Miracle-dz/UniFAR-FTUs huggingface dataset:
Virological and Immunological Factors Associated with HIV-1 Differential Disease Progression in HLA-B*58:01-Positive Individuals

ABSTRACT Molecular epidemiology studies have identified HLA-B*58:01 as a protective HIV allele. However, not all B*58:01-expressing persons exhibit slow HIV disease progression. We followed six HLA-B*58:01-positive, HIV subtype C-infected individuals for up to 31 months from the onset of infection and observed substantial variability in their clinical progression despite comparable total breadths of T cell responses. We therefore investigated additional immunological and virological factors that could explain their different disease trajectories. Cytotoxic T-lymphocyte (CTL) responses during acute infection predominantly targeted the TW10 and KF9 epitopes in p24Gag and Nef, respectively. Failure to target the TW10 epitope in one B*58:01-positive individual was associated with low CD4+ counts and rapid disease progression. Among those targeting TW10, escape mutations arose within 2 to 15 weeks of infection. Rapid escape was associated with preexisting compensatory mutations in the transmitted viruses, which were present at a high frequency (69%) in the study population. At 1 year postinfection, B*58:01-positive individuals who targeted and developed escape mutations in the TW10 epitope (n = 5) retained significantly higher CD4+ counts (P = 0.04), but not lower viral loads, than non-B*58:01-positive individuals (n = 17). The high population-level frequency of these compensatory mutations may be limiting the protective effect of the B*58:01 allele.
Evaluating assumptions of weighting class methods for partial response using a selection model

In survey sampling, information about the prevalence of a health outcome Y for a defined target population is frequently obtained using a two‐stage data collection process. In the first stage, households that have members of the target population are identified and socio‐demographic data that are believed to be associated with Y are collected. At the end of the first stage of data collection, permission is requested to contact the member's health providers so that accurate information about Y can be obtained. When permission is obtained, a second phase of data collection is conducted in which those health providers are contacted and Y is obtained. A ‘complete response’ results when data are obtained from both the first and the second phases of the survey. A ‘partial response’ results when data are collected from the first phase, but Y is not obtained in the second phase. To adjust for selection bias in estimating the prevalence of Y caused by partial responders' missing Y values, potential differences between complete and partial responders are typically taken into account by using weighting class methods. These methods assume that missing Y values are missing at random (MAR). This paper describes statistical tests for evaluating whether missing data are missing completely at random or MAR. Copyright © 2008 John Wiley & Sons, Ltd.
Caring community and relationship centred care on an end-stage dementia special care unit.

BACKGROUND of the estimated 1.4 million residents of US nursing homes, over half have dementia. In the final stages of dementia, caregiving is complicated by the inability of care recipients to speak intelligibly or express their needs. AIM to examine the ways in which a nursing home end-stage dementia special care unit (SCU) functioned as a caring community for people near the end of life. RESEARCH DESIGN AND METHODS a qualitative, ethnographic case study was conducted in a highly-regarded SCU. Over 175 hours of scheduled activity observations were completed over 2 years, bolstered by 30 hours of caregiving observations on the end-stage dementia unit and 19 interviews with SCU carers. Inductive coding was completed independently by two researchers, emerging themes reconciled by consensus, and qualitative analysis conducted iteratively until the endpoint of thematic saturation. FINDINGS on the SCU, employees and volunteers fostered relationships based upon a model of family. They formed a caring community that included professionals, volunteers, friends and family. Relationships were supported through (1) the use of reminiscence to evoke intact long-term memories, (2) the use of verbal communication long after care-recipients could no longer speak and (3) the use of intentional nonverbal communication, including daily music, pet visits, and sensory stimulation. CONCLUSIONS through detailed examination of daily life, this study identified articulated beliefs and observable behaviour through which to develop relationship-centred care in the context of end-stage dementia. The caring community offers primary source data for the development of mid-level theory and the generation of new hypotheses.
Influence of parametric uncertainties and their interactions on small‐signal stability: A case example of parallel‐connected active loads in a DC microgrid

