Miracle-dz/UniFAR-FTUs huggingface dataset:
Low serum testosterone is associated with adverse outcome in men with cirrhosis independent of the model for end‐stage liver disease score

Low serum testosterone has been retrospectively associated with mortality in men on the liver transplant waiting list. The impact of testosterone deficiency on other outcomes has not previously been assessed. We conducted a single center prospective observational study of all men with cirrhosis seen between 2013 and 2014. Baseline data included sex hormone profile, Model for End‐Stage Liver Disease (MELD) score, and standard biochemistry. Outcomes were recorded over 12 months including major infection, liver transplantation, and death. Of 268 cirrhotic men, the median MELD score was 10 (interquartile range [IQR], 8‐15) and median serum testosterone was 17.4 nmol/L (IQR, 8.9‐25.0 nmol/L). During the study period, 32 (12%) men died, 18 (7%) received a liver transplant, and 51 (19%) suffered a major infection. Mortality markedly increased when total testosterone fell below a threshold value of 8.3 nmol/L, and this cutoff was used for further analysis. Testosterone below 8.3 nmol/L was associated with the combined outcome of death or transplantation independently of the MELD score (hazard ratio [HR], 2.36; IQR, 1.16‐4.81; P = 0.02) for testosterone (and HR, 1.22; IQR, 1.18‐1.27; P < 0.001 for MELD). Low total testosterone was also an independent risk factor for major infection (HR, 3.61; IQR, 1.61‐8.06; P < 0.001) and nearly significant for mortality alone (HR, 2.39; IQR, 0.97‐5.88; P = 0.057). Low free testosterone (<139 pmol/L) was similarly independently associated with death or transplantation (HR, 2.43; IQR, 1.12‐5.29; P = 0.03) and infection (HR, 3.3; IQR, 1.46‐7.46; P = 0.004). In conclusion, low testosterone is a novel prognostic marker in men with cirrhosis that is numerically associated with increased mortality or need for transplantation, as well as risk for major infection. Interventional studies of testosterone therapy are required to investigate whether correcting low testosterone can reduce mortality and improve other clinical outcomes. Liver Transplantation 22 1482–1490 2016 AASLD.
Simulation and Analysis of GNSS-R Composite Waveforms Using GPS and Galileo Signals

Nowadays, several global navigation satellite system (GNSS) services coexist at L-band and some more will be available in the near future. These new signals were originally conceived to enhance the location accuracy, but they also offer a promising opportunity for improved GNSS-reflectometry (GNSS-R) retrievals. This work gives closed form expressions for GNSS-R waveform simulation using the composite GPS L1 and L5 and Galileo E1, E5, and E6 signals as function of the receiver bandwidth. The impact of the observation geometry and sea state on the waveform shape is studied in airborne and spaceborne conditions. Finally, the altimetric height bias using the derivative method is analyzed as function of the receiver bandwidth.
Human-powered Sorts and Joins

Crowdsourcing markets like Amazon's Mechanical Turk (MTurk) make it possible to task people with small jobs, such as labeling images or looking up phone numbers, via a programmatic interface. MTurk tasks for processing datasets with humans are currently designed with significant reimplementation of common workflows and ad-hoc selection of parameters such as price to pay per task. We describe how we have integrated crowds into a declarative workflow engine called Qurk to reduce the burden on workflow designers. In this paper, we focus on how to use humans to compare items for sorting and joining data, two of the most common operations in DBMSs. We describe our basic query interface and the user interface of the tasks we post to MTurk. We also propose a number of optimizations, including task batching, replacing pairwise comparisons with numerical ratings, and pre-filtering tables before joining them, which dramatically reduce the overall cost of running sorts and joins on the crowd. In an experiment joining two sets of images, we reduce the overall cost from $67 in a naive implementation to about $3, without substantially affecting accuracy or latency. In an end-to-end experiment, we reduced cost by a factor of 14.5.
Introduction to the Special Topic on Grammar Induction, Representation of Language and Language Learning

