Miracle-dz/UniFAR-FTUs huggingface dataset:
Reproductive success mediates the effects of climate change and grassland management on plant populations dynamics

Climate change is one of the largest threats to grassland plant species, which can be modified by land management. Although climate change and land management can separately and interactively influence plant demography this has been rarely considered within one experimental set-up. We used a large-scale experiment to quantify the effects of grassland management, climate change and their joint effect on the demography and population growth rate of 11 native plant species. We parameterized integral projection models with four years of demographic data to project the population growth rate. We hypothesized, plants would perform better in ambient than in the future climate treatment that creates hotter and drier summer conditions and that plant performance in grazing vs. mowing would vary across species and depend on their traits. Due to extreme drought events, over half of our study species went quasi extinct, which highlights how extreme climate events can influence long term experimental results. Of the persistent species, only one supported our expectations, and the rest either had higher population growth rates in the future climate treatment or showed no significant difference in population growth between climate treatments. Species with shorter flowering durations performed better in the mowing treatment while those with longer flowering durations performed better in the grazing treatment. The population growth rates of these species were sensitive to changes in vital rates related to reproduction and recruitment. Depending on the species we found effects of land management and climate change on population growth rates but we did not find strong support for interactive effects among both factors. Experiments combined with measuring plant demographic responses provide a way to isolate the effects of different drivers on the long-term persistence of species, and to identify the demographic vital rates that are critical to manage in the future. Our study suggests that it will become increasingly difficult to maintain species with preferences for moister soil conditions, that traits such as flowering duration might predict responses to management, and that vital rates such as reproduction and recruitment are disproportionately important.
Synthetic Frizzled agonist and LRP antagonist for high-efficiency Wnt/β-catenin signaling manipulation in organoid cultures and in vivo

Wnt/β-catenin signaling and its dysregulation play critical roles in the fate determination of stem cells and the pathology of various diseases. However, the application of translated Wnt ligand in regenerative medicine is hampered by its hydrophobicity and cross-reactivity with Frizzled (FZD) receptors. Here, we generate an engineered water-soluble, FZD subtype-specific agonist, RRP-pbFn, for high-efficiency Wnt/β-catenin signaling activation. In the absence of direct binding to LRP5/6, RRP-pbFn stimulates Wnt/β-catenin signaling more potently than surrogate Wnt. RRP-pbFn supports the growth of a variety of mouse and human organoids, and induces the expansion of liver and intestine progenitors in vivo. Meanwhile, we develop a synthetic LRP antagonist, RRP-Dkk1c, which exhibits heightened effectiveness in attenuating Wnt/β-catenin signaling activity compared to Dkk1, thereby abolishing the formation of CT26-derived colon cancer xenograft in vivo. Together, these two paired Wnt/β-catenin signaling manipulators hold great promise for biomedical research and potential therapeutics.
A Dual Color Pax7 and Myf5 In Vivo Reporter to Investigate Muscle Stem Cell Heterogeneity in Regeneration and Aging

Increasing evidence suggests heterogeneity in the muscle stem cell (MuSC) pool. In particular, a rare subset of Pax7 positive MuSCs that has never expressed the myogenic regulatory factor Myf5 has enhanced self-renewal and engraftment characteristics. However, the scarcity and limited availability of protein markers make the characterization of these cells challenging. We describe the generation of StemRep reporter mice allowing to monitor Pax7 and Myf5 protein based on equimolar levels of dual nuclear fluorescence. High levels of Pax7 protein and low levels of Myf5 delineate a deeply quiescent MuSC subpopulation with distinct molecular signatures and dynamics of activation, proliferation, and commitment. Aging decreases the number of these cells, and skews the MuSC pool towards Myf5-High cells with impaired quiescence. Altogether, we describe a novel deeply quiescent MuSC subpopulation whose maintenance is impaired in old muscles, and establish the StemRep line as a versatile tool to study quiescence and MuSC heterogeneity.
Effect of temperature on betacyanins synthesis and the transcriptome of Suaeda salsa

