Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Detection of Gene Coexpression Domains Showing Linkage to Regions Enriched with Polymorphic Retrotransposons in Recombinant Inbred Mouse Strains

Although gene coexpression domains have been reported in most eukaryotic organisms, data available to date suggest that coexpression rarely concerns more than doublets or triplets of adjacent genes in mammals. Using expression data from hearts of mice from the panel of AxB/BxA recombinant inbred mice, we detected (according to window sizes) 42−53 loci linked to the expression levels of clusters of three or more neighboring genes. These loci thus formed “cis-expression quantitative trait loci (eQTL) clusters” because their position matched that of the genes whose expression was linked to the loci. Compared with matching control regions, genes contained within cis-eQTL clusters showed much greater levels of coexpression. Corresponding regions showed: (1) a greater abundance of polymorphic elements (mostly short interspersed element retrotransposons), and (2) significant enrichment for the motifs of binding sites for various transcription factors, with binding sites for the chromatin-organizing CCCTC-binding factor showing the greatest levels of enrichment in polymorphic short interspersed elements. Similar cis-eQTL clusters also were detected when we used data obtained with several tissues from BxD recombinant inbred mice. In addition to strengthening the evidence for gene expression domains in mammalian genomes, our data suggest a possible mechanism whereby noncoding polymorphisms could affect the coordinate expression of several neighboring genes.
Trust Building in Recommender Agents

Trust has long been regarded as an important factor influencing users’ decision to buy a product in an online shop or to return to the shop for more product information. However, most notions of trust focus on the aspects of benevolence and integrity, and less on competence. Although benefits clearly exist for websites to employ competent recommender agents, the exact nature of these benefits to users’ trusting intentions remains unclear. This paper presents some preliminary results of these issues based on a trust model that we have developed for recommender agents. We describe a carefully constructed survey in an attempt to reveal the relationship between users’ perception of the agent’s trustworthiness based on its competence and consumer trusting intentions, and more importantly, the role of explanation-based recommendation interfaces and their media format on trust promotion.
Will Big Data Close the Missing Heritability Gap?

Modern biobanks that collect genotype-phenotype information from hundreds of thousands of individuals bring unprecedented opportunities for genomic. Despite the important discoveries reported by genome-wide association (GWA) studies, for most traits and diseases the prediction R-squared (R-sq.) achieved with genetic scores remains considerably lower than the trait heritability. Modern biobanks will soon deliver unprecedentedly large biomedical data sets: Will the advent of big data close the gap between the trait heritability and the proportion of variance that can be explained by a genomic predictor? We addressed this question using Bayesian methods and a data analysis approach that produces a surface response relating prediction R-sq. with sample size and model complexity (e.g., number of SNPs). We applied the methodology to data from the interim release of the UK Biobank. Focusing on human height as a model trait and using 80,000 records for model training, we achieved a prediction R-sq. in testing (n = 22,221) of 0.24 (95% C.I.: 0.23–0.25). Our estimates show that prediction R-sq. increases with sample size, reaching an estimated plateau at values that ranged from 0.1 to 0.37 for models using 500 and 50,000 (GWA-selected) SNPs, respectively. Soon much larger data sets will become available. Using the estimated surface response, we forecast that larger sample sizes will lead to further improvements in prediction R-sq. We conclude that big data will lead to a substantial reduction of the gap between trait heritability and the proportion of interindividual differences that can be explained with a genomic predictor. However, even with the power of big data, for complex traits we anticipate that the gap between prediction R-sq. and trait heritability will not be fully closed.
Performance Analysis of Distributed Single Carrier Systems With Distributed Cyclic Delay Diversity

This paper investigates a distributed cyclic delay diversity (CDD) transmission scheme for cyclic-prefixed single carrier systems in non-identically and identically distributed frequency selective fading channels. The distinguishable feature of the proposed scheme lies in providing a transmit diversity gain while reducing the burden of estimating the channel state information, which is a challenging task in distributed and cooperative systems. To effectively use the distributed CDD scheme at the transmitters, two sufficient conditions are derived to eliminate the intersymbol interference at the receiver and leveraged to convert the multi-input single-output channel into a single-input single-output channel. These conditions allow the system to achieve the maximum diversity for frequency selective fading channels at a full rate. To achieve this maximum diversity, a fixed number of CDD transmitters are selected based on the channel conditions, symbol block size, and maximum time dispersion of the channel, and a new two-stage transmission mode is proposed. Based on the distributed CDD and the proposed selection schemes, a new expression for the signal-to-noise ratio at the receiver is obtained with the aid of order statistics, and then closed-form expressions for the outage probability and average symbol error rate (ASER) are derived. As far as the identically distributed frequency selective fading channel model is concerned, the achievable maximum diversity gain is proved, with the aid of asymptotic analysis, to be equal to the product of the total number of transmitters in the system and the number of multipath components. Link-level simulations are also conducted to validate the analytical expressions for outage probability, ASER, and maximum achievable diversity gain.
Principal correlation of PVC melt elongational properties with foam cell morphology

