bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lp‐PLA2 levels in HIV‐infected patients
Authors: Díaz‐Pollán Beatriz , Estrada Vicente , Fuentes‐Ferrer Manuel , Gómez‐Garré Dulcenombre , San Román‐Montero Jesús 
Published: November 2014

IntroductionHIV‐infected patients show an increased risk of cardiovascular disease (CVD). In the general population, lipoprotein‐associated phospholipase A2 (Lp‐PLA2) appears to be an independent predictor of CVD. We aimed to study associations between Lp‐PLA2 plasma levels and other risk factors for CVD in HIV patients.Materials and MethodsA cross‐sectional, comparative study of two series of cases (HIV patients, n=116 and age‐matched non‐HIV healthy controls, n=113) was conducted. Eighty‐seven percent HIV patients on antiretroviral therapy (ART), 72.4% with HIV‐1 viral load <50 cop/mL. Inflammatory biomarkers (CRP, Lp‐PLA2) and internal carotid intima‐media thickness (IMT) were measured and CVD risk (Framingham and SCORE algorithms) was calculated. Univariate and multivariable associations between these variables were performed.ResultsHIV patients presented higher Lp‐PLA2 levels [276.81 ng/mL (209.71–356.58)] than uninfected healthy controls [220.80 ng/mL (172.70–256.90)], p≤0.01. In univariate analysis of the global sample, only cigarette smoking was associated with higher Lp‐PLA2 levels, p≤0.001. In HIV group, female and smoker patients showed higher Lp‐PLA2 levels, p≤0.05. No significant association was found between Lp‐PLA2 levels and another CVD risk factors, carotid IMT, Framingham and SCORE algorithms, ART, HIV‐1 viral load neither and CD4+ T lymphocyte count. In multivariate analysis, cigarette smoking remained significantly associated with Lp‐PLA2 levels [β=64.8 (95% CI 10.8–118.9) ng/mL, p=0.020].ConclusionsHIV‐infected patients present higher Lp‐PLA2 levels than healthy controls, and in this population, tobacco smoking is significantly associated with increased Lp‐PLA2 levels. Smoking cessation should be a priority in CVD prevention in HIV‐infected patients.
Liver fibrosis is associated with cognitive impairment in HIV‐positive patients
Authors: Ciccarelli Nicoletta , Fabbiani Massimiliano , Grima Pierfrancesco , Limiti Silio , Fanti Iuri , Mondi Annalisa , Gagliardini Roberta , D'Avino Alessandro , Borghetti Alberto , Cauda Roberto , Di Giambenedetto Simona 
Published: November 2014

IntroductionThe aim of our study was to investigate the potential relationship between liver fibrosis (LF) and cognitive performance in HIV+ patients.Materials and MethodsWe performed a cross‐sectional cohort study by consecutively enrolling HIV+ patients during routine outpatient visits at two clinical centres in Italy. Subjects with decompensated liver disease were excluded. All subjects underwent a comprehensive neuropsychological battery exploring memory, attention, psychomotor speed and language; cognitive impairment was defined as at least two abnormal [1.5 SD below the mean for appropriate norms] cognitive domains. LF was explored by calculating FIB4 index; in a subgroup of patients, LF was also assessed by transient elastography. Factors associated with cognitive impairment were investigated by logistic regression models.ResultsA total of 413 patients [77% males, median age 46 (IQR 39–52), 17% with past AIDS‐defining events, 19% past IDU, 3% with diabetes, 94% on cART, 90% with HIV RNA <50 copies/mL, 18% co‐infected with HCV] were enrolled. Seventeen patients (4%) had FIB4 >3.25 and 14/129 (3%) had liver stiffness >14KPa. Forty‐seven patients (11%) were diagnosed with cognitive impairment. At multivariate analyses patients with FIB4 >1.45 showed a higher risk of cognitive impairment in comparison with those with lower values (OR 2.19, 95% CI 1.02–4.72; p=0.044) after adjusting for education (OR 0.79, 95% CI 0.71–0.88; p<0.001), past