Takshan/R1 huggingface dataset:
Remission in Depression and Associated Factors at Different Assessment Times in Primary Care in Chile.

Objective: To determine the factors associated with remission at 3, 6, 9 and 12 months among depressive adult patients in primary care [PHC] in Chile. Methods: This is a one-year naturalistic study that followed 297 patients admitted for treatment of depression in eight primary care clinics in Chile. Initially, patients were evaluated using: the International Mini-Neuropsychiatric Interview [MINI], a screening for Childhood Trauma Events [CTEs], the Life Experiences Survey and a partner violence scale. The Hamilton Depression Scale [HDRS] was used to follow the patients during the observation time. Associations between the factors studied and the primary outcome remission [HDRS ≤ 7] were assessed using a dichotomous logistic regression and a multivariate Poisson regression. The significance level was 0.05. Results: Remission [HDRS ≤ 7] ranged between 36.7% at 3 months and 53.9% at 12 months. Factors that predicted poor remission during the observation time were: CTEs [Wald X2 = 4.88, Exp B=0.94, CI 0.90-0.92, p=0.27]; psychiatric comorbidities [Wald X2 = 10.73, Exp B=0.90, CI 0.85-0.96, p=0.01]; suicidal tendencies [Wald X2 = 4.66, Exp B=0.88, CI 0.79-0.98, p=0.03] and prior treatment for depression [Wald X2 = 4.50, Exp B=0.81, CI 0.68-0.85, p=0.03]. Discussion: Almost 50% of this sample failed remission in depression at 12 months. Psychiatric comorbidities and CTEs are factors that should be considered for a poor outcome in depressed Chilean patients. These factors need more recognition and a better approach in PHC.
DSigDB: drug signatures database for gene set analysis.

UNLABELLED: We report the creation of Drug Signatures Database (DSigDB), a new gene set resource that relates drugs/compounds and their target genes, for gene set enrichment analysis (GSEA). DSigDB currently holds 22 527 gene sets, consists of 17 389 unique compounds covering 19 531 genes. We also developed an online DSigDB resource that allows users to search, view and download drugs/compounds and gene sets. DSigDB gene sets provide seamless integration to GSEA software for linking gene expressions with drugs/compounds for drug repurposing and translational research. AVAILABILITY AND IMPLEMENTATION: DSigDB is freely available for non-commercial use at http://tanlab.ucdenver.edu/DSigDB. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: aikchoon.tan@ucdenver.edu.
Circulating tumor cells, tumor-derived extracellular vesicles and plasma cytokeratins in castration-resistant prostate cancer patients.

Purpose: The presence of Circulating Tumor Cells (CTCs) in Castration-Resistant Prostate Cancer (CRPC) patients is associated with poor prognosis. In this study, we evaluated the association of clinical outcome in 129 CRPC patients with CTCs, tumor-derived Extracellular Vesicles (tdEVs) and plasma levels of total (CK18) and caspase-cleaved cytokeratin 18 (ccCK18). Experimental Design: CTCs and tdEVs were isolated with the CellSearch system and automatically enumerated. Cut-off values dichotomizing patients into favorable and unfavorable groups of overall survival were set on a retrospective data set of 84 patients and validated on a prospective data set of 45 patients. Plasma levels of CK18 and ccCK18 were assessed by ELISAs. Results: CTCs, tdEVs and both cytokeratin plasma levels were significantly increased in CRPC patients compared to healthy donors (HDs). All biomarkers except for ccCK18 were prognostic showing a decreased median overall survival for the unfavorable groups of 9.2 vs 21.1, 8.1 vs 23.0 and 10.0 vs 21.5 months respectively. In multivariable Cox regression analysis, tdEVs remained significant. Conclusions: Automated CTC and tdEV enumeration allows fast and reliable scoring eliminating inter- and intra- operator variability. tdEVs provide similar prognostic information to CTC counts.
Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health.

