Miracle-dz/UniFAR-FTUs huggingface dataset:
Survey of Extreme Solvent Tolerance in Gram-Positive Cocci: Membrane Fatty Acid Changes in Staphylococcus haemolyticus Grown in Toluene

ABSTRACT We exploited the unique ecological niche of oil fly larval guts to isolate a strain of Staphylococcus haemolyticus which may be the most solvent-tolerant gram-positive bacterium yet described. This organism is able to tolerate 100% toluene, benzene, and p-xylene on plate overlays and saturating levels of these solvents in monophasic liquid cultures. A comparison of membrane fatty acids by gas chromatography after growth in liquid media with and without toluene showed that in cells continuously exposed to solvent the proportion of anteiso fatty acids increased from 25.8 to 33.7% while the proportion of 20:0 straight-chain fatty acids decreased from 19.3 to 10.1%. No changes in the membrane phospholipid composition were noted. Thus, S. haemolyticus alters its membrane fluidity via fatty acid composition to become more fluid when it is exposed to solvent. This response is opposite that commonly found in gram-negative bacteria, which change their fatty acids so that the cytoplasmic membrane is less fluid. Extreme solvent tolerance in S. haemolyticus is not accompanied by abnormal resistance to anionic or cationic detergents. Finally, six strains of Staphylococcus aureus and five strains of Staphylococcus epidermidis, which were not obtained by solvent selection, also exhibited exceptional solvent tolerance.
Discovering gapped binding sites of yeast transcription factors

A gapped transcription factor-binding site (TFBS) contains one or more highly degenerate positions. Discovering gapped motifs is difficult, because allowing highly degenerate positions in a motif greatly enlarges the search space and complicates the discovery process. Here, we propose a method for discovering TFBSs, especially gapped motifs. We use ChIP-chip data to judge the binding strength of a TF to a putative target promoter and use orthologous sequences from related species to judge the degree of evolutionary conservation of a predicted TFBS. Candidate motifs are constructed by growing compact motif blocks and by concatenating two candidate blocks, allowing 0–15 degenerate positions in between. The resultant patterns are statistically evaluated for their ability to distinguish between target and nontarget genes. Then, a position-based ranking procedure is proposed to enhance the signals of true motifs by collecting position concurrences. Empirical tests on 32 known yeast TFBSs show that the method is highly accurate in identifying gapped motifs, outperforming current methods, and it also works well on ungapped motifs. Predictions on additional 54 TFs successfully discover 11 gapped and 38 ungapped motifs supported by literature. Our method achieves high sensitivity and specificity for predicting experimentally verified TFBSs.
Transgenic Rodent Assay for Quantifying Male Germ Cell Mutant Frequency

De novo mutations arise mostly in the male germline and may contribute to adverse health outcomes in subsequent generations. Traditional methods for assessing the induction of germ cell mutations require the use of large numbers of animals, making them impractical. As such, germ cell mutagenicity is rarely assessed during chemical testing and risk assessment. Herein, we describe an in vivo male germ cell mutation assay using a transgenic rodent model that is based on a recently approved Organisation for Economic Co-operation and Development (OECD) test guideline. This method uses an in vitro positive selection assay to measure in vivo mutations induced in a transgenic λgt10 vector bearing a reporter gene directly in the germ cells of exposed males. We further describe how the detection of mutations in the transgene recovered from germ cells can be used to characterize the stage-specific sensitivity of the various spermatogenic cell types to mutagen exposure by controlling three experimental parameters: the duration of exposure (administration time), the time between exposure and sample collection (sampling time), and the cell population collected for analysis. Because a large number of germ cells can be assayed from a single male, this method has superior sensitivity compared with traditional methods, requires fewer animals and therefore much less time and resources.
Analysis and Optimal Design for Association Studies Using Next‐Generation Sequencing With Case‐Control Pools

