Miracle-dz/UniFAR-FTUs huggingface dataset:
Uneven recombination rate and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.)

Recombination (R) rate and linkage disequilibrium (LD) analyses are the basis for plant breeding. These vary by breeding system, by generation of inbreeding or outcrossing and by region in the chromosome. Common bean (Phaseolus vulgaris L.) is a favored food legume with a small sequenced genome (514 Mb) and n = 11 chromosomes. The goal of this study was to describe R and LD in the common bean genome using a 768-marker array of single nucleotide polymorphisms (SNP) based on Trans-legume Orthologous Group (TOG) genes along with an advanced-generation Recombinant Inbred Line reference mapping population (BAT93 x Jalo EEP558) and an internationally available diversity panel. A whole genome genetic map was created that covered all eleven linkage groups (LG). The LGs were linked to the physical map by sequence data of the TOGs compared to each chromosome sequence of common bean. The genetic map length in total was smaller than for previous maps reflecting the precision of allele calling and mapping with SNP technology as well as the use of gene-based markers. A total of 91.4% of TOG markers had singleton hits with annotated Pv genes and all mapped outside of regions of resistance gene clusters. LD levels were found to be stronger within the Mesoamerican genepool and decay more rapidly within the Andean genepool. The recombination rate across the genome was 2.13 cM / Mb but R was found to be highly repressed around centromeres and frequent outside peri-centromeric regions. These results have important implications for association and genetic mapping or crop improvement in common bean.
Problematic gaming behaviour and health-related outcomes: A systematic review and meta-analysis

This systematic review and meta-analysis aimed to investigate the interplay between problematic gaming behaviour and health-related outcomes at different developmental stages. A total of 50 empirical studies met the specified inclusion criteria, and a meta-analysis using correlation coefficients was used for the studies that reported adverse health implications regarding the impact of problematic gaming behaviour on depression, anxiety, obsessive–compulsive disorder and somatisation. Overall, the results suggested that problematic gaming behaviour is significantly associated with a wide range of detrimental health-related outcomes. Finally, the limitations of this review alongside its implications were discussed and considered for future research.
Analysis and Enhancement of Wikification for Microblogs with Context Expansion

Disambiguation to Wikipedia (D2W) is the task of linking mentions of concepts in text to their corresponding Wikipedia entries. Most previous work has focused on linking terms in formal texts (e.g. newswire) to Wikipedia. Linking terms in short informal texts (e.g. tweets) is difficult for systems and humans alike as they lack a rich disambiguation context. We first evaluate an existing Twitter dataset as well as the D2W task in general. We then test the effects of two tweet context expansion methods, based on tweet authorship and topic-based clustering, on a state-of-the-art D2W system and evaluate the results.
A novel learning algorithm to predict individual survival after liver transplantation for primary sclerosing cholangitis

Deciding who should receive a liver transplant (LT) depends on both urgency and utility. Most survival scores are validated through discriminative tests, which compare predicted outcomes between patients. Assessing post-transplant survival utility is not discriminate, but should be “calibrated” to be effective. There are currently no such calibrated models. We developed and validated a novel calibrated model to predict individual survival after LT for Primary Sclerosing Cholangitis (PSC). We applied a software tool, PSSP, to adult patients in the Scientific Registry of Transplant Recipients (n = 2769) who received a LT for PSC between 2002 and 2013; this produced a model for predicting individual survival distributions for novel patients. We also developed an appropriate evaluation measure, D-calibration, to validate this model. The learned PSSP model showed an excellent D-calibration (p = 1.0), and passed the single-time calibration test (Hosmer-Lemeshow p-value of over 0.05) at 0.25, 1, 5 and 10 years. In contrast, the model based on traditional Cox regression showed worse calibration on long-term survival and failed at 10 years (Hosmer-Lemeshow p value = 0.027). The calculator and visualizer are available at: http://pssp.srv. ualberta.ca/calculator/liver_transplant_2002. In conclusion we present a new tool that accurately estimates individual post liver transplantation survival.
Correlation in Statistics and in Data Compression

