Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Puccinia punctiformis on Cirsium arvense performance in a simulated crop sequence

Cirsium arvense (Canada thistle) is a perennial weed that causes significant economic losses in agriculture. An extensive rhizomatous root system makes C. arvense difficult to manage, particularly in agricultural systems that use tillage as a primary management tool. There is a need for the development of integrated weed management toolsets that include C. arvense biological controls. Puccinia punctiformis (thistle rust) is an autoecious fungal pathogen that systemically infects C. arvense, with the potential to reduce host vigor over time. The goal of this study was to integrate the P. punctiformis biocontrol with a simulated annual cropping sequence in a greenhouse environment and evaluate C. arvense’s above-and belowground biomass production, and its competitive ability. Repeated P. punctiformis inoculations produced systemically infected C. arvense stems in greenhouse pots over time. Cirsium arvense that was inoculated with P. punctiformis had 1.6 grams/pot (p = 0.0019) less aboveground biomass and 5.6 grams/pot (p< 0.001) less belowground biomass, compared to the non-inoculated (control). Puccinia punctiformis and crop competition interacted additively to lower aboveground (p<0.001) and belowground (p<0.001) C. arvense biomass more than individual use of either the biocontrol or competition alone. The aboveground competition intensity of C. arvense in a mixed crop sequence, relative to non-inoculated C. arvense grown in a monoculture, was moderately impacted by the P. punctiformis biocontrol (p = 0.0987). These results indicate that systemic infection can reduce biomass production and the competitive ability of C. arvense. Overall, P. punctiformis can be integrated into competitive annual cropping sequences with the potential to reduce C. arvense vigor over time.
Effect of farm machinery adoption on household income and food security: evidence from a nationwide household survey in India

An increase in farm productivity and income is crucially linked to farm mechanization. Labour shortage in rural areas and frequent extreme weather events have made a resounding pitch for the deepening of farm mechanization in India. Our study examines the effect of agricultural machinery adoption on net agricultural income, household income, and household consumption in India; the latter is considered as an indicator of food security. A nationwide household survey of 10253 households drawn from the majority of states of India has been used. To assess the impact of machinery adoption on the outcome variables, the endogenous switching regression (ESR) model is used. Of the three types of machineries investigated, such as tractors, electric pumps, and diesel pumps, the average adoption rates are found to be low in the country, i.e., 8% for tractors, 24% for electric pumps, and 14% for diesel pumps. The wide heterogeneity in terms of adoption is mostly rooted in the large geographical differences among the states of India, as machinery adoption is concentrated in the north and north-central plains of the country. The first stage of ESR, which is a probit model, reveals the determinants of mechanization as access to credit, climatic shocks, access to irrigation, and farmer cooperative membership. The average treatment effect estimates from the second stage outcome regression reveal that the adoption of machineries has increased net agricultural income by 31%, household income by 19%, and food consumption by 5%. Given these demonstrable positive effects of mechanization in agriculture, there is a need for deepening of low-cost scale appropriate farm machines suitable for small holders. Government support would play a pivotal role in this direction by making farm credits accessible to smallholders, providing timely subsidies on machinery purchase, and providing required extension services.
Evaluating longitudinal relationships between parental monitoring and substance use in a multi-year, intensive longitudinal study of 670 adolescent twins

