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Cells are the singular building blocks of life, and a comprehensive understanding of morphology, among other properties, is crucial to the assessment of underlying heterogeneity. We developed Computational Sorting and Mapping of Single Cells (COSMOS), a platform based on Artificial Intelligence (AI) and microfluidics to characterize and sort single cells based on real-time deep learning interpretation of high-resolution brightfield images. Supervised deep learning models were applied to characterize and sort cell lines and dissociated primary tissue based on high-dimensional embedding vectors of morphology without the need for biomarker labels and stains/dyes. We demonstrate COSMOS capabilities with multiple human cell lines and tissue samples. These early results suggest that our neural networks embedding space can capture and recapitulate deep visual characteristics and can be used to efficiently purify unlabeled viable cells with desired morphological traits. Our approach resolves a technical gap in the ability to perform real-time deep learning assessment and sorting of cells based on high-resolution brightfield images., (© 2023. Springer Nature Limited.)

Nipah virus (NiV) is a zoonotic, single-stranded RNA virus from the family Paramyxoviridae, genus Henipavirus. NiV is a biosafety-level-4 pathogen that is mostly spread by Pteropus species, which serve as its natural reservoir host. NiV is one of the major public health challenges in South and South East Asia. However, few molecular studies have been conducted to characterise NiV in a specific region. The main objective of this review is to understand the epidemiology, pathogenesis, molecular surveillance, transmission dynamics, genetic diversity, reservoir host, clinical characteristics, and phylogenetics of NiV. South and South East Asian nations have experienced NiV outbreaks. Phylogenetic analysis confirmed that two primary clades of NiV are in circulation. In humans, NiV causes severe respiratory illness and/or deadly encephalitis. NiV is mainly diagnosed by ELISA along with PCR. Therefore, we recommend that the governments of the region support the One Health approach to reducing the risk of zoonotic disease transmission in their respective countries., (© 2023. Japanese Society of Tropical Medicine.)

Limited evidence is available concerning the household-level costs of prevailing diseases and the potential cost of climate adaptation in Nepal. This study estimates these costs and assesses the relationships between prevalent diseases and climate adaptation at the household level using survey data from 420 households. An ingredients-based approach was used to estimate the cost of health and adaptation, and a Probit regression model was used to analyze the relationship between prevalent diseases and climate adaptation costs. Household direct curative costs are the highest among health cost components. Two-thirds of total health costs are direct costs for households. On average, 15.90% of household income is used for direct cost of health care. The climate hazard cost among afflicted households is estimated to be high. In addition, diseases like malaria, typhoid and jaundice, their costs, climate awareness program, droughts, family size and loss of per capita income are more likely to raise the cost of climate adaptation. The occurrence of gastritis, prevalence of diarrhea and cold waves are less likely to affect the cost. Policymakers should implement health financing schemes and adaptation strategies to prevent the loss of human health in western Nepal., Competing Interests: The authors declare no conflict of interest., (© 2020 The Authors. Published by Elsevier Ltd.)

Background: Governments have committed to eliminate malaria. But a decline in government investment in malaria interventions, particularly in developing countries such as Nepal, reveals a limited emphasis on malaria elimination that may be due to lack of strong evidence on benefits of the investment. This paper empirically analyses curative and preventive costs and benefits of Nepal's malaria elimination program from the perspectives of both service providers in the public sector and people who are at risk., Methods: Cost benefit analysis of both curative and preventive interventions for malaria elimination was conducted using case and non-case household survey data. Secondary data were obtained from government sources. Ingredient approach and step-down methods were used to estimate costs of malaria elimination interventions, and willingness to pay (WTP) method and case averted approach to estimate benefits., Results: Curative intervention of malaria elimination program is economically viable in Nepal with a net present value (NPV) of USD 23 million, benefit cost ratio (BCR) of 1.58 and internal rate of return of 63%. Malaria preventive intervention is highly beneficial with NPV of USD 435 million and BCR of 2.13. An annual investment of USD 36.59 million is required to continue the current pattern of malaria reduction that can generate societal benefits of USD 92.81 million. From this investment, the government can save USD 132 million by the end of 2025. The maximum WTP of case households for the intervention is USD 57 per household which is 63% higher than that of non-case households., Conclusion: Malaria elimination program in Nepal is economically viable and investment worthy. As the preventive intervention generates much higher net benefits than the curative intervention, the government should emphasize on preventive intervention while continuing the curative interventions., (© 2020 Published by Elsevier Ltd.)

