bluuebunny/crossref_metadata_2025 huggingface dataset:
Mining candidate genes for rice cadmium accumulation in the shoot through a genome-wide association study and transcriptomic analysis
Authors: Wang Jian , Yang Wu , Zhang Shaohong , Dong Jingfang , Yang Tifeng , Ma Yamei , Zhou Lian , Chen Jiansong , Liu Bin , Zhao Junliang
Published: August 2022

High cadmium (Cd) accumulation in rice is a serious threat to human health. The genetic mechanism of Cd accumulation in rice is highly complicated. To identify the low Cd accumulation in rice germplasm, investigate the genetic mechanism underlying Cd accumulation, and mine the elite genes of significant importance for rice breeding of low Cd accumulation varieties, we performed a genome-wide association study (GWAS) for rice Cd concentration in the shoot. The rice accessions were 315 diverse indica rice accessions selected from the 1568 rice accessions with 700,000 SNPs. Within the high rate of linkage disequilibrium (LD) decay, eight QTLs related to rice Cd accumulation were identified. Transcriptomic analysis showed there were 799 differentially expressed genes (DEGs) in the root and 857 DEGs in the shoot, which are probably considered to be the cause of the significant difference in Cd accumulation between high and low Cd accumulation varieties. In qCd11-1, we detected a crucial candidate gene, LOC_Os11g11050, which encodes an initiation factor, expressed differently in the root between the high and low Cd accumulation varieties. Furthermore, under Cd treatment, the expression levels of LOC_Os11g11050 significantly decreased in both the high and low Cd accumulation varieties. Sequence comparison and qRT-PCR revealed that there were indel sequences and base substitutions in the promoter region of LOC_Os11g11050 correlated with the LOC_Os11g11050 expression level, as well as the phenotype of Cd concentration differences in shoot between the high and low Cd accumulation accessions. LOC_Os11g11050 might play important roles in Cd accumulation. The results of our study provide valuable resources for low Cd accumulation in indica varieties and the candidate functional gene, as well as molecular mechanisms for Cd accumulation in indica rice. The genetic architecture underlying Cd accumulation in indica can be used for further applying the low Cd gene existing in indica for decreasing Cd accumulation in rice.
Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome
Authors: Rabapane Kgodiso J. , Ijoma Grace N. , Matambo Tonderayi S.
Published: August 2022

Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.
Molecular mediators of the association between child obesity and mental health
Authors: Handakas Evangelos , Xu Yiwen , Segal Alexa Blair , Huerta Maria Carmen , Bowman Kirsty , Howe Laura D. , Sassi Franco , Robinson Oliver
Published: August 2022

Biological mechanisms underlying the association between obesity and depression remain unclear. We investigated the role of metabolites and DNA methylation as mediators of the relationship between childhood obesity and subsequent poor mental health in the English Avon Longitudinal Study of Parents and Children. Obesity was defined according to United Kingdom Growth charts at age 7 years and mental health through the Short Mood and Feelings Questionnaire (SMFQ) completed at age 11 years. Metabolites and DNA methylation were measured by nuclear magnetic resonance spectroscopy and Illumina array in blood at the age of 7 years. The associations between obesity and SMFQ score, as continuous count data or using cut-offs to define depressive symptoms (SMFQ >7) or depression (SMFQ >11), were tested using adjusted Poisson and logistic regression. Candidate metabolite mediators were identified through metabolome-wide association scans for obesity and SMFQ score, correcting for false-discovery rate. Candidate DNA methylation mediators were identified through testing the association of putative BMI-associated CpG sites with SMFQ scores, correcting for look-up false-discovery rate. Mediation by candidate molecular markers was tested. Two-sample Mendelian randomization (MR) analyses were additionally applied to test causal associations of metabolites with depression in independent adult samples. 4,018 and 768 children were included for metabolomics and epigenetics analyses, respectively. Obesity at 7 years was associated with a 14% increase in SMFQ score (95% CI: 1.04, 1.25) and greater odds of depression (OR: 1.46 (95% CI: 0.78, 2.38) at 11 years. Natural indirect effects (mediating pathways) between obesity and depression for tyrosine, leucine and conjugated linoleic acid were 1.06 (95% CI: 1.00, 1.13, proportion mediated (PM): 15%), 1.04 (95% CI: 0.99, 1.10, PM: 9.6%) and 1.06 (95% CI: 1.00, 1.12, PM: 13.9%) respectively. In MR analysis, one unit increase in tyrosine was associated with 0.13 higher log odds of depression (p = 0.1). Methylation at cg17128312, located in the FBXW9 gene, had a natural indirect effect of 1.05 (95% CI: 1.01,1.13, PM: 27%) as a mediator of obesity and SMFQ score. Potential biologically plausible mechanisms involving these identified molecular features include neurotransmitter regulation, inflammation, and gut microbiome modulation. These results require replication in further observational and mechanistic studies.
Identifying hub genes and miRNAs in Crohn’s disease by bioinformatics analysis
Authors: Sun Yuxin , Cai Daxing , Hu Weitao , Fang Taiyong
Published: August 2022

Introduction:Crohn’s disease (CD) is a disease that manifests mainly as chronic inflammation of the gastrointestinal tract, which is still not well understood in terms of its pathogenesis. The aim of this study was to use bioinformatics analysis to identify differentially expressed genes (DEGs) and miRNAs with diagnostic and therapeutic potential in CD.

