Miracle-dz/UniFAR-FTUs huggingface dataset:
Interstrain Variation in the Human Cytomegalovirus DNA Polymerase Sequence and Its Effect on Genotypic Diagnosis of Antiviral Drug Resistance

ABSTRACT The polymerase (pol) coding sequence was determined for 40 independent clinical cytomegalovirus isolates sensitive to ganciclovir and foscarnet. Sequence alignments showed >98% interstrain homology and amino acid variation in only 4% of the 1,237 codons. Almost all variation occurred outside of conserved functional domains where resistance mutations have been identified.
Nutrition and the Lung

The use of surfactant replacement, ‘kinder gentler’ modes of ventilation combined with prenatal corticosteroids have all played a role in improved survival rates of very-low-birth-weight infants but have not reduced the prevalence of chronic lung disease. The increased rates of prematurity being observed in the United States along with the increased survival makes the overall problem of treatment of infants with established disease expensive spanning neonatology, pediatric critical care and general pediatrics and involving a myriad of specialists over the life of the surviving infant. However, none of the therapies used over the years have proven to be effective or have long-term adverse effects, nor have they been accepted as methods to prevent chronic lung disease. Although intuitively an appropriate nutritional therapy may be a useful adjunct in the care of the premature sick infant, perinatal malnutrition remains a major problem. The role of nutrition therapy in health and disease as it pertains to the lung will be reviewed.
Diversity in unity: The biochemical composition of the endothelial cell surface varies between the vascular beds

The vascular endothelium represents a population of squamous epithelial cells characterized by a particular histological localization (intima of blood vessels) and by several physiological functions such as the transport of substances between blood and tissues, the modulation of the vascular tone, the control of blood coagulation and that of the leukocyte extravasation. In spite of all these elements in common and of an identical embryonic origin, endothelial cells show definite morphological and physiological variations that divide them into types and subtypes, each specifically associated to various categories of organs. Even within the vasculature of the same organ, there are clear segmental (arterial/capillary/venous) differentiations of the endothelial cells. While the morphological and physiological differences between endothelial cells are well documented, there are very few data on the biochemistry underlying this heterogeneity. This work presents several data suggesting that, at present, the domain is ripe for a comprehensive analysis of this biochemical diversity, at least in what concerns the luminal aspect of the endothelial plasmalemma, a compartment of crucial importance in the biology and pathology of the cardiovascular system. Microsc. Res. Tech. 57:381–389, 2002. © 2002 Wiley‐Liss, Inc.
Altered Utilization of N-Acetyl-d-Galactosamine by Escherichia coli O157:H7 from the 2006 Spinach Outbreak

ABSTRACT In silico analyses of previously sequenced strains of Escherichia coli O157:H7, EDL933 and Sakai, localized the gene cluster for the utilization of N-acetyl-d-galactosamine (Aga) and d-galactosamine (Gam). This gene cluster encodes the Aga phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) and other catabolic enzymes responsible for transport and catabolism of Aga. As the complete coding sequences for enzyme IIA (EIIA)Aga/Gam, EIIBAga, EIICAga, and EIIDAga of the Aga PTS are present, E. coli O157:H7 strains normally are able to utilize Aga as a sole carbon source. The Gam PTS complex, in contrast, lacks EIICGam, and consequently, E. coli O157:H7 strains cannot utilize Gam. Phenotypic analyses of 120 independent isolates of E. coli O157:H7 from our culture collection revealed that the overwhelming majority (118/120) displayed the expected Aga+ Gam− phenotype. Yet, when 194 individual isolates, derived from a 2006 spinach-associated E. coli O157:H7 outbreak, were analyzed, all (194/194) displayed an Aga− Gam− phenotype. Comparison of aga/gam sequences from two spinach isolates with those of EDL933 and Sakai revealed a single nucleotide change (G:C→A:T) in the agaF gene in the spinach-associated isolates. The base substitution in agaF, which encodes EIIAAga/Gam of the PTS, changes a conserved glycine residue to serine (Gly91Ser). Pyrosequencing of this region showed that all spinach-associated E. coli O157:H7 isolates harbored this same G:C→A:T substitution. Notably, when agaF + was cloned into an expression vector and transformed into six spinach isolates, all (6/6) were able to grow on Aga, thus demonstrating that the Gly91Ser substitution underlies the Aga− phenotype in these isolates.
Abnormal respiratory‐related evoked potentials in untreated awake patients with severe obstructive sleep apnoea syndrome

