Miracle-dz/UniFAR-FTUs huggingface dataset:
Swimming through sand: connectivity of aquatic fauna in deserts

Abstract Freshwater ecosystems in arid regions range from highly fragmented to highly connected, and connectivity has been assumed to be a major factor in the persistence of aquatic biota in arid environments. This review sought to synthesize existing research on genetic estimation of population connectivity in desert freshwaters, identify knowledge gaps, and set priorities for future studies of connectivity in these environments. From an extensive literature search, we synthesized the approaches applied, systems studied, and conclusions about connectivity reached in population genetic research concerning desert freshwater connectivity globally. We restrict our scope to obligate aquatic fauna that disperse largely via freshwaters and exclude those with active aerial dispersal abilities. We examined 92 papers, comprising 133 studies, published from 1987 to 2014. Most described studies of fishes and invertebrates in the deserts of Australia and North America. Connectivity declined with increasing scale, but did not differ significantly among arid regions or taxonomic classes. There were significant differences in connectivity patterns between species with different dispersal abilities, and between spring and riverine habitats at local scales. Population connectivity in desert freshwaters is typically most influenced by the ecology of the species concerned and hydrological connectivity. Most studies did not assess predefined models of connectivity, but described gene flow and/or genetic structure. Climate change and anthropogenic impacts worldwide are likely to increase the incidence and impact of habitat fragmentation in already threatened desert freshwaters. To reduce this risk, biodiversity conservation and environmental management must address connectivity, but often the required information does not exist. Researchers can provide this by explicitly considering the effects of hydrology and species’ ecology on connectivity, and incorporating these into connectivity models, which are vital for understanding connectivity in desert freshwaters.
Software Defined Infrastructure: Rethinking Cybersecurity with a More Capable Toolset

In Software Defined Infrastructure (SDI), virtualization techniques are used to decouple applications and higher-level services from their underlying physical compute, storage, and network resources. The approach offers a set of powerful new capabilities (isolation, encapsulation, portability, interposition), including the formation of a software-based, infrastructure-wide control plane for orchestrated management. In this position paper, we identify opportunities for revisiting ongoing cybersecurity challenges using SDI as a powerful new toolset. Benefits of this approach can be broadly utilized in public, private, and hybrid clouds, data centers, enterprise computing, IoT deployments, and more. The discussion motivates the research challenge underlying VMware's partnership with the National Science Foundation to fund novel and foundational research in this area. Known as the NSF/VMware Partnership on Software Defined Infrastructure as a Foundation for Clean-Slate Computing Security (SDI-CSCS), the jointly funded university research program is set to begin in the fall of 2017.
Immigration-induced phase transition in a regulated multispecies birth-death process

Power-law-distributed species counts or clone counts arise in many biological settings such as multispecies cell populations, population genetics, and ecology. This empirical observation that the number of species ck represented by k individuals scales as negative powers of k is also supported by a series of theoretical birth–death–immigration (BDI) models that consistently predict many low-population species, a few intermediate-population species, and very high-population species. However, we show how a simple global population-dependent regulation in a neutral BDI model destroys the power law distributions. Simulation of the regulated BDI model shows a high probability of observing a high-population species that dominates the total population. Further analysis reveals that the origin of this breakdown is associated with the failure of a mean-field approximation for the expected species abundance distribution. We find an accurate estimate for the expected distribution by mapping the problem to a lower-dimensional Moran process, allowing us to also straightforwardly calculate the covariances . Finally, we exploit the concepts associated with energy landscapes to explain the failure of the mean-field assumption by identifying a phase transition in the quasi-steady-state species counts triggered by a decreasing immigration rate.
Corneal epithelial toxicity with intravitreal methotrexate in a case of B-cell lymphoma with ocular involvement

