Miracle-dz/UniFAR-FTUs huggingface dataset:
Generalizing PageRank: damping functions for link-based ranking algorithms

This paper introduces a family of link-based ranking algorithms that propagate page importance through links. In these algorithms there is a damping function that decreases with distance, so a direct link implies more endorsement than a link through a long path. PageRank is the most widely known ranking function of this family.The main objective of this paper is to determine whether this family of ranking techniques has some interest per se, and how different choices for the damping function impact on rank quality and on convergence speed. Even though our results suggest that PageRank can be approximated with other simpler forms of rankings that may be computed more efficiently, our focus is of more speculative nature, in that it aims at separating the kernel of PageRank, that is, link-based importance propagation, from the way propagation decays over paths.We focus on three damping functions, having linear, exponential, and hyperbolic decay on the lengths of the paths. The exponential decay corresponds to PageRank, and the other functions are new. Our presentation includes algorithms, analysis, comparisons and experiments that study their behavior under different parameters in real Web graph data.Among other results, we show how to calculate a linear approximation that induces a page ordering that is almost identical to PageRank's using a fixed small number of iterations; comparisons were performed using Kendall's τ on large domain datasets.
Genetic Alterations within the DENND1A Gene in Patients with Polycystic Ovary Syndrome (PCOS)

Polycystic ovary syndrome (PCOS), the most common endocrine disease among premenopausal women, is caused by both genes and environment. We and others previously reported association between single nucleotide polymorphisms (SNPs) in the DENND1A gene and PCOS. We therefore sequenced the DENND1A gene in white patients with PCOS to identify possible alterations that may be implicated in the PCOS pathogenesis. Patients were referred with PCOS and/or hirsutism between 1998 and 2011 (n = 261). PCOS was diagnosed according to the Rotterdam criteria (n = 165). Sequence analysis was performed in 10 patients with PCOS. Additional patients (n = 251) and healthy female controls (n = 248) were included for SNP genotyping. Patients underwent clinical examination including Ferriman-Gallwey score (FG-score), biochemical analyses and transvaginal ultrasound. Mutation analysis was carried out by bidirectional sequencing. SNP genotyping was tested by allelic discrimination in real-time PCR in the additional patients and controls. Sequencing of the DENND1A gene identified eight SNPs; seven were not known to be associated with any diseases. One missense SNP was detected (rs189947178, A/C), potentially altering the structural conformation of the DENND1A protein. SNP genotyping of rs189947178 showed significantly more carriers among patients with PCOS and moderate hirsutism compared to controls. However, due to small sample size and lack of multiple regression analysis supporting an association between rs189947178 and FG-score or PCOS diagnosis, this could be a false positive finding. In conclusion, sequence analysis of the DENND1A gene of patients with PCOS did not identify alterations that alone could be responsible for the PCOS pathogenesis, but a missense SNP (rs189947178) was identified in one patient and significantly more carriers of rs189947178 were found among patients with PCOS and moderate hirsutism vs. controls. Additional studies with independent cohort are needed to confirm this due to the small sample size of this study.
Treatment approaches and antibiotic use for emergency dental treatment in Turkey

The purpose of this study was to gather information about Turkish general dental practitioners’ treatment approaches towards endodontic emergencies, antibiotic-prescribing habits, and their participation in lifelong learning programs. Questionnaires were given to dentists who attended the 16th National Congress organized by the Turkish Dental Association. From 1,400 questionnaires distributed, 589 (43%) were deemed usable in this study. This survey dealt with questions that were subdivided into two main topics: dental emergency treatment approaches, and antibiotic prescription and information on lifelong learning program participation. The statistical analysis was conducted with a χ2 test at a significance level of P<0.05. For irreversible pulpitis cases in vital teeth, most of the dental practitioners (65.3%) preferred single-visit root canal treatments. For teeth presenting a periapical lesion, the preferred treatment approach was root canal treatment (91.5%). The rate of prescription of analgesics and antibiotics was 21.7% in untreated acute apical periodontitis cases and 41% in acute apical abscess cases. Frequently prescribed antibiotics were amoxicillin–clavulanate (61.8%) and amoxicillin (46.5%). There was a tendency for practitioners to attend congresses as their years of professional practice increased (P<0.0001). There have been discrepancies between taught and observed practice. Educational initiatives are needed to prevent inappropriate prescription of antibiotics.
Terminal short arm domains of basement membrane laminin are critical for its self-assembly

