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Objectives: To evaluate the efficacy and safety of Janus kinase inhibitors (JAKi) in the treatment of refractory anti-synthetase syndrome (ASS) in real-world clinical settings., Methods: The medical records of all refractory ASS patients who were treated with JAKi from October 2020 to June 2023 were retrospectively reviewed., Results: Twenty patients were included, and all (100 %) patients had interstitial lung disease (ILD). After treatment with JAKi, 14 (70 %) of the refractory ASS patients showed significant improvement in clinical manifestations, including arthritis (56.3 % vs. 6.3 %, p = 0.002), rash (77.8 % vs. 27.8 %, p = 0.012), shortness of breath (55.6 % vs. 16.7 %, p = 0.039), cough (61.1 % vs. 11.1 %, p = 0.012). Improvement was noted for myalgia (50 % vs. 11.1 %, p = 0.016) and muscular weakness (61.1 % vs. 11.1 %, p = 0.012), while creatine kinase (CK) levels, which were abnormally elevated in five patients prior treatment, were significantly lowered (1096 ± 1042.98 IU/L vs. 199.2 ± 144.66 IU/L, p = 0.043). A decrease in levels of inflammatory markers, including erythrocyte sedimentation rate (ESR) (p = 0.001) and C-reactive protein (CRP) (p = 0.023) was observed in the patients. In ASS-ILD, the CT score reduced (188.75 ± 69.67 vs. 156.35 ± 74.62, p = 0.001). Furthermore, the glucocorticoid dose significantly reduced (21.42 ± 13.26 mg vs. 11.32 ± 8.59 mg; p = 0.001)., Conclusions: JAKi were effective in most refractory ASS patients as evidenced by improved skin rash, myositis, and ILD. However, larger prospective controlled studies are required to evaluate its efficacy., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. The author is not an Editorial Board Member/Editor-in-Chief/Associate Editor/Guest Editor for any journal, including [Seminars in Arthritis and Rheumatism] and was not involved in the editorial review or the decision to publish this article.The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: None, (Copyright © 2024. Published by Elsevier Inc.)

The issue of material failure attributed to microbiologically influenced corrosion (MIC) is escalating in seriousness. Microorganisms not only facilitate corrosion but certain beneficial microorganisms also impede its occurrence. This study explored the impact of marine B. velezensis on the corrosion behavior of X65 steel in simulated offshore oilfield produced water. B. velezensis exhibited rapid growth in the initial stages, and the organic acid metabolites were found to promote corrosion. Subsequently, there was an increase in cross-linked "networked" biofilms products, a significant rise in the prismatic shape of corrosion products, and a tendency for continuous development in the middle and late stages. The organic/inorganic mineralized film layer formed on the surface remained consistently complete. Metabolic products of amino acid corrosion inhibitors were also observed to be adsorbed into the film. B. velezensis altered the kinetics of the X65 steel cathodic reaction, resulting in a deceleration of the electrochemical reaction rate. The mineralization induced by B. velezensis effectively slowed down the corrosion rate of X65 steel., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Objective: To investigate the clinical features, severity and prognosis of interstitial lung disease (ILD) in patients with mixed connective tissue disease (MCTD)., Methods: We performed a retrospective study on clinical data of MCTD patients admitted to China-Japan Friendship Hospital between October 2012 and October 2022. Data including long-term follow-up were retrieved from medical records. We compared MCTD patients with and without ILD in terms of clinical features, laboratory and imaging findings, severity and treatment response., Results: A total of 59 patients were included, with a mean age of 46 years, among which 91.5% (n = 54) were females. Symptoms of pulmonary involvement were present in 44 patients (74.6%, 95% CI: 62.3-84.9%). Based on lung high-resolution computed tomography (HRCT), ILD was diagnosed in 39 (66.1%) patients, among which 31 (79.5%) showed nonspecific interstitial pneumonia (NSIP) as the radiological pattern, 21 (53.9%) showed a reticulation pattern, while 24 (61.5%) showed ground glass opacity (GGO). Eight (13.6%) patients had pulmonary arterial hypertension (PAH), and 7 (11.9%) had pleural effusions. Based on pulmonary function tests (PFTs), 27 patients were divided into the mild 13 (48.1%) and moderate 14 (51.9%) groups. Multivariate analysis showed that gastroesophageal reflux (GER; OR=5.28, p=0.010) and cough (OR=4.61, p=0.043) were the predictive factors for ILD. With a median follow-up of 50 months, the mortality rate was 2.38%., Conclusion: ILD is common in MCTD patients, with NSIP as the common imaging pattern. Patients with GER and cough are relevant factors in the development of ILD. The majority of MCTD patients with ILD are mild to moderate in severity., Competing Interests: The authors declare that they have no competing interests in this work., (© 2024 Shan and Ge.)

