Miracle-dz/UniFAR-FTUs huggingface dataset:
Bases of motifs for generating repeated patterns with wild cards

Motif inference represents one of the most important areas of research in computational biology, and one of its oldest ones. Despite this, the problem remains very much open in the sense that no existing definition is fully satisfying, either in formal terms, or in relation to the biological questions that involve finding such motifs. Two main types of motifs have been considered in the literature: matrices (of letter frequency per position in the motif) and patterns. There is no conclusive evidence in favor of either, and recent work has attempted to integrate the two types into a single model. In this paper, we address the formal issue in relation to motifs as patterns. This is essential to get at a better understanding of motifs in general. In particular, we consider a promising idea that was recently proposed, which attempted to avoid the combinatorial explosion in the number of motifs by means of a generator set for the motifs. Instead of exhibiting a complete list of motifs satisfying some input constraints, what is produced is a basis of such motifs from which all the other ones can be generated. We study the computational cost of determining such a basis of repeated motifs with wild cards in a sequence. We give new upper and lower bounds on such a cost, introducing a notion of basis that is provably contained in (and, thus, smaller) than previously defined ones. Our basis can be computed in less time and space, and is still able to generate the same set of motifs. We also prove that the number of motifs in all bases defined so far grows exponentially with the quorum, that is, with the minimal number of times a motif must appear in a sequence, something unnoticed in previous work. We show that there is no hope to efficiently compute such bases unless the quorum is fixed.
Ligand Activation of Peroxisome Proliferator–Activated Receptor b / d (PPAR b / d ) Attenuates Carbon Tetrachloride Hepatotoxicity by Downregulating Proinﬂammatory Gene Expression

Peroxisome proliferator–activated receptor (PPAR) b / d –null mice exhibit exacerbated hepatotoxicity in response to administration of carbon tetrachloride (CCl 4 ). To determine whether ligand activation of the receptor protects against chemical toxicity in the liver, wild-type and PPAR b / d -null mice were administered CCl 4 with or without coadministration of the highly speciﬁc PPAR b / d ligand GW0742. Biomarkers of liver toxicity, including serum alanine aminotransferase (ALT) and hepatic tumor necrosis factor (TNF) a mRNA, were signiﬁcantly higher in CCl 4 -treated PPAR b / d -null mice compared to wild-type mice. Hepatic expression of TNF-like weak inducer of apoptosis receptor (TWEAKr) and S100 calcium–binding protein A6 (S100A6/calcyclin), genes involved in nuclear factor kappa B signaling, was higher in the CCl 4 -treated PPAR b / d -null mice compared to wild-type mice. GW0742 treatment resulted in reduced serum ALT concentration and lower expression of CCl 4 -induced TNF- a , S100A6, monocyte chemoattractant protein-1 (MCP1), and TWEAKr in wild-type mice, and these effects were not observed in PPAR b / d -null mice. Expression of TNF- a was higher in PPAR b / d -null primary hepatocytes in response to interleukin-1 b treatment compared to wild-type hepatocytes, but GW0742 did not signiﬁcantly modulate TNF- a expression in hepatocytes from either genotype. While PPAR b / d -null hepatic stellate exhibited higher rates of proliferation compared to wild-type cells, GW0742 did not affect a -smooth muscle actin expression in these cells. Combined, these ﬁndings demonstrate that ligand activation of PPAR b / d protects against chemically induced hepatotoxicity by downregulating expression of proinﬂammatory genes. Hepatocytes and hepatic stellate cells do not appear to directly mediate the inhibitory effects of ligand activation of PPAR b / d in liver, suggesting the involvement of paracrine and autocrine events mediated by hepatic cells.
Sleep indices and eating behaviours in young adults: findings from Project EAT

