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https://www.readbyqxmd.com/read/29345933/large-scale-functional-group-symmetry-adapted-perturbation-theory-on-graphical-processing-units
#1
Robert M Parrish, Keiran C Thompson, Todd J Martínez
Symmetry-adapted perturbation theory (SAPT) is a valuable method for analyzing intermolecular interactions. The functional group SAPT partition (F-SAPT) has been introduced to provide additional insight into the origins of noncovalent interactions. Until now, SAPT analysis has been too costly for large ligand-protein complexes where it could provide key insights for chemical modifications that might improve ligand binding. In this paper, we present a large-scale implementation of F-SAPT which is especially efficient when one of the interacting monomers is significantly larger than the other, as is usually the case for drug-protein interactions...
January 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29337848/identifying-pre-existing-ns3-and-ns5a-resistance-associated-variants-and-transmission-chains-in-the-polish-hiv-hcv-genotype-1-epidemic-impact-on-prevention-and-treatment
#2
Miłosz Parczewski, Iwona Cielniak, Justyna Kordek, Bogusz Aksak-Wąs, Anna Urbańska, Magdalena Leszczyszyn-Pynka, Ewa Siwak, Monika Bociąga-Jasik, Anna Nowak, Aleksandra Szymczak, Małgorzata Zalewska, Władysław Łojewski, Anne-Mieke Vandamme, Nadine Lübke, Lize Cuypers
BACKGROUND: Hepatitis C virus (HCV) resistance-associated variants (RAVs) have been shown to adversely affect treatment response of direct-acting antivirals (DAAs). Identifying pre-existing RAVs and transmission networks among HIV/HCV genotype 1 (G1) infected patients from Poland will assist in shaping surveillance strategies for HCV. METHODS: NS3 and NS5A sequences were obtained from samples of 112 DAA-naive G1 patients (45 G1a, 67 G1b), of which 74 were chronically infected and 38 were diagnosed with acute hepatitis C (AHC)...
January 15, 2018: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/29335428/analysis-of-the-hiv-2-protease-s-adaptation-to-various-ligands-characterization-of-backbone-asymmetry-using-a-structural-alphabet
#3
Dhoha Triki, Mario Enrique Cano Contreras, Delphine Flatters, Benoit Visseaux, Diane Descamps, Anne-Claude Camproux, Leslie Regad
The HIV-2 protease (PR2) is a homodimer of 99 residues with asymmetric assembly and binding various ligands. We propose an exhaustive study of the local structural asymmetry between the two monomers of all available PR2 structures complexed with various inhibitors using a structural alphabet approach. On average, PR2 exhibits asymmetry in 31% of its positions-i.e., exhibiting different backbone local conformations in the two monomers. This asymmetry was observed all along its structure, particularly in the elbow and flap regions...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29334546/impact-of-early-antiretroviral-therapy-eligibility-on-hiv-acquisition-household-level-evidence-from-rural-south-africa
#4
Catherine E Oldenburg, Jacob Bor, Guy Harling, Frank Tanser, Tinofa Mutevedzi, Maryam Shahmanesh, George R Seage, Victor De Gruttola, Matthew J Mimiaga, Kenneth H Mayer, Deenan Pillay, Till Bärnighausen
OBJECTIVES: We investigate the effect of immediate ART eligibility on HIV incidence among HIV-uninfected household members. DESIGN: Regression discontinuity study arising from a population-based cohort. METHODS: Household members of patients seeking care at the Hlabisa HIV Treatment and Care Programme in rural KwaZulu-Natal South Africa between January 2007 and August 2011 with CD4 counts up to 350 cells/μl were eligible for inclusion if they had at least two HIV tests and were HIV-uninfected at the time the index patient linked to care (N = 4,115)...
January 13, 2018: AIDS
https://www.readbyqxmd.com/read/29329426/a-practical-guide-to-estimating-the-heritability-of-pathogen-traits
#5
Venelin Mitov, Tanja Stadler
Pathogen traits, such as the virulence of an infection, can vary significantly between patients. A major challenge is to measure the extent to which genetic differences between infecting strains explain the observed variation of the trait. This is quantified by the trait's broad-sense heritability, H2. A recent discrepancy between estimates of the heritability of HIV-virulence has opened a debate on the estimators' accuracy. Here, we show that the discrepancy originates from model limitations and important lifecycle differences between sexually reproducing organisms and transmittable pathogens...
