bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel pathogenic variants of DNAH5 associated with clinical and genetic spectra of primary ciliary dyskinesia in an Arab population
Authors: Al-Mutairi Dalal A. , Alsabah Basel H. , Pennekamp Petra , Omran Heymut
Published: July 2024

Introduction: Primary ciliary dyskinesia (PCD) is caused by the dysfunction of motile cilia resulting in insufficient mucociliary clearance of the lungs. This study aimed to map novel PCD variants and determine their pathogenicity in PCD patients in Kuwait.

Methods: Herein, we present five PCD individuals belonging to a cohort of 105 PCD individuals recruited from different hospitals in Kuwait. Genomic DNAs from the family members were analysed to screen for pathogenic PCD variants. Transmission electron microscopy (TEM) and immunofluorescence (IF) analyses were performed on the nasal biopsies to detect specific structural abnormalities within the ciliated cells.

Results: Genetic screening and functional analyses confirmed that the five PCD individuals carried novel pathogenic variants of DNAH5 causing PCD in three Arabic families. Of these, one multiplex family with two affected individuals showed two novel homozygous missense variants in DNAH5 causing PCD with situs inversus; another multiplex family with two affected individuals showed two newly identified compound heterozygous variants in DNAH5 causing PCD with situs solitus. In addition, novel heterozygous variants were identified in a child with PCD and situs solitus from a singleton family with unrelated parents. TEM analysis demonstrated the lack of outer dynein arms (ODAs) in all analysed samples, and IF analysis confirmed the absence of the dynein arm component of DNAH5 from the ciliary axoneme.

Conclusion: The newly identified pathogenic variants of DNAH5 are associated with PCD as well as variable pulmonary clinical manifestations in Arabic families.
DNA methylation patterns in the peripheral blood of Xinjiang brown cattle with variable somatic cell counts
Authors: Wang Dan , Ma Shengchao , Yan Mengjie , Dong Mingming , Zhang Menghua , Zhang Tao , Zhang Tao , Zhang Xiaoxue , Xu Lei , Huang Xixia
Published: July 2024

The use of wide-ranging dairy herd improvement (DHI) measurements has resulted in the investigation of somatic cell count (SCC) and the identification of many genes associated with mastitis resistance. In this study, blood samples of Xinjiang brown cattle with different SCCs were collected, and genome-wide DNA methylation was analyzed by MeDIP-seq. The results showed that peaks were mostly in intergenic regions, followed by introns, exons, and promoters. A total of 1,934 differentially expressed genes (DEGs) associated with mastitis resistance in Xinjiang brown cattle were identified. The enrichment of differentially methylated CpG islands of the TRAPPC9 and CD4 genes was analyzed by bisulfate genome sequencing. The methylation rate of differentially methylated CpGs was higher in the TRAPPC9 gene of cattle with clinical mastitis (mastitis group) compared with healthy cattle (control group), while methylation of differentially methylated CpGs was significantly lower in CD4 of the mastitis group compared with the control group. RT-qRCR analysis showed that the mastitis group had significantly reduced expression of CD4 and TRAPPC9 genes compared to the control group (p < 0.05). Furthermore, Mac-T cells treated with lipopolysaccharide and lipoteichoic acid showed significant downregulation of the TRAPPC9 gene in the mastitis group compared with the control group. The identified epigenetic biomarkers provide theoretical reference for treating cow mastitis, breeding management, and the genetic improvement of mastitis resistance in Xinjiang brown cattle.
Development of a subunit vaccine against the cholangiocarcinoma causing Opisthorchis viverrini: a computational approach
Authors: Shah Mohibullah , Sitara Farva , Sarfraz Asifa , Shehroz Muhammad , Wara Tehreem Ul , Perveen Asia , Ullah Najeeb , Zaman Aqal , Nishan Umar , Ahmed Sarfraz , Ullah Riaz , Ali Essam A. , Ojha Suvash Chandra
Published: July 2024

Opisthorchis viverrini is the etiological agent of the disease opisthorchiasis and related cholangiocarcinoma (CCA). It infects fish-eating mammals and more than 10 million people in Southeast Asia suffered from opisthorchiasis with a high fatality rate. The only effective drug against this parasite is Praziquantel, which has significant side effects. Due to the lack of appropriate treatment options and the high death rate, there is a dire need to develop novel therapies against this pathogen. In this study, we designed a multi-epitope chimeric vaccine design against O. viverrini by using immunoinformatics approaches. Non-allergenic and immunogenic MHC-1, MHC-2, and B cell epitopes of three candidate proteins thioredoxin peroxidase (Ov-TPx-1), cathepsin F1 (Ov-CF-1) and calreticulin (Ov-CALR) of O. viverrini, were predicted to construct a potent multiepitope vaccine. The coverage of the HLA-alleles of these selected epitopes was determined globally. Four vaccine constructs made by different adjuvants and linkers were evaluated in the context of their physicochemical properties, antigenicity, and allergenicity. Protein-protein docking and MD simulation found that vaccines 3 was more stable and had a higher binding affinity for TLR2 and TLR4 immune receptors. In-silico restriction cloning of vaccine model led to the formation of plasmid constructs for expression in a suitable host. Finally, the immune simulation showed strong immunological reactions to the engineered vaccine. These findings suggest that the final vaccine construct has the potential to be validated by in vivo and in vitro experiments to confirm its efficacy against the CCA causing O. viverrini.
The causal relationship between gut microbiota and nine infectious diseases: a two-sample Mendelian randomization analysis
Authors: Wang Song , Yin Fangxu , Sun Wei , Li Rui , Guo Zheng , Wang Yuchao , Zhang Yiyuan , Sun Chao , Sun Daqing
Published: July 2024

Background

Evidence from observational studies and clinical trials has associated gut microbiota with infectious diseases. However, the causal relationship between gut microbiota and infectious diseases remains unclear.

