Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Origins and Sex-Biased Admixture of the Huis

Abstract The Hui people are unique among Chinese ethnic minorities in that they speak the same language as Han Chinese (HAN) but practice Islam. However, as the second-largest minority group in China numbering well over 10 million, the Huis are under-represented in both global and regional genomic studies. Here, we present the first whole-genome sequencing effort of 234 Hui individuals (NXH) aged over 60 who have been living in Ningxia, where the Huis are mostly concentrated. NXH are genetically more similar to East Asian than to any other global populations. In particular, the genetic differentiation between NXH and HAN (FST = 0.0015) is only slightly larger than that between northern and southern HAN (FST = 0.0010), largely attributed to the western ancestry in NXH (∼10%). Highly differentiated functional variants between NXH and HAN were identified in genes associated with skin pigmentation (e.g., SLC24A5), facial morphology (e.g., EDAR), and lipid metabolism (e.g., ABCG8). The Huis are also distinct from other Muslim groups such as the Uyghurs (FST = 0.0187), especially, NXH derived much less western ancestry (∼10%) compared with the Uyghurs (∼50%). Modeling admixture history indicated that NXH experienced an episode of two-wave admixture. An ancient admixture occurred ∼1,025 years ago, reflecting the intensive west–east contacts during the late Tang Dynasty, and the Five Dynasties and Ten Kingdoms period. A recent admixture occurred ∼500 years ago, corresponding to the Ming Dynasty. Notably, we identified considerable sex-biased admixture, that is, excess of western males and eastern females contributing to the NXH gene pool. The origins and the genomic diversity of the Hui people imply the complex history of contacts between western and eastern Eurasians.
Ecological risk assessment and long-term environmental pollution caused by obsolete undisposed organochlorine pesticides

Abstract Obsolete organochlorine pesticides (OSPs) are currently prohibited as persistent organic pollutants that contaminate the environment. If undisposed, they continue to pollute soil and water, to accumulate in the food chain and to harm plants, animals and the human body. The aim of the study was to assess water and soil pollution around the storehouses of undisposed, banned OSPs and their possible genotoxic effect. The storehouses in four villages near Almaty, Kazakhstan were investigated. Chemical analysis confirmed contamination of water and soil around storehouses with OSPs. The genotoxic effect of water and soil samples was evaluated using model objects: S.typhymurium, D.melanogaster, sheep lymphocytes cultures and human lymphocytes cultures. It was found that water and soil samples caused mutagenic effect in all model systems. They increased the frequency of revertants in Salmonella, the frequency of lethal mutations in Drosophila chromosomes, and the frequency of chromosome aberrations in cultures of human and sheep lymphocytes. Although a genotoxic effect was demonstrated for each of these models, various models showed different sensitivity to the effects of pesticides and they varied degree of response. The association between the total content of OCPs in soil and the level of mutations for different model systems was discovered.
Evolution of large males is associated with female‐skewed adult sex ratios in amniotes

Body size often differs between the sexes (leading to sexual size dimorphism, SSD), as a consequence of differential responses by males and females to selection pressures. Adult sex ratio (ASR, the proportion of males in the adult population) should influence SSD because ASR relates to both the number of competitors and available mates, which shape the intensity of mating competition and thereby promotes SSD evolution. However, whether ASR correlates with SSD variation among species has not been yet tested across a broad range of taxa. Using phylogenetic comparative analyses of 462 amniotes (i.e., reptiles, birds, and mammals), we fill this knowledge gap by showing that male bias in SSD increases with increasingly female‐skewed ASRs in both mammals and birds. This relationship is not explained by the higher mortality of the larger sex because SSD is not associated with sex differences in either juvenile or adult mortality. Phylogenetic path analysis indicates that higher mortality in one sex leads to skewed ASR, which in turn may generate selection for SSD biased toward the rare sex. Taken together, our findings provide evidence that skewed ASRs in amniote populations can result in the rarer sex evolving large size to capitalize on enhanced mating opportunities.
The role of non-standard translation in Candida albicans pathogenesis

