Miracle-dz/UniFAR-FTUs huggingface dataset:
Two distinct ATP‐binding domains are needed to promote protein export by Escherichia coli SecA ATPase

Six putative ATP‐binding motifs of SecA protein were altered by oligonucleotide‐directed mutagenesis to try to define the ATP‐binding regions of this multifunctional protein. The effects of the mutations were analysed by genetic and biochemical assays. The results show that SecA contains two essential ATP‐binding domains. One domain is responsible for high‐affinity ATP binding and contains motifs AO and BO, located at amino acid residues 102‐109 and 198‐210, respectively. A second domain is responsible for low‐affinity ATP binding and contains motifs A3 and a predicted B motif located at amino acid residues 503‐511 and 631‐653, respectively. The ATP‐binding properties of both domains were essential for SecA‐dependent translocation ATPase and in vitro protein translocation activities. The significance of these findings for the mechanism of SecA‐dependent protein translocation is discussed.
PRIME-MD: Its Utility in Detecting Mental Disorders in American Indians

Objective: To examine the utility of using PRIME-MD (Primary Care Evaluation of Mental Disorders) for diagnosing mental disorders in American Indians. Method: One hundred randomly selected, adult, American-Indian patients who receive health care services at an urban Indian Health Service primary care clinic were evaluated for mental disorder by three primary care physicians using the PRIME-MD diagnostic assessment procedure. The main outcome measures were PRIME-MD diagnoses, diagnoses by an independent mental health professional, and treatment/referral decisions. Results: Eighteen percent of the patients had a threshold (met full DSM-IV criteria) PRIME-MD diagnosis, and an additional 17 percent had a subthreshold PRIME-MD diagnosis. The most frequently occurring PRIME-MD diagnoses were: probable alcohol abuse/dependence, major depressive disorder, and generalized anxiety disorder. Over 60 percent of the patients with a PRIME-MD diagnosis who were known “somewhat” or “fairly well” to their physician had not been recognized as having that psychiatric disorder prior to the PRIME-MD assessment. Therapy and/or referral was initiated for nineteen of the twenty-seven patients with a PRIME-MD diagnosis who were not previously receiving treatment. The primary care physicians were able to complete the PRIME-MD evaluations within an average of 7.8 minutes. There was a fair agreement between the PRIME-MD diagnoses and the diagnoses of the mental health professional (kappa = 0.56; overall accuracy rate = 79%). Conclusions: The present study represents the first formal examination of the use of PRIME-MD with American Indians. The results are encouraging. Further studies using PRIME-MD with other urban groups and reservation populations are recommended.
CryoEM structure of Drosophila flight muscle thick filaments at 7 Å resolution

Relaxed thick filaments from Drosophila flight muscle show disordered myosin heads, a ribbon arrangement of myosin tails and a novel protein, stretchin-klp, on the filament surface. Striated muscle thick filaments are composed of myosin II and several non-myosin proteins. Myosin II’s long α-helical coiled-coil tail forms the dense protein backbone of filaments, whereas its N-terminal globular head containing the catalytic and actin-binding activities extends outward from the backbone. Here, we report the structure of thick filaments of the flight muscle of the fruit fly Drosophila melanogaster at 7 Å resolution. Its myosin tails are arranged in curved molecular crystalline layers identical to flight muscles of the giant water bug Lethocerus indicus. Four non-myosin densities are observed, three of which correspond to ones found in Lethocerus; one new density, possibly stretchin-mlck, is found on the backbone outer surface. Surprisingly, the myosin heads are disordered rather than ordered along the filament backbone. Our results show striking myosin tail similarity within flight muscle filaments of two insect orders separated by several hundred million years of evolution.
GIT-GVU-0427 11 / 17 / 04 Tightening : Curvature-Limiting Morphological Simplification

Given a planar set S of arbitrary topology and a radius r , we show how to construct an r -tightening of S , which is a set whose boundary has a radius of curvature everywhere greater than or equal to r and which only differs from S in a morphologically-defined tolerance zone we call the mortar. The mortar consists of the thin or highly curved parts of S , such as corners, gaps, and small connected components, while the boundary of a tightening consists of minimum-length loops through the mortar. Tightenings are defined independently of shape representation, and it may be possible to find them using a variety of algorithms. We describe how to approximately compute tightenings for sets represented as binary images using constrained, level-set curvature flow.
A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb targets