Aim: Obstructive sleep apnoeas generate an intense afferent traffic leading to arousal and apnoea termination. Yet a decrease in the sensitivity of the afferents has been described in patients with obstructive sleep apnoea, and could be a determinant of disease severity. How mechanical changes within the respiratory system are processed in the brain can be studied through the analysis of airway occlusion‐related respiratory‐related evoked potentials. Respiratory‐related evoked potentials have been found altered during sleep in mild and moderate obstructive sleep apnoea syndrome, with contradictory results during wake. We hypothesized that respiratory‐related evoked potentials’ alterations during wake, if indeed a feature of the obstructive sleep apnoea syndrome, should be present in untreated severe patients.
Enhanced Protective Efficacy of Nonpathogenic Recombinant Leishmania tarentolae Expressing Cysteine Proteinases Combined with a Sand Fly Salivary Antigen

Background Novel vaccination approaches are needed to prevent leishmaniasis. Live attenuated vaccines are the gold standard for protection against intracellular pathogens such as Leishmania and there have been new developments in this field. The nonpathogenic to humans lizard protozoan parasite, Leishmania (L) tarentolae, has been used effectively as a vaccine platform against visceral leishmaniasis in experimental animal models. Correspondingly, pre-exposure to sand fly saliva or immunization with a salivary protein has been shown to protect mice against cutaneous leishmaniasis. Methodology/Principal Findings Here, we tested the efficacy of a novel combination of established protective parasite antigens expressed by L. tarentolae together with a sand fly salivary antigen as a vaccine strategy against L. major infection. The immunogenicity and protective efficacy of different DNA/Live and Live/Live prime-boost vaccination modalities with live recombinant L. tarentolae stably expressing cysteine proteinases (type I and II, CPA/CPB) and PpSP15, an immunogenic salivary protein from Phlebotomus papatasi, a natural vector of L. major, were tested both in susceptible BALB/c and resistant C57BL/6 mice. Both humoral and cellular immune responses were assessed before challenge and at 3 and 10 weeks after Leishmania infection. In both strains of mice, the strongest protective effect was observed when priming with PpSP15 DNA and boosting with PpSP15 DNA and live recombinant L. tarentolae stably expressing cysteine proteinase genes. Conclusion/Significance The present study is the first to use a combination of recombinant L. tarentolae with a sand fly salivary antigen (PpSP15) and represents a novel promising vaccination approach against leishmaniasis.
Fabrication of polymer/microwave‐reduced graphite oxide nanocomposites by ball‐milling assisted wet compounding

Microwave-induced reduction of graphite oxide (GO) is a promising method for rapid and scalable production of graphene. However, homogeneous incorporation of thus prepared graphene into polymer matrix is still a hard task. In this article, we present a ball-milling assisted wet compounding method for the fabrications of microwave-reduced GO (MRGO)/polymer composites. MRGO powders were added into a solution of polystyrene (PS) and then mechanically exfoliated in a stirring mill. Scanning electron microscopy and transmission electron microscopy investigations show that the graphene sheets have been homogeneously dispersed in the PS matrix. The composites show pronouncedly improved properties. The thermal degradation temperature of composites increased by 34°C with the addition of 5wt% MRGO in PS. Up to 76% improvement of storage modulus (at 30°C) is achieved by compounding with 10wt% MRGO.POLYM. COMPOS. , 2013. © 2013 Society of Plastics Engineers
Introgression patterns in the mosaic hybrid zone between Mytilus edulis and M. galloprovincialis