Materials and methods:Three CD datasets (GSE179285, GSE102133, GSE75214) were downloaded from the Gene Expression Omnibus (GEO) database. DEGs between normal and CD tissues were identified using the GEO2R online tool. The Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs were conducted using the clusterProfiler function in the R package. Protein-protein interaction network (PPI) analysis and visualization were performed with STRING and Cytoscape. Ten hub genes were identified using cytoHubba’s MCC algorithm and validated with datasets GSE6731 and GSE52746. Finally, the miRNA gene regulatory network was constructed by Cytoscape and NetworkAnalyst to predict potential microRNAs (miRNAs) associated with DEGs.

Results:A total of 97 DEGs were identified, consisting of 88 downregulated genes and 9 upregulated genes. The enriched functions and pathways of the DEGs include immune system process, response to stress, response to cytokine and extracellular region. KEGG pathway analysis indicates that the genes were significantly enriched in Cytokine-cytokine receptor interaction, IL-17 signaling pathway, Rheumatoid arthritis and TNF signaling pathway. In combination with the results of the protein-protein interaction (PPI) network and CytoHubba, 10 hub genes including IL1B, CXCL8, CXCL10, CXCL1, CXCL2, CXCL5, ICAM1, IL1RN, TIMP1 and MMP3 were selected. Based on the DEG-miRNAs network construction, 5 miRNAs including hsa-mir-21-5p, hsa-mir-93-5p, hsa-mir-98-5p, hsa-mir-1-3p and hsa-mir-335-5p were identified as potential critical miRNAs.

Conclusion:In conclusion, a total of 97 DEGs, 10 hub genes and 5 miRNAs that may be involved in the progression or occurrence of CD were identified in this study, which could be regarded as biomarkers of CD.
Peroxidase is a novel potential marker in glioblastoma through bioinformatics method and experimental validation
Authors: Shi Weiwei , Ding Wenjie , Zhao Zixuan , Wang Rui , Wang Fengxu , Tang Yanfen , Zhu Jinfeng , Su Chengcheng , Zhao Xinyuan , Liu Lei
Published: August 2022

Peroxidase (PXDN), a specific extracellular matrix (ECM)-associated protein, has been determined as a tumor indicator and therapeutic target in various tumors. However, the effects of PXDN in prognostic performance and clinical implications in glioblastoma multiforme (GBM) remains unknown. Here, we assessed PXDN expression pattern and its performance on prognosis among GBM cases from TCGA and CGGA databases. PXDN was up-regulated within GBM samples in comparison with normal control. High PXDN expression was a dismal prognostic indicator in GBM. Single cell RNA analysis was conducted to detect the cell localization of PXDN. We also set up a PPI network to explore the interacting protein associated with PXDN, including TSKU, COL4A1 and COL5A1. Consistently, functional enrichment analysis revealed that several cancer hallmarks were enriched in the GBM cases with high PXDN expression, such as epithelial-mesenchymal transition (EMT), fatty acid metabolism, glycolysis, hypoxia, inflammatory response, and Wnt/beta-catenin signaling pathway. Next, this study analyzed the association of PXDN expression and immunocyte infiltration. PXDN expression was in direct proportion to the infiltrating degrees of NK cells resting, T cells regulatory, M0 macrophage, monocytes and eosinophils. The roles of PXDN on immunity were further estimated by PXDN-associated immunomodulators. In addition, four prognosis-related lncRNAs co-expressed with PXDN were identified. Finally, we observed that PXDN depletion inhibits GBM cell proliferation and migration by in vitro experiments. Our data suggested that PXDN has the potential to be a powerful prognostic biomarker, which might offer a basis for developing therapeutic targets for GBM.
Cellular senescence is a key mediator of lung aging and susceptibility to infection
Authors: Torrance Blake L. , Haynes Laura
Published: August 2022

Aging results in systemic changes that leave older adults at much higher risk for adverse outcomes following respiratory infections. Much work has been done over the years to characterize and describe the varied changes that occur with aging from the molecular/cellular up to the organismal level. In recent years, the systemic accumulation of senescent cells has emerged as a key mediator of many age-related declines and diseases of aging. Many of these age-related changes can impair the normal function of the respiratory system and its capability to respond appropriately to potential pathogens that are encountered daily. In this review, we aim to establish the effects of cellular senescence on the disruption of normal lung function with aging and describe how these effects compound to leave an aged respiratory system at great risk when exposed to a pathogen. We will also discuss the role cellular senescence may play in the inability of most vaccines to confer protection against respiratory infections when administered to older adults. We posit that cellular senescence may be the point of convergence of many age-related immunological declines. Enhanced investigation into this area could provide much needed insight to understand the aging immune system and how to effectively ameliorate responses to pathogens that continue to disproportionately harm this vulnerable population.
Orange-derived and dexamethasone-encapsulated extracellular vesicles reduced proteinuria and alleviated pathological lesions in IgA nephropathy by targeting intestinal lymphocytes
Authors: Zhang Wang , Yuan Ye , Li Xiang , Luo Jiao , Zhou Zhanmei , Yu Lei , Wang Guobao
Published: August 2022