With its potential to discover a much greater amount of genetic variation, next‐generation sequencing is fast becoming an emergent tool for genetic association studies. However, the cost of sequencing all individuals in a large‐scale population study is still high in comparison to most alternative genotyping options. While the ability to identify individual‐level data is lost (without bar‐coding), sequencing pooled samples can substantially lower costs without compromising the power to detect significant associations. We propose a hierarchical Bayesian model that estimates the association of each variant using pools of cases and controls, accounting for the variation in read depth across pools and sequencing error. To investigate the performance of our method across a range of number of pools, number of individuals within each pool, and average coverage, we undertook extensive simulations varying effect sizes, minor allele frequencies, and sequencing error rates. In general, the number of pools and pool size have dramatic effects on power while the total depth of coverage per pool has only a moderate impact. This information can guide the selection of a study design that maximizes power subject to cost, sample size, or other laboratory constraints. We provide an R package (hiPOD: hierarchical Pooled Optimal Design) to find the optimal design, allowing the user to specify a cost function, cost, and sample size limitations, and distributions of effect size, minor allele frequency, and sequencing error rate.
Gene Expression Analysis Exposes Mitochondrial Abnormalities in a Mouse Model of Rett Syndrome

ABSTRACT Rett syndrome (RTT) is a severe neurological disorder caused by mutations in the X-linked MECP2 gene, which encodes a methyl-CpG binding transcriptional repressor. Using the Mecp2-null mouse (an animal model for RTT) and differential display, we found that mice with neurological symptoms overexpress the nuclear gene for ubiquinol-cytochrome c reductase core protein 1 (Uqcrc1). Chromatin immunoprecipitation demonstrated that MeCP2 interacts with the Uqcrc1 promoter. Uqcrc1 encodes a subunit of mitochondrial respiratory complex III, and isolated mitochondria from the Mecp2-null brain showed elevated respiration rates associated with respiratory complex III and an overall reduction in coupling. A causal link between Uqcrc1 gene overexpression and enhanced complex III activity was established in neuroblastoma cells. Our findings raise the possibility that mitochondrial dysfunction contributes to pathology of the Mecp2-null mouse and may contribute to the long-known resemblance between Rett syndrome and certain mitochondrial disorders.
FDI, banking crises and growth: direct and spill over effects

ABSTRACT This study suggests a new decomposition of the effect of foreign direct investment (FDI) on the long-term growth of developing countries. It reveals that FDI not only has a direct positive effect on growth, but also increases it by reducing the recessionary effect resulting from a banking crisis. However, these advantages are conditioned by the FDI threshold, which in turn depends on the ‘absorption capacity’ of the host country.
How to read a nephrology systematic review

A systematic review provides the best summary of evidence for clinical decision‐making in nephrology by summarizing all the primary studies that evaluate a specific clinical question. By using rigorous and pre‐specified methods, conclusions about the overall effect of an intervention can be more reliable, precise and comprehensive in a systematic review than those derived from individual studies. In this article, we describe the key components of a systematic review and meta‐analysis. We summarize the features of a systematic review that should be looked for when considering the accuracy and validity of its results – particularly when applying the outcomes of a systematic review to a clinical question.
The association between saliva control, silent saliva penetration, aspiration, and videofluoroscopic findings in Parkinson's disease patients

Background: Dysphagia is a common disorder among patients with Parkinson′s disease (PD). It occurs in up to 80% of all (PD) patients during the early stages of the disease and up to 95% in the advanced stages; but professionals may not hear from the patients about dysphagia symptoms until these symptoms reach an advanced stage and lead to medical complications. Materials and Methods: Thirty-three PD patients (mean age 66.09 ± 9.4 years; 24 men, nine women) participated in this study at our Neurology Institute, between April 20, 2013, and October 26, 2013. They were asked two questions; one about saliva control and the other about silent saliva penetration and aspiration. Next, they underwent the videofluoroscopic swallowing study (VFSS). Results: The Pearson Correlation coefficient between the Penetration-Aspiration Scale (PAS) scores and question 1 scores was 0.48 (P < 0.05, =0.25), and there was a significant correlation between the PAS scores and question 2 scores, and also question 1 scores + question 2 scores (r = 0.589, P < 0.05, =0 and r = 0589, P < 0.05, =0). Conclusions: This study showed a significant correlation between the questions about saliva control, silent saliva penetration, and aspiration, and laryngeal penetration and aspiration during VFSS. Therefore, by using these two questions, the potential silent laryngeal penetration and aspiration during meals could be detected before it led to aspiration pneumonia. Taking the benefit of these questions, as a part of the swallowing assessment of PD patients, is recommended.
Automated semantic leaf image categorization by geometric analysis

