bluuebunny/crossref_metadata_2025_split huggingface dataset:
PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites
Authors: Panjkovich Alejandro , Daura Xavier 
Published: January 2014

Abstract
Summary: The regulation of protein activity is a key aspect of life at the molecular level. Unveiling its details is thus crucial to understanding signalling and metabolic pathways. The most common and powerful mechanism of protein-function regulation is allostery, which has been increasingly calling the attention of medicinal chemists due to its potential for the discovery of novel therapeutics. In this context, PARS is a simple and fast method that queries protein dynamics and structural conservation to identify pockets on a protein structure that may exert a regulatory effect on the binding of a small-molecule ligand.
Availability: PARS is freely available as a web server at http://bioinf.uab.cat/pars.
Contact: xavier.daura@uab.cat
Supplementary information: Supplementary data are available at Bioinformatics online.
BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution
Authors: Ye Chengxi , Hsiao Chiaowen , Corrada Bravo Héctor 
Published: January 2014

Abstract
Motivation: Base-calling of sequencing data produced by high-throughput sequencing platforms is a fundamental process in current bioinformatics analysis. However, existing third-party probabilistic or machine-learning methods that significantly improve the accuracy of base-calls on these platforms are impractical for production use due to their computational inefficiency.
Results: We directly formulate base-calling as a blind deconvolution problem and implemented BlindCall as an efficient solver to this inverse problem. BlindCall produced base-calls at accuracy comparable to state-of-the-art probabilistic methods while processing data at rates 10 times faster in most cases. The computational complexity of BlindCall scales linearly with read length making it better suited for new long-read sequencing technologies.
Availability and Implementation: BlindCall is implemented as a set of Matlab scripts available for download at http://cbcb.umd.edu/∼hcorrada/secgen.
Contact: hcorrada@umiacs.umd.edu
Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT)
Authors: Durbin Richard 
Published: January 2014

Abstract
Motivation: Over the last few years, methods based on suffix arrays using the Burrows–Wheeler Transform have been widely used for DNA sequence read matching and assembly. These provide very fast search algorithms, linear in the search pattern size, on a highly compressible representation of the dataset being searched. Meanwhile, algorithmic development for genotype data has concentrated on statistical methods for phasing and imputation, based on probabilistic matching to hidden Markov model representations of the reference data, which while powerful are much less computationally efficient. Here a theory of haplotype matching using suffix array ideas is developed, which should scale too much larger datasets than those currently handled by genotype algorithms.
Results: Given M sequences with N bi-allelic variable sites, an O(NM) algorithm to derive a representation of the data based on positional prefix arrays is given, which is termed the positional Burrows–Wheeler transform (PBWT). On large datasets this compresses with run-length encoding by more than a factor of a hundred smaller than using gzip on the raw data. Using this representation a method is given to find all maximal haplotype matches within the set in O(NM) time rather than O(NM2) as expected from naive pairwise comparison, and also a fast algorithm, empirically independent of M given sufficient memory for indexes, to find maximal matches between a new sequence and the set. The discussion includes some proposals about how these approaches could be used for imputation and phasing.
Availability: http://github.com/richarddurbin/pbwt
Contact: richard.durbin@sanger.ac.uk
Standardizing compositional data for stock assessment
Authors: Thorson James T. 
Published: January 2014

Abstract
Stock assessment models frequently integrate abundance index and compositional (e.g. age, length, sex) data. Abundance indices are generally estimated using index standardization models, which provide estimates of index standard errors while accounting for: (i) differences in sampling intensity spatially or over time; (ii) non-independence of available data; and (iii) the effect of covariates. However, compositional data are not generally processed using a standardization model, so effective sample size is not routinely estimated and these three issues are unresolved. I therefore propose a computationally simple “normal approximation” method for standardizing compositional data and compare this with design-based and Dirichlet-multinomial (D-M) methods for analysing compositional data. Using simulated data from a population with multiple spatial strata, heterogeneity within strata, differences in sampling intensity, and additional overdispersion, I show that the normal-approximation method provided unbiased estimates of abundance-at-age and estimates of effective sample size that are consistent with the imprecision of these estimates. A conventional design-based method also produced unbiased age compositions estimates but no estimate of effective sample size. The D-M failed to account for known differences in sampling intensity (the proportion of catch for each fishing trip that is sampled for age) and hence provides biased estimates when sampling intensity is correlated with variation in abundance-at-age data. I end by discussing uses for “composition-standardization models” and propose that future research develop methods to impute compositional data in strata with missing data.
G-Quadruplex binding enantiomers show chiral selective interactions with human telomere
Authors: Wang Jiasi , Chen Yong , Ren Jinsong , Zhao Chuanqi , Qu Xiaogang 
Published: January 2014