Current evidence highlights the critical role of the gut-kidney axis in the pathogenesis of IgA nephropathy (IgAN). However, few attempts have been made to explore targeted intestinal immunity therapy. This research aims to develop an oral intestine targeting medication based on extracellular vesicles (EVs) and investigate its therapeutic efficacy in IgAN. EVs were isolated from orange juice and electroporated with dexamethasone sodium phosphate (DexP). After oral administration, EVs-DexP was picked up by lymphocytes in the submucosal area of ileocecum. EVs-DexP outperformed DexP not only in suppressing lymphocyte stimulation in vitro but also in alleviating renal pathological lesions in the IgAN mouse model. Clinical improvement was accompanied by a reducing IgA secreted by the intestine and a decreasing IgA + B220 + lymphocytes in Peyer’s patches. The present study develops a cost-effective, biofriendly EVs-based glucocorticoid strategy for IgAN.
Significant difference in Th1/Th2 paradigm induced by tuberculosis-specific antigens between IGRA-positive and IGRA-negative patients
Authors: Li Qiang , Ren Weicong , Yuan Jinfeng , Guo Haiping , Shang Yuanyuan , Wang Wei , Pan Junhua , Gao Mengqiu , Pang Yu
Published: August 2022

False negative interferon-γ release assay (IGRA) results constitute the major dilemma for the diagnosis of tuberculosis (TB) infections. Herein, we conducted a cohort study to compare the host immunological response to TB-specific antigens between active TB patients with positive and negative IGRA results and control groups. A total of 274 laboratory-confirmed TB patients were included in our analysis, consisting of 221 were IGRA positive and 53 were IGRA negative. Patients with the elderly were identified as an independent risk factor for negative IGRA results. In addition, the elevated level of IL-4 and the decreased levels of IFN-γ, IL-2, IL-6, IL-1β, and IL-12 in IGRA negative TB relative to IGRA positive TB group, demonstrating a significant difference in Th1/Th2 paradigm between two groups. The IFN-γ&IL-2 based assay could correctly identify 247 out of 307 MTB-infected individuals [271 TB patients and 36 individuals with latent TB infection (LTBI)], demonstrating a sensitivity of 80.5%. Then the IFN-γ and IL-4 were applied to distinguish healthy control and IGRA-negative group. When using the stepwise algorithm, the sensitivity for detecting Mycobacterium tuberculosis (MTB) infections was significantly increased from 80.5% to 89.6%. Additionally, patients with negative IGRA results had a conversion to culture-negative status longer than those with positive IGRA results. In conclusion, a stepwise algorithm outperforms IGRA assays to accurately identify MTB infections by the combination IFN-γ, IL-2, and IL-4. Further study is needed to evaluate the accuracy of our diagnostic algorithm in the LTBI population.
Cryoablation reshapes the immune microenvironment in the distal tumor and enhances the anti-tumor immunity
Authors: Wu Ying , Cao Fei , Zhou Danyang , Chen Shuanggang , Qi Han , Huang Tao , Tan Hongtong , Shen Lujun , Fan Weijun
Published: August 2022

As one of the local treatments, cryoablation plays an increasingly important role in the comprehensive treatment of malignant tumors with its advantages of less trauma, high reproducibility, and minimally invasive. Activation of anti-tumor immunity, another characteristic of cryoablation, has attracted more and more attention with the extensive application of immunotherapy. Unfortunately, the mechanism by which cryoablation enhances anti-tumor immunity is still unclear. In this study, we applied a multi-omics approach to investigate the effects of local cryoablation in the distal tumor microenvironment. The results revealed that large amounts of tumor antigens were released post-cryoablation, leading to a sterile inflammatory response in distant tumors. During this period, activated lysosome-related pathways result in over-expression of SNAP23 (Synaptosome associated protein 23) and STXBP2 (Syntaxin binding protein 2), activation of immune effector cells, suppression of the release of immunosuppressive factors, and finally enhancement of anti-tumor immunity, which shows a broad prospect in combined immunotherapy.
Comparative immunogenicity analysis of intradermal versus intramuscular immunization with a recombinant human adenovirus type 5 vaccine against Ebola virus
Authors: Zhang Zhe , Zhao ZhengHao , Wang Yudong , Wu Shipo , Wang Busen , Zhang Jinlong , Song Xiaohong , Chen Yi , Lv Peng , Hou Lihua
Published: August 2022

The proper route for vaccine delivery plays an important role in activating a robust immune response. Several viral vector-based vaccines against Ebola disease administered intramuscularly have been found to have excellent immunogenicity and protectiveness. In this study, we evaluated different vaccine routes for Ad5-EBOV delivery by comparing humoral and cellular responses, germinal center reactions, dendritic cell activation and antigen expression. Mice injected intramuscularly with the vaccine exhibited an advantage in antigen expression, leading to more robust germinal center and humoral responses, while intradermal injection recruited more migrating DCs and induced a more polyfunctional cellular response. Our study provides more data for future use of viral vector-based vaccines.
Efficacy of metal nanoparticles as a control tool against adult mosquito vectors: A review
Authors: Blore Kai , Baldwin Rebecca , Batich Christopher D. , Koehler Phillip , Pereira Roberto , Jack Cameron J. , Qualls Whitney A. , Xue Rui-De
Published: August 2022

