{"id":"https://openalex.org/W2217898077","doi":"https://doi.org/10.1109/bibm.2015.7359813","title":"Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus","display_name":"Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2217898077","doi":"https://doi.org/10.1109/bibm.2015.7359813","mag":"2217898077"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2015.7359813","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359813","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008692578","display_name":"Ishwor Thapa","orcid":"https://orcid.org/0000-0002-3594-1631"},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ishwor Thapa","raw_affiliation_strings":["College of IS&T, University of Nebraska, Omaha, NE"],"affiliations":[{"raw_affiliation_string":"College of IS&T, University of Nebraska, Omaha, NE","institution_ids":["https://openalex.org/I122266389"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061418721","display_name":"Howard S. Fox","orcid":"https://orcid.org/0000-0003-2032-374X"},"institutions":[{"id":"https://openalex.org/I59130452","display_name":"University of Nebraska Medical Center","ror":"https://ror.org/00thqtb16","country_code":"US","type":"funder","lineage":["https://openalex.org/I59130452"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Howard S. Fox","raw_affiliation_strings":["Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE"],"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE","institution_ids":["https://openalex.org/I59130452"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102932572","display_name":"Dhundy R. Bastola","orcid":"https://orcid.org/0000-0002-5630-7576"},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dhundy R. Bastola","raw_affiliation_strings":["College of IS&T, University of Nebraska, Omaha, NE"],"affiliations":[{"raw_affiliation_string":"College of IS&T, University of Nebraska, Omaha, NE","institution_ids":["https://openalex.org/I122266389"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5008692578"],"corresponding_institution_ids":["https://openalex.org/I122266389"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08729875,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"962","last_page":"968"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10082","display_name":"HIV/AIDS Research and Interventions","score":0.9850000143051147,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9621000289916992,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/methamphetamine","display_name":"Methamphetamine","score":0.9019021987915039},{"id":"https://openalex.org/keywords/neurocognitive","display_name":"Neurocognitive","score":0.7262430191040039},{"id":"https://openalex.org/keywords/cart","display_name":"Cart","score":0.7069568037986755},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.6532677412033081},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.5222764015197754},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5053904056549072},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.4752984941005707},{"id":"https://openalex.org/keywords/viral-load","display_name":"Viral load","score":0.4641168713569641},{"id":"https://openalex.org/keywords/neurodegeneration","display_name":"Neurodegeneration","score":0.45570501685142517},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4451867938041687},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.4271664023399353},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.4245275557041168},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.3319038450717926},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2682081460952759},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2532638907432556},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.19008305668830872},{"id":"https://openalex.org/keywords/psychiatry","display_name":"Psychiatry","score":0.1450168490409851},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1413363814353943},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.09836333990097046},{"id":"https://openalex.org/keywords/cognition","display_name":"Cognition","score":0.08089888095855713}],"concepts":[{"id":"https://openalex.org/C2780376393","wikidata":"https://www.wikidata.org/wiki/Q191924","display_name":"Methamphetamine","level":2,"score":0.9019021987915039},{"id":"https://openalex.org/C172467417","wikidata":"https://www.wikidata.org/wiki/Q1670397","display_name":"Neurocognitive","level":3,"score":0.7262430191040039},{"id":"https://openalex.org/C2777275308","wikidata":"https://www.wikidata.org/wiki/Q234668","display_name":"Cart","level":2,"score":0.7069568037986755},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.6532677412033081},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.5222764015197754},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5053904056549072},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.4752984941005707},{"id":"https://openalex.org/C142462285","wikidata":"https://www.wikidata.org/wiki/Q2528140","display_name":"Viral