Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive Assignment of Roles for Salmonella Typhimurium Genes in Intestinal Colonization of Food-Producing Animals

Chickens, pigs, and cattle are key reservoirs of Salmonella enterica, a foodborne pathogen of worldwide importance. Though a decade has elapsed since publication of the first Salmonella genome, thousands of genes remain of hypothetical or unknown function, and the basis of colonization of reservoir hosts is ill-defined. Moreover, previous surveys of the role of Salmonella genes in vivo have focused on systemic virulence in murine typhoid models, and the genetic basis of intestinal persistence and thus zoonotic transmission have received little study. We therefore screened pools of random insertion mutants of S. enterica serovar Typhimurium in chickens, pigs, and cattle by transposon-directed insertion-site sequencing (TraDIS). The identity and relative fitness in each host of 7,702 mutants was simultaneously assigned by massively parallel sequencing of transposon-flanking regions. Phenotypes were assigned to 2,715 different genes, providing a phenotype–genotype map of unprecedented resolution. The data are self-consistent in that multiple independent mutations in a given gene or pathway were observed to exert a similar fitness cost. Phenotypes were further validated by screening defined null mutants in chickens. Our data indicate that a core set of genes is required for infection of all three host species, and smaller sets of genes may mediate persistence in specific hosts. By assigning roles to thousands of Salmonella genes in key reservoir hosts, our data facilitate systems approaches to understand pathogenesis and the rational design of novel cross-protective vaccines and inhibitors. Moreover, by simultaneously assigning the genotype and phenotype of over 90% of mutants screened in complex pools, our data establish TraDIS as a powerful tool to apply rich functional annotation to microbial genomes with minimal animal use.
Determinants of functional decline in community-dwelling older adults

ion Babcock (1994) also reported unique age-related variance attributed to other abilities; namely, identification of rules (i.e., inducing abstract relations), application of such rules. According to Conway et al. (2002), the link between working memory (includes central executive component) and general fluid intelligence is the demand for active maintenance of information in the face of concurrent processing of information and/or attention shifts, and this is a demand for controlled attention. It is clear that controlled attention (Engle et al., 1999) contributes to the variance in fluid intelligence, but it is also clear that Gf is fundamentally more than controlled attention (Birney et al, 2006). Tasks that require controlled attention processes involve operations such as inhibition, divided attention, and set switching (Anum, 2006), but even with regard to these executive functions, Friedman et al. (2006) noted that only 57% of the variance in fluid intelligence was accounted for by executive abilities, namely, inhibiting, updating, and shifting. The view that working memory is not synonymous with Gf is not uncommon among neuroscience or neuropsychology researchers (Kane et al., 2005). In fact, a recent meta-analysis concerning these two abilities concluded that that individual tests of working memory capacity and Gf (or reasoning) share only about 20% of their variance, on average (Ackerman et al., 2005). Garlick and Sennowski (2006) point out that, in addition to working memory and executive function, neurobiological models of fluid intelligence would be bolstered by the inclusion of abstraction, as all fluid intelligence problems involve abstraction. These authors also point out that abstraction has historically been recognized as the hallmark of intelligence (Synderman & Rothman, 1987). Both scaling studies and factor analyses show that tests that require reasoning, or reflect the products of past reasoning, fall in the
It is all in the noise: Efficient multi-task Gaussian process inference with structured residuals

Multi-task prediction methods are widely used to couple regressors or classification models by sharing information across related tasks. We propose a multi-task Gaussian process approach for modeling both the relatedness between regressors and the task correlations in the residuals, in order to more accurately identify true sharing between regressors. The resulting Gaussian model has a covariance term in form of a sum of Kronecker products, for which efficient parameter inference and out of sample prediction are feasible. On both synthetic examples and applications to phenotype prediction in genetics, we find substantial benefits of modeling structured noise compared to established alternatives.
Teaching strategies, learning strategies, and communication in the mainstream biology classroom. A study of the perspective of deaf students

This qualitative pilot research study explores the perceptions of deaf students who are a minority in the mainstream college classroom. It focuses upon the effectiveness of teaching and learning strategies used in the biology classroom, and how communication with hearing peers affects the deaf student's ability to learn in the classroom. Through questionnaires and interviews, participants provided insight on their experiences in the mainstream biology setting. Through research articles and interview responses, suggestions for effective teaching, learning, and communication were constructed and are provided to benefit all in the education profession.
Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing

