Miracle-dz/UniFAR-FTUs huggingface dataset:
Soil application of effective microorganisms and nitrogen alleviates salt stress in hot pepper (Capsicum annum L.) plants

The application of effective microorganisms (EMs) and/or nitrogen (N) have a stimulating effect on plants against abiotic stress conditions. The aim of the present study was to determine the impact of the co-application of EMs and N on growth, physio-biochemical attributes, anatomical structures, nutrients acquisition, capsaicin, protein, and osmoprotectant contents, as well as the antioxidative defense system of hot pepper (Capsicum annum L.) plants. In the field trials, EMs were not applied (EMs-) or applied (EMs+) along with three N rates of 120, 150, and 180 kg unit N ha-1 (designated as N120, N150, and N180, respectively) to hot pepper plants grown in saline soils (9.6 dS m-1). The application of EMs and/or high N levels attenuated the salt-induced damages to hot pepper growth and yield. The application of EMs+ with either N150 or N180 increased the number, average weight and yield of fruits by 14.4 or 17.0%, 20.8 or 20.8% and 28.4 or 27.5%, respectively, compared to hot pepper plants treated with the recommended dose (EMs- × N150). When EMs+ was individually applied or combined with either N150 or N180, increased accumulation of capsaicin were observed by 16.7 or 20.8%, protein by 12.5 or 16.7%, proline by 19.0 or 14.3%, and total soluble sugars by 3.7 or 7.4%, respectively, in comparison with those treated with the integrative EMs- × N150. In addition, the non-enzymatic contents (ascorbate, and glutathione) and enzymatic activities (catalase, superoxide dismutase, and glutathione reductase) of the antioxidant defense systems significantly increased in hot pepper plants treated with EMs+ alone or combined with N150 or N180 under salt stress conditions. Higher accumulation of nutrients (N, P, K+, and Ca2+) along with reduced Na+ acquisition was also evidenced in response to EMs+ or/and high N levels. Most anatomical features of stems and leaves recovered in hot pepper plants grown in saline soils and supplied with EMs+ and N. The application of EMs and N is undoubtedly opening new sustainable approaches toward enhancing abiotic stress tolerance in crops (e.g. hot pepper).
Perturbed actin cap as a new personalized biomarker in primary fibroblasts of Huntington’s disease patients

Primary fibroblasts from patient’s skin biopsies are directly isolated without any alteration in the genome, retaining in culture conditions their endogenous cellular characteristics and biochemical properties. The aim of this study was to identify a distinctive cell phenotype for potential drug evaluation in fibroblasts from Huntington’s Disease (HD) patients, using image-based high content analysis. We show that HD fibroblasts have a distinctive nuclear morphology associated with a nuclear actin cap deficiency. This in turn affects cell motility in a similar manner to fibroblasts from Hutchinson-Gilford progeria syndrome (HGPS) patients used as known actin cap deficient cells. Moreover, treatment of the HD cells with either Latrunculin B, used to disrupt actin cap formation, or the antioxidant agent Mitoquinone, used to improve mitochondrial activity, show expected opposite effects on actin cap associated morphological features and cell motility. Deep data analysis allows strong cluster classification within HD cells according to patients’ disease severity score which is distinct from HGPS and matching controls supporting that actin cap is a biomarker in HD patients’ cells correlated with HD severity status that could be modulated by pharmacological agents as tool for personalized drug evaluation.
Microplastics in mainstem Mississippi River fishes

