Miracle-dz/UniFAR-FTUs huggingface dataset:
Distributed coding of three sources using punctured turbo codes

This paper describes a distributed coding system based on punctured turbo codes to compress three correlated memoryless binary and Gaussian sources. The performance bounds given by the Slepian-Wolf and Wyner-Ziv theorems are provided for three sources. The simulation results are analyzed against those provided by the same asymmetric system based on punctured turbo codes used for distributed coding of two sources.
Cloud computing paradigms for pleasingly parallel biomedical applications

Cloud computing offers exciting new approaches for scientific computing that leverage major commercial players’ hardware and software investments in large‐scale data centers. Loosely coupled problems are very important in many scientific fields, and with the ongoing move towards data‐intensive computing, they are on the rise. There exist several different approaches to leveraging clouds and cloud‐oriented data processing frameworks to perform pleasingly parallel (also called embarrassingly parallel) computations. In this paper, we present three pleasingly parallel biomedical applications: (i) assembly of genome fragments; (ii) sequence alignment and similarity search; and (iii) dimension reduction in the analysis of chemical structures, which are implemented utilizing a cloud infrastructure service‐based utility computing models of Amazon Web Services (http://Amazon.com Inc., Seattle, WA, USA) and Microsoft Windows Azure (Microsoft Corp., Redmond, WA, USA) as well as utilizing MapReduce‐based data processing frameworks Apache Hadoop (Apache Software Foundation, Los Angeles, CA, USA) and Microsoft DryadLINQ. We review and compare each of these frameworks, performing a comparative study among them based on performance, cost, and usability. High latency, eventually consistent cloud infrastructure service‐based frameworks that rely on off‐the‐node cloud storage were able to exhibit performance efficiencies and scalability comparable to the MapReduce‐based frameworks with local disk‐based storage for the applications considered. In this paper, we also analyze variations in cost among the different platform choices (e.g., Elastic Compute Cloud instance types), highlighting the importance of selecting an appropriate platform based on the nature of the computation. Copyright © 2011 John Wiley & Sons, Ltd.
Identification of Genes Involved in Polysaccharide-Independent Staphylococcus aureus Biofilm Formation

Staphylococcus aureus is a potent biofilm former on host tissue and medical implants, and biofilm growth is a critical virulence determinant for chronic infections. Recent studies suggest that many clinical isolates form polysaccharide-independent biofilms. However, a systematic screen for defective mutants has not been performed to identify factors important for biofilm formation in these strains. We created a library of 14,880 mariner transposon mutants in a S. aureus strain that generates a proteinaceous and extracellular DNA based biofilm matrix. The library was screened for biofilm defects and 31 transposon mutants conferred a reproducible phenotype. In the pool, 16 mutants overproduced extracellular proteases and the protease inhibitor α2-macroglobulin restored biofilm capacity to 13 of these mutants. The other 15 mutants in the pool displayed normal protease levels and had defects in genes involved in autolysis, osmoregulation, or uncharacterized membrane proteins. Two transposon mutants of interest in the GraRS two-component system and a putative inositol monophosphatase were confirmed in a flow cell biofilm model, genetically complemented, and further verified in a community-associated methicillin-resistant S. aureus (CA-MRSA) isolate. Collectively, our screen for biofilm defective mutants identified novel loci involved in S. aureus biofilm formation and underscored the importance of extracellular protease activity and autolysis in biofilm development.
Topic modeling for expert finding using latent Dirichlet allocation

The task of expert finding is to rank the experts in the search space given a field of expertise as an input query. In this paper, we propose a topic modeling approach for this task. The proposed model uses latent Dirichlet allocation (LDA) to induce probabilistic topics. In the first step of our algorithm, the main topics of a document collection are extracted using LDA. The extracted topics present the connection between expert candidates and user queries. In the second step, the topics are used as a bridge to find the probability of selecting each candidate for a given query. The candidates are then ranked based on these probabilities. The experimental results on the Text REtrieval Conference (TREC) Enterprise track for 2005 and 2006 show that the proposed topic‐based approach outperforms the state‐of‐the‐art profile‐ and document‐based models, which use information retrieval methods to rank experts. Moreover, we present the superiority of the proposed topic‐based approach to the improved document‐based expert finding systems, which consider additional information such as local context, candidate prior, and query expansion.
Effectiveness of advanced nursing care on depression in patients with ovarian cancer