Abstract Objective To test the associations between sleep indices and eating behaviours in young adults, a group vulnerable to suboptimal sleep. Design Cross-sectional analysis of survey measures of sleep (i.e. time in bed, variability, timing and quality) and dietary patterns (i.e. breakfast skipping, eating at fast-food restaurants, consumption of sports and energy drinks, and sugar-free, sugar-sweetened and caffeinated beverages). Setting Minneapolis/St. Paul metropolitan area of Minnesota (USA). Subjects A total of 1854 respondents (20–30 years, 55·6 % female) from the 2008–2009 survey conducted for the third wave of the population-based Project EAT (Eating and Activity in Teens and Young Adults) study. Results After adjustment for demographic and behavioural covariates in linear regression models, those who went to bed after 00.30 hours consumed 0·3 more servings of sugar-sweetened beverages per day, consumed 1·7 times more energy drinks, skipped breakfast 1·8 more times per week and consumed fast food 0·3 more times per week compared with those who went to bed before 22.30 hours. Reported sleep quality in the lowest (Q1) v. highest (Q3) tertile was associated with more intake of energy drinks (Q3 v. Q1, prevalence ratio, 95 % CI: 1·79, 1·24, 2·34), sports drinks (1·28, 1·00, 1·55) and breakfast skipping (adjusted mean, 95 % CI: Q1: 4·03, 3·81, 4·26; Q3: 3·43, 3·17, 3·69). Time in bed and sleep variability were associated with few eating behaviours. Conclusions Some, but not all, sleep indices were related to problematic eating behaviours. Sleep habits may be important to address in interventions and policies that target improvements in eating patterns and health outcomes.
Different Apathy Profile in Behavioral Variant of Frontotemporal Dementia and Alzheimer's Disease: A Preliminary Investigation

Apathy is one of the most common behavioral symptoms of dementia; it is one of the salient features of behavioral variant of frontotemporal dementia (bvFTD) but is also very frequent in Alzheimer's disease. This preliminary investigation was aimed at assessing the type of apathy-related symptoms in a population of bvFTD and AD subjects showing comparable apathy severity. Each patient underwent a comprehensive neuropsychological assessment; behavioral changes were investigated by the neuropsychiatric inventory (NPI), using the NPI-apathy subscale to detect apathetic symptoms. At univariate analysis, bvFTD subjects showed lack of initiation (χ 2 = 4.602, p = 0.032), reduced emotional output (χ 2 = 6.493, p = 0.008), and reduced interest toward friends and family members (χ 2 = 4.898, p = 0.027), more frequently than AD subjects. BvFTD displayed higher scores than AD on NPI total score (p = 0.005) and on subscales assessing agitation (p = 0.004), disinhibition (p = 0.007) and sleep disturbances (p = 0.025); conversely, AD subjects were more impaired on memory, constructional abilities, and attention. On multivariate logistic regression, reduced emotional output was highly predictive of bvFTD (OR = 18.266; p = 0.008). Our preliminary findings support the hypothesis that apathy is a complex phenomenon, whose clinical expression is conditioned by the site of anatomical damage. Furthermore, apathy profile may help in differentiating bvFTD from AD.
Emerging infectious diseases.

Until 1995, Trichinella pseudospiralis, a nonencapsulating species of the genus Trichinella and the only species that infects both mammals and birds, was not considered a potential pathogen of humans and domestic animals, since it had been detected only in sylvatic animals (raccoon dog, corsac fox, tiger cat, tawny eagle, and rook) in remote regions (Caucasus, Kazakhstan, Tasmania) (1). However, this pathogen has since been detected in wildlife in the United States (2), in domestic and synanthropic animals and humans in Russia (3), and in humans in Thailand (4). In October 1999, a human outbreak of trichinellosis in France was traced to infected wild boar meat. We describe the epidemiologic, clinical, and laboratory investigations that confirmed T. pseudospiralis as the etiologic agent.
Disordered Eating Behaviors and Substance Use in Women: A Comparison of Perceived Adverse Consequences

The study investigated the adverse consequences on varied life domains of dieting, bingeing, vomiting and laxative use and compared them to the adverse consequences of alcohol drinking, tobacco smoking, and marijuana use. Results showed that the percentages of women who reported adverse consequences related to eating disordered behaviors were often comparable, if not higher, than the percentages of women who reported adverse consequences related to their substance use. This is the first study to compare the adverse consequences of disordered eating patterns and substance use behaviors. Results suggest the importance of recognizing the adverse consequences of disordered eating patterns.
Experimental and numerical analysis of short sisal fiber-cement composites produced with recycled matrix