CpG Island promoter genes make up more than half of human genes, and a subset regulated by Polycomb-Repressive Complex 2 (PRC2+-CGI) become DNA methylated and silenced in cancer. Here, we perform a systematic regulatory analysis of CGI genes across TCGA cancer types, finding that PRC2+-CGI genes are frequently prone to transcriptional upregulation as well. These upregulated PRC2+-CGI genes control important pathways such as Epithelial-Mesenchymal Transition and TNFα-associated inflammatory response, and have the greatest cancer-type specificity among any class of CGI genes. Using publicly available chromatin datasets and genetic perturbations, we show that transcription factor binding sites (TFBSs) within distal enhancers underlie transcriptional activation of PRC2+-CGI genes, in contrast to PRC2-free CGI genes which are predominantly regulated by promoter TFBSs. Surprisingly, a large subset of PRC2+-CGI genes that are upregulated in one cancer type are also hypermethylated/silenced in at least one other cancer type, highlighting the high degree of regulatory plasticity likely derived from their complex regulatory patterns during normal development.
A General Strategy to Uncover Transcription Factor Properties Identifies a New Regulator of Drug Resistance in Yeast*

We demonstrate a genomewide approach to determine the physiological role of a putative transcription factor, Ylr266, identified through yeast genome sequencing program. We constructed activated forms of the zinc finger (Zn2Cys6) protein Ylr266, and we analyzed the corresponding transcriptomes with DNA microarrays to characterize the up-regulated genes. The direct target genes of Ylr266 were further identified by in vivo chromatin immunoprecipitation procedure. The functions of the genes directly controlled byYLR266c are in agreement with the observed drug-resistance phenotype of the cell expressing an activated form of Ylr266. These target genes code for ATP-binding cassette or major facilitator superfamily transporters such as PDR15, YOR1, or AZR1 or for other proteins such as SNG1,YJL216c, or YLL056c which are already known to be involved in the yeast pleiotropic drug resistance (PDR) phenomenon. YLR266c could thus be named PDR8. Overlaps with the other PDR networks argue in favor of a new specific role forPDR8 in connection with the well known PDR regulatorsPDR1/PDR3 and YRR1. This strategy to identify the regulatory properties of an anonymous transcription factor is likely to be generalized to all the Zn2Cys6transcription factors from Saccharomyces cerevisiae and related yeasts.
Advances in generator control and automatic synchronization - Eliminating the need for standalone synchronization systems

Flexibility in the control of electric power generation within an industrial facility can be improved through the implementation of technology associated with recent advances in electrical system measurement techniques and communications protocols. While generator speed governing and synchronization technology has remained relatively static in recent years, advancements in generator control, including the ability to eliminate the need for standalone bus synchronization systems, are described in this paper. For such advanced systems, time-synchronized measurement and control of generators are required, using technology such as IEEE C37.118 (synchronized phasor measurements). Time-synchronized measurements implemented in each generator governor controller allow precise control of a power system island or group of islands relative to each other or to a master reference. Accordingly, independent, perpetually synchronized power system islands were tested in a laboratory using time-synchronized governor controllers. The results are documented, and conclusions are drawn regarding the feasibility and usefulness of such technology. Additionally, challenges related to control and synchronization difficulties faced at a variety of industrial facilities are discussed, as well as how this new control technology can help overcome such difficulties.
A parallel computer clusters for convolutional network

Convolution neural network can gain optional solution by training dataset many times. But persons without experiments are very difficult to seek a good learning rate or a good convergence criterion. We propose a framework, which only are composed by many cheap computers, and by improved convolution network to handle this problem. In the framework, we use terminal server to dispatch initial parameter to each calculate unit (computer) and receive their final result. Single unit's collapse will not affect framework's final result, so framework has strong superiority and robustness.
Salamander-like tail regeneration in the West African lungfish

Salamanders, frog tadpoles, and diverse lizards have the remarkable ability to regenerate tails. Paleontological data suggests that this capacity is plesiomorphic, yet when the developmental and genetic architecture of tail regeneration arose is poorly understood. Here we show morphological and molecular hallmarks of tetrapod tail regeneration in the West African lungfish Protopterus annectens, a living representative of the sister group of tetrapods. As in salamanders, lungfish tail regeneration occurs via formation of a proliferative blastema and restores original structures, including muscle, skeleton and spinal cord. In contrast to lizards and similar to salamanders and frogs, lungfish regenerate spinal cord neurons and reconstitute dorsoventral patterning of the tail. Similar to salamander and frog tadpoles, Shh is required for lungfish tail regeneration. Through RNA-seq analysis of uninjured and regenerating tail blastema, we show that the genetic program deployed during lungfish tail regeneration maintains extensive overlap with that of tetrapods, with the upregulation of genes and signaling pathways previously implicated in amphibian and lizard tail regeneration. Furthermore, the lungfish tail blastema showed marked upregulation of genes encoding post-transcriptional RNA processing components and transposon-derived genes. Our results show that developmental processes and genetic program of tetrapod tail regeneration were present at least near the base of the sarcopterygian clade and establish the lungfish as a valuable research system for regenerative biology.
The e-Visibility Maturity Model - Assessing Stages of Visibility Evolution for e-Business

