Miracle-dz/UniFAR-FTUs huggingface dataset:
Persistent High Burden of Invasive Pneumococcal Disease in South African HIV-Infected Adults in the Era of an Antiretroviral Treatment Program

Background Highly active antiretroviral treatment (HAART) programs have been associated with declines in the burden of invasive pneumococcal disease (IPD) in industrialized countries. The aim of this study was to evaluate trends in IPD hospitalizations in HIV-infected adults in Soweto, South Africa, associated with up-scaling of the HAART program from 2003 to 2008. Methods Laboratory-confirmed IPD cases were identified from 2003 through 2008 through an existing surveillance program. The period 2003-04 was designated as the early-HAART era, 2005–06 as the intermediate-HAART era and 2007–08 as the established-HAART era. The incidence of IPD was compared between the early-HAART and established-HAART eras in HIV-infected and–uninfected individuals. Results A total of 2,567 IPD cases among individuals older than 18 years were reported from 2003 through 2008. Overall incidence of IPD (per 100,000) did not change during the study period in HIV-infected adults (207.4 cases in the early-HAART and 214.0 cases in the established-HAART era; p = 0.55). IPD incidence, actually increased 1.16-fold (95% CI: 1.01; 1.62) in HIV-infected females between the early-and established-HAART eras (212.1 cases and 246.2 cases, respectively; p = 0.03). The incidence of IPD remained unchanged in HIV-uninfected adults across the three time periods. Conclusion Despite a stable prevalence of HIV and the increased roll-out of HAART for treatment of AIDS patients in our setting, the burden of IPD has not decreased among HIV-infected adults. The study indicates a need for ongoing monitoring of disease and HAART program effectiveness to reduce opportunistic infections in African adults with HIV/AIDS, as well as the need to consider alternate strategies including pneumococcal conjugate vaccine immunization for the prevention of IPD in HIV-infected adults.
Remodeling of Axonal Connections Contributes to Recovery in an Animal Model of Multiple Sclerosis

In multiple sclerosis (MS), inflammation in the central nervous system (CNS) leads to damage of axons and myelin. Early during the clinical course, patients can compensate this damage, but little is known about the changes that underlie this improvement of neurological function. To study axonal changes that may contribute to recovery, we made use of an animal model of MS, which allows us to target inflammatory lesions to the corticospinal tract (CST), a major descending motor pathway. We demonstrate that axons remodel at multiple levels in response to a single neuroinflammatory lesion as follows: (a) surrounding the lesion, local interneurons show regenerative sprouting; (b) above the lesion, descending CST axons extend new collaterals that establish a “detour” circuit to the lumbar target area, whereas below the lesion, spared CST axons increase their terminal branching; and (c) in the motor cortex, the distribution of projection neurons is remodeled, and new neurons are recruited to the cortical motor pool. Behavioral tests directly show the importance of these changes for recovery. This paper provides evidence for a highly plastic response of the motor system to a single neuroinflammatory lesion. This framework will help to understand the endogenous repair capacity of the CNS and to develop therapeutic strategies to support it.
Feature Sensitive Remeshing

Remeshing artifacts are a fundamental problem when converting a given geometry into a triangle mesh. We propose a new remeshing technique that is sensitive to features. First, the resolution of the mesh is iteratively adapted by a global restructuring process which additionally optimizes the connectivity. Then a particle system approach evenly distributes the vertices across the original geometry. To exactly find the features we extend this relaxation procedure by an effective mechanism to attract the vertices to feature edges. The attracting force is imposed by means of a hierarchical curvature field and does not require any thresholding parameters to classify the features.
Discriminative Relational Topic Models

Relational topic models (RTMs) provide a probabilistic generative process to describe both the link structure and document contents for document networks, and they have shown promise on predicting network structures and discovering latent topic representations. However, existing RTMs have limitations in both the restricted model expressiveness and incapability of dealing with imbalanced network data. To expand the scope and improve the inference accuracy of RTMs, this paper presents three extensions: 1) unlike the common link likelihood with a diagonal weight matrix that allows the-same-topic interactions only, we generalize it to use a full weight matrix that captures all pairwise topic interactions and is applicable to asymmetric networks; 2) instead of doing standard Bayesian inference, we perform regularized Bayesian inference (RegBayes) with a regularization parameter to deal with the imbalanced link structure issue in real networks and improve the discriminative ability of learned latent representations; and 3) instead of doing variational approximation with strict mean-field assumptions, we present collapsed Gibbs sampling algorithms for the generalized relational topic models by exploring data augmentation without making restricting assumptions. Under the generic RegBayes framework, we carefully investigate two popular discriminative loss functions, namely, the logistic log-loss and the max-margin hinge loss. Experimental results on several real network datasets demonstrate the significance of these extensions on improving prediction performance.
How Much Knowledge Can They Gain? Women's Information Behavior on Government Health Websites in the Context of HIV/AIDS Prevention

