Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Eight Different Bioinformatics Tools To Predict Viral Tropism in Different Human Immunodeficiency Virus Type 1 Subtypes

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) tropism can be assessed using phenotypic assays, but this is quite laborious, expensive, and time-consuming and can be made only in sophisticated laboratories. More accessible albeit reliable tools for testing of HIV-1 tropism are needed in view of the prompt introduction of CCR5 antagonists in clinical practice. Bioinformatics tools based on V3 sequences might help to predict HIV-1 tropism; however, most of these methods have been designed by taking only genetic information derived from HIV-1 subtype B into consideration. The aim of this study was to evaluate the performances of several genotypic tools to predict HIV-1 tropism in non-B subtypes, as data on this issue are scarce. Plasma samples were tested using a new phenotypic tropism assay (Phenoscript-tropism; Eurofins), and results were compared with estimates of coreceptor usage using eight different genotypic predictor softwares (Support Vector Machine [SVM], C4.5, C4.5 with positions 8 to 12 only, PART, Charge Rule, geno2pheno coreceptor, Position-Specific Scoring Matrix X4R5 [PSSMX4R5], and PSSMsinsi). A total of 150 samples were tested, with 115 belonging to patients infected with non-B subtypes and 35 drawn from subtype B-infected patients, which were taken as controls. When non-B subtypes were tested, the concordances between the results obtained using the phenotypic assay and distinct genotypic tools were as follows: 78.8% for SVM, 77.5% for C4.5, 82.5% for C4.5 with positions 8 to 12 only, 82.5% for PART, 82.5% for Charge Rule, 82.5% for PSSMX4R5, 83.8% for PSSMsinsi, and 71.3% for geno2pheno. When clade B viruses were tested, the best concordances were seen for PSSMX4R5 (91.4%), PSSMsinsi (88.6%), and geno2pheno (88.6%). The sensitivity for detecting X4 variants was lower for non-B than for B viruses, especially in the case of PSSMsinsi (38.4% versus 100%, respectively), SVMwetcat (46% versus 100%, respectively), and PART (30% versus 90%, respectively). In summary, while inferences of HIV-1 coreceptor usage using genotypic tools seem to be reliable for clade B viruses, their performances are poor for non-B subtypes, in which they particularly fail to detect X4 variants.
Colonization resistance of the digestive tract of mice during systemic antibiotic treatment

SUMMARY During systemic treatment of mice with ampicillin or streptomycin, oral contaminations with exogenous bacterial species resulted in an abnormal colonization pattern. The contaminants persisted much longer and in much higher concentrations in the caecum of systemically treated mice than in control animals. Spread of the contaminant into the mesenteric lymph nodes and the spleen was found much more often in the antibiotic treated group. This, however, was only seen when the contaminant was ‘resistant’ to the antibiotic injected. The experiments suggest that the ‘CR-inducing species’ of the microflora live in close contact with the mucosa and therefore could be identical with the anaerobic tapered rods described by Savage & Dubos (1968).
Human platelets activate porcine endothelial cells through a CD154-dependent pathway.

BACKGROUND Delayed xenograft rejection is associated with endothelial cell activation, platelet sequestration, and subsequent thrombosis. We evaluated whether human platelets could directly activate porcine endothelium (PEC), and if so, whether this was mediated by an interaction between platelet-bound CD154 and PEC CD40. METHODS Platelet activation was achieved by thrombin exposure and confirmed by evaluation of up-regulated CD62P and CD154. Co-incubation of platelets or D1.1 cells with PEC was performed, and PEC activation was evaluated by up-regulation of CD62E. RESULTS Co-incubation of resting platelets that lacked significant expression of CD62P and were void of CD154 did not activate PEC. In contrast, thrombin-activated human platelets expressing considerable amounts of both CD62P and CD154 induced PEC activation. This activation could be completely inhibited by coincubation with a humanized monoclonal antibody directed at human CD154 (hu5c8). Similarly, human D1.1 cells expressing CD154 were shown to activate PEC in a CD154-dependent manner. CONCLUSION Human CD154 expressed on activated human platelets or on T cells interacts with CD40 expressed on PEC leading to PEC activation. This interaction can be inhibited by a monoclonal antibody directed against CD154, suggesting that an interaction between human CD154 and PEC CD40 is at least in part responsible for PEC activation seen in delayed xenograft rejection. These data strengthen the rationale for the use of CD154-directed therapy in discordant xenotransplantation.
Epidemiology Data on 108 MEN 1 Patients From the GTE With Isolated Nonfunctioning Tumors of the Pancreas

