Miracle-dz/UniFAR-FTUs huggingface dataset:
Preprocessing and analyzing genetic data with complex networks: An application to Obstructive Nephropathy

Many diseases have a genetic origin, and a great effort is being made to detect the genes that are responsible for their insurgence. One of the most promising techniques is the analysis of genetic information through the use of complex networks theory. Yet, a practical problem of this approach is its computational cost, which scales as the square of the number of features included in the initial dataset. In this paper, we propose the use of an iterative feature selection strategy to identify reduced subsets of relevant features, and show an application to the analysis of congenital Obstructive Nephropathy. Results demonstrate that, besides achieving a drastic reduction of the computational cost, the topologies of the obtained networks still hold all the relevant information, and are thus able to fully characterize the severity of the disease.
New Methods for Quantification of Visual Photosensitivity Threshold and Symptoms

Purpose Visual photosensitivity is a common symptom difficult to measure and diagnose, and is found in many ocular and neurological disorders. We developed two novel reproducible quantitative assessments of visual photosensitivity. Methods We designed and built the ocular photosensitivity analyzer (OPA), an automated instrument to determine light intensity visual photosensitivity threshold (VPT), and developed the Visual Light Sensitivity Questionnaire-8 (VLSQ-8), an eight-question survey to assess the presence and severity of photosensitivity symptoms. We evaluated the test–retest variability and obtained normative values of these two approaches in 35 healthy normal subjects, distributed evenly over five age groups from eight to 60 years. Each subject underwent two test sessions, each with VLSQ-8, eye examination, and OPA, four weeks apart, between April 2015 and June 2016. Results Log-transformed VPTs (log10lux) and VLSQ-8 results were highly reproducible between the two sessions (VPT intraclass correlation coefficient [ICC] = 0.86; 95% confidence interval [CI] = 0.71–0.93; binocular testing, VLSQ-items ICC range = 0.53–0.87). No consistent significant differences in VPTs were found with monocular (P = 0.053, session 1) or binocular (P = 0.26) testing. Subjects in age group >30 to 40 years had significantly higher VPTs than those in other age groups (P ≤ 0.011) except the >40 to 50 years age group (P = 0.11). Photosensitivity symptoms assessed by the VLSQ-8 generally were low and highly reproducible with ≥88% of responses between the 2 sessions being within one category of each other. Conclusions Our results provide reliability data and normative results toward validation of two novel approaches to quantify visual photosensitivity and provide support for their potential use in ocular and neurologic conditions as well as in clinical trials. Translational Relevance The new quantitative photosensitivity approaches are potential measures to characterize disease severity, monitor disease progression, and evaluate treatment efficacy.
Mesenchymal stem cell mechanobiology and emerging experimental platforms

Experimental control over progenitor cell lineage specification can be achieved by modulating properties of the cell's microenvironment. These include physical properties of the cell adhesion substrate, such as rigidity, topography and deformation owing to dynamic mechanical forces. Multipotent mesenchymal stem cells (MSCs) generate contractile forces to sense and remodel their extracellular microenvironments and thereby obtain information that directs broad aspects of MSC function, including lineage specification. Various physical factors are important regulators of MSC function, but improved understanding of MSC mechanobiology requires novel experimental platforms. Engineers are bridging this gap by developing tools to control mechanical factors with improved precision and throughput, thereby enabling biological investigation of mechanics-driven MSC function. In this review, we introduce MSC mechanobiology and review emerging cell culture platforms that enable new insights into mechanobiological control of MSCs. Our main goals are to provide engineers and microtechnology developers with an up-to-date description of MSC mechanobiology that is relevant to the design of experimental platforms and to introduce biologists to these emerging platforms.
Web-supported Matching and Classification of Business Opportunities

