Miracle-dz/UniFAR-FTUs huggingface dataset:
Precompetitional Weight Reduction Modifies Prooxidative-Antioxidative Status in Judokas

Objective The main aim of the study was an assessment of the influence of rapid weight loss on oxidative stress parameters in judokas differing in weight reduction value. Materials and Methods The study included 30 judokas with an age range of 18-30 years (mean age: 22.4 ± 3.40 years). Enzymatic and nonenzymatic antioxidative markers, lipid peroxidation markers, and total oxidative stress were assessed three times: one week before a competition (the first stage), after gaining the desired weight (the second stage), and one week after the competition (the third stage). Results Between the first and the second stage, the concentration of lipid hydroperoxides (LPH) decreased significantly. The superoxide dismutase (SOD), copper- and zinc-containing superoxide dismutase (Cu,Zn-SOD), ceruloplasmin (CER), malondialdehyde (MDA), LPH, and total oxidative stress (TOS) concentrations were the lowest one week after the competition. Linear regression indicated that the emphases on increased weight reduction increased the activity of glutathione peroxidase (GPx), glutathione reductase (GR), glutathione S-transferase (GST), and protein sulfhydryl (PSH) between the first and the second stage of the study. Moderate weight reduction (2-5%) resulted in elevated levels of SOD, Mn-SOD, LPH, MDA, and TOS in comparison to low and high reductions. An opposite relation was observed in PSH. In judokas, the precompetitional weight reduction range was 0.44-6.10% (mean: 2.93% ± 1.76%) of the initial body weight. Concentrations of superoxide dismutase (SOD; p < .01), manganese-dependent superoxide dismutase (Mn-SOD; p < .001), and ceruloplasmin (CER; p < .05) decreased between the first and the third stage of the study as well between the second and third one. Before competitions, a decrease in lipid hydroperoxide (LPH; p < .01) concentration was observed. A reduction of malondialdehyde (MDA; p < .05), LPH (p < .01), and total oxidative stress (TOS; p < .05) levels between the first and the final stage occurred. The increase in weight reduction was linearly correlated with the rise of glutathione peroxidase (GPx; p < .05), glutathione reductase (GR; p < .05), glutathione S-transferase (GST; p < .05), and protein sulfhydryl (PSH; p < .05) concentrations between the first and the second stage of the study. Moderate weight reduction (2-5%) resulted in elevated levels of SOD (p < .05), Mn-SOD (p < .05), LPH (p < .05), MDA (p < .05), and TOS (p < .05) in comparison to low and high reductions. An opposite relation was observed in PSH (p < .005). Conclusions The effect of weight reduction in judo athletes on prooxidative-antioxidative system diversity depends on the weight reduction value.
Experimental evolution reveals a general role for the methyltransferase Hmt1 in noise buffering

Cell-to-cell heterogeneity within an isogenic population has been observed in prokaryotic and eukaryotic cells. Such heterogeneity often manifests at the level of individual protein abundance and may have evolutionary benefits, especially for organisms in fluctuating environments. Although general features and the origins of cellular noise have been revealed, details of the molecular pathways underlying noise regulation remain elusive. Here, we used experimental evolution of Saccharomyces cerevisiae to select for mutations that increase reporter protein noise. By combining bulk segregant analysis and CRISPR/Cas9-based reconstitution, we identified the methyltransferase Hmt1 as a general regulator of noise buffering. Hmt1 methylation activity is critical for the evolved phenotype, and noise buffering is primarily achieved via two Hmt1 methylation targets. Hmt1 functions as an environmental sensor to adjust noise levels in response to environmental cues. Moreover, Hmt1-mediated noise buffering is conserved in an evolutionarily distant yeast species, suggesting broad significance of noise regulation. Author Summary Cell-to-cell heterogeneity within an isogenic population has been observed in prokaryotic and eukaryotic cells. Such heterogeneity often manifests at the level of individual protein abundance and may have evolutionary benefits, especially for organisms in fluctuating environments. Here, we used experimental evolution of Saccharomyces cerevisiae to select for mutations that increase reporter protein noise and identified the methyltransferase Hmt1 as a general regulator of noise buffering. Hmt1 is a central hub protein that is involved in multiple basic cellular pathways, including chromatin remodeling/transcription, translation, ribosome biogenesis, and post-transcriptional regulation. Our results show that Hmt1 constrains the noise level of multiple cellular pathways under normal conditions, so the physiology of individual cells in a population will not deviate too much from optimal peak fitness. However, when cells encounter environmental stresses, HMT1 is quickly down-regulated and expression noise is enhanced to increase the likelihood of population survival. Moreover, the noise buffering function of Hmt1 is conserved in Schizosaccharomyces pombe that diverged from the common ancestor of Saccharomyces cerevisiae more than 400 million years ago. Since the Hmt1 network is conserved from yeast cells to human, it is quite possible that Hmt1-mediated noise buffering also operates in multicellular organisms.
Stock-production functions resembling Beverton-Holt

