Miracle-dz/UniFAR-FTUs huggingface dataset:
Repeatability of methane emission measurements in Australian beef cattle

Records on 175 young Angus heifer and bull progeny from 46 sires, measured for methane production in respiration chambers, were used to evaluate the repeatability of methane measurement over short- and long-term periods. The traits assessed were dry matter intake (DMI), methane production rate (MPR), methane yield (MPR per unit DMI), and four residual methane (RMP) traits. The RMP traits were computed as actual MPR minus expected MPR, where the expected MPR for the first three RMP traits were calculated from three different published and widely used equations. The expected MPR for the fourth was computed by regressing MPR on DMI, using the data from the study. Animals underwent an initial (first) methane measurement test for 48 h, and one repeat methane measurement test up to 450 days after the first test. Repeat tests were classified into four different time periods: tested across consecutive days; re-tested within 60 days of first test; re-tested 61–120 days after first test; and re-tested 121–450 days after first test. Repeatabilities were calculated for all traits across all time periods, and phenotypic correlations for the same trait measured over time were obtained from bivariate analyses. Methane traits from tests conducted over consecutive days were highly repeatable (0.75–0.94) and highly phenotypically correlated (0.85–0.95). Repeatabilities from tests conducted within 60 days of the first test were moderate to high (0.59–0.91), whereas phenotypic correlations were, in general, moderate (0.30–0.44), with the exception of MPR (0.78). Results for both longer-term time periods (61–120 days and 121–450 days after the first test) were very similar, with low estimates of repeatabilities (0.16–0.27) and phenotypic correlations (0.12–0.27). Correlations between sire progeny means from the first and repeat methane test were moderate (0.46–0.77) for all traits except RMPR (0.19). Results from this study indicate that methane traits from tests conducted either on consecutive days or within a short-term time frame afterward (~60 days) are highly repeatable and highly phenotypically correlated. However, methane tests conducted over longer-term time frames are substantially, but consistently, less repeatable and are lowly phenotypically correlated, which indicates that multiple measures may be required to accurately record methane traits over the life time of an animal.
The Systematics and Evolution of the Crocodilia as Suggested by Restriction Endonuclease Analysis of Mitochondrial and Nuclear Ribosomal DNA

We present restriction fragment analyses of mitochondrial and ribosomal DNAs in an effort to resolve some critical systematic questions among extant members of the order Crocodilia. This paper concentrates on interspecific relationships among all the species of the circumtropical genus Crocodylus (the true crocodiles), the relationship of Crocodylus to Osteolaemus (the dwarf-African crocodile) and tests the hypothesis that the two gharial genera, Gavialis and Tomistoma, are more closely related to one another than to any other group of living crocodilians. This first extensive molecular phylogeny of the true crocodiles not only aligns some species that are found in the same hemisphere but also places organisms that currently have disjunct distributions in the same clade. We also include a method of analysis (compatible parsimony) for restriction fragment data that appears to combine compatibility and parsimony criteria.
Multidisciplinary rehabilitation in persons with multiple trauma: A systematic review.

OBJECTIVE To determine the effectiveness of multidisciplinary rehabilitation in improving functional and psychological outcomes in person with multiple trauma. DATE SOURCES A comprehensive literature review was conducted using medical and health science electronic databases up to February 2019. DATA EXTRACTION Two independent reviewers selected studies, extracted data and assessed study quality using the Critical Appraisal Skills Programme (CASP) checklists and Grading of Recommendations, Assessment, Development and Evaluations (GRADE). DATA SYNTHESIS One randomized controlled trial, 1 clinical controlled trial and 4 observational studies (1 with 2 reports) were included. Qualitative analysis was used to synthesize the evidence due to the heterogeneity of included trials. The quality of the studies varied (CASP approach); the majority were of "low quality". The findings suggest "very low to moderate" evidence (GRADE) for the effectiveness of multidisciplinary rehabilitation in improving functional ability and participation. The majority of studies (n = 6) reported functional improvements after multidisciplinary rehabilitation in the short-term. CONCLUSION The lack of "high-quality" evidence for multidisciplinary rehabilitation in improving outcomes following trauma highlights gaps in the available evidence, signifying the need for more robust studies.
Effect of aeration of the nutrient solution on the growth and quality of purslane (Portulaca oleracea)