Methods

We identified gut microbiota based on phylum, class, order, family, and genus classifications, and obtained infectious disease datasets from the IEU OpenGWAS database. The two-sample Mendelian Randomization (MR) analysis was then performed to determine whether the gut microbiota were causally associated with different infectious diseases. In addition, we performed reverse MR analysis to test for causality.

Results

Herein, we characterized causal relationships between genetic predispositions in the gut microbiota and nine infectious diseases. Eight strong associations were found between genetic predisposition in the gut microbiota and infectious diseases. Specifically, the abundance of class Coriobacteriia, order Coriobacteriales, and family Coriobacteriaceae was found to be positively associated with the risk of lower respiratory tract infections (LRTIs). On the other hand, family Acidaminococcaceae, genus Clostridiumsensustricto1, and class Bacilli were positively associated with the risk of endocarditis, cellulitis, and osteomyelitis, respectively. We also discovered that the abundance of class Lentisphaeria and order Victivallales lowered the risk of sepsis.

Conclusion

Through MR analysis, we found that gut microbiota were causally associated with infectious diseases. This finding offers new insights into the microbe-mediated infection mechanisms for further clinical research.
Natural products as promising modulators of breast cancer immunotherapy
Authors: Alqathama Aljawharah
Published: July 2024

Breast cancer (BC) is the most common malignancy among women and is considered a major global health challenge worldwide due to its high incidence and mortality rates. Treatment strategies for BC is wide-ranging and include surgery, radiotherapy, chemotherapy, targeted hormonal therapy and immunotherapy. Immunotherapy has gained popularity recently and is often integrated as a component of personalized cancer care because it aims to strengthen the immune system and enable it to recognize and eradicate transformed cells. It has fewer side-effects and lower toxicity than other treatment strategies, such as chemotherapy. Many natural products are being investigated for a wide range of therapeutic pharmacological properties, such as immune system modulation and activity against infection, auto-immune disease, and cancer. This review presents an overview of the major immune response-related pathways in BC, followed by detailed explanation of how natural compounds can act as immunomodulatory agents against biomolecular targets. Research has been carried out on many forms of natural products, including extracts, isolated entities, synthetic derivatives, nanoparticles, and combinations of natural compounds. Findings have shown significant regulatory effects on immune cells and immune cytokines that lead to immunogenic cancer cell death, as well as upregulation of macrophages and CD+8 T cells, and increased natural killer cell and dendritic cell activity. Natural products have also been found to inhibit some immuno-suppressive cells such as Treg and myeloid-derived suppressor cells, and to decrease immunosuppressive factors such as TGF-β and IL-10. Also, some natural compounds have been found to target and hinder immune checkpoints such as PD-L1.
T-cell responses in colorectal peritoneal metastases are recapitulated in a humanized immune system mouse model
Authors: Saris Job , Bootsma Sanne , Verhoeff Jan , Tuynman Jurriaan B. , Wildenberg Manon E. , Rijnstra Esther Siteur-van , Lenos Kristiaan J. , Garcia Vallejo Juan J. , Vermeulen Louis , Grootjans Joep
Published: July 2024

Background

The occurrence of peritoneal metastasis (PM) in patients with colorectal cancer (CRC) has a dismal prognosis. There is often limited response to systemic- and immunotherapy, even in microsatellite unstable (MSI) CRC. To overcome therapy resistance, it is critical to understand local immune environment in the peritoneal cavity, and to develop models to study anti-tumor immune responses. Here, we defined the peritoneal immune system (PerIS) in PM-CRC patients and evaluate the pre-clinical potential of a humanized immune system (HIS) mouse model for PM-CRC.

Methods

We studied the human PerIS in PM-CRC patients (n=20; MSS 19/20; 95%) and in healthy controls (n=3). HIS mice (NODscid gamma background; n=18) were generated, followed by intraperitoneal injection of either saline (HIS control; n=3) or human MSS/MSI CRC cell lines HUTU80, MDST8 and HCT116 (HIS-PM, n=15). Immune cells in peritoneal fluid and peritoneal tumors were analyzed using cytometry by time of flight (CyTOF).

Results

The human and HIS mouse homeostatic PerIS was equally populated by NK cells and CD4+- and CD8+ T cells, however differences were observed in macrophage and B cell abundance. In HIS mice, successful peritoneal engraftment of both MSI and MSS tumors was observed (15/15; 100%). Both in human PM-CRC and in the HIS mouse PM-CRC model, we observed that MSS PM-CRC triggered a CD4+ Treg response in the PerIS, while MSI PM-CRC drives CD8+ TEMs responses.

