Miracle-dz/UniFAR-FTUs huggingface dataset:
Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

Gene set analysis (GSA) is used to elucidate genome-wide data, in particular transcriptome data. A multitude of methods have been proposed for this step of the analysis, and many of them have been compared and evaluated. Unfortunately, there is no consolidated opinion regarding what methods should be preferred, and the variety of available GSA software and implementations pose a difficulty for the end-user who wants to try out different methods. To address this, we have developed the R package Piano that collects a range of GSA methods into the same system, for the benefit of the end-user. Further on we refine the GSA workflow by using modifications of the gene-level statistics. This enables us to divide the resulting gene set P-values into three classes, describing different aspects of gene expression directionality at gene set level. We use our fully implemented workflow to investigate the impact of the individual components of GSA by using microarray and RNA-seq data. The results show that the evaluated methods are globally similar and the major separation correlates well with our defined directionality classes. As a consequence of this, we suggest to use a consensus scoring approach, based on multiple GSA runs. In combination with the directionality classes, this constitutes a more thorough basis for an enriched biological interpretation.
Socioeconomic and lifestyle determinants of obesity in a transitional southeast European population.

OBJECTIVE We aimed to assess the prevalence and socioeconomic and behavioral correlates of obesity in adult population of Albania, a transitional country in the western Balkans. METHODS A cross-sectional study was conducted in 2007-2009 in the Albanian capital, including a sex-stratified random sample of 997 Tirana residents aged 25-65 years (83% response). A structured interview included data on demographic and socioeconomic characteristics and lifestyle factors. Physical examination included measurement of height, weight, and hips and waist circumferences. Binary logistic regression was used to assess the association of obesity with covariates. RESULTS Half of participants were overweight, and about 30% were obese (36% women and 24% men). Obesity was positively associated with age, but inversely related to education and economic level. Almost every day drinkers were more likely to be obese compared to non-drinkers (OR = 2.2, 95% CI = 1.4-2.9). Fat and carbohydrate intake were both positively associated with obesity (for fat intake OR [low-moderate vs. high intake] = 3.1, 95% CI = 2.0-4.2) and for carbohydrate intake OR [low-moderate vs. high intake] = 2.8; 95% CI = 1.9-3.3). CONCLUSIONS Our findings indicate that overweight and obesity pose serious public health concerns in this post-communist country. Health professionals and policy makers should focus particularly on the modifiable risk factors as an effective means of controlling the burden of obesity in Albania.
TRF1 negotiates TTAGGG repeat-associated replication problems by recruiting the BLM helicase and the TPP1/POT1 repressor of ATR signaling

The semiconservative replication of telomeres is facilitated by the shelterin component TRF1. Zimmermann et al. establish that TRF1 binds BLM to facilitate lagging but not leading strand telomeric DNA synthesis. TRF1 also deploys TIN2 and the TPP1/POT1 heterodimers in shelterin to prevent ATR during telomere replication and repress the accompanying sister telomere associations.
A step towards refining prognostication in individual patients with bladder cancer

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Efficacy and safety of orally disintegrating tamsulosin tablets in Taiwanese patients with benign prostatic hyperplasia

Objectives: Tamsulosin is an alpha-1 adrenoceptor antagonist applied in treating lower urinary tract symptoms (LUTS) suggestive of benign prostatic hyperplasia (BPH). This study aimed to evaluate safety, efficacy and acceptance of newly formulated orally disintegrating tamsulosin tablets in Taiwanese patients with LUTS/BPH. Methods: This single center, non-comparative, observational study enrolled 45 male patients over age 50 years. All patients received 0.2 mg tamsulosin orally disintegrating tablets daily and were evaluated at weeks 0, 4, 8, 12 of the 12-week treatment period. Tamsulosin efficacy was evaluated by International Prostate Symptom Score (I-PSS) with 7 questions on urinary symptoms and one disease-specific quality-of-life question, with scores ranging from 0 (no symptoms) to 35 (highly symptomatic). Maximum flow rate (ml/s), voided volume (ml), flow time (s), and mean flow rate (ml/s) were measured. Danish prostatic symptom sexual function scale rated severity and associated concerns of erection quality, ejaculatory function and pain/discomfort were also assessed. Results: Patients’ mean ± SD age was 62.47 ± 7.77 (range: 50–89) and mean ± SD I-PSS was 13.98 ± 5.50. Statistically significant changes from baseline were found in post-test I-PSS and quality of life (both P < 0.001). Mean ± SD I-PSS decreased from 14.30 ± 9.34 to 6.73 ± 0.88 at patients’ final visit. Statistically significant increases in mean maximum flow rate and mean flow rate were found over 12-week study period (P < 0.05). No adverse events were reported. No significant differences were found in pulse, SBP/DBP or sexual function. Conclusion: Orally disintegrating tamsulosin tablets demonstrate acceptable safety and efficacy for acceptance and well tolerance by Taiwanese LUTS/BPH patients.
Creutzfeldt-Jakob disease and related transmissible spongiform encephalopathies.

