Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors influencing reversion from virus infection in sweetpotato

Viruses limit sweetpotato (Ipomoea batatas) production worldwide. Many sweetpotato landraces in East Africa are, however, largely virus-free. Moreover, some plants infected by the prevalent Sweet potato feathery mottle virus (SPFMV) may be able to revert to virus-free status. In this study, we analysed reversion from SPFMV, Sweet potato virus C, Sweet potato mild mottle virus, Sweet potato chlorotic stunt virus (SPCSV) and Sweet potato leaf curl Uganda virus using the indicator plant I. setosa and PCR/reverse-transcriptase PCR. We also investigated environmental factors (temperature and soil nutrients) that may influence reversion from virus infection. We tested reversion in the East African cultivars New Kawogo, NASPOT 1 and NASPOT 11, and the United States cultivars Resisto and Beauregard. Reverted plants were asymptomatic and virus was undetectable in assayed parts of the plant. After graft inoculation, only the East African cultivars mostly reverted at a high rate and from most viruses though cultivar Beauregard fully reverted following sap inoculation with Sweet potato virus C. None of the tested cultivars fully reverted from single or double infections involving SPCSV, and reversion was only observed in co-infections involving potyviruses. Root sprouts derived from SPFMV-reverted plants were also virus free. Reversion generally increased with increasing temperature and by improved soil nutrition. Overall, these results indicate variation in reversion by cultivar and that the natural ability of sweetpotato plants to revert from viruses is malleable, which has implications for both breeding and virus control.
Diet and parasitism in Leposternon polystegum (Amphisbaenia, Amphisbaenidae) from coastal areas in the Brazilian Northeast

ABSTRACT Amphisbaenids are fossorial reptiles with morphological adaptations to subterraneous life. These reptiles feed mainly on arthropods and may act as hosts of several parasite groups. This study analysed specimens of Leposternon polystegum regarding their diet and helminths occurrence, sampled in coastal areas of Ceará State, Brazilian Northeast. The most common prey categories in the diet were Isoptera, Formicidae, and larvae of Coleoptera. Termites were predominant in frequency (48.6%), number (60.9%), and volume (66.5%). There was no difference between sexes in relation to number, volume, and size of preys consumed. Only the nematode species Aplectana nordestina was found, with prevalence of 65.9% and mean intensity of infection of 72 ± 9.1 (7–215). Males and females did not different in their parasite infection intensity. Amphisbaenids are commonly host to nematodes, as well as termites are fundamental prey in their diet.
Ageing before birth: pace and stability of prenatal growth affect telomere dynamics

Pre-natal effects on telomere length are increasingly recognized as a potential contributor to the developmental origin of health and adult diseases. While it is becoming clear that telomere length is strongly influenced by pre-natal conditions, the factors affecting telomere dynamics during embryogenesis remain poorly understood. We manipulated both the pace and stability of prenatal growth using incubation temperature in Japanese quail and investigated the impact on telomere dynamics from embryogenesis to adulthood, along with potential drivers of telomere shortening such as oxidative damage and prenatal glucocorticoid levels. Telomere length was not affected by these manipulations for the first 75% of prenatal development, but was reduced at hatching in response to both experimentally induced fast embryo growth and growth instability. These early-life effects on telomere length persisted until adulthood. The effect of developmental instability on telomere length at hatching was potentially mediated by an increased secretion of glucocorticoid hormones during development. Both the pace and the stability of prenatal growth appear as key factors determining telomere length and dynamics up to adulthood, with fast and unstable embryo growth leading to short telomeres with the potential for adverse associated outcomes in terms of reduced longevity and greater risk of disease.
Educational and Economic Outcomes of an Intervention to Improve Early Testing and Treatment of HIV