Abstract
Chiral recognition of DNA molecules is important because DNA chiral transition and its different conformations are involved in a series of important life events. Among them, polymorphic human telomere DNA has attracted great interests in recent years because of its important roles in chromosome structural integrity. In this report, we examine the short-term effect of chiral metallo-supramolecular complex enantiomers treatment on tumor cells, and find that a zinc-finger-like alpha helical chiral metallo-supramolecular complex, [Ni2L3]4+-P enantiomer (NiP), can selectively provoke the rapid telomere uncapping, trigger DNA damage responses at telomere and degradation of G-overhang and the delocalization of telomeric protein from telomeres. Further studies indicate that NiP can induce an acute cellular apoptosis and senescence in cancer cells rather than normal cells. These results are further evidenced by the upregulation of p21 and p16 proteins. Moreover, NiP can cause translocation of hTERT from nuclear to cytoplasm through Tyr 707 phosphorylation. While its enantiomer, [Ni2L3]4+-M (NiM), has no such mentioned effects, these results clearly demonstrate the compound’s chiral selectivity in cancer cells. Our work will shed light on design of chiral anticancer drugs targeting G-quadruplex DNA, and developing telomere and telomerase modulation agents.
CpG domains downstream of TSSs promote high levels of gene expression
Authors: Krinner Simone , Heitzer Asli P. , Diermeier Sarah D. , Obermeier Ingrid , Längst Gernot , Wagner Ralf 
Published: January 2014

Abstract
CpG dinucleotides are known to play a crucial role in regulatory domains, affecting gene expression in their natural context. Here, we demonstrate that intragenic CpG frequency and distribution impacts transgene and genomic gene expression levels in mammalian cells. As shown for the Macrophage Inflammatory Protein 1α, de novo RNA synthesis correlates with the number of CpG dinucleotides, whereas RNA splicing, stability, nuclear export and translation are not affected by the sequence modification. Differences in chromatin accessibility in vivo and altered nucleosome positioning in vitro suggest that increased CpG levels destabilize the chromatin structure. Moreover, enriched CpG levels correlate with increased RNA polymerase II elongation rates in vivo. Interestingly, elevated CpG levels particularly at the 5′ end of the gene promote efficient transcription. We show that this is a genome-wide feature of highly expressed genes, by identifying a domain of ∼700 bp with high CpG content downstream of the transcription start site, correlating with high levels of transcription. We suggest that these 5′ CpG domains are required to distort the chromatin structure and to increase gene activity.
Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences
Authors: Lippold Sebastian , Xu Hongyang , Ko Albert , Li Mingkun , Renaud Gabriel , Butthof Anne , Schröder Roland , Stoneking Mark 
Published: January 2014

AbstractTo investigate in detail the paternal and maternal demographic histories of humans, we obtained ∼500 kb of non-recombining Y chromosome (NRY) sequences and complete mtDNA genome sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). Our results: confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA; suggest very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations; and indicate that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf. However, we also find substantial differences in patterns of mtDNA vs. NRY variation in different regional groups; thus, global patterns of variation are not necessarily representative of specific geographic regions.
A Hydraulic Model Is Compatible with Rapid Changes in Leaf Elongation under Fluctuating Evaporative Demand and Soil Water Status
Authors: Caldeira Cecilio F. , Bosio Mickael , Parent Boris , Jeanguenin Linda , Chaumont François , Tardieu François 
Published: January 2014

Abstract
Plants are constantly facing rapid changes in evaporative demand and soil water content, which affect their water status and growth. In apparent contradiction to a hydraulic hypothesis, leaf elongation rate (LER) declined in the morning and recovered upon soil rehydration considerably quicker than transpiration rate and leaf water potential (typical half-times of 30 min versus 1–2 h). The morning decline of LER began at very low light and transpiration and closely followed the stomatal opening of leaves receiving direct light, which represent a small fraction of leaf area. A simulation model in maize (Zea mays) suggests that these findings are still compatible with a hydraulic hypothesis. The small water flux linked to stomatal aperture would be sufficient to decrease water potentials of the xylem and growing tissues, thereby causing a rapid decline of simulated LER, while the simulated water potential of mature tissues declines more slowly due to a high hydraulic capacitance. The model also captured growth patterns in the evening or upon soil rehydration. Changes in plant hydraulic conductance partly counteracted those of transpiration. Root hydraulic conductivity increased continuously in the morning, consistent with the transcript abundance of Zea maize Plasma Membrane Intrinsic Protein aquaporins. Transgenic lines underproducing abscisic acid, with lower hydraulic conductivity and higher stomatal conductance, had a LER declining more rapidly than wild-type plants. Whole-genome transcriptome and phosphoproteome analyses suggested that the hydraulic processes proposed here might be associated with other rapidly occurring mechanisms. Overall, the mechanisms and model presented here may be an essential component of drought tolerance in naturally fluctuating evaporative demand and soil moisture.
Reversible basal ganglia lesions in neuropsychiatric lupus: a report of three pediatric cases
Authors: Sato Satoshi , Nakajima Junya , Shimura Masaru , Kawashima Hisashi , Yoshio Taku , Hara Yuko 
Published: January 2014

