Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotypic Homogeneity of Multidrug Resistant S. Typhimurium Infecting Distinct Adult and Childhood Susceptibility Groups in Blantyre, Malawi

Nontyphoidal Salmonella (NTS) serovars are a common cause of bacteraemia in young children and HIV-infected adults in Malawi and elsewhere in sub-Saharan Africa. These patient populations provide diverse host-immune environments that have the potential to drive bacterial adaptation and evolution. We therefore investigated the diversity of 27 multidrug resistant (MDR) Salmonella Typhimurium strains isolated over 6 years (2002–2008) from HIV-infected adults and children and HIV-uninfected children. Sequence reads from whole-genome sequencing of these isolates using the Illumina GA platform were mapped to the genome of the laboratory strain S. Typhimurium SL1344 excluding homoplastic regions that contained prophage and insertion elements. A phylogenetic tree generated from single nucleotide polymorphisms showed that all 27 strains clustered with the prototypical MDR strain D23580. There was no clustering of strains based on host HIV status or age, suggesting that these susceptible populations acquire S. Typhimurium from common sources or that isolates are transmitted freely between these populations. However, 7/14 of the most recent isolates (2006/2008) formed a distinct clade that branched off 22 SNPs away from the cluster containing earlier isolates. These data suggest that the MDR bacterial population is not static, but is undergoing microevolution which might result in further epidemiology change.
Single-carrier transmission frequency-domain equalization based on a wiener filter

Recently, frequency-domain equalization for single-carrier transmission (SC-FDE) has been given much attention. For example, the up-link in the 3.9 generation mobile phone long term evolution (LTE) system, an SC-FDMA method using SC-FDE and multiple access will be adopted. However in previous research, there are many papers describing the features and advantages of SC-FDE based on a comparison of SC-FDE and orthogonal frequency-division multiplexing (OFDM) systems. In this paper, we discuss single-carrier transmission equalization in the time-domain (SC-TDE) and SC-FDE in a unified way centered on the Wiener filter based on the minimum mean square error (MMSE) criterion. As a result, we could get useful information and pointers, especially for when we want to replace existing SC-TDE technology with SC-FDE technology.
The Persian, Last 7-day, Long form of the International Physical Activity Questionnaire: Translation and Validation Study

Purpose To translate long form, interview-administered International Physical Activity Questionnaire (IPAQ) from English to Persian and evaluate its validity, reliability and reproducibility. Methods A forward-backward translation procedure was followed to develop the Persian version of the IPAQ. A total of 218 respondents (53.7% women, aged 22–76 yr) completed the Persian version in Tehran, Iran. To examine the test–retest reliability, 48 healthy volunteers completed the IPAQ twice during a 7-day period. The PA indicators derived from the IPAQ were assessed for reliability and were compared with aerobic fitness and body mass index (BMI) for construct validity. Results In general, the questionnaire was received well and all domains met the minimum reliability standards (intra-class correlation [ICC]>0.7), except for Leisure-time physical activity (PA). Aerobic fitness showed a weak positive correlation with all of the PA results derived from the IPAQ. A significant correlation was observed between the IPAQ data for total PA and both aerobic fitness (r=0.33, P<0.001) and BMI (r=0.26, P<0.001). Performing a known group comparison analysis, the results indicated that the questionnaire was discriminated well between the subgroups of the study samples expected to be different in their physical activity. Conclusions The Persian version of the long form, interview-administered IPAQ had an acceptable reliability and validity for assessing total PA in our Iranian sample of individuals. It may be a useful instrument for generating internationally comparable data on PA.
How Large a Corpus Do We Need: Statistical Method Versus Rule-based Method

We investigate the impact of input data scale in corpus-based learning using a study style of Zipfs law. In our research, Chinese word segmentation is chosen as the study case and a series of experiments are specially conducted for it, in which two types of segmentation techniques, statistical learning and rule-based methods, are examined. The empirical results show that a linear performance improvement in statistical learning requires an exponential increasing of training corpus size at least. As for the rule-based method, an approximate negative inverse relationship between the performance and the size of the input lexicon can be observed.
Arginine Consumption by the Intestinal Parasite Giardia intestinalis Reduces Proliferation of Intestinal Epithelial Cells