Presently, there is a need to develop effective and novel modes of control for mosquitoes, which remain a key driver of infectious disease transmission throughout the world. Control methods for these vectors have historically relied on a limited number of active ingredients (AIs) that have not experienced significant change in usage since the mid-20th century. The resulting development of widespread insecticide resistance has consequently increased the risk for future vector-borne disease outbreaks. Recently, metal nanoparticles have been explored for potential use in mosquito control due to their demonstrated toxicity against mosquitoes at all life stages. However, the majority of studies to date have focused on the larvicidal efficacy of metal nanoparticles with few studies examining their adulticidal potential. In this review, we analyze the current literature on green synthesized metal nanoparticles and their effect on adult mosquitoes.
STAT3 mutations in “gray-zone” cases of T-cell large granular lymphocytic leukemia associated with autoimmune rheumatic diseases
Authors: Gorodetskiy Vadim , Sidorova Yulia , Biderman Bella , Kupryshina Natalia , Ryzhikova Natalya , Sudarikov Andrey
Published: August 2022

A persistently increased T-cell large granular lymphocyte (T-LGL) count in the blood of more than 2 × 109/L for at least 6 months is necessary for a reliable diagnosis of T-LGL leukemia. In cases with LGL counts of approximately 0.5–2 × 109/L, a diagnosis of T-LGL leukemia can be made if clonal rearrangement of T-cell receptor (TCR) genes is present and if the patient shows typical manifestations of T-LGL leukemia, such as cytopenia, splenomegaly, or concomitant autoimmune disease. However, in cases with LGL counts of less than 0.5 × 109/L, the diagnosis of T-LGL leukemia is questionable (termed as “gray-zone” cases). Although mutations in signal transducer and activator of transcription 3 (STAT3) gene are the molecular hallmark of T-LGL leukemia, their diagnostic value in the “gray-zone” cases of T-LGL leukemia has not been evaluated – our study has been aimed to examine the prevalence of STAT3 mutations in these cases. Herein, we describe 25 patients with autoimmune rheumatic diseases, neutropenia, clonal rearrangement of TCR genes, and circulating LGL count of less than 0.5 × 109/L. Splenomegaly was observed in 19 (76%) patients. Mutations in the STAT3 were detected in 56% of patients using next-generation sequencing. Importantly, in 3 patients, no involvement of the blood and bone marrow by malignant LGLs was noted, but examination of splenic tissue revealed infiltration by clonal cytotoxic T-lymphocytes within the red pulp, with greater prominence in the cords. We suggest using the term “splenic variant of T-LGL leukemia” for such cases.
Effect of low-dose dexmedetomidine on sleep quality in postoperative patients with mechanical ventilation in the intensive care unit: A pilot randomized trial
Authors: Sun Yue-Ming , Zhu Sai-Nan , Zhang Cheng , Li Shuang-Ling , Wang Dong-Xin
Published: August 2022

Background

Sleep disturbances are prevalent in patients requiring invasive mechanical ventilation in the intensive care unit (ICU) and are associated with worse outcomes. Sedative-dose dexmedetomidine may improve sleep quality in this patient population but is associated with adverse events. Herein, we tested the effect of low-dose dexmedetomidine infusion on nighttime sleep quality in postoperative ICU patients with invasive ventilation.

Methods

In this pilot randomized trial, 80 adult patients who were admitted to the ICU after non-cardiac surgery and required invasive mechanical ventilation were randomized to receive either low-dose dexmedetomidine (0.1 to 0.2 μg/kg/h, n = 40) or placebo (n = 40) for up to 72 h. The primary endpoint was overall subjective sleep quality measured using the Richards–Campbell Sleep Questionnaire (score ranges from 0 to 100, with a higher score indicating better quality) in the night of surgery. Secondary outcomes included sleep structure parameters monitored with polysomnography from 9:00 PM on the day of surgery to the next 6:00 AM.

Results

All 80 patients were included in the intention-to-treat analysis. The overall subjective sleep quality was median 52 (interquartile 20, 66) with placebo vs. 61 (27, 79) with dexmedetomidine, and the difference was not statistically significant (median difference 8; 95% CI: −2, 22; P = 0.120). Among 68 patients included in sleep structure analysis, those in the dexmedetomidine group tended to have longer total sleep time [median difference 54 min (95% CI: −4, 120); P = 0.061], higher sleep efficiency [median difference 10.0% (95% CI: −0.8%, 22.3%); P = 0.060], lower percentage of stage N1 sleep [median difference −3.9% (95% CI: −11.8%, 0.5%); P = 0.090], higher percentage of stage N3 sleep [median difference 0.0% (95% CI: 0.0%, 0.4%); P = 0.057], and lower arousal index [median difference −0.9 (95% CI −2.2, 0.1); P = 0.091] but not statistically significant. There were no differences between the two groups regarding the incidence of adverse events.

Conclusion

Among patients admitted to the ICU after surgery with intubation and mechanical ventilation, low-dose dexmedetomidine infusion did not significantly improve the sleep quality pattern, although there were trends of improvement. Our findings support the conduct of a large randomized trial to investigate the effect of low-dose dexmedetomidine in this patient population.