Microplastics are ubiquitous in Earth’s ecosystems and many efforts have begun to understand their distributions. Large rivers, like the Mississippi River, provide a unique system in which to look at large-scale patterns of microplastic distribution. In this study, we sampled four species of widely-distributed fishes from five sites along the mainstem Mississippi River, from Minnesota to Louisiana, United States. Microplastics were found in all fish species and at all sites; however, microplastics increased in occurrence in the Lower Mississippi River. Fragments were the most common morphologies and polypropylene was the most common polymer detected. We also examined the hypothesis that microplastic loads in fishes increased downstream, but found support for this hypothesis only when examining Largemouth Bass; Flathead Catfish, Shortnose Gar, and Bluegill were all found to have similar microplastic loads along the mainstem Mississippi River. It is clear that microplastics are heterogeneously distributed throughout ecosystems, and further understanding of microplastic distributional patterns and varying species burdens are needed to fully understand threats that microplastics present.
Whole-genome DNA methylome analysis of different developmental stages of the entomopathogenic fungus Beauveria bassiana NCHU-157 by nanopore sequencing

The entomopathogenic fungus (EPF), Beauveria bassiana, is an important and commonly used EPF for microbial control. However, the role of DNA methylation has not been thoroughly studied. Therefore, the whole genomic DNA methylome of one promising EPF isolate, B. bassiana NCHU-157 (Bb-NCHU-157), was investigated by Oxford Nanopore Technologies (ONT). First, the whole genome of Bb-NCHU-157 was sequenced by next-generation sequencing (NGS) and ONT. The genome of Bb-NCHU-157 contains 16 contigs with 34.19 Mb and 50% GC content, which are composed of 10,848 putative protein-coding genes. Two putative DNA methyltransferases (DNMTs) were found, including Dim-2 and C-5 cytosine-specific DNA methylases. Both DNMTs showed higher expression levels in the mycelium stage than in the conidia stage, indicating that development of DNA methylation in Bb-NCHU-157 might occur in the mycelium stage. The global methylation level of the mycelium stage (5 mC = 4.56%, CG = 3.33%, CHG = 0.74%, CHH = 0.49%) was higher than that of the conidial stage (5 mC = 2.99%, CG = 1.99%, CHG = 0.63%, CHH = 0.37%) in both the gene and transposable element (TE) regions. Furthermore, the TE regions showed higher methylation frequencies than the gene regions, especially for CHH site methylation, suggesting regulation of genomic stabilization during mycelium development. In the gene regions, high methylation frequencies were found around the transcription start site (TSS) and transcription end site (TES). Moreover, CG and CHG methylation mainly occur in the promoter and intergenic regions, while CHH methylation occurs in the TE region. Among the methylated regions, 371, 661, and 756 differentially DNA methylated regions (DMRs) were hypermethylated in the mycelium in CG, CHG, and CHH, while only 13 and 7 DMRs were hypomethylated in the mycelium in CHG, and CHH, respectively. Genes located in the DMR shared the GO terms, DNA binding (GO: 0003677), and sequence-specific DNA binding (GO: 0043565) for hypermethylation in the mycelium, suggesting that methylation might regulate gene expression from the initial process. Evaluation of the DNA methylome in Bb-NCHU-157 by ONT provided new insight into this field. These data will be further validated, and epigenetic regulation during the development of B. bassiana will be explored.
Extension of a Compressible Code Toward the Incompressible Limit

Pressure is used as a dependent variable for consistent extension toward incompressible flows. The proposed method exploits the fact that the divergence-free constraint on the velocity field for incompressible flow derives from the energy equation. In the compressible regime the implicit elliptic pressure equation transforms into an explicit hyperbolic equation, leading to the common formulation used in explicit compressible codes. The method strictly respects the strong conservation form, and reliable shock capturing is established by the use of a proven approximate Riemann solver for flux computation
Immune infiltration analysis reveals immune cell signatures in salivary gland tissue of primary Sjögren’s syndrome

