Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylodynamics and Dispersal of HRSV Entails Its Permanence in the General Population in between Yearly Outbreaks in Children

Background Human respiratory syncytial virus (HRSV) is one of the major etiologic agents of respiratory tract infections among children worldwide. Methodology/Principal Findings Here through a comprehensive analysis of the two major HRSV groups A and B (n = 1983) which comprise of several genotypes, we present a complex pattern of population dynamics of HRSV over a time period of 50 years (1956–2006). Circulation pattern of HRSV revealed a series of expansions and fluctuations of co-circulating lineages with a predominance of HRSVA. Positively selected amino acid substitutions of the G glycoprotein occurred upon population growth of GB3 with a 60-nucleotide insertion (GB3 Insert), while other genotypes acquired substitutions upon both population growth and decrease, thus possibly reflecting a role for immune selected epitopes in linkage to the traced substitution sites that may have important relevance for vaccine design. Analysis evidenced the co-circulation and predominance of distinct HRSV genotypes in Brazil and suggested a year-round presence of the virus. In Brazil, GA2 and GA5 were the main culprits of HRSV outbreaks until recently, when the GB3 Insert became highly prevalent. Using Bayesian methods, we determined the dispersal patterns of genotypes through several inferred migratory routes. Conclusions/Significance Genotypes spread across continents and between neighboring areas. Crucially, genotypes also remained at any given region for extended periods, independent of seasonal outbreaks possibly maintained by re-infecting the general population.
The Role of Apoptosis in the Pathology of Pancreatic Cancer

Pancreatic cancer is a disease with high resistance to most common therapies and therefore has a poor prognosis, which is partly due to a lack of reaction to apoptotic stimuli. Signal transduction of such stimuli includes a death receptor-mediated extrinsic pathway as well as an intrinsic pathway linked to the mitochondria. Defects in apoptotic pathways and the deregulation of apoptotic proteins, such as Survivin, Bcl-2, Bcl-xL and Mcl-1, play decisive roles in the development of pancreatic cancer. Investigation of the molecular mechanism allowing tumors to resist apoptotic cell death would lead to an improved understanding of the physiology and the development of new molecular strategies in pancreatic cancer.
Towards Optimal Bayes Decision for Speech Recognition

This paper presents a new speech recognition framework towards fulfilling optimal Bayes decision theory, which is essential for general pattern recognition. The recognition procedure is developed through minimizing the Bayes risk, or equivalently the expected loss due to classification action. Typically, loss function measures the penalty/evidence of choosing a candidate hypothesis. This function was manually specified or empirically calculated. Here, we exploit a novel Bayes loss function via testing the hypotheses whether the classification action produces loss or not. A Bayes factor is derived to measure loss in a statistical and meaningful way. Attractively, Bayes loss function using predictive distributions is robust to the uncertainty of environments. Also, optimizing this Bayes criterion equals to minimizing classification errors of test data. The relation between the minimum classification error (MCE) classifier and the proposed optimal Bayes classifier (OBC) is bridged. Specifically, the logarithm of Bayes factor in OBC is analogous to the misclassification measure in MCE when using predictive distribution as the discriminant function. We accordingly build a robust and discriminative classification for large vocabulary continuous speech recognition. In the experiments on broadcast news transcription, the new OBC rule significantly outperforms traditional maximum a posteriori classification
Epidemiology, Seasonality and Treatment of Hospitalized Adults and Adolescents with Influenza in Jingzhou, China, 2010-2012