Summary The aim of this work was to assess the influence of three levels of aeration of the nutrient solution (high, low, or no aeration) on the growth and quality of two cultivars of purslane (Portulaca oleracea L.): the commercial cultivar, ‘Golden Purslane’, and a local Spanish accession, C-215. Both were grown in a floating system over four crop cycles. Our results showed purslane to be a crop that exhibited little sensitivity to oxygen depletion in the rooting medium, since it was able to adapt to a gradual reduction in oxygen content. Under such conditions, purslane plants created an aerenchyma tissue (equivalent to approx. 10% of root sections in the non-aerated treatments in both cultivars) that helped to maintain growth. Under conditions in which no aeration was provided, there was a slight decrease in plant growth. The final quality of the product was improved because leaf nitrate concentrations were reduced (by more than 1,300 mg kg–1 FW) compared with the high aeration treatment, and the content of functional phytochemicals and SPAD values (chlorophyll contents) were increased.
Radiographic predictive findings of neck pain in patients with ankylosing spondylitis

Abstract Objective The aim of this study was to investigate the relationship between neck pain and radiological findings in ankylosing spondylitis (AS) patients. Methods The study groups comprised 257 AS and 50 normal patients. Of the AS patients, 91 had axial neck pain (group 1) and 166 did not (group 2). Full-length radiographs of the spine in the anteroposterior and lateral planes were taken. Radiographic parameters such as the chin brow vertical angle (CBVA), McGregor slope (McGS), slope of the Line of Sight (SLS), C2 slope, C2-C7 lordosis (CL), C2-C7 sagittal vertical axis (C2-C7 SVA), and T1 slope were measured. Statistical analysis was performed. Results The AS and normal patients were found to have significantly different CBVA, McGS, C2 slope, C2-C7 SVA, and T1 slope. However, no significant difference was observed for SLS and CL. Between groups 1 and 2, there were significant differences in the McGS, CL, and T1 slope. However, no significant difference between these two groups was observed for CBVA, SLS, C2 slope, and C2-C7 SVA. Logistic regression analysis was performed to identify statistically significant predictors of neck pain in AS patients and it revealed that the T1 slope and McGS were two such predictors. The T1 slope showed superior discriminatory power to McGS and CL in the receiver operating characteristic curve analysis. Conclusions This study shows that a high T1 slope and McGS are independent radiological predictors of neck pain in AS. Further well-designed studies would be necessary to substantiate our results.
Genome-Wide Identification and Expression Analysis of the Strawberry FvbZIP Gene Family and the Role of Key Gene FabZIP46 in Fruit Resistance to Gray Mold

A total of 54 FvbZIP genes were identified from the strawberry genome. These genes were found to be unevenly distributed on seven different chromosomes, and two of the genes had no matching chromosomal localization. FvbZIP genes were divided into 10 subfamilies according to protein sequence, and the structures of these genes were found to be highly conserved. Based on the bioinformatics analysis of FvbZIP genes, the expression of FabZIP genes changed during different stages of its growth and of its infection with gray mold disease. FabZIP46 was substantially upregulated, and its expression remained relatively high. FabZIP46 was cloned from cultivated strawberries by homologous cloning. The results of a transient transgenic assay revealed that the damage to the fruit tissue was markedly alleviated in strawberries overexpressing FabZIP46, with the incidence rate being substantially lower than that in the control group. By contrast, a brief silencing of FabZIP46 had the opposite effect. The results revealed that FabZIP46 played a positive role in the resistance of strawberries to Botrytis cinerea. The study findings provide valuable insights into the role of bZIP transcription factors as well as a theoretical reference for the regulation of resistance to gray mold disease in strawberry fruit.
Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic

Background: During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden. Methods: We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 14 May 2020. Results: We identified 14 variant sites ≥5% frequency in the population. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. The variant sites can distinguish 11 mutational profiles in Sweden. Nine of the profiles appeared in Stockholm in March 2020. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10−3 substitutions per year. Conclusions: Our study provides novel knowledge on the spatio-temporal dynamics of Swedish SARS-CoV-2 variants during the early pandemic. Characterization of these viral variants can provide precious insights on viral pathogenesis and can be valuable for diagnostic and drug development approaches.
A new measure of treatment effect in clinical trials involving competing risks based on generalized pairwise comparisons

In survival analysis with competing risks, the treatment effect is typically expressed using cause‐specific or subdistribution hazard ratios, both relying on proportional hazards assumptions. This paper proposes a nonparametric approach to analyze competing risks data based on generalized pairwise comparisons (GPC). GPC estimate the net benefit, defined as the probability that a patient from the treatment group has a better outcome than a patient from the control group minus the probability of the opposite situation, by comparing all pairs of patients taking one patient from each group. GPC allow using clinically relevant thresholds and simultaneously analyzing multiple prioritized endpoints. We show that under proportional subdistribution hazards, the net benefit for competing risks settings can be expressed as a decreasing function of the subdistribution hazard ratio, taking a value 0 when the latter equals 1. We propose four net benefit estimators dealing differently with censoring. Among them, the Péron estimator uses the Aalen–Johansen estimator of the cumulative incidence functions to classify the pairs for which the patient with the best outcome could not be determined due to censoring. We use simulations to study the bias of these estimators and the size and power of the tests based on the net benefit. The Péron estimator was approximately unbiased when the sample size was large and the censoring distribution's support sufficiently wide. With one endpoint, our approach showed a comparable power to a proportional subdistribution hazards model even under proportional subdistribution hazards. An application of the methodology in oncology is provided.
Predicting the fMRI Signal Fluctuation with Recurrent Neural Networks Trained on Vascular Network Dynamics

