Miracle-dz/UniFAR-FTUs huggingface dataset:
A neural network method for prediction of ?-turn types in proteins using evolutionary information

MOTIVATION The prediction of beta-turns is an important element of protein secondary structure prediction. Recently, a highly accurate neural network based method Betatpred2 has been developed for predicting beta-turns in proteins using position-specific scoring matrices (PSSM) generated by PSI-BLAST and secondary structure information predicted by PSIPRED. However, the major limitation of Betatpred2 is that it predicts only beta-turn and non-beta-turn residues and does not provide any information of different beta-turn types. Thus, there is a need to predict beta-turn types using an approach based on multiple sequence alignment, which will be useful in overall tertiary structure prediction. RESULTS In the present work, a method has been developed for the prediction of beta-turn types I, II, IV and VIII. For each turn type, two consecutive feed-forward back-propagation networks with a single hidden layer have been used where the first sequence-to-structure network has been trained on single sequences as well as on PSI-BLAST PSSM. The output from the first network along with PSIPRED predicted secondary structure has been used as input for the second-level structure-to-structure network. The networks have been trained and tested on a non-homologous dataset of 426 proteins chains by 7-fold cross-validation. It has been observed that the prediction performance for each turn type is improved significantly by using multiple sequence alignment. The performance has been further improved by using a second level structure-to-structure network and PSIPRED predicted secondary structure information. It has been observed that Type I and II beta-turns have better prediction performance than Type IV and VIII beta-turns. The final network yields an overall accuracy of 74.5, 93.5, 67.9 and 96.5% with MCC values of 0.29, 0.29, 0.23 and 0.02 for Type I, II, IV and VIII beta-turns, respectively, and is better than random prediction. AVAILABILITY A web server for prediction of beta-turn types I, II, IV and VIII based on above approach is available at http://www.imtech. res.in/raghava/betaturns/ and http://bioinformatics.uams. edu/mirror/betaturns/ (mirror site).
microRNAs in Spinal Cord Injury: Potential Roles and Therapeutic Implications

microRNAs (miRNAs) are a novel class of small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. miRNAs can modulate gene expression and thus play important roles in diverse neurobiological processes, such as cell differentiation, growth, proliferation and neural activity, as well as the pathogenic processes of spinal cord injury (SCI) like inflammation, oxidation, demyelination and apoptosis. Results from animal studies have revealed the temporal alterations in the expression of a large set of miRNAs following SCI in adult rats, and the expressional changes in miRNAs following SCI is bidirectional (increase or decrease). In addition, several miRNAs have distinct roles in prognosis of SCI (protective, detrimental and varied). Taken together, the existing evidence suggests that abnormal miRNA expression following SCI contributes to the pathogenesis of SCI, and miRNAs may become potential targets for the therapy of SCI.
Enhancement of Salinity Tolerance during Rice Seed Germination by Presoaking with Hemoglobin

Salinity stress is an important environmental constraint limiting the productivity of many crops worldwide. In this report, experiments were conducted to investigate the effects of seed presoaking by bovine hemoglobin, an inducer of heme oxygenase-1 (HO-1), on salinity tolerance in rice (Oryza sativa) plants. The results showed that different concentrations of the hemoglobin (0.01, 0.05, 0.2, 1.0, and 5.0 g/L) differentially alleviated the inhibition of rice seed germination and thereafter seedling shoot growth caused by 100 mM NaCl stress, and the responses of 1.0 g/L hemoglobin was the most obvious. Further analyses showed that application of hemoglobin not only increased the HO-1 gene expression, but also differentially induced catalase (CAT), ascorbate peroxidase (APX), and superoxide dismutase (SOD) activities or transcripts, thus decreasing the lipid peroxidation in germinating rice seeds subjected to salt stress. Compared with non-hemoglobin treatment, hemoglobin presoaking also increased the potassium (K) to sodium (Na) ratio both in the root and shoot parts after salinity stress. The effect is specific for HO-1 since the potent HO-1 inhibitor zinc protoporphyrin IX (ZnPPIX) blocked the positive actions of hemoglobin on seed germination and seedling shoot growth. Overall, these results suggested that hemoglobin performs an advantageous role in enhancement of salinity tolerance during rice seed germination.
Bilingually Motivated Domain-Adapted Word Segmentation for Statistical Machine Translation

We introduce a word segmentation approach to languages where word boundaries are not orthographically marked, with application to Phrase-Based Statistical Machine Translation (PB-SMT). Instead of using manually segmented monolingual domain-specific corpora to train segmenters, we make use of bilingual corpora and statistical word alignment techniques. First of all, our approach is adapted for the specific translation task at hand by taking the corresponding source (target) language into account. Secondly, this approach does not rely on manually segmented training data so that it can be automatically adapted for different domains. We evaluate the performance of our segmentation approach on PB-SMT tasks from two domains and demonstrate that our approach scores consistently among the best results across different data conditions.
Heterogeneous tissue distribution of a mitochondrial DNA polymorphism in heteroplasmic subjects without mitochondrial disorders