Objective:To analyze the penetrance and clinical course of isolated nonfunctioning tumors of the pancreas (NFTP) in MEN 1 patients, and to propose a strategy for managing them. Summary Background Data:Pancreaticoduodenal tumors develop in a majority of MEN 1 patients and are a major cause of death. The natural history of NFTP is poorly defined, and no clear-cut guidelines have been widely accepted regarding treatment. Methods:Data on 108 patients with isolated NFTP among 579 MEN 1 patients from the French Endocrine Tumor Study Group (GTE) were analyzed. Survival rates were calculated using the Kaplan-Meier method. Results:The penetrance of NFTP was 34% at age 50, making it the most frequent pancreaticoduodenal tumor in MEN 1 patients. Forty-three patients (40%) underwent surgery, 32 of them curatively. No patient died because of surgery. Average life expectancy for patients with NFTP was shorter than that for MEN 1 patients who did not have pancreaticoduodenal tumors. Thirteen patients died during follow-up, 10 due to NFTP. Tumor size was correlated with the risks of metastasis and death. These risks were low for patients with tumors ≤20 mm. Conclusions:NFTP are currently the most common tumors of the pancreaticoduodenal region in patients with MEN 1. Prevention of tumor spread by surgery should be balanced with potential operative mortality and morbidity. We do not recommend routine surgery for NFTP ≤20 mm.
Neonatal Sleep Predicts Attention Orienting and Distractibility

Objective: Children with sleep disorders tend to experience attention problems, yet little is known about the relationship between sleep and attention in early development. This prospective follow-up study investigated the longitudinal relationships between neonatal sleep, attention, and distraction in infants born preterm. Method: We used actigraphy and sleep-wake diaries in the neonatal intensive care unit (NICU, N = 65), attention orienting in a visual-recognition-memory task (VRM) at age 4 months, and structured observation of attention and distractibility at age 18 months. Results: Infants with poorer neonatal sleep (n = 31) exhibited longer first gaze durations in the VRM at 4 months and longer distraction episodes at 18 months relative to neonatal controls who slept well (p < .01). Hierarchical regression models support relations between neonatal sleep and gaze behavior at 4 months and distractibility at 18 months; moreover, alterations in orienting attention at 4 months predicted the likelihood of being distracted during the second year of life. Conclusion: Findings underscore the importance of early sleep-wake and attention regulation in the development of distraction in infants born preterm.
A Fuzzy Recommender System for Public Library Catalogs

Recommendation engines are one of the “discovery” products built into integrated library systems. These are a subclass of enterprise systems designed specifically for public and research libraries that incorporate an electronic card catalogue, circulation and inventory management, personnel and payroll systems, etc. The system vendors offer customizations for different contexts of specific library systems, but cannot create a bespoke solution for every customer. Our partner, an Edmonton‐area company, is filling this gap for a consortium of rural libraries in Alberta by creating a mobile app that interfaces with their electronic card catalog. Rural libraries are generally smaller than major urban public libraries, meaning that their holdings are limited overall, and within any given genre. This poses a severe problem for traditional collaborative‐filtering recommender algorithms, as the item sets for recommendations are limited by supply rather than by readers’ interests. The library's relatively small clientele also limits the item sets available for comparison. To deal with this ongoing “cold‐start” problem, we propose a hybridization of collaborative filtering with a content filter using a fuzzy taste vector. Experiments on two benchmark recommender data sets show that this approach is at least as accurate as existing fuzzy recommenders and is particularly effective on sparse data sets.
A comparative gene-expression analysis of CD34+ hematopoietic stem and progenitor cells grown in static and stirred culture systems