The proper use of renewable or recycled source materials can contribute significantly to reducing the environmental impact of construction industry. In this work, cement-based composites reinforced with natural fibres were developed and their mechanical behaviour was characterised. To ensure the composite sustainability and durability, the ordinary Portland cement matrix was modified by adding metakaolin and the natural aggregate was substituted by 10 and 20% of recycled concrete aggregate. Compression and splitting tensile tests indicated that mechanical strength did not seem to be affected by recycled content. Flat sheets were cast in a self-compacted cement matrix and bending tests were performed to determine the first crack, postpeak strength and cracking behaviour of the composites. The use of short sisal fibre as reinforcement of recycled cement matrices results in a composite with multiple cracking and increment in strength after first crack. The modelling of composites using the finite-element method allowed to determine the tensile stress−strain behaviour of material and to design possible applications of this new sustainable material.
Activation of natural killer cells by hepatitis C virus particles in vitro

Little is known about the ability of hepatitis C virus (HCV) to alter early innate immune responses in infected patients. Previous studies have shown that natural killer (NK) cells are functionally impaired after interaction of recombinant HCV glycoprotein E2 with the co‐stimulatory CD81 molecule in vitro; however, the functional consequences of a prolonged contact of NK cells with HCV particles have remained unclear. We have examined the phenotypes of purified, interleukin‐2‐activated NK cells from healthy donors and HCV genotype 1b patients after culture for 5 days with HCV pseudoparticles (HCVpp) and serum samples containing HCV genotype 1b. NK cells from healthy donors and chronic HCV patients were found to up‐regulate receptors associated with activation (NKp46, NKp44, NKp30, NKG2D), while NK receptors from the killer cell immunoglobulin‐like receptor family (KIR/CD158), predominantly having an inhibitory function, were significantly down‐modulated after culture in the presence of HCV particles compared with control cultures of NK cells. HCV‐infected sera and HCVpp elicited significantly higher secretion of the NK effector lymphokines interferon‐γ and tumour necrosis factor‐α. Furthermore, HCV stimulated the cytotoxic potential of NK cells from normal donors and patients. The enhanced activation of NK cells after prolonged culture with HCVpp or HCV‐containing sera for 5 days suggests that these innate effector cells may play an important role in viral control during early phases of HCV infection.
Novel Crohn Disease Locus Identified by Genome-Wide Association Maps to a Gene Desert on 5p13.1 and Modulates Expression of PTGER4

To identify novel susceptibility loci for Crohn disease (CD), we undertook a genome-wide association study with more than 300,000 SNPs characterized in 547 patients and 928 controls. We found three chromosome regions that provided evidence of disease association with p-values between 10−6 and 10−9. Two of these (IL23R on Chromosome 1 and CARD15 on Chromosome 16) correspond to genes previously reported to be associated with CD. In addition, a 250-kb region of Chromosome 5p13.1 was found to contain multiple markers with strongly suggestive evidence of disease association (including four markers with p < 10−7). We replicated the results for 5p13.1 by studying 1,266 additional CD patients, 559 additional controls, and 428 trios. Significant evidence of association (p < 4 × 10−4) was found in case/control comparisons with the replication data, while associated alleles were over-transmitted to affected offspring (p < 0.05), thus confirming that the 5p13.1 locus contributes to CD susceptibility. The CD-associated 250-kb region was saturated with 111 SNP markers. Haplotype analysis supports a complex locus architecture with multiple variants contributing to disease susceptibility. The novel 5p13.1 CD locus is contained within a 1.25-Mb gene desert. We present evidence that disease-associated alleles correlate with quantitative expression levels of the prostaglandin receptor EP4, PTGER4, the gene that resides closest to the associated region. Our results identify a major new susceptibility locus for CD, and suggest that genetic variants associated with disease risk at this locus could modulate cis-acting regulatory elements of PTGER4.
Downregulation of microRNA-301a inhibited proliferation, migration and invasion of non-small cell lung cancer by directly targeting DLC1