Grammar induction refers to the process of learning grammars and languages from data; this finds a variety of applications in syntactic pattern recognition, the modeling of natural language acquisition, data mining and machine translation. This special topic contains several papers presenting some of recent developments in the area of grammar induction and language learning, as applied to various problems in Natural Language Processing, including supervised and unsupervised parsing and statistical machine translation.
Children’s experience of sport in Australia

Australia is known as a ‘sporting nation’ and sport is central to its cultural identity. Children’s participation in leisure activities, including sport, is considered to be of such importance that it is enshrined as an international human right. There is a growing awareness, however, that children’s experience of sport is not always positive and that abuse and harm may occur in organised sport. This paper reports on a study designed to explore children’s experiences of organised sport, as recounted by young adults between the ages of 18 and 25 years. A mixed methods study design was implemented, which resulted in 107 survey responses and 10 follow-up interviews with young adults. Overwhelmingly, young people reported the lasting developmental benefits of participation in organised sport as children. More than 50% also reported negative experiences, including emotional and physical harm and sexual harassment. The reasons for these apparently contradictory findings are explored. The role of coaches, peers, parents and the wider sporting association ethos are investigated and suggestions made for future research.
MATRAS: a program for protein 3D structure comparison

The recent accumulation of large amounts of 3D structural data warrants a sensitive and automatic method to compare and classify these structures. We developed a web server for comparing protein 3D structures using the program Matras (http://biunit.aist-nara.ac.jp/matras). An advantage of Matras is its structure similarity score, which is defined as the log-odds of the probabilities, similar to Dayhoff's substitution model of amino acids. This score is designed to detect evolutionarily related (homologous) structural similarities. Our web server has three main services. The first one is a pairwise 3D alignment, which is simply align two structures. A user can assign structures by either inputting PDB codes or by uploading PDB format files in the local machine. The second service is a multiple 3D alignment, which compares several protein structures. This program employs the progressive alignment algorithm, in which pairwise 3D alignments are assembled in the proper order. The third service is a 3D library search, which compares one query structure against a large number of library structures. We hope this server provides useful tools for insights into protein 3D structures.
An Efficient Self-Transposing Memory Structure for 32-bit Video Processors

Many 2D data processing applications can be simplified and represented by use of 1D operations. Such tools, however, require applying both vertical and horizontal operations to the data blocks. The data transposing units is preferred to be used by the designers rather than applying individual operations for horizontal and vertical directions. Hence, designing a cost efficient and extendible transposing memory is a key issue for these applications. This paper proposes an efficient management strategy for using the SRAM modules in order to make a self-transposing memory architecture (STMA). In addition to its lower cost compared to flip-flop based buffers, the proposed architecture is more than 29% faster than usual SRAM based memory units. Simulations indicate that using the STMA in the H.264/AVC deblocking filter results in 60% speed improvement
Safety and cost effectiveness of early hospital discharge of lower risk children with cancer admitted for fever and neutropenia

Background. Standard treatment for fever during periods of chemotherapy‐induced neutropenia includes hospitalization and administration of intravenous antibiotics until the patient is afebrile and no longer neutropenic. This study prospectively evaluates the safety and cost‐effectiveness of early discharge of selected low risk children before recovery from neutropenia.
Ethnically diverse causes of Walker‐Warburg syndrome (WWS): FCMD mutations are a more common cause of WWS outside of the Middle East

Walker‐Warburg syndrome (WWS) is a genetically heterogeneous autosomal recessive disease characterized by congenital muscular dystrophy, cobblestone lissencephaly, and ocular malformations. Mutations in six genes involved in the glycosylation of á‐dystroglycan (POMT1, POMT2, POMGNT1, FCMD, FKRP and LARGE) have been identified in WWS patients, but account for only a portion of WWS cases. To better understand the genetics of WWS and establish the frequency and distribution of mutations across WWS genes, we genotyped all known loci in a cohort of 43 WWS patients of varying geographical and ethnic origin. Surprisingly, we reached a molecular diagnosis for 40% of our patients and found mutations in POMT1, POMT2, FCMD and FKRP, many of which were novel alleles, but no mutations in POMGNT1 or LARGE. Notably, the FCMD gene was a more common cause of WWS than previously expected in the European/American subset of our cohort, including all Ashkenazi Jewish cases, who carried the same founder mutation. © 2008 Wiley‐Liss, Inc.
An Improved Support Vector Regression Modeling for Taiwan Stock Exchange Market Weighted Index Forecasting

