Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatics Study of Functional Associations Observed in Multiple Sources of Human Genome Data

High-throughput genome analysis techniques produce the ever increasing number of heterogeneous large-scale datasets. Studies of these mutually complementary sources of data promise insights into a global picture of the living cell. Here, we present a simple bioinformatics methodology for the analysis of multiple heterogeneous sources of 'omic' (ge- nomic, proteomic, etc) data. We apply this methodology to study associations among four types of human 'omic' data: protein-protein interactions, gene expression, transcription factor binding sites, and functional pathways. The results of our study indicate that the proposed approach can be used to identify and rank statistically significant functional associa- tions among genes. We show that combinations of multiple data types provide additional insights into the properties of functional pathways. The proposed methodology can also be used as a quantitative procedure for evaluating the quality of 'omic' datasets.
Learning Models and Technology Strategy in Catching-up *

Learning is central to knowledge-bas ed development. It is through learning that innovation capabilities of firm and social capabilities to adapt to change get improved. This paper focuses on learning at firm and in cluster in developing countries. Three distinctive paths or models of industrial latecomer learning are analyzed: a) individual firm-based latecomer learning, with Korean firms as prototype; b) network-based latecomer learning, with Taiwanese firms as prototype; c) ‘re-combinati on’ latecomer learning which takes place during profound transition in economic regimes, with Chinese firms as prototype. Machinery and ICT (information and communications technology) industries are the sectoral background of analysis. Reviewing three learning models rather than one model is intended to, and merely intended to, expand our understanding that models or trajectories of learning by industrial latecomers are plural. The analysis leads to identificatio n that, firstly, learning of industrial latecomers is difficult. It entails discontinuous knowledge and skills acquisition, and is a process away from the state of equilibrium. Secondly, in latecomer learning the role of human capital is very central. It makes up the major input from the learner’s part so that the intrinsic difficulties involved are possible to be surmounted. Thirdly, internationally migratory technological knowledge has developed much more extensive and multi-form. It provides latecomer learners reference points to entry. The paper then summarizes the implications in terms of technology strategy in catchingup, including technological choices for entry and the nature of catching-up, which is now open to redress from the perspective of learning.
No evidence for a relationship between testosterone hair samples and 2D:4D ratio or risk taking

Using a recently developed alternative assay procedure to measure hormone levels from hair samples, we examined the relationships between testosterone, cortisol, 2D:4D ratio, overconfidence and risk taking. A total of 162 (53 male) participants provided a 3 cm sample of hair, a scanned image of their right and left hands from which we determined 2D:4D ratios, and completed measures of overconfidence and behavioral risk taking. While our sample size for males was less than ideal, our results revealed no evidence for a relationship between hair testosterone concentrations, 2D:4D ratios and risk taking. No relationships with overconfidence emerged. Partially consistent with the Dual Hormone Hypothesis, we did find evidence for the interacting effect of testosterone and cortisol on risk taking but only in men. Hair testosterone concentrations were positively related to risk taking when levels of hair cortisol concentrations were low, in men. Our results lend support to the suggestion that endogenous testosterone and 2D:4D ratio are unrelated and might then exert diverging activating vs. organizing effects on behavior. Comparing our results to those reported in the existing literature we speculate that behavioral correlates of testosterone such as direct effects on risk taking may be more sensitive to state-based fluctuations than baseline levels of testosterone.
Classifying soft error vulnerabilities in extreme-Scale scientific applications using a binary instrumentation tool

Extreme-scale scientific applications are at a significant risk of being hit by soft errors on supercomputers as the scale of these systems and the component density continues to increase. In order to better understand the specific soft error vulnerabilities in scientific applications, we have built an empirical fault injection and consequence analysis tool - BIFIT -that allows us to evaluate how soft errors impact applications. In particular, BIFIT is designed with capability to inject faults at very specific targets: an arbitrarily-chosen execution point and any specific data structure. We apply BIFIT to three mission-critical scientific applications and investigate the applications vulnerability to soft errors by performing thousands of statistical tests. We, then, classify each applications individual data structures based on their sensitivity to these vulnerabilities, and generalize these classifications across applications. Subsequently, these classifications can be used to apply appropriate resiliency solutions to each data structure within an application. Our study reveals that these scientific applications have a wide range of sensitivities to both the time and the location of a soft error; yet, we are able to identify intrinsic relationships between application vulnerabilities and specific types of data objects. In this regard, BIFIT enables new opportunities for future resiliency research.
Gap Junction Communication and Connexin 43 Gene Expression in a Rat Granulosa Cell Line: Regulation by Follicle-Stimulating Hormone1