Abstract Resting-state functional MRI (rs-fMRI) studies have revealed specific low-frequency hemodynamic signal fluctuations (<0.1 Hz) in the brain, which could be related to neuronal oscillations through the neurovascular coupling mechanism. Given the vascular origin of the fMRI signal, it remains challenging to separate the neural correlates of global rs-fMRI signal fluctuations from other confounding sources. However, the slow-oscillation detected from individual vessels by single-vessel fMRI presents strong correlation to neural oscillations. Here, we use recurrent neural networks (RNNs) to predict the future temporal evolution of the rs-fMRI slow oscillation from both rodent and human brains. The RNNs trained with vessel-specific rs-fMRI signals encode the unique brain oscillatory dynamic feature, presenting more effective prediction than the conventional autoregressive model. This RNN-based predictive modeling of rs-fMRI datasets from the Human Connectome Project (HCP) reveals brain state-specific characteristics, demonstrating an inverse relationship between the global rs-fMRI signal fluctuation with the internal default-mode network (DMN) correlation. The RNN prediction method presents a unique data-driven encoding scheme to specify potential brain state differences based on the global fMRI signal fluctuation, but not solely dependent on the global variance.
Leveraging on the genomics and immunopathology of SARS-CoV-2 for vaccines development: prospects and challenges

ABSTRACT The incidence and case-fatality rates (CFRs) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, the etiological agent for Coronavirus Disease 2019 (COVID-19), have been rising unabated. Even though the entire world has been implementing infection prevention and control measures, the pandemic continues to spread. It has been widely accepted that preventive vaccination strategies are the public health measures for countering this pandemic. This study critically reviews the latest scientific advancement in genomics, replication pattern, pathogenesis, and immunopathology of SARS-CoV-2 infection and how these concepts could be used in the development of vaccines. We also offer a detailed discussion on the anticipated potency, efficacy, safety, and pharmaco-economic issues that are and will be associated with candidate COVID-19 vaccines.
Alterations in Gastric Microbial Communities Are Associated with Risk of Gastric Cancer in a Korean Population: A Case-Control Study

Simple Summary The gastric microbial community has been identified as a specific risk factor for the gastric cancer (GC) risk in recent molecular epidemiology studies. The equilibrium of the gastric microbial community and their functions are very important to keep a proper gastric related health. However, dysbiosis where there is an imbalance of the microbiome in gastric environment leads to several pathological conditions including GC. Thus, understanding how alterations in gastric microbial communities are associated with GC risk in large population-based studies is needed to implement possible preventive and curative strategies in the future. We derived a microbial dysbiosis index to observe the association with GC risk. Further, we predicted the microbial functions that are associated with GC risk. The findings of our study are important to understand certain pathogenic bacteria and their functions associated with GC risk. It might be helpful to develop novel preventive guidelines to prevent GC risk. Abstract Although the microbiome has a potential role in gastric cancer (GC), little is known about microbial dysbiosis and its functions. This study aimed to observe the associations between the alterations in gastric microbial communities and GC risk. The study participants included 268 GC patients and 288 controls. The 16S rRNA gene sequencing was performed to characterize the microbiome. Streptococcus_NCVM and Prevotella melaninogenica species were highly enriched in cases and controls, respectively. Those who were in the third tertile of P. melaninogenica showed a significantly decreased risk of GC in total (odds ratio (OR): 0.91, 95% confidence interval (CI): 0.38–0.96, p-trend = 0.071). Class Bacilli was phylogenetically enriched in cases, while phylum Actinobacteria, class Actinobacteria were related to the controls. The microbial dysbiosis index (MDI) was significantly higher for the cases compared with the healthy controls in the female population (p = 0.002). Females in the third tertile of the MDI showed a significantly increased risk of GC (OR: 2.66, 95% CI: 1.19-5.99, p-trend = 0.017). Secondary bile acid synthesis and biosynthesis of ansamycins pathways were highly abundant in cases and controls, respectively. Dysbiosis of gastric microbial communities is associated with an increased risk of GC specifically in females.
Associations between Household Water Fluoridation Status and Plain Tap or Bottled Water Consumption