More and more business opportunities are published on the Web; however, it is difficult to collect and process them automatically. This paper describes a tool and techniques to help users discovering relevant business opportunities, in particular, calls for tenders. The tool includes spidering, information extraction, classification, and a search interface. Our focus in this paper is on classification, which aims to organize calls for tenders into classes, so as to facilitate user’s browsing. We describe a new approach to classification of business opportunities on the Web using language modeling (LM) approach. This utilization is strongly inspired by the recent success of LM in IR experiments. However, few attempts have been made to use LM for text classification so far. Our goal is to investigate whether LM can bring improvement to text classification. Our experiments are conducted on two corpora: Reuters containing newswire articles and FedBizOpps (FBO) containing calls for tenders (CFTs) published on the Web. The experimental results show that LM-based classification can significantly improve the classification performance on both test corpora, compared with the traditional Naive Bayes (NB) classifier. In particular, it seems to have stronger impact on FBO than on Reuters. This result shows that LM can greatly improve classification on the Web.
Is Spousal Violence Being “Vertically Transmitted” through Victims? Findings from the Pakistan Demographic and Health Survey 2012-13

Introduction Violence against women is regarded as a major violation of human rights, and several socio-behavioral aspects among victims have been identified as important determinants of spousal violence experience. Pakistani nationally representative contextual evidence is scarce in this regard. We aimed to estimate prevalence of spousal violence, and explore its association with intergenerational transfer, and attitudinal acceptance of violence, among Pakistani ever-married women. Materials and Methods Data of 3,687 ever-married women from Pakistan Demographic and Health Survey, 2012-13 was used to perform secondary analysis. Logistic regression analyses were conducted. Association between the different forms of spousal violence and the independent variables: intergenerational transfer of spousal violence (mother also beaten up by father); and attitudinal acceptance of spousal violence (beating is justifies if wife argues with husband) were reported as Odds ratios with 95% confidence intervals (CI). Results Overall, more than a third (n=1344, 37.9%)of ever-married women reported that they experienced spousal violence. Almost 68% (n=539) of the women who reported that their mothers were also beaten up by their fathers, were victims of spousal violence; and almost 47% (n=603) of the women who agreed that beating was justified if the wife argues with her husband, also suffered spousal violence. Intergenerational transfer (OR =5.71, 95%CI 4.40-7.41, p-value <0.01), and attitudinal acceptance (OR =1.66, 95%CI 1.27-2.15, p-value <0.01) were significantly associated with experience of physical violence even after adjusting for respondents’ age at marriage, education level, wealth index, parity, employment status, and empowerment status. Conclusions Spousal violence continues to haunt the lives of women in Pakistan, and is being transmitted as a learned behavior from mothers to daughters who tend to accept such violation of human rights. Girl children from such unfortunate homes may continue to transmit such behaviors, and thus may be targeted for future anti-domestic violence efforts.
Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa

Let There Be Light Retinitis pigmentosa, a disease that can result from a wide variety of genetic defects, causes degeneration of photoreceptor cells in the retina and leads to blindness. In the course of the disease, it is generally the rod photoreceptor cells that degenerate first. Cone photoreceptor cells may persist, but in a damaged and nonfunctional state. Busskamp et al. (p. 413, published online 24 June; see the cover; see the Perspective by Cepko) have now applied a gene therapy approach to mouse models of retinitis pigmentosa. Inducing expression of a bacterial light-activated ion pump, halorho dopsin, in the damaged cone cells improved visual responses in the diseased mouse retinas. Thus, it may be possible to rescue cone photoreceptors therapeutically, even after they have already been damaged. A bacterial ion pump rescues visual function in damaged cone-photoreceptor cells in mouse models of retinitis pigmentosa. Retinitis pigmentosa refers to a diverse group of hereditary diseases that lead to incurable blindness, affecting two million people worldwide. As a common pathology, rod photoreceptors die early, whereas light-insensitive, morphologically altered cone photoreceptors persist longer. It is unknown if these cones are accessible for therapeutic intervention. Here, we show that expression of archaebacterial halorhodopsin in light-insensitive cones can substitute for the native phototransduction cascade and restore light sensitivity in mouse models of retinitis pigmentosa. Resensitized photoreceptors activate all retinal cone pathways, drive sophisticated retinal circuit functions (including directional selectivity), activate cortical circuits, and mediate visually guided behaviors. Using human ex vivo retinas, we show that halorhodopsin can reactivate light-insensitive human photoreceptors. Finally, we identified blind patients with persisting, light-insensitive cones for potential halorhodopsin-based therapy.
The Meaning of Body Image for Women with Eating Disorders

