Miracle-dz/UniFAR-FTUs huggingface dataset:
Methicillin Resistance Transfer from Staphylocccus epidermidis to Methicillin-Susceptible Staphylococcus aureus in a Patient during Antibiotic Therapy

Background The mecA gene, encoding methicillin resistance in staphylococci, is located on a mobile genetic element called Staphylococcal Cassette Chromosome mec (SCCmec). Horizontal, interspecies transfer of this element could be an important factor in the dissemination of methicillin-resistant S. aureus (MRSA). Previously, we reported the isolation of a closely related methicillin-susceptible Staphylococcus aureus (MSSA), MRSA and potential SCCmec donor Staphylococcus epidermidis isolate from the same patient. Based on fingerprint techniques we hypothesized that the S. epidermidis had transferred SCCmec to the MSSA to become MRSA. The aim of this study was to show that these isolates form an isogenic pair and that interspecies horizontal SCCmec transfer occurred. Methodology/Results Whole genome sequencing of both isolates was performed and for the MSSA gaps were closed by conventional sequencing. The SCCmec of the S. epidermidis was also sequenced by conventional methods. The results show no difference in nucleotide sequence between the two isolates except for the presence of SCCmec in the MRSA. The SCCmec of the S. epidermidis and the MRSA are identical except for a single nucleotide in the ccrB gene, which results in a valine to alanine substitution. The main difference with the closely related EMRSA-16 is the presence of SaPI2 encoding toxic shock syndrome toxin and exfoliative toxin A in the MSSA-MRSA pair. No transfer of SCCmec from the S. epidermidis to the MSSA could be demonstrated in vitro. Conclusion The MSSA and MRSA form an isogenic pair except for SCCmec. This strongly supports our hypothesis that the MRSA was derived from the MSSA by interspecies horizontal transfer of SCCmec from S. epidermidis O7.1.
Studying College Students in the 21st Century: Meeting New Challenges

The confluence of several demographic, institutional, economic, and technological changes may not only alter fundamentally the way we think about what it means to go to college but also change the methodologies we now use to assess the impact of college. In this article, we outline and discuss the implications of four such forces: the changing undergraduate student population, the increasing importance of community colleges, shrinking financial support for higher education, and the rise of information technology.
Increased adhesion of the promyelocytic leukaemia cell line, NB4, to fibronectin and thrombospondin upon all‐trans‐retinoic acid treatment

We have evaluated the effects of all‐trans‐retinoic acid (RA) on the adhesion of the human promyelocytic cell line NB4 to various components of the extracellular matrix. NB4 cells, radiolabelled with 111Indium, showed a 2–3‐fold increase (P < 0.001) in adhesion to fibronectin and thrombospondi‘n upon RA (3 × 10−7 m) treatment, whereas adhesion to collagen I, laminin and vitronectin was not modified. The increase in cell adhesion, observed as early as day 1, preceded cell differentiation and was concomitant with tyrosine phosphorylation events. Using flow cytometry, we analysed the expression of major receptors for fibronectin (α4β1 and α5β1) and for thrombospondin (αvβ3, αIIbβ3, CD36 and CD47) on NB4 cells before and after RA treatment. Except for αIIbβ3, which was induced on RA‐treated cells, we found no significant increase in the expression of the other receptors, and a decrease in the expression of CD36, upon RA treatment. Preincubation of RA‐treated cells with blocking antibodies demonstrated a role for α4β1 and α5β1 in cell adhesion to fibronectin and α5β1, αIIbβ3, CD36 and CD47 in cell adhesion to thrombospondin. Experiments with the synthetic peptides GRGDS (0.2 mm) and CSVTCG (0.2 mm) confirmed the participation of integrins, and integrins and CD36, in adhesion of RA‐treated cells to fibronectin and thrombospondin, respectively. Further inhibition by heparin (10 μg/ml) and/or recombinant heparin‐binding domain of thrombospondin (TSP18) indicated the additional participation of heparin‐like receptors in cell adhesion to thrombospondin. Our results indicate that increase in NB4 cell adhesion to fibronectin and thrombospondin upon RA treatment is likely to occur through a modulation of the functional state of several receptors for these proteins.
Training Efficiently in Virtual Environments: Determinants of Distance Perception of Stationary Observers Viewing Stationary Objects

