Takshan/R1 huggingface dataset:
Bacillus spp. from rainforest soil promote plant growth under limited nitrogen conditions.

AIMS: The aim of this study was to evaluate effects of PGPR (plant growth-promoting rhizobacteria) isolated from rainforest soil on different plants under limited nitrogen conditions. METHODS AND RESULTS: Bacterial isolates from a Peruvian rainforest soil were screened for plant growth-promoting effects on Arabidopsis (Col-0). Four selected isolates including one Bacillus subtilis, two B. atrophaeus and one B. pumilus significantly promoted growth of Zea mays L. and Solanum lycopersicum under greenhouse conditions. Moreover, the PGPRs significantly promoted growth of S. lycopersicum in both low and nitrogen-amended soil conditions. These PGPR strains were further studied to obtain insights into possible mechanisms of plant growth promotion. Volatile chemicals from those isolates promoted Arabidopsis growth, and the expression of genes related to IAA production was induced in the Arabidopsis plants treated with PGPRs. Further, selected PGPR strains triggered induced systemic resistance (ISR) against Pseudomonas syringae pv tomato DC3000 in Arabidopsis. CONCLUSIONS: PGPR strains isolated from the rainforest soil promoted the plant growth of Arabidopsis, corn and tomato. SIGNIFICANCE AND IMPACT OF THE STUDY: New PGPR that have wider adaptability to different crops, soils and environmental conditions are needed to decrease our reliance on agricultural amendments derived from fossil-based fuels. The PGPRs isolated from a nonagricultural site constitute new plant growth-promoting strains that could be developed for agricultural uses.
Cancer dormancy and criticality from a game theory perspective.

Background: The physics of cancer dormancy, the time between initial cancer treatment and re-emergence after a protracted period, is a puzzle. Cancer cells interact with host cells via complex, non-linear population dynamics, which can lead to very non-intuitive but perhaps deterministic and understandable progression dynamics of cancer and dormancy. Results: We explore here the dynamics of host-cancer cell populations in the presence of (1) payoffs gradients and (2) perturbations due to cell migration. Conclusions: We determine to what extent the time-dependence of the populations can be quantitively understood in spite of the underlying complexity of the individual agents and model the phenomena of dormancy.
Frequency of BRCA1 and BRCA2 causative founder variants in ovarian cancer patients in South-East Poland.

Background: Causative variants in BRCA1 and BRCA2 are well-established risk factors for breast and ovarian cancer. In Poland, the causative founder variants in the BRCA1 are responsible for a significant proportion of ovarian cancer cases, however, regional differences in the frequencies of various mutations may exist. The spectrum and frequency of BRCA1/2 mutations between ovarian cancer patients have not yet been studied in the region of South-East Poland. Methods: We examined 158 consecutive unselected cases of ovarian cancer patients from the region of Podkarpacie. We studied 13 Polish causative founder variants in BRCA1 (c.5266dupC, c.4035delA, c.5251C > T, c.181 T > G, c.676delT, c.68_69delAG, c.3700_3704delGTAAA, c.1687C > T, c.3756_3759delGTCT) and in BRCA2 (c.658_659delGT, c.7910_7914delCCTTT, c.3847_3848delGT, c.5946delT). Results: A BRCA1 causative founder variants were detected in 10 of the 158 (6.3%) ovarian cancer cases. BRCA2 causative founder variants were not observed. The c.5266dupC mutation was detected in 6 patients, c.181 T > G mutation in 3 patients and the c.676delT mutation in 1 patient. The median age of diagnosis of the 10 hereditary ovarian cancers was 55.5 years of age. Conclusions: The frequency of 13 causative founder variants in Podkarpacie was lower than in other regions of Poland. Testing of three BRCA1 mutations (c.5266dupC, c.181 T > G, c.676delT) should be considered a sensitive test panel.
Preliminary assessment of the computer-based Taenia solium educational program 'The Vicious Worm' on knowledge uptake in primary school students in rural areas in eastern Zambia.

