2,056 results on '"Goedert, James"'
Search Results
2. Early Oligocene kelp holdfasts and stepwise evolution of the kelp ecosystem in the North Pacific
- Author
-
Kiel, Steffen, Goedert, James L, Huynh, Tony L, Krings, Michael, Parkinson, Dula, Romero, Rosemary, and Looy, Cindy V
- Subjects
Physical Geography and Environmental Geoscience ,Biological Sciences ,Ecology ,Evolutionary Biology ,Earth Sciences ,Climate Change Science ,Animals ,Ecosystem ,Kelp ,Forests ,Climate ,Pacific Ocean ,Mammals ,Desmostylia ,Laminariales ,kelp forest - Abstract
Kelp forests are highly productive and economically important ecosystems worldwide, especially in the North Pacific Ocean. However, current hypotheses for their evolutionary origins are reliant on a scant fossil record. Here, we report fossil hapteral kelp holdfasts from western Washington State, USA, indicating that kelp has existed in the northeastern Pacific Ocean since the earliest Oligocene. This is consistent with the proposed North Pacific origin of kelp associated with global cooling around the Eocene-Oligocene transition. These fossils also support the hypotheses that a hapteral holdfast, rather than a discoid holdfast, is the ancestral state in complex kelps and suggest that early kelps likely had a flexible rather than a stiff stipe. Early kelps were possibly grazed upon by mammals like desmostylians, but fossil evidence of the complex ecological interactions known from extant kelp forests is lacking. The fossil record further indicates that the present-day, multi-story kelp forest had developed at latest after the mid-Miocene climate optimum. In summary, the fossils signify a stepwise evolution of the kelp ecosystem in the North Pacific, likely enabled by changes in the ocean-climate system.
- Published
- 2024
3. First Eocene record of a bangialean rhodophyte (the endolithic microboring Conchocelichnus seilacheri) and coralline red algae from the Pacific Coast of North America
- Author
-
Kočí, Tomáš, Veselská, Martina Kočová, Goedert, James L., Buckeridge, John S., Reitner, Joachim, and Váchová, Lenka
- Published
- 2024
- Full Text
- View/download PDF
4. Plasma metabolites in childhood Burkitt lymphoma cases and cancer-free controls in Uganda
- Author
-
Huang, Jiaqi, Nabalende, Hadijah, Camargo, M. Constanza, Lovett, Jacqueline, Otim, Isaac, Legason, Ismail D., Ogwang, Martin D., Kerchan, Patrick, Kinyera, Tobias, Ayers, Leona W., Bhatia, Kishor, Goedert, James J., Reynolds, Steven J., Crompton, Peter D., Moore, Steven C., Moaddel, Ruin, Albanes, Demetrius, and Mbulaiteye, Sam M.
- Published
- 2024
- Full Text
- View/download PDF
5. New Challenges to Health: The Threat of Virus Infection (review)
- Author
-
Goedert, James J
- Published
- 2002
- Full Text
- View/download PDF
6. Africa-specific human genetic variation near CHD1L associates with HIV-1 load
- Author
-
McLaren, Paul J., Porreca, Immacolata, Iaconis, Gennaro, Mok, Hoi Ping, Mukhopadhyay, Subhankar, Karakoc, Emre, Cristinelli, Sara, Pomilla, Cristina, Bartha, István, Thorball, Christian W., Tough, Riley H., Angelino, Paolo, Kiar, Cher S., Carstensen, Tommy, Fatumo, Segun, Porter, Tarryn, Jarvis, Isobel, Skarnes, William C., Bassett, Andrew, DeGorter, Marianne K., Sathya Moorthy, Mohana Prasad, Tuff, Jeffrey F., Kim, Eun-Young, Walter, Miriam, Simons, Lacy M., Bashirova, Arman, Buchbinder, Susan, Carrington, Mary, Cossarizza, Andrea, De Luca, Andrea, Goedert, James J., Goldstein, David B., Haas, David W., Herbeck, Joshua T., Johnson, Eric O., Kaleebu, Pontiano, Kilembe, William, Kirk, Gregory D., Kootstra, Neeltje A., Kral, Alex H., Lambotte, Olivier, Luo, Ma, Mallal, Simon, Martinez-Picado, Javier, Meyer, Laurence, Miro, José M., Moodley, Pravi, Motala, Ayesha A., Mullins, James I., Nam, Kireem, Obel, Niels, Pirie, Fraser, Plummer, Francis A., Poli, Guido, Price, Matthew A., Rauch, Andri, Theodorou, Ioannis, Trkola, Alexandra, Walker, Bruce D., Winkler, Cheryl A., Zagury, Jean-François, Montgomery, Stephen B., Ciuffi, Angela, Hultquist, Judd F., Wolinsky, Steven M., Dougan, Gordon, Lever, Andrew M. L., Gurdasani, Deepti, Groom, Harriet, Sandhu, Manjinder S., and Fellay, Jacques
- Published
- 2023
- Full Text
- View/download PDF
7. Mosaic chromosomal alterations in peripheral blood leukocytes of children in sub-Saharan Africa
- Author
-
Zhou, Weiyin, Fischer, Anja, Ogwang, Martin D., Luo, Wen, Kerchan, Patrick, Reynolds, Steven J., Tenge, Constance N., Were, Pamela A., Kuremu, Robert T., Wekesa, Walter N., Masalu, Nestory, Kawira, Esther, Kinyera, Tobias, Otim, Isaac, Legason, Ismail D., Nabalende, Hadijah, Ayers, Leona W., Bhatia, Kishor, Goedert, James J., Gouveia, Mateus H., Cole, Nathan, Hicks, Belynda, Jones, Kristine, Hummel, Michael, Schlesner, Mathias, Chagaluka, George, Mutalima, Nora, Borgstein, Eric, Liomba, George N., Kamiza, Steve, Mkandawire, Nyengo, Mitambo, Collins, Molyneux, Elizabeth M., Newton, Robert, Glaser, Selina, Kretzmer, Helene, Manning, Michelle, Hutchinson, Amy, Hsing, Ann W., Tettey, Yao, Adjei, Andrew A., Chanock, Stephen J., Siebert, Reiner, Yeager, Meredith, Prokunina-Olsson, Ludmila, Machiela, Mitchell J., and Mbulaiteye, Sam M.
- Published
- 2023
- Full Text
- View/download PDF
8. Trans-ancestral fine-mapping of MHC reveals key amino acids associated with spontaneous clearance of hepatitis C in HLA-DQβ1
- Author
-
Valencia, Ana, Vergara, Candelaria, Thio, Chloe L, Vince, Nicolas, Douillard, Venceslas, Grifoni, Alba, Cox, Andrea L, Johnson, Eric O, Kral, Alex H, Goedert, James J, Mangia, Alessandra, Piazzolla, Valeria, Mehta, Shruti H, Kirk, Gregory D, Kim, Arthur Y, Lauer, Georg M, Chung, Raymond T, Price, Jennifer C, Khakoo, Salim I, Alric, Laurent, Cramp, Matthew E, Donfield, Sharyne M, Edlin, Brian R, Busch, Michael P, Alexander, Graeme, Rosen, Hugo R, Murphy, Edward L, Wojcik, Genevieve L, Carrington, Mary, Gourraud, Pierre-Antoine, Sette, Alessandro, Thomas, David L, and Duggal, Priya
- Subjects
Biological Sciences ,Biomedical and Clinical Sciences ,Immunology ,Genetics ,Digestive Diseases ,Chronic Liver Disease and Cirrhosis ,Infectious Diseases ,Hepatitis ,Hepatitis - C ,Liver Disease ,Emerging Infectious Diseases ,Prevention ,Good Health and Well Being ,Acute Disease ,Alleles ,Amino Acid Substitution ,Black People ,Female ,Gene Expression ,Genome-Wide Association Study ,Genotype ,HLA-DQ beta-Chains ,Hepacivirus ,Hepatitis C ,Host-Pathogen Interactions ,Humans ,Leucine ,Male ,Polymorphism ,Single Nucleotide ,Proline ,Protein Isoforms ,Remission ,Spontaneous ,White People ,GWAS ,HCV clearance ,HLA imputation ,HLA-DQβ1 ,MHC ,fine-mapping ,hepatitis C virus ,host genetics ,infection ,trans-ancestral ,Medical and Health Sciences ,Genetics & Heredity ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
Spontaneous clearance of acute hepatitis C virus (HCV) infection is associated with single nucleotide polymorphisms (SNPs) on the MHC class II. We fine-mapped the MHC region in European (n = 1,600; 594 HCV clearance/1,006 HCV persistence) and African (n = 1,869; 340 HCV clearance/1,529 HCV persistence) ancestry individuals and evaluated HCV peptide binding affinity of classical alleles. In both populations, HLA-DQβ1Leu26 (p valueMeta = 1.24 × 10-14) located in pocket 4 was negatively associated with HCV spontaneous clearance and HLA-DQβ1Pro55 (p valueMeta = 8.23 × 10-11) located in the peptide binding region was positively associated, independently of HLA-DQβ1Leu26. These two amino acids are not in linkage disequilibrium (r2 < 0.1) and explain the SNPs and classical allele associations represented by rs2647011, rs9274711, HLA-DQB1∗03:01, and HLA-DRB1∗01:01. Additionally, HCV persistence classical alleles tagged by HLA-DQβ1Leu26 had fewer HCV binding epitopes and lower predicted binding affinities compared to clearance alleles (geometric mean of combined IC50 nM of persistence versus clearance; 2,321 nM versus 761.7 nM, p value = 1.35 × 10-38). In summary, MHC class II fine-mapping revealed key amino acids in HLA-DQβ1 explaining allelic and SNP associations with HCV outcomes. This mechanistic advance in understanding of natural recovery and immunogenetics of HCV might set the stage for much needed enhancement and design of vaccine to promote spontaneous clearance of HCV infection.
- Published
- 2022
9. A Multiancestry Sex-Stratified Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus
- Author
-
Vergara, Candelaria, Valencia, Ana, Thio, Chloe L, Goedert, James J, Mangia, Alessandra, Piazzolla, Valeria, Johnson, Eric, Kral, Alex H, O’Brien, Thomas R, Mehta, Shruti H, Kirk, Gregory D, Kim, Arthur Y, Lauer, Georg M, Chung, Raymond T, Cox, Andrea L, Peters, Marion G, Khakoo, Salim I, Alric, Laurent, Cramp, Matthew E, Donfield, Sharyne M, Edlin, Brian R, Busch, Michael P, Alexander, Graeme, Rosen, Hugo R, Murphy, Edward L, Wojcik, Genevieve L, Taub, Margaret A, Thomas, David L, and Duggal, Priya
- Subjects
Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Human Genome ,Vaccine Related ,Hepatitis ,Liver Disease ,Women's Health ,Emerging Infectious Diseases ,Prevention ,Infectious Diseases ,Digestive Diseases ,Chronic Liver Disease and Cirrhosis ,Biotechnology ,Immunization ,Hepatitis - C ,Aetiology ,2.1 Biological and endogenous factors ,2.2 Factors relating to the physical environment ,Infection ,Good Health and Well Being ,Female ,Genome-Wide Association Study ,Hepacivirus ,Hepatitis C ,Humans ,Male ,Polymorphism ,Single Nucleotide ,Ribosomal Proteins ,Septins ,Sex Factors ,Viral Load ,HCV ,GWAS ,Sex ,X chromosome ,ARL5B ,Septin 6 ,Host-genetics ,infection ,immune ,Medical and Health Sciences ,Microbiology ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundSpontaneous clearance of acute hepatitis C virus (HCV) infection is more common in women than in men, independent of known risk factors.MethodsTo identify sex-specific genetic loci, we studied 4423 HCV-infected individuals (2903 male, 1520 female) of European, African, and Hispanic ancestry. We performed autosomal, and X chromosome sex-stratified and combined association analyses in each ancestry group.ResultsA male-specific region near the adenosine diphosphate-ribosylation factor-like 5B (ARL5B) gene was identified. Individuals with the C allele of rs76398191 were about 30% more likely to have chronic HCV infection than individuals with the T allele (OR, 0.69; P = 1.98 × 10-07), and this was not seen in females. The ARL5B gene encodes an interferon-stimulated gene that inhibits immune response to double-stranded RNA viruses. We also identified suggestive associations near septin 6 and ribosomal protein L39 genes on the X chromosome. In box sexes, allele G of rs12852885 was associated with a 40% increase in HCV clearance compared with the A allele (OR, 1.4; P = 2.46 × 10-06). Septin 6 facilitates HCV replication via interaction with the HCV NS5b protein, and ribosomal protein L39 acts as an HCV core interactor.ConclusionsThese novel gene associations support differential mechanisms of HCV clearance between the sexes and provide biological targets for treatment or vaccine development.