Laminin self-assembles into large polymers by a cooperative two-step calcium-dependent mechanism (Yurchenco, P. D., E. C. Tsilibary, A. S. Charonis, and H. Furthmayr. 1985. J. Biol. Chem. 260:7636-7644). The domain specificity of this process was investigated using defined proteolytically generated fragments corresponding to the NH2-terminal globule and adjacent stem of the short arm of the B1 chain (E4), a complex of the two short arms of the A and B2 chains attached to the proximal stem of a third short arm (E1'), a similar complex lacking the globular domains (P1'), and the distal half of the long arm attached to the adjacent portion of the large globule (E8). Polymerization, followed by an increase of turbidity at 360 nm in neutral isotonic TBS containing CaCl2 at 35 degrees C, was quantitatively inhibited in a concentration-dependent manner with laminin fragments E4 and E1' but not with fragments E8 and P1'. Affinity retardation chromatography was used for further characterization of the binding of laminin domains. The migration of fragment E4, but not of fragments E8 and P1', was retarded in a temperature- and calcium-dependent fashion on a laminin affinity column but not on a similar BSA column. These data are evidence that laminin fragments E4 and E1' possess essential terminal binding domains for the self-aggregation of laminin, while fragments E8 and P1' do not. Furthermore, the individual domain-specific interactions that contribute to assembly are calcium dependent and of low affinity.
The prevalence of symptoms associated with pulmonary tuberculosis in randomly selected children from a high burden community

Background: Diagnosis of childhood tuberculosis is problematic and symptom based diagnostic approaches are often promoted in high burden settings. This study aimed (i) to document the prevalence of symptoms associated with tuberculosis among randomly selected children living in a high burden community, and (ii) to compare the prevalence of these symptoms in children without tuberculosis to those in children with newly diagnosed tuberculosis. Methods: A cross sectional, community based survey was performed on a 15% random sample of residential addresses. A symptom based questionnaire and tuberculin skin test (TST) were completed in all children. Chest radiographs were performed according to South African National Tuberculosis Control Program guidelines. Results: Results were available in 1415 children of whom 451 (31.9%) were TST positive. Tuberculosis was diagnosed in 18 (1.3%) children. Of the 1397 children without tuberculosis, 253 (26.4%) reported a cough during the preceding 3 months. Comparison of individual symptoms (cough, dyspnoea, chest pain, haemoptysis, anorexia, weight loss, fatigue, fever, night sweats) in children with and without tuberculosis revealed that only weight loss differed significantly (OR = 4.5, 95% CI 1.5 to 12.3), while the combination of cough and weight loss was most significant (OR = 5.4, 95% CI 1.7 to 16.9). Children with newly diagnosed tuberculosis reported no symptoms in 50% of cases. Conclusion: Children from this high burden community frequently reported symptoms associated with tuberculosis. These symptoms had limited value to differentiate children diagnosed with tuberculosis from those without tuberculosis. Improved case definitions and symptom characterisation are required when evaluating the diagnostic value of symptoms.
HUMAN LAND USE INFLUENCES CHRONIC WASTING DISEASE PREVALENCE IN MULE DEER

Human alteration of landscapes can affect the distribution, abundance, and behavior of wildlife. We explored the effects of human land use on the prevalence of chronic wasting disease (CWD) in mule deer (Odocoileus hemionus) populations residing in north-central Colorado. We chose best approximating models estimating CWD prevalence in relation to differences in human land use, sex, and geographic location. Prevalence was higher in developed areas and among male deer, suggesting anthropogenic influences on the occurrence of disease. We also found a relatively high degree of variation in prevalence across the three study sites, suggesting that spatial patterns in disease may be influenced by other factors operating at a broader, landscape scale. Our results suggest that multiple factors, including changes in land use, differences in exposure risk between sexes, and landscape-scaled heterogeneity, are associated with CWD prevalence in north-central Colorado.
An Embodiment Perspective on Number–Space Mapping in 3.5‐Year‐Old Dutch Children