Background: Education is needed to address professional practice gaps in testing, linkage to care, and treatment of human immunodeficiency virus (HIV) in the primary care setting. Further, little is known about the economic impact of continuing medical education in this area. Methods: We executed one online and two live continuing education activities designed to enhance competence in testing and treating HIV. Competence was measured using pre- and post-activity case vignettes. Costs averted when participants implemented learning into their clinical practices were estimated using the outcomes impact analysis (OIA) model. We modeled: 1) decreased transmission of HIV resulting from awareness of infection and 2) earlier initiation of antiretroviral therapy (ART). The perspective was that of the healthcare payer and the time span was one year. Results: Participants from the live (n = 64) and online (n = 230) activities demonstrated educationally and statistically significant improvement in all 3 competencies (P ≤ .01 for all). Evaluations demonstrated a strong commitment to change and the intention to incorporate learning into practice. For the first OIA model, the estimated costs averted were be $10,731,517 when testing related awareness led to decreased transmission. For the second OIA model, earlier treatment comparing ART initiation at 351-500 CD4 cells/μL versus 201-350 CD4 cells/μL, the estimated costs averted were $11,685,686. When we compared initiating ART at 351-500 CD4 cells/μL versus < 200 CD4 cells/μL, the costs averted were estimated to be $39,521,676. Conclusions: An educational intervention improved competence in testing, linkage to care, and treatment of HIV. Estimates of the economic impact suggest that implementation of learning from the activity is associated with substantial cost savings.
WITOD: A Tool for Within-Taxon Operational Taxonomic Unit Diversity Analysis

Motivation Taxonomic analysis of microbiomes based on 16S rRNA amplicons has so far been usually restricted to abundance analysis of operational taxonomic units (OTUs), which are usually mapped to genus, as the furthest level for a balance between accuracy and speed. Biodiversity within taxa has been little studied, due to lack of proper computational tools. Within-taxon diversity reflects genetic polymorphism within the taxa to reveal whether there are potentially more variants/lineages for some microbiome-associated traits, e.g., diseases or bioconversion efficiency. The diversity will aid diagnosis decisions. Results Here we introduce a tool, WITOD, for the WIthin-Taxon Operational taxonomic unit Diversity analysis. WITOD works on the alignment of all the OTU sequences within a taxon to get a non-redundant alignment with consensus regions on both ends (due to the conservation of the 16S regions used). Then the relative abundance of identical OTUs is combined; more specific taxonomy is obtained through BLASTn of these OTU sequences against the Silva database. One of the outputs is an OTU table with these unique OTUs with new taxonomy, combined relative abundance. In addition, another table can be constructed which we call the diversity table that associates the number of OTUs for a specific Taxa and the relative abundance in that environment. This can be used to further discover the importance of differing diversity in a given environment. Conclusions In this paper, we have introduced a python program WITOD which is a computational tool to analyze the within-taxon biodiversity of microbiome composition. It will be useful in revealing the genetic polymorphism in general and aiding identifying the causative human pathogens or environmental disease vectors. WITOD is available at https://github.com/johncava/WITOD
A guide for mental health practitioners working with collective trauma victims from Latin America: An experiential approach

A resource guide for mental health practitioners working with Latino victims of collective trauma was developed based on a review of the literature. The development of the resource was also informed by two structured interviews with experts in the field of collective trauma within the Latino population. Review of the literature and structured interviews were used to develop culturally sensitive treatment approaches for victims of collective trauma from Latin America. The resource guide offers clinicians culturally adapted interventions, including PTSD measures, a table to identify culture bound syndromes, PTSD psychoeducation handouts (provided in Spanish and English), relaxation skills (e.g. breathing techniques, progressive muscle relaxation, the use of music, meditation), interoceptive exposure protocols, and tools to help clients live a life of meaning as well as restore their roles in the community and within their family. An additional two experts in the field evaluated the resource guide for validity, content, and applicability to the Latino population. Feedback from the evaluators will be used for future versions of the resource guide. Results indicated that the resource guide may be advantageous for Latino victims of collective trauma and may therefore serve as an adjunct to current treatment protocols. The resource guide may assist mental health practitioners in modifying their approach to treatment as well as offer culturally appropriate interventions in order to enhance cultural sensitivity, thus leading to a stronger therapeutic alliance.
Modeling Dragons: Using linked mechanistic physiological and microclimate models to explore environmental, physiological, and morphological constraints on the early evolution of dinosaurs