The aim of this document is to illuminate the concept of correlation as used in data compression. The correlation between pixels is what makes image compression possible, so this type of correlation deserves a better understanding. Such an understanding is provided here in the form of a quantitative treatment of this concept. We start with a discussion of how the correlation between two variables (arrays of numbers) is measured in statistics. The Pearson correlation coefficient R is then introduced and explained. This is compared to the term " correlation " as used in data compression, i.e., the correlation between elements (pixels or audio samples) of a single variable (an image row or column or an audio file). Next, we propose two ways to quantitatively measure the correlation between elements of a single variable, and support these proposals with experiments performed on real data. The Correlation Coefficient. We start with a discussion of the concept of correlation and how it is measured statistically. In statistics, correlation is measured between two random variables (arrays of numbers) a and b. We say that the two variables are positively correlated if the numbers feature the same behavior. The two variables are strongly (and positively) correlated, since a i > a i−1 implies b i > b i−1 and a i < a i−1 implies b i < b i−1. In other words, knowing a helps in predicting b. The correlation coefficient should be defined such that its value for these two variables would be large positive. If we reverse one of the variables, they become negatively correlated, since a i > a i−1 now implies b i < b i−1. Knowing a in this case also helps in predicting b, but we want the correlation coefficient to be negative. If the relation a i > a i−1 tells us nothing about the relation between b i and b i−1 , then there is no association between the variables, they are decorrelated and their correlation coefficient should be zero. The English statistician Karl Pearson [1857–1936] was the first to approach the study of correlation scientifically. He measured the heights of 1078 fathers and their sons (at maturity) and arranged the results in a scatter diagram, similar to those of Figure 1b,c,d. Each point on the diagram corresponds to the heights of a father-son pair. Pearson realized that such a diagram can be the basis for …
D 2 . 4 Qualitative Analysis of Rumours , Sources , and Diffusers across Media and Languages

FP7-ICT Collaborative Project ICT-2013-611233 PHEME Deliverable D2.4 (WP2) This deliverable describes the work conducted in Work Package 2 for the study of conversations around rumours in social media. It describes our efforts towards developing an annotation scheme for analysing each of the messages that participate in rumourous conversations, and we put it into practice by creating a large-scale corpus of annotated tweets in English and German, including links to other media. This report also summarises our qualitative analysis of conversations around different types of rumours, looking at the diffusion across different media and languages. A sample of the corpus produced in this process is released along with this deliverable, which will be extended with the release of the whole corpus in December 2015. Keyword list: rumours, veracity, annotation scheme, social media, analysis Copyright c © 2015 University of Warwick Project Delivery Date Contractual Date Nature Reviewed By Web links Dissemination PHEME No. 611233 July 13, 2015 June 30, 2015 Report Kalina Bontcheva, Thierry Declerck http://www.pheme. eu/ PU
‘The Forms of Tissues, or Cell-aggregates’: D'Arcy Thompson's influence and its limits

In two chapters of his book On Growth and Form, D'Arcy Thompson used numerous biological and physical observations to show how principles from mathematics and physics – such as pressure differences, surface tension and viscosity – could explain cell shapes and packing within tissues. In this Review, we depict influences that enabled the genesis of his ideas, report examples of his visionary observations and trace his impact over the past 100 years. Recently, his ideas have been revisited as a new field of research emerged, linking cell-level physics with epithelial tissue structure and development. We critically discuss the potential and the limitations of both Thompson's and the modern approaches. Summary: This Review considers how Thompson's sometimes oversimplified explanations of the geometries and tensions underlying cell and tissue packing have informed modern cell-level physics but also should be viewed with due scrutiny.
Field testing the strength of thin-layer mortars using the pull-out method

Reinforced steel bar (rebar) mesh and thin-layer mortar are applied to reinforce sintered clay brick walls in a construction site. Their strengths are measured using the pre-installed pull-out method, the post-installed pull-out method and the standard cube compression strength test. Nine strength grades of cement mortars, namely, M10, M15, M20, M25, M30, M35, M40, M45 and M50, are chosen for the test; the pre-installed and post-installed pull-out tests consist of 54 samples of each. By fitting the experimental results, a formula for the compressive strength of the thin-layer mortar for the pre-installed and post-installed pull-out tests is developed. The regression function is validated and an interval prediction of the specific compressive strength for the pre-installed pull-out test is proposed. This study provides a basis for wider application of the pull-out test for thin-layer mortar and the establishment of its technical standards.
Nanoparticle Agglomeration via Ionic Colloidal Destabilization as a Novel Approach to Dry Powder Formulations for Pulmonary Drug Delivery

Efficient administration of poorly water soluble drugs represents a leading challenge in pulmonary medicine. This route of administration has been used for steroidal treatments for some time, but with room for advancement. New inhalable medicines require a more reliable and effective dosing regimen due to narrow therapeutic indices, and specific and enhanced deposition in the lungs is also desired. This thesis investigates a general method for producing micron sized dry powders for a general class of drugs, poorly water soluble small molecule drugs, for their use in pulmonary drug delivery. Formulation methods already exist for inhalable aerosols, but the resulting powders often show limited deposition efficiency in the deep lung. In this body of work, an alternative formulation strategy is provided for inhalable dry powders using nanoparticle agglomeration that results in a potentially more efficient line of therapy. The model drug used in this study was nifedipine, a well known calcium channel blocker used to treat various symptoms of hypertension. The results indicated that nanoparticle agglomeration is a viable means of creating dry powders with suitable characteristics for pulmonary drug delivery as an alternative to more expensive and less controllable formulation strategies.
New apparatus for measuring elastic modulus based on elastic contact deformation of sphere and flat: An apparatus based on Hertzian theory