- Published
- 2021
10. Effects of processed meat and drinking water nitrate on oral and fecal microbial populations in a controlled feeding study
- Author
-
Sinha, Rashmi, Zhao, Ni, Goedert, James J, Byrd, Doratha A, Wan, Yunhu, Hua, Xing, Hullings, Autumn G, Knight, Rob, van Breda, Simone, Mathijs, Karen, de Kok, Theo M, Ward, Mary H, members, PHYTOME consortium, Pieters, Harm-Jan, Sági-Kiss, Virág, Kuhnle, Gunter G, Georgiadis, Panagiotis, Saccani, Giovanna, Parolari, Giovanni, Virgili, Roberta, Hemke, Gert, Hung, Yung, Verbeke, Wim, Masclee, Ad A, Vleugels-Simon, Carla B, van Bodegraven, Adriaan A, Dobbelaere, Dirk, Vandewynkel, Anneleen, van der Kruijk, Richard, Egberts, Frans, and van Helvoirt, Jan-Hein
- Subjects
Biological Sciences ,Environmental Sciences ,Chemical Sciences ,Digestive Diseases ,Nutrition ,Cancer ,Oral and gastrointestinal ,Diet ,Drinking Water ,Humans ,Meat ,Nitrates ,Nitrites ,RNA ,Ribosomal ,16S ,Processed meat ,Water nitrate ,Nitrite ,Oral and fecal microbiome ,Phytochemicals ,PHYTOME consortium members ,Toxicology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
BackgroundOne mechanism that can explain the link between processed meat consumption and colorectal cancer (CRC) is the production of carcinogenic N-nitroso compounds (NOCs) in the gastrointestinal tract. Oral and gut microbes metabolize ingested proteins (a source of secondary and tertiary amines and amides) and can reduce nitrate to nitrite, generating potentially carcinogenic NOCs.ObjectiveWe evaluated whether nitrate/nitrite in processed meat or water influences the fecal or salivary microbiota.DesignIn this dietary intervention study, 63 volunteers consumed diets high in conventional processed meats for two weeks, switched to diets high in poultry for two weeks, and then consumed phytochemical-enriched conventional processed or low-nitrite processed meat diets for two weeks. During the intervention, they drank water with low nitrate concentrations and consumed a healthy diet with low antioxidants. Then the volunteers drank nitrate-enriched water for 1 week, in combination with one of the four different diets. We measured creatinine-adjusted urinary nitrate levels and characterized the oral and fecal microbiota using 16S rRNA amplicon sequencing.ResultsUsing linear mixed models, we found that, compared to baseline, urinary nitrate levels were reduced during the phytochemical-enriched low-nitrite meat diet (p-value = 0.009) and modestly during the poultry diet (p-value = 0.048). In contrast, urinary nitrate increased after 1-week of drinking nitrate-enriched water (p-value
- Published
- 2021
11. Associations of fecal microbial profiles with breast cancer and nonmalignant breast disease in the Ghana Breast Health Study
- Author
-
Byrd, Doratha A, Vogtmann, Emily, Wu, Zeni, Han, Yongli, Wan, Yunhu, Clegg‐Lamptey, Joe‐Nat, Yarney, Joel, Wiafe‐Addai, Beatrice, Wiafe, Seth, Awuah, Baffour, Ansong, Daniel, Nyarko, Kofi, Hullings, Autumn G, Hua, Xing, Ahearn, Thomas, Goedert, James J, Shi, Jianxin, Knight, Rob, Figueroa, Jonine D, Brinton, Louise A, Garcia‐Closas, Montserrat, and Sinha, Rashmi
- Subjects
Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Breast Cancer ,Aging ,Cancer ,Good Health and Well Being ,Adult ,Aged ,Bacteria ,Breast Diseases ,Breast Neoplasms ,Case-Control Studies ,DNA ,Bacterial ,DNA ,Ribosomal ,Feces ,Female ,Gastrointestinal Microbiome ,Ghana ,High-Throughput Nucleotide Sequencing ,Humans ,Logistic Models ,Middle Aged ,Odds Ratio ,Phylogeny ,RNA ,Ribosomal ,16S ,Sequence Analysis ,DNA ,Young Adult ,breast cancer ,microbiome ,nonmalignant breast diseases ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
The gut microbiota may play a role in breast cancer etiology by regulating hormonal, metabolic and immunologic pathways. We investigated associations of fecal bacteria with breast cancer and nonmalignant breast disease in a case-control study conducted in Ghana, a country with rising breast cancer incidence and mortality. To do this, we sequenced the V4 region of the 16S rRNA gene to characterize bacteria in fecal samples collected at the time of breast biopsy (N = 379 breast cancer cases, N = 102 nonmalignant breast disease cases, N = 414 population-based controls). We estimated associations of alpha diversity (observed amplicon sequence variants [ASVs], Shannon index, and Faith's phylogenetic diversity), beta diversity (Bray-Curtis and unweighted/weighted UniFrac distance), and the presence and relative abundance of select taxa with breast cancer and nonmalignant breast disease using multivariable unconditional polytomous logistic regression. All alpha diversity metrics were strongly, inversely associated with odds of breast cancer and for those in the highest relative to lowest tertile of observed ASVs, the odds ratio (95% confidence interval) was 0.21 (0.13-0.36; Ptrend
- Published
- 2021
12. Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection
- Author
-
Vergara, Candelaria, Duggal, Priya, Thio, Chloe L, Valencia, Ana, O’Brien, Thomas R, Latanich, Rachel, Timp, Winston, Johnson, Eric O, Kral, Alex H, Mangia, Alessandra, Goedert, James J, Piazzola, Valeria, Mehta, Shruti H, Kirk, Gregory D, Peters, Marion G, Donfield, Sharyne M, Edlin, Brian R, Busch, Michael P, Alexander, Graeme, Murphy, Edward L, Kim, Arthur Y, Lauer, Georg M, Chung, Raymond T, Cramp, Matthew E, Cox, Andrea L, Khakoo, Salim I, Rosen, Hugo R, Alric, Laurent, Wheelan, Sarah J, Wojcik, Genevieve L, Thomas, David L, and Taub, Margaret A
- Subjects
Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Emerging Infectious Diseases ,Infectious Diseases ,Chronic Liver Disease and Cirrhosis ,Hepatitis ,Digestive Diseases ,Liver Disease ,Hepatitis - C ,2.1 Biological and endogenous factors ,Aetiology ,Good Health and Well Being ,Black People ,Haplotypes ,Hepatitis C ,Humans ,Interferons ,Phenotype ,Polymorphism ,Single Nucleotide ,White People ,Immunology - Abstract
Clearance of acute infection with hepatitis C virus (HCV) is associated with the chr19q13.13 region containing the rs368234815 (TT/ΔG) polymorphism. We fine-mapped this region to detect possible causal variants that may contribute to HCV clearance. First, we performed sequencing of IFNL1-IFNL4 region in 64 individuals sampled according to rs368234815 genotype: TT/clearance (N = 16) and ΔG/persistent (N = 15) (genotype-outcome concordant) or TT/persistent (N = 19) and ΔG/clearance (N = 14) (discordant). 25 SNPs had a difference in counts of alternative allele >5 between clearance and persistence individuals. Then, we evaluated those markers in an association analysis of HCV clearance conditioning on rs368234815 in two groups of European (692 clearance/1 025 persistence) and African ancestry (320 clearance/1 515 persistence) individuals. 10/25 variants were associated (P
- Published
- 2020
13. Eocene tube-dwelling annelids (Polychaeta: Sedentaria) from the Black Hills, western Washington State: the first record of Neodexiospira from North America
- Author
-
Kočí, Tomáš, Goedert, James L., and Buckeridge, John S.
- Published
- 2022
- Full Text
- View/download PDF
14. Author Correction: Africa-specific human genetic variation near CHD1L associates with HIV-1 load
- Author
-
McLaren, Paul J., Porreca, Immacolata, Iaconis, Gennaro, Mok, Hoi Ping, Mukhopadhyay, Subhankar, Karakoc, Emre, Cristinelli, Sara, Pomilla, Cristina, Bartha, István, Thorball, Christian W., Tough, Riley H., Angelino, Paolo, Kiar, Cher S., Carstensen, Tommy, Fatumo, Segun, Porter, Tarryn, Jarvis, Isobel, Skarnes, William C., Bassett, Andrew, DeGorter, Marianne K., Sathya Moorthy, Mohana Prasad, Tuff, Jeffrey F., Kim, Eun-Young, Walter, Miriam, Simons, Lacy M., Bashirova, Arman, Buchbinder, Susan, Carrington, Mary, Cossarizza, Andrea, De Luca, Andrea, Goedert, James J., Goldstein, David B., Haas, David W., Herbeck, Joshua T., Johnson, Eric O., Kaleebu, Pontiano, Kilembe, William, Kirk, Gregory D., Kootstra, Neeltje A., Kral, Alex H., Lambotte, Olivier, Luo, Ma, Mallal, Simon, Martinez-Picado, Javier, Meyer, Laurence, Miro, José M., Moodley, Pravi, Motala, Ayesha A., Mullins, James I., Nam, Kireem, Obel, Niels, Pirie, Fraser, Plummer, Francis A., Poli, Guido, Price, Matthew A., Rauch, Andri, Theodorou, Ioannis, Trkola, Alexandra, Walker, Bruce D., Winkler, Cheryl A., Zagury, Jean-François, Montgomery, Stephen B., Ciuffi, Angela, Hultquist, Judd F., Wolinsky, Steven M., Dougan, Gordon, Lever, Andrew M. L., Gurdasani, Deepti, Groom, Harriet, Sandhu, Manjinder S., and Fellay, Jacques
- Published
- 2023
- Full Text
- View/download PDF
15. CCR5AS lncRNA variation differentially regulates CCR5, influencing HIV disease outcome
- Author
-
Kulkarni, Smita, Lied, Alexandra, Kulkarni, Viraj, Rucevic, Marijana, Martin, Maureen P, Walker-Sperling, Victoria, Anderson, Stephen K, Ewy, Rodger, Singh, Sukhvinder, Nguyen, Hoang, McLaren, Paul J, Viard, Mathias, Naranbhai, Vivek, Zou, Chengcheng, Lin, Zhansong, Gatanaga, Hiroyuki, Oka, Shinichi, Takiguchi, Masafumi, Thio, Chloe L, Margolick, Joseph, Kirk, Gregory D, Goedert, James J, Hoots, W Keith, Deeks, Steven G, Haas, David W, Michael, Nelson, Walker, Bruce, Le Gall, Sylvie, Chowdhury, Fatema Z, Yu, Xu G, and Carrington, Mary
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Immunology ,Sexually Transmitted Infections ,Genetics ,Human Genome ,Infectious Diseases ,HIV/AIDS ,2.1 Biological and endogenous factors ,Infection ,Good Health and Well Being ,3' Untranslated Regions ,Alleles ,Biomarkers ,CD4-Positive T-Lymphocytes ,Cell Membrane ,Gene Expression Regulation ,Genes ,Reporter ,Genetic Variation ,Genotype ,HIV Infections ,HIV-1 ,Humans ,Linkage Disequilibrium ,Polymorphism ,Single Nucleotide ,Population Groups ,Prognosis ,RNA Stability ,RNA ,Antisense ,RNA ,Long Noncoding ,RNA ,Messenger ,Receptors ,CCR5 ,Viral Load ,Biochemistry and cell biology - Abstract
Multiple genome-wide studies have identified associations between outcome of human immunodeficiency virus (HIV) infection and polymorphisms in and around the gene encoding the HIV co-receptor CCR5, but the functional basis for the strongest of these associations, rs1015164A/G, is unknown. We found that rs1015164 marks variation in an activating transcription factor 1 binding site that controls expression of the antisense long noncoding RNA (lncRNA) CCR5AS. Knockdown or enhancement of CCR5AS expression resulted in a corresponding change in CCR5 expression on CD4+ T cells. CCR5AS interfered with interactions between the RNA-binding protein Raly and the CCR5 3' untranslated region, protecting CCR5 messenger RNA from Raly-mediated degradation. Reduction in CCR5 expression through inhibition of CCR5AS diminished infection of CD4+ T cells with CCR5-tropic HIV in vitro. These data represent a rare determination of the functional importance of a genome-wide disease association where expression of a lncRNA affects HIV infection and disease progression.