A 49-year-old woman, known case of diffuse large B-cell lymphoma, presented with complaints of floater in both eyes since 3 days. On examination, visual acuity was 0.18 logMAR in both eyes. Indirect ophthalmoscopy revealed presence of vitreous clumps. Vitreous biopsy was done and the histopathological report suggested a diagnosis of ocular lymphoma. The patient was treated with weekly injections of intravitreal methotrexate in both eyes. The patient developed severe photophobia, watering, redness and diminution of vision in the both eyes 2 days following the fifth dose of intravitreal methotrexate. Severe limbitis with annular corneal epitheliopathy and corneal haze was noted on slit-lamp examination. The patient was started on topical lubricants, antibiotic, ciclosporin, loteprednol, folinic acid and oral folic acid. Complete resolution was noted at 2-week follow-up. The patient, however, refused further injections and was kept on close follow-up to look for recurrence of the disease.
Local adaptation and the evolution of inversions on sex chromosomes and autosomes

Spatially varying selection with gene flow can favour the evolution of inversions that bind locally adapted alleles together, facilitate local adaptation and ultimately drive genomic divergence between species. Several studies have shown that the rates of spread and establishment of new inversions capturing locally adaptive alleles depend on a suite of evolutionary factors, including the strength of selection for local adaptation, rates of gene flow and recombination, and the deleterious mutation load carried by inversions. Because the balance of these factors is expected to differ between X (or Z) chromosomes and autosomes, opportunities for inversion evolution are likely to systematically differ between these genomic regions, though such scenarios have not been formally modelled. Here, we consider the evolutionary dynamics of X-linked and autosomal inversions in populations evolving at a balance between migration and local selection. We identify three factors that lead to asymmetric rates of X-linked and autosome inversion establishment: (1) sex-biased migration, (2) dominance of locally adapted alleles and (3) chromosome-specific deleterious mutation loads. This theory predicts an elevated rate of fixation, and depressed opportunities for polymorphism, for X-linked inversions. Our survey of data on the genomic distribution of polymorphic and fixed inversions supports both theoretical predictions. This article is part of the theme issue ‘Linking local adaptation with the evolution of sex differences'.
Treatment of developmental dysplasia of the hip with the Pavlik harness in children under six months of age: indications, results and failures

Purpose The aim of this article is to review the current concepts in the indications, results and failure causes of the treatment of developmental dysplasia of the hip (DDH) with the Pavlik harness. Methods The reported variables influencing the outcome in the Pavlik harness treatment were analyzed. Results Significant discrepancies about the clinical and radiological outcomes, the rates of failure and complications as well as the variables influencing the treatment outcome occur in the published studies due to the heterogeneity of the data and the differences in the methods used. The overall short-, mid- or long-term success rate of the treatment ranges from 45% to 100% and it is commonly over 75%. The rate of osteonecrosis of the femoral head ranges from 1% to 30%. Age, gender, laterality, radiological or clinical severity of the initial hip pathology and parents’ compliance are the commonly reported determinants of failure of the treatment. Conclusion The failure in treatment with the Pavlik harness is multifactorial, initial type of hip dysplasia being the most prominent followed by the treatment initiation age. This type of treatment cannot be considered as the best option in Graf IV hips (hip ultrasonography) or highly dislocated hips (plain radiography) and in infants older than three months of age, as the risk of failure and development of complications including osteonecrosis and femoral nerve palsy seem to increase in such circumstances. Large-scale, comparative studies including homogenous data are needed to answer the unsolved questions concerning indications.
Targeting TGF-β Signaling in Kidney Fibrosis

Renal fibrosis is the final common pathway of numerous progressive kidney diseases, and transforming growth factor-β (TGF-β) has an important role in tissue fibrosis by up-regulating matrix protein synthesis, inhibiting matrix degradation, and altering cell-cell interaction. Many strategies targeting TGF-β, including inhibition of production, activation, binding to the receptor, and intracellular signaling, have been developed. Some of them were examined in clinical studies against kidney fibrosis, and some are applied to other fibrotic diseases or cancer. Here, I review the approaches targeting TGF-β signaling in kidney fibrosis.
Closed reduction in late-detected developmental dysplasia of the hip: indications, results and complications

