Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples

ABSTRACT Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice.
Cytosolic Nucleotides Block and Regulate the Arabidopsis Vacuolar Anion Channel AtALMT9*

Background: AtALMT9 is an intracellular anion channel regulating stomata aperture. Results: ATP interacts with the pore of AtALMT9 competing with vacuolar anions and modifying the voltage dependence of this ion channel. Conclusion: Cytosolic nucleotides and vacuolar anions directly modulate the transport activity of AtALMT9. Significance: Regulation of intracellular transporters is crucial for their physiological functions. The aluminum-activated malate transporters (ALMTs) form a membrane protein family exhibiting different physiological roles in plants, varying from conferring tolerance to environmental Al3+ to the regulation of stomatal movement. The regulation of the anion channels of the ALMT family is largely unknown. Identifying intracellular modulators of the activity of anion channels is fundamental to understanding their physiological functions. In this study we investigated the role of cytosolic nucleotides in regulating the activity of the vacuolar anion channel AtALMT9. We found that cytosolic nucleotides modulate the transport activity of AtALMT9. This modulation was based on a direct block of the pore of the channel at negative membrane potentials (open channel block) by the nucleotide and not by a phosphorylation mechanism. The block by nucleotides of AtALMT9-mediated currents was voltage dependent. The blocking efficiency of intracellular nucleotides increased with the number of phosphate groups and ATP was the most effective cellular blocker. Interestingly, the ATP block induced a marked modification of the current-voltage characteristic of AtALMT9. In addition, increased concentrations of vacuolar anions were able to shift the ATP block threshold to a more negative membrane potential. The block of AtALMT9-mediated anion currents by ATP at negative membrane potentials acts as a gate of the channel and vacuolar anion tune this gating mechanism. Our results suggest that anion transport across the vacuolar membrane in plant cells is controlled by cytosolic nucleotides and the energetic status of the cell.
Novel Ranking-Based Lexical Similarity Measure for Word Embedding

Distributional semantics models derive word space from linguistic items in context. Meaning is obtained by defining a distance measure between vectors corresponding to lexical entities. Such vectors present several problems. In this paper we provide a guideline for post process improvements to the baseline vectors. We focus on refining the similarity aspect, address imperfections of the model by applying the hubness reduction method, implementing relational knowledge into the model, and providing a new ranking similarity definition that give maximum weight to the top 1 component value. This feature ranking is similar to the one used in information retrieval. All these enrichments outperform current literature results for joint ESL and TOEF sets comparison. Since single word embedding is a basic element of any semantic task one can expect a significant improvement of results for these tasks. Moreover, our improved method of text processing can be translated to continuous distributed representation of biological sequences for deep proteomics and genomics.
Improving performance of construction projects: multi-cultural perspective

This paper reveals the national culture of the migrant construction employees in the UAE. The study is based on the national culture dimensions proposed by Hofstede. These include the power distance index (PDI), individualism (IND), masculinity (MAS), the uncertainty avoidance index (UAI) and long term orientation (LTO). The data was collected through observations, narratives and semi-structured interviews. The research covers multi-cultural construction team members from India, Pakistan, Bangladesh and China. The results show Indian construction employees were having high UAI, Pakistani employees showed high MAS, Bangladeshi employees revealed low LTO and IND and Chinese construction employees showed high IND and LTO. The study suggests that the management of cultural differences may help the successful completion of projects, which could be beneficial for both the migrant sending country and the host country and also for the individual migrant and his family.
Modeling and Analysis of Passive Switching Crossbar Arrays

Emerging technologies have enabled efficient, high-speed realizations of ultra-dense crossbar arrays, driving the need for better insight in the transient operation of such systems. Previous work focused mostly on the effect of line resistance and its impact on steady-state response. In this paper, we develop a compact <inline-formula> <tex-math notation="LaTeX">$RC$ </tex-math></inline-formula> framework that includes the effects of parasitics. We use memristors as an exemplar device where interconnect parasitics (resistance, inductance, capacitance, and conductance) are extracted using ANSYS Q3D extractor for 5- and 50-<inline-formula> <tex-math notation="LaTeX">$nm$ </tex-math></inline-formula> feature sizes. A model for the crossbar is presented, considering the stray and coupling capacitive parasitics of the crossbar. The derived model is based on state-space representation and provides more insight into the behavior of crossbar arrays containing either linear or nonlinear switching devices. The framework provides a closed-form solution to evaluate Elmore delay, as well as the steady-state response of the system. Signal delay is evaluated and compared for both grounded and floating interconnect inputs and verified against HSPICE, showing a perfect match.
The prognostic importance of severity and type of post‐transplant proteinuria

