Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary Protein Affects Gene Expression and Prevents Lipid Accumulation in the Liver in Mice

Background and Aims High protein (HP) diets are suggested to positively modulate obesity and associated increased prevalence of non-alcoholic fatty liver (NAFLD) disease in humans and rodents. The aim of our study was to detect mechanisms by which a HP diet affects hepatic lipid accumulation. Methods To investigate the acute and long term effect of high protein ingestion on hepatic lipid accumulation under both low and high fat (HF) conditions, mice were fed combinations of high (35 energy%) or low (10 energy%) fat and high (50 energy%) or normal (15 energy%) protein diets for 1 or 12 weeks. Effects on body composition, liver fat, VLDL production rate and the hepatic transcriptome were investigated. Results Mice fed the HP diets displayed a lower body weight, developed less adiposity and decreased hepatic lipid accumulation, which could be attributed to a combination of several processes. Next to an increased hepatic VLDL production rate, increased energy utilisation due to enhanced protein catabolic processes, such as transamination, TCA cycle and oxidative phosphorylation was found upon high protein ingestion. Conclusion Feeding a HP diet prevented the development of NAFLD by enhancing lipid secretion into VLDL particles and a less efficient use of ingested calories.
Lightweight computation tree tracing for lazy functional languages

A computation tree of a program execution describes computations of functions and their dependencies. A computation tree describes how a program works and is at the heart of algorithmic debugging. To generate a computation tree, existing algorithmic debuggers either use a complex implementation or yield a less informative approximation. We present a method for lazy functional languages that requires only a simple tracing library to generate a detailed computation tree. With our algorithmic debugger a programmer can debug any Haskell program by only importing our library and annotating suspected functions.
Toward an exact adjoint : semicircle versus hyperbola

The correctness of an adjoint operator entirely depends on the correctness of the corresponding forward modeling operator. In migration, the input-oriented algorithm implies more correct forward modeling than the output-oriented algorithm does. One big difference between the two algorithms is the domain of interpolation, and this is one of the major sources of migration artifacts. Whereas the input-oriented algorithm requires interpolation in the model space, the output-oriented algorithm requires interpolation in the data space. For Kirchhoff migration, the method of semicircle superposition and the method of hyperbola summation correspond to the input-oriented and output-oriented algorithms, respectively. The same analogy can be applied to Stolt migration. Levin (1994) suggested the input-oriented algorithm that is the counterpart to the output-oriented algorithm suggested by the SEP “in-time" group (Popovici et al., 1993; Lin et al.,1993; Blondel and Muir, 1993)
The MITLL-AFRL IWSLT 2016 Systems

This report summarizes the MITLL-AFRL MT and ASR systems and the experiments run during the 2016 IWSLT evaluation campaign. Building on lessons learned from previous years’ results, we refine our ASR systems and examine the explosion of neural machine translation systems and techniques developed in the past year. We experiment with a variety of phrase-based, hierarchical and neural-network approaches in machine translation and utilize system combination to create a composite system with the best characteristics of all attempted MT approaches.
ec 1 99 8 Stable Oscillations of Black Hole Accretion Discs

The study of stable accretion disc oscillations relevant to black hole candidate (BHC) systems dates back over twenty years. Prior work has focused on both unstable and (potentially) stable disc oscillations. The former has often been suspected of being the underlying cause for the observed broad-band variability in BHC, whereas the latter has had little observational motivation until quite recently. In this article, we review both the observations and theory of (predominantly) stable oscillations in BHC systems. We discuss how variability, both broad-band and quasi-periodic, is characterized in BHC. We review previous claims of low frequency features in BHC, and we discuss the recent observational evidence for stable, high frequency oscillations in so-called ‘galactic microquasars’. As a potential explanation for the latter observations, we concentrate on a class of theories– with a rich history of study– that we call ‘diskoseismology’. We also discuss other recent alternative theories, namely Lense-Thirring precession of tilted rings near the disc inner edge. We discuss the advantages and disadvantages of each of these theories, and discuss possible future directions for study.
Association between glutathione S-transferase M1/T1 gene polymorphisms and susceptibility to endometriosis: A systematic review and meta-analysis