- Published
- 2019
16. Multi-Ancestry Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus
- Author
-
Vergara, Candelaria, Thio, Chloe L, Johnson, Eric, Kral, Alex H, O'Brien, Thomas R, Goedert, James J, Mangia, Alessandra, Piazzolla, Valeria, Mehta, Shruti H, Kirk, Gregory D, Kim, Arthur Y, Lauer, Georg M, Chung, Raymond T, Cox, Andrea L, Peters, Marion G, Khakoo, Salim I, Alric, Laurent, Cramp, Matthew E, Donfield, Sharyne M, Edlin, Brian R, Busch, Michael P, Alexander, Graeme, Rosen, Hugo R, Murphy, Edward L, Latanich, Rachel, Wojcik, Genevieve L, Taub, Margaret A, Valencia, Ana, Thomas, David L, and Duggal, Priya
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Nutrition and Dietetics ,Hepatitis - C ,Emerging Infectious Diseases ,Hepatitis ,Infectious Diseases ,Genetics ,Chronic Liver Disease and Cirrhosis ,Digestive Diseases ,Human Genome ,Liver Disease ,Infection ,Good Health and Well Being ,Black People ,Female ,Genome-Wide Association Study ,Hepacivirus ,Hepatitis C ,Hispanic or Latino ,Host-Pathogen Interactions ,Humans ,Interferons ,Interleukins ,Major Histocompatibility Complex ,Male ,Receptors ,G-Protein-Coupled ,Remission ,Spontaneous ,United States ,Viral Load ,White People ,GWAS ,SNP ,Risk ,Cytokine ,Neurosciences ,Paediatrics and Reproductive Medicine ,Gastroenterology & Hepatology ,Clinical sciences ,Nutrition and dietetics - Abstract
Background & aimsSpontaneous clearance of hepatitis C virus (HCV) occurs in approximately 30% of infected persons and less often in populations of African ancestry. Variants in major histocompatibility complex (MHC) and in interferon lambda genes are associated with spontaneous HCV clearance, but there have been few studies of these variants in persons of African ancestry. We performed a dense multi-ancestry genome-wide association study of spontaneous clearance of HCV, focusing on individuals of African ancestry.MethodsWe performed genotype analyses of 4423 people from 3 ancestry groups: 2201 persons of African ancestry (445 with HCV clearance and 1756 with HCV persistence), 1739 persons of European ancestry (701 with HCV clearance and 1036 with HCV persistence), and 486 multi-ancestry Hispanic persons (173 with HCV clearance and 313 with HCV persistence). Samples were genotyped using Illumina (San Diego, CA) arrays and statistically imputed to the 1000 Genomes Project. For each ancestry group, the association of single-nucleotide polymorphisms with HCV clearance was tested by log-additive analysis, and then a meta-analysis was performed.ResultsIn the meta-analysis, significant associations with HCV clearance were confirmed at the interferon lambda gene locus IFNL4-IFNL3 (19q13.2) (P = 5.99 × 10-50) and the MHC locus 6p21.32 (P = 1.15 × 10-21). We also associated HCV clearance with polymorphisms in the G-protein-coupled receptor 158 gene (GPR158) at 10p12.1 (P = 1.80 × 10-07). These 3 loci had independent, additive effects of HCV clearance, and account for 6.8% and 5.9% of the variance of HCV clearance in persons of European and African ancestry, respectively. Persons of African or European ancestry carrying all 6 variants were 24-fold and 11-fold, respectively, more likely to clear HCV infection compared with individuals carrying none or 1 of the clearance-associated variants.ConclusionsIn a meta-analysis of data from 3 studies, we found variants in MHC genes, IFNL4-IFNL3, and GPR158 to increase odds of HCV clearance in patients of European and African ancestry. These findings could increase our understanding of immune response to and clearance of HCV infection.
- Published
- 2019
17. Cranium of an Eocene/Oligocene pheasant-sized galliform bird from western North America, with the description of a vascular autapomorphy of the Galliformes
- Author
-
Mayr, Gerald, Goedert, James L., and Rabenstein, Renate
- Published
- 2022
- Full Text
- View/download PDF
18. Reusing a prepaid health plan’s fecal immunochemical tests for microbiome associations with colorectal adenoma
- Author
-
Goedert, James J., Wu, Zhenyi, Yonehara, Cyndee H., Frankland, Timothy B., Sinha, Rashmi, Jones, Gieira S., Wan, Yunhu, Ravel, Jacques, Zhao, Ni, and Honda, Stacey A.
- Published
- 2022
- Full Text
- View/download PDF
19. HLA tapasin independence : broader peptide repertoire and HIV control
- Author
-
Bashirova, Arman A., Viard, Mathias, Naranbhai, Vivek, Grifoni, Alba, Garcia-Beltran, Wilfredo, Akdag, Marjan, Yuki, Yuko, Gao, Xiaojiang, O’hUigin, Colm, Raghavan, Malini, Wolinsky, Steven, Bream, Jay H., Duggal, Priya, Martinson, Jeremy, Michael, Nelson L., Kirk, Gregory D., Buchbinder, Susan P., Haas, David, Goedert, James J., Deeks, Steven G., Fellay, Jacques, Walker, Bruce, Goulder, Philip, Cresswell, Peter, Elliott, Tim, Sette, Alessandro, Carlson, Jonathan, and Carrington, Mary
- Published
- 2020
20. Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1
- Author
-
Martin, Maureen P, Naranbhai, Vivek, Shea, Patrick R, Qi, Ying, Ramsuran, Veron, Vince, Nicolas, Gao, Xiaojiang, Thomas, Rasmi, Brumme, Zabrina L, Carlson, Jonathan M, Wolinsky, Steven M, Goedert, James J, Walker, Bruce D, Segal, Florencia P, Deeks, Steven G, Haas, David W, Migueles, Stephen A, Connors, Mark, Michael, Nelson, Fellay, Jacques, Gostick, Emma, Llewellyn-Lacey, Sian, Price, David A, Lafont, Bernard A, Pymm, Phillip, Saunders, Philippa M, Widjaja, Jacqueline, Wong, Shu Cheng, Vivian, Julian P, Rossjohn, Jamie, Brooks, Andrew G, and Carrington, Mary
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Immunology ,Infectious Diseases ,Genetics ,HIV/AIDS ,Human Genome ,Clinical Research ,Sexually Transmitted Infections ,2.1 Biological and endogenous factors ,Aetiology ,Infection ,Good Health and Well Being ,Adult ,Cohort Studies ,Female ,Genetic Variation ,HIV Infections ,HIV-1 ,HLA-B Antigens ,Humans ,Male ,Middle Aged ,Receptors ,KIR3DL1 ,AIDS/HIV ,Innate immunity ,MHC class 1 ,NK cells ,Medical and Health Sciences ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
HLA-B*57 control of HIV involves enhanced CD8+ T cell responses against infected cells, but extensive heterogeneity exists in the level of HIV control among B*57+ individuals. Using whole-genome sequencing of untreated B*57+ HIV-1-infected controllers and noncontrollers, we identified a single variant (rs643347A/G) encoding an isoleucine-to-valine substitution at position 47 (I47V) of the inhibitory killer cell immunoglobulin-like receptor KIR3DL1 as the only significant modifier of B*57 protection. The association was replicated in an independent cohort and across multiple outcomes. The modifying effect of I47V was confined to B*57:01 and was not observed for the closely related B*57:03. Positions 2, 47, and 54 tracked one another nearly perfectly, and 2 KIR3DL1 allotypes differing only at these 3 positions showed significant differences in binding B*57:01 tetramers, whereas the protective allotype showed lower binding. Thus, variation in an immune NK cell receptor that binds B*57:01 modifies its protection. These data highlight the exquisite specificity of KIR-HLA interactions in human health and disease.
- Published
- 2018
21. Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells
- Author
-
Ramsuran, Veron, Naranbhai, Vivek, Horowitz, Amir, Qi, Ying, Martin, Maureen P, Yuki, Yuko, Gao, Xiaojiang, Walker-Sperling, Victoria, Del Prete, Gregory Q, Schneider, Douglas K, Lifson, Jeffrey D, Fellay, Jacques, Deeks, Steven G, Martin, Jeffrey N, Goedert, James J, Wolinsky, Steven M, Michael, Nelson L, Kirk, Gregory D, Buchbinder, Susan, Haas, David, Ndung’u, Thumbi, Goulder, Philip, Parham, Peter, Walker, Bruce D, Carlson, Jonathan M, and Carrington, Mary
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Immunology ,Sexually Transmitted Infections ,HIV/AIDS ,Women's Health ,Infectious Diseases ,Aetiology ,2.1 Biological and endogenous factors ,Development of treatments and therapeutic interventions ,5.1 Pharmaceuticals ,Infection ,Alleles ,CD4 Lymphocyte Count ,Cohort Studies ,HIV ,HIV Infections ,HLA Antigens ,Humans ,Killer Cells ,Natural ,Ligands ,NK Cell Lectin-Like Receptor Subfamily C ,Protein Sorting Signals ,Viremia ,General Science & Technology - Abstract
The highly polymorphic human leukocyte antigen (HLA) locus encodes cell surface proteins that are critical for immunity. HLA-A expression levels vary in an allele-dependent manner, diversifying allele-specific effects beyond peptide-binding preference. Analysis of 9763 HIV-infected individuals from 21 cohorts shows that higher HLA-A levels confer poorer control of HIV. Elevated HLA-A expression provides enhanced levels of an HLA-A-derived signal peptide that specifically binds and determines expression levels of HLA-E, the ligand for the inhibitory NKG2A natural killer (NK) cell receptor. HLA-B haplotypes that favor NKG2A-mediated NK cell licensing (i.e., education) exacerbate the deleterious effect of high HLA-A on HIV control, consistent with NKG2A-mediated inhibition impairing NK cell clearance of HIV-infected targets. Therapeutic blockade of HLA-E:NKG2A interaction may yield benefit in HIV disease.
- Published
- 2018
22. HLA-B*14:02-Restricted Env-Specific CD8+ T-Cell Activity Has Highly Potent Antiviral Efficacy Associated with Immune Control of HIV Infection
- Author
-
Leitman, Ellen M, Willberg, Christian B, Tsai, Ming-Han, Chen, Huabiao, Buus, Søren, Chen, Fabian, Riddell, Lynn, Haas, David, Fellay, Jacques, Goedert, James J, Piechocka-Trocha, Alicja, Walker, Bruce D, Martin, Jeffrey, Deeks, Steven, Wolinsky, Steven M, Martinson, Jeremy, Martin, Maureen, Qi, Ying, Sáez-Cirión, Asier, Yang, Otto O, Matthews, Philippa C, Carrington, Mary, and Goulder, Philip JR
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Immunology ,Infectious Diseases ,Immunization ,Vaccine Related ,HIV/AIDS ,Sexually Transmitted Infections ,Clinical Research ,Prevention ,Vaccine Related (AIDS) ,2.1 Biological and endogenous factors ,Inflammatory and immune system ,Infection ,Good Health and Well Being ,Adult ,CD8-Positive T-Lymphocytes ,HIV Envelope Protein gp160 ,HIV Infections ,HIV-1 ,HLA-B14 Antigen ,Humans ,Immunity ,Cellular ,Peptides ,gag Gene Products ,Human Immunodeficiency Virus ,CD8(+) T cells ,HIV ,HLA-B*14 ,immune control ,CD8+ T cells ,Biological Sciences ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Virology ,Agricultural ,veterinary and food sciences ,Biological sciences ,Biomedical and clinical sciences - Abstract
Immune control of human immunodeficiency virus type 1 (HIV) infection is typically associated with effective Gag-specific CD8+ T-cell responses. We here focus on HLA-B*14, which protects against HIV disease progression, but the immunodominant HLA-B*14-restricted anti-HIV response is Env specific (ERYLKDQQL, HLA-B*14-EL9). A subdominant HLA-B*14-restricted response targets Gag (DRYFKTLRA, HLA-B*14-DA9). Using HLA-B*14/peptide-saporin-conjugated tetramers, we show that HLA-B*14-EL9 is substantially more potent at inhibiting viral replication than HLA-B*14-DA9. HLA-B*14-EL9 also has significantly higher functional avidity (P < 0.0001) and drives stronger selection pressure on the virus than HLA-B*14-DA9. However, these differences were HLA-B*14 subtype specific, applying only to HLA-B*14:02 and not to HLA-B*14:01. Furthermore, the HLA-B*14-associated protection against HIV disease progression is significantly greater for HLA-B*14:02 than for HLA-B*14:01, consistent with the superior antiviral efficacy of the HLA-B*14-EL9 response. Thus, although Gag-specific CD8+ T-cell responses may usually have greater anti-HIV efficacy, factors independent of protein specificity, including functional avidity of individual responses, are also critically important to immune control of HIV.IMPORTANCE In HIV infection, although cytotoxic T lymphocytes (CTL) play a potentially critical role in eradication of viral reservoirs, the features that constitute an effective response remain poorly defined. We focus on HLA-B*14, unique among HLAs associated with control of HIV in that the dominant CTL response is Env specific, not Gag specific. We demonstrate that Env-specific HLA-B*14-restricted activity is substantially more efficacious than the subdominant HLA-B*14-restricted Gag response. Env immunodominance over Gag and strong Env-mediated selection pressure on HIV are observed only in subjects expressing HLA-B*14:02, and not HLA-B*14:01. This reflects the increased functional avidity of the Env response over Gag, substantially more marked for HLA-B*14:02. Finally, we show that HLA-B*14:02 is significantly more strongly associated with viremic control than HLA-B*14:01. These findings indicate that, although Gag-specific CTL may usually have greater anti-HIV efficacy than Env responses, factors independent of protein specificity, including functional avidity, may carry greater weight in mediating effective control of HIV.
