Miracle-dz/UniFAR-FTUs huggingface dataset:
Ethnicity and Gender Differences in Lipodystrophy of HIV-Positive Individuals Taking Antiretroviral Therapy in Ontario, Canada

Abstract Purpose: This study assessed ethnicity and gender differences in prevalence, type, and severity of antiretroviral-associated lipodystrophy in HIV-positive individuals in Ontario. Methods: This was a cross-sectional analysis of the Ontario Cohort Study (OCS), a prospective study of HIV-positive patients in Ontario. Lipodystrophy was defined as at least 1 major or 2 minor self-reported changes of peripheral lipoatrophy and/or central lipohypertrophy. Prevalence, type, and severity were compared by ethnicity (Black, White, or Other) and gender. Univariate and multivariate logistic regression analyses identified predictors of lipodystrophy. Results: Data were available for 778 participants (659 men, 119 women). There were 517 Whites, 121 Blacks, and 140 patients of Other ethnicities. In univariate analyses, Whites reported more peripheral lipoatrophy (P = .004) and abdominal lipohypertrophy (P = .04); these ethnic differences were observed in males (P = .05 and P = .03, respectively) but not females. Males reported more peripheral lipoatrophy (P = .01), whereas females had more central lipohypertrophy (P < .0001) and mixed fat redistribution (P < .0001). Multivariable regression analyses revealed Black women to be most vulnerable to lipodystrophy (P = .02), particularly lipohypertrophy (P < .0001). Conclusions: Ethnicity and gender are important factors influencing lipodystrophy. Combining lipoatrophy and lipohypertrophy into a single entity is not appropriate. Black women were most vulnerable to lipohypertrophy, which has important implications for antiretroviral therapy roll-out in Africa.
Vulnerability to Climate Change Related Disasters in the Eastern Cape Province: An Application of the Household Vulnerability Index (HVI)

Abstract Globally there is now a consensus that extreme climatic events are occurring and pose significant challenges, particularly for resource poor rural households. This paper assesses household vulnerability to climate change related disasters in the Eastern Cape (EC) Province in South Africa. The Household Vulnerability Index (HVI) was used to determine the levels of vulnerability to climate change related disasters by households. Data from 1546 households was collected, however only 1510 questionnaires were used for analysis. The majority (83%) of the households were found to be moderately vulnerable to climate change related disasters. A Tobit censored regression, used to determine the factors influencing household vulnerability to climate change related disasters, established that socio-economic factors including age, marital status, highest level of education, employment status, health status, ownership of farm assets, receiving external support, income generating activities, livestock ownership and extension access were significant. The findings suggest that households need to be empowered in terms of their socio-economic attributes, a move that will enhance adaptation and resilience under extreme climatic conditions.
Accuracy of estimating intra-abdominal fat in obese women

ACCURACY OF ESTIMATING INTRA-ABDOMINAL FAT IN OBESE WOMEN. Stephen D. Ball, Pamela D. Swan. JEPonline. 2003;6(4):1-7. Intra-abdominal fatness (IAF) has been linked to a cluster of risk factors for cardiovascular disease. An accurate assessment of IAF is therefore critical for clinicians when assessing disease risk. The aim of this investigation was to examine the accuracy of a previously developed equation by Treuth, Hunter, and Kekes-Szabo (1) using dual-energy absorptiometry (DXA) combined with anthropometry for predicting IAF in obese women. Thirty-five peri- and post-menopausal obese women (age: 47.0 yr±7.0; BMI: 32.2±6.3 kg/m 2 ; and percent fat: 43.5±6.7 %) underwent a single-slice computed tomography (CT) scan at the level of L4-L5. In addition, a total body DXA scan and anthropometric measures including waist circumference and supine sagittal diameter measures at the level of the umbilicus, were also made. DXA-IAF was predicted using the equation: -208.2 + 4.62(SD) + 0.75(A) + 1.73(W) + 0.78(DXA). (SD=anthropometric sagittal diameter, cm; A=age, yrs; W=waist circ., cm; DXA=DXA trunk fat, %). DXA-IAF was significantly correlated with CT-IAF (r=0.628, P<0.001, SEE=53.0 cm 2 ). However, DXA-IAF values (172.2±46.9 cm 2 ) significantly overestimated CT-IAF (114.0±67.1 cm 2 ) in this population. The results from the current study indicate that the Treuth et al. equation was not able to adequately estimate IAF in obese women. Although this equation was originally generated on a wide selection of women, a limited number of the original cohort were obese. In summary, this equation may be more generalizable for normal weight women than for obese women.
Color Correction by Estimation of Dominant Chromaticity in Multi-Scaled Retinex