The conserved pre-mRNA splicing factor SF1 is implicated in 3′ splice site recognition by binding directly to the intron branch site. However, because SF1 is not essential for constitutive splicing, its role in pre-mRNA processing has remained mysterious. Here, we used crosslinking and immunoprecipitation (CLIP) to analyze short RNAs directly bound by human SF1 in vivo. SF1 bound mainly pre-mRNAs, with 77% of target sites in introns. Binding to target RNAs in vitro was dependent on the newly defined SF1 binding motif ACUNAC, strongly resembling human branch sites. Surprisingly, the majority of SF1 binding sites did not map to the expected position near 3′ splice sites. Instead, target sites were distributed throughout introns, and a smaller but significant fraction occurred in exons within coding and untranslated regions. These data suggest a more complex role for SF1 in splicing regulation. Indeed, SF1 silencing affected alternative splicing of endogenous transcripts, establishing a previously unexpected role for SF1 and branch site-like sequences in splice site selection.
Designing Parallel Algorithms for Hierarchical SMP Clusters

Clusters of symmetric multiprocessor nodes (SMP clusters) are one of the most important parallel architectures at the moment. The architecture consists of shared-memory nodes with multiple processors and a fast interconnection network between the nodes. New programming models try to exploit this architecture by using threads in the nodes and using message-passing-libraries for inter-node communication. In order to develop efficient algorithms, it is necessary to consider the hybrid nature of the architecture and of the programming models. We present the κNUMA-model and a methodology that build a good base for designing efficient algorithms for SMP clusters. The κNUMA-model is a computational model that extends the bulk-synchronous parallel (BSP) model with the characteristics of SMP clusters and new hybrid programming models. The κNUMA-methodology suggests to develop efficient overall algorithms by developing efficient algorithms for each level in the hierarchy. We use the problem of personalized one-to-all-broadcast and the dense matrix-vector-multiplication for the presentation. The theoretical results of the analysis of the dense matrix-vector-multiplication are verified practically. We show results of experiments, made on a Linux-cluster of dual Pentium-III nodes.
Characterization of the TGN exit signal of the human mannose 6-phosphate uncovering enzyme

The human mannose 6-phosphate uncovering enzyme participates in the uncovering of the mannose 6-phosphate recognition tag on lysosomal enzymes, a process that facilitates recognition of those enzymes by mannose 6-phosphate receptors to ensure delivery to lysosomes. Uncovering enzyme has been identified on the trans-Golgi network at steady state. It has been shown to traffic to the plasma membrane from where it is rapidly internalized via endosomal structures, the process being mediated by a tyrosine-based internalization motif, Y488HPL, in its cytoplasmic tail. Using immunogold electron microscopy a GFP-uncovering enzyme fusion construct was found to be colocalized with the cation-dependent mannose 6-phosophate receptor in regions of the trans-Golgi network, suggesting that uncovering enzyme might follow a similar pathway of exit from the trans-Golgi network as that of the cation-dependent mannose 6-phosohate receptor. In this study, we identified the signal sequence in the cytoplasmic tail of uncovering enzyme responsible for its exit from the trans-Golgi network. Using GFP fusion constructs of the transmembrane and cytoplasmic domains of uncovering enzyme, we could show, by automated analysis of confocal immunofluorescence images, that residues Q492EMN in the cytoplasmic tail of uncovering enzyme are involved in its exit from the trans-Golgi network. Detailed characterization of the exit signal revealed that residue Q492 is the most important to the exit function while M494 and N495 also contribute. The cytoplasmic tail of the uncovering enzyme does not possess any of the known canonical signal sequences for interaction with Golgi-associated gamma ear-containing adaptor proteins. The identification of a trans-Golgi network exit signal in its cytoplasmic tail elucidates the trafficking pathway of uncovering enzyme, a crucial player in the process of lysosomal biogenesis.
Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs

Human and mouse embryonic stem cells (ESCs) are derived from blastocyst-stage embryos but have very different biological properties, and molecular analyses suggest that the pluripotent state of human ESCs isolated so far corresponds to that of mouse-derived epiblast stem cells (EpiSCs). Here we rewire the identity of conventional human ESCs into a more immature state that extensively shares defining features with pluripotent mouse ESCs. This was achieved by ectopic induction of Oct4, Klf4, and Klf2 factors combined with LIF and inhibitors of glycogen synthase kinase 3β (GSK3β) and mitogen-activated protein kinase (ERK1/2) pathway. Forskolin, a protein kinase A pathway agonist which can induce Klf4 and Klf2 expression, transiently substitutes for the requirement for ectopic transgene expression. In contrast to conventional human ESCs, these epigenetically converted cells have growth properties, an X-chromosome activation state (XaXa), a gene expression profile, and a signaling pathway dependence that are highly similar to those of mouse ESCs. Finally, the same growth conditions allow the derivation of human induced pluripotent stem (iPS) cells with similar properties as mouse iPS cells. The generation of validated “naïve” human ESCs will allow the molecular dissection of a previously undefined pluripotent state in humans and may open up new opportunities for patient-specific, disease-relevant research.
A double-blind, placebo-controlled, crossover study of osmotic release oral system methylphenidate in adults with ADHD with assessment of oppositional and emotional dimensions of the disorder.