CONTEXT Several maternally inherited point mutations of the mitochondrial genome cause mitochondrial disorders, but the correlation between genotype and phenotype remains obscure in many cases. The same mutation may cause various diseases, probably because of a different tissue distribution. OBJECTIVE To assess the role of random somatic segregation in generating interperson differences by analysis of an apparently neutral polymorphism. DESIGN Screening of 81 brain samples from subjects without mitochondrial disorders and selection of five necropsy cases showing a high level of heteroplasmy for the polymorphism. MAIN OUTCOME MEASURES A proportion of various distinct genotypes in the mtDNA pool of the tissues, identified by fluorescent PCR products, representing a short polycytosine tract of variable length in the mitochondrial displacement loop. RESULTS Differences were found between organs or groups of organs within subjects, pointing towards somatic segregation of mtDNA. In addition, marked differences of this organ distribution occurred between subjects, which cannot be explained by tissue specific selection. CONCLUSIONS The observed interperson differences can be explained by somatic segregation, which occurs randomly at various developmental stages. Besides tissue specific selection, this process might participate in the distribution of pathogenic mtDNA mutations.
The Interpretation of Functional Heads: Using Comparatives to Explore the Mass/Count Distinction

Comparative judgments for mass and count nouns yield two generalizations. First, all words that can be used in both mass and count syntax (e.g., rock, string, apple, water) always denote individuals when used in count syntax but never when used in mass syntax (e.g. too many rocks vs. too much rock). Second, some mass nouns denote individuals (e.g., furniture) while others do not (e.g., water). In this article, we show that no current theory of mass-count semantics can capture these two facts and argue for an alternative theory that can. We propose that lexical roots are not specified as mass or count. Rather, a root becomes a mass noun or count noun by combining with a functional head. Some roots have denotations with individuals while others do not. The count head is interpreted as a function that maps denotations without individuals to those with individuals. The mass head is interpreted as an identity function making the interpretation of a mass noun equivalent to the interpretation of the root. As a result, all count nouns have individuals in their denotation, whereas mass counterparts of count nouns do not. Also, some roots that have individuals in their denotations can be used as mass nouns to denote individuals.
Environmental Determinants of Cardiovascular Diseases Risk Factors: A Qualitative Directed Content Analysis

Background: Cardiovascular diseases (CVDs) are the number one cause of death in the world. In most analyses of health problems, environment plays a significant and modifiable role in causing the problem either directly or indirectly through behavior. Objectives: This study aims to understand the patients and healthcare providers’ experiences about the environmental determinants of CVD risk factors based on the Precede Model. Patients and Methods: This qualitative study conducted over six months in 2012 at Diabetes Units of Health Centers associated with Alborz University of Medical Sciences and Health Services which is located in Karaj, Iran. The data were collected based on individual semi-structured interviews with 50 patients and 12 healthcare providers. Data analysis was performed simultaneous with data collection using the content analysis directed method. Results: Lack of behaviors like stress control, healthy eating and physical activity were the roots of the risk factors for CVD. The environmental factor is one of the barriers for conducting these behaviors. The environmental barriers included of structural environment including “availability and accessibility of health resources”, “new skills”, and “law and policies” which are located in enabling category and social environment including “social support”, “motivation to comply” and “consequences of behavior” which are located in reinforcing category. The most barriers to performing health behaviors were often structural. Conclusions: The environmental factors were barriers for doing healthy behaviors. These factors need to be considered to design health promotion interventions. Policymakers should not only focus on patients’ education but also should provide specific facilities to enhance economic, social and cultural status.
PcrV Immunization Enhances Survival of Burned Pseudomonas aeruginosa-Infected Mice

ABSTRACT Burned Pseudomonas aeruginosa-infected mice immunized against PcrV, a type III virulence system translocating protein, showed significantly enhanced survival compared to controls. Survival was non-O serotype specific and correlated with a reduced systemic microbial load. Infection with a high-level toxin A-producing strain required supplemental antitoxin treatment to enhance survival.
Sulfotransferase gene copy number variation: pharmacogenetics and function