Unravelling mysteries of the diversity of the plant community is a crucial issue both for the development of many botanical industries as well as for the conservation of ecosystem biodiversity. Traditionally, botanists have proposed detailed dichotomous key descriptions (called also characters or concepts) about the morphology of plants and particularly of leaves that allow them to construct relationships between different plants and between plants and their environment. However, extracting these concepts is complicated, painstaking and can only be carried out by experts. One way to accelerate and broaden the use of these concepts is to automatically extract them directly from images. In this paper, we focus on one of the most basic and important concepts: the leaf arrangement. According to this concept, leaves are divided into four categories: simple, pinnnately compound, palmately compound and compound trifoliate. To accomplish this task, we follow a hierarchical scheme, reducing ambiguity between categories from the most different shapes to the most similar ones. The choice of appropriate features is performed based on botanical observations and validated by a statistical study. The method was tested on real world leaf images (the Pl@ntLeaves scans). Experimental results show its robustness for a high number of leaf species (70 species) and even in the presence of some distortions (such as rotation and partial leaf overlapping).
Oxaliplatin plus irinotecan compared with irinotecan alone as second-line treatment after single-agent fluoropyrimidine therapy for metastatic colorectal carcinoma.

UNLABELLED PURPOSE To determine whether irinotecan plus oxaliplatin (IROX) is superior to irinotecan alone in patients with metastatic colorectal cancer (CRC) previously treated with single-agent fluoropyrimidines. PATIENTS AND METHODS A phase III, randomized, open-label, multicenter study of patients with metastatic or recurrent CRC that had progressed or recurred during or after adjuvant or first-line fluoropyrimidines (fluorouracil/leucovorin or capecitabine, the latter only for metastatic CRC). Patients received IROX (irinotecan 200 mg/m(2) plus oxaliplatin 85 mg/m(2)) or irinotecan alone (350 mg/m(2)) every 3 weeks. RESULTS At the data cutoff (when 447 of 628 randomly assigned patients had died), median overall survival was 13.4 months (95% CI, 12.4 to 14.7 months) and 11.1 month (95% CI, 10.0 to 12.7 months) in the IROX and irinotecan groups, respectively (hazard ratio = 0.78; 95% CI, 0.65 to 0.94; P = .0072). Overall response rate (22% v 7%, respectively; P < .0001), median time to progression (5.3 v 2.8 months, respectively; P < .0001), and improvement in tumor-related symptoms (32% v 19%, respectively; P = .0072) were also improved with IROX as compared with irinotecan. With the exception of granulocytopenia (25% v 13%), diarrhea (28% v 23%), and sensory disturbances (5% v 0%), grade 3 to 4 toxicities were comparable between the IROX and irinotecan groups, respectively. CONCLUSION IROX is an effective treatment for metastatic CRC that has progressed after first-line fluoropyrimidine therapy. IROX improves efficacy compared with irinotecan alone, providing an additional option in the postadjuvant or second-line treatment setting for patients who experience treatment failure with single-agent fluoropyrimidine therapy.
Differential effects of n-3 and n-6 polyunsaturated fatty acids on BRCA1 and BRCA2 gene expression in breast cell lines