We employed the widely-tested biophysiological modeling software, Niche Mapper™ to investigate the metabolic function of Late Triassic dinosaurs Plateosaurus and Coelophysis during global greenhouse conditions. We tested them under a variety of assumptions about resting metabolic rate, evaluated within six microclimate models that bound paleoenvironmental conditions at 12° N paleolatitude, as determined by sedimentological and isotopic proxies for climate within the Chinle Formation of the southwestern United States. Sensitivity testing of metabolic variables and simulated “metabolic chamber” analyses support elevated “ratite-like” metabolic rates and intermediate “monotreme-like” core temperature ranges in these species of early saurischian dinosaur. Our results suggest small theropods may have needed partial to full epidermal insulation in temperate environments, while fully grown prosauropods would have likely been heat stressed in open, hot environments and should have been restricted to cooler microclimates such as dense forests (under any vegitative cover) or those seen at higher latitudes and elevations. This is in agreement with the Late Triassic fossil record and may have contributed to the latitudinal gap in the Triassic prosauropod record.
Fully-automated cell-type identification with specific markers extracted from single-cell transcriptomic data

Single-cell transcriptomics enables systematic charting of cellular composition of complex tissues. Identification of cell populations often relies on unsupervised clustering of cells based on the similarity of the scRNA-seq profiles, followed by manual annotation of cell clusters using established marker genes. However, manual selection of marker genes for cell-type annotation is a laborious and error-prone task since the selected markers must be specific both to the individual cell clusters and various cell types. Here, we developed a computational method, termed ScType, which enables data-driven selection of marker genes based solely on given scRNA-seq data. Using a compendium of 7 scRNA-seq datasets from various human and mouse tissues, we demonstrate how ScType enables unbiased, accurate and fully-automated single-cell type annotation by guaranteeing the specificity of marker genes both across cell clusters and cell types. The widely-applicable method is implemented as an interactive web-tool (https://sctype.fimm.fi), connected with comprehensive database of specific markers.
Cross-species machine learning improves diagnostic classification of human psychiatric disorders

Psychiatric disorders often exhibit shared (co-morbid) symptoms, raising controversies over accurate diagnosis and the overlap of their neural underpinnings. Because the complexity of data generated by clinical studies poses a formidable challenge, we have pursued a reductionist framework using brain imaging data of a transgenic primate model of autism spectrum disorder (ASD). Here we report an interpretable cross-species machine learning approach which extracts transgene-related core regions in the monkey brain to construct the classifier for diagnostic classification in humans. The cross-species classifier based on core regions, mainly distributed in frontal and temporal cortex, identified from the transgenic primate model, achieved an accuracy of 82.14% in one clinical ASD cohort obtained from Autism Brain Imaging Data Exchange (ABIDE-I), significantly higher than the human-based classifier (61.31%, p < 0.001), which was validated in another independent ASD cohort obtained from ABIDE-II. Such monkey-based classifier generalized to achieve a better classification in obsessive-compulsive disorder (OCD) cohorts, and enabled parsing of differential connections to right ventrolateral prefrontal cortex being attributable to distinct traits in patients with ASD and OCD. These findings underscore the importance of investigating biologically homogeneous samples, particularly in the absence of real-world data adequate for deconstructing heterogeneity inherited in the clinical cohorts. One Sentence Summary Features learned from transgenic monkeys enable improved diagnosis of autism-related disorders and dissection of their underlying circuits.
Oxygen challenge MRI: development of a novel technique and application to acute stroke patients

