Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Resolution Melting Analysis for the Rapid Detection of Fluoroquinolone and Streptomycin Resistance in Mycobacterium tuberculosis

Background Molecular methods for the detection of drug-resistant tuberculosis are potentially more rapid than conventional culture-based drug susceptibility testing, facilitating the commencement of appropriate treatment for patients with drug resistant tuberculosis. We aimed to develop and evaluate high-resolution melting (HRM) assays for the detection of mutations within gyrA, rpsL, and rrs, for the determination of fluoroquinolone and streptomycin resistance in Mycobacterium tuberculosis (MTB). Methodology/Principal Findings A blinded series of DNA samples extracted from a total of 92 clinical isolates of MTB were analyzed by HRM analysis, and the results were verified using DNA sequencing. The sensitivity and specificity of the HRM assays in comparison with drug susceptibility testing were 74.1% and 100.0% for the detection of fluoroquinolone resistance, and 87.5% and 100.0% for streptomycin resistance. Five isolates with low level resistance to ofloxacin had no mutations detected in gyrA, possibly due to the action of efflux pumps, or false negativity due to mixed infections. One fluoroquinolone-resistant isolate had a mutation in a region of gyrA not encompassed by our assay. Six streptomycin-resistant strains had undetectable mutations by HRM and DNA sequencing, which may be explained by the fact that not all streptomycin-resistant isolates have mutations within rpsL and rrs, and suggesting that other targets may be involved. Conclusion The HRM assays described here are potentially useful adjunct tests for the efficient determination of fluoroquinolone and streptomycin resistance in MTB, and could facilitate the timely administration of appropriate treatment for patients infected with drug-resistant TB.
Effects of irrigation deprivation during the harvest period on yield determinants in mature almond trees.

Effects of irrigation deprivation during the harvest period on yield determinants in mature almond (Prunus dulcis (Mill.) D.A. Webb cv. Nonpareil) trees were investigated during a 3-year field experiment. Return bloom and fruit set were measured on 2185 individually tagged spurs. Water stress resulting from irrigation deprivation during the harvest period, which purportedly coincides with the time of flower initiation, had no effect on the percentage of spurs that flowered or set fruit during subsequent years. Although water stress had no apparent effect on spur mortality, 66% of the tagged spurs died within 3 years. In addition, many spurs were vegetative by the third year, indicating the importance of spur renewal for sustained fruit production. Reductions in nut yield were evident after two successive years of irrigation deprivation during the harvest period. Regression analysis indicated a loss in yield of 7.7 kg tree(-1) in response to each 1 MPa decrease in stem water potential below -1.2 MPa during the previous seasons. The number of fruiting positions per tree (estimated indirectly for whole trees based on weight of current-year shoots > 5 cm in length) was negatively associated with water stress. Yield reduction in response to water stress during harvest appears to be a compound, multiyear effect, associated with reduced annual growth and renewal of fruiting positions.
In Vitro Cytotoxic Activity and Structure Activity Relationships of Iridoid Glucosides Derived from Veronica species

This study was an investigation of the cytotoxic activity of iridoid glucosides, including aucubin, catalpol, 6‐O‐acetylcatalpol, veronicoside, catalposide, verproside, amphicoside, veratroylcatalposide, verminoside, aquaticosides B and C isolated from different Veronica species. The cytotoxic activity was determined against Hep‐2 (human epidermoid carcinoma), RD (human rhabdomyosarcoma), L‐20B (transgenic murine L‐cells) cancer cell lines and Vero (African green monkey kidney cells) non‐cancerous cell line using the MTT method. While verminoside, amphicoside and veronicoside were found to exhibit cytotoxic activity in the concentration range of 70–355 µ m, acetylcatalpol, aquaticosides B and C, catalposide, veratroylcatalposide and verproside showed cytostatic activity. Apoptotic cell death was observed as the effect of verminoside in the histological analysis of the tested cell lines. In conclusion, iridoid glucosides are considered to show a biphasic effect on cancer cells that is both cytostatic and cytotoxic, depending on the chemical structure and the type of cancer cell. Copyright © 2011 John Wiley & Sons, Ltd.
Threshold region performance of maximum likelihood direction of arrival estimators

