ErmineJ: Tool for functional analysis of gene expression data sets

BACKGROUND: It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution (or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported. RESULTS: We introduce ErmineJ, a multiplatform user-friendly stand-alone software tool for the analysis of functionally-relevant sets of genes in the context of microarray gene expression data. ErmineJ implements multiple algorithms for gene set analysis, including over-representation and resampling-based methods that focus on gene scores or correlation of gene expression profiles. In addition to a graphical user interface, ErmineJ has a command line interface and an application programming interface that can be used to automate analyses. The graphical user interface includes tools for creating and modifying gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression data. ErmineJ comes with a complete user manual, and is open-source software licensed under the Gnu Public License. CONCLUSION: The availability of multiple analysis algorithms, together with a rich feature set and simple graphical interface, should make ErmineJ a useful addition to the biologist's informatics toolbox. ErmineJ is available from

Factors affecting the productivity of coffee in Gulmi and Arghakhanchi districts of Nepal

Coffee is one of the major potential cash crops with lucrative export value grown in mid-hills of Nepal. Nepalese coffee production has suffered long by low productivity. Research was conducted from February to May, 2019 to analyze the factors affecting the productivity of coffee in Arghakhanchi and Gulmi districts of Nepal. These two districts were, purposively selected for this study taking account of comparative advantage and past studies recommendations for coffee sector. Altogether, 100 coffee growing households 50 from each, Arghakhanchi and Gulmi, were sampled by using multistage sampling technique. A pre-tested semi-structured interview schedule was used to collect the primary information while secondary information was collected reviewing the relevant publications. Ordinary Least Square (OLS) regression model was used to determine the factors affecting the productivity of coffee. The study revealed that the number of active family members involved in coffee production (0.000), adoption of income diversification through intercropping (0.005), training (0.072) and technical assistance (0.021) had positive and significant effect on coffee productivity. Encouraging the household to have coffee production as their primary occupation, providing technical assistance on rational land utilization and intercropping and strengthening the skill and knowledge of farmers through trainings could significantly support in increasing the productivity of coffee

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Physico-Chemical Determination of Pollution in Groundwater Sources in Sangamner Tahsil, 422605, Dist. Ahmednagar, MS, India

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Study of effects of total and visceral fat on cardiovascular sympathetic functions

Background : Obesity is characterized by an excessive deposition and storage of fat in the body, which alters the cardiovascular autonomic functions. Autonomic nervous system through its Sympathetic and Parasympathetic division regulates and modulates most of the visceral functions of the body. Methods :This was a cross sectional study with the primary data that includes 200 healthy volunteer male subjects between 20 to 35 years of age, in and around Shivpuri. For all the subjects anthropometric data was collected by Karada scan and cardiovascular sympathetic functions were assessed by sphygmomanometry and electrocardiogram. Observation and results: Descriptive statistics was done by using SPSS software version 16 for windows with descriptive analysis done by ANOVA analysis test which suggested increase in sympathetic and decrease in parasympathetic activity as visceral fat% increases. Conclusion: Study concludes that with increase in visceral fat% cardiovascular morbidity and mortality increases as compared to increase in total body fat %

DESIGN AND MANUFACTURING OF LOOP WHEEL WITH DAMPER

Polluted air is one of the major environmental problems in India. Around 20% of total air pollution is from vehicles. The polluted air is very hazardous to human health and it is observed that all the metropolitans are facing severe consequences of polluted air. To reduce pollution created due to two wheelers, many countries are supporting the use of bicycles. It will not only reduce pollution but also helpful to keep human healthy. Problem associated with conventional bicycles is poor suspension and uncomfortable seating arrangement hence it is avoided to use over long distances. Authors have designed a wheel for bicycles with inbuilt suspension. CAD design of a wheel with hardware structure development is presented by authors in this paper. It is suggested to use the wheel for improvement in suspension for better ride experience

Visceral leishmaniasis in the hills of western Nepal: A transmission assessment.

In Nepal, visceral leishmaniasis (VL) has been targeted for elimination as a public health problem by 2026. Recently, increasing numbers of VL cases have been reported from districts of doubtful endemicity including hills and mountains, threatening the ongoing VL elimination program in Nepal. We conducted a multi-disciplinary, descriptive cross-sectional survey to assess the local transmission of Leishmania donovani in seven such districts situated at altitudes of up to 1,764 meters in western Nepal from March to December 2019. House-to-house surveys were performed for socio-demographic data and data on past and current VL cases. Venous blood was collected from all consenting individuals aged ≥2 years and tested with the rK39 RDT. Blood samples were also tested with direct agglutination test, and a titer of ≥1:1600 was taken as a marker of infection. A Leishmania donovani species-specific PCR (SSU-rDNA) was performed for parasite species confirmation. We also captured sand flies using CDC light traps and mouth aspirators. The house-to-house surveys documented 28 past and six new VL cases of which 82% (28/34) were without travel exposure. Overall, 4.1% (54/1320) of healthy participants tested positive for L. donovani on at least one serological or molecular test. Among asymptomatic individuals, 17% (9/54) were household contacts of past VL cases, compared to 0.5% (6/1266) among non-infected individuals. Phlebotomus argentipes, the vector of L. donovani, was found in all districts except in Bajura. L. donovani was confirmed in two asymptomatic individuals and one pool of sand flies of Phlebotomus (Adlerius) sp. We found epidemiological and entomological evidence for local transmission of L. donovani in areas previously considered as non-endemic for VL. The national VL elimination program should revise the endemicity status of these districts and extend surveillance and control activities to curb further transmission of the disease