Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance metrics and auditing framework using application kernels for high‐performance computer systems

This paper describes XSEDE Metrics on Demand, a comprehensive auditing framework for use by high‐performance computing centers, which provides metrics regarding resource utilization, resource performance, and impact on scholarship and research. This role‐based framework is designed to meet the following objectives: (1) provide the user community with a tool to manage their allocations and optimize their resource utilization; (2) provide operational staff with the ability to monitor and tune resource performance; (3) provide management with a tool to monitor utilization, user base, and performance of resources; and (4) provide metrics to help measure scientific impact. Although initially focused on the XSEDE program, XSEDE Metrics on Demand can be adapted to any high‐performance computing environment. The framework includes a computationally lightweight application kernel auditing system that utilizes performance kernels to measure overall system performance. This allows continuous resource auditing to measure all aspects of system performance including filesystem performance, processor and memory performance, and network latency and bandwidth. Metrics that focus on scientific impact, such as publications, citations and external funding, will be included to help quantify the important role high‐performance computing centers play in advancing research and scholarship. Copyright © 2012 John Wiley & Sons, Ltd.
A pathway for cell wall anchorage of Saccharomyces cerevisiae alpha-agglutinin

Saccharomyces cerevisiae alpha-agglutinin is a cell wall-anchored adhesion glycoprotein. The previously identified 140-kDa form, which contains a glycosyl-phosphatidylinositol (GPI) anchor (D. Wojciechowicz, C.-F. Lu, J. Kurjan, and P. N. Lipke, Mol. Cell. Biol. 13:2554-2563, 1993), and additional forms of 80, 150, 250 to 300, and > 300 kDa had the properties of intermediates in a transport and cell wall anchorage pathway. N glycosylation and additional modifications resulted in successive increases in size during transport. The 150- and 250- to 300-kDa forms were membrane associated and are likely to be intermediates between the 140-kDa form and a cell surface GPI-anchored form of > 300 kDa. A soluble form of > 300 kDa that lacked the GPI anchor had properties of a periplasmic intermediate between the plasma membrane form and the > 300-kDa cell wall-anchored form. These results constitute experimental support for the hypothesis that GPI anchors act to localize alpha-agglutinin to the plasma membrane and that cell wall anchorage involves release from the GPI anchor to produce a periplasmic intermediate followed by linkage to the cell wall.
Evidence for Population-Specific Positive Selection on Immune Genes of Anopheles gambiae

Host-pathogen interactions can be powerful drivers of adaptive evolution, shaping the patterns of molecular variation at the genes involved. In this study, we sequenced alleles from 28 immune-related loci in wild samples of multiple genetic subpopulations of the African malaria mosquito Anopheles gambiae, obtaining unprecedented sample sizes and providing the first opportunity to contrast patterns of molecular evolution at immune-related loci in the recently discovered GOUNDRY population to those of the indoor-resting M and S molecular forms. In contrast to previous studies that focused on immune genes identified in laboratory studies, we centered our analysis on genes that fall within a quantitative trait locus associated with resistance to Plasmodium falciparum in natural populations of A. gambiae. Analyses of haplotypic and genetic diversity at these 28 loci revealed striking differences among populations in levels of genetic diversity and allele frequencies in coding sequence. Putative signals of positive selection were identified at 11 loci, but only one was shared by two subgroups of A. gambiae. Striking patterns of linkage disequilibrium were observed at several loci. We discuss these results with respect to ecological differences among these strata as well as potential implications for disease transmission.
Glucose Tolerance and Insulin Response to Glucose Load in Body Builders*

