Miracle-dz/UniFAR-FTUs huggingface dataset:
PSPP: A Protein Structure Prediction Pipeline for Computing Clusters

Background Protein structures are critical for understanding the mechanisms of biological systems and, subsequently, for drug and vaccine design. Unfortunately, protein sequence data exceed structural data by a factor of more than 200 to 1. This gap can be partially filled by using computational protein structure prediction. While structure prediction Web servers are a notable option, they often restrict the number of sequence queries and/or provide a limited set of prediction methodologies. Therefore, we present a standalone protein structure prediction software package suitable for high-throughput structural genomic applications that performs all three classes of prediction methodologies: comparative modeling, fold recognition, and ab initio. This software can be deployed on a user's own high-performance computing cluster. Methodology/Principal Findings The pipeline consists of a Perl core that integrates more than 20 individual software packages and databases, most of which are freely available from other research laboratories. The query protein sequences are first divided into domains either by domain boundary recognition or Bayesian statistics. The structures of the individual domains are then predicted using template-based modeling or ab initio modeling. The predicted models are scored with a statistical potential and an all-atom force field. The top-scoring ab initio models are annotated by structural comparison against the Structural Classification of Proteins (SCOP) fold database. Furthermore, secondary structure, solvent accessibility, transmembrane helices, and structural disorder are predicted. The results are generated in text, tab-delimited, and hypertext markup language (HTML) formats. So far, the pipeline has been used to study viral and bacterial proteomes. Conclusions The standalone pipeline that we introduce here, unlike protein structure prediction Web servers, allows users to devote their own computing assets to process a potentially unlimited number of queries as well as perform resource-intensive ab initio structure prediction.
Shiftwork and Diurnal Salivary Cortisol Patterns Among Police Officers

Objective: To investigate associations between shiftwork and diurnal salivary cortisol among 319 police officers (77.7% men). Methods: Information on shiftwork was obtained from the City of Buffalo, NY electronic payroll records. Saliva was collected using Salivettes at seven time points and analyzed for free cortisol concentrations (nmol/L) using a chemiluminescence immunoassay. Mean slopes and areas under the curve were compared across shift schedule using analysis of variance (ANOVA)/analysis of covariance (ANCOVA). Results: Officers working primarily on the night shift had a significantly shallower slope. Mean slope (nmol/L/minutes) of the cortisol curve varied significantly across shifts (day: −0.00332 ± 0.00017, afternoon: −0.00313 ± 0.00018, night: −0.00257 ± 0.0002); adjusted P = 0.023. Conclusions: Our results suggest that night shiftwork is a workplace factor that may alter the response of the hypothalamic–pituitary–adrenal (HPA) axis to the circadian cues responsible for the pattern of the diurnal cortisol curve.
Experimental residual stress evaluation of hydraulic expansion transitions in Alloy 690 steam generator tubing

Nuclear Steam Generator (SG) service reliability and longevity have been seriously affected worldwide by corrosion at the tube-to-tubesheet joint expansion. Current SG designs for new facilities and replacement projects enhance corrosion resistance through the use of advanced tubing materials and improved joint design and fabrication techniques. Here, transition zones of hydraulic expansions have undergone detailed experimental evaluation to define residual stress and cold-work distribution on and below the secondary-side surface. Using X-ray diffraction techniques, with supporting finite element analysis, variations are compared in tubing metallurgical condition, tube/pitch geometry, expansion pressure, and tube-to-hole clearance. Initial measurements to characterize the unexpanded tube reveal compressive stresses associated with a thin work-hardened layer on the outer surface of the tube. The gradient of cold-work was measured as 3% to 0% within . 001 inch of the surface. The levels and character of residual stresses following hydraulic expansion are primarily dependent on this work-hardened surface layer and initial stress state that is unique to each tube fabrication process. Tensile stresses following expansion are less than 25% of the local yield stress and are found on the transition in a narrow circumferential band at the immediate tube surface (< .0002 inch/0.005 mm depth). The measurements otherwise indicatemore » a predominance of compressive stresses on and below the secondary-side surface of the transition zone. Excellent resistance to SWSCC initiation is offered by the low levels of tensile stress and cold-work. Propagation of any possible cracking would be deterred by the compressive stress field that surrounds this small volume of tensile material. « less
Information-thermodynamic characterization of stochastic Boolean networks