Researchers dissatisfied with the performance of the Beverton-Holt model, in contexts where “Beverton-Holt-like” behavior is expected, have introduced a plethora of alternative model forms. This paper presents a formalization of what constitutes “Beverton-Holt-like behavior” which includes many of these forms, and shows that the class of functions so defined has a coherent and non-trivial mathematical theory. Data from the stock production database assembled by Ransom Myers is used to illustrate why such generalizations have been sought in the first place, and to highlight the difficulties in choosing between model forms on purely empirical grounds. Special attention is given to a parametric family of functions within this class, here called “θ-BH” functions. These functions cover a broad range of shapes, including both the Beverton-Holt and hockey stick functions, and share useful properties with these two widely-used models.
Ultrasound improves the outcomes of cardiopulmonary resuscitation in rats by stimulating the cholinergic anti-inflammatory pathway

The present study investigated the effects of the ultrasound (US), a noninvasive technique, on ischemia-reperfusion injury (IRI) following cardiopulmonary resuscitation (CPR). The animals used in the present study were randomized into five groups (n=8 per group) as follows: i) The CPR group, where the rats underwent 6 min of untreated ventricular fibrillation (VF) followed by CPR and defibrillation; ii) the US group, in which the treatment was identical to the CPR group with the exception that rats were exposed to US treatment 24 h prior to CPR; iii) the MLA group, in which the treatment was identical to the US group with the exception that the α7 nicotinic acetylcholine receptor (α7nAChR) antagonist MLA (4 mg/kg) was administered 30 min prior to US and VF respectively; iv) the GTS group, in which the treatment was identical to the CPR group with the exception that the α7nAChR agonist GTS-21 (4 mg/kg) was injected 30 min prior to VF; and v) the SHAM group, in which the rats were exposed to surgical preparation without CPR and US application. At 1 day prior to CPR, the US treatment was administered to the left kidney by US pulses (contrast general mode with 9 MHz) with a bursting mechanical index of 0.72 for 2 min. Following treatment of the left kidney, the right kidney was exposed to identical US treatment for an additional 2 min. The results demonstrated that US preconditioning decreased the number of defibrillations required and shortened the duration of CPR. US also suppressed tumor necrosis factor-α and interleukin-6 levels following resuscitation (P<0.05), and a significantly longer overall survival time was observed in the US-treated animals (P<0.01). In addition, US attenuated neuronal injury and promoted the expression of α7nAChR in hippocampal neurons (P<0.05). However, the protective effects of US were abolished by MLA and imitated by GTS-21. The results of the present study demonstrated that prior exposure to US may improve animal outcomes following CPR, and the protective effects of US may be dependent on the cholinergic anti-inflammatory pathway (CAP) via α7nAChR.
Identification of core genes and pathways in type 2 diabetes mellitus by bioinformatics analysis

