bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome analysis of Bacillus amyloliquefaciens TA-1, a promising biocontrol agent against Cercospora arachidicola pathogen of early leaf spot in Arachis hypogaea L
Authors: Wang Chen , Ahsan Taswar , Ding Ao , Han Di , Zang Chao-Qun , Huang Yu-Qian , Hussain Khalid 
Published: September 2023

Abstract
Background
Early leaf spot disease, caused by Cercospora arachidicola, is a devastating peanut disease that has severely impacted peanut production and quality. Chemical fungicides pollute the environment; however, Bacillus bacteria can be used as an environmentally friendly alternative to chemical fungicides. To understand the novel bacterial strain and unravel its molecular mechanism, De novo whole-genome sequencing emerges as a rapid and efficient omics approach.

Results
In the current study, we identified an antagonistic strain, Bacillus amyloliquefaciens TA-1. In-vitro assay showed that the TA-1 strain was a strong antagonist against C. arachidicola, with an inhibition zone of 88.9 mm. In a greenhouse assay, results showed that the TA-1 strain had a significant biocontrol effect of 95% on peanut early leaf spot disease. De novo whole-genome sequencing analysis, shows that strain TA-1 has a single circular chromosome with 4172 protein-coding genes and a 45.91% guanine and cytosine (GC) content. Gene function was annotated using non-redundant proteins from the National Center for Biotechnology Information (NCBI), Swiss-Prot, the Kyoto Encyclopedia of Genes and Genomes (KEGG), clusters of orthologous groups of proteins, gene ontology, pathogen-host interactions, and carbohydrate-active enZYmes. antiSMASH analysis predicted that strain TA-1 can produce the secondary metabolites siderophore, tailcyclized peptide, myxochelin, bacillibactin, paenibactin, myxochelin, griseobactin, benarthin, tailcyclized, and samylocyclicin.

Conclusion
The strain TA-1 had a significant biological control effect against peanut early leaf spot disease in-vitro and in greenhouse assays. Whole genome analysis revealed that, TA-1 strain belongs to B. amyloliquefaciens and could produce the antifungal secondary metabolites.
Enhanced detection rate of Mycoplasma genitalium in urine overtime by transcription-mediated amplification in comparison to real-time PCR
Authors: Adriaens Nikki , Pennekamp Anne-Marije , van Dam Alje P. , Bruisten Sylvia M. 
Published: September 2023

Abstract
Background
Diagnosis of infected individuals with Mycoplasma genitalium (MG) is often performed by real-time PCR or transcription-mediated amplification (TMA). A limitation of the MG-TMA assay is the relatively short time span of 24 h in which the collected urine is required to be transferred into a Urine Specimen Transport Tube, according to the manufacturer’s guidelines. If not transferred within 24 h, the manufacturer’s claimed sensitivity cannot be guaranteed anymore, and samples may instead be tested with an in-house validated real-time PCR, despite its recognized lower sensitivity. This study aimed to validate an exception to the sample transport and storage conditions of the MG-TMA assay as set by the manufacturer, being the prolongation of the acceptable testing time limit of 24 h.

Methods
From June to December 2022, first-void urines were collected from clients attending the clinic for sexual health in Amsterdam, the Netherlands. Urine samples that tested positive for MG by TMA assay at the day of collection were concomitantly stored at room (18–24 °C) and refrigerator temperature (4–8 °C) for 15 days. The stored urine samples were tested with both an in-house validated real-time PCR and MG-TMA assay after transfer of the original urine samples to the respective test tubes at 3, 7, 12 and 15 days post collection.

Results
In total, 47 MG-positive urine samples were collected, stored and tested for MG by real-time PCR and TMA assays. After storage at room temperature, the MG-detection rate by TMA was significantly higher compared to real-time PCR, at days 0 (p ≤ 0.001), 7 (p ≤ 0.001) and 12 (p < 0.05). After storage at refrigerator temperature, the MG-detection rate determined by TMA assay was significantly enhanced in comparison with real-time PCR at days 3 (p < 0.01), 7 (p ≤ 0.001) and 15 (p < 0.01).