This paper presents a performance analysis of the maximum likelihood (ML) estimator for finding the directions of arrival (DOAs) with a sensor array. The asymptotic properties of this estimator are well known. In this paper, the performance under conditions of low signal-to-noise ratio (SNR) and a small number of array snapshots is investigated. It is well known that the ML estimator exhibits a threshold effect, i.e., a rapid deterioration of estimation accuracy below a certain SNR or number of snapshots. This effect is caused by outliers and is not captured by standard techniques such as the Crame/spl acute/r-Rao bound and asymptotic analysis. In this paper, approximations to the mean square estimation error and probability of outlier are derived that can be used to predict the threshold region performance of the ML estimator with high accuracy. Both the deterministic ML and stochastic ML estimators are treated for the single-source and multisource estimation problems. These approximations alleviate the need for time-consuming computer simulations when evaluating the threshold region performance. For the special case of a single stochastic source signal and a single snapshot, it is shown that the ML estimator is not statistically efficient as SNR/spl rarr//spl infin/ due to the effect of outliers.
An Association between Emotional Responsiveness and Smoking Behavior

Introduction. Emotional responsiveness (ER) has been theorized to play a protective role in pathways to tobacco initiation, regular use, and dependence, yet a possible association between ER and smoking behavior has not been studied. Our aim was to test whether measuring ER to a neutral stimulus was associated with decreased odds of current smoking. Methods. We measured ER and smoking status (current, former, and never) in two datasets: a cross-sectional dataset of persons with diabetes (n = 127) and a prospective dataset of depressed patients (n = 107) from an urban primary care system. Because there were few former smokers in the datasets, smoking status was dichotomized (current versus former/never) and measured at baseline (cross-sectional dataset) or at 36 weeks after-baseline (prospective dataset). ER was ascertained with response to a neutral facial expression (any ER versus none). Results. Compared to their nonresponsive counterparts, adjusted odds of current smoking were lower among participants endorsing emotional responsiveness in both the cross-sectional and prospective datasets (ORs = .29 and .32, P's <.02, resp.). Discussion. ER may be protective against current smoking behavior. Further research investigating the association between ER and decreased smoking may hold potential to inform treatment approaches to improve smoking prevalence.
The Association of Early Childhood Cognitive Development and Behavioural Difficulties with Pre-Adolescent Problematic Eating Attitudes

Objectives Few studies have prospectively investigated associations of child cognitive ability and behavioural difficulties with later eating attitudes. We investigated associations of intelligence quotient (IQ), academic performance and behavioural difficulties at 6.5 years with eating attitudes five years later. Methods We conducted an observational cohort study nested within the Promotion of Breastfeeding Intervention Trial, Belarus. Of 17,046 infants enrolled at birth, 13,751 (80.7%) completed the Children's Eating Attitude Test (ChEAT) at 11.5 years, most with information on IQ (n = 12,667), academic performance (n = 9,954) and behavioural difficulties (n = 11,098) at 6.5 years. The main outcome was a ChEAT score ≥85th percentile, indicative of problematic eating attitudes. Results Boys with higher IQ at 6.5 years reported fewer problematic eating attitudes, as assessed by ChEAT scores ≥85th percentile, at 11.5 years (OR per SD increase in full-scale IQ = 0.87; 0.79, 0.94). No such association was observed in girls (1.01; 0.93, 1.10) (p for sex-interaction = 0.016). In both boys and girls, teacher-assessed academic performance in non-verbal subjects was inversely associated with high ChEAT scores five years later (OR per unit increase in mathematics ability = 0.88; 0.82, 0.94; and OR per unit increase in ability for other non-verbal subjects = 0.86; 0.79, 0.94). Behavioural difficulties were positively associated with high ChEAT scores five years later (OR per SD increase in teacher-assessed rating = 1.13; 1.07, 1.19). Conclusion Lower IQ, worse non-verbal academic performance and behavioural problems at early school age are positively associated with risk of problematic eating attitudes in early adolescence.
A Grouped-Iterative Framework for MIMO Detection

