Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative transcriptomic analysis reveals gene expression changes during early stages of Plasmodiophora brassicae infection in cabbage (Brassica oleracea var. capitata L.)

Abstract Clubroot caused by Plasmodiophora brassicae is an economically important disease of crucifer crops throughout the world and is a major threat to the quality and yield of cabbage (Brassica oleracea var. capitata L.) in China. Host resistance is essential for clubroot management. Although two cabbage lines (clubroot-resistant line CR21 and clubroot-susceptible line CS54) have been identified through screening 80 cabbage accessions, the molecular mechanisms underlying differential responses to clubroot remain elusive. Herein, RNA-seq analysis was performed to characterize the transcriptomic changes in CR21 and CS54 at 3 days after P. brassicae inoculation (DAI). In total, 1057 and 4741 differentially expressed genes (DEGs) were found in CR21 and CS54, respectively. Moreover, 541 genes were up-regulated in CR21, but showed either no significant change or were down-regulated in CS54. Gene Ontology (GO) analysis showed that most DEGs were involved in metabolism, transport, signal transduction and defence. Compared with the identified putative defence response genes in Arabidopsis thaliana, 165 resistance-related DEGs were obtained, including PAMPs-triggered immunity (PTI)-related genes and Effector-triggered-immunity (ETI)-related genes. Interestingly, the co-supported defence response DEGs contained the defence-related genes, wound response genes, RBOHB, WRKY28, TIR-NBS-LRR class (RPS4 etc.), pathogenesis-related (PR) gene (Bo7g005050), lipid transfer protein class (LTP1 etc.), plant hormone-related genes, ethylene signalling transduction (HRE1-like gene and EIN3), ABA signalling (PP2C and PYL13), and cell wall modification related genes (EXP17 and PME44, beta-1,3-glucanase and cytochrome P450 genes). Taken together, this study provided a comprehensive insight into transcriptomic responses to P. brassicae infection in two different cabbage lines, and identified several candidate genes that might contribute to clubroot resistance in cabbage and other Brassica crops.
Supplementation of fungal and/or bacterial phytase in broiler diets formulated with reduced phosphorus level and different calcium contents

ABSTRACT The objective of the current study was to evaluate the effects of three calcium:available phosphorus (Ca:aP) ratios and different supplementation with phytases from different origins on performance and ash, Ca, and P contents in the tibia of broilers. A total of 900 male broilers (22 to 35 days old) were fed ten dietary treatments in a completely randomized design. A 3 × 3 + 1 factorial scheme was used, corresponding to three Ca:aP ratios (4.5:1.0, 6.0:1.0, and 7.5:1.0) and [. ]
The Developmental Transcriptome for Lytechinus variegatus Exhibits Temporally Punctuated Gene Expression Changes

Embryonic development is arguably the most complex process an organism undergoes during its lifetime, and understanding this complexity is best approached with a systems-level perspective. The sea urchin has become a highly valuable model organism for understanding developmental specification, morphogenesis, and evolution. As a non-chordate deuterostome, the sea urchin occupies an important evolutionary niche between protostomes and vertebrates. Lytechinus variegatus (Lv) is an Atlantic species that has been well studied, and which has provided important insights into signal transduction, patterning, and morphogenetic changes during embryonic and larval development. The Pacific species, Strongylocentrotus purpuratus (Sp), is another well-studied sea urchin, particularly for gene regulatory networks (GRNs) and cis-regulatory analyses. A well-annotated genome and transcriptome for Sp are available, but similar resources have not been developed for Lv. Here, we provide an analysis of the Lv transcriptome at 11 timepoints during embryonic and larval development. The data indicate that the gene regulatory networks that underlie specification are well-conserved among sea urchin species. We show that the major transitions in variation of embryonic transcription divide the developmental time series into four distinct, temporally sequential phases. Our work shows that sea urchin development occurs via sequential intervals of relatively stable gene expression states that are punctuated by abrupt transitions. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which . http://dx.doi. org/10.1101/572388 doi: bioRxiv preprint first posted online Mar. 8, 2019;
Wearable Multiple Modality Bio-Signal Recording and Processing on Chip: A Review

Remote home monitoring via wearables is rapidly gaining popularity, thanks to ever more complex vital signs recording and data analytics that are embedded into single devices. True system-on-chips (SoCs) push the envelope of power and form factor, while wearables are becoming more common-place, novel health sensing paradigms appear. Non-contact sensing technologies enable vital signs sensing without requiring any physical contact with the human body. This article reviews existing multiple-modality bio-signal recording and processing SoCs, circuit techniques for individual bio-signal readout channels including electrocardiography (ECG), Electroencephalography (EEG), Bio-impedance (BioZ), photoplethysmography (PPG), and non-contact sensing with high user comfort. The state-of-the-art wearable sensor interfaces and systems together with future development trends are provided.
Multi-site sampling and risk prioritization reveals the public health relevance of antibiotic resistance genes found in wastewater environments