Abstract Follicle-stimulating hormone is the major regulator of growth and development of antral follicles in the ovary. Granulosa cells (GCs) in these follicles are coupled via gap junctions (GJs) consisting of connexin 43 (Cx 43). Because we and others have found that Cx 43 and GJs, respectively, are more abundant in large antral follicles compared with small antral and preantral follicles, we hypothesized that FSH may control Cx 43 gene expression, GJ formation, and intercellular communication. To directly address these points, we chose a rat GC line (GFSHR-17) expressing the FSH receptor and the Cx 43 gene. The functionality of FSH receptors was shown by the effects of porcine FSH, namely cell rounding, reduced cellular proliferation, and stimulation of progesterone production of GFSHR-17 cells, which are effects that were detectable within hours. Treatment with FSH also statistically significantly increased Cx 43 mRNA levels, as shown after 6 to 9 h in Northern blots. These effects were antedated by altered GJ communication, which was observed within seconds. Using a single-cell/whole-cell patch clamp technique, we showed that FSH rapidly and reversibly enhanced electrical cell coupling of GFSHR-17 cells. Increased GJ communication was associated with statistically significantly decreased phosphorylation of Cx 43, which was observed within 10 min after FSH addition, during immunoprecipitation experiments. Our results demonstrate, to our knowledge for the first time, that the gonadotropin FSH acutely and directly stimulates intercellular communication of GFSHR-17 cells through existing GJs. Moreover, FSH also increases levels of Cx 43 mRNA. These changes are associated with reduced proliferation and enhanced differentiation of GFSHR-17 cells. In vivo factors in addition to FSH may be involved in the regulation of GJ/GJ communication between GCs in the follicle, but our results suggest that improved cell-to-cell coupling, enhanced Cx 43 gene expression, and possibly, formation of new GJs are direct consequences of FSH receptor activation and may antedate and/or initiate the pivotal effects of FSH on GCs.
Computing consistent query answers using conflict hypergraphs

A consistent query answer in a possibly inconsistent database is an answer which is true in every (minimal) repair of the database. We present here a practical framework for computing consistent query answers for large, possibly inconsistent relational databases. We consider relational algebra queries without projection, and denial constraints. Because our framework handles union queries, we can effectively (and efficiently) extract indefinite disjunctive information from an inconsistent database. We describe a number of novel optimization techniques applicable in this context and summarize experimental results that validate our approach.
Role of the Extracytoplasmic Function Sigma Factor RpoE4 in Oxidative and Osmotic Stress Responses in Rhizobium etli

ABSTRACT The aims of this study were to functionally characterize and analyze the transcriptional regulation and transcriptome of the Rhizobium etli rpoE4 gene. An R. etli rpoE4 mutant was sensitive to oxidative, saline, and osmotic stresses. Using transcriptional fusions, we determined that RpoE4 controls its own transcription and that it is negatively regulated by rseF (regulator of sigma rpoE4; CH03274), which is cotranscribed with rpoE4. rpoE4 expression was induced not only after oxidative, saline, and osmotic shocks, but also under microaerobic and stationary-phase growth conditions. The transcriptome analyses of an rpoE4 mutant and an rpoE4-overexpressing strain revealed that the RpoE4 extracytoplasmic function sigma factor regulates about 98 genes; 50 of them have the rpoE4 promoter motifs in the upstream regulatory regions. Interestingly, 16 of 38 genes upregulated in the rpoE4-overexpressing strain encode unknown putative cell envelope proteins. Other genes controlled by RpoE4 include rpoH2, CH00462, CH02434, CH03474, and xthA1, which encode proteins involved in the stress response (a heat shock sigma factor, a putative Mn-catalase, an alkylation DNA repair protein, pyridoxine phosphate oxidase, and exonuclease III, respectively), as well as several genes, such as CH01253, CH03555, and PF00247, encoding putative proteins involved in cell envelope biogenesis (a putative peptidoglycan binding protein, a cell wall degradation protein, and phospholipase D, respectively). These results suggest that rpoE4 has a relevant function in cell envelope biogenesis and that it plays a role as a general regulator in the responses to several kinds of stress.
Chemotaxis Inhibitory Protein of Staphylococcus aureus, a Bacterial Antiinflammatory Agent