ABSTRACT Candida albicans typically resides in the human gastrointestinal tract and mucosal membranes as a commensal organism. To adapt and cope with the host immune system, it has evolved a variety of mechanisms of adaptation such as stress-induced mutagenesis and epigenetic regulation. Niche-specific patterns of gene expression also allow the fungus to fine-tune its response to specific microenvironments in the host and switch from harmless commensal to invasive pathogen. Proteome plasticity produced by CUG ambiguity, on the other hand is emerging as a new layer of complexity in C. albicans adaptation, pathogenesis, and drug resistance. Such proteome plasticity is the result of a genetic code alteration where the leucine CUG codon is translated mainly as serine (97%), but maintains some level of leucine (3%) assignment. In this review, we dissect the link between C. albicans non-standard CUG translation, proteome plasticity, host adaptation and pathogenesis. We discuss published work showing how this pathogen uses the fidelity of protein synthesis to spawn novel virulence traits.
Development of an ELISA for distinguishing convalescent sera with Mycoplasma hyopneumoniae infection from hyperimmune sera responses to bacterin vaccination in pigs

Abstract Vaccination with inactivated bacterin is the most popular and practical measure to control enzootic pneumonia. After immunisation with inactivated bacterin, Mycoplasma hyopneumoniae colonised on the respiratory tract and lung stimulates the humoural immune responses and produces IgG and IgA antibodies. ELISA is a widely used serological method to detect M. hyopneumoniae antibodies. However, commercial IgG‐ELISA kit cannot distinguish between inactivated bacterin‐induced hyperimmune sera and convalescent sera stimulated by natural infection. SIgA‐ELISA method needs to collect nasal swabs, but collecting nasal swabs is not easy to operate. Establishment of a discriminative ELISA detecting humoural IgG from convalescent sera but not hyperimmune sera facilitates to evaluate the natural infection of M. hyopneumoniae after inactivated bacterin vaccination. We expressed and purified a recombinant protein named Mhp366‐N which contains an epitope recognised by the convalescent sera but not hyperimmune sera. The developed discriminative IgG‐ELISA could discriminate between inactivated bacterin‐induced hyperimmune sera and convalescent sera and was reproducible, sensitive and specific to M. hyopneumoniae antibody produced by natural infection. Compared to SIgA‐ELISA method, discriminative IgG‐ELISA was more convenient to detect IgG antibody from sera than IgA from nasal swabs, although it has limited sensitivity in the early stages of infection. Additionally, to some extent, it has a potential to avoid the interference of maternally derived IgG antibodies. The established discriminative IgG‐ELISA was efficient to judge the serological IgG antibodies induced from natural infection or inactivated vaccine stimulation and provided a useful method to investigate and evaluate the live organism infection after the application of inactivated bacterin.
Sequential administration of Prevnar 13™ and PNEUMOVAX™ 23 in healthy participants 50 years of age and older

ABSTRACT In most countries worldwide, pneumococcal conjugate vaccines have been included in the infant immunization program, resulting in a significant reduction in the burden of pneumococcal disease in children and adults. Shifting serotype distribution due to the indirect effect of infant vaccination with the 13-valent pneumococcal conjugate vaccine (PCV13) may continue to increase the gap between 23-valent pneumococcal polysaccharide vaccine (PPSV23) and PCV13 serotype coverage for older adults in the coming years. This clinical study (V110-029; NCT02225587) evaluated the safety and immunogenicity of sequential administration of PCV13 followed approximately 8 weeks later, or approximately 26 weeks later, by PPSV23 in healthy adults ≥50 years of age. Both dosing intervals were generally well tolerated as measured by the nature, frequency, and intensity of reported adverse events (AEs) in both vaccination groups. Serotype-specific opsonophagocytic activity (OPA) geometric mean titers (GMTs) measured 30 days following receipt of PPSV23 in either group and at Week 30 were generally comparable between the 2 groups for 6 serotypes unique to PPSV23 and 12 serotypes shared between PCV13 and PPSV23, regardless of the interval between receipt of PCV13 and PPSV23. In addition, administration of PPSV23 given either 8 weeks or 26 weeks following PCV13 did not negatively impact immune responses induced by PCV13. Furthermore, administration of PPSV23 given either 8 weeks or 26 weeks after PCV13 elicited serotype-specific OPA GMTs to serotypes unique to PPSV23, which could provide earlier protection against pneumococcal disease caused by these serotypes in comparison with the current Advisory Committee on Immunization Practices recommended interval of at least 12 months.
Ischemic Heart Disease: Noninvasive Imaging Techniques and Findings