The spread of bacterial antibiotic resistance across human and environmental habitats is a global public health challenge. Wastewater has been implicated as a major source of antibiotic resistance in the environment, as it carries resistant bacteria and resistance genes from humans into natural ecosystems. However, different wastewater environments and antibiotic resistance genes in wastewater do not all present the same level of risk to human health. In this study, we investigate the public health relevance of antibiotic resistance found in wastewater by combining metagenomic sequencing with risk prioritization of resistance genes, analyzing samples across urban sewage system environments in multiple countries. We find that many of the resistance genes commonly found in wastewater are not readily present in humans. Ranking antibiotic resistance genes based on their potential pathogenicity and mobility reveals that most of the resistance genes in wastewater are not clinically relevant. Additionally, we show that residential wastewater resistomes pose greater risk to human health than those in wastewater treatment plant samples, and that residential wastewater can be as risky as hospital effluent. Across countries, differences in antibiotic resistance in residential wastewater can, in some cases, reflect differences in antibiotic drug consumption. Finally, we find that the flow of antibiotic resistance genes is influenced by geographical distance and environmental selection. Taken together, we demonstrate how different analytical approaches can provide greater insights into the public health relevance of antibiotic resistance in wastewater.
The relationship of breakfast and snack foods with cognitive and academic performance and physical activity levels of adolescent students

ABSTRACT The aim of the present study was to examine the relationship of breakfast and snack consumption with academic and cognitive performance and physical activity (PA) status in adolescent students. In a cross-sectional study, 600 participants (age: 13.9±2.7 years; height: 161.1±2.6 cm; weight: 53.4±3.9 kg) in the first grade of high school were selected for the study. Demographic characteristics, breakfast and snack consumption were, respectively, collected by self-administered and 24-h calorie intake questionnaires. Academic and cognitive performance were, respectively, measured by the final exams scores and cognitive function questionnaire and PA status were measured using the international physical activity questionnaire. The results indicated that breakfast and snack meals had significant effects on cognitive functions (p<0.05) and physical activity level (p<0.05). The results also indicated that the breakfast meal had a significant effect on academic performance (p<0.05). However, the non-significant effect was found for snack meal (p=0.94). It was shown that breakfast and snack meals predict 79% of the cognitive performance, 77% of the academic performance and 70% of the PA levels. In conclusion, breakfast and snack consumption had a beneficial effect on students' cognitive functions, academic performance as well as PA levels.
Determinants of Exclusive Breastfeeding in Lebanon: An Online Survey

Background: Breastfeeding is the ultimate food source for infants and exclusive breastfeeding is recommended until six months postpartum. In Lebanon, the exclusive breastfeeding rates until six months postpartum are amongst the lowest worldwide, and the factors affecting exclusive breastfeeding have rarely been investigated. Objectives: The aim of this study was to explore the association between certain novel demographic, social and cultural factors with exclusive breastfeeding for the six months postpartum across Lebanon. Methods: 593 mothers recruited via social media completed an online questionnaire. Data analysis consisted of bivariate analysis and multivariate logistic regressions. Results: The findings show that exclusive breastfeeding until six months postpartum is not associated with the housekeeper presence, positively associated with having a prenatal plan to breastfeed, the mother disagreeing that free formula samples should be distributed to the mothers after delivery at the hospital, having the baby’s crib kept by the mother’s bed side at the hospital, not being offered a free formula sample at the hospital, the mother’s partner perceiving breastfeeding as very important, not having the mother’s father living in the same household besides the partner and children when the child was between zero and six months and being non-Lebanese. Conclusions: This is the first study conducted in low and middle-income countries to explore novel factors and their association with exclusive breastfeeding until six months postpartum. This study shows that ensuring appropriate systems and support for mothers, while applying the social-ecological model, should be a priority to improve maternal and child health.
Functional Connectivity of the Anterior and Posterior Hippocampus: Differential Effects of Glucose in Younger and Older Adults