Purpose The aim of the study was a review of the literature in order to evaluate the results and complications of closed reduction in late-detected developmental dysplasia of the hip (DDH). Methods This study consisted of an analysis of the literature relative to late-detected DDH treatment options considering hip congruency, rates of re-dislocation and of avascular necrosis. Results Gradual closed reduction (Petit-Morel method) appears to be an effective method concerning joint congruency restitution. Dislocation relapse and avascular necrosis are more efficiently prevented with closed versus open reduction. The tendency for spontaneous correction of acetabular dysplasia decreases if closed reduction is performed after 18 months of age. Patient age at the beginning of traction should be considered for the prognosis, with a lower rate of satisfactory results showing after the age of 3 years. Conclusion In our opinion, the Petit-Morel method is a suitable treatment option for children aged between six months and three years with idiopathic DDH.
Supporting out of office software development using personal devices

Software developers typically use multiple large screens in their office setup. However, they often work away from the office where such a setup is not available, instead only working with a laptop computer and drastically reduced screen real estate. We explore how developers can be better supported in ad-hoc scenarios, for example when they work in a cafe, an airport, or at a client's site. We present insights into current work practices and challenges when working away from the usual office desk sourced from a survey of professional software developers. Based on these insights, we introduce an IDE that makes use of additional personal devices, such as a phone or a tablet. Parts of the IDE can be offloaded to these mobile devices, for example the application that is being developed, a debugging console or navigational elements. A qualitative evaluation with professional software developers showed that they appreciate the increased screen real estate.
Theory-Driven Automated Content Analysis of Suicidal Tweets : Using Typicality-Based Classification for LDA Dataset

This study provides a methodological framework for the computer to classify tweets according to variables of the Theory of Planned Behavior. We present a sequential process of automated text analysis which combined supervised approach and unsupervised approach in order to make the computer to detect one of TPB variables in each tweet. We conducted Latent Dirichlet Allocation (LDA), Nearest Neighbor, and then assessed "typicality" of newly labeled tweets in order to predict classification boundary. Furthermore, this study reports findings from a content analysis of suicide-related tweets which identify traits of information environment in Twitter. Consistent with extant literature about suicide coverage, the findings demonstrate that tweets often contain information which prompt perceived behavior control of committing suicide, while rarely provided deterring information on suicide. We conclude by highlighting implications for methodological advances and empirical theory studies.
Educational Case: Pheochromocytoma

The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see http://journals.sagepub. com/doi/10.1177/2374289517715040.
Systemic Inflammation and Acute-on-Chronic Liver Failure: Too Much, Not Enough

ACLF is a specific, but complex and multifactorial form of acute decompensation of cirrhosis and is characterized by an extraordinary dynamic natural course, rapidly evolving organ failure, and high short-term mortality. Dysbalanced immune function is central to its pathogenesis and outcome with an initial excessive systemic inflammatory response that drives organ failure and mortality. Later in its course, immuno-exhaustion/immunoparalysis prevails predisposing the patient to secondary infectious events and reescalation in end-organ dysfunction and mortality. The management of patients with ACLF is still poorly defined. However, as its pathophysiology is gradually being unravelled, potential therapeutic targets emerge that warrant further study such as restoring or substituting albumin via plasma exchange or via albumin dialysis and evaluating usefulness of TLR4 antagonists, modulators of gut dysbiosis (pre- or probiotics), and FXR-agonists.
Auto-switching list search interface for touchscreen smartwatches

