Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of origanum oil, hydrolysable tannins and tea saponin in mitigating ruminant methane: In vitro and in vivo methods

Abstract The objective of this study was to investigate the effects of origanum oil (ORO), hydrolysable tannins (HYT) and tea saponin (TES) on methane (CH4) emission, rumen fermentation, productive performance and gas exchange in sheep by using in vitro and in vivo methods. The ORO, HYT and TES additive levels were normalized per kg dry matter (DM) in both in vitro and in vivo experiments: ORO‐0, 10, 20 and 40 ml/kg; HYT‐0, 15, 30 and 60 g/kg; and TES‐0, 15, 30 and 60 g/kg, respectively. During in vitro incubation, 40 ml/kg ORO linearly decreased CH4 emission (p < 0.05); 20 and 40 ml/kg ORO cubically decreased carbon dioxide (CO2) production (p < 0.05), and rumen pH was cubically raised with the increasing ORO additive level (p < 0.01). The 60 g/kg HYT cubically decreased CH4 production (p < 0.05). The pH of 60 g/kg HYT was higher than that of 15 and 30 g/kg (p < 0.01); the pH of 20 g/kg TES was higher than that of 5 g/kg (p < 0.05). In the in vivo experiments, 40 ml/kg ORO inhibited dry matter intake (p < 0.01) cubically and reduced average daily gain (ADG) and feed conversion ratio (FCR) cubically (p < 0.05), and 20 or 40 ml/kg ORO linearly decreased CH4 production based on per day or metabolic weight (W0.75) (p < 0.05). Both 30 and 60 g/kg HYT linearly inhibited CH4 emission on the bases of per day and W0.75 (p < 0.05). The 20 g/kg TES improved the apparent digestibility of crude protein (p < 0.05), 10 and 20 g/kg of TES decreased CH4 emission (p < 0.05), and 5 g/kg of TES reduced O2 consumption and CO2 production (p < 0.05). In conclusion, these three plant extracts all showed the abilities on mitigating CH4 emission of sheep with appropriate additive ranges.
Human subjects exploit a cognitive map for credit assignment

Significance Credit assignment (CA) to relevant actions poses a challenge because one is often flooded with reward feedback that is not easily causally attributed. We addressed this issue in a reinforcement learning framework wherein choice is mutually controlled by value-caching model-free (MF) and prospective, planning model-based (MB) systems. We find knowledge, stored in a cognitive map, filters exuberant reward feedback to guide CA in both systems but based on different attribute dimensions. In MF, CA is boosted for outcomes that are relevant (causally related) to one’s choice, whereas in MB, CA is enhanced for outcomes that attract greater attention during the deliberation process that preceded a choice. We consider normative and mechanistic accounts, including how these processes are instrumental to adaptation. An influential reinforcement learning framework proposes that behavior is jointly governed by model-free (MF) and model-based (MB) controllers. The former learns the values of actions directly from past encounters, and the latter exploits a cognitive map of the task to calculate these prospectively. Considerable attention has been paid to how these systems interact during choice, but how and whether knowledge of a cognitive map contributes to the way MF and MB controllers assign credit (i.e., to how they revaluate actions and states following the receipt of an outcome) remains underexplored. Here, we examine such sophisticated credit assignment using a dual-outcome bandit task. We provide evidence that knowledge of a cognitive map influences credit assignment in both MF and MB systems, mediating subtly different aspects of apparent relevance. Specifically, we show MF credit assignment is enhanced for those rewards that are related to a choice, and this contrasted with choice-unrelated rewards that reinforced subsequent choices negatively. This modulation is only possible based on knowledge of task structure. On the other hand, MB credit assignment was boosted for outcomes that impacted on differences in values between offered bandits. We consider mechanistic accounts and the normative status of these findings. We suggest the findings extend the scope and sophistication of cognitive map-based credit assignment during reinforcement learning, with implications for understanding behavioral control.
Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail

Seasonal flu is an acute respiratory disease that exacts a massive toll on human populations, healthcare systems and economies. The disease is caused by an enveloped Influenza virus containing eight ribonucleoprotein (RNP) complexes. Each RNP incorporates multiple copies of nucleoprotein (NP), a fragment of the viral genome (vRNA), and a viral RNA-dependent RNA polymerase (POL), and is responsible for packaging the viral genome and performing critical functions including replication and transcription. A complete model of an Influenza RNP in atomic detail can elucidate the structural basis for viral genome functions, and identify potential targets for viral therapeutics. In this work we construct a model of a complete Influenza A RNP complex in atomic detail using multiple sources of structural and sequence information and a series of homology-modeling techniques, including a motif-matching fragment assembly method. Our final model provides a rationale for experimentally-observed changes to viral polymerase activity in numerous mutational assays. Further, our model reveals specific interactions between the three primary structural components of the RNP, including potential targets for blocking POL-binding to the NP-vRNA complex. The methods developed in this work open the possibility of elucidating other functionally-relevant atomic-scale interactions in additional RNP structures and other biomolecular complexes.
Antioxidant and Cytoprotective Potential of the Essential Oil Pistacia lentiscus var. chia and Its Major Components Myrcene and α-Pinene

The antioxidant, cytoprotective, and wound-healing potential of the essential oil from the resin of Pistacia lentiscus var. chia (mastic oil) was evaluated, along with that of its major components, myrcene and α-pinene. Antioxidant potential was monitored as: (i) direct antioxidant activity as assessed by 2,2-di-phenyl-1-picrylhydrazyl (DPPH), 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), and ABTS assays; (ii) DNA damage protection activity; and (iii) cytoprotective activity as assessed via induction of transcription of genes related to the antioxidant response in human keratinocyte cells (HaCaT). The cytoprotective potential of the test substances was further evaluated against ultraviolet radiation B (UVB)- or H2O2-induced oxidative damage, whereas their regenerative capability was accessed by monitoring the wound closure rate in HaCaT. Μastic oil and major components did not show significant direct antioxidant activity, however they increased the mRNA levels of antioxidant response genes, suggesting indirect antioxidant activity. Treatment of HaCaT with the test substances before and after UVB irradiation resulted in increased cell viability in the cases of pre-treatment with mastic oil or post-treatment with myrcene. Increased cytoprotection was also observed in the case of cell treatment with mastic oil or its major components prior to H2O2 exposure. Finally, mastic oil and myrcene demonstrated a favorable dose-dependent effect for cell migration and wound closure. Collectively, mastic essential oil may exert its promising cytoprotective properties through indirect antioxidant mechanisms.
Multi-omics analyses of cognitive traits and psychiatric disorders highlight brain-dependent mechanisms

Abstract Integrating findings from genome-wide association studies with molecular datasets can help develop insight into the underlying functional mechanisms responsible for trait-associated genetic variants. We have applied the principles of Mendelian randomization to investigate whether brain-derived gene expression (n = 1194) may be responsible for mediating the effect of genetic variants on eight cognitive and psychological outcomes (attention-deficit hyperactivity disorder, Alzheimer’s disease, bipolar disorder, depression, intelligence, insomnia, neuroticism and schizophrenia). Transcriptome-wide analyses identified 83 genes associated with at least one outcome (PBonferroni < 6.72 × 10−6), with multiple trait colocalization also implicating changes to brain-derived DNA methylation at nine of these loci. Comparing effects between outcomes identified the evidence of enrichment, which may reflect putative causal relationships, such as an inverse relationship between genetic liability towards schizophrenia risk and cognitive ability in later life. Repeating these analyses in whole blood (n = 31 684), we replicated 58.2% of brain-derived effects (based on P < 0.05). Finally, we undertook phenome-wide evaluations at associated loci to investigate pleiotropic effects with 700 complex traits. This highlighted pleiotropic loci such as FURIN [initially implicated in schizophrenia risk (P = 1.05 × 10−7)], which had evidence of an effect on 28 other outcomes, as well as genes which may have a more specific role in disease pathogenesis [e.g. SLC12A5 which only provided evidence of an effect on depression (P = 7.13 × 10−10)]. Our results support the utility of whole blood as a valuable proxy for future studies analysing molecular datasets, but also suggest that conducting analyses in a tissue-specific manner may be more comprehensive.
Health of war-affected Karen adults 5 years post-resettlement.

