Miracle-dz/UniFAR-FTUs huggingface dataset:
What do we know about the microbiome of I. ricinus?

I. ricinus is an obligate hematophagous parasitic arthropod that is responsible for the transmission of a wide range of zoonotic pathogens including spirochetes of the genus Borrelia, Rickettsia spp. , C. burnetii, Anaplasma phagocytophilum and Francisella tularensis, which are part the tick´s microbiome. Most of the studies focus on “pathogens” and only very few elucidate the role of “non-pathogenic” symbiotic microorganisms in I. ricinus. While most of the members of the microbiome are leading an intracellular lifestyle, they are able to complement tick´s nutrition and stress response having a great impact on tick´s survival and transmission of pathogens. The composition of the tick´s microbiome is not consistent and can be tied to the environment, tick species, developmental stage, or specific organ or tissue. Ovarian tissue harbors a stable microbiome consisting mainly but not exclusively of endosymbiotic bacteria, while the microbiome of the digestive system is rather unstable, and together with salivary glands, is mostly comprised of pathogens. The most prevalent endosymbionts found in ticks are Rickettsia spp. , Ricketsiella spp. , Coxiella-like and Francisella-like endosymbionts, Spiroplasma spp. and Candidatus Midichloria spp. Since microorganisms can modify ticks’ behavior, such as mobility, feeding or saliva production, which results in increased survival rates, we aimed to elucidate the potential, tight relationship, and interaction between bacteria of the I. ricinus microbiome. Here we show that endosymbionts including Coxiella-like spp. , can provide I. ricinus with different types of vitamin B (B2, B6, B7, B9) essential for eukaryotic organisms. Furthermore, we hypothesize that survival of Wolbachia spp. , or the bacterial pathogen A. phagocytophilum can be supported by the tick itself since coinfection with symbiotic Spiroplasma ixodetis provides I. ricinus with complete metabolic pathway of folate biosynthesis necessary for DNA synthesis and cell division. Manipulation of tick´s endosymbiotic microbiome could present a perspective way of I. ricinus control and regulation of spread of emerging bacterial pathogens.
The first session is the one that counts: An exploratory study of therapeutic alliance

Background The controversy about whether psychotherapy outcome is the consequence of the techniques themselves, common factors or both is still current. The importance of common factors has been demonstrated, although it is also known that they alone are insufficient. At the present time, the contextual model grants heavy weight to the therapeutic alliance in the first sessions and seems to predict positive final results. Furthermore, monitoring sessions has demonstrated that this alliance improves. Objectives To analyze the relationship between the therapeutic alliance and patient’s perceived improvement during the first five sessions of therapy, and find out whether the therapeutic alliance is maintained or unstable within that timeframe. Methods Thirty-four patients at a university psychological care service who had had at least five therapy sessions participated. Of these, 70.46% were women (Mage = 24.24, SD = 6.73). The patients filled out the Outcome Rating Scale and Session Rating Scale the week before each session. Data were analyzed by the Dual STATIS method. Results The compromise matrix explained 77.36% of the variability. The position of the vectors and the distribution of the position of the patients on the graph show that as their perception increased, therapeutic alliance remained stable. Moreover, the position of the vectors shows that the therapeutic alliance was forged in the first session and remained stable during the following sessions. Conclusion This exploratory study demonstrated the importance of the first session in establishing the therapeutic alliance, and for it to remain stable, regardless of whether the rest of the therapeutic process has variations or changes. Novel use of the STATIS method for analyzing measurements in the first five sessions, showed that beginning the therapeutic intervention with a strong alliance, produced the favorable, lasting effects necessary for development of the intervention.
Representing bacteria with unique genomic signatures