January 9, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29325134/continued-propagation-of-the-crf19_cpx-variant-among-hiv-positive-msm-patients-in-spain
#6
S Pérez-Parra, M Álvarez, J A Fernandez-Caballero, A B Pérez, J Santos, O Bisbal, A Aguilera, M Rivero, L García-Fraile, F García
Objectives: The HIV-1 CRF19_cpx genetic form has been recently associated with greater pathogenicity. We used CoRIS, a national cohort of 31 reference hospitals in Spain, to investigate the current epidemiological situation of this variant in Spain. Patients and methods: We analysed 4734 naive HIV-1-positive patients diagnosed during the 2007-15 period with an available pol gene sequence in the CoRIS resistance database. HIV-1 CRF19_cpx was ascribed through REGA3...
January 8, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29315303/genome-wide-comparison-of-ethiopian-leishmania-donovani-strains-reveals-differences-potentially-related-to-parasite-survival
#7
Arie Zackay, James A Cotton, Mandy Sanders, Asrat Hailu, Abedelmajeed Nasereddin, Alon Warburg, Charles L Jaffe
Leishmania donovani is the main cause of visceral leishmaniasis (VL) in East Africa. Differences between northern Ethiopia/Sudan (NE) and southern Ethiopia (SE) in ecology, vectors, and patient sensitivity to drug treatment have been described, however the relationship between differences in parasite genotype between these two foci and phenotype is unknown. Whole genomic sequencing (WGS) was carried out for 41 L. donovani strains and clones from VL and VL/HIV co-infected patients in NE (n = 28) and SE (n = 13)...
January 9, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29311557/publisher-correction-the-%C3%AE-20-%C3%AE-21-of-gp120-is-a-regulatory-switch-for-hiv-1-env-conformational-transitions
#8
Alon Herschhorn, Christopher Gu, Francesca Moraca, Xiaochu Ma, Mark Farrell, Amos B Smith, Marie Pancera, Peter D Kwong, Arne Schön, Ernesto Freire, Cameron Abrams, Scott C Blanchard, Walther Mothes, Joseph G Sodroski
The original version of this Article contained an error in the spelling of the author Amos B. Smith, III, which was incorrectly given as Amos B. SmithIII. This has now been corrected in both the PDF and HTML versions of the Article.
January 8, 2018: Nature Communications
https://www.readbyqxmd.com/read/29310975/influence-of-birth-origin-and-risk-factor-profile-on-hepatitis-b-mortality-philadelphia-pa-2003-2013
#9
Dana C Higgins, Danica E Kuncio, Caroline C Johnson, Kendra M Viner
PURPOSE: Chronic hepatitis B virus (HBV) affects specific subpopulations in the United States, including individuals born in HBV-endemic countries and persons engaging in high-risk behaviors. METHODS: The 2003-2013 HBV registry data and surveillance investigations for Philadelphia, PA were matched to death certificate data to examine demographic, risk factor, and cause of death characteristics among HBV-infected populations. Bivariate analysis compared investigated foreign-born (FB) and US-born chronic HBV individuals...
December 22, 2017: Annals of Epidemiology
https://www.readbyqxmd.com/read/29303690/erratum
#10
(no author information available yet)
Mayer KH, Loo S, Crawford PM, et al. Excess clinical comorbidity among HIV-infected patients accessing primary care in US community health centers. Public Health Rep. 2018;133:109-118. (Original DOI: 10.1177/0033354917748670) In the above referenced article, Table 3 was published with duplicate information in the initial OnlineFirst version. The correct Table 3 is given below. The article, as published in volume 133, issue 1, reflects the corrected table. [Table: see text].
January 2018: Public Health Reports
https://www.readbyqxmd.com/read/29299966/ancient-dna-investigation-of-a-medieval-german-cemetery-confirms-long-term-stability-of-ccr5-%C3%AE-32-allele-frequencies-in-central-europe
#11
Abigail Bouwman, Natallia Shved, Gülfirde Akgül, Frank Rühli, Christina Warinner
The CCR5-Δ32 mutation present in European populations is among the most prominently debated cases of recent positive selection in humans. This allele, a 32-bp deletion that renders the T-cell CCR5 receptor nonfunctional, has important epidemiological and public health significance, as homozygous carriers are resistant to several HIV strains. However, although the function of this allele in preventing HIV infection is now well described, its human evolutionary origin is poorly understood. Initial attempts to determine the emergence of the CCR5-Δ32 allele pointed to selection during the 14th-century Black Death pandemic; however, subsequent analyses suggest that the allele rose in frequency more than 5,000 years ago, possibly through drift...