This study applies a novel neural network technique, support vector regression (SVR), to Taiwan stock exchange market weighted index (TAIEX) forecasting. To build an effective SVR model, SVR's parameters must be set carefully. This study proposes a novel approach, known as GA-SVR, which searches for SVR s optimal parameters using real value genetic algorithms. The experimental results demonstrate that SVR outperforms the ANN and RW models based on the normalized mean square error (NMSE), mean square error (MSE) and mean absolute percentage error (MAPE). Moreover, in order to test the importance and understand the features of SVR model, this study examines the effects of the number of input node
Is there an association between PPARGC1A genotypes and endurance capacity in Chinese men?

Our purpose was to determine the possible association between genotypes of three polymorphisms (Gly482Ser, Thr394Thr and A2962G) of the peroxisome proliferator‐activated receptor γ coactivator 1α (PPARGC1A) gene, on one hand, and both the pre‐ (baseline) and post‐training levels of maximal (i.e., maximal oxygen uptake [VO2max]) and submaximal human endurance capacity (i.e., running economy [RE]). We studied 102 young males (physically active, non‐athletes; age: 19±1 yrs) from Northern China (of Han origin) who underwent a 18‐week endurance training (running) program and were tested on a treadmill (for VO2max and RE determination) before and after training. None of the VO2max and RE related traits were associated with the Gly482Ser and Thr394Thr polymorphisms at baseline or after training. The A2962G polymorphism was however associated with VO2max at baseline, as carriers of the G allele (AG+GG genotypes; n=49) had higher levels of VO2max than the AA group (n=53) (58.2±4.3 vs 56.3±3.9 mL/kg/min; P=0.017). Our results do not support previous data on Caucasians showing an association between the Gly482Ser variant and VO2max but suggest the potential role of another polymorphism (A2962G) to explain individual VO2max differences in Chinese men.
Premise Selection and External Provers for HOL4

Learning-assisted automated reasoning has recently gained popularity among the users of Isabelle/HOL, HOL Light, and Mizar. In this paper, we present an add-on to the HOL4 proof assistant and an adaptation of the HOL(y)Hammer system that provides machine learning-based premise selection and automated reasoning also for HOL4. We efficiently record the HOL4 dependencies and extract features from the theorem statements, which form a basis for premise selection. HOL(y)Hammer transforms the HOL4 statements in the various TPTP-ATP proof formats, which are then processed by the ATPs. We discuss the different evaluation settings: ATPs, accessible lemmas, and premise numbers. We measure the performance of HOL(y)Hammer on the HOL4 standard library. The results are combined accordingly and compared with the HOL Light experiments, showing a comparably high quality of predictions. The system directly benefits HOL4 users by automatically finding proofs dependencies that can be reconstructed by Metis.
Isolation and characterization of epinectin, a novel adhesion protein for epithelial cells

