Miracle-dz/UniFAR-FTUs huggingface dataset:
Tobacco use and self-reported morbidity among rural Indian adults

Aim To measure the prevalence of self-reported morbidity and its associated factors among adults (aged ⩾15 years) in a select rural Indian population. Background Self-reporting of smoking has been validated as population-based surveys using self-reported data provide reasonably consistent estimates of smoking prevalence, and are generally considered to be sufficiently accurate for tracking the general pattern of morbidity associated with tobacco use in populations. However, to gauge the true disease burden using self-reported morbidity data requires cautious interpretation. Methods During 2010–2011, a cross-sectional survey was conducted under the banner of the Health and Demographic Surveillance System, Birbhum, an initiative of the Department of Health and Family Welfare, Government of West Bengal, India. With over 93.6% response rate from the population living in 12 300 households, this study uses the responses from 16 354 individuals: 8012 smokers, and 8333 smokeless tobacco users. Smokers and smokeless tobacco users were asked whether they have developed any morbidity symptoms due to smoking, or smokeless tobacco use. Bivariate, as well as multivariate logistic regression analyses were deployed to attain the study objective. Findings Over 20% of smokers and over 9% of smokeless tobacco users reported any morbidity. Odds ratio (OR) with 95% confidence interval (CI) estimated using logistic regression shows that women are less likely to report any morbidity attributable to smoking (OR: 0.69; CI: 0.54–0.87), and more likely to report any morbidity due to smokeless tobacco use (OR: 1.68; CI: 1.36–2.09). Non-Hindus have higher odds, whereas the wealthiest respondents have lower odds of reporting any morbidity. With a culturally appropriate intervention to change behaviour, youth (both men and women) could be targeted with comprehensive tobacco cessation assistance programmes. A focussed intervention could be designed for unprocessed tobacco users to curb hazardous effects of tobacco use.
Embryo defective 14 encodes a plastid-targeted cGTPase essential for embryogenesis in maize.

The embryo defective (emb) mutants in maize genetically define a unique class of loci that is required for embryogenesis but not endosperm development, allowing dissection of two developmental processes of seed formation. Through characterization of the emb14 mutant, we report here that Emb14 gene encodes a circular permuted, YqeH class GTPase protein that likely functions in 30S ribosome formation in plastids. Loss of Emb14 function in the null mutant arrests embryogenesis at the early transition stage. Emb14 was cloned by transposon tagging and was confirmed by analysis of four alleles. Subcellular localization indicated that the EMB14 is targeted to chloroplasts. Recombinant EMB14 is shown to hydrolyze GTP in vitro (Km = 2.42 ± 0.3 μm). Emb14 was constitutively expressed in all tissues examined and high level of expression was found in transition stage embryos. Comparison of emb14 and WT indicated that loss of EMB14 function severely impairs accumulation of 16S rRNA and several plastid encoded ribosomal genes. We show that an EMB14 transgene complements the pale green, slow growth phenotype conditioned by mutations in AtNOA1, a closely related YqeH GTPase of Arabidopsis. Taken together, we propose that the EMB14/AtNOA1/YqeH class GTPases function in assembly of the 30S subunit of the chloroplast ribosome, and that this function is essential to embryogenesis in plants.
Health team for the elderly: a feasibility study for preventive home visits