To find out to what extent body composition affects glucose tolerance, blood glucose (BG) and insulin (IRI) responses to a 100-g oral glucose tolerance test (OGTT) were compared in 10 male body builders, 11 untrained lean control subjects, and 11 mildly obese men, all of similar age (19-35 years). In comparison with the remaining two groups, the body builders had the lowest percentage of fat, although their lean body mass (LBM) in absolute terms did not differ from that in obese subjects. Both BG and IRI concentrations during the OGTT were the lowest in body builders, medium in controls, and the highest in obese men. The differences in glucose tolerance between the groups were also demonstrated by comparison of the subjects' BG levels during the OGTT with the respective mean BG values obtained in a reference group of 42 healthy nonobese men aged from 20 to 55 years. The data indicate that body builders show better glucose tolerance and improved insulin action in comparison with untrained, nonobese subjects of similar age and body weight. Lean body mass in absolute terms cannot, however, be considered as a sole determinant of the insulin action in the body since in mildly obese subjects glucose tolerance was considerably reduced in spite of the fact that their LBM was similar to that in body builders. Either muscle hypertrophy or reduced adiposity may account for the beneficial effects of body building on glucose metabolism.
Analysis of El Niño and IOD Phenomenon 2015/2016 and Their Impact on Rainfall Variability in Indonesia

The El Niño phenomenon that occurs in 2015/2016 fell into category of strong intensity. The El Niño phenomenon had a very large impact on meteorological droughts in Indonesia. The aim of this study is to determine the dynamics of the atmosphere and the sea during the phenomenon of El Nino 2015/2016 and its impact on rainfall in the Indonesia region. The research methods consisted of several steps, in order to obtain an overview of the spatial conditions of rainfall during the El Niño period, data processing of both accumulation and anomaly of rainfall per-season (MAM, JJA, SON, DJF) were evaluated. The results showed that strong intensity of the El Niño occurred from early July 2015 to early March 2016. The shift of the convection center occurred in the Pacific Ocean during this period where the sea surface temperature anomaly in the eastern Pacific appeared warmer 2-3°C than normal temperature (1981-2010). In 2015, the positive Indian Ocean Dipole (IOD) also occurred in the Indian Ocean from August to November. These phenomena resulted wider drought impacts throughout Indonesia especially during the transition from dry season to wet season period (September-November).
Spina bifida and parental occupation in a Swedish register-based study.

OBJECTIVES To gather more evidence on a possible relation between spina bifida and agricultural and other occupations of parents, a register-based linkage study was conducted in Sweden. METHODS Four hundred and eighty-two cases of spina bifida in infants born between 1976 and 1991 were identified from the Swedish Register of Congenital Malformations. Nine hundred and sixty-four referents without spina bifida were selected from the Medical Birth Register and matched for year of birth of the child, maternal age, and parity. Information on occupation was obtained from the Medical Birth Register from 1983 on, and from the census, which is performed every fifth year. RESULTS A slightly increased odds ratio (OR) was observed for women in agricultural occupations [OR 1.8, 95% confidence interval (95% CI) 0.8-4.2]. For all women who had an agricultural occupation or lived on a farm, the OR was 2.2 (95% CI 1.3-3.8). The OR values of most of the other occupational groups were close to unity. CONCLUSIONS The results suggest an increased risk of spina bifida for the infants of women in agricultural occupations, but they do not provide insight into any specific occupational risk factors.
A Packet-In Message Filtering Mechanism for Protection of Control Plane in OpenFlow Switches

Protecting control planes in networking hardware from high rate packets is a critical issue for networks under operation. One common approach for conventional networking hardware is to offload expensive functions onto hard-wired offload engines as ASICs. This approach is inadequate for OpenFlow networks because it restricts a certain amount of flexibility for network control that OpenFlow tries to provide. Therefore, we need a control plane protection mechanism in OpenFlow switches as a last resort, while preserving flexibility for network control. In this paper, we propose a mechanism to filter out Packet-In messages, which include packets handled by the control plane in OpenFlow networks, without dropping important ones for network control. Switches record values of packet header fields before sending Packet-In messages, and filter out packets that have the same values as the recorded ones. The controllers set the header fields in advance whose values must be recorded, and the header fields are selected based on controller design. We have implemented and evaluated the proposed mechanism on a prototype software switch, concluding that it dramatically reduces CPU loads on switches while passes important Packet-In messages for network control. key words: network security, software-defined networking, OpenFlow
Flexible Background Subtraction with Self-Balanced Local Sensitivity