Objective: To propose a theoretical model accounting for the meaning and function of body image disturbances for individuals with eating disorders. This model departs from available conceptualizations of body image focused on attractiveness and emphasizes the role of body image preoccupations in the regulation of self-esteem and affect. Method: This model was developed on the basis of the author's clinical observations and the available empirical research. Results: Three main functions of body image are described. The first one, “affiliation,” consists of using one's appearance in the establishment of interpersonal relationships, both at the level of friendship and romance. The second function, “avoidance,” consists of using one's body image to avoid abuse, be it psychological, physical, or sexual. The third function, “expression,” consists of using one's body image to communicate to the self and others one's capacity for accomplishment or one's inner feelings of dejection. Conclusion: This model is designed to be a therapeutic tool within body image therapy. Body image therapy can be most effective when focused on the unique meaning of body image for each individual patient.
Signal and Spectrum Coordination for Next Generation DSL Networks (Signaal- en spectrumcoördinatie voor next generation DSL netwerken)

The ability to easily exchange and access data has transformed the way we work, study, inform and entertain ourselves. In particular, the Internet has had an effect on people’s lives in the past two decades that is profound. Profound as this effect may be, people seem not to grow tired of it. On the contrary: as of today, the Internet revolution is far from over. The thirst for bigger amounts of data at higher speeds and ubiquitous connectivity seem not to abate. This thirst for more, faster and better quality data is both a huge challenge and a huge opportunity for the broadband access industry. The opportunity lies on the fact that, as of the end of 2012, there were 600 million subscribers to broadband services around the world. Plus, even though the market is already enormous, it still has big growth potential. The challenge lies on the connections between the network backbone and the user, the so-called local loop. In the local loop the network thins out and usually consists of lower quality channels in comparison to the network backbone. Of the technologies currently available to bridge this local loop, digital subscriber lines (DSL) is by far the market leader. This technology uses twisted copper pairs, the same used for decades for standard telephony services. If on the plus side the telephone network infrastructure is ubiquitous through the globe, making costs of installation very small, on the minus side DSL operates in a medium not initially designed for broadband communications. One of the consequences of this is severe levels of multi-user interference, commonly known as crosstalk. In this thesis, we develop signal and spectrum coordination techniques that aim at avoiding, minimizing or even profiting from crosstalk. The collection of these techniques is commonly known in the literature as dynamic spectrum management (DSM). DSM has repeatedly been shown to provide formidable gains in the performance of DSL networks. It is an enabler for next generation
Evolutionary Roots of Arginase Expression and Regulation

Two main types of macrophage functions are known: classical (M1), producing nitric oxide, NO, and M2, in which arginase activity is primarily expressed. Ornithine, the product of arginase, is a substrate for synthesis of polyamines and collagen, important for growth and ontogeny of animals. M2 macrophages, expressing high level of mitochondrial arginase, have been implicated in promoting cell division and deposition of collagen during ontogeny and wound repair. Arginase expression is the default mode of tissue macrophages, but can also be amplified by signals, such as IL-4/13 or transforming growth factor-β (TGF-β) that accelerates wound healing and tissue repair. In worms, the induction of collagen gene is coupled with induction of immune response genes, both depending on the same TGF-β-like pathway. This suggests that the main function of M2 “heal” type macrophages is originally connected with the TGF-β superfamily of proteins, which are involved in regulation of tissue and organ differentiation in embryogenesis. Excretory–secretory products of metazoan parasites are able to induce M2-type of macrophage responses promoting wound healing without participation of Th2 cytokines IL-4/IL-13. The expression of arginase in lower animals can be induced by the presence of parasite antigens and TGF-β signals leading to collagen synthesis. This also means that the main proteins, which, in primitive metazoans, are involved in regulation of tissue and organ differentiation in embryogenesis are produced by innate immunity. The signaling function of NO is known already from the sponge stage of animal evolution. The cytotoxic role of NO molecule appeared later, as documented in immunity of marine mollusks and some insects. This implies that the M2-wound healing promoting function predates the defensive role of NO, a characteristic of M1 macrophages. Understanding when and how the M1 and M2 activities came to be in animals is useful for understanding how macrophage immunity, and immune responses operate.
A Combined Predictor for Item-Based Collaborative Filtering