Background: This systematic review will assess the effectiveness of advanced nursing care (ANC) on depression in patients with ovarian cancer (OC). Methods: We will identify any relevant randomized controlled trial from Cochrane Library, MEDLINE, Embase, Web of Science, Springer, Chinese Biomedical Literature Database, and China National Knowledge Infrastructure from their inceptions to March 5, 2019. The primary outcome includes depression. The secondary outcomes consist of anxiety, quality of life, and adverse events. Data that meets all the eligibility criteria will be extracted, pooled, and analyzed by using RevMan 5.3 software. Methodological quality for each eligible study will be assessed by using Cochrane risk of bias tool. Results: This study will analyze depression, anxiety, quality of life, and adverse events of ANC on depression in patients with OC. Conclusion: The findings of this study will provide the latest evidence for the effectiveness and adverse events of ANC on depression in patients with OC. Ethics and dissemination: No ethic approval is required for this study, because all the data will be extracted from previous published studies. The results of this study will be presented at conference or will be published at a peer-reviewed journal. PROSPERO registration number: PROSPERO CRD42019126374.
The Fibronectin Domain ED-A Is Crucial for Myofibroblastic Phenotype Induction by Transforming Growth Factor-β1

Transforming growth factor-β1 (TGFβ1), a major promoter of myofibroblast differentiation, induces α-smooth muscle (sn) actin, modulates the expression of adhesive receptors, and enhances the synthesis of extracellular matrix (ECM) molecules including ED-A fibronectin (FN), an isoform de novo expressed during wound healing and fibrotic changes. We report here that ED-A FN deposition precedes α-SM actin expression by fibroblasts during granulation tissue evolution in vivo and after TGFβ1 stimulation in vitro. Moreover, there is a correlation between in vitro expression of α-SM actin and ED-A FN in different fibroblastic populations. Seeding fibroblasts on ED-A FN does not elicit per se α-SM actin expression; however, incubation of fibroblasts with the anti-ED-A monoclonal antibody IST-9 specifically blocks the TGFβ1-triggered enhancement of α-SM actin and collagen type I, but not that of plasminogen activator inhibitor-1 mRNA. Interestingly, the same inhibiting action is exerted by the soluble recombinant domain ED-A, but neither of these inhibitory agents alter FN matrix assembly. Our findings indicate that ED-A–containing polymerized FN is necessary for the induction of the myofibroblastic phenotype by TGFβ1 and identify a hitherto unknown mechanism of cytokine-determined gene stimulation based on the generation of an ECM-derived permissive outside in signaling, under the control of the cytokine itself.
Deletion of IL-4Rα on CD4 T Cells Renders BALB/c Mice Resistant to Leishmania major Infection

Effector responses induced by polarized CD4+ T helper 2 (Th2) cells drive nonhealing responses in BALB/c mice infected with Leishmania major. Th2 cytokines IL-4 and IL-13 are known susceptibility factors for L. major infection in BALB/c mice and induce their biological functions through a common receptor, the IL-4 receptor α chain (IL-4Rα). IL-4Rα–deficient BALB/c mice, however, remain susceptible to L. major infection, indicating that IL-4/IL-13 may induce protective responses. Therefore, the roles of polarized Th2 CD4+ T cells and IL-4/IL-13 responsiveness of non-CD4+ T cells in inducing nonhealer or healer responses have yet to be elucidated. CD4+ T cell–specific IL-4Rα (LckcreIL-4Rα−/lox) deficient BALB/c mice were generated and characterized to elucidate the importance of IL-4Rα signaling during cutaneous leishmaniasis in the absence of IL-4–responsive CD4+ T cells. Efficient deletion was confirmed by loss of IL-4Rα expression on CD4+ T cells and impaired IL-4–induced CD4+ T cell proliferation and Th2 differentiation. CD8+, γδ+, and NK–T cells expressed residual IL-4Rα, and representative non–T cell populations maintained IL-4/IL-13 responsiveness. In contrast to IL-4Rα−/lox BALB/c mice, which developed ulcerating lesions following infection with L. major, LckcreIL-4Rα−/lox mice were resistant and showed protection to rechallenge, similar to healer C57BL/6 mice. Resistance to L. major in LckcreIL-4Rα−/lox mice correlated with reduced numbers of IL-10–secreting cells and early IL-12p35 mRNA induction, leading to increased delayed type hypersensitivity responses, interferon-γ production, and elevated ratios of inducible nitric oxide synthase mRNA/parasite, similar to C57BL/6 mice. These data demonstrate that abrogation of IL-4 signaling in CD4+ T cells is required to transform nonhealer BALB/c mice to a healer phenotype. Furthermore, a beneficial role for IL-4Rα signaling in L. major infection is revealed in which IL-4/IL-13–responsive non-CD4+ T cells induce protective responses.
Staged memory scheduling: Achieving high performance and scalability in heterogeneous systems