Introduction Suaeda salsa (Linn.) Pall. is an important tourist resource and ecological restoration species in coastal wetlands. Environmental factors such as low temperature, darkness, phytohormone, salt stress and seawater flflooding, and light can induce betalain synthesis in S. salsa, which plays an important role in plant adaptation to abiotic stress processes and in shaping the beautiful “red beach” landscape. Methods In this study, Illumina sequencing was used to profifile the transcriptome sequence (RNA-Seq) of S. salsa leaves at different temperatures (5° C, 10°C, 15°C, 20°C, 25°C, and 30°C) and to validate differentially expressed genes (DEGs) indicated by real-time PCR (RT-qPCR). Results The betacyanin content was highest in S. salsa leaves at 15°C. Transcription group data showed that compared to the control group (15°C), the “betacyanin biosynthesis pathway” was signifificantly enriched in the fifive different temperature groups. KEGG analysis showed that the DEGs were mainly involved in pathways of phenylpropanoid biosynthesis, carbon fifixation in photosynthetic organisms, flflavonoid biosynthesis, and betacyanin biosynthesis. Among the key enzymes involved in biosynthesis of betacyanin, genes for tyrosinase, CYP76AD1 and 4,5-DOPA dioxygenase were signifificantly upregulated and most abundantly expressed at 15°C. It is possible that the gene for betacyanin synthesis from S. salsa is primarily regulated by the MYB1R1 and MYB1 transcription factor. Four DEGs were randomly selected for quantitative PCR analysis, and DEG expression was generally consistent with the RNA-Seq data, verifying the validity of the transcriptome sequencing data. Discussion Relative to other temperatures, 15°C was optimum for S. salsa betacyanin synthesis, and this provides a theoretical reference for coastal wetland ecological remediation, reveals mechanisms of S. salsa discoloration, and further mines its potential application for landscape vegetation.
Design of a Low Distortion Head-Mounted Display with Freeform Reflective Mirror Based on Two Ellipsoids Structure

A new method to design a low distortion, even relative illumination, optical see-through head-mounted display (HMD) with a freeform reflective mirror (FFRM) based on the two similar ellipsoids structure is proposed. The HMD we have realized has a simple structure which consists of two similar ellipsoid surfaces, an FFRM, a 7-piece co-axis relay lens, and an OLED. This structure can be applied to offset distortion, reach even relative illumination, and correct the off-axis aberrations. The HMD we finally have realized has a near 3% low distortion, a higher than 80% relative illumination, and a 40°×30° field of view (FOV).
An anatomically detailed arterial-venous network model. Cerebral and coronary circulation

In recent years, several works have addressed the problem of modeling blood flow phenomena in veins, as a response to increasing interest in modeling pathological conditions occurring in the venous network and their connection with the rest of the circulatory system. In this context, one-dimensional models have proven to be extremely efficient in delivering predictions in agreement with in-vivo observations. Pursuing the increase of anatomical accuracy and its connection to physiological principles in haemodynamics simulations, the main aim of this work is to describe a novel closed-loop Anatomically-Detailed Arterial-Venous Network (ADAVN) model. An extremely refined description of the arterial network consisting of 2,185 arterial vessels is coupled to a novel venous network featuring high level of anatomical detail in cerebral and coronary vascular territories. The entire venous network comprises 189 venous vessels, 79 of which drain the brain and 14 are coronary veins. Fundamental physiological mechanisms accounting for the interaction of brain blood flow with the cerebro-spinal fluid and of the coronary circulation with the cardiac mechanics are considered. Several issues related to the coupling of arterial and venous vessels at the microcirculation level are discussed in detail. Numerical simulations are compared to patient records published in the literature to show the descriptive capabilities of the model. Furthermore, a local sensitivity analysis is performed, evidencing the high impact of the venous circulation on main cardiovascular variables.
Diagnostic performance and clinical impact of blood metagenomic next-generation sequencing in ICU patients suspected monomicrobial and polymicrobial bloodstream infections