Collaborative filtering is one of most important technologies in the field of recommender systems, the process of making predictions about user preferences for products or services by learning known user-item relationships. In this paper, slope one and item-based nearest neighbor collaborative filtering algorithms are analyzed on the Movie Lens dataset. In order to obtain better accuracy and rationality, a new combined approach is proposed that takes advantages of slope one and item-based nearest neighbor model. In addition, simple gradient descent and bias effects are used further to improve performance. Finally, some experiments are implemented on the dataset, and the experimental results show that the proposed final solution achieves great improvement of prediction accuracy when compared to the method of using slope one or item-based nearest neighbor model alone.
Outcomes in Women and Minorities Compared With White Men 1 Year After Everolimus-Eluting Stent Implantation: Insights and Results From the PLATINUM Diversity and PROMUS Element Plus Post-Approval Study Pooled Analysis

Importance There exist limited outcomes data for women and minorities after contemporary percutaneous coronary intervention (PCI). Objective To examine 1-year outcomes in women and minorities vs white men after PCI with everolimus-eluting stents. Design, Settings, and Participants The PLATINUM Diversity study was a single-arm study enrolling women and minorities. Patient-level pooling with the PROMUS Element Plus Post-Approval Study was prespecified. Data on social determinants of health and language were collected in the PLATINUM Diversity cohort, which included 1501 patients at 52 US sites. The PROMUS Element Plus Post-Approval study enrolled 2681 patients at 52 US sites with some site overlap and included an “all-comers” population. All patients were enrolled beginning in October 2014 and were followed for 12 months. Analyses began in August 2016. Interventions Patients received 1 or more everolimus-eluting stent implantation. Main Outcomes and Measures The primary end point was 1-year major adverse cardiac events (MACE), which included death/myocardial infarction (MI)/target vessel revascularization. Secondary ischemic end points were also evaluated. Results The pooled study consisted of 4182 patients: 1635 white men (39.1%), 1863 women (white and minority) (44.5%), and 1059 minority patients (women and men) (25.3%). Women and minorities had a higher prevalence of diabetes, prior stroke, hypertension, renal disease, and congestive heart failure than white men but lower rates of multivessel disease, prior coronary artery bypass graft surgery, prior MI, and smoking. Unadjusted 1-year MACE rates (white men, 7.6%; women, 8.6%; minorities, 9.6%) were similar between groups with no significant differences after risk adjustment. The adjusted risk of death/MI was higher among women (odds ratio, 1.6; 95% CI, 1.1-2.4) and minorities (odds ratio, 1.9; 95% CI, 1.2-2.8) compared with white men and the adjusted risk of MI was higher in minorities (odds ratio, 2.6; 95% CI, 1.4-4.8). These differences were driven primarily by nonstent-related MIs. Within the PLATINUM Diversity cohort, the independent predictors of MACE were cardiogenic shock, renal disease, history of peripheral vascular disease, multivessel disease, widowhood, and lack of private insurance. Conclusions and Relevance After contemporary everolimus-eluting stent implantation, women and minorities experience a similar risk of 1-year MACE but a higher adjusted risk of recurrent ischemic events primarily because of nonstent-related MIs. Both clinical and angiographic factors and social determinants of health, including widowhood and insurance status, contribute to 1-year MACE among women and minorities.
Intrapartum Clinical, Sonographic, and Parous Patients' Estimates of Newborn Birth Weight

