Miracle-dz/UniFAR-FTUs huggingface dataset:
The application of projected conjugate gradient solvers on graphical processing units

Graphical processing units introduce the capability for large scale computation at the desktop. Presented numerical results verify that efficiencies and accuracies of basic linear algebra subroutines of all levels when implemented in CUDA and Jacket are comparable. But experimental results demonstrate that the basic linear algebra subroutines of level three offer the greatest potential for improving efficiency of basic numerical algorithms. We consider the solution of the multiple right hand side set of linear equations using Krylov subspace-based solvers. Thus, for the multiple right hand side case, it is more efficient to make use of a block implementation of the conjugate gradient algorithm, rather than to solve each system independently. Jacket is used for the implementation. Furthermore, including projection from one system to another improves efficiency. A relevant example, for which simulated results are provided, is the reconstruction of a three dimensional medical image volume acquired from a positron emission tomography scanner. Efficiency of the reconstruction is improved by using projection across nearby slices.
A Method to Combine Local Heat Transfer and Flow Visualization of Flow Boiling in Frame-and-plate Heat Exchanger

This paper presents the development of a novel method to combine measurement of local heat transfer coefficient and flow visualization in frame-and-plate heat exchanger (FPHE). A special plate was instrumented using two original chevron plates and clay as thermal infills. Thermocouples were deployed on the inner surfaces of the two plates. With the known thickness and thermal conductivity of the clay, the instrumented plate functions as a heat flux sensor. After calibration, this plate was installed to measure fluid heat transfer from one side, while leaving visual access from the other. Preliminary results of water-water single-phase heat transfer and R245fa-water flow boiling were presented. Combined with visualization, the method provides a viable solution to relate local heat transfer with flow regime within a plate channel, while preserving the real geometry and operating condition.
Perceived Autonomy Support, Personal Goal Content, and Emotional Well-Being among Elite Athletes: Mediating Effects of Reasons for Goals

The relations between perceived support of autonomy from coaches, characteristics of personal goals, and emotional well-being from the perspective of self-determination theory was examined among 95 elite athletes (59% men; M = 21.6 yr., SD = 6.1) from Track and Field, Greco-Roman Wrestling, Taekwondo, and Power Lifting. Elite athletes were those representing their country in their sport. It was hypothesized that having autonomous reasons for goals would mediate the positive associations between perceived autonomy support and intrinsic goal content with subjective positive emotional well-being, and that controlled reasons for goals would mediate the association between extrinsic goal content and subjective negative emotional well-being. An idiographic approach to measures of personal goals and the autonomous and controlled reasons and intrinsic and extrinsic contents were performed. Perceived autonomy support from the coach was assessed with the Sport Climate Questionnaire and subjective emotional well-being was assessed with the Positive and Negative Affect Schedule. All hypotheses were supported by path analyses using LISREL.
Integrated perception with recurrent multi-task neural networks

Modern discriminative predictors have been shown to match natural intelligences in specific perceptual tasks in image classification, object and part detection, boundary extraction, etc. However, a major advantage that natural intelligences still have is that they work well for "all" perceptual problems together, solving them efficiently and coherently in an "integrated manner". In order to capture some of these advantages in machine perception, we ask two questions: whether deep neural networks can learn universal image representations, useful not only for a single task but for all of them, and how the solutions to the different tasks can be integrated in this framework. We answer by proposing a new architecture, which we call "MultiNet", in which not only deep image features are shared between tasks, but where tasks can interact in a recurrent manner by encoding the results of their analysis in a common shared representation of the data. In this manner, we show that the performance of individual tasks in standard benchmarks can be improved first by sharing features between them and then, more significantly, by integrating their solutions in the common representation.
Revising Bayesian Network Parameters Using

