Takshan/R1 huggingface dataset:
Impact of a direct-to-consumer information campaign on prescription patterns for overactive bladder.

BACKGROUND: Direct-to-consumer information (DTCI) campaign is a new medium to inform and empower patients in their decision-making without directly promoting specific drugs. However, little is known about the impact of DTCI campaigns, expanding rapidly in developed countries, on changes in prescription patterns. We sought to determine whether a DTCI campaign on overactive bladder increases the prescription rate for overactive bladder treatment drugs. METHODS: We performed a 3-year retrospective cohort study of 1332 participants who were diagnosed overactive bladder but not prescribed treatment drugs prior to the examined DTCI campaign (exposure), using the health insurance claims dataset of the Japan Medical Data Center (November 19, 2010 to November 18, 2013). The DTCI campaign for overactive bladder included television, Internet, and print advertising (November 19, 2011 to December 22, 2011). We divided the study period into Pre-Campaign Year (2010-2011), Year 1 (2011-2012), and Year 2 (2012-2013). Each year began on November 19 and included Period 1 (weeks 1-5) through Period 10 (weeks 46-50). The main outcome was first-time prescription of the treatment drug for each patient, measured by 5-week periods. Using Period 10 in the Pre-Campaign Year as the referent period, we applied the Cox proportional hazard model for each period. Additionally, we performed the interrupted time series analysis (ITSA) for the first-time prescription rate per 5-week period. RESULTS: Following the DTCI campaign, patients were about seven times more likely to receive a first prescription of a treatment drug during Period 4 in Year 1 (hazard ratio 7.09; 95% CI, 2.11-23.8; p-value<.01) compared with the reference period. Similar increases were also observed for subsequent Periods 5 and 6 in Year 1. The ITSA confirmed the DTCI campaign impact on the level of prescription rate (one-time increase in the regression-intercept) that increased by 1128.1 [per standardized 100,000 persons] (p < .05) during Period 4 in Year 1. CONCLUSIONS: The examined DTCI campaign appeared to increase the prescription rate among patients with overactive bladder for 15 weeks with a 15-week delay. Clinical outcomes of the patients with targeted diseases need to be monitored after DTCI campaigns by a future study.
Notos - a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types.

BACKGROUND: DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it remains challenging to infer kingdom-wide general rules about the functions and evolutionary conservation of DNA methylation. Methylated cytosine is often found in specific CpN dinucleotides, and the frequency distributions of, for instance, CpG observed/expected (CpG o/e) ratios have been used to infer DNA methylation types based on higher mutability of methylated CpG. RESULTS: Predominantly model-based approaches essentially founded on mixtures of Gaussian distributions are currently used to investigate questions related to the number and position of modes of CpG o/e ratios. These approaches require the selection of an appropriate criterion for determining the best model and will fail if empirical distributions are complex or even merely moderately skewed. We use a kernel density estimation (KDE) based technique for robust and precise characterization of complex CpN o/e distributions without a priori assumptions about the underlying distributions. CONCLUSIONS: We show that KDE delivers robust descriptions of CpN o/e distributions. For straightforward processing, we have developed a Galaxy tool, called Notos and available at the ToolShed, that calculates these ratios of input FASTA files and fits a density to their empirical distribution. Based on the estimated density the number and shape of modes of the distribution is determined, providing a rational for the prediction of the number and the types of different methylation classes. Notos is written in R and Perl.
Mitochondrial Effects of Teucrium Polium and Prosopis Farcta Extracts in Colorectal Cancer Cells

Background: Teucrium Polium and Prosopis Farcta have been traditionally employed in cancer treatment. In this study we evaluated the effects of methanolic extracts of these two plants in HT-29 cells. Methods: IC50s of extracts were obtained via MTT assay and the levels of ROS production, cell death, collapse of mitochondrial membrane potential and Sirt3 enzyme activity were determined. Results: After 48 hours exposure, IC50s for Teucrium and Prosopis extracts were 3 and 2μg/ml, respectively. Extracts induced higher ROS production after 6 hours than after 12 hours. Mitochondrial membrane potential collapse and cell death rate were also increased; Teucrium caused greater cell death than Prosopis. Extracts from both plants increased Sirt3 activity in its normal form, but only Teucrium extract caused a significant increase in activity of Sirt3 enzyme isolated from cancer cells. Conclusion: Teucrium and Prosopis extracts exert anticancer activity via mitochondrial alterations, as exemplified by increased ROS levels, Sirt3 activity and cell death in HT-29 colorectal cancer cells.
Effects of substrate binding site residue substitutions of xynA from Bacillus amyloliquefaciens on substrate specificity.