Ischemic heart disease is a leading cause of death worldwide and comprises a large proportion of annual health care expenditure. Management of ischemic heart disease is now best guided by the physiologic significance of coronary artery stenosis. Invasive coronary angiography is the standard for diagnosing coronary artery stenosis. However, it is expensive and has risks including vascular access site complications and contrast material–induced nephropathy. Invasive coronary angiography requires fractional flow reserve (FFR) measurement to determine the physiologic significance of a coronary artery stenosis. Multiple noninvasive cardiac imaging modalities can also anatomically delineate or functionally assess for significant coronary artery stenosis, as well as detect the presence of myocardial infarction (MI). While coronary CT angiography can help assess the degree of anatomic stenosis, its inability to assess the physiologic significance of lesions limits its specificity. Physiologic significance of coronary artery stenosis can be determined by cardiac MR vasodilator or dobutamine stress imaging, CT stress perfusion imaging, FFR CT, PET myocardial perfusion imaging (MPI), SPECT MPI, and stress echocardiography. Clinically unrecognized MI, another clear indicator of physiologically significant coronary artery disease, is relatively common and is best evaluated with cardiac MRI. The authors illustrate the spectrum of imaging findings of ischemic heart disease (coronary artery disease, myocardial ischemia, and MI); highlight the advantages and disadvantages of the various noninvasive imaging methods used to assess ischemic heart disease, as illustrated by recent clinical trials; and summarize current indications and contraindications for noninvasive imaging techniques for detection of ischemic heart disease. Online supplemental material is available for this article. Published under a CC BY 4.0 license.
Radii of Gyration of Ring-Shaped Polystyrenes with High Purity in Dilute Solutions.

Ring polystyrenes (PSs) were synthesized by anionic polymerization technique and purified with preparative size-exclusion chromatography (SEC). Seven ring PSs with their weight-average molecular weight (Mw) ranging from 17k to 570k were prepared and they were confirmed to have high purities all over 96% by liquid chromatography at the chromatographic critical condition (LCCC) analyses. Their radii of gyration (Rgs) were determined in benzene-d6 as a good solvent and in cyclohexane-d12 or cyclohexane-h12 as Θ solvents by small-angle neutron scattering (SANS) or light scattering (LS). It has been found that Rgs of ring polymers are scaled with Mw as Rg∝Mw0.60 in a good solvent and as Rg∝Mw0.53 in Θ solvents. Moreover it was confirmed that g factors, Rg2(Ring)/Rg2(Linear), obtained in Θ solvents are meaningfully larger than theoretically predicted values owing to the topological effect stored in ring molecules.
Longitudinal stability of a multimodal visco-elastic polyacrylamide gel phantom for magnetic resonance and ultrasound shear-wave elastography

We evaluated the long-term stability of a newly developed viscoelastic phantom made of polyacrylamide (PAAm) gel for magnetic resonance elastography (MRE) and ultrasound-based shear-wave elastography (US SWE). The stiffness of the cylindrical phantom was measured at 0, 13 and 18 months. Storage and loss moduli were measured with MRE, and shear-wave speed (SWS) was measured with US SWE. Long-term stability was evaluated in accordance with the Quantitative Imaging Biomarker Alliance (QIBA) profiles for each modality. The initial storage and loss moduli of the phantom were 5.01±0.22 and 1.11±0.15 respectively, and SWS was 2.57±0.04 m/s. The weight of the phantom decreased by 0.6% over the 18 months. When measured with MRE, the stiffness of the phantom decreased and changes to the storage and loss moduli were -3.0% and -4.6% between 0 and 13 months, and -4.3% and 0.0% between 0 and 18 months. The US measurements found that SWS decreased by 2.4% over the first 13 months and 3.6% at 18 months. These changes were smaller than the tolerances specified in the QIBA profiles, so the viscoelastic PAAm gel phantom fulfilled the condition for long-term stability. This new phantom has the potential to be used as a quality assurance and quality control phantom for MRE and US SWE.
The Mechanisms of chemical reaction between silicate glass and attacking agents: Part 1. Electrophilic and nucleophilic mechanisms of attack

