Miracle-dz/UniFAR-FTUs huggingface dataset:
Near infrared spectroscopy calibration strategies to predict multiple nutritional parameters of pasture species from different functional groups

Near infrared reflectance (NIR) spectroscopy has been used by the agricultural industry as a rapid and inexpensive technique to quantify nutritional chemistry in plants. The aim of this study was to evaluate the performance of NIR calibrations in predicting the nutritional composition of ten pasture species that underpin livestock industries in many countries. The species comprised a range of functional diversity (C3 legumes; C3/C4 grasses; annuals/perennials) and origins (tropical/temperate; introduced/native) that grew under varied environmental conditions (control and experimentally induced warming and drought) over a period of more than two years (n = 2622). A maximal calibration set including 391 samples was used to develop and evaluate calibrations for all ten pasture species (global calibrations), as well as for subsets comprised of the plant functional groups. This study found that the global calibrations were appropriate to predict the six key nutritional quality parameters for the studied pasture species, with the highest estimation quality found for ash (ASH), crude protein (CP), amylase-treated neutral detergent fibre (aNDF) and acid detergent fibre (ADF), and the lowest for ether extract (EE) and acid detergent lignin (ADL) parameters. The plant functional group calibrations for C3 grasses performed better than the global calibrations for ASH, CP, ADF and EE parameters, whereas for C3 legumes and C4 grasses the functional group calibrations performed less well than the global calibrations for all nutritional parameters of these groups. Additionally, the calibrations were able to capture the range of variation in forage nutritional quality caused by future climate scenarios of warming and severe drought.
Selective logging shows no impact on the dietary breadth of the fawn leaf-nosed bat (Hipposideros cervinus)

Logging activities degrade forest habitats across large areas of the tropics, but the impacts on trophic interactions that underpin forest ecosystems are poorly understood. DNA metabarcoding provides an invaluable tool to investigate such interactions, allowing analysis at a far greater scale and resolution than has previously been possible. We analysed the diet of the insectivorous fawn leaf-nosed bat Hipposideros cervinus across a forest disturbance gradient in Borneo, using a dataset of ecological interactions from an unprecedented number of bat-derived faecal samples. Bats predominantly consumed insects from the orders Lepidoptera, Blattodea, Diptera and Coleoptera, and the taxonomic composition of their diet remained relatively consistent across sites regardless of logging disturbance. There was little difference in the richness of prey consumed in each logging treatment, indicating potential resilience of this species to habitat degradation. In fact, bats consumed a high richness of prey items, and intensive sampling is needed to reliably compare feeding ecology over multiple sites regardless of the bioinformatic procedures used.
Evolutionary Dynamics of Indels in SARS-CoV-2 Spike Glycoprotein

SARS-CoV-2, responsible for the current COVID-19 pandemic that claimed over 5.0 million lives, belongs to a class of enveloped viruses that undergo quick evolutionary adjustments under selection pressure. Numerous variants have emerged in SARS-CoV-2, posing a serious challenge to the global vaccination effort and COVID-19 management. The evolutionary dynamics of this virus are only beginning to be explored. In this work, we have analysed 1.79 million spike glycoprotein sequences of SARS-CoV-2 and found that the virus is fine-tuning the spike with numerous amino acid insertions and deletions (indels). Indels seem to have a selective advantage as the proportions of sequences with indels steadily increased over time, currently at over 89%, with similar trends across countries/variants. There were as many as 420 unique indel positions and 447 unique combinations of indels. Despite their high frequency, indels resulted in only minimal alteration of N-glycosylation sites, including both gain and loss. As indels and point mutations are positively correlated and sequences with indels have significantly more point mutations, they have implications in the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein.
Naked Mole-Rat Hematopoietic Stem and Progenitors are Highly Quiescent with an Inherent Myeloid Bias