Abstract : The accurate perception and estimation of distance is an important element of many military tasks. It is necessary for orienting oneself on the battlefield, for making optimal use of terrain features during navigation, and for judging the distance from one point to another. It is also a component of both route and configuration knowledge and acquisition. In order to maximize transfer from Virtual Environment (VE) to the real world, it is important to develop an understanding of the capabilities and limitations of this new training medium. Toward that end, the present study sought to gain insight about the conditions affecting distance estimation of VEs. The purpose of this research is to examine factors that influence the perception of distance in VEs. Two experiments were designed to investigate the relative effects of such factors on distance estimates of a stationary observer positioned at near and medium distances from an object. Factors found to improve distance estimates in these experiments will be incorporated into the design of VEs for subsequent investigations.
A review of association and linkage studies for genetical analyses of learning disorders

Learning disorders (LD) commonly comprise of a heterogeneous group of disorders manifested by unexpected problems in some children's experiences in the academic performance arena. These problems especially comprise of a variety of disorders which may be subclassified to attention‐deficit hyperactivity disorder (ADHD), reading disability (RD), specific language impairment (SLI), speech‐sound disorder (SSD), and dyspraxia. The aim of this review is to summarize the current molecular studies and some of the most exciting recent developments in molecular genetic research on LD. The findings for the association and linkage of LD with candidate genes will help to set the research agendas for future studies to follow. © 2007 Wiley‐Liss, Inc.
Gain Scheduling Control of Gas Turbine Engines: Stability by Computing a Single Quadratic Lyapunov Function

We develop and describe a stable gain scheduling controller for a gas turbine engine that drives a variable pitch propeller. A stability proof is developed for gain scheduled closed-loop system using global linearization and linear matrix inequality (LMI) techniques. Using convex optimization tools, a single quadratic Lyapunov function is computed for multiple linearizations near equilibrium and non-equilibrium points of the nonlinear closed-loop system. This approach guarantees stability of the closed-loop gas turbine engine system. Simulation results show the developed gain scheduling controller is capable of regulating a turboshaft engine for large thrust commands in a stable fashion with proper tracking performance.Copyright © 2013 by ASME
Increasing Scholarly Activity Productivity During Residency: A Systematic Review

Purpose Although resident participation in scholarly activity is mandated by the Accreditation Council for Graduate Medical Education, programmatic factors associated with success are not defined. This systematic review’s objective was to determine which interventions are effective in increasing resident scholarly activity productivity (RSAP), as measured by participation in scholarly activity, presentations, or publications. Method The PubMed, MEDLINE, Cochrane Library of Systematic Reviews, PsycINFO, CINAHL, and ERIC databases were searched through October 2013. English-language articles evaluating interventions to increase RSAP in U.S. or Canadian residency programs were included, without date limits. Two independent reviewers selected articles for inclusion and extracted data. Discrepancies were resolved by consensus. Results Of the 6,248 records screened, 80 studies underwent data abstraction. Twenty-six described outcomes without a comparison group, leaving 54 studies representing 13 medical and surgical specialties. Interventions included required scholarly activity participation, protected research time, research curricula, research directors, dedicated research days, and research tracks. Focusing on the 35 studies reporting statistical analysis, RSAP was associated with all interventions. There were some differences in intervention effectiveness between medical and surgical specialties. Conclusions Interventions, including protected time, research curricula, or specialized research tracks, generally result in increased participation in scholarly activity in residency programs, with mixed effects on resident presentations or publications. In many studies, interventions were bundled, suggesting that programs may need to provide increased structure and rigor through multiple pathways. The findings highlight the need for a clear definition of resident scholarly activity success aligned specifically to individual program and resident aims.
Are you making an impression? : The visual aesthetics of career websites

The field of HCI has begun to realize the importance of visual aesthetics. Recent studies have investigated visual aesthetics related to first impressions and found that judgments can be made almost instantaneously. This thesis builds upon previous research related to visual aesthetics and first impressions. Two different approaches were used to investigate university student’s subjective impressions of career websites of organizations. The first approach investigated first impressions, were users rated the websites on their visual appeal, after viewing a screenshot of the website for only 500 milliseconds. In the second approach, the viewing time was not restricted, and the users rated the screenshots on four statements of the VisAWI-S questionnaire. The subjective ratings collected in the two studies were compared objective characteristics such as number of images, number of visual objects and the average RGB-value of the screenshots. Strong correlations was found between the subjective ratings given in the two studies. Both methods was found useful for evaluating the visual aesthetics of websites, and the context of the study should also guide the choice of method. No correlations were found between the objective characteristics and the subjective ratings, with the exception to the average RGB-values. There was an indication that the students preferred websites with darker colors.
Etiology of Diarrhea in Older Children, Adolescents and Adults: A Systematic Review