BACKGROUND An estimated 140 000 refugees from Burma have resettled to the USA since 2009, comprising 21% of total resettlement in the USA over the last decade. Our objective was to describe patterns of longitudinal health outcomes in a cohort of Karen refugees resettled in the USA for 5 years, and to translate these findings to a primary healthcare context. METHODS The study was a retrospective cohort study focused on the analysis of the first 5 years of electronic health records of a sample of 143 Karen refugees who were initially resettled between May 2011 and May 2013. RESULTS Through descriptive, inferential and survival statistics, we described patterns of retention in primary care, biometric trends, condition prevalence and survival probabilities. Highest prevalence health conditions documented at any point in the 5-year period included diagnoses or symptoms associated with pain (52%); gastrointestinal disturbance (41%); metabolic disorder (41%); infectious process (34%); mental health condition (31%) and central nervous system disorder (24%). CONCLUSIONS This study is the first retrospective longitudinal analysis of patterns of health in Karen refugees originating from Burma and resettled to the USA. Findings identified in the 5-year, the post-resettlement period provided important clinical insights into the health trajectories of war-affected populations. Burden of illness was high although results did not demonstrate the extent of trauma-associated physical health conditions reported in the literature. Indicators such as significant increases in body mass index (BMI), the overall prevalence of dyslipidaemia and others suggested that the cohort may be exhibiting an early trajectory towards the development of these conditions. Authors summarize potential protective factors experienced by the cohort that promoted aspects of health frequently challenged in forced migration.
Evaluation of Abbott BinaxNOW Rapid Antigen Test for SARS-CoV-2 Infection at Two Community-Based Testing Sites — Pima County, Arizona, November 3–17, 2020

Rapid antigen tests, such as the Abbott BinaxNOW COVID-19 Ag Card (BinaxNOW), offer results more rapidly (approximately 15-30 minutes) and at a lower cost than do highly sensitive nucleic acid amplification tests (NAATs) (1). Rapid antigen tests have received Food and Drug Administration (FDA) Emergency Use Authorization (EUA) for use in symptomatic persons (2), but data are lacking on test performance in asymptomatic persons to inform expanded screening testing to rapidly identify and isolate infected persons (3). To evaluate the performance of the BinaxNOW rapid antigen test, it was used along with real-time reverse transcription-polymerase chain reaction (RT-PCR) testing to analyze 3,419 paired specimens collected from persons aged ≥10 years at two community testing sites in Pima County, Arizona, during November 3-17, 2020. Viral culture was performed on 274 of 303 residual real-time RT-PCR specimens with positive results by either test (29 were not available for culture). Compared with real-time RT-PCR testing, the BinaxNOW antigen test had a sensitivity of 64.2% for specimens from symptomatic persons and 35.8% for specimens from asymptomatic persons, with near 100% specificity in specimens from both groups. Virus was cultured from 96 of 274 (35.0%) specimens, including 85 (57.8%) of 147 with concordant antigen and real-time RT-PCR positive results, 11 (8.9%) of 124 with false-negative antigen test results, and none of three with false-positive antigen test results. Among specimens positive for viral culture, sensitivity was 92.6% for symptomatic and 78.6% for asymptomatic individuals. When the pretest probability for receiving positive test results for SARS-CoV-2 is elevated (e.g., in symptomatic persons or in persons with a known COVID-19 exposure), a negative antigen test result should be confirmed by NAAT (1). Despite a lower sensitivity to detect infection, rapid antigen tests can be an important tool for screening because of their quick turnaround time, lower costs and resource needs, high specificity, and high positive predictive value (PPV) in settings of high pretest probability. The faster turnaround time of the antigen test can help limit transmission by more rapidly identifying infectious persons for isolation, particularly when used as a component of serial testing strategies.
Effects of Prior Voluntary Hyperventilation on the 3-min All-Out Cycling Test in Men