Classical stability analysis techniques based on nominal models do not consider the uncertainty of system parameters, their interactions, and nonlinearity, which are important characteristics of practical highly coupled microgrids. In this work, variance-based sensitivity analysis is used to identify parameter combinations that have a significant impact on the small-signal stability of a microgrid featuring two parallel active loads. The analysis indicates that the effectiveness of source-side damping is reduced when resonant frequencies of load input filters become matched. Further results using derivative-based sensitivity analysis reveal that source-side resistance can exhibit drastically different effects on the stability if load input filter resonant frequencies are matched with respect to the case when they are well separated. These behaviours are verified using time-domain switching models.
Effect of desferrioxamine and metals on the hydroxylases in the oxygen sensing pathway

Hypoxia‐inducible transcription factor (HIF) is regulated by two oxygen‐dependent events that are catalyzed by the HIF prolyl 4‐hydroxylases (HIF‐P4Hs) and HIF asparaginyl hydroxylase (FIH). We have purified the three recombinant human HIF‐P4Hs to near homogeneity and characterized their catalytic properties and inhibition and those of FIH. The specific activities of the HIF‐P4Hs were at least 40–50 mol/mol/min, and they and FIH catalyzed an uncoupled decarboxylation of 2‐oxoglutarate in the absence of any peptide substrate. The purified HIF‐P4Hs showed considerable activities even without added Fe2+, their apparent Km values for iron being markedly lower than that of FIH. Desferrioxamine and several metals were effective inhibitors of FIH, but surprisingly, ineffective inhibitors of the HIF‐P4Hs in vitro, especially of HIF‐P4H‐2. Desferrioxamine and cobalt were more effective in cultured insect cells synthesizing recombinant HIF‐P4H‐2, but complete inhibition was not achieved and most of the enzyme was inactivated irreversibly. Cobalt also rapidly inactivated HIF‐P4Hs during storage at 4°C. The well‐known stabilization of HIF‐α by cobalt and nickel is thus not due to a simple competitive inhibition of HIF‐P4Hs. The effective inhibition of FIH by these metals and zinc probably leads to full transcriptional activity of HIF‐α even in concentrations that produce no stabilization of HIF‐α.
Plasma MicroRNA Profiling Reveals Loss of Endothelial MiR-126 and Other MicroRNAs in Type 2 Diabetes

Rationale: MicroRNAs (miRNAs) have been implicated in the epigenetic regulation of key metabolic, inflammatory, and antiangiogenic pathways in type 2 diabetes (DM) and may contribute to common disease complications. Objective: In this study, we explore plasma miRNA profiles in patients with DM. Methods and Results: Total RNA was extracted from plasma samples of the prospective population-based Bruneck study. A total of 13 candidate miRNAs identified by microarray screening and miRNA network inference were quantified by quantitative PCR in all diabetic patients of the Bruneck study and age- and sex-matched controls (1995 evaluation, n=80 each). Quantitative PCR assessment revealed lower plasma levels of miR-20b, miR-21, miR-24, miR-15a, miR-126, miR-191, miR-197, miR-223, miR-320, and miR-486 in prevalent DM, but a modest increase of miR-28-3p. Findings emerged as robust in multivariable analysis and were independent of the standardization procedure applied. For endothelial miR-126, results were confirmed in the entire Bruneck cohort (n=822) in univariate (odds ratio [95% confidence interval], 0.38 [0.26 to 0.55]; P=2.72×10−7) and multivariate analyses (0.57 [0.37 to 0.86]; P=0.0082). Importantly, reduced miR-15a, miR-29b, miR-126, miR-223, and elevated miR-28-3p levels antedated the manifestation of disease. Most differences in miRNA levels were replicated in plasma obtained from hyperglycemic Lepob mice. High glucose concentrations reduced the miR-126 content of endothelial apoptotic bodies. Similarly in patients with DM, the reduction of miR-126 was confined to circulating vesicles in plasma. Conclusions: We reveal a plasma miRNA signature for DM that includes loss of endothelial miR-126. These findings might explain the impaired peripheral angiogenic signaling in patients with DM.
Coupled pulsation and translation of two gas bubbles in a liquid