Background: Macrophage activation syndrome (MAS) is a severe and life-threatening syndrome associated with autoimmune diseases. The coexistence of MAS and juvenile dermatomyositis (JDM) is not well reported. This report describes a case of JDM with MAS and summarizes the clinical characteristics and prognosis of MAS in patients with JDM., Case Presentation: The patient was a 15-year-old female with JDM, presenting with heliotrope rash, muscle weakness, increased muscle enzyme, anti-nuclear matrix protein 2 (NXP2) antibody, and muscle biopsy consistent with JDM. The patient developed fever, cytopenia, and hyperferritinemia three months after the first manifestations. Hemophagocytosis was found in the bone marrow. The final diagnosis was JDM combined with MAS. Despite intensive treatment, the patient died of MAS. By reviewing the literature, we found 17 similar cases. Together with the present case, 18 patients were identified, the median age of disease onset was 13.5 years, and male to female ratio was 1.25: 1. Nine out of 16 (56.3%) patients were complicated with interstitial lung disease (ILD). The median time interval between JDM onset and MAS diagnosis was 9 weeks. At the onset of MAS, all (100%) patients had elevated levels of ferritin and serum liver enzymes. Among 18 patients, 14 (77.8%) had fever, 14/17 (82.4%) had cytopenia, 11/11 (100%) had hepatosplenomegaly, and 13/14 (92.9%) had hemophagocytosis. Five (27.8%) patients showed central nervous system (CNS) involvement. The mortality of MAS rate of in patients with JDM was 16.7%, despite various treatment methods., Conclusion: . The coexistence of JDM and MAS is underestimated with increased mortality. Hepatosplenomegaly and increased serum levels of ferritin in patients with JDM should raise clinical suspicion for MAS., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is widely used in proteomics studies. Hundreds of proteins extracted from a biological sample can be separated and visualized on a 2D-PAGE gel. The interpretation of protein expression levels relies on the comparison of areas and intensities of the corresponding protein spots in 2D-PAGE gel images. However, determination of protein spot areas by the manual selection method is time-consuming and error-prone. The purpose of this research is to develop a highly automated program for the simultaneous detection and quantification of protein spots across a large number of 2D-PAGE protein gel images by using MATLAB image processing toolbox. This program will enhance the potential of using 2D-PAGE technique as a high throughput quantitative protein expression study tool. We developed MatGel, a simple and efficient program for protein spot area detection and intensity quantification from 2D-PAGE protein gel images. MatGel can detect and output the areas and mean intensities of corresponding protein spots across a large number of 2D-PAGE gel images simultaneously. Users also have options to adjust preferences at each step of image analysis. Basic knowledge with MATLAB programming language is required to run the program.•We developed MATLAB program MatGel to automate the determination of protein spots on 2D-PAGE protein gel images.•MatGel can analyze a large number of 2D-PAGE gel images simultaneously to minimize human errors.•MatGel is flexible and easy to use., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)

The roles of signaling pathway genes related to the aflatoxin reduction trait in maize were studied for the improvement of maize resistance to the fungal pathogen Aspergillus flavus ( A. flavus ). In this study, 55 maize genes in plant-pathogen interaction signaling pathways were investigated among 12 maize near-isogenic lines (NILs) that carry maize quantitative trait loci (QTL) associated with aflatoxin reduction. These maize NILs were developed from maize inbred lines Mp313E (resistant donor parent) and Va35 (susceptible recurrent parent). The quantitative RT-PCR (qRT-PCR) technique was used to study the gene expression patterns. Seven calcium-dependent protein kinases and one respiratory burst oxidase displayed significant differential expression levels among the maize QTL-NILs. In addition, the gene expression profiles of WRKY transcription factors were also examined. Maize WRKY 52, WRKY 71, and WRKY83 genes displayed significantly differential expression levels among the QTL-NILs. The elucidation of differentially expressed signaling pathway genes involving maize resistance to A. flavus can provide insights into maize disease resistance and enhance maize molecular breeding., (Copyright © 2019 Parish, Williams, Windham and Shan.)