Conclusion

In conclusion, T cell responses in PM-CRC in HIS mice mirror those in human PM-CRC, making this model suitable to study antitumor T cell responses in PM-CRC.
A comprehensive meta-analysis of tissue resident memory T cells and their roles in shaping immune microenvironment and patient prognosis in non-small cell lung cancer
Authors: Shen Aidan , Garrett Aliesha , Chao Cheng-Chi , Liu Dongliang , Cheng Chao , Wang Zhaohui , Qian Chen , Zhu Yangzhi , Mai Junhua , Jiang Chongming
Published: July 2024

Tissue-resident memory T cells (TRM) are a specialized subset of long-lived memory T cells that reside in peripheral tissues. However, the impact of TRM-related immunosurveillance on the tumor-immune microenvironment (TIME) and tumor progression across various non-small-cell lung cancer (NSCLC) patient populations is yet to be elucidated. Our comprehensive analysis of multiple independent single-cell and bulk RNA-seq datasets of patient NSCLC samples generated reliable, unique TRM signatures, through which we inferred the abundance of TRM in NSCLC. We discovered that TRM abundance is consistently positively correlated with CD4+ T helper 1 cells, M1 macrophages, and resting dendritic cells in the TIME. In addition, TRM signatures are strongly associated with immune checkpoint and stimulatory genes and the prognosis of NSCLC patients. A TRM-based machine learning model to predict patient survival was validated and an 18-gene risk score was further developed to effectively stratify patients into low-risk and high-risk categories, wherein patients with high-risk scores had significantly lower overall survival than patients with low-risk. The prognostic value of the risk score was independently validated by the Cancer Genome Atlas Program (TCGA) dataset and multiple independent NSCLC patient datasets. Notably, low-risk NSCLC patients with higher TRM infiltration exhibited enhanced T-cell immunity, nature killer cell activation, and other TIME immune responses related pathways, indicating a more active immune profile benefitting from immunotherapy. However, the TRM signature revealed low TRM abundance and a lack of prognostic association among lung squamous cell carcinoma patients in contrast to adenocarcinoma, indicating that the two NSCLC subtypes are driven by distinct TIMEs. Altogether, this study provides valuable insights into the complex interactions between TRM and TIME and their impact on NSCLC patient prognosis. The development of a simplified 18-gene risk score provides a practical prognostic marker for risk stratification.
The role of HDAC3 in inflammation: mechanisms and therapeutic implications
Authors: Watson Noah , Kuppuswamy Sivaraman , Ledford William Luke , Sukumari-Ramesh Sangeetha
Published: July 2024

Histone deacetylases (HDACs) are critical regulators of inflammatory gene expression, and the efficacy of pan-HDAC inhibitors has been implicated in various disease conditions. However, it remains largely unclear how HDACs precisely regulate inflammation. To this end, evaluating the isoform-specific function of HDACs is critical, and the isoform-specific targeting could also circumvent the off-target effects of pan-HDAC inhibitors. This review provides an overview of the roles of HDAC3, a class I HDAC isoform, in modulating inflammatory responses and discusses the molecular mechanisms by which HDAC3 regulates inflammation associated with brain pathology, arthritis, cardiovascular diseases, lung pathology, allergic conditions, and kidney disorders. The articles also identify knowledge gaps in the field for future studies. Despite some conflicting reports, the selective inhibition of HDAC3 has been demonstrated to play a beneficial role in various inflammatory pathologies. Exploring the potential of HDAC3 inhibition to improve disease prognosis is a promising avenue requiring further investigation.
Pemphigoid diseases in patients with end-stage kidney diseases: pathogenesis and treatment
Authors: Yang Liu-Yi-Yi , Wang Yu-Lu , Zuo Ya-Gang
Published: July 2024

Background

Pemphigoid diseases constitute a group of autoimmune blistering disorders characterized by subepithelial blistering. The association between pemphigoid diseases and both end-stage kidney disease (ESKD) and its treatment is notable. However, there is limited evidence about the management of pemphigoid diseases in patients with ESKD. This systematic review compiled case reports and relevant studies, summarized the underlying mechanisms of pemphigoid diseases in patients with ESKD, and summarized the efficacy of various therapies.

Methods

A systematic search of PubMed and Embase was performed for articles published between 1982 to June 2, 2024.

Results

Fifty-three case reports and eight relevant studies were included. Triggers for pemphigoids in patients with ESKD included materials used to treat ESKD, immune dysregulation of patients with ESKD, and rejection of renal allograft. Treatment for these patients included removing triggers, as well as administering of corticosteroids, mycophenolate mofetil (MMF), tetracyclines, rituximab, methotrexate, dapsone, azathioprine, cyclosporine, intravenous immunoglobin (IVIG), plasmapheresis, and Janus kinase inhibitors.