Most background subtraction approaches offer decent results in baseline scenarios, but adaptive and flexible solutions are still uncommon as many require scenario-specific parameter tuning to achieve optimal performance. In this paper, we introduce a new strategy to tackle this problem that focuses on balancing the inner workings of a non-parametric model based on pixel-level feedback loops. Pixels are modeled using a spatiotemporal feature descriptor for increased sensitivity. Using the video sequences and ground truth annotations of the 2012 and 2014 CVPR Change Detection Workshops, we demonstrate that our approach outperforms all previously ranked methods in the original dataset while achieving good results in the most recent one.
A Coding Scheme Development Methodology Using Grounded Theory for Qualitative Analysis of Pair Programming

A number of quantitative studies of pair programmin g (the practice of two programmers working together using just one compute r) have partially conflicting results. Qualitative studies are needed to explain what is really going on. We support such studies by taking a grounded theory (GT) appro ach for deriving a coding scheme for the objective conceptual description of specifi c pair programming sessions independent of a particular research goal. The pres ent article explains why our initial attempts at using GT failed and describes how to av oid these difficulties by a predetermined perspective on the data, concept nami ng rules, an analysis results metamodel, and pair coding. These practices may be helpful in all GT situations, particularly those involving very rich data such as video data. We illustrate the operation and usefulness of these practices by real examples derived from our coding work and present a few preliminary hypotheses regar ding pair programming that have surfaced.
Generation 2.5 Antisense Oligonucleotides Targeting the Androgen Receptor and Its Splice Variants Suppress Enzalutamide-Resistant Prostate Cancer Cell Growth

Purpose: Enzalutamide (ENZ) is a potent androgen receptor (AR) antagonist with activity in castration-resistant prostate cancer (CRPC); however, progression to ENZ-resistant (ENZ-R) CRPC frequently occurs with rising serum PSA levels, implicating AR full-length (ARFL) or variants (AR-Vs) in disease progression. Experimental Design: To define functional roles of ARFL and AR-Vs in ENZ-R CRPC, we designed 3 antisense oligonucleotides (ASO) targeting exon-1, intron-1, and exon-8 in AR pre-mRNA to knockdown ARFL alone or with AR-Vs, and examined their effects in three CRPC cell lines and patient-derived xenografts. Results: ENZ-R-LNCaP cells express high levels of both ARFL and AR-V7 compared with CRPC-LNCaP; in particular, ARFL levels were approximately 12-fold higher than AR-V7. Both ARFL and AR-V7 are highly expressed in the nuclear fractions of ENZ-R-LNCaP cells even in the absence of exogenous androgens. In ENZ-R-LNCaP cells, knockdown of ARFL alone, or ARFL plus AR-Vs, similarly induced apoptosis, suppressed cell growth and AR-regulated gene expression, and delayed tumor growth in vivo. In 22Rv1 cells that are inherently ENZ-resistant, knockdown of both ARFL and AR-Vs more potently suppressed cell growth, AR transcriptional activity, and AR-regulated gene expression than knockdown of ARFL alone. Exon-1 AR-ASO also inhibited tumor growth of LTL-313BR patient-derived CRPC xenografts. Conclusions: These data identify the AR as an important driver of ENZ resistance, and while the contributions of ARFL and AR-Vs can vary across cell systems, ARFL is the key driver in the ENZ-R LNCaP model. AR targeting strategies against both ARFL and AR-Vs is a rational approach for AR-dependent CRPC. Clin Cancer Res; 21(7); 1675–87. ©2015 AACR.
Perceive the difference: Vehicle pitch motions as feedback for the driver

The feedback of state transitions and intentions of the automation system is very important for obtaining and/or increasing the driver's awareness of the automation system's state during partially automated driving. In this paper, the feedback is realized via rotational vehicle motions and not, as usual, visually. The detailed design of active pitch motions for feeding back state transitions and intentions of the automation system is evaluated in a driving study on a test track. In doing so, the lateral and longitudinal vehicle guidance is carried out by the automation system.
Mass balance estimation using geodetic method for glaciers in Baspa basin, Western Himalaya