p-type ternary oxides can be extensively explored as alternative sensing channels to binary oxides with diverse structural and compositional versatilities. Seeking a novel approach to magnify their sensitivities toward gas molecules, e.g., volatile organic compounds (VOCs), will definitely expand their applications in the frontier area of healthcare and air-quality monitoring. In this work, delafossite CuCrO 2 (CCO) nanoparticles with different grain sizes have been utilized as p-type ternary oxide sensors. It was found that singly ionized oxygen vacancies (V o • ) defects, compared with the grain size of CCO nanoparticles, play an important role in enhancing the charge exchange at the VOCs molecules/CCO interface. In addition to suppressing the hole concentration of the sensor channel, the unpaired electron trapped in V o • provides an active site for chemisorptions of environmental oxygen and VOCs molecules. The synergetic effect is responsible for the observed increase of sensitivity. Furthermore, the sensitive (V o • defect-rich) CCO sensor exhibits good reproducibility and stability under a moderate operation temperature (<325 °C). Our work highlights that V o • defects, created via either in situ synthesis or postannealing treatment, could be explored to rationally boost the performance of p-type ternary oxide sensors.

Antimicrobial peptides (AMPs) are small defense proteins present in various organisms. Major groups of AMPs include beta-barrelin, hevein, knottin, lipid transfer protein (LTP), thionin, defensin, snakin, and cyclotide. Most plant AMPs involve host plant resistance to pathogens such as fungi, viruses, and bacteria, whereas a few plant AMPs from the cyclotide family carry insecticidal functions. In this research, a genome-wide investigation on antimicrobial peptide genes in maize genome was conducted. AMPs previously identified from various plant species were used as query sequences for maize genome data mining. Thirty-nine new maize AMPs were identified in addition to seven known maize AMPs. Protein sequence analysis revealed 10 distinguishable maize AMP groups. Analysis of mRNA expression of maize AMP genes by quantitative real-time polymerase chain reaction (qRT-PCR) revealed different expression patterns in a panel of 10 maize inbred lines. Five maize AMP genes were found significantly associated with insect or fungus resistance. Identification of maize antimicrobial peptide genes will facilitate the breeding of host plant resistance and improve maize production., Competing Interests: The authors declare no conflict of interest.

The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

Aflatoxins are carcinogenic mycotoxins produced by some species in the Aspergillus genus, such as A. flavus and A. parasiticus. Contamination of aflatoxins in corn profusely happens at pre-harvest stage when heat and drought field conditions favor A. flavus colonization. Commercial corn hybrids are generally susceptible to A. flavus infection. An ideal strategy for preventing aflatoxin contamination is through the enhancement of corn host resistance to Aspergillus infection and aflatoxin production. Constant efforts have been made by corn breeders to develop resistant corn genotypes. Significantly low levels of aflatoxin accumulation have been determined in certain resistant corn inbred lines. A number of reports of quantitative trait loci have provided compelling evidence supporting the quantitative trait genetic basis of corn host resistance to aflatoxin accumulation. Important findings have also been obtained from the investigation on candidate resistance genes through transcriptomics approach. Elucidation of molecular mechanisms will provide in-depth understanding of the host-pathogen interactions and hence facilitate the breeding of corn with resistance to A. flavus infection and aflatoxin accumulation.

Aspergillus flavus is a pathogenic fungus infecting maize and producing aflatoxins that are health hazards to humans and animals. Characterizing host defense mechanism and prioritizing candidate resistance genes are important to the development of resistant maize germplasm. We investigated methods amenable for the analysis of the significance and relations among maize candidate genes based on the empirical gene expression data obtained by RT-qPCR technique from maize inbred lines. We optimized a pipeline of analysis tools chosen from various programs to provide rigorous statistical analysis and state of the art data visualization. A network-based method was also explored to construct the empirical gene expression relational structures. Maize genes at the centers in the network were considered as important candidate genes for maize DNA marker studies. The methods in this research can be used to analyze large RT-qPCR datasets and establish complex empirical gene relational structures across multiple experimental conditions.