Until 30 years ago, Creutzfeldt–Jakob disease was an obscure form of dementia unknown to most physicians. The name is now familiar to the medical community as the major transmissible spongiform encephalopathy (or prion disease) in humans and to research scientists because of its strange causative agent with novel modes of replication and transmission. Furthermore, the term “Creutzfeldt–Jakob disease” has caused distress to patients who have been notified that they may have received tainted blood or blood products, and it has been popularized by extensive media coverage of bovine spongiform encephalopathy (“mad cow disease”), with its profound economic impact in Europe .
Cyclopean Tilt Aftereffects Can Be Induced Monocularly: Is There a Purely Binocular Process?

A series of experiments have been reported by Wolfe and Held which they have taken as evidence for the existence of more than one binocular process in human vision, specifically a simple binocular process (OR-gate) and a purely binocular process (AND-gate). In one of their studies, it was shown that tilt aftereffects induced with cyclopean stimuli produced measurable effects only when testing was binocular, which suggested that cyclopean adaptation affects only the AND-gate mechanism. If the two alleged mechanisms (AND or OR) are independent, monocular adaptation with luminance contrast stimuli should produce aftereffects which can only be measured with luminance contrast test stimuli. Cyclopean test displays would probe only the unadapted AND-mechanism. Results to the contrary are reported, casting doubt upon the functional independence, perhaps even the existence, of the so-called purely binocular process.
A STUDY OF DUST AND GAS AT MARS FROM COMET C/2013 A1 (SIDING SPRING)

Although the nucleus of comet C/2013 A1 (Siding Spring) will safely pass Mars in 2014 October, the dust in the coma and tail will more closely approach the planet. Using a dynamical model of comet dust, we estimate the impact fluence. Based on our nominal model no impacts are expected at Mars. Relaxing our nominal model's parameters, the fluence is no greater than ∼10−7 grains m−2 for grain radii larger than 10 μm. Mars-orbiting spacecraft are unlikely to be impacted by large dust grains, but Mars may receive as many as ∼107 grains, or ∼100 kg of total dust. We also estimate the flux of impacting gas molecules commonly observed in comet comae.
Expert recommender systems in practice: evaluating semi-automatic profile generation

Expert recommender systems (ERS) are considered a promising technology in knowledge management. However, there are very few studies which evaluated their appropriation in practice. In this paper, we present results of a case study of expert recommender technology in a large European industrial association. Unlike existing expert recommender approaches, the system involves users in selecting textual documents for semi-automatic profile generation. Our study focuses on the appropriation of this functionality and discusses impacts from an organizational perspective.
Verifying equivalence of memories using a first order logic theorem prover

We propose a new method for equivalence checking of RTL and schematic descriptions of memories using translation into first-order logic. Our method is based on a powerful abstraction of memories and address decoders within them. We propose two ways of axiomatizing some of the bit-vector operations, decoders, and memories. The first axiomatization uses an algebra of operations on bit-vectors. The second axiomatization considers a bit-vector as a unary relation and memory as a relation of larger arity. For some designs, including real-life designs, the second axiomatization results in a first-order problem falling into a known decidable fragment of first-order logic and suitable for solving by modern first-order provers. Equivalence of real-life memories can be verified in seconds with our approach.
Clinical Behaviour of Prostatic Specific Antigen and Prostatic Acid Phosphatase: A Comparative Study