OBJECTIVE: The zoonotic helminth Taenia solium is endemic in Zambia, causing human (taeniasis and (neuro)cysticercosis) and pig (porcine cysticercosis) diseases with high health, social and economic burdens. We aimed to evaluate the impact of a health educational program intended to lead to powerful and cumulative improvements in knowledge, attitudes and practices that decrease parasite transmission and disease occurrence. METHODS: Half-day health education workshops were conducted in three primary schools in the highly endemic Eastern Province of Zambia, using the computer-based T. solium educational program 'The Vicious Worm'. Questionnaires were administered before and after the educational component to determine the program's impact on knowledge uptake in primary school students. RESULTS: In total, 99 students participated: 38 males and 61 females, with a median age of 14 years (range 10-18 years). Baseline general knowledge of T. solium, including awareness of the different human and pig disease states, and disease diagnosis, treatment and prevention, was quite high (average score 62%) and consistent across all three study areas. Participants' knowledge had significantly increased after the educational component, particularly regarding parasite transmission and disease prevention. CONCLUSION: Preliminary assessment of 'The Vicious Worm' indicates it is an effective tool for the short-term T. solium education of primary school students in Zambia. Follow-up studies are planned to assess the longer term impact of the program on knowledge uptake in the study neighbourhoods. Inclusion of tailored 'The Vicious Worm' educational workshops should be considered in integrated cysticercosis control programs in endemic areas of sub-Saharan Africa.
Family Physician-Led Group Visits for Lifestyle Modification in Women with Weight Problems: A Pilot Intervention and Follow-Up Study.

OBJECTIVE: Lifestyle modification requires extensive information sharing and counseling. However, one-on-one primary care consultations are lacking to cover all necessary components due to time constraints. This preliminary study aims to investigate the feasibility and effects of lifestyle-changing intervention by family physician-led group visits (GVs) on weight management in overweight and obese women. METHODS: 60 volunteers fulfilling the inclusion criteria were enrolled. Baseline and 6th month assessments consisted of anthropometric measurements, SF-36 Health Survey, blood variables, exercise test, and resting metabolic rate. Weight maintenance was controlled at the 12th month. RESULTS: Although weight loss among participants varied, the mean body weights were significantly decreased by 8.2% in full-attenders (n = 30). A significant increase in HDL-cholesterol and decreases in heart rate and blood pressure were found. SF-36 summary scales were significantly improved. Weight change was moderately correlated with exercise duration, compliance to diet, and baseline mental component score. It was determined that 62.5% of the participants either lost or maintained body weight at the 12th month. CONCLUSION: Significant weight loss and quality of life improvement was achieved in this pilot study. GVs may be a promising alternative to primary care consultations for obesity management; however, the high dropout level and diverse outcomes need further assessment.
Different Effects of Oral Contraceptive and Dydrogesterone Treatment on Oxidative Stress Levels in Premenopausal Women.

Background: The aim of the study was to observe the changes in blood oxidative stress levels by oral contraceptive (OC) and/or dydrogesterone (DG) treatment. Methods: A retrospective cohort of 27 premenopausal women with primary dysmenorrhea consisted of the OC treatment group (N = 17) and the DG treatment group (N = 10) by choice of the initial treatment. The OC group included two subgroups: patients with continuous OC treatment (treated for at least 15 months, N = 10) and patients with discontinuous OC treatment (switched to DG treatment after approximately 6 months of initial OC treatment: N = 7). The DG group had 15 months of continuous DG treatment. Blood parameters, including diacron-reactive oxygen metabolites (d-ROMs: an oxidative stress marker), were measured. Results: The d-ROMs level was elevated in the OC group 3 months after initial treatment (mean: from 321 (at baseline) to 512 Carratelli Units (Carr U); P < 0.01), while such changes were not observed in the DG group. The d-ROMs level was reduced in the discontinuous OC subgroup 15 months after initial treatment (from 508 (3 months after initial treatment) to 372 Carr U; P < 0.01), while such changes were not observed in the continuous OC subgroup. The DG group displayed unchanged the d-ROMs level. Conclusion: Replacing OC with DG can attenuate oxidative stress as elevated by OC, thereby alleviating the possible vascular risks with OC treatment.
Pathogenesis and mechanisms of antibody-mediated hemolysis.

