.edu/attachments/91069400/download_file?s=profile"><span><i class="fa fa-arrow-down"></i></span><span>Download</span></a><span class="wp-workCard--action visible-if-viewed-by-owner inline-block" style="display: none;"><span class="js-profile-work-strip-edit-button-wrapper profile-work-strip-edit-button-wrapper" data-work-id="86670683"><a class="js-profile-work-strip-edit-button" tabindex="0"><span><i class="fa fa-pencil"></i></span><span>Edit</span></a></span></span></div><div class="wp-workCard_item wp-workCard--stats"><span><span><span class="js-view-count view-count u-mr2x" data-work-id="86670683"><i class="fa fa-spinner fa-spin"></i></span><script>$(function () { var workId = 86670683; 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