Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening the Influence of Biomarkers for Metabolic Syndrome in Occupational Population Based on the Lasso Algorithm

Aim: Metabolic syndrome (MS) screening is essential for the early detection of the occupational population. This study aimed to screen out biomarkers related to MS and establish a risk assessment and prediction model for the routine physical examination of an occupational population. Methods: The least absolute shrinkage and selection operator (Lasso) regression algorithm of machine learning was used to screen biomarkers related to MS. Then, the accuracy of the logistic regression model was further verified based on the Lasso regression algorithm. The areas under the receiving operating characteristic curves were used to evaluate the selection accuracy of biomarkers in identifying MS subjects with risk. The screened biomarkers were used to establish a logistic regression model and calculate the odds ratio (OR) of the corresponding biomarkers. A nomogram risk prediction model was established based on the selected biomarkers, and the consistency index (C-index) and calibration curve were derived. Results: A total of 2,844 occupational workers were included, and 10 biomarkers related to MS were screened. The number of non-MS cases was 2,189 and that of MS was 655. The area under the curve (AUC) value for non-Lasso and Lasso logistic regression was 0.652 and 0.907, respectively. The established risk assessment model revealed that the main risk biomarkers were absolute basophil count (OR: 3.38, CI:1.05–6.85), platelet packed volume (OR: 2.63, CI:2.31–3.79), leukocyte count (OR: 2.01, CI:1.79–2.19), red blood cell count (OR: 1.99, CI:1.80–2.71), and alanine aminotransferase level (OR: 1.53, CI:1.12–1.98). Furthermore, favorable results with C-indexes (0.840) and calibration curves closer to ideal curves indicated the accurate predictive ability of this nomogram. Conclusions: The risk assessment model based on the Lasso logistic regression algorithm helped identify MS with high accuracy in physically examining an occupational population.
Imaging Flow Cytometry and Confocal Immunofluorescence Microscopy of Virus-Host Cell Interactions

Viruses are diverse pathogens that use host factors to enter cells and cause disease. Imaging the entry and replication phases of viruses and their interactions with host factors is key to fully understanding viral infections. This review will discuss how confocal microscopy and imaging flow cytometry are used to investigate virus entry and replication mechanisms in fixed and live cells. Quantification of viral images and the use of cryo-electron microscopy to gather structural information of viruses is also explored. Using imaging to understand how viruses replicate and interact with host factors, we gain insight into cellular processes and identify novel targets to develop antiviral therapeutics and vaccines.
State of Shark and Ray Genomics in an Era of Extinction

Chondrichthyan species (sharks, rays, skates, and chimeras) are a class of high ecological, economic, and cultural significance, and yet they are the most threatened taxa in the marine environment. The creation of reference chromosome-length genome assemblies allows for conservation genomics methods, such as population and ecological genomics, to be utilized. Despite being greatly threatened and of great importance in maintaining ecosystem function, chondrichthyan species have been repeatedly absent from conservation-based genome sequencing projects. Less than 1% of these species have a genome sequence, despite their almost 50% either threatened or Data Deficient conservation status. Most notably, there are seven orders within this class without any genome representation. In this review, we identify gaps in chondrichthyan genomic resources and demonstrate how the lack of genomic resources for this major taxonomic class is limiting the conservation of these already difficult to conserve species. We highlight other applications for chondrichthyans genomics, such as evolutionary and developmental biology. Likely, the mismatching sampling protocols and limited computational skills and communication between fields have been preventing the integration of marine and molecular sciences. Here, we propose that this field is in dire need to move forward quickly to increase protection for marine species and ecosystems through improved collaboration between marine, molecular, and computer sciences.
Experiences of Honours Research Students and Supervisors During the COVID-19 Pandemic: A Pilot Study Framed by Self-Determination Theory

This study evaluated the impact of the COVID-19 pandemic in a sample of Honours students (n = 21) and Honours supervisors (n = 41) at a major Australian university. Data were collected from voluntary, online, anonymous surveys, which included ratings of the pandemic’s impact on their 1) experience of Honours research activities, and 2) sense of relatedness, competence, autonomy, and wellbeing. Self-determination theory (SDT), which posits that the psychological needs of relatedness, competence, and autonomy lead to a sense of wellbeing, provided a theoretical framework for understanding student and supervisor experience during the pandemic. Both students and supervisors indicated significant impact of the pandemic on the students’ research projects, and the degree of perceived impact did not differ between students and supervisors. There was no relationship between the severity of impact and student or supervisor wellbeing. Student wellbeing was low, but the hypotheses that student SDT needs would not be met were only partly supported. Overall, the extent to which Honours students’ SDT needs were met predicted wellbeing; the outcome was similar for supervisors. Our hypothesis that SDT needs and wellbeing would be higher for supervisors than for students was supported. The theoretical and practical implications of these findings are discussed, including recommendations for Honours programs as we move through the current pandemic.
Metal oxide hollow nanocapsule and a method for preparing the same