Conclusion

Removing triggers is the most effective strategy. Despite their suboptimal efficacy, corticosteroids remain the most commonly used agents in this patient population. MMF, tetracyclines, and rituximab are less used but with benefits. There are significant adverse effects associated with methotrexate treatment. Other treatment may also be beneficial and require further investigation. These findings may enable clinicians to optimize the therapeutic approach for these patients.
Verification of the reactivity of immunoglobulins in dried blood spots collected for onchocerciasis sero-surveillance by an Escherichia coli ELISA
Authors: Hassan Hassan K. , Miley Kristi M. , Unnasch Thomas R.
Published: July 2024

The World Health Organization guidelines for verification of onchocerciasis elimination include demonstrating that the prevalence of exposure to the parasite in individuals born since transmission was interrupted needs to be less than 0.1%. The guidelines recommend using seropositivity to an Onchocerca volvulus specific antigen (Ov16) for this purpose. Ov16 seropositivity has most often been assessed using the Ov16 ELISA assay. Currently, the Ov16 ELISA assay includes internal positive and negative controls to monitor for proper assay performance but does not control for the quality of the dried blood spots (DBS) being tested. Previous studies have reported a high prevalence of antibodies recognizing Escherichia coli in children. Through the development of an ELISA assay to detect antibodies recognizing E. coli, a common commensal in humans, DBS may be prescreened for quality assurance prior to testing for Ov16. Results demonstrated antibodies to E. coli were detected in 100% of randomly selected serum samples collected from O. volvulus infected individuals residing in an onchocerciasis hyperendemic area. Furthermore, when DBS were improperly stored, the E. coli antibodies were found to decay over a period of one week, while remaining unchanged over the same period in properly stored samples. Similarly, E. coli antibodies were detected in 100% of a batch of field collected properly stored DBS, while being present only in 5% of a batch of improperly stored spots. This study demonstrates the value of E. coli ELISA for DBS quality control testing and validation of proper storage of collections of DBS for the Ov16 ELISA.
Case report: Challenging kidney transplantation in an adolescent patient with tetralogy of Fallot
Authors: Jakšić Ante , Barbalić Berislav , Orlić Lidija , Župan Željko , Vujičić Božidar , Gršković Antun , Ćelić Tanja , Chinchella Ivana Koraca , Čače Neven , Flajšman-Raspor Sanja , Bubić Ivan , Španjol Josip , Markić Dean
Published: July 2024

Tetralogy of Fallot is the most common cyanotic congenital heart disease. This severe disorder of cardiac physiology can impair renal function and lead to the development of cardiorenal syndrome and eventually to end-stage renal disease. Kidney transplantation may be the best option for renal replacement treatment in patients with tetralogy of Fallot, but only after correcting cardiac abnormalities and optimizing cardiac functions, all of which require a multidisciplinary approach. We report the first case of kidney transplantation in an adolescent patient with tetralogy of Fallot. Our findings confirms that kidney transplantation is a valuable treatment option in selected congenital heart disease cases.
Application effect of the online and offline mixed education mode in nursing practice based on the SMCR communication model
Authors: Chen Qian , Jin Yanhong , Zhong Lixia , Li Yingying , Fu Li , Zhang Weiwei , Xu Qiuying
Published: July 2024

Objective

To explore the application effect of the online and offline mixed teaching mode in nursing practice teaching based on the Source Message Channel Receiver (SMCR) communication model.

Methods

By using the convenience sampling method, 15 nursing students who practiced their internship in the Department of Critical Care Medicine at Beijing Friendship Hospital affiliated to Capital Medical University for 4 weeks, from 1 April 2022 to 31 December 2023, were selected as the experimental group. A total of 16 nursing students who practiced in the same hospital in 2021 were selected as the control group. The control group used traditional teaching mode for teaching, and the experimental group used the online and offline teaching mode for teaching. The theoretical and practical achievements, competency, and teaching satisfaction of the two groups of nursing students were compared and analyzed after the internship.

Results

The theoretical knowledge, operational performance, competence of the nurses, and satisfaction with the teaching in the experimental group were higher than those of the control group (P < 0.05).

Conclusion

Based on the SMCR communication model, exploring the online and offline mixed teaching mode plays an important role in the teaching process of nursing practice, which can not only effectively improve the comprehensive performance of nursing students but also help to improve their satisfaction with teaching and has a positive impact on the cultivation of high-quality nursing talents.
Clinical efficacy of CO2 fractional laser combined with compound betamethasone in treating vitiligo and its impact on inflammatory factors
Authors: Zhang Lina , Zhang Jianzhong , Wang Xin , Zhao Zhonglin , Li Zhifeng , Miao Guoying , Lv Chao
Published: July 2024

Objective

To analyze the clinical efficacy of CO2 fractional laser combined with compound betamethasone in treating vitiligo and its impact on inflammatory factors.

Methods

The clinical treatment effects, levels of inflammatory factors [interleukin-17 (IL-17), interferon-gamma (IFN-γ), interleukin-10 (IL-10)], prognosis regarding repigmentation and relapse, psychological health (satisfaction).

Results

① Clinical treatment effects: the total effective rate in Group A was 92.73%, Group B was 74.55%, and Group C was 67.27%, with Group A showing significantly higher effectiveness than Groups B and C (p < 0.05). ② Inflammatory factors: prior to treatment, there was no significant difference in IL-17, IFN-γ, and IL-10 levels among the three groups (p > 0.05); after 3 and 6 months of treatment, the levels of IL-17 and IFN-γ decreased significantly while IL-10 levels increased significantly across all three groups, with Group A showing a more pronounced change compared to Groups B and C (p < 0.05). ③ Prognosis regarding repigmentation and relapse: after 3 and 6 months of treatment, Group A exhibited significantly higher repigmentation rates compared to Groups B and C (p < 0.05); in terms of relapse, Group A had a relapse rate of 5.45%, Group B had 21.82%, and Group C had 23.64%, with Group A showing significantly lower relapse rates compared to Groups B and C (p < 0.05). ④ Quality of life and psychological health: at the end of the 6 month follow-up, the quality of life and psychological health of patients in Group A were significantly higher than those in Groups B and C (p < 0.05). ⑤ Occurrence of adverse reactions: the incidence of adverse reactions was 12.73% in Group A, 10.91% in Group B, and 9.09% in Group C, with no significant difference observed among the three groups (p > 0.05).