AbstractAimCentral nervous system involvement represents a serious and common complication of systemiclupus erythematosus (SLE). We describe the characteristics of patients with neuropsychiatric (NP) SLE complicated with reversible basal ganglia lesions.MethodsWe describe the cases of three NPSLE patients.ResultsThey presented with NP manifestations such as headache, cognitive dysfunction, tremors, seizures, and mood disorder. The levels of autoantibodies to NMDA (N‐methyl‐d‐aspartate) receptor antibodies and antiribosomal‐P antibodies were elevated, indicating the presence of an acute phase. Marked elevation of interleukin‐6 in cerebrospinal fluid was noted when these patients showed NP symptoms. Moreover, the patients presented with high‐intensity lesions in the basal ganglia on T2‐weighted images, fluid‐attenuated inversion recovery (FLAIR) images, diffusion‐weighted images (DWI) and apparent diffusion coefficient (ADC) maps. Following immunosuppressive treatment, almost complete improvement of the lesions was noted.ConclusionThe reported cases indicate that reversible vasculopathies represent vasogenic edema localized in basal ganglia lesions and that activation of the autoimmune system and inflammation could lead to NP manifestations in SLE.
The impact of thyroid autoimmunity on arterial stiffness in postmenopausal patients with fibromyalgia
Authors: Cho Kyoung Im , Lee Ji Hyun 
Published: January 2014

AbstractObjectiveThe exact mechanism of arterial stiffness in fibromyalgia (FM) remains unclear. The present study aimed to evaluate the association between thyroid function and markers of arterial function in postmenopausal FM patients.MethodsThis study included 163 postmenopausal FM patients without any known cardiovascular diseases and within a normal reference range of thyroid‐stimulating hormone (TSH) level. Clinical parameters including the Fibromyalgia Impact Questionnaire (FIQ), the pain visual analogical scale (VAS) and tender point counts were measured. Vascular function was assessed by brachial‐ankle pulse wave velocity (baPWV) and flow‐mediated dilation (FMD). We evaluated the associations between arterial markers and serum TSH, free thyroxin, as well as serum thyroidperoxidase autoantibody (TPO Ab).ResultsPatients with a high baPWV (≥ 1490 cm/s) showed more positive TPO Ab (65% vs. 10%, P = 0.006) than those with a normal baPWV. Additionally, the baPWV values of patients with positive TPO Ab were significantly different from those with negative TPO Ab. Age, FIQ and TPO Ab were significantly correlated with baPWV and FMD (all P < 0.05). Multiple linear regression analysis revealed that the only significant predictors of baPWV were age, FIQ and the presence of TPO Ab after adjustment for traditional risk factors. A significant association was also found between FMD and positive TPO Ab.ConclusionAge, functional status and presence of TPO Ab were significantly associated with increased arterial stiffness in postmenopausal FM patients. Given the combined thyroid autoimmunity in FM patients, a re‐evaluation of the effects on the vasculature may be necessary.
Chronic glucocorticoid treatment enhances lipogenic activity in visceral adipocytes of male Wistar rats
Authors: Chimin P. , Farias T. da S. M. , Torres‐Leal F. L. , Bolsoni‐Lopes A. , Campaña A. B. , Andreotti S. , Lima F. B. 
Published: January 2014

AbstractAimGlucocorticoid (GC) in excess promotes the redistribution of adipose tissue from peripheral to central sites of the body. In this study, we characterized an experimental condition of prolonged GC excess and investigated its effect on the lipogenic metabolism in white adipose tissue.MethodsTwenty male Wistar rats were divided into control (CON) and dexamethasone‐treated (DEX) groups. DEX group received dexamethasone (0.25 mg kg−1 day−1) during 4 weeks, while CON group received saline. Animals were killed and subcutaneous (SC), retroperitoneal (RP) and mesenteric (MS) fat pads were excised, weighed and processed for adipocyte isolation, morphometric cell analysis and incorporation of glucose into lipids.ResultsThe treatment effectively blocked hypothalamic–pituitary–adrenal axis, as verified by a 58% decrease in plasma corticosterone levels and 19% atrophy in adrenal glands in DEX group. Animals from DEX group presented insulin resistance, glucose intolerance, dyslipidaemia and increased insulin and leptin plasma levels and hypertrophied adipocytes. They showed increased lipogenesis in RP and MS depots, with increased incorporation of glucose into fatty acids of triacylglycerol. Increased activity of lipogenic enzymes ATP‐citrate lyase, fatty acid synthase, glucose‐6‐phosphate dehydrogenase and malic was only seen in the MS depot in DEX group, while gene expression of these enzymes was enhanced in SC and MS fat depots.ConclusionThe adaptations promoted by GC treatment in adipose metabolism seemed to be mainly due to the increased activity of enzymes that supply the NADPH required for lipogenesis than to the increase in enzymes that more directly deal with fatty acid synthesis itself.
Policy intermediaries and the reform of e‐Education inSouthAfrica
Authors: Vandeyar Thirusellvan 
Published: January 2014

