Miracle-dz/UniFAR-FTUs huggingface dataset:
Coal mining and lung disease in the 21st century.

PURPOSE OF REVIEW To review the impact of coal mining and resurgence of coal workers' pneumoconiosis (CWP) in 21st century and effect of ambient air pollution on lung function. RECENT FINDINGS At the beginning of 21st century, statistics by National Institute for Occupational Safety and Health showed a steep rise in pneumoconiosis. This was followed by numerous epidemiologic and pathologic studies that confirmed increasing CWP prevalence as well as disease in younger miners and those with a shorter mining tenure. Recent studies have demonstrated that poor dust control in mines, a relative shift in composition of the coal mine dust, small sized mines and increase in surface mining are all possible contributors to this resurgence. There is also growing literature evaluating the effects of worsening air pollution on health, including decreasing lung function and development of emphysema, worsening quality of life measures and lung cancer. SUMMARY This irreversible but preventable disease currently haunts approximately 60 000 miners across United States and millions across the world. Its resurgence despite the strict dust regulations is a setback from the public health standpoint. The continued reliance on coal for energy will continue to place coal miners at danger of developing disease as well as the world.
Cephalopod Biology: At the Intersection Between Genomic and Organismal Novelties.

Cephalopods are resourceful marine predators that have fascinated generations of researchers as well as the public owing to their advanced behavior, complex nervous system, and significance in evolutionary studies. Recent advances in genomics have accelerated the pace of cephalopod research. Many traditional areas focusing on evolution, development, behavior, and neurobiology, primarily on the morphological level, are now transitioning to molecular approaches. This review addresses the recent progress and impact of genomic and other molecular resources on research in cephalopods. We outline several key directions in which significant progress in cephalopod research is expected and discuss its impact on our understanding of the genetic background behind cephalopod biology and beyond. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 8 is February 15, 2020. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Characterising risk of homicide in a population-based cohort

Background Homicide is an extreme expression of violence that has attracted less attention from public health researchers and policy makers interested in prevention. The purpose of this study was to examine the socioeconomic gradient of homicide and to determine whether risk differs by immigration status. Methods We conducted a population-based cohort study using linked vital statistics, census and population data sets that included all deaths by homicide from 1992 to 2012 in Ontario, Canada. We calculated age-adjusted death rates for homicide by material deprivation quintiles, stratified by immigration status. Count-based negative binomial regression models were used to calculate unadjusted and adjusted rate ratios with predictors of interest being age, urban residence, material deprivation and immigration status. A subanalysis containing immigrants only examined the effect of time since immigration and immigration class. Results There were 3345 homicide deaths registered between 1992 and 2012. Relative to low material deprivation areas, age-adjusted rates of homicide deaths in high materially deprived areas were similar among refugees (RR: 48.49; 95% CI 36.99 to 62.45) and long-term residents (RR: 47.67; 95% CI 44.66 to 50.83), but were slightly lower for non-refugee immigrants (RR: 38.53; 95% CI 32.42 to 45.45). Female refugees experienced a 1.31 (95% CI 0.88 to 1.94) higher rate and male refugees experienced a 1.23 (95% CI 0.90 to 1.67) higher rate of homicide victimisation compared with long-term residents. In an immigrant only analysis, the risk of homicide among refugees increased with duration of residence. Conclusions Given the large area-level, socioeconomic status gradients observed in homicides among refugees, community-level and culturally appropriate prevention approaches are important.
Calpain fosters the hyperexcitability of motoneurons after spinal cord injury and leads to spasticity