Type 2 diabetes mellitus (T2DM) is a metabolic disorder. Numerous proteins have been identified that are associated with the occurrence and development of T2DM. This study aimed to identify potential core genes and pathways involved in T2DM, through exhaustive bioinformatic analyses using GSE20966 microarray profiles of pancreatic β-cells obtained from healthy controls and patients with T2DM. The original microarray data were downloaded from the Gene Expression Omnibus database. Data were processed by the limma package in R software and the differentially expressed genes (DEGs) were identified. Gene Ontology functional analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were carried out to identify potential biological functions and pathways of the DEGs. Key transcription factors were identified using the WEB-based GEne SeT AnaLysis Toolkit (WebGestalt) and Enrichr. The Search Tool for the Retrieval of Interacting Genes (STRING) database was used to establish a protein-protein interaction (PPI) network for the DEGs. In total, 329 DEGs were involved in T2DM, with 208 upregulated genes enriched in pancreatic secretion and the complement and coagulation cascades, and 121 downregulated genes enriched in insulin secretion, carbohydrate digestion and absorption, and the Toll-like receptor pathway. Furthermore, hepatocyte nuclear factor 1-alpha (HNF1A), signal transducer and activator of transcription 3 (STAT3) and glucocorticoid receptor (GR) were key transcription factors in T2DM. Twenty important nodes were detected in the PPI network. Finally, two core genes, serpin family G member 1 (SERPING1) and alanyl aminopeptidase, membrane (ANPEP), were shown to be associated with the development of T2DM. On the whole, the findings of this study enhance our understanding of the potential molecular mechanisms of T2DM and provide potential targets for further research.
Single-Cell Transcriptomics Reveals Spatial and Temporal Turnover of Keratinocyte Differentiation Regulators

Keratinocyte differentiation requires intricately coordinated spatiotemporal expression changes that specify epidermis structure and function. This article utilizes single-cell RNA-seq data from 22,338 human foreskin keratinocytes to reconstruct the transcriptional regulation of skin development and homeostasis genes, organizing them by differentiation stage and also into transcription factor (TF)–associated modules. We identify groups of TFs characterized by coordinate expression changes during progression from the undifferentiated basal to the differentiated state and show that these TFs also have concordant differential predicted binding enrichment in the super-enhancers previously reported to turn over between the two states. The identified TFs form a core subset of the regulators controlling gene modules essential for basal and differentiated keratinocyte functions, supporting their nomination as master coordinators of keratinocyte differentiation. Experimental depletion of the TFs ZBED2 and ETV4, both predicted to promote the basal state, induces differentiation. Furthermore, our single-cell RNA expression analysis reveals preferential expression of antioxidant genes in the basal state, suggesting keratinocytes actively suppress reactive oxygen species to maintain the undifferentiated state. Overall, our work demonstrates diverse computational methods to advance our understanding of dynamic gene regulation in development.
Identifying hetero-protein complexes in the nuclear envelope