The problem of learning Bayesian networks with hidden variables is known to be a hard problem. Even the simpler task of learning just the conditional probabilities on a Bayesian network with hidden variables is hard. In this paper, we present an approach that learns the conditional probabilities on a Bayesian network with hidden variables by transforming it into a multi-layer feedforward neural network (ANN). The conditional probabilities are mapped onto weights in the ANN, which are then learned using standard backpropagation techniques. To avoid the problem of exponentially large ANNs, we focus on Bayesian networks with noisy-or and noisy-and nodes. Experiments on real world classiication problems demonstrate the eeectiveness of our technique.
Measures to Control an Outbreak of Pertussis in a Neonatal Intermediate Care Nursery After Exposure to a Healthcare Worker

Background. Hospitalized premature infants are particularly vulnerable to morbidity and mortality from pertussis. Effective prevention and investigative and control measures are not well described. Objective. To identify the source of nosocomial pertussis in a 2-month-old premature infant in a neonatal intermediate care nursery (ICN) and to critically review the investigation and outbreak control measures. Setting. An ICN and a neonatal intensive care unit. Methods. We queried healthcare workers (HCWs) and family members about cough illness and contacted potentially exposed patients to determine whether they had symptoms of pertussis. Culture and polymerase chain reaction (PCR) testing for Bordetella pertussis were performed by the hospital laboratory with specimens collected from symptomatic patients and HCWs. Levels of pertussis toxin immunoglobulin G antibodies were measured in HCWs with cough of at least 14 days' duration at a public health laboratory. Extensive control measures were instituted. Results. Four ICN HCWs met the clinical case definition for presence of pertussis. Serologic test results were positive for 3 of the HCWs. The primary case patient was a 36-year-old HCW with a cough illness of 3-weeks' duration that was accompanied by paroxysms, whoop, posttussive emesis, and pneumothorax. Among the 4 affected HCWs, the duration of cough illness prior to identification of the infant index patient ranged from 11 to 25 days. Outbreak control measures included isolation of the infant case patient, furlough and treatment of symptomatic HCWs, administration of chemoprophylaxis to contacts, and surveillance for additional cases. Seventy-two infant patients and 72 HCWs were exposed and were given antibiotic prophylaxis. One additional case of pertussis, confirmed by PCR and culture, occurred in a resident physician who declined prophylaxis; she had cared for the index patient but had no contact with symptomatic HCWs. Conclusion. HCWs or patients may serve as the source of pertussis in nosocomial outbreaks, which can result in substantial morbidity and outlay of resources for control measures. Our review suggested that a diagnosis of pertussis should be an early consideration for HCWs with cough illness. Targeted pertussis immunization of HCWs, employee health policies that provide for testing and furlough of HCWs with prolonged cough, and monitoring of HCWs for compliance with infection control measures could reduce the morbidity and costs associated with pertussis outbreaks. These measures will require evaluation of their effectiveness.
Immunologic injury of cultured cells infected with measles virus. I. role of IfG antibody and the alternative complement pathway

In these studies, a number of human cell lines including epithelial, neural, glial, and lymphoid cells infected with several strains of measles virus were found to be lysed upon incubation with fresh sera from humans containing antibody measles virus. In all instances, the cytolytic event was mediated by alternative complement (C) pathway without a significant contribution from classical pathway. In contrast, isolated measles virus in conjunction with antibody was found to selectively activate the classical C pathway. Measles antibodies of the IgG class, but not the IgA class, possessed cytolytic potential against cells infected with measles virus. Human IgG antibodies could directly activate the alternative C pathway. No defect was found in cytolytic measles antibody in sera or cerebrospinal fluid from patients with subacute sclerosing panencephalitis, nor was the alternative C pathway impaired in sera from these patients. Sera from newborn humans exhibited a functional alternative C pathway.
A Visual Data Mining Tool that Facilitates Reconstruction of Transcription Regulatory Networks