In the field of infectious diseases the multifaceted amino acid arginine has reached special attention as substrate for the host´s production of the antimicrobial agent nitric oxide (NO). A variety of infectious organisms interfere with this part of the host immune response by reducing the availability of arginine. This prompted us to further investigate additional roles of arginine during pathogen infections. As a model we used the intestinal parasite Giardia intestinalis that actively consumes arginine as main energy source and secretes an arginine-consuming enzyme, arginine deiminase (ADI). Reduced intestinal epithelial cell (IEC) proliferation is a common theme during bacterial and viral intestinal infections, but it has never been connected to arginine-consumption. Our specific question was thereby, whether the arginine-consumption by Giardia leads to reduced IEC proliferation, in addition to NO reduction. In vitro cultivation of human IEC lines in arginine-free or arginine/citrulline-complemented medium, as well as in interaction with different G. intestinalis isolates, were used to study effects on host cell replication by MTT assay. IEC proliferation was further analyzed by DNA content analysis, polyamine measurements and expressional analysis of cell cycle regulatory genes. IEC proliferation was reduced upon arginine-withdrawal and also in an arginine-dependent manner upon interaction with G. intestinalis or addition of Giardia ADI. We show that arginine-withdrawal by intestinal pathogens leads to a halt in the cell cycle in IECs through reduced polyamine levels and upregulated cell cycle inhibitory genes. This is of importance with regards to intestinal tissue homeostasis that is affected through reduced cell proliferation. Thus, the slower epithelial cell turnover helps the pathogen to maintain a more stable niche for colonization. This study also shows why supplementation therapy of diarrhea patients with arginine/citrulline is helpful and that citrulline especially should gain further attention in future treatment strategies.
Examining the Relationship between Socialization and Improved Software Development Skills in the Scratch Code Learning Environment

In the last years, socialization of the software development process has been proven to be an emergent practice, becoming social development platforms (such as GitHub or GitLab) very popular among software developers. However, little is still known about how social factors influence software development. In particular, in this paper we focus on how socialization affects the learning of programming skills, as developing software can be considered, in part, a continuous learning process. Aiming to shed some light in this regard, we analyze the social interactions of almost 70,000 users and the sophistication of over 1.5 million software products authored by them in the Scratch platform, the most popular social coding site for learning to program. The results indicate that there is a relationship between the social conducts of users and the improvement of their programming abilities, showing that more social actions performed by users is positively associated with more sophistication in their programs. Furthermore, the results also provide evidence that the relationship of social factors with the development of software programming skills tends to grow with time.
Image Understanding in a Nonparametric Bayesian Framework

We explore recently proposed nonparametric Bayesian stati stic l models of image partitions. These models are attractive because they adapt to images of different complexity, successfully modeling uncertainty in size, sh ape, and structure of human segmentations of natural scenes. We improve upon them in a number of key ways to achieve performance comparable to state-of-the-ar t methods. Our first major contribution is a novel discrete search based posteri r inference algorithm which, compared to previous approaches, is significantly mo re r bust and accurate. We then present a low rank version of the spatially depe ndent Pitman-Yor processes model, critical for efficient inference. Further more, we show how the Gaussian process covariance functions underlying the prop osed models can be calibrated to accurately match the statistics of human segm entations. Finally, we present accurate segmentations of complex scenes as well as multiple hypothesized image partitions (capturing the inherent uncertaint y in human scene interpretations) produced by our method.
An Efficient Technique to Implement Similarity Measures in Text Document Clustering using Artificial Neural Networks Algorithm

Pattern recognition, envisaging supervised and unsupervised method, optimization, associative memory and control process are some of the diversified troubles that can be resolved by artificial neural networks. Problem identified: Of late, discovering the required information in massive quantity of data is the challenging tasks. The model of similarity evaluation is the central element in accomplishing a perceptive of variables and perception that encourage behavior and mediate concern. This study proposes Artificial Neural Networks algorithms to resolve similarity measures. In order to apply singular value decomposition the frequency of word pair is established in the given document. (1) Tokenization: The splitting up of a stream of text into words, phrases, signs, or other significant parts is called tokenization. (2) Stop words: Preceding or succeeding to processing natural language data, the words that are segregated is called stop words. (3) Porter stemming: The main utilization of this algorithm is as part of a phrase normalization development that is characteristically completed while setting up in rank recovery technique. (4) WordNet: The compilation of lexical data base for the English language is called as WordNet Based on Artificial Neural Networks, the core part of this study work extends n-gram proposed algorithm. All the phonemes, syllables, letters, words or base pair corresponds in accordance to the application. Future work extends the application of this same similarity measures in various other neural network algorithms to accomplish improved results.
Crowdsourcing the Verification of Relationships in Biomedical Ontologies

Biomedical ontologies are often large and complex, making ontology development and maintenance a challenge. To address this challenge, scientists use automated techniques to alleviate the difficulty of ontology development. However, for many ontology-engineering tasks, human judgment is still necessary. Microtask crowdsourcing, wherein human workers receive remuneration to complete simple, short tasks, is one method to obtain contributions by humans at a large scale. Previously, we developed and refined an effective method to verify ontology hierarchy using microtask crowdsourcing. In this work, we report on applying this method to find errors in the SNOMED CT CORE subset. By using crowdsourcing via Amazon Mechanical Turk with a Bayesian inference model, we correctly verified 86% of the relations from the CORE subset of SNOMED CT in which Rector and colleagues previously identified errors via manual inspection. Our results demonstrate that an ontology developer could deploy this method in order to audit large-scale ontologies quickly and relatively cheaply.
Modeling Changes to Streamflow, Sediment, and Nutrient Loading from Land Use Changes Due to Potential Natural Gas Development