Introduction Early and effective application of antimicrobial medication has been evidenced to improve outcomes of patients with bloodstream infection (BSI). However, conventional microbiological tests (CMTs) have a number of limitations that hamper a rapid diagnosis. Methods We retrospectively collected 162 cases suspected BSI from intensive care unit with blood metagenomics next-generation sequencing (mNGS) results, to comparatively evaluate the diagnostic performance and the clinical impact on antibiotics usage of mNGS. Results and discussion Results showed that compared with blood culture, mNGS detected a greater number of pathogens, especially for Aspergillus spp, and yielded a significantly higher positive rate. With the final clinical diagnosis as the standard, the sensitivity of mNGS (excluding viruses) was 58.06%, significantly higher than that of blood culture (34.68%, P<0.001). Combing blood mNGS and culture results, the sensitivity improved to 72.58%. Forty-six patients had infected by mixed pathogens, among which Klebsiella pneumoniae and Acinetobacter baumannii contributed most. Compared to monomicrobial, cases with polymicrobial BSI exhibited dramatically higher level of SOFA, AST, hospitalized mortality and 90-day mortality (P<0.05). A total of 101 patients underwent antibiotics adjustment, among which 85 were adjusted according to microbiological results, including 45 cases based on the mNGS results (40 cases escalation and 5 cases de-escalation) and 32 cases on blood culture. Collectively, for patients suspected BSI in critical condition, mNGS results can provide valuable diagnostic information and contribute to the optimizing of antibiotic treatment. Combining conventional tests with mNGS may significantly improve the detection rate for pathogens and optimize antibiotic treatment in critically ill patients with BSI.
Role of autophagy-related proteins ATG8f and ATG8h in the maintenance of autophagic activity in Arabidopsis roots under phosphate starvation

Nutrient starvation-induced autophagy is a conserved process in eukaryotes. Plants defective in autophagy show hypersensitivity to carbon and nitrogen limitation. However, the role of autophagy in plant phosphate (Pi) starvation response is relatively less explored. Among the core autophagy-related (ATG) genes, ATG8 encodes a ubiquitin-like protein involved in autophagosome formation and selective cargo recruitment. The Arabidopsis thaliana ATG8 genes, AtATG8f and AtATG8h, are notably induced in roots under low Pi. In this study, we show that such upregulation correlates with their promoter activities and can be suppressed in the phosphate response 1 (phr1) mutant. Yeast one-hybrid analysis failed to attest the binding of the AtPHR1 transcription factor to the promoter regions of AtATG8f and AtATG8h. Dual luciferase reporter assays in Arabidopsis mesophyll protoplasts also indicated that AtPHR1 could not transactivate the expression of both genes. Loss of AtATG8f and AtATG8h leads to decreased root microsomal-enriched ATG8 but increased ATG8 lipidation. Moreover, atg8f/atg8h mutants exhibit reduced autophagic flux estimated by the vacuolar degradation of ATG8 in the Pi-limited root but maintain normal cellular Pi homeostasis with reduced number of lateral roots. While the expression patterns of AtATG8f and AtATG8h overlap in the root stele, AtATG8f is more strongly expressed in the root apex and root hair and remarkably at sites where lateral root primordia develop. We hypothesize that Pi starvation-induction of AtATG8f and AtATG8h may not directly contribute to Pi recycling but rely on a second wave of transcriptional activation triggered by PHR1 that fine-tunes cell type-specific autophagic activity.
Effects of the COVID-19 pandemic on Czech citizens: how do depression and anxiety symptoms influence cognitive, behavioral, and emotional changes?