The present invention is an invention relating to the iron oxide produced from a hollow nano-capsule manufacturing method and a hollow which the metal oxide nano-capsules in a well-dispersed in the water system. Production method of the metal oxide hollow nanocapsules according to the invention are metal oxy After dispersing the hydroxide particles to aqueous the metal oxy-hydroxide, after forming the silica coating layer on the particles, the heat treatment by oxidizing the metal layer of the hollow in the inner silica coating layer it is formed It characterized in that formed in a process to remove silica and then. As the metal oxide produced by the process of the invention a hollow nano-capsule is a water-based dispersion it is excellent, and have a uniform particle size distribution, but there is an effect that it is possible to carry the bioactive material to the interior hollow. Further, iron oxide nano-capsules according to the present invention is a bearing of a biomolecule it has a medium-pore (meso pore) of at least 100 m Metal oxy-hydroxides, the hollow nano-capsule, iron oxide
DNA Damage Repair Deficiency in Pancreatic Ductal Adenocarcinoma: Preclinical Models and Clinical Perspectives

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers worldwide, and survival rates have barely improved in decades. In the era of precision medicine, treatment strategies tailored to disease mutations have revolutionized cancer therapy. Next generation sequencing has found that up to a third of all PDAC tumors contain deleterious mutations in DNA damage repair (DDR) genes, highlighting the importance of these genes in PDAC. The mechanisms by which DDR gene mutations promote tumorigenesis, therapeutic response, and subsequent resistance are still not fully understood. Therefore, an opportunity exists to elucidate these processes and to uncover relevant therapeutic drug combinations and strategies to target DDR deficiency in PDAC. However, a constraint to preclinical research is due to limitations in appropriate laboratory experimental models. Models that effectively recapitulate their original cancer tend to provide high levels of predictivity and effective translation of preclinical findings to the clinic. In this review, we outline the occurrence and role of DDR deficiency in PDAC and provide an overview of clinical trials that target these pathways and the preclinical models such as 2D cell lines, 3D organoids and mouse models [genetically engineered mouse model (GEMM), and patient-derived xenograft (PDX)] used in PDAC DDR deficiency research.
Rapid Increase of Oral Bacteria in Nasopharyngeal Microbiota After Antibiotic Treatment in Children With Invasive Pneumococcal Disease

Introduction Antibiotics are commonly prescribed to young children for treating bacterial infections such as invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae. Despite the obvious benefits of antibiotics, little is known about their possible side effects on children’s nasopharyngeal microbiota. In other ecological niches, antibiotics have been described to perturb the balanced microbiota with short- and long-term effects on children’s health. The present study aims to evaluate and compare the nasopharyngeal microbiota of children with IPD and different degree of antibiotic exposure. Methods We investigated differences in nasopharyngeal microbiota of two groups of children <18 years with IPD: children not exposed to antibiotics before sample collection (n=27) compared to children previously exposed (n=54). Epidemiological/clinical data were collected from subjects, and microbiota was characterized by Illumina sequencing of V3-V4 amplicons of the 16S rRNA gene. Results Main epidemiological/clinical factors were similar across groups. Antibiotic-exposed patients were treated during a median of 4 days (IQR: 3–6) with at least one beta-lactam (100.0%). Higher bacterial richness and diversity were found in the group exposed to antibiotics. Different streptococcal amplicon sequence variants (ASVs) were differentially abundant across groups: antibiotic use was associated to lower relative abundances of Streptococcus ASV2 and Streptococcus ASV11 (phylogenetically close to S. pneumoniae), and higher relative abundances of Streptococcus ASV3 and Streptococcus ASV12 (phylogenetically close to viridans group streptococci). ASVs assigned to typical bacteria from the oral cavity, including Veillonella, Alloprevotella, Porphyromonas, Granulicatella, or Capnocytophaga, were associated to the antibiotic-exposed group. Common nosocomial genera such as Staphylococcus, Acinetobacter, and Pseudomonas were also enriched in the group exposed to antibiotics. Conclusion Our results point toward a reduction of S. pneumoniae abundance on the nasopharynx of children with IPD after antibiotic treatment and a short-term repopulation of this altered niche by oral and nosocomial bacteria. Future research studies will have to evaluate the clinical implications of these findings and if these populations would benefit from the probiotic/prebiotic administration or even from the improvement on oral hygiene practices frequently neglected among hospitalized children.
Arylmalonate Decarboxylase—A Versatile Biocatalyst for the Synthesis of Optically Pure Carboxylic Acids