AbstractUtilising a case study approach and backward mapping principles to policy implementation, this study set out to explore how well district and province's e‐learning officials are equipped for the task of implementing the national e‐Education policy. Qualitative methods were employed to capture data through interviews and document analysis. Data were analysed using grounded theory methods. Analyses of e‐learning official's constructions about information and communication technology implementation in schools yielded patterns in their understandings of policy implementation. Findings were fourfold. First, district and provincial e‐learning leaders superficially understood the e‐Education policy, missing policy intent of their role as policy intermediaries. Second, they perceived their role mainly as policy conduits focusing on the dissemination of the policy to schools. Third, the compartmentalisation of directorates performing the same function lacked communication, interaction and coherence. Fourth, district's capacity and lack of competence impacted negatively on their ability to implement policy and support schools. This study suggests that for intermediaries to be effective implementers of policy, they need to become teachers of policy. In order to achieve this, it becomes necessary and crucial for them to participate in the process of policy formulation, appropriation, interpretation and the learning of policy.However much policy makers may have wished the districts to be able to perform what official policy aspired to, the reality is otherwise.
Optimising by response surface methodology the dyeing of polyester with a liposome‐encapsulated disperse dye
Authors: Sadr Dadras Farahnaz , Gharanjig Kamaladin , Raissi Sadigh 
Published: January 2014

Optimisation of conditions for dyeing polyester with liposome‐encapsulated CI Disperse Red 50 was performed using response surface methodology. The effects of temperature, time, and lecithin:dye ratio on the colour strength of dyed fabrics were investigated by a central composite design. The coefficient of determination, the probability value in analysis of variance, and the normality plot of residuals demonstrated sufficient significance of the proposed fitness function. It was found that the temperature and time of the dyeing cycle were effective factors in the dyeing of polyester fabrics with encapsulated dye. It was also established that the colour yield of dyed fabrics was above 25 in the case of a dyeing time of >80 min, a lecithin:dye ratio of ≤2, and a temperature of ca. 128 °C. Comparison of colour strengths produced by liposome‐encapsulated dye and commercial dye revealed that there was approximately the same build‐up on polyester. Dyeings from encapsulated CI Disperse Red 50 exhibited very similar fastness to dyeings from conventional CI Disperse Red 50.
Sequence‐specific procedural learning deficits in children with specific language impairment
Authors: Hsu Hsinjen Julie , Bishop Dorothy V.M. 
Published: January 2014

AbstractThis study tested the procedural deficit hypothesis of specific language impairment (SLI) by comparing children's performance in two motor procedural learning tasks and an implicit verbal sequence learning task. Participants were 7‐ to 11‐year‐old children with SLI (n = 48), typically developing age‐matched children (n = 20) and younger typically developing children matched for receptive grammar (n = 28). In a serial reaction time task, the children with SLI performed at the same level as the grammar‐matched children, but poorer than age‐matched controls in learning motor sequences. When tested with a motor procedural learning task that did not involve learning sequential relationships between discrete elements (i.e. pursuit rotor), the children with SLI performed comparably with age‐matched children and better than younger grammar‐matched controls. In addition, poor implicit learning of word sequences in a verbal memory task (the Hebb effect) was found in the children with SLI. Together, these findings suggest that SLI might be characterized by deficits in learning sequence‐specific information, rather than generally weak procedural learning.
Shared understanding and idiosyncratic expression in early vocabularies
Authors: Mayor Julien , Plunkett Kim 
Published: January 2014

AbstractTo what extent do toddlers have shared vocabularies? We examined CDI data collected from 14,607 infants and toddlers in five countries and measured the amount of variability between individual lexicons during development for both comprehension and production. Early lexicons are highly overlapping. However, beyond 100 words, toddlers share more words with other toddlers in comprehension than in production, even when matched for lexicon sizes. This finding points to a structural difference in early comprehension and production: Toddlers are generalists in comprehension but develop a unique, expressive voice. Variability in production decreases after two years of age, suggesting convergence to a common expressive core vocabulary. We discuss potential exogenous and endogenous contributions to the inverted U‐shaped development observed in young children's expressive lexical variability.