In image capture a scene with nonuniform illumination has an influence on the image quality, especially the contrast and detail in dark regions. Generally, the tone curve or histogram of an image is modified to improve the contrast and detail, yet this is in- sufficient as the intensity and chromaticity of the illumination vary with geometric position. Thus, the multi-scaled retinex algorithm has been proposed, where the influence of nonuniform illumination is reduced by partitioning the original image using local average im- ages that are estimated based on Gaussian filtering of the original image. However, the multi-scaled retinex algorithm produces color distortion as the local average images are independently estimated for each channel. In particular, if the chromatic distribution of the original image is not uniform and is dominated by a certain chroma- ticity, the local average image includes not only the intensity and chromaticity of the illumination but also the dominant chromaticity through the Gaussian filtering, thereby distorting the color. Accord- ingly, this article proposes a multi-scaled retinex using a modified local average image to reduce the color distortion by the dominant chromaticity of the original image. As with the multi-scaled retinex algorithm, the local average image is obtained through Gaussian filtering of the original image. The local average image is then di- vided by the average chromaticity value of the original image to reduce the influence of the dominant chromaticity. However, be- cause the average chromaticity value includes the dominant chro- maticity of the original image and the chromaticity of the illumination, the chromaticity removed from the illumination in the local average image needs to be compensated. Therefore, the chromaticity of the illumination is estimated based on the chromaticity of the highlight regions in the original image. The chromaticity of the local average image is then modified by the estimated chromaticity. In experi- ments, the proposed method was found to improve local contrast and reduce the color distortion. © 2009 Society for Imaging Science and Technology. DOI: 10.2352/J.ImagingSci. Technol.2009. 53.5. 050502
A Brief Review on Diagnosis of Foot-and-Mouth Disease of Livestock: Conventional to Molecular Tools

Foot-and-mouth disease (FMD) is one of the highly contagious diseases of domestic animals. Effective control of this disease needs sensitive, specific, and quick diagnostic tools at each tier of control strategy. In this paper we have outlined various diagnostic approaches from old to new generation in a nutshell. Presently FMD diagnosis is being carried out using techniques such as Virus Isolation (VI), Sandwich-ELISA (S-ELISA), Liquid-Phase Blocking ELISA (LPBE), Multiplex-PCR (m-PCR), and indirect ELISA (DIVA), and real time-PCR can be used for detection of antibody against nonstructural proteins. Nucleotide sequencing for serotyping, microarray as well as recombinant antigen-based detection, biosensor, phage display, and nucleic-acid-based diagnostic are on the way for rapid and specific detection of FMDV. Various pen side tests, namely, lateral flow, RT-LAMP, Immunostrip tests, and so forth. are also developed for detection of the virus in field condition.
以語音辨識與評分輔助口說英文學習 (Spoken English Learning Based on Speech Recognition and Assessment) [In Chinese]

本論文提出利用音訊處理和語音辨識的技術,進行英文語音評分。 依英文發音的特有性,進行評分系統的各個 模組之設計、製作及實驗,期許建立一套合理的英文語音評分系統。 本論文結合三項技術 ― 「說話驗證」、「語音訊號切割」和「英文語音評分」達成輔助口說英文之學習。 「說話驗證」利用說話驗證的可信度評估,依此拒絕文句內容(context)不正確的評分語句。 「語音訊號切割」 提供一個將語音訊號切割出每個音素時間區段的方法,以預先訓練好的英文發音聲學模型當作切割依據,爾後 經由語音辨認技術,以合適的聲學模型切割出正確的發音區段。 「英文語音評分」為評分系統的核心,使用的評分方式是比較標準語音和評分語音的相似度。 本文採用四 個評分參數 ― 音量強度曲線、基頻軌跡曲線、發聲急緩變化及 HMM 對數機率差異進行語音相似度評分。 經 由實驗,對於一個合理的評分系統,我們得到音量強度曲線的權重為 7.45%,基頻軌跡曲線的權重為 22.40%, 發聲急緩變化的權重為 17.24%,HMM 對數機率差異的權重為 52.91%,經由實驗證實本系統之語音評分與人 工評分具有約 60%的正相關性。
Latitude is significantly associated with the prevalence of multiple sclerosis: a meta-analysis

