Miracle-dz/UniFAR-FTUs huggingface dataset:
Translational Analysis of Moderate to Severe Asthma GWAS Signals Into Candidate Causal Genes and Their Functional, Tissue-Dependent and Disease-Related Associations

Asthma affects more than 300 million people globally and is both under diagnosed and under treated. The most recent and largest genome-wide association study investigating moderate to severe asthma to date was carried out in 2019 and identified 25 independent signals. However, as new and in-depth downstream databases become available, the translational analysis of these signals into target genes and pathways is timely. In this study, unique (U-BIOPRED) and publicly available datasets (HaploReg, Open Target Genetics and GTEx) were investigated for the 25 GWAS signals to identify 37 candidate causal genes. Additional traits associated with these signals were identified through PheWAS using the UK Biobank resource, with asthma and eosinophilic traits amongst the strongest associated. Gene expression omnibus dataset examination identified 13 candidate genes with altered expression profiles in the airways and blood of asthmatic subjects, including MUC5AC and STAT6. Gene expression analysis through publicly available datasets highlighted lung tissue cell specific expression, with both MUC5AC and SLC22A4 genes showing enriched expression in ciliated cells. Gene enrichment pathway and interaction analysis highlighted the dominance of the HLA-DQA1/A2/B1/B2 gene cluster across many immunological diseases including asthma, type I diabetes, and rheumatoid arthritis. Interaction and prediction analyses found IL33 and IL18R1 to be key co-localization partners for other genes, predicted that CD274 forms co-expression relationships with 13 other genes, including the HLA-DQA1/A2/B1/B2 gene cluster and that MUC5AC and IL37 are co-expressed. Drug interaction analysis revealed that 11 of the candidate genes have an interaction with available therapeutics. This study provides significant insight into these GWAS signals in the context of cell expression, function, and disease relationship with the view of informing future research and drug development efforts for moderate-severe asthma.
Single-Cell Analysis of Antigen-Specific CD8+ T-Cell Transcripts Reveals Profiles Specific to mRNA or Adjuvanted Protein Vaccines

CD8+ T cells play a key role in mediating protective immunity after immune challenges such as infection or vaccination. Several subsets of differentiated CD8+ T cells have been identified, however, a deeper understanding of the molecular mechanism that underlies T-cell differentiation is lacking. Conventional approaches to the study of immune responses are typically limited to the analysis of bulk groups of cells that mask the cells’ heterogeneity (RNA-seq, microarray) and to the assessment of a relatively limited number of biomarkers that can be evaluated simultaneously at the population level (flow and mass cytometry). Single-cell analysis, on the other hand, represents a possible alternative that enables a deeper characterization of the underlying cellular heterogeneity. In this study, a murine model was used to characterize immunodominant hemagglutinin (HA533-541)-specific CD8+ T-cell responses to nucleic- and protein-based influenza vaccine candidates, using single-cell sorting followed by transcriptomic analysis. Investigation of single-cell gene expression profiles enabled the discovery of unique subsets of CD8+ T cells that co-expressed cytotoxic genes after vaccination. Moreover, this method enabled the characterization of antigen specific CD8+ T cells that were previously undetected. Single-cell transcriptome profiling has the potential to allow for qualitative discrimination of cells, which could lead to novel insights on biological pathways involved in cellular responses. This approach could be further validated and allow for more informed decision making in preclinical and clinical settings.
Association Analysis Between the Functional Single Nucleotide Variants in miR-146a, miR-196a-2, miR-499a, and miR-612 With Acute Lymphoblastic Leukemia