Background After the 2009 influenza A (H1N1) pandemic, we conducted hospital-based severe acute respiratory infection (SARI) surveillance in one central Chinese city to assess disease burden attributable to influenza among adults and adolescents. Methods We defined an adult SARI case as a hospitalized patient aged ≥ 15 years with temperature ≥38.0°C and at least one of the following: cough, sore throat, tachypnea, difficulty breathing, abnormal breath sounds on auscultation, sputum production, hemoptysis, chest pain, or chest radiograph consistent with pneumonia. For each enrolled SARI case-patient, we completed a standardized case report form, and collected a nasopharyngeal swab within 24 hours of admission. Specimens were tested for influenza viruses by real-time reverse transcription polymerase chain reaction (rRT-PCR). We analyzed data from adult SARI cases in four hospitals in Jingzhou, China from April 2010 to April 2012. Results Of 1,790 adult SARI patients enrolled, 40% were aged ≥ 65 years old. The median duration of hospitalization was 9 days. Nearly all were prescribed antibiotics during their hospitalization, less than 1% were prescribed oseltamivir, and 28% were prescribed corticosteroids. Only 0.1% reported receiving influenza vaccination in the past year. Of 1,704 samples tested, 16% were positive for influenza. Influenza activity in all age groups showed winter-spring and summer peaks. Influenza-positive patients had a longer duration from illness onset to hospitalization and a shorter duration from hospital admission to discharge or death compared to influenza negative SARI patients. Conclusions There is substantial burden of influenza-associated SARI hospitalizations in Jingzhou, China, especially among older adults. More effective promotion of annual seasonal influenza vaccination and timely oseltamivir treatment among high risk groups may improve influenza prevention and control in China.
Accelerating the Convergence of the Subspace Decomposition Channel Estimation Algorithm in OFDM System

The ESPRIT algorithm is suitable for parametric channel estimation of slow varying channel of OFDM system. In this algorithm, the subspace decomposition technology is usually first used to estimate the multipath delay information of the channel, and then the channel is reconstructed through the estimate of the multipath delay information. This paper focuses on fast subspace tracking technology, and by using the frequency hopping principle, the convergence speed of the subspace tracking is accelerated. Theoretical analysis and simulation results show that, with applying this technology, subspace tracking performance is more stable, and the requirement that channel conditions should maintain unchanged over a longer period of time is not necessary.
Joint downlink transmit and receive beamforming under per-antenna power constraints

Conditioned with per-antenna power constraints, power allocation over transmit antennas must be controlled in joint optimization of transmit beamformers and receive beam-formers in multi-user Multiple-Input Multiple-Output (MIMO) downlink. In this paper, it is shown the Lagrangian dual of the per-antenna power constrained optimization problem is related to the network dual of a weighted sum power optimization problem without power constraints. From this perspective, the virtual uplink noises are found to be playing important roles. A scheme to manage power allocation over antennas by adjusting the virtual uplink noises during optimization is proposed. Under this scheme, two algorithms with different functions are designed and show good performance in simulations.
A user dependent Web service QoS collaborative prediction approach using neighborhood regularized matrix factorization

With the advent of service-oriented computing, Web service QoS prediction have become crucial for the success of many service-based distributed systems due to its significant role in evaluating Web services to satisfy user personalized needs. Previous studies underestimate the role of implicit relationship of neighborhood with respect to both users and Web services. It is natural and reasonable to assume that the QoS Web services perform and the choices users make are significantly influenced by their neighbors, thus it will be beneficial to incorporate this new source of information in QoS prediction. In this paper, we propose a neighborhood regularized matrix factorization method for collaborative Web service QoS prediction by properly incorporating both user and Web service neighborhood relationships aiming to improve the accuracy of prediction as well as alleviate the data sparsity issue. Experimental results demonstrate that the proposed approach achieves more accurate prediction than other well-known methods.
Du dépistage à la confirmation du diagnostic de trouble du spectre autistique : dispositif, outils et suivi du développement en population tout venant