BACKGROUND: The aromatic residues of xylanase enzyme, W187, Y124, W144, Y128 and W63 of substrate binding pocket from Bacillus amyloliquefaciens were investigated for their role in substrate binding by homology modelling and sequence analysis. These residues are highly conserved and play an important role in substrate binding through steric hindrance. The substitution of these residues with alanine allows the enzyme to accommodate nonspecific substrates. RESULTS: Wild type and mutated genes were cloned and overexpressed in BL21. Optimum pH and temperature of rBAxn exhibited pH 9.0 and 50 °C respectively and it was stable up to 215 h. Along with the physical properties of rBAxn, kinetic parameters (Km 19.34 ± 0.72 mg/ml; kcat 6449.12 ± 155.37 min- 1 and kcat/Km 333.83 ± 6.78 ml min- 1 mg- 1) were also compared with engineered enzymes. Out of five mutations, W63A, Y128A and W144A lost almost 90% activity and Y124A and W187A retained almost 40-45% xylanase activity. CONCLUSIONS: The site-specific single mutation, led to alteration in substrate specificity from xylan to CMC while in case of double mutant the substrate specificity was altered from xylan to CMC, FP and avicel, indicating the role of aromatic residues on substrate binding, catalytic process and overall catalytic efficiency.
MOCAT2: a metagenomic assembly, annotation and profiling framework.

UNLABELLED: MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes. AVAILABILITY AND IMPLEMENTATION: MOCAT2 is implemented in Perl 5 and Python 2.7, designed for 64-bit UNIX systems and offers support for high-performance computer usage via LSF, PBS or SGE queuing systems; source code is freely available under the GPL3 license at http://mocat.embl.de CONTACT: : bork@embl.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
On the Diagnosis of Mycotic Aortic Aneurysms.

Objective: There is striking paucity in consensus on the terminology, definition, and diagnostic criteria of mycotic aortic aneurysms. This literature study aims to elucidate this scientific omission, discuss its consequences, and present a proposition for reporting items on this disease. Methods: A systematic literature review on PubMed and Medline using mycotic and infected aortic aneurysms between 1850 and 2017 was performed. Articles were assessed according to a protocol regarding terminology, definition, and diagnostic criteria. Case series with less than 5 patients were excluded. Results: A total of 49 articles were included. The most prevalent term was mycotic aortic aneurysm but there was no widely accepted definition. Most modern publications used a diagnostic workup based on a combination on clinical presentation, laboratory results, imaging findings, and intraoperative findings. How these protean variables should be balanced was unclear. A proposition of reporting items was framed and consisted of definition of disease used, basis of diagnostic workup, exclusion criteria, patient characteristics, laboratory and imaging findings, aneurysm anatomy, details on treatment, pre/postoperative antibiotic treatment, and details on follow-up. Conclusions: This article emphasizes the need to standardize definition, terminology, and diagnostic criteria for mycotic aortic aneurysms and proposes reporting items enhancing comparability between studies.
CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation, and visualization.

Summary: Identifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes , an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization. The input and output of each step in the framework are packaged in the same data format, making it convenience to compare different methods. The package is useful for inferring cancer subtypes from an input genomic dataset, comparing the predictions from different well-known methods and testing new subtype discovery methods, as shown with different application scenarios in the Supplementary Material. Availability: The package is implemented in R and available under GPL-2 license from the Bioconductor website( http://bioconductor.org/packages/CancerSubtypes/ ). Contact: Thuc. Le@unisa.edu.au , jiuyong.li@unisa.edu.au.
Inferring condition-specific miRNA activity from matched miRNA and mRNA expression data.

MOTIVATION: MicroRNAs (miRNAs) play crucial roles in complex cellular networks by binding to the messenger RNAs (mRNAs) of protein coding genes. It has been found that miRNA regulation is often condition-specific. A number of computational approaches have been developed to identify miRNA activity specific to a condition of interest using gene expression data. However, most of the methods only use the data in a single condition, and thus, the activity discovered may not be unique to the condition of interest. Additionally, these methods are based on statistical associations between the gene expression levels of miRNAs and mRNAs, so they may not be able to reveal real gene regulatory relationships, which are causal relationships. RESULTS: We propose a novel method to infer condition-specific miRNA activity by considering (i) the difference between the regulatory behavior that an miRNA has in the condition of interest and its behavior in the other conditions; (ii) the causal semantics of miRNA-mRNA relationships. The method is applied to the epithelial-mesenchymal transition (EMT) and multi-class cancer (MCC) datasets. The validation by the results of transfection experiments shows that our approach is effective in discovering significant miRNA-mRNA interactions. Functional and pathway analysis and literature validation indicate that the identified active miRNAs are closely associated with the specific biological processes, diseases and pathways. More detailed analysis of the activity of the active miRNAs implies that some active miRNAs show different regulation types in different conditions, but some have the same regulation types and their activity only differs in different conditions in the strengths of regulation. AVAILABILITY AND IMPLEMENTATION: The R and Matlab scripts are in the Supplementary materials.
Exploring the molecular mechanisms of Traditional Chinese Medicine components using gene expression signatures and connectivity map.