BACKGROUND: To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. METHODOLOGY/PRINCIPAL FINDINGS: We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. CONCLUSIONS/SIGNIFICANCE: After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems.
Mice with miR-146a deficiency develop severe gouty arthritis via dysregulation of TRAF 6, IRAK 1 and NALP3 inflammasome.

BACKGROUND: MicroRNAs (miRNAs) serve as important regulators of inflammatory and immune responses and are implicated in several immune disorders including gouty arthritis. The expression of miR-146a is upregulated in the peripheral blood mononuclear cells of patients with inter-critical gout when compared to normouricemic and hyperuricemic controls and those patients with acute gout flares. However, the role of miR-146a in the development of gout remains unknown. Here, we used miR-146a knockout (KO) mice to test miR-146a function in a monosodium urate (MSU)-induced gouty arthritis model. METHODS: The footpad or ankle joint of miR-146a KO and wild-type (WT) mice were injected with an MSU suspension to induce acute gouty arthritis. Bone marrow-derived macrophages (BMDMs) were stimulated with MSU and the gene expression of miR-146a; interleukin 1 beta (IL-1β); tumor necrosis factor-α (TNF-α); and the NACHT, LRR and PYD domains-containing protein 3 (NALP3) inflammasome was evaluated. TNF-α and IL-1β protein levels in BMDMs were assessed by fluorescence-activated cell sorting and western blot analyses. Gene and protein levels of TNF receptor-associated factor 6 (TRAF6) and IL-1 receptor-associated kinase (IRAK1), the targets of miR-146a, were also measured. RESULTS: Significantly increased paw swelling and index and ankle joint swelling were observed in miR-146a KO mice compared to WT controls after MSU treatment. MiR-146a expression in BMDMs from WT mice was dramatically upregulated at 4 h following MSU stimulation. Additionally, the expression of IL-1β, TNF-α, and NALP3 was higher in BMDMs from miR-146a KO mice after exposure to MSU crystals compared to those from WT mice. Consistent with the observed gene expression, the IL-1β and TNF-α proteins were upregulated in miR-146a KO mice. Additionally quantitative RT-PCR and western blot demonstrated that TRAF6 and IRAK1 were dramatically upregulated in BMDMs from miR-146 KO mice compared to those from WT mice. CONCLUSIONS: Collectively, these observations suggest that miR-146a provides negative feedback regulation of gouty arthritis development and lack of miR-146a enhances gouty arthritis via upregulation of TRAK6, IRAK-1, and the NALP3 inflammasome function.
Renal Protective Effects of N-Acetyl-Seryl-Aspartyl-Lysyl-Proline (Ac-SDKP) in Obese Rats on a High-Salt Diet.

BACKGROUND: Obesity is a public health problem, associated with salt sensitive hypertension, kidney inflammation, and fibrosis. N-acetyl-seryl-aspartyl-lysyl-proline (Ac-SDKP) is a tetra peptide with anti-inflammatory and anti-fibrotic properties. However, its effect on preventing kidney damage in obesity is unknown. We hypothesized that Zucker obese (ZO) rats on a high-salt (HS) diet develop renal damage, inflammation, fibrosis, and this is prevented with Ac-SDKP treatment. METHODS: Zucker lean (ZL) and ZO rats (8 weeks old) were treated with Ac-SDKP (1.6 mg/kg/day) while maintained on either a normal-salt (NS; 0.4%) or HS (4%) diet for 8 weeks. Systolic blood pressure (SBP), albuminuria, renal inflammation, and fibrosis were evaluated. RESULTS: HS diet increased macrophage infiltration in the kidneys of both ZL and ZO rats but was significantly higher in ZO rats receiving the HS diet (ZL + NS, 13.9 ± 1.3 vs. ZL + HS, 19.14 ± 1.5 and ZO + NS, 25.5 ± 1.4 vs. ZO + HS, 87.8 ± 10.8 cells/mm2; P < 0.05). Ac-SDKP prevented macrophage infiltration in ZO rats (ZO + HS + Ac-SDKP, 32.18 ± 2.4 cells/mm2; P < 0.05). Similarly, glomerulosclerosis, cortical, and medullary interstitial fibrosis were increased in ZO rats fed the HS diet, and Ac-SDKP attenuated these alterations (P < 0.05). SBP was increased in ZO rats fed the HS diet (ZO + NS, 121.3 ± 8.9 vs. ZO + HS, 164 ± 6.9 mm Hg; P < 0.05), and it was significantly decreased with Ac-SDKP treatment (ZO + HS + Ac-SDKP, 144.05 ± 14.1 mm Hg; P = 0.004). Albuminuria was higher in ZO rats than in ZL rats; however, neither HS nor Ac-SDKP treatment affected it. CONCLUSIONS: Ac-SDKP treatment in ZO rats fed a HS diet prevented renal damage by reducing inflammation, fibrosis, and SBP.
Gout, Hyperuricemia, and Crystal-Associated Disease Network Consensus Statement Regarding Labels and Definitions for Disease Elements in Gout.