A lab-scale method developed in this work offers new possibilities to polymer foam manufacturers to significantly reduce the number of experiments required on production extruders to optimise PVC foam formulations. Rheotens elongation experiments were applied to analyse PVC foam formulations without a blowing agent with regard to their melt elongational properties such as melt strength and elongation at break. The uni-axial state of deformation represented by these experiments offers an approximation of the melt behaviour in a multi-axial deformation such as foam extrusion. The evaluated foam formulations were foamed on an extruder under identical processing conditions and the resulting cell morphologies were investigated by Scanning Electron Microscopy. Image analysis of the obtained SEM-images confirmed a principal correlation between the melt elongational properties and the foam cell morphology. It appears, that the PVC melt strength mainly influences the mean cell size and the cell size distribution. In addition, the fraction of open cells is decreasing with increasing melt strength.
53BP1 Mediates ATR-Chk1 Signaling and Protects Replication Forks under Conditions of Replication Stress

ABSTRACT Complete replication of the genome is an essential prerequisite for normal cell division, but a variety of factors can block the replisome, triggering replication stress and potentially causing mutation or cell death. The cellular response to replication stress involves recruitment of proteins to stabilize the replication fork and transmit a stress signal to pause the cell cycle and allow fork restart. We find that the ubiquitously expressed DNA damage response factor 53BP1 is required for the normal response to replication stress. Using primary, ex vivo B cells, we showed that a population of 53BP1−/− cells in early S phase is hypersensitive to short-term exposure to three different agents that induce replication stress. 53BP1 localizes to a subset of replication forks following induced replication stress, and an absence of 53BP1 leads to defective ATR-Chk1-p53 signaling and caspase 3-mediated cell death. Nascent replicated DNA additionally undergoes degradation in 53BP1−/− cells. These results show that 53BP1 plays an important role in protecting replication forks during the cellular response to replication stress, in addition to the previously characterized role of 53BP1 in DNA double-strand break repair.
Immunizations and Autism: A Review of the Literature

ABSTRACT: Because of a temporal correlation between the first notable signs and symptoms of autism and the routine childhood vaccination schedule, many parents have become increasingly concerned regarding the possible etiologic role vaccines may play in the development of autism. In particular, some have suggested an association between the Measles-Mumps-Rubella vaccine and autism. Our literature review found very few studies supporting this theory, with the overwhelming majority showing no causal association between the Measles-Mumps-Rubella vaccine and autism. The vaccine preservative thimerosal has alternatively been hypothesized to have a possible causal role in autism. Again, no convincing evidence was found to support this claim, nor for the use of chelation therapy in autism. With decreasing uptake of immunizations in children and the inevitable occurrence of measles outbreaks, it is important that clinicians be aware of the literature concerning vaccinations and autism so that they may have informed discussions with parents and caregivers.
Vitamin D deficiency and low ionized calcium are linked with semen quality and sex steroid levels in infertile men.

STUDY QUESTION Are low vitamin D levels linked with semen quality and sex steroids in infertile men? SUMMARY ANSWER Infertile men with vitamin D deficiency had lower sperm motility, total numbers of motile sperm, Inhibin B, sex-hormone-binding-globulin (SHBG) and testosterone/estradiol ratio, but higher levels of free sex steroids, than infertile men with normal vitamin D levels. WHAT IS KNOWN ALREADY Low vitamin D levels have been associated with decreased sperm motility in healthy men, but a relationship between vitamin D and calcium with semen quality and especially sex steroids has not been sufficiently described in infertile men. STUDY DESIGN, SIZE, DURATION This study comprises baseline characteristics of 1427 infertile men screened from 2011 to 2014 for inclusion in a randomized clinical trial, the Copenhagen-Bone-Gonadal Study. PARTICIPANTS/MATERIALS, SETTING, METHODS In total 1427 infertile men, consecutively referred to our tertiary andrological centre for fertility workup, underwent a physical examination and had semen quality assessed based on two samples and blood analysed for serum testosterone, SHBG, estradiol, inhibin B, luteinizing hormone, follicle-stimulating hormone (FSH), 25-hydroxyvitamin D (25-OHD), ionized calcium (Ca(2+)) and karyotype. There were 179 men excluded due to serious comorbidities or anabolic steroid usage, leaving 1248 patients for analyses. MAIN RESULTS AND THE ROLE OF CHANCE Men with 25-OHD >75 nmol/l had higher sperm motility and 66 and 111% higher total numbers of motile spermatozoa after 45 and 262 min, respectively, than men with 25-OHD <25 nmol/l (all P < 0.05). SHBG levels and testosterone/estradiol ratios were 15 and 14% lower, respectively, while free testosterone and estradiol ratios were 6 and 13% higher, respectively, in men with 25-OHD <25 nmol/l (all P < 0.05). Men with lower Ca(2+) levels had higher progressive sperm motility and inhibin B/FSH ratio but lower testosterone/estradiol ratio (all P < 0.05). LIMITATIONS, REASONS FOR CAUTION All outcomes presented are predefined end-points but inferral of causality is compromised by the descriptive study design. It remains to be shown whether the links between vitamin D, calcium, semen quality and sex steroids in infertile men are causal. WIDER IMPLICATIONS OF THE FINDINGS The associations between vitamin D deficiency and low calcium with semen quality and sex steroids support the existence of a cross-link between regulators of calcium homeostasis and gonadal function in infertile men. STUDY FUNDING/COMPETING INTERESTS This study was supported by the Danish Agency for Science, Technology and Innovation, Hørslev Fonden, Danish Cancer Society and Novo Nordisk Foundation. There are no conflicts of interest. TRIAL REGISTRATION NUMBER NCT01304927. DATE OF TRIAL REGISTRATION 25 February 2011. DATE OF ENROLMENT OF FIRST PATIENT 8 March 2011.
A high-reproducibility and high-accuracy method for automated topic classification