In this paper, we propose one grouped-iterative framework to generate a family of the MIMO detection algorithms. The presented framework not only includes the conventional iterative, grouped, and Chase detection algorithms, but also derives a new low-complexity MIMO detection algorithm. The proposed detection can adjust some parameters to achieve a range of trade-offs between performance and complexity. In (4,4) system with uncoded 16-QAM inputs, one instance of the proposed detection algorithm not only substantially reduces the multiplication complexity by 26.3% but also outperforms the BODF algorithm about 5 dB. Another instance of the proposed algorithm can save multiplication complexity by 34% at the penalty of 1 dB loss compared with the B-Chase detector.
HandyDepth: Example-based stereoscopic hand depth estimation using Eigen Leaf Node Features

This paper presents a data-driven method to estimate a high quality depth map of a hand from a stereoscopic camera input by introducing a novel regression framework. The method first computes disparity using a robust stereo matching technique. Then, it applies Random Forest (RF) to learn the mapping between the estimated, noisy disparity and actual depth given ground truth data. We introduce Eigen Leaf Node Features (ELNFs) that perform feature selection at the leaf node in each RF tree to identify features that are most discriminative for depth regression. Experimental results demonstrate the promise of the method to produce high quality depth images of a hand using an inexpensive stereo camera.
A collaborative awareness framework for mobile tourist recommender system

Tourism industry is expected to grow tremendously in Malaysia. Mobile technology such as smart phones can be use as a tourist recommender system. This paper proposed a collaborative awareness framework in order to design a usable mobile system. The collaborative awareness framework takes into account of tourist types, tourism activities, tourist experiences, visiting phases, mobile technology capabilities and limitations. The proposed mobile tourist recommender system will be able to provide both location-based and person-based awareness.
A multicenter evaluation of tests for diagnosis of histoplasmosis.

BACKGROUND The sensitivity of the MVista Histoplasma antigen enzyme immunoassay (MiraVista Diagnostics) has been evaluated in disseminated histoplasmosis in patients with AIDS and in the "epidemic" form of acute pneumonia. Moreover, there has been no evaluation of the sensitivity of antigenemia detection in disseminated histoplasmosis after the implementation of methods to dissociate immune complexes and denature released antibodies. The goal of this study was to determine the sensitivity of the current antigen assay in different categories of histoplasmosis. METHODS Urine and serum specimens obtained from 218 patients with histoplasmosis and 229 control subjects, including 30 with blastomycosis, were tested. RESULTS Antigenuria was detected in 91.8% of 158 patients with disseminated histoplasmosis, 83.3% of 6 patients with acute histoplasmosis, 30.4% of 46 patients with subacute histoplasmosis, and 87.5% of 8 patients with chronic pulmonary histoplasmosis; antigenemia was present in 100% of 31 tested cases of disseminated histoplasmosis. Among patients with disseminated cases, antigenuria was detected more often and at higher concentrations in immunocompromised patients and those with severe disease. Specificity was 99.0% for patients with nonfungal infections (n = 130) and in healthy subjects (n = 69), but cross-reactivity occurred in 90% of patients with blastomycosis. CONCLUSIONS The sensitivity of antigen detection in disseminated histoplasmosis is higher in immunocompromised patients than in immunocompetent patients and in patients with more severe illness. The sensitivity for detection of antigenemia is similar to that for antigenuria in disseminated infection.
Disturbed Cross Talk between Insulin-Like Growth Factor I and AMP-Activated Protein Kinase as a Possible Cause of Vascular Dysfunction in the Amyloid Precursor Protein/Presenilin 2 Mouse Model of Alzheimer's Disease