We present and analyse a model for the spherical pulsations and translational motions of a pair of interacting gas bubbles in an incompressible liquid. The model is derived rigorously in the context of potential flow theory and contains all terms up to and including fourth order in the inverse separation distance between the bubbles. We use this model to study the cases of both weak and moderate applied acoustic forcing. For weak acoustic forcing, the radial pulsations of the bubbles are weakly coupled, which allows us to obtain a nonlinear time-averaged model for the relative distance between the bubbles. The two parameters of the time-averaged model classify four different dynamical regimes of relative translational motion, two of which correspond to the attraction and repulsion of classical secondary Bjerknes theory. Also predicted is a pattern in which the bubbles exhibit stable, time-periodic translational oscillations along the line connecting their centres, and another pattern in which there is an unstable separation distance such that bubble pairs can either attract or repel each other depending on whether their initial separation distance is smaller or larger than this value. Moreover, it is shown that the full governing equations possess the dynamics predicted by the time-averaged model. We also study the case of moderateamplitude acoustic forcing, in which the bubble pulsations are more strongly coupled to each other and bubble translation also affects the radial pulsations. Here, radial harmonics and nonlinear phase shifting play a significant role, as bubble pairs near resonances are observed to translate in patterns opposite to those predicted by classical secondary Bjerknes theory. In this work, dynamical systems techniques and the method of averaging are the primary mathematical methods that are employed.
Recognition of emotional states using EEG signals based on time-frequency analysis and SVM classifier

The recognition of emotions is a vast significance and a high developing field of research in the recent years. The applications of emotion recognition have left an exceptional mark in various fields including education and research. Traditional approaches used facial expressions or voice intonation to detect emotions, however, facial gestures and spoken language can lead to biased and ambiguous results. This is why, researchers have started to use electroencephalogram (EEG) technique which is well defined method for emotion recognition. Some approaches used standard and pre-defined methods of the signal processing area and some worked with either fewer channels or fewer subjects to record EEG signals for their research. This paper proposed an emotion detection method based on time-frequency domain statistical features. Box-and-whisker plot is used to select the optimal features, which are later feed to SVM classifier for training and testing the DEAP dataset, where 32 participants with different gender and age groups are considered. The experimental results show that the proposed method exhibits 92.36% accuracy for our tested dataset. In addition, the proposed method outperforms than the state-of-art methods by exhibiting higher accuracy.
Imposing Tax and Rebate Policy for Addressing Game Addiction Problem

Massively Multiplayer Online Games (MMOGs) are popular worldwide. Especially in Korea, there were about 19 million gamers in 2006. Despite this wide popularity, some players have become seriously addicted to online games, causing a serious social problem. However, studies and/or trials to address game addiction problems have rarely been performed. In this paper, we investigate the relationships among interested parties in the game industry and propose a base model to explain them. From the base model, we expect that casual gamers increase until some point of time, but decline afterward. The growth rate of total revenue from online games is decreased due to a reduced number of casual gamers over time and a negative image of online games. To resolve game addiction problems, we analyzed a self regulation policy and a tax and rebate policy in the base model. Through the analysis of the policies, we found that a tax and rebate policy is preferable to a self regulation policy. Under the tax and rebate policy, the total revenue of online games increases contrary to the concern of game companies, the social image of online games is improved and the number of game addicts decreases.
Automatic estimation of speaking rate in multilingual spontaneous speech