Introduction Parental monitoring is a key intervention target for adolescent substance use, however this practice is largely supported by causally uninformative cross-sectional or sparse-longitudinal observational research designs. Methods We therefore evaluated relationships between adolescent substance use (assessed weekly) and parental monitoring (assessed every two months) in 670 adolescent twins for two years. This allowed us to assess how individual-level parental monitoring and substance use trajectories were related and, via the twin design, to quantify genetic and environmental contributions to these relationships. Furthermore, we attempted to devise additional measures of parental monitoring by collecting quasi-continuous GPS locations and calculating a) time spent at home between midnight and 5am and b) time spent at school between 8am-3pm. Results ACE-decomposed latent growth models found alcohol and cannabis use increased with age while parental monitoring, time at home, and time at school decreased. Baseline alcohol and cannabis use were correlated (r = .65) and associated with baseline parental monitoring (r = −.24 to −.29) but not with baseline GPS measures (r = −.06 to −.16). Longitudinally, changes in substance use and parental monitoring were not significantly correlated. Geospatial measures were largely unrelated to parental monitoring, though changes in cannabis use and time at home were highly correlated (r = −.53 to −.90), with genetic correlations suggesting their relationship was substantially genetically mediated. Due to power constraints, ACE estimates and biometric correlations were imprecisely estimated. Most of the substance use and parental monitoring phenotypes were substantially heritable, but genetic correlations between them were not significantly different from 0. Discussion Overall, we found developmental changes in each phenotype, baseline correlations between substance use and parental monitoring, co-occurring changes and mutual genetic influences for time at home and cannabis use, and substantial genetic influences on many substance use and parental monitoring phenotypes. However, our geospatial variables were mostly unrelated to parental monitoring, suggesting they poorly measured this construct. Furthermore, though we did not detect evidence of genetic confounding, changes in parental monitoring and substance use were not significantly correlated, suggesting that, at least in community samples of mid-to-late adolescents, the two may not be causally related.
A narrative action on the battle against hunger using mushroom, peanut, and soybean-based wastes

Numerous generations have been affected by hunger, which still affects hundreds of millions of people worldwide. The hunger crisis is worsening although many efforts have been made to minimize it. Besides that, food waste is one of the critical problems faced by most countries worldwide. It has disrupted the food chain system due to inefficient waste management, while negatively impacting the environment. The majority of the waste is from the food production process, resulting in a net zero production for food manufacturers while also harnessing its potential. Most food production wastes are high in nutritional and functional values, yet most of them end up as low-cost animal feed and plant fertilizers. This review identified key emerging wastes from the production line of mushroom, peanut, and soybean (MPS). These wastes (MPS) provide a new source for food conversion due to their high nutritional content, which contributes to a circular economy in the post-pandemic era and ensures food security. In order to achieve carbon neutrality and effective waste management for the production of alternative foods, biotechnological processes such as digestive, fermentative, and enzymatic conversions are essential. The article provides a narrative action on the critical potential application and challenges of MPS as future foods in the battle against hunger.
A mini-review of the role of vesicular glutamate transporters in Parkinson’s disease

Parkinson’s disease (PD) is a common neurodegenerative disease implicated in multiple interacting neurotransmitter pathways. Glutamate is the central excitatory neurotransmitter in the brain and plays critical influence in the control of neuronal activity. Impaired Glutamate homeostasis has been shown to be closely associated with PD. Glutamate is synthesized in the cytoplasm and stored in synaptic vesicles by vesicular glutamate transporters (VGLUTs). Following its exocytotic release, Glutamate activates Glutamate receptors (GluRs) and mediates excitatory neurotransmission. While Glutamate is quickly removed by excitatory amino acid transporters (EAATs) to maintain its relatively low extracellular concentration and prevent excitotoxicity. The involvement of GluRs and EAATs in the pathophysiology of PD has been widely studied, but little is known about the role of VGLUTs in the PD. In this review, we highlight the role of VGLUTs in neurotransmitter and synaptic communication, as well as the massive alterations in Glutamate transmission and VGLUTs levels in PD. Among them, adaptive changes in the expression level and function of VGLUTs may exert a crucial role in excitatory damage in PD, and VGLUTs are considered as novel potential therapeutic targets for PD.
Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis

The collection of whole microbial communities (bacteria, archaea, fungi, and viruses) together constitutes the gut microbiome. Diet, age, stress, host genetics, and diseases cause increases or decreases in the relative abundance and diversity of bacterial species (dysbiosis). We aimed to investigate the gut microbial composition at different taxonomic levels of healthy controls (HCs) with active Crohn’s disease (CD), ulcerative colitis (UC), and ischemic colitis (IC) using culture- and non-culture-based approaches and identify biomarkers to discriminate CD, UC, or IC. We determined the specific changes in the gut microbial profile using culture-independent (16S rRNA gene amplicon sequencing) as well as culture-based (culturomic) approaches. Biomarkers were validated using quantitative Real-Time PCR (qPCR). In both methods, bacterial diversity and species richness decreased in disease-associated conditions compared with that in HCs. Highly reduced abundance of Faecalibacterium prausnitzii and Prevotella sp. and an increased abundance of potentially pathogenic bacteria such as Enterococcus faecium, Enterococcus faecalis, and Escherichia coli in all CD, UC, or IC conditions were observed. We noted a high abundance of Latilactobacillus sakei in CD patients; Ligilactobacillus ruminis in UC patients; and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC patients. Highly reduced abundance of Faecalibacterium prausnitzii in all cases, and increased abundance of Latilactobacillus sakei and Enterococcus faecium in CD, Ligilactobacillus ruminis and Enterococcus faecium in UC, and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC could be biomarkers for CD, UC, and IC, respectively. These biomarkers may help in IBD (CD or UC) and IC diagnosis.
Culture, executive functions, and academic achievement

Although it is well known that children of East Asian immigrants show higher academic achievement than native-born North American children, the social-cognitive determinants of this difference remain poorly understood. Given the importance of executive functions (EF) for academic achievement, and evidence that EF develops more quickly in East Asian compared to North American cultures, it is conceivable that differences in academic achievement might be rooted in EF differences between these groups. We examine this possibility by reviewing evidence of cross-cultural differences in EF development but find core concepts and findings limited in several key respects. To address these limitations, we propose a framework for relating EF, culture, and academic achievement that draws on new theoretical ideas about the nature of EF and its relation to social context. We conclude by discussing avenues for future research on the relations between culture, executive functions, and academic achievement.
Chemical suppression of harmaline-induced body tremor yields recovery of pairwise neuronal coherence in cerebellar nuclei neurons

Neuronal oscillations occur in health and disease; however, their characteristics can differ across conditions. During voluntary movement in freely moving rats, cerebellar nuclei (CN) neurons display intermittent but coherent oscillations in the theta frequency band (4–12 Hz). However, in the rat harmaline model of essential tremor, a disorder attributed to cerebellar malfunction, CN neurons display aberrant oscillations concomitantly with the emergence of body tremor. To identify the oscillation features that may underlie the emergence of body tremor, we analyzed neuronal activity recorded chronically from the rat CN under three conditions: in freely behaving animals, in harmaline-treated animals, and during chemical suppression of the harmaline-induced body tremor. Suppression of body tremor did not restore single neuron firing characteristics such as firing rate, the global and local coefficients of variation, the likelihood of a neuron to fire in bursts or their tendency to oscillate at a variety of dominant frequencies. Similarly, the fraction of simultaneously recorded neuronal pairs oscillating at a similar dominant frequency (<1 Hz deviation) and the mean frequency deviation within pairs remained similar to the harmaline condition. Moreover, the likelihood that pairs of CN neurons would co-oscillate was not only significantly lower than that measured in freely moving animals, but was significantly worse than chance. By contrast, the chemical suppression of body tremor fully restored pairwise neuronal coherence; that is, unlike in the harmaline condition, pairs of neurons that oscillated at the same time and frequency displayed high coherence, as in the controls. We suggest that oscillation coherence in CN neurons is essential for the execution of smooth movement and its loss likely underlies the emergence of body tremor.
Alterations of the Ca2+ clearing mechanisms by type 2 diabetes in aortic smooth muscle cells of Zucker diabetic fatty rat