Author(s): Chong, Jing | Abstract: Using a theoretical framework extended from Rimal and Real’s (2003) Risk Perception Attitude framework, this research examines women’s information behavior, specifically information finding and reaction to information, on government health websites in the context of HIV/AIDS prevention. In the empirical study, think aloud and structured individual interview were used to collect data from 40 female university students in the U.S. in their completion of an information seeking task and an interview. Factors that influence women’s information finding and reaction to information were identified. This research challenges and extends Rimal and Real’s (2003) Risk Perception Attitude framework by proposing an Extended Risk Perception Attitude framework. This research also exemplifies Gupta’s (2000) categories of social construction of gender and sexuality in the HIV/AIDS discourse, and adds new evidence that proves their validity. In addition, this research enriches the literature in health-related information behavior by switching the research focus to other information behaviors than information seeking.
GeNMR: a web server for rapid NMR-based protein structure determination

GeNMR (GEnerate NMR structures) is a web server for rapidly generating accurate 3D protein structures using sequence data, NOE-based distance restraints and/or NMR chemical shifts as input. GeNMR accepts distance restraints in XPLOR or CYANA format as well as chemical shift files in either SHIFTY or BMRB formats. The web server produces an ensemble of PDB coordinates for the protein within 15–25 min, depending on model complexity and completeness of experimental restraints. GeNMR uses a pipeline of several pre-existing programs and servers to calculate the actual protein structure. In particular, GeNMR combines genetic algorithms for structure optimization along with homology modeling, chemical shift threading, torsion angle and distance predictions from chemical shifts/NOEs as well as ROSETTA-based structure generation and simulated annealing with XPLOR-NIH to generate and/or refine protein coordinates. GeNMR greatly simplifies the task of protein structure determination as users do not have to install or become familiar with complex stand-alone programs or obscure format conversion utilities. Tests conducted on a sample of 90 proteins from the BioMagResBank indicate that GeNMR produces high-quality models for all protein queries, regardless of the type of NMR input data. GeNMR was developed to facilitate rapid, user-friendly structure determination of protein structures via NMR spectroscopy. GeNMR is accessible at http://www.genmr. ca.
Ammonium perfluorooctanoate substantially alters phenotype and cytokine secretion of human monocyte-derived dendritic cells in vitro

Perfluoroalkyl carboxylic acids (PFCA) are commercially used for their surfactant properties combined with chemical and thermal stability. Differentiation of peripheral monocytes to immature dendritic cells (DCs) in the presence of the PFCA, ammonium perfluorooctanoate (APFO, 200 μM) led to a considerably increased expression of CD86 and HLA-DR on immature DCs. However, these phenotypic changes were not reflected by an increased T cell-stimulatory capacity of the cells. Notably, activated, fully mature APFO-treated DCs secreted significantly less IL-12 and IL-10 than control cells. Thus, APFO at non-cytotoxic concentration affects the phenotype and cytokine secretion of human DCs.
An SOA-Based Model for the Integrated Provisioning of Cloud and Grid Resources

In the last years, the availability and models of use of networked computing resources within reach of e-Science are rapidly changing and see the coexistence of many disparate paradigms: high-performance computing, grid, and recently cloud. Unfortunately, none of these paradigms is recognized as the ultimate solution, and a convergence of them all should be pursued. At the same time, recent works have proposed a number of models and tools to address the growing needs and expectations in the field of e-Science. In particular, they have shown the advantages and the feasibility ofmodeling e-Science environments and infrastructures according to the service-oriented architecture. In this paper, we suggest a model to promote the convergence and the integration of the different computing paradigms and infrastructures for the dynamic on-demand provisioning of resources from multiple providers as a cohesive aggregate, leveraging the service-oriented architecture. In addition, we propose a design aimed at endorsing a flexible, modular, workflow-based computing model for e-Science. The model is supplemented by a working prototype implementation together with a case study in the applicative domain of bioinformatics, which is used to validate the presented approach and to carry out some performance and scalability measurements.
[Characteristics of "Tojikomori" and "Tojikomerare" among home disabled elderly: daily life of housebound elderly].