IDU (OR 1.69, 95% CI 0.67–4.23; p=0.264), diabetes (OR 2.35, 95% CI 0.62–8.86; p=0.207), HIV RNA <50 copies/mL (OR 0.47, 95% CI 0.19–1.14; p=0.095) and HCV co‐infection (OR 0.88, 95% CI 0.33–2.39; p=0.807). Analyzing any single cognitive domain, a higher risk of abnormal psychomotor speed was associated with fibroscan score >14KPa in comparison with fibroscan score <7KPa (OR 285.07; 95% CI 2.42–33574.06; p=0.020) after adjusting for education (OR 0.54, 95% CI 0.31–0.92; p=0.024), age (for 10 years increase) (OR 2.03, 95% CI 0.55–7.53; p=0.288), past IDU (OR 4.43, 95% CI 0.35–7.57; p=0.526), HIV RNA <50 copies/mL (OR 0.01, 95% CI 0.00–0.18; p=0.003), HIV history (for 1 year increase) (OR 0.96, 95% CI 0.83–1.12; p=0.641), CD4 cells count at nadir (OR 1.10, 95% CI 0.56–2.16; p=0.779), and HCV co‐infection (OR 0.06; 95% CI 0.00–1.93; p=0.113).ConclusionsIn HIV‐infected patients higher LF, estimated through non‐invasive methods, is associated to a higher risk of cognitive impairment.
Viral escape in the CNS with multidrug‐resistant HIV‐1
Authors: Béguelin Charles , Vázquez Miriam , Bertschi Manuel , Yerly Sabine , de Jong Denise , Rauch Andri , Cusini Alexia 
Published: November 2014

IntroductionHIV‐1 viral escape in the cerebrospinal fluid (CSF) despite viral suppression in plasma is rare [1,2]. We describe the case of a 50‐year‐old HIV‐1 infected patient who was diagnosed with HIV‐1 in 1995. Antiretroviral therapy (ART) was started in 1998 with a CD4 T cell count of 71 cells/ìL and HIV‐viremia of 46,000 copies/mL. ART with zidovudine (AZT), lamivudine (3TC) and efavirenz achieved full viral suppression. After the patient had interrupted ART for two years, treatment was re‐introduced with tenofovir (TDF), emtricitabin (FTC) and ritonavir boosted atazanavir (ATVr). This regimen suppressed HIV‐1 in plasma for nine years and CD4 cells stabilized around 600 cells/ìL. Since July 2013, the patient complained about severe gait ataxia and decreased concentration.Materials and MethodsAdditionally to a neurological examination, two lumbar punctures, a cerebral MRI and a neuropsycological test were performed. HIV‐1 viral load in plasma and in CSF was quantified using Cobas TaqMan HIV‐1 version 2.0 (Cobas Ampliprep, Roche diagnostic, Basel, Switzerland) with a detection limit of 20 copies/mL. Drug resistance mutations in HIV‐1 reverse transcriptase and protease were evaluated using bulk sequencing.ResultsThe CSF in January 2014 showed a pleocytosis with 75 cells/ìL (100% mononuclear) and 1,184 HIV‐1 RNA copies/mL, while HIV‐1 in plasma was below 20 copies/mL. The resistance testing of the CSF‐HIV‐1 RNA showed two NRTI resistance‐associated mutations (M184V and K65R) and one NNRTI resistance‐associated mutation (K103N). The cerebral MRI showed increased signal on T2‐weighted images in the subcortical and periventricular white matter, in the basal ganglia and thalamus. Four months after ART intensification with AZT, 3TC, boosted darunavir and raltegravir, the pleocytosis in CSF cell count normalized to 1 cell/ìL and HIV viral load was suppressed. The neurological symptoms improved; however, equilibrium disturbances and impaired memory persisted. The neuro‐psychological evaluation confirmed neurocognitive impairments in executive functions, attention, working and nonverbal memory, speed of information processing, visuospatial abilities and motor skills.ConclusionsHIV‐1 infected patients with neurological complaints prompt further investigations of the CSF including measurement of HIV viral load and genotypic resistance testing since isolated replication of HIV with drug resistant variants can rarely occur despite viral suppression in plasma. Optimizing ART by using drugs with improved CNS penetration may achieve viral suppression in CSF with improvement of neurological symptoms.