Background This study examined the impact of anxiety and depression symptoms during the first stage of the COVID-19 pandemic on the behavioral, cognitive, and emotional changes of the Czech population. Methods The research sample (n = 2363; 48.83 ± 16.53 years; 50.15% men) was obtained using an online survey. Depression and anxiety symptoms were measured using the Overall Depression Severity and Impairment Scale (ODSIS) and the Overall Anxiety Severity and Impairment Scale (OASIS) and associations were adjusted for age, gender, and economic status. Results The results showed that increased symptoms of anxiety and depression were significantly linked to feelings of loneliness, helplessness, reduced quality of relationship with a partner, higher probabilities of alcohol abuse, food consumption, and contemplation of existential questions. Higher symptoms of anxiety were associated with feelings of being threatened. Higher symptoms of depression symptoms increased tobacco abuse. Conclusion During the first stage of the COVID-19 pandemic, higher symptoms of anxiety and depression among Czech citizens were associated with behavioral, cognitive, and emotional changes.
In silico-in vitro modeling to uncover cues involved in establishing microglia identity: TGF-β3 and laminin can drive microglia signature gene expression

Microglia are the resident macrophages of the central nervous system (CNS) and play a key role in CNS development, homeostasis, and disease. Good in vitro models are indispensable to study their cellular biology, and although much progress has been made, in vitro cultures of primary microglia still only partially recapitulate the transcriptome of in vivo microglia. In this study, we explored a combination of in silico and in vitro methodologies to gain insight into cues that are involved in the induction or maintenance of the ex vivo microglia reference transcriptome. First, we used the in silico tool NicheNet to investigate which (CNS-derived) cues could underlie the differences between the transcriptomes of ex vivo and in vitro microglia. Modeling on basis of gene products that were found to be upregulated in vitro, predicted that high mobility group box 2 (HMGB2)- and interleukin (IL)-1β-associated signaling pathways were driving their expression. Modeling on basis of gene products that were found to be downregulated in vitro, did not lead to predictions on the involvement of specific signaling pathways. This is consistent with the idea that in vivo microenvironmental cues that determine microglial identity are for most part of inhibitory nature. In a second approach, primary microglia were exposed to conditioned medium from different CNS cell types. Conditioned medium from spheres composed of microglia, oligodendrocytes, and radial glia, increased the mRNA expression levels of the microglia signature gene P2RY12. NicheNet analyses of ligands expressed by oligodendrocytes and radial glia predicted transforming growth factor beta 3 (TGF-β3) and LAMA2 as drivers of microglia signature gene expression. In a third approach, we exposed microglia to TGF-β3 and laminin. In vitro exposure to TGF-β3 increased the mRNA expression levels of the microglia signature gene TREM2. Microglia cultured on laminin-coated substrates were characterized by reduced mRNA expression levels of extracellular matrix-associated genes MMP3 and MMP7, and by increased mRNA expression levels of the microglia signature genes GPR34 and P2RY13. Together, our results suggest to explore inhibition of HMGB2- and IL-1β-associated pathways in in vitro microglia. In addition, exposure to TGF-β3 and cultivation on laminin-coated substrates are suggested as potential improvements to current in vitro microglia culture protocols.
Prolonged voluntary wheel running reveals unique adaptations in mdx mice treated with microdystrophin constructs ± the nNOS-binding site