BACKGROUND: The clinical consequences of antibodies to red blood cells (RBCs) have been studied for a century. Most clinically relevant antibodies can be detected by sensitive in vitro assays. Several mechanisms of antibody-mediated hemolysis are well understood. Such hemolysis after transfusion is reliably avoided in a donor-recipient pair, if one individual is negative for the cognate antigen to which the other has the antibody. STUDY DESIGN AND RESULTS: Mechanisms of antibody-mediated hemolysis were reviewed based on a presentation at the Strategies to Address Hemolytic Complications of Immune Globulin Infusions Workshop addressing intravenous immunoglobulin (IVIG) and ABO antibodies. The presented topics included the rates of intravascular and extravascular hemolysis; immunoglobulin (Ig)M and IgG isoagglutinins; auto- and alloantibodies; antibody specificity; A, B, A,B, and A1 antigens; A1 versus A2 phenotypes; monocytes-macrophages, other immune cells, and complement; monocyte monolayer assay; antibody-dependent cell-mediated cytotoxicity; and transfusion reactions due to ABO and other antibodies. CONCLUSION: Several clinically relevant questions remained unresolved, and diagnostic tools were lacking to routinely and reliably predict the clinical consequences of RBC antibodies. Most hemolytic transfusion reactions associated with IVIG were due to ABO antibodies. Reducing the titers of such antibodies in IVIG may lower the frequency of this kind of adverse event. The only way to stop these events is to have no anti-A or anti-B in the IVIG products.
Identification of miRNA-mRNA regulatory modules by exploring collective group relationships.

BACKGROUND: microRNAs (miRNAs) play an essential role in the post-transcriptional gene regulation in plants and animals. They regulate a wide range of biological processes by targeting messenger RNAs (mRNAs). Evidence suggests that miRNAs and mRNAs interact collectively in gene regulatory networks. The collective relationships between groups of miRNAs and groups of mRNAs may be more readily interpreted than those between individual miRNAs and mRNAs, and thus are useful for gaining insight into gene regulation and cell functions. Several computational approaches have been developed to discover miRNA-mRNA regulatory modules (MMRMs) with a common aim to elucidate miRNA-mRNA regulatory relationships. However, most existing methods do not consider the collective relationships between a group of miRNAs and the group of targeted mRNAs in the process of discovering MMRMs. Our aim is to develop a framework to discover MMRMs and reveal miRNA-mRNA regulatory relationships from the heterogeneous expression data based on the collective relationships. RESULTS: We propose DIscovering COllective group RElationships (DICORE), an effective computational framework for revealing miRNA-mRNA regulatory relationships. We utilize the notation of collective group relationships to build the computational framework. The method computes the collaboration scores of the miRNAs and mRNAs on the basis of their interactions with mRNAs and miRNAs, respectively. Then it determines the groups of miRNAs and groups of mRNAs separately based on their respective collaboration scores. Next, it calculates the strength of the collective relationship between each pair of miRNA group and mRNA group using canonical correlation analysis, and the group pairs with significant canonical correlations are considered as the MMRMs. We applied this method to three gene expression datasets, and validated the computational discoveries. CONCLUSIONS: Analysis of the results demonstrates that a large portion of the regulatory relationships discovered by DICORE is consistent with the experimentally confirmed databases. Furthermore, it is observed that the top mRNAs that are regulated by the miRNAs in the identified MMRMs are highly relevant to the biological conditions of the given datasets. It is also shown that the MMRMs identified by DICORE are more biologically significant and functionally enriched.
Forced air warming during sedation in the cardiac catheterisation laboratory: a randomised controlled trial.

