Miracle-dz/UniFAR-FTUs huggingface dataset:
A condition for regeneration of a cell chain inspired by the Dachsous-Fat system

Regeneration phenomena in cricket legs and Planarians have recently been studied at the single cellular level. Within a cell, Dachsous and Fat molecules, and between cells, Dachsous- Fat heterodimers, are considered related to regeneration phenomena. Inspired by recent studies on Dachsous and Fat, we modeled a cell chain with heterodimers and analyzed it. We parameterized redistribution of heterodimers during cell division, which is poorly understood. We then derived equations in parameters to regenerate the heterodimeric pattern even if part of the cell chain is excised. This excision model contained eight parameters, and hence we used a few algebraic methods to suit models that are described by a set of polynomials. A number of biological phenomena have recently been analyzed through algebraic methods; thereby, we can directly derive equations in parameters. The derived equations show that some specific relation between the redistribution ratio of heterodimers allows a cell chain to regenerate its heterodimeric pattern.
Early energy restriction in premature infants and bronchopulmonary dysplasia: a cohort study

Abstract Bronchopulmonary dysplasia (BPD) is a multifactor pathology. Animal studies and cohort studies suggest that poor nutrient intake after birth increases the risk of BPD. The objective of the present study was to determine the existence of association between BPD in very low birth weight (VLBW) and energy intake during the first week of life. We recorded in a retrospective cohort study the intake of enteral and parenteral macronutrients during this period by examining the nutritional and clinical history of 450 VLBW newborns admitted to the neonatal intensive care unit. After applying the relevant exclusion criteria, data for 389 VLBW infants were analysed, of whom 159 developed some degree of BPD. Among the newborns with BPD, energy and lipid intake was significantly lower and fluid intake was significantly higher. The energy intake for the 25th percentile in the group without BPD was 1778·2 kJ/kg during the first week of life. An energy intake <1778·2 kJ/kg in this period was associated with a 2-fold increase in the adjusted risk of BPD (OR 2·63, 95 % CI 1·30, 5·34). The early nutrition and the increase of energy intake in the first week of life are associated in our sample with a lower risk of BPD developing.
The Effect of Aerobic Training with Vitamin D on Extrinsic Pathway of Apoptosis and Anti-Apoptotic Indices of Heart Tissue of Rats Exposed to Oxidative Damage Induced by H 2 O 2

Introduction: Apoptosis plays an important role in the development of cardiovascular diseases. The aim of this study was to investigate the effect of aerobic training (AT) with Vitamin D (VD) on extrinsic pathway of apoptosis and antiapoptotic indices of heart tissue of rats exposed to oxidative damage induced by H2O2. Methods: In this experimental study, 60 rats were selected and randomly placed into 10 groups of six, including 1) 1 mmol / kg H2O2, 2) 2 mmol / kg H2O2, 3) VD + 1 mmol / kg H2O2, 4) AT + 1 mmol / kg H2O2, 5) AT + VD + 1 mmol / kg H2O2, 6) VD + 2 mmol / kg H2O2, 7) AT + 2 mmol / kg H2O2, 8) AT + VD + 2 mmol / kg H2O2, 9) sham and 10) control. During eight weeks, the rats in groups 1-9 were subjected to intraperitoneal injection of H2O2 at specific doses three times a week; the rats in groups 4, 5, 7 and 8 performed aerobic trainings, and the rats in groups 3, 5, 6 and 8 received 0.5 μg / kg of vitamin D3 intraperitoneally daily. Protein concentrations of Caspase 8, Fas and FLIP were measured in rat heart tissue. For analysis of the research findings, KolmogorovSmirnov, one-way ANOVA, two-way ANOVA along with Bonferroni post hoc tests were used (p≤0.05). Results: H2O2 has a significant effect on the increase of Caspase 8, Fas and FLIP in the heart tissue of rats (p≤0.05); eight weeks of aerobic training and Vitamin D intake has a significant effect on decreasing the concentration of Caspase 8, Fas and increase of FLIP in the heart tissue of rats exposed to oxidative damage induced by 1 and 2 m/mol/kg H2O2 (p ≤0.05); aerobic training and Vitamin D intake has significant interactions in the reduction of Caspase 8, Fas in the heart tissue of rats exposed to oxidative damage induced by 1 and 2 m/mol/kg H2O2 (p≤0.05), however, it does not have interactive effect on the increased FLIP of the heart tissue of rats exposed to oxidative damage induced by 1 and 2 m/mol/kg H2O2 (p≥0.05). Conclusion: It seems that performing aerobic training activities and simultaneous consumption of vitamin D supplement has interactive effects on reducing some of the extrinsic pathway indices of apoptosis in the heart tissue of H2O2-rats exposed to oxidative damage induced by H2O2.
β-Sitosterol Attenuates High Grain Diet-Induced Inflammatory Stress and Modifies Rumen Fermentation and Microbiota in Sheep