Increasing evidence has indicated that the abnormal expression of microRNAs contributes to tumorigenesis and tumor development. Understanding the roles of microRNAs in non-small cell lung cancer (NSCLC) might provide valuable information for therapeutic strategies in the therapy for patients with NSCLC. In the present study, significant upregulation of microRNA (miR)-301a was observed in NSCLC tissues and cell lines compared with normal adjacent tissues and a normal human bronchial epithelial cell line. The inhibition of miR-301a suppressed proliferation, migration and invasion of NSCLC cells. Functional analyses indicated that DLC1 was a direct target of miR-301a in NSCLC. Inhibiting miR-301a expression decreased DLC1 expression at mRNA and protein levels. Moreover, DLC1 knockdown partially reversed the inhibition of proliferation, migration and invasion induced by miR-301a knockdown in NSCLC cells. Therefore, these findings may provide novel insights into the molecular mechanisms of miR-301a in proliferation, migration and invasion of NSCLC cells. The findings also indicated that miR-301a may act as a novel potential therapeutic target for patients with NSCLC.
Alteration of the Ileal Microbiota of Weanling Piglets by the Growth-Promoting Antibiotic Chlortetracycline

ABSTRACT Antibiotics such as chlortetracycline (CTC) have been used to promote growth of pigs for decades, but concerns over increased antibiotic-resistant infections in humans have prompted the development of alternative strategies. Developing alternatives to antibiotic growth promoters (AGPs) could be informed by information on the mechanisms of growth promotion, notably, how AGPs affect the microbial populations of the gastrointestinal tract. Pigs from three sows were aseptically delivered by cesarean section. Six piglets were distributed to each of two foster mothers until weaning, when piglets were fed a diet with or without 50 mg/kg CTC for 2 weeks. The ileal bacterial microbiota was characterized by using a cultivation-independent approach based on DNA extraction, PCR amplification, cloning, and sequencing of the 16S rRNA gene pool. The ileal and mucosal communities of these growing pigs were dominated by Lactobacillus bacteria, various members of the family Clostridiaceae, and members of the poorly known genus Turicibacter. Overall, CTC treatment resulted in three shifts: a decrease in Lactobacillusjohnsonii, an increase in L. amylovorus, and a decrease in Turicibacter phylotypes. The composition of the microbiota varied considerably between individual pigs, as revealed by shared operational taxonomic units (OTUs) and similarity (SONS) analysis (θYC values). While the observed variation between untreated pigs obscured the possible effect of CTC, ∫-LIBSHUFF and SONS analyses of pooled libraries indicated a significant shift due to CTC in both the lumen and the mucosa, with some OTUs unique to either treated or control ileum. DOTUR analysis revealed little overlap between control and treated communities at the 3% difference level, indicating unique ileal communities in the presence of CTC.
Seed Germination and Dormancy

Seeds are a vital component of the world’s diet. Cereal grains alone, which comprise -90% of all cultivated seeds, contribute up to half of the global per capita energy intake. Not surprisingly then, seed biology is one of the most extensively researched areas in plant physiology. Even in relation to the topics reviewed here, a casual perusal of the Agricola database reveals that well over 5000 publications on seed germination and 700 on seed dormancy have appeared in the last decade. Yet we still cannot answer two fundamental questions: how does the embryo emerge from the seed to complete germination, and how is embryo emergence blocked so that seeds can be maintained in the dormant state? Obviously, with such a large literature on the subject, this review is far from comprehensive. Nevertheless, it provides both an overview of the essential processes that are associated with germination and a description of the possible impediments thereto that may result in dormancy. With the seed, the independence of the next generation of plants begins. The seed, containing the embryo as the new plant in miniature, is structurally and physiologically equipped for its role as a dispersa1 unit and is well provided with food reserves to sustain the growing seedling until it establishes itself as a self-sufficient, autotrophic organism. Because the function of a seed is to establish a new plant, it may seem peculiar that dormancy, an intrinsic block to germination, exists. But it may not be advantageous for a seed to germinate freely, even in seemingly favorable conditions. For example, germination of annuals in the spring allows time for vegetative growth and the subsequent production of offspring, whereas germination in similar conditions in the fall could lead to the demise of the vegetative plant during the winter. Thus, dormancy is an adaptive trait that optimizes the distribution of germination over time in a population of seeds. Seed dormancy is generally an undesirable characteristic in agricultural crops, where rapid germination and growth are required. However, some degree of dormancy is advantageous, at least during seed development. This is particularly true for cereal crops because it prevents germination of grains while still on the ear of the parent plant (preharvest sprouting), a phenomenon that results in major losses to the
Stochastic derivatives for fractional diffusions.