A new apparatus for measuring elastic modulus is developed, which quickly estimates it by measuring the relative normal approach between a flat and a sphere as the function of a normal load during the indentation. Then the elastic modulus of the flat or the sphere specimen can be calculated using the Hertzian theory. The apparatus possesses the following advantages to estimate the elastic modulus: the specimens used are the only one or two small disks (plates) which can be easily made, and the test can be made as quickly as a hardness test. In addition, the apparatus can also measure the elastic modulus of sphere in shape.
DeepEye: Towards Automatic Data Visualization

Data visualization is invaluable for explaining the significance of data to people who are visually oriented. The central task of automatic data visualization is, given a dataset, to visualize its compelling stories by transforming the data (e.g., selecting attributes, grouping and binning values) and deciding the right type of visualization (e.g., bar or line charts). We present DEEPEYE, a novel system for automatic data visualization that tackles three problems: (1) Visualization recognition: given a visualization, is it "good or "bad"? (2) Visualization ranking: given two visualizations, which one is "better"? And (3) Visualization selection: given a dataset, how to find top-k visualizations? DEEPEYE addresses (1) by training a binary classifier to decide whether a particular visualization is good or bad. It solves (2) from two perspectives: (i) Machine learning: it uses a supervised learning-to-rank model to rank visualizations; and (ii) Expert rules: it relies on experts' knowledge to specify partial orders as rules. Moreover, a "boring" dataset may become interesting after data transformations (e.g., binning and grouping), which forms a large search space. We also discuss optimizations to efficiently compute top-k visualizations, for approaching (3). Extensive experiments verify the effectiveness of DEEPEYE. "
Causes and Timing of Mortality and Morbidity Among Late Presenters Starting Antiretroviral Therapy in the REALITY Trial

Abstract Background In sub-Saharan Africa, 20%–25% of people starting antiretroviral therapy (ART) have severe immunosuppression; approximately 10% die within 3 months. In the Reduction of EArly mortaLITY (REALITY) randomized trial, a broad enhanced anti-infection prophylaxis bundle reduced mortality vs cotrimoxazole. We investigate the contribution and timing of different causes of mortality/morbidity. Methods Participants started ART with a CD4 count <100 cells/µL; enhanced prophylaxis comprised cotrimoxazole plus 12 weeks of isoniazid + fluconazole, single-dose albendazole, and 5 days of azithromycin. A blinded committee adjudicated events and causes of death as (non–mutually exclusively) tuberculosis, cryptococcosis, severe bacterial infection (SBI), other potentially azithromycin-responsive infections, other events, and unknown. Results Median pre-ART CD4 count was 37 cells/µL. Among 1805 participants, 225 (12.7%) died by week 48. Fatal/nonfatal events occurred early (median 4 weeks); rates then declined exponentially. One hundred fifty-four deaths had single and 71 had multiple causes, including tuberculosis in 4.5% participants, cryptococcosis in 1.1%, SBI in 1.9%, other potentially azithromycin-responsive infections in 1.3%, other events in 3.6%, and unknown in 5.0%. Enhanced prophylaxis reduced deaths from cryptococcosis and unknown causes (P < .05) but not tuberculosis, SBI, potentially azithromycin-responsive infections, or other causes (P > .3); and reduced nonfatal/fatal tuberculosis and cryptococcosis (P < .05), but not SBI, other potentially azithromycin-responsive infections, or other events (P > .2). Conclusions Enhanced prophylaxis reduced mortality from cryptococcosis and unknown causes and nonfatal tuberculosis and cryptococcosis. High early incidence of fatal/nonfatal events highlights the need for starting enhanced-prophylaxis with ART in advanced disease. Clinical Trials Registration ISRCTN43622374.
Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal

Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically identical parasite strains, coincident with increased deployment of malaria control interventions and decreased malaria deaths. Parasite genotypes in some cases persisted clonally across dry seasons. The increase in frequency of genetically identical parasite strains corresponded with decrease in the probability of multiple infections. Further, these observations support evidence of both clonal and epidemic population structures. These data provide the first evidence of a temporal correlation between the appearance of identical parasite types and increased malaria control efforts in Africa, which here included distribution of insecticide treated nets (ITNs), use of rapid diagnostic tests (RDTs) for malaria detection, and deployment of artemisinin combination therapy (ACT). Our results imply that genetic surveillance can be used to evaluate the effectiveness of disease control strategies and assist a rational global malaria eradication campaign.
Sensitivity of composite materials to ambient light and clinical working time