Introduction Mouse models are the basis for primary Sjögren’s syndrome (pSS) research. However, the depth of comparisons between mice and humans in salivary gland (SG) immune cells remains limited. Methods The gene expression profiles of SGs from normal subjects and pSS patients were downloaded from the Gene Expression Comprehensive Database. The proportion of infiltrating immune cell subsets was then assessed by cell type identification by estimating relative subsets of RNA transcripts (CIBERSORT). An experimental Sjögren’s syndrome (ESS) mouse model was successfully constructed using SG protein. Based on mouse SG tissue RNA-Seq data, the seq-ImmuCC model was used to quantitatively analyze the compositional ratios of 10 immune cells in pSS patients and mouse model SG tissues. Results Computed and obtained 31 human data samples using the CIBERSORT deconvolution method. The immune cell infiltration results showed that, compared to normal human SG tissue, the content of gamma delta T cells was significantly different from naive CD4+ T cells and significantly increased, while the plasma cell content decreased. Principal component analysis indicated differences in immune cell infiltration between pSS patients and normal subjects. Meanwhile, for ESS model mouse data analysis, we found that the proportion of macrophages increased, while the proportion of CD4+ T cells, B cells, and monocytes decreased. Furthermore, we found that the proportion of monocytes was decreased, while the proportion of macrophages was increased in the SG tissues of pSS patients and model mice. The infiltration of CD4+ T, CD8+ T, and B cells also showed some differences. Discussion We comprehensively analyzed SG immune infiltration in pSS patients and model mice. We demonstrated conserved and nonconserved aspects of the immune system in mice and humans at the level of immune cells to help explain the primary regulation of immune mechanisms during the development of Sjögren’s syndrome.
Structural boundary and deep contact relationship between the Yangtze and Cathaysia Blocks from crustal thickness gradients

The deep boundary and contact relationship between the Yangtze and Cathaysia Blocks (the major tectonic units of the Southern China Block), as well as the tectonic attributes of the Jiangnan Orogenic Belt, have remained unknown or controversial. Using data recorded by 128 portable broadband stations and 96 permanent stations, we obtained high-resolution images of crustal thickness and Poisson’s ratio in the study area. The influences of crustal anisotropy and inclined interface were eliminated by using the newly proposed receiver function H–κ–c stacking method. We then used a gradient analysis method to obtain crustal thickness gradients at the boundary of the Yangtze and Cathaysia Blocks for the first time. Our results reveal that the crustal thickness varies from >38 km in the Qinling–Dabie Orogenic Belt to <30 km east of the Tanlu Fault and Cathaysia Block. Areas with high Poisson’s ratios (>0.27) are concentrated on the flanks of the deep fault zone and the continental margin of the study area; those with low Poisson’s ratios (<0.23) are concentrated in the Jiangnan Orogenic Belt. Large crustal thickness gradients are found beneath the eastern part of the Jiujiang–Shitai buried fault (>5 km/°). Combined with the velocity structure and discontinuity characteristics at different depths, these findings suggest that the Jiujiang–Shitai fault may constitute a deep tectonic boundary dividing the Yangtze and Cathaysia Blocks on the lithospheric scale. Moreover, our results support that the Cathaysia Block subducted northwest-ward toward the southeastern margin of the Yangtze Block in the Neoproterozoic, and that the Jiujiang–Shitai buried fault and Jiangshan–Shaoxing fault are the deep and shallow crustal contact boundaries of the two Blocks, respectively; that is, the Yangtze Block overlaps the Cathaysia Block.
Can public–private partnership investment in energy (PPPI) mitigate CO2 emissions in South Africa? Fresh evidence from the novel dynamic ARDL simulations approach