Natural gas development using hydraulic fracturing has many potential environmental impacts, but among the most certain is the land disturbance required to build the well pads and other infrastructure required to drill and extract the gas. We used the Soil and Water Assessment Tool (SWAT) model to investigate how natural gas development could impact streamflow and sediment, total nitrogen (TN), and total phosphorous (TP) loadings in the upper Delaware River Basin (DRB), a relatively undeveloped watershed of 7,950 km2 that lies above the Marcellus Shale formation. If gas development was permitted, our projections show the DRB could experience development of over 600 well pads to extract natural gas at build out, which, with supporting infrastructure (roads, gathering pipelines), could convert over 5,000 ha from existing land uses in the study area. In subbasins with development activity we found sediment, TN, and TP yields could increase by an average of 15, 0.08, and 0.03 kg/ha/yr, respectively (an increase of 2, 3, and 15%, respectively) for each one percent of subbasin land area converted into natural gas infrastructure. At the study area outlet on the Delaware River at Port Jervis, New York, we found increases in the annual average streamflow and sediment, nitrogen, and phosphorus loads of up to 0.01, 0.2, 0.2, and 1%, respectively, for a rapid development year, and 0.08, 1.3, 2.0, and 11%, respectively, for the full development scenario. Editor's note: This paper is part of the featured series on SWAT Applications for Emerging Hydrologic and Water Quality Challenges. See the February 2017 issue for the introduction and background to the series.
Natural Current Balancing of Multicell Current Source Converters

This paper explores the issue of balancing the intermediate inductor currents of a multilevel current source inverter (CSI). The paper begins by identifying that single-phase multicell CSIs and flying capacitor voltage source inverters (FCVSIs) form a topological dual pair. This allows the established understanding of the natural balance process of the FCVSI intermediate capacitor voltages to suggest that the intermediate inductor currents of the CSI should also settle to their target balance values when phase-shifted carrier (PSC) pulse width modulation (PWM) is used. This concept is confirmed by full switched simulations. Next, an analytic model is developed to explore the dynamic response and robustness of the balancing process, using a double Fourier series representation of the converter switching signals to linearise a nonlinear transient circuit model. The model is verified against simulations, and predicts that the resistance of the intermediate inductors can perturb the steady state balancing point. The model further predicts that the resistance of the inductance must be small compared to the load resistance to minimize this effect. Results obtained on a five-level experimental CSI precisely match the theoretical model and hence support these conclusions.
Unravelling the Relationship between Animal Growth and Immune Response during Micro-Parasitic Infections

Background Both host genetic potentials for growth and disease resistance, as well as nutrition are known to affect responses of individuals challenged with micro-parasites, but their interactive effects are difficult to predict from experimental studies alone. Methodology/Principal Findings Here, a mathematical model is proposed to explore the hypothesis that a host's response to pathogen challenge largely depends on the interaction between a host's genetic capacities for growth or disease resistance and the nutritional environment. As might be expected, the model predicts that if nutritional availability is high, hosts with higher growth capacities will also grow faster under micro-parasitic challenge, and more resistant animals will exhibit a more effective immune response. Growth capacity has little effect on immune response and resistance capacity has little effect on achieved growth. However, the influence of host genetics on phenotypic performance changes drastically if nutrient availability is scarce. In this case achieved growth and immune response depend simultaneously on both capacities for growth and disease resistance. A higher growth capacity (achieved e.g. through genetic selection) would be detrimental for the animal's ability to cope with pathogens and greater resistance may reduce growth in the short-term. Significance Our model can thus explain contradicting outcomes of genetic selection observed in experimental studies and provides the necessary biological background for understanding the influence of selection and/or changes in the nutritional environment on phenotypic growth and immune response.
Clinicopathological correlation of congenital corneal opacification using ultrasound biomicroscopy