Analysis of transmitted HIV‐1 drug resistance using 454 ultra‐deep‐sequencing and the DeepChek®‐HIV system
Authors: Garcia‐Diaz Ana , McCormick Adele , Booth Clare , Gonzalez Dimitri , Sayada Chalom , Haque Tanzina , Johnson Margaret , Webster Daniel 
Published: November 2014

IntroductionNext‐generation sequencing (NGS) is capable of detecting resistance‐associated mutations (RAMs) present at frequencies of 1% or below. Several studies have found that baseline low‐frequency RAMs are associated with failure to first‐line HAART. One major limitation to the expansion of this technology in routine diagnostics is the complexity and laboriousness integral to bioinformatics analysis. DeepChek (ABL, TherapyEdge) is a CE‐marked software that allows automated analysis and resistance interpretation of NGS data.ObjectiveTo evaluate the use of 454 ultra‐deep‐sequencing (Roche® 454, Life Sciences; 454‐UDS) and DeepChek for routine baseline resistance testing in a clinical diagnostic laboratory.Methods107 newly diagnosed HIV‐1‐infected patients (subtypes: A, n=9; B, n=52; C, n=21; D, n=2; F, n=3; G, n=1; CRF01, n=7; CRF02, n=7; CRF06, n=1; CRF07, n=1; CRF10, n=1 and unassigned complex, n=2) with a median plasma viral load of 88,727 copies/mL (range: 1380–2,143,543) were tested by 454‐UDS and Sanger sequencing for the detection of protease and reverse transcriptase RAMs. In addition, integrase RAMs were investigated in 57 of them. Sequence analysis and resistance interpretation were performed using DeepChek applying 1% and 20% thresholds for variant detections; filters applied were comparison between Sanger and 454‐UDS, and Stanford and IAS list for resistance interpretation.ResultsThe time elapsed from generation of raw 454 data (between 2,000–5,000 sequences/sample) to elaboration of a resistance report was approximately 10 minutes per sample, equivalent to the time required for the same process using Sanger sequencing. Four patients (3.7%) showed baseline resistance by Sanger and 454‐UDS at frequencies above 20%, which affected both NRTIs (n=2) and NNRTIs (n=2). In addition, 12 patients (11.2%) showed transmitted drug resistance (TDR) by 454‐UDS at frequencies below 20% affecting NRTIs (n=9), NNRTIs (n=7) and PIs (n=2). Integrase resistance was not detected at baseline by 454‐UDS or Sanger sequencing.ConclusionsDeepChek allowed easy and rapid analysis and interpretation of NGS data, thus facilitating the incorporation of this technology in routine diagnostics. The use of NGS considerably increased the detection rates of TDR to NRTI, NNRTIs and PIs. No transmitted resistance to integrase inhibitors was found in our population by Sanger sequencing or UDS.