Leukocyte migration is a key event both in host defense against invading pathogens as well as in inflammation. Bacteria generate chemoattractants primarily by excretion (formylated peptides), complement activation (C5a), and subsequently through activation of leukocytes (e.g., leukotriene B4, platelet-activating factor, and interleukin 8). Here we describe a new protein secreted by Staphylococcus aureus that specifically impairs the response of neutrophils and monocytes to formylated peptides and C5a. This chemotaxis inhibitory protein of S. aureus (CHIPS) is a 14.1-kD protein encoded on a bacteriophage and is found in >60% of clinical isolates. CHIPS reduces the neutrophil recruitment toward C5a in a mouse peritonitis model, even though its activity is much more potent on human than on mouse cells. These findings suggest a new immune escape mechanism of S. aureus and put forward CHIPS as a potential new antiinflammatory therapeutic compound.
Adaptive controller design for uncertain nonlinear systems with input magnitude and rate limitations

An adaptive controller for a class of multiple input-multiple-output (MIMO) uncertain nonlinear systems with extern disturbance and control input limitations is presented in this paper. The controller is designed with a priori consideration of input limitation effects, hence it can generate control signals satisfying input limitations. This controller uses adaptive radial basis function (RBF) neural networks to approximate the unknown nonlinearities. To compensate the effects of input limitations, an auxiliary system is constructed and used in neural network parameter update laws. Furthermore, in order to deal with approximation errors for unknown nonlinearities and extern disturbances, a supervisory control is designed, which guarantees that the closed loop system achieves a desired level H∞ tracking performance. The closed loop system performance is analyzed by Lyapunov method. Steady state and transient tracking performance index are established and can be adjusted by design parameters. Computer simulations are presented to illustrate the efficiency and tracking performance of the proposed controller.
Prevalence of ADHD Among Students of Zahedan University of Medical Science in Iran

Objective: Attention-deficit/hyperactivity disorder (ADHD) is a common mental disorder in adults that was under-diagnosed until recently. Due to probable consequences of ADHD such as occupational and educational dysfunctions and substance use, this disorder is becoming more and more of a concern. This study aimed to investigate ADHD symptoms among students of Zahedan University of medical sciences, Iran. Methods: This cross-sectional study was performed in Zahedan University of Medical Sciences from 2008 to 2009. Our sample included 1500 individuals who were chosen using simple sampling method. Considering the goal of the investigation, two questionnaires were distributed among students including demographic information form and the Conners' Adult ADHD Rating Scales–Self Report (Screening Version, CAARS-S:SV). Data analysis was done using descriptive and analytical statistics in SPSS software. Results: Out of 1500 questionnaires distributed among students, 913 were completed. 589 students (64.5%) were female and 324 (35.5%) were male. The Mean age of participants was 21.7 ± 3.2 years. ADHD symptoms were defined based on the Conner’s adult test. Based on CAARS-S: SV, inattention/memory, hyperactivity/restlessness, impulsiveness/emotional lability, and problems with self-concept subscale symptoms were found in 107 (11.7%), 109 (12%), 121 (13.2%), and 30 (3.3%) respondents, respectively. These findings were significantly higher than average. Conclusions: According to our results, it seems that the prevalence of ADHD is high among students. Thus, more screening is required in this population in order to diagnose and treat the disorder earlier and prevent its consequences, such as substance abuse. Declaration of interest: None.
Prognostic value of the modified american college of Cardiology/American heart association stenosis morphology classification for long-term angiographic and clinical outcome after coronary stent placement.