The treatment of hyperacute ischaemic stroke has been revolutionised by the concept of potentially salvageable tissue – the ‘ischaemic penumbra’. However, current therapeutic practice is to administer thrombolytic therapy with recombinant tissue plasminogen activator after exclusion of intra-cerebral haemorrhage, with ‘time since onset’ used as a surrogate marker for the presence or absence of the ischaemic penumbra. The ability to identify the penumbra on an individual basis would enable bespoke treatment plans on the basis of underlying pathophysiology. The most commonly employed penumbral image technique is multi-modal magnetic resonance imaging (MRI) to identify a region of perfusion-diffusion mismatch. However, this approach remains to be validated. Moreover, a systematic review presented as an appendix to this thesis highlights the marked heterogeneity for its application. This thesis focusses on the development of a novel MRI technique (Oxygen Challenge) and is the first to report findings from human acute ischaemic stroke. The rationale for this technique is that it is sensitive to deoxyhaemoglobin, which is produced as a consequence of oxidative metabolism. It therefore has the potential to discriminate tissue compartments based on metabolic activity. For this study, 35 subjects with acute ischaemic stroke were imaged with transient hyperoxia (Oxygen Challenge) applied during continuous T2*-weighted MRI. Exploratory analyses suggested the following; •Oxygen Challenge precipitates a T2*-weighted signal increase in healthy tissue •This signal increase is partly dependent on the underlying cerebral blood volume, as suggested by univariate and multivariate analyses •In general, higher concentrations of oxygen precipitate greater T2*-weighted signal increases, but oxygen may influence T2*-weighted signal intensity in a bi-modal manner •The signal changes in operationally defined infarct core are attenuated, suggesting a metabolic influence on Oxygen Challenge results •Signal increases in the hyperacute perfusion-diffusion mismatch region were sometimes exaggerated, consistent with increased oxygen extraction fraction. However, small volumes of tissue acquired from only a few subjects limited definitive conclusions in this study •Oxygen Challenge may detect regions of crossed cerebellar diaschsis, although further confirmation is required •Maps of ‘percentage signal change’ allowed rapid evaluation of whole brain Oxygen Challenge data •Improvements in signal-to-noise ratio are required before this technique can be applied in clinical practice. On the basis of these data it is concluded that the technique is encouraging and further validation is warranted.
Genetic Parameter Contributing to Lodging Resistance of F2 Population in Red Rice

The effectiveness and successful of selection depend on the value of genetic variability, heritability and genetic advance estimation. The purpose of this research is to measure the value of genetic parameters (variability, heritability and genetic advance) of F2 lines derived from crossing of mutant red rice, local accession of red rice, and commercial upland rice varieties. This research used single plant design. The rice materials used in this research was the F2 seeds derived from hibridization between MR1512 X Inpago 8, MR1512 X Banyuasin, Inpago 8 X Balok, Balok X Banyuasin and Balok X Inpago 8. Selection intensity used is 10%. The filled grains and grain weight have a wide phenotypic variability, whereas the plant height and the productive tiller numbers have wide genotypic variability. The high heritability value was found in the plant height, flowering time, and harvest time. The high genetic advance was found in plant height, productive tillers number, flowering time, and harvest time. In the present work, it has been shown that the plant height, productive tiller numbers, flowering time, and harvest time are the important traits for use in rice lodging tolerance breeding program.
GENETIC BEHAVIOR OF YIELD, GRAIN QUALITY, STEM BORER AND STORAGE INSECT INFESTATION TRAITS FOR SOME RICE GENOTYPES AT DIFFERENT SOWING DATES.