April 2017: Human Biology
https://www.readbyqxmd.com/read/29299858/hydrogeochemical-and-biomedical-insights-into-germanium-potential-of-curative-waters-a-case-study-of-health-resorts-in-the-sudetes-mountains-poland
#12
Dariusz Dobrzyński, Anna Boguszewska-Czubara, Kenji Sugimori
Germanium is considered to be a non-essential element; however, little is still known about its significance for living organisms. It exerts prophylactic and therapeutic effects in the treatment of serious diseases such as cancer, HIV infection, and others. Germanium does not exhibit acute toxicity, but, as it tends to accumulate in various organs and tissues, undesirable and even dangerous side effects have been reported after prolonged and/or high dosage application. In general, inorganic compounds of germanium are more toxic than its organic compounds...
January 3, 2018: Environmental Geochemistry and Health
https://www.readbyqxmd.com/read/29285638/the-use-of-online-posts-to-identify-barriers-to-and-facilitators-of-hiv-pre-exposure-prophylaxis-prep-among-men-who-have-sex-with-men-a-comparison-to-a-systematic-review-of-the-peer-reviewed-literature
#13
Alisse Hannaford, Madeleine Lipshie-Williams, Joanna L Starrels, Julia H Arnsten, Jessica Rizzuto, Phillip Cohen, Damon Jacobs, Viraj V Patel
Pre-exposure prophylaxis (PrEP) remains an under-utilized HIV prevention tool among men who have sex with men (MSM). To more comprehensively elucidate barriers and facilitators to PrEP use among US MSM, we conducted a systematic review of peer-reviewed published articles and content analysis of online posts about PrEP. We searched peer-reviewed databases (Medline, Web of Science, Google Scholar) using MESH headings and keywords about PrEP and/or HIV prevention from 2005 to 2015. We included original studies among MSM in the US that reported on barriers, facilitators, or other factors related to PrEP use...
December 28, 2017: AIDS and Behavior
https://www.readbyqxmd.com/read/29282092/reporting-quality-of-randomized-controlled-trials-in-patients-with-hiv-on-antiretroviral-therapy-a-systematic-review
#14
REVIEW
Kaori Nagai, Akiko M Saito, Toshiki I Saito, Noriyo Kaneko
BACKGROUND: To allow for correct evaluation of clinical trial results, readers require comprehensive, clear, and highly transparent information on the methodology used and the results obtained. This study aimed to evaluate the quality of reporting in articles on randomized controlled trials (RCTs) of antiretroviral therapy (ART) in the field of HIV/AIDS. METHODS: We searched for original articles on RCTs of ART developed in the field of HIV/AIDS in PubMed database by 5 April 2016...
December 28, 2017: Trials
https://www.readbyqxmd.com/read/29281620/dual-strain-genital-herpes-simplex-virus-type-2-hsv-2-infection-in-the-us-peru-and-8-countries-in-sub-saharan-africa-a-nested-cross-sectional-viral-genotyping-study
#15
Christine Johnston, Amalia Magaret, Pavitra Roychoudhury, Alexander L Greninger, Daniel Reeves, Joshua Schiffer, Keith R Jerome, Cassandra Sather, Kurt Diem, Jairam R Lingappa, Connie Celum, David M Koelle, Anna Wald
BACKGROUND: Quantitative estimation of the extent to which the immune system's protective effect against one herpes simplex virus type 2 (HSV-2) infection protects against infection with additional HSV-2 strains is important for understanding the potential for HSV-2 vaccine development. Using viral genotyping, we estimated the prevalence of HSV-2 dual-strain infection and identified risk factors. METHODS AND FINDINGS: People with and without HIV infection participating in HSV-2 natural history studies (University of Washington Virology Research Clinic) and HIV prevention trials (HIV Prevention Trials Network 039 and Partners in Prevention HSV/HIV Transmission Study) in the US, Africa, and Peru with 2 genital specimens each containing ≥105 copies herpes simplex virus DNA/ml collected a median of 5 months apart (IQR: 2-11 months) were included...