Up-regulation of the persistent sodium current (INaP) and down-regulation of the potassium/chloride extruder KCC2 lead to spasticity after spinal cord injury (SCI). We here identified calpain as the driver of the up- and down-regulation of INaP and KCC2, respectively, in neonatal rat lumbar motoneurons. Few days after SCI, neonatal rats developed behavioral signs of spasticity with the emergence of both hyperreflexia and abnormal involuntary muscle contractions on hindlimbs. At the same time, in vitro isolated lumbar spinal cords became hyperreflexive and displayed numerous spontaneous motor outputs. Calpain-I expression paralleled with a proteolysis of voltage-gated sodium (Nav) channels and KCC2. Acute inhibition of calpains reduced this proteolysis, restored the motoneuronal expression of Nav and KCC2, normalized INaP and KCC2 function, and curtailed spasticity. In sum, by up- and down-regulating INaP and KCC2, the calpain-mediated proteolysis of Nav and KCC2 drives the hyperexcitability of motoneurons which leads to spasticity after SCI.
Diet and Genetics Influence Beef Cattle Performance and Meat Quality Characteristics

A comprehensive review of the impact of tropical pasture grazing, nutritional supplementation during feedlot finishing and fat metabolism-related genes on beef cattle performance and meat-eating traits is presented. Grazing beef cattle on low quality tropical forages with less than 5.6% crude protein, 10% soluble starches and 55% digestibility experience liveweight loss. However, backgrounding beef cattle on high quality leguminous forages and feedlot finishing on high-energy diets increase meat flavour, tenderness and juiciness due to improved intramuscular fat deposition and enhanced mono- and polyunsaturated fatty acids. This paper also reviews the roles of stearoyl-CoA desaturase, fatty acid binding protein 4 and fatty acid synthase genes and correlations with meat traits. The review argues that backgrounding of beef cattle on Desmanthus, an environmentally well-adapted and vigorous tropical legume that can persistently survive under harsh tropical and subtropical conditions, has the potential to improve animal performance. It also identifies existing knowledge gaps and research opportunities in nutrition-genetics interactions aimed at a greater understanding of grazing nutrition, feedlot finishing performance, and carcass traits of northern Australian tropical beef cattle to enable red meat industry players to work on marbling, juiciness, tenderness and overall meat-eating characteristics.
The effects of heavy metals on human metabolism

Abstract As technology continues to advance, heavy metals in drinking water have exceeded recommended limits from regulators around the world. The main source of human exposure to heavy metals is from contaminated drinking water. The effects of drinking water contaminated with heavy metals, such as arsenic, lead, nickel, cadmium and mercury, have gradually caught the attention of the relevant departments and personnel. It is well known that occupational exposure to heavy metals occurs as a result of using these metals in a variety of industrial processes in and/or a variety of materials, including color pigments and alloys. A series of adverse effects on human metabolism has resulted from exposure to heavy metal-contaminated drinking water, which has been recorded from around the world. The general mechanism of heavy metal toxicity is through the production of reactive oxygen species, the appearance of oxidative damage, and subsequent adverse effects on health. Therefore, water contaminated with heavy metals causes high morbidity and mortality worldwide. In order to address concern regarding the health effects of different heavy metals, this paper reviews its sources, distribution and effects of heavy metal on human metabolism. HIGHLIGHTS The accumulation of heavy metals such as lead, arsenic, mercury, cadmium and nickel will destroy the main metabolic process of human body. Redox reactions in biological systems are caused by carcinogenic metal ions such as nickel and arsenic. The free radicals produced by these reactions cause oxidative damage to proteins and DNA. The accumulation of heavy metals eventually produces reactive oxygen species that can cause oxidative stress, which may lead to the production of various diseases.
Convergence between Microglia and Peripheral Macrophages Phenotype during Development and Neuroinflammation