Background: Aspergillus flavus infection and aflatoxin contamination of maize pose negative impacts in agriculture and health. Commercial maize hybrids are generally susceptible to this fungus. Significant levels of host plant resistance have been observed in certain maize inbred lines. This study was conducted to identify maize genes associated with host plant resistance or susceptibility to A. flavus infection and aflatoxin accumulation., Results: Genome wide gene expression levels with or without A. flavus inoculation were compared in two resistant maize inbred lines (Mp313E and Mp04:86) in contrast to two susceptible maize inbred lines (Va35 and B73) by microarray analysis. Principal component analysis (PCA) was used to find genes contributing to the larger variances associated with the resistant or susceptible maize inbred lines. The significance levels of gene expression were determined by using SAS and LIMMA programs. Fifty candidate genes were selected and further investigated by quantitative RT-PCR (qRT-PCR) in a time-course study on Mp313E and Va35. Sixteen of the candidate genes were found to be highly expressed in Mp313E and fifteen in Va35. Out of the 31 highly expressed genes, eight were mapped to seven previously identified quantitative trait locus (QTL) regions. A gene encoding glycine-rich RNA binding protein 2 was found to be associated with the host hypersensitivity and susceptibility in Va35. A nuclear pore complex protein YUP85-like gene was found to be involved in the host resistance in Mp313E., Conclusion: Maize genes associated with host plant resistance or susceptibility were identified by a combination of microarray analysis, qRT-PCR analysis, and QTL mapping methods. Our findings suggest that multiple mechanisms are involved in maize host plant defense systems in response to Aspergillus flavus infection and aflatoxin accumulation. These findings will be important in identification of DNA markers for breeding maize lines resistant to aflatoxin accumulation.

A public candidate gene testing pipeline for resistance to aflatoxin accumulation or Aspergillus flavus infection in maize is presented here. The pipeline consists of steps for identifying, testing, and verifying the association of selected maize gene sequences with resistance under field conditions. Resources include a database of genetic and protein sequences associated with the reduction in aflatoxin contamination from previous studies; eight diverse inbred maize lines for polymorphism identification within any maize gene sequence; four Quantitative Trait Loci (QTL) mapping populations and one association mapping panel, all phenotyped for aflatoxin accumulation resistance and associated phenotypes; and capacity for Insertion/Deletion (InDel) and SNP genotyping in the population(s) for mapping. To date, ten genes have been identified as possible candidate genes and put through the candidate gene testing pipeline, and results are presented here to demonstrate the utility of the pipeline.

Background: Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian., Results: The C. porosus BAC library consists of 101,760 individually archived clones stored in 384-well microtiter plates. NotI digestion of random clones indicates an average insert size of 102 kb. Based on a genome size estimate of 2778 Mb, the library affords 3.7 fold (3.7x) coverage of the C. porosus genome. To investigate the utility of the library in studying sequence distribution, probes derived from CR1a and CR1b, two crocodilian CR1-like retrotransposon subfamilies, were hybridized to C. porosus macroarrays. The results indicate that there are a minimum of 20,000 CR1a/b elements in C. porosus and that their distribution throughout the genome is decidedly non-random. To demonstrate the utility of the library in gene isolation, we probed the C. porosus macroarrays with an overgo designed from a C-mos (oocyte maturation factor) partial cDNA. A BAC containing C-mos was identified and the C-mos locus was sequenced. Nucleotide and amino acid sequence alignment of the C. porosus C-mos coding sequence with avian and reptilian C-mos orthologs reveals greater sequence similarity between C. porosus and birds (specifically chicken and zebra finch) than between C. porosus and squamates (green anole)., Conclusion: We have demonstrated the utility of the Crocodylus porosus BAC library as a tool in genomics research. The BAC library should expedite complete genome sequencing of C. porosus and facilitate detailed analysis of genome evolution within Crocodylia and between crocodilians and diverse amniote lineages including birds, mammals, and other non-avian reptiles.