OBJECTIVE: Forced air warming (FAW) during general anaesthesia is a safe and effective intervention used to reduce hypothermia. The objective of this study was to determine if FAW reduces hypothermia when used for procedures performed with sedation in the cardiac catheterisation laboratory. METHODS: A parallel-group randomised controlled trial was conducted. Adults receiving sedation in a cardiac catheterisation laboratory at two sites were randomised to receive FAW or usual care, which involved passive warming with heated cotton blankets. Hypothermia, defined as a temperature less than 36°C measured with a sublingual digital thermometer after procedures, was the primary outcome. Other outcomes were postprocedure temperature, shivering, thermal comfort and major complications. RESULTS: A total of 140 participants were randomised. Fewer participants who received FAW were hypothermic (39/70, 56% vs 48/69, 70%, difference 14%; adjusted RR 0.75, 95% CI=0.60 to 0.94), and body temperature was 0.3°C higher (95% CI=0.1 to 0.5, p=0.004). FAW increased thermal comfort (63/70, 90% vs51/69, 74% difference 16%, RR 1.21, 95% CI=1.04 to 1.42). The incidence of shivering was similar (3/69, 4% vs 0/71 0%, difference 4%, 95% CI=-1.1 to 9.8). One patient in the control group required reintervention for bleeding. No other major complications occurred. CONCLUSION: FAW reduced hypothermia and improved thermal comfort. The difference in temperature between groups was modest and less than that observed in previous studies where use of FAW decreased risk of surgical complications. Therefore, it should not be considered clinically significant. TRIAL REGISTRATION NUMBER: ACTRN12616000013460.
Mining heterogeneous causal effects for personalized cancer treatment.

Motivation: Cancer is not a single disease and involves different subtypes characterized by different sets of molecules. Patients with different subtypes of cancer often react heterogeneously towards the same treatment. Currently, clinical diagnoses rather than molecular profiles are used to determine the most suitable treatment. A molecular level approach will allow a more precise and informed way for making treatment decisions, leading to a better survival chance and less suffering of patients. Although many computational methods have been proposed to identify cancer subtypes at molecular level, to the best of our knowledge none of them are designed to discover subtypes with heterogeneous treatment responses. Results: In this article we propose the Survival Causal Tree (SCT) method. SCT is designed to discover patient subgroups with heterogeneous treatment effects from censored observational data. Results on TCGA breast invasive carcinoma and glioma datasets have shown that for each subtype identified by SCT, the patients treated with radiotherapy exhibit significantly different relapse free survival pattern when compared to patients without the treatment. With the capability to identify cancer subtypes with heterogeneous treatment responses, SCT is useful in helping to choose the most suitable treatment for individual patients. Availability and Implementation: Data and code are available at https://github.com/WeijiaZhang24/SurvivalCausalTree . Contact: weijia.zhang@mymail.uinsa.edu.au. Supplementary information: Supplementary data are available at Bioinformatics online.
Use of intervention mapping to adapt a health behavior change intervention for endometrial cancer survivors: the shape-up following cancer treatment program.

BACKGROUND: About 80% of endometrial cancer survivors (ECS) are overweight or obese and have sedentary behaviors. Lifestyle behavior interventions are promising for improving dietary and physical activity behaviors, but the constructs associated with their effectiveness are often inadequately reported. The aim of this study was to systematically adapt an evidence-based behavior change program to improve healthy lifestyle behaviors in ECS. METHODS: Following a review of the literature, focus groups and interviews were conducted with ECS (n = 16). An intervention mapping protocol was used for the program adaptation, which consisted of six steps: a needs assessment, formulation of matrices of change objectives, selection of theoretical methods and practical applications, program production, adoption and implementation planning, and evaluation planning. Social Cognitive Theory and Control Theory guided the adaptation of the intervention. RESULTS: The process consisted of eight 90-min group sessions focusing on shaping outcome expectations, knowledge, self-efficacy, and goals about healthy eating and physical activity. The adapted performance objectives included establishment of regular eating, balanced diet, and portion sizes, reduction in sedentary behaviors, increase in lifestyle and organized activities, formulation of a discrepancy-reducing feedback loop for all above behaviors, and trigger management. Information on managing fatigue and bowel issues unique to ECS were added. CONCLUSIONS: Systematic intervention mapping provided a framework to design a cancer survivor-centered lifestyle intervention. ECS welcomed the intervention and provided essential feedback for its adaptation. The program has been evaluated through a randomized controlled trial.
The effect of an eye health promotion program on the health protective behaviors of primary school students.