Cerebrovascular dysfunction appears to be involved in Alzheimer's disease (AD). In double mutant amyloid precursor protein/presenilin 2 (APP/PS2) mice, a transgenic model of AD, vessel homeostasis is disturbed. These mice have elevated levels of vascular endothelial growth factor (VEGF) and increased brain endothelial cell division but abnormally low brain vessel density. Examination of the potential involvement of insulin-like growth factor I (IGF-I) in these alterations revealed that treatment with IGF-I, a potent vessel growth promoter in the brain that ameliorates cognitive dysfunction in APP/PS2 mice, counteracted vascular dysfunction as follows: VEGF levels and endothelial cell proliferation were reduced, whereas vascular density was normalized. Notably, abnormally elevated brain IGF-I receptor levels in APP/PS2 mice were also normalized by IGF-I treatment. Analysis of possible processes involved in these alterations indicated that AMP-activated protein kinase (AMPK), a cell energy sensor that intervenes in angiogenic signaling and interacts with IGF-I, was also abnormally activated in APP/PS2 brains. Examination of the consequences of AMPK activation on cultured brain endothelial cells revealed increased VEGF levels together with enhanced endothelial cell proliferation and metabolism. Although these effects were also independently elicited by IGF-I, when both IGF-I and AMPK pathways were simultaneously activated on brain endothelial cells, VEGF production and endothelial cell proliferation ceased while cells remained metabolically activated (glucose use, peroxide production, and mitochondrial activity were elevated) and became more resistant to oxidative stress. Therefore, high IGF-I receptor and phosphoAMPK levels in APP/PS2 brains may reflect imbalanced IGF-I and AMPK angiogenic cross talk that could underlie vascular dysfunction in this model of AD.
Enhanced Production and Secretion of Heterologous Proteins by the Filamentous Fungus Aspergillus oryzae via Disruption of Vacuolar Protein Sorting Receptor Gene Aovps10

ABSTRACT Filamentous fungi have received attention as hosts for heterologous protein production because of their high secretion capability and eukaryotic posttranslational modifications. However, despite these positive attributes, a bottleneck in posttranscriptional processing limits protein yields. The vacuolar protein sorting gene VPS10 encodes a sorting receptor for the recognition and delivery of several yeast vacuolar proteins. Although it can also target recombinant and aberrant proteins for vacuolar degradation, there is limited knowledge of the effect of its disruption on heterologous protein production. In this study, cDNA encoding AoVps10 from the filamentous fungus Aspergillus oryzae was cloned and sequenced. Microscopic observation of the transformant expressing AoVps10 fused with enhanced green fluorescent protein showed that the fusion protein localized at the Golgi and prevacuolar compartments. Moreover, disruption of the Aovps10 gene resulted in missorting and secretion of vacuolar carboxypeptidase AoCpyA into the medium, indicating that AoVps10 is required for sorting of vacuolar proteins to vacuoles. To investigate the extracellular production levels of heterologous proteins, ΔAovps10 mutants expressing either bovine chymosin (CHY) or human lysozyme (HLY) were constructed. Interestingly, the ΔAovps10 mutation increased the maximum extracellular production levels of CHY and HLY by 3- and 2.2-fold, respectively. Western blot analysis of extracellular heterologous proteins also demonstrated an improvement in productivity. These results suggest that AoVps10 plays a role in the regulation of heterologous protein secretion in A. oryzae and may be involved in the vacuolar protein degradation through the Golgi apparatus.
The Validity Issue in Mixed Research

In quantitative research, the importance of validity has been long accepted. In qualitative research, discussions of validity have been more contentious and different typologies and terms have been produced. In mixed methods research, wherein quantitative and qualitative approaches are combined, discussions about “validity” issues are in their infancy. We argue that because mixed research involves combining complementary strengths and nonoverlapping weaknesses of quantitative and qualitative research, assessing the validity of findings is particularly complex; we call this the problem of integration. We recommend that validity in mixed research be termed legitimation in order to use a bilingual nomenclature. Tashakkori and Teddlie’s (2003, 2006) evaluation criteria frameworks involving the concept of inference quality are summarized. Although providing a framework for assessing legitimation in mixed research always will be incomplete, it is important to address several legitimation types that come to the fore as a result of combining inferences from the quantitative and qualitative components of the study into the formation of meta-inferences. Nine types of legitimation are described here in order to continue this emerging and important dialogue among researchers and methodologists.
Selection of T‐cell receptors with a recurrent CDR3β peptide‐contact motif within the repertoire of alloreactive CD8+ T cells