Conclusions
This validation study showed that the MG-TMA assay has a superior detection rate in urine compared to real-time PCR, up to 15 days post sample collection and irrespective of storage temperature. Accepting urines older than 24 h to be tested by TMA will improve clinical diagnosis of MG infections.
SARS-CoV-2 vaccine breakthrough infection in the older adults: a meta-analysis and systematic review
Authors: Jing Xiaohui , Han Menglin , Wang Xiaoxuan , Zhou Li 
Published: September 2023

AbstractBackgroundCorona Virus Disease 2019 (COVID-19) mRNA vaccine effectiveness (VE) has recently declined, and reports about COVID-19 breakthrough infection have increased. We aimed to conduct a meta-analysis on population-based studies of the prevalence and incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) breakthrough infection amongst older adults worldwide.MethodsStudies from PubMed, Embase, Cochrane Library, and Web of Science were systematically screened to determine the prevalence and incidence of SARS-CoV-2 breakthrough infection in older adults from inception to November 2, 2022. Our meta-analysis included 30 studies, all published in English. Pooled estimates were calculated using a random-effect model through the inverse variance method. Publication bias was tested through funnel plots and Egger’s regression test, and sensitivity analyses were performed to confirm the robustness of the results. This research was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.ResultsThirty publications were included in this meta-analysis (17 on prevalence, 17 on incidence, and 4 on both). The pooled prevalence of COVID-19 breakthrough infection among older adults was 7.7 per 1,000 persons (95% confidence interval [95%CI] 4.0–15.0). At the same time, the pooled incidence was 29.1 per 1000 person-years (95%CI 15.2–55.7).ConclusionsThis meta-analysis provides estimates of prevalence and incidence in older adults. We concluded that the prevalence and incidence of SARS-CoV-19 breakthrough infection in older people was low. The prevalence and incidence of breakthrough infection admitted to hospital, severe-critical, and deathly was significantly lower. Otherwise, there was considerable heterogeneity among estimates in this study, which should be considered when interpreting the results.
The role of ultrasonography in diagnosing acute closed volar plate injury of proximal interphalangeal joint
Authors: Wang Tiezheng , Guo Fei , Qi Hengtao , Cui Liyuan , Liu Lihua , Bao Shougang , Teng Jianbo 
Published: September 2023

Abstract
Background
Acute closed volar plate injury of the proximal interphalangeal joint (PIP) is a common hand injury. In the past, there were few objective evaluation imaging methods for the degree of volar plate injury. The purpose of this study was to investigate the role of high frequency ultrasonography in diagnosing volar plate injury, and to explore whether ultrasound can provide a beneficial guidance to clinical decision-making and appropriate treatment adopting through accurate US classification of volar plate injury.

Methods
From May 2019 to may 2022, 41 patients diagnosed with volar plate injury were included in this study. All patients underwent ultrasonography and X-ray examinations. The sonographic features were analyzed. A new kind of classification of volar plate injury based on ultrasonography findings was described.

Results
Either an injury of volar plate or an avulsion fracture of middle phalangeal base was identified clearly on ultrasonography, according to which volar plate injury could be divided into three types: A, B and C. Type A, avulsion fracture of the middle phalangeal base without volar plate rupture; Type B, full thickness tear of the volar plate without avulsion fracture; Type C, partial thickness tear of the volar plate. The average thickness of the three types of injured volar plate measured by ultrasound was 0.33 ± 0.05 cm, and the average thickness of the volar plate at the same site of the corresponding finger on the contralateral side was 0.22 ± 0.03 cm. There was significant difference between the two group (t = 11.823, p = 1.2476 *10^(-14)).

Conclusions
High frequency ultrasonography could be a reliable, accurate, convenient and non-radioactive diagnostic imaging technique in the evaluation of acute closed volar plate injury of PIP. And ultrasound could provide a beneficial guidance to clinical decision-making and appropriate treatment adopting through accurate US classification.
TET2 inhibits the proliferation and metastasis of lung adenocarcinoma cells via activation of the cGAS-STING signalling pathway
Authors: Cheng Gui , Wu Jun , Ji Mei , Hu Wenwei , Wu Changping , Jiang Jingting 
Published: September 2023

Abstract
Background
Effective identification and development of new molecular methods for the diagnosis, treatment and prognosis of lung adenocarcinoma (LUAD) remains an urgent clinical need. DNA methylation patterns at cytosine bases in the genome are closely related to gene expression, and abnormal DNA methylation is frequently observed in various cancers. The ten-eleven translocation (TET) enzymes oxidize 5-methylcytosine (5mC) and promote locus-specific DNA methylation reversal. This study aimed to explore the role of the TET2 protein and its downstream effector, 5-hmC/5-mC DNA modification, in LUAD progression.