Endometriosis is a polygenic/multifactorial disease caused by interactions between multiple genes and the environment. Findings from studies evaluating the association between the glutathione S-transferase (GST) M1/T1 null genotype and susceptibility to endometriosis are inconsistent. This meta-analysis updated and reevaluated the possible associations between GSTM1, GSTT1 and combined GSTM1/GSTT1 (null genotype versus wild-type) gene polymorphisms and susceptibility to endometriosis. The PubMed, Embase and Chinese BioMedical Literature databases and Google Scholar were searched for case-control genetic association studies on GSTM1/GSTT1 (null genotype versus wild-type) gene polymorphisms and endometriosis in comparison with non-endometriosis or healthy controls. Fixed-effect and random-effect meta-analytical techniques were conducted for the outcome measure and subgroup analyses. The meta-analysis demonstrated significant associations between the GSTM1 [odds ratio (OR)=1.56; 95% confidence interval (CI): 1.25–1.95; P<0.0001), GSTT1 (OR=1.31; 95% CI: 1.02–1.68; P=0.037) and GSTM1/GSTT1 (OR=1.68; 95% CI: 1.29–2.17; P<0.0001) null genotypes and increased risk for endometriosis. The results suggest that the GSTM1, GSTT1, and combined GSTM1/GSTT1 null genotypes increase susceptibility to endometriosis. Additional well-designed studies and precise analyses are warranted to confirm these findings.
Identification of new stress-induced microRNA and their targets in wheat using computational approach

MicroRNAs (miRNAs) are a class of short endogenous non-coding small RNA molecules of about 18–22 nucleotides in length. Their main function is to downregulate gene expression in different manners like translational repression, mRNA cleavage and epigenetic modification. Computational predictions have raised the number of miRNAs in wheat significantly using an EST based approach. Hence, a combinatorial approach which is amalgamation of bioinformatics software and perl script was used to identify new miRNA to add to the growing database of wheat miRNA. Identification of miRNAs was initiated by mining the EST (Expressed Sequence Tags) database available at National Center for Biotechnology Information. In this investigation, 4677 mature microRNA sequences belonging to 50 miRNA families from different plant species were used to predict miRNA in wheat. A total of five abiotic stress-responsive new miRNAs were predicted and named Ta-miR5653, Ta-miR855, Ta-miR819k, Ta-miR3708 and Ta-miR5156. In addition, four previously identified miRNA, i.e., Ta-miR1122, miR1117, Ta-miR1134 and Ta-miR1133 were predicted in newly identified EST sequence and 14 potential target genes were subsequently predicted, most of which seems to encode ubiquitin carrier protein, serine/threonine protein kinase, 40S ribosomal protein, F-box/kelch-repeat protein, BTB/POZ domain-containing protein, transcription factors which are involved in growth, development, metabolism and stress response. Our result has increased the number of miRNAs in wheat, which should be useful for further investigation into the biological functions and evolution of miRNAs in wheat and other plant species.
Polyomavirus nephropathy in native kidneys and renal allografts: an update on an escalating threat

Polyomavirus nephropathy, also termed BK‐virus nephropathy (BKN) after the main causative agent, the polyoma‐BK‐virus strain, is a significant complication after kidney transplantation. BKN is the most common viral infection that affects renal allografts with a prevalence of 1–9% on average 8–13 months post surgery. It can also occur sporadically in native kidneys. Viral nephropathy is caused by the (re)activation of latent BK viruses that enter into a replicative cycle under sustained and intensive immunosuppression. Pure productive kidney infections with JC‐ and SV‐40 polyomaviruses are exceptionally rare. BKN is morphologically defined by the presence of intranuclear viral inclusion bodies in epithelial cells and tubular injury, which is the morphological correlate for renal dysfunction. Renal disease can progress through different histologic stages (from early BKN stage A to late fibrotic stage C) that carry prognostic significance; disease stages B and C often result in chronic kidney (allograft) dysfunction and end‐stage renal disease. The clinical goal is to diagnose viral nephropathy in disease stage A and to limit chronic renal injury. Strategies to recognize, classify, and manage BKN are critically discussed including ancillary techniques for risk assessment and patient monitoring: (i) urine cytology and the search for so‐called ‘decoy cells’; (ii) PCR analyses for viral load measurements in the plasma and urine; and (iii) negative staining urine electron microscopy to identify viral particles.
What's hot and what's not: Windowed developer topic analysis

As development on a software project progresses, developers shift their focus between different topics and tasks many times. Managers and newcomer developers often seek ways of understanding what tasks have recently been worked on and how much effort has gone into each; for example, a manager might wonder what unexpected tasks occupied their team's attention during a period when they were supposed to have been implementing new features. Tools such as Latent Dirichlet Allocation (LDA) and Latent Semantic Indexing (LSI) can be used to extract a set of independent topics from a corpus of commit-log comments. Previous work in the area has created a single set of topics by analyzing comments from the entire lifetime of the project. In this paper, we propose windowing the topic analysis to give a more nuanced view of the system's evolution. By using a defined time-window of, for example, one month, we can track which topics come and go over time, and which ones recur. We propose visualizations of this model that allows us to explore the evolving stream of topics of development occurring over time. We demonstrate that windowed topic analysis offers advantages over topic analysis applied to a project's lifetime because many topics are quite local.
How people talk when teaching a robot