Global warming presents a worrisome condition that necessitates important actions across the planet. One promising strategy is encouraging investments through public–private partnership investment (PPPI) in green ventures. The Environmental Kuznets Curve (EKC) hypothesis framework is used in the current study to examine the relationship between the aforementioned factor and the level of carbon dioxide (CO2) emissions in South Africa between 1960 and 2020. Using the recently developed novel dynamic autoregressive distributed lag (ARDL) simulations framework, the results showed that (i) public–private partnership investment in energy contribute to deteriorating environmental quality; (ii) while the technique effect (TE) improves environmental quality, the scale effect (SE) largely contributes to escalating CO2 emissions, thus confirming that the EKC hypothesis holds; iii) energy consumption, foreign direct investment, trade openness, and industrial growth escalate CO2 emissions, but technological innovation reduces it; and iv) public–private partnership investment in energy, technological innovation, scale effect, technique effect, foreign direct investment, energy consumption, industrial growth, and trade openness Granger-cause CO2 emissions in the short, medium, and long run, showing that these variables are fundamental to determining environmental quality. Our empirical findings suggest that PPPIs should be accomplished in environmentally friendly sectors and industries, and South Africa’s government and policymakers should take further initiatives to ensure the implementation of policies that enable the change from non-renewable energy sources to renewable ones to promote efficiency in the production processes and curtail CO2 emissions in the country.
The association of the paraoxonase 1 Q192R polymorphism with coronary artery disease (CAD) and cardiometabolic risk factors in Iranian patients suspected of CAD

Introduction The present study aimed to investigate the association of the paraoxonase 1 (PON1) Q192R polymorphism with coronary artery disease (CAD) and cardiometabolic risk factors in Iranian patients suspected of CAD. Methods This cross-sectional study was conducted on 428 patients undergoing angiography. The data related to demographic information and physical activity were collected by valid and reliable questionnaires. The PON-1 genotypes were detected by the polymerase chain reaction-restriction fragment length polymorphism (RFLP-PCR) technique. The Gensini and SYNTAX score, anthropometric measurements, and biochemical and clinical parameters were measured by standard protocols. Results and discussion Findings indicated that the odds of obesity was significantly higher in people with the RR genotype compared to the QQ genotype carriers (OR: 2.95 CI: 1.25–6.93, P = 0.014) and also odds of low high-density lipoprotein cholesterol (HDL-C) was marginally higher (OR: 2.31 CI: 0.97–5.49, P = 0.056). There was no significant association between other CAD risk factors with PON1 Q192R polymorphism (P > 0.05). Further analysis showed a significant interaction between sex and 192QR (P = 0.019) and 192 RR (P = 0.007) genotypes on body mass index (BMI). More specifically, the risk of obesity in men carrying the RR genotype was 3.38 times (OR: 3.38 CI: 1.08–10.58, P = 0.036). Also, a significant joint effect of the RR genotype and sex on HDL-C was seen (P = 0.003). The stratification based on sex showed that the risk of low HDL-C is significantly higher in women carrying the RR genotype (OR: 6.18 CI: 1.21–31.46, P = 0.028). A marginal sex-genotype interaction was also found in the risk of elevated alanine aminotransferase (ALT) (P = 0.057). In summary, the findings showed that the risk of obesity and low HDL-C was higher in people carrying the RR genotype. On the other hand, a Q192R polymorphism-sex interaction was observed on the risk of obesity, elevated ALT, and low HDL-C.
A machine learning approach to quantify gender bias in collaboration practices of mathematicians

Collaboration practices have been shown to be crucial determinants of scientific careers. We examine the effect of gender on coauthorship-based collaboration in mathematics, a discipline in which women continue to be underrepresented, especially in higher academic positions. We focus on two key aspects of scientific collaboration—the number of different coauthors and the number of single authorships. A higher number of coauthors has a positive effect on, e.g., the number of citations and productivity, while single authorships, for example, serve as evidence of scientific maturity and help to send a clear signal of one's proficiency to the community. Using machine learning-based methods, we show that collaboration networks of female mathematicians are slightly larger than those of their male colleagues when potential confounders such as seniority or total number of publications are controlled, while they author significantly fewer papers on their own. This confirms previous descriptive explorations and provides more precise models for the role of gender in collaboration in mathematics.
Specificity of the innate immune responses to different classes of non-tuberculous mycobacteria