Methods
The expression of TET2 was analysed by real-time PCR, Western blotting and immunohistochemistry. The 5-hmC DNA content was determined by a colorimetric kit. Activation of the cGAS-STING signalling pathway was evaluated by Western blotting. CCK-8, wound healing and Transwell assays were performed to evaluate the effect of TET2 on cell proliferation, migration and invasion abilities. A xenograft model was used to analyse the effect of TET2 on the tumorigenic ability of A549 cells.

Results
TET2 overexpression decreased proliferation and metastasis of A549 and H1975 cells in vitro and in vivo. However, TET2 knockdown dramatically enhanced the proliferation, migration and invasion of A549 and H1975 cells. Mechanistically, activation of the cGAS-STING signalling pathway is critical for the TET2-mediated suppression of LUAD cell tumorigenesis and metastasis.

Conclusion
In this study, we demonstrate a tumour suppressor role of TET2 in LUAD, providing new potential molecular therapeutic targets and clinical therapies for patients with non-small cell lung cancer.
MALAT1-regulated gene expression profiling in lung cancer cell lines
Authors: Roh Jungwook , Kim Boseong , Im Mijung , Jang Wonyi , Chae Yeonsoo , Kang JiHoon , Youn BuHyun , Kim Wanyeon 
Published: September 2023

Abstract
Background
Non-small cell lung cancer (NSCLC) is the most common type of lung cancer and has a poor prognosis. Identifying biomarkers based on molecular mechanisms is critical for early diagnosis, timely treatment, and improved prognosis of lung cancer. MALAT1 has been reported to have overexpressed and tumor-promoting functions in NSCLC. It has been proposed as a potential biomarker for the diagnosis and prognosis of cancer. Therefore, this study was conducted to profile the changes in gene expression according to the regulation of expression of MALAT1 in NSCLC cell lines and to investigate the correlation through bioinformatic analysis of differentially expressed genes (DEGs).

Methods
MALAT1 expression levels were measured using RT-qPCR. The biological functions of MALAT1 in NSCLC were analyzed by cell counting, colony forming, wound-healing, and Transwell invasion assays. In addition, gene expression profiling in response to the knockdown of MALAT1 was analyzed by transcriptome sequencing, and differentially expressed genes regulated by MALAT1 were performed by GO and KEGG pathway enrichment analyses. Bioinformatic databases were used for gene expression analysis and overall survival analysis.

Results
Comparative analysis versus MALAT1 expression in MRC5 cells (a normal lung cell line) and the three NSCLC cell lines showed that MALAT1 expression was significantly higher in the NSCLC cells. MALAT1 knockdown decreased cell survival, proliferation, migration, and invasion in all three NSCLC cell lines. RNA-seq analysis of DEGs in NSCLC cells showed 198 DEGs were upregulated and 266 DEGs downregulated by MALAT1 knockdown in all three NSCLC cell lines. Survival analysis on these common DEGs performed using the OncoLnc database resulted in the selection of five DEGs, phosphoglycerate mutase 1 (PGAM1), phosphoglycerate mutase 4 (PGAM4), nucleolar protein 6 (NOL6), nucleosome assembly protein 1 like 5 (NAP1L5), and sestrin1 (SESN1). The gene expression levels of these selected DEGs were proved to gene expression analysis using the TNMplot database.