load","level":3,"score":0.4641168713569641},{"id":"https://openalex.org/C2776925932","wikidata":"https://www.wikidata.org/wiki/Q1755122","display_name":"Neurodegeneration","level":3,"score":0.45570501685142517},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4451867938041687},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.4271664023399353},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.4245275557041168},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.3319038450717926},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2682081460952759},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2532638907432556},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.19008305668830872},{"id":"https://openalex.org/C118552586","wikidata":"https://www.wikidata.org/wiki/Q7867","display_name":"Psychiatry","level":1,"score":0.1450168490409851},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1413363814353943},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.09836333990097046},{"id":"https://openalex.org/C169900460","wikidata":"https://www.wikidata.org/wiki/Q2200417","display_name":"Cognition","level":2,"score":0.08089888095855713},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2015.7359813","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359813","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.8600000143051147}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332162","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1547888106","https://openalex.org/W1574896709","https://openalex.org/W1753464271","https://openalex.org/W1964916693","https://openalex.org/W1979339518","https://openalex.org/W1981509058","https://openalex.org/W1987994679","https://openalex.org/W1995746794","https://openalex.org/W2009455549","https://openalex.org/W2020914845","https://openalex.org/W2021341670","https://openalex.org/W2055845329","https://openalex.org/W2057567758","https://openalex.org/W2070342831","https://openalex.org/W2089082039","https://openalex.org/W2093530590","https://openalex.org/W2096599172","https://openalex.org/W2099574296","https://openalex.org/W2108234281","https://openalex.org/W2109669557","https://openalex.org/W2115322174","https://openalex.org/W2117131162","https://openalex.org/W2126492433","https://openalex.org/W2140729960","https://openalex.org/W2160588949","https://openalex.org/W2170551349","https://openalex.org/W2468314239","https://openalex.org/W4242710713"],"related_works":["https://openalex.org/W4400093351","https://openalex.org/W3193909393","https://openalex.org/W2322350723","https://openalex.org/W2618011907","https://openalex.org/W4226229889","https://openalex.org/W2945144341","https://openalex.org/W2974098477","https://openalex.org/W3126687991","https://openalex.org/W2913272324","https://openalex.org/W2024873351"],"abstract_inverted_index":{"The":[0,39,135],"use":[1,40,85,123],"of":[2,6,17,29,41,48,55,86,93,95,113,124,138,140,154],"methamphetamine":[3,42,132],"and":[4,20,32,63,83,148],"infection":[5],"HIV":[7,49],"are":[8],"both":[9,33],"considered":[10],"public":[11],"health":[12],"issues":[13],"by":[14,109],"the":[15,27,35,46,53,56,70,75,84,99,106,111,122,141,152],"Centers":[16],"Disease":[18],"Control":[19],"Prevention":[21],"(CDC).":[22],"Many":[23],"studies":[24,67],"have":[25,68],"shown":[26],"effect":[28,104],"methamphetamine,":[30,87],"HIV,":[31],"to":[34,61,78,157],"central":[36],"nervous":[37],"system.":[38],"not":[43],"only":[44],"increases":[45],"tendency":[47],"transmission,":[50],"but":[51,88],"also":[52],"severity":[54],"infection,":[57,80],"which":[58],"may":[59],"lead":[60],"neurodegeneration":[62],"neurocognitive":[64],"disorders.":[65],"Several":[66],"examined":[69],"gene":[71],"expression":[72,136],"changes":[73],"in":[74],"host":[76],"due":[77],"viral":[79,128],"antiretroviral":[81,125],"treatment,":[82],"there":[89],"is":[90],"a":[91],"lack":[92],"understanding":[94],"their":[96,103,158],"impact":[97],"on":[98,105],"virus.":[100],"We":[101,119],"investigated":[102],"HIV-1":[107,142],"virus":[108],"analyzing":[110],"amount":[112],"reads":[114,155],"obtained":[115],"from":[116,151],"RNA":[117],"sequencing.":[118],"showed":[120,161],"that":[121],"drugs":[126],"reduced":[127],"read":[129],"levels,":[130],"whereas":[131],"increased":[133],"them.":[134],"level":[137],"some":[139],"genes":[143],"such":[144],"as":[145],"gag,":[146],"pol,":[147],"nef,":[149],"inferred":[150],"count":[153],"mapped":[156],"genomic":[159],"locations,":[160],"different":[162],"temporal":[163],"states":[164],"among":[165],"our":[166],"biological":[167],"samples.":[168]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