Classifying or identifying bacteria in metagenomic samples is an important problem in the analysis of metagenomic data. This task can be computationally expensive since microbial communities usually consist of hundreds to thousands of environmental microbial species. We proposed a new method for representing bacteria in a microbial community using genomic signatures of those bacteria. With respect to the microbial community, the genomic signatures of each bacterium are unique to that bacterium; they do not exist in other bacteria in the community. Further, since the genomic signatures of a bacterium are much smaller than its genome size, the approach allows for a compressed representation of the microbial community. This approach uses a modified Bloom filter to store short k-mers with hash values that are unique to each bacterium. We show that most bacteria in many microbiomes can be represented uniquely using the proposed genomic signatures. This approach paves the way toward new methods for classifying bacteria in metagenomic samples.
Screening of short-day onions for resistance to Stemphylium leaf blight in the seed-to-bulb stage (stage I) and bulb-to-seed stage (stage II)

Stemphylium leaf blight, caused by Stemphylium vesicarium, is a very important fungal disease in onions since its epidemics are able to affect both the bulb yield and the seed quality. The aim of this study was to screen onion genotypes at stage I (seed to bulb) and further screen the identified resistant and susceptible genotypes at stage II (bulb to seed). One hundred and fifty-seven genotypes were screened against SLB under artificially inoculated field conditions. Results revealed a significant variation among the morphological and biochemical traits studied. Correlation studies revealed a significant and negative correlation between percent disease incidence (PDI), pseudostem width, neck thickness, and dry matter. Fifteen genotypes were identified as moderately resistant, and the rest were categorized as susceptible. Bulbs of the genotypes, identified as moderately resistant, were again screened for resistance in stage II. All the genotypes were categorized as moderately susceptible. Biochemical analysis revealed that total foliar phenol content, pyruvic acid, catalase, and peroxidase increased up to 20 days after inoculation (DAI) and thereafter declined. Protein content was highest in the initial stage and declined at 10, 20, and 30 DAI. The higher biochemical activity was observed in moderately resistant category genotypes compared with the susceptible ones. Correlation analysis showed a highly significant and negative correlation of PDI with total foliar phenol content (TFPC), pyruvic acid, catalase, peroxidase, and protein content. To conclude, it was observed that screening against SLB should be done at both the stages (stage I and Stage II) to identify resistant onion genotypes. Direction selection for genotypes with high dry matter, higher phenols, and enzymes may be an alternative pathway to select genotypes for a robust resistance breeding program.
Advances in microbial metagenomics and artificial intelligence analysis in forensic identification

Microorganisms, which are widely distributed in nature and human body, show unique application value in forensic identification. Recent advances in high-throughput sequencing technology and significant reductions in analysis costs have markedly promoted the development of forensic microbiology and metagenomics. The rapid progression of artificial intelligence (AI) methods and computational approaches has shown their unique application value in forensics and their potential to address relevant forensic questions. Here, we summarize the current status of microbial metagenomics and AI analysis in forensic microbiology, including postmortem interval inference, individual identification, geolocation, and tissue/fluid identification.
Regulation of T cell function by protein S-acylation

S-acylation, the reversible lipidation of free cysteine residues with long-chain fatty acids, is a highly dynamic post-translational protein modification that has recently emerged as an important regulator of the T cell function. The reversible nature of S-acylation sets this modification apart from other forms of protein lipidation and allows it to play a unique role in intracellular signal transduction. In recent years, a significant number of T cell proteins, including receptors, enzymes, ion channels, and adaptor proteins, were identified as S-acylated. It has been shown that S-acylation critically contributes to their function by regulating protein localization, stability and protein-protein interactions. Furthermore, it has been demonstrated that zDHHC protein acyltransferases, the family of enzymes mediating this modification, also play a prominent role in T cell activation and differentiation. In this review, we aim to highlight the diversity of proteins undergoing S-acylation in T cells, elucidate the mechanisms by which reversible lipidation can impact protein function, and introduce protein acyltransferases as a novel class of regulatory T cell proteins.
How does artificial intelligence empower EFL teaching and learning nowadays? A review on artificial intelligence in the EFL context