Type 2 Diabetes Mellitus (T2DM) is a rapidly rising disease with cardiovascular complications constituting the most common cause of death among diabetic patients. Chronic hyperglycemia can induce vascular dysfunction through damage of the components of the vascular wall, such as vascular smooth muscle cells (VSMCs), which regulate vascular tone and contribute to vascular repair and remodeling. These functions are dependent on intracellular Ca2+ changes. The mechanisms by which T2DM affects Ca2+ handling in VSMCs still remain poorly understood. Therefore, the objective of this study was to determine whether and how T2DM affects Ca2+ homeostasis in VSMCs. We evaluated intracellular Ca2+ signaling in VSMCs from Zucker Diabetic Fatty rats using Ca2+ imaging with Fura-2/AM. Our results indicate that T2DM decreases Ca2+ release from the sarcoplasmic reticulum (SR) and increases the activity of store-operated channels (SOCs). Moreover, we were able to identify an enhancement of the activity of the main Ca2+ extrusion mechanisms (SERCA, PMCA and NCX) during the early stage of the decay of the ATP-induced Ca2+ transient. In addition, we found an increase in Ca2+ entry through the reverse mode of NCX and a decrease in SERCA and PMCA activity during the late stage of the signal decay. These effects were appreciated as a shortening of ATP-induced Ca2+ transient during the early stage of the decay, as well as an increase in the amplitude of the following plateau. Enhanced cytosolic Ca2+ activity in VSMCs could contribute to vascular dysfunction associated with T2DM.
Economic impact of COVID-19 on income and use of livelihoods related coping mechanisms in Chad

Introduction Impacts of the economic slowdown due to COVID-19 were prevalent in SubSaharan African countries. Using four nationally representative surveys collected in 2020 (rural n = 13,208; urban n = 1736) and 2021 (n = 14,730; n = 2,231), this secondary analysis evaluates economic impacts of the pandemic on household income and use of livelihoods-related coping mechanisms in Chad. Methods Univariate and multivariate regression, accounting for the survey design and sampling weights, was used to examine risk factors for reported income reduction and coping mechanism use and the associations with food expenditures and food security. Results The economic impact of COVID-19 was greater in urban areas than rural areas in 2020 with improvement in urban areas and deterioration in rural areas in 2021. The reported income reduction was associated with female and unmarried household heads, living in the Saharan zone, and in rural areas, non-agricultural income sources. In urban areas, having skilled/unskilled labor as the primary income source was protective. Risk factors for the adoption of livelihoods-related coping mechanisms were similar to those of income reduction, with findings related to poor living conditions. Income reduction due to COVID-19 was associated with the use of stress and crisis coping strategies and lower household expenditure in both years and poor food consumption in rural areas in 2020. Discussion This study elucidates the potential impact pathways of COVID-19 from a household economic downturn to limited food spending, poor food consumption, and increased use of coping mechanisms. Findings are relevant for informing the targeting of assistance in future economic shocks and suggest prioritizing socioeconomically vulnerable households.
Hamilton, Rodrigues, and the Quaternion Scandal

The invention of the calculus of quaternions is a step towards the knowledge of quantities related to space which can only be compared, for its importance, with the invention of triple coordinates by Descartes. The ideas of this calculus, as distinguished from its operations and symbols, are fitted to be of the greatest use in all parts of science. Such robust language as Lord Kelvin's may now be largely forgotten, but the fact remains that the man in the street is strangely averse to using quaternions. Side by side with matrices and vectors, now the lingua franca of all physical scientists, quaternions appear to exude an air of nineteenth-century decay, as a rather unsuccess- ful species in the struggle-for-life of mathematical ideas. Mathematicians, admittedly, still keep a warm place in their hearts for the remarkable algebraic properties of quaternions, but such enthusiasm means little to the harder-headed physical scientist. This article will attempt to highlight certain problems of interpretation as regards quaternions which may seriously have affected their progress, and which might explain their present parlous status. For claims were made for quaternions which quaternions could not possibly fulfil, and this made it difficult to grasp what quater- nions are excellent at, which is handling rotations and double groups. It is
Long-term functional recovery and associated microbial community structure after sediment drying and bedform migration