Les troubles du Spectre Autistique (TSA) sont des troubles neuro-developpementaux, d’apparition precoce et qui affectent le developpement de l’individu tout au long de sa vie. La prevalence des TSA est estimee aux alentours de 1% de la population generale. Des interventions precoces peuvent minimiser le handicap resultant de ce trouble et ameliorer la qualite de vie et l’insertion sociale des enfants. L’opportunite de beneficier d’une intervention precoce depend de l’âge du diagnostic. Aujourd’hui, l’âge moyen du diagnostic des TSA en France est de 5 ans en moyenne. Un diagnostic precoce est pourtant possible des l’âge de 24 mois. Un depistage precoce des TSA permettrait de diminuer l’âge du diagnostic et par consequent l’âge du debut de l’intervention, maximisant ainsi les benefices. L'objectif general de ce travail, organise autour de 3 etudes, est de participer a l’amelioration des pratiques de depistage et de diagnostic precoce des TSA en evaluant la pertinence de differents outils pour aider les professionnels a reperer et orienter les enfants a risque de TSA. La premiere etude a pour objectif d’evaluer la faisabilite d’un depistage systematique des TSA chez les enfants âges de 24 mois. Un dispositif de depistage a ete developpe avec pour prealables la formation des professionnels de premiere ligne et la validation d’outils de depistage specifiques aux TSA : le CHAT et le M-CHAT. La seconde etude a pour objectif d’ameliorer l’orientation diagnostique des enfants reperes pour une suspicion de TSA. Dans cette optique, cette etude vise a evaluer la pertinence de l’utilisation du module 1 de l’ADOS-G pour confirmer ou infirmer la presence d’un risque de TSA chez les enfants de moins de 3 ans. Enfin, l’objectif de la derniere etude est d’evaluer l’apport eventuel des donnees issues de l’evaluation developpementale dans le dispositif. L’evaluation developpementale des enfants permet de mettre en evidence leur profil et ainsi de proposer un plan d’intervention dans l’attente de la confirmation diagnostique. Les resultats de ces etudes temoignent de la possibilite de reperer les enfants a risque de TSA a 24 mois. Les professionnels impliques dans la pratique de depistage ont aujourd’hui a leur disposition deux outils valides sur un echantillon francais: le CHAT et le M-CHAT. Ces outils presentent des proprietes psychometriques satisfaisantes pour une utilisation en population generale. L’utilisation du module 1 de l’ADOS-G permet de differencier les enfants de moins de 3 ans presentant un TSA des enfants avec une autre problematique developpementale. Cet outil apparait donc important pour ameliorer la specificite du depistage precoce. L’evaluation developpementale apporte quant a elle des informations sur les profils des enfants avec un TSA, marques notamment par des deficits dans les domaines de l’imitation et du jeu. Les implications cliniques de ces etudes sont discutees et de nouvelles pistes de recherche sont proposees.
Design , synthesis and evaluation of acridin-9-yl hydrazide derivatives as BACE-1 inhibitors

BACE-1, an aspartyl protease is implicated in Alzheimer’s disease. In this paper, we report BACE-1 inhibitory potential of acridin-9-yl hydrazide derivatives, known to inhibit other aspartyl proteases. The derivatives were designed based on the docking study, synthesized and assessed for BACE-1 inhibition in vitro. Docking simulation predicted the binding of prototype acridin-9-yl hydrazide at BACE-1 active site. The enzyme–inhibitor complex was primarily stabilized by hydrogen bonds between the hydrazide part of the inhibitor and side chain of Gly11, which is important amino acid of 10s loop. The acridinyl moiety showed p–p stacking with Tyr71 while the phenyl ring was buried in S1 cavity. Enzyme inhibition experiments showed that the synthesized compounds had moderate activity with compound AA-13 having 54.54 % inhibition at 10 lM concentration.
A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance

A recent study revealed that TATA boxes and initiator sequences have a common anomalous mechanical property, i.e. they comprise distinctive flexible and rigid sequences when compared with the other parts of the promoter region. In the present study, using the flexibility parameters from two different models, we calculated the average flexibility profiles of 1004 human promoters that do not contain canonical promoter elements, such as a TATA box, initiator (Inr) sequence, downstream promoter element or a GC box, and those of 382 human promoters that contain the GC box only. Here, we show that they have a common characteristic mechanical property that is strikingly similar to those of the TATA box-containing or Inr-containing promoters. Their most interesting feature is that the TATA- or Inr-corresponding region lies in the several nucleotides around the transcription start site. We have also found that a dinucleotide step from −1 to +1 (transcription start site) has a slight tendency to adopt CA that is known to be flexible. We also demonstrate that certain synthetic DNA fragments designed to mimic the average mechanical property of these 1386 promoters can drive transcription. This distinctive mechanical property may be the hallmark of a promoter.
SLEEP mode techniques for small cell deployments