Pharmacogenetics is the study of the role of inheritance in variation to drug response. Drug response phenotypes can vary from adverse drug reactions at one end of the spectrum to equally serious lack of the desired effect of drug therapy at the other. Many of the current important examples of pharmacogenetics involve inherited variation in drug metabolism. Sulfate conjugation catalyzed by cytosolic sulfotransferase (SULT) enzymes, particularly SULT1A1, is a major pathway for drug metabolism in humans. Pharmacogenetic studies of SULT1A1 began over a quarter of a century ago and have advanced from biochemical genetic experiments to include cDNA and gene cloning, gene resequencing, and functional studies of the effects of single nucleotide polymorphisms (SNPs). SNP genotyping, in turn, led to the discovery of functionally important copy number variations (CNVs) in the SULT1A1 gene. This review will briefly describe the evolution of our understanding of SULT1A1 pharmacogenetics and CNV, as well as challenges involved in utilizing both SNP and CNV data in an attempt to predict SULT1A1 function. SULT1A1 represents one example of the potential importance of CNV for the evolving disciplines of pharmacogenetics and pharmacogenomics.
The nature of fault exposure ratio

The fault exposure ratio K is an important factor that controls the per-fault hazard rate, and hence the effectiveness of software testing. The paper examines the variations of K with fault density which declines with testing time. Because faults get harder to find, K should decline if testing is strictly random. However, it is shown that at lower fault densities K tends to increase, suggesting that real testing is more efficient than random testing. Data sets from several different projects are analyzed. Models for the two factors controlling K are suggested, which jointly lead to the logarithmic model. <<ETX>>
Hidden Parameter Markov Decision Processes: A Semiparametric Regression Approach for Discovering Latent Task Parametrizations

Control applications often feature tasks with similar, but not identical, dynamics. We introduce the Hidden Parameter Markov Decision Process (HiP-MDP), a framework that parametrizes a family of related dynamical systems with a low-dimensional set of latent factors, and introduce a semiparametric regression approach for learning its structure from data. We show that a learned HiP-MDP rapidly identifies the dynamics of new task instances in several settings, flexibly adapting to task variation.
Association of Apolipoprotein E4 and Haplotypes of the Apolipoprotein E Gene With Lobar Intracerebral Hemorrhage

Background and Purpose— Conflicting reports in the literature exist with regard to the association of apolipoprotein E (apo E) alleles and lobar intracerebral hemorrhage (ICH). We genotyped 12 single-nucleotide polymorphisms in the 5′ upstream regulatory, exonic, and intronic regions of the apo E gene and performed genotype and haplotype association analyses. Methods— We prospectively enrolled subjects with hemorrhagic stroke and matched them with 2 controls based on age, race, and sex. Each case was reviewed by a physician to determine case status and location of the ICH. Multivariate logistic-regression modeling with backward elimination was used to determine significant risk factors for lobar ICH. Associations at the genotype and haplotype levels and linkage disequilibrium were conducted according to standard statistical methods. Results— Between May 1997 and December 2002, 315 cases of ICH were recruited, of whom 107 were lobar ICH cases matched to 205 controls. No association was found for apo E2, E3, or E4 with nonlobar ICH. Independent, significant risk factors for lobar ICH included apo E4, untreated hypertension, anticoagulant use, a first-degree relative with ICH, and ≤high school education (compared with >high school education). Treated hypercholesterolemia compared with “no history of hypercholesterolemia” was associated with a decreased risk of lobar ICH. Haplotype association analysis demonstrated a significant association of the apo E gene with lobar ICH among whites (P<0.0001) and blacks (P=0.0024). Conclusions— Apo E4 is independently associated with lobar ICH but not nonlobar ICH. Haplotypes of the apo E gene are associated with lobar ICH. Untreated hypertension is a risk factor for lobar ICH.
Wideband LNA Compatible for Differential and Single-Ended Inputs

This letter presents a wideband low-noise amplifier (LNA) that supports both differential and single-ended inputs, while providing differential output. The LNA is implemented in 0.13 mum CMOS technology. For sub-1 GHz wideband applications, this LNA achieves 22.5 dB voltage gain, +1 dBm IIP3, and 2.5 dB NF in the differential receiving mode, while achieving 23 dB voltage gain, -0.5 dBm IIP3, and 2.65 dB NF in the single-ended receiving mode. The LNA core circuit draws 2.5 mA from 1.2 V supply voltage, and occupies a small chip area of 0.06 mm2.
’ s repository of research publications and other research outputs A new efficient similarity metric and generic computation strategy for pattern-based very low bit-rate video coding Conference Item

In the context of very low bit-rate video coding, pattern representations of a moving region (MR) in block-based motion estimation and compensation has become increasingly attractive. Generally, all existing pattern-matching algorithms apply a similarity metric involving elementary operations, to compute the mismatch between a MR and a particular fixed pattern in order to select the best-matching pattern from a fixed-size codebook of predefined patterns. In this paper, an efficient similarity metric together a new generic computation strategy is presented by considering only the mismatch areas of MRs. It is theoretically proven that for a specific MR in a macroblock, the new similarity metric selects exactly the same pattern as existing metrics, while the resulting computational coding efficiency is improved by between 21% and 58% compared with the H.263 low bit-rate coding standard.
CONVERGENCE ACROSS INDUSTRIES AND PROVINCES IN TURKEY