Climate change and erosion from agricultural areas cause increased drying periods and bedform migration of riverbeds, respectively, worldwide. Both sediment drying and bedform migration can independently stress the microbial community residing in the riverbed. Here, we investigated the microbial response after exposure to these stressors with a focus on long-term recovery. We conducted an in situ experiment to investigate the long-term (8 months) functional and structural recovery of benthic microbial communities from either sediment drying (episodic severe stressor) or bedform migration (frequent moderate stressor). Stressed sediment associated communities were rewetted (dried sediments) and immobilized (migrated sediments) and exposed in the River Spree (north-eastern Germany) to initiate the recovery process. We then evaluated the microbial function (community respiration, net community production and extracellular enzymatic activities) as well as the bacterial, fungal and diatom community structure (16S rRNA gene and ITS region metabarcoding, and microscopic diatom morphotype classification). We observed different recovery times for community respiration (less than 7 days) and gross primary production (more than 5 months), implying a shift toward net heterotrophy in the first few months after stress exposure. Similarly, we observed a strong autotrophic community response (particularly associated with the diatoms Navicula and Fragilaria), especially in migrated sediments. The bacterial and fungal community response to sediment drying was stronger than to bedform migration (particularly associated with the bacterium Flavobacterium and the fungi Alternaria sp. and Aureobasidium pullulans). Our results show that sediment drying and bedform migration had a significant impact on the microbial community function and structure, which persisted for several months after the stress. Due to the surprising long period of recovery, successive stress events combined with seasonal effects will likely hamper the ongoing recovery process with severe alterations to the microbial function and structure. These findings extend the concept of ecosystem resilience and stability on the dimensions of timescale and seasonal environmental variations. Legacy effects are expected to play a key role when facing future stress.
A quadruplex real-time PCR assay combined with a conventional PCR for the differential detection of Marek’s disease virus vaccines and field strains

To evaluate the effect of the vaccine and differentiate vaccine from virulent MDV, a new quadruplex real-time PCR assay based on TaqMan probes was developed to differentiate and accurately quantify HVT, CVI988 and virulent MDV-1. The results showed that the limit of detection (LOD) of the new assay was 10 copies with correlation coefficients >0.994 of CVI988, HVT and virulent MDV DNA molecules without cross-reactivity with other avian disease viruses. The intra-assay and inter-assay coefficients of variation (CVs) of Ct values for the new assay were less than 3%. Analysis of replication kinetics of CVI988 and virulent MDV of collected feathers between 7 and 60 days post-infection (dpi) showed MD5 had no significant effect on the genomic load of CVI988 (p > 0.05), while vaccination with CVI988 could significantly reduce the viral load of MD5 (p < 0.05). Combined with meq gene PCR, this method can effectively identify virulent MDV infections in immunized chickens. These results demonstrated that this assay could distinguish between the vaccine and virulent MDV strains and had the advantages of being reliable, sensitive and specific to confirm the immunization status and monitor the circulation of virulent MDV strains.
Free fatty acids support oligodendrocyte survival in a mouse model of amyotrophic lateral sclerosis

Introduction Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the white matter degeneration. Although changes in blood lipids are involved in the pathogenesis of neurological diseases, the pathological role of blood lipids in ALS remains unclear. Methods and results We performed lipidome analysis on the plasma of ALS model mice, mutant superoxide dismutase 1 (SOD1G93A) mice, and found that the concentration of free fatty acids (FFAs), including oleic acid (OA) and linoleic acid (LA), decreased prior to disease onset. An in vitro study revealed that OA and LA directly inhibited glutamate-induced oligodendrocytes cell death via free fatty acid receptor 1 (FFAR1). A cocktail containing OA/LA suppressed oligodendrocyte cell death in the spinal cord of SOD1G93A mice. Discussion These results suggested that the reduction of FFAs in the plasma is a pathogenic biomarker for ALS in the early stages, and supplying a deficiency in FFAs is a potential therapeutic approach for ALS by preventing oligodendrocyte cell death.