Recent progress in experimental techniques has enabled us to quantitatively study stochastic and flexible behavior of biological systems. For example, gene regulatory networks perform stochastic information processing and their functionalities have been extensively studied. In gene regulatory networks, there are specific subgraphs called network motifs that occur at frequencies much higher than those found in randomized networks. Further understanding of the designing principle of such networks is highly desirable. In a different context, information thermodynamics has been devel- oped as a theoretical framework that generalizes non-equilibrium thermodynamics to stochastically fluctuating systems with information. Here we systematically characterize gene regulatory networks on the basis of information thermodynamics. We model three-node gene regulatory patterns by a stochastic Boolean model, which receive one or two input signals that carry external information. For the case of a single input, we found that all the three-node patterns are classified into four types by using information-thermodynamic quantities such as dissipation and mutual information, and reveal to which type each network motif belongs. Next, we consider the case where there are two inputs, and evaluate the capacity of logical operation of the three-node patterns by using tripartite mutual information, and argue the reason why patterns with fewer edges are preferred in natural selection. This result may also explain the difference of the occurrence frequencies among different types of feedforward-loop network motifs, and therefore suggests a guiding principle of the network formation.
Tracking Emotions of Bloggers - A Case Study for Bengali

The present paper describes the identification and tracking of bloggers' emotions with respect to time from the structured Bengali blog documents. The assignment of Ekman's six basic emotions to the bloggers' comments is carried out at sentence and paragraph level granularities. The Referential Informative Chain (RIC ) developed for each blogger consists of the nodes representing the emotional states of that blogger. Each node of a RIC contains the identification information of its associated blogger, timestamp, section and emotional sentences. The nodes are arranged in each RIC based on the ascending order of the associated timestamps. An affect scoring technique has been employed to capture the emotions from each of the nodes of a blogger's RIC . The incorporation of self emotions and influential emotions as extracted from other bloggers plays a significant role in detecting the emotions of a blogger's present state. The Extrinsic evaluation produces precision (P), recall (R) and F-Measure of 61.05%, 69.81% and 65.13% respectively for evaluating the total of 193 emotional states of 20 bloggers. The Intrinsic evaluation has been conducted using a manual rater with the help of a statistical agreement coefficient, Krippendorff's alpha 6. Two types of alpha, namely nominal alpha and interval alpha produce the average scores of 0.67 and 0.72, respectively.
Rehabilitation of stroke patients with plegic hands: Randomized controlled trial of expanded Constraint-Induced Movement therapy.

PURPOSE To evaluate the efficacy of an expanded form of Constraint-Induced Movement Therapy (eCIMT) that renders CIMT, originally designed for treating mild-to-moderate upper-extremity hemiparesis, suitable for treating severe hemiparesis. METHODS Twenty-one adults ≥1 year after stroke with severe upper-extremity hemiparesis (with little or no capacity to make movements with the more-affected hand) were randomly assigned to eCIMT (n = 10), a placebo-control procedure (n = 4), or usual care (n = 7). The participants who received usual care were crossed over to eCIMT four months after enrollment. The CIMT protocol was altered to include fitting of orthotics and adaptive equipment, selected neurodevelopmental techniques, and electromyography-triggered functional electrical stimulation. Treatment was given for 15 consecutive weekdays with 6 hours of therapy scheduled daily for the immediate eCIMT group and 3.5 hours daily for the cross-over eCIMT group. RESULTS At post-treatment, the immediate eCIMT group showed significant gains relative to the combination of the control groups on the Grade-4/5 Motor Activity Log (MAL; mean = 1.5 points, P < 0.001, f = 4.2) and a convergent measure, the Canadian Occupational Performance Measure (COPM; mean = 2.3, P = 0.014, f = 1.1; f values ≥0.4 are considered large, on the COPM changes ≥2 are considered clinically meaningful). At 1-year follow-up, the MAL gains in the immediate eCIMT group were only 13% less than at post-treatment. The short and long-term outcomes of the crossover eCIMT group were similar to those of the immediate eCIMT group. CONCLUSIONS This small, randomized controlled trial (RCT) suggests that eCIMT produces a large, meaningful, and persistent improvement in everyday use of the more-affected arm in adults with severe upper-extremity hemiparesis long after stroke. These promising findings warrant confirmation by a large RCT.
Further Characterisation of the Molecular Signature of Quiescent and Activated Mouse Muscle Satellite Cells

Satellite cells are the resident stem cells of adult skeletal muscle. To date though, there is a paucity of native markers that can be used to easily identify quiescent satellite cells, with Pax7 probably being the best that is currently available. Here we have further characterized a number of recently described satellite cell markers, and also describe novel ones. Caveolin-1, integrin α7 and the calcitonin receptor proved reliable markers for quiescent satellite cells, being expressed by all satellite cells identified with Pax7. These three markers remained expressed as satellite cells were activated and underwent proliferation. The nuclear envelope proteins lamin A/C and emerin, mutations in which underlie Emery-Dreifuss muscular dystrophy, were also expressed in both quiescent and proliferating satellite cells. Conversely, Jagged-1, a Notch ligand, was not expressed in quiescent satellite cells but was induced upon activation. These findings further contribute to defining the molecular signature of muscle satellite cells.
A Novel Harmonic Field Based Method for Femoral Head Segmentation from Challenging CT Data