Background Diarrhea is an important cause of morbidity and mortality in all regions of the world and among all ages, yet little is known about the fraction of diarrhea episodes and deaths due to each pathogen. Methodology/Principal Findings We conducted a systematic literature review to identify all papers reporting the proportion of diarrhea episodes with positive laboratory tests for at least one pathogen in inpatient, outpatient and community settings that met our inclusion and exclusion criteria. We identified a total of 25,701 papers with possible etiology data and after final screening included 22 papers that met all inclusion and exclusion criteria. Enterotoxigenic Escherichia coli and V. cholerae O1/O139 were the leading causes of hospitalizations. In outpatient settings, Salmonella spp. , Shigella spp. , and E. histolytica were the most frequently isolated pathogens. Conclusions/Significance This is the first systematic review which has considered the relative importance of multiple diarrhea pathogens. The few studies identified suggest that there is a great need for additional prospective studies around the world in these age groups to better understand the burden of disease and the variation by region.
Experimental evidence of human recreational disturbance effects on bird-territory establishment

The worldwide increase in human outdoor activities raises concerns for wildlife. Human disturbances, even at low levels, are likely to impact species during sensitive periods of the annual cycle. However, experimental studies during the putative sensitive period of territory establishment of birds which not only investigate low disturbance levels, but which also exclude the effect of habitat modification (e.g. walking trails) are lacking. Here, we experimentally disturbed birds in forest plots by walking through twice a day during territory establishment. Later we compared the breeding bird community of experimentally disturbed plots with that of undisturbed control plots. We discovered that the number of territories (−15.0%) and species richness (−15.2%) in disturbed plots were substantially reduced compared with control plots. Species most affected included those sensitive to human presence (assessed by flight-initiation distances), open-cup nesters and above-ground foragers. Long-distance migrants, however, were unaffected due to their arrival after experimental disturbance took place. These findings highlight how territory establishment is a sensitive period for birds, when even low levels of human recreation may be perceived as threatening, and alter settlement decisions. This can have important implications for the conservation of species, which might go unnoticed when focusing only on already established birds.
Degree of corticospinal tract damage correlates with motor function after stroke

Direct injury to the corticospinal tract (CST) is a major factor defining motor impairment after stroke. Diffusion tensor imaging (DTI) tractography allows definition of the CST. We sought to determine whether DTI‐based assessment of the degree of CST damage correlates with motor impairment at each phase of ischemic stroke.
Human Validation of Genes Associated With a Murine Atherosclerotic Phenotype

Objective— The genetically modified mouse is the most commonly used animal model for studying the pathogenesis of atherosclerotic disease. We aimed to assess if mice atherosclerosis-related genes could be validated in human disease through examination of results from genome-wide association studies. Approach and Results— We performed a systematic review to identify atherosclerosis-causing genes in mice and carried out gene-based association tests of their human orthologs for an association with human coronary artery disease and human large artery ischemic stroke. Moreover, we investigated the association of these genes with human atherosclerotic plaque characteristics. In addition, we assessed the presence of tissue-specific cis-acting expression quantitative trait loci for these genes in humans. Finally, using pathway analyses we show that the putative atherosclerosis-causing genes revealed few associations with human coronary artery disease, large artery ischemic stroke, or atherosclerotic plaque characteristics, despite the fact that the majority of these genes have cis-acting expression quantitative trait loci. Conclusions— A role for genes that has been observed in mice for atherosclerotic lesion development could scarcely be confirmed by studying associations of disease development with common human genetic variants. The value of murine atherosclerotic models for selection of therapeutic targets in human disease remains unclear.
Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

Summary: The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. Availability and implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). Contact: contact@workflow4metabolomics.org
The Combination of Phylogenetic Analysis with Epidemiological and Serological Data to Track HIV-1 Transmission in a Sexual Transmission Case

Objective To investigate the linkage of HIV transmission from a man to a woman through unprotected sexual contact without disclosing his HIV-positive status. Methods Combined with epidemiological information and serological tests, phylogenetic analysis was used to test the a priori hypothesis of HIV transmission from the man to the woman. Control subjects, infected with HIV through heterosexual intercourse, from the same location were also sampled. Phylogenetic analyses were performed using the consensus gag, pol and env sequences obtained from blood samples of the man, the woman and the local control subjects. The env quasispecies of the man, the woman, and two controls were also obtained using single genome amplification and sequencing (SGA/S) to explore the paraphyletic relationship by phylogenetic analysis. Results Epidemiological information and serological tests indicated that the man was infected with HIV-1 earlier than the woman. Phylogenetic analyses of the consensus sequences showed a monophyletic cluster for the man and woman in all three genomic regions. Furthermore, gag sequences of the man and woman shared a unique recombination pattern from subtype B and C, which was different from those of CRF07_BC or CRF08_BC observed in the local samples. These indicated that the viral sequences from the two subjects display a high level of similarity. Further, viral quasispecies from the man exhibited a paraphyletic relationship with those from the woman in the Bayesian and maximum-likelihood (ML) phylogenetic trees of the env region, which supported the transmission direction from the man to the woman. Conclusions In the context of epidemiological and serological evidence, the results of phylogenetic analyses support the transmission from the man to the woman.
The center for research.