Aim: To investigate the correlation between clinical, high frequency ultrasound biomicroscopy (UBM) and, where possible, histological findings in cases of congenital corneal opacification presenting to the departments of ophthalmology, Great Ormond Street Hospital for Children, London, and the Hospital for Sick Children, Toronto, Canada. Method: 22 eyes of 13 children (age range 3–225 days) with congenitally opaque corneas were examined. UBM was performed using the ultrasound biomicroscope (Allergan-Humphrey). All eyes underwent penetrating keratoplasties (PKP) except five. The host corneas were all sent for histological examination. Results: The final diagnosis in our series was Peters' anomaly in nine cases (70%), corneal dystrophy in two cases (15%), and sclerocornea in two cases (15%). The UBM findings changed the clinical diagnosis in five cases (38%). In these five cases histology was available in four and confirmed the UBM diagnosis in each case. In no case of the 13 where histology was available did it contradict the UBM findings. In two cases a hypoechoic region in the anterior stroma was seen on UBM which correlated histologically with absent Bowman's layer and oedema. In two cases UBM revealed aniridia and in one, congenital aphakia, which was not apparent clinically. Conclusion: UBM examination is not only very useful in evaluating the clinical diagnosis in congenital corneal opacification, it also acts as a preoperative guide in cases undergoing PKP by detecting keratolenticular and iridocorneal adhesions and other ocular abnormalities such as aniridia and congenital aphakia. In all cases where PKP was performed the UBM diagnosis was confirmed histologically. The clinical diagnosis was incorrect in five cases. This has important implications in studies of phenotype/genotype correlation of congenital corneal opacification.
DIFFERENTIAL IMMUNOFLUORESCENCE OF FERTILIZED MOUSE EGGS WITH H-2 AND NON H-2 ANTIBODY

Mouse embryos at the two-cell and blastocyst stages, as well as unfertilized eggs, have been studied by indirect immunofluorescence for the expression of H-2 and non-H-2 histocompatibility antigens on surface membranes. Serologically-specific reactivity to non-H-2 antibody (H-3 and H-6) was observed as diffuse, patchy staining over the entire surface of the blastomeres at the two-cell stage. In contrast, no reactivity of two-cell or unfertilized egg embryos of four inbred strains was observed when antisera containing only multispecific H-2 cytolytic antibody were used. Antisera containing H-2 along with non-H-2 antibody of unknown specificity showed varying degrees of reactivity, which could be shown by absorption studies to be due to the non-H-2 content of the serum. The results suggest that the initial expression of histocompatibility genes varies and support the hypothesis that the appearance of these cell components may relate to specific stages of differentiation.
Eye Position Influence on the Parieto‐occipital Area PO (V6) of the Macaque Monkey

The aim of this work was to study the effect of eye position on the activity of neurons of area PO (V6), a cortical region located in the most posterior part of the superior parietal lobule. Experiments were carried out on three awake macaque monkeys. Animals sat in a primate chair in front of a large screen, and fixated a small spot of light projected in different screen locations while the activity of single neurons was extracellularly recorded. Both visual and non‐visual neurons were found. About 48% of visual and 32% of non‐visual neurons showed eye position‐related activity in total darkness, while in ˜61% of visual neurons the visual response was modulated by eye position in the orbit. Eye position fields and/or gain fields were different from cell to cell, going from large and quite planar fields up to peak‐shaped fields localized in more or less restricted regions of the animal's field of view. The spatial distribution of fixation point locations evoking peak activity in the eye position‐sensitive population did not show any evident laterality effect, or significant top/bottom asymmetry. Moreover, the cortical distribution of eye position‐sensitive neurons was quite uniform all over the cortical region studied, suggesting the absence of segregation for this property within area PO (V6). In the great majority of visual neurons, the receptive field‘moved’with gaze according to eye displacements, remaining at the same retinotopic coordinates, as is usual for visual neurons. In some cases, the receptive field did not move with gaze, remaining anchored to the same spatial location regardless of eye movements (‘real‐position cells'). A model is proposed suggesting how eye position‐sensitive visual neurons might build up real‐position cells in local networks within area PO (V6). The presence in area PO (V6) of real‐position cells together with a high percentage of eye position‐sensitive neurons, most of them visual in nature, suggests that this cortical area is engaged in the spatial encoding of extrapersonal visual space. Since lesions of the superior parietal lobule in humans produce deficits in visual localization of targets as well as in arm‐reaching for them, and taking into account that the monkey's area PO (V6) is reported to be connected with the premotor area 6, we suggest that area PO (V6) supplies the premotor cortex with the visuo‐spatial information required for the visual control of arm‐reaching movements.
Association between Income and the Hippocampus

Facets of the post-natal environment including the type and complexity of environmental stimuli, the quality of parenting behaviors, and the amount and type of stress experienced by a child affects brain and behavioral functioning. Poverty is a type of pervasive experience that is likely to influence biobehavioral processes because children developing in such environments often encounter high levels of stress and reduced environmental stimulation. This study explores the association between socioeconomic status and the hippocampus, a brain region involved in learning and memory that is known to be affected by stress. We employ a voxel-based morphometry analytic framework with region of interest drawing for structural brain images acquired from participants across the socioeconomic spectrum (n = 317). Children from lower income backgrounds had lower hippocampal gray matter density, a measure of volume. This finding is discussed in terms of disparities in education and health that are observed across the socioeconomic spectrum.