Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploiting functional parallelism of POWER2 to design high-performance numerical algorithms

We describe the algorithms and architecture approach to produce high-performance codes for numerically intensive computations. In this approach, for a given computation, we design algorithms so that they perform optimally when run on a target machine-in this case, the new POWERS'" machines from the RSl6000 family of RISC processors. The algorithmic features that we emphasize are functional parallelism, cachelregister blocking, algorithmic prefetching, loop unrolling, and algorithmic restructuring. The architectural features of the POWER2 machine that we describe and that lead to high performance are multiple functional units, high bandwidth between registers, cache, and memory, a large number of fixedand floating-point registers, and a large cache and TLB (translation lookaside buffer). The paper gives two examples that illustrate how the algorithms and architectural features interplay to produce high-performance codes. They are B U S (basic linear algebra subroutines) and narrow-band matrix routines. These routines are included in ESSL (Engineering and Scientific Subroutine Library); an overview of ESSL is also given in the paper.
Genome of Methylobacillus flagellatus, Molecular Basis for Obligate Methylotrophy, and Polyphyletic Origin of Methylotrophy

ABSTRACT Along with methane, methanol and methylated amines represent important biogenic atmospheric constituents; thus, not only methanotrophs but also nonmethanotrophic methylotrophs play a significant role in global carbon cycling. The complete genome of a model obligate methanol and methylamine utilizer, Methylobacillus flagellatus (strain KT) was sequenced. The genome is represented by a single circular chromosome of approximately 3 Mbp, potentially encoding a total of 2,766 proteins. Based on genome analysis as well as the results from previous genetic and mutational analyses, methylotrophy is enabled by methanol and methylamine dehydrogenases and their specific electron transport chain components, the tetrahydromethanopterin-linked formaldehyde oxidation pathway and the assimilatory and dissimilatory ribulose monophosphate cycles, and by a formate dehydrogenase. Some of the methylotrophy genes are present in more than one (identical or nonidentical) copy. The obligate dependence on single-carbon compounds appears to be due to the incomplete tricarboxylic acid cycle, as no genes potentially encoding alpha-ketoglutarate, malate, or succinate dehydrogenases are identifiable. The genome of M. flagellatus was compared in terms of methylotrophy functions to the previously sequenced genomes of three methylotrophs, Methylobacterium extorquens (an alphaproteobacterium, 7 Mbp), Methylibium petroleiphilum (a betaproteobacterium, 4 Mbp), and Methylococcus capsulatus (a gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or phylogenetically, the methylotrophy functions in M. flagellatus were more similar to those in M. capsulatus and M. extorquens than to the ones in the more closely related M. petroleiphilum species, providing the first genomic evidence for the polyphyletic origin of methylotrophy in Betaproteobacteria.
M2L at SemEval-2016 Task 8: AMR Parsing with Neural Networks

This paper describes our contribution to the SemEval 2016 Workshop. We participated in the Shared Task 8 on Meaning Representation parsing using a transition-based approach, which builds upon the system of Wang et al. (2015a) and Wang et al. (2015b), with additions that utilize a Feedforward Neural Network classifier and an enriched feature set. We observed that exploiting Neural Networks in
Simulation in University Education:The Artificial Agent PSI as a Teaching Tool

One weakness of undergraduate psychology education in Germany is that students do not have many opportunities to practice their theoretical knowledge. To fill this gap, a new teaching approach has been introduced to the curriculum at the University of Bamberg, Germany.The students conduct experiments with an artificial agent, a computer simulation originating from a cognitive modeling approach. The agent, called “PSI” (see http://web.uni-bamberg.de/ppp/insttheopsy/software for various versions), is the implementation of the PSI theory (see Dörner, D., 1999, Bauplan für eine Seele, Rowohlt, Reinbek). The PSI theory integrates approaches to cognition, emotions, motivation, human action regulation, and perception. One major benefit of the work with the simulation (besides the students gaining practical experience) is that it is possible to convey knowledge about psychological processes and that interaction of different processes difficult to isolate in natural agents become clearly visible to students. In the evaluation of the course, students rated the course as a valuable addendum to the traditional education in psychology.
Dual Embeddings and Metrics for Relational Similarity