Conclusion
MALAT1 might function as an oncogene that enhances NSCLC cell survival, proliferation, colony formation, and invasion. RNA-seq and bioinformatic analyses resulted in the selection of five DEGs, PGAM1, PGAM4, NOL6, NAP1L5, and SESN1, which were found to be closely related to patient survival and tumorigenesis. We believe that further investigation of these five DEGs will provide valuable information on the oncogenic role of MALAT1 in NSCLC.
Validity of a novel optical coherence tomography angiography flow index in a cohort of primary open angle glaucoma
Authors: Ameen Ismail Ahmed , Sadek Sherin , Kamal Mahmoud , Hatata Ragai 
Published: September 2023

Abstract
Background
Vascular mechanisms are implicated in many ocular diseases. Therefore, different vascular imaging modalities are used in management of such conditions. Optical coherence tomography angiography (OCTA) has high spatial resolution and segmentable 3D volumetric sampling enabling isolation of retinal and peripapillary vascular beds. However, OCTA only indirectly derives quantitative flow data i.e. velocimetry through methods and algorithms liable to limitations like signal saturation. This study introduces and validates novel mathematical OCTA flow indices that may compensate for some OCTA velocimetric limitations.

Methods
Thirty-seven eyes of 23 POAG patients were included. Each underwent baseline and follow-up assessment one month thereafter. Assessment comprised full ophthalmological examination, intraocular pressure (IOP), systemic arterial blood pressure (SABP) and OCTA macula and ONH. Angiograms were processed using ImageJ to calculate OCTA intensity-based flow indices (FIOs), for superficial vascular plexus (SVP), deep vascular plexus (DVP) and optic nerve head vascular plexus (ONH-RPC), i.e. SFIO, DFIO and ONHFIO respectively. Mean ocular perfusion pressure (MOPP) was calculated using IOP and SABP. OCTA vascular densities (VD) and MOPP were used to calculate three respective mathematical flow indices (FIMs) for SVP, DVP and ONH-RPC, based on Hagen-Poiseuille law, i.e. SFIM, DFIM, ONHFIM respectively. Pearson test was used for correlation between the two sets of indices. Intraclass correlation coefficient (ICC) was tested for baseline and follow-up values for each index.

Results
There was positive correlation between the three FIMs and their respective FIOs at baseline and follow-up ranging between high and moderate. Correlation coefficients (CCs) were 0.773 and 0.609 for SFIM and SFIO P-value < 0.001, 0.829 and 0.624 for DFIM and DFIO P-value < 0.001 and 0.516 and 0.737 for ONHFIM P-value = 0.001 for baseline and follow-up respectively. ICCs were 0.772 P-value < 0.001, 0.328 P-value = 0.022 and 0.888 P-value < 0.001 for SFIM, DFIM and ONHFIM respectively. For SFIO, DFIO and ONHFIO, ICCs were 0.420 P-value = 0.004, 0.079 P-value = 0.320 and 0.833 P-value < 0.001 respectively.

Conclusion
The novel FIMs are reliable alternatives to FIOs and may compensate for OCTA signal saturation in extremes of MOPP. SFIM and ONHFIM showed high ICCs with excellent reliability. While DFIM demonstrated low ICC indicating poor reliability, it still performed better than its corresponding DFIO.
Associations between constructs related to social relationships and mental health conditions and symptoms: an umbrella review
Authors: Pearce Eiluned , Birken Mary , Pais Sarah , Tamworth Millie , Ng Yutung , Wang Jingyi , Chipp Beverley , Crane Ellena , Schlief Merle , Yang Jinyan , Stamos Aggelos , Cheng Lui Kwan , Condon Maria , Lloyd-Evans Brynmor , Kirkbride James B. , Osborn David , Pitman Alexandra , Johnson Sonia 
Published: September 2023

Abstract
Background
Loneliness and social isolation are increasingly recognised as prevalent among people with mental health problems, and as potential targets for interventions to improve quality of life and outcomes, as well as for preventive strategies. Understanding the relationship between quality and quantity of social relationships and a range of mental health conditions is a helpful step towards development of such interventions.

Purpose
Our aim was to give an overview of associations between constructs related to social relationships (including loneliness and social isolation) and diagnosed mental conditions and mental health symptoms, as reported in systematic reviews of observational studies.

Methods
For this umbrella review (systematic review of systematic reviews) we searched five databases (PsycINFO, MEDLINE, EMBASE, CINAHL, Web of Science) and relevant online resources (PROSPERO, Campbell Collaboration, Joanna Briggs Institute Evidence Synthesis Journal). We included systematic reviews of studies of associations between constructs related to social relationships and mental health diagnoses or psychiatric symptom severity, in clinical or general population samples. We also included reviews of general population studies investigating the relationship between loneliness and risk of onset of mental health problems.