- Published
- 2017
23. The oldest mysticete in the Northern Hemisphere
- Author
-
Tsai, Cheng-Hsiu, primary, Goedert, James L., additional, and Boessenecker, Robert W., additional
- Published
- 2024
- Full Text
- View/download PDF
24. Impact of HLA class I functional divergence on HIV control
- Author
-
Viard, Mathias, primary, O’hUigin, Colm, additional, Yuki, Yuko, additional, Bashirova, Arman A., additional, Collins, David R., additional, Urbach, Jonathan M., additional, Wolinsky, Steven, additional, Buchbinder, Susan, additional, Kirk, Gregory D., additional, Goedert, James J., additional, Michael, Nelson L., additional, Haas, David W., additional, Deeks, Steven G., additional, Walker, Bruce D., additional, Yu, Xu, additional, and Carrington, Mary, additional
- Published
- 2024
- Full Text
- View/download PDF
25. Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma
- Author
-
Liu, Zhiwei, primary, Luo, Yang, additional, Kirimunda, Samuel, additional, Verboom, Murielle, additional, Onabajo, Olusegun O., additional, Gouveia, Mateus H., additional, Ogwang, Martin D., additional, Kerchan, Patrick, additional, Reynolds, Steven J., additional, Tenge, Constance N., additional, Were, Pamela A., additional, Kuremu, Robert T., additional, Wekesa, Walter N., additional, Masalu, Nestory, additional, Kawira, Esther, additional, Kinyera, Tobias, additional, Otim, Isaac, additional, Legason, Ismail D., additional, Nabalende, Hadijah, additional, Dhudha, Herry, additional, Ayers, Leona W., additional, Bhatia, Kishor, additional, Goedert, James J., additional, Cole, Nathan, additional, Luo, Wen, additional, Liu, Jia, additional, Manning, Michelle, additional, Hicks, Belynda, additional, Prokunina-Olsson, Ludmila, additional, Chagaluka, George, additional, Johnston, W. Thomas, additional, Mutalima, Nora, additional, Borgstein, Eric, additional, Liomba, George N., additional, Kamiza, Steve, additional, Mkandawire, Nyengo, additional, Mitambo, Collins, additional, Molyneux, Elizabeth M., additional, Newton, Robert, additional, Hsing, Ann W., additional, Mensah, James E., additional, Adjei, Anthony A., additional, Hutchinson, Amy, additional, Carrington, Mary, additional, Yeager, Meredith, additional, Blasczyk, Rainer, additional, Chanock, Stephen J., additional, Raychaudhuri, Soumya, additional, and Mbulaiteye, Sam M., additional
- Published
- 2024
- Full Text
- View/download PDF
26. Cancer-Attributable Mortality Among People With Treated Human Immunodeficiency Virus Infection in North America
- Author
-
Engels, Eric A, Yanik, Elizabeth L, Wheeler, Willian, Gill, M John, Shiels, Meredith S, Dubrow, Robert, Althoff, Keri N, Silverberg, Michael J, Brooks, John T, Kitahata, Mari M, Goedert, James J, Grover, Surbhi, Mayor, Angel M, Moore, Richard D, Park, Lesley S, Rachlis, Anita, Sigel, Keith, Sterling, Timothy R, Thorne, Jennifer E, Pfeiffer, Ruth M, Benson, Constance A, Bosch, Ronald J, Kirk, Gregory D, Boswell, Stephen, Mayer, Kenneth H, Grasso, Chris, Hogg, Robert S, Harrigan, P Richard, Montaner, Julio SG, Yip, Benita, Zhu, Julia, Salters, Kate, Gabler, Karyn, Buchacz, Kate, Gebo, Kelly A, Carey, John T, Rodriguez, Benigno, Horberg, Michael A, Rabkin, Charles, Jacobson, Lisa P, D’Souza, Gypsyamber, Klein, Marina B, Rourke, Sean B, Rachlis, Anita R, Globerman, Jason, Kopansky-Giles, Madison, Hunter-Mellado, Robert F, Deeks, Steven G, Martin, Jeffrey N, Patel, Pragna, Saag, Michael S, Mugavero, Michael J, Willig, James, Eron, Joseph J, Napravnik, Sonia, Crane, Heidi M, Drozd, Daniel R, Haas, David, Rebeiro, Peter, Turner, Megan, Bebawy, Sally, Rogers, Ben, Justice, Amy C, Fiellin, David, Gange, Stephen J, Anastos, Kathryn, McKaig, Rosemary G, Freeman, Aimee M, Lent, Carol, Van Rompaey, Stephen E, Morton, Liz, McReynolds, Justin, Lober, William B, Abraham, Alison G, Lau, Bryan, Zhang, Jinbing, and Jing, Jerry
- Subjects
Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Lung ,Sexually Transmitted Infections ,Hematology ,Lymphatic Research ,HIV/AIDS ,Infectious Diseases ,Cancer ,Lymphoma ,Rare Diseases ,Lung Cancer ,2.1 Biological and endogenous factors ,2.4 Surveillance and distribution ,Aetiology ,Infection ,Good Health and Well Being ,Adolescent ,Adult ,CD4 Lymphocyte Count ,Female ,HIV Infections ,Humans ,Male ,Middle Aged ,Neoplasms ,North America ,Proportional Hazards Models ,Retrospective Studies ,Viral Load ,Young Adult ,HIV ,AIDS ,cancer ,mortality ,aging ,North American AIDS Cohort Collaboration on Research and Design of the International Epidemiologic Databases to Evaluate AIDS ,North American AIDS Cohort Collaboration on Research and Design of the International Epidemiologic Databases to Evaluate AIDS ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Clinical sciences - Abstract
BackgroundCancer remains an important cause of morbidity and mortality in people with human immunodeficiency virus (PWHIV) on effective antiretroviral therapy (ART). Estimates of cancer-attributable mortality can inform public health efforts.MethodsWe evaluated 46956 PWHIV receiving ART in North American HIV cohorts (1995-2009). Using information on incident cancers and deaths, we calculated population-attributable fractions (PAFs), estimating the proportion of deaths due to cancer. Calculations were based on proportional hazards models adjusted for age, sex, race, HIV risk group, calendar year, cohort, CD4 count, and viral load.ResultsThere were 1997 incident cancers and 8956 deaths during 267145 person-years of follow-up, and 11.9% of decedents had a prior cancer. An estimated 9.8% of deaths were attributable to cancer (cancer-attributable mortality rate 327 per 100000 person-years). PAFs were 2.6% for AIDS-defining cancers (ADCs, including non-Hodgkin lymphoma, 2.0% of deaths) and 7.1% for non-AIDS-defining cancers (NADCs: lung cancer, 2.3%; liver cancer, 0.9%). PAFs for NADCs were higher in males and increased strongly with age, reaching 12.5% in PWHIV aged 55+ years. Mortality rates attributable to ADCs and NADCs were highest for PWHIV with CD4 counts
- Published
- 2017
27. Association of CD4+ T-cell Count, HIV-1 RNA Viral Load, and Antiretroviral Therapy With Kaposi Sarcoma Risk Among HIV-infected Persons in the United States and Canada
- Author
-
Dubrow, Robert, Qin, Li, Lin, Haiqun, Hernández-Ramírez, Raúl U, Neugebauer, Romain S, Leyden, Wendy, Althoff, Keri N, Achenbach, Chad J, Hessol, Nancy A, Modur, Sharada P, D'Souza, Gypsyamber, Bosch, Ronald J, Grover, Surbhi, Horberg, Michael A, Kitahata, Mari M, Mayor, Angel M, Novak, Richard M, Rabkin, Charles S, Sterling, Timothy R, Goedert, James J, Justice, Amy C, Engels, Eric A, Moore, Richard D, and Silverberg, Michael J
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Public Health ,Health Sciences ,HIV/AIDS ,Infectious Diseases ,Emerging Infectious Diseases ,Sexually Transmitted Infections ,Prevention ,Infection ,Adult ,Anti-HIV Agents ,CD4 Lymphocyte Count ,CD4-Positive T-Lymphocytes ,Canada ,Cohort Studies ,Female ,HIV Infections ,Humans ,Male ,Middle Aged ,Proportional Hazards Models ,RNA ,Viral ,Sarcoma ,Kaposi ,United States ,Viral Load ,Kaposi sarcoma ,HIV infection ,acquired immunodeficiency syndrome ,CD4(+) T-cell count ,HIV-1 RNA viral load ,antiretroviral therapy ,North American AIDS Cohort Collaboration on Research and Design of the International Epidemiologic Databases to Evaluate AIDS ,Clinical Sciences ,Public Health and Health Services ,Virology ,Clinical sciences ,Epidemiology ,Public health - Abstract
BackgroundKaposi sarcoma (KS) remains common among HIV-infected persons. To better understand KS etiology and to help target prevention efforts, we comprehensively examined a variety of CD4 T-cell count and HIV-1 RNA viral load (VL) measures, as well as antiretroviral therapy (ART) use, to determine independent predictors of KS risk.SettingNorth American AIDS Cohort Collaboration on Research and Design.MethodsWe followed HIV-infected persons during 1996-2009 from 18 cohorts. We used time-updated Cox regression to model relationships between KS risk and recent, lagged, trajectory, and cumulative CD4 count or VL measures, as well as ART use. We used Akaike's information criterion and global P values to derive a final model.ResultsIn separate models, the relationship between each measure and KS risk was highly significant (P < 0.0001). Our final mutually adjusted model included recent CD4 count [hazard ratio (HR) for
- Published
- 2017
28. HIV Infection, Immunosuppression, and Age at Diagnosis of Non-AIDS-Defining Cancers
- Author
-
Shiels, Meredith S, Althoff, Keri N, Pfeiffer, Ruth M, Achenbach, Chad J, Abraham, Alison G, Castilho, Jessica, Cescon, Angela, D’Souza, Gypsyamber, Dubrow, Robert, Eron, Joseph J, Gebo, Kelly, Gill, M John, Goedert, James J, Grover, Surbhi, Hessol, Nancy A, Justice, Amy, Kitahata, Mari, Mayor, Angel, Moore, Richard D, Napravnik, Sonia, Novak, Richard M, Thorne, Jennifer E, Silverberg, Michael J, Engels, Eric A, and AIDS, for the North American AIDS Cohort Collaboration on Research and Design of the International Epidemiologic Databases to Evaluate
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Lung Cancer ,Rare Diseases ,Health Disparities ,Cancer ,Lung ,Sexually Transmitted Infections ,Infectious Diseases ,HIV/AIDS ,Aetiology ,2.1 Biological and endogenous factors ,Adult ,Age Factors ,Aged ,CD4 Lymphocyte Count ,Cohort Studies ,Female ,HIV Infections ,Humans ,Immune Tolerance ,Male ,Middle Aged ,Neoplasms ,Young Adult ,HIV ,cancer ,immunosuppression ,AIDS ,aging ,North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) of the International Epidemiologic Databases to Evaluate AIDS ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Clinical sciences - Abstract
BackgroundIt is unclear whether immunosuppression leads to younger ages at cancer diagnosis among people living with human immunodeficiency virus (PLWH). A previous study found that most cancers are not diagnosed at a younger age in people with AIDS, with the exception of anal and lung cancers. This study extends prior work to include all PLWH and examines associations between AIDS, CD4 count, and age at cancer diagnosis.MethodsWe compared the median age at cancer diagnosis between PLWH in the North American AIDS Cohort Collaboration on Research and Design and the general population using data from the Surveillance, Epidemiology and End Results Program. We used statistical weights to adjust for population differences. We also compared median age at cancer diagnosis by AIDS status and CD4 count.ResultsAfter adjusting for population differences, younger ages at diagnosis (P < .05) were observed for PLWH compared with the general population for lung (difference in medians = 4 years), anal (difference = 4), oral cavity/pharynx (difference = 2), and kidney cancers (difference = 2) and myeloma (difference = 4). Among PLWH, having an AIDS-defining event was associated with a younger age at myeloma diagnosis (difference = 4; P = .01), and CD4 count
- Published
- 2017
29. Risk of End-Stage Liver Disease in HIV-Viral Hepatitis Coinfected Persons in North America From the Early to Modern Antiretroviral Therapy Eras
- Author
-
Klein, Marina B, Althoff, Keri N, Jing, Yuezhou, Lau, Bryan, Kitahata, Mari, Re, Vincent Lo, Kirk, Gregory D, Hull, Mark, Kim, H Nina, Sebastiani, Giada, Moodie, Erica EM, Silverberg, Michael J, Sterling, Timothy R, Thorne, Jennifer E, Cescon, Angela, Napravnik, Sonia, Eron, Joe, Gill, M John, Justice, Amy, Peters, Marion G, Goedert, James J, Mayor, Angel, Thio, Chloe L, Cachay, Edward R, Moore, Richard, Research and Design of IeDEA, for the North American AIDS Cohort Collaboration on, Benson, Constance A, Bosch, Ronald J, Boswell, Stephen, Mayer, Kenneth H, Grasso, Chris, Hogg, Robert S, Harrigan, P Richard, Montaner, Julio SG, Samji, Hasina, Brooks, John T, Buchacz, Kate, Gebo, Kelly A, Moore, Richard D, Rodriguez, Benigno, Horberg, Michael A, Jacobsonc, Lisa P, D'Souza, Gypsyamber, Rourke, Sean B, Burchell, Ann N, Rachlis, Anita R, Hunter-Mellado, Robert F, Mayor, Angel M, Deeks, Steven G, Martin, Jeffrey N, Patel, Pragna, Saag, Michael S, Mugavero, Michael J, Willig, James, Eron, Joseph J, Kitahata, Mari M, Crane, Heidi M, Drozd, Daniel R, Haas, David, Bebawy, Sally, Turner, Megan, Justice, Amy C, Dubrow, Robert, Fiellin, David, Gange, Stephen J, Anastos, Kathryn, McKaig, Rosemary G, Freeman, Aimee M, Lent, Carol, Van Rompaey, Stephen E, Morton, Liz, McReynolds, Justin, Lober, William B, and Abraham, Alison G