December 2017: PLoS Medicine
https://www.readbyqxmd.com/read/29280055/sirtuin-1-chromatin-binding-dynamics-points-to-a-common-mechanism-regulating-inflammatory-targets-in-siv-infection-and-in-the-aging-brain
#16
Nikki Bortell, Liana Basova, Julia A Najera, Brenda Morsey, Howard S Fox, Maria Cecilia Garibaldi Marcondes
Microglia and macrophages are the main non-neuronal subsets of myeloid origin in the brain, and are critical regulators in neurodegenerative disorders, where inflammation is a key factor. Since HIV infection results in neurological perturbations that are similar to those in aging, we examined microglial and infiltrating myeloid subsets in the search for changes that might resemble the ones in aging. For that, we used the SIV infection in rhesus macaques to model neuroAIDS. We found that Sirt-1, a molecule that impacts survival and health in many models, was decreased in cell preparations containing a majority of microglia and myeloid cells from the brain of infected macaques...
December 26, 2017: Journal of Neuroimmune Pharmacology: the Official Journal of the Society on NeuroImmune Pharmacology
https://www.readbyqxmd.com/read/29273442/pharmaceutical-interactions-between-antiretroviral-and-antimalarial-drugs-used-in-chemoprophylaxis
#17
REVIEW
Andreas Erich Zautner, Ottmar Herchenröder, Awatef El Moussi, Norbert Georg Schwarz, Dorothea Franziska Wiemer, Uwe Groß, Hagen Frickmann
Human immunodeficiency virus (HIV) is the causative agent of the Acquired Immunodeficiency Syndrome (AIDS). The pandemic is believed to have originated within the Northern Congo basin covering large parts of the Democratic Republic of Congo, the Republic of Congo, the Central African Republic, Cameroon and Gabon. Although over decades, HIV-1 has spread throughout the World leaving no country unaffected, sub-Saharan Africa remains the region with more than 80% of all infected individuals. The HIV-2 epidemic has largely remained restricted to West Africa along the Upper Guinean forests...
December 19, 2017: Acta Tropica
https://www.readbyqxmd.com/read/29258916/potential-of-selected-lamiaceae-plants-in-anti-retro-viral-therapy
#18
REVIEW
Maja Bekut, Snežana Brkić, Nebojša Kladar, Gordana Dragović, Neda Gavarić, Biljana Božin
Constant search for new drugs with antiviral properties often extends to products of natural origin. Lamiaceae is one of the most important herbal families, well known for various biological and medicinal effects of a variety of aromatic spices, including thyme, mint, oregano, basil, sage, savory, rosemary, self-heal, hyssop, lemon balm and many others. The paper provides a review of antiviral potential of previously mentioned plants which has been demonstrated so far, with special emphasis on anti-HIV properties...
December 16, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29258326/origin-and-spread-of-hiv-1-subtype-b-among-heterosexual-individuals-in-bulgaria
#19
Ivailo Alexiev, Alessandra Lo Presti, Reneta Dimitrova, Brian Thomas Foley, Anna Gancheva, Asya Kostadinova, Lora Nikolova, Silvia Angeletti, Eleonora Cella, Ivaylo Elenkov, Mariana Stoycheva, Daniela Nikolova, Tsetsa Doychinova, Liliya Pekova, Massimo Ciccozzi
Human Immunodeficiency Virus (HIV) was originally introduced in Bulgaria through heterosexual transmission (HET) and later transferred to other vulnerable groups along with numerous more recent introductions from outside Bulgaria. To define the diversity, origins and dynamics of the HIV-1 subtypes prevalent in HET population in Bulgaria we applied phylogenetic and phylodynamic analyses using polymerase (pol) sequences from HET individuals to infer the spatiotemporal evolutionary history of the HIV-1 epidemic in this population in Bulgaria...
December 19, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/29258320/characterization-of-a-novel-hiv-1-circulating-recombinant-form-crf01_ae-b-c-crf96_cpx-in-yunnan-china
#20
Jing Miao, Jieyu Ran, Yindi Song, Yang Liu, Li Gao, Zhijiang Miao, Chunyue Zhang, Yue Feng, Xueshan Xia
Currently, complex HIV-1 recombination among the B', C, and CRF01_AE genotypes have frequently arisen in Yunnan, China. A novel HIV-1 complex circulating recombinant form (CRF) consisting of B', C, and CRF01_AE (CRF96_cpx) was recently characterized from three epidemiologically unlinked individuals. Two strains of them were isolated from the injecting drug users in this study, the remaining one strain (JL. RL01) obtained from a previous report in Jilin province. Phylogenetic analysis based on near full-length genome (NFLG) revealed that CRF96_cpx formed a distinct monophyletic cluster supported by a high bootstrap value of 100%, distantly related to all known HIV-1 subtypes/CRFs...
December 19, 2017: AIDS Research and Human Retroviruses
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