Miracle-dz/UniFAR-FTUs huggingface dataset:
Labelling effect in insects: cue associations influence perceived food value in ants

Humans usually assess things not in terms of absolute value, but relative to reference points. The framing of alternatives can strongly affect human decision-making, leading to different choices depending on the context within which options are presented. Similar reference-point effects have been recently reported in ants, in which foragers show a contrast effect: ants overvalue a medium-quality food source if they were expecting a poor one, and vice versa for expectations of good food. However, studies of human consumer psychology have demonstrated that expectations, for example from product labels, can drive value perception in the other direction via assimilation. For example, an expensive bottle of wine is perceived as more enjoyable compared to a cheaper bottle, even if the wine is the same. In this study, we demonstrate a similar labelling-association effect in an insect: ants showed assimilation effects by spending twice as long drinking at a medium quality food source if it was scented with an odour previously associated with high quality than if it was scented with a poor-quality label. The presence of odour cues in the food during consumption and evaluation is critical, as without them, odour-driven expectations of quality result in contrast, not assimilation effects. The addition of a quality label in the food thus reverses contrast effects and causes value to be aligned with expectations, rather than being contrasted against them. As value judgement is a key element in decision-making, relative value perception strongly influences which option is chosen, and ultimately how choices are made.
The Development of Literate Potential in Literature-Based and Skills-Based Classrooms

This study examined young children’s developing understand ing of written discourse in two instructional settings: literature-based and skills-based. Forty-one first graders were each requested to dictate two “written” stories for others to read at the beginning and end of the school year. The 82 texts were analyzed for their cohesive harmony, conformity to the socioculturally-codified genre conventions, and use of specific written language features. Quantitative analysis revealed statistically sig nificant increases in cohesion and genre scores, but only marginal gains in the written language features measures. Further, the development of such written discourse knowledge was not significantly impacted by the instructional context. Qualitative analysis revealed that the children’s texts demonstrated impressive advances in the written mode of organiz ing and communicating information to others, despite evidence of traces of oral discourse patterns and immature control over diverse genres. These findings are discussed in light of relevant literacy research and practice.
Attempt of using median filter as an aiding device of noncoherent matched filter code acquisition of DS receiver in continuous tone jamming

The paper introduces analysis and simulation results regarding a DS spread spectrum system in which the principle of noncoherent matched filter synchronization for acquisition of the code synchronization is used. Approximations of the probabilities of detection and false alarms and the mean acquisition times of noncoherent matched filter synchronization in continuous tone jamming are introduced when a complementary code pair is used as a spreading code. The idea of using median type filtering as an aid for the matched filter is tested for the noncoherent case. It is shown that continuous jamming can have a very dramatic influence on P/sub d/, P/sub fa/, and T/sub MA/. The influence can be decreased efficiently by using a median filter. <<ETX>>
The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken

Scope: As DNA methylation is one of the key epigenetic mechanisms involved in embryonic muscle development, elucidating its relationship with non-coding RNAs and genes is essential for understanding early muscle development. The methylome profiles of pre-hatching chicken across multiple developmental stages remain incomplete although several related studies have been reported. Methods: In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq of broilers and layers in different embryonic development points (E10, E13, E16 and E19) to explore the genetic basis of embryonic muscle development in chicken. The differential methylated regions and novel lncRNAs were identified for association analyses. Through genomic position and correlation analysis between DMRs and lncRNAs, the target lncRNAs were detected to participate in the embryonic muscle formation and the results were then verified in vitro experiments. Results: Comparison of methylome profiles between two chicken lines revealed that lower methylation in broilers might contribute to muscle development in embryonic period. Differential methylated region analysis showed that the majority of differential methylated regions were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, we identified a long non-coding RNA MyH1-AS that potentially regulated embryonic muscle development, proved by the regulatory network construction and further in vitro experiments. Conclusion: Our study revealed an integrative landscape of middle- to late-stage of embryonic myogenesis in chicken, gave rise to a comprehensive understanding of epigenetic and transcriptional regulation in muscle development. Moreover, we provided a reliable data resource for further embryonic muscle development studies.
Improved statistical methods for k-means clustering of noisy and directional data