We examine affective vocalizations provided by human teachers to robotic learners. In unscripted one-on-one interactions, participants provided vocal input to a robotic dinosaur as the robot selected toy buildings to knock down. We find that (1) people vary their vocal input depending on the learner's performance history, (2) people do not wait until a robotic learner completes an action before they provide input and (3) people naïvely and spontaneously use intensely affective vocalizations. Our findings suggest modifications may be needed to traditional machine learning models to better fit observed human tendencies. Our observations of human behavior contradict the popular assumptions made by machine learning algorithms (in particular, reinforcement learning) that the reward function is stationary and path-independent for social learning interactions. We also propose an interaction taxonomy that describes three phases of a human-teacher's vocalizations: direction, spoken before an action is taken; guidance, spoken as the learner communicates an intended action; and feedback, spoken in response to a completed action.
Chronic Activation of Heme Free Guanylate Cyclase Leads to Renal Protection in Dahl Salt-Sensitive Rats

The nitric oxide (NO)/soluble guanylate cyclase (sGC)/cyclic guanosine monophasphate (cGMP)-signalling pathway is impaired under oxidative stress conditions due to oxidation and subsequent loss of the prosthetic sGC heme group as observed in particular in chronic renal failure. Thus, the pool of heme free sGC is increased under pathological conditions. sGC activators such as cinaciguat selectively activate the heme free form of sGC and target the disease associated enzyme. In this study, a therapeutic effect of long-term activation of heme free sGC by the sGC activator cinaciguat was investigated in an experimental model of salt-sensitive hypertension, a condition that is associated with increased oxidative stress, heme loss from sGC and development of chronic renal failure. For that purpose Dahl/ss rats, which develop severe hypertension upon high salt intake, were fed a high salt diet (8% NaCl) containing either placebo or cinaciguat for 21 weeks. Cinaciguat markedly improved survival and ameliorated the salt-induced increase in blood pressure upon treatment with cinaciguat compared to placebo. Renal function was significantly improved in the cinaciguat group compared to the placebo group as indicated by a significantly improved glomerular filtration rate and reduced urinary protein excretion. This was due to anti-fibrotic and anti-inflammatory effects of the cinaciguat treatment. Taken together, this is the first study showing that long-term activation of heme free sGC leads to renal protection in an experimental model of hypertension and chronic kidney disease. These results underline the promising potential of cinaciguat to treat renal diseases by targeting the disease associated heme free form of sGC.
Assessment of the Rotation Motion at the Papillary Muscle Short-Axis Plane with Normal Subjects by Two-Dimensional Speckle Tracking Imaging: A Basic Clinical Study

Background The aim of this study was to observe the rotation patterns at the papillary muscle plane in the Left Ventricle(LV) with normal subjects using two-dimensional speckle tracking imaging(2D-STI). Methods We acquired standard of the basal, the papillary muscle and the apical short-axis images of the LV in 64 subjects to estimate the LV rotation motion by 2D-STI. The rotational degrees at the papillary muscle short-axis plane were measured at 15 different time points in the analysis of two heart cycles. Results There were counterclockwise rotation, clockwise rotation, and counterclockwise to clockwise rotation at the papillary muscle plane in the LV with normal subjects, respectively. The ROC analysis of the rotational degrees was performed at the papillary muscle short-axis plane at the peak LV torsion for predicting whether the turnaround point of twist to untwist motion pattern was located at the papillary muscle level. Sensitivity and specificity were 97% and 67%, respectively, with a cut-off value of 0.34°, and an area under the ROC curve of 0.8. At the peak LV torsion, there was no correlation between the rotational degrees at the papillary muscle short-axis plane and the LVEF in the normal subjects(r = 0.000, p = 0.998). Conclusions In the study, we conclude that there were three rotation patterns at the papillary muscle short-axis levels, and the transition from basal clockwise rotation to apical counterclockwise rotation is located at the papillary muscle level.
Measurement and Analysis of Quality of Service of Mobile Networks in Afghanistan End User Perspective

Enhanced Quality of Service (QoS) and satisfaction of mobile phone user are major concerns of a service provider. In order to manage network efficiently and to provide enhanced end – to – end Quality of Experience (QoE), operator is expected to measure and analyze QoS from various perspectives and at different relevant points of network. The scope of this paper is measurement and statistically analysis of QoS of mobile networks from end user perspective in Afghanistan. The study is based on primary data collected on random basis from 1,515 mobile phone users of five cellular operators. The paper furthermore proposes adequate technical solutions to mobile operators in order to address existing challenges in the area of QoS and to remain competitive in the market. Based on the result of processed data, considering geographical locations, population and telecom regulations of the government, authors recommend deployment of small cells (SCs), increasing number of regular performance tests, optimal placement of base stations, increasing number of carriers, and high order sectorization as proposed technical solutions.
Picking the Fresh from the Rotten : Quote and Sentiment Extraction from Rotten Tomatoes Movie Reviews