Abstract . In this work, we study the problem of relational similarity by combining different word embeddings learned from different types of contexts. The word2vec model with linear bag-of-words contexts can capture more topical and less functional similarity, while the dependency-based word embeddings with syntactic contexts can capture more functional and less topical similarity. We explore topical space and functional space simultaneously by considering these two word embed-dings and different metrics. We evaluate our model on relational similarity framework, and report state-of-the-art performance on standard test collections
Manufacturing Technology of α-Fe Bonded Grinding Wheel Free Abrasive

ELID ultra-precision grinding mirror surface can achieve nanometer precision. However, after the grinding wheel passivates the abrasive particles in electrolysis, it is easy to scratch the ultra-precision ELID grinding surface into the grinding process. In order to solve this problem, a non-abrasive grain α-Fe bonded grinding wheel is propose, which contains no abrasive particles. After electrolysis, oxide film is formed on the surface of the wheel. In ultra-precision ELID grinding, there is no abrasive particles involved, only the polishing effect of oxide film. There is no need to worry about the scratching of exfoliated abrasive particles that have been machined on ultra-precision ELID surfaces. Thus achieving extremely high surface accuracy.
Outage capacity regions of multicarrier DF relaying in underwater acoustic channels

In this paper, we investigate the information theoretical limits on the performance of cooperative multicarrier underwater acoustic (UWA) communication systems. We assume decode-and-forward (DF) relaying and consider non-orthogonal half-duplex cooperation. Under the assumptions of sparse and frequency-selective Rician fading channel and correlated Gaussian ambient noise, we derive the maximum achievable sum-rate and common/individual outage capacity regions for the cooperation protocol under consideration. We further investigate the effect of several parameters such as underwater temperature, carrier frequency, etc. on the outage capacity regions.
The measurement manifesto

Useful measurement data is badly needed to help monitor and control large networks. Current approaches to solving measurement problems often assume minimal support from routers and protocols (e.g., active measurement) or place the entire burden on the router to support heavy-weight mechanisms (e.g., NetFlow). In this paper we argue that the research agenda in measurement must change to consider measurement solutions which enlist the cooperation of routers, protocols, and tools. We believe that the need is so urgent that the deployment issues associated with such holistic solutions can be finessed by cooperation between a few key ISPs and a few key router vendors. If this agenda is accepted, there is a rich vein of technical problems, hitherto considered only from an active measurement perspective, for which there can be new and effective orchestrated solutions. We illustrate this thesis using two examples. Our major example is that of measuring traffic matrices using class counters and class sampling (as opposed to the implementation cost of per-prefix counters, or the errors inherent in tomography). We also provide a smaller example of measuring route stability by modifying route computation. Beyond specific techniques, we hope the guidelines in this paper can provide a focus for discussion among researchers, router vendors, protocol designers, and network operators---the stakeholders in the measurement enterprise.
Cross-Cultural Adaptation of the Social Vulnerability Index for Use in the Dutch Context

Being able to identify socially frail older adults is essential for designing interventions and policy and for the prediction of health outcomes, both on the level of individual older adults and of the population. The aim of the present study was to adapt the Social Vulnerability Index (SVI) to the Dutch language and culture for those purposes. A systematic cross-cultural adaptation of the initial Social Vulnerability Index was performed following five steps: initial translation, synthesis of translations, back translation, a Delphi procedure, and a test for face validity and feasibility. The main result of this study is a face-valid 32 item Dutch version of the Social Vulnerability Index (SVI-D) that is feasible in health care and social care settings. The SVI-D is a useful index to measure social frailty in Dutch-language countries and offers a broad, holistic quantification of older people’s social circumstances related to the risk of adverse health outcomes.
Characterization of glycopeptide-resistant enterococci from U.S. hospitals