Introduction. The aim of this study was to determine sensitivity of composite materials to ambient light by a modified standard ISO 4049:2000 and clinical working time. Materials and Methods. The following materials were tested: nano-hybrid Herculite XRV Ultra (Kerr), micro-hybrid Herculite XRV (Kerr), Zmack (Zhermack), SuperCor (SpofaDental) and Valux Plus (3M ESPE). Five samples in each group were exposed to ambient light of 8000 lx, which comprised dental unit light and natural light. After 60 sec of exposure, each sample was visually examined for signs of inhomogeneity meaning that material did not pass the test. Clinical working time was studied by applying a custom-built, standardized indenter into composite specimens of about 2 mm thickness during the same exposure to ambient light. Completion of polymerization was tested by dissolving samples in ethanol and measuring the difference in thickness before and after the test. Results were statistically analyzed using ANOVA at the significance level of 0.05. Results. Only Herculite XRV Ultra passed the test of sensitivity to ambient light, while other materials showed signs of inhomogeneity. Herculite XRV Ultra showed significantly longer working time than other composites, the average was 250 sec (p<0.05). The mean values of working time for other materials ranged between 117-131 sec and there was no significant difference between them (p>0.05). Conclusion. Due to the lower sensitivity to ambient light and significantly longer clinical working time compared to micro-hybrid composites, Herculite XRV Ultra can be recommended for clinical procedures that require prolonged working time with material in plastic condition. [Projekat Ministarstva nauke Republike Srbije, br. ON172007]
Seasonal, sexual and developmental differences in hoopoe Upupa epops preen gland morphology and secretions: evidence for a role of bacteria

The uropygial glands of birds serve multiple functions, and there is great interspecific variability in the composition and properties of their secretions. A special case is the secretion in the hoopoes Upupa epops, and green woodhoopoes Phoeniculus purpureus, which, contrary to the commonly white and odourless secretions, are dark with pungent odour. Recently, bacteria have been isolated from glands of both woodhoopoes and hoopoes and here we test the hypothesis that bacteria are responsible of some of the special properties of glands and secretions of this group of birds. We explore natural seasonal changes and intersexual differences in the properties of hoopoe glands and secretions, check the natural occurrence of bacteria within secretions, and analyse the effect of experimental injection of antibiotics on uropygial gland properties. Male glands underwent no seasonal changes, and their secretions were invariably white and odourless, very similar to female glands outside the breeding season. However, in comparison to the uropygial gland of non-breeding females, those of incubating females showed a marked increase in size and volume of secretion produced, which became dark and pungent. All these parameters increased until the hatching date and returned to values similar to those in the prelaying phase towards the end of the nestling period. Nestling glands produced secretions similar to those of females in colour and odour. Gland size of both females and nestlings predicted the amount of secretion produced. Microscopic techniques confirmed the presence of bacteria at high density and in active division in all dark secretions examined. The antibiotic treatment significantly reduced the load of enterococci in nestling glands, did not affect size of glands, but diminished the volume of secretion, which was lighter in colour than that of control nestlings. In nesting females, the experimental injection of antibiotic affected some measurements of gland size and secretion colour. Because the experiment did not affect general health estimates (immunocompetence, body condition or growing) of nestlings, our results suggest that some of the special properties of hoopoe glands are mediated by the presence of symbiotic bacteria.
Comprehensive landscape of subtype-specific coding and non-coding RNA transcripts in breast cancer

Molecular classification of breast cancer into clinically relevant subtypes helps improve prognosis and adjuvant-treatment decisions. The aim of this study is to provide a better characterization of the molecular subtypes by providing a comprehensive landscape of subtype-specific isoforms including coding, long non-coding RNA and microRNA transcripts. Isoform-level expression of all coding and non-coding RNAs is estimated from RNA-sequence data of 1168 breast samples obtained from The Cancer Genome Atlas (TCGA) project. We then search the whole transcriptome systematically for subtype-specific isoforms using a novel algorithm based on a robust quasi-Poisson model. We discover 5451 isoforms specific to single subtypes. A total of 27% of the subtype-specific isoforms have better accuracy in classifying the intrinsic subtypes than that of their corresponding genes. We find three subtype-specific miRNA and 707 subtype-specific long non-coding RNAs. The isoforms from long non-coding RNAs also show high performance for separation between Luminal A and Luminal B subtypes with an AUC of 0.97 in the discovery set and 0.90 in the validation set. In addition, we discover 1500 isoforms preferentially co-expressed in two subtypes, including 369 isoforms co-expressed in both Normal-like and Basal subtypes, which are commonly considered to have distinct ER-receptor status. Finally, analyses at protein level reveal four subtype-specific proteins and two subtype co-expression proteins that successfully validate results from the isoform level.