This paper suggests a model to measure e-visibility — the e-Visibility Maturity Model (e-VM model) that is used to assess the visibility of a company or set of companies in the global e-business market. The visibility is measured using company's involvement in electronic interactions with customers that is externalized by the integration of the Social Software (SoS) in its other means of online presence. This approach allows evaluating company's adaptation to the challenges of the social web and scaling the evaluation to industry or country level. The evaluation of the maturity can be completed based on external presentation, i.e., the website, of the company allowing an efficient evaluation process. The suggested maturity model for assessing e-visibility is based on related work in the area of maturity assessment in e-business. Its application is illustrated in a case where the e-VM for specific countries across industries is assessed, based on a sample of 1600 enterprises from four countries.
Risk of dementia in Parkinson’s disease

Objective: To calculate the incidence of and determine possible risk factors for dementia in PD. Background: Dementia has important clinical consequences for patients with PD and their caregivers, but the incidence is unknown. Methods: A population-based cohort of nondemented patients with PD (n = 171) from the county of Rogaland, Norway, was assessed at baseline and 4.2 years later with a comprehensive evaluation of motor, cognitive, and neuropsychiatric symptoms. The diagnosis of dementia was made according to the Diagnostic and Statistical Manual of Mental Disorders, 3rd edition, revised (DSM-III-R) criteria, based on interview of the patient and a caregiver, cognitive rating scales, and neuropsychologic tests. A representative sample of 3,062 nondemented elderly subjects without PD served as control group. Results: Forty-three patients with PD were demented at follow-up evaluation, equivalent to an incidence rate of 95.3 per 1,000 person-years (95% CI, 68.2 to 122.0). The risk for the development of dementia in patients with PD relative to the control subjects after adjusting for age, sex, and education was 5.9 (95% CI, 3.9 to 9.1). Predictive factors at baseline for dementia in PD in addition to age were Hoehn & Yahr score >2 (OR, 3.4; 95% CI, 1.3 to 8.6) and Mini-Mental State Examination score <29 (OR, 3.3; 95% CI, 1.3 to 8.2). Conclusions: Patients with PD have an almost sixfold increased risk for becoming demented compared with subjects without PD.
Temperature-Dependent Parasitic Relationship between Legionella pneumophila and a Free-Living Amoeba (Acanthamoeba castellanii)

ABSTRACT We analyzed the effects of temperature on the interaction of Legionella pneumophila with Acanthamoeba castellanii. At <20°C, overexpression of type 1 metacaspase, a stimulator of A. castellanii encystation, was associated with a reduced number of bacteria within amoeba. At low temperatures, A. castellanii seems to eliminate L. pneumophila by encystation and digestion.
Influence of nucleotide modifications at the C2’ position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA

Abstract Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2′-deoxyribose, 2′-O-methyl-ribose, 2′-deoxy-2′-fluoro-ribose, arabinose and 2′-deoxy-2′-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2’ modifications gave a variety of effects. Arabinose and 2′-deoxy-2′-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2′-O-methyl and 2′-deoxy-2′-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability.
The minimum number of scanning windows required for effective maximum likelihood estimation of image texture parameters and additive noise variance

In this paper, we dealt with the problem of noise variance estimation from additive mixture of the noise and an underlying image texture. Assuming fBm-model for image texture, the number Me(H,SNR)of SWs has been obtained such that statistical efficiency e of the previously designed ML noise variance estimator is close to a predefined level e = 0.9. The value Me defines a boundary between asymptotic and non-asymptotic modes of the ML estimator with respect to image fragment size (number of SWs available). For fixed SNR, Me takes minimum values for smooth textures ( H close to 0.8) and increases fast as H approaches 0. As a function of SNR, Me has minimum at approximately SNR = 1.5 and increases fast as SNR deviates from this value. These results are useful for establishing the area of applicability of noise variance estimators and to assure the quality of estimates obtained from an image texture of a given size, roughness and SNR.
Response of satellite cells to focal skeletal muscle injury

The time course and pattern of the initiation of satellite cell mitoses was studied following a crush injury of the distal third of the 30‐day‐old rat extensor digitorum longus, a muscle in which myofibers run the entire length of the belly. Satellite cell mitotic activity was monitored using autoradiography after injection of 3H‐thymidine. Satellite cell labeling rose above control values by 15 hours post injury at the injured site and by 20 hours in the middle third or adjacent undamaged portion of the muscle. Labeling decreased in the proximal third of the muscle, so that by 25 hours post injury, a gradient of labeling was established along the muscle length. Electron microscopy (EM) quantitation showed that the reduced labeling in the proximal third resulted from a reduction in satellite cell numbers. The results suggest that mitotic activity of satelite cells after localized injury occurs mainly at or near the site of injury, but that many of the dividing cells have migrated from undamaged areas distant from the lesion site.
Determinants of risk behavior for human immunodeficiency virus/acquired immunodeficiency syndrome in people with severe mental illness.