Background There is a striking latitudinal gradient in multiple sclerosis (MS) prevalence, but exceptions in Mediterranean Europe and northern Scandinavia, and some systematic reviews, have suggested that the gradient may be an artefact. The authors sought to evaluate the association between MS prevalence and latitude by meta-regression. Methods and findings Studies were sourced from online databases, reference mining and author referral. Prevalence estimates were age-standardised to the 2009 European population. Analyses were carried out by means of random-effects meta-regression, weighted with the inverse of within-study variance. The authors included 650 prevalence estimates from 321 peer-reviewed studies; 239 were age-standardised, and 159 provided sex-specific data. The authors found a significant positive association (change in prevalence per degree-latitude) between age-standardised prevalence (1.04, p<0.001) and latitude that diminished at high latitudes. Adjustment for prevalence year strengthened the association with latitude (2.60, p<0.001). An inverse gradient in the Italian region reversed on adjustment for MS-associated HLA-DRB1 allele distributions. Adjustment for HLA-DRB1 allele frequencies did not appreciably alter the gradient in Europe. Adjustment for some potential sources of bias did not affect the observed associations. Conclusion This, the most comprehensive review of MS prevalence to date, has confirmed a statistically significant positive association between MS prevalence and latitude globally. Exceptions to the gradient in the Italian region and northern Scandinavia are likely a result of genetic and behavioural–cultural variations. The persistence of a positive gradient in Europe after adjustment for HLA-DRB1 allele frequencies strongly supports a role for environmental factors which vary with latitude, the most prominent candidates being ultraviolet radiation (UVR)/vitamin D.
The Underlying Mechanisms for Olanzapine-induced Hypertriglyceridemia

Olanzapine is an efficacious antipsychotic drug often used in the treatment for schizophrenia or bipolar disorder, however, sometimes induces metabolic disorders. We will introduce a patient with bipolar disorder, who has been treated by olanzapine and showed severe hypertriglyceridemia. As a result of measurements of parameters associated with lipid metabolism, very-low density lipoprotein was most important lipoprotein for olanzapin-induced hypertriglyceridemia. The cessation of olanzapine significantly decreased high-sensitivity C-reactive protein and increased adiponectin, proposing that inflammation and reduced adiponectin level may be associated with olanzapin-induced hypertriglyceridemia.
Autoantibody Epitope Spreading in the Pre-Clinical Phase Predicts Progression to Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a prototypical autoimmune arthritis affecting nearly 1% of the world population and is a significant cause of worldwide disability. Though prior studies have demonstrated the appearance of RA-related autoantibodies years before the onset of clinical RA, the pattern of immunologic events preceding the development of RA remains unclear. To characterize the evolution of the autoantibody response in the preclinical phase of RA, we used a novel multiplex autoantigen array to evaluate development of the anti-citrullinated protein antibodies (ACPA) and to determine if epitope spread correlates with rise in serum cytokines and imminent onset of clinical RA. To do so, we utilized a cohort of 81 patients with clinical RA for whom stored serum was available from 1–12 years prior to disease onset. We evaluated the accumulation of ACPA subtypes over time and correlated this accumulation with elevations in serum cytokines. We then used logistic regression to identify a profile of biomarkers which predicts the imminent onset of clinical RA (defined as within 2 years of testing). We observed a time-dependent expansion of ACPA specificity with the number of ACPA subtypes. At the earliest timepoints, we found autoantibodies targeting several innate immune ligands including citrullinated histones, fibrinogen, and biglycan, thus providing insights into the earliest autoantigen targets and potential mechanisms underlying the onset and development of autoimmunity in RA. Additionally, expansion of the ACPA response strongly predicted elevations in many inflammatory cytokines including TNF-α, IL-6, IL-12p70, and IFN-γ. Thus, we observe that the preclinical phase of RA is characterized by an accumulation of multiple autoantibody specificities reflecting the process of epitope spread. Epitope expansion is closely correlated with the appearance of preclinical inflammation, and we identify a biomarker profile including autoantibodies and cytokines which predicts the imminent onset of clinical arthritis.
A layered approach to in situ data management on a wireless sensor network