BACKGROUND The realization that attention-deficit/hyperactivity disorder (ADHD) often persists into adulthood has led to increased frequency of diagnosis and treatment in adults. Osmotic release oral system (OROS) methylpheni-date is a long-acting stimulant demonstrated to be effective in the treatment of children and adolescents with ADHD. METHOD Forty-seven adults entered and 41 completed this double-blind, placebo-controlled, crossover trial of OROS methylphenidate. Each double-blind arm lasted 4 weeks; data were collected from August 2004 through December 2005. Subjects met both DSM-IV-TR and Utah Criteria for ADHD in adults. Outcome measures included the Wender-Reimherr Adult Attention Deficit Disorder Scale (WRAADDS), the adult ADHD-Rating Scale (ADHD-RS), and the Clinical Global Impressions-Improvement scale (CGI-I). At baseline, subjects were categorized as having significant emotional symptoms with the WRAADDS and/or significant oppositional-defiant symptoms using a self-report scale assessing the DSM-IV criteria for oppositional defiant disorder. RESULTS 17% of the sample (N = 8) had ADHD alone, 38% (N = 18) had ADHD plus significant emotional symptoms, and 40% (N = 19) had ADHD with both significant emotional and oppositional symptoms. At a mean +/- SD dose of 64.0 +/- 23.3 (0.75 mg/kg), OROS methylphenidate proved superior to placebo for all clinical measures: total WRAADDS score decrease of 42% versus 13%, respectively, p < . 001 and total ADHD-RS score decrease of 41% versus 14%, respectively, p = . 003, plus the subscales addressing inattention, hyperactivity/ impulsivity, and emotional dysregulation. CONCLUSIONS OROS methylphenidate proved effective in treating adult ADHD. ADHD alone was relatively uncommon. Over 80% of our patients had ADHD with a combination of emotional and/or oppositional symptoms.
Outage-constrained source-sum-power minimization in multiple-sensor single-DF-relay networks with direct links

This paper considers minimizing source-sum-power consumption under outage constraints in a wireless multiple-sensor single-relay network with direct link communication. We consider decode-and-forward (DF) relaying. It is difficult to find the exact expression of the optimal solution to the problem. A suboptimal power allocation and lower bound of the minimum source power consumption are provided. Numerical results show that the performance gap between the proposed suboptimal power allocation and the lower bound becomes small as relay power capacity increases.
An A Contrario Model for Matching Interest Points under Geometric and Photometric Constraints

Finding point correspondences between two views is generally based on the matching of local photometric descriptors. A subsequent geometric constraint ensures that the set of matching points is consistent with a realistic camera motion. Starting from a paper by Moisan and Stival, we propose an a contrario model for matching interest points based on descriptor similarity and geometric constraints. The resulting algorithm has adaptive matching thresholds and is able to detect point correspondences whose associated descriptors are not the first nearest neighbor. We also discuss the specific difficulties raised by images containing repeated patterns which are likely to introduce correspondences beyond the nearest neighbor.
What do untrained conversation partners know about communicating with people with aphasia

This study was undertaken as part of the final year undergraduate degree programme at De Montfort University. In 2006 Turner & Whitworth identified that teaching conversational partners about supportive communication strategies was a key theme of the three main approaches to conversational therapy; the conversational analysis approach, the supported conversation approach and the conversational coaching approach. This research project was designed to investigate whether potential conversation partners who had not received conversational partner training could identify ways to support conversations with people with aphasia.
Antinociceptive and Anti-Inflammatory Activities of the Sesame Oil and Sesamin

Sesame oil is widely consumed as nutritious food, cooking oil, and in pharmaceuticals and food. In this study, the antinociceptive and anti-inflammatory properties of the sesame oil and sesamin were investigated. The sesame oil and sesamin reduced the number of abdominal contortions at the doses 100, 200, or 400 mg/kg. The first and second phases of the time paw licking were inhibited by sesame oil and sesamin (100, 200, or 400 mg/kg). After 90 min of treatment, sesame oil and sesamin increased the reaction time on a hot plate (200 or 400 mg/kg). Considering the tail-immersion assay, the sesame oil and sesamin produced significant effect after 60 min at the doses of 100, 200, or 400 mg/kg. After 4 h of application of the carrageenan, the sesame oil and sesamin were effective against the paw edema. The exudate volume and leucocyte migration were also reduced by sesame oil and sesamin. These results suggest that sesamin is one of the active compounds found in sesame oil and justify the antinociceptive and anti-inflammatory properties of this product.
Steering a Tractor by Means of an EMG-Based Human-Machine Interface