Static and stirred culture systems are widely used to expand hematopoietic cells, but differential culture performances are observed between these systems. We hypothesize that these differential culture outcomes are caused by the physiological responses of CD34+ hematopoietic stem and progenitor cells (HSPCs) to the different physical microenvironments created in these culture devices. To understand the genetic changes provoked by culture microenvironments, the gene expression profiling of CD34+ HSPCs grown in static and stirred culture systems was compared using SMART-PCR and cDNA arrays. The results revealed that 103 and 99 genes were significantly expressed in CD34+ cells from static and stirred systems, respectively. Of those, 91 have similar levels of expression, while 12 show differential transcription levels. These differentially expressed genes are mainly involved in anti-oxidation, DNA repair, apoptosis, and chemotactic activity. A quantitative molecular understanding of the influences of growth microenvironments on transcriptional events in CD34+ HSPCs should give new insights into optimizing culture strategies to produce hematopoietic cells.
Nucleotide sequence of core and envelope genes of the hepatitis C virus genome derived directly from human healthy carriers.

Hepatitis C virus (HCV) is the major causative agent of post transfusion non-A, non-B hepatitis throughout the world. We isolated and sequenced eDNA clones of the HCV genome from RNA extracted from healthy Japanese HCV carrier plasma samples by reverse polymerase chain reaction (rPCR) methods (1, 2). Primers were designed from the nucleotide sequence of HCV derived from an experimentally transmitted chimpanzee (3, 4). Here we report the complete nucleotide and amino acid sequences of the structural gene ofHCV (Figure 1). Clones from three different but overlapping regions were isolated after rPCR. From each region, three clones were independently isolated and sequenced at both strands in order to deduce the consensus nucleotide sequence. We consider nucleotide (nt) 1 to ca. nt 570 as a coding gene for the nucleocapsid (core) protein because of (i) high nucleotide (90.5%) and amino acid (97.4%) sequence identity to those of the original HCV isolate (4), (ii) lack of N-glycosylation signal, (iii) existence of a highly hydrophobic domain particularly at its C-terminus, and (iv) detection of a 22-kilodalton protein expressed in mammalian cells by introducing this eDNA sequence under the control of a foreign promoter (5). The region from ca. nt 570 to ca. nt 1140 was considered to be the putative envelope gene. The deduced amino acid sequence was mostly hydrophobic and had 6 possible N
The thermal analysis of a satellite by an in-house computer code based on Thermal Network Method and Monte Carlo Ray Tracing Technique

In this paper, the development of an in-house computer code for the thermal analysis of satellites is discussed. The code is based on Thermal Network Method (TNM) in conjunction with Method of Lines (MOL) for the solution of energy equation. The view factors required for the computation of radiative exchange factors which are used in TNM are calculated by a newly developed module based on Monte-Carlo Ray Tracing Technique. The predictive accuracy of the code including the new module was assessed on a realistic test problem involving a satellite orbiting the earth at an altitude of 700 km. Comparison of transient results obtained by the in-house code and a commercial thermal analysis software package (Thermica-SINDA/G) has shown that the in-house code predictions mimic the ones obtained by Thermica-SINDA/G very accurately.
The Relative Effectiveness of Liquid Methionine Hydroxy Analogue Compared to DL-methionine in Broilers

The present experiment was conducted to assess the efficacy of liquid methionine hydroxy analogue-free acid (MHA- FA) in comparison to DL-methionine (DL-Met) in broilers. 567 day-old Avian chicks were divided into 7 treatments with 5 replicates of 16 birds each. During the 35d (7-42 d) experimental periods chicks were given two basal diets. From 7 to 21d of age, a starting basal diet containing 19.5% protein and 0.33% methionine was supplemented with two graded levels of DL-Met (0.070 and 0.160%) or four levels of MHA-FA (0.118, 0.143, 0.221 and 0.268%). From 22 to 42d of age DL-Met (0.050 and 0.080%) or MHA-FA (0.071, 0.074, 0.112 and 0.140%) were added to a finishing basal diet with 18.0% protein and 0.28% methionine. Chicks fed on supplemental DL-Met or MHA-FA had significantly higher (p<0.05) body weight gain and feed conversion ratio (FCR) than the control group from 7-21d of age. During the finishing phase (22-42 d), body weight and weight gain of chicks in DL-Met or MHA-FA treatments were similar to those in the control, but FCR was improved (p<0.05) with supplementation of DL-Met or MHA-FA. Breast yield was higher (p<0.05) on DL-Met or MHA-FA supplemented than un-supplemented diets. The thigh meat yields emanating from diets with DL-Met or MHA-FA were lower (p<0.05) than that in control. Abdominal fat was also higher in broilers fed the control diet than in DL-Met or MHA-FA supplemented treatments. Methionine requirement of broilers was calculated to be 0.44 and 0.35% and cystine requirement was 0.35 and 0.31% for the starting (7-21 d) and finishing phase (22-42 d), respectively. The efficacy of MHA-FA in comparison to DL-Met for weight gain was 64 and 85% and for FCR was 55 and 60% at 7-21 and 22-42 d of age, respectively, while it was 74, 72, 52 and 48% for breast yield, thigh meat production, body energy content and energy deposition ratio at 42 d of age, respectively. In conclusion, in practical diet formulation for broiler chicks the average bioavailability of MHA-FA relative to DL-Met could be considered as 60 and 73% for 7 to 21d and 22 to 42 d of age, respectively. (Key Words : DL-Met, MHA-FA, Broiler, Growth Performance, Carcass Traits)
Education in ambulatory settings: developing valid measures of educational outcomes, and other research priorities