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Clinical Sciences ,Hepatitis ,Emerging Infectious Diseases ,Chronic Liver Disease and Cirrhosis ,Hepatitis - C ,Digestive Diseases ,Liver Disease ,Hepatitis - B ,Sexually Transmitted Infections ,Infectious Diseases ,HIV/AIDS ,6.1 Pharmaceuticals ,Evaluation of treatments and therapeutic interventions ,Infection ,Good Health and Well Being ,Adult ,Aged ,Alcohol Drinking ,Anti-HIV Agents ,Canada ,Cohort Studies ,Coinfection ,End Stage Liver Disease ,Female ,HIV Infections ,Hepatitis B ,Hepatitis C ,Humans ,Incidence ,Male ,Middle Aged ,Risk Factors ,United States ,HIV ,hepatitis C virus ,hepatitis B virus ,coinfection ,end-stage liver disease ,North American AIDS Cohort Collaboration on Research and Design of IeDEA ,North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) of IeDEA ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Clinical sciences - Abstract
BackgroundHuman immunodeficiency virus (HIV)-infected patients coinfected with hepatitis B (HBV) and C (HCV) viruses are at increased risk of end-stage liver disease (ESLD). Whether modern antiretroviral therapy has reduced ESLD risk is unknown.MethodsTwelve clinical cohorts in the United States and Canada participating in the North American AIDS Cohort Collaboration on Research and Design validated ESLD events from 1996 to 2010. ESLD incidence rates and rate ratios according to hepatitis status adjusted for age, sex, race, cohort, time-updated CD4 cell count and HIV RNA were estimated in calendar periods corresponding to major changes in antiretroviral therapy: early (1996-2000), middle (2001-2005), and modern (2006-2010) eras.ResultsAmong 34 119 HIV-infected adults followed for 129 818 person-years, 380 incident ESLD outcomes occurred. ESLD incidence (per 1000 person-years) was highest in triply infected (11.57) followed by HBV- (8.72) and HCV- (6.10) coinfected vs 1.27 in HIV-monoinfected patients. Adjusted incidence rate ratios (95% confidence intervals) comparing the modern to the early antiretroviral era were 0.95 (.61-1.47) for HCV, 0.95 (.40-2.26) for HBV, and 1.52 (.46-5.02) for triply infected patients. Use of antiretrovirals dually activity against HBV increased over time. However, in the modern era, 35% of HBV-coinfected patients were not receiving tenofovir. There was little use of HCV therapy.ConclusionsDespite increasing use of antiretrovirals, no clear reduction in ESLD risk was observed over 15 years. Treatment with direct-acting antivirals for HCV and wider use of tenofovir-based regimens for HBV should be prioritized for coinfected patients.
- Published
- 2016
30. A lower jaw of the nautiloid Aturia angustata (Conrad, 1849) from Oligocene cold seep limestone, Washington State, U.S.A.
- Author
-
Goedert, James L. and Kiel, Steffen
- Subjects
Oligocene ,nautiloid jaw ,Aturia ,Washington State - Abstract
Fossil shells of the extinct nautiloid genus Aturia have been found in Cenozoic strata in many parts of the world, and yet there have only been two previous records of fossils of any part of the jaw apparatus of Aturia. This suggests that the jaws were only preserved by virtue of special, highly localized conditions. A fossilized lower jaw referable to Aturia has been found in western Washington State, USA, associated with two shells of Aturia angustata within a piece of limestone that formed as a result of localized hydrocarbon seepage on the deep-sea floor. This is the first report of a nautiloid jaw from Cenozoic strata of western North America, and the first report of any part of the jaw apparatus for A. angustata.
- Published
- 2016
31. Fluid expulsion system and tectonic architecture of the incipient Cascadia convergent margin as revealed by Nd, Sr and stable isotope composition of mid-Eocene methane seep carbonates
- Author
-
Jakubowicz, Michal, Kiel, Steffen, Goedert, James L., Dopieralska, Jolanta, and Belka, Zdzislaw
- Published
- 2020
- Full Text
- View/download PDF
32. First report of the megathyridid (Terebratellidina) brachiopod Argyrotheca from a hydrocarbon seep deposit, middle Eocene Humptulips Formation, Washington State, USA
- Author
-
Goedert, James L., Sandy, Michael R., and Peckmann, Jörn
- Published
- 2021
- Full Text
- View/download PDF
33. Incidence of AIDS-Defining Opportunistic Infections in a Multicohort Analysis of HIV-infected Persons in the United States and Canada, 2000–2010
- Author
-
Buchacz, Kate, Lau, Bryan, Jing, Yuezhou, Bosch, Ronald, Abraham, Alison G, Gill, M John, Silverberg, Michael J, Goedert, James J, Sterling, Timothy R, Althoff, Keri N, Martin, Jeffrey N, Burkholder, Greer, Gandhi, Neel, Samji, Hasina, Patel, Pragna, Rachlis, Anita, Thorne, Jennifer E, Napravnik, Sonia, Henry, Keith, Mayor, Angel, Gebo, Kelly, Gange, Stephen J, Moore, Richard D, Brooks, John T, Research and Design of IeDEA, for the North American AIDS Cohort Collaboration on, Kirk, Gregory D, Benson, Constance A, Bosch, Ronald J, Boswell, Stephen, Mayer, Kenneth H, Grasso, Chris, Hogg, Robert S, Harrigan, P Richard, Montaner, Julio SG, Cescon, Angela, Gebo, Kelly A, Carey, John T, Rodriguez, Benigno, Horberg, Michael A, Jacobson, Lisa P, D'Souza, Gypsyamber, Klein, Marina B, Rourke, Sean B, Burchell, Ann N, Rachlis, Anita R, Hunter-Mellado, Robert F, Mayor, Angel M, Deeks, Steven G, Saag, Michael S, Mugavero, Michael J, Willig, James, Eron, Joseph J, Kitahata, Mari M, Crane, Heidi M, Drozd, Daniel R, Rebeiro, Peter F, Haas, David, Bebawy, Sally, Turner, Megan, Justice, Amy C, Dubrow, Robert, Fiellin, David, and Anastos, Kathryn
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Clinical Sciences ,Sexually Transmitted Infections ,Infectious Diseases ,Clinical Research ,HIV/AIDS ,Infection ,AIDS-Related Opportunistic Infections ,Adult ,Canada ,Cohort Studies ,Female ,Humans ,Incidence ,Male ,Middle Aged ,Survival Analysis ,United States ,AIDS-related opportunistic infections ,HIV cohort studies ,incidence ,prophylaxis ,combination antiretroviral therapy ,CD4(+) T-lymphocyte count ,epidemiology ,North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) of IeDEA ,CD4+ T-lymphocyte count ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundThere are few recent data on the rates of AIDS-defining opportunistic infections (OIs) among human immunodeficiency virus (HIV)-infected patients in care in the United States and Canada.MethodsWe studied HIV-infected participants in 16 cohorts in the North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) during 2000-2010. After excluding 16 737 (21%) with any AIDS-defining clinical events documented before NA-ACCORD enrollment, we analyzed incident OIs among the remaining 63 541 persons, most of whom received antiretroviral therapy during the observation. We calculated incidence rates per 100 person-years of observation (hereafter, "person-years") with 95% confidence intervals (CIs) for the first occurrence of any OI and select individual OIs during 2000-2003, 2004-2007, and 2008-2010.ResultsA total of 63 541 persons contributed 261 573 person-years, of whom 5836 (9%) developed at least 1 OI. The incidence rate of any first OI decreased over the 3 observation periods, with 3.0 cases, 2.4 cases, and 1.5 cases per 100 person-years of observation during 2000-2003, 2004-2007, and 2008-2010, respectively (Ptrend
- Published
- 2016
34. Sickle cell allele HBB‐rs334(T) is associated with decreased risk of childhood Burkitt lymphoma in East Africa
- Author
-
Hong, Hyokyoung G., primary, Gouveia, Mateus H., additional, Ogwang, Martin D., additional, Kerchan, Patrick, additional, Reynolds, Steven J., additional, Tenge, Constance N., additional, Were, Pamela A., additional, Kuremu, Robert T., additional, Wekesa, Walter N., additional, Masalu, Nestory, additional, Kawira, Esther, additional, Kinyera, Tobias, additional, Wang, Xunde, additional, Zhou, Jiefu, additional, Leal, Thiago Peixoto, additional, Otim, Isaac, additional, Legason, Ismail D., additional, Nabalende, Hadijah, additional, Dhudha, Herry, additional, Mumia, Mediatrix, additional, Baker, Francine S., additional, Okusolubo, Temiloluwa, additional, Ayers, Leona W., additional, Bhatia, Kishor, additional, Goedert, James J., additional, Woo, Joshua, additional, Manning, Michelle, additional, Cole, Nathan, additional, Luo, Wen, additional, Hicks, Belynda, additional, Chagaluka, George, additional, Johnston, W. Thomas, additional, Mutalima, Nora, additional, Borgstein, Eric, additional, Liomba, George N., additional, Kamiza, Steve, additional, Mkandawire, Nyengo, additional, Mitambo, Collins, additional, Molyneux, Elizabeth M., additional, Newton, Robert, additional, Hutchinson, Amy, additional, Yeager, Meredith, additional, Adeyemo, Adebowale A., additional, Thein, Swee Lay, additional, Rotimi, Charles N., additional, Chanock, Stephen J., additional, Prokunina‐Olsson, Ludmila, additional, and Mbulaiteye, Sam M., additional
- Published
- 2023
- Full Text
- View/download PDF
35. Cumulative Incidence of Cancer Among Persons With HIV in North America: A Cohort Study.
- Author
-
Silverberg, Michael J, Lau, Bryan, Achenbach, Chad J, Jing, Yuezhou, Althoff, Keri N, D'Souza, Gypsyamber, Engels, Eric A, Hessol, Nancy A, Brooks, John T, Burchell, Ann N, Gill, M John, Goedert, James J, Hogg, Robert, Horberg, Michael A, Kirk, Gregory D, Kitahata, Mari M, Korthuis, Philip T, Mathews, William C, Mayor, Angel, Modur, Sharada P, Napravnik, Sonia, Novak, Richard M, Patel, Pragna, Rachlis, Anita R, Sterling, Timothy R, Willig, James H, Justice, Amy C, Moore, Richard D, Dubrow, Robert, and North American AIDS Cohort Collaboration on Research and Design of the International Epidemiologic Databases to Evaluate AIDS
- Subjects
North American AIDS Cohort Collaboration on Research and Design of the International Epidemiologic Databases to Evaluate AIDS ,Humans ,Sarcoma ,Kaposi ,HIV Infections ,Neoplasms ,Lymphoma ,Non-Hodgkin ,Colorectal Neoplasms ,Anus Neoplasms ,Liver Neoplasms ,Lung Neoplasms ,Incidence ,Proportional Hazards Models ,Cohort Studies ,Comorbidity ,Age Distribution ,Adult ,Aged ,Middle Aged ,North America ,Female ,Male ,Sarcoma ,Kaposi ,Lymphoma ,Non-Hodgkin ,General & Internal Medicine ,Medical and Health Sciences - Abstract
BackgroundCancer is increasingly common among persons with HIV.ObjectiveTo examine calendar trends in cumulative cancer incidence and hazard rate by HIV status.DesignCohort study.SettingNorth American AIDS Cohort Collaboration on Research and Design during 1996 to 2009.Participants86 620 persons with HIV and 196 987 uninfected adults.MeasurementsCancer type-specific cumulative incidence by age 75 years and calendar trends in cumulative incidence and hazard rates, each by HIV status.ResultsCumulative incidences of cancer by age 75 years for persons with and without HIV, respectively, were as follows: Kaposi sarcoma, 4.4% and 0.01%; non-Hodgkin lymphoma, 4.5% and 0.7%; lung cancer, 3.4% and 2.8%; anal cancer, 1.5% and 0.05%; colorectal cancer, 1.0% and 1.5%; liver cancer, 1.1% and 0.4%; Hodgkin lymphoma, 0.9% and 0.09%; melanoma, 0.5% and 0.6%; and oral cavity/pharyngeal cancer, 0.8% and 0.8%. Among persons with HIV, calendar trends in cumulative incidence and hazard rate decreased for Kaposi sarcoma and non-Hodgkin lymphoma. For anal, colorectal, and liver cancer, increasing cumulative incidence, but not hazard rate trends, were due to the decreasing mortality rate trend (-9% per year), allowing greater opportunity to be diagnosed. Despite decreasing hazard rate trends for lung cancer, Hodgkin lymphoma, and melanoma, cumulative incidence trends were not seen because of the compensating effect of the declining mortality rate.LimitationSecular trends in screening, smoking, and viral co-infections were not evaluated.ConclusionCumulative cancer incidence by age 75 years, approximating lifetime risk in persons with HIV, may have clinical utility in this population. The high cumulative incidences by age 75 years for Kaposi sarcoma, non-Hodgkin lymphoma, and lung cancer support early and sustained antiretroviral therapy and smoking cessation.