Bacterial arylmalonate decarboxylase (AMDase) is an intriguing cofactor-independent enzyme with a broad substrate spectrum. Particularly, the highly stereoselective transformation of diverse arylmalonic acids into the corresponding chiral α-arylpropionates has contributed to the broad recognition of this biocatalyst. While, more than 30 years after its discovery, the native substrate and function of AMDase still remain undiscovered, contributions from multiple fields have ever since brought forth a powerful collection of AMDase variants to access a wide variety of optically pure α-substituted propionates. This review aims at providing a comprehensive overview of the development of AMDase from an enzyme with unknown function up to a powerful tailored biocatalyst for the synthesis of industrially relevant optically pure α-arylpropionates. Historical perspectives as well as recent achievements in the field will be covered within this work.
Lactobacillus reuteri Alleviates Gastrointestinal Toxicity of Rituximab by Regulating the Proinflammatory T Cells in vivo

Rituximab (RTX) is a widely used anticancer drug with gastrointestinal side effects, such as nausea, vomiting, and diarrhea. The reason for these side effects is still poorly understood. Previous studies have reported that the intestinal microbiota is associated with the occurrence of disease and the therapeutic effect of drugs. In this study, we observed mucosal damage, inflammatory cell infiltration and increased intestinal inflammatory factor expression in RTX-treated mice. RTX also changed the diversity of the intestinal microbiota in mice, and decreased abundance of Lactobacillus reuteri was observed in RTX-treated mice. Further experiments revealed that intragastric administration of L. reuteri in RTX-treated mice attenuated the intestinal inflammatory response induced by RTX and regulated the proportion of helper T (Th) cells. In conclusion, our data characterize the effect of the intestinal microbiota on RTX-induced intestinal inflammation, suggesting that modifying the gut microbiota may represent a positive strategy for managing adverse reactions.
Transforming Growth Factor-β: An Agent of Change in the Tumor Microenvironment

Transforming Growth Factor-β (TGF-β) is a key regulator of embryonic development, adult tissue homeostasis, and lesion repair. In tumors, TGF-β is a potent inhibitor of early stage tumorigenesis and promotes late stage tumor progression and metastasis. Here, we review the roles of TGF-β as well as components of its signaling pathways in tumorigenesis. We will discuss how a core property of TGF-β, namely its ability to change cell differentiation, leads to the transition of epithelial cells, endothelial cells and fibroblasts to a myofibroblastoid phenotype, changes differentiation and polarization of immune cells, and induces metabolic reprogramming of cells, all of which contribute to the progression of epithelial tumors.
Membrane Depolarization and Apoptosis-Like Cell Death in an Alkaline Environment in the Rice Pathogen Burkholderia glumae

The rice pathogen Burkholderia glumae uses amino acids as a principal carbon source and thus produces ammonia in amino acid-rich culture medium such as Luria–Bertani (LB) broth. To counteract ammonia-mediated environmental alkaline toxicity, the bacterium produces a public good, oxalate, in a quorum sensing (QS)-dependent manner. QS mutants of B. glumae experience alkaline toxicity and may undergo cell death at the stationary phase when grown in LB medium. Here, we show that the cell-death processes of QS mutants due to alkaline environmental conditions are similar to the apoptosis-like cell death reported in other bacteria. Staining QS mutants with bis-(1,3-dibutylbarbituric acid)-trimethine oxonol revealed membrane depolarization. CellROX™ staining showed excessive generation of reactive oxygen species (ROS) in QS mutants. The expression of genes encoding HNH endonuclease (BGLU_1G15690), oligoribonuclease (BGLU_1G09120), ribonuclease E (BGLU_1G09400), and Hu-beta (BGLU_1G13530) was significantly elevated in QS mutants compared to that in wild-type BGR1, consistent with the degradation of cellular materials as observed under transmission electron microscopy (TEM). A homeostatic neutral pH was not attainable by QS mutants grown in LB broth or by wild-type BGR1 grown in an artificially amended alkaline environment. At an artificially adjusted alkaline pH, wild-type BGR1 underwent apoptosis-like cell death similar to that observed in QS mutants. These results show that environmental alkaline stress interferes with homeostatic neutral cellular pH, induces membrane depolarization, and causes apoptosis-like cell death in B. glumae.
Differences in Diet and Gut Microbiota Between Lactating and Non-lactating Asian Particolored Bats (Vespertilio sinensis): Implication for a Connection Between Diet and Gut Microbiota