We examined 105 clinical isolates of glycopeptide-resistant enterococci collected from 31 U.S. hospitals in 14 states during May 1988 to July 1992. The isolates included 82 Enterococcus faecium, 8 E. faecalis, 6 Enterococcus spp. , 5 E. gallinarum, 3 E. casseliflavus, and 1 E. raffinosus. The isolates were categorized into the following four phenotypes of glycopeptide resistance on the basis of their MIC patterns: (i) 70 VanA (vancomycin [Vm] MIC, > or = 64 micrograms/ml; teicoplanin [Tei] MIC, 16 to > or = 128 micrograms/ml), (ii) 26 VanB (Vm MIC, 16 to 1,024 micrograms/ml; Tei MIC, < or = 2 micrograms/ml), (iii) 5 VanC (Vm MIC, 4 to 16 micrograms/ml; Tei MIC, < or = 2 micrograms/ml) in E. gallinarum, and (iv) 3 E. casseliflavus and 1 E. raffinosus isolates for which Vm MICs were 4 to 16 micrograms/ml and Tei MICs were < or = 1 micrograms/ml were called unclassified. Of the 101 isolates with the VanA, VanB, and VanC phenotypes, 99 were confirmed by production of a specific 1,030-, 433-, or 796-bp polymerase chain reaction product, respectively, and hybridization with the respective gene probe. The vanA gene was also detected in the E. raffinosus isolate for which the Vm MIC was 16 micrograms/ml and the Tei MIC was 1 microgram/ml. The vanA gene was located on either a 34- or a 60-kb plasmid in all of the U.S. isolates examined. Pulsed-field gel electrophoresis demonstrated both intrahospital and interhospital diversity among Vmr enterococci in the United States and was more useful than plasmid analysis for epidemiologic studies.
Black hole entropy as entanglement entropy: A Holographic derivation

We study the possibility that black hole entropy be identified as entropy of entanglement across the horizon of the vacuum of a quantum field in the presence of the black hole. We argue that a recent proposal for computing entanglement entropy using AdS/CFT holography implies that black hole entropy can be exactly equated with entanglement entropy. The implementation of entanglement entropy in this context solves all the problems (such as cutoff dependence and the species problem) typically associated with this identification.
The expression of glucocorticoid receptor is negatively regulated by active androgen receptor signaling in prostate tumors

The glucocorticoid and androgen receptors (GR and AR) can commonly regulate up to 50% of their target genes in prostate cancer (PCa) cells. GR expression is stimulated by castration therapy, which has been proposed to be one mechanism that compensates for AR signaling blockade and promotes castration‐resistant PCa (CRPC) progression. However, whether GR functions as a driver for CRPC or a marker reflecting AR activity remains unclear. Here, we applied PCa tissue microarrays to show that GR protein levels were elevated by castration therapy, but reduced to pre‐castration levels when tumors were at the CRPC stage. Using subrenal capsule xenograft models, we showed that GR expression was inversely correlated with AR and PSA expressions. GR expression levels are not associated with tumor invasion and metastasis phenotypes. In castration‐resistant C4‐2 xenografts expressing AR shRNA, regressing tumors induced by AR knockdown expressed higher levels of GR and lower levels of PSA than non‐regressing tumors. Immunoblotting and real‐time PCR assays further showed that AR knockdown or AR antagonists increased GR expression at both mRNA and protein levels. ChIP combined with DNA sequencing techniques identified a negative androgen responsive element (nARE) 160K base pairs upstream of the GR gene. Gel shift assays confirmed that AR directly interacted with the nARE and luciferase assays demonstrated that the nARE could mediate transcription repression by ligand‐activated AR. In conclusion, GR expression is negatively regulated by AR signaling and may serve as a marker for AR signaling in prostate tumors.
The association between co-morbidities and physical performance in people with chronic obstructive pulmonary disease