Naked mole-rats (NMRs) are the longest-lived rodents yet their stem cell characteristics remain enigmatic. Here we comprehensively mapped the NMR hematopoietic landscape and identified unique features likely contributing to longevity. Adult NMRs form red blood cells in spleen and marrow, which is a neotenic trait. A myeloid bias towards granulopoiesis in concert with decreased B-lymphopoiesis defines the marrow composition, resembling fetal leukopoiesis. Very similar to primates, the primitive stem cell compartment is marked by CD34 and THY1. Remarkably, stem and progenitor respiration rates are as low as in human cells, while NMR cells show a strong expression signature for fatty acid metabolism. The pool of quiescent stem cells is higher than in mice, and the cell cycle of hematopoietic cells is prolonged. Our work provides a platform to study immunology and stem cell biology in an animal model of exceptional longevity. Teaser Juvenile features of hematopoiesis shape the blood system of the longest-lived rodent.
Prognostic Value of Interleukin-17 A Gene Polymorphism and Serum IL-17 Levels in Adult Acute Myeloid Leukaemia Patients

Background: T helper 17 (Th17) cells play a role in the pathogenesis and prognosis of acute myeloid leukemia (AML). Th17 cells produce interleukin (IL)-17A and IL-17F, that share strong surface expression and homology of the IL-23 receptor (IL-23R). Objective: To evaluate the expression of IL-17A gene polymorphism and IL-17 serum level in adult AML patients and to clarify its prognostic significance. Patients and methods: In this prospective study, 48 patients with de novo AML and 48 healthy matched controls were enrolled. Cases were diagnosed at clinical pathology and managed in Medical Oncology Departments. We evaluated both serum IL-17 levels, measured by ELISA, and IL-17A (rs2275913) gene polymorphism was assessed using realtime polymerase chain reaction (PCR) in all patients and control. All patients received “3+7” as induction, responders received 3-4 courses of high dose cytarabine as consolidation, while non-responders received salvage therapy. Results: Serum levels of IL-17 were higher in AML patients (median 27 pg/ml) vs 17 pg/ml in the control group (P < 0.001). Also, serum IL 17 level was higher in non-responders with median 37.5 (pg/ml) vs 23 (pg/ml) in responders (P < 0.001). while IL-17A mutant genotypes and alleles showed no significant relation between expression of IL-17 A gene polymorphism and response to treatment or outcome of studied AML cases. Conclusion: Serum IL-17 levels can be considered a useful diagnostic and prognostic factor in AML patients, unlike IL-17 A gene polymorphisms.
Clinical Features and Survival Outcome of Early-Stage Primary Pulmonary MALT Lymphoma After Surgical Treatment

Background: We aimed to study the clinical features and survival outcomes of patients with early-stage primary pulmonary mucosa-associated lymphoid tissue (MALT) lymphoma who underwent surgery. Methods: This is a retrospective, single-center study including 32 patients with early-stage primary pulmonary MALT lymphoma. Univariate and multivariate Cox analyses were performed to select independent prognostic factors. The overall survival (OS) was analyzed by the Kaplan-Meier method and was compared with the log-rank test. Results: Among the 32 patients included, there were 16 men (50.0%) and 16 women (50.0%). The average age was 59.2 years old. Ten patients had non-specific clinical symptoms including cough, expectoration, and chest pain, and four patients had B symptoms. CT images are not specific and can be shown as peripheral, central, solid, and ground glass but more peripheral (93.8%) and solid (75.0%). In prognostic analysis, univariate analysis showed that tumor stage and size were associated with relapse-free survival (RFS) and OS [hazard ratio (HR) = 1.105, 95% CI: 1.021–1.197, P = 0.011; HR = 1.211, 95% CI: 1.158–1.968, P = 0.003, respectively]. It seems to indicate that higher stage and larger size indicate a worse prognosis, but we could not find statistically significant predictors in multivariate analysis. Sublobectomy was performed in 21 (65.6) cases, lobectomy was performed in the other 11 (34.4) cases, both of them can achieve good prognosis (5-year RFS and OS are both 100%), and there is no significant difference between them. Conclusions: The clinical manifestation of early-stage primary pulmonary MALT lymphoma is not significantly specific, and surgical resection is an effective treatment.
Epidemiology of Bleeding in Critically Ill Children