Current evidence strongly supports a role for the breast tumour suppressor genes, BRCA1 and BRCA2, in both normal development and carcinogenesis. In vitro observations reported that BRCA1 and BRCA2 are expressed in a cell cycle-dependent manner. Interestingly, differences in the actions of n-3 and n-6 polyunsaturated fatty acids have been observed: while the n-3 polyunsaturated fatty acids have been described to reduce pathological cell growth, the n-6 polyunsaturated fatty acids have been found to induce tumour proliferation. Here, we examined the expression of BRCA1 and BRCA2 in breast cell lines after treatment with polyunsaturated fatty acids. Real-time quantitative polymerase chain reaction determinations conclusively demonstrated increases in BRCA1 and BRCA2 mRNA expressions in MCF7 and MDA-MB 231 tumour cell lines after treatment with n-3 polyunsaturated fatty acids (eicosapentaenoic acid and docosahexaenoic acid), but no variation was noticed with the n-6 polyunsaturated fatty acid (arachidonic acid). On the other hand, no variation of the expression of BRCA1 and BRCA2 mRNA was detected in MCF10a normal breast cell line treated by polyunsaturated fatty acids. The level of BRCA1 and BRCA2 proteins quantified by affinity chromatography remained unchanged in tumour (MCF7, MDA-MB 231) and normal (MCF10a) breast cell lines. We suggest the presence of a possible transcriptional or post-transcriptional regulation of BRCA1 and BRCA2 after n-3 polyunsaturated fatty acid treatment in breast tumour cells.
Price Transmission, Volatility and Discovery of Gram in Some Selected Markets in Rajathan State, India

Market integration in many agricultural commodities had been extensively studied for the insight it provides into the functioning of such markets, thus giving valuable information about the dynamics of market adjustment, and whether there exist market imperfection, which may justify government intervention. This study empirically investigated price transmission, volatility and discovery of gram across four wholesale gram markets, viz. Jaipur, Kishangarh, Chomu and Malpura in Rajasthan state of India using Johansen’s multivariate cointegration approach, VECM, Granger causality tests, GARCH, EGARCH and ARIMA. Monthly wholesale gram price data spanning from January 2011 to December 2015 sourced from AGMARKNET were used. Multivariate cointegration showed that all the selected gram markets were cointegarted in the long-run, meaning long-run price association among these markets. The degree of market integration observed is consistent with the view that Rajasthan state gram markets are quite competitive; thus, provide little justification for extensive and costly government intervention designed to enhance market efficiency through improve competitiveness. Therefore, in order to sustain the present system of market integration, there is need to evolve mechanism that will generate market information and market intelligence which would serve as a platform for guiding farmers in marketing their produce.
Effect of creatine and weight training on muscle creatine and performance in vegetarians.

PURPOSE To compare the change in muscle creatine, fiber morphology, body composition, hydration status, and exercise performance between vegetarians and nonvegetarians with 8 wk of creatine supplementation and resistance training. METHODS Eighteen VG and 24 NV subjects (19-55 yr) were randomly assigned (double blind) to four groups: VG + creatine (VGCr, N=10), VG + placebo (VGPl, N=8), NV + creatine (NVCr, N=12), and NV + placebo (NVPl, N=12). Before and at the end of the study, muscle biopsies were taken from the vastus lateralis m, body composition was assessed by DXA, and strength was assessed using 1-RM bench press and leg press. Subjects participated in the same 8-wk resistance-training program. Creatine dosage was based on lean tissue mass (0.25 g.kg(-1) LTM.d(-1) x 7 d; 0.0625 g.kg(-1) LTM.d(-1) x 49 d). RESULTS Biopsy samples indicated that total creatine (TCr=free Cr + PCr) was significantly lower in VG compared with NV at baseline (VG=117 mmol.kg(-1); NV=130 mmol.kg(-1); P<0.05). For Cr subjects, there was a greater increase in PCr, TCr, bench-press strength, isokinetic work, Type II fiber area, and whole-body lean tissue compared with subjects on placebo (P<0.05). Vegetarians who took Cr had a greater increase in TCr, PCr, lean tissue, and total work performance than nonvegetarians who took Cr (P<0.05). The change in muscle TCr was significantly correlated with initial muscle TCr, and the change in lean tissue mass and exercise performance. These findings confirm an ergogenic effect of Cr during resistance training and suggest that subjects with initially low levels of intramuscular Cr (vegetarians) are more responsive to supplementation.
Transmit Power Control for D2D-Underlaid Cellular Networks Based on Statistical Features