The aim was to describe the development, utilization and feasibility of a model of preventive home visits, in an urban and a rural municipality in Norway. Background Older people >65 years will rise significantly in coming years. Increased age is associated with risk of disability, illness and need for public health services. Preventive home visits is assumed to help older people to maintain their functional level longer, delaying disease and thus delaying the need for health care. Method Descriptive explorative design describing the development, utilization and feasibility of preventive home visits in two different settings. All 77-year-old persons living at home in an urban municipality and all 75 years and older in a rural municipality were invited to participate. A questionnaire including a substantial number of tests concerning; fall, nutrition, polypharmacy and cognitive impairment was used by Health Team Nurses as base for a risk assessment. Pilot studies were conducted to validate the questionnaire including an inter-rater reliability study of the risk assessment tool. A multiprofessional team, Health Team for the Elderly met each week to evaluate risk assessments and make recommendations to be sent to each respective general practitioner. Data were analysed using descriptive and inferential statistics. In total, 167 persons (109 from the urban municipality and 58 from the rural municipality) participated, corresponding to 60% of the approached individuals. The mean time for the visits was 108 minutes (SD 20). Missing data were identified for; Do you feel safe in your municipality (17.5%) and Are you looking forward to ageing (11.4%). In total, 36 persons (21.7%) were identified with increased risk for developing illness. We suggest that a structured model of preventive home visits and collaboration between highly specialized health care professionals are important factors for reliable health promoting risk assessments of elderly home dwellers.
Evaluation of a pilot service to facilitate discharge of patients with stable long-term mental health needs from secondary to primary care: the role of Primary Care Mental Health Specialists

Aim We aimed to evaluate a pilot service to facilitate discharge of patients with stable long-term mental health needs from secondary to primary care. Background Patients with stable long-term mental health conditions are often not discharged from secondary mental health services when no longer needed due to insufficient systems and processes to enable safe, effective, recovery-focussed treatment and support. The Primary Care Mental Health Specialist (PCMHS) Service was developed to address this gap; new PCMHS posts were introduced to act as a conduit for patients being discharged from secondary care and a single point of referral back into secondary care, should it be required. The two-year pilot, across six Clinical Commissioning Groups in South East England, began in March 2013. Methods Interviews were conducted with all PCMHS employed in the pilot service (n=13) and a sample of service users (n=12). The views of professionals working alongside the service, including GPs, Psychiatrists and Mental Health Nurses, were captured using a brief online questionnaire (n=50). Time and Activity Recording Sheets were used to capture data required for economic analysis. Findings Our findings indicate that the service is working well from the perspective of patients; staff employed within the service and professionals working alongside the service. Patients described the service as a ‘safety net’ they could fall back on in case of difficulties, whereas staff used the analogy of a ‘bridge’ to describe the way the service improved communication and collaboration between the various professionals and organisations involved in the patient’s care. Improvements in well-being were seen to result from increased support for those transitioning from secondary to primary care, a more pro-active approach to relapse prevention and increased engagement in daily activities. Each PCMHS covered 36 patients in a one-month period, with a unit cost of £73.01 per patient.
Three-Dimensional Gas Exchange Pathways in Pome Fruit Characterized by Synchrotron X-Ray Computed Tomography1[C][W][OA]

Our understanding of the gas exchange mechanisms in plant organs critically depends on insights in the three-dimensional (3-D) structural arrangement of cells and voids. Using synchrotron radiation x-ray tomography, we obtained for the first time high-contrast 3-D absorption images of in vivo fruit tissues of high moisture content at 1.4-μm resolution and 3-D phase contrast images of cell assemblies at a resolution as low as 0.7 μm, enabling visualization of individual cell morphology, cell walls, and entire void networks that were previously unknown. Intercellular spaces were always clear of water. The apple (Malus domestica) cortex contains considerably larger parenchyma cells and voids than pear (Pyrus communis) parenchyma. Voids in apple often are larger than the surrounding cells and some cells are not connected to void spaces. The main voids in apple stretch hundreds of micrometers but are disconnected. Voids in pear cortex tissue are always smaller than parenchyma cells, but each cell is surrounded by a tight and continuous network of voids, except near brachyssclereid groups. Vascular and dermal tissues were also measured. The visualized network architecture was consistent over different picking dates and shelf life. The differences in void fraction (5.1% for pear cortex and 23.0% for apple cortex) and in gas network architecture helps explain the ability of tissues to facilitate or impede gas exchange. Structural changes and anisotropy of tissues may eventually lead to physiological disorders. A combined tomography and internal gas analysis during growth are needed to make progress on the understanding of void formation in fruit.
Effects of Balance Training on Stability and Neuromuscular Drive in Older Women