Clinical trial registration

ClinicalTrial.gov, identifier: NCT03335527.
Third dose of anti-SARS-CoV-2 inactivated vaccine for patients with RA: Focusing on immunogenicity and effects of RA drugs
Authors: Zhao Ting , Wang Bo , Shen Jiayan , Wei Yuanyuan , Zhu Youyang , Tian Xiaofang , Wen Guangfen , Xu Bonan , Fu Chenyang , Xie Zhaohu , Xi Yujiang , Li Zhenmin , Peng Jiangyun , Wu Yang , Tang Xiaohu , Wan Chunping , Pan Lei , Zhu Wenxin , Li Zhaofu , Qin Dongdong
Published: August 2022

Objectives

To evaluate the immunogenicity of the third dose of inactivated SARS-CoV-2 vaccine in rheumatoid arthritis (RA) patients and explore the effect of RA drugs on vaccine immunogenicity.

Methods

We recruited RA patients (n = 222) and healthy controls (HC, n = 177) who had been injected with a third dose of inactivated SARS-CoV-2 vaccine, and their neutralizing antibody (NAb) titer levels were assessed.

Results

RA patients and HC were age- and gender-matched, and the mean interval between 3rd vaccination and sampling was comparable. The NAb titers were significantly lower in RA patients after the third immunization compared with HC. The positive rate of NAb in HC group was 90.4%, while that in RA patients was 80.18%, and the difference was significant. Furthermore, comparison of NAb titers between RA treatment subgroups and HC showed that the patients in the conventional synthetic (cs) disease-modifying anti-rheumatic drugs (DMARDs) group exhibited no significant change in NAb titers, while in those receiving the treatment of biological DMARDs (bDMARDs), Janus Kinase (JAK) inhibitors, and prednisone, the NAb titers were significantly lower. Spearman correlation analysis revealed that NAb responses to SARS-CoV-2 in HC did differ significantly according to the interval between 3rd vaccination and sampling, but this finding was not observed in RA patients. In addition, NAb titers were not significantly correlated with RA-related laboratory indicators, including RF-IgA, RF-IgG, RF-IgM, anti-CCP antibody; C-RP; ESR; NEUT% and LYMPH%.

Conclusion

Serum antibody responses to the third dose of vaccine in RA patients were weaker than HC. Our study will help to evaluate the efficacy and safety of booster vaccination in RA patients and provide further guidance for adjusting vaccination strategies.
Acceptance of clinical artificial intelligence among physicians and medical students: A systematic review with cross-sectional survey
Authors: Chen Mingyang , Zhang Bo , Cai Ziting , Seery Samuel , Gonzalez Maria J. , Ali Nasra M. , Ren Ran , Qiao Youlin , Xue Peng , Jiang Yu
Published: August 2022

Background

Artificial intelligence (AI) needs to be accepted and understood by physicians and medical students, but few have systematically assessed their attitudes. We investigated clinical AI acceptance among physicians and medical students around the world to provide implementation guidance.

Materials and methods

We conducted a two-stage study, involving a foundational systematic review of physician and medical student acceptance of clinical AI. This enabled us to design a suitable web-based questionnaire which was then distributed among practitioners and trainees around the world.

Results

Sixty studies were included in this systematic review, and 758 respondents from 39 countries completed the online questionnaire. Five (62.50%) of eight studies reported 65% or higher awareness regarding the application of clinical AI. Although, only 10–30% had actually used AI and 26 (74.28%) of 35 studies suggested there was a lack of AI knowledge. Our questionnaire uncovered 38% awareness rate and 20% utility rate of clinical AI, although 53% lacked basic knowledge of clinical AI. Forty-five studies mentioned attitudes toward clinical AI, and over 60% from 38 (84.44%) studies were positive about AI, although they were also concerned about the potential for unpredictable, incorrect results. Seventy-seven percent were optimistic about the prospect of clinical AI. The support rate for the statement that AI could replace physicians ranged from 6 to 78% across 40 studies which mentioned this topic. Five studies recommended that efforts should be made to increase collaboration. Our questionnaire showed 68% disagreed that AI would become a surrogate physician, but believed it should assist in clinical decision-making. Participants with different identities, experience and from different countries hold similar but subtly different attitudes.

Conclusion

Most physicians and medical students appear aware of the increasing application of clinical AI, but lack practical experience and related knowledge. Overall, participants have positive but reserved attitudes about AI. In spite of the mixed opinions around clinical AI becoming a surrogate physician, there was a consensus that collaborations between the two should be strengthened. Further education should be conducted to alleviate anxieties associated with change and adopting new technologies.
Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal pathogen
Authors: Yin Chuntao , Hagerty Christina H. , Paulitz Timothy C.
Published: August 2022

Synthetic microbial communities (SynComs) could potentially enhance some functions of the plant microbiome and emerge as a promising inoculant for improving crop performance. Here, we characterized a collection of bacteria, previously isolated from the wheat rhizosphere, for their antifungal activity against soilborne fungal pathogens. Ten SynComs with different compositions from 14 bacterial strains were created. Seven SynComs protected wheat from Rhizoctonia solani AG8 infection, although SynComs were not more effective than single strains in reducing wheat root rot disease. Further, the mechanisms of interaction of the tested bacteria with each other and plants were explored. We found that nine bacteria and nine SynComs impacted the root growth of Arabidopsis. Nine bacteria and four SynComs significantly inhibited the growth of AG8 by producing volatiles. The cell-free supernatants from six bacteria inhibited the growth of AG8. Together, this study provided the potential for improving crop resilience by creating SynComs.
Prognosis of COVID-19 in the middle eastern population, knowns and unknowns
Authors: Dandachi Iman , Aljabr Waleed
Published: August 2022