BACKGROUND AND PURPOSE A Japanese word Tojikomori means shutting oneself in a room or house, or generally withdrawing. It has been pointed out that Tojikomori results in a decline in mobility among disabled elderly living at home. As a result of the qualitative study, we have attempted to define two types of Tojikomori. The first type, or the narrowly defined Tojikomori, is the elderly who are housebound-inactive but have a high mobility level. The second type, Tojikomerare (the passive of Tojikomori), is the elderly who are housebound-inactive because of their low mobility. The purpose of this study is to describe characteristics of Tojikomori and Tojikomerare. METHODS 321 disabled elderly (male: 122, female: 199, mean age 78.8) were interviewed at home by nurses in Wajima City, Japan, in 1998. The subjects were selected from the list of used in a screening survey, the Whole Wajima Elderly Survey. Mobility, life space, activity, physical function, psychosocial factors, caregiver's burden and caregiver's care to elderly were measured. The Tojikomerare subjects were operationally defined as the housebound-inactive elderly who were unable to walk. The Tojikomori were identified as the housebound-inactive elderly who were able to walk 5 yards but were unable to take a bus. RESULTS Results obtained were as follows: 1. Housebound were not found among elders able to go out bus. There were 16 Tojikomori (10.1%) in subjects who were able to walk 5 yards (n = 153). Among the subjects who were unable to walk (n = 72), 49 people (68.1%) were classified as Tojikomerare. 2. The physical function, autonomy and social network of the Tojikomerare subjects were lowest among subjects unable to walk. They used day care least and received least care from their caregivers. In addition, their caregivers' burdens were modest. 3. Among the elderly who were able to walk 5 yards, autonomy and social network of the Tojikomori ranked lowest, although physical function was not low. CONCLUSION Tojikomerare had lowest physical and psychosocial function, but they were cared for the least by caregivers. Tojikomori had the lowest psychosocial function among elderly who can walk 5 yards. The results suggest that it is important to evaluate the mobility, life space, and activity of the housebound elderly when providing community-based services.
Detection of Antibody to Avian Influenza A (H5N1) Virus in Human Serum by Using a Combination of Serologic Assays

ABSTRACT From May to December 1997, 18 cases of mild to severe respiratory illness caused by avian influenza A (H5N1) viruses were identified in Hong Kong. The emergence of an avian virus in the human population prompted an epidemiological investigation to determine the extent of human-to-human transmission of the virus and risk factors associated with infection. The hemagglutination inhibition (HI) assay, the standard method for serologic detection of influenza virus infection in humans, has been shown to be less sensitive for the detection of antibodies induced by avian influenza viruses. Therefore, we developed a more sensitive microneutralization assay to detect antibodies to avian influenza in humans. Direct comparison of an HI assay and the microneutralization assay demonstrated that the latter was substantially more sensitive in detecting human antibodies to H5N1 virus in infected individuals. An H5-specific indirect enzyme-linked immunosorbent assay (ELISA) was also established to test children’s sera. The sensitivity and specificity of the microneutralization assay were compared with those of an H5-specific indirect ELISA. When combined with a confirmatory H5-specific Western blot test, the specificities of both assays were improved. Maximum sensitivity (80%) and specificity (96%) for the detection of anti-H5 antibody in adults aged 18 to 59 years were achieved by using the microneutralization assay combined with Western blotting. Maximum sensitivity (100%) and specificity (100%) in detecting anti-H5 antibody in sera obtained from children less than 15 years of age were achieved by using ELISA combined with Western blotting. This new test algorithm is being used for the seroepidemiologic investigations of the avian H5N1 influenza outbreak.
A Unified Theory of U.S. Lawmaking: Preferences, Institutions, and Party Discipline

We develop a unified theory of lawmaking that integrates preferences, institutional features, and imperfect party discipline. This model both parsimoniously subsumes numerous extant models and allows for examination of heretofore unexplored equilibria behavior. To demonstrate this, we pinpoint what effects the kinds of changes that reformers often focus on—strengthening parties and loosening the filibuster rule—might have on the equilibrium gridlock interval and generate a number of nonintuitive results. We also find that our unified model's empirical implications are consistent with the gridlock pattern found in the data. We conclude that this model is theoretically important and empirically relevant.
Indices of slowness of information processing in head injury patients: Tests for selective attention related to ERP latencies

We explored the relation between neuropsychological (attention tests involving time constraints) and neurophysiological (N2 and P3 event-related potential (ERP) latencies) indices of slowness of information processing after closed head injury (CHI). A group of 44 CHI patients performed worse than healthy controls on most neuropsychological indices, and had significantly longer ERP latencies. Significant correlations between neuropsychological measures and ERP latencies were found only for the 3 subtasks of the Stroop test. In additional multiple regression analyses P3 latency appeared the best predictor in Stroop Color only. A possible explanation is that stimulus evaluation processes comprise a relatively large part of performance on this subtask. In Stroop Color-Word, response related processes are supposed to play a greater role, reducing the role of the preceding input related processes. The absence of significant correlations between P3 latency and scores on the other attention tests suggests a relatively small role of stimulus evaluation processes in these tasks, implying that these tasks are not sensitive to slowness of these processes. The Stroop test appears to be the only attention test administered in which slowness in stimulus evaluation processes requiring selective attention contributes significantly to the delay in final performance on the task. (JINS, 2004, 10, 851–861.)
Synchronization and Bifurcations in Networks of Coupled Hindmarsh-Rose Neurons