We assayed prostatic specific antigen (PSA) and prostatic acid phosphatase (PAP) serum levels in 1383 patients using a double antibody radioimmunoassay (RIA) I125. Establishing the upper normal limit in 10 ng/ml PSA and 2.5 ng/ml for PAP, the false positive results were only 1.9 and 5.1 percent in men with non-prostatic benign or malignant pathology and respectively 0 and 2.2 percent in women. We detected false positive levels for these two tumoral markers in 3.5 and 4.7 percent of patients with non-complicated benign prostatic hypertrophy, 64.8 and 19.2 percent in complicated benign prostatic hypertrophy, 24 and 16 percent in acute prostatitis and 3.3 percent in chronic prostatitis. The sensitivity in patients with prostate cancer was 87.2 percent for PSA and 64.1 percent for PAP, and there was a better correlation with PSA than PAP for tumoral spread and histological grading. Finally, clinical efficacy was higher with PSA and was no better when both markers were assayed.
Narcolepsy: a review

Narcolepsy is a lifelong sleep disorder characterized by a classic tetrad of excessive daytime sleepiness with irresistible sleep attacks, cataplexy (sudden bilateral loss of muscle tone), hypnagogic hallucination, and sleep paralysis. There are two distinct groups of patients, ie, those having narcolepsy with cataplexy and those having narcolepsy without cataplexy. Narcolepsy affects 0.05% of the population. It has a negative effect on the quality of life of its sufferers and can restrict them from certain careers and activities. There have been advances in the understanding of the pathogenesis of narcolepsy. It is thought that narcolepsy with cataplexy is secondary to loss of hypothalamic hypocretin neurons in those genetically predisposed to the disorder by possession of human leukocyte antigen DQB1*0602. The diagnostic criteria for narcolepsy are based on symptoms, laboratory sleep tests, and serum levels of hypocretin. There is no cure for narcolepsy, and the present mainstay of treatment is pharmacological treatment along with lifestyle changes. Some novel treatments are also being developed and tried. This article critically appraises the evidence for diagnosis and treatment of narcolepsy.
Circulating anticoagulant to factor 8 associated with rheumatoid arthritis.

which are often used to illustrate this type of data, give disproportionately large values in subjects with a low initial F.E. V.1 and must be corrected to the normal distribution if used for analysis-for example, by a logit transformation (Oldham, 1968). A simple alternative method, which has been used here, is to consider only the actual changes in F.E. V.1. Neither method is entirely satisfactory, since they cannot allow for variation due to the interesting relation between the severity of the asthma and the degree of response obtainable from the use of bronchodilator aerosols (Hume and Gandevia, 1957; Hume and Rhys Jones, 1961). These results suggest that the aerosol administration of a naturally occurring substance, prostaglandin E, can cause a substantial reduction in airways obstruction in asthmatic subjects. It is probable that this action of PGE1 is not mediated through the stimulation of sympathetic a-receptors. The relation of the prostaglandins to the function of respiratory smooth muscle obviously merits further investigation.
What Drives ICT Diffusion in Developing Countries? Evidence from Paraguay

The diffusion of Information and Communication Technologies (ICTs) has been identified by international policy-makers and schol ars as an important driver for economic development. In this perspective, research on the determinants of technology adoption appears particularly relevant. However, while the empirical literature on ICT adoption in workplace is relative ly abundant, few studies have been elaborated on their penetration in households. Addi tionally, academic work has focused on industrialized countries and it is still missing a comprehensive analysis on developing world. In this paper we contribute to fill this gap, evaluating the main socio-economic determinants of the presence of computer and Internet connection in Paraguayan households. Non-parametric statistics sh ow that Paraguay has relatively low levels of ICT penetration. Moreover, technology diffusion follows a heterogeneous pattern, reflecting pre-existing ineq ualities in other socio-economic dimensions. Econometrically, we model the probability that a ho usehold has or has not adopted computer technologies and Internet acce ss. The results confirm that conventional variables such as income and education are key determinants of ICT diffusion, but there is also evidence of the presen ce of geographical network effects and of complementarities between Internet use at di fferent locations.
How to teach digital library data to swim into research