The booming Artificial Intelligence (AI) provides fertile ground for AI in education. So far, few reviews have been deployed to explore how AI empowers English as Foreign Language (EFL) teaching and learning. This study attempts to give a brief yet profound overview of AI in the EFL context by summarizing and delineating six dominant forms of AI application, including Automatic Evaluation Systems, Neural Machine Translation Tools, Intelligent Tutoring Systems (ITSs), AI Chatting Robots, Intelligent Virtual Environment, and Affective Computing (AC) in ITSs. The review furthermore uncovers a current paucity of research on applying AC in the EFL context and exploring pedagogical and ethical implications of AI in the EFL context. Ultimately, challenges from technical and teachers' perspectives, as well as future research directions, are illuminated, hopefully proffering new insights for the future study.
Starch–protein interaction effects on lipid metabolism and gut microbes in host

The purpose of this experiment was to investigate the effects of different starch and protein levels on lipid metabolism and gut microbes in mice of different genders. A total of 160 male mice were randomly assigned to sixteen groups and fed a 4 × 4 Latin square design with dietary protein concentrations of 16, 18, 20, and 22%, and starch concentrations of 50, 52, 54, and 56%, respectively. The results of the study showed that different proportions of starch and protein had obvious effects on the liver index of mice, and there was a significant interaction between starch and protein on the liver index (p = 0.005). Compared with other protein ratio diets, 18% protein diet significantly increased the serum TBA concentration of mice (p < 0.001), and different starch ratio diets had no effect on serum TBA concentration (p = 0.442). It was proved from the results of ileal tissue HE staining that the low protein diet and the low starch diet were more favorable. There was a significant interaction between diets with different starch and protein levels on Bacteroidetes, Firmicutes and Proteobacteria abundance in feces of mice (p < 0.001). Compared with 16 and 18% protein ratio diets, both 20 and 22% protein diets significantly decreased the Parabacteroides and Alistipes abundance in feces of mice (p < 0.05), and 52% starch ratio diet significantly decreased the Parabacteroides and Alistipes abundance than 50% starch ratio diet of mice (p < 0.05). There was a significant interaction between diets with different starch and protein levels on Parabacteroides (p = 0.014) and Alistipes (p = 0.001) abundance in feces of mice. Taken together, our results suggest that a low protein and starch diet can alter lipid metabolism and gut microbes in mice.
Observation of Landau-level-like quantization at 77 K along a strained-induced graphene ridge

Recent studies show that the electronic structures of graphene can be modified by strain and it was predicted that strain in graphene can induce peaks in the local density of states (LDOS) mimicking Landau levels (LLs) generated in the presence of a large magnetic field. Here we report scanning tunnelling spectroscopy (STS) observation of nine strain-induced peaks in LDOS at 77 K along a graphene ridge created when the graphene layer was cleaved from a sample of highly oriented pyrolytic graphite (HOPG). The energies of these peaks follow the progression of LLs of massless 'Dirac fermions' (DFs) in a magnetic field of 230 T. The results presented here suggest a possible route to realize zero-field quantum Hall-like effects at 77 K.
Attachment Patterns of Human and Avian Influenza Viruses to Trachea and Colon of 26 Bird Species – Support for the Community Concept

Avian influenza A viruses (AIVs) have a broad host range, but are most intimately associated with waterfowl (Anseriformes) and, in the case of the H13 and H16 subtypes, gulls (Charadriiformes). Host associations are multifactorial, but a key factor is the ability of the virus to bind host cell receptors and thereby initiate infection. The current study aims at investigating the tissue attachment pattern of a panel of AIVs, comprising H3N2, H6N1, H12N5, and H16N3, to avian trachea and colon tissue samples obtained from host species of different orders. Virus attachment was not restricted to the bird species or order from which the virus was isolated. Instead, extensive virus attachment was observed to several distantly related avian species. In general, more virus attachment and receptor expression were observed in trachea than in colon samples. Additionally, a human seasonal H3N2 virus was studied. Unlike the studied AIVs, this virus mainly attached to tracheae from Charadriiformes and a very limited set of avian cola. In conclusion, the reported results highlight the importance of AIV attachment to trachea in many avian species. Finally, the importance of chickens and mallards in AIVs dynamics was illustrated by the abundant AIV attachment observed.
Integrated energy system region model with renewable energy and optimal control method