By analogy with the mechanisms of reaction of certain organic substances a scheme is presented to explain the reactions of silicate glasses with various reagents, including water and alkaline solutions. Two types of general attack are considered: attack on non-bridging oxygen atoms by reagents with electron deficit and attack on network silicon atoms by reagents with electron excess.
Long-read whole-genome methylation patterning using enzymatic base conversion and nanopore sequencing

Abstract Long-read whole-genome sequencing analysis of DNA methylation would provide useful information on the chromosomal context of gene expression regulation. Here we describe the development of a method that improves the read length generated by using the bisulfite-sequencing-based approach. In this method, we combined recently developed enzymatic base conversion, where an unmethylated cytosine (C) should be converted to thymine (T), with nanopore sequencing. After methylation-sensitive base conversion, the sequencing library was constructed using long-range polymerase chain reaction. This type of analysis is possible using a minimum of 1 ng genomic DNA, and an N50 read length of 3.4–7.6 kb is achieved. To analyze the produced data, which contained a substantial number of base mismatches due to sequence conversion and an inaccurate base read of the nanopore sequencing, a new analytical pipeline was constructed. To demonstrate the performance of long-read methylation sequencing, breast cancer cell lines and clinical specimens were subjected to analysis, which revealed the chromosomal methylation context of key cancer-related genes, allele-specific methylated genes, and repetitive or deletion regions. This method should convert the intractable specimens for which the amount of available genomic DNA is limited to the tractable targets.
Mechanistic Evaluation of Linalool Effect against Renal Ischemia- Reperfusion Injury in Rats

Abstract Background Kidney ischemia reperfusion (IR) is an important cause of renal dysfunction. The hypoxic conditions in ischemic damage result in the formation of free radicals and apoptotic death of renal cells. We evaluated the renoprotective effects of linalool in IR- induced renal injury. Methods Wistar rats were divided into three groups of six rats; namely, control group, IR group, and linalool + IR group. The animals were unilaterally nephrectomized and subjected to 45 min of renal pedicle occlusion followed by 24 h reperfusion. Linalool (40mg/kg) was administered before ischemia. After 24h reperfusion, the kidney tissues were obtained for detection of miR-21, HSP 70 and caspase-3 expression levels and histological studies. Also, the blood samples were collected for the measurement of biochemical parameters. Results IR significantly increased the expression of miR-21, HSP70 and capase-3 and the serum levels of BUN-Cr, ALT, AST and ALP enzymes. Furthermore, histological findings of the IR group confirmed that there were acute tubular necrosis and lymphocyte infiltration in the renal tissues. Treatment with linalool improved the renal function and morphological changes. Conclusion It seems that linalool could exert a nephroprotective effect via a number of mechanisms in renal IR injury.
The neuronal ceroid lipofuscinosis‐related protein CLN8 regulates endo‐lysosomal dynamics and dendritic morphology

The endo‐lysosomal system (ELS) comprises a set of membranous organelles responsible for transporting intracellular and extracellular components within cells. Defects in lysosomal proteins usually affect a large variety of processes and underlie many diseases, most of them with a strong neuronal impact. Mutations in the endoplasmic reticulum‐resident CLN8 protein cause CLN8 disease. This condition is one of the 14 known neuronal ceroid lipofuscinoses (NCLs), a group of inherited diseases characterised by accumulation of lipofuscin‐like pigments within lysosomes. Besides mediating the transport of soluble lysosomal proteins, recent research suggested a role for CLN8 in the transport of vesicles and lipids, and autophagy. However, the consequences of CLN8 deficiency on ELS structure and activity, as well as the potential impact on neuronal development, remain poorly characterised. Therefore, we performed CLN8 knockdown in neuronal and non‐neuronal cell models to analyse structural, dynamic and functional changes in the ELS and to assess the impact of CLN8 deficiency on axodendritic development.
The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-Ι