OBJECTIVE: The language currently used to describe gout lacks standardization. The aim of this project was to develop a consensus statement on the labels and definitions used to describe the basic disease elements of gout. METHODS: Experts in gout (n = 130) were invited to participate in a Delphi exercise and face-to-face consensus meeting to reach consensus on the labeling and definitions for the basic disease elements of gout. Disease elements and labels in current use were derived from a content analysis of the contemporary medical literature, and the results of this analysis were used for item selection in the Delphi exercise and face-to-face consensus meeting. RESULTS: There were 51 respondents to the Delphi exercise and 30 attendees at the face-to-face meeting. Consensus agreement (≥80%) was achieved for the labels of 8 disease elements through the Delphi exercise; the remaining 3 labels reached consensus agreement through the face-to-face consensus meeting. The agreed labels were monosodium urate crystals, urate, hyperuric(a)emia, tophus, subcutaneous tophus, gout flare, intercritical gout, chronic gouty arthritis, imaging evidence of monosodium urate crystal deposition, gouty bone erosion, and podagra. Participants at the face-to-face meeting achieved consensus agreement for the definitions of all 11 elements and a recommendation that the label "chronic gout" should not be used. CONCLUSION: Consensus agreement was achieved for the labels and definitions of 11 elements representing the fundamental components of gout etiology, pathophysiology, and clinical presentation. The Gout, Hyperuricemia, and Crystal-Associated Disease Network recommends the use of these labels when describing the basic disease elements of gout.
Connecting tubule glomerular feedback mediates tubuloglomerular feedback resetting post-unilateral nephrectomy.

Unilaterally nephrectomized rats (UNx) have higher glomerular capillary pressure (PGC) that can cause significant glomerular injury in the remnant kidney. PGC is controlled by the ratio of afferent (Af-Art) and efferent arteriole resistance. Af-Art resistance in turn is regulated by two intrinsic feedback mechanisms: 1) Tubuloglomerular feedback (TGF) that causes Af-Art constriction in response to increased NaCl in the macula densa and 2) connecting tubule glomerular feedback (CTGF) that causes Af-Art dilatation in response to an increase in NaCl transport in the connecting tubule via the epithelial sodium channel (ENaC). Resetting of TGF post-UNx can allow systemic pressure to be transmitted to the glomerulus and cause renal damage, but the mechanism behind this resetting is unclear. Since CTGF is an Af-Art dilatory mechanism, we hypothesized that CTGF is increased after UNx, and contributes to TGF resetting. To test this hypothesis, we performed UNx in Sprague Dawley (SD) rats. Twenty-four hours after surgery, we performed micropuncture of individual nephrons and measured stop-flow pressure (PSF). PSF is an indirect measurement of PGC. Maximal TGF response at 40nl/min was 8.9 ± 1.24 mmHg in sham-UNx rats and 1.39 ± 1.02 mmHg in UNx rats indicating TGF resetting after UNx. When CTGF was inhibited with the ENaC blocker Benzamil (1μM/L), the TGF response was 12.29 ± 2.01 mmHg in UNx rats and 13.03 ± 1.25 mmHg in sham-UNx rats, indicating restoration of the TGF responses in UNx. We conclude that enhanced CTGF contributes to TGF resetting after UNx.
Disruptive behavior scale for adolescents (DISBA): development and psychometric properties.