Background-The modified American College of Cardiology/American Heart Association (ACC/AHA) lesion morphology criteria are predictive of early outcome after various coronary catheter interventions. Their potential prognostic value after stent implantation and, in particular, for restenosis and long-term clinical outcome has not been studied. We assessed the prognostic value of the modified ACC/AHA criteria for the long-term angiographic and clinical outcome of patients after coronary stenting. Methods and Results-This study includes 2944 consecutive patients with symptomatic coronary artery disease treated with coronary stent placement. Modified ACC/AHA lesion morphology criteria were used to qualitatively assess the angiograms; type A and B1 lesions were categorized as simple, and type B2 and C lesions were designated complex. Primary end points were angiographic restenosis and 1-year event-free survival. Restenosis rate was 33.2% in complex lesions and 24.9% in simple lesions (P<0.001). It was 21. 7% for type A, 26.3% for type B1, 33.7% for type B2, and 32.6% for type C lesions. One-year event-free survival was 75.6% for patients with complex lesions and 81.1% for patients with simple lesions (P<0. 001). It was 85.2% for patients with type A, 79.4% for type B1, 75. 9% for type B2, and 75.2% type C lesions. The higher risk for restenosis and an adverse outcome associated with complex lesions was also maintained after multivariate adjustment for other clinical and angiographic characteristics. Conclusions-The modified ACC/AHA lesion morphology scheme has significant prognostic value for the outcome of patients after coronary stent placement. Lesion morphology is able to influence the restenosis process and thus the entire 1-year clinical course of these patients.
Epigenetic Silencing of Human Immunodeficiency Virus (HIV) Transcription by Formation of Restrictive Chromatin Structures at the Viral Long Terminal Repeat Drives the Progressive Entry of HIV into Latency

ABSTRACT The molecular mechanisms utilized by human immunodeficiency virus (HIV) to enter latency are poorly understood. Following the infection of Jurkat T cells with lentiviral vectors that express Tat in cis, gene expression is progressively silenced. Silencing is greatly enhanced when the lentiviral vectors carry an attenuated Tat gene with the H13L mutation. Individual clones of lentivirus-infected cells showed a wide range of shutdown rates, with the majority showing a 50% silencing frequency between 30 to 80 days. The silenced clones characteristically contained a small fraction (0 to 15%) of activated cells that continued to express d2EGFP. When d2EGFP+ and d2EGFP− cell populations were isolated from the shutdown clones, they quickly reverted to the original distribution of inactive and active cells, suggesting that the d2EGFP+ cells arise from stochastic fluctuations in gene expression. The detailed analysis of transcription initiation and elongation using chromatin immunoprecipitation (ChIP) assays confirms that Tat levels are restricted in the latently infected cells but gradually rise during proviral reactivation. ChIP assays using clones of latently infected cells demonstrate that the latent proviruses carry high levels of deacetylated histones and trimethylated histones. In contrast, the cellular genes IκBα and GAPDH had high levels of acetylated histones and no trimethylated histones. The levels of trimethylated histone H3 and HP1-α associated with HIV proviruses fell rapidly after tumor necrosis factor alpha activation. The progressive shutdown of HIV transcription following infection suggests that epigenetic mechanisms targeting chromatin structures selectively restrict HIV transcription initiation. This decreases Tat production below the levels that are required to sustain HIV gene expression.
Nonintubated Surfactant Application vs Conventional Therapy in Extremely Preterm Infants: A Randomized Clinical Trial.