Peptide/MHC complexes recognized by alloreactive T lymphocytes (TLs) have been identified, but their contribution to in vivo allo‐rejection is not known. We previously characterized the peptide pBM1, highly represented among endogenous H‐2Kb (Kb)‐associated peptides and critically required to induce full activation of H‐2k monoclonal CD8+ TLs expressing the cognate TCR‐BM3.3. Here, we asked whether a pBM1/Kb‐specific TL subset could be detected within a polyclonal TL population rejecting allogeneic cells in vivo. We show that the proportion of pBM1/Kb‐binding CD8+ TLs increased from <0.04% in naïve mice to 3% of activated CD44+ CD8+ TLs in H‐2k mice rejecting Kb‐expressing cells. Among these, TCR‐Vβ2 usage was greatly enriched, and 75% of them shared a TCR‐Vβ2 CDR3β motif with the prototype TCR‐BM3.3. Fewer than 5% of Kb‐reactive CD44+ CD8+ TLs not binding pBM1/Kb displayed this CDR3β motif. We found that the recurrent CDR3β motif of pBM1/Kb‐binding TLs was assembled from distinct V/D/J recombination events, suggesting that it is recruited upon immunization for its optimal TCR‐peptide/MHC fit. Thus, a CDR3β motif generated by a process akin to “convergent recombination” accounts for a sizable fraction of the alloreactive anti‐Kb TCR repertoire.
Study on Exothermic Oxidation of Acrylonitrile-butadiene-styrene (ABS) Resin Powder with Application to ABS Processing Safety

Oxidative degradation of commercial grade ABS (Acrylonitrile-butadiene-styrene) resin powders was studied by thermal analysis. The instabilities of ABS containing different polybutadiene (PB) contents with respect to temperature were studied by Differential Scanning Calorimeter (DSC). Thermograms of isothermal test and dynamic scanning were performed. Three exothermic peaks were observed and related to auto-oxidation, degradation and oxidative decomposition, respectively. Onset temperature of the auto-oxidation was determined to be around 193 °C. However, threshold temperature of oxidation was found to be as low as 140 °C by DSC isothermal testing. Another scan of the powder after degeneration in air showed an onset temperature of 127 °C. Reactive hazards of ABS powders were verified to be the exothermic oxidation of unsaturated PB domains, not the SAN (poly(styrene-acrylonitrile)) matrix. Heat of oxidation was first determined to be 2,800 ± 40 J per gram of ABS or 4,720 ± 20 J per gram of PB. Thermal hazards of processing ABS powder are assessed by adiabatic temperature rise at process conditions. IR spectroscopy associated with heat of oxidation verified the oxidative mechanism, and these evidences excluded the heat source from the degradation of SAN. A specially prepared powder of ABS without adding anti-oxidant was analyzed by DSC for comparing the exothermic behaviors. Exothermic onset temperatures were determined to be 120 °C and 80 °C by dynamic scanning and isothermal test, respectively. The assessment successfully explained fires and explosions in an ABS powder dryer and an ABS extruder.
Association of adiponectin gene variations with risk of incident myocardial infarction and ischemic stroke: a nested case-control study.

BACKGROUND Adiponectin (ADIPOQ) gene variations are associated with risk of cardiovascular disease in patients with diabetes. No prospective data are available, however, on the risk of atherothrombotic disorders in persons with ADIPOQ variations who do not have diabetes. METHODS From a group of DNA samples collected at baseline in a prospective cohort of 14 916 initially healthy American men, we assessed the presence of 5 ADIPOQ genetic variants (rs266729, rs182052, rs822396, rs2241766, and rs1501299) in samples from 600 Caucasian men who subsequently suffered an atherothrombotic event (incident myocardial infarction or ischemic stroke) and from 600 age- and smoking-matched Caucasian men who remained free of reported vascular disease during follow-up (controls). RESULTS Genotype distributions for the variations tested were in Hardy-Weinberg equilibrium. Marker-by-marker conditional logistic regression analysis, adjusted for potential risk factors, showed an association of rs266729 [recessive: odds ratio (OR), 0.26; 95% confidence interval (CI), 0.10-0.64; P=0.004] and rs182052 (recessive: OR, 0.40; 95% CI, 0.21-0.76; P=0.006) with decreased risk of ischemic stroke. These findings remained significant after Bonferroni correction. Haplotype-based (constituted by rs266729, rs182052, and rs822396) conditional logistic regression analysis, adjusted for the same potential risk factors, showed an association of haplotype G-A-G (OR, 0.28; 95% CI, 0.09-0.87; P=0.03) with decreased risk of ischemic stroke. Prespecified analysis limited to participants without baseline diabetes showed similar significant findings. CONCLUSIONS The present prospective investigation provides further evidence for a protective role of adiponectin gene variation in the risk of ischemic stroke that was independent of the presence of diabetes.