Simple Summary Over the years, rumen acidosis is considered as the most common disease in ruminants, which affects animal health and brings huge economic losses of the ruminant industry. Antibiotic have been considered as effective to alleviate the occurrence of ruminal acidosis. However, antibiotic usage in food animals has been absolutely banned by European Union and strictly restricted in other countries. It is necessary to search for safe, effective and healthy additives alternative to antibiotics for ruminants. β-sitosterol is a plant compound known as phytosterol, which has many biological activities. In this study, sheep were feed four levels with β-sitosterol supplementation (0, 0.25, 0.5, and 1.0 g/kg). We concluded that β-sitosterol could attenuate high grain diet-induced inflammatory response and modify ruminal fermentation. These findings provide updated insight for preventing the occurrence of rumen acidosis. Abstract β-sitosterol (BSS) is a plant-derived natural bioactive compound, its cellular mechanism of anti-inflammatory activity has been proven recently. Little information is available regarding the application of BSS on ruminants under high grain diet. The objective of this study was to evaluate the effects of dietary BSS supplementation on inflammatory response, ruminal fermentation characteristics and the composition of the ruminal bacterial community under high grain diet. Eight rumen-cannulated Hu sheep (59.7 ± 4.8 kg of initial body weight) were randomly assigned into a replicated 4 × 4 Latin square design trial. Sheep were fed a high grain diet (non-fiber carbohydrate: neutral detergent fiber = 2.03) supplemented either with 0.25 (LBS), 0.5 (MBS), 1.0 (HBS) or without (CON) g BSS /kg dry matter diet. On day 21 of each period, rumen content samples were obtained at 6 h postfeeding, and blood samples were obtained before morning feeding. The data showed that compared with control group, Dietary BSS supplementation decreased serum concentrations of tumor necrosis factor, interleukin (IL)-6, and IL-1β. The ruminal pH and acetate concentration for BSS treatment were improved, while concentration of propionate, butyrate and lactate was decreased. The result of Illumina MiSeq sequencing of 16S rRNA gene revealed that BSS addition can increase the proportion of Prevotella_1, Rikenellaceae_RC9_gut_group, Prevotella_7, and Selenomonas_1, and decrease the proportion of Lachnospiraceae_NK3A20_group. These results indicated that BSS attenuates high grain diet-induced inflammatory response and modifies ruminal fermentation. In addition, the BSS dietary supplementation at the level of 0.5 g/kg is recommended in sheep.
The translucens group of Xanthomonas translucens: Complicated and important pathogens causing bacterial leaf streak on cereals