In mammals, lactation is considered the most energetically costly phase for females. To meet nutritional and energy demands, lactating females usually change feeding patterns by eating food that is higher in protein and calories. Their gut microbes respond accordingly to help adapt to the changes in diet. In this study, we examined differences in diet and gut microbial composition between lactating and non-lactating Asian particolored bats (Vespertilio sinensis) using COI and 16S amplicon sequencing. When compared with non-lactating bats, we found that the diversity and composition of lactating bats’ diets differed; the proportion of Diptera increased and Coleoptera and Orthoptera decreased significantly. This could be attributed to the easy availability and high protein content of Diptera. Comparative analysis of the gut microbiota of lactating and non-lactating females showed that although the diversity of gut microbiota did not change, the relative abundance of specific gut microbiota associated with a particular diet did change. For example, when the consumption of Coleoptera decreased in lactating bats, the relative abundance of Lactobacillaceae was also reduced. Lactobacillaceae are thought to be involved in the digestion of Coleopteran exoskeletons. This study suggests that during lactation, Asian particolored bats eat a diet that yields higher levels of protein, and at the same time, the abundance of specific gut microbes change to help their hosts adapt to these changes in diet.
Anthocyanin Genes Involved in the Flower Coloration Mechanisms of Cymbidium kanran

The Orchidaceae, otherwise known as orchids, is one of the largest plant families and is renowned for its spectacular flowers and ecological adaptations. Various polymorphisms of orchid flower colour can attract pollinators and be recognised as valuable horticultural ornamentals. As one of the longest historic cultured orchids, Cymbidium kanran has been domesticated for more than 2,500 years and is an ideal species to study coloration mechanisms because of plentiful variations in floral coloration and abundant traditional varieties. In this study, we used two distinct colour-type flowers of C. kanran as experimental materials to elucidate the mechanism of flower coloration. High-performance liquid chromatography (HPLC) analysis revealed that anthocyanins in purple-red-type flowers include three types of anthocyanidin aglycones, peonidin, malvidin, and cyanidin, whereas anthocyanins are lacking in white-type flowers. Through comparative transcriptome sequencing, 102 candidate genes were identified as putative homologues of colour-related genes. Based on comprehensive correlation analysis between colour-related compounds and gene expression profiles, four candidates from 102 captured genes showed a positive correlation with anthocyanidin biosynthesis. Furthermore, transient expression of CkCHS-1, CkDFR, and CkANS by particle bombardment confirmed that recovery of their expression completed the anthocyanin pathway and produced anthocyanin compounds in white-type flowers. Collectively, this study provided a comprehensive transcriptomic dataset for Cymbidium, which significantly facilitate our understanding of the molecular mechanisms of regulating floral pigment accumulation in orchids.
Transforming Growth Factor Beta 1 Alters Glucose Uptake but Not Insulin Signalling in Human Primary Myotubes From Women With and Without Polycystic Ovary Syndrome

Women with polycystic ovary syndrome (PCOS), commonly have profound skeletal muscle insulin resistance which can worsen other clinical features. The heterogeneity of the condition has made it challenging to identify the precise mechanisms that cause this insulin resistance. A possible explanation for the underlying insulin resistance may be the dysregulation of Transforming Growth Factor-beta (TGFβ) signalling. TGFβ signalling contributes to the remodelling of reproductive and hepatic tissues in women with PCOS. Given the systemic nature of TGFβ signalling and its role in skeletal muscle homeostasis, it may be possible that these adverse effects extend to other peripheral tissues. We aimed to determine if TGFβ1 could negatively regulate glucose uptake and insulin signalling in skeletal muscle of women with PCOS. We show that both myotubes from women with PCOS and healthy women displayed an increase in glucose uptake, independent of changes in insulin signalling, following short term (16 hr) TGFβ1 treatment. This increase occurred despite pro-fibrotic signalling increasing via SMAD3 and connective tissue growth factor in both groups following treatment with TGFβ1. Collectively, our findings show that short-term treatment with TGFβ1 does not appear to influence insulin signalling or promote insulin resistance in myotubes. These findings suggest that aberrant TGFβ signalling is unlikely to directly contribute to skeletal muscle insulin resistance in women with PCOS in the short term but does not rule out indirect or longer-term effects.
Influence of Response-Option Combinations when Measuring Sense of Efficacy for Teaching: Trivial, or Substantial and Substantive?

Certain combinations of number and labeling of response options on Likert scales might, because of their interaction, influence psychometric outcomes. In order to explore this possibility with an experimental design, two versions of a scale for assessing sense of efficacy for teaching (SET) were administered to preservice teachers. One version had seven response options with labels at odd-numbered points; the other had nine response options with labels only at the extremes. Before outliers in the data were adjusted, the first version produced a range of more desirable psychometric outcomes but poorer test–retest reliability. After outliers were addressed, the second version had more undesirable attributes than before, and its previously high test–retest reliability dropped to poor. These results are discussed in relation to the design of scales for assessing SET and other constructs as well as in relation to the need for researchers to examine their data carefully, consider the need to address outlying data, and conduct analyses appropriately and transparently.