Himalayan glaciers, which contribute to water security for almost 1.3 billion people in Asia, are now under threat due to climate change. Assessment of glacier mass balance changes is crucial to determine the implications of climate change, but in situ measurements are limited due to rugged terrain and harsh climate of the Himalaya. Remote sensing-based geodetic method is therefore important for studying the evolution of Himalayan glaciers at a large scale. In this study, the mass balance of glaciers located in Baspa basin (Western Himalaya) is estimated for a period of 11 years between 2000 and 2011, using geodetic method. Out of 89 glaciers in the basin, 42 glaciers (greater than 1 km(2)) covering an area of similar to 72% (215 km(2)) of the total glaciated area were selected for the study. A mean thinning of similar to 50 +/- 11 m and mean accumulation of similar to 35 +/- 11 m was observed during the study period, with the cumulative mass balance varying between -36.9 +/- 1.98 and 6.47 +/- 1.98 m.w.e. A mean annual mass loss of -1.09 +/- 0.32 m. w.e. a(-1) was observed for the entire basin, suggesting that the glaciers in Baspa basin are losing mass at higher rate compared to the glaciers in central and eastern Himalayas. This study demonstrates the utility of geodetic method to estimate mass balance of glaciers at basin scale, which will be useful to assess future changes in glacial extent and stream run-off.
Early childhood computer experience and cognitive and motor development.

OBJECTIVES To explore the association between early computer experience (both accessibility and frequency of use) and cognitive and psychomotor development among young children. METHODS The participants were 122 preschool children enrolled in a rural county Head Start program in the United States during 2001-2002. The following tests were administered to the children: the Bender Visual Motor Gestalt Test; the Boehm Test of Basic Concepts, Third Edition Preschool; the Test of Gross Motor Development, Second Edition; and a short form of the Wechsler Preschool and Primary Scales of Intelligence-Revised. Information pertaining to family characteristics and children's early computer experience was collected from parents. Both bivariate and multivariate analyses were used to assess the association between early computer experience and cognitive and motor development. RESULTS Of the participating children, 53% had a computer at home. Among families who had a computer, 83% had children's software on the computer. According to parents' reports, 29% of these children played on the home computer on a daily basis, and an additional 44% of the children played on the computer at least weekly. Of those families who did not have a home computer, 49% reported that their children had access to a computer somewhere outside home. Among these children, 10% had daily access to the computer and 33% had weekly access. The presence of a computer in the home was significantly associated with the family's income and the educational attainment of the parents. There was no gender difference in computer accessibility and frequency use among the participating children. Children who had access to a computer performed better on measures of school readiness and cognitive development, controlling for children's developmental stage and family socioeconomic status. The data in the current study did not suggest a relationship between computer experience and visual motor or gross motor skills among the participating children. CONCLUSION The findings in the present study suggest that early computer exposure before or during the preschool years is associated with development of preschool concepts and cognition among young children. However, frequency of use did not reveal such a relationship; neither did the ownership of other child electronic or video games in the household.
Chaotic simulated annealing with decaying chaotic noise

By adding chaotic noise to each neuron of the discrete-time continuous-output Hopfield neural network (HNN) and gradually reducing the noise, a chaotic neural network is proposed so that it is initially chaotic but eventually convergent, and, thus, has richer and more flexible dynamics compared to the HNN. The proposed network is applied to the traveling salesman problem (TSP) and that results are highly satisfactory. That is, the transient chaos enables the network to escape from local energy minima and to find global minima in 100% of the simulations for four-city and ten-city TSPs, as well as near-optimal solutions in most of runs for a 48-city TSP.
Improvement of the visual servoing task with a new trajectory predictor - the fuzzy kalman filter