Hybrid zones are fascinating systems to investigate the structure of genetic barriers. Marine hybrid zones deserve more investigation because of the generally high dispersion potential of planktonic larvae which allows migration on scales unrivalled by terrestrial species. Here we analyse the genetic structure of the mosaic hybrid zone between the marine mussels Mytilus edulis and M. galloprovincialis, using three length‐polymorphic PCR loci as neutral and diagnostic markers on 32 samples along the Atlantic coast of Europe. Instead of a single genetic gradient from M. galloprovincialis on the Iberian Peninsula to M. edulis populations in the North Sea, three successive transitions were observed in France. From South to North, the frequency of alleles typical of M. galloprovincialis first decreases in the southern Bay of Biscay, remains low in Charente, then increases in South Brittany, remains high in most of Brittany, and finally decreases again in South Normandy. The two enclosed patches observed in the midst of the mosaic hybrid zone in Charente and Brittany, although predominantly M. edulis‐like and M. galloprovincialis‐like, respectively, are genetically original in two respects. First, considering only the various alleles typical of one species, the patches show differentiated frequencies compared to the reference external populations. Second, each patch is partly introgressed by alleles of the other species. When introgression is taken into account, linkage disequilibria appear close to their maximum possible values, indicating a strong genetic barrier within all transition zones. Some pre‐ or postzygotic isolation mechanisms (habitat specialization, spawning asynchrony, assortative fertilization and hybrid depression) have been documented in previous studies, although their relative importance remains to be evaluated. We also provided evidence for a recent migratory ‘short‐cut’ connecting M. edulis‐like populations of the Charente patch to an external M. edulis population in Normandy and thought to reflect artificial transfer of spat for aquaculture.
Regulation of High-Density Lipoprotein on Hematopoietic Stem/Progenitor Cells in Atherosclerosis Requires Scavenger Receptor Type BI Expression

Objective— Recently, we demonstrated that scavenger receptor type BI (SR-BI), a high-density lipoprotein (HDL) receptor, was expressed on murine hematopoietic stem/progenitor cells (HSPC) and infusion of reconstituted HDL and purified human apolipoprotein A-I (apoA-I) suppressed HSPC proliferation. We hypothesized that SR-B1 expression is required for the observed antiproliferative effects of HDL on HSPC. Approach and Results— SR-BI–deficient (SR-BI−/−) mice and wild-type controls were fed on chow or high-fat diet (HFD) for 8 to 10 weeks. Under chow diet, a significant increase in Lin− Sca1+ cKit+ cells (LSK cells, so-called HSPC) was found in the bone marrow of SR-BI−/− mice when compared with wild-type mice. HFD induced a further expansion of CD150+CD48- LSK cells (HSC), HSPC, and granulocyte monocyte progenitors in SR-BI−/− mice. Injection of reactive oxygen species inhibitor N-acetylcysteine attenuated HFD-induced HSPC expansion, leukocytosis, and atherosclerosis in SR-BI−/− mice. ApoA-I infusion inhibited HSPC cell proliferation, Akt phosphorylation and reactive oxygen species production in HSPC and plaque progression in low-density lipoprotein receptor knockout (LDLr−/−) apoA-I−/− mice on HFD but had no effect on SR-BI−/− mice on HFD. Transplantation of SR-BI−/− bone marrow cells into irradiated LDLr−/− recipients resulted in enhanced white blood cells reconstitution, inflammatory cell production, and plaque development. In patients with coronary heart disease, HDL levels were negatively correlated with white blood cells count and HSPC frequency in the peripheral blood. By flow cytometry, SR-BI expression was detected on human HSPC. Conclusions— SR-BI plays a critical role in the HDL-mediated regulation HSPC proliferation and differentiation, which is associated with atherosclerosis progression.
Moving a formative test from a paper-based to a computer-based format. A student viewpoint