Conclusion

The application of CO2 fractional laser combined with compound betamethasone in vitiligo patients demonstrates significant efficacy. Compared to sole treatment with CO2 fractional laser or compound betamethasone injections, this combined approach further improves the levels of inflammatory factors in vitiligo patients, reduces the risk of relapse, enhances skin repigmentation, improves quality of life, psychological well-being, without increasing the risk of related adverse reactions. This combined approach merits clinical promotion and application.
Obesity and adiposity promote the development of non-suppurative otitis media: a Mendelian randomization study
Authors: Yan Xin , Chen Suhua
Published: July 2024

Background

Observational studies have found that obesity is associated with the development of non-suppurative otitis media (NSOM), but the causality and pathogenesis are unclear. This study aimed to investigate the association between obesity, lipid metabolism, and NSOM at the genetic level.

Methods

We performed a bidirectional two-sample Mendelian randomization (MR) study to examine the causal relationship between obesity, lipid metabolism-related factors, and NSOM by using the datasets obtained from the IEU Open genome-wide association studies (GWAS) Project. Furthermore, a multivariate MR (MVMR) analysis on lipid indicators was conducted to validate the results. We then used obesity or body mass index (BMI) as the exposure and NSOM as the outcome to search for possible mediators in lipids and adipokines.

Results

Using NSOM as the outcome, we found nine positive exposure results related to obesity and lipid metabolism. Among them, obesity, BMI, body fat percentage, waist circumference, hip circumference, and resistin were risk factors, while apolipoprotein A1 (apoA1), high-density lipoprotein cholesterol (HDL-C), and nerve growth factor (NGF) were protective factors. Then, we used the obesity and lipid metabolism-related factors as outcomes and NSOM as the exposure to perform the MR analysis, which failed to obtain positive results. In the MVMR analysis, we found that HDL cholesterol and apoA1 remained causally associated with NSOM after correction for other potential confounders. Simultaneously, when obesity or BMI was used as the exposure and NSOM as the outcome, HDL cholesterol or apoA1 served as mediators through a two-step MR analysis. The MR analysis for mediation, obesity, and BMI reduced the production of HDL or apoA1, which served as protective factors affecting the development of NSOM.

Conclusion

At the genetic level, obesity and adiposity may promote the development of NSOM, while NSOM has no effect on obesity and adiposity. Obesity can also encourage the progress of NSOM by reducing HDL cholesterol/apoA1. Resistin may be a potential risk factor for NSOM, whereas NGF may be a potential protective factor.
Advancing musculoskeletal diagnosis and therapy: a comprehensive review of trigger point theory and muscle pain patterns
Authors: Zhai Tianjun , Jiang Fengyan , Chen Yeping , Wang Jie , Feng Wei
Published: July 2024

Musculoskeletal disorders, especially chronic muscle pain, have a significant impact on public health, affecting millions worldwide. This review examines recent advancements in the diagnosis and management of myofascial pain, with a focus on the refined application of trigger point theory. This theory now incorporates an intricate model that blends biomechanical and neurophysiological mechanisms, essential for understanding the initiation and persistence of pain, and necessitating targeted therapeutic interventions. Utilizing a methodical approach, this paper categorizes muscle pain into three types: Muscle Belly Pain, Origin-Insertion Pain, and Referred Pain, as delineated in the most recent edition of “Myofascial Pain and Dysfunction—The Trigger Point Manual.” Such classification enhances diagnostic precision and therapeutic effectiveness by establishing a specific treatment protocol for each type of pain. The paper discusses the implications of various treatments, such as dry needling and manual therapy, which are informed by empirically derived trigger point charts. These charts are instrumental in pinpointing the exact locations of pain sources and customizing treatment plans. Moreover, this review critically assesses the evolving nature of trigger point charts and champions a holistic approach to pain management. It underscores the necessity of integrating biomechanics, kinesiology, and compensatory mechanisms to provide a comprehensive understanding that allows practitioners to address not only symptomatic pain but also the root causes of musculoskeletal disorders, thereby enhancing long-term patient care outcomes in clinical environments.
Exploring the occurrence of Listeria in biofilms and deciphering the bacterial community in a frozen vegetable producing environment
Authors: Pracser Nadja , Voglauer Eva M. , Thalguter Sarah , Pietzka Ariane , Selberherr Evelyne , Wagner Martin , Rychli Kathrin
Published: July 2024