Background: Growing evidence indicates that if disruptive behavior is left unidentified and untreated, a significant proportion of these problems will persist and may develop into problems linked with delinquency, substance abuse, and violence. Research is needed to develop valid and reliable measures of disruptive behavior to assist recognition and impact of treatments on disruptive behavior. The aim of this study was to develop and evaluate the psychometric properties of a scale for disruptive behavior in adolescents. Methods: Six hundred high school students (50% girls), ages ranged 15-18 years old, selected through multi stage random sampling. Psychometrics of the disruptive behavior scale for adolescents (DISBA) (Persian version) was assessed through content validity, explanatory factor analysis (EFA) using Varimax rotation and confirmatory factor analysis (CFA). The reliability of this scale was assessed via internal consistency and test-retest reliability. Results: EFA revealed four factors accounting for 59% of observed variance. The final 29-item scale contained four factors: (1) aggressive school behavior, (2) classroom defiant behavior, (3) unimportance of school, and (4) defiance to school authorities. Furthermore, CFA produced a sufficient Goodness of Fit Index > 0.90. Test-retest and internal consistency reliabilities were acceptable at 0.85 and 0.89, respectively. Conclusions: The findings from this study suggest that the Iranian version of DISBA questionnaire has content validity. Further studies are needed to evaluate stronger psychometric properties for DISBA.
Investigations on the interplays between Schistosoma mansoni, praziquantel and the gut microbiome.

BACKGROUND: Schistosomiasis is a neglected tropical disease burdening millions of people. One drug, praziquantel, is currently used for treatment and control. Clinically relevant drug resistance has not yet been described, but there is considerable heterogeneity in treatment outcomes, ranging from cure to only moderate egg reduction rates. The objectives of this study are to investigate potential worm-induced dysbacteriosis of the gut microbiota and to assess whether a specific microbiome profile could influence praziquantel response. METHODS: Using V3 and V4 regions of 16S rRNA genes, we screened the gut microbiota of 34 Schistosoma mansoni infected and uninfected children from Côte d'Ivoire. From each infected child one pre-treatment, one 24-hour and one 21-day follow-up sample after administering 60 mg/kg praziquantel or placebo, were collected. RESULTS: Overall taxonomic profiling and diversity indicators were found to be close to a "healthy" gut structure in all children. Slight overall compositional changes were observed between S. mansoni-infected and non-infected children. Praziquantel treatment was not linked to a major shift in the gut taxonomic profiles, thus reinforcing the good safety profile of the drug by ruling out off-targets effects on the gut microbes.16S rRNA gene of the Fusobacteriales order was significantly more abundant in cured individuals, both at baseline and 24 hours post-treatment. A real-time qPCR confirmed the over-abundance of Fusobacterium spp. in cured children. Fusobacterium spp. abundance could also be correlated with treatment induced S. mansoni egg-reduction. CONCLUSIONS: Our study suggests that neither a S. mansoni infection nor praziquantel administration triggers a significant effect on the microbial composition and that a higher abundance of Fusobacterium spp., before treatment, is associated with higher efficacy of praziquantel in the treatment of S. mansoni infections. TRIAL REGISTRATION: International Standard Randomised Controlled Trial, number ISRCTN15280205 .
Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer.