Background: A paper-based test was changed to a computer-based format. Students completed the test over a 2-week period on any computer with internet access. Aim: To determine the acceptability to students of the computer-based format, whether resources were used by students during the test, the value of receiving an immediate score, positive aspects of the computer format and areas for improvement. Methods: Students completed an online survey containing closed questions (Likert scale) and free text questions. Results: A large majority of respondents had easy access to a computer, found it easy to complete the test in the time given and did not use resources to answer the test questions. The most cited benefits were flexibility and convenience in being able to choose both the location and time for taking the test. A smaller majority found it useful to get immediate feedback. The possibility of students ‘cheating’ because of the ability to use resources during the test was seen as problematic. Some students felt that the test appeared to lack importance because of the flexibility permitted. Conclusions: From a student perspective, the computer was an acceptable platform for delivering a formative assessment comprising multiple choice questions (MCQs).
Vaccine candidate discovery for the next generation of malaria vaccines

Although epidemiological observations, IgG passive transfer studies and experimental infections in humans all support the feasibility of developing highly effective malaria vaccines, the precise antigens that induce protective immunity remain uncertain. Here, we review the methodologies applied to vaccine candidate discovery for Plasmodium falciparum malaria from the pre‐ to post‐genomic era. Probing of genomic and cDNA libraries with antibodies of defined specificities or functional activity predominated the former, whereas reverse vaccinology encompassing high throughput in silico analyses of genomic, transcriptomic or proteomic parasite data sets is the mainstay of the latter. Antibody‐guided vaccine design spanned both eras but currently benefits from technological advances facilitating high‐throughput screening and downstream applications. We make the case that although we have exponentially increased our ability to identify numerous potential vaccine candidates in a relatively short space of time, a significant bottleneck remains in their validation and prioritization for evaluation in clinical trials. Longitudinal cohort studies provide supportive evidence but results are often conflicting between studies. Demonstration of antigen‐specific antibody function is valuable but the relative importance of one mechanism over another with regards to protection remains undetermined. Animal models offer useful insights but may not accurately reflect human disease. Challenge studies in humans are preferable but prohibitively expensive. In the absence of reliable correlates of protection, suitable animal models or a better understanding of the mechanisms underlying protective immunity in humans, vaccine candidate discovery per se may not be sufficient to provide the paradigm shift necessary to develop the next generation of highly effective subunit malaria vaccines.
The association between various smoking behaviors, cotinine biomarkers and skin autofluorescence, a marker for advanced glycation end product accumulation

Background Skin autofluorescence, a biomarker for advanced glycation end products (AGEs) accumulation, has been shown to predict diabetes-related cardiovascular complications and is associated with several environmental and lifestyle factors. In the present study, we examined the association between various smoking behaviors and skin autofluorescence, as well as the association between several cotinine biomarkers and skin autofluorescence, using both epidemiological and metabolomics data. Methods In a cross-sectional study, we evaluated participants from the LifeLines Cohort Study and the Qatar Metabolomics Study on Diabetes (QMDiab). In the LifeLines Cohort Study smoking behavior and secondhand smoking were assessed in 8,905 individuals including 309 individuals (3.5%) with type 2 diabetes. In QMDiab, cotinine biomarkers were measured in saliva, plasma and urine in 364 individuals of whom 188 (51%) had type 2 diabetes. Skin autofluorescence was measured non-invasively in all participants using the AGE Reader. Results Skin autofluorescence levels increased with a higher number of hours being exposed to secondhand smoking. Skin autofluorescence levels of former smokers approached levels of never smokers after around 15 years of smoking cessation. Urinary cotinine N-oxide, a biomarker of nicotine exposure, was found to be positively associated with skin autofluorescence in the QMDiab study (p = 0.03). Conclusions In the present study, we have demonstrated that secondhand smoking is associated with higher skin autofluorescence levels whereas smoking cessation has a beneficial effect on skin autofluorescence. Finally, urinary cotinine N-oxide might be used as an alternative way for questionnaires to examine the effect of (environmental) tobacco smoking on skin autofluorescence.
Activity of glucose-fructose oxidoreductase in fresh and permeabilised cells of Zymomonas mobilis grown in different glucose concentrations