Visual Servoing is an important issue in robotic vision but one of the main problems is to cope with the delay introduced by acquisition and image processing. This delay is the reason for the limited velocity and acceleration of tracking systems. The use of predictive techniques is one of the solutions to solve this problem. In this paper, we present a Fuzzy predictor. This predictor decreases the tracking error compared with the classicKalmanfilter (KF) for abrupt changes of direction and can be used for an unknown object’s dynamics. The Fuzzy predictor proposed in this work is based on several cases of the Kalmanfiltering, therefore, we have named it: FuzzyKalmanFilter (FKF). The robustness and feasibility of the proposed algorithm is validated by a great number of experiments and is compared with other robust methods.
All-at-once Optimization for Coupled Matrix and Tensor Factorizations

Joint analysis of data from multiple sources has the potential to improve our understanding of the underlying structures in complex data sets. For instance, in restaurant recommendation systems, recommendations can be based on rating histories of customers. In addition to rating histories, customers' social networks (e.g., Facebook friendships) and restaurant categories information (e.g., Thai or Italian) can also be used to make better recommendations. The task of fusing data, however, is challenging since data sets can be incomplete and heterogeneous, i.e., data consist of both matrices, e.g., the person by person social network matrix or the restaurant by category matrix, and higher-order tensors, e.g., the "ratings" tensor of the form restaurant by meal by person. In this paper, we are particularly interested in fusing data sets with the goal of capturing their underlying latent structures. We formulate this problem as a coupled matrix and tensor factorization (CMTF) problem where heterogeneous data sets are modeled by fitting outer-product models to higher-order tensors and matrices in a coupled manner. Unlike traditional approaches solving this problem using alternating algorithms, we propose an all-at-once optimization approach called CMTF-OPT (CMTF-OPTimization), which is a gradient-based optimization approach for joint analysis of matrices and higher-order tensors. We also extend the algorithm to handle coupled incomplete data sets. Using numerical experiments, we demonstrate that the proposed all-at-once approach is more accurate than the alternating least squares approach.
pKa analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications.

To quantitatively explore the applicability of the generalized solvent boundary potential (GSBP) based QM/MM approach as a "multiscale" framework for studying chemical reactions in biomolecules, the structural and energetic properties of the Human Carbonic Anhydrase II (CAII) are analyzed and compared to those from periodic boundary condition (PBC) simulations and available experimental data. Although the atomic fluctuations from GSBP based simulations are consistently lower compared to those from PBC simulations or crystallographic data, the fluctuations and internal coordinate distributions for residues in the proximity of the active site as well as diffusion constants of active-site water molecules are fairly well described by GSBP simulations. The pKa of the zinc-bound water, calculated with a SCC-DFTB/MM-GSBP based thermodynamic integration approach, agrees well with experiments for the wild type CAII. For the E106Q mutant, however, a 9 pKa unit downward shift relative to the wild type is found in contrast with previous experiments that found little change. This dramatic discrepancy signals a possible change in the mechanism for the interconversion between CO2/HCO3- in the E106Q mutant, which may be similar to the bicarbonate mediated mechanism proposed for the Co2+ substituted CAII (J. Am. Chem. Soc. 2001, 123, 5861). 1 The study highlights pKa analyses as a valuable approach for quantitatively validating the computational model for complex biomolecules as well as for revealing energetic properties intimately related to the chemical process of interest.
Young People Learning to Live With Inflammatory Bowel Disease

In a longitudinal study we investigated how young people come to live with a chronic disease, and asked them to record an audio diary on a regular basis. We also interviewed each participant every 6 weeks. Our analysis focused within and across the diary sets of 6 young people diagnosed with inflammatory bowel disease. All were aged between 11 and 16 years, and their recordings provided an insight into the experience of living within and beyond disease, and of negotiating health in the context of adolescence. This data collection method, which became known as the unclosed diary, was well received by the young people, who made use of their diaries in different ways. Three key aspects of their diary use, immediacy and intimacy, conversation, and reflection, demonstrate the flexibility of the method both as a means of accessing young people’s lives at a time of change and development, and as a personal resource for the participants.