The hippocampus features structurally and functionally distinct anterior and posterior segments. Relatively few studies have examined how these change during aging or in response to pharmacological interventions. Alterations in hippocampal connectivity and changes in glucose regulation have each been associated with cognitive decline in aging. A distinct line of research suggests that administration of glucose can lead to a transient improvement in hippocampus-dependent memory. Here we probe age, glucose and human cognition with a special emphasis on resting state functional connectivity (rsFC) of the hippocampus along its longitudinal axis to the rest of the brain. Using a randomized, placebo-controlled, double-blind, crossover design thirty-two healthy adults (16 young and 16 older) ingested a drink containing 25g glucose or placebo across two counterbalanced sessions. They then underwent resting state functional magnetic resonance imaging and cognitive testing. There was a clear dissociation in the effects of glucose by age. In older participants rsFC between posterior hippocampus (pHPC) and medial prefrontal cortex (mPFC) increased after glucose ingestion, whereas in younger participants connectivity decreased. Magnitude change in rsFC from pHPC to mPFC was correlated with individual glucose regulation and gains in performance on a spatial navigation task. Our results demonstrate that glucose administration can attenuate cognitive performance deficits in older adults with impaired glucose regulation and suggest that increases in pHPC-mPFC rsFC are beneficial for navigation task performance in older participants. This study is the first to demonstrate the selective modulation of pHPC connectivity in the acute setting.
Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics

Human iPSC-derived kidney organoids have the potential to revolutionize discovery, but assessing their consistency and reproducibility across iPSC lines, and reducing the generation of off-target cells remain an open challenge. Here, we used single cell RNA-Seq (scRNA-Seq) to profile 415,775 cells to show that organoid composition and development are comparable to human fetal and adult kidneys. Although cell classes were largely reproducible across iPSC lines, time points, protocols, and replicates, cell proportions were variable between different iPSC lines. Off-target cell proportions were the most variable. Prolonged in vitro culture did not alter cell types, but organoid transplantation under the mouse kidney capsule diminished off-target cells. Our work shows how scRNA-seq can help score organoids for reproducibility, faithfulness and quality, that kidney organoids derived from different iPSC lines are comparable surrogates for human kidney, and that transplantation enhances their formation by diminishing off-target cells.
The structure of morphological variation in the shape of occlusal surface of permanent teeth in pikas Ochotona (Lagomorpha: Ochotonidae)

Variation in the shape of the occlusal surface of permanent teeth was examined in 102 skulls of four species of pikas. Variance components analysis was carried out on Procrustean coordinates retrieved from 71 and 65 landmarks positioned on the lower and upper teeth rows respectively. The main variance was related to the within-group variation, which indicates general instability in the shape of the enamel loops. Sexual variation explained the smallest amount of variance among all factors examined. The highest percentage of age-related variation was found in the premolars of both teeth rows, especially in p3 and P3. The amount of variance due to interspecies variation was relatively low in all analyses, even in the anterior part of p3, which is regularly recommended for the identification of pikas species. There was no evidence of a phylogenetic signal either. Thus we suggest more careful investigation of the role of features of the shape of teeth occlusal surface for species identification. How to cite this article: Volkova V.R. , Lissovsky A.A. 2018. The structure of morphological variation in the shape of occlusal surface of permanent teeth in pikas Ochotona (Lagomorpha: Ochotonidae) // Russian J. Theriol. Vol.17. No.2. P.91–99. doi: 10.15298/rusjtheriol.17. 2.05
A reformulation of the selection ratio shed light on resource selection functions and leads to a unified framework for habitat selection studies

The selection ratio (SR), i.e. the ratio of proportional use of a habitat over proportional availability of this habitat, has for long been the standard metric of habitat selection analyses. It is easy to compute and directly estimates disproportionate use. Its apparent restriction to habitat selection analyses using categorical predictors led to the development of the resource selection functions (RSF) approach, which has now become the norm. The RSF approach has however led to debates and confusion. For instance, what functional form can be used remains debated, and the concept of relative probability of selection is often misunderstood. I propose a reformulation of the SR demonstrating that it can be estimated in a regression context, and thus even with continuous predictors. This reformulation suggests that RSF can be seen as an intermediate step in the calculation of SR. This reformulation also clarifies some longstanding debates about RSF and data-selection/fitting practices. I further suggest that SR estimates the strength of habitat selection, but that the contribution of selection in determining use, which should be more directly linked to fitness than selection per se, should be estimated by another metric, the selection effect on use (SE). SE could be estimated simply as the difference between proportional use and proportional availability, and can be computed from SR and a density estimation of availability. I conduct a habitat selection analysis of plains zebras to demonstrate the added-value of going beyond RSF scores and using SR estimated in a regression context, and of combining SR and SE. Overall, I highlight the inter-relation between various metrics used to study habitat selection (i.e., SR, other selection indices, RSF scores, marginality). I conclude by proposing that SR and SE can be the unifying metrics of habitat selection, as together they offer a comprehensive view on the strength of habitat selection and its effect on habitat use.
Changes of Lymphocyte, Interleukin-6 and Inflammatory Indexes in Patients with Coronavirus Disease 2019 under Different Conditions of Disease in Northeast Division of Chongqing/ 渝东北片区新型冠状病毒肺炎患者不同病情状态下淋巴细胞、白细胞介素-6及炎症指标的变化