Abstract Xanthomonas translucens is a group of gram‐negative bacteria that can cause important diseases in cereal crops and forage grasses. Different pathovars have been defined according to their host ranges, and molecular and biochemical characteristics. Pathovars have been placed into two major groups: translucens and graminis. The translucens group contains the pathovars causing bacterial leaf streak (BLS) on cereal crops such as wheat, barley, triticale, rye, and oat. In recent years, BLS has re‐emerged as a major problem for many wheat‐ and barley‐producing areas worldwide. The biology of the pathogens and the host–pathogen interactions in cereal BLS diseases were poorly understood. However, recent genome sequence data have provided an insight into the bacterial phylogeny and identification and pathogenicity/virulence. Furthermore, identification of sources of resistance to BLS and mapping of the resistance genes have been initiated. Taxonomy Kingdom Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadacea e; Genus Xanthomonas; Species X. translucens; translucens group pathovars: undulosa, translucens, cerealis, hordei, and secalis; graminis group pathovars: arrhenatheri, graminis, poae, phlei; newly established pathovar: pistaciae. Host range X. translucens mainly infects plant species in the Poaceae with the translucens group on cereal crop species and the graminis group on forage grass species. However, some strains have been isolated from, and are able to infect, ornamental asparagus and pistachio trees. Most pathovars have a narrow host range, while a few can infect a broad range of hosts. Genome The complete genome sequence is available for two X. translucens pv. undulosa strains and one pv. translucens strain. A draft genome sequence is also available for at least one strain from each pathovar. The X. translucens pv. undulosa strain Xt4699 was the first to have its complete genome sequenced, which consists of 4,561,137 bp with total GC content approximately at 68% and 3,528 predicted genes. Virulence mechanisms Like most xanthomonads, X. translucens utilizes a type III secretion system (T3SS) to deliver a suite of T3SS effectors (T3Es) inside plant cells. Transcription activator‐like effectors, a special group of T3Es, have been identified in most of the X. translucens genomes, some of which have been implicated in virulence. Genetic factors determining host range virulence have also been identified.
Backscratching in Hierarchical Organizations

In this paper we investigate the role of reciprocity in sustaining the emergence of implicit collusive agreements in hierarchical organizations. We conduct a laboratory experiment in which an agent hires, on behalf of the principal, one worker out of two candidates. The two candidates differ in their ability and, once employed, the worker chooses a level of non-contractible effort to exert in two tasks: one benefits the organization (that is both the principal and the agent) while the other one is less profitable, only benefits the agent and provides him with higher earnings. We provide evidence that: i) low ability workers are more likely to exert effort in the task that is exclusively beneficial to the agent; ii) as a consequence, agents distort the hiring process in favor of the low ability workers and iii) sharing a small part of the organization's profits with the workers alleviates their effort distortion.
Identification and functional characterization of a novel heterozygous missense variant in the LPL associated with recurrent hypertriglyceridemia‐induced acute pancreatitis in pregnancy

Acute pancreatitis in pregnancy (APIP) is a life‐threatening disease for both mother and fetus. To date, only three patients with recurrent hypertriglyceridemia‐induced APIP (HTG‐APIP) have been reported to carry rare variants in the lipoprotein lipase (LPL) gene, which encodes the key enzyme responsible for triglyceride (TG) metabolism. Coincidently, all three patients harbored LPL variants on both alleles and presented with complete or severe LPL deficiency.
Comparison of Element Concentrations (Ba, Mn, Pb, Sr, Zn) in the Bones and Teeth of Wild Ruminants from the West Carpathians and the Tian-Shan Mountains as Indicators of Air Pollution

Through analyzing the concentrations of selected heavy metals (Ba, Mn, Pb, Sr, Zn) in the bones and teeth of wild living and ecologically equivalent ruminants from the Tian-Shan (Capra sibirica and Ovis ammon polii) and the West Carpathians (Rupicapra rupicapra tatrica) we compared the environmental pollution levels of these two mountain ranges. The samples were analyzed by X-ray fluorescence. Significantly higher contents of Zn and Mn as well as a higher frequency of measurable occurrences of Mn, Ba, and Pb in samples from the West Carpathians confirmed the results of our previous study, that the West Carpathians are relatively more polluted by heavy metals than the Tian-Shan Mountains. The most probably contamination sources are mining and smelting as well as traffic emissions, which can reach remote mountain ranges through long distance atmospheric transport.
The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica

ABSTRACT The McMurdo Dry Valleys (MDV) in Antarctica harbor a diverse assemblage of mat-forming diazotrophic cyanobacteria that play a key role in nitrogen cycling. Prior research showed that heterotrophic diazotrophs also make a substantial contribution to nitrogen fixation in MDV. The goals of this study were to survey autotrophic and heterotrophic diazotrophs across the MDV to investigate factors that regulate the distribution and relative ecological roles of each group. Results indicated that diazotrophs were present only in samples with mats, suggesting a metabolic coupling between autotrophic and heterotrophic diazotrophs. Analysis of 16S rRNA and nifH gene sequences also showed that diazotrophs were significantly correlated to the broader bacterial community, while co-occurrence network analysis revealed potential interspecific interactions. Consistent with previous studies, heterotrophic diazotrophs in MDV were diverse, but largely limited to lakes and their outlet streams, or other environments protected from desiccation. Despite the limited distribution, heterotrophic diazotrophs may make a substantial contribution to the nitrogen budget of MDV due to larger surface area and longer residence times of lakes. This work contributes to our understanding of key drivers of bacterial community structure in polar deserts and informs future efforts to investigate the contribution of nitrogen fixation to MDV ecosystems.
How Bacterial Chemoreceptors Evolve Novel Ligand Specificities

Many bacteria possess a large number of chemoreceptors that recognize a variety of different compounds. More than 60% of the genomes analyzed in this study contain paralogous chemoreceptors, suggesting that they emerge with high frequency. We provide first insight on how paralogous receptors have evolved and show that two chemoreceptors with a narrow ligand range have evolved from an ancestral protein with a broad chemoeffector spectrum. Protein structures show that multiple changes in the ligand-binding site account for the differences in the ligand spectrum. This work lays the ground for further studies aimed at establishing whether the principles of ligand-binding evolution reported here can be generalized for a wider spectrum of sensory proteins in bacteria. ABSTRACT Chemoreceptor-based signaling pathways are among the major modes of bacterial signal transduction, and Pseudomonas aeruginosa PAO1 is an important model to study their function. Of the 26 chemoreceptors of this strain, PctA has a broad ligand range and responds to most of the proteinogenic amino acids, whereas PctB and PctC have a much narrower range and show strong ligand preference for l-glutamine and γ-aminobutyrate, respectively. Using several comparative genomics approaches, we show that these receptors are paralogs: pctA gene duplication in the common ancestor of the genus Pseudomonas led to pctC, whereas pctB originated through another, independent pctA duplication in the common ancestor of P. aeruginosa. Thus, the broad-range amino acid chemoreceptor was evolutionarily older, and chemoreceptors that complemented “missing” amino acid sensing abilities arose later in specific Pseudomonas lineages. Using comparative sequence analysis, newly solved crystal structures of PctA, PctB, and PctC ligand-binding domains, and their molecular dynamics simulations, we identified a conserved amino acid recognition motif and changes in the ligand-binding pocket that led to novel ligand specificities. In addition, we determined major forces driving the evolution of this group of chemoreceptors. IMPORTANCE Many bacteria possess a large number of chemoreceptors that recognize a variety of different compounds. More than 60% of the genomes analyzed in this study contain paralogous chemoreceptors, suggesting that they emerge with high frequency. We provide first insight on how paralogous receptors have evolved and show that two chemoreceptors with a narrow ligand range have evolved from an ancestral protein with a broad chemoeffector spectrum. Protein structures show that multiple changes in the ligand-binding site account for the differences in the ligand spectrum. This work lays the ground for further studies aimed at establishing whether the principles of ligand-binding evolution reported here can be generalized for a wider spectrum of sensory proteins in bacteria.
Looking Back: An Examination of Hindsight Bias in Change Detection Ability

This study examines hindsight bias in relation to performance in the change detection (i.e., ‘flicker’) paradigm. In order to determine confidence ratings and predictions about performance, participants provided ratings at three time points. Following a verbal description of the flicker paradigm, the pre-test was administered. Next, three flicker trials were administered, followed by the mid-session test, three more flicker trials, and finally the post-test. Critically, the post-test asked participants to remember and report their initial confidence ratings and predictions about their performance. The hypotheses were that the participants would have an initial overestimate of ability to detect change that would decrease after participation in the change detection paradigm, and that post-test responses would be significantly different than the initial ratings, showing hindsight bias. Results showed that there was an initial overestimate of confidence in change detection ability, and that hindsight bias was evident in the measure of predicted performance level, but not in confidence ratings. These findings are important in many aspects of life that require us to understand the role of hindsight bias in recalling past events, such as in legal settings involving remembered reports of witnessing a crime.
The utility of anthopometric indicators to identify cardiovascular risk factors in Vietnamese children