Since its emergence in China in 2019, the SARS-CoV-2 virus has affected all countries worldwide. The virus is easily transmitted from one person to another via infected aerosols or contaminated surfaces. Unlike its counterparts, the prognosis of COVID-19 ranges from asymptomatic to critical disease or death. Several factors play a role in determining the severity of the disease in infected patients. Among others, is the pre-existence of an underlying medical condition such as diabetes, cancer, and others. Furthermore, although children are less prone to the severe form of the COVID-19 disease, they require attention due to the report of many atypical presentations of the infection, post-asymptomatic exposure. In the Middle East, little is known about the prognosis of the SARS-CoV-2 infection in high-risk categories, notably patients with diabetes, cancer, and pregnant women. The aim of this review is to summarize the current knowledge about this group of population in the middle eastern region as well as to highlight the gap in the literature. We have found that the majority of the papers were from the Gulf countries. Although, few studies were conducted; high-risk patients appear to have an increased risk of morbidity and mortality from COVID-19 compared to their counterparts. Higher levels of inflammatory markers, C-reactive protein, erythrocyte sedimentation rate, D-dimer, and ferritin levels were also observed. Children are often asymptomatic or present with atypical presentations. More studies should be conducted to determine the clinical biomarkers of COVID-19 in high-risk categories to help in patient risk stratification and management in the middle eastern population.
Metabarcoding of harmful algal bloom species in sediments from four coastal areas of the southeast China
Authors: Wang Zhaohui , Peng Liang , Xie Changliang , Wang Wenting , Zhang Yuning , Xiao Lijuan , Tang Yali , Yang Yufeng
Published: August 2022

In the past three decades, harmful algal blooms (HAB) have become more frequent and widespread in southeast Chinese sea areas. Resting stages are regarded as the “seed bank” of algal blooms, and play an important role in initiating HABs. The distribution of resting stages in sediments especially those of HAB species can make good predictions about the potential risk of future blooms, however with limited reports. In this study, surface sediment samples were collected in the four sea areas along the southeast Chinese coasts, including Dafeng Port (DF) in the southern Yellow Sea, Xiangshan Bay (XS), Funing Bay (FN), and Dongshan Bay (DS) in the East China Sea. Diversity and community structure of eukaryotic microalgae in surface sediments were assessed by metabarcoding V4 region of the 18S rDNA, focusing on the distribution of HAB species. Biogenic elements including total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP), biogenic silicon (BSi), and moisture content (MC) were analyzed. A total of 454 eukaryotic algal OTUs were detected, which belonged to 31 classes of 9 phyla. Altogether 149 algal species were detected in this study, and 59 taxa have been reported to form resting stages. Eukaryotic algal community was similar in XS, FN and DS of the East China Sea, which were predominated by dinoflagellates. However, algal community was different in DF of the Yellow Sea, and characterized by the dominance of chrysophytes and low OTU richness. The distribution of most abundant HAB species showed positive correlations with TN, BSi, and TOC, suggesting that eutrophication and consequent increase in diatom productivity may have a significant influence on the distribution of HAB species and facilitate the occurrence of HABs. Furthermore, HAB species occurred more abundantly and widely in FN. Our results suggest high potential risks of HABs in the southeast Chinese coast especially in Funing Bay.
Impact of queuosine modification of endogenous E. coli tRNAs on sense codon reassignment
Authors: Tittle Jillyn M. , Schwark David G. , Biddle Wil , Schmitt Margaret A. , Fisk John D.
Published: August 2022

The extent to which alteration of endogenous tRNA modifications may be exploited to improve genetic code expansion efforts has not been broadly investigated. Modifications of tRNAs are strongly conserved evolutionarily, but the vast majority of E. coli tRNA modifications are not essential. We identified queuosine (Q), a non-essential, hypermodified guanosine nucleoside found in position 34 of the anticodons of four E. coli tRNAs as a modification that could potentially be utilized to improve sense codon reassignment. One suggested purpose of queuosine modification is to reduce the preference of tRNAs with guanosine (G) at position 34 of the anticodon for decoding cytosine (C) ending codons over uridine (U) ending codons. We hypothesized that introduced orthogonal translation machinery with adenine (A) at position 34 would reassign U-ending codons more effectively in queuosine-deficient E. coli. We evaluated the ability of introduced orthogonal tRNAs with AUN anticodons to reassign three of the four U-ending codons normally decoded by Q34 endogenous tRNAs: histidine CAU, asparagine AAU, and aspartic acid GAU in the presence and absence of queuosine modification. We found that sense codon reassignment efficiencies in queuosine-deficient strains are slightly improved at Asn AAU, equivalent at His CAU, and less efficient at Asp GAU codons. Utilization of orthogonal pair-directed sense codon reassignment to evaluate competition events that do not occur in the standard genetic code suggests that tRNAs with inosine (I, 6-deaminated A) at position 34 compete much more favorably against G34 tRNAs than Q34 tRNAs. Continued evaluation of sense codon reassignment following targeted alterations to endogenous tRNA modifications has the potential to shed new light on the web of interactions that combine to preserve the fidelity of the genetic code as well as identify opportunities for exploitation in systems with expanded genetic codes.
Fatty acid export (FAX) proteins contribute to oil production in the green microalga Chlamydomonas reinhardtii
Authors: Peter Janick , Huleux Marie , Spaniol Benjamin , Sommer Frederik , Neunzig Jens , Schroda Michael , Li-Beisson Yonghua , Philippar Katrin
Published: August 2022