In the context of global energy transition, integrated regional energy systems containing renewable energy sources play an important role. While improving the economic and carbon efficiency of energy utilization, renewable energy sources also bring research challenges to the safe and reliable operation of energy systems. Based on the region concept, a region model and optimal control method for integrated energy systems containing renewable energy are proposed. Firstly, the key pipeline is taken as the observation object, and the feasible region model of the integrated energy system is determined according to the capacity of key equipment and its pipeline capacity with the multi-energy balance equation as the feasible constraint. Then, considering the mutual backup relationship of different equipment and pipelines, the regional integrated energy system security region model is constructed based on the N-1 security criterion, and the optimal control method based on the region concept is proposed. Finally, the validity of the model is analyzed with arithmetic examples, and the influence of the access capacity and access location of renewable energy on the feasible and safe regions of the regional integrated energy system is discussed. And according to the actual situation of the working state point, the optimal adjustment strategy based on the efficiency function and security constraint is given.
Knowledge and participation in exercise and physical activity among pregnant women in Ho, Ghana

Background Physical activity (PA) and exercise have been identified to improve the general fitness and health. Although, the Pregnancy Physical Activity Questionnaire (PPAQ) has been validated for use in assessing PA in pregnant women. However, understanding the knowledge and participation levels of PA in pregnant women in the underdeveloped regions of Ghana is of clinical relevance to foster education and promotion of PA. In Ghana, pregnant women believe the “myth” (mostly in rural areas and underdeveloped regions) that exercising in the first trimester might lead to miscarriage. Thus, the main objective of this study was to investigate the extent of knowledge and participation levels in PA among pregnant women in Ho, Ghana using a self-developed questionnaire which consisted of some questions adapted from the PPAQ. Methods Seventy-seven (n = 77) pregnant women between the ages of 18–50 years were recruited from three hospitals across the Ho municipality of Ghana. A self-developed questionnaire which consisted of some questions taken from the PPAQ was administered to participants under the researchers' supervision. Spearman's correlation analysis was used to find the association between the level of participation in PA, knowledge of PA and gestational age among pregnant women. Results From the total participants (n = 77) recruited, 57 (74%) of the participants scored high in PA knowledge. Most of the participants 48 (62.3%) answered that PA promotes healthy pregnancy. Participants who reported barriers to PA during pregnancy were no exercise habits 51 (66.2%), having no time 17 (22.1%) and fear of miscarriage 9 (11.7%). There was a significant (p < 0.05) association between the level of participation and gestational age. No significant (p > 0.05) association between the level of participation and knowledge of PA was observed. Conclusion There is a high level of knowledge of PA among pregnant women in Ho, Ghana. However, most pregnant women rather engage in PA as their gestational age increases. Thus, to foster sustainable exercise participation during pregnancy, all healthcare providers saddled with the responsibility of providing maternal healthcare must strengthen the education and promotion of exercise and PA among pregnant women in Ho, Ghana.
Gender differences in association of urbanization with psychological stress in Chinese adults: A population-based study

Objective To investigate the gender-specific associations between exposure to urbanization and psychological stress in China experiencing rapid urbanization. Methods Data were obtained from the 2015 China Health and Nutrition Survey. A total of 4,388 men and 5,098 women aged at least 18 years were obtained from 288 communities across 12 provinces and municipalities. Tertiles of the urbanization index, summarizing 12 urbanization dimensions at the community level, were used to define low, medium, and high levels of urbanization. The psychological stress was measured based on the 10-item Perceived Stress Scale. The gender-stratified multilevel analysis (Level-1: Individuals, Level-2: Communities, and Level-3: provinces/municipalities) was used to estimate the association between exposure to urbanization and psychological stress. Results After controlling for age, education status, marital status, work status, household income per capita, current smoking, alcohol drinking, sleep duration, BMI, and chronic conditions, the urbanization index was negatively associated with psychological stress in women (Ptrend = 0.017) but not men (Ptrend = 0.476). More specifically, a one-standard deviation increase in the score of community population density (β = −0.329, P = 0.329), modern markets (β = −0.247, P = 0.044), education (β = −0.448, P = 0.002), and housing (β = −0.380, P = 0.005) was negatively associated with psychological stress only in women, separately. Conclusion Our data revealed that living in the most urbanized communities is associated with lower levels of psychological stress for women but not men. Thus, this study can help empower decision-makers to accurately target vulnerable communities and plan effective strategies to address psychological outcomes.
DhMYB2 and DhbHLH1 regulates anthocyanin accumulation via activation of late biosynthesis genes in Phalaenopsis-type Dendrobium