The establishment of Listeria (L.) monocytogenes within food processing environments constitutes a significant public health concern. This versatile bacterium demonstrates an exceptional capacity to endure challenging environmental conditions in the food processing environment, where contamination of food products regularly occurs. The diverse repertoire of stress resistance genes, the potential to colonize biofilms, and the support of a co-existing microbiota have been proposed as root causes for the survival of L. monocytogenes in food processing environments. In this study, 71 sites were sampled after cleaning and disinfection in a European frozen vegetable processing facility, where L. monocytogenes in-house clones persisted for years. L. monocytogenes and L. innocua were detected by a culture-dependent method at 14 sampling sites, primarily on conveyor belts and associated parts. The presence of biofilms, as determined by the quantification of bacterial load and the analysis of extracellular matrix components (carbohydrates, proteins, extracellular DNA) was confirmed at nine sites (12.7%). In two cases, L. innocua was detected in a biofilm. Furthermore, we explored the resident microbial community in the processing environment and on biofilm-positive sites, as well as the co-occurrence of bacterial taxa with Listeria by 16S rRNA gene sequencing. Pseudomonas, Acinetobacter, and Exiguobacterium dominated the microbial community of the processing environment. Using differential abundance analysis, amplicon sequence variants (ASVs) assigned to Enterobacterales (Enterobacter, Serratia, unclassified Enterobacteriaceae) and Carnobacterium were found to be significantly higher abundant in Listeria-positive samples. Several Pseudomonas ASVs were less abundant in Listeria-positive compared to Listeria-negative samples. Acinetobacter, Pseudomonas, Janthinobacterium, Brevundimonas, and Exiguobacterium were key players in the microbial community in biofilms, and Exiguobacterium and Janthinobacterium were more relatively abundant in biofilms. Further, the microbial composition varied between the different areas and the surface materials.
Bifid triple viable preparation combined with enteral nutrition as a supportive treatment for acute ischemic stroke: a systematic review and meta-analysis
Authors: Kong Yumeng , Yu Yunfeng , Deng Juan , Yu Rong , Liu Xiu
Published: July 2024

Background

The benefits and risks of bifid triple viable preparations in patients with acute ischemic stroke (AIS) are still controversial. This study aimed to assess the efficacy and safety of bifid triple viable preparations in combination with enteral nutrition for the management of AIS.

Methods

Eight public databases including China National Knowledge Infrastructure, China Biology Medicine, VIP, WanFang, EBSCO, PubMed, Cochrane Library, and Web of Science were searched for relevant clinical literature, published through January 2024. These data were then used in the present meta-analysis.

Results

A total of 15 studies involving 1,544 patients were included in the meta-analysis. In terms of nutritional status, the results showed that compared with enteral nutrition alone, the bifid triple viable preparation combination group increased the levels of total protein (mean difference [MD], 5.53; 95%confidence interval [CI], 1.94–9.12; p = 0.003), albumin (MD, 4.01; 95%CI, 2.96–5.06; p < 0.00001), prealbumin (MD, 23.08; 95%CI, 16.22–29.95; p < 0.00001), hemoglobin (MD, 9.31; 95%CI, 6.34–12.27; p < 0.00001), and transferrin (MD, 0.64; 95%CI, 0.23–1.05; p = 0.002); in terms of neurological function, it improved the Glasgow Coma Scale (MD, 2.09; 95%CI, 0.69–3.49; p = 0.003), National Institute of Health Stroke Scale (MD, −3.07; 95%CI, −3.73 to −2.40; p < 0.00001), and Neurological Disability Score (MD, −6.68; 95%CI, -7.29 to −6.08; p < 0.00001); in terms of intestinal barrier function, it reduced the levels of endotoxin (MD, −0.55; 95%CI, −0.71 to −0.39; p < 0.00001), D-lactic acid (MD, −3.17; 95%CI, −4.07 to −2.26; p < 0.00001), diamine oxidase (MD, −4.39; 95%CI, −6.20 to −2.57; p < 0.00001), and endothelin (MD, −21.35; 95%CI, −27.86 to −14.83; p < 0.00001); in terms of immune function, it increased the levels of immunoglobulin G (MD, 1.01; 95%CI, 0.20–1.82; p = 0.01) and immunoglobulin M (MD, 0.16; 95%CI, 0.02–0.30; p = 0.03). Additionally, it reduced the incidence of pulmonary infection, vomiting, constipation, and diarrhea, while there were no significant differences in total adverse events, abdominal distension, anorexia, reflux, gastrointestinal bleeding, or electrolyte disturbance.

Conclusion

The addition of bifid triple viable preparation to enteral nutrition improved the nutritional status, neurological function, intestinal barrier function, and immune function of patients with AIS, and reduced the risk of infection and gastrointestinal events.
Soil-derived cellulose-degrading bacteria: screening, identification, the optimization of fermentation conditions, and their whole genome sequencing
Authors: Ma Degao , Chen Haoyu , Liu Duxuan , Feng Chenwei , Hua Yanhong , Gu Tianxiao , Guo Xiao , Zhou Yuchen , Wang Houjun , Tong Guifeng , Li Hua , Zhang Kun
Published: July 2024