When multiple processor (CPU) cores and a GPU integrated together on the same chip share the off-chip main memory, requests from the GPU can heavily interfere with requests from the CPU cores, leading to low system performance and starvation of CPU cores. Unfortunately, state-of-the-art application-aware memory scheduling algorithms are ineffective at solving this problem at low complexity due to the large amount of GPU traffic. A large and costly request buffer is needed to provide these algorithms with enough visibility across the global request stream, requiring relatively complex hardware implementations. This paper proposes a fundamentally new approach that decouples the memory controller's three primary tasks into three significantly simpler structures that together improve system performance and fairness, especially in integrated CPU-GPU systems. Our three-stage memory controller first groups requests based on row-buffer locality. This grouping allows the second stage to focus only on inter-application request scheduling. These two stages enforce high-level policies regarding performance and fairness, and therefore the last stage consists of simple per-bank FIFO queues (no further command reordering within each bank) and straightforward logic that deals only with low-level DRAM commands and timing. We evaluate the design trade-offs involved in our Staged Memory Scheduler (SMS) and compare it against three state-of-the-art memory controller designs. Our evaluations show that SMS improves CPU performance without degrading GPU frame rate beyond a generally acceptable level, while being significantly less complex to implement than previous application-aware schedulers. Furthermore, SMS can be configured by the system software to prioritize the CPU or the GPU at varying levels to address different performance needs.
Working with audio: integrating personal tape recorders and desktop computers

Audio data is rarely used on desktop computers today, although audio is otherwise widely used for communication tasks. This paper describes early work aimed at creating computer tools that support the ways users may want to work with audio data. User needs for the system were determined by intervieweing people already working with audio data, using existing devices such as portable tape recorders. A preliminary prototype system – consisting of a personal tape recorder for recording and simultaneously marking audio and a Macintosh application for browsing these recordings – was built. Informal field user tests of this prototype system have indicated areas for improvement and directions for future work.
Prevalence of the Equol-Producer Phenotype and Its Relationship with Dietary Isoflavone and Serum Lipids in Healthy Chinese Adults

Background Studies have suggested that daidzein-metabolizing phenotypes have beneficial effects on a range of health outcomes. We investigated the prevalence of equol producers and the relationship of equol phenotype with habitual isoflavone consumption and serum lipid concentrations in 200 Chinese adults in Beijing. Methods After the baseline survey and dietary records, 200 healthy adults in Beijing were challenged with a soy-isoflavone supplement for 3 days; 24-hour urine samples were collected before and after the challenge. Isoflavones and their metabolites in urine were measured to determine equol phenotype. Serum lipids, uric acid, and other biochemical markers were also measured. Results Only 26.8% of the participants excreted equol when on a regular diet, as compared with 60.4% after the challenge. After the challenge, urinary isoflavonoid excretion increased in all participants, while equol excretion increased only in equol producers. Isoflavone intake was correlated with urinary isoflavone (range r = 0.49–0.58, P < 0.01). As compared with nonproducers, equol producers were less likely to consume cereals (P < 0.001). There was no significant correlation between serum lipids and isoflavone intake. Serum lipids were not significantly affected by equol phenotype. Conclusions Urinary equol excretion was detected in about 25% of participants under their usual dietary conditions. Their potential to produce equol was increased after the challenge. Urinary isoflavone levels may serve as a useful biomarker for isoflavone intake in populations. We observed an association between equol phenotype and cereal intake. Our findings also suggest that dietary isoflavone intake has no significant effect on serum lipids in healthy participants, regardless of equol phenotype.
Sports activities related to injuries? A survey among 9–19 year olds in Switzerland