Background Acute lymphoblastic leukemia (ALL) is characterized by an abnormal proliferation of immature lymphocytes, in whose development involves both environmental and genetic factors. It is well known that single nucleotide polymorphisms (SNPs) in coding and noncoding genes contribute to the susceptibility to ALL. This study aims to determine whether SNPs in miR-146a, miR-196a-2, miR-499a, and miR-612 genes are associated with the risk to ALL in pediatric Mexican population. Methods A multicenter case-control study was carried out including patients with de novo diagnosis of ALL and healthy subjects as control group. The DNA samples were obtained from saliva and peripheral blood, and the genotyping of rs2910164, rs12803915, rs11614913, and rs3746444 was performed using the 5′exonuclease technique. Gene-gene interaction was evaluated by the multifactor dimensionality reduction (MDR) software. Results miR-499a rs3746444 showed significant differences among cases and controls. The rs3746444G allele was found as a risk factor to ALL (OR, 1.6 [95% CI, 1.05–2.5]; p = 0.028). The homozygous GG genotype of rs3746444 confers higher risk to ALL than the AA genotype (OR, 5.3 [95% CI, 1.23–23.4]; p = 0.01). Moreover, GG genotype highly increases the risk to ALL in male group (OR, 17.6 [95% CI, 1.04–298.9]; p = 0.00393). In addition, an association in a gender-dependent manner among SNPs located in miR-146a and miR-196a-2 genes and ALL susceptibility was found. Conclusion Our findings suggest that SNP located in miR-499a, miR-146a, and miR-196a-2 genes confer risk to ALL in Mexican children. Experimental analysis to decipher the role of these SNPs in human hematopoiesis could improve our understanding of the molecular mechanism underlying the development of ALL.
Transcriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques

Atherosclerosis is a chronic inflammatory disease with high prevalence and mortality. The rupture of atherosclerotic plaque is the main reason for the clinical events caused by atherosclerosis. Making clear the transcriptomic and proteomic profiles between the stabe and unstable atherosclerotic plaques is crucial to prevent the clinical manifestations. In the present study, 5 stable and 5 unstable human carotid atherosclerotic plaques were obtained by carotid endarterectomy. The samples were used for the whole transcriptome sequencing (RNA-Seq) by the Next-Generation Sequencing using the Illumina HiSeq, and for proteome analysis by HPLC-MS/MS. The lncRNA-targeted genes and circRNA-originated genes were identified by analyzing their location and sequence. Gene Ontology and KEGG enrichment was carried out to analyze the functions of differentially expressed RNAs and proteins. The protein-protein interactions (PPI) network was constructed by the online tool STRING. The consistency of transcriptome and proteome were analyzed, and the lncRNA/circRNA-miRNA-mRNA interactions were predicted. As a result, 202 mRNAs, 488 lncRNAs, 91 circRNAs, and 293 proteins were identified to be differentially expressed between stable and unstable atherosclerotic plaques. The 488 lncRNAs might target 381 protein-coding genes by cis-acting mechanisms. Sequence analysis indicated the 91 differentially expressed circRNAs were originated from 97 protein-coding genes. These differentially expressed RNAs and proteins were mainly enriched in the terms of the cellular response to stress or stimulus, the regulation of gene transcription, the immune response, the nervous system functions, the hematologic activities, and the endocrine system. These results were consistent with the previous reported data in the dataset GSE41571. Further analysis identified CD5L, S100A12, CKB (target gene of lncRNA MSTRG.11455.17), CEMIP (target gene of lncRNA MSTRG.12845), and SH3GLB1 (originated gene of hsacirc_000411) to be critical genes in regulating the stability of atherosclerotic plaques. Our results provided a comprehensive transcriptomic and proteomic knowledge on the stability of atherosclerotic plaques.
Post-Transplant Nivolumab Plus Unselected Autologous Lymphocytes in Refractory Hodgkin Lymphoma: A Feasible and Promising Salvage Therapy Associated With Expansion and Maturation of NK Cells