An automatic estimation of speaking rate is developed in this paper. It is based on an unsupervised vowel detection algorithm and thus may be costlessly applied to any language. Validation is driven on a spontaneous speech subset of the OGI Multilingual Telephone Speech Corpus. The correlation coefficient between the estimated and real speaking rates (evaluated in term of vowel-per-second rates) is 0.84 on average among the 6 languages for which a phonetic transcription is available (English, German, Hindi, Japanese, Mandarin and Spanish).
Gliosis and brain remodeling after treatment of stroke in rats with marrow stromal cells

The long‐term (4‐month) responses to treatment of stroke in the older adult rat, using rat bone marrow stromal cells (MSCs), have not been investigated. Retired breeder rats were subjected to middle cerebral artery occlusion (MCAo) alone, or injected intravenously with 3 × 106 MSCs, at 7 days after MCAo. Functional recovery was measured using an adhesive‐removal patch test and a modified neurological severity score. Bromodeoxyuridine, a cell proliferation marker, was injected daily for 14 before sacrifice. Animals were sacrificed 4 months after stroke. Double immunostaining was used to identify cell proliferation and cell types for axons, astrocytes, microglia, and oligodendrocytes. MSC treatment induced significant improvement in neurological outcome after MCAo compared with control rats. MSC treatment reduced the thickness of the scar wall (P < 0.05) and reduced the numbers of microglia/macrophages within the scar wall (P < 0.01). Double staining showed increased expression of an axonal marker (GAP‐43), among reactive astrocytes in the scar boundary zone and in the subventricular zone in the treated rats. Bromodeoxyuridine in cells preferentially colocalized with markers of astrocytes (GFAP) and oligodendrocytes (RIP) in the ipsilateral hemisphere, and gliogenesis was enhanced in the subventricular zone of the rats treated with MSCs. This is the first report to show that MSCs injected at 7 days after stroke improve long‐term neurological outcome in older animals. Brain tissue repair is an ongoing process with reactive gliosis, which persists for at least 4 months after stroke. Reactive astrocytes responding to MSC treatment of ischemia may also promote axonal regeneration during long‐term recovery. © 2004 Wiley‐Liss, Inc.
WTF-LOD - A New Resource for Large-Scale NER Evaluation

This paper introduces the Web TextFull linkage to Linked Open Data (WTF-LOD) dataset intended for large-scale evaluation of named entity recognition (NER) systems. First, we present the process of collecting data from the largest publically-available textual corpora, including Wikipedia dumps, monthly runs of the CommonCrawl, and ClueWeb09/12. We discuss similarities and differences of related initiatives such as WikiLinks and WikiReverse. Our work primarily focuses on links from “textfull” documents (links surrounded by a text that provides a useful context for entity linking), de-duplication of the data and advanced cleaning procedures. Presented statistics demonstrate that the collected data forms one of the largest available resource of its kind. They also prove suitability of the result for complex NER evaluation campaigns, including an analysis of the most ambiguous name mentions appearing in the data.
Trust Based Security Mechanisms for Social Networks

Inspired by the similarities between human trust and physical measurements, we have proposed a trust framework for social networks, including defining new trust metrics and their combinations, which captures both human trust level and its uncertainty, while being intuitive and user friendly. Based on our trust framework, we propose several security mechanisms, including filtering information on social networks and increasing the efficiency of advertisement and influence on social networks. Experiments on synthesized and real social networks validate the potential of our trust framework to develop trust based mechanisms for social networks.
Intonation: A Dataset of Quality Vocal Performances Refined by Spectral Clustering on Pitch Congruence

We introduce the "Intonation" dataset of amateur vocal performances with a tendency for good intonation, collected from Smule, Inc. The dataset can be used for music information retrieval tasks such as autotuning, query by humming, and singing style analysis. It is available upon request on the Stanford CCRMA DAMP website.1 We describe a semi-supervised approach to selecting the audio recordings from a larger collection of performances based on intonation patterns. The approach can be applied in other situations where a researcher needs to extract a subset of data samples from a large database. A comparison of the "Intonation" dataset and the remaining collection of performances shows that the two have different intonation behavior distributions.
A multimodal approach to simulation fidelity