A systematic review was conducted to examine the association between co-morbidity and physical performance in people with chronic obstructive pulmonary disease (COPD). MEDLINE, EMBASE, CINAHL, SCOPUS and Cochrane Central Register of Controlled Trials were searched from inception to end-February 2013, using keywords ‘COPD’, ‘exercise’, ‘physical activity’, ‘rehabilitation’, ‘co-morbidity’ and individual co-morbid conditions. Studies reporting associations of co-morbidities in COPD with at least one objective measure of physical performance were included. Study quality was appraised using the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) checklist. Nine studies met inclusion criteria. Mean (standard deviation (SD)) STROBE score was 16 (3) (maximum score = 21). Four studies examined anxiety as a co-morbid condition; three examined depression; two examined obesity and two examined a range of conditions. Reduced physical performance was associated with higher Charlson score (odds ratio (OR) = 0.72, 95% confidence interval (CI) = 0.54–0.98), metabolic disease (OR = 0.58, 95% CI = 0.49–0.67), anxiety (OR = 0.37, 95% CI = 0.23–0.59) and osteoporosis (OR = 0.28, 95% CI = 0.11–0.70). Depression had minimal association with physical performance but was associated with higher dropout rates from pulmonary rehabilitation programmes. Obesity was negatively associated with baseline physical performance but not with change from an exercise intervention. The presence of co-morbid conditions in people with COPD may negatively affect physical performance and should be identified and accounted for analysis of interventions.
Incremental LL(1) Parsing in Language-Based Editors

This paper introduces an efficient incremental LL(1) parsing algorithm for use in language-based editors that use the structure recognition approach. It is designed to parse user input at intervals of very small granularity and to limit the amount of incremental parsing needed when changes are made internal to the editing buffer. The algorithm uses the editing focus as a guide in restricting parsing. It has been implemented in the Fred language-based editor. >
Tensor clustering with algebraic constraints gives interpretable groups of crosstalk mechanisms in breast cancer

We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. This framework is designed to enable detection of clusters of data in the presence of structural requirements which we encode as algebraic constraints in a linear program. Our clustering method is general and can be tailored to a variety of applications in science and industry. We illustrate our method on a collection of experiments measuring the response of genetically diverse breast cancer cell lines to an array of ligands. Each experiment consists of a cell line–ligand combination, and contains time-course measurements of the early signalling kinases MAPK and AKT at two different ligand dose levels. By imposing appropriate structural constraints and respecting the multi-indexed structure of the data, the analysis of clusters can be optimized for biological interpretation and therapeutic understanding. We then perform a systematic, large-scale exploration of mechanistic models of MAPK–AKT crosstalk for each cluster. This analysis allows us to quantify the heterogeneity of breast cancer cell subtypes, and leads to hypotheses about the signalling mechanisms that mediate the response of the cell lines to ligands.
The Role of Knowledge in Economic Growth

Figure 1 sets the stage for our discussion. The kink of the curve signifies the ”onset” of an important historical process, commonly called the industrial revolution. Around that kink a number of events took place. First of all, and probably most important (Eliasson 1991c) the production system of Sweden and the now industrialized mature economies was thoroughly deregulated by the rapid removal of the craft system. Parallel to this, however, significant investments in public schooling were initiated, Also, and third, at that time the new technology of the industrial revolution, based on the invention and increased sophistication of the machine tools since the second half of the 18 century in England was rapidly being introduced among the now mature industrial economies, allowing for fundamental reorganization of production. Great opportunities were created, but even though the new technology was to a large extent internationally available, only a handful of countries made it onto the faster growth track, under significant social disruption and effort. The local ability to put the new technology to industrial use (Receiver competence, Eliasson 1990a) mattered. Since that time and until recently a diminishing income inequality could be observed in the industrializing economies, as people left agriculture and the handicrafts to earn higher and steadily increasing wages in firms enjoying, for a long time, steadily increasing returns. Several questions can be asked. The important one today is what kind of knowledge capital played the role of a moving force behind this development.
An Efficient Performance Estimation Method for Configurable Multi-layer Bus-based SoC