A 70,000-mol-wt protein was isolated from A431 carcinoma cell extracellular matrix that promotes cell substratum adhesion of these epidermoid tumor cells. Extracellular matrix was isolated by a modification of a procedure described by Hedman et al. (Hedman, K., M. Kurkinen, K. Alitalo, A. Vaheri, S. Johansson, and M. Hook, 1979 J. Cell Biol., 81:83-91) and Yamada and Weston (Yamada, K., and J. A. Weston, 1974, Proc. Natl. Acad. Sci. USA, 71:3492-3496). Cells were solubilized with 0.5% deoxycholate, 10 mM Tris, 0.9% NaCl, and 1 mM phenylmethylsulfonyl fluoride, pH 8.0. The residual matrix was then removed from the plates with 6 M urea and 1 mM phenylmethylsulfonyl fluoride and phosphate-buffered saline. SDS PAGE gels of the 6 M urea extract showed one major band at 70,000-mol-wt by Coomassie Blue staining. A 70,000-mol-wt isotopically-labeled band could also be extracted from the matrix of cells incubated with [35S]methionine. Because of the presence of this protein on squamous-derived epithelial cells we have called the 70,000-mol-wt molecule epinectin. Indirect immunofluorescence with polyclonal rabbit antibodies against epinectin stained A431 cells pericellularly in dense punctate accumulations and along the plasma membrane. Enzyme-linked immunoassays and gel-transfer immunolocalization studies showed that the extract did not cross-react with antibodies to fibronectin, laminin, serum-spreading factor, epibolin, or keratin. Additionally, antibodies to epinectin did not cross-react with these proteins. Further studies showed that epinectin does not bind to gelatin. Cell-adhesion assay, using radiolabeled A431 carcinoma cells on various adhesion-promoting substrates, showed that epinectin has similar adhesion-promoting capacity as serum-spreading factor, was somewhat less active than fibronectin, but more effective than laminin or epibolin. Epinectin appears to be a unique protein isolated from epidermoid tumor cells that is distinct from other known adhesion proteins.
Effects of Ocean Acidification on Juvenile Red King Crab (Paralithodes camtschaticus) and Tanner Crab (Chionoecetes bairdi) Growth, Condition, Calcification, and Survival

Ocean acidification, a decrease in the pH in marine waters associated with rising atmospheric CO2 levels, is a serious threat to marine ecosystems. In this paper, we determine the effects of long-term exposure to near-future levels of ocean acidification on the growth, condition, calcification, and survival of juvenile red king crabs, Paralithodes camtschaticus, and Tanner crabs, Chionoecetes bairdi. Juveniles were reared in individual containers for nearly 200 days in flowing control (pH 8.0), pH 7.8, and pH 7.5 seawater at ambient temperatures (range 4.4–11.9 °C). In both species, survival decreased with pH, with 100% mortality of red king crabs occurring after 95 days in pH 7.5 water. Though the morphology of neither species was affected by acidification, both species grew slower in acidified water. At the end of the experiment, calcium concentration was measured in each crab and the dry mass and condition index of each crab were determined. Ocean acidification did not affect the calcium content of red king crab but did decrease the condition index, while it had the opposite effect on Tanner crabs, decreasing calcium content but leaving the condition index unchanged. This suggests that red king crab may be able to maintain calcification rates, but at a high energetic cost. The decrease in survival and growth of each species is likely to have a serious negative effect on their populations in the absence of evolutionary adaptation or acclimatization over the coming decades.
Film Colorization, Using Artificial Neural Networks and Laws Filters

In this study a new artificial neural network based approach to automatic or semi-automatic colorization of black and white film footages is introduced. Different features of black and white images are tried as the input of a MLP neural network which has been trained to colorize the movie using its first frame as the ground truth. Amongst the features tried, e.g. position, relaxed position, luminance, and so on, we are most interested on the texture features namely the Laws filter responses, and what their performance would be in the process of colorization. Also, the network parameter optimization, the effects of color reduction, and relaxed x-y position of pixels as the feature, are investigated in this study. The results are promising and show that the combination of MLP and texture features is effective in this application.
Hose rate control for P2P-TV streaming systems

In this paper we consider mesh based P2P streaming systems focusing on the problem of regulating peer upload rate to match the system demand while not overloading each peer upload link capacity. We propose Hose Rate Control (HRC), a novel scheme to control the speed at which peers offer chunks to other peers, ultimately controlling peer uplink capacity utilization. This is of critical importance for heterogeneous scenarios like the one faced in the Internet, where peer upload capacity is unknown and varies widely. HRC nicely adapts to the actual peer available upload bandwidth and system demand, so that users' Quality of Experience is greatly enhanced. Both simulations and actual experiments involving up to 1000 peers are presented to assess performance in real scenarios. Results show that HRC consistently outperforms the Quality of Experience achieved by non-adaptive schemes.
Module placement with boundary constraints using B*-trees