High frequency of antiviral drug resistance and non‐b subtypes in HIV‐1 patients failing antiviral therapy in Cuba
Authors: Kouri Vivian , Alemán Yoan , Pérez Lissette , Pérez Jorge , Fonseca Carlos , Correa Consuelo , Aragonés Carlos , Campos Jorge , Álvarez Delmis , Schrooten Yoeri , Vinken Lore , Limia Celia , Soto Yudira , Vandamme Anne‐Mieke , Van Laethem Kristel 
Published: November 2014

IntroductionEmergence of HIV‐1 drug resistance may limit the sustained benefits of antiretroviral therapy (ART) in settings with limited laboratory monitoring and drug options. The objective is to implement the surveillance of drug resistance and subtypes in HIV‐1 patients failing ART in Cuba.MethodsThis study compiled clinical and genotypic drug resistance data 588 ART‐experienced HIV‐1 patients attending a clinical center in Havana in 2009–2013. Drug resistance testing was performed as part of routine clinical care. Drug resistance mutations and levels were determined using Rega version 8.0.2.ResultsEighty‐three percent received solely ART containing at least three drugs. Patients from 2009 to 2010 were longer treated (median: 4.9 vs 2.7 years) and exposed to more ART regimens (median: 4 vs 2 regimens) compared to patients from 2011–2013. Nucleoside reverse transcriptase inhibitor (NRTI), non‐nucleoside RTI (NNRTI) and PI mutations were present in 83.5, 77.4 and 52.0%. Full‐class resistance (FCR) to NRTI, NNRTI, PI and multidrug resistance (MDR) were detected in 25.0, 33.7, 11.4 and 6.3%. FCR to NRTI, NNRTI, PI and MDR were present in 12.8, 28.7, 0 and 0% after first‐line failure (164 patients) and in 23.1, 34.6, 3.8 and 3.1% after second‐line failure (130 patients). Subtype B (32.5%), BG recombinants (19.6%) and CRF19_cpx (16.2%) were the most prevalent genetic forms. Subtype distribution did not change significantly between 2009–2010 and 2011–2013, except for BG recombinants that increased from 12.2 to 21.3% (p=0.002).ConclusionsOur study found a high prevalence of drug resistance and supports the need for appropriate laboratory monitoring in clinical practice and access to drug options in case of virological failure.
Use of dolutegravir in two INI‐experienced patients with multiclass resistance resulted in excellent virological and immunological responses
Authors: Marije Hofstra Laura , Nijhuis Monique , Mudrikova Tania , Fun Axel , Schipper Pauline , Schneider Margriet , Wensing Annemarie 
Published: November 2014

IntroductionDolutegravir is a second generation integrase inhibitor with a proposed high genetic barrier to resistance. However, in clinical trials, decreased virological response was seen in a subset of patients with prior exposure to raltegravir and multiple integrase resistance mutations.MethodsWe describe two cases of HIV subtype B‐infected patients starting dolutegravir after previous failure on a raltegravir‐containing regimen with extensive resistance. Genotypic analysis was performed using population sequencing and 454 ultradeep sequencing of integrase at time of raltegravir exposure.ResultsBoth patients were diagnosed in early 1990s and received mono‐ and dual therapy, followed by several cART‐regimens. Due to presence of extensive resistance, the genotypic susceptibility score of these regimens never reached a score >2 and never resulted in sustained virological suppression despite good adherence. Early 2012, the clinical condition of patient 1 worsened during persistent failure of a mega‐cART regimen despite excellent drug levels. Six major PI, six minor PI, seven NRTI, six NNRTI and two INI mutations plus DM‐virus were detected (Table 1). Ultra‐deep sequencing of integrase showed the selection of Q148R, E138K+Q148K, and N155H variants and phenotypic raltegravir resistance was demonstrated. After addition of dolutegravir and enfuvirtide to the failing regimen (zidovudine, lamivudine, tenofovir, etravirine, darunavir/ritonavir, maraviroc), viral load (VL) decreased from 244,000 to <20 cps/mL within five months, CD4‐count increased (33 to 272 mm3) and the clinical condition improved substantially. In patient 2, similar worsening of the clinical condition was observed late 2012 during persistent failure on mega‐cART. Five major PI, six minor PI, nine NRTI, seven NNRTI and one INI mutation plus DM‐virus were detected. Ultra‐deep sequencing showed selection of N155H, followed by Q95K and V151I variants and phenotypic raltegravir resistance was demonstrated. Dolutegravir was added to his failing regimen (zidovudine, lamivudine, etravirine, atazanavir/ritonavir, maraviroc) at a VL of 39,000 cps/mL. Sustained virological suppression was reached within five months with considerable increase of CD4‐count (41 to 175 mm3) and slight improvement of clinical condition.ConclusionsWe present the first patients with extensive integrase resistance who were treated with dolutegravir in clinical practice and who achieved excellent virological and immunological success. These cases demonstrate the high genetic barrier of dolutegravir.