Abstract The purpose of this study was to examine the effects of an 8-week proprioceptive balance training program on dynamic stability, neuromuscular drive, clinical performance measures, and physical activity in older women. Thirteen females (76.2 ±1.2 yrs) completed an 8-week balance training program (3 X/week). Measurements were performed at 0, 4, and 8 weeks. In general the balance training program resulted in significant improvement in the computerized balance and stability measurements tested. Normalized IEMG values increased (p < 0.05) at the high level of stability with the gastrocnemius (0.515 ±0.019 to 0.613 ±0.029), lower leg muscles combined (0.458 ±0.043 to 0.597 ±0.027) and total leg IEMG (0.486 ±0.035 to 0.620 ±0.027). In addition, there were significant differences in normalized IEMG values at the low level of stability in the total leg IEMG. The results from the current investigation indicate that a specific dynamic balance training program is effective and efficient at improving dynamic stability.
Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR KINASE Proteins Serve Brassinosteroid-Dependent and -Independent Signaling Pathways1[C][W]

The Arabidopsis (Arabidopsis thaliana) SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) genes belong to a small family of five plant receptor kinases that are involved in at least five different signaling pathways. One member of this family, BRASSINOSTEROID INSENSITIVE1 (BRI1)-ASSOCIATED KINASE1 (BAK1), also known as SERK3, is the coreceptor of the brassinolide (BR)-perceiving receptor BRI1, a function that is BR dependent and partially redundant with SERK1. BAK1 (SERK3) alone controls plant innate immunity, is also the coreceptor of the flagellin receptor FLS2, and, together with SERK4, can mediate cell death control, all three in a BR-independent fashion. SERK1 and SERK2 are essential for male microsporogenesis, again independent from BR. SERK5 does not appear to have any function under the conditions tested. Here, we show that the different SERK members are only redundant in pairs, whereas higher order mutant combinations only show additive phenotypes. Surprisingly, SERK members that are redundant within one are not redundant in another pathway. We also show that this evolution of functional pairs occurred by a change in protein function and not by differences in spatial expression. We propose that, in plants, closely related receptor kinases have a minimal homo- or heterodimeric configuration to achieve specificity.
Citrus Chlorophyllase Dynamics at Ethylene-Induced Fruit Color-Break: A Study of Chlorophyllase Expression, Posttranslational Processing Kinetics, and in Situ Intracellular Localization1[OA]

Fruit color-break is the visual manifestation of the developmentally regulated transition of chloroplasts to chromoplasts during fruit ripening and often involves biosynthesis of copious amounts of carotenoids concomitant with massive breakdown of chlorophyll. Regulation of chlorophyll breakdown at different physiological and developmental stages of the plant life cycle, particularly at fruit color-break, is still not well understood. Here, we present the dynamics of native chlorophyllase (Chlase) and chlorophyll breakdown in lemon (Citrus limon) fruit during ethylene-induced color-break. We show, using in situ immunofluorescence on ethylene-treated fruit peel (flavedo) tissue, that citrus Chlase is located in the plastid, in contrast to recent reports suggesting cytoplasmic localization of Arabidopsis (Arabidopsis thaliana) Chlases. At the intra-organellar level, Chlase signal was found to overlap mostly with chlorophyll fluorescence, suggesting association of most of the Chlase protein with the photosynthetic membranes. Confocal microscopy analysis showed that the kinetics of chlorophyll breakdown was not uniform in the flavedo cells. Chlorophyll quantity at the cellular level was negatively correlated with plastid Chlase accumulation; plastids with reduced chlorophyll content were found by in situ immunofluorescence to contain significant levels of Chlase, while plastids containing still-intact chlorophyll lacked any Chlase signal. Immunoblot and protein-mass spectrometry analyses were used to demonstrate that citrus Chlase initially accumulates as an approximately 35-kD precursor, which is subsequently N-terminally processed to approximately 33-kD mature forms by cleavage at either of three consecutive amino acid positions. Chlase plastid localization, expression kinetics, and the negative correlation with chlorophyll levels support the central role of the enzyme in chlorophyll breakdown during citrus fruit color-break.
Systematic molecular genetic analysis of congenital sideroblastic anemia: Evidence for genetic heterogeneity and identification of novel mutations