Synchronization plays central role in processing of information in many systems. In this work we propose a method for both to predict the behavior of the synchronous state of a network of Hindmarsh-Rose neurons and to synthesize such a network with a prescribed time-domain evolution. This method combines the synchronization conditions of the network and the bifurcation diagram of the synchronous state.
The Challenges of Implementing Next Generation Sequencing Across a Large Healthcare System, and the Molecular Epidemiology and Antibiotic Susceptibilities of Carbapenemase-Producing Bacteria in the Healthcare System of the U.S. Department of Defense

Objective We sought to: 1) provide an overview of the genomic epidemiology of an extensive collection of carbapenemase-producing bacteria (CPB) collected in the U.S. Department of Defense health system; 2) increase awareness of the public availability of the sequences, isolates, and customized antimicrobial resistance database of that system; and 3) illustrate challenges and offer mitigations for implementing next generation sequencing (NGS) across large health systems. Design Prospective surveillance and system-wide implementation of NGS. Setting 288-hospital healthcare network. Methods All phenotypically carbapenem resistant bacteria underwent CarbaNP® testing and PCR, followed by NGS. Commercial (Newbler and Geneious), on-line (ResFinder), and open-source software (Btrim, FLASh, Bowtie2, an Samtools) were used for assembly, SNP detection and clustering. Laboratory capacity, throughput, and response time were assessed. Results From 2009 through 2015, 27,000 multidrug-resistant Gram-negative isolates were submitted. 225 contained carbapenemase-encoding genes (most commonly blaKPC, blaNDM, and blaOXA23). These were found in 15 species from 146 inpatients in 19 facilities. Genetically related CPB were found in more than one hospital. Other clusters or outbreaks were not clonal and involved genetically related plasmids, while some involved several unrelated plasmids. Relatedness depended on the clustering algorithm used. Transmission patterns of plasmids and other mobile genetic elements could not be determined without ultra-long read, single-molecule real-time sequencing. 80% of carbapenem-resistant phenotypes retained susceptibility to aminoglycosides, and 70% retained susceptibility to fluoroquinolones. However, among the CPB-confirmed genotypes, fewer than 25% retained susceptibility to aminoglycosides or fluoroquinolones. Conclusion Although NGS is increasingly acclaimed to revolutionize clinical practice, resource-constrained environments, large or geographically dispersed healthcare networks, and military or government-funded public health laboratories are likely to encounter constraints and challenges as they implement NGS across their health systems. These include lack of standardized definitions and quality control metrics, limitations of short-read sequencing, insufficient bandwidth, and the current limited availability of very expensive and scarcely available sequencing platforms. Possible solutions and mitigations are also proposed.
The making of a reader

This volume helps parents and early childhood educators understand the nature of early literacy at home and at school. Ways in which nursery school structures support and extend childrens's literacy are explored. This volume, based on an 18-month ethnographic study of story reading and other literacy events in nursery school, describes parents' attitudes, beliefs, and values about literacy, nursery school organization of time and space, how reading and writing is used by nursery school participants and how story reading events help children learn to make sense of books and use books to learn about the world.
Joint feature and model training for minimum detection errors applied to speech subword detection

This paper presents methods and results for joint optimization of the feature extraction and the model parameters of a detector. We further define a discriminative training criterion called Minimum Detection Error (MDE). The criterion can optimize the F-score or any other detection performance metric. The methods are used to design detectors of subwords in continuous speech, i.e. to spot phones and articulatory features. For each subword detector the MFCC filterbank matrix and the Gaussian means in the HMM models are jointly optimized. For experiments on TIMIT, the optimized detectors clearly outperform the baseline detectors and also our previous MCE based detectors. The results indicate that the same performance metric should be used for training and test and that accuracy outperforms F-score with respect to relative improvement. Furter, the optimized filterbanks usually reflect typical acoustic properties of the corresponding detection classes.
Involuntary Autobiographical Memories: An Introduction to the Unbidden Past

1. Introduction to the unbidden past 2. Theoretical backgrounds 3. Ways to study the unbidden past 4. How special are involuntary autobiographical memories? 5. How do they come to mind? 6. Differences between involuntary and voluntary autobiographical memories 7. Involuntary memories of traumatic events 8. Future and past.