Early clinical response and presence of viral resistant minority variants: a proof of concept study
Authors: Callegaro Annapaola , Di Filippo Elisa , Astuti Noemi , Andrea Serna Ortega Paula , Rizzi Marco , Farina Claudio , Valenti Daniela , Maggiolo Franco 
Published: November 2014

IntroductionTraditional genotyping assays detect viral variants present in at least 15–25% of the entire virus population. We tested the Next generation GS Junior System (NGS) setted with a detection limit of 0.05% and evaluated the clinical relevance of low prevalent mutations.MethodsNGS was performed on the plasma of 26 infected individuals who started a TDF/FTC/RPV (15 subjects) or TDF/FTC/EFV (11 subjects) cART after a routine HIV‐1 drug‐resistance negative test by Viroseq HIV‐1 Genotyping System. Amplicon Sequencing of HIV‐1 RT and PR Plate (Roche) was performed following the manufacturer's instructions. HIV‐1 variants were analyzed by a specific HIV‐1 tool by AVA software v. 2.7. The updated IAS resistance mutations list (March 2013) was considered for the analysis of resistance positions. Patients were followed testing viral load and immunologic parameters.ResultsTwenty four males and two females with a mean age of 43 years were included. Twenty‐one were nave for cART. At baseline, median HIV‐RNA was 4.57 log copies/mL (range 2.15–6.57) and CD4 count 315 cells/mcL (range 16–648). In 18 patients, NGS did not detect any additional variant relevant for the selected cART compared to population genotyping. In the remaining eight patients resistance conferring mutations to part of the ongoing regimen were detected. Single mutations E138K (two cases) and M184V in three distinct patients and V90I+G190E; M184V+A98S; Y215F+V118I+T215I; L210S+T215I+F227L; and A62V+D67G+K70N+188H in the remaining five subjects. In all cases, the mutation prevalence was inferior to 5%. The mean daily reduction of VL was −3759 copies/mL in patients without NGS detected mutations and −1045 copies/mL in those with mutations. The median KM estimates for reaching an HIV‐RNA blood level <50 copies/mL were 127 days and 161 days, respectively. One patient without baseline resistance selected for M184I+E138K+T215I (NGS) after four months of TDF/FTC/RPV therapy.ConclusionsNGS detected low‐frequency HIV‐1 variants harbouring RT drug resistance mutations that could have affected the therapy outcome. However, viral decay in an early cART phase was not affected by the presence of resistant minority variants. The low prevalence of the detected mutation, the limited effect on the combination regimen and the potency of cART components could be possible explanations of our findings. Longer follow‐up and larger casuistries are needed to determine the clinical relevance of NGS in routine clinical practice and eventually define a clinically relevant mutations' prevalence.