Sideroblastic anemias are heterogeneous congenital and acquired bone marrow disorders characterized by pathologic iron deposits in mitochondria of erythroid precursors. Among the congenital sideroblastic anemias (CSAs), the most common form is X‐linked sideroblastic anemia, due to mutations in 5‐aminolevulinate synthase (ALAS2). A novel autosomal recessive CSA, caused by mutations in the erythroid specific mitochondrial transporter SLC25A38, was recently defined. Other known etiologies include mutations in genes encoding the thiamine transporter SLC19A2, the RNA‐modifying enzyme pseudouridine synthase 1 (PUS1), a mitochondrial ATP‐binding cassette transporter (ABCB7), glutaredoxin 5 (GLRX5), as well as mitochondrial DNA deletions. Despite these known diverse causes, in a substantial portion of CSA cases a presumed genetic defect remains unknown.
A γ-Glutamyl Transpeptidase-Independent Pathway of Glutathione Catabolism to Glutamate via 5-Oxoproline in Arabidopsis1[W][OA]

The degradation pathway of glutathione (GSH) in plants is not well understood. In mammals, GSH is predominantly metabolized through the γ-glutamyl cycle, where GSH is degraded by the sequential reaction of γ-glutamyl transpeptidase (GGT), γ-glutamyl cyclotransferase, and 5-oxoprolinase to yield glutamate (Glu) and dipeptides that are subject to peptidase action. In this study, we examined if GSH is degraded through the same pathway in Arabidopsis (Arabidopsis thaliana) as occurs in mammals. In Arabidopsis, the oxoprolinase knockout mutants (oxp1-1 and oxp1-2) accumulate more 5-oxoproline (5OP) and less Glu than wild-type plants, suggesting substantial metabolite flux though 5OP and that 5OP is a major contributor to Glu steady-state levels. In the ggt1-1/ggt4-1/oxp1-1 triple mutant with no GGT activity in any organs except young siliques, the 5OP concentration in leaves was not different from that in oxp1-1, suggesting that GGTs are not major contributors to 5OP production in Arabidopsis. 5OP formation strongly tracked the level of GSH in Arabidopsis plants, suggesting that GSH is the precursor of 5OP in a GGT-independent reaction. Kinetics analysis suggests that γ-glutamyl cyclotransferase is the major source of GSH degradation and 5OP formation in Arabidopsis. This discovery led us to propose a new pathway for GSH turnover in plants where GSH is converted to 5OP and then to Glu by the combined action of γ-glutamyl cyclotransferase and 5-oxoprolinase in the cytoplasm.
The Vigna unguiculata Gene Expression Atlas (VuGEA) from de novo assembly and quantification of RNA-seq data provides insights into seed maturation mechanisms.

Legume research and cultivar development are important for sustainable food production, especially of high-protein seed. Thanks to the development of deep-sequencing technologies, crop species have been taken to the front line, even without completion of their genome sequences. Black-eyed pea (Vigna unguiculata) is a legume species widely grown in semi-arid regions, which has high potential to provide stable seed protein production in a broad range of environments, including drought conditions. The black-eyed pea reference genotype has been used to generate a gene expression atlas of the major plant tissues (i.e. leaf, root, stem, flower, pod and seed), with a developmental time series for pods and seeds. From these various organs, 27 cDNA libraries were generated and sequenced, resulting in more than one billion reads. Following filtering, these reads were de novo assembled into 36 529 transcript sequences that were annotated and quantified across the different tissues. A set of 24 866 unique transcript sequences, called Unigenes, was identified. All the information related to transcript identification, annotation and quantification were stored into a gene expression atlas webserver (http://vugea.noble.org), providing a user-friendly interface and necessary tools to analyse transcript expression in black-eyed pea organs and to compare data with other legume species. Using this gene expression atlas, we inferred details of molecular processes that are active during seed development, and identified key putative regulators of seed maturation. Additionally, we found evidence for conservation of regulatory mechanisms involving miRNA in plant tissues subjected to drought and seeds undergoing desiccation.
Differential deposition of H2A.Z in combination with histone modifications within related genes in Oryza sativa callus and seedling