BACKGROUND AND OBJECTIVE: Traditional Chinese Medicine (TCM) has been practiced over thousands of years in China and other Asian countries for treating various symptoms and diseases. However, the underlying molecular mechanisms of TCM are poorly understood, partly due to the "multi-component, multi-target" nature of TCM. To uncover the molecular mechanisms of TCM, we perform comprehensive gene expression analysis using connectivity map. METHODS: We interrogated gene expression signatures obtained 102 TCM components using the next generation Connectivity Map (CMap) resource. We performed systematic data mining and analysis on the mechanism of action (MoA) of these TCM components based on the CMap results. RESULTS: We clustered the 102 TCM components into four groups based on their MoAs using next generation CMap resource. We performed gene set enrichment analysis on these components to provide additional supports for explaining these molecular mechanisms. We also provided literature evidence to validate the MoAs identified through this bioinformatics analysis. Finally, we developed the Traditional Chinese Medicine Drug Repurposing Hub (TCM Hub) - a connectivity map resource to facilitate the elucidation of TCM MoA for drug repurposing research. TCMHub is freely available in http://tanlab.ucdenver.edu/TCMHub. CONCLUSIONS: Molecular mechanisms of TCM could be uncovered by using gene expression signatures and connectivity map. Through this analysis, we identified many of the TCM components possess diverse MoAs, this may explain the applications of TCM in treating various symptoms and diseases.
IMPACT web portal: oncology database integrating molecular profiles with actionable therapeutics.

BACKGROUND: With the advancement of next generation sequencing technology, researchers are now able to identify important variants and structural changes in DNA and RNA in cancer patient samples. With this information, we can now correlate specific variants and/or structural changes with actionable therapeutics known to inhibit these variants. We introduce the creation of the IMPACT Web Portal, a new online resource that connects molecular profiles of tumors to approved drugs, investigational therapeutics and pharmacogenetics associated drugs. RESULTS: IMPACT Web Portal contains a total of 776 drugs connected to 1326 target genes and 435 target variants, fusion, and copy number alterations. The online IMPACT Web Portal allows users to search for various genetic alterations and connects them to three levels of actionable therapeutics. The results are categorized into 3 levels: Level 1 contains approved drugs separated into two groups; Level 1A contains approved drugs with variant specific information while Level 1B contains approved drugs with gene level information. Level 2 contains drugs currently in oncology clinical trials. Level 3 provides pharmacogenetic associations between approved drugs and genes. CONCLUSION: IMPACT Web Portal allows for sequencing data to be linked to actionable therapeutics for translational and drug repurposing research. The IMPACT Web Portal online resource allows users to query genes and variants to approved and investigational drugs. We envision that this resource will be a valuable database for personalized medicine and drug repurposing. IMPACT Web Portal is freely available for non-commercial use at http://tanlab.ucdenver.edu/IMPACT .
Over-expression of a NAC 67 transcription factor from finger millet (Eleusine coracana L.) confers tolerance against salinity and drought stress in rice.

BACKGROUND: NAC proteins (NAM (No apical meristem), ATAF (Arabidopsis transcription activation factor) and CUC (cup-shaped cotyledon)) are plant-specific transcription factors reported to be involved in regulating growth, development and stress responses. Salinity responsive transcriptome profiling in a set of contrasting finger millet genotypes through RNA-sequencing resulted in the identification of a NAC homolog (EcNAC 67) exhibiting differential salinity responsive expression pattern. METHODS: Full length cDNA of EcNAC67 was isolated, characterized and validated for its role in abiotic stress tolerance through agrobacterium mediated genetic transformation in a rice cultivar ASD16. RESULTS: Bioinformatics analysis of putative NAC transcription factor (TF) isolated from a salinity tolerant finger millet showed its genetic relatedness to NAC67 family TFs in related cereals. Putative transgenic lines of rice over-expressing EcNAC67 were generated through Agrobacterium mediated transformation and presence/integration of transgene was confirmed through PCR and southern hybridization analysis. Transgenic rice plants harboring EcNAC67 showed enhanced tolerance against drought and salinity under greenhouse conditions. Transgenic rice plants were found to possess higher root and shoot biomass during stress and showed better revival ability upon relief from salinity stress. Upon drought stress, transgenic lines were found to maintain higher relative water content and lesser reduction in grain yield when compared to non-transgenic ASD16 plants. Drought induced spikelet sterility was found to be much lower in the transgenic lines than the non-transgenic ASD16. CONCLUSION: Results revealed the significant role of EcNAC67 in modulating responses against dehydration stress in rice. No detectable abnormalities in the phenotypic traits were observed in the transgenic plants under normal growth conditions. Results indicate that EcNAC67 can be used as a novel source for engineering tolerance against drought and salinity stress in rice and other crop plants.
LchERF, a novel ethylene-responsive transcription factor from Lycium chinense, confers salt tolerance in transgenic tobacco.