Proteinuria, developing after renal transplantation may influence allograft and patient outcomes. This study aimed to investigate the effect of proteinuria on patient and allograft survival. Among 514 patients, 56 (11%) patients with good allograft function and proteinuria were evaluated retrospectively. Patients with proteinuria were classified as group P (20 patients with permanent proteinuria, Male/Female: 16/4) and group T (36 patients with temporary proteinuria, M/F: 29/7) according to the type of proteinuria. Also, considering the amount of proteinuria, patients were classified as group M (32 patients with massive proteinuria, M/F: 29/3) and group NM (24 patients with non‐massive proteinuria, M/F: 16/8). The mean time interval between transplantation and appearance of proteinuria was 23.7 months (range 0–121 months) and no difference was found between groups. Two‐ and 5‐yr allograft survival rates were found to be 85 and 80% in group M, and 95 and 82% in group NM, respectively (p=0.24). In terms of type of proteinuria, 2‐ and 5‐yr allograft survival rates were found to be 70 and 58% in group P and 92 and 87% in group T, respectively. The difference between groups P and T was found to be statistically significant (p=0.02). Most (85%) of the patients with permanent proteinuria also had massive proteinuria. In conclusion, we found a significant relation between type and severity of proteinuria. The type of post‐transplant proteinuria had a stronger effect on allograft outcome than the severity of proteinuria.
Improvements in fundamental movement skill competency mediate the effect of the SCORES intervention on physical activity and cardiorespiratory fitness in children

Abstract Numerous studies have identified a positive association between fundamental movement skill (FMS) competency and physical activity in children; however, the causal pathways have not been established. The aim of this study is to determine if changes in FMS competency mediated the effect of the Supporting Children’s Outcomes using Rewards, Exercise and Skills (SCORES) intervention on physical activity and cardiorespiratory fitness in children. Eight primary schools (25 classes) and 460 children (aged 8.5 ± 0.6, 54% girls) were randomised to the SCORES intervention or control group for the 12-month study. The outcomes were accelerometer-determined moderate-to-vigorous physical activity (MVPA) and cardiorespiratory fitness. The hypothesised mediators were actual FMS competency and perceived sport competence. Mediation analyses were conducted using multilevel linear analysis in MPlus. From the original sample, 138 (30.0%) and 370 (80.4%) children provided useable physical activity and cardiorespiratory fitness data at post-test assessments. There were significant treatment effects for locomotor skills and overall FMSs. Changes in MVPA were associated with changes in object-control skills, overall FMSs and perceived competence. The overall FMSs had a significant mediating effect on MVPA (AB = 2.09, CI = 0.01–4.55). Overall FMSs (AB = 1.19, CI = 0.002–2.79) and locomotor skills (AB = 0.74, CI = 0.01–1.69) had a significant mediating effect on cardiorespiratory fitness. The results of this study conclude that actual but not perceived movement skill competency mediated the effect of the SCORES intervention on physical activity and cardiorespiratory fitness.
Analyzing Moir's Curve: A Quantitative Look at Attitudinal Changes in Induction-Year Agricultural Educators.

With the challenge of creating a competent workforce to fill the shortage of agricultural educators nationwide, researchers have suggested a detailed examination of induction-year teachers to increase retention is critical. Multiple studies have depicted the importance of examining attitudes of induction-year and early career agricultural educators to develop quality induction-level support for this group. Moir (1990) conducted a qualitative study that resulted in the suggestion of six attitudinal phases all induction-year teachers experience, and described a predictive curvilinear relationship between attitude and time over the course of their first year teaching. As part of a larger study, the purpose of this study was to investigate the relationship among demographic variables and induction-year teachers’ attitudes toward teaching. Using a repeated measures design, induction-year teachers’ (n=197) attitudes were measured at six points during the 2011-12 school year in relation to the Moir’s (1990) model. Findings showed that although minor changes in attitude among respondents occurred, respondents were generally positive in attitude toward their career and did not experience the high levels of fluctuation as suggested by Moir (1990). Additionally, upon completion of a forced entry linear regression, demographic characteristics were not found to be significant predictors of induction-year teachers’ attitudes toward teaching.
Contribution of individual targets to the antitumor efficacy of the multitargeted receptor tyrosine kinase inhibitor SU11248