By allowing two nearby mobile devices to communicate via a direct link between them, device-to-device (D2D) communications can efficiently increase the capacity of D2D-underlaid cellular networks, in which D2D and cellular communications share the same frequency band. However, the coexistence of D2D and cellular communications in the same frequency band will cause interference between the D2D and cellular users, thus degrading their performance. One may control the transmit power based on the real-time channel-state information (CSI) to mitigate this interference, but it is difficult to acquire the real-time CSI between D2D/cellular transmitters and D2D receivers. To overcome this difficulty, we propose novel statistical-feature-based power control (SFPC), which determines the transmit power based on statistical (instead of real-time) CSI. The proposed SFPC combines the power control—that is aware of D2D success likelihood—with opportunistic access control to 1) reduce the interference caused by D2D communications and 2) maximize the area spectral efficiency of D2D communications. Specifically, it aims to minimize the D2D transmit power and optimize the selection of access threshold. Our simulation results show that SFPC can increase both the cellular communication success probability and the energy efficiency of D2D communications, as well as reduce the average D2D transmit power.
Enhancing momentum with volatility and risk management : an empirical analysis of momentum in US equities

In this thesis, we examine two approaches to enhance the performance of a momentum strategy. First, we investigate if stocks with similar cumulative returns but different daily standard deviation during the formation period perform differently in the holding period. We find a large variation in the performance of portfolios within each decile formed on cumulative returns, where the most volatile portfolio clearly underperforms. We construct a volatility dependent momentum strategy, that excludes the most volatile winners and losers. We find that our volatility dependent momentum strategy outperforms a generic momentum strategy, with an annualized Sharpe ratio of 0.43 versus 0.35. Similar to other momentum strategies, we find that our volatility dependent momentum strategy inherits the risk of large drawdowns in periods when the market rebounds after a major decline. In order to reduce the impact of momentum crashes, we introduce a new risk management approach. We exit our volatility dependent momentum strategy when the 12-month cumulative return of the market is negative. Risk management further enhances the Sharpe ratio from 0.43 to 0.81. We find that the combination of taking volatility and risk management into account generates a monthly alpha of 0.62% after controlling for Fama/French 5 Factors including momentum.
Abnormal intestinal motility in diabetics with the gastroparesis syndrome

Abstract. Gastroparesis syndrome is a recognized complication of longstanding diabetes mellitus and is attributed to reduced gastric contractility due to ‘autovagotomy’. However, motor abnormalities associated with this syndrome may not be limited to the stomach. To test this hypothesis we have studied the fasting and fed manometric profiles of the proximal small intestine of fourteen patients with the clinical diagnosis of gastroparesis. Abnormal intestinal manometric patterns were observed in twelve out of the fourteen patients. In four patients there was reduced duodenojejunal phasic pressure activity, whereas in nine there were non‐propagated long bursts of powerful contractions. Furthermore, while the majority of patients (eleven out of fourteen) exhibited the expected reduction in antral pressure activity and gastric phase III, a small subgroup of three patients exhibited a peculiar continuous 3 min‐1 antral contractile activity.
Semen quality and sexual hormones in greenhouse workers.

OBJECTIVES This study focused on determining the testicular function of greenhouse workers exposed to pesticides. METHODS Semen was examined for 122 of 199 eligible men (61%) from 30 ornamental flower greenhouses. Sperm concentration, morphology, and viability were measured according to World Health Organization guidelines, and the curvilinear sperm velocity was determined by a computer-assisted analysis of video recordings. Three groups were formed according to expert judgment of current exposure to pesticides from cultures, pesticide formulations, and the transfer of pesticide residues from leaves to hands, and also ranked according to years of work in a greenhouse. The risk estimates were adjusted for the effects of sexual abstinence and other potentially confounding factors. RESULTS According to current exposure the median values of sperm concentration and the proportion of normal spermatozoa were 60% and 14% lower, respectively, in the high-level exposure group (N=13) than in the low-level group (N=44), and the values of the intermediate group fell in between. The adjusted differences between the high-level and low-level exposure groups were statistically significant, while no differences were observed for the viability and velocity of sperm and sexual hormones. The median sperm concentration was 40% lower for the men with > 10 years' experience in a greenhouse than for those with < 5 years' experience. The age-adjusted testosterone/sex-hormone-binding globulin ratio declined 1.9% (95% confidence interval 0.4-3.4%) per year of work. CONCLUSIONS The results are compatible with the hypothesis that male fecundity may be at risk from exposure to pesticides in the manual handling of cultures in greenhouses.