Differently from other myeloid cells, microglia derive exclusively from precursors originating within the yolk sac and migrate to the CNS under development, without any contribution from fetal liver or postnatal hematopoiesis. Consistent with their unique ontology, microglia may express specific physiological markers, which have been partly described in recent years. Here we wondered whether profiles distinguishing microglia from peripheral macrophages vary with age and under pathology. To this goal, we profiled transcriptomes of microglia throughout the lifespan and included a parallel comparison with peripheral macrophages under physiological and neuroinflammatory settings using age- and sex-matched wild-type and bone marrow chimera mouse models. This comprehensive approach demonstrated that the phenotypic differentiation between microglia and peripheral macrophages is age-dependent and that peripheral macrophages do express some of the most commonly described microglia-specific markers early during development, such as Fcrls, P2ry12, Tmem119, and Trem2. Further, during chronic neuroinflammation CNS-infiltrating macrophages and not peripheral myeloid cells acquire microglial markers, indicating that the CNS niche may instruct peripheral myeloid cells to gain the phenotype and, presumably, the function of the microglia cell. In conclusion, our data provide further evidence about the plasticity of the myeloid cell and suggest caution in the strict definition and application of microglia-specific markers. SIGNIFICANCE STATEMENT Understanding the respective role of microglia and infiltrating monocytes in neuroinflammatory conditions has recently seemed possible by the identification of a specific microglia signature. Here instead we provide evidence that peripheral macrophages may express some of the most commonly described microglia markers at some developmental stages or pathological conditions, in particular during chronic neuroinflammation. Further, our data support the hypothesis about phenotypic plasticity and convergence among distinct myeloid cells so that they may act as a functional unit rather than as different entities, boosting their mutual functions in different phases of disease. This holds relevant implications in the view of the growing use of myeloid cell therapies to treat brain disease in humans.
Interleukin 31 in insect bite hypersensitivity—Alleviating clinical symptoms by active vaccination against itch

Insect bite hypersensitivity (IBH) is the most common seasonal pruritic allergic dermatitis of horses occurring upon insect bites. In recent years, a major role for IL‐31 in allergic pruritus of humans, monkeys, dogs, and mice was acknowledged. Here, we investigate the role of IL‐31 in IBH of horses and developed a therapeutic vaccine against equine IL‐31 (eIL‐31).
Atrial Fibrillation in Athletes—Features of Development, Current Approaches to the Treatment, and Prevention of Complications

Atrial fibrillation (AF) is one of the most common types of cardiac arrhythmias. This review article highlights the problem of the development of atrial fibrillation in individuals engaged in physical activity and sports. Predisposing factors, causes, and development mechanisms of atrial fibrillation in athletes from the perspective of the authors are described. Methods of treatment, as well as prevention of thromboembolic complications, are discussed. Directions for further studies of this problem and prevention of complications are proposed.
Point-of-care ultrasound (POCUS) for hospitalists and general internists

ABSTRACT Point-of-care ultrasound (POCUS) is currently implemented in various medical fields by clinicians for the bedside examination of patients. Evidence supports the fact that adding an ultrasound technology in daily practice (hand-held ultrasound device), called by some ‘stethoscope of the future’, improves patient care and allows an earlier diagnosis in a hospital setting. In this article, we reviewed the historical evolution of the use of ultrasound in medicine and the possibilities of using POCUS for hospitalists and general internists based on the existing scientific literature.
A Functional 3′ UTR Polymorphism of FADS2 Affects Cow Milk Composition through Modifying Mir-744 Binding