Recent achievements in the development of multitargeted molecular inhibitors necessitate a better understanding of the contribution of activity against individual targets to their efficacy. SU11248, a small-molecule inhibitor targeting class III/V receptor tyrosine kinases, including the platelet-derived growth factor (PDGF) and vascular endothelial growth factor (VEGF) receptors, KIT and FLT3, exhibits direct effects on cancer cells as well as antiangiogenic activity. Here, we investigated the contributions of inhibiting individual SU11248 target receptors to its overall antitumor efficacy in tumor models representing diverse signaling paradigms. Consistent with previous results, SU11248 was highly efficacious (frequently cytoreductive) in all models tested. To elucidate the specific contributions of inhibition of PDGF and VEGF receptors to the in vivo efficacy of SU11248, we employed two selective inhibitors, SU10944 (VEGF receptor inhibitor) and Gleevec (PDGF receptor inhibitor). SU10944 alone induced a tumor growth delay in all models evaluated, consistent with a primarily antiangiogenic mode of action. In contrast, Gleevec resulted in modest growth inhibition in tumor models in which the cancer cells expressed its targets (PDGFRβ and KIT), but was not efficacious against tumors not driven by these target receptor tyrosine kinases. Strikingly, in all but one tumor model evaluated, the antitumor efficacy of SU10944 combined with Gleevec was similar to that of single-agent SU11248, and was greatly superior to that of each compound alone, indicating that the antitumor potency of SU11248 in these models stems from combined inhibition of both PDGF and VEGF receptors. The one exception was a model driven by an activated mutant of FLT3, in which the activity of SU11248, which targets FLT3, was greater than that of SU10944 plus Gleevec. Moreover, SU10944 combined with Gleevec inhibited tumor neoangiogenesis to an extent comparable to that of SU11248. Thus, the potent efficacy of SU11248 in models representing diverse signaling paradigms results from simultaneous inhibition of individual target receptors expressed both in cancer cells and in the tumor neovasculature, supporting the hypothesis that multitargeted inhibitors have the cumulative antitumor efficacy of combined single-target inhibitors. [Mol Cancer Ther 2006;5(5);1280–9]
Testing of Diagnostic Methods for Detection of Influenza Virus for Optimal Performance in the Context of an Influenza Surveillance Network

ABSTRACT Influenza surveillance networks must detect early the viruses that will cause the forthcoming annual epidemics and isolate the strains for further characterization. We obtained the highest sensitivity (95.4%) with a diagnostic tool that combined a shell-vial assay and reverse transcription-PCR on cell culture supernatants at 48 h, and indeed, recovered the strain.
Switched inverter - A new technique for sample data low-voltage and low-power applications

In this paper, a new technique called 'switched inverter' for analog sample data signal processing is proposed. The circuit is based on the conventional CMOS inverter operating as a transconductor. The proposed circuit does not require linear capacitors and employs switches that operate at fixed channel voltage. Owing to the use of inverters, the proposed structure presents class-AB operation. A 8'th taps FIR filter has been designed in a standard 0.35-μm CMOS technology at 0.6 V supply.
Relative Role of Akt, ERK and CREB in Alcohol-Induced Microglia P2X4R Receptor Expression.

AIMS Previously we have demonstrated altered microglia P2X4R expression in response to alcohol and pharmacological blockade with a selective P2X4R antagonist can reverse the action, suggesting that P2X4R play a role in mediating alcohol-induced effects on microglia. In the present study, we investigated the underlying signaling mediators, which may play a role in modulating P2X4R expression in microglia cells in response to alcohol. METHODS Embryonic stem cell-derived microglia (ESdM) cells were used to investigate the potential mechanisms involved in the regulation of P2X4R in response to alcohol. Selective P2X4R antagonist and kinase inhibitors were used to further corroborate the signal transduction pathway through which alcohol modulates P2X4R expression in microglia. RESULTS Alcohol (100 mM) suppressed phosphorylated AKT and ERK cascades in native ESdM cells. This alcohol-induced suppression was confirmed to be P2X4R-dependent through the use of a selective P2X4R antagonist and knockdown of P2XR4 by siRNA. Alcohol increased transcriptional activity of CREB. P2X4R antagonist blocked alcohol-induced effects on CREB, suggesting a P2X4R-mediated effect. CONCLUSION These findings provide important clues to the underlying mechanism of purinoceptors in alcohol-induced microglia immune suppression.
Development of a model of the coronary arterial tree for the 4D XCAT phantom