Objective: Bleeding can be a severe complication of critical illness, but its true epidemiologic impact on children has seldom been studied. Our objective is to describe the epidemiology of bleeding in critically ill children, using a validated clinical tool, as well as the hemostatic interventions and clinical outcomes associated with bleeding. Design: Prospective observational cohort study. Setting: Tertiary pediatric critical care unit Patients: All consecutive patients (1 month to 18 years of age) admitted to a tertiary pediatric critical care unit Measurements and Main Results: Bleeding events were categorized as minimal, moderate, severe, or fatal, according to the Bleeding Assessment Scale in Critically Ill Children. We collected demographics and severity at admission, as evaluated by the Pediatric Index of Mortality. We used regression models to compare the severity of bleeding with outcomes adjusting for age, surgery, and severity. Over 12 months, 902 critically ill patients were enrolled. The median age was 64 months (IQR 17; 159), the median admission predicted risk of mortality was 0.5% (IQR 0.2; 1.4), and 24% were post-surgical. Eighteen percent of patients experienced at least one bleeding event. The highest severity of bleeding was minimal for 7.9% of patients, moderate for 5.8%, severe for 3.8%, and fatal for 0.1%. Adjusting for age, severity at admission, medical diagnosis, type of surgery, and duration of surgery, bleeding severity was independently associated with fewer ventilator-free days (p < 0.001) and fewer PICU-free days (p < 0.001). Adjusting for the same variables, bleeding severity was independently associated with an increased risk of mortality (adjusted odds ratio for each bleeding category 2.4, 95% CI 1.5; 3.7, p < 0.001). Conclusion: Our data indicate bleeding occurs in nearly one-fifth of all critically ill children, and that higher severity of bleeding was independently associated with worse clinical outcome. Further multicenter studies are required to better understand the impact of bleeding in critically ill children.
Spiritual Inspiration of Village Cadres and Inclusive Innovation of Bricolage in Rural Autonomy in China

In the rural autonomous context of China, inclusive innovation of bricolage is a widespread phenomenon. However, the existing research rarely considers villagers as the main actors of innovation. In a research survey of 23 provinces in China, we studied the internal mechanism of inclusive innovation of bricolage. We found that the spiritual inspiration of the village cadres is positively related to inclusive innovation of bricolage behavior of villagers. Moreover, the results revealed that affective commitment to the village of the villagers plays a mediating role in the relationship between the spiritual inspiration of the village cadres and inclusive innovation of bricolage behavior of villagers. In addition, our findings reveal that resilience of villagers plays a moderating role in the relationship between the spiritual inspiration of the village cadres and inclusive innovation of bricolage behavior of villagers.
Cloning, Heterologous Expression, and Characterization of a βκ-Carrageenase From Marine Bacterium Wenyingzhuangia funcanilytica: A Specific Enzyme for the Hybrid Carrageenan–Furcellaran

Carrageenan is a group of important food polysaccharides with high structural heterogeneity. Furcellaran is a typical hybrid carrageenan, which contains the structure consisted of alternative β-carrageenan and κ-carrageenan motifs. Although several furcellaran-hydrolyzing enzymes have been characterized, their specificity for the glycosidic linkage was still unclear. In this study, we cloned, expressed, and characterized a novel GH16_13 furcellaran-hydrolyzing enzyme Cgbk16A_Wf from the marine bacterium Wenyingzhuangia fucanilytica CZ1127. Cgbk16A_Wf exhibited its maximum activity at 50°C and pH 6.0 and showed high thermal stability. The oligosaccharides in enzymatic products were identified by liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) and nuclear magnetic resonance (NMR) spectroscopy. It was confirmed that Cgbk16A_Wf specifically cleaves the β-1,4 linkages between β-carrageenan and κ-carrageenan motifs from non-reducing end to reducing end. Considering the structural heterogeneity of carrageenan and for the unambiguous indication of the specificity, we recommended to name the furcellaran-hydrolyzing activity represented by Cgbk16A as “βκ-carrageenase” instead of “furcellaranase”.
Examination of CA1 Hippocampal DNA Methylation as a Mechanism for Closing of Estrogen’s Critical Window

