Comparative analysis of the transcriptome across distant species.

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

Participatory Women's Groups with Cash Transfers Can Increase Dietary Diversity and Micronutrient Adequacy during Pregnancy, whereas Women's Groups with Food Transfers Can Increase Equity in Intrahousehold Energy Allocation.

Background: There is scarce evidence on the impacts of food transfers, cash transfers, or women's groups on food sharing, dietary intakes, or nutrition during pregnancy, when nutritional needs are elevated. Objective: This study measured the effects of 3 pregnancy-focused nutrition interventions on intrahousehold food allocation, dietary adequacy, and maternal nutritional status in Nepal. Methods: Interventions tested in a cluster-randomized controlled trial (ISRCTN 75964374) were "Participatory Learning and Action" (PLA) monthly women's groups, PLA with transfers of 10 kg fortified flour ("Super Cereal"), and PLA plus transfers of 750 Nepalese rupees (∼US$7.5) to pregnant women. Control clusters received usual government services. Primary outcomes were Relative Dietary Energy Adequacy Ratios (RDEARs) between pregnant women and male household heads and pregnant women and their mothers-in-law. Diets were measured by repeated 24-h dietary recalls. Results: Relative to control, RDEARs between pregnant women and their mothers-in-law were 12% higher in the PLA plus food arm (log-RDEAR coefficient = 0.12; 95% CI: 0.02, 0.21; P = 0.014), but 10% lower in the PLA-only arm between pregnant women and male household heads (-0.11; 95% CI: -0.19, -0.02; P = 0.020). In all interventions, pregnant women's energy intakes did not improve, but odds of pregnant women consuming iron-folate supplements were 2.5-4.6 times higher, odds of pregnant women consuming more animal-source foods than the household head were 1.7-2.4 times higher, and midupper arm circumference was higher relative to control. Dietary diversity was 0.4 food groups higher in the PLA plus cash arm than in the control arm. Conclusions: All interventions improved maternal diets and nutritional status in pregnancy. PLA women's groups with food transfers increased equity in energy allocation, whereas PLA with cash improved dietary diversity. PLA alone improved diets, but effects were mixed. Scale-up of these interventions in marginalized populations is a policy option, but researchers should find ways to increase adherence to interventions. This trial was registered at www.controlled-trials.com as ISRCTN 75964374.

Landscape of transcription in human cells.

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

Smartphone tool to collect repeated 24 h dietary recall data in Nepal.

OBJECTIVE: To outline the development of a smartphone-based tool to collect thrice-repeated 24 h dietary recall data in rural Nepal, and to describe energy intakes, common errors and researchers' experiences using the tool. DESIGN: We designed a novel tool to collect multi-pass 24 h dietary recalls in rural Nepal by combining the use of a CommCare questionnaire on smartphones, a paper form, a QR (quick response)-coded list of foods and a photographic atlas of portion sizes. Twenty interviewers collected dietary data on three non-consecutive days per respondent, with three respondents per household. Intakes were converted into nutrients using databases on nutritional composition of foods, recipes and portion sizes. SETTING: Dhanusha and Mahottari districts, Nepal. SUBJECTS: Pregnant women, their mothers-in-law and male household heads. Energy intakes assessed in 150 households; data corrections and our experiences reported from 805 households and 6765 individual recalls. RESULTS: Dietary intake estimates gave plausible values, with male household heads appearing to have higher energy intakes (median (25th-75th centile): 12 079 (9293-14 108) kJ/d) than female members (8979 (7234-11 042) kJ/d for pregnant women). Manual editing of data was required when interviewers mistook portions for food codes and for coding items not on the food list. Smartphones enabled quick monitoring of data and interviewer performance, but we initially faced technical challenges with CommCare forms crashing. CONCLUSIONS: With sufficient time dedicated to development and pre-testing, this novel smartphone-based tool provides a useful method to collect data. Future work is needed to further validate this tool and adapt it for other contexts.

Protocol of the Low Birth Weight South Asia Trial (LBWSAT), a cluster-randomised controlled trial testing impact on birth weight and infant nutrition of Participatory Learning and Action through women's groups, with and without unconditional transfers of fortified food or cash during pregnancy in Nepal.