Background: Asthma is widely prevalent in Nepal, but the causes are not well known aside from some general associations with ambient air pollution and microbial exposures. Information on the wide-ranging determinants of asthma prevalence among the population at risk can help policy makers to reduce risk., Objective: The present study is a preliminary investigation of the environmental, socioeconomic and behavioral determinants of asthma prevalence in western Nepal., Methods: A survey was conducted among 420 randomly selected households in western Nepal. A cross-sectional analytical study design was employed with the primary data using econometric tools of probit and logistic regression., Results: Environmental variables such as extreme cold winter, deteriorating river water quality and air pollution were associated with an increase in asthma prevalence. However, individual or household characteristics such as advancing age of household head, use of pesticides in the home for the control of pests, piped drinking water with old pipes and lack of participation in awareness programs were associated with an increase in asthma prevalence., Discussion: Among environmental factors, decreasing river water quality, increasing air pollution, and extremely cold winters are more likely to contribute to asthma prevalence. In light of the effects of environmental factors on the prevalence of asthma in Nepal, the high public and private costs of asthma could further impoverish the rural poor., Conclusions: Environmental health policy makers should design adaptation strategies along with additional community programs addressing asthma-instigating factors. Programs to reduce environmental pollution can reduce morbidity due to asthma., Participant Consent: Obtained., Ethics Approval: This study was approved by the Ethical Committee of the Nepal Health Research Council., Competing Interests: The authors declare no competing financial interests., (© Pure Earth 2020.)

Wetlands support livelihoods of millions of people in developing countries. However, wetland land cover change, as a result of growing population and subsequent anthropogenic activities, has been evident at a global scale, and ongoing micro-climate alteration has further deteriorating its ecological condition. Nepal is equally vulnerable to wetland changes that can have direct effects on the sustenance of local wetland-dependent people. This study thus attempts to look at how wetland areas of Nepal are undergoing changes, taking a case of Ghodaghodi Lake Complex (GLC). Remote sensing technique, climate, and population data were used in the analysis aided by focus group discussions and key informant interviews. Results showed that total population of the study area has been increased drastically in recent decades. Landsat image analysis for 25 years (1989-2016) depicts changes in the GLC in its land cover, with maximum expansion observed in settlement followed by river and banks, whereas maximum reduction was observed in forests, followed by areas of agricultural land and lake. Similarly, diurnal temperature is increasing while total annual rainfall is slightly decreasing during the same period. Locals have perceived ecological degradation in the GLC due to both anthropogenic pressure and climatic variability. The study outlines linkage of drivers for GLC degradation and finally makes recommendations to achieve longer term sustainability of the lake complex.

Climate change (CC) threatens ecosystems in both developed and developing countries. As the impacts of CC are pervasive, global, and mostly irreversible, it is gaining worldwide attention. Here we review vulnerability and impacts of CC on forest and freshwater wetland ecosystems. We particularly look at investigations undertaken at different geographic regions in order to identify existing knowledge gaps and possible implications from such vulnerability in the context of Nepal along with available adaptation programs and national-level policy supports. Different categories of impacts which are attributed to disrupting structure, function, and habitat of both forest and wetland ecosystems are identified and discussed. We show that though still unaccounted, many facets of forest and freshwater wetland ecosystems of Nepal are vulnerable and likely to be impacted by CC in the near future. Provisioning ecosystem services and landscape-level ecosystem conservation are anticipated to be highly threatened with future CC. Finally, the need for prioritizing CC research in Nepal is highlighted to close the existing knowledge gap along with the implementation of adaptation measures based on existing location specific traditional socio-ecological system.

Recent advances in whole-genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ∼100 picograms of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants were assembled into long haplotype contigs. Removal of false positive single nucleotide variants not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 megabases. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications.

Biomass fuels are used by the majority of resource poor households in low-income countries. Though biomass fuels, such as dung-briquette and firewood are apparently cheaper than the modern fuels indoor pollution from burning biomass fuels incurs high health costs. But, the health costs of these conventional fuels, mostly being indirect, are poorly understood. To address this gap, this study develops probit regression models using survey data generated through interviews from households using either dung-briquette or biogas as the primary source of fuel for cooking. The study investigates factors affecting the use of dung-briquette, assesses its impact on human health, and estimates the associated household health costs. Analysis suggests significant effects of dung-briquette on asthma and eye diseases. Despite of the perception of it being a cheap fuel, the annual health cost per household due to burning dung-briquette (US$ 16.94) is 61.3% higher than the annual cost of biogas (US$ 10.38), an alternative cleaner fuel for rural households. For reducing the use of dung-briquette and its indirect health costs, the study recommends three interventions: (1) educate women and aboriginal people, in particular, and make them aware of the benefits of switching to biogas; (2) facilitate tree planting in communal as well as private lands; and (3) create rural employment and income generation opportunities.