The module placement problem is to determine the co-ordinates of logic modules in a chip such that no two modules overlap and some cost (e.g. silicon area, interconnection length, etc.) is optimised. To shorten connections between inputs and outputs and/or make related modules adjacent, it is desired to place some modules along the specific boundaries of a chip. To deal with such boundary constraints, we explore the feasibility conditions of a B*-tree with boundary constraints and develop a simulated annealing-based algorithm using B*-trees. Unlike most previous work, the proposed algorithm guarantees a feasible B*-tree with boundary constraints for each perturbation. Experimental results show that the algorithm can obtain a smaller silicon area than the most recent work based on sequence pairs.
Ecological education and action research: A transformative blend for formal and nonformal educators

Action research, within the context of an ecological education graduate degree, can result in transformative learning experiences for formal and nonformal educators. Encountering layers of hegemony and awakening to relations of power facilitated a profound shift within these teacher-researchers, engendering a newly felt sense of empowerment. Integral to the transformative learning process were opportunities for reflection fostering greater balance between the personal and professional, learning to accept feelings of confusion and disorientation, and evolving a deeper understanding of ecological education. Moreover, this investigation reveals the existence of a synergistic relationship between ecological education, action research, and transformative learning. This kinship is substantiated through analysis of data from four cohorts of students engaged in capstone action research projects.
CRISPR-Cas9 Mediated Telomere Removal Leads to Mitochondrial Stress and Protein Aggregation

Aging is considered the major risk factor for neurodegenerative diseases including Parkinson’s disease (PD). Telomere shortening is associated with cellular senescence. In this regard, pharmacological or genetic inhibition of telomerase activity has been used to model cellular aging. Here, we employed CRISPR-Cas9 technology to instantly remove the telomere to induce aging in a neuroblastoma cell line. Expression of both Cas9 and guide RNA targeting telomere repeats ablated the telomere, leading to retardation of cell proliferation. Instant deletion of telomere in SH-SY5Y cells impaired mitochondrial function with diminished mitochondrial respiration and cell viability. Supporting the pathological relevance of cell aging by CRISPR-Cas9 mediated telomere removal, alterations were observed in the levels of PD-associated proteins including PTEN-induced putative kinase 1, peroxisome proliferator-activated receptor γ coactivator 1-α, nuclear respiratory factor 1, parkin, and aminoacyl tRNA synthetase complex interacting multifunctional protein 2. Significantly, α-synuclein expression in the background of telomere removal led to the enhancement of protein aggregation, suggesting positive feed-forward interaction between aging and PD pathogenesis. Collectively, our results demonstrate that CRISPR-Cas9 can be used to efficiently model cellular aging and PD.
Reduced Glucose Sensation Can Increase the Fitness of Saccharomyces cerevisiae Lacking Mitochondrial DNA

Damage to the mitochondrial genome (mtDNA) can lead to diseases for which there are no clearly effective treatments. Since mitochondrial function and biogenesis are controlled by the nutrient environment of the cell, it is possible that perturbation of conserved, nutrient-sensing pathways may successfully treat mitochondrial disease. We found that restricting glucose or otherwise reducing the activity of the protein kinase A (PKA) pathway can lead to improved proliferation of Saccharomyces cerevisiae cells lacking mtDNA and that the transcriptional response to mtDNA loss is reduced in cells with diminished PKA activity. We have excluded many pathways and proteins from being individually responsible for the benefits provided to cells lacking mtDNA by PKA inhibition, and we found that robust import of mitochondrial polytopic membrane proteins may be required in order for cells without mtDNA to receive the full benefits of PKA reduction. Finally, we have discovered that the transcription of genes involved in arginine biosynthesis and aromatic amino acid catabolism is altered after mtDNA damage. Our results highlight the potential importance of nutrient detection and availability on the outcome of mitochondrial dysfunction.