Background Although the use of microarray technology has seen exponential growth, analysis of microarray data remains a challenge to many investigators. One difficulty lies in the interpretation of a list of differentially expressed genes, or in how to plan new experiments given that knowledge. Clustering methods can be used to identify groups of genes with similar expression patterns, and genes with unknown function can be provisionally annotated based on the concept of “guilt by association”, where function is tentatively inferred from the known functions of genes with similar expression patterns. These methods frequently suffer from two limitations: (1) visualization usually only gives access to group membership, rather than specific information about nearest neighbors, and (2) the resolution or quality of the relationships are not easily inferred. Methodology/Principal Findings We have addressed these issues by improving the precision of similarity detection over that of a single experiment and by creating a tool to visualize tractable association networks: we (1) performed meta-analysis computation of correlation coefficients for all gene pairs in a heterogeneous data set collected from 2,145 publicly available micorarray samples in mouse, (2) filtered the resulting distribution of over 130 million correlation coefficients to build new, more tractable distributions from the strongest correlations, and (3) designed and implemented a new Web based tool (StarNet, http://vanburenlab.medicine.tamhsc.edu/starnet.html) for visualization of sub-networks of the correlation coefficients built according to user specified parameters. Conclusions/Significance Correlations were calculated across a heterogeneous collection of publicly available microarray data. Users can access this analysis using a new freely available Web-based application for visualizing tractable correlation networks that are flexibly specified by the user. This new resource enables rapid hypothesis development for transcription regulatory relationships.
Assessment and Classroom Learning

ABSTRACT This article is a review of the literature on classroom formative assessment. Several studies show firm evidence that innovations designed to strengthen the frequent feedback that students receive about their learning yield substantial learning gains. The perceptions of students and their role in self‐assessment are considered alongside analysis of the strategies used by teachers and the formative strategies incorporated in such systemic approaches as mastery learning. There follows a more detailed and theoretical analysis of the nature of feedback, which provides a basis for a discussion of the development of theoretical models for formative assessment and of the prospects for the improvement of practice.
Conflicts in Thailand during 2013-14: An Analysis of Conflict News in Mass Media

Thailand’s current conflicts have strikingly increased political, social, and economic instability, reduced legitimacy of governance, and undermined the rule of law. The purpose of this research was to examine types of conflicts in 6 social situations in Thailand during 2013-14. A sample of 1,200 conflict news reports from 3 daily newspapers, 2 weekly newspapers, and 3 television news channels were analyzed using content analysis and discourse analysis. The findings revealed that the conflict news reported from the deep southern regions of Thailand showed more violent behaviors than the other five conflict situations- the political conflict, the economic conflict, the environmental conflict, the public policy, and the violence against children and adolescents. All conflict news showed higher proportion of structural conflicts rather than other types of conflict. Moreover, conflict news during the 3 political periods showed differences based on writer’s biased opinion and personal ideology. Keywords : news analysis, conflicts in Thailand
Glycated and carbamylated albumin are more "nephrotoxic" than unmodified albumin in the amphibian kidney.

There is increasing evidence that proteins in tubular fluid are "nephrotoxic. " In vivo it is difficult to study protein loading of tubular epithelial cells in isolation, i.e., without concomitant glomerular damage or changes of renal hemodynamics, etc. Recently, a unique amphibian model has been described which takes advantage of the special anatomy of the amphibian kidney in which a subset of nephrons drains the peritoneal cavity (open nephrons) so that intraperitoneal injection of protein selectively causes protein storage in and peritubular fibrosis around open but not around closed tubules. There is an ongoing debate as to what degree albumin per se is nephrotoxic and whether modification of albumin alters its nephrotoxicity. We tested the hypothesis that carbamylation and glycation render albumin more nephrotoxic compared with native albumin and alternative albumin modifications, e.g., lipid oxidation and lipid depletion. Preparations of native and modified albumin were injected into the axolotl peritoneum. The kidneys were retrieved after 10 days and studied by light microscopy as well as by immunohistochemistry [transforming growth factor (TGF)-β, PDGF, NF-κB, collagen I and IV, RAGE], nonradioactive in situ hybridization, and Western blotting. Two investigators unaware of the animal groups evaluated and scored renal histology. Compared with unmodified albumin, glycated and carbamylated albumin caused more pronounced protein storage. After no more than 10 days, selective peritubular fibrosis was seen around nephrons draining the peritoneal cavity (open nephrons), but not around closed nephrons. Additionally, more intense expression of RAGE, NF-κB, as well as PDGF, TGF-β, EGF, ET-1, and others was noted by histochemistry and confirmed by RT-PCR for fibronectin and TGF-β as well as nonradioactive in situ hybridization for TGF-β and fibronectin. The data indicate that carbamylation and glycation increase the capacity of albumin to cause tubular cell damage and peritubular fibrosis.
Second order statistics of bilinear forms of robust scatter estimators