Immune checkpoint inhibitors (CI) have demonstrated clinical activity in Hodgkin Lymphoma (HL) patients relapsing after autologous stem cell transplantation (ASCT), although only 20% complete response (CR) rate was observed. The efficacy of CI is strictly related to the host immune competence, which is impaired in heavily pre-treated HL patients. Here, we aimed to enhance the activity of early post-ASCT CI (nivolumab) administration with the infusion of autologous lymphocytes (ALI). Twelve patients with relapse/refractory (R/R) HL (median age 28.5 years; range 18-65), underwent lymphocyte apheresis after first line chemotherapy and then proceeded to salvage therapy. Subsequently, 9 patients with progressive disease at ASCT received early post-transplant CI supported with four ALI, whereas 3 responding patients received ALI alone, as a control cohort. No severe adverse events were recorded. HL-treated patients achieved negative PET scan CR and 8 are alive and disease-free after a median follow-up of 28 months. Four patients underwent subsequent allogeneic SCT. Phenotypic analysis of circulating cells showed a faster expansion of highly differentiated NK cells in ALI plus nivolumab-treated patients as compared to control patients. Our data show anti-tumor activity with good tolerability of ALI + CI for R/R HL and suggest that this setting may accelerate NK cell development/maturation and favor the expansion of the “adaptive” NK cell compartment in patients with HCMV seropositivity, in the absence of HCMV reactivation.
De Novo Variants in the DYNC1H1 Gene Associated With Infantile Spasms

Objective: The DYNC1H1 gene is related to a variety of diseases, including spinal muscular atrophy with lower extremity–predominant 1, Charcot–Marie–Tooth disease type 2O, and mental retardation, autosomal dominant13 (MRD13). Some patients with DYNC1H1 variant also had epilepsy. This study aimed to detect DYNC1H1 variants in Chinese patients with infantile spasms (ISs). Methods: We reviewed clinical information, video electroencephalogram (V-EEG), and neuroimaging of a newly identified cohort of five patients with de novo DYNC1H1gene variants. Results: Five patients with four DYNC1H1variants from four families were included. All patients had epileptic spasms (ESs), the median age at seizure onset was 7.5 months (range from 5 months to 2 years 7 months), and the interictal V-EEG results were hypsarrhythmia. Four of five patients had brain magnetic resonance imaging (MRI) abnormalities. Four de novo DYNC1H1 variants were identified, including two novel variants (p.N1117K, p.M3405L) and two reported variants (p.R1962C, p.F1093S). As for the variant site, two variants are located in the tail domain, one variant is located in the motor domain, and one variant is located in the stalk domain. All patients had tried more than five kinds of antiepileptic drugs. One patient has been controlled well by vigabatrin (VGB) for 4 years, and another patient by VGB and steroids for 1.5 years. The other three patients still had frequent ESs. All patients had severe intellectual disability and development delays. Significance: IS was one of the phenotypes of DYNC1H1 variants. Most patients had non-specific brain MRI abnormality. Two of four DYNC1H1 variants were novel, expanding the variant spectrum. The IS phenotype was related to the variant's domains of DYNC1H1 variant sites. All patients were drug-refractory and showed development delays.
Immune Infiltration-Related Signature Predicts Risk Stratification and Immunotherapy Efficacy in Grade II and III Gliomas

Background: Tumor microenvironment, especially infiltrating immune cell, is crucial for solid tumors including glioma. However, the hub genes as well as their effects on patient prognosis and immunotherapy efficacy remain obscure. Methods: We employed a total of 952 lower grade glioma (LGG) patients from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases, and 24 samples in our hospital for subsequent analyses. Abundances of immune infiltrates were evaluated using CIBERSORT and ImmuCellAI. Their correlations with prognosis were assessed by log-rank test. Immune infiltration-related hub genes were obtained from overlapped differential expressed genes (DEGs) in various subsets of survival-related immune cell types. The risk signature was constructed by Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analysis. The functional analyses were estimated by GVSA and Gene Set Enrichment Analysis (GSEA) algorithms. And protein–protein interaction enrichment analysis was carried out with the Metascape database integrating STRING, BioGrid, OmniPath, and InWeb_IM. Results: Among the 21 infiltrates, the abundances of five immune infiltrates were correlated with overall survival (OS) in LGG patients. Higher abundances of naïve CD4+ T cells (p = 0.002), activated mast cells (p = 0.015), and monocytes (p = 0.014) were correlated with better prognosis, while higher abundances of resting memory CD4+ T cells (p = 0.015) and M1 macrophages (p = 0.020) correlated with poorer OS. We finally obtained 44 hub genes and constructed an immune infiltration-related signature (IIRS). The IIRS correlates with clinicopathological characteristics and exhibited potential power in predicting the immunotherapy efficacy. The IRRS correlates with cancer related pathways, especially “epithelial-mesenchymal transition (EMT),” and cytotoxic T lymphocytes. Conclusion: Our study constructed and validated a novel signature for risk stratification and prediction of immunotherapy response in grade II and III gliomas, which was closely associated with glioma immune microenvironment and could serve as a promising prognostic biomarker for glioma patients.
Going Up Inflame: Reviewing the Underexplored Role of Inflammatory Programming in Stress-Induced Intrauterine Growth Restricted Livestock