In this paper, we introduce some fundamental notions related to the so-called stochastic derivatives with respect to a given �-fieldQ. In our framework, we recall well-known results about Markov–Wiener diffusions. We then focus mainly on the case where X is a fractional diffusion and where Q is the past, the future or the present of X. We treat some crucial examples and our main result is the existence of stochastic derivatives with respect to the present of X when X solves a stochastic differential equation driven by a fractional Brownian motion with Hurst index H > 1/2. We give explicit formulas. 1. Introduction. There exist various ways to generalize the notion of differentiation on deterministic functions. We may think of fractional derivatives or differentiation in the sense of the theory of distributions. In both cases, we lose a dynamical or geometric interpretation of tangent vectors (velocities, e.g.). In the present work, we seek to construct derivatives on stochastic processes which conserve a dynamical meaning. Our goal is motivated by the stochastic embedding of dynamical systems introduced in [2]. This procedure aims at comprehending the following question: how can we write an equation which contains the dynamical meaning of an initial ordinary differential equation and which extends this dynamical meaning to stochastic processes? We refer to [3] for more details. Unfortunately, for most of the stochastic processes used in physical models, the limit Zt+h −Zt h
Surprisingly Simple Mechanical Behavior of a Complex Embryonic Tissue

Background Previous studies suggest that mechanical feedback could coordinate morphogenetic events in embryos. Furthermore, embryonic tissues have complex structure and composition and undergo large deformations during morphogenesis. Hence we expect highly non-linear and loading-rate dependent tissue mechanical properties in embryos. Methodology/Principal Findings We used micro-aspiration to test whether a simple linear viscoelastic model was sufficient to describe the mechanical behavior of gastrula stage Xenopus laevis embryonic tissue in vivo. We tested whether these embryonic tissues change their mechanical properties in response to mechanical stimuli but found no evidence of changes in the viscoelastic properties of the tissue in response to stress or stress application rate. We used this model to test hypotheses about the pattern of force generation during electrically induced tissue contractions. The dependence of contractions on suction pressure was most consistent with apical tension, and was inconsistent with isotropic contraction. Finally, stiffer clutches generated stronger contractions, suggesting that force generation and stiffness may be coupled in the embryo. Conclusions/Significance The mechanical behavior of a complex, active embryonic tissue can be surprisingly well described by a simple linear viscoelastic model with power law creep compliance, even at high deformations. We found no evidence of mechanical feedback in this system. Together these results show that very simple mechanical models can be useful in describing embryo mechanics.
Convention and Innovation in Social Networks

To depict the mechanisms that have enabled the emergence of semantic meaning, philosophers and researchers particularly access a game-theoretic model: the signaling game. In this article I will argue that this model is also quite appropriate to analyze not only the emergence of semantic meaning, but also semantic change. In other words, signaling games might help to depict mechanisms of language change. For that purpose the signaling game will be i) combined with innovative reinforcement learning and ii) conducted repeatedly as simulation runs in a multi-agent account, where agents are arranged in social network structures: scale-free networks with small-world properties. The results will give a deeper understanding of the role of environmental variables that might promote semantic change or support solidity of semantic conventions.
Effect of Sediment Properties on the Thermal Performance of Submarine HV Cables

The thermal performance of high-voltage submarine cables is controlled by the effectiveness of heat transfer through the sediments in which they are buried. This paper assesses the influence of sediment parameters on this heat transfer using finite-element simulations. Particular attention is paid to the role of convective heat transfer, with a method being developed to define installation scenarios where this may become significant. This paper shows that the permeability is the dominant factor and can have a significant impact on cable temperatures, even though it is typically neglected in conventional models.