Big things come in small packages; a particularly apt description of small cell deployment in cellular networks. Small cells have a big role to play in orchestrating a cellular network that can overcome the explosive mobile traffic upsurge at little cost to the network operator. However, if left unchecked, a large-scale small cell deployment can substantially increase the network energy consumption with strong ecological and economic implications. In this article, we introduce energy-efficient SLEEP mode algorithms for small cell base stations in a bid to reduce cellular networks' power consumption. The designed algorithms allow the hardware components in the BS to be astutely switched off in idle conditions, such that the energy consumption is modulated over the variations in traffic load. Three different strategies for algorithm control are discussed, relying on small cell driven, core network driven, and user equipment driven approaches. Based on a mixed voice and data traffic model, the algorithms present energy saving opportunities of approximately 10-60 percent in the network with respect to no SLEEP mode activation in small cells, coupled with additional capacity incentives.
The pathophysiology of chronic graft-versus-host disease: the unveiling of an enigma

Chronic graft-versus-host disease (CGVHD) is one of the most significant complications of long-term survivors after allogeneic hematopoietic stem cell transplantation (allo-HSCT). CGVHD may have protean manifestations and can pose unique diagnostic and therapeutic challenges. New recommendations that emphasize the importance of qualitative differences, as opposed to time of onset after HSCT, are now being used to standardize the diagnosis and clinical assessment of CGVHD, but they require validation. During the past 3 decades, experimental studies and clinical observations have elucidated the mechanisms of acute GVHD, but its biology is much less well-understood. Experimental studies have generated at least 4 theories to explain the pathophysiology of CGVHD: (1) thymic damage and the defective negative selection of T cells, (2) regulatory T cell deficiencies, (3) auto-antibody production by aberrant B cells, and (4) the formation of profibrotic lesions. Mouse models have provided important insights into the pathophysiology of CGVHD, and these have helped improve clinical outcomes following allo-HSCT, but no animal model fully replicates all of the features of CGVHD in humans. In this article, recent clinical changes, the pathogenesis of CGHVD, the cellular and cytokine networks implicated in its pathogenesis, and the animal models used to devise strategies to prevent and treat CGVHD are reviewed.
Relativistic Programming in Haskell Using Types to Enforce a Critical Section Discipline

Relativistic programming (RP) is a concurrent programming model in which readers can safely access shared data concurrently with writers that are modifying it. RP has been used extensively in operating system kernels, most notably in Linux, and is widely credited with improving the performance and scalability of Linux on highly concurrent architectures. However, using RP primitives safely is tricky, and existing implementations of RP do not identify most unsafe uses statically. This work introduces Monadic RP, a GHC Haskell library for RP, and presents an example of its use. To our knowledge, Monadic RP is the ﬁrst RP implementation in Haskell. It provides a novel mechanism to statically rule out a subset of unsafe relativistic programs by using types to separate read-side and write-side critical sections, and to restrict the operations available in each. This work describes the current status of our implementation, presents a brief experimental evaluation of it, and discusses directions for ongoing and future work.
Protection from distributed denial of service attacks using history-based IP filtering

In this paper, we introduce a practical scheme to defend against distributed denial of service (DDoS) attacks based on IP source address filtering. The edge router keeps a history of all the legitimate IP addresses which have previously appeared in the network. When the edge router is overloaded, this history is used to decide whether to admit an incoming Ip packet. Unlike other proposals to defend against DDoS attacks, our scheme works well during highly-distributed DDoS attacks, i.e., from a large number of sources. We present several heuristic methods to make the IP address database accurate and robust, and we present experimental results that demonstrate the effectiveness of our scheme in defending against highly-distributed DDoS attacks.
Estimating the Long-Term Costs Of Ischemic and Hemorrhagic Stroke for Australia: New Evidence Derived From the North East Melbourne Stroke Incidence Study (NEMESIS)