The impact of intrauterine growth restriction (IUGR) on health in humans is well-recognized. It is the second leading cause of perinatal mortality worldwide, and it is associated with deficits in metabolism and muscle growth that increase lifelong risk for hypertension, obesity, hyperlipidemia, and type 2 diabetes. Comparatively, the barrier that IUGR imposes on livestock production is less recognized by the industry. Meat animals born with low birthweight due to IUGR are beset with greater early death loss, inefficient growth, and reduced carcass merit. These animals exhibit poor feed-to-gain ratios, less lean mass, and greater fat deposition, which increase production costs and decrease value. Ultimately, this reduces the amount of meat produced by each animal and threatens the economic sustainability of livestock industries. Intrauterine growth restriction is most commonly the result of fetal programming responses to placental insufficiency, but the exact mechanisms by which this occurs are not well-understood. In uncompromised pregnancies, inflammatory cytokines are produced at modest rates by placental and fetal tissues and play an important role in fetal development. However, unfavorable intrauterine conditions can cause cytokine activity to be excessive during critical windows of fetal development. Our recent evidence indicates that this impacts developmental programming of muscle growth and metabolism and contributes to the IUGR phenotype. In this review, we outline the role of inflammatory cytokine activity in the development of normal and IUGR phenotypes. We also highlight the contributions of sheep and other animal models in identifying mechanisms for IUGR pathologies.
Antimicrobial Use and Susceptibility of Indicator Escherichia coli in Finnish Integrated Pork Production

In pigs, antimicrobial use (AMU) practices vary at different production phases between herds and between countries. Antimicrobial resistance (AMR) development is linked to AMU but recognized as a multi-factorial issue, and thus, any information increasing knowledge of AMU and AMR relationships is valuable. We described AMU and screened the carriage of different AMR phenotypes of indicator Escherichia coli in 25 selected Finnish piglet-producing and finishing herds that formed nine birth-to-slaughter production lines. Moreover, we studied associations between AMU and AMR in both herd types and throughout the production line. Treatment records were obtained from the national Sikava register for 1year, and AMU was quantified as mg/PCU (population correction unit) and TIs (treatment incidences). For phenotypic antimicrobial susceptibility testing, ten pen-level pooled feces samples (n=250) in each herd were collected from one room representing the oldest weaned piglets or the oldest finishing pigs. Majority of the medications (96.8%) was administered parenterally, and penicillin was the predominant antimicrobial in every herd. More different antimicrobial substances were used in piglet-producing than in finishing herds (median 5 and 1, respectively, p<0.001). As mg/PCU, sows had the highest AMU and suckling piglets had the highest TIs, whereas finishing pigs were the least treated age group. The proportion of susceptible indicator E. coli isolates of all studied isolates was 59.6%. Resistance was found most commonly against tetracycline, sulfamethoxazole, trimethoprim, and ampicillin, and multi-resistant (MR) isolates (46.5% of all resistant isolates) were resistant to a maximum of four different antimicrobials. Quinolone resistance was rare, and no resistance against 3rd-generation cephalosporins, meropenem, azithromycin, colistin, gentamicin, or tigecycline was detected. The main associations between AMU and AMR were found at antimicrobial group level when use was compared with the presence of AMR phenotypes. The proportion of resistant isolates was not associated with AMU, and herd size was not associated with either AMU or AMR. We suggest that the use of narrow-spectrum beta-lactams as a primary treatment option and lack of wide application of oral group medications potentially favors a good resistance pattern in integrated pork production.
Methodological Aspects for Numerical Analysis of Lid Systems for SNF and HLW Transport Packages