Efforts to redesign education in ambulatory settings are hampered by a lack of rigorous and coherent research on the learning process in these settings and the desired outcomes of the educational experiences. The authors present 13 priority research topics and 51 important research questions concerning education in ambulatory settings that were defined by a distinguished group of medical educators, clinicians, and policymakers who attended an invitational conference on education in ambulatory settings in 1996. The need to establish valid and reliable measures of quality and outcomes of educational programs and instructional interventions stood out as the major prerequisite for conducting research on education in ambulatory settings. Issues of theory building, research priorities, and research design are discussed, and policy recommendations are made for the development of valid measures of educational outcomes. The creation of a “Medical Education Outcomes Commission” is proposed to act as a repository for measures and instruments, and to provide the field with mechanism to validate instruments and uniform recommendations to conduct studies of quality. The authors urge funding agencies with missions that support medical education to invest in basic research on the outcomes of education in ambulatory settings.
A Gender Comparison of Motivations for Physical Dating Violence Among College Students

There are limited empirical investigations that directly compare men and women’s motivations, or reasons, for perpetrating physical dating violence (DV). In an attempt to further understand whether men and women have similar or different motives for physical DV, the purpose of the current study was to conduct a gender comparison of motives in a sample of male (n = 163) and female (n = 319) college students. Motivations for physical DV were classified according to seven broad categories proposed by Langhinrichsen-Rohling and colleagues: (a) power/control, (b) self-defense, (c) expression of negative emotion (e.g., anger), (d) communication difficulties, (e) retaliation, (f) jealousy, and (g) other (e.g., because it was sexually arousing, the influence of alcohol, the influence of drugs). The prevalence of physical violence perpetration in the overall sample was 29.4%. Results indicated that communication difficulties and self-defense were among the most frequently endorsed motive categories for both male and female perpetrated DV. In addition, results demonstrated gender similarity in all of the examined motive categories. Research and clinical implications are discussed.
Suppression of transcription polarity in the Escherichia coli haemolysin operon by a short upstream element shared by polysaccharide and DNA transfer determinants

Expression of the Escherichia coli hlyCABD operon encoding synthesis, maturation and export of haemolysin toxin was strongly dependent upon a 35 bp DNA sequence, spanning the element GGCGGTAG, located 2 kbp upstream. When the hly operon was placed under the control of the inducible tac promoter, expression remained dependent upon this element, when transcribed in its native orientation 3′ of the promoter. The increase in ptac‐directed transcription was strongest for the distal, export genes of the hly operon, and was particularly striking when ptac and the element were placed far upstream. The element did not influence transcript stability, and we suggest that it is a key component of a novel regulatory mechanism may suppresses transcription polarity within operons. The mechanism that be of widespread importance in bacterial gene expression because the 8 bp element is present in many Gram‐negative species as an upstream component of operons encoding the production of toxins and the surface assembly of polysaccharides and components required for the conjugal transfer of DNA. We name it the ops element for operon polarity suppressor.
Plasma immunoglobulin concentrations in an African (Gambian) community in relation to season, malaria and other infections and pregnancy.