Previous research suggests that block adding, subtracting and counting direction are early forms of number–space mapping. In this study, an embodiment perspective on these skills was taken. Embodiment theory assumes that cognition emerges through sensory–motor interaction with the environment. In line with this assumption, it was investigated if counting and adding/subtracting direction in young children is related to the hand they use during task performance. Forty‐eight 3.5‐year‐old children completed a block adding, subtracting and counting task. They had to add and remove a block from a row of three blocks and count a row of five blocks. Adding, subtracting and counting direction were related to the hand the children used for task performance. Most children who used their right hand added, removed and started counting the blocks at the right side of the row. Most children who used their left hand added, removed and started counting the blocks at the left side of the row. It can be concluded that number–space mapping, as measured by direction of adding, subtracting and counting blocks, in young children is embodied: It is not fixed, but is related to the situation. © 2016 The Authors Infant and Child Development Published by John Wiley & Sons, Ltd.
Influence of Enhanced Recovery Pathway on Surgical Site Infection after Colonic Surgery

Background The present study aimed to evaluate a potential effect of ERAS on surgical site infections (SSI). Methods Colonic surgical patients operated between May 2011 and September 2015 constituted the cohort for this retrospective analysis. Over 100 items related to demographics, surgical details, compliance, and outcome were retrieved from a prospectively maintained database. SSI were traced by an independent National surveillance program. Risk factors for SSI were identified by univariate and multinomial logistic regression. Results Fifty-four out of 397 patients (14%) developed SSI. Independent risk factors for SSI were emergency surgery (OR 1.56; 95% CI 1.09–1.78, p = 0.026), previous abdominal surgery (OR 1.7; 95% CI 1.32–1.87, p = 0.004), smoking (OR 1.71; 95% CI 1.22–1.89, p = 0.014), and oral bowel preparation (OR 1.86; 95% CI 1.34–1.97, p = 0.013), while minimally invasive surgery (OR 0.3; 95% CI 0.16–0.56, p < 0.001) protected against SSI. Compliance to ERAS items of >70% was not retained as a protective factor for SSI after multivariate analysis (OR 0.94; 95% CI 0.46–1.92, p = 0.86). Conclusions Smoking, open and emergency surgery, and bowel preparation were risk factors for SSI. ERAS pathway had no independent impact while minimally invasive approach did. This study was registered under ResearchRegistry.com (UIN researchregistry2614).
EuroSense: Automatic Harvesting of Multilingual Sense Annotations from Parallel Text

Parallel corpora are widely used in a variety of Natural Language Processing tasks, from Machine Translation to cross-lingual Word Sense Disambiguation, where parallel sentences can be exploited to automatically generate high-quality sense annotations on a large scale. In this paper we present EuroSense, a multilingual sense-annotated resource based on the joint disambiguation of the Europarl parallel corpus, with almost 123 million sense annotations for over 155 thousand distinct concepts and entities from a language-independent unified sense inventory. We evaluate the quality of our sense annotations intrinsically and extrinsically, showing their effectiveness as training data for Word Sense Disambiguation.
The Ontogeny and Evolution of Sex-Biased Gene Expression in Drosophila melanogaster