The regulatory compliance of the containment system is of essential importance for the design assessment of transport packages for radioactive materials. The requirements of the IAEA transport regulations SSR-6 for accident conditions implies high load on the containment system of Type B(U) packages. The integrity of the containment system has to be ensured under the mechanical and thermal tests.The containment system of German transport packages for spent nuclear fuel (SNF) and high level waste (HLW) usually includes bolted lids with metal gaskets. BAM Federal Institute for Materials Research and Testing as the German competent authority for the mechanical and thermal design assessment of approved transport packages has developed the guideline BAM-GGR 012 for the analysis of bolted lid and trunnion systems. According to this guideline the finite element (FE) method is recommended for the calculations. FE analyses provide more accurate and detailed information about loading and deformation of such kind of structures. The results allow the strength assessment of the lid and bolts as well as the evaluation of relative displacements between the lid and the cask body in the area of the gasket groove.This paper discusses aspects concerning FE simulation of lid systems for SNF and HLW transport packages. The work is based on the experiences of BAM within safety assessment procedures. The issues considered are the assessment methods used in the BAM-GGR 012 for bolted lid systems along with the nominal stress concept which is applied for bolts according to that guideline. Additionally, modeling strategies, analysis techniques and the interpretation of the results are illustrated by the example of a generalized bolted lid systems under selected accident conditions of transport.Copyright © 2014 by ASME
Refinement of the Micro‐Distillation Technique for Isotopic Analysis of Geological Samples with pg‐Level Osmium Contents

In recent years, the 187Re–187Os isotope system has been increasingly used to study samples containing very small quantities of Os. For such samples, optimisation of measurement procedures is essential to minimise the loss of Os before mass spectrometric measurements. Micro‐distillation is a necessary purification step that is applied after the main Os chemical separation procedure, prior to Os isotope ratio measurements by negative‐thermal ionisation mass spectrometry (N‐TIMS). However, unlike the other separation steps, this procedure has not yet been optimised for small samples. In this study, we present a refined micro‐distillation method that achieved higher yields and allowed high‐precision R(187Os/188Os) expressed as 187Os/188Os measurements for small‐sized geological samples that contain only a few pg Os. The Os recovery in the micro‐distillation step was tested by changing the operating conditions including heating time and temperature, and amounts of oxidant and reductant. Recoveries were measured by the isotope dilution ICP‐MS method after the addition of 190Os‐enriched spike solution. We found that the most critical factor controlling the chemical yield of Os during micro‐distillation is the extent of dilution of the reductant (HBr) by H2O evaporated from the oxidant. A refined micro‐distillation method, in which the amount of oxidant solution is reduced from the conventional method, achieved an improved chemical yield of Os (~ 90%). This refined method was applied to the measurement of 187Os/188Os by N‐TIMS of varying test portions of the geological reference material BIR‐1a. The resulting 187Os/188Os ratios of BIR‐1a matched the literature data, with propagated uncertainties of 0.2, 1.1 and 11% digested sample quantities containing 150, 10 and 1 pg of Os, respectively.
Effect Of High And Low Velocity Ballistic Training On Acceleration Speed Among Novice College Athletes

The purpose of the study was to find out the effect of high and low velocity ballistics training on acceleration speed. To achieve this purpose of the study, forty fivemale students studying in department of physical education, Annamalai university, Chidambaram, Tamil Nadu, India, were randomly selected and divided into three groups of fifteen each. The age of the subjects were ranged from 18 to 24 years. This study consisted of two experimental variables (high velocityballistic training (HVBT) and low velocityballistic training (LVBT)). The allotment of these groups was done at random, thus Group-I underwent high velocityballistic training, Group-II underwent low velocityballistic trainingfor three days per week for twelve weeks, Group-III acted as control. All the subjects were tested prior to and after the experimentation period. The collected data were statistically treated by using ANCOVA, and 0.05 level of confidence was fixed to test the significance. When the obtained ‘F’ ratio was significant, Scheffe’s post hoc test was used to find out the paired mean difference. The results of the study revealed that there was a significant difference among high velocityballistic training group, low velocityballistic training group as compared to control group on acceleration speed. And also it was found that there was significant improvement on acceleration speeddue to high velocityballistic training group as comparedto low velocityballistic training group.