IMPORTANCE Treatment of respiratory distress syndrome in premature infants with continuous positive airway pressure (CPAP) preserves surfactant and keeps the lung open but is insufficient in severe surfactant deficiency. Traditional surfactant administration is related to short periods of positive pressure ventilation and implies the risk of lung injury. CPAP with surfactant but without any positive pressure ventilation may work synergistically. This randomized trial investigated a less invasive surfactant application protocol (LISA). OBJECTIVE To test the hypothesis that LISA increases survival without bronchopulmonary dysplasia (BPD) at 36 weeks' gestational age in extremely preterm infants. DESIGN, SETTING, AND PARTICIPANTS The Nonintubated Surfactant Application trial was a multicenter, randomized, clinical, parallel-group study conducted between April 15, 2009, and March 25, 2012, in 13 level III neonatal intensive care units in Germany. The final follow-up date was June 21, 2012. Participants included 211 of 558 eligible (37.8%) spontaneously breathing preterm infants born between 23.0 and 26.8 weeks' gestational age with signs of respiratory distress syndrome. In an intention-to-treat design, infants were randomly assigned to receive surfactant either via a thin endotracheal catheter during CPAP-assisted spontaneous breathing (intervention group) or after conventional endotracheal intubation during mechanical ventilation (control group). Analysis was conducted from September 6, 2012, to June 20, 2013. INTERVENTION LISA via a thin catheter. MAIN OUTCOMES AND MEASURES Survival without BPD at 36 weeks' gestational age. RESULTS Of 211 infants who were randomized, 104 were randomized to the control group and 107 to the LISA group. Of the infants who received LISA, 72 (67.3%) survived without BPD compared with 61 (58.7%) of those in the control group. The reduction in absolute risk was 8.6% (95% CI, -5.0% to 21.9%; P = .20). Intervention group infants were less frequently intubated (80 infants [74.8%] vs 103 [99.0%]; P < .001) and required fewer days of mechanical ventilation. Significant reductions were seen in pneumothorax (5 of 105 intervention group infants [4.8%] vs 13 of 103 12.6%]; P = .04) and severe intraventricular hemorrhage (11 infants [10.3%] vs 23 [22.1%]; P = .02), and the combined survival without severe adverse events was increased in the intervention group (54 infants [50.5%] vs 37 [35.6%]; P = .02; absolute risk reduction, 14.9; 95% CI, 1.4 to 28.2). CONCLUSIONS AND RELEVANCE LISA did not increase survival without BPD but was associated with increased survival without major complications. Because major complications are related to lifelong disabilities, LISA may be a promising therapy for extremely preterm infants. TRIAL REGISTRATION isrctn.org Identifier: ISRCTN64011614.
Dietary Advanced Glycation End Products Consumption as a Direct Modulator of Insulin Sensitivity in Overweight Humans: A Study Protocol for a Double-Blind, Randomized, Two Period Cross-Over Trial

Background Advanced glycation end products (AGEs) are formed during the processing, storage, and cooking of foods. As part of a western diet, AGEs are consumed in excess and impair glucose metabolism in patients with type 2 diabetes. In the absence of diabetes, AGE-mediated decreases in insulin sensitivity and signaling have been postulated. However, randomized studies to test this relationship in humans are limited. Objective The primary aim of this trial is to determine whether dietary consumption of AGEs will decrease insulin sensitivity in healthy overweight adults. A secondary aim is to determine the effects of dietary AGEs on insulin secretion, circulating soluble receptor for AGEs (sRAGE), and inflammation markers. Methods Overweight, but otherwise healthy, non-diabetic adults (N=20) aged 18-50 years old will complete a randomized cross-over design intervention study alternating low and high (4-fold increase) AGE diets (2-week duration). At baseline, participants will undergo a medical review including an intravenous glucose tolerance test (IVGTT), a hyperinsulinemic-euglycemic clamp, and anthropometric measures and questionnaires assessing diet, physical activity, and general wellness. Each test diet will be followed for 14 days, followed by a 4-week washout period before commencement of the second alternate dietary period. Energy, macronutrient, and AGE intake will be calculated for each dietary period. Additionally, the AGE content of foods used in the study will be measured by ultra performance liquid chromatography mass spectrometry. All measurements will be repeated at the beginning and end of each dietary period. Primary and secondary outcomes will be expressed as a change over the dietary period for insulin sensitivity, secretion, anthropometric parameters, sRAGE, and inflammation markers and compared by paired t test and analysis of variance (ANOVA). Results The study will be completed in early 2016. Conclusion The proposed trial will provide much needed clinical evidence on the impact of excess dietary AGE consumption on insulin sensitivity and will indicate whether lowering dietary AGE intake can improve insulin sensitivity and/or secretion, thereby decreasing risk for type 2 diabetes. Trial Registration Clinicaltrials.gov NCT00422253; https://clinicaltrials.gov/ct2/show/NCT00422253 (Archived by Webcite at http://www.webcitation.org/6ZXLhT89c)