The nucleus is delineated by the nuclear envelope (NE), which is a double membrane barrier composed of the inner and outer nuclear membranes as well as a ~40 nm wide lumen. In addition to its barrier function, the NE acts as a critical signaling node for a variety of cellular processes which are mediated by protein complexes within this subcellular compartment. While fluorescence fluctuation spectroscopy (FFS) is a powerful tool for characterizing protein complexes in living cells, it was recently demonstrated that conventional FFS methods are not suitable for applications in the NE because of the presence of slow nuclear membrane undulations. We previously addressed this challenge by developing time-shifted mean-segmented Q (tsMSQ) analysis and applied it to successfully characterize protein homo-oligomerization in the NE. However, many NE complexes, such as the linker of the nucleoskeleton and cytoskeleton (LINC) complex, are formed by heterotypic interactions, which single-color tsMSQ is unable to characterize. Here, we describe the development of dual-color (DC) tsMSQ to analyze NE hetero-protein complexes built from proteins that carry two spectrally distinct fluorescent labels. Experiments performed on model systems demonstrate that DC tsMSQ properly identifies hetero-protein complexes and their stoichiometry in the NE by accounting for spectral crosstalk and local volume fluctuations. Finally, we applied DC tsMSQ to study the assembly of the LINC complex, a hetero-protein complex composed of Klarsicht/ANC-1/SYNE homology (KASH) and Sad1/UNC-84 (SUN) proteins, in the NE of living cells. Using DC tsMSQ, we demonstrate the ability of the SUN protein SUN2 and the KASH protein nesprin-2 to form a hetero-complex in vivo. Our results are consistent with previously published in vitro studies and demonstrate the utility of the DC tsMSQ technique for characterizing NE hetero-protein complexes. Statement of Significance Protein complexes found within the nuclear envelope (NE) play a vital role in regulating cellular functions ranging from gene expression to cellular movement. However, the assembly state of these complexes within their native environment remains poorly understood, which is compounded by a general lack of fluorescence techniques suitable for quantifying the oligomeric state of NE protein complexes. This study aims at addressing this issue by introducing dual-color time-shifted mean-segmented Q analysis as a fluorescence fluctuation method specifically designed to identify the average oligomeric state of hetero-protein complexes within the NE of living cells.
Polyamino-Isoprenyl Derivatives as Antibiotic Adjuvants and Motility Inhibitors for Bordetella bronchiseptica Porcine Pulmonary Infection Treatment

The spreading of multidrug-resistant bacteria and the lack of novel antibiotic molecules leave clinicians and veterinarians with very limited options to treat bacterial infections, especially those caused by Gram-negative pathogens. To reduce the selection of antibiotic resistance mechanisms and their transfer to human pathogens, veterinary pharmaceutical companies have dramatically decreased the number of antibiotics used. Among all the investigated alternate solutions, chemosensitizers, which decrease the amount of the used drugs, appear to be one of the most promising strategies. In this study, we reported that polyamino-isoprenyl derivatives can potentiate florfenicol activity against veterinary sensitive reference strains as well as clinical isolates. These molecules induce inner membrane depolarization and subsequently inhibit efflux pumps by collapsing the proton-motive force (PMF). Considering that Bordetella bronchiseptica rotor flagellum is highly PMF dependent and that flagellar motility represents an important factor involved in colonization, we monitored the swimming and swarming motilities of bacteria and showed a strong inhibition in the presence of the lead selected compound. Taken together, our results suggest that this class of molecules are able to increase treatment efficacy and decrease drug consumption.
Drivers of Household Decision-Making on Land-Use Transformation: An Example of Woodlot Establishment in Masindi District, Uganda

Land use transformation at the farm level is attributed to household decision-making, reflected by the behavior and activities of smallholder farmers. Unfortunately, household decision-making in local communities and its determinants are site-specific and hardly understood. This study uses multistage purposive selection of households as a unit for the analysis to investigate the transformation from pure agriculture to farm forest mosaics, especially through woodlot establishment. We use key informants, household surveys, and observations to obtain data on decision-making amongst 84 farm households in Nyantonzi parish, Masindi district, Uganda, as an example. Specifically, the study addresses four research questions. Firstly, what is the current status of gender-based decision-making at the household level? Secondly, is decision making within farm households individualistic or collective? Thirdly, which factors are considered to select annual, perennial and tree-crop farm management regimes? Fourthly, what determinants influence the decision-making process and the likelihood of woodlot establishment? A multilevel analysis comprising parametric statistical models and binary logistic regression is applied to assess difference in household natural, physical, human, and social capital, highlight gender roles, and obtain factors associated to selection of crops and determinants of woodlot establishment at the farm level, respectively. Results reveal that gender based decision-making is clearly disaggregated on the basis of husbands and wives and it is individualistic, mostly dominated by husbands with lower participation by wives and other family members. Households consider various factors before making any decisions, e.g., market prices for both annual and perennial crops, food consumption for annual crops, ease of management, and yields from the previous season for the tree-crop management regimes. The likelihood for woodlot establishment is positively influenced by the willingness and intention of households to establish woodlots and relative age of household head. However, knowledge of land use Policies, Laws, and Regulations (PLRs) in relation to tree planting and harvesting and access to non-farm income reduce the likelihood of woodlot establishment. Here, we recommend that current and future forest land restoration initiatives focus on reducing the gender gap and increase women’s participation in decision making, provide market information platforms on wood products, and include woodlot farmers in social organization. Current PLRs on tree tenure should be improved and clearly communicated by using the existing communication assets and social gatherings as channels of change and influence for decision-making.
The complete chloroplast genome of Aster hypoleucus (Asteraceae: Astereae): an endemic species from China