Much of human knowledge sits in large databases of unstructured text. Leveraging this knowledge requires algorithms that extract and record metadata on unstructured text documents. Assigning topics to documents will enable intelligent search, statistical characterization, and meaningful classification. Latent Dirichlet allocation (LDA) is the state-of-the-art in topic classification. Here, we perform a systematic theoretical and numerical analysis that demonstrates that current optimization techniques for LDA often yield results which are not accurate in inferring the most suitable model parameters. Adapting approaches for community detection in networks, we propose a new algorithm which displays high-reproducibility and high-accuracy, and also has high computational efficiency. We apply it to a large set of documents in the English Wikipedia and reveal its hierarchical structure. Our algorithm promises to make "big data" text analysis systems more reliable.
Predictors of adolescent weight status and central obesity in rural South Africa

Abstract Objective To investigate predictors of adolescent obesity in rural South Africa. Design Cross-sectional study. Height, weight and waist circumference were measured using standard procedures. Overweight and obesity in adolescents aged 10–17 years were assessed using the International Obesity Taskforce cut-offs, while the WHO adult cut-offs were used for participants aged 18–20 years. Waist-to-height ratio of >0·5 defined central obesity in those at Tanner stages 3–5. Linear and logistic regression analysis was used to evaluate risk factors. Setting Agincourt sub-district, rural South Africa. Subjects Participants (n 1848) were aged 10–20 years. Results Combined overweight and obesity was higher in girls (15 %) than boys (4 %), as was central obesity (15 % and 2 %, respectively). With regard to overweight/obesity, fourfold higher odds were observed for girls and twofold higher odds were observed for participants from households with the highest socio-economic status (SES). The odds for overweight/obesity were 40 % lower if the household head had not completed secondary level education. For central obesity, the odds increased 10 % for each unit increase in age; girls had sevenfold higher odds v. boys; post-pubertal participants had threefold higher odds v. pubertal participants; those with older mothers aged 50+ years had twofold higher odds v. those whose mothers were aged 35–49 years; those in highest SES households had twofold higher odds v. those in lowest SES households. Conclusions In rural South Africa, adolescent females are most at risk of obesity which increases with age and appears to be associated with higher SES. To intervene effectively, it is essential to understand how household factors influence food choice, diet and exercise.
Associations between meal and snack frequency and overweight and abdominal obesity in US children and adolescents from National Health and Nutrition Examination Survey (NHANES) 2003–2012

Abstract The association between eating frequency (EF) and adiposity in young populations is inconsistent. This cross-sectional study examined associations of EF, meal frequency (MF) and snack frequency (SF) with adiposity measures in US children aged 6–11 years (n 4346) and adolescents aged 12–19 years (n 6338) participating in the National Health and Nutrition Examination Survey 2003–2012. Using data from two 24-h dietary recalls, all eating occasions providing ≥210 kJ of energy were divided into meals or snacks based on contribution to energy intake (≥15 or <15 %), self-report and time (06.00–09.00, 12.00–14.00 and 17.00–20.00 hours or others). When analysed without adjustment for the ratio of reported energy intake:estimated energy requirement (EI:EER), all measures of EF, MF and SF showed inverse or null associations with overweight (BMI≥85th percentile of BMI-for-age) and abdominal obesity (waist circumference≥90th percentile) in both children and adolescents. After adjustment for EI:EER, however, EF and SF, but not MF, showed positive associations in children, irrespective of the definition of meals and snacks. In adolescents, after adjustment for EI:EER, positive associations were observed for EF (abdominal obesity only), SF based on energy contribution and MF based on self-report, whereas there was an inverse association between MF based on energy contribution and overweight. In conclusion, higher SF and EF, but not MF, were associated with higher risks of overweight and abdominal obesity in children, whereas associations varied in adolescents, depending on the definition of meals and snacks. Prospective studies are needed to establish the associations observed here.
The Ring Vortex: Concepts for a Novel Complex Flow Phantom for Medical Imaging