There is a critical window for estrogen replacement therapy, beyond which estradiol (E2) fails to enhance cognition and N-methyl-D-aspartate (NMDA) receptor function, and E2-responsive transcription decreases. Much less attention has been given to the mechanism for closing of the critical window, which is thought to involve the decline in estrogen signaling cascades, possibly involving epigenetic mechanisms, including DNA methylation. This study investigated changes in DNA methylation in region CA1 of the hippocampus of ovariectomized female rats over the course of brain aging and in response to E2-treatment, using whole genome bisulfite sequencing. Differential methylation of CpG and non-CpG (CHG and CHH) sites and associated genes were characterized in aged controls (AC), middle-age controls (MC), and young controls (YC) and differential methylation in response to E2-treatment (T) was examined in each age group (AT-AC, MT-MC, and YT-YC). Possible candidate genes for the closing of the critical window were defined as those that were hypomethylated by E2-treatment in younger animals, but were unresponsive in aged animals. Gene ontology categories for possible critical window genes were linked to response to hormones (Adcyap1, Agtr2, Apob, Ahr, Andpro, Calm2, Cyp4a2, Htr1b, Nr3c2, Pitx2, Pth, Pdk4, Slc2a2, Tnc, and Wnt5a), including G-protein receptor signaling (Gpr22 and Rgs4). Other possible critical window genes were linked to glutamate synapses (Nedd4, Grm1, Grm7, and Grin3a). These results suggest that decreased E2 signaling with advanced age, and/or prolonged E2 deprivation, results in methylation of E2-responsive genes, including those involved in rapid E2 signaling, which may limit subsequent transcription.
A Cross-Platform Metabolomics Comparison Identifies Serum Metabolite Signatures of Liver Fibrosis Progression in Chronic Hepatitis C Patients

Metabolomics offers new insights into disease mechanisms that is enhanced when adopting orthogonal instrumental platforms to expand metabolome coverage, while also reducing false discoveries by independent replication. Herein, we report the first inter-method comparison when using multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS) and nuclear magnetic resonance (NMR) spectroscopy for characterizing the serum metabolome of patients with liver fibrosis in chronic hepatitis C virus (HCV) infection (n = 20) and non-HCV controls (n = 14). In this study, 60 and 30 serum metabolites were detected frequently (>75%) with good technical precision (median CV < 10%) from serum filtrate samples (n = 34) when using standardized protocols for MSI-CE-MS and NMR, respectively. Also, 20 serum metabolite concentrations were consistently measured by both methods over a 500-fold concentration range with an overall mean bias of 9.5% (n = 660). Multivariate and univariate statistical analyses independently confirmed that serum choline and histidine were consistently elevated (p < 0.05) in HCV patients with late-stage (F2-F4) as compared to early-stage (F0-F1) liver fibrosis. Overall, the ratio of serum choline to uric acid provided optimal differentiation of liver disease severity (AUC = 0.848, p = 0.00766) using a receiver operating characteristic curve, which was positively correlated with liver stiffness measurements by ultrasound imaging (r = 0.606, p = 0.0047). Moreover, serum 5-oxo-proline concentrations were higher in HCV patients as compared to non-HCV controls (F = 4.29, p = 0.0240) after adjustment for covariates (age, sex, BMI), indicative of elevated oxidative stress from glutathione depletion with the onset and progression of liver fibrosis. Both instrumental techniques enable rapid yet reliable quantification of serum metabolites in large-scale metabolomic studies with good overlap for biomarker replication. Advantages of MSI-CE-MS include greater metabolome coverage, lower operating costs, and smaller sample volume requirements, whereas NMR offers a robust platform supported by automated spectral and data processing software.
Magnetic Molecularly Imprinted Polymers: Synthesis and Applications in the Selective Extraction of Antibiotics

Recently, magnetic molecularly imprinted polymers (MMIPs) have integrated molecular imprinting technology (MIT) and magnetic separation technology and become a novel material with specific recognition and effective separation of target molecules. Based on their special function, they can be widely used to detect contaminants such as antibiotics. The antibiotic residues in the environment not only cause harm to the balance of the ecosystem but also induce bacterial resistance to specific antibiotics. Given the above consideration, it is especially important to develop sensitive and selective methods for measuring antibiotics in the complex matrix. The combination of MMIPs and conventional analytical methods provides a rapid approach to separate and determine antibiotics residues. This article gives a systematic overview of synthetic approaches of the novel MMIPs materials, briefly introduces their use in sample pretreatment prior to antibiotic detection, and provides a perspective for future research.
Neural Network Differential Equations For Ion Channel Modelling