In algae and land plants, transport of fatty acids (FAs) from their site of synthesis in the plastid stroma to the endoplasmic reticulum (ER) for assembly into acyl lipids is crucial for cellular lipid homeostasis, including the biosynthesis of triacylglycerol (TAG) for energy storage. In the unicellular green alga Chlamydomonas reinhardtii, understanding and engineering of these processes is of particular interest for microalga-based biofuel and biomaterial production. Whereas in the model plant Arabidopsis thaliana, FAX (fatty acid export) proteins have been associated with a function in plastid FA-export and hence TAG synthesis in the ER, the knowledge on the function and subcellular localization of this protein family in Chlamydomonas is still scarce. Among the four FAX proteins encoded in the Chlamydomonas genome, we found Cr-FAX1 and Cr-FAX5 to be involved in TAG production by functioning in chloroplast and ER membranes, respectively. By in situ immunolocalization, we show that Cr-FAX1 inserts into the chloroplast envelope, while Cr-FAX5 is located in ER membranes. Severe reduction of Cr-FAX1 or Cr-FAX5 proteins by an artificial microRNA approach results in a strong decrease of the TAG content in the mutant strains. Further, overexpression of chloroplast Cr-FAX1, but not of ER-intrinsic Cr-FAX5, doubled the content of TAG in Chlamydomonas cells. We therefore propose that Cr-FAX1 in chloroplast envelopes and Cr-FAX5 in ER membranes represent a basic set of FAX proteins to ensure shuttling of FAs from chloroplasts to the ER and are crucial for oil production in Chlamydomonas.
Exported J domain proteins of the human malaria parasite
Authors: Almaazmi Shaikha Y. , Singh Harpreet , Dutta Tanima , Blatch Gregory L.
Published: August 2022

The heat shock protein 40 (Hsp40) family, also called J domain proteins (JDPs), regulate their Hsp70 partners by ensuring that they are engaging the right substrate at the right time and in the right location within the cell. A number of JDPs can serve as co-chaperone for a particular Hsp70, and so one generally finds many more JDPs than Hsp70s in the cell. In humans there are 13 Hsp70s and 49 JDPs. The human malaria parasite, Plasmodium falciparum, has dedicated an unusually large proportion of its genome to molecular chaperones, with a disproportionately high number of JDPs (PfJDPs) of 49 members. Interestingly, just under half of the PfJDPs are exported into the host cell during the asexual stage of the life cycle, when the malaria parasite invades mature red blood cells. Recent evidence suggests that these PfJDPs may be functionalizing both host and parasite Hsp70s within the infected red blood cell, and thereby driving the renovation of the host cell towards pathological ends. PfJDPs have been found to localize to the host cytosol, mobile structures within the host cytosol (so called “J Dots”), the host plasma membrane, and specialized structures associated with malaria pathology such as the knobs. A number of these exported PfJDPs are essential, and there is growing experimental evidence that they are important for the survival and pathogenesis of the malaria parasite. This review critiques our understanding of the important role these exported PfJDPs play at the host-parasite interface.
SARS-CoV-2 and extracellular vesicles: An intricate interplay in pathogenesis, diagnosis and treatment
Authors: Sbarigia C. , Vardanyan D. , Buccini L. , Tacconi S. , Dini L.
Published: August 2022

Extracellular vesicles (EVs) are widely recognized as intercellular communication mediators. Among the different biological processes, EVs play a role in viral infections, supporting virus entrance and spread into host cells and immune response evasion. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection became an urgent public health issue with significant morbidity and mortality worldwide, being responsible for the current COVID-19 pandemic. Since EVs are implicated in SARS-CoV-2 infection in a morphological and functional level, they have gained growing interest for a better understanding of SARS-CoV-2 pathogenesis and represent possible diagnostic tools to track the disease progression. Furthermore, thanks to their biocompatibility and efficient immune activation, the use of EVs may also represent a promising strategy for the development of new therapeutic strategies against COVID-19. In this review, we explore the role of EVs in viral infections with a focus on SARS-CoV-2 biology and pathogenesis, considering recent morphometric studies. The common biogenesis aspects and structural similarities between EVs and SARS-CoV-2 will be examined, offering a panoramic of their multifaceted interplay and presenting EVs as a machinery supporting the viral cycle. On the other hand, EVs may be exploited as early diagnostic biomarkers and efficient carriers for drug delivery and vaccination, and ongoing studies will be reviewed to highlight EVs as potential alternative therapeutic strategies against SARS-CoV-2 infection.
Skill-learning by observation-training with patients after traumatic brain injury
Authors: Avraham Einat , Sacher Yaron , Maaravi-Hesseg Rinatia , Karni Avi , Doron Ravid
Published: August 2022