Due to the weak boundary, narrow or even disappeared joint space and varying topology in challenging CT, accurate segmentation of the femur from hip joint is still a difficult task. To address this problem, the proposed method combines anatomical information of relative location of bone tissues and neighboring slices to predict a statistical model for Joint space identification. A novel idea in this paper for separating the femur head from the rest parts is the usage of barrier line, and the characteristic of improved harmonic field make the barrier line smoother and attracts the barrier to boundary of femur more closely, which guarantees the accuracy in segmenting the bone tissues with narrow space. We have evaluated our method on 40 hips including pathologies. The experimental results demonstrate the effectiveness and accuracy of the proposed approach.
Early detection of Alzheimer's disease using histograms in a dissimilarity-based classification framework

Classification methods have been proposed to detect early-stage Alzheimer’s disease using Magnetic Resonance images. In particular, dissimilarity-based classification has been applied using a deformation-based distance measure. However, such approach is not only computationally expensive but it also considers large-scale alterations in the brain only. In this work, we propose the use of image histogram distance measures, determined both globally and locally, to detect very mild to mild Alzheimer’s disease. Using an ensemble of local patches over the entire brain, we obtain an accuracy of 84% (sensitivity 80% and specificity 88%).
Riboflavin-Responsive Multiple Acyl-CoA Dehydrogenase Deficiency Associated with Hepatoencephalomyopathy and White Matter Signal Abnormalities on Brain MRI

Abstract Multiple acyl-CoA dehydrogenase deficiency (MADD) is a rare inborn error of metabolism affecting both fatty acid and amino acid oxidation. It can manifest at any age, but riboflavin-responsiveness has mainly been described in less severely affected patients. We describe an infant with severe MADD presenting with profound hypotonia and hepatomegaly. Treatment with riboflavin improved his muscle strength, liver size, and biochemical markers. A homozygous mutation of electron transfer flavoprotein dehydrogenase (ETFDH) was found. His motor skills continued to progress until a fatal infection-triggered deterioration at the age of 34 months. We show changes in brain magnetic resonance imaging over the course of the disease, with profound white matter abnormalities during the deterioration phase. Aggregates of mitochondria with abnormal cristae in muscle electron microscopy were noticed already in infancy. An unusual lactate dehydrogenase (LDH) isoenzyme pattern with LDH-1 predominance was additionally observed. This case demonstrates riboflavin-responsiveness in a severely affected infant with both muscular and extramuscular involvement and further underlines the variable nature of this disease.
Implementation of five level charging scheme in lithium ion batteries for enabling fast charging in plug-in hybrid electric vehicles

Electrical machine is getting emerged as modern-day propulsion medium in transportation due to its several advantages over conventional internal combustion engine (ICE). The advantages include reduced emissions, less fuel costs, better control and operation. Inspite of the aforementioned advantages, the uses of electrical machine based Plug-in hybrid electric vehicles (PHEVs) are not up to the expected level due to some of its major drawbacks; One of those is high charging time required to charge the battery bank used to drive the electrical motor. Lithium-ion (Li-ion) batteries are one of the potential candidates to be used in PHEV application. With advancement of charging system in the recent time, a fast and safe charging of battery, five level charging method is proposed in few years back. The present work focuses on implementation of the five-level charging scheme for Li-ion battery. A charging system is proposed to implement the charging scheme. Conventional charging scheme and the five-level charging scheme are simulated in PSIM software, and the later scheme is experimentally verified for a 1 Ah, 3.7 V Li-ion battery. A comparison between the two changing methods is also presented.
Promotion of neurological recovery in rat spinal cord injury by mesenchymal stem cells loaded on nerve‐guided collagen scaffold through increasing alternatively activated macrophage polarization