The present investigation was carried out at Rice Research and Training Center and lab of Plant Protection Institute, Sakha, Kafr EL-Sheikh, Egypt, during 2011 and 2012 seasons. The objectives of this investigation is amid to study the genetic behavior of ten rice genotypes under three sowing dates (May1 st , May 15 th and May30 th ), the effect of different sowing dates on grain quality characters, and on the infestation by stem borer and to evaluate the susceptibility of certain rice varieties against the infestation by Lesser grain borer, Rhizopertha dominica (F.). The tested genotypes were; Giza177, Giza 178, Sakha 101, Giza 182, GZ 9057-6-1-3-2, GZ 9577-4-1-1, GZ 9523-2-1-1-1, GZ 9461-4-2-3-1, Egyptian Yasmin, and SK2034 H1. Giza 178 cultivar produced maximum grain yield and it remained statistically at par with SK2034 genotype. Egyptian Yasmin gave minimum grain yield. Grain yield averaged across all the genotypes seems to be maximum at sowing date of 1 st May. However, the lowest yield was recorded in sowing date of 30 th May. Sowing dates significantly affected the milled rice % in the first season only and highest milled rice % belonged to the second planting date in the first season. Highest milled rice % were obtained for Giza 177 and GZ 9523-2-1-1-1; the lowest percentages were observed for GZ 9577-4-1-1 and Giza 178. For Stem borer (Chilo agamemnon Bles.), Giza 178, Sakha101, GZ 9577-4-1-1 and GZ 9461-4-2-3-1 were resistant (R) with 1.44, 0.83, 2.66 and 1.93 WH%, respectively. While, five genotypes (Giza177, Giza182, GZ 9057, GZ 9577-4-1-1 and SK2034 H1) were moderately resistant (MR) with 4.18, 4.14, 5.94, 3.46, and 5.36 WH%, respectively. On the other hand, one genotype (Egyptian Yasmin) was moderately susceptible (MS) with 6.32 WH%. The number of adult emergence of Rhizopertha dominica ranged from 1.08 insects (Sakha101) to 8.25 insects (GZ9577-4-1-1) (low susceptibility varieties to insect infestation). Also, the number of adult emergence ranged from 13.08 insects (Giza182) to 17.58 insects (Giza177) for moderate susceptibility varieties to insect infestation. Also, the number of adult emergence ranged from 21.08 insects (Egyptian Yasmin) to 22.58 insects (GZ 9057-6-1-3-2) which proved to be high susceptibility varieties to insect infestation. Clustering analysis for varieties, based on similarity of quantitative characters, produced two large distinct groups. The first one included five rice genotypes; Giza 178, Giza 182, GZ 9523-2-1-1-1, Egyptian Yasmin and SK2034 H1. These genotypes were Indica and Indica-Japonica types except Gz 9523-2-1-1-1 was Japonica type. While, the second group included Giza 177, Sakha 101, GZ 9057-6-1-3-2, GZ 95774-1-1 and GZ 9461-4-2-3-1, these genotypes were Japonica types and similar in duration and grain yield characters.
Bioefficacy of insecticides against predatory spider in soybean

Field experiments was conducted in kharif season during 2017 and 2018 to evaluate bio-efficacy of insecticides against spider in soybean. The pooled data of both the years indicated that there were highest population of spider recorded in control plot (0.97 spider/mrl), chlorantraniliprole 0.4 GR (0.92 spider/mrl) and thiamethoxam 30 FS (0.89 spider/mrl). The lowest population found in imidacloprid 48 FS (0.82 spider/mrl) and phorate 10 CG (0.85 spider/mrl) followed by fipronil 0.3GR (0.87 spider/mrl) and clothiniadin 50 WDG (0.88 spider/mrl). The pooled data of two years indicated that the maximum yield of soybean was recorded in chlorantraniliprole 0.4 GR (26.46 q/ha) followed by clothianidin 50 WDG (25.93 q/ha), fipronil 0.3 GR (25.22 q/ha) and thiamethoxam 30 FS (23.42 q/ha) at par with each other. whereas the lowest yield was found in control plot (18.02 q/ha) and phorate 10 CG (22.40 q/ha).
High-fiber, noncaloric flour substitute for baked foods. Properties of alkaline peroxide-treated lignocellulose

Treatment of lignocellulosic materials such as wheat straw, corn stalks, cereal brans, or vegetable and fruit pulps with an alkaline (pH 11.5) solution of hydrogen peroxide dramatically increased their ability to absorb water, soften, and swell when hydrated. Substitution of alkaline hydrogen peroxide treated lignocellulose for cornstarch-dextrose mixtures in the diets of nonruminant animals (rats, chicks) reduced the digestibility of the diets without increasing the amount of feed consumed. As a result, the rate and efficiency and weight gain were reduced for animals consuming the diets containing treated lignocellulose. The low digestibility of alkaline peroxide-treated lignocellulose by nonruminants, in conjunction with its enhanced physical properties compared with other cellulosic ingredients for baked foods, suggests that this material may be useful as an ingredient for reducing caloric density and/or increasing dietary fiber content of baked products.