Background and Purpose— Stroke is associated with considerable societal costs. Cost-of-illness studies have been undertaken to estimate lifetime costs; most incorporating data up to 12 months after stroke. Costs of stroke, incorporating data collected up to 12 months, have previously been reported from the North East Melbourne Stroke Incidence Study (NEMESIS). NEMESIS now has patient-level resource use data for 5 years. We aimed to recalculate the long-term resource utilization of first-ever stroke patients and compare these to previous estimates obtained using data collected to 12 months. Methods— Population structure, life expectancy, and unit prices within the original cost-of-illness models were updated from 1997 to 2004. New Australian stroke survival and recurrence data up to 10 years were incorporated, as well as cross-sectional resource utilization data at 3, 4, and 5 years from NEMESIS. To enable comparisons, 1997 costs were inflated to 2004 prices and discounting was standardized. Results— In 2004, 27 291 ischemic stroke (IS) and 4291 intracerebral hemorrhagic stroke (ICH) first-ever events were estimated. Average annual resource use after 12 months was AU$6022 for IS and AU$3977 for ICH. This is greater than the 1997 estimates for IS (AU$4848) and less than those for ICH (previously AU$10 692). The recalculated average lifetime costs per first-ever case differed for IS (AU$57 106 versus AU$52 855 [1997]), but differed more for ICH (AU$49 995 versus AU$92 308 [1997]). Conclusion— Basing lifetime cost estimates on short-term data overestimated the costs for ICH and underestimated those for IS. Patterns of resource use varied by stroke subtype and, overall, the societal cost impact was large.
Psychological Differences toward Pedestrian Red Light Crossing between University Students and Their Peers

Based on our site investigation conducted in 2013, we found that the pedestrian red light crossing at the midblock connecting the campus of Southwest University and living area was low, where most of pedestrians are university students and staff. This paper reports a supplementary work applying the Theory of Planned Behaviour (TPB) to identify any psychological differences toward pedestrian red light crossing between university students and their peers. Three social groups participated in the investigation. The first group is the university students in Grade one (Group 1), the other two groups are their previous senior middle school classmates who are now working full time (Group 2) or who are now out of work and school (Group 3). The statistical results indicated The TPB components accounted for 42.9%, 55.3% and 55.4% of the variance of red signal crossing intention for Group 1, Group 2 and Group 3 in the depicted road crossing scenario. The data also showed that there are obvious differences among the participants’ responses to “refrain from crossing” between university students and others, and the subsequent regression analysis revealed the ability to “refrain from crossing” played the most important role in the intention of red light crossing in the depicted scenario.
On-the-Fly Computing on Many-Core Processors in Nuclear Applications (Selected Papers of the Joint International Conference of Supercomputing in Nuclear Applications and Monte Carlo : SNA + MC 2010)

Many nuclear applications still require more computational power than the current computers can provide. Furthermore, some of them require dedicated machines, because they must run constantly or no delay is allowed. To satisfy these requirements, we introduce computer accelerators which can provide higher computational power with lower prices than the current commodity processors. However, the feasibility of accelerators had not well investigated on nuclear applications. Thus, we applied the Cell and GPGPU to plasma stability monitoring and infrasound propagation analysis, respectively. In the plasma monitoring, the eigenvalue solver was focused on. To obtain sufficient power, we connected Cells with Ethernet, and implemented a preconditioned conjugate gradient method. Moreover, we applied a hierarchical parallelization method to minimize communications among the Cells. Finally, we could solve the block tri-diagonal Hermitian matrix that had 1, 024 diagonal blocks, and each block was 128 × 128, within one second. On the basis of these results, we showed the potential of plasma monitoring by using our Cell cluster system. In infrasound propagation analysis, we accelerated two-dimensional parabolic equation (PE) method by using GPGPU. PE is one of the most accurate methods, but it requires higher computational power than other methods. By applying softwarepipelining and memory layout optimization, we obtained ×18.3 speedup on GPU from CPU. Our achieved computing speed could be comparable to faster but more inaccurate method.