Summary As a histone variant, H2A.Z is highly conserved among species and plays a significant role in diverse cellular processes. Here, we generated genome‐wide maps of H2A.Z in Oryza sativa (rice) callus and seedling by combining chromatin immunoprecipitation using H2A.Z antibody and high‐throughput sequencing. We found a significantly high peak and a small peak of H2A.Z distributed at the 5′ and 3′ ends of highly expressed genes, respectively. H2A.Z was also associated with inactive genes in both tissues. H3 lysine 4 trimethylation was associated with H2A.Z deposition at the 5′ end of expressed genes, and H3 lysine 27 trimethylation peaks were partially associated with H2A.Z. In summary, our study provides global analysis data for the distribution of H2A.Z in the rice genome. Our results demonstrate that the differential deposition of H2A.Z might play important roles in gene transcription during rice development. Significance Statement Regulation of chromatin structure is important in modulating genome activities. The histone variant H2A.Z is highly conserved between species and plays a significant role, but how H2A.Z nucleosome occupancy mediates differential transcription in plants other than Arabidopsis is still poorly understood. Here, we performed a genome‐wide distribution of H2A.Z in rice seedlings and callus. We conclude that differential deposition of H2A.Z, in combination with other chromatin marks, affects gene transcription during rice development.
ABI4 represses the expression of type‐A ARRs to inhibit seed germination in Arabidopsis

Summary The plant hormone abscisic acid (ABA) plays a crucial role in regulating seed germination and post‐germination growth. ABSCISIC ACID INSENSITIVE4 (ABI4), an APETALA2 (AP2)‐type transcription factor, is required for the ABA‐mediated inhibition of seed germination. Cytokinins promote seed germination and seedling growth by antagonizing ABA signaling. However, the interaction between ABA and cytokinin signaling during seed germination remains unclear. Here, we report that ABA signaling downregulates Arabidopsis response regulators (ARRs), a class of cytokinin‐inducible genes, during seed germination and cotyledon greening. We found that the application of exogenous ABA repressed the expression of type‐A ARRs in Arabidopsis seeds and seedlings. Among the type‐A ARR family members, the expression of ARR6, ARR7 and ARR15 was upregulated in ABA‐deficient mutants, indicating that the transcriptional inhibition of type‐A ARRs requires the ABA signaling pathway. Single and multiple mutations of these ARRs resulted in increased ABA sensitivity during germination and cotyledon greening; overexpression of ARR7 or ARR15 led to an ABA‐insensitive phenotype. These observations suggest that type‐A ARRs inhibit the ABA response during seed germination and cotyledon greening. Further analysis showed that ABI4 negatively regulated the transcription of ARR6, ARR7 and ARR15 by directly binding to their promoters. Genetic analysis showed that loss‐of‐function mutations of ARR7 and ARR15 partially rescued the ABA insensitivity of abi4‐1. Thus, this study revealed that ABI4 plays a key role in ABA and cytokinin signaling by inhibiting the transcription of type‐A ARRs to inhibit seed germination and cotyledon greening. Significance Statement The plant hormone abscisic acid (ABA) suppresses seed germination, while cytokinin promotes seed germination and seedling growth. The detailed molecular mechanisms underlying ABA and cytokinin antagonism during seed germination remain elusive. Here we report that the transcription factor ABI4 negatively regulates the expression of Arabidopsis response regulators (ARRs), a class of cytokinin‐inducible genes. Thus ABI4 is a key node that integrates ABA and cytokinin signalling to modulate seed germination and cotyledon greening.