A new methodology is proposed for clustering datasets in the presence of scattered observations. Scattered observations are defined as unlike any other, so traditional approaches that force them into groups can lead to erroneous conclusions. Our suggested approach is a scheme which, under assumption of homogeneous spherical clusters, iteratively builds cores around their centers and groups points within each core while identifying points outside as scatter. In the absence of scatter, the algorithm reduces to k-means. We also provide methodology to initialize the algorithm and to estimate the number of clusters in the dataset. Results in experimental situations show excellent performance, especially when clusters are elliptically symmetric. The methodology is applied to the analysis of the United States Environmental Protection Agency (EPA)’s Toxic Release Inventory (TRI) reports on industrial releases of mercury for the year 2000.
Aldose Reductase Inhibitors of Plant Origin in the Prevention and Treatment of Alcoholic Liver Disease: A Minireview

Alcoholic liver disease (ALD) is caused by heavy alcohol consumption over a long period. Acetaldehyde-mediated toxicity, oxidative stress, and imbalance of lipid metabolism are generally considered involved in the initiation of ALD. There is an increasing requirement for alternative and natural medicine to treat ALD. Recently, aldose reductase (AR) has been reported to be involved in the development of ALD by affecting inflammatory cytokines, oxidative stress, and lipid metabolism. Here, we review the effect of plant-derived AR inhibitors on ALD in rodents. And we conclude that AR inhibitors of plant origin may enhance antioxidant capacity, inhibit lipid peroxidation and inflammatory cytokines expression, and activate AMP-activated protein kinase thereby subsequently suppressing alcohol-induced lipid synthesis in liver to achieve ALD protection. This review reveals that natural AR inhibitor may be potential therapeutic agent for ALD.
Molecular phylogenetic analysis resolves Trisetum (Poaceae: Pooideae: Koeleriinae) polyphyletic: Evidence for a new genus, Sibirotrisetum and resurrection of Acrospelion

To investigate the evolutionary relationships among the species of Trisetum and other members of subtribe Koeleriinae, a phylogeny based on DNA sequences from four gene regions (ITS, rpl32‐trnL spacer, rps16‐trnK spacer, and rps16 intron) is presented. The analyses, including type species of all genera in Koeleriinae (Acrospelion, Avellinia, Cinnagrostis, Gaudinia, Koeleria, Leptophyllochloa, Limnodea, Peyritschia, Rostraria, Sphenopholis, Trisetaria, Trisetopsis, Trisetum), along with three outgroups, confirm previous indications of extensive polyphyly of Trisetum. We focus on the monophyletic Trisetum sect. Sibirica clade that we interpret here as a distinct genus, Sibirotrisetum gen. nov. We include a description of Sibirotrisetum with the following seven new combinations: Sibirotrisetum aeneum, S. bifidum, S. henryi, S. scitulum, S. sibiricum, S. sibiricum subsp. litorale, and S. turcicum; and a single new combination in Acrospelion: A. distichophyllum. Trisetum s.s. is limited to one, two or three species, pending further study.
Rhizosphere metagenomics of mine tailings colonizing plants: assembling and selecting synthetic bacterial communities to enhance in situ bioremediation