Abstract This study was the first report about complete chloroplast genome of Aster hypoleucus (Asteraceae, Astereae), an endemic species in Xizang (China). The circular whole cp genome of A. hypoleucus was 152,300 bp in length, contained a large single-copy (LSC) region of 84,031 bp and a small single-copy (SSC) region of 18,269 bp. These two regions were separated by a pair of inverted repeat regions (IRa and IRb), each of them 25,000 bp in length. A total of 134 functional genes were encoded, consisted of 89 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the chloroplast genome sequence was 37.3%, and the GC contents of the LSC, SSC, and IR regions were 35.2%, 31.2%, and 43.0%, respectively.
Complete mitochondrial genome of Gymnocanthus intermedius and Gymnocanthus herzensteini (Scorpaeniformes: Cottidae)

Abstract Here, we report the complete mitochondrial genomes of the Sculpins species Gymnocanthus intermedius and Gymnocanthus herzensteini. The mitogenomes were determined to be 16,639 bp for G. intermedius and 16,691 bp for G. herzensteini. The mitogenomes comprised 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding region. We then used the mitogenome data to construct a phylogenetic tree for these two species and an additional three species within the order Scorpaeniformes.
GENETIC CHARACTERIZATION OF INFECTIOUS BURSAL DISEASE VIRUS ISOLATES IN UKRAINE

The objective of the investigation was to characterize infectious bursal disease viruses (IBDV) circulating in commercial poultry farms in Ukraine between 2014 and 2016. IBDV genetic material was amplified directly from bursa. The nucleotide sequence for VP2 hypervariable region of 16 IBDVs were determined by RT-PCR method, sequenced and compared to well characterised IBDV isolates worldwide. Neighbor-joining method was used for phylogenetic analyses. In result of the studyUkrainian IBDVs represented two genetic lineages: very virulent (vv) IBDVs and classical IBDV closely related to attenuated vaccine stains. The nucleotide identity among UkrainianvvIBDVs ranged between 87.2% and 99,8%. Ukrainian vvIBDV strains clustered together with very virulent strains from other counties like: United Kingdom, Egypt, China, Netherlands and Spain. In conclusion this report demonstrates the circulation of vvIBDV in commercial poultry farms in Ukraine.
Vbargain: A Market-Driven Quality Oriented Incentive for Mobile Video Offloading

With the increasing popularity of video delivery among mobile users, the problem of explosive traffic growth becomes more and more serious for the mobile wireless networks. To deal with this problem, in this paper we propose to exploit opportunistic transmission and the idea of crowdsourcing to offload mobile video traffic. Based on this idea, a Quality of VIDEO (QoV) oriented pricing incentive scheme, namely Vbargain, is proposed to stimulate mobile users to deliver video data collaboratively. More specifically, in our scheme, the network is regarded as a Virtual Market, and the video packets are treated as commodities, which are dynamically priced according to their expected marginal gains on the quality of reconstructed video; the process of video delivery is regarded as a sequence of packet transactions which are modeled as two-person cooperative games. Driven by the profit-hunting nature of mobile users, the video data is delivered from the source to its destination. In order to gain deep insight into our scheme, we also analyze the overhead and the influence of start-up capital on the performance of video delivered theoretically, and give its lower bound and upper bound. Our simulation results, based on both the synthetic and real-life traces of mobile users, verify the efficiency of our scheme and analysis.