As smartwatch functions expand, target selection among many items will probably become a common task. List search interfaces (LSIs) for a smartwatch use a prefix matching query to search for items, and need two modes because of the small screen size: query input mode and list navigation mode. Despite the modes, LSIs may be more efficient than list interfaces (LIs), which involve no text querying, for large pools. Actually, we could show that the LSI outperformed the LI for pool sizes over 60. However, we also found that the LSI users experience overhead when deciding whether to switch the modes or not. To reduce the overhead, we designed two auto-switching LSIs: input-length-based auto-switching LSI (IA-LSI) and list-size-based auto-switching LSI (LA-LSI). We could show both auto-switching LSIs outperformed the conventional LSI for pool sizes over 60. We also conducted experiments with the auto-switching LSIs for various pool sizes, and provided their results and guidelines for the optimal switching criteria for the LSIs.
Size and topology modulate the effects of frustration in protein folding

Significance Frustration is a central concept in the study of protein folding kinetics. While it has been proposed that most proteins are minimally frustrated, recent experiments have found systems with surprisingly slow reconfiguration dynamics, suggesting an underlying landscape that is frustrated or “rough. ” Our results suggest that protein size and topology play a role in determining how sensitive a protein is to frustration. The presence of conflicting interactions, or frustration, determines how fast biomolecules can explore their configurational landscapes. Recent experiments have provided cases of systems with slow reconfiguration dynamics, perhaps arising from frustration. While it is well known that protein folding speed and mechanism are strongly affected by the protein native structure, it is still unknown how the response to frustration is modulated by the protein topology. We explore the effects of nonnative interactions in the reconfigurational and folding dynamics of proteins with different sizes and topologies. We find that structural correlations related to the folded state size and topology play an important role in determining the folding kinetics of proteins that otherwise have the same amount of nonnative interactions. In particular, we find that the reconfiguration dynamics of α-helical proteins are more susceptible to frustration than β-sheet proteins of the same size. Our results may explain recent experimental findings and suggest that attempts to measure the degree of frustration due to nonnative interactions might be more successful with α-helical proteins.
Retrospective comparison of the efficacy and the toxicity of standard and modified FOLFIRINOX regimens in patients with metastatic pancreatic adenocarcinoma.

Background FOLFIRINOX stands a major breakthrough in the management of metastatic pancreatic adenocarcinoma (MPA). Nonetheless, significant side-effects have been reported using standard FOLFIRINOX. We aimed to compare survival outcomes, response rates and toxicity of patients treated with standard or modified FOLFIRINOX in MPA. Methods We included patients aged ≥18 years old, with pathologically confirmed MPA, treated with FOLFIRINOX in the first-line setting. Patients submitted to at least one cycle of full-dose FOLFIRINOX were grouped in the standard FOLFIRINOX group. Results Patients treated with standard FOLFIRINOX were younger and had less comorbidity. We observed no differences in overall survival or in progression-free survival between the two treatment arms. The only variable independently associated with OS was log10[neutrophil-to-lymphocyte ratio (NLR)]. Modified FOLFIRINOX was associated with a lower dose reduction rate, but a slightly increased incidence of severe toxicity. Conclusions Modified FOLFIRINOX presents the same activity against MPA as standard FOLFIRINOX. We found no significant differences in toxicity, possibly due to patient selection and a higher dose reduction rate in the standard FOLFIRINOX arm. NLR stood as an important prognostic marker and further research is needed to comprehend its biological meaning in pancreatic cancer.
Deeply Supervised Depth Map Super-Resolution as Novel View Synthesis