A detailed three-dimensional (3D) model of the coronary artery tree with cardiac motion has great potential for applications in a wide variety of medical imaging research areas. In this work, we first developed a computer-generated 3D model of the coronary arterial tree for the heart in the extended cardiac-torso (XCAT) phantom, thereby creating a realistic computer model of the human anatomy. The coronary arterial tree model was based on two datasets: (1) a gated cardiac dual-source computed tomography (CT) angiographic dataset obtained from a normal human subject and (2) statistical morphometric data of porcine hearts. The initial proximal segments of the vasculature and the anatomical details of the boundaries of the ventricles were defined by segmenting the CT data. An iterative rule-based generation method was developed and applied to extend the coronary arterial tree beyond the initial proximal segments. The algorithm was governed by three factors: (1) statistical morphometric measurements of the connectivity, lengths and diameters of the arterial segments; (2) avoidance forces from other vessel segments and the boundaries of the myocardium, and (3) optimality principles which minimize the drag force at the bifurcations of the generated tree. Using this algorithm, the 3D computational model of the largest six orders of the coronary arterial tree was generated, which spread across the myocardium of the left and right ventricles. The 3D coronary arterial tree model was then extended to 4D to simulate different cardiac phases by deforming the original 3D model according to the motion vector map of the 4D cardiac model of the XCAT phantom at the corresponding phases. As a result, a detailed and realistic 4D model of the coronary arterial tree was developed for the XCAT phantom by imposing constraints of anatomical and physiological characteristics of the coronary vasculature. This new 4D coronary artery tree model provides a unique simulation tool that can be used in the development and evaluation of instrumentation and methods for imaging normal and pathological hearts with myocardial perfusion defects.
Taking the Skill Bias Out of Global Migration

Global migration is heavily skill-biased, with tertiary-educated workers being four times more likely to migrate than workers with a lower education. In this paper, we quantify the global impact of this skill bias in migration. Based on a quantitative multi-country model with trade, we compare the current world to a counterfactual with the same number of migrants, where all migrants are neutrally selected from their countries of origin. We find that most receiving countries benefit from the skill bias in migration, while a small number of sending countries is significantly worse off. The negative effect in many sending countries is completely eliminated — and often reversed — once we account for remittances and additional migration-related externalities. In a model with all our extensions, the average welfare effect of skill-biased migration in both OECD and non-OECD countries is positive.
Human tumor microRNA signatures derived from large‐scale oligonucleotide microarray datasets

The expression profiles of microRNAs (miRNAs) are associated with the initiation and progression of human tumors. DNA microarrays are widely used to explore the expression patterns of miRNAs. Because of the limited sample size and experimental expense, the statistical power of individual research projects is not sufficient to yield a robust conclusion. However, collected microarray datasets of expression profiles provide opportunities to compile the information of individual studies. Our study carried out a comprehensive meta‐analysis of miRNA expression microarray datasets from 28 published tumor studies; it comprises 33 comparisons and nearly 4,000 tumor and corresponding nontumorous samples. This work reports 52 miRNAs as common signatures that are dysregulated in tumors. In addition to the commonly altered miRNAs, five solid cancers displayed specific tissue patterns of altered miRNAs as well. The meta‐analysis also revealed some novel tumor‐related miRNAs such as hsa‐miR‐144, hsa‐miR‐130b, hsa‐miR‐132, hsa‐miR‐154, hsa‐miR‐192 and hsa‐miR‐345. We further validated the expression pattern of hsa‐miR‐154 in human hepatocellular carcinoma by RT‐PCR. Restoration of intracellular miR‐154 inhibited tumor cell malignance and the G1/S transition in cancer cells. Both bioinformatic prediction and western blotting demonstrated that miR‐154 could target CCND2. In addition, expression patterns of miR‐154 were inversely correlated with those of CCND2 in hepatocellular carcinoma. Overall, this study used a large‐scale data analysis to identify a qualified list of miRNAs that are consistently changed in tumors, which could lead to a better understanding of human tumor etiology.
Application of Equivalent Linearization Algorithm on Voltage Transformer Protection during Fundamental Resonance in Power System

Ferroresonance is a common phenomenon and the type of the fundamental resonance occurs frequently in the power system. The overvoltage and overcurrent generated by the resonance will damage the voltage transformer (VT) or other facilities, and lower the power quality in the power system. In this paper, an adapted equivalent linearization algorithm is applied to analyze the fundamental resonance of a typical resonance circuit in the power network for the VT protection. The resonance region and safe region of the circuit can be obtained by the algorithm. On the base of the equivalent linearization algorithm the fundamental resonance can be avoided, and VTs can be efficiently protected from the resonance