This paper lies in the lineage of recent works studying the asymptotic behaviour of robust-scatter estimators in the case where the number of observations and the dimension of the population covariance matrix grow at infinity with the same pace. In particular, we analyze the fluctuations of bilinear forms of the robust shrinkage estimator of covariance matrix. We show that this result can be leveraged in order to improve the design of robust detection methods. As an example, we provide an improved generalized likelihood ratio based detector which combines robustness to impulsive observations and optimality across the shrinkage parameter, the optimality being considered for the false alarm regulation.
SALT frameworks to tackle surveillance and privacy concerns

This paper elaborates on the need to take into account the different views of the stakeholders involved in the development of surveillance systems and civil society, during the design process. It first provides an overview on privacy-by-design approaches. It then identifies three principles essential to integrate privacy concerns into the design of surveillance systems. It consequently proposes a design process based on social-contextual, ethical, legal and technical frameworks (SALT) and the challenges for its creation and use. It finally provides a specification of a resulting SALT framework management tool based on modelling techniques.
A Randomized Controlled Trial of Chloroquine for the Treatment of Dengue in Vietnamese Adults

Background There is currently no licensed antiviral drug for treatment of dengue. Chloroquine (CQ) inhibits the replication of dengue virus (DENV) in vitro. Methods and Findings A double-blind, randomized, placebo-controlled trial of CQ in 307 adults hospitalized for suspected DENV infection was conducted at the Hospital for Tropical Diseases (Ho Chi Minh City, Vietnam) between May 2007 and July 2008. Patients with illness histories of 72 hours or less were randomized to a 3-day course of CQ (n = 153) or placebo (n = 154). Laboratory-confirmation of DENV infection was made in 257 (84%) patients. The primary endpoints were time to resolution of DENV viraemia and time to resolution of DENV NS1 antigenaemia. In patients treated with CQ there was a trend toward a longer duration of DENV viraemia (hazard ratio (HR) = 0.80, 95% CI 0.62–1.05), but we did not find any difference for the time to resolution of NS1 antigenaemia (HR = 1.07, 95% CI 0.76–1.51). Interestingly, CQ was associated with a significant reduction in fever clearance time in the intention-to-treat population (HR = 1.37, 95% CI 1.08–1.74) but not in the per-protocol population. There was also a trend towards a lower incidence of dengue hemorrhagic fever (odds ratio = 0.60, PP 95% CI 0.34–1.04) in patients treated with CQ. Differences in levels of T cell activation or pro- or anti-inflammatory plasma cytokine concentrations between CQ- and placebo-treated patients did not explain the trend towards less dengue hemorrhagic fever in the CQ arm. CQ was associated with significantly more adverse events, primarily vomiting. Conclusions CQ does not reduce the durations of viraemia and NS1 antigenaemia in dengue patients. Further trials, with appropriate endpoints, would be required to determine if CQ treatment has any clinical benefit in dengue. Trial Registration Current Controlled Trials number ISRCTN38002730.
Absolute and Relative Strength Performance Following Creatine Monohydrate Supplementation Combined With Periodized Resistance Training