Mine tailings phytostabilization has been proposed as a bioremediation strategy to constrain the contaminants dispersion using plants to limit the effects of erosion. Rhizospheric bacteria impact plant health and facilitate plant establishment through their metabolic functions, which could be relevant in bioremediation strategies. We studied both culturable and metagenomic diversity or rhizospheric bacteria of mine tailings colonizing plants of an abandoned mine operation in Nacozari de García, Sonora, Mexico. Diversity was described through amplification of the 16S rRNA gene and whole metagenome shotgun sequencing of both environmental and cultured rhizosphere associated microbes. The culturable bacteria were assembled in a synthetic community (SC; 235 bacteria genera). Subsequently, we performed an experimental evolution setup with the SC, selecting for heavy metal resistance, microbial competition, and the ability for growing in plant-derived nutrient sources. The selection experiment show that bacteria diversity decreases from the environmental culture-free microbiomes to the mine tailings rhizospheres and the experimental evolution outcome: the synthetic community (FSC; 43 bacteria genera). The rhizosphere communities shifted from the dominance of Actinobacteria in their environment to Proteobacteria in the cultivated consortia and the synthetic communities. Both environmental and cultured metagenomes contained plant-growth promotion, heavy-metal homeostasis, and antibiotic resistance predicted genes. The FSC included predicted proteins related to plant-growth promotion such as siderophore production and plant hormone regulation proteins. We reconstructed a metagenome assembled genomic sequence named Enterobacter sp. , Nacozari. The recovered Enterobacter sp. Nacozari, have predicted coding genes for direct and indirect plant growth promotion along with adhesion and oxidative stress-related proteins. The metabolic potential of the FSC presents promising features that might make it useful for plant-growth promotion in tailored phytostabilization strategies for the abandoned mine-tailings of Nacozari.
Resolving ESCRT-III spirals at the intercellular bridge of dividing cells using 3D STORM imaging

The ESCRT machinery mediates membrane fission in a verity of processes in cells. According to the proposed mechanism, ESCRT-III proteins drive membrane fission by assembling into helical filaments on membranes. Yet, ESCRT-III filaments have never been directly visualized in a cellular process that utilizes this machinery for its function. Here we used 3D STORM imaging of endogenous ESCRT-III component IST1, to describe the structural organization of ESCRT-III during mammalian cytokinetic abscission. Using this approach, ESCRT-III ring and spiral assemblies were resolved at the intercellular tube of cells undergoing abscission. Characterization of these structures indicates the ESCRT-III helical filament undergoes remodeling during abscission. This work provides the first evidence that ESCRT-III proteins assemble into helical filaments in physiological context, indicating that the ESCRT-III machine indeed derives its contractile activity through spiral assemblies. Moreover, it provides new structural information on ESCRT-III filaments, which raise new mechanistic scenarios for ESCRT driven membrane constriction.
Mitochondrial D-loop DNA analyses of Norway lobster (Nephrops norvegicus) reveals genetic isolation between Atlantic and East Mediterranean populations

Abstract Nephrops norvegicus is a commercially valuable demersal fisheries species. Relatively little is understood about this species’ population dynamics across its distribution with previous mitochondrial and microsatellite studies failing to identify significant population-level differentiation. In this study, sequence variation in the mitochondrial (mtDNA) D-loop was analysed from samples across the distribution range, and compared with COI sequences for this species retrieved from GenBank. Analysis of a 375 bp fragment of the D-loop revealed significant genetic differentiation between samples from the North-east Atlantic and the east Mediterranean (FST = 0.107, P < 0.001). Tau (τ), theta (θ0 and θ1) and Fu's FS values suggest the species spread between 10,500 to 19,000 ybp and subsequently expanded rapidly across the Atlantic.
Benefits of an 8-form Tai Chi Training Exercise on Balance Performance, Falling Risk, and Muscle Strengths in Elderly with Limited Strength: A Feasibility Study