Background—Most data on sports injuries are gathered in clinical settings so that their epidemiology in the general population is not well known. Objective—To explore the link between sports injuries with the type and the amount of sports activity and biological factors. Methods—In 1996, 3609 in-school adolescents 10–19 years (1847 girls and 1762 boys) participated in a regional survey. This included anthropometric measurements and a self administered questionnaire. Results—Altogether 28.2% of girls and 35.9% of boys reported one or more sports injuries during the previous year and 2.1% of girls and 6.5% of boys reported at least one hospitalization due to a sports injury. Using the mean rate of injuries as reference level, some sports are highly related to injury occurrence: body building (relative risk (RR) 1.7, 95% confidence interval (CI) 1.5 to 1.9), skateboarding and rollerskating (RR 1.6, 1.4 to 1.8), athletics (RR 1.5, 1.3 to 1.7), snowboarding (RR 1.5, 1.4 to 1.6), basketball (RR 1.3, 1.2 to 1.4), soccer (RR 1.3, 1.2 to 1.4), and ice hockey (RR 1.2, 1.1 to 1.3). Using a logistic regression, several variables associated with a higher risk of injury were identified: the amount of physical activity, high risk sports, and Tanner pubertal stages. Conclusion—The risk of sports injury increases not so much with age but with exposure to specific sports and with pubertal development.
Identifying frail older people using predictive modeling.

OBJECTIVES To determine whether a designation of frailty using the Adjusted Clinical Groups-diagnoses based computerized predictive model (ACG Dx-PM) can identify an elderly population who (1) have the clinical characteristics of frailty and (2) are frail as determined by the validated Vulnerable Elders Survey (VES), and to determine the ability of these tools to predict adverse outcomes. STUDY DESIGN Secondary analysis of administrative and survey data. METHODS Participants over age 65 years (n = 195) in an outpatient comprehensive geriatric assessment study at an Israeli health maintenance organization (HMO) were screened for frailty using the ACG Dx-PM and VES. Administrative and demographic data were also gathered. RESULTS Compared with ACG nonfrail patients, ACG frail patients were older and less likely to be married; had a higher rate of falls, incontinence, and need for personal care; and had a poorer quality of life consistent with a clinical picture of frailty. The ACG frailty tag identified a frail population using the VES frailty determination as the accepted standard with moderate success (area under the curve 0.62). Adjusting for sex and functional status in backward logistic regression, the ACG frailty tag predicted hospitalizations (P <.032) and the VES frailty tool predicted emergency department visits (P <.016). CONCLUSIONS The ACG frailty tag identified an elderly population with clinical characteristics of frailty and performed with moderate success compared with the VES. Both tools predicted adverse outcomes in older HMO members. A combined screening approach for frailty using predictive modeling with a function-based survey deserves further study.
Sentiment in Twitter events

The microblogging site Twitter generates a constant stream of communication, some of which concerns events of general interest. An analysis of Twitter may, therefore, give insights into why particular events resonate with the population. This article reports a study of a month of English Twitter posts, assessing whether popular events are typically associated with increases in sentiment strength, as seems intuitively likely. Using the top 30 events, determined by a measure of relative increase in (general) term usage, the results give strong evidence that popular events are normally associated with increases in negative sentiment strength and some evidence that peaks of interest in events have stronger positive sentiment than the time before the peak. It seems that many positive events, such as the Oscars, are capable of generating increased negative sentiment in reaction to them. Nevertheless, the surprisingly small average change in sentiment associated with popular events (typically 1% and only 6% for Tiger Woods' confessions) is consistent with events affording posters opportunities to satisfy pre-existing personal goals more often than eliciting instinctive reactions. © 2011 Wiley Periodicals, Inc.
Natural Language Instruction for Analogical Reasoning: An Initial Report