Sexually dimorphic phenotypes are thought to largely result from sex differences in gene expression, and genes with sex-biased expression have been well characterized in adults of many species. Although most sexual dimorphisms manifest in adults, many result from sex-specific developmental trajectories, implying that juveniles may exhibit significant levels of sex-biased expression. However, it is unclear how much sex-biased expression occurs before reproductive maturity and whether preadult sex-biased genes should exhibit the same evolutionary dynamics observed for adult sex-biased genes. In order to understand the continuity, or lack thereof, and evolutionary dynamics of sex-biased expression throughout the life cycle, we examined sex-biased genes in pre-gonad tissue of two preadult stages and compared them with the adult gonad of Drosophila melanogaster. We found that the majority of the genome is sex-biased at some point in the life cycle, with some genes exhibiting conserved sex-biased expression and others displaying stage-specific sex bias. Our results also reveal a far more complex pattern of evolution for sex-biased genes throughout development. The most rapid evolutionary divergence occurred in genes expressed only in larvae within each sex, compared with continuously expressed genes. In females—but not males—this pattern appeared to be due to relaxed purifying selection in larva-limited genes. Furthermore, genes that retained male bias throughout life evolved more rapidly than stage-specific male-biased genes, due to stronger purifying selection in stage-specific genes. However, female-biased genes that were specific to larvae evolved most rapidly, a pattern that could not be definitively attributed to differences in adaptive evolution or purifying selection, suggesting that pleiotropic constraints on protein-coding sequences can arise when genes are broadly expressed across developmental stages. These results indicate that the signature of sex-specific selection can be detected well before reproductive maturity and is strongest during development.
Relationship of Sleep Duration With All‐Cause Mortality and Cardiovascular Events: A Systematic Review and Dose‐Response Meta‐Analysis of Prospective Cohort Studies

Background Effects of extreme sleep duration on risk of mortality and cardiovascular outcomes remain controversial. We aimed to quantify the dose‐response relationships of sleep duration with risk of all‐cause mortality, total cardiovascular disease, coronary heart disease, and stroke. Methods and Results PubMed and Embase were systematically searched for prospective cohort studies published before December 1, 2016, that examined the associations between sleep duration and at least 1 of the 4 outcomes in generally healthy populations. U‐shaped associations were indicated between sleep duration and risk of all outcomes, with the lowest risk observed for ≈7‐hour sleep duration per day, which was varied little by sex. For all‐cause mortality, when sleep duration was <7 hours per day, the pooled relative risk (RR) was 1.06 (95% CI, 1.04–1.07) per 1‐hour reduction; when sleep duration was >7 hours per day, the pooled RR was 1.13 (95% CI, 1.11–1.15) per 1‐hour increment. For total cardiovascular disease, the pooled RR was 1.06 (95% CI, 1.03–1.08) per 1‐hour reduction and 1.12 (95% CI, 1.08–1.16) per 1‐hour increment of sleep duration. For coronary heart disease, the pooled RR was 1.07 (95% CI, 1.03–1.12) per 1‐hour reduction and 1.05 (95% CI, 1.00–1.10) per 1‐hour increment of sleep duration. For stroke, the pooled RR was 1.05 (95% CI, 1.01–1.09) per 1‐hour reduction and 1.18 (95% CI, 1.14–1.21) per 1‐hour increment of sleep duration. Conclusions Our findings indicate that both short and long sleep duration is associated with an increased risk of all‐cause mortality and cardiovascular events.
Preliminary evaluations on development of new materials for hip joint femoral head

Development and selection of a proper biomaterial with diverse properties (i.e. physical, mechanical, wear, corrosion, and many others) for hip femoral head is one of the most exigent tasks. Improper material often causes component failure during functioning. Therefore, in this study, a series of implant materials containing tungsten of different weight percentages were fabricated by high temperature vacuum casting induction furnace and the physical, mechanical, wear, and corrosion properties were examined. The proportions were varied from 0 wt% to 4 wt% in a cobalt–chromium alloy (Co–30Cr–4Mo–1Ni). The mechanical properties were tested by the micro-hardness tester and the compression testing machine, while the wear performance was analyzed through a pin-on-disc tribometer under different operating conditions at room temperature. Corrosion resistance was analyzed under NaCl solution by the electrochemical test method. Due to the conflict between the properties obtained, the Vise Kriterijumska Optimizacija Kompromisno Resenjemeaning (VIKOR) method integrated with analytic hierarchy process (AHP) was applied to choose the best material among the set of alternatives, where AHP was used to determine criteria weights, and VIKOR approach was used to rank the alternatives. From the results obtained, it was found that Co–30Cr–4Mo–1Ni implant material containing 2 wt% tungsten provides the best combination of the properties for a given application (i.e. hip femoral head).
A General Framework for the Analysis of Phenotypic Trajectories in Evolutionary Studies