144‐week outcomes of lopinavir/ritonavir (LPV/r)‐based first‐line ART in 1,409 HIV‐infected patients: data from the German STAR/STELLA cohort
Authors: Wolf Eva , Trein Andreas , Baumgarten Axel , Stephan Christoph , Jaeger Hans , Hillenbrand Heribert , Koeppe Siegfried , Lutz Thomas , Koenig Bettina , Stellbrink Hans‐Juergen 
Published: November 2014

IntroductionSTAR/STELLA is a prospective[TS1] cohort of HIV patients initiated on LPV/r‐based ART in routine clinical practice. Here, virologic/immunologic outcomes and safety data of LPV/r‐based first‐line ART over a period of 144 weeks are presented.MethodsAnalysis included ART‐naïve patients who started on LPV/r before July 2011 (i.e. patients with ≥144 weeks since ART initiation). Safety evaluation included adverse events (AEs), discontinuations (disc.) due to AEs, and symptoms assessed with the self‐report ACTG Symptom Distress Module (ASDM; high score=high distress).Results1409 patients were included (84% men; 76% on TDF+FTC), with a large proportion in advanced stages of HIV disease at ART initiation: 48% had a CD4 count <200/µL, 55% had HIV RNA levels >100,000 c/mL. 53% of patients (n=746) remained on LPV/r for at least 144 weeks. Time on drug was longer for patients initiated before 2008 than in subsequent years (HRadj, 1.2; 95% CI, 1.0–1.4; p=0.04; hazard ratio adjusted for CD4 <200/µL and HIV RNA >100,000 c/mL). Main reasons for d/c were: AEs (19.3%), patient wish (9.2%), virologic/immunologic failure (4.1%), and noncompliance (2.8%); 1.6% of patients died. By week 144, 33% of patients had >750 CD4/µL (Kaplan–Meier estimate): time to CD4 count >750 c/ µL, stratified by BL CD4 count, is shown in Figure 1.ITT snapshot analysis of HIV RNA <50 c/mL at week 144 showed 51% responders (failure=d/c due to virologic/immunologic failure, AEs, noncompliance, death). In patients on LPV/r for 144 weeks, median CD4 change was +314/µL (IQR, 205–440/µL), 87% had HIV RNA levels <50 c/mL. In patients who discontinued therapy prior to week 144, 56% had an HIV RNA level <50 c/mL. In 51% of patients, ≥1 AE was reported (most commonly diarrhoea, 35%); 11% of patients had ≥1 AE of grade 3 or 4 (diarrhoea, 4.5%). In patients who remained on LPV/r based ART through 144 weeks, median ASDM score decreased significantly from 9 at BL (IQR, 3–21) to 2.5 at Week 144 (IQR, 0–8.5, p<0.001).ConclusionIn the STAR/STELLA observational cohort, LPV/r‐based ART demonstrated good virologic outcomes and immune recovery in ART‐naïve patients over 144 weeks, with significant improvements in symptom distress. Over three years, <5% of patients discontinued LPV/r due to virologic/immunologic failure, and 19% of patients discontinued for tolerability reasons.
Analysis of Protein Composition Using Multidimensional Chromatography and Mass Spectrometry
Authors: Link Andrew J. , Washburn Michael P. 
Published: November 2014

AbstractMultidimensional liquid chromatography of peptides produced by protease digestion of complex protein mixtures followed by tandem mass spectrometry can be coupled with automated database searching to identify large numbers of proteins in complex samples. These methods avoid the limitations of gel electrophoresis and in‐gel digestions by directly identifying protein mixtures in solution. One method used extensively is named Multidimensional Protein Identification Technology (MudPIT), where reversed‐phase chromatography and strong cation–exchange chromatography are coupled directly in a microcapillary column. This column is then placed in line between an HPLC and a mass spectrometer for complex mixture analysis. MudPIT remains a powerful approach for analyzing complex mixtures like whole proteomes and protein complexes. MudPIT is used for quantitative proteomic analysis of complex mixtures to generate novel biological insights. © 2014 by John Wiley & Sons, Inc.
Sampling of Intestinal Microbiota and Targeted Amplification of Bacterial 16S rRNA Genes for Microbial Ecologic Analysis
Authors: Tong Maomeng , Jacobs Jonathan P. , McHardy Ian H. , Braun Jonathan 
Published: November 2014

AbstractDysbiosis of host‐associated commensal microbiota is emerging as an important factor in risk and phenotype of immunologic, metabolic, and behavioral diseases. Accurate analysis of microbial composition and functional state in humans or mice requires appropriate collection and pre‐processing of biospecimens. Methods to sample luminal and mucosal microbiota from human or mouse intestines and to profile microbial phylogenetic composition using 16S rRNA sequencing are presented here. Data generated using the methods in this unit can be used for downstream quantitative analysis of microbial ecology. © 2014 by John Wiley & Sons, Inc.