TASK DEFINITION: In this task, you are given a passage which has a question and the context. You have to generate an answer to the question based on the information present in the context.
PROBLEM: Context: To determine the extent of genetic variation among internationally collected HIV-1 isolates, to analyse phylogenetic relationships and the geographic distribution of different variants.', 'Phylogenetic comparison of 70 HIV-1 isolates collected in 15 countries on four continents.', 'To sequence the complete gag genome of HIV-1 isolates, build multiple sequence alignments and construct phylogenetic trees using distance matrix methods and maximum parsimony algorithms.', 'Phylogenetic tree analysis identified seven distinct genotypes. The seven genotypes were evident by both distance matrix methods and maximum parsimony analysis, and were strongly supported by bootstrap resampling of the data. The intra-genotypic gag distances averaged 7%, whereas the inter-genotypic distances averaged 14%. The geographic distribution of variants was complex. Some genotypes have apparently migrated to several continents and many areas harbor a mixture of genotypes. Related variants may cluster in certain areas, particularly isolates from a single city collected over a short time.\Question: Does phylogenetic analysis of gag genes from 70 international HIV-1 isolates provide evidence for multiple genotypes?

SOLUTION: The genetic variation among HIV-1 isolates is more extensive than previously appreciated. At least seven distinct HIV-1 genotypes can be identified. Diversification, migration and establishment of local, temporal 'blooms' of particular variants may all occur concomitantly.

PROBLEM: Context: Obstructive sleep apnea (OSA) is a common disorder characterized by chronic intermittent hypoxia (CIH). OSA is prevalent in obese subjects and is associated with endothelial dysfunction and cardiovascular disorders. We tested the hypothesis that the deleterious effects of IH could be further modulated by diet-induced obesity.', 'Thirty adult (8-10 weeks) male C57BL/6J mice were divided into four groups. Mice were subjected to CIH or intermittent air (IA) for 12h a day and fed either a high fat (HF) or a low fat control diet (CD) for 6weeks. We analyzed endothelial function using a wire myograph, and measured markers of oxidative stress (plasma malondialdehyde (MDA) and total antioxidant capacity (TAC)) using colorimetrical assays. We also measured C-reactive protein (CRP) using ELISA and endothelial nitric oxide (eNOS) gene expression using real time PCR.', 'Stimulated endothelial dependent dilation was significantly impaired only in the group fed high fat diet and subjected to CIH (Emax: HFIH 78±2%, p<0.0001) when compared to the other groups (Emax: HFIA 95±0.7%, CDIH 94±2%, CDIA 97±1%). Also basal endothelial dependant dilation was attenuated in the HFIH group compared to the HFIA group (Emax: HFIH: 179±10% vs. HFIA: 149±11% in the presence of L-NAME). Levels of MDA were elevated in the CDIH group when compared to CDIA (0.68±0.04 vs. 0.41±0.03 μM, p<0.05) but were greatest in the HFIH group (0.83±0.08 μM, p<0.05). However, there was no significant increase in MDA levels in the HFIA group (0.45±0.03 μM, p=NS) when compared to all other groups. Similar effects were observed with CRP levels; CRP levels were significantly higher in the CDIH group compared with intermittent air (10.39±0.38 vs. 8.70±0.21 μg/ml, p<0.05) but the HFIH had the greatest levels of CRP (11.87±0.31 μg/ml, p<0.05). In the HFIA group, CRP levels were not elevated (9.96±0.37 μg/ml, p=NS). Nevertheless, total antioxidant capacity and eNOS gene expression were not significantly different in the groups.\Question: Does chronic intermittent hypoxia cause endothelial dysfunction in a mouse model of diet-induced obesity?

SOLUTION: CIH caused endothelial dysfunction in mice fed an obesogenic diet. Inflammation and oxidative stress were increased in CIH and an obesogenic diet exacerbated these effects.

PROBLEM: Context: Device-related infections remain a considerable problem of left-ventricular support. We compared the device-related-infections between the HeartMate left ventricular assist device (LVAD) and the Jarvik 2000 permanent LVAD, a device with a novel retroauricular power-supply.', 'Between December 2000 and September 2002 we implanted the HeartMate-vented, electrical-system in 11 patients and the permanent Jarvik 2000 in six patients. Total support time was 1626 patient-days (HeartMate, 26-271 days) versus 1246 patient-days (Jarvik 2000, 8-411 days). As potential risk factors for infection we analyzed age, preoperative hospital-days, total protein, cardiac index, maximal oxygen uptake, use of inotropes, LVAD risk-score-index and Aaronson-Mancini-score, intubation time, and intensive care unit stay. We used the Center of Disease Control definitions for surgical site infections.', 'HeartMate-patients were younger than Jarvik 2000 patients (46+/-13 versus 58+/-6 years, P=0.056), there were no other differences in the risk factors. Four HeartMate-patients needed late (>or=48 h) surgical revisions for bleeding/hematomas versus no revisions in the Jarvik 2000 patients. In the HeartMate-patients, there were seven (64%) driveline-infections, five (45%) device-pocket infections, and three (27%) bloodstream-infections, or 0.43 device-related infections/100 patient-days. Infections occurred early (34+/-31 days). Three patients required urgent transplantation due to bloodstream infection. There were no adverse outcomes in the HeartMate-group due to infection. In the Jarvik 2000 patients, there was one driveline-infection (16%) after 270 days of support (0.08 device-related infections/100 patient-days), significantly less than in the HeartMate-group (P=0.044). Driveline infections resolved with antibiotics and local wound care in the Jarvik 2000 patient, but only in one of seven HeartMate-patients.\Question: Is the Jarvik 2000 associated with less infections than the HeartMate left ventricular assist device?

SOLUTION:
Implantation of the Jarvik 2000 is associated with less device-related infections than the HeartMate-LVAD. The power-supply of the permanent Jarvik 2000 is suitable for long-term mechanical support.