Significance We report that SARS-CoV-2 utilizes its ORF8 protein as a unique mechanism to alter the expression of surface MHC-Ι expression to evade immune surveillance. Our study is significant for providing an understanding of the pathogenesis of SARS-CoV-2 and will provide additional perspective to the intensive ongoing investigation into the mechanism and function of T cell antiviral immunity in COVID-19. COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic and has claimed over 2 million lives worldwide. Although the genetic sequences of SARS-CoV and SARS-CoV-2 have high homology, the clinical and pathological characteristics of COVID-19 differ significantly from those of SARS. How and whether SARS-CoV-2 evades (cellular) immune surveillance requires further elucidation. In this study, we show that SARS-CoV-2 infection leads to major histocompability complex class Ι (MHC-Ι) down-regulation both in vitro and in vivo. The viral protein encoded by open reading frame 8 (ORF8) of SARS-CoV-2, which shares the least homology with SARS-CoV among all viral proteins, directly interacts with MHC-Ι molecules and mediates their down-regulation. In ORF8-expressing cells, MHC-Ι molecules are selectively targeted for lysosomal degradation via autophagy. Thus, SARS-CoV-2–infected cells are much less sensitive to lysis by cytotoxic T lymphocytes. Because ORF8 protein impairs the antigen presentation system, inhibition of ORF8 could be a strategy to improve immune surveillance.
Twelve tips for learners to succeed in a CBME program

Abstract The international movement to competency-based medical education (CBME) marks a major transition in medical education that requires a shift in educators’ and learners’ approach to clinical experiences, the way assessment data are collected and integrated, and in learners’ mindsets. Learners entering a CBME curriculum must actively drive their learning experiences and education goals. For some, this expectation may be a significant change from their previous approach to learning in medicine. This paper highlights 12 tips to help learners succeed within a CBME model.
Investigating the Multifaceted Nature of Radiation-Induced Coagulopathies in a Göttingen Minipig Model of Hematopoietic Acute Radiation Syndrome

Coagulopathies are well documented after acute radiation exposure at hematopoietic doses, and radiation-induced bleeding is notably one of the two main causes of mortality in the hematopoietic acute radiation syndrome. Despite this, understanding of the mechanisms by which radiation alters hemostasis and induces bleeding is still lacking. Here, male Göttingen minipigs received hematopoietic doses of 60Co gamma irradiation (total body) and coagulopathies were characterized by assessing bleeding, blood cytopenia, fibrin deposition, changes in hemostatic properties, coagulant/anticoagulant enzyme levels, and markers of inflammation, endothelial dysfunction, and barrier integrity to understand if a relationship exists between bleeding, hemostatic defects, bone marrow aplasia, inflammation, endothelial dysfunction and loss of barrier integrity. Acute radiation exposure induced coagulopathies in the Göttingen minipig model of hematopoietic acute radiation syndrome; instances of bleeding were not dependent upon thrombocytopenia. Neutropenia, alterations in hemostatic parameters and damage to the glycocalyx occurred in all animals irrespective of occurrence of bleeding. Radiation-induced bleeding was concurrent with simultaneous thrombocytopenia, anemia, neutropenia, inflammation, increased heart rate, decreased nitric oxide bioavailability and endothelial dysfunction; bleeding was not observed with the sole occurrence of a single aforementioned parameter in the absence of the others. Alteration of barrier function or clotting proteins was not observed in all cases of bleeding. Additionally, fibrin deposition was observed in the heart and lungs of decedent animals but no evidence of DIC was noted, suggesting a unique pathophysiology of radiation-induced coagulopathies. These findings suggest radiation-induced coagulopathies are the result of simultaneous damage to several key organs and biological functions, including the immune system, the inflammatory response, the bone marrow and the cardiovasculature.