Phalaenopsis-type Dendrobium is a popular orchid with good ornamental and market value. Despite their popularity, molecular regulation of anthocyanin biosynthesis during flower development remains poorly understood. In this study, we systematically investigated the regulatory roles of the transcription factors DhMYB2 and DhbHLH1 in anthocyanins biosynthesis. Gene expression analyses indicated that both DhMYB2 and DhbHLH1 are specifically expressed in flowers and have similar expression patterns, showing high expression in purple floral tissues with anthocyanin accumulation. Transcriptomic analyses showed 29 differentially expressed genes corresponding to eight enzymes in anthocyanin biosynthesis pathway have similar expression patterns to DhMYB2 and DhbHLH1, with higher expression in the purple lips than the yellow petals and sepals of Dendrobium ‘Suriya Gold’. Further gene expression analyses and Pearson correlation matrix analyses of Dendrobium hybrid progenies revealed expression profiles of DhMYB2 and DhbHLH1 were positively correlated with the structural genes DhF3’H1, DhF3’5’H2, DhDFR, DhANS, and DhGT4. Yeast one-hybrid and dual‐luciferase reporter assays revealed DhMYB2 and DhbHLH1 can bind to promoter regions of DhF3’H1, DhF3’5’H2, DhDFR, DhANS and DhGT4, suggesting a role as transcriptional activators. These results provide new evidence of the molecular mechanisms of DhMYB2 and DhbHLH1 in anthocyanin biosynthesis in Phalaenopsis-type Dendrobium.
Nutrient turnover by large sulfur bacteria on the Namibian mud belt during the low productivity season

Surface sediments of the coastal mud belt in the Benguela Upwelling System (BUS) off Namibia host extensive communities of chemotrophic large sulfur bacteria (LSB) of the family Beggiatoaceae such as Thiomargarita spp. and Candidatus Maribeggiatoa spp. In order to understand the role of these bacteria in N and P cycling, biogeochemical data from three sites in the mud belt were simulated with a biogeochemical model including LSB catabolic pathways. Organic carbon remineralization was dominated by the reduction of sulfate to hydrogen sulfide (5.0–7.7 mmol C m−2 d−1). At the two stations where LSB were observed, produced hydrogen sulfide was almost completely oxidized by LSB using nitrate as the electron acceptor. Modeled rates of nitrate reduction to N2 by LSB were over two times higher than nitrate reduction to ammonium. This points toward a potential negative feedback by LSB on primary production. Furthermore, loss of fixed N strongly enriched the benthic fluxes in P relative to N. Although the model included intracellular polyphosphate accumulation by LSB and subsequent breakdown to phosphate, a clear link between polyphosphate dynamics and hydroxyapatite precipitation and burial could not be clearly substantiated. This is partly due to simplifying assumptions in the model and analytical uncertainties in distinguishing between authigenic hydroxyapatite and allochthonous hydroxyapatite (e.g., fish bones), both of which are major components of particulate P in the BUS. Our modeling suggests a significant control of LSB on benthic N and P fluxes to the water column. Given the extensive coverage of LSB on the shelf (>30,000 km2), more accurate forecasts of nutrient cycling and primary production in the BUS necessitate a closer inspection of benthic P sources and sinks in the mud belt and a clearer understanding of the controls on the end product of nitrate reduction by LSB.