Mesenchymal stem cells (MSCs) are characterized by multidifferentiation and immunoregulatory potential and have been used in the treatment of spinal cord injury (SCI), but direct transplantation may limit effectiveness due to their quick diffusion. The role of macrophages in healing is being increasingly recognized because of their ability to polarize into pro‐ and anti‐inflammatory phenotypes. In the present study, nerve‐guide collagen scaffold (CS) combined with rat MSCs was developed. After CS was confirmed to minimize MSC distribution in vivo by positron emission tomography (PET) imaging, the repair capacity of combined implantation of CS and MSCs and the effect on classically activated macrophage/alternatively activated macrophage (M2) polarization was assessed in a hemisected SCI rat model. In vivo studies showed that, compared to the control group, the rats in the combined implantation group exhibited more significant recovery of nerve function evidenced by the 21‐point Basso–Beattie–Bresnahan score and footprint analysis. Morphological staining showed less macrophage infiltration, apoptosis and glial fibrillary acidic protein, and more neurofilaments, and the fibres were guided to grow through the implant. More M2 were observed in the combined implantation group. The data suggest that the combined implantation could support MSCs to play a protective role of SCI, not only through inhibiting chronic scar formation and providing linear guidance for the nerve, but also benefitting M2 polarization to form an anti‐inflammatory environment. Thus, the combination of biomaterial and MSCs might be a prominent therapeutic treatment for SCI. Copyright © 2016 John Wiley & Sons, Ltd.
Are individuals with loss‐of‐control eating more prone to dietary lapse in behavioural weight loss treatment? An ecological momentary assessment study

OBJECTIVE Individuals with overweight/obesity and loss-of-control eating (LOC) may experience poorer outcomes from behavioural weight loss due to reactivity to internal (e.g., affective and physical) states that impact treatment adherence (e.g., dietary lapses). This study examined (a) whether the presence of LOC increased risk for dietary lapses and (b) the moderating role of LOC on the relation between internal states and dietary lapses. METHOD Individuals (n = 189) with overweight and obesity completed ecological momentary assessment early in behavioural weight loss. RESULTS LOC was positively associated with dietary lapse. LOC did not moderate the relation between momentary changes in internal states and dietary lapses. However, the effect of average levels of internal states on lapses was attenuated for those with LOC. DISCUSSION Results suggest that those with LOC are at higher risk of dietary lapse, whereas elevated average levels of internal states may contribute to early inadherence for those without LOC.
The prospective association between sleep deprivation and depression among adolescents.

STUDY OBJECTIVES To examine the prospective, reciprocal association between sleep deprivation and depression among adolescents. DESIGN A community-based two-wave cohort study. SETTING A metropolitan area with a population of over 4 million. PARTICIPANTS 4,175 youths 11-17 at baseline, and 3,134 of these followed up a year later. MEASUREMENTS Depression is measured using both symptoms of depression and DSM-IV major depression. Sleep deprivation is defined as ≤ 6 h of sleep per night. RESULTS Sleep deprivation at baseline predicted both measures of depression at follow-up, controlling for depression at baseline. Examining the reciprocal association, major depression at baseline, but not symptoms predicted sleep deprivation at follow-up. CONCLUSION These results are the first to document reciprocal effects for major depression and sleep deprivation among adolescents using prospective data. The data suggest reduced quantity of sleep increases risk for major depression, which in turn increases risk for decreased sleep.
On the operational space control of industrial robots using their own joint velocity PI controllers

Operational space control of industrial robots is addressed in this document. We analyze a two-loop hierarchical control with the resolved motion rate controller as outer loop and the joint velocity PI controller as inner loop; the later is the typical internal velocity controller used in industrial robots. We prove, by the first time, that these simple controllers make the solutions of the closed-loop system uniformly ultimately bounded.
Fimbria-Encoding Gene yadC Has a Pleiotropic Effect on Several Biological Characteristics and Plays a Role in Avian Pathogenic Escherichia coli Pathogenicity

ABSTRACT The extraintestinal pathogen termed avian pathogenic Escherichia coli (APEC) is known to cause colibacillosis in chickens. The molecular basis of APEC pathogenesis is not fully elucidated yet. In this work, we deleted a component of the Yad gene cluster (yadC) in order to understand the role of Yad in the pathogenicity of the APEC strain SCI-07. In vitro, the transcription level of yadC was upregulated at 41°C and downregulated at 22°C. The yadC expression in vivo was more pronounced in lungs than in spleen, suggesting a role in the early steps of the infection. Chicks infected with the wild-type and mutant strains presented, respectively, 80% and 50% mortality rates. The ΔyadC strain presented a slightly decreased ability to adhere to HeLa cells with or without the d-mannose analog compared with the wild type. Real-time PCR (RT-PCR) assays showed that fimH was downregulated (P < 0.05) and csgA and ecpA were slightly upregulated in the mutant strain, showing that yadC modulates expression of other fimbriae. Bacterial internalization studies showed that the ΔyadC strain had a lower number of intracellular bacteria recovered from Hep-2 cells and HD11 cells than the wild-type strain (P < 0.05). Motility assays in soft agar demonstrated that the ΔyadC strain was less motile than the wild type (P < 0.01). Curiously, flagellum-associated genes were not dramatically downregulated in the ΔyadC strain. Taken together, the results show that the fimbrial adhesin Yad contributes to the pathogenicity and modulates different biological characteristics of the APEC strain SCI-07.