ABSTRACT Introduction The ergogenic effects of respiratory alkalosis induced by prior voluntary hyperventilation (VH) are controversial. This study examined the effects of prior VH on derived parameters from the 3-min all-out cycling test (3MT). Methods Eleven men ( V̇ O 2max = 46 ± 8 mL·kg−1·min−1) performed a 3MT preceded by 15 min of rest (CONT) or VH ( V̇E = 38 ± 5 L·min−1) with PETCO2 reduced to 21 ± 1 mm Hg (HYP). End-test power (EP; synonymous with critical power) was calculated as the mean power output over the last 30 s of the 3MT, and the work done above EP (WEP; synonymous with W′) was calculated as the power–time integral above EP. Results At the start of the 3MT, capillary blood PCO2 and [H+] were lower in HYP (25.2 ± 3.0 mm Hg, 27.1 ± 2.6 nmol·L−1) than CONT (43.2 ± 2.0 mm Hg, 40.0 ± 1.5 nmol·L−1) (P < 0.001). At the end of the 3MT, blood PCO2 was still lower in HYP (35.7 ± 5.4 mm Hg) than CONT (40.6 ± 5.0 mm Hg) (P < 0.001). WEP was 10% higher in HYP (19.4 ± 7.0 kJ) than CONT (17.6 ± 6.4 kJ) (P = 0.006), whereas EP was 5% lower in HYP (246 ± 69 W) than CONT (260 ± 74 W) (P = 0.007). The ΔWEP (J·kg−1) between CONT and HYP correlated positively with the PCO2 immediately before the 3MT in HYP (r = 0.77, P = 0.006). Conclusion These findings suggest that acid–base changes elicited by prior VH increase WEP but decrease EP during the all-out 3MT.
Aerosol assisted chemical vapor deposition of conductive and photocatalytically active tantalum doped titanium dioxide films

This paper shows the aerosol assisted chemical vapour deposition of transparent, blue coloured and conductive tantalum doped titanium dioxide films from the CVD reaction of Ti(OEt)4 and Ta(OEt)5. Hall effect measurements showed the doped films to have excellent n-type electrical conductivity showing, to the best of our knowledge, the lowest reported sheet resistance ever recorded for Ta-doped TiO2 of 14 Ω sq−1. The Ta 6 atom% doped TiO2 film also showed the best electrical results with a charge carrier concentration of 1.60 × 1021 cm−3 and mobility of 1.44 cm2 V−1 s−1 making it a suitable electrode in photovoltaic devices. The doped films were multifunctional, showing good photocatalytic activity under UV-light illumination. XPS and XRD studies gave strong evidence that the Ta was entering the TiO2 lattice as Ta5+ and that a reduction of some Ti4+ to Ti3+ was observed.
Polarizing and depolarizing charge injection through a thin dielectric layer in a ferroelectric-dielectric bilayer.

Charge injection from the near-by-electrode can occur during ferroelectric switching in the ferroelectric-dielectric bilayer due to the high field applied to the adjacent dielectric layers. The aim of this study is to investigate the effect of the charge injection by separating the amount of switched polarization and the injected charge density. A dynamic model of the injection-involved switching is developed and exploited to elucidate the mechanism. The model demonstrates that the amount of injected charges, which compensates for the bound charge of the polarization, can be larger, smaller, or identical to that of the polarization. This model further describes the analytical conditions of this compensation state. The model predictions are validated by the newly introduced ramping pulse measurements involving the serially connected TiN/Hf0.5Zr0. 5O2/TiN and TiN/amorphous Al2O3/TiN, which are capable of separating the injected charge from the switched polarization. The dynamic model, along with the electrical measurements, enables the quantitative prediction and estimation of the internal potential and the effective charge, which is the sum of the bound and injected charges in the bilayer. This work provides fundamental insights into field-effect devices such as the next-generation ferroelectric-field-effect-transistors with NAND architecture based on uncompensated ferroelectric charges.
A link between promoter polymorphisms of the transforming growth factor β1 (TGFB1) and TGF-β1 receptor II (TGFBR2) genes and relapsing-remitting multiple sclerosis.