Previously grown cells of the ethanologenic bacterium Zymomonas mobilis produce sorbitol and gluconic acid, in reactions catalysed by the periplasmic enzymes glucose-fructose oxidoreductase (GFOR) and glucono-d-lactonase (GL). The GFOR/GL system activity, in cells to be used in this bioconversion, depends on growth conditions. In batch runs, with initial glucose concentrations (S0) from 42 to 230 g/L, the highest specific and total GFOR/GL activities were obtained with S0 = 153 g/L (12.6 U/g cells and 62 U/L). Higher S0 led to decreasing activities in fresh cells. With S0 = 209 g/L, the final specific activity was only 7.0 U/g. After disruption of cells, however, an activity over 15 U/g was revealed. Since growth inhibition with S0 over 153 g/L was observed in batch mode, fed-batch runs, equivalent to a batch of 230 g/L, were done. Although no growth inhibition occurred in fed-batch cultivation, enzyme activity remained low (5.2 U/g). A further fed-batch experiment, carried out under low pressure to remove ethanol from the medium, resulted in a specific activity of 9.8 U/g and a total activity of 68.7 U/L. These results indicate that the low GFOR/GL activities in Z. mobilis cells grown on higher S0 were due to changes in the cell wall, caused by high concentration of ethanol, that hindered the transport of the substrate to the intracellular enzymes in biconversion runs. This conclusion was confirmed by bioconversion runs with cells cultivated under different conditions.
Plague Circulation and Population Genetics of the Reservoir Rattus rattus: The Influence of Topographic Relief on the Distribution of the Disease within the Madagascan Focus

Background Landscape may affect the distribution of infectious diseases by influencing the population density and dispersal of hosts and vectors. Plague (Yersinia pestis infection) is a highly virulent, re-emerging disease, the ecology of which has been scarcely studied in Africa. Human seroprevalence data for the major plague focus of Madagascar suggest that plague spreads heterogeneously across the landscape as a function of the relief. Plague is primarily a disease of rodents. We therefore investigated the relationship between disease distribution and the population genetic structure of the black rat, Rattus rattus, the main reservoir of plague in Madagascar. Methodology/Principal Findings We conducted a comparative study of plague seroprevalence and genetic structure (15 microsatellite markers) in rat populations from four geographic areas differing in topology, each covering about 150–200 km2 within the Madagascan plague focus. The seroprevalence levels in the rat populations mimicked those previously reported for humans. As expected, rat populations clearly displayed a more marked genetic structure with increasing relief. However, the relationship between seroprevalence data and genetic structure differs between areas, suggesting that plague distribution is not related everywhere to the effective dispersal of rats. Conclusions/Significance Genetic diversity estimates suggested that plague epizootics had only a weak impact on rat population sizes. In the highlands of Madagascar, plague dissemination cannot be accounted for solely by the effective dispersal of the reservoir. Human social activities may also be involved in spreading the disease in rat and human populations.
Design and optimization of DFIGs with alternate voltage and speed ratings for wind applications

Induction machines 100 kW to 7.5 MW are designed for Low Voltage (LV) 460 V, 690 V or Medium Voltages (MV) 2.4 kV to 4 kV and 12 kV in special cases. The objective of this paper is to compare doubly fed induction generators (DFIGs) with different voltage and speed ratings for wind energy systems. This paper investigates the effect of alternate number of poles and voltage ratings on the performance of a DFIG. The design of a DFIG has been optimized by means of an analytical model and a Genetic Algorithm (GA). Several optimized DFIG designs were generated in this manner, and then matched with a suitable single-stage gear box and a back-to-back converter connected to the rotor. This paper suggests an improved system by considering the quality of output power, voltage and number of poles.
Representation of Perceived Object Shape by the Human Lateral Occipital Complex

The human lateral occipital complex (LOC) has been implicated in object recognition, but it is unknown whether this region represents low-level image features or perceived object shape. We used an event-related functional magnetic resonance imaging adaptation paradigm in which the response to pairs of successively presented stimuli is lower when they are identical than when they are different. Adaptation across a change between the two stimuli in a pair provides evidence for a common neural representation invariant to that change. We found adaptation in the LOC when perceived shape was identical but contours differed, but not when contours were identical but perceived shape differed. These data indicate that the LOC represents not simple image features, but rather higher level shape information.