Virtual research environments (VREs) aim to enhance research practice and have been identified as drivers for changes in libraries. This paper argues that VREs in combination with Semantic Web technologies offer a range of possibilities to align research with library practices. This main claim of the article is exemplified by a metadata integration process of bibliographic data from libraries to a VRE which is based on Semantic MediaWiki. The integration process rests on three pillars: MediaWiki as a web-based repository, Semantic MediaWiki annotation mechanisms, and semi-automatic workflow management for the integration of digital resources. Thereby, needs of scholarly research practices and capacities for interactions are taken into account. The integration process is part of the design of Semantic MediaWiki for Collaborative Corpora Analysis (SMW-CorA) which uses a concrete research project in the history of education as a reference point for an infrastructural distribution. Semantic MediaWiki thus provides a light-weight environment offering a framework for re-using heterogeneous resources and a flexible collaborative way of conducting research.
A New Method to Estimate Ligand-Receptor Energetics*

In the discovery of new drugs, lead identification and optimization have assumed critical importance given the number of drug targets generated from genetic, genomics, and proteomic technologies. High-throughput experimental screening assays have been complemented recently by “virtual screening” approaches to identify and filter potential ligands when the characteristics of a target receptor structure of interest are known. Virtual screening mandates a reliable procedure for automatic ranking of structurally distinct ligands in compound library databases. Computing a rank score requires the accurate prediction of binding affinities between these ligands and the target. Many current scoring strategies require information about the target three-dimensional structure. In this study, a new method to estimate the free binding energy between a ligand and receptor is proposed. We extend a central idea previously reported (Bock, J. R., and Gough, D. A. (2001) Predicting protein-protein interactions from primary structure. Bioinformatics 17, 455–460; Bock, J. R. , and Gough, D. A. (2002) Whole-proteome interaction mining. Bioinformatics, in press) that uses simple descriptors to represent biomolecules as input examples to train a support vector machine (Smola, A. J., and Schölkopf, B. (1998) A Tutorial on Support Vector Regression, NeuroCOLT Technical Report NC-TR-98-030, Royal Holloway College, University of London, UK) and the application of the trained system to previously unseen pairs, estimating their propensity for interaction. Here we seek to learn the function that maps features of a receptor-ligand pair onto their equilibrium free binding energy. These features do not comprise any direct information about the three-dimensional structures of ligand or target. In cross-validation experiments, it is demonstrated that objective measurements of prediction error rate and rank-ordering statistics are competitive with those of several other investigations, most of which depend on three-dimensional structural data. The size of the sample (n = 2,671) indicates that this approach is robust and may have widespread applicability beyond restricted families of receptor types. It is concluded that newly sequenced proteins, or those for which three-dimensional crystal structures are not easily obtained, can be rapidly analyzed for their binding potential against a library of ligands using this methodology.
Mandibular bone mineral density changes in complete and removable partial denture wearers: a 6-month follow-up study.

PURPOSE The purpose of the study was to determine the changes in bone mineral density of the mandible in complete and removable free-end saddle denture wearers over a 6-month period. MATERIALS AND METHODS Twenty removable partial denture patients and 20 complete denture wearers participated. Two dental panoramic radiographs were taken from each patient, the first prior to denture delivery and the second after 6 months of denture wearing. Bone mineral density measurements were performed on panoramic radiographs with a five-step copper stepwedge attached to each film cassette. Bone mineral density values of the measured regions of interest were expressed in equivalents of the stepwedge thickness (mm). RESULTS The results revealed minor changes in bone mineral density values of the examined regions in the 6-month period. Under the distal end of complete denture saddles, the bone mineral density values decreased, whereas the values under the distal end of removable partial dentures increased. However, the difference between the first and second measurements was not significant. In each of the examined groups, the bone mineral density values at the gonion increased significantly by approximately 20%. This was attributed to the increased strain forces of the masseter muscle at the gonion after denture delivery. CONCLUSION Significant increase of bone mineral density values was registered 2 mm above the gonion in both complete and removable partial denture wearers. Age and gender were not related to the bone mineral density changes over a 6-month period.