Abstract BMI, waist circumference (WC) and waist-to-height ratio (WHtR) can be used for discriminating children and adolescents at risk of CVD. However, consensus on how to use these anthropometric indicators is lacking for children and adolescents in Asia. Discrete criteria are promoted internationally, but continuous variables could be used. Data from a survey of 10 949 Vietnamese school-aged children (6–18 years) were used to evaluate the performance of anthropometric indicators to identify elevated blood pressure (BP), dyslipidaemia or at least three cardiovascular risk factors (CVRF). Weight, height, WC and BP were measured using standardised protocols; 1009 participants who had blood lipids were analysed. AUC was used to assess the performance, and the Youden index to identify optimal cut-offs. The prevalence of elevated BP, dyslipidaemia and CVRF was 26·5, 49·3 and 12·2 %, respectively. BMI, WC and WHtR had low capacity to identify elevated BP and dyslipidaemia (AUC range 0·61–0·66) but moderate capacity to identify CVRF (0·72–0·74). Optimal BMIZ cut-offs to identify elevated BP, dyslipidaemia and CVRF were 0·40, 1·01 and 1·1 sd; for WC z-score, they were 0·06, 0·49 and 0·62 sd; for WHtR, optimal cut-offs were close to 0·5. A BMIZ cut-off of 1·0 sd and a WHtR cut-off of 0·5 would, therefore, be useful criteria to identify Vietnamese children who are likely to have CVRF. However, further validation of these criteria in other studies of Asian children and adolescents is needed.
Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality

Metabolic adaptation is linked to the ability of the opportunistic pathogen Candida albicans to colonize and cause infection in diverse host tissues. One way that C. albicans controls its metabolism is through the glucose repression pathway, where expression of alternative carbon source utilization genes is repressed in the presence of its preferred carbon source, glucose. Here we carry out genetic and gene expression studies that identify transcription factors Mig1 and Mig2 as mediators of glucose repression in C. albicans. The well-studied Mig1/2 orthologs ScMig1/2 mediate glucose repression in the yeast Saccharomyces cerevisiae; our data argue that C. albicans Mig1/2 function similarly as repressors of alternative carbon source utilization genes. However, Mig1/2 functions have several distinctive features in C. albicans. First, Mig1 and Mig2 have more co-equal roles in gene regulation than their S. cerevisiae orthologs. Second, Mig1 is regulated at the level of protein accumulation, more akin to ScMig2 than ScMig1. Third, Mig1 and Mig2 are together required for a unique aspect of C. albicans biology, the expression of several pathogenicity traits. Such Mig1/2-dependent traits include the abilities to form hyphae and biofilm, tolerance of cell wall inhibitors, and ability to damage macrophage-like cells and human endothelial cells. Finally, Mig1 is required for a puzzling feature of C. albicans biology that is not shared with S. cerevisiae: the essentiality of the Snf1 protein kinase, a central eukaryotic carbon metabolism regulator. Our results integrate Mig1 and Mig2 into the C. albicans glucose repression pathway and illuminate connections among carbon control, pathogenicity, and Snf1 essentiality.
Sources of Welfare Disparities Across and Within Regions of Brazil: Evidence from the 2002-03 Household Budget Survey

Brazil's inequalities in welfare and poverty across and within regions can be accounted for by differences in household attributes and returns to those attributes. This paper uses Oaxaca-Blinder decompositions at the mean as well as at different quantiles of welfare distributions on regionally representative household survey data (2002-03 Household Budget Survey). The analysis finds that household attributes account for most of the welfare differences between urban and rural areas within regions. However, comparing the lagging Northeast region with the leading Southeast region, differences in returns to attributes account for a large part of the welfare disparities, in particular in metropolitan areas, supporting the presence of agglomeration effects in booming areas.