Simple Summary Fatty acid desaturase 2 (FADS2) is the rate-limiting enzyme involved in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFAs). Many studies have suggested that polymorphisms in the FADS2 gene can modify its delta-6 desaturase activity. However, much remains unknown in regards to the regulatory mechanisms interpreting how DNA variants influence the function of FADS2. A previous study has suggested that c.1571G>A is located within the miR-744 binding site, indicating that this single nucleotide polymorphism (SNP) may be functional. Therefore, the aim of the present study was to determine the association of SNP c.1571G>A with milk PUFAs content and to further elucidate how this SNP contributes to regulating FADS2 expression. Our results support the use of SNP c.1571G>A as a potential genetic marker in the selective breeding of cattle to increase beneficial FAs content in milk. Abstract This study determined the associations of FADS2 c.1571G>A with milk FAs content and revealed that cows with the GG genotype had improved levels of delta-6 desaturase substrates (linoleic acid, C18:2n-6; p < 0.001) and decreased levels of desaturase products (gamma-linolenic acid, C18:3n-6; p < 0.001), indicating a reduction in FADS2 expression or delta-6 desaturase activity caused by this polymorphism. Computer alignment demonstrated that c.1571G>A occurred within a potential miR-744 binding site. When the c.1571G allele was present, the luciferase activity of reporter constructs was significantly suppressed by miR-744, while no such effect was observed with the A allele. Overexpression of miR-744 in bovine mammary epithelial cells (with the 1571GG genotype) downregulated FADS2 expression at both mRNA and protein levels. In contrast, inhibition of endogenous miR-744 with a specific inhibitor dramatically upregulated FADS2 expression. Taken together, these lines of evidence indicated that the c.1571A minor allele abolished the ability of miR-744 to bind FADS2, with a consequent increase in FADS2 expression levels and synthesis of omega-6 LC-PUFAs.
Systematic processing of ribosomal RNA gene amplicon sequencing data

Abstract Background With the advent of high-throughput sequencing, microbiology is becoming increasingly data-intensive. Because of its low cost, robust databases, and established bioinformatic workflows, sequencing of 16S/18S/ITS ribosomal RNA (rRNA) gene amplicons, which provides a marker of choice for phylogenetic studies, has become ubiquitous. Many established end-to-end bioinformatic pipelines are available to perform short amplicon sequence data analysis. These pipelines suit a general audience, but few options exist for more specialized users who are experienced in code scripting, Linux-based systems, and high-performance computing (HPC) environments. For such an audience, existing pipelines can be limiting to fully leverage modern HPC capabilities and perform tweaking and optimization operations. Moreover, a wealth of stand-alone software packages that perform specific targeted bioinformatic tasks are increasingly accessible, and finding a way to easily integrate these applications in a pipeline is critical to the evolution of bioinformatic methodologies. Results Here we describe AmpliconTagger, a short rRNA marker gene amplicon pipeline coded in a Python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. It is designed to work within an HPC environment, supporting a complex network of job dependencies with a smart-restart mechanism in case of job failure or parameter modifications. As proof of concept, we present end results obtained with AmpliconTagger using 16S, 18S, ITS rRNA short gene amplicons and Pacific Biosciences long-read amplicon data types as input. Conclusions Using a selection of published algorithms for generating operational taxonomic units and amplicon sequence variants and for computing downstream taxonomic summaries and diversity metrics, we demonstrate the performance and versatility of our pipeline for systematic analyses of amplicon sequence data.
TNIP1 Inhibits Proliferation And Promotes Apoptosis In Clear Cell Renal Carcinoma Through Targeting C/Ebpβ

Background/Purpose TNF-α-induced protein 3-interacting protein 1 (TNIP1) is active in various cancers, but its expression and function in renal cell carcinoma (RCC) have not been described. This study investigated the role of TNIP1 in clear cell renal cell carcinomas (ccRCC), which accounts for 75–80% of RCC and has a poor prognosis. Methods The expression of TNIP1 in human ccRCC tissues and cells was detected by real-time quantitative reverse transcription–polymerase chain reaction (qRT-PCR), Western blot (WB), and immunohistochemical (IHC) staining. Cell proliferation was assayed by a cell counting kit (CCK)-8 assay; cell cycle analysis and apoptosis assay were done by flow cytometry. Results TNIP1 is downregulated in both ccRCC human tissues and cells. Besides, TNIP1 downregulation promoted cell proliferation with more cell cycle entry, and inhibited apoptosis. TNIP1 downregulation was associated with increased of expression of the Bcl-2 anti-apoptosis gene and decreased expression of the Bax apoptosis-promoting gene and cleaved-caspase-3 by negatively regulating C/EBPβ expression. Conclusion TNIP1 acted as a tumor-inhibitor in ccRCC by targeting C/EBPβ. The results warrant study of TNIP1 as a potential diagnostic marker and therapeutic target of ccRCC.
Numerical and Experimental Investigation of Morphological Modification on Fused Silica Using CO2 Laser Ablation