Hepatitis B virus (HBV) infection is a leading risk factor for hepatocellular carcinoma (HCC). HBV integration into the host genome has been reported, but its scale, impact and contribution to HCC development is not clear. Here, we sequenced the tumor and nontumor genomes (>80× coverage) and transcriptomes of four HCC patients and identified 255 HBV integration sites. Increased sequencing to 240× coverage revealed a proportionally higher number of integration sites. Clonal expansion of HBV-integrated hepatocytes was found specifically in tumor samples. We observe a diverse collection of genomic perturbations near viral integration sites, including direct gene disruption, viral promoter-driven human transcription, viral-human transcript fusion, and DNA copy number alteration. Thus, we report the most comprehensive characterization of HBV integration in hepatocellular carcinoma patients. Such widespread random viral integration will likely increase carcinogenic opportunities in HBV-infected individuals.

Unchained base reads on self-assembling DNA nanoarrays have recently emerged as a promising approach to low-cost, high-quality resequencing of human genomes. Because of unique characteristics of these mated pair reads, existing computational methods for resequencing assembly, such as those based on map-consensus calling, are not adequate for accurate variant calling. We describe novel computational methods developed for accurate calling of SNPs and short substitutions and indels (<100 bp); the same methods apply to evaluation of hypothesized larger, structural variations. We use an optimization process that iteratively adjusts the genome sequence to maximize its a posteriori probability given the observed reads. For each candidate sequence, this probability is computed using Bayesian statistics with a simple read generation model and simplifying assumptions that make the problem computationally tractable. The optimization process iteratively applies one-base substitutions, insertions, and deletions until convergence is achieved to an optimum diploid sequence. A local de novo assembly procedure that generalizes approaches based on De Bruijn graphs is used to seed the optimization process in order to reduce the chance of converging to local optima. Finally, a correlation-based filter is applied to reduce the false positive rate caused by the presence of repetitive regions in the reference genome.

Introduction: Dengue fever is an emerging mosquito borne disease in Nepal claiming substantial morbidity and mortality. The objective of the study was to find out frequency of acute dengue infection in patients from the hospitals of the western Nepal., Methods: The study was conducted between August 2007 and July 2008 in patients visiting hospitals of the western terai of Nepal with chief complains of fever. The sero-diagnosis of acute dengue infection was determined by enzyme linked immunosorbent assay among 239 patients visiting Lumbini Zonal Hospital, Butwal; Bheri Zonal Hospital, Nepalgunj; Bardiya District Hospital, Bardiya and Mahakali Zonal Hospital, Mahendranagar., Results: The anti-dengue IgM positivity was 29.3%. There was slight male preponderance with a male to female ratio of 1.2:1. Out of the total positive cases, the highest positive cases (75.7%) were from the age group 15 - 50 years followed by < 15 years old (15.7%). Out of four hospitals, the highest positive cases (54.3%) were in Lumbini Zonal Hospital, Butwal. The age and gender were independent predictors to dengue virus infection. The highest numbers of dengue positive cases were in October (52.6%). The association between dengue disease and the month was statistically significant., Conclusions: The dengue positivity was estimated in acute patients from hospitals of western Nepal by enzyme immunoassay. Therefore, the serological marker can be used to diagnose acute patients of dengue during outbreaks.

Lung cancer is the leading cause of cancer-related mortality worldwide, with non-small-cell lung carcinomas in smokers being the predominant form of the disease. Although previous studies have identified important common somatic mutations in lung cancers, they have primarily focused on a limited set of genes and have thus provided a constrained view of the mutational spectrum. Recent cancer sequencing efforts have used next-generation sequencing technologies to provide a genome-wide view of mutations in leukaemia, breast cancer and cancer cell lines. Here we present the complete sequences of a primary lung tumour (60x coverage) and adjacent normal tissue (46x). Comparing the two genomes, we identify a wide variety of somatic variations, including >50,000 high-confidence single nucleotide variants. We validated 530 somatic single nucleotide variants in this tumour, including one in the KRAS proto-oncogene and 391 others in coding regions, as well as 43 large-scale structural variations. These constitute a large set of new somatic mutations and yield an estimated 17.7 per megabase genome-wide somatic mutation rate. Notably, we observe a distinct pattern of selection against mutations within expressed genes compared to non-expressed genes and in promoter regions up to 5 kilobases upstream of all protein-coding genes. Furthermore, we observe a higher rate of amino acid-changing mutations in kinase genes. We present a comprehensive view of somatic alterations in a single lung tumour, and provide the first evidence, to our knowledge, of distinct selective pressures present within the tumour environment.