Mycobacterium avium is the most common nontuberculous mycobacterium (NTM) species causing infectious disease. Here, we characterized a M. avium infection model in zebrafish larvae, and compared it to M. marinum infection, a model of tuberculosis. M. avium bacteria are efficiently phagocytosed and frequently induce granuloma-like structures in zebrafish larvae. Although macrophages can respond to both mycobacterial infections, their migration speed is faster in infections caused by M. marinum. Tlr2 is conservatively involved in most aspects of the defense against both mycobacterial infections. However, Tlr2 has a function in the migration speed of macrophages and neutrophils to infection sites with M. marinum that is not observed with M. avium. Using RNAseq analysis, we found a distinct transcriptome response in cytokine-cytokine receptor interaction for M. avium and M. marinum infection. In addition, we found differences in gene expression in metabolic pathways, phagosome formation, matrix remodeling, and apoptosis in response to these mycobacterial infections. In conclusion, we characterized a new M. avium infection model in zebrafish that can be further used in studying pathological mechanisms for NTM-caused diseases.
Analysis and Design of Dual Band High Directive EBG Resonator Antenna Using Square Loop FSS as Superstrate Layer

A superstrate layer is used to enhance the directivity of the small radiation sources such as Microstrip Patch Antennas. In this paper, we use square loop frequency selective surface (SLFSS) configuration to design the superstrate layer. To compact the structure, we propose a new single layer square loop FSS configuration that operates in two frequency bands such as multi-layer SL-FSS. Simulation results are shown to have good agreement with experimental results.
Case report: A novel de novo loss of function variant in the DNA-binding domain of TBX2 causes severe osteochondrodysplasia

Background: T-box family members are transcription factors characterized by highly conserved residues corresponding to the DNA-binding domain known as the T-box. TBX2 has been implicated in several developmental processes, such as coordinating cell fate, patterning, and morphogenesis of a wide range of tissues and organs, including lungs, limbs, heart, kidneys, craniofacial structures, and mammary glands. Methods: In the present study, we have clinically and genetically characterized a proband showing a severe form of chondrodysplasia with developmental delay. Whole-exome sequencing (WES), Sanger sequencing, and 3D protein modeling were performed in the present investigation. Results: Whole-exome sequencing revealed a novel nonsense variant (c.529A>T; p.Lys177*; NM_005994.4) in TBX2. 3D-TBX2 protein modeling revealed a substantial reduction of the mutated protein, which might lead to a loss of function (LOF) or nonsense-mediated decay (NMD). Conclusion: This study has not only expanded the mutation spectrum in the gene TBX2 but also facilitated the diagnosis and genetic counseling of related features in affected families.
CFD supported scale up of perfusion bioreactors in biopharma

The robust scale up of perfusion systems requires comparable conditions over all scales to ensure equivalent cell culture performance. As cells in continuous processes circulate outside the bioreactor, performance losses may arise if jet flow and stirring cause a direct connection between perfusion feed and return. Computational fluid dynamics can be used to identify such short circuit flows, assess mixing efficiencies, and eventually adapt the perfusion setup. This study investigates the scale up from a 2 L glass bioreactor to 100 L and 500 L disposable pilot scale systems. Highly resolved Lattice Boltzmann Large Eddy simulations were performed in single phase and mixing efficiencies (Emix) furthermore experimentally validated in the 2 L system. This evaluation gives insight into the flow pattern, the mixing behavior and information on cell residence time inside the bioreactors. No geometric adaptations in the pilot scale systems were necessary as Emix was greater than 90% for all conditions tested. Two different setups were evaluated in 2 L scale where the direction of flow was changed, yielding a difference in mixing efficiency of 10%. Nevertheless, since Emix was confirmed to be >90% also for both 2 L setups and the determined mixing times were in a similar range for all scales, the 2 L system was deemed to be a suitable scale down model. The results demonstrate how computational fluid dynamic models can be used for rational process design of intensified production processes in the biopharmaceutical industry.