We examined the prevalence and correlates of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) risk behaviors in a large sample of severely mentally ill (SMI) patients. Risk levels were correlated with demographic factors, diagnosis, symptom severity, trauma history, post-traumatic stress disorder (PTSD), substance use disorder (SUD), and sexual orientation. SMI clients from urban and rural settings (N = 275) were assessed regarding HIV/AIDS risk behaviors, and hypothesized risk factors. Patients exhibited substantial levels of risky behavior, particularly sexual risk. Correlates of increased risk included SUD, trauma, male homosexual orientation, younger age, and symptom severity. Structural equation modeling identified SUD and sexual orientation as the primary determinants of both drug and sexual risk behavior. We conclude that specific illness related variables appear to have less impact on risk behavior among people with SMI than previously hypothesized. Substance abuse prevention and treatment may be the most effective means of reducing HIV risk in this population.
Robust 3-d Object Detection and Feature Extraction for Multi-Robot Cooperation

This paper develops a computer vision system for multi-robot cooperation in rescue operations. The work is focused on providing robust and fast vision capabilities to the robots to meet the expected level of performance. Enhanced versions of existing techniques and new techniques are utilized to develop an adaptive vision system architecture for use in an unstructured environment of multi-robot activity in an emergency scenario. Different types of object detection methods are selected in real time in the developed system according to the requirements of a robot. To validate the developed system for use in a multi-robot application, rigorous experiments are conducted in a typical unstructured environment. Features such as invariance of scale, rotation, illumination, and occlusion are tested with different types of objects, for various methods. Generally, good results are obtained.
Effect of Training on Antioxidant Capacity, Tissue Damage, and Endurance of Adult Male Rats

We studied the effects of physical training on antioxidant defences and susceptibility to damage induced by exhaustive exercise in tissues of adult (12 mo) rats. Therefore, untrained animals were sacrificed either at rest (n = 8) or immediately after swimming to exhaustion (n = 8). Rats trained to swim for 10 weeks were also sacrificed, 48 hr after the last exercise, either at rest (n = 8) or after exhaustive swimming (n = 8). Integrity of mitochondria and sarcoplasmic (SR) or endoplasmic (ER) reticulum of liver, heart, and muscle was assessed by measuring mitochondrial respiratory control and latency of alkaline phosphatase activity. Lipid peroxidation was measured by determination of malondialdehyde and hydroperoxides. Additionally, the effect of training on tissue antioxidant systems was examined by determining the glutathione peroxidase (GPX) and glutathione reductase (GR) activity and the overall antioxidant capacity (CA). Membrane integrity was unaffected by training in liver and muscle, and improved in heart of at rest animals, whereas lipid peroxidation was reduced in both liver and heart. Glutathione peroxidase and glutathione reductase activity, and overall antioxidant capacity were increased (p < 0.05) by training in liver and muscle. In heart, antioxidant capacity was increased from 0.21+/-0.01 to 0.33+/-0.02 (p<0.05), but glutathione peroxidase activity remained unchanged (p>0.05), and glutathione reductase activity was decreased from 3.56+/-0.08 to 2.27+/-0.10 micromol x min(-1) x g(-1) (p < 0.05). The exhaustive exercise gave rise to tissue damage irrespective of trained state, as documented by similar loss of SR and ER integrity, and increase (p<0.05) in lipid peroxidation found in exhausted trained and untrained rats. However, the above changes were elicited by exercise of greater duration in trained than in untrained rats (340+/-17 min and 233+/-6 min, respectively). These findings support the view that free radical-induced damage in muscle could be one of the factors involved in muscle fatigue. If so, the increased endurance in trained rats should reflect lengthening of the time required for the oxidative processes to sufficiently impair cell functions so as to make further exercise impossible.
Are individual differences in speech reception related to individual differences in cognitive ability? A survey of twenty experimental studies with normal and hearing-impaired adults

This paper summarizes twenty studies, published since 1989, that have measured experimentally the relationship between speech recognition in noise and some aspect of cognition, using statistical techniques such as correlation or factor analysis. The results demonstrate that there is a link, but it is secondary to the predictive effects of hearing loss, and it is somewhat mixed across study. No one cognitive test always gave a significant result, but measures of working memory (especially reading span) were mostly effective, whereas measures of general ability, such as IQ, were mostly ineffective. Some of the studies included aided listening, and two reported the benefits from aided listening: again mixed results were found, and in some circumstances cognition was a useful predictor of hearing-aid benefit.