IgG, IgA, IgM and IgD concentrations in plasma were measured at three surveys of a rural Gambian community made over 13 months. 3523 samples were analysed. The pattern of change with age of mean levels of each immunoglobulin class was similar at each survey, although IgM levels were highest in the survey made at the end of the wet season. Immunoglobulin levels in the same individual were found to be relatively stable in adults over the study period. Only minor correlations were found between the levels of different immunoglobulin classes in plasma from the same individual. Malarial parasitaemia was associated with increased mean IgG levels in age groups up to 20 years but with increased IgM levels only in the first 2 years of life. Plasma which contained precipitating antibodies to malarial antigens showed higher mean levels of IgG and IgM in most age groups. In association with splenomegaly mean IgG levels were increased throughout childhood while mean IgM levels were elevated only in the first 2 years. No consistent relationship between malaria and mean levels of IgA and IgD were noted. The only relationship found between haemoglobin concentration and immunoglobulin levels was a small negative correlation in respect of IgM. Clinical infection, other than malaria, was associated with increased mean levels of IgG and IgA in all age groups and of IgM in young children. Lower levels of IgG, IgA and IgM occurred in pregnancy; IgG levels seemed to fall progressively as pregnancy advanced. At certain ages mean levels of IgM and IgD were higher in females than males.
Effect of Simulated Visual Impairment on Nighttime Driving Performance

Purpose. This study investigated the effects of simulated visual impairment on nighttime driving performance and pedestrian recognition under real-road conditions. Methods. Closed road nighttime driving performance was measured for 20 young visually normal participants (M = 27.5 ± 6.1 years) under three visual conditions: normal vision, simulated cataracts, and refractive blur that were incorporated in modified goggles. The visual acuity levels for the cataract and blur conditions were matched for each participant. Driving measures included sign recognition, avoidance of low contrast road hazards, time to complete the course, and lane keeping. Pedestrian recognition was measured for pedestrians wearing either black clothing or black clothing with retroreflective markings on the moveable joints to create the perception of biological motion (“biomotion”). Results. Simulated visual impairment significantly reduced participants' ability to recognize road signs, avoid road hazards, and increased the time taken to complete the driving course (p < 0.05); the effect was greatest for the cataract condition, even though the cataract and blur conditions were matched for visual acuity. Although visual impairment also significantly reduced the ability to recognize the pedestrian wearing black clothing, the pedestrian wearing “biomotion” was seen 80% of the time. Conclusions. Driving performance under nighttime conditions was significantly degraded by modest visual impairment; these effects were greatest for the cataract condition. Pedestrian recognition was greatly enhanced by marking limb joints in the pattern of “biomotion,” which was relatively robust to the effects of visual impairment.
Hepatocyte Growth Factor-induced Differential Activation of Phospholipase Cγ1 and Phosphatidylinositol 3-Kinase Is Regulated by Tyrosine Phosphatase SHP-1 in Astrocytes*

Hepatocyte growth factor (HGF) elicits pleiotropic effects on various types of cells through the c-Met receptor tyrosine kinase. However, the mechanisms underlying the diverse responses of cells remain unknown. We show here that HGF promoted chemokinesis of rat primary astrocytes through the activation of phosphatidylinositol 3 (PI3)-kinase without any influence on mitogenesis of the cells. Under the same condition, phospholipase Cγ1 (PLCγ1), which is another signal mediator of c-Met, was not tyrosine-phosphorylated during HGF stimulation. However, treatment of the cells with orthovanadate, a tyrosine phosphatase inhibitor, restored the HGF-induced tyrosine phosphorylation of PLCγ1. A tyrosine phosphatase, SHP-1, was associated with both PI3-kinase and PLCγ1 before HGF stimulation, but it was dissociated only from PI3-kinase after the stimulation. Furthermore, transfectants of catalytically inactive mutant of SHP-1 showed tyrosine phosphorylation of PLCγ1 and mitogenic responses to HGF, and the mitogenic response was blocked with U73122, an inhibitor of phosphatidylinositol-specific PLC, and calphostin C, an inhibitor of protein kinase C downstream of the PLCγ1. These results indicate that PLCγ1 is selectively prevented from being a signal mediator by constitutive association of SHP-1, and that this selective inhibition of PLCγ1 may determine the cellular response of astrocytes to HGF.