- Published
- 2015
36. Inverse association of falciparum positivity with endemic Burkitt lymphoma is robust in analyses adjusting for pre-enrollment malaria in the EMBLEM case-control study
- Author
-
Peprah, Sally, Ogwang, Martin D., Kerchan, Patrick, Reynolds, Steven J., Tenge, Constance N., Were, Pamela A., Kuremu, Robert T., Wekesa, Walter N., Masalu, Nestory, Kawira, Esther, Otim, Isaac, Legason, Ismail D., Ayers, Leona W., Bhatia, Kishor, Goedert, James J., Pfeiffer, Ruth M., and Mbulaiteye, Sam M.
- Published
- 2021
- Full Text
- View/download PDF
37. End-Stage Renal Disease Among HIV-Infected Adults in North America
- Author
-
Abraham, Alison G, Althoff, Keri N, Jing, Yuezhou, Estrella, Michelle M, Kitahata, Mari M, Wester, C William, Bosch, Ronald J, Crane, Heidi, Eron, Joseph, Gill, M John, Horberg, Michael A, Justice, Amy C, Klein, Marina, Mayor, Angel M, Moore, Richard D, Palella, Frank J, Parikh, Chirag R, Silverberg, Michael J, Golub, Elizabeth T, Jacobson, Lisa P, Napravnik, Sonia, Lucas, Gregory M, AIDS, for the North American AIDS Cohort Collaboration on Research and Design of the International Epidemiologic Databases to Evaluate, Kirk, Gregory D, Benson, Constance A, Collier, Ann C, Boswell, Stephen, Grasso, Chris, Mayer, Ken, Hogg, Robert S, Harrigan, Richard, Montaner, Julio, Cescon, Angela, Brooks, John T, Buchacz, Kate, Gebo, Kelly A, Carey, John T, Rodriguez, Benigno, Thorne, Jennifer E, Goedert, James J, Klein, Marina B, Rourke, Sean B, Burchell, Ann, Rachlis, Anita R, Hunter-Mellado, Robert F, Deeks, Steven G, Martin, Jeffrey N, Saag, Michael S, Mugavero, Michael J, Willig, James, Eron, Joseph J, Crane, Heidi M, Dubrow, Robert, Fiellin, David, Sterling, Timothy R, Haas, David, Bebawy, Sally, Turner, Megan, Gange, Stephen J, Anastos, Kathryn, McKaig, Rosemary G, Freeman, Aimee M, Lent, Carol, Van Rompaey, Stephen E, Webster, Eric, Morton, Liz, Simon, Brenda, Lau, Bryan, Zhang, Jinbing, Jing, Jerry, Golub, Elizabeth, Modur, Shari, Hanna, David B, Rebeiro, Peter, Wong, Cherise, and Mendes, Adell
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Clinical Sciences ,Infectious Diseases ,Clinical Research ,HIV/AIDS ,Prevention ,Kidney Disease ,Infection ,Good Health and Well Being ,Adolescent ,Adult ,Black or African American ,Aged ,Aged ,80 and over ,Cohort Studies ,Comorbidity ,Diabetes Mellitus ,Female ,HIV Infections ,Hepatitis C ,Humans ,Hypertension ,Incidence ,Kidney Failure ,Chronic ,Kidney Transplantation ,Male ,Middle Aged ,North America ,Prevalence ,Risk Factors ,Viral Load ,Young Adult ,end-stage renal disease ,chronic kidney disease ,HIV infection/AIDS ,glomerular filtration rate ,North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) of the International Epidemiologic Databases to Evaluate AIDS ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Clinical sciences - Abstract
BackgroundHuman immunodeficiency virus (HIV)-infected adults, particularly those of black race, are at high-risk for end-stage renal disease (ESRD), but contributing factors are evolving. We hypothesized that improvements in HIV treatment have led to declines in risk of ESRD, particularly among HIV-infected blacks.MethodsUsing data from the North American AIDS Cohort Collaboration for Research and Design from January 2000 to December 2009, we validated 286 incident ESRD cases using abstracted medical evidence of dialysis (lasting >6 months) or renal transplant. A total of 38 354 HIV-infected adults aged 18-80 years contributed 159 825 person-years (PYs). Age- and sex-standardized incidence ratios (SIRs) were estimated by race. Poisson regression was used to identify predictors of ESRD.ResultsHIV-infected ESRD cases were more likely to be of black race, have diabetes mellitus or hypertension, inject drugs, and/or have a prior AIDS-defining illness. The overall SIR was 3.2 (95% confidence interval [CI], 2.8-3.6) but was significantly higher among black patients (4.5 [95% CI, 3.9-5.2]). ESRD incidence declined from 532 to 303 per 100 000 PYs and 138 to 34 per 100 000 PYs over the time period for blacks and nonblacks, respectively, coincident with notable increases in both the prevalence of viral suppression and the prevalence of ESRD risk factors including diabetes mellitus, hypertension, and hepatitis C virus coinfection.ConclusionsThe risk of ESRD remains high among HIV-infected individuals in care but is declining with improvements in virologic suppression. HIV-infected black persons continue to comprise the majority of cases, as a result of higher viral loads, comorbidities, and genetic susceptibility.
- Published
- 2015
38. Risk of Breast Cancer With CXCR4-Using HIV Defined by V3 Loop Sequencing
- Author
-
Goedert, James J, Swenson, Luke C, Napolitano, Laura A, Haddad, Mojgan, Anastos, Kathryn, Minkoff, Howard, Young, Mary, Levine, Alexandra, Adeyemi, Oluwatoyin, Seaberg, Eric C, Aouizerat, Bradley, Rabkin, Charles S, Harrigan, P Richard, and Hessol, Nancy A
- Subjects
Biomedical and Clinical Sciences ,Health Sciences ,Oncology and Carcinogenesis ,Clinical Research ,Cancer ,Breast Cancer ,Adult ,Breast Neoplasms ,Case-Control Studies ,Female ,Genetic Predisposition to Disease ,HIV ,HIV Infections ,Humans ,Middle Aged ,Receptors ,CXCR4 ,chemokine receptors ,AIDS ,breast cancer ,parallel sequencing ,women ,Clinical Sciences ,Public Health and Health Services ,Virology ,Clinical sciences ,Epidemiology ,Public health - Abstract
ObjectiveEvaluate the risk of female breast cancer associated with HIV-CXCR4 (X4) tropism as determined by various genotypic measures.MethodsA breast cancer case-control study, with pairwise comparisons of tropism determination methods, was conducted. From the Women's Interagency HIV Study repository, one stored plasma specimen was selected from 25 HIV-infected cases near the breast cancer diagnosis date and 75 HIV-infected control women matched for age and calendar date. HIV-gp120 V3 sequences were derived by Sanger population sequencing (PS) and 454-pyro deep sequencing (DS). Sequencing-based HIV-X4 tropism was defined using the geno2pheno algorithm, with both high-stringency DS [false-positive rate (3.5) and 2% X4 cutoff], and lower stringency DS (false-positive rate, 5.75 and 15% X4 cutoff). Concordance of tropism results by PS, DS, and previously performed phenotyping was assessed with kappa (κ) statistics. Case-control comparisons used exact P values and conditional logistic regression.ResultsIn 74 women (19 cases, 55 controls) with complete results, prevalence of HIV-X4 by PS was 5% in cases vs 29% in controls (P = 0.06; odds ratio, 0.14; confidence interval: 0.003 to 1.03). Smaller case-control prevalence differences were found with high-stringency DS (21% vs 36%, P = 0.32), lower stringency DS (16% vs 35%, P = 0.18), and phenotyping (11% vs 31%, P = 0.10). HIV-X4 tropism concordance was best between PS and lower stringency DS (93%, κ = 0.83). Other pairwise concordances were 82%-92% (κ = 0.56-0.81). Concordance was similar among cases and controls.ConclusionsHIV-X4 defined by population sequencing (PS) had good agreement with lower stringency DS and was significantly associated with lower odds of breast cancer.
- Published
- 2015
39. Regulatory Variation in HIV-1 Dependency Factor ZNRD1 Associates with Host Resistance to HIV-1 Acquisition
- Author
-
An, Ping, Goedert, James J, Donfield, Sharyne, Buchbinder, Susan, Kirk, Gregory D, Detels, Roger, and Winkler, Cheryl A
- Subjects
Infectious Diseases ,Clinical Research ,Biotechnology ,Genetics ,Human Genome ,Prevention ,HIV/AIDS ,2.1 Biological and endogenous factors ,Aetiology ,Infection ,Good Health and Well Being ,Cohort Studies ,DNA-Binding Proteins ,Disease Resistance ,HIV-1 ,Humans ,Longitudinal Studies ,Male ,Polymorphism ,Single Nucleotide ,United States ,infection ,host susceptibility ,AIDS ,SNP ,single nucleotide polymorphism ,ZNRD1 ,genetic association ,Biological Sciences ,Medical and Health Sciences ,Microbiology - Abstract
BackgroundZNRD1 was identified as a host protein required for the completion of the human immunodeficiency virus (HIV) lifecycle in a genome-wide screen using small interfering RNA gene silencing. Subsequently, a genome-wide association study (GWAS) of host determinants for HIV-1 disease identified an association of single nucleotide polymorphisms (SNPs) in the ZNRD1 region with CD4(+) T-cell depletion.MethodsWe investigated the effects of SNPs in the ZNRD1 region on human immunodeficiency virus type 1 (HIV-1) infection and progression to clinical outcomes in 5 US-based HIV-1 longitudinal cohorts consisting of men who have sex with men, males with hemophilia, and injection drug users (IDUs) (n = 1865). SNP function was evaluated by electrophoretic mobility shift assay and promoter luciferase assay.ResultsA haplotype in the ZNRD1 gene showed significant association with a 35% decreased risk of HIV-1 acquisition (OR = 0.65, 95% CI, .47-.89), independent of HLA-C rs9264942, in European Americans. The SNP rs3132130 tagging this haplotype, located in the ZNRD1 5' upstream region, caused a loss of nuclear factor binding and decrease in ZNRD1 promoter activity. ZNRD1 variants also affected HIV-1 disease progression in European- and African-American cohorts.ConclusionsThis study provides novel evidence that ZNRD1 polymorphism may confer host resistance to HIV-1 acquisition.