BACKGROUND: Low birth weight (LBW, < 2500 g) affects one third of newborn infants in rural south Asia and compromises child survival, infant growth, educational performance and economic prospects. We aimed to assess the impact on birth weight and weight-for-age Z-score in children aged 0-16 months of a nutrition Participatory Learning and Action behaviour change strategy (PLA) for pregnant women through women's groups, with or without unconditional transfers of food or cash to pregnant women in two districts of southern Nepal. METHODS: The study is a cluster randomised controlled trial (non-blinded). PLA comprises women's groups that discuss, and form strategies about, nutrition in pregnancy, low birth weight and hygiene. Women receive up to 7 monthly transfers per pregnancy: cash is NPR 750 (~US$7) and food is 10 kg of fortified sweetened wheat-soya Super Cereal per month. The unit of randomisation is a rural village development committee (VDC) cluster (population 4000-9200, mean 6150) in southern Dhanusha or Mahottari districts. 80 VDCs are randomised to four arms using a participatory 'tombola' method. Twenty clusters each receive: PLA; PLA plus food; PLA plus cash; and standard care (control). Participants are (mostly Maithili-speaking) pregnant women identified from 8 weeks' gestation onwards, and their infants (target sample size 8880 birth weights). After pregnancy verification, mothers may be followed up in early and late pregnancy, within 72 h, after 42 days and within 22 months of birth. Outcomes pertain to the individual level. Primary outcomes include birth weight within 72 h of birth and infant weight-for-age Z-score measured cross-sectionally on children born of the study. Secondary outcomes include prevalence of LBW, eating behaviour and weight during pregnancy, maternal and newborn illness, preterm delivery, miscarriage, stillbirth or neonatal mortality, infant Z-scores for length-for-age and weight-for-length, head circumference, and postnatal maternal BMI and mid-upper arm circumference. Exposure to women's groups, food or cash transfers, home visits, and group interventions are measured. DISCUSSION: Determining the relative importance to birth weight and early childhood nutrition of adding food or cash transfers to PLA women's groups will inform design of nutrition interventions in pregnancy. TRIAL REGISTRATION: ISRCTN75964374 , 12 Jul 2013.

STAR: ultrafast universal RNA-seq aligner.

MOTIVATION: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. RESULTS: To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. AVAILABILITY AND IMPLEMENTATION: STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.

Understanding psychological distress among mothers in rural Nepal: a qualitative grounded theory exploration.

BACKGROUND: There is a large burden of psychological distress in low and middle-income countries, and culturally relevant interventions must be developed to address it. This requires an understanding of how distress is experienced. We conducted a qualitative grounded theory study to understand how mothers experience and manage distress in Dhanusha, a low-resource setting in rural Nepal. We also explored how distressed mothers interact with their families and the wider community. METHODS: Participants were identified during a cluster-randomised controlled trial in which mothers were screened for psychological distress using the 12-item General Health Questionnaire (GHQ-12). We conducted 22 semi-structured interviews with distressed mothers (GHQ-12 score ≥ 5) and one with a traditional healer (dhami), as well as 12 focus group discussions with community members. Data were analysed using grounded theory methods and a model was developed to explain psychological distress in this setting. RESULTS: We found that distress was termed tension by participants and mainly described in terms of physical symptoms. Key perceived causes of distress were poor health, lack of sons, and fertility problems. Tension developed in a context of limited autonomy for women and perceived duty towards the family. Distressed mothers discussed several strategies to alleviate tension, including seeking treatment for perceived physical health problems and tension from doctors or dhamis, having repeated pregnancies until a son was delivered, manipulating social circumstances in the household, and deciding to accept their fate. Their ability to implement these strategies depended on whether they were able to negotiate with their in-laws or husbands for resources. CONCLUSIONS: Vulnerability, as a consequence of gender and social disadvantage, manifests as psychological distress among mothers in Dhanusha. Screening tools incorporating physical symptoms of tension should be envisaged, along with interventions to address gender inequity, support marital relationships, and improve access to perinatal healthcare.

Harmine Acts as an Indirect Inhibitor of Intracellular Protein Aggregation.