Results
We identified 53 relevant systematic reviews, including them in a narrative synthesis. We found evidence regarding associations between (i) loneliness, social isolation, social support, social network size and composition, and individual-level social capital and (ii) diagnoses of mental health conditions and severity of various mental health symptoms. Depression (including post-natal) and psychosis were most often reported on, with few systematic reviews on eating disorders or post-traumatic stress disorder (PTSD), and only four related to anxiety. Social support was the most commonly included social construct. Our findings were limited by low quality of reviews and their inclusion of mainly cross-sectional evidence.

Conclusion
Good quality evidence is needed on a wider range of social constructs, on conditions other than depression, and on longitudinal relationships between social constructs and mental health symptoms and conditions.
Factor structure of the Social Phobia Scale (SPS) and the Social Interaction Anxiety Scale (SIAS) in a clinical sample recruited from the community
Authors: Šipka Dajana , Brodbeck Jeannette , Schulz Ava , Stolz Timo , Berger Thomas 
Published: September 2023

Abstract
Background
The Social Phobia Scale (SPS) and the Social Interaction Anxiety Scale (SIAS) are widely used self-report questionnaires to assess symptoms of social anxiety. While SPS measures social performance anxiety, SIAS measures social interaction anxiety. They are mostly reported simultaneously, but there have not been consistent results of the joint factor structure and therefore no consistent recommendations on how to use and evaluate the questionnaires. This study aimed (1) to evaluate the underlying joint factor structure of the SPS and SIAS and (2) to test whether SPS and SIAS are reliable scales to assess two different aspects of social anxiety.

Methods
The one-factor, two-factor, and bifactor models were tested in a clinical sample recruited from the community and diagnosed with a social anxiety disorder. Exploratory and confirmatory factor analyses were conducted, bifactor-specific indices were calculated, and the content of the less fitting items was examined.

Results
Confirmatory factor analyses showed that the best-fitting model was the bifactor model with a reduced set of items. The bifactor-specific indices showed that the factor structure cannot be considered unidimensional and that SPS and SIAS are reliable subscales. A closer examination of the less fitting item content and implications for future studies are discussed.

Conclusions
In conclusion, SPS and SIAS can be reported together as an overall score of social anxiety and are separately reliable measures to assess different aspects of social anxiety.

Trial registration
This is a secondary analysis of data from two trials registered under ISRCTN75894275 and ISRCTN10627379.
Correlates of severity in a clinical staging model of schizophrenia: a cross-sectional study among 158 subjects
Authors: Hamieh Fatima , Hallit Souheil , Haddad Chadia , Obeid Sahar , Kazour Francois 
Published: September 2023

Abstract
Background
Clinical staging has been widely used to predict and optimize the treatment of medical disorders. Different models have been proposed to map the development, progression, and extension of psychiatric disorders over time, mainly for schizophrenia. The primary objective of this study was to classify patients with psychosis according to the McGorry staging model and compare factors between the different stages.

Methods
This was a cross-sectional study, collecting data from 158 patients hospitalized for schizophrenia/psychosis. The survey included the Mini International Neuropsychiatric Interview (MINI), Positive and Negative Symptom Scale (PANSS), Montgomery-Asberg Depression Rating Scale (MADRS), Yong Mania Rating Scale (YMRS), Clinical Global Impression (CGI) scale, and the McGorry staging model.

Results
Patients have been classified into three clinical stages: relapse of psychotic disorder (43%), multiple relapses (47.5%), and persistent and severe illness (9.5%). A higher mean duration of hospitalization, psychotic symptoms (PANSS total scale and subscales), chlorpromazine equivalent dose, and number of antipsychotic treatments were found among participants in Stage 4 as compared to the other groups. However, a significantly higher mean GAF scale was found among participants in stage 3b as compared to the other groups.

Conclusion
Each stage in the McGorry staging model of schizophrenia is associated with well-defined clinical presentations, which help decide the appropriate treatment. Using such models in psychiatry can improve the diagnostic process and potential therapeutic interventions for patients suffering from mental disorders.