This paper investigates convergence across Turkish provinces between 1975 and 1995. The evidence shows that convergence across Turkish provinces is conditional unlike the absolute convergence pattern found for the regions within the developed nations. Using a fixed effects model it has been shown that estimated steady states differ significantly and the major determinant of the position of the steady states is the initial condition. The paper also investigates the sources of convergence by examining sectoral convergence pattern. It is found that productivity levels and productivity growth vary across sectors and across provinces. Changes in sectoral employment contribute significantly both to productivity growth and convergence at the aggregate level
Modeling of very low frequency motions during RIPEX

Numerical computations are used to explain the presence of very low frequency motions (VLFs), with frequencies less than 0.004 Hz, in the rip current velocity signals observed during the Rip-current field Experiment (RIPEX) field experiment. Observations show that the VLF motions are most intense within the surfzone and then quickly taper off in the offshore direction. By comparing computed VLF intensity (URMS,vlf) distributions in both the cross-shore and alongshore direction with observations in a qualitative sense, the most important contributions to the VLF dynamics are established. VLF motions at neighboring rip-channels are seen to interact in the computations, with stronger surfzone intensity for increasing bathymetric variation. The intermittent forcing by spatially varying wave groups is essential in obtaining the correct URMS,vlf distribution in the cross-shore direction, suggesting this is the predominant mechanism responsible for the generation of the VLF motions observed during RIPEX. Computations also suggest that VLF motions can occasionally propagate offshore but are mostly confined to the surfzone corresponding to surfzone eddies. A quantitative comparison shows good correspondence between model computations and measurements of URMS,vlf with a model skill of O(0.7), with generally increased (decreased) URMS,vlf during mean low (high) water levels.
Linear and curvilinear correlations of brain gray matter volume and density with age using voxel‐based morphometry with the Akaike information criterion in 291 healthy children

We examined linear and curvilinear correlations of gray matter volume and density in cortical and subcortical gray matter with age using magnetic resonance images (MRI) in a large number of healthy children. We applied voxel‐based morphometry (VBM) and region‐of‐interest (ROI) analyses with the Akaike information criterion (AIC), which was used to determine the best‐fit model by selecting which predictor terms should be included. We collected data on brain structural MRI in 291 healthy children aged 5–18 years. Structural MRI data were segmented and normalized using a custom template by applying the diffeomorphic anatomical registration using exponentiated lie algebra (DARTEL) procedure. Next, we analyzed the correlations of gray matter volume and density with age in VBM with AIC by estimating linear, quadratic, and cubic polynomial functions. Several regions such as the prefrontal cortex, the precentral gyrus, and cerebellum showed significant linear or curvilinear correlations between gray matter volume and age on an increasing trajectory, and between gray matter density and age on a decreasing trajectory in VBM and ROI analyses with AIC. Because the trajectory of gray matter volume and density with age suggests the progress of brain maturation, our results may contribute to clarifying brain maturation in healthy children from the viewpoint of brain structure. Hum Brain Mapp, 2013. © 2012 Wiley Periodicals, Inc.
404 not found: the stability and persistence of URLs published in MEDLINE

MOTIVATION The advent of the World Wide Web has enabled unprecedented supplementation of traditional journal publications, allowing access to resources, such as video, sound, software, databases, datasets too large to publish, and even supplementary information and discussion. However, unlike traditional publications, continued availability of these online resources is not guaranteed. An automated survey was conducted to quantify the growth in Uniform Resource Locators (URLs) published to date in MEDLINE abstracts, their current availability and distribution by journal. RESULTS Of 1630 unique URLs identified, formatting and/or spelling errors were detected within 201 (12%) of them as published. After corrections were made, a survey revealed that approximately 63% of these URLs were consistently available, and another 19% were available intermittently. The rate of failure was far worse for anonymous login to FTP sites, with only 12 of 33 sites (36%) responding. This survey also shows that journals vary disproportionately in the number of web citations published, suggesting policy implementation among a few could have a profound impact overall. Out of the 306 journals with a URL published in an abstract, Bioinformatics published the most (12% of total). AVAILABILITY URL database and program available by request.
Causes of eating disorders.

Anorexia nervosa and bulimia nervosa have emerged as the predominant eating disorders. We review the recent research evidence pertaining to the development of these disorders, including sociocultural factors (e.g., media and peer influences), family factors (e.g., enmeshment and criticism), negative affect, low self-esteem, and body dissatisfaction. Also reviewed are cognitive and biological aspects of eating disorders. Some contributory factors appear to be necessary for the appearance of eating disorders, but none is sufficient. Eating disorders may represent a way of coping with problems of identity and personal control.