Calibration of medical imaging systems that provide quantitative measures relating to complex physiological flows is challenging. Physical test objects available for the purpose either offer a known simple flow far removed from the complexity of pathology (e.g. parabolic flow in a straight pipe) or complex relevant flows in which the details of the flow behaviour are unknown. This paper presents the ring vortex as a candidate for a complex flow phantom, since it is marked by inherently complex flow features that are controllable, predictable, reproducible and stable. These characteristics are demonstrated by a combination of analytical, numerical (CFD) and experimental methods. Together they provide a consistent perspective on ring vortex behaviour and highlight qualities relevant to phantom design. Discussion of the results indicates that a liquid phantom based on the ring vortex may have merit as a complex flow phantom for multimodal imaging. Furthermore, availability of such a flow reference may also serve as a benchmark for quality assurance of simulation methodologies.
A Benchmarking Environment for Reinforcement Learning Based Task Oriented Dialogue Management

Dialogue assistants are rapidly becoming an indispensable daily aid. To avoid the significant effort needed to hand-craft the required dialogue flow, the Dialogue Management (DM) module can be cast as a continuous Markov Decision Process (MDP) and trained through Reinforcement Learning (RL). Several RL models have been investigated over recent years. However, the lack of a common benchmarking framework makes it difficult to perform a fair comparison between different models and their capability to generalise to different environments. Therefore, this paper proposes a set of challenging simulated environments for dialogue model development and evaluation. To provide some baselines, we investigate a number of representative parametric algorithms, namely deep reinforcement learning algorithms - DQN, A2C and Natural Actor-Critic and compare them to a non-parametric model, GP-SARSA. Both the environments and policy models are implemented using the publicly available PyDial toolkit and released on-line, in order to establish a testbed framework for further experiments and to facilitate experimental reproducibility.
Theory of Solvation-Controlled Reactions in Stimuli-Responsive Nanoreactors

Metallic nanoparticles embedded in stimuli-responsive polymers can be regarded as nanoreactors because their catalytic activity can be changed within wide limits: the physicochemical properties of the polymer network can be tuned and switched by external parameters, for example, temperature or pH, and thus allow a selective control of reactant mobility and concentration close to the reaction site. Combining Debye’s model of diffusion through an energy landscape and a two-state model for the polymer, here we develop an analytical expression for the observed reaction rate constant, kobs. Our formula shows an exponential dependence of this rate on the solvation free-enthalpy change ΔGsol, a quantity that describes the partitioning of the reactant in the network versus bulk. Thus, changes in ΔGsol, and not in the diffusion coefficient, will be the decisive factor affecting the reaction rate in most cases. A comparison with recent experimental data on switchable, thermosensitive nanoreactors demonstrates the.
Real World Use of an Internet Intervention for Pediatric Encopresis

Background The Internet is a significant source of medical information and is now being shown to be an important conduit for delivering various health-related interventions. Objective This paper aimed to examine the utility and impact of an Internet intervention for childhood encopresis as part of standard medical care in a “real world” setting. Methods Patients diagnosed with encopresis were given a Web-based information prescription to use an Internet intervention for pediatric encopresis. A total of 22 families utilized the intervention between July 2004 and June 2006. A chart review and phone interview were undertaken to collect user characteristics; defecation-related information, including frequency of soiling, bowel movements (BMs) in the toilet, and amount of pain associated with defecation; and information on computer/Internet usage. Three questionnaires were used to examine the utility of, impact of, and adherence to the Internet intervention. Program utilization was obtained from a data tracking system that monitored usage in real time. Results Overall, parents rated the Internet intervention as enjoyable, understandable, and easy to use. They indicated that the Internet intervention positively affected their children, decreasing overall accidents and increasing child comfort on the toilet at home. Of the 20 children who initially reported fecal accidents, 19 (95%) experienced at least a 50% improvement, with a reduction of accident frequency from one fecal accident per day to one accident per week. Although it is not clear whether this improvement is directly related to the use of the Internet intervention, patient feedback suggests that the program was an important element, further establishing Internet interventions as a viable and desirable addition to standard medical care for pediatric encopresis. Conclusions To our knowledge, this is the first time a pediatric Internet intervention has been examined as part of a “real world” setting. This is an important step toward establishing Internet interventions as an adjunctive component to treatment of pediatric patients in a clinical setting, particularly given the positive user feedback, possible cost savings, and significant potential for large-scale dissemination.