Protein aggregation and oxidative stress are two pathological hallmarks of a number of protein misfolding diseases, including Huntington's disease (HD). Whether protein aggregation precedes elevation of oxidative stress or follows it remains ambiguous. We have investigated the role of harmine, a beta-carboline alkaloid, in aggregation of a mutant huntingtin fragment (103Q-htt) in a yeast model of HD. We observed that harmine was able to decrease intracellular aggregation of 103Q-htt, and this reduction was higher than that observed with trehalose, a conventional protein stabilizer. The presence of harmine also decreased prion formation. Decreased protein aggregation was accompanied by reduction in oxidative stress. However, harmine had no effect on aggregation of the mutant huntingtin fragment in vitro. Thus, based on experimental data, we conclude that the antioxidant harmine lowers aggregation-induced elevation in oxidative stress, which slows down intracellular protein aggregation.

Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence.

Coronaviruses are a large family of viruses that are known to infect both humans and animals. However, the evidence of inter-transmission of coronavirus between humans and companion animals is still a debatable issue. There is substantial evidence that the virus outbreak is fueled by zoonotic transmission because this new virus belongs to the same family of viruses as SARS-CoV associated with civet cats, and MERS-CoV associated with dromedary camels. While the whole world is investigating the possibility about the transmission of this virus, the transmission among humans is established, but the interface between humans and animals is not much evident. Not only are the lives of human beings at risk, but there is an equal potential threat to the animal world. With multiple reports claiming about much possibility of transmission of COVID-19 from humans to animals, there has been a significant increase in the number of pets being abandoned by their owners. Additionally, the risk of reverse transmission of COVID-19 virus from companion pets like cats and dogs at home is yet another area of concern. The present article highlights different evidence of human-animal interface and necessitates the precautionary measures required to combat with the consequences of this interface. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) have suggested various ways to promote awareness and corroborate practices for helping people as well as animals to stay secure and healthy.

Status and determinants of intra-household food allocation in rural Nepal.

BACKGROUND/OBJECTIVES: Understanding of the patterns and predictors of intra-household food allocation could enable nutrition programmes to better target nutritionally vulnerable individuals. This study aims to characterise the status and determinants of intra-household food and nutrient allocation in Nepal. SUBJECTS/METHODS: Pregnant women, their mothers-in-law and male household heads from Dhanusha and Mahottari districts in Nepal responded to 24-h dietary recalls, thrice repeated on non-consecutive days (n = 150 households; 1278 individual recalls). Intra-household inequity was measured using ratios between household members in food intakes (food shares); food-energy intake proportions ('food shares-to-energy shares', FS:ES); calorie-requirement proportions ('relative dietary energy adequacy ratios', RDEARs) and mean probability of adequacy for 11 micronutrients (MPA ratios). Hypothesised determinants were collected during the recalls, and their associations with the outcomes were tested using multivariable mixed-effects linear regression models. RESULTS: Women's diets (pregnant women and mothers-in-law) consisted of larger FS:ES of starchy foods, pulses, fruits and vegetables than male household heads, whereas men had larger FS:ES of animal-source foods. Pregnant women had the lowest MPA (37%) followed by their mothers-in-law (52%), and male household heads (57%). RDEARs between pregnant women and household heads were 31% higher (log-RDEAR coeff=0.27 (95% CI 0.12, 0.42), P < 0.001) when pregnant women earned more or the same as their spouse, and log-MPA ratios between pregnant women and mothers-in-law were positively associated with household-level calorie intakes (coeff=0.43 (0.23, 0.63), P < 0.001, per 1000 kcal). CONCLUSIONS: Pregnant women receive inequitably lower shares of food and nutrients, but this could be improved by increasing pregnant women's cash earnings and household food security.

Impact on birth weight and child growth of Participatory Learning and Action women's groups with and without transfers of food or cash during pregnancy: Findings of the low birth weight South Asia cluster-randomised controlled trial (LBWSAT) in Nepal.