Deep convolutional neural network (DCNN) has been successfully applied to depth map super-resolution and outperforms existing methods by a wide margin. However, there still exist two major issues with these DCNN-based depth map super-resolution methods that hinder the performance: 1) the low-resolution depth maps either need to be up-sampled before feeding into the network or substantial deconvolution has to be used and 2) the supervision (high-resolution depth maps) is only applied at the end of the network, thus it is difficult to handle large up-sampling factors, such as <inline-formula> <tex-math notation="LaTeX">$\times 8$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\times 16$ </tex-math></inline-formula>. In this paper, we propose a new framework to tackle the above problems. First, we propose to represent the task of depth map super-resolution as a series of novel view synthesis sub-tasks. The novel view synthesis sub-task aims at generating (synthesizing) a depth map from a different camera pose, which could be learned in parallel. Second, to handle large up-sampling factors, we present a deeply supervised network structure to enforce strong supervision in each stage of the network. Third, a multi-scale fusion strategy is proposed to effectively exploit the feature maps at different scales and handle the blocking effect. In this way, our proposed framework could deal with challenging depth map super-resolution efficiently under large up-sampling factors (e.g., <inline-formula> <tex-math notation="LaTeX">$\times 8$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\times 16$ </tex-math></inline-formula>). Our method only uses the low-resolution depth map as input, and the support of color image is not needed, which greatly reduces the restriction of our method. Extensive experiments on various benchmarking data sets demonstrate the superiority of our method over current state-of-the-art depth map super-resolution methods.
Computing or Estimating Extensions' Probabilities over Structured Probabilistic Argumentation Frameworks

Probabilistic argumentation combines Dung’s abstract argumentation framework with probability theory in order to model uncertainty in argumentation. In this setting, we address the fundamental problem of computing the probability that a set of arguments is an extension according to a given semantics over structured probabilistic argumentation frameworks. We focus on the most popular semantics (i.e., admissible, stable, complete, grounded, and preferred), for which the problem of computing extension’s probabilities over structured probabilistic argumentation frameworks was shown to be FP#P -complete. Our aim is that of experimentally establishing when, due to the complexity of the problem and the size of the structured probabilistic argumentation framework, estimating the extension’s probabilities is preferable to computing it (as computing the probability cannot be done in reasonable time). To do this, we devise two algorithms: the naive one, which computes the extension’s probabilities, and the Monte-Carlo simulation one, which estimates the extension’s probabilities, and evaluate both algorithms over two datasets to compare their efficiency.
mpact of Tricuspid egurgitation on Long-Term Survival

OBJECTIVES The goal of this study was to examine mortality associated with tricuspid regurgitation (TR) after controlling for left ventricular ejection fraction (LVEF), right ventricular (RV) dilation and dysfunction, and pulmonary artery systolic pressure (PASP). BACKGROUND Tricuspid regurgitation is a frequent echocardiographic finding; however, the association with prognosis is unclear. METHODS We retrospectively identified 5,223 patients (age 66.5 12.8 years; predominantly male) undergoing echocardiography at one of three Veterans Affairs Medical Center laboratories over a period of four years. Follow-up data were available for four years (mean 498 402 days). Kaplan-Meier and proportional hazards methods were used to compare differences in survival among TR grades. RESULTS Mortality increased with increasing severity of TR. The one-year survival was 91.7% with no TR, 90.3% with mild TR, 78.9% with moderate TR, and 63.9% with severe TR. Moderate or greater TR was associated with increased mortality regardless of PASP (hazard ratio [HR] 1.31, 95% confidence interval [CI] 1.16 to 1.49 for PASP 40 mm Hg; HR 1.32, 95% CI 1.05 to 1.62 for PASP 40 mm Hg) and LVEF (HR 1.49, 95% CI 1.34 to 1.66 for EF 50%; HR 1.54, 95% CI 1.37 to 1.71 for EF 50%). When adjusted for age, LVEF, inferior vena cava size, and RV size and function, survival was worse for patients with moderate (HR 1.17, 95% CI 0.96 to 1.42) and severe TR (HR 1.31, 95% CI 1.05 to 1.66) than for those with no TR. CONCLUSIONS We conclude that increasing TR severity is associated with worse survival in men regardless of LVEF or pulmonary artery pressure. Severe TR is associated with a poor prognosis, independent of age, biventricular systolic function, RV size, and dilation of the inferior vena cava. (J Am Coll Cardiol 2004;43:405–9) © 2004 by the American College of Cardiology Foundation