BACKGROUND: Recent studies have shown that the crosstalk between microRNA (miRNA) sponges plays an important role in human cancers. However, the co-regulation roles of miRNA sponges in protein-protein interactions (PPIs) are still unknown. RESULTS: In this study, we propose a multi-step method called miRSCoPPI to infer miRNA sponge co-regulation of PPIs. We focus on investigating breast cancer (BRCA) related miRNA sponge co-regulation, by integrating heterogeneous data, including miRNA, long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression data, experimentally validated miRNA-target interactions, PPIs and lncRNA-target interactions, and the list of breast cancer genes. We find that the inferred BRCA-related miRSCoPPI network is highly connected and scale free. The top 10% hub genes in the BRCA-related miRSCoPPI network have potential biological implications in breast cancer. By utilizing a graph clustering method, we discover 17 BRCA-related miRSCoPPI modules. Through pathway enrichment analysis of the modules, we find that several modules are significantly enriched in pathways associated with breast cancer. Moreover, 10 modules have good performance in classifying breast tumor and normal samples, and can act as module signatures for prognostication. By using putative computationally predicted miRNA-target interactions, we have consistent results with those obtained using experimentally validated miRNA-target interactions, indicating that miRSCoPPI is robust in inferring miRNA sponge co-regulation of PPIs in human breast cancer. CONCLUSIONS: Taken together, the results demonstrate that miRSCoPPI is a promising tool for inferring BRCA-related miRNA sponge co-regulation of PPIs and it can help with the understanding of the co-regulation roles of miRNA sponges on the PPIs.
Identifying miRNA sponge modules using biclustering and regulatory scores.

BACKGROUND: MicroRNA (miRNA) sponges with multiple tandem miRNA binding sequences can sequester miRNAs from their endogenous target mRNAs. Therefore, miRNA sponge acting as a decoy is extremely important for long-term loss-of-function studies both in vivo and in silico. Recently, a growing number of in silico methods have been used as an effective technique to generate hypotheses for in vivo methods for studying the biological functions and regulatory mechanisms of miRNA sponges. However, most existing in silico methods only focus on studying miRNA sponge interactions or networks in cancer, the module-level properties of miRNA sponges in cancer is still largely unknown. RESULTS: We propose a novel in silico method, called miRSM (miRNA Sponge Module) to infer miRNA sponge modules in breast cancer. We apply miRSM to the breast invasive carcinoma (BRCA) dataset provided by The Cancer Genome Altas (TCGA), and make functional validation of the computational results. We discover that most miRNA sponge interactions are module-conserved across two modules, and a minority of miRNA sponge interactions are module-specific, existing only in a single module. Through functional annotation and differential expression analysis, we also find that the modules discovered using miRSM are functional miRNA sponge modules associated with BRCA. Moreover, the module-specific miRNA sponge interactions among miRNA sponge modules may be involved in the progression and development of BRCA. Our experimental results show that miRSM is comparable to the benchmark methods in recovering experimentally confirmed miRNA sponge interactions, and miRSM outperforms the benchmark methods in identifying interactions that are related to breast cancer. CONCLUSIONS: Altogether, the functional validation results demonstrate that miRSM is a promising method to identify miRNA sponge modules and interactions, and may provide new insights for understanding the roles of miRNA sponges in cancer progression and development.
Computational methods for identifying miRNA sponge interactions.

Recent findings show that coding genes are not the only targets that miRNAs interact with. In fact, there is a pool of different RNAs competing with each other to attract miRNAs for interactions, thus acting as competing endogenous RNAs (ceRNAs). The ceRNAs indirectly regulate each other via the titration mechanism, i.e. the increasing concentration of a ceRNA will decrease the number of miRNAs that are available for interacting with other targets. The cross-talks between ceRNAs, i.e. their interactions mediated by miRNAs, have been identified as the drivers in many disease conditions, including cancers. In recent years, some computational methods have emerged for identifying ceRNA-ceRNA interactions. However, there remain great challenges and opportunities for developing computational methods to provide new insights into ceRNA regulatory mechanisms. In this paper, we review the publically available databases of ceRNA-ceRNA interactions and the computational methods for identifying ceRNA-ceRNA interactions (also known as miRNA sponge interactions). We also conduct a comparison study of the methods with a breast cancer dataset. Our aim is to provide a current snapshot of the advances of the computational methods in identifying miRNA sponge interactions and to discuss the remaining challenges.