Straw cellulose is an abundant renewable resource in nature. In recent years, the conversion of cellulose from waste straw into biofuel by specific microorganisms’ fragmentation has attracted extensive attention. Although many bacteria with the ability to degrade cellulose have been identified, comprehensive bioinformatics analyses of these bacteria remain limited, and research exploring optimal fragmentation conditions is scarce. Our study involved the isolation and screening of bacteria from various locations in Yangzhou using carboxymethyl cellulose (CMC) media. Then, the cellulose-degrading bacteria were identified using 16S rRNA and seven candidate bacterial strains with cellulose degrading ability were identified in Yangzhou city for the first time. The cellulase activity was determined by the 3,5-dinitrosalicylic acid (DNS) method in different fragmentation conditions, and finally two bacteria strains with the strongest cellulose degradation ability were selected for whole genome sequencing analysis. Sequencing results revealed that the genome sizes of Rhodococcus wratislaviensis YZ02 and Pseudomonas Xanthosomatis YZ03 were 8.51 Mb and 6.66 Mb, containing 8,466 and 5,745 genes, respectively. A large number of cellulose degradation-related genes were identified and annotated using KEGG, GO and COG analyses. In addition, genomic CAZyme analysis indicated that both R. wratislaviensis YZ02 and P. Xanthosomatis YZ03 harbor a series of glycoside hydrolase family (GH) genes and other genes related to cellulose degradation. Our finding provides new options for the development of cellulose-degrading bacteria and a theoretical basis for improving the cellulose utilization of straw.
Genetic markers associated with host status and clonal expansion of Group B Streptococcus in the Netherlands
Authors: Khan Uzma Basit , Dyster Victoria , Chaguza Chrispin , van Sorge Nina M. , van de Beek Diederik , Man Wing Kit , Bentley Stephen D. , Bijlsma Merijn W. , Jamrozy Dorota
Published: July 2024

Objectives

Certain Group B Streptococcus (GBS) genotypes are associated with invasive disease in neonates. We conducted a comparative genomic analysis of GBS isolates from neonatal disease and maternal carriage in the Netherlands to determine distribution of genetic markers between the two host groups.

Methods

Whole genome sequencing was used to characterise 685 neonatal invasive isolates (2006–2021) and 733 maternal carriage isolates (2017–2021) collected in the Netherlands.

Results

Clonal complex (CC) 17 and serotype III were significantly more common in disease while carriage isolates were associated with serotypes II, IV, V as well as CC1. Previously reported CC17-A1 sub-lineage was dominant among disease isolates and significantly less common in carriage. The phiStag1 phage, previously associated with expansion of invasive CC17 isolates in the Netherlands, was more common among disease isolates compared to carriage isolates overall, however it was equally distributed between CC17 isolates from carriage and disease. Prevalence of antimicrobial resistance genes was overall lower in disease compared to carriage isolates, but increased significantly over time, mediated by rise in prevalence of a multidrug resistance element ICESag37 among disease isolates.

Conclusion

There is a stable association between certain GBS genotypes and invasive disease, which suggests opportunities for developing more precise disease prevention strategies based on GBS targeted screening. In contrast, GBS mobile genetic elements appear less likely to be correlated with carriage or disease, and instead are associated with clonal expansion events across the GBS population.
Surveillance of fluoroquinolones resistance in rifampicin-susceptible tuberculosis in eastern China with whole-genome sequencing-based approach
Authors: Che Yang , Lu Yewei , Zhu Yelei , He Tianfeng , Li Xiangchen , Gao Junli , Gao Junshun , Wang Xiaomeng , Liu Zhengwei , Tong Feng
Published: July 2024

Background

Leveraging well-established DNA-level drug resistance mechanisms, whole-genome sequencing (WGS) has emerged as a valuable methodology for predicting drug resistance. As the most effective second-line anti-tuberculosis (anti-TB) drugs, fluoroquinoloness (FQs) are generally used to treat multidrug-resistant tuberculosis (MDR-TB, defined as being resistant to resistant to rifampicin and isoniazid) or rifampicin-resistant tuberculosis (RR-TB). However, FQs are also commonly used in the management of other bacterial infections. There are few published data on the rates of FQs resistance among rifampicin-susceptible TB. The prevalence of FQs resistance among TB patients who are rifampicin-susceptible has not been studied in Zhejiang Province, China. The goal of this study was to provide a baseline characterization of the prevalence of FQs resistance, particularly among rifampicin-susceptible TB in Zhejiang Province, China.

Methods

Based on WGS, we have investigated the prevalence of FQs resistance among rifampicin-susceptible TB in Zhejiang Province. All pulmonary TB patients with positive cultures who were identified in Zhejiang area during TB drug resistance surveillance from 2018 to 2019 have enrolled in this population-based retrospective study.

Results

The rate of FQs resistance was 4.6% (32/698) among TB, 4.0% (27/676) among rifampicin-susceptible TB, and 22.7% (5/22) among RR-TB. According to WGS, strains that differ within 12 single-nucleotide polymorphisms (SNPs) were considered to be transmission of FQ-resistant strains. Specifically, 3.7% (1/27) of FQs resistance was caused by the transmission of FQs-resistant strains among the rifampicin-susceptible TB and 40.7% (11/27) of FQs resistance was identified as hetero-resistance.