Introduction: The benefits of community water fluoridation for preventing dental caries are attenuated if people do not consume tap water. Objectives: We examined associations between household water fluoride content and consuming plain tap or bottled water among US youth. Methods: We used National Health and Nutrition Examination Survey data for 2013 to 2016 for 5,193 youth aged 2 to 19 y. Fluoride content in youth’s household tap water samples was measured electrometrically with ion-specific electrodes and designated low (<0.6 mg/L) or about optimal (0.6 to 1.2 mg/L). Plain tap and bottled water consumption was obtained from one 24-h dietary recall. We used binomial regression models to estimate adjusted prevalence ratios (APRs) and 95% CIs for consuming plain tap water (including tap only or both tap and bottled) and consuming only bottled water as related to household water fluoride content (low or about optimal) and sociodemographic characteristics. Results: On a given day, 52.6% of youth consumed plain tap water (43.8% exclusively and 8.8% both tap and bottled) and 28%, only bottled water. Neither tap water (APR, 0.96; 95% CI, 0.84 to 1.10) nor only bottled water (APR, 1.03; 95% CI, 0.86 to 1.22) consumption was associated with household water fluoride content. Non-Hispanic Black youth and Hispanic youth were about 30% relatively less likely to consume tap water and 60% to 80% relatively more likely to consume only bottled water than non-Hispanic Whites. Low income, low parental education, and no past-year dental visit were associated with not consuming tap water. Conclusion: Half of youth consumed plain tap water on a given day. Consuming plain tap water was not associated with community water fluoridation status. This study is the first to find that up to 50% of the population served by fluoridated water may not receive its full caries-preventive benefits due to not consuming plain tap water. Knowledge Transfer Statement: Half of US youth consumed plain tap water on a given day. Consuming plain tap water was not associated with community water fluoridation status. This finding suggests that up to 50% of the population served by fluoridated water systems may not receive its full caries-preventive benefits due to not consuming plain tap water. Our findings add support for the need to identify and address barriers to tap water consumption and promote health benefits of fluoridation.
Green Open Innovation Activities and Green Co-Innovation Performance in Taiwan’s Manufacturing Sector

This study investigates the positive effects of an appropriability regime and perceived similarity to green co-innovation performance when considering green open innovation activities as the mediator. It proposes a novel construct, i.e., green open innovation activities, and employs structural equation modeling to test its hypotheses. 190 valid questionnaires were collected from executives in Taiwanese manufacturing companies. Manufacturing activities are regarded as a major source of pollution. Consequently, given the broad concern for the environment among governments and consumers, adopting green practices has become critical for manufacturing companies. All the proposed hypotheses were supported by the analysis results. An appropriability regime is positively associated with green open innovation activities and green co-innovation performance. Perceived similarity is positively associated with green open innovation activities and green co-innovation performance. Moreover, green open innovation activities are positively associated with green co-innovation performance. A major finding is that if a company introduces one, the longer the duration of a green project is, the stronger the green open innovation activities and green co-innovation performance are. This study aimed to determine the simultaneous effects of both factors, i.e., appropriability regime, and perceived similarity on green open innovation activities and green co-innovation performance. The contribution of this study highlights the simultaneous importance of appropriability regimes and perceived similarity to determine a company’s green practices. While companies have tended to increase their green co-innovation performance, they need to improve their appropriability regime, perceived similarity, and green open innovation activities.
F-Box Gene D5RF Is Regulated by Agrobacterium Virulence Protein VirD5 and Essential for Agrobacterium-Mediated Plant Transformation

We previously reported that the Agrobacterium virulence protein VirD5 possesses transcriptional activation activity, binds to a specific DNA element D5RE, and is required for Agrobacterium-mediated stable transformation, but not for transient transformation. However, direct evidence for a role of VirD5 in plant transcriptional regulation has been lacking. In this study, we found that the Arabidopsis gene D5RF (coding for VirD5 response F-box protein, At3G49480) is regulated by VirD5. D5RF has two alternative transcripts of 930 bp and 1594 bp that encode F-box proteins of 309 and 449 amino acids, designated as D5RF.1 and D5RF.2, respectively. D5RF.2 has a N-terminal extension of 140 amino acids compared to D5RF.1, and both of them are located in the plant cell nucleus. The promoter of the D5RF.1 contains two D5RE elements and can be activated by VirD5. The expression of D5RF is downregulated when the host plant is infected with virD5 deleted Agrobacterium. Similar to VirD5, D5RF also affects the stable but not transient transformation efficiency of Agrobacterium. Some pathogen-responsive genes are downregulated in the d5rf mutant. In conclusion, this study further confirmed Agrobacterium VirD5 as the plant transcription activator and identified Arabidopsis thaliana D5RF.1 as the first target gene of VirD5 in regulation.