Twenty-one men (20–26 years old) were randomly assigned to one of 3 groups: an acute creatine monohydrate (Cr) 5-day load and maintenance placebo (AL); an acute Cr 5-day load and 32-day maintenance dose (ALM), and a placebo group (PL). The AL and ALM groups received Cr dissolved in a flavored drink at a dosage of 0.3g·kg−1·d−1 for 5 days for the acute load and the ALM group ingested Cr at 0.03g·kg−1·d−1 for the maintenance phase. The PL group ingested the drink only. While supplementing, all groups participated in a periodized resistance training program performing the same relative load and volume of training regardless of their assigned experimental group. Bench press (BP) and incline leg press (ILP) absolute strength (1 repetition maximum [1RM]), total lifting volume (80% of 1RM to failure), and strength per mass ratio were assessed initially (T1), after a 5-day acute load (T2), and following the 32-day maintenance phase (T3). No differences were observed in 1RMs, total lifting volume, or strength per mass ratio between experimental groups over time except in the AL group, which showed a significant improvement in the total lifting volume for BP after the acute Cr load. All groups significantly improved 1RM, total lifting volume, and strength per mass ratio from T1 to T3, with no changes observed from T1 to T2 in BP and ILP. The findings suggest that Cr supplementation combined with resistance training when relative loads and volumes are the same as a placebo group does not result in a training advantage in absolute or relative strength performance.
POMDP approach to robotized clothes separation

Rigid object manipulation with robots has mainly relied on precise, expensive models and deterministic sequences. Given the great complexity of accurately modeling deformable objects, their manipulation seems to call for a rather different approach. This paper proposes a probabilistic planner, based on a Partially Observable Markov Decision Process (POMDP), targeted at reducing the inherent uncertainty of deformable object sorting. It is shown that a small set of unreliable actions and inaccurate perceptions suffices to accomplish the task, provided faithful statistics on both of them are collected beforehand. The planner has been applied to a clothes sorting task in a real case context with a depth and color sensor and a robotic arm. Experimental results show the promise of the approach since more than 95% certainty of having isolated a piece of clothing is reached in an average of four steps for quite entangled initial clothing configurations.
Modelling the Dynamics of Anti-HBV Infection Therapy with Chinese Herbs

Effective treatment of chronic Hepatitis B virus (HBV) patients aims to prevent progression of chronic hepatitis B to cirrhosis, hepatocellular carcinoma, and eventually death. The use of mathematical modelling to explain the anti-HBV infection therapy has made a significant contribution for understanding the dynamics of host cells, viruses, the immune system. Chinese herbs are playing important roles for anti-HBV infec- tion treatment. Recently a new type of Chinese herbs (NTCH) has been proved to be effective for anti-HBV infection therapy. Based on a patient's anti-hepatitis B virus (HBV) infection therapy clinical data with the NTCH and our previous modified basic virus infection model (1), a new differential equation model with an immune variable is set up. The numerical simulations of the model show that the evolution of the HBV DNA of the model is agreement with in the patient's clinic plasma HBV DNA levels. The model predicts that it needs to prolong the treatment time to 4.3 years to eliminate NTCH the HBV virus in the patient's infected hepatocytes. Otherwise earlier cessation of the therapy will make the patient's HBV DNA levels return rapidly.
Exchange Bias Effects in Iron Oxide-Based Nanoparticle Systems

The exploration of exchange bias (EB) on the nanoscale provides a novel approach to improving the anisotropic properties of magnetic nanoparticles for prospective applications in nanospintronics and nanomedicine. However, the physical origin of EB is not fully understood. Recent advances in chemical synthesis provide a unique opportunity to explore EB in a variety of iron oxide-based nanostructures ranging from core/shell to hollow and hybrid composite nanoparticles. Experimental and atomistic Monte Carlo studies have shed light on the roles of interface and surface spins in these nanosystems. This review paper aims to provide a thorough understanding of the EB and related phenomena in iron oxide-based nanoparticle systems, knowledge of which is essential to tune the anisotropic magnetic properties of exchange-coupled nanoparticle systems for potential applications.