Being able to quickly determine whether a movie is worth watching is one of the major appeals of the movie review website Rotten Tomatoes (www.rottentomatoes.com). The site gathers reviews from known movie critics, with each critic's review assigned a binary rating expressing the review’s sentiment, fresh (positive) or rotten (negative), and a quote, the single sentence/phrase from the review that best exemplifies that rating. This form capsule summarization allows users the ability to discern the consensus of a group of critics at a glance. A system was constructed to perform the "Rotten Tomatoes Task" of identifying the quote and rating from an unlabeled review. A maximum entropy classifier was trained on a corpus of reviews from Rotten Tomatoes that had their ratings and accompanying quotes identified. Lexical and positional features were used. In addition, the notion of regional coherence, from text-segmentation work, was applied to create features that would help identify potential quotes from a review. A discussion of the nature of this "Rotten Tomatoes Task" is given, as well as future avenues of investigation, including alternative evaluation methods.
On the measurement of Fragmentation

In this paper we propose a new party-system fragmentation measure as equivalent number of parties that fully takes into account the pivotal power of parties. The novel approach we adopt in the method of construction for an index of fragmentation allows us to take advantage of the theory of generalized means. We first construct the (class of) quasi-arithmetic mean(s) with Banzhaf power weight function for the party sizes and then, given the average size, we derive an equivalent-number of parties.
Effect of Electrode Shape on Impedance of Single HeLa Cell: A COMSOL Simulation

In disease prophylaxis, single cell inspection provides more detailed data compared to conventional examinations. At the individual cell level, the electrical properties of the cell are helpful for understanding the effects of cellular behavior. The electric field distribution affects the results of single cell impedance measurements whereas the electrode geometry affects the electric field distributions. Therefore, this study obtained numerical solutions by using the COMSOL multiphysics package to perform FEM simulations of the effects of electrode geometry on microfluidic devices. An equivalent circuit model incorporating the PBS solution, a pair of electrodes, and a cell is used to obtain the impedance of a single HeLa cell. Simulations indicated that the circle and parallel electrodes provide higher electric field strength compared to cross and standard electrodes at the same operating voltage. Additionally, increasing the operating voltage reduces the impedance magnitude of a single HeLa cell in all electrode shapes. Decreasing impedance magnitude of the single HeLa cell increases measurement sensitivity, but higher operational voltage will damage single HeLa cell.
Periodic retinoic acid–STRA8 signaling intersects with periodic germ-cell competencies to regulate spermatogenesis

Significance As male sex cells mature into sperm, two pivotal transitions are spermatogonial differentiation (exit from the stem cell pool) and meiotic initiation. These transitions occur in physical proximity, with 8.6-d periodicity. We report that the gene Stra8, essential for meiotic initiation, also promotes (but is not required for) spermatogonial differentiation. Moreover, injected RA induces both transitions to occur precociously. We conclude that a periodic RA signal, acting instructively through the common target Stra8, coordinates these transitions. This RA signal intersects with two distinct windows of sex-cell competency, which both begin while RA levels are low; sex cells respond quickly to rising RA. These mechanisms help account for the elaborate organization of sperm production, and its prodigious output. Mammalian spermatogenesis—the transformation of stem cells into millions of haploid spermatozoa—is elaborately organized in time and space. We explored the underlying regulatory mechanisms by genetically and chemically perturbing spermatogenesis in vivo, focusing on spermatogonial differentiation, which begins a series of amplifying divisions, and meiotic initiation, which ends these divisions. We first found that, in mice lacking the retinoic acid (RA) target gene Stimulated by retinoic acid gene 8 (Stra8), undifferentiated spermatogonia accumulated in unusually high numbers as early as 10 d after birth, whereas differentiating spermatogonia were depleted. We thus conclude that Stra8, previously shown to be required for meiotic initiation, also promotes (but is not strictly required for) spermatogonial differentiation. Second, we found that injection of RA into wild-type adult males induced, independently, precocious spermatogonial differentiation and precocious meiotic initiation; thus, RA acts instructively on germ cells at both transitions. Third, the competencies of germ cells to undergo spermatogonial differentiation or meiotic initiation in response to RA were found to be distinct, periodic, and limited to particular seminiferous stages. Competencies for both transitions begin while RA levels are low, so that the germ cells respond as soon as RA levels rise. Together with other findings, our results demonstrate that periodic RA–STRA8 signaling intersects with periodic germ-cell competencies to regulate two distinct, cell-type-specific responses: spermatogonial differentiation and meiotic initiation. This simple mechanism, with one signal both starting and ending the amplifying divisions, contributes to the prodigious output of spermatozoa and to the elaborate organization of spermatogenesis.