Traumatic brain injury (TBI) is a major cause of death and disability in Western society, and often results in functional and neuropsychological abnormalities. Memory impairment is one of the most significant cognitive implications after TBI. In the current study we investigated procedural memory acquisition by observational training in TBI patients. It was previously found that while practicing a new motor skill, patients engage in all three phases of skill learning–fast acquisition, between-session consolidation, and long-term retention, though their pattern of learning is atypical compared to healthy participants. A different set of studies showed that training by observing a motor task, generally prompted effective acquisition and consolidation of procedural knowledge in healthy participants. The aim of our study was to (i) evaluate the potential benefit of action observation in TBI patients. (ii) Examine the possibility of general improvement in performance between the first (24 h post-training) and second (2 weeks post-training) stage of the study. (iii) Investigate the link between patients’ ability to benefit from observational learning (viaperformance gains–speed and accuracy) and common measures of injury (such as severity of injury, functional and cognitive measures).

Materials and methods

Patients hospitalized after moderate to severe TBI, were trained by observation for the finger opposition sequence (FOS) motor task. They were then tested for the observation-trained sequence (A) and a similar control sequence (B), at two different time-points (24 h post-training and 2 weeks later).

Results revealed

(i) a significant difference in performance between the trained (A) and untrained (B) sequences, in favor of the trained sequence. (ii) An increase in performance for both sequences A and B toward the second (retention) session. (iii) The advantage for sequence A was stable and preserved also in the second session. (iv) Participants with lower moderate Functional Independence Measure (FIM) scores gained more from observational-procedural learning, compared with patients with higher functional abilities.

Conclusion

Overall, these findings support the notion that TBI patients may achieve procedural memory consolidation and retention through observational learning. Moreover, different functional traits may predict the outcomes of observational training in different patients. These findings may have significant practical implications in the future, regarding skill acquisition methods in TBI patients.
Application value of a deep learning method based on a 3D V-Net convolutional neural network in the recognition and segmentation of the auditory ossicles
Authors: Wang Xing-Rui , Ma Xi , Jin Liu-Xu , Gao Yan-Jun , Xue Yong-Jie , Li Jing-Long , Bai Wei-Xian , Han Miao-Fei , Zhou Qing , Shi Feng , Wang Jing
Published: August 2022

Objective

To explore the feasibility of a deep learning three-dimensional (3D) V-Net convolutional neural network to construct high-resolution computed tomography (HRCT)-based auditory ossicle structure recognition and segmentation models.

Methods

The temporal bone HRCT images of 158 patients were collected retrospectively, and the malleus, incus, and stapes were manually segmented. The 3D V-Net and U-Net convolutional neural networks were selected as the deep learning methods for segmenting the auditory ossicles. The temporal bone images were randomized into a training set (126 cases), a test set (16 cases), and a validation set (16 cases). Taking the results of manual segmentation as a control, the segmentation results of each model were compared.

Results

The Dice similarity coefficients (DSCs) of the malleus, incus, and stapes, which were automatically segmented with a 3D V-Net convolutional neural network and manually segmented from the HRCT images, were 0.920 ± 0.014, 0.925 ± 0.014, and 0.835 ± 0.035, respectively. The average surface distance (ASD) was 0.257 ± 0.054, 0.236 ± 0.047, and 0.258 ± 0.077, respectively. The Hausdorff distance (HD) 95 was 1.016 ± 0.080, 1.000 ± 0.000, and 1.027 ± 0.102, respectively. The DSCs of the malleus, incus, and stapes, which were automatically segmented using the 3D U-Net convolutional neural network and manually segmented from the HRCT images, were 0.876 ± 0.025, 0.889 ± 0.023, and 0.758 ± 0.044, respectively. The ASD was 0.439 ± 0.208, 0.361 ± 0.077, and 0.433 ± 0.108, respectively. The HD 95 was 1.361 ± 0.872, 1.174 ± 0.350, and 1.455 ± 0.618, respectively. As these results demonstrated, there was a statistically significant difference between the two groups (P < 0.001).

Conclusion

The 3D V-Net convolutional neural network yielded automatic recognition and segmentation of the auditory ossicles and produced similar accuracy to manual segmentation results.
The carbon footprint of Italian schools meals: An optimal choice of dishes in vegan, vegetarian, and omnivorous menus
Authors: Benvenuti Luca , De Santis Alberto , Ferrari Marika , Martone Deborah , Rossi Laura
Published: August 2022

This study aims to assess the carbon footprint associated with vegan, vegetarian, and omnivorous menus for primary school lunches in Italy. For this purpose, healthy and acceptable menus with minimal greenhouse gas emissions have been designed by a binary linear programming model. The results show that the adoption of a specific diet may help in reducing the carbon footprint of menus, but it is the optimal selection of dishes that ultimately makes the difference. Interestingly enough, the optimal choice of dishes and the restriction of meat consumption in omnivorous menus can lead up to a 40% emission reduction compared to the current school lunch menu of the municipality of Rome. Moreover, the optimal choice of dishes in vegan menus provides the menu with the lowest carbon footprint among all kinds of diets.