Many evolutionary studies require an understanding of phenotypic change. However, while analyses of phenotypic variation across pairs of evolutionary levels (populations or time steps) are well established, methods for testing hypotheses that compare evolutionary sequences across multiple levels are less developed. Here we describe a general analytical procedure for quantifying and comparing patterns of phenotypic evolution. The phenotypic evolution of a lineage is defined as a trajectory across a set of evolutionary levels in a multivariate phenotype space. Attributes of these trajectories (their size, direction, and shape), are quantified, and statistically compared across pairs of taxa, and a summary statistic is used to determine the extent to which patterns of phenotypic evolution are concordant across multiple taxa. This approach provides a direct quantitative description of how patterns of phenotypic evolution differ, as well as a statistical assessment of the degree of repeatability in the evolutionary responses to selection among taxa. We describe how this approach can quantify phenotypic trajectories from many ecological and evolutionary processes, whose data encode multivariate characterizations of the phenotype, including: phenotypic plasticity, ecological selection, ontogeny and growth, local adaptation, and biomechanics. We illustrate the approach by examining the phenotypic evolution of several fossil lineages of Globorotalia.
Flexible Thick Film Electroluminescent Devices: Influence of the Mechanical Stress on Layers Behavior

The influence of the mechanical bending on flexible screen-printed organic light emitting devices upon their electrical properties has been examined. Our measurements showed that flexible printed coatings can be bent to small radii (5 mm and 2.5 mm) of curvature and still function, despite the increase of the electrical resistance of the electrodes from 45 to 62.1 Ohms/sq. This is ascribed to the mixture of two classes organic compounds (low molecular weight and polymeric) in suitable ratio, which guarantee high adhesion and stability against strain. Device failure is caused mainly by the transparent indium tin oxide (ITO) electrode that is not resistant to continuous bending at radius 5 mm, as well as to repeated bending over 2 000 that lead to cracks occurring. Internal stress induced in organic electroluminescent layers with different thickness was determined to be in the range |1|-|7| MPa, based on the radius of curvature. Current-voltage characteristics clearly show the limit of bending, at which current flow stops, because of electrodes degradation.
Multicenter study using paraffin-embedded tumor tissue testing PITX2 DNA methylation as a marker for outcome prediction in tamoxifen-treated, node-negative breast cancer patients.

PURPOSE We recently reported DNA methylation of the paired-like homeodomain transcription factor 2 (PITX2) gene to be strongly correlated with increased risk of recurrence in node-negative, hormone receptor-positive, tamoxifen-treated breast cancer patients using fresh frozen specimens. Aims of the present study were to establish determination of PITX2 methylation for routine analysis in formalin-fixed paraffin-embedded (FFPE) breast cancer tissue and to test PITX2 DNA methylation as a biomarker for outcome prediction in an independent patient cohort. PATIENTS AND METHODS Real-time polymerase chain reaction (PCR) technology was validated for FFPE tissue by comparing methylation measurements in FFPE specimens with those in fresh frozen specimens from the same tumor. The impact of PITX2 methylation on time to distant metastasis was then evaluated in FFPE specimens from hormone receptor-positive, node-negative breast cancer patients (n = 399, adjuvant tamoxifen monotherapy). RESULTS Reproducibility of the PCR assay in replicate measurements (r(s) > or = 0.95; n = 150) and concordant measurements between fresh frozen and FFPE tissues (r(s) = 0.81; n = 89) were demonstrated. In a multivariate model, PITX2 methylation added significant information (hazard ratio = 2.35; 95% CI, 1.20 to 4.60) to established prognostic factors (tumor size, grade, and age). CONCLUSION PITX2 methylation can be reliably assessed by real-time PCR technology in FFPE tissue. Together with our earlier studies, we have accumulated substantial evidence that PITX2 methylation analysis holds promise as a practical assay for routine clinical use to predict outcome in node-negative, tamoxifen-treated breast cancer, which might allow, based on future validation studies, the identification of low-risk patients who may be treated by tamoxifen alone.