BACKGROUND: Undernutrition during pregnancy leads to low birthweight, poor growth and inter-generational undernutrition. We did a non-blinded cluster-randomised controlled trial in the plains districts of Dhanusha and Mahottari, Nepal to assess the impact on birthweight and weight-for-age z-scores among children aged 0-16 months of community-based participatory learning and action (PLA) women's groups, with and without food or cash transfers to pregnant women. METHODS: We randomly allocated 20 clusters per arm to four arms (average population/cluster = 6150). All consenting married women aged 10-49 years, who had not had tubal ligation and whose husbands had not had vasectomy, were monitored for missed menses. Between 29 Dec 2013 and 28 Feb 2015 we recruited 25,092 pregnant women to surveillance and interventions: PLA alone (n = 5626); PLA plus food (10 kg/month of fortified wheat-soya 'Super Cereal', n = 6884); PLA plus cash (NPR750≈US$7.5/month, n = 7272); control (existing government programmes, n = 5310). 539 PLA groups discussed and implemented strategies to improve low birthweight, nutrition in pregnancy and hand washing. Primary outcomes were birthweight within 72 hours of delivery and weight-for-age z-scores at endline (age 0-16 months). Only children born to permanent residents between 4 June 2014 and 20 June 2015 were eligible for intention to treat analyses (n = 10936), while in-migrating women and children born before interventions had been running for 16 weeks were excluded. Trial status: completed. RESULTS: In PLA plus food/cash arms, 94-97% of pregnant women attended groups and received a mean of four transfers over their pregnancies. In the PLA only arm, 49% of pregnant women attended groups. Due to unrest, the response rate for birthweight was low at 22% (n = 2087), but response rate for endline nutritional and dietary measures exceeded 83% (n = 9242). Compared to the control arm (n = 464), mean birthweight was significantly higher in the PLA plus food arm by 78·0 g (95% CI 13·9, 142·0; n = 626) and not significantly higher in PLA only and PLA plus cash arms by 28·9 g (95% CI -37·7, 95·4; n = 488) and 50·5 g (95% CI -15·0, 116·1; n = 509) respectively. Mean weight-for-age z-scores of children aged 0-16 months (average age 9 months) sampled cross-sectionally at endpoint, were not significantly different from those in the control arm (n = 2091). Differences in weight for-age z-score were as follows: PLA only -0·026 (95% CI -0·117, 0·065; n = 2095); PLA plus cash -0·045 (95% CI -0·133, 0·044; n = 2545); PLA plus food -0·033 (95% CI -0·121, 0·056; n = 2507). Amongst many secondary outcomes tested, compared with control, more institutional deliveries (OR: 1.46 95% CI 1.03, 2.06; n = 2651) and less colostrum discarding (OR:0.71 95% CI 0.54, 0.93; n = 2548) were found in the PLA plus food arm but not in PLA alone or in PLA plus cash arms. INTERPRETATION: Food supplements in pregnancy with PLA women's groups increased birthweight more than PLA plus cash or PLA alone but differences were not sustained. Nutrition interventions throughout the thousand-day period are recommended. TRIAL REGISTRATION: ISRCTN75964374.

Experiences in running a complex electronic data capture system using mobile phones in a large-scale population trial in southern Nepal.

The increasing availability and capabilities of mobile phones make them a feasible means of data collection. Electronic Data Capture (EDC) systems have been used widely for public health monitoring and surveillance activities, but documentation of their use in complicated research studies requiring multiple systems is limited. This paper shares our experiences of designing and implementing a complex multi-component EDC system for a community-based four-armed cluster-Randomised Controlled Trial in the rural plains of Nepal, to help other researchers planning to use EDC for complex studies in low-income settings. We designed and implemented three interrelated mobile phone data collection systems to enrol and follow-up pregnant women (trial participants), and to support the implementation of trial interventions (women's groups, food and cash transfers). 720 field staff used basic phones to send simple coded text messages, 539 women's group facilitators used Android smartphones with Open Data Kit Collect, and 112 Interviewers, Coordinators and Supervisors used smartphones with CommCare. Barcoded photo ID cards encoded with participant information were generated for each enrolled woman. Automated systems were developed to download, recode and merge data for nearly real-time access by researchers. The systems were successfully rolled out and used by 1371 staff. A total of 25,089 pregnant women were enrolled, and 17,839 follow-up forms completed. Women's group facilitators recorded 5717 women's groups and the distribution of 14,647 food and 13,482 cash transfers. Using EDC sped up data collection and processing, although time needed for programming and set-up delayed the study inception. EDC using three interlinked mobile data management systems (FrontlineSMS, ODK and CommCare) was a feasible and effective method of data capture in a complex large-scale trial in the plains of Nepal. Despite challenges including prolonged set-up times, the systems met multiple data collection needs for users with varying levels of literacy and experience.