INTRODUCTION: Undiagnosed and uncorrected refractive errors in childhood can negatively affect the development of vision and cause students to have low academic success and even quit school before graduation. This study aims to determine the effects of an eye health promotion program on the health protective behaviors of primary school students. MATERIALS AND METHODS: This experimental study using a pretest-posttest design with a control group was conducted in three public primary schools in Aydın, a city in the Western Anatolia Region of Turkey, between April and November 2014. The eye health promotion program was provided by the researchers to the experimental Group 2 days in 4 weeks. The data were analyzed using the t-test, Chi-square analysis, the Mann-Whitney U-test, the Wilcoxon signed-rank test, and the McNemar test. RESULTS: The average age of the students was identified as 9.0 ± 3.64 years. The students wearing glasses all in the experimental group and 53.3% in the control group were found to always wear their glasses after the education program was completed (P < 0.05). These students, 97.9% in the experimental group and 58.1% in the control group underwent eye examinations from an ophthalmologist (P < 0.05). The eye health protective behaviors of the experimental group were found to have positively changed in the final follow-up, compared to the control group (P < 0.05). CONCLUSION: The eye health promotion program was found to be effective in improving eye health protective behaviors within the experimental group.
A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip.

BACKGROUND: DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has been accepted as one of the most efficient technologies. However, challenges exist in analysis of DNA methylation data generated by this technology due to widespread biases. RESULTS: Here we proposed a generalized framework for evaluating data analysis methods for Illumina 450K array. This framework considers the following steps towards a successful analysis: importing data, quality control, within-array normalization, correcting type bias, detecting differentially methylated probes or regions and biological interpretation. CONCLUSIONS: We evaluated five methods using three real datasets, and proposed outperform methods for the Illumina 450K array data analysis. Minfi and methylumi are optimal choice when analyzing small dataset. BMIQ and RCP are proper to correcting type bias and the normalized result of them can be used to discover DMPs. R package missMethyl is suitable for GO term enrichment analysis and biological interpretation.
PhenoDis: a comprehensive database for phenotypic characterization of rare cardiac diseases.

BACKGROUND: Thoroughly annotated data resources are a key requirement in phenotype dependent analysis and diagnosis of diseases in the area of precision medicine. Recent work has shown that curation and systematic annotation of human phenome data can significantly improve the quality and selectivity for the interpretation of inherited diseases. We have therefore developed PhenoDis, a comprehensive, manually annotated database providing symptomatic, genetic and imprinting information about rare cardiac diseases. RESULTS: PhenoDis includes 214 rare cardiac diseases from Orphanet and 94 more from OMIM. For phenotypic characterization of the diseases, we performed manual annotation of diseases with articles from the biomedical literature. Detailed description of disease symptoms required the use of 2247 different terms from the Human Phenotype Ontology (HPO). Diseases listed in PhenoDis frequently cover a broad spectrum of symptoms with 28% from the branch of 'cardiovascular abnormality' and others from areas such as neurological (11.5%) and metabolism (6%). We collected extensive information on the frequency of symptoms in respective diseases as well as on disease-associated genes and imprinting data. The analysis of the abundance of symptoms in patient studies revealed that most of the annotated symptoms (71%) are found in less than half of the patients of a particular disease. Comprehensive and systematic characterization of symptoms including their frequency is a pivotal prerequisite for computer based prediction of diseases and disease causing genetic variants. To this end, PhenoDis provides in-depth annotation for a complete group of rare diseases, including information on pathogenic and likely pathogenic genetic variants for 206 diseases as listed in ClinVar. We integrated all results in an online database ( http://mips.helmholtz-muenchen.de/phenodis/ ) with multiple search options and provide the complete dataset for download. CONCLUSION: PhenoDis provides a comprehensive set of manually annotated rare cardiac diseases that enables computational approaches for disease prediction via decision support systems and phenotype-driven strategies for the identification of disease causing genes.