We analyzed the whole-genome sequences of a family of four, consisting of two siblings and their parents. Family-based sequencing allowed us to delineate recombination sites precisely, identify 70% of the sequencing errors (resulting in > 99.999% accuracy), and identify very rare single-nucleotide polymorphisms. We also directly estimated a human intergeneration mutation rate of approximately 1.1 x 10(-8) per position per haploid genome. Both offspring in this family have two recessive disorders: Miller syndrome, for which the gene was concurrently identified, and primary ciliary dyskinesia, for which causative genes have been previously identified. Family-based genome analysis enabled us to narrow the candidate genes for both of these Mendelian disorders to only four. Our results demonstrate the value of complete genome sequencing in families.

Genome sequencing of large numbers of individuals promises to advance the understanding, treatment, and prevention of human diseases, among other applications. We describe a genome sequencing platform that achieves efficient imaging and low reagent consumption with combinatorial probe anchor ligation chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs. We sequenced three human genomes with this platform, generating an average of 45- to 87-fold coverage per genome and identifying 3.2 to 4.5 million sequence variants per genome. Validation of one genome data set demonstrates a sequence accuracy of about 1 false variant per 100 kilobases. The high accuracy, affordable cost of $4400 for sequencing consumables, and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies.

Data on 4112 Muzaffarnagari sheep, maintained at the Central Institute for Research on Goats, Makhdoom, Mathura, India, and recorded between 1976 and 1999, were analysed to study the growth-related traits and their genetic control. The average weights at birth, and at 12 months of age were 3.1 +/- 0.2 and 28.0 +/- 0.6 kg, respectively. The pre- and post-weaning average daily weight gains were 127.8 +/- 3.3 g and 49.4 +/- 1.6 g. and the associated growth efficiencies were 3.59 +/- 0.08 and 0.95 +/- 0.03. Significant differences associated with the year of lambing were observed in body weight, weight gain and efficiency in weight gain at different stages of growth. The lambs born in the dam's second parity were generally of heavier weight and higher daily weight gain than those born in other parities. Males were heavier and had a higher weight gain than females at almost all stages of growth and the differences tended to increase with age. Single-born lambs had a distinct advantage over those born in multiple births at all stages of growth. The heritabilities of all body weights, weight gains and efficiency in weight gains at different stages of growth were moderate (0.18-0.26), except for birth weight, which was of low heritability (0.068 +/- 0.01). The phenotypic and genetic correlations among the different body weights were positive and high, except for birth weight. The genetic correlation of the pre- and post-weaning average daily weight gains with body weights were high and positive.

Three breeds of sheep, Brazilian Somali, Morada Nova and Santa Inês which are indigenous to hot tropical semi-arid north-east Brazil were studied for their early growth. There were large breed differences in size at birth, at the 86th day and at 6 months. The Santa Inês was the largest and the Brazilian Somali the smallest. The type of birth (single vs. multiple) had a profound effect on weight at virtually all stages of growth which was similar for male and female lambs. Sex effects tended to become significant at around the 86th day, female lambs slightly outweighing males but marked sex differences appeared around 6 months when males outweighed females. The 7-day variation in age of lambs when the weights were taken around the 15th day had a marked effect on weight and correction for age would be necessary in future studies. However, the 7-day variation in age around the 86th day and thereafter did not affect the weights. The birth weight and weights at the 15th, 86th and 112 days and at 6 months were significantly correlated.

The seasons in the 1 year study were classified as rainy, transitional rainy-dry, dry, and transitional dry-rainy. Semen pH and the consistency of the testes did not vary between seasons or among rams. All other characteristics of semen and testis varied between rams. Significant seasonal differences were observed for ejaculate volume, mass, % motility, forward motility score and concentration of spermatozoa, and linear testis measurements. The total number of spermatozoa per ejaculate did not vary seasonally. The magnitude of the seasonal effects was not sufficient to prevent the rams being used for breeding throughout the year.

This study reports the incidence of abscesses in relation to Corynebacterium pseudotuberculosis infection in goats in north-east Brazil. Among 656 goats examined periodically over almost two years 41.6% were found with superficially palpable abscesses. Most of the infected areas were in the anterior half of the body in front of the pre-scapular region; the inguinal region formed the other prominent area. Among 486 dead or slaughtered goats, 56 (11.5%) revealed abscesses in the internal organs. Lungs and epididymis were affected most, liver, spleen, udder and lateropharyngeal nodes were next in order and kidneys and mediastinal nodes were least affected. Thus the overall incidence of external and internal abscesses was 28.8%; of all the abscesses 27.7% were due to C. pseudotuberculosis and the rest due to infections of Corynebacterium pyogenes and several species of streptococci or staphylococci. The growth of C. pseudotuberculosis-infected and non-infected goats was of the same order and it seems that caseous lymphadenitis is not the cause of much financial loss in north-east Brazil but in view of its high incidence remedial measures should be considered necessary in regions where the goat meat industry is likely to become more intensive and important.