A process oriented view of a multimodal approach to simulation fidelity is discussed in the context of system verification and validation in industry. An overview of classical simulation product development is given and the problem of developing models through the inclusion of simulation objectives is presented in terms of this process. A multi modal approach for improving the syntactic fidelity of simulation by using meta-modeling techniques and semantic web principles is presented in an operational context. The domain model is briefly presented and a concept of operating mode is proposed in the model teleological framework of Structure, Behavior, Function and Interface. The relation with the study of formal techniques on semantic or behavioral fidelity is briefly discussed along with an overview on the challenges ahead and future work.
Communication-Free Data Allocation Techniques for Parallelizing Compilers on Multicomputers

In this paper, we devote our efforts to the techniques of allocatiing array elements of nested loops onto multicomputers in a communication-free fashion for parallelizing compilers. The arrays can be partitioned under the communication free criteria with non-duplicate or duplicate data. In addition, the performance of the strategies with non-duplicate and dupli cate array data is compared.
Key influences on motivations for utility cycling (cycling for transport to and from places).

ISSUE ADDRESSED Although increases in cycling in Brisbane are encouraging, bicycle mode share to work (the proportion of people travelling to work by bicycle) in the state of Queensland remains low. The aim of this qualitative study was to draw upon the lived experiences of Queensland cyclists to understand the main motivators for utility cycling (cycling as a means to get to and from places) and compare motivators between utility cyclists (those who cycle for utility as well as for recreation) and non-utility cyclists (those who cycle only for recreation). METHODS For an online survey, members of a bicycle group (831 utility cyclists and 931 non-utility cyclists, aged 18-90 years) were asked to describe, unprompted, what would motivate them to engage in utility cycling (more often). Responses were coded into themes within four levels of an ecological model. RESULTS Within an ecological model, built environment influences on motivation were grouped according to whether they related to appeal (safety), convenience (accessibility) or attractiveness (more amenities) and included adequate infrastructure for short trips, bikeway connectivity, end-of-trip facilities at public locations and easy and safe bicycle access to destinations outside of cities. A key social-cultural influence related to improved interactions among different road users. CONCLUSIONS The built and social-cultural environments need to be more supportive of utility cycling before even current utility and non-utility cyclists will be motivated to engage (more often) in utility cycling. SO WHAT? : Additional government strategies and more and better infrastructure that support utility cycling beyond commuter cycling may encourage a utility cycling culture.
Arm Use After Left or Right Hemiparesis Is Influenced by Hand Preference

Background and Purpose— Despite strong evidence for hand preference and its impact on motor performance, its influence on stroke rehabilitation has not been routinely considered. Previous research demonstrates that patients with hemiparetic stroke use their ipsilesional, nonparetic arm 5 to 6 times more frequently than their paretic arm, but it is unknown if such use varies with laterality of hemiparesis. The purpose of our study was to determine if the right arm is used more frequently in right-handed patients with stroke. Methods— We assessed relative use of the right, left, and both arms with wrist accelerometers on patients with unilateral, paretic stroke matched for degree of paresis (12 with right hemisphere damage, 17 with left hemisphere damage) and 25 neurologically intact control participants as they performed the Arm Motor Ability Test. Results— We showed: (1) ipsilesional arm use was greater after right hemisphere damage than left hemisphere damage; (2) the left hemisphere damage group used both arms together more often than the right hemisphere damage group but less often than the control group; and (3) both stroke groups used their contralesional, paretic arm to the same degree. Conclusions— These findings emphasize the influence of hand preference on arm use after stroke for the ipsilesional but not the contralesional arm. Although both stroke groups used their ipsilesional more than their contralesional arm, the difference was greater for the right hemisphere damage group who used their ipsilesional arm 4 times more frequently than their contralesional arm, whereas the left hemisphere damage group used their ipsilesional arm 2 times more frequently than their contralesional arm.