This paper proposes an efficient performance estimation method for configurable multi-layer bus-based SoC, which evaluates system performance in an early stage of design process. The proposed method uses data flow information obtained from a system-level profiling, an architecture-independent loosely-timed transaction level simulation, and constructs a system-level execution dependency graph. Then, based on each architecture-level model, the architecture-level execution dependency graph is constructed and analyzed to estimate the performance of each architecture. In the analysis, the behavior details of shared buses and multi-layer bus are determined based on the analyzed dynamic bus contention and bus protocols’ features. Experiments were conducted by modeling the multi-layer AHB and applying the method to estimate performance of the architectures executing JPEG encoder application. The proposed method estimates the performance of SoC with less than 8% of errors comparing to the results from accurate RTL simulations.
Ischemia-Reperfusion Lung Injury Is Attenuated in MyD88-Deficient Mice

Ischemia-reperfusion lung injury is a common cause of acute morbidity and mortality in lung transplant recipients and has been associated with subsequent development of bronchiolitis obliterans syndrome. Recognition of endogenous ligands released during cellular injury (damage-associated molecular patterns; DAMPs) by Toll-like receptors (TLRs), especially TLR4, has increasingly been recognized as a mechanism for inflammation resulting from tissue damage. TLR4 is implicated in the pathogenesis of ischemia-reperfusion injury of multiple organs including heart, liver, kidney and lung. Additionally, activation of TLRs other than TLR4 by DAMPs has been identified in tissues other than the lung. Because all known TLRs, with the exception of TLR3, signal via the MyD88 adapter protein, we hypothesized that lung ischemia-reperfusion injury was mediated by MyD88-dependent signaling. To test this hypothesis, we subjected C57BL/6 wildtype, Myd88 -/-, and Tlr4 -/- mice to 1 hr of left lung warm ischemia followed by 4 hr of reperfusion. We found that Myd88 -/- mice had significantly less MCP-1/CCL2 in the left lung following ischemia-reperfusion as compared with wildtype mice. This difference was associated with dramatically reduced lung permeability. Interestingly, Tlr4 -/- mice had only partial protection from ischemia-reperfusion as compared to Myd88 -/- mice, implicating other MyD88-dependent pathways in lung injury following ischemia-reperfusion. We also found that left lung ischemia-reperfusion caused remote inflammation in the right lung. Finally, using chimeric mice with MyD88 expression restricted to either myeloid or non-myeloid cells, we found that MyD88-dependent signaling in myeloid cells was necessary for ischemia-reperfusion induced lung permeability. We conclude that MyD88-dependent signaling through multiple receptors is important in the pathogenesis of acute lung inflammation and injury following ischemia and reperfusion.
Processed red meat contribution to dietary patterns and the associated cardio-metabolic outcomes

Abstract Evidence suggests that processed red meat consumption is a risk factor for CVD and type 2 diabetes (T2D). This analysis investigates the association between dietary patterns, their processed red meat contributions, and association with blood biomarkers of CVD and T2D, in 786 Irish adults (18–90 years) using cross-sectional data from a 2011 national food consumption survey. All meat-containing foods consumed were assigned to four food groups (n 502) on the basis of whether they contained red or white meat and whether they were processed or unprocessed. The remaining foods (n 2050) were assigned to twenty-nine food groups. Two-step and k-means cluster analyses were applied to derive dietary patterns. Nutrient intakes, plasma fatty acids and biomarkers of CVD and T2D were assessed. A total of four dietary patterns were derived. In comparison with the pattern with lower contributions from processed red meat, the dietary pattern with greater processed red meat intakes presented a poorer Alternate Healthy Eating Index (21·2 (sd 7·7)), a greater proportion of smokers (29 %) and lower plasma EPA (1·34 (sd 0·72) %) and DHA (2·21 (sd 0·84) %) levels (P<0·001). There were no differences in classical biomarkers of CVD and T2D, including serum cholesterol and insulin, across dietary patterns. This suggests that the consideration of processed red meat consumption as a risk factor for CVD and T2D may need to be re-assessed.