- Published
- 2014
40. Disparities in the Quality of HIV Care When Using US Department of Health and Human Services Indicators
- Author
-
Althoff, Keri N, Rebeiro, Peter, Brooks, John T, Buchacz, Kate, Gebo, Kelly, Martin, Jeffrey, Hogg, Robert, Thorne, Jennifer E, Klein, Marina, Gill, M John, Sterling, Timothy R, Yehia, Baligh, Silverberg, Michael J, Crane, Heidi, Justice, Amy C, Gange, Stephen J, Moore, Richard, Kitahata, Mari M, Horberg, Michael A, Research and Design, for the North American AIDS Cohort Collaboration on, Kirk, Gregory D, Benson, Constance A, Bosch, Ronald J, Collier, Ann C, Boswell, Stephen, Grasso, Chris, Mayer, Kenneth H, Hogg, Robert S, Harrigan, P Richard, Montaner, Julio SG, Cescon, Angela, Samji, Hasina, Gebo, Kelly A, Moore, Richard D, Carey, John T, Goedert, James J, Jacobson, Lisa P, Klein, Marina B, Rourke, Sean B, Burchell, Ann N, Rachlis, Anita R, Hunter-Mellado, Robert F, Mayor, Angel M, Deeks, Steven G, Martin, Jeffrey N, Saag, Michael S, Mugavero, Michael J, Willig, James, Eron, Joseph J, Napravnik, Sonia, Crane, Heidi M, Dubrow, Robert, Fiellin, David, Haas, David, Bebawy, Sally, Turner, Megan, Anastos, Kathryn, McKaig, Rosemary G, Freeman, Aimee M, Lent, Carol, Van Rompaey, Stephen E, Morton, Liz, McReynolds, Justin, Lober, William B, Abraham, Alison G, Lau, Bryan, Zhang, Jinbing, Jing, Jerry, Golub, Elizabeth, Modur, Shari, Hanna, David B, Wong, Cherise, and Mendes, Adell
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Infectious Diseases ,Behavioral and Social Science ,Prevention ,Sexually Transmitted Infections ,Health Services ,Women's Health ,HIV/AIDS ,Clinical Research ,Infection ,Good Health and Well Being ,Adult ,Aged ,Aged ,80 and over ,Anti-Retroviral Agents ,Cohort Studies ,Continuity of Patient Care ,Cross-Sectional Studies ,Female ,HIV Infections ,Healthcare Disparities ,Humans ,Male ,Middle Aged ,United States ,United States Dept. of Health and Human Services ,Viral Load ,HIV ,quality of care ,retention in care ,antiretroviral therapy ,HIV RNA suppression ,North American AIDS Cohort Collaboration on Research and Design ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Clinical sciences - Abstract
We estimated US Department of Health and Human Services (DHHS)-approved human immunodeficiency virus (HIV) indicators. Among patients, 71% were retained in care, 82% were prescribed treatment, and 78% had HIV RNA ≤200 copies/mL; younger adults, women, blacks, and injection drug users had poorer outcomes. Interventions are needed to reduce retention- and treatment-related disparities.
- Published
- 2014
41. Complex taphonomic and depositional history of a new species of Carcinidae (Decapoda: Brachyura: Portunoidea) from Washington state, USA
- Author
-
Feldmann, Rodney M., Schweitzer, Carrie E., and Goedert, James L.
- Published
- 2018
42. Hepatitis C Viremia and the Risk of Chronic Kidney Disease in HIV-Infected Individuals
- Author
-
Lucas, Gregory M, Jing, Yuezhou, Sulkowski, Mark, Abraham, Alison G, Estrella, Michelle M, Atta, Mohamed G, Fine, Derek M, Klein, Marina B, Silverberg, Michael J, Gill, M John, Moore, Richard D, Gebo, Kelly A, Sterling, Timothy R, Butt, Adeel A, for the NA-ACCORD of the IeDEA, Kirk, Gregory D, Benson, Constance A, Bosch, Ronald J, Collier, Ann C, Boswell, Stephen, Grasso, Chris, Mayer, Ken, Hogg, Robert S, Harrigan, Richard, Montaner, Julio, Cescon, Angela, Brooks, John T, Buchacz, Kate, Carey, John T, Rodriguez, Benigno, Horberg, Michael A, Thorne, Jennifer E, Goedert, James J, Jacobson, Lisa P, Rourke, Sean B, Burchell, Ann, Rachlis, Anita R, Rico, Puerto, Hunter-Mellado, Robert F, Mayor, Angel M, Deeks, Steven G, Martin, Jeffrey N, Patel, Pragna, Saag, Michael S, Mugavero, Michael J, Willig, James, Eron, Joseph J, Napravnik, Sonia, Kitahata, Mari M, Crane, Heidi M, Justice, Amy C, Dubrow, Robert, Fiellin, David, Haas, David, Bebawy, Sally, Turner, Megan, Gange, Stephen J, Anastos, Kathryn, McKaig, Rosemary G, Freeman, Aimee M, Lent, Carol, Van Rompaey, Stephen E, Webster, Eric, Morton, Liz, Simon, Brenda, Althoff, Keri N, Lau, Bryan, Zhang, Jinbing, Jing, Jerry, Golub, Elizabeth, Modur, Shari, Hanna, David B, Rebeiro, Peter, Wong, Cherise, and Mendes, Adell
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Kidney Disease ,Infectious Diseases ,Liver Disease ,Chronic Liver Disease and Cirrhosis ,HIV/AIDS ,Hepatitis ,Digestive Diseases ,Emerging Infectious Diseases ,Sexually Transmitted Infections ,Clinical Research ,Hepatitis - C ,Renal and urogenital ,Infection ,Good Health and Well Being ,Adult ,Canada ,Chi-Square Distribution ,Cohort Studies ,Female ,Glomerular Filtration Rate ,HIV Infections ,Hepacivirus ,Hepatitis C ,Humans ,Incidence ,Male ,Middle Aged ,Proportional Hazards Models ,RNA ,Viral ,Renal Insufficiency ,Chronic ,Risk Factors ,Substance Abuse ,Intravenous ,United States ,Viremia ,NA-ACCORD of the IeDEA ,HIV ,chronic kidney disease ,cohort study ,glomerular filtration rate ,hepatitis C RNA ,hepatitis C virus ,injection drug use ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
Background The role of active hepatitis C virus (HCV) replication in chronic kidney disease (CKD) risk has not been clarified.Methods We compared CKD incidence in a large cohort of HIV-infected subjects who were HCV seronegative, HCV viremic (detectable HCV RNA), or HCV aviremic (HCV seropositive, undetectable HCV RNA). Stages 3 and 5 CKD were defined according to standard criteria. Progressive CKD was defined as a sustained 25% glomerular filtration rate (GFR) decrease from baseline to a GFR < 60 mL/min/1.73 m2. We used Cox models to calculate adjusted hazard ratios (HRs) and 95% confidence intervals (CIs).Results A total of 52 602 HCV seronegative, 9508 HCV viremic, and 913 HCV aviremic subjects were included. Compared with HCV seronegative subjects, HCV viremic subjects were at increased risk for stage 3 CKD (adjusted HR 1.36 [95% CI, 1.26, 1.46]), stage 5 CKD (1.95 [1.64, 2.31]), and progressive CKD (1.31 [1.19, 1.44]), while HCV aviremic subjects were also at increased risk for stage 3 CKD (1.19 [0.98, 1.45]), stage 5 CKD (1.69 [1.07, 2.65]), and progressive CKD (1.31 [1.02, 1.68]).Conclusions Compared with HIV-infected subjects who were HCV seronegative, both HCV viremic and HCV aviremic individuals were at increased risk for moderate and advanced CKD.
- Published
- 2013
43. First record of a tarsometatarsus of Tonsala hildegardae (Plotopteridae) and other avian remains from the late Eocene/early Oligocene of Washington State (USA)
- Author
-
Mayr, Gerald and Goedert, James L.
- Published
- 2018
- Full Text
- View/download PDF
44. Trends and Disparities in Antiretroviral Therapy Initiation and Virologic Suppression Among Newly Treatment-Eligible HIV-Infected Individuals in North America, 2001–2009
- Author
-
Hanna, David B, Buchacz, Kate, Gebo, Kelly A, Hessol, Nancy A, Horberg, Michael A, Jacobson, Lisa P, Kirk, Gregory D, Kitahata, Mari M, Korthuis, P Todd, Moore, Richard D, Napravnik, Sonia, Patel, Pragna, Silverberg, Michael J, Sterling, Timothy R, Willig, James H, Lau, Bryan, Althoff, Keri N, Crane, Heidi M, Collier, Ann C, Samji, Hasina, Thorne, Jennifer E, Gill, M John, Klein, Marina B, Martin, Jeffrey N, Rodriguez, Benigno, Rourke, Sean B, Gange, Stephen J, AIDS, for the North American AIDS Cohort Collaboration on Research and Design of the International Epidemiologic Databases to Evaluate, Benson, A, Bosch, Ronald J, Boswell, Stephen, Grasso, Chris, Mayer, Ken, Hogg, Robert S, Harrigan, Richard, Montaner, Julio, Cescon, Angela, Brooks, John T, Goedert, James J, Burchell, Ann, Rachlis, Anita R, Hunter-Mellado, Robert F, Mayor, Angel M, Deeks, Steven G, Saag, Michael S, Mugavero, Michael J, Willig, James, Eron, Joseph J, Justice, Amy C, Dubrow, Robert, Fiellin, David, Haas, David, Bebawy, Sally, Turner, Megan, Anastos, Kathryn, McKaig, Rosemary G, Freeman, Aimee M, Lent, Carol, Platt, Aaron, Van Rompaey, Stephen E, Webster, Eric, Morton, Liz, Simon, Brenda, Abraham, Alison G, Zhang, Jinbing, Jing, Jerry, Golub, Elizabeth, Modur, Shari, and Rebeiro, Peter
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Substance Misuse ,Sexually Transmitted Infections ,Women's Health ,HIV/AIDS ,Infectious Diseases ,Clinical Research ,6.1 Pharmaceuticals ,Evaluation of treatments and therapeutic interventions ,Infection ,Good Health and Well Being ,Adolescent ,Adult ,Anti-HIV Agents ,Canada ,Female ,HIV Infections ,Healthcare Disparities ,Humans ,Incidence ,Male ,Middle Aged ,Multivariate Analysis ,Proportional Hazards Models ,Treatment Outcome ,United States ,Viral Load ,Young Adult ,antiretroviral therapy ,healthcare disparities ,HIV ,time factors ,viral load ,North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) of the International Epidemiologic Databases to Evaluate AIDS ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Clinical sciences - Abstract
BackgroundSince the mid-1990s, effective antiretroviral therapy (ART) regimens have improved in potency, tolerability, ease of use, and class diversity. We sought to examine trends in treatment initiation and resulting human immunodeficiency virus (HIV) virologic suppression in North America between 2001 and 2009, and demographic and geographic disparities in these outcomes.MethodsWe analyzed data on HIV-infected individuals newly clinically eligible for ART (ie, first reported CD4+ count
- Published
- 2013
45. Influence of HLA-C Expression Level on HIV Control
- Author
-
Apps, Richard, Qi, Ying, Carlson, Jonathan M, Chen, Haoyan, Gao, Xiaojiang, Thomas, Rasmi, Yuki, Yuko, Del Prete, Greg Q, Goulder, Philip, Brumme, Zabrina L, Brumme, Chanson J, John, Mina, Mallal, Simon, Nelson, George, Bosch, Ronald, Heckerman, David, Stein, Judy L, Soderberg, Kelly A, Moody, M Anthony, Denny, Thomas N, Zeng, Xue, Fang, Jingyuan, Moffett, Ashley, Lifson, Jeffrey D, Goedert, James J, Buchbinder, Susan, Kirk, Gregory D, Fellay, Jacques, McLaren, Paul, Deeks, Steven G, Pereyra, Florencia, Walker, Bruce, Michael, Nelson L, Weintrob, Amy, Wolinsky, Steven, Liao, Wilson, and Carrington, Mary
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Immunology ,Genetics ,Sexually Transmitted Infections ,Infectious Diseases ,Clinical Research ,HIV/AIDS ,Cancer ,2.1 Biological and endogenous factors ,Aetiology ,Infection ,Inflammatory and immune system ,Black or African American ,Alleles ,Amino Acid Sequence ,Anti-Retroviral Agents ,Crohn Disease ,Gene Expression Regulation ,HIV ,HIV Infections ,HLA-C Antigens ,Humans ,Immunodominant Epitopes ,Molecular Sequence Data ,Mutation ,Peptide Fragments ,Polymorphism ,Single Nucleotide ,T-Lymphocytes ,Cytotoxic ,Viral Load ,General Science & Technology - Abstract
A variant upstream of human leukocyte antigen C (HLA-C) shows the most significant genome-wide effect on HIV control in European Americans and is also associated with the level of HLA-C expression. We characterized the differential cell surface expression levels of all common HLA-C allotypes and tested directly for effects of HLA-C expression on outcomes of HIV infection in 5243 individuals. Increasing HLA-C expression was associated with protection against multiple outcomes independently of individual HLA allelic effects in both African and European Americans, regardless of their distinct HLA-C frequencies and linkage relationships with HLA-B and HLA-A. Higher HLA-C expression was correlated with increased likelihood of cytotoxic T lymphocyte responses and frequency of viral escape mutation. In contrast, high HLA-C expression had a deleterious effect in Crohn's disease, suggesting a broader influence of HLA expression levels in human disease.