The aim of this study was to determine the effectiveness of an 8-form Tai Chi training exercise on balance performance, falling risk, and muscle strengths in elderly with limited strength. Twenty-six females between 70-85 years old with balance problem and moderate lower extremity muscular strengths (grade 2+ to 3+) without prior Tai Chi training volunteered for the study. The participants underwent the 8-form Tai Chi training exercise for 45 minutes/session, 3 sessions a week for 12 weeks. Balance performance (m-CTSIB, Postural Stability Balance Test, and 8-foot up-and-go Test), falling risk (Fall Risk Overall Stability Test and Fear of Falling Assessment), and muscle strengths (30-second Chair Stand Test and Pressure Biofeedback Unit Test) were assessed during pretest, mid-test, and post-test. One-way repeated measures ANOVA was conducted at the significant level of 0.05. The results after 6 weeks of training showed that balance and falling risk were improved where 8 foot up-and-go test and fear of falling assessment were significantly better than pre-experiment, while after 12 weeks, balance, falling risk, and lower extremity muscular strengths were significantly improved when compared to the pre-experiment. The 12-week 8-form Tai Chi training exercise was safe and effective in improving balance, falling risk, and lower extremity muscular strengths in ageing people with limited strengths.
A Novel Approach to Enhance the Urease Activity of Sporosarcina pasteurii and its Application on Microbial-Induced Calcium Carbonate Precipitation for Sand

Abstract Urease is involved in the formation of carbonate sediments by microbial-induced calcium carbonate precipitation (MICP), and Sporosarcina pasteurii used extensively in this technique owing to its high urease production. In this study, a simple two-step culture method with the appropriate medium was developed to enhance the urease activity of S. pasteurii. Urea played an important role in the culture process, particularly during the pre-cultivation step and the newly developed method improved both urease activity and specific urease activity. Furthermore, the increase in urease activity by MICP resulted in increased production of calcium carbonate and better strength of bio-cemented sand.
Redox-mediated kick-start of mitochondrial energy metabolism drives resource-efficient seed germination

Significance Seeds are the main human food source and germination characteristics are critical in modern agriculture. For plants, seeds allow propagation over long distances and time periods and provide protection of progeny from hostile environments. For germination and seedling establishment the embryo relies fully on its stored energy resources. We report a sharp transition in mitochondrial metabolic activity and thiol redox status that coincides with seed rehydration. Hundreds of Cys-based redox switches are operated, providing early and direct metabolic regulation, long before gene expression-based control is established to underpin hormonal checkpoints. Seeds lacking proteins of the mitochondrial thiol redox machinery use their resources less efficiently, suggesting that the early reset of thiol redox status orchestrates metabolic efficiency for successful germination. Seeds preserve a far developed plant embryo in a quiescent state. Seed metabolism relies on stored resources and is reactivated to drive germination when the external conditions are favorable. Since the switchover from quiescence to reactivation provides a remarkable case of a cell physiological transition we investigated the earliest events in energy and redox metabolism of Arabidopsis seeds at imbibition. By developing fluorescent protein biosensing in intact seeds, we observed ATP accumulation and oxygen uptake within minutes, indicating rapid activation of mitochondrial respiration, which coincided with a sharp transition from an oxidizing to a more reducing thiol redox environment in the mitochondrial matrix. To identify individual operational protein thiol switches, we captured the fast release of metabolic quiescence in organello and devised quantitative iodoacetyl tandem mass tag (iodoTMT)-based thiol redox proteomics. The redox state across all Cys peptides was shifted toward reduction from 27.1% down to 13.0% oxidized thiol. A large number of Cys peptides (412) were redox switched, representing central pathways of mitochondrial energy metabolism, including the respiratory chain and each enzymatic step of the tricarboxylic acid (TCA) cycle. Active site Cys peptides of glutathione reductase 2, NADPH-thioredoxin reductase a/b, and thioredoxin-o1 showed the strongest responses. Germination of seeds lacking those redox proteins was associated with markedly enhanced respiration and deregulated TCA cycle dynamics suggesting decreased resource efficiency of energy metabolism. Germination in aged seeds was strongly impaired. We identify a global operation of thiol redox switches that is required for optimal usage of energy stores by the mitochondria to drive efficient germination.
Null model analyses of temporal patterns of bird assemblages and their foraging guilds revealed the predominance of positive and random associations