Objective To analyze the changes of lymphocyte, interleukin-6 (IL6) and inflammatory indexes in patients with coronavirus disease 2019 under different conditions of disease in northeast division of Chongqing Methods A total of 74 patients with coronavirus disease 2019 in Chongqing Three Gorges Central Hospital from January 28, 2020 to February 21, 2020 were selected, which including 27 severe cases, 18 critical cases and 29 mild cases They were divided into five groups according to their disease status, among whom the critically ill patients were divided into groups A, B, C and D, and the mild ill patients into group E Some patients were counted several times due to disease progression Flow cytometer and blood routine analyzer were used to detect the levels of lymphocyte, IL-6 and inflammatory indexes in patients with different conditions of disease Results The levels of IL-6 and CRP in severe patients with different conditions of disease were significantly higher than those in mild patients (P 0 05) Conclusion IL-6, lymphocyte and CRP can predict the change of coronavirus disease 2019
Designing CAST: A Computer-Assisted Shadowing Trainer for Self-Regulated Foreign Language Listening Practice

Shadowing, i.e., listening to recorded native speech and simultaneously vocalizing the words, is a popular language-learning technique that is known to improve listening skills. However, despite strong evidence for its efficacy as a listening exercise, existing shadowing systems do not adequately support listening-focused practice, especially in self-regulated learning environments with no external feedback. To bridge this gap, we introduce Computer-Assisted Shadowing Trainer (CAST), a shadowing system that makes self-regulation easy and effective through four novel design elements — (i) in-the-moment highlights for tracking and visualizing progress, (ii) contextual blurring for inducing self-reflection on misheard words, (iii) self-listening comparators for post-practice self-evaluation, and (iv) adjustable pause-handles for self-paced practice. We base CAST on a formative user study (N=15) that provides fresh empirical grounds on the needs and challenges of shadowers. We validate our design through a summative evaluation (N=12) that shows learners can successfully self-regulate their shadowing practice with CAST while retaining focus on listening.
Environmental influence on phytoplankton communities in the northern Benguela ecosystem

An investigation of surface phytoplankton communities was undertaken on the shelf of the northern Benguela upwelling ecosystem during austral autumn (May) and spring (September), along latitudinal transects at 20° S and 23° S, from 2 to 70 nautical miles offshore, as well as on a zigzag grid located between these transects. Microscopic identification of the phytoplankton and CHEMTAX analysis of pigment biomarkers were used to characterise the community composition. During May 2014, warmer, more-saline water with a shallower upper mixed layer corresponding to periods of less-intense offshore Ekman transport was encountered on the shelf. Satellite imagery indicated high phytoplankton biomass extending for a considerable distance from the coast, and CHEMTAX indicated diatoms as dominant at most of the stations (52–92%), although dinoflagellates were dominant at some inshore localities (57–74%). Species of Chaetoceros, Bacteriastrum and Cylindrotheca were the most abundant, with abundance of the Pseudo-nitzschia ‘seriata-group’ being particularly high at a number of stations. In September 2014, more-intense wind-forcing resulted in a deeper upper mixed layer and stronger upwelling of colder, less-saline water. Elevated phytoplankton biomass was confined close to the coast, where diatoms accounted for most of the population (54–87%), whereas small flagellates, such as prasinophytes, haptophytes and cryptophytes, as well as the cyanobacterium Synechococcus, dominated the communities (58–90%) farther from the coast. It is hypothesised that stronger upwelling and deeper vertical mixing in September of that year were not conducive for widespread diatom growth, and that small flagellates populated the water column by being entrained from offshore onto the shelf in the upwelled water that moved in towards the coast.
Magnetic Field Generation System of the Magnetic Probe With Diamond Quantum Sensor and Ferromagnetic Materials for the Detection of Sentinel Lymph Nodes With Magnetic Nanoparticles

We have developed the magnetic probe with a diamond quantum sensor and electromagnetic coils to detect sentinel lymph nodes (SLNs), as the medical application of diamond quantum sensing. The probe magnetizes magnetic nanoparticles (MNPs) accumulated in SLNs and detect the magnetic fields of magnetized MNPs. In this study, we designed a ferromagnetic core that has a unique shape and optimized the magnetic field generation system for improving the detection performance such as the magnetic sensitivity and detectable distance. The proposed magnetic core enhances an excitation magnetic field strength at a longer distance and suppresses a bias field strength at a location of the diamond quantum sensor. The increment of the excitation field is approximately 370% and the decrement of the bias field is approximately 45%. In addition to the proposed magnetic core, even applying a cancellation coil, the excitation field strength is tenfold compared with the coil only structure, suggesting the larger magnetization of MNPs generates the large magnetic field for longer detectable distance.