- Published
- 2013
46. Invasive Cervical Cancer Risk Among HIV-Infected Women
- Author
-
Abraham, Alison G, D’Souza, Gypsyamber, Jing, Yuezhou, Gange, Stephen J, Sterling, Timothy R, Silverberg, Michael J, Saag, Michael S, Rourke, Sean B, Rachlis, Anita, Napravnik, Sonia, Moore, Richard D, Klein, Marina B, Kitahata, Mari M, Kirk, Gregory D, Hogg, Robert S, Hessol, Nancy A, Goedert, James J, Gill, M John, Gebo, Kelly A, Eron, Joseph J, Engels, Eric A, Dubrow, Robert, Crane, Heidi M, Brooks, John T, Bosch, Ronald J, and Strickler, Howard D
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Health Sciences ,Cancer ,Cervical Cancer ,Women's Health ,Infectious Diseases ,HIV/AIDS ,Prevention ,Sexually Transmitted Infections ,Clinical Research ,2.1 Biological and endogenous factors ,2.2 Factors relating to the physical environment ,Aetiology ,Infection ,Adult ,Cohort Studies ,Female ,HIV Infections ,Humans ,Mass Screening ,Neoplasm Invasiveness ,North America ,Risk Factors ,Uterine Cervical Neoplasms ,human papillomavirus ,HIV-infection ,invasive cervical cancer ,immunosuppression ,North American AIDS Cohort Collaboration on Research and Design of IeDEA ,Clinical Sciences ,Public Health and Health Services ,Virology ,Clinical sciences ,Epidemiology ,Public health - Abstract
ObjectiveHIV infection and low CD4+ T-cell count are associated with an increased risk of persistent oncogenic human papillomavirus infection-the major risk factor for cervical cancer. Few reported prospective cohort studies have characterized the incidence of invasive cervical cancer (ICC) in HIV-infected women.MethodsData were obtained from HIV-infected and -uninfected female participants in the North American AIDS Cohort Collaboration on Research and Design with no history of ICC at enrollment. Participants were followed from study entry or January 1996 through ICC, loss to follow-up, or December 2010. The relationship of HIV infection and CD4+ T-cell count with risk of ICC was assessed using age-adjusted Poisson regression models and standardized incidence ratios. All cases were confirmed by cancer registry records and/or pathology reports. Cervical cytology screening history was assessed through medical record abstraction.ResultsA total of 13,690 HIV-infected and 12,021 HIV-uninfected women contributed 66,249 and 70,815 person-years of observation, respectively. Incident ICC was diagnosed in 17 HIV-infected and 4 HIV-uninfected women (incidence rate of 26 and 6 per 100,000 person-years, respectively). HIV-infected women with baseline CD4+ T-cells of ≥350, 200-349, and
- Published
- 2013
47. Genome-wide association study of spontaneous resolution of hepatitis C virus infection: data from multiple cohorts.
- Author
-
Duggal, Priya, Thio, Chloe L, Wojcik, Genevieve L, Goedert, James J, Mangia, Alessandra, Latanich, Rachel, Kim, Arthur Y, Lauer, Georg M, Chung, Raymond T, Peters, Marion G, Kirk, Gregory D, Mehta, Shruti H, Cox, Andrea L, Khakoo, Salim I, Alric, Laurent, Cramp, Matthew E, Donfield, Sharyne M, Edlin, Brian R, Tobler, Leslie H, Busch, Michael P, Alexander, Graeme, Rosen, Hugo R, Gao, Xiaojiang, Abdel-Hamid, Mohamed, Apps, Richard, Carrington, Mary, and Thomas, David L
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Liver Disease ,Infectious Diseases ,Digestive Diseases ,Hepatitis - C ,Hepatitis ,Genetics ,Emerging Infectious Diseases ,Chronic Liver Disease and Cirrhosis ,Clinical Research ,Human Genome ,2.1 Biological and endogenous factors ,Aetiology ,Infection ,Good Health and Well Being ,Black or African American ,Female ,Gene Frequency ,Genome-Wide Association Study ,Genotype ,HLA-DQ beta-Chains ,Hepatitis C ,Hepatitis C Antibodies ,Humans ,Interferons ,Interleukins ,Male ,Polymorphism ,Single Nucleotide ,RNA ,Viral ,Remission ,Spontaneous ,Public Health and Health Services - Abstract
UnlabelledChinese translationBackgroundHepatitis C virus (HCV) infections occur worldwide and either spontaneously resolve or persist and markedly increase the person's lifetime risk for cirrhosis and hepatocellular carcinoma. Although HCV persistence occurs more often in persons of African ancestry and persons with genetic variants near interleukin-28B (IL-28B), the genetic basis is not well-understood.ObjectiveTo evaluate the host genetic basis for spontaneous resolution of HCV infection.Design2-stage, genome-wide association study.Setting13 international multicenter study sites.Patients919 persons with serum HCV antibodies but no HCV RNA (spontaneous resolution) and 1482 persons with serum HCV antibodies and HCV RNA (persistence).MeasurementsFrequencies of 792 721 single nucleotide polymorphisms (SNPs).ResultsDifferences in allele frequencies between persons with spontaneous resolution and persistence were identified on chromosomes 19q13.13 and 6p21.32. On chromosome 19, allele frequency differences localized near IL-28B and included rs12979860 (overall per-allele OR, 0.45; P = 2.17 × 10-30) and 10 additional SNPs spanning 55 000 base pairs. On chromosome 6, allele frequency differences localized near genes for HLA class II and included rs4273729 (overall per-allele OR, 0.59; P = 1.71 × 10-16) near DQB1*03:01 and an additional 116 SNPs spanning 1 090 000 base pairs. The associations in chromosomes 19 and 6 were independent and additive and explain an estimated 14.9% (95% CI, 8.5% to 22.6%) and 15.8% (CI, 4.4% to 31.0%) of the variation in HCV resolution in persons of European and African ancestry, respectively. Replication of the chromosome 6 SNP, rs4272729, in an additional 745 persons confirmed the findings (P = 0.015).LimitationEpigenetic effects were not studied.ConclusionIL-28B and HLA class II are independently associated with spontaneous resolution of HCV infection, and SNPs marking IL-28B and DQB1*03:01 may explain approximately 15% of spontaneous resolution of HCV infection.
- Published
- 2013
48. Predictive Accuracy of the Veterans Aging Cohort Study Index for Mortality With HIV Infection
- Author
-
Justice, Amy C, Modur, Sharada P, Tate, Janet P, Althoff, Keri N, Jacobson, Lisa P, Gebo, Kelly A, Kitahata, Mari M, Horberg, Michael A, Brooks, John T, Buchacz, Kate, Rourke, Sean B, Rachlis, Anita, Napravnik, Sonia, Eron, Joseph, Willig, James H, Moore, Richard, Kirk, Gregory D, Bosch, Ronald, Rodriguez, Benigno, Hogg, Robert S, Thorne, Jennifer, Goedert, James J, Klein, Marina, Gill, John, Deeks, Steven, Sterling, Timothy R, Anastos, Kathryn, and Gange, Stephen J
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Public Health ,Health Sciences ,Sexually Transmitted Infections ,Aging ,HIV/AIDS ,Minority Health ,Infectious Diseases ,Infection ,Good Health and Well Being ,Age Factors ,Alanine Transaminase ,Anti-Retroviral Agents ,Aspartate Aminotransferases ,Biomarkers ,CD4 Lymphocyte Count ,Cohort Studies ,Creatinine ,Female ,HIV Infections ,HIV-1 ,Hemoglobins ,Hepatitis C ,Humans ,Kaplan-Meier Estimate ,Male ,Middle Aged ,North America ,Platelet Count ,Predictive Value of Tests ,RNA ,Viral ,Risk Assessment ,Sex Factors ,HIV ,aging ,prognosis ,NA-ACCORD and VACS Project Teams ,Clinical Sciences ,Public Health and Health Services ,Virology ,Clinical sciences ,Epidemiology ,Public health - Abstract
BackgroundBy supplementing an index composed of HIV biomarkers and age (restricted index) with measures of organ injury, the Veterans Aging Cohort Study (VACS) index more completely reflects risk of mortality. We compare the accuracy of the VACS and restricted indices (1) among subjects outside the Veterans Affairs Healthcare System, (2) more than 1-5 years of prior exposure to antiretroviral therapy (ART), and (3) within important patient subgroups.MethodsWe used data from 13 cohorts in the North American AIDS Cohort Collaboration (n = 10, 835) limiting analyses to HIV-infected subjects with at least 12 months exposure to ART. Variables included demographic, laboratory (CD4 count, HIV-1 RNA, hemoglobin, platelets, aspartate and alanine transaminase, creatinine, and hepatitis C status), and survival. We used C-statistics and net reclassification improvement (NRI) to test discrimination varying prior ART exposure from 1 to 5 years. We then combined Veterans Affairs Healthcare System (n = 5066) and North American AIDS Cohort Collaboration data, fit a parametric survival model, and compared predicted to observed mortality by cohort, gender, age, race, and HIV-1 RNA level.ResultsMean follow-up was 3.3 years (655 deaths). Compared with the restricted index, the VACS index showed greater discrimination (C-statistics: 0.77 vs. 0.74; NRI: 12%; P < 0.0001). NRI was highest among those with HIV-1 RNA
- Published
- 2013
49. Closing the Gap: Increases in Life Expectancy among Treated HIV-Positive Individuals in the United States and Canada
- Author
-
Samji, Hasina, Cescon, Angela, Hogg, Robert S, Modur, Sharada P, Althoff, Keri N, Buchacz, Kate, Burchell, Ann N, Cohen, Mardge, Gebo, Kelly A, Gill, M John, Justice, Amy, Kirk, Gregory, Klein, Marina B, Korthuis, P Todd, Martin, Jeff, Napravnik, Sonia, Rourke, Sean B, Sterling, Timothy R, Silverberg, Michael J, Deeks, Stephen, Jacobson, Lisa P, Bosch, Ronald J, Kitahata, Mari M, Goedert, James J, Moore, Richard, Gange, Stephen J, and Research and Design of IeDEA, for The North American AIDS Cohort Collaboration on
- Subjects
Biomedical and Clinical Sciences ,Public Health ,Health Sciences ,Human Society ,Clinical Sciences ,Behavioral and Social Science ,Infectious Diseases ,Aging ,Sexually Transmitted Infections ,Clinical Research ,HIV/AIDS ,Evaluation of treatments and therapeutic interventions ,6.1 Pharmaceuticals ,Infection ,Good Health and Well Being ,Adult ,Canada ,Female ,HIV Infections ,Humans ,Life Expectancy ,Male ,Middle Aged ,United States ,Young Adult ,North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) of IeDEA ,General Science & Technology - Abstract
BackgroundCombination antiretroviral therapy (ART) has significantly increased survival among HIV-positive adults in the United States (U.S.) and Canada, but gains in life expectancy for this region have not been well characterized. We aim to estimate temporal changes in life expectancy among HIV-positive adults on ART from 2000-2007 in the U.S. and Canada.MethodsParticipants were from the North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD), aged ≥20 years and on ART. Mortality rates were calculated using participants' person-time from January 1, 2000 or ART initiation until death, loss to follow-up, or administrative censoring December 31, 2007. Life expectancy at age 20, defined as the average number of additional years that a person of a specific age will live, provided the current age-specific mortality rates remain constant, was estimated using abridged life tables.ResultsThe crude mortality rate was 19.8/1,000 person-years, among 22,937 individuals contributing 82,022 person-years and 1,622 deaths. Life expectancy increased from 36.1 [standard error (SE) 0.5] to 51.4 [SE 0.5] years from 2000-2002 to 2006-2007. Men and women had comparable life expectancies in all periods except the last (2006-2007). Life expectancy was lower for individuals with a history of injection drug use, non-whites, and in patients with baseline CD4 counts
- Published
- 2013
50. CD4 count at presentation for HIV care in the United States and Canada: Are those over 50 years more likely to have a delayed presentation?
- Author
-
Althoff, Keri N, Gebo, Kelly A, Gange, Stephen J, Klein, Marina B, Brooks, John T, Hogg, Robert S, Bosch, Ronald J, Horberg, Michael A, Saag, Michael S, Kitahata, Mari M, Eron, Joseph J, Napravnik, Sonia, Rourke, Sean B, Gill, M John, Rodriguez, Benigno, Sterling, Timothy R, Deeks, Steven G, Martin, Jeffrey N, Jacobson, Lisa P, Kirk, Gregory D, Collier, Ann C, Benson, Constance A, Silverberg, Michael J, Goedert, James J, McKaig, Rosemary G, Thorne, Jennifer, Rachlis, Anita, Moore, Richard D, and Justice, Amy C
- Abstract
Abstract We assessed CD4 count at initial presentation for HIV care among ≥50-year-olds from 1997-2007 in 13 US and Canadian clinical cohorts and compared to
- Published
- 2010
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.