In this paper, a numerical model based on the finite-element method for predicting the morphological evolution during CO2 laser ablation on fused silica is developed and examined experimentally. Adopting the optimized parameters that were obtained from the model, a typical cone-shaped multi-stage structure with a diameter of 2 mm and a slope angle of 10.4° was sufficiently polished. Both the roughness and the transparency of the surface structure were significantly improved. The characterized slope angle of the continuous surface is exactly consistent with the predicted value, and the ablation depth is 32 ± 1.247 µm with a deviation of 1.7% (RMS, root mean square). The deviation is principally caused by the neglect of melting displacement in simulation and the irregularity in actual stepping structures. These results indicate that the numerical model can simulate morphological modification of CO2 laser ablation with a high degree of reliability. It could further be used to optimize processing parameters for customizing continuous fused silica surfaces, which could facilitate industrial manufacturing of freeform optics.
School-Related Risk Factors of Internet Use Disorders

A growing body of research focusing on the risk factors of Internet use disorder (IUD) underlines the effect of sociodemographic variables like age and gender or comorbid mental disorders on IUD symptoms. The relation between IUD symptoms and school-related variables has to date been insufficiently studied. The present study closes this gap by investigating the relation between school-relevant factors such as absenteeism, school grades, procrastination, school-related social behavior, and learning behavior and IUD symptoms in a high-risk sample. n = 418 students between 11 and 21 years of age (M = 15.10, SD = 1.97), screened for elevated risk of IUD, participated in the study. Sociodemographic data, school grades and absent days, Internet use variables (time spent online and gaming), as well as school-related psychological variables (procrastination, learning behavior, and social behavior) were assessed via self-report questionnaires. IUD symptoms were assessed with an adapted version of the German Video Game Dependency Scale (CSAS), which is based on the 9 criteria for Internet gaming disorder in the DSM-5. The instrument was adapted to include the assessment of non-gaming IUD symptoms. Taking the hierarchical structure of the data into account, a multilevel modeling approach was used to analyze the data. Procrastination, time spent online, and gaming were significant predictors of IUD symptoms at the individual level, whereas social behavior significantly predicted symptoms of IUD at the school level. In addition to previous findings on risk factors of IUD, this study indicates the importance of school-related factors in the development of IUD, especially psychological factors that play a role in the school setting. The early age of IUD onset and the high relevance of prevention of IUD at the school age underline the relevance of this finding.
The Fusion of Lipid and DNA Nanotechnology

Lipid membranes form the boundary of many biological compartments, including organelles and cells. Consisting of two leaflets of amphipathic molecules, the bilayer membrane forms an impermeable barrier to ions and small molecules. Controlled transport of molecules across lipid membranes is a fundamental biological process that is facilitated by a diverse range of membrane proteins, including ion-channels and pores. However, biological membranes and their associated proteins are challenging to experimentally characterize. These challenges have motivated recent advances in nanotechnology towards building and manipulating synthetic lipid systems. Liposomes—aqueous droplets enclosed by a bilayer membrane—can be synthesised in vitro and used as a synthetic model for the cell membrane. In DNA nanotechnology, DNA is used as programmable building material for self-assembling biocompatible nanostructures. DNA nanostructures can be functionalised with hydrophobic chemical modifications, which bind to or bridge lipid membranes. Here, we review approaches that combine techniques from lipid and DNA nanotechnology to engineer the topography, permeability, and surface interactions of membranes, and to direct the fusion and formation of liposomes. These approaches have been used to study the properties of membrane proteins, to build biosensors, and as a pathway towards assembling synthetic multicellular systems.