A multi-layered algorithm is proposed that provides a scalable and adaptive method for handling data on a wireless sensor network. Statistical tests, local feedback and global genetic style material exchange ensure limited resources, such as battery and bandwidth, are used efficiently by manipulating data at the source and important features in the time series are not lost when compression needs to be made. The approach leads to a more 'hands off' implementation which is demonstrated by a real world oceanographic deployment of the system.
NADPH oxidase and aging drive microglial activation, oxidative stress, and dopaminergic neurodegeneration following systemic LPS administration

Parkinson's disease is characterized by a progressive degeneration of substantia nigra (SN) dopaminergic neurons with age. We previously found that a single systemic lipopolysaccharide (LPS, 5 mg/kg, i.p.) injection caused a slow progressive loss of tyrosine hydroxylase immunoreactive (TH+IR) neurons in SN associated with increasing motor dysfunction. In this study, we investigated the role of NADPH oxidase (NOX) in inflammation‐mediated SN neurotoxicity. A comparison of control (NOX2+/+) mice with NOX subunit gp91phox‐deficient (NOX2−/−) mice 10 months after LPS administration (5 mg/kg, i.p.) resulted in a 39% (P < 0.01) loss of TH+IR neurons in NOX2+/+ mice, whereas NOX2−/− mice did not show a significant decrease. Microglia (Iba1+IR) showed morphological activation in NOX2+/+ mice, but not in NOX2−/− mice at 1 hr. Treatment of NOX2+/+ mice with LPS resulted in a 12‐fold increase in NOX2 mRNA in midbrain and 5.5–6.5‐fold increases in NOX2 protein (+IR) in SN compared with the saline controls. Brain reactive oxygen species (ROS), determined using diphenyliodonium histochemistry, was increased by LPS in SN between 1 hr and 20 months. Diphenyliodonium (DPI), an NOX inhibitor, blocked LPS‐induced activation of microglia and production of ROS, TNFα, IL‐1β, and MCP‐1. Although LPS increased microglial activation and ROS at all ages studied, saline control NOX2+/+ mice showed age‐related increases in microglial activation, NOX, and ROS levels at 12 and 22 months of age. Together, these results suggest that NOX contributes to persistent microglial activation, ROS production, and dopaminergic neurodegeneration that persist and continue to increase with age. © 147.
Calling louder and longer: how bats use biosonar under severe acoustic interference from other bats

Active-sensing systems such as echolocation provide animals with distinct advantages in dark environments. For social animals, however, like many bat species, active sensing can present problems as well: when many individuals emit bio-sonar calls simultaneously, detecting and recognizing the faint echoes generated by one's own calls amid the general cacophony of the group becomes challenging. This problem is often termed ‘jamming’ and bats have been hypothesized to solve it by shifting the spectral content of their calls to decrease the overlap with the jamming signals. We tested bats’ response in situations of extreme interference, mimicking a high density of bats. We played-back bat echolocation calls from multiple speakers, to jam flying Pipistrellus kuhlii bats, simulating a naturally occurring situation of many bats flying in proximity. We examined behavioural and echolocation parameters during search phase and target approach. Under severe interference, bats emitted calls of higher intensity and longer duration, and called more often. Slight spectral shifts were observed but they did not decrease the spectral overlap with jamming signals. We also found that pre-existing inter-individual spectral differences could allow self-call recognition. Results suggest that the bats’ response aimed to increase the signal-to-noise ratio and not to avoid spectral overlap.
Ligand Exchange between Proteins