Informed Consent More than just a form, Informed Consent is a process that ensures respect for people by offering them thoughtful consent to voluntarily participate. Informed consent is achieved when voluntary participants fully understand their rights and the expectations, risks and benefits of participating in a research project. The process is designed to provide potential participants sufficient information, in terms they can understand, so they can make an educated decision whether or not to participate in a research project.
Perceptual contrast versus reciprocal concession as mediators of induced compliance

This study examined two explanations for the success of a compliance strategy in which a second moderate-sized request is asked immediately after the refusal of a first largesized request. The reciprocal concessions explanation argues that the change from the first request to the second is viewed as a concession on the part of the requestor that compels the subject to make a concession of his own, i.e., agree to the second request. The perceptual contrast explanation proposes that the first request establishes a comparison standard against which the second request appears to be less costly; without the first request, the second request might be compared with the possibility of doing nothing for the requestor. The results supported the view that the critical manipulation in eliciting compliance is the reduction of relative cost to the subject and not the personal concession shown by the requestor.
An Examination of Test-Taking Attitudes and Response Distortion on a Personality Test

Psychology (ABSTRACT) This study examined test-taking attitudes and response distortion on a personality test. Consistent with our hypotheses, applicants were found to have significantly more positive test-taking attitudes and exhibit a greater degree of response distortion as compared to incumbents. In addition, test-taking attitudes were significantly associated with response distortion. However, test-taking attitudes failed to affect work performance or validity in the incumbent samples. Limitations and implications for future research are discussed. Acknowledgments This manuscript could not have been completed without the help and guidance of Dr. Roseanne Foti and Dr. Neil Hauenstein. They have made my graduate career a fulfilling and worthwhile experience that I will always remember. I would also like to thank my committee members, Dr. and Dr. Joseph Sgro, for their insight and support throughout the entire process.
STRUCTURAL ENCODING PRECLUDES RECOGNITION OF FACE PARTS IN PROSOPAGNOSIA

The extent and the impact of spared processing of facial stimuli in the prosopagnosic patient LH is examined using the inversion effect and the face context effect. Our study asked how the deficit in individual face recognition is related to two perceptual abilities that are spared in this patient but between which there is interference when both are applied to the face stimulus, i.e. structural encoding of the face and parts-based matching procedures. Three experiments studied this relationship with task demands and stimulus properties designed to trigger the parts-based processes. In the first experiment, human and animal faces are presented upright or inverted with good performance only for the inverted condition. In Experiment 2 normals show a clear face context effect (matching of upright faces easier than scrambled or inverted ones) in the full face matching task whereas in the parts matching task the face superiority effect disappears. In contrast, LH shows a face inferiority effect when matching full faces but also when matching an isolated face part to a face part in a full face context. The results show that structural encoding of the face overrules parts-based procedures that could otherwise be helpful to tell individual faces apart.
Growth rate of 147 mammary carcinomas

In 147 cases of mammary carcinoma, 388 serial mammographies were performed before final treatment. The average retrospective observation time was 27 months with a range of two months to 11 years. The number of serial mammographies per case ranged between two and 11. The tumor volume doubling times (Tv); obtained by measuring the growth of the tumor nucleus shadow in the mammographies, ranged from 44 to 1869 days with an average of 212 days. No correlation between volume doubling time and histoldgic differentiation could be found. One hundred of these cancer patients were found in a screening population of 22,000 women receiving serial mammographies in a time period ranging from two to 16 years. An additional 40 cancer patients surfaced in this group without roentgenologic but with foregoing clinical or thermographic abnormalities before final diagnosis. An additional 21 cancer patients surfaced without any foregoing abnormalities. The follow‐up tumor ranged between three months and two years with a mean time of one year and nine months. Not considering tumor size, pathologic‐thermographic signs appeared with greater frequency the faster the tumor grew. Theoretically, an average of more than 16 years should elapse before an initial tumor cell develops into a 10‐mm primary mammary carcinoma (30 doubling times). Therefore the length of time necessary for a 2‐mm tumor to grow to a size of 10‐mm is, on the average, four years.