Mathematical models of cardiac ion channels have been widely used to study and predict the behaviour of ion currents. Typically models are built using biophysically-based mechanistic principles such as Hodgkin-Huxley or Markov state transitions. These models provide an abstract description of the underlying conformational changes of the ion channels. However, due to the abstracted conformation states and assumptions for the rates of transition between them, there are differences between the models and reality—termed model discrepancy or misspecification. In this paper, we demonstrate the feasibility of using a mechanistically-inspired neural network differential equation model, a hybrid non-parametric model, to model ion channel kinetics. We apply it to the hERG potassium ion channel as an example, with the aim of providing an alternative modelling approach that could alleviate certain limitations of the traditional approach. We compare and discuss multiple ways of using a neural network to approximate extra hidden states or alternative transition rates. In particular we assess their ability to learn the missing dynamics, and ask whether we can use these models to handle model discrepancy. Finally, we discuss the practicality and limitations of using neural networks and their potential applications.
Levels of Reading Comprehension in Higher Education: Systematic Review and Meta-Analysis

Higher education aims for university students to produce knowledge from the critical reflection of scientific texts. Therefore, it is necessary to develop a deep mental representation of written information. The objective of this research was to determine through a systematic review and meta-analysis the proportion of university students who have an optimal performance at each level of reading comprehension. Systematic review of empirical studies has been limited from 2010 to March 2021 using the Web of Science, Scopus, Medline, and PsycINFO databases. Two reviewers performed data extraction independently. A random-effects model of proportions was used for the meta-analysis and heterogeneity was assessed with I2. To analyze the influence of moderating variables, meta-regression was used and two ways were used to study publication bias. Seven articles were identified with a total sample of the seven of 1,044. The proportion of students at the literal level was 56% (95% CI = 39–72%, I2 = 96.3%), inferential level 33% (95% CI = 19–46%, I2 = 95.2%), critical level 22% (95% CI = 9–35%, I2 = 99.04%), and organizational level 22% (95% CI = 6–37%, I2 = 99.67%). Comparing reading comprehension levels, there is a significant higher proportion of university students who have an optimal level of literal compared to the rest of the reading comprehension levels. The results have to be interpreted with caution but are a guide for future research.
Study of Terpenoid Synthesis and Prenyltransferase in Roots of Rehmannia glutinosa Based on iTRAQ Quantitative Proteomics

Rehmannia glutinosa has important medicinal value; terpenoid is one of the main active components in R. glutinosa. In this study, iTRAQ technique was used to analyze the relative abundance of proteins in roots of R. glutinosa, and 6,752 reliable proteins were quantified. GO enrichment results indicated that most proteins were involved in metabolic process or cellular process, 57.63% proteins had catalytic activity, and 65.80% proteins were enriched in membrane-bounded organelle. In roots of R. glutinosa, there were 38 KEGG enrichments with significance, more DEPs were found in some pathways, especially the proteasome pathway and TCA cycle with 15.0% DEPs between elongation stage and expansion stage of roots. Furthermore, five KEGG pathways of terpenoid synthesis were found. Most prenyltransferases belong to FPP/GGPP synthase family, involved in terpenoid backbone biosynthesis, and all interacted with biotin carboxylase CAC2. Compared with that at the elongation stage, many prenyltransferases exhibited higher expression at the expansion stage or maturation stage of roots. In addition, eight FPP/GGPP synthase encoding genes were cloned from R. glutinosa, namely FPPS, FPPS1, GGPS, GGPS3, GGPS4, GGPS5, GPPS and GPPS2, introns were also found in FPPS, FPPS1, GGPS5 and GGPS2, and FPP/GPP synthases were more conservative in organisms, especially in viridiplantae, in which the co-occurrence of GPPS or GPPS2 was significantly higher in plants. Further analysis found that FPP/GGPP synthases of R. glutinosa were divided into three kinds, GGPS, GPPS and FPPS, and their gene expression was significantly diverse in different varieties, growth periods, or tissues of R. glutinosa. Compared with that of GGPS, the expression of GPPS and FPPS was much higher in R. glutinosa, especially at the expansion stage and maturation stage. Thus, the synthesis of terpenoids in roots of R. glutinosa is intricately regulated and needs to be further studied.