We have studied the structural elements that affect ligand exchange between the two high affinity biotin-binding proteins, egg white avidin and its bacterial analogue, streptavidin. For this purpose, we have developed a simple assay based on the antipodal behavior of the two proteins toward hydrolysis of biotinyl p-nitrophenyl ester (BNP). The assay provided the experimental basis for these studies. It was found that biotin migrates unidirectionally from streptavidin to avidin. Conversely, the biotin derivative, BNP, is transferred in the opposite direction, from avidin to streptavidin. A previous crystallographic study (Huberman, T., Eisenberg-Domovich, Y., Gitlin, G., Kulik, T., Bayer, E. A., Wilchek, M., and Livnah, O. (2001) J. Biol. Chem. 276, 32031–32039) provided insight into a plausible explanation for these results. These data revealed that the non-hydrolyzable BNP analogue, biotinylp-nitroanilide, was almost completely sheltered in streptavidin as opposed to avidin in which the disordered conformation of a critical loop resulted in the loss of several hydrogen bonds and concomitant exposure of the analogue to the solvent. In order to determine the minimal modification of the biotin molecule required to cause the disordered loop conformation, the structures of avidin and streptavidin were determined with norbiotin, homobiotin, and a common long-chain biotin derivative, biotinyl ε-aminocaproic acid. Six new crystal structures of the avidin and streptavidin complexes with the latter biotin analogues and derivatives were thus elucidated. It was found that extending the biotin side chain by a single CH2 group (i.e. homobiotin) is sufficient to result in this remarkable conformational change in the loop of avidin. These results bear significant biotechnological importance, suggesting that complexes containing biotinylated probes with streptavidin would be more stable than those with avidin. These findings should be heeded when developing new drugs based on lead compounds because it is difficult to predict the structural and conformational consequences on the resultant protein-ligand interactions.
Chloride Sensing by WNK1 Involves Inhibition of Autophosphorylation

Structural analysis reveals how chloride inhibits the activation of a kinase implicated in hypertension. Inhibited by Chloride in the Active Site Chloride ions are essential for regulation of blood pressure and electrolyte homeostasis. Kinases of the WNK family are involved in the phosphorylation-mediated regulation of chloride cotransporters and ion channels involved in salt regulation; mutations in WNK1 or WNK4 produce hypertension, hyperkalemia, and hyperchloremia. Piala et al. found that chloride ions stabilized the WNK1 kinase domain and inhibited its autophosphorylation activity and kinase activity toward substrates. Analysis of crystal structures of the kinase domain with either bromide or chloride revealed that the ion bound in the catalytic site, and mutation of the residues involved in binding the ion rendered the kinase less sensitive to inhibition of autophosphorylation activity by chloride salts. Thus, these results provide a molecular explanation for how these kinases function as sensors of intracellular chloride. WNK1 [with no lysine (K)] is a serine-threonine kinase associated with a form of familial hypertension. WNK1 is at the top of a kinase cascade, leading to phosphorylation of several cotransporters, in particular those transporting sodium, potassium, and chloride (NKCC), sodium and chloride (NCC), and potassium and chloride (KCC). The responsiveness of NKCC, NCC, and KCC to changes in extracellular chloride parallels their phosphorylation state, provoking the proposal that these transporters are controlled by a chloride-sensitive protein kinase. We found that chloride stabilizes the inactive conformation of WNK1, preventing kinase autophosphorylation and activation. Crystallographic studies of inactive WNK1 in the presence of chloride revealed that chloride binds directly to the catalytic site, providing a basis for the unique position of the catalytic lysine. Mutagenesis of the chloride-binding site rendered the kinase less sensitive to inhibition of autophosphorylation by chloride, validating the binding site. Thus, these data suggest that WNK1 functions as a chloride sensor through direct binding of a regulatory chloride ion to the active site, which inhibits autophosphorylation.
Understanding software through numbers: A metric based approach to program comprehension

There are many approaches to try to comprehend software. Code can be statically analysed and its structure and content displayed as lists, tables or graphs. Most of the literature on software comprehension deals with this approach. Code can also be dynamically executed and its reaction to impulses from outside registered and documented. This is a useful approach to understanding object-orientated systems. A third approach is not to deal with the code at all, but instead to extract information from existing documents and to combine it into a whole. The problem here is that important documents are often missing and those that are available are out of date. A fourth approach is to interview the experts and to aggregate their views of the software, how it is composed and how it functions as opposed to how it should be composed and how it should function. All of these approaches have been examined and reported on by the participants of the ESPRIT DOCKET Project (1992). A fifth approach to software understanding, the one to be presented here, is that of comprehension through numbers by software managers, i.e. using metrics to support the decision making process.