KEY MESSAGE: An ERF gene, LchERF , was cloned from L. chinense for the first time. Overexpression of LchERF conferred salt stress tolerance in transgenic tobacco lines during seed germination and vegetative growth. Ethylene-responsive transcription factors (ERFs) play important roles in tolerance to biotic and abiotic stresses by regulating the expression of stress-responsive genes. Although the ERF proteins involved in defense responses against biotic stresses have been extensively documented, the mechanisms by which ERF subfamily genes regulate plant responses to abiotic stresses are largely unknown. In this study, a novel ethylene-responsive transcription factor, named LchERF, was isolated from Lycium chinense (a salinity-resistant plant). Analysis of the LchERF-deduced protein sequence showed that it had a typical AP2/ERF domain and belonged to the B-3 subgroup of the ERF subfamily. The expression of LchERF was found to be tissue specific in L. chinense under normal conditions. Upon treatment with NaCl, polyethylene glycol (PEG) or ethephon (ET), transcript levels of LchERF rapidly increased in L. chinense. Overexpression of LchERF conferred salt stress tolerance in transgenic tobacco during seed germination and vegetative growth. Compared with control lines, LchERF-overexpressing plants showed higher chlorophyll and proline contents, and were associated with lower H2O2 content under salt stress. Overall, our results demonstrate that LchERF might play an important role in the regulation of plant responses to abiotic stresses and mediate various physiological pathways that enhance salt stress tolerance in plants.
Overexpression of VaPAT1, a GRAS transcription factor from Vitis amurensis, confers abiotic stress tolerance in Arabidopsis.

KEY MESSAGE: VaPAT1 functions as a stress-inducible GRAS gene and enhanced cold, drought and salt tolerance in transgenic Arabidopsis via modulation of the expression of a series of stress-related genes. The plant-specific GRAS transcription factor family regulates diverse processes involved in plant growth, development and stress responses. In this study, VaPAT1, a GRAS gene from Vitis amurensis was isolated and functionally characterized. Sequence alignment and phylogenetic analysis showed that VaPAT1 has a high sequence identity to CmsGRAS and OsCIGR1, which belong to PAT1 branch of GRAS family and function in stress resistance. The transcription of VaPAT1 was markedly induced by stress-related phytohormone abscisic acid (ABA) and various abiotic stress treatments such as cold, drought and high salinity, however, it was repressed by exogenous gibberellic acid (GA) application. Overexpression of VaPAT1 increased the cold, drought and high salinity tolerance in transgenic Arabidopsis. When compared with wild type (WT) seedlings, the VaPAT1-overexpression lines accumulated higher levels of proline and soluble sugar under these stress treatments. Moreover, stress-related genes such as AtSIZ1, AtCBF1, AtATR1/MYB34, AtMYC2, AtCOR15A, AtRD29A and AtRD29B showed higher expression levels in VaPAT1 transgenic lines than in WT Arabidopsis under normal growth conditions. Together, our results indicated that VaPAT1 functions as a positive transcriptional regulator involved in grapevine abiotic stress responses.
Two NAC transcription factors from Caragana intermedia altered salt tolerance of the transgenic Arabidopsis.

BACKGROUND: Plants are continuously challenged by different environment stresses, and they vary widely in their adjustability. NAC (NAM, ATAF and CUC) transcription factors are known to be crucial in plants tolerance response to abiotic stresses, such as drought and salinity. ANAC019, ANAC055, and ANAC072, belong to the stress-NAC TFs, confer the Arabidopsis abiotic stress tolerance. RESULTS: Here we isolated two stress-responsive NACs, CiNAC3 and CiNAC4, from Caragana intermedia, which were induced by ABA and various abiotic stresses. Localization assays revealed that CiNAC3 and CiNAC4 localized in the nuclei, consistent with their roles as transcription factors. Histochemistry assay using Pro(CiNAC4)::GUS transgenic Arabidopsis showed that the expression of the GUS reporter was observed in many tissues of the transgenic plants, especially in the root vascular system. Overexpression of CiNAC3 and CiNAC4 reduced ABA sensitivity during seed germination, and enhanced salt tolerance of the transgenic Arabidopsis. CONCLUSIONS: We characterised CiNAC3 and CiNAC4 and found that they were induced by numerous abiotic stresses and ABA. GUS histochemical assay of CiNAC4 promoter suggested that root, flower and local damaged tissues were the strongest stained tissues. Overexpression assay revealed that CiNAC4 play essential roles not only in promoting lateral roots formation, but also in responding to salinity and ABA treatment of Arabidopsis.