A challenge for any case-based reasoning system is how to acquire the cases with which to reason. Here we explore acquiring cases via natural language instruction by a person. We show how, using microstories (1-3 sentence stories) expressed in simplified English syntax, small cases – called common sense units – can be incrementally added to improve analogical reasoning performance.
Active touch point selection with travel cost in tactile exploration for fast shape estimation of unknown objects

Tactile sensing for object shape estimation is a key ingredient for real world robots that need to do grasping and manipulation of unknown objects. Since the vision sensors are noisy and suffer from occlusions, the touch to sense approach is beneficial for complementary obtaining local but accurate shape information of objects. Executing exhaustive touches for an object is time consuming and unrealistic, therefore, actively selecting touch points that effectively contribute on the shape estimation is crucial. Prior work suggested to touch the most uncertain part of the estimated shape for minimizing the required number of touches. However, the number of touches may not be the best objective for active touch point selection because it may require an unnecessarily long travel distance and result in an unreasonable execution time. In this paper, we present an alternative approach for active touch point selection by considering the travel costs to the touch points from the current sensor position in addition to the uncertainty of the estimated shape. To estimate the travel costs for all the candidates of touches, we present a graph-based efficient path planning method based on stochastic optimal control. Simulations and real robot experiments with 7DOFs anthropomorphic arm with a single finger device equipped with a tactile sensor are conducted. All the experimental results with several comparisons verify the effectiveness of our method.
Phragmoplast of the green alga Spirogyra is functionally distinct from the higher plant phragmoplast

Cytokinesis in the green alga Spirogyra (Zygnemataceae) is characterized by centripetal growth of a septum, which impinges on a persistent, centrifugally expanding telophase spindle, leading to a phragmoplast-like structure of potential phylogenetic significance (Fowke, L. C., and J. D. Pickett-Heaps. 1969. J. Phycol. 5:273-281). Combining fluorescent tagging of the cytoskeleton in situ and video- enhanced differential interference contrast microscopy of live cells, the process of cytokinesis was investigated with emphasis on cytoskeletal reorganization and concomitant redistribution of organelles. Based on a sequence of cytoskeletal arrangements and the effects of cytoskeletal inhibitors thereon, cytokinetic progression could be divided into three functional stages with respect to the contribution of microfilaments (MFs) and microtubules (MTs): (1) Initiation: in early prophase, a cross wall initial was formed independently of MFs and MTs at the presumptive site of wall growth. (2) Septum ingrowth: numerous organelles accumulated at the cross wall initial concomitant with reorganization of the extensive peripheral interphase MF array into a distinct circumferential MF array. This array guided the ingrowing septum until it contacted the expanding interzonal MT array. (3) Cross wall closure: MFs at the growing edge of the septum coaligned with and extended along the interzonal MTs toward the daughter nuclei. Thus, actin-based transportation of small organelles during this third stage occurred, in part, along a scaffold previously deployed in space by MTs. Displacement of the nuclei- associated interzonal MT array by centrifugation and depolymerization of the phragmoplast-like structure showed that the success of cytokinesis at the third stage depends on the interaction of both MF and MT cytoskeletons. Important features of the phragmoplast-like structure in Spirogyra were different from the higher plant phragmoplast: in particular, MFs were responsible for the positioning of organelles at the fusion site, contrary to the proposed role of MTs in the higher plant phragmoplast.
SPAN: Integrating Problem-Solving Tactics

This paper describes SPAN, a system designed to integrate a variety of problem solving tactics in a coherent package. The paper discusses some of the tactics that had been used in previous systems to overcome the combinatorial explosion that is inherent in any planning problem. It then continues with a description of SPAN architecture. Two case studies are presented. The first, from the blocks world, is already implemented, and the second, from the domain of bridge playing, is in the coding stage. SPANS limitations are discussed and directions for further research are considered.