We tested the effects of prolonged voluntary wheel running on the muscle function of mdx mice treated with one of two different microdystrophin constructs. At 7 weeks of age mdx mice were injected with a single dose of AAV9-CK8-microdystrophin with (gene therapy 1, GT1) or without (gene therapy 2, GT2) the nNOS-binding domain and were assigned to one of four gene therapy treated groups: mdxRGT1 (run, GT1), mdxGT1 (no run, GT1), or mdxRGT2 (run,GT2), mdxGT2 (no run, GT2). There were two mdx untreated groups injected with excipient: mdxR (run, no gene therapy) and mdx (no run, no gene therapy). A third no treatment group, Wildtype (WT) received no injection and did not run. mdxRGT1, mdxRGT2 and mdxR performed voluntary wheel running for 52 weeks; WT and remaining mdx groups were cage active. Robust expression of microdystrophin occurred in diaphragm, quadriceps, and heart muscles of all treated mice. Dystrophic muscle pathology was high in diaphragms of non-treated mdx and mdxR mice and improved in all treated groups. Endurance capacity was rescued by both voluntary wheel running and gene therapy alone, but their combination was most beneficial. All treated groups increased in vivo plantarflexor torque over both mdx and mdxR mice. mdx and mdxR mice displayed ∼3-fold lower diaphragm force and power compared to WT values. Treated groups demonstrated partial improvements in diaphragm force and power, with mdxRGT2 mice experiencing the greatest improvement at ∼60% of WT values. Evaluation of oxidative red quadriceps fibers revealed the greatest improvements in mitochondrial respiration in mdxRGT1 mice, reaching WT levels. Interestingly, mdxGT2 mice displayed diaphragm mitochondrial respiration values similar to WT but mdxRGT2 animals showed relative decreases compared to the no run group. Collectively, these data demonstrate that either microdystrophin construct combined with voluntary wheel running increased in vivo maximal muscle strength, power, and endurance. However, these data also highlighted important differences between the two microdystrophin constructs. GT1, with the nNOS-binding site, improved more markers of exercise-driven adaptations in metabolic enzyme activity of limb muscles, while GT2, without the nNOS-binding site, demonstrated greater protection of diaphragm strength after chronic voluntary endurance exercise but decreased mitochondrial respiration in the context of running.
Administration strategy of energy management in smart grid: system view and optimization path

Power generation and transmission infrastructure is vulnerable to the interaction of various Distributed Generations (DG), which leads to the imbalance of power system operation, frequent voltage drops or spikes, and even power outages. This phenomenon not only wastes energy, but also affects grid security. The main reason is a delayed feedback of circuit failure and load changes, and the optimization of energy management system and path is an effective way to solve the above problems. In this paper, a method of multi-objective optimization based on ANFIS algorithm is proposed which can help to improve the demand response, energy storage and management of smart power grid, reduce the volatility of DGs, reducing electricity costs and improving energy efficiency. Firstly, based on the ANFIS algorithm, the distributed power generation control mode, inverter control, real-time electricity price calculation method, energy transfer and storage scheme are improved, and the optimization path of the energy management system is defined. Secondly, the advantages of ANFIS algorithm in response speed and running stability are verified by comparing with other algorithms. Finally, a distributed energy microgrid is constructed for simulation verification. The results show that :(1) ANFIS optimization algorithm has good adaptability in smart grid, and has advantages in large amount of data processing and information transmission; (2) The verification model based on ANFIS has strong elasticity and efficient response speed. The research results will help solve various problems in the smart grid, including establishing a clear energy management system path, maintaining the stable operation of the power system, providing users with more reasonable power plans and the lowest cost of electricity.
The role and features of peer assessment feedback in college English writing

Peer assessment is a common pedagogical practice for evaluating students’ writing in college English classrooms. However, in-depth research on the learning outcomes after peer assessment is scarce and inconsistent; how peer feedback is used has not been fully explored either. This study compared peer feedback to teacher feedback and explored the different features of feedback and its impact on draft revision. Two specific research questions were answered in this study: (1) In which aspects can peer feedback supplement teacher feedback in improving the linguistic features in writing? (2) What are the differences in features of peer feedback versus teacher feedback? And how do they connect to feedback take-in? Two writing tasks were assigned to 94 students. One received teacher feedback and the other peer feedback. Pre-feedback and post-feedback writings in both tasks (4 sets in total) were scored and human ratings were adjusted using Many-Facet Rasch modeling to control for differences in leniency. Drawing on three natural language processing (NLP) tools, this study also assessed writing qualities by comparing 22 selected indices related to the scoring rubrics for human raters, which involve three dimensions: cohesion, lexical quality and syntactic complexity. Peer and teacher feedback was then coded based on features of feedback to explore their influence on draft revision. The results showed that both peer and teacher feedback had positive effects on rating scores. We confirmed peer feedback as an effective classroom approach to improve writing, though limited compared to teacher feedback as reflected in the indices. In terms of feedback features, students often stopped at identifying the language problems, while the teacher provided more explanations, solutions or suggestions regarding the problems identified. Implications for peer feedback research and implementation of peer assessment activities are provided.