Abstract Patterns of species associations have been commonly used to infer interactions among species. If species positively co‐occur, they may form predominantly neutral assemblages, and such patterns suggest a relatively weak role for compensatory dynamics. The main objective of this study was to test this prediction on temporal samples of bird assemblages (n = 19, 10–57 years) by the presence/absence and quantitative null models on assemblage and guild levels. These null model outcomes were further analyzed to evaluate the effects of various data set characteristics on the outcomes of the null models. The analysis of two binary null models in combination with three association indices revealed 20% with significant aggregations, 61% with random associations, and only 19% with significant segregations (n = 95 simulations). The results of the quantitative null model simulations detected more none‐random associations: 61% aggregations, 6% random associations, and 33% segregations (n = 114 simulations). Similarly, quantitative analyses on guild levels showed 58% aggregations, 20% segregations, and 22% random associations (n = 450 simulations). Bayesian GLMs detected that the outcomes of the binary and quantitative null models applied to the assemblage analyses were significantly related to census plot size, whereas the outcomes of the quantitative analyses were also related to the mean population densities of species in the data matrices. In guild‐level analyses, only 9% of the GLMs showed a significant influence of matrix properties (plot size, matrix size, species richness, and mean species population densities) on the null model outcomes. The results did not show the prevalence of negative associations that would have supported compensatory dynamics. Instead, we assume that a similar response of the majority of species to climate‐driven and stochastic factors may be responsible for the revealed predominance of positive associations.
Ethnic variation in osteoporosis risk factors: dietary calcium, vitamin D intake
and body mass index (BMI)

Osteoporosis is the most common bone disease in humans, representing a major public health problem. Few studies have investigated osteoporosis risk factors such as calcium and vitamin D intake, quality of life and body mass index (BMI) among multi-ethnic adults in the Malaysian context. This study aimed to determine the ethnic variation in osteoporosis risk factors among students in Universiti Malaysia Terengganu (UMT). A cross-sectional study via a self-administrated questionnaire was carried out among 198 respondents aged 19 to 25 years from UMT. The data in the present study included a three -day food record and anthropometric measurements. Nutritionist ProTM analysis software version 5.3 was used to calculate dietary calcium and vitamin D intake from the diet histories, based on the Nutrient Composition of Malaysian Food Database guidance for the dietary calcium intake and the United States Department of Agriculture (USDA) for vitamin D intake. The data were analyzed using Kruskal-Wallis, Mann-Whitney and ChiSquare tests. The findings indicate the median calcium intake was 348.3 mg/day while for vitamin D intake was only 1.37 µg/day. Indian participants had a significantly lower intake level of calcium (243.5 mg/day), followed by Chinese (362.3 mg/day) and Malays (440.4 mg/day). The median vitamin D intakes of Malay, Chinese, and Indian adults were 2.15 μg/day, 1.37 μg/day and 1.14 μg/day, respectively. Furthermore, the BMI among respondents at 20.88 (6.4) kg/m2 categorized as normal weight. It was found that there was no significant difference (p> 0.05) in BMI across ethnicity. Lastly, there was a significant association (p< 0.05) between ethnicity and calcium intake (p = 0.001).
Single cell analysis reveals immune cell–adipocyte crosstalk regulating the transcription of thermogenic adipocytes

Immune cells are vital constituents of the adipose microenvironment that influence both local and systemic lipid metabolism. Mice lacking IL10 have enhanced thermogenesis, but the roles of specific cell types in the metabolic response to IL10 remain to be defined. We demonstrate here that selective loss of IL10 receptor α in adipocytes recapitulates the beneficial effects of global IL10 deletion, and that local crosstalk between IL10-producing immune cells and adipocytes is a determinant of thermogenesis and systemic energy balance. Single Nuclei Adipocyte RNA-sequencing (SNAP-seq) of subcutaneous adipose tissue defined a metabolically-active mature adipocyte subtype characterized by robust expression of genes involved in thermogenesis whose transcriptome was selectively responsive to IL10Rα deletion. Furthermore, single-cell transcriptomic analysis of adipose stromal populations identified lymphocytes as a key source of IL10 production in response to thermogenic stimuli. These findings implicate adaptive immune cell-adipocyte communication in the maintenance of adipose subtype identity and function.