An electromiographic (EMG)-based human-machine interface (HMI) is a communication pathway between a human and a machine that operates by means of the acquisition and processing of EMG signals. This article explores the use of EMG-based HMIs in the steering of farm tractors. An EPOC, a low-cost human-computer interface (HCI) from the Emotiv Company, was employed. This device, by means of 14 saline sensors, measures and processes EMG and electroencephalographic (EEG) signals from the scalp of the driver. In our tests, the HMI took into account only the detection of four trained muscular events on the driver’s scalp: eyes looking to the right and jaw opened, eyes looking to the right and jaw closed, eyes looking to the left and jaw opened, and eyes looking to the left and jaw closed. The EMG-based HMI guidance was compared with manual guidance and with autonomous GPS guidance. A driver tested these three guidance systems along three different trajectories: a straight line, a step, and a circumference. The accuracy of the EMG-based HMI guidance was lower than the accuracy obtained by manual guidance, which was lower in turn than the accuracy obtained by the autonomous GPS guidance; the computed standard deviations of error to the desired trajectory in the straight line were 16 cm, 9 cm, and 4 cm, respectively. Since the standard deviation between the manual guidance and the EMG-based HMI guidance differed only 7 cm, and this difference is not relevant in agricultural steering, it can be concluded that it is possible to steer a tractor by an EMG-based HMI with almost the same accuracy as with manual steering.
A Review of Key Issues That Concern the Feasibility of Mobile Cloud Computing

Recently, the arising of cloud computing (CC) concept and explosive growth of mobile applications induce a novel technology, i.e., mobile cloud computing (MCC). By integrating CC into mobile environment, MCC alleviates limitations of mobile devices and proliferates a variety of new fascinating mobile services. The key to enable MCC is to equip mobile users with the data processing and storage abilities in the clouds via wireless networks. In this paper, aiming at facilitating the research of MCC and inducing more research topics regarding MCC, we offer a review of the key issues that concern the feasibility of MCC and identify the corresponding novel techniques to mitigate these key issues. Moreover, we propose a potential framework to enhance the robustness of MCC incorporating these novel techniques.
SSDExplorer: A virtual platform for fine-grained design space exploration of Solid State Drives

Solid State Drives (SSDs) are gaining particular momentum in various frameworks such as multimedia, large data centers and cloud environments. Unfortunately, efficient CAD tools for SSD design space exploration able to assess the optimization of the device microarchitecture w.r. t. the target performance are still missing. This paper tries to close this gap by proposing SSDExplorer, a tool for fine-grained and fast design space exploration of SSD devices. SSDExplorer provides unprecedented insights into the architecture behavior and subcomponent interaction efficiency, while avoiding the need for the actual implementation of an FTL or of key hardware components. This is achieved by the introduction of suitable abstractions of the different components. This is confirmed by the thorough validation of SSDExplorer against a commercial SSD device.
Soil Organic Carbon Pool and Its Chemical Composition in Phyllostachy pubescens Forests at Two Altitudes in Jian-ou City, China

Phyllostachys pubescens forests play an important role in soil organic carbon (SOC) sequestration in terrestrial ecosystems. However, the estimation and mechanism of SOC sequestration by P. pubescens forests remain unclear. In this study, the effect of P. pubescens forest distribution with elevation was investigated at two altitude sites in Jian-ou City, Southeast China. SOC storage was estimated and its chemical composition was obtained via 13C-nuclear magnetic resonance (NMR), chemical classification, and spectral analysis. Results showed that the SOC contents and stocks were significantly higher at the high-altitude site than at the low-altitude site in the entire soil profile (0–60 cm). The C contents of the three combined humus forms exhibited similar responses to the elevation change, and all of these forms were higher at the high-altitude site than at the low-altitude site regardless of soil layer. However, the proportions of the three combined humus C showed no significant differences between the two altitudes. The results of 13C-NMR showed that the SOC chemical composition did not significantly vary with elevation as well. This finding was consistent with the E465/E665 of the loosely combined humus. Overall, the results suggested that altitude should be considered during regional SOC estimation and that altitude affected the quantity rather than the quality of the SOC under the same P. pubescens vegetation.
Non-intrusive Viral Marketing Based on Percolation Centrality

Viral marketing can become an effective marketing technique in social networks. Initiating from a set of influential seed users, it can activate a “chain-reaction” driven by word-of-mouth. The effectiveness of viral marketing lies in the fact that it conveys an implied endorsement from social ties. However, not all viral marketing campaign become successful some stop even before the number of activated users of the network reaches critical mass. In this paper we propose a new approach to viral marketing that will allow marketers to increase the performance of the stopped campaign by initiating new “waves” of the campaign. But in order to not overwhelm users that were already exposed to the initial campaign, the activation of seeds is performed in a non-intrusive way by suggesting users to follow recommendations of their friends. The proposed method for seed selection for the next “wave” is based on percolation centrality that takes into account already activated nodes and uses their social connections to boost the word-of-mouth propagation that already happens in the network.