The accuracy of estimating birth weight clinically, sono-graphically (using femur length and abdominal circumference), and by maternal prediction was studied prospectively in 106 term parous women who were in active labor. Estimates of birth weight by these women had lower standardized error (86.8 ± 78.0 g/kg) than either clinical estimates (90.2 ± 84.8 g/kg) or sonographically derived estimates (155.8 ± 118.0 g/kg) of birth weight (P = not significant). Maternal estimates of birth weight were within ± 10% of the actual weight in 69.8%, compared with 66.1% for clinical estimates and 42.4% for sonography. A term parous woman in labor can predict the birth weight with accuracy comparable to a clinical estimation by a physician or a sonographic estimate based on infant measurements.
Distributed under Creative Commons Cc-by 4.0 Physortr: a Fast, Flexible Tool for Sorting Phylogenetic Trees in R

A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R package for classifying phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa based on tip labels (i.e., leaves) on a tree, with customisable options to assess clades within the context of the whole tree. Using simulated and empirical datasets, we demonstrate the potential and scalability of PhySortR in analysis of thousands of phylogenetic trees without a priori assumption of tree-rooting, and in yielding readily interpretable trees that unambiguously satisfy the query. PhySortR is a command-line tool that is freely available and easily automatable.
Severity of Cardiovascular Disease Outcomes Among Patients With HIV Is Related to Markers of Inflammation and Coagulation

Background In the general population, raised levels of inflammatory markers are stronger predictors of fatal than nonfatal cardiovascular disease (CVD) events. People with HIV have elevated levels of interleukin‐6 (IL‐6), high‐sensitivity C‐reactive protein (hsCRP), and D‐dimer; HIV‐induced activation of inflammatory and coagulation pathways may be responsible for their greater risk of CVD. Whether the enhanced inflammation and coagulation associated with HIV is associated with more fatal CVD events has not been investigated. Methods and Results Biomarkers were measured at baseline for 9764 patients with HIV and no history of CVD. Of these patients, we focus on the 288 that experienced either a fatal (n=74) or nonfatal (n=214) CVD event over a median of 5 years. Odds ratios (ORs) (fatal versus nonfatal CVD) (95% confidence intervals [CIs]) associated with a doubling of IL‐6, D‐dimer, hsCRP, and a 1‐unit increase in an IL‐6 and D‐dimer score, measured a median of 2.6 years before the event, were 1.39 (1.07 to 1.79), 1.40 (1.10 to 1.78), 1.09 (0.93 to 1.28), and 1.51 (1.15 to 1.97), respectively. Of the 214 patients with nonfatal CVD, 23 died during follow‐up. Hazard ratios (95% CI) for all‐cause mortality were 1.72 (1.28 to 2.31), 1.73 (1.27 to 2.36), 1.44 (1.15 to 1.80), and 1.88 (1.39 to 2.55), respectively, for IL‐6, D‐dimer, hsCRP, and the IL‐6 and D‐dimer score. Conclusions Higher IL‐6 and D‐dimer levels reflecting enhanced inflammation and coagulation associated with HIV are associated with a greater risk of fatal CVD and a greater risk of death after a nonfatal CVD event. Clinical Trial Registration URL: http://www.clinicaltrial. gov Unique identifier: SMART: NCT00027352, ESPRIT: NCT00004978, SILCAAT: NCT00013611.
Improved Algorithm for Gradient Vector Flow Based Active Contour Model Using Global and Local Information

Active contour models are used to extract object boundary from digital image, but there is poor convergence for the targets with deep concavities. We proposed an improved approach based on existing gradient vector flow methods. Main contributions of this paper are a new algorithm to determine the false part of active contour with higher accuracy from the global force of gradient vector flow and a new algorithm to update the external force field together with the local information of magnetostatic force. Our method has a semidynamic external force field, which is adjusted only when the false active contour exists. Thus, active contours have more chances to approximate the complex boundary, while the computational cost is limited effectively. The new algorithm is tested on irregular shapes and then on real images such as MRI and ultrasound medical data. Experimental results illustrate the efficiency of our method, and the computational complexity is also analyzed.