Conclusion

The prevalence of FQs resistance among TB patients who were rifampicin-susceptible was severe in Zhejiang. The emergence of FQs resistance in TB isolates that are rifampicin-susceptible was mainly caused by the selection of drug-resistant strains. In order to prevent the emergence of FQs resistance, the WGS-based surveillance system for TB should be urgently established, and clinical awareness of the responsible use of FQs for respiratory infections should be enhanced.
Melodious tuning of microbial dynamics in biofloc, cage, and pond culturing system: a study on Pangasius pangasius fish gut microbiome
Authors: Vala Foram D. , Lende Smit R. , Solanki Vishal K. , Jora Kiran , Desai Riya , Sharma Parth , Nathani Neelam , Mootapally Chandrashekar
Published: July 2024

Aquaculture, a rapidly expanding sector, meets the global surging demand for aquatic food. Pangasius, a highly valued freshwater species, has seen a significant increase in demand due to its adaptability and potential for high yields, making it a promising candidate for aquaculture in India. This study investigates the gut microbiome composition of Pangasius pangasius fish cultured in three different systems (biofloc, cage, and pond). Metagenomic DNA extraction and 16S rRNA gene-targeted sequencing were performed. Outcomes revealed distinct microbial compositions across culture types, with significant differences in species richness and diversity, specifically in the biofloc system, compared to cages and ponds. Taxonomic analysis identified prevalent phyla such as Firmicutes and Fusobacteriota, with varying abundances among culture systems. The genus-level analysis highlighted dominant genera such as Cetobacterium and WWE3. Functional profiling indicated differences in enzymatic activity and metabolic pathways, emphasizing each culture sample type's unique microbial community structures. Notably, the microbiota from BF samples exhibited significant differences and unique metabolic pathways compared to the microbiota from C and P samples, which showed greater similarity and shared several common metabolic pathways. These findings highlight substantial differences in microbial diversity across the culturing systems, reflecting the microbiota's ability to adapt to specific environments and their potential role in promoting fish growth within those environments. Overall, this study provides insights into the gut microbiome diversity and functionality in Pangasius pangasius across different aquaculture environments, contributing to a better understanding of host–microbe interactions and aquaculture management strategies.
Artificial intelligence in ischemic stroke images: current applications and future directions
Authors: Liu Ying , Wen Zhongjian , Wang Yiren , Zhong Yuxin , Wang Jianxiong , Hu Yiheng , Zhou Ping , Guo Shengmin
Published: July 2024

This paper reviews the current research progress in the application of Artificial Intelligence (AI) based on ischemic stroke imaging, analyzes the main challenges, and explores future research directions. This study emphasizes the application of AI in areas such as automatic segmentation of infarct areas, detection of large vessel occlusion, prediction of stroke outcomes, assessment of hemorrhagic transformation risk, forecasting of recurrent ischemic stroke risk, and automatic grading of collateral circulation. The research indicates that Machine Learning (ML) and Deep Learning (DL) technologies have tremendous potential for improving diagnostic accuracy, accelerating disease identification, and predicting disease progression and treatment responses. However, the clinical application of these technologies still faces challenges such as limitations in data volume, model interpretability, and the need for real-time monitoring and updating. Additionally, this paper discusses the prospects of applying large language models, such as the transformer architecture, in ischemic stroke imaging analysis, emphasizing the importance of establishing large public databases and the need for future research to focus on the interpretability of algorithms and the comprehensiveness of clinical decision support. Overall, AI has significant application value in the management of ischemic stroke; however, existing technological and practical challenges must be overcome to achieve its widespread application in clinical practice.
Hospital outcomes of acute COVID-19 infection among patients with neurological conditions: a single-center study
Authors: Desouky Adam , Fuentes Venessa , Tiwari Chhitij , Usui Hikari , Smith Ayala Arthor H. , Wilson Susan E. , Diaz Monica M.
Published: July 2024

Background

Coronavirus disease 2019 (COVID-19) infection has been associated with severe neurological consequences, including stroke or seizures, and less severe neurological sequelae, including headaches, dizziness, and anosmia. Earlier COVID-19 variants were associated with high morbidity and mortality; however, knowledge of the impact of neurological conditions in the setting of COVID-19 on healthcare outcomes is limited. We sought to determine the impact of acute neurological conditions and acute COVID-19 infection on inpatient hospitalization outcomes.

Methods

This was a retrospective, observational study of adult patients who were admitted to a large academic medical center in the Southeastern US between April 2020 and December 2021 with acute COVID-19 infection and a neurological diagnosis. Patient demographics, medical history, neurological diagnoses, and hospitalization outcomes were obtained from the medical record. Descriptive statistics and unadjusted and adjusted logistic regression analyses were performed.

Results

Of the 1,387 patients included in this study, 27% died and 23% were kept under ventilation during hospitalization. The mean +/− standard deviation (SD) age was 64.6+/−16.9 years, with 52.8% women and 30.1% identifying as Black/African American. The most common neurological conditions included ischemic stroke (35.0%), movement disorder (12.0%), and hemorrhagic stroke (10.7%). In-hospital death was most common among those with epilepsy (p = 0.024), headache (p = 0.026), and dementia (p < 0.0001) compared to individuals without those conditions. Ventilation support was given more commonly to dementia patients (p = 0.020). Age was a significant risk factor for death (p < 0.001) and hospital length of stay (LOS) for ventilation (p < 0.001), but no neurological condition was a significant factor in adjusted logistic regression analyses.

Discussion

Mortality was high in this study, with more than one-quarter of patients dying in the hospital. Death was the most common among those with epilepsy, headache, or dementia, but no neurological condition increased the risk of in-hospital mortality or ventilation. Future studies would determine the long-term neurological sequelae of those discharged from the hospital with COVID-19 and a neurological condition.