INTRODUCTION Multiple sclerosis (MS) is a chronic progressive autoimmune disease characterised by nerve demyelination, mediated by myelin-specific Th1 autoreactive cells. Transforming growth factor 1 (TGF-1) is a regulatory cytokine involved in MS aetiology by maintaining CD4+ cell differentiation and preventing autoimmune responses. Because of the important role of the TGF-1 signalling pathway in MS aetiopathogenesis, we aimed to investigate the association of two DNA polymorphisms: TGFB1C[-509]T and TGFBR2G[-875]A and their combined genotypes with the risk of MS development in a cohort of Bulgarian patients. The effect of the two promoter polymorphisms on the disease onset was also assessed. MATERIAL AND METHODS In the study, a cohort of 183 patients with relapsing-remitting multiple sclerosis (RRMS) and 307 sex- and age-matched healthy subjects were recruited. Genotyping of the TGFB1C[-509]T (rs1800469) and TGFBR2G[-875]A (rs3087465) polymorphisms was performed by PCR-RFLP and PIRA-PCR approaches. RESULTS Frequencies of the TGFB1T[-509]T genotype and TGFB1[-509]*T-allele were lower in RRMS men than in control healthy men (15.7% vs. 26.9%, 37.3% vs. 50.7%, respectively). Among males, the TGFB1T[-509]T genotype was related to a significantly reduced risk of RRMS (OR = 0.360, 95% CI: 0.126-1.028, p = 0.05) in comparison to the TGFB1C[-509]C genotype. Also, TGFB1[-509]*T-allele was more common in men with RRMS than in healthy men relative to the TGFB1[-509]*C-allele and was associated with a statistically significant protective effect (OR = 0.576, 95% CI: 0.341-0.974, p = 0.039). The combination of TGFB1T[-509]T/TGFB1T[-509]C and TGFBR2G[-875]A genotypes among men was associated with a significant protective effect compared to the wild-type homozygous TGFB1C[-509]C and TGFBR2G[-875]G genotypes (OR = 0.268, 95% CI: 0.088-0.818, p = 0.018). No significant association between rs1800469 and rs3087465 was observed among females with and without (controls) RRMS. CONCLUSIONS In summary, we suggest that in males, a higher TGF-1 level determined by TGFB1T[-509]T genotype in combination with the TGFBR2G[-875]A genotype might be a protective factor against RRMS development.
Housing conditions as predictors of common childhood illness: Evidence from Nigeria Demographic and Health Surveys, 2008–2018

Several studies have examined the impacts of water, sanitation, hygiene, and general housing conditions on childhood health in developing countries. However, up-to-date knowledge and change pattern in common childhood illness prevalence over time are scarce in Nigeria. To contribute toward meeting the Sustainable Development Goals three and six, we used pooled data (N = 94,053) from the Nigeria Demographic Health Surveys from 2008 to 2018 to examine the trend and determinants of four childhood illnesses: diarrhea, fever, cough, and respiratory infection. Multivariate logistic regression was used to estimate the determinants of the four health outcomes. Our results indicate that between 2008 and 2018, the prevalence of childhood diarrhea, cough, and fever slowly declined. However, there was a drastic decline in childhood-related respiratory illness. Housing conditions, sanitation facilities, and water sources were significantly associated with childhood illness based on the logistic regression analysis. Based on our findings, we recommend general improvement in housing conditions that can eradicate childhood cough, fever, and respiratory infections.
Is Intestinal Bacterial Diversity Enhanced by Trans-Species Spread in the Mixed-Species Flock of Hooded Crane (Grus monacha) and Bean Goose (Anser fabalis) Wintering in the Lower and Middle Yangtze River Floodplain?

Simple Summary Intestinal microbes play an indispensable role in host physiology and their alteration can produce serious effects on vertebrates. In this study, we analyzed the characteristics of intestinal bacterial community of hooded crane and bean goose whose niches overlap at Shengjin Lake, China, and investigated how host internal factors and inter-species interactions affected the diversity and spread of intestinal bacteria of the two species over three wintering periods. We have found that direct or indirect contact with each other increased the diversity of host intestinal bacteria and caused bacteria to spread among species in the mixed-species flock. In addition, a total of 63 pathogens were identified, of which 38 (60.3%) were found in the gut of both species. These findings could help our understanding of the factors that influence gut bacteria in wild waterbirds, which are also major contributors to the spread of pathogens worldwide. Abstract Diversity of gut microbes is influenced by many aspects, including the host internal factors and even direct or indirect contact with other birds, which is particularly important for mixed-species wintering waterbird flocks. In this study, Illumina high-throughput sequencing was used to analyze the intestinal bacteria of the hooded crane and bean goose whose niches overlap at Shengjin Lake. We tested whether contact time enhances the trans-species spread of gut bacteria. Results indicate alpha-diversity and microbial composition displayed significant separation between the two hosts in every wintering period, although the number of bacteria types shared increased with increasing contact time. For the same species, with the lengthening of contact time, alpha-diversity and the number of operational taxonomic units (OTUs) in the host intestine augmented, and the common OTUs and structural similarity of microflora in the middle and late periods were more than in the early and middle periods. In addition, we found a very high proportion of shared pathogens. Our results indicate that, although intestinal microflora of different species were separated, direct or indirect contact in the mixed-species flock caused the spread of gut bacteria trans-species, indicating that more attention should be paid to intestinal pathogens in wild birds.