bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic insights into the composition and function of the gut microbiota of mice infected with Toxoplasma gondii
Authors: Meng Jin-Xin , Wei Xin-Yu , Guo Huanping , Chen Yu , Wang Wei , Geng Hong-Li , Yang Xing , Jiang Jiang , Zhang Xiao-Xuan 
Published: April 2023

IntroductionDespite Toxoplasma gondii infection leading to dysbiosis and enteritis, the function of gut microbiota in toxoplasmosis has not been explored.MethodsHere, shotgun metagenomics was employed to characterize the composition and function of mouse microbial community during acute and chronic T. gondii infection, respectively.ResultsThe results revealed that the diversity of gut bacteria was decreased immediately after T. gondii infection, and was increased with the duration of infection. In addition, T. gondii infection led to gut microbiota dysbiosis both in acute and chronic infection periods. Therein, several signatures, including depression of Firmicutes to Bacteroidetes ratio and infection-enriched Proteobacteria, were observed in the chronic period, which may contribute to aggravated gut inflammation and disease severity. Functional analysis showed that a large amount of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and carbohydrate-active enzymes (CAZy) family displayed distinct variation in abundance between infected and healthy mice. The lipopolysaccharide biosynthesis related pathways were activated in the chronic infection period, which might lead to immune system imbalance and involve in intestinal inflammation. Moreover, microbial and functional spectrums were more disordered in chronic than acute infection periods, thus implying gut microbiota was more likely to participate in disease process in the chronically infected mice, even exacerbated immunologic derangement and disease progression.DiscussionOur data indicate that the gut microbiota plays a potentially important role in protecting mice from T. gondii infection, and contributes to better understand the association between gut microbiota and toxoplasmosis.
Severe COVID-19 and non-COVID-19 severe sepsis converge transcriptionally after a week in the intensive care unit, indicating common disease mechanisms
Authors: An Andy Y. , Baghela Arjun , Zhang Peter , Falsafi Reza , Lee Amy H. , Trahtemberg Uriel , Baker Andrew J. , dos Santos Claudia C. , Hancock Robert E. W. 
Published: April 2023

IntroductionSevere COVID-19 and non-COVID-19 pulmonary sepsis share pathophysiological, immunological, and clinical features. To what extent they share mechanistically-based gene expression trajectories throughout hospitalization was unknown. Our objective was to compare gene expression trajectories between severe COVID-19 patients and contemporaneous non-COVID-19 severe sepsis patients in the intensive care unit (ICU).MethodsIn this prospective single-center observational cohort study, whole blood was drawn from 20 COVID-19 patients and 22 non-COVID-19 adult sepsis patients at two timepoints: ICU admission and approximately a week later. RNA-Seq was performed on whole blood to identify differentially expressed genes and significantly enriched pathways.ResultsAt ICU admission, despite COVID-19 patients being almost clinically indistinguishable from non-COVID-19 sepsis patients, COVID-19 patients had 1,215 differentially expressed genes compared to non-COVID-19 sepsis patients. After one week in the ICU, the number of differentially expressed genes dropped to just 9 genes. This drop coincided with decreased expression of antiviral genes and relatively increased expression of heme metabolism genes over time in COVID-19 patients, eventually reaching expression levels seen in non-COVID-19 sepsis patients. Both groups also had similar underlying immune dysfunction, with upregulation of immune processes such as “Interleukin-1 signaling” and “Interleukin-6/JAK/STAT3 signaling” throughout disease compared to healthy controls.DiscussionEarly on, COVID-19 patients had elevated antiviral responses and suppressed heme metabolism processes compared to non-COVID-19 severe sepsis patients, although both had similar underlying immune dysfunction. However, after one week in the ICU, these diseases became indistinguishable on a gene expression level. These findings highlight the importance of early antiviral treatment for COVID-19, the potential for heme-related therapeutics, and consideration of immunomodulatory therapies for both diseases to treat shared immune dysfunction.
Dose-response relationship of resistance training for muscle morphology and strength in elderly cancer patients: A meta-analysis
Authors: Zhai Haiting , Wei Hongwen , Xia Jixiang , Wang Wei 
Published: April 2023

ObjectiveTo systematically evaluate the effects of resistance training (RT) on muscle strength and muscle hypertrophy in elderly cancer patients, and to provide dose–response relationships of RT variables that could improve muscle strength and morphology in elderly cancer patients.MethodThe Review Manager 5.3 was applied to analyze the 12 literatures (616 participants) through random or fixed effects model and global effect size to examine upper limb strength, lower extremity strength, and muscle hypertrophy. Sub-group analysis was made on five variables: the total number of repeated training times/week, load intensity, exercise frequency/week, exercise duration and gender. This study also examines the heterogeneity and publication bias.ResultsTwelve literatures (616 participants, 60–80 years) were included in meta-analysis. RT significantly increased the upper limb muscular strength (SMD = 0.51, 95% CI: 0.10–0.93; Z = 2.41; p = 0.02) and lower extremity strength (SMD = 0.48, 95% CI: 0.28–0.67; Z = 4.82; p &lt; 0.00001), but had no significant effect on muscle morphology(SMD = 0.21, 95% CI: 0.01–0.42; Z = 1.88; p = 0.06). In subgroup analysis for lower extremity muscle strength in elderly male cancer patients, it was found that male intensity of 70–90%1RM, volume of 400–500 times per week, frequencies of 3 times per week, and session of 12–24 weeks, revealed the greatest effect. Funnel plot of the three studies shows that the results were reliable, and no publication bias was found.ConclusionRT had medium effects on improving muscle strength in elderly cancer patients, but it is not effective in improving muscle hypertrophy. In addition, when RT is performed, different training protocols can have an effect on the growth of muscle strength. Therefore, a lower extremity training protocol with a training intensity of 70–90% 1RM, a total of 400–500 repetitions per week, 3 times per week, and an exercise session of 12–24 weeks is most effective in improving lower extremity strength in elderly male cancer patients.
Different endoscopic treatments for small colorectal polyps: A systematic review, pair-wise, and network meta-analysis
Authors: Li Xuanhan , Zhu He , Li Fudong , Li Ri , Xu Hong 
Published: April 2023

Background and study aimsIn recent years, cold snare polypectomy (CSP) has been increasingly used for small polyps (&lt;10 mm) instead of hot snare polypectomy (HSP). However, evidence-based research regarding the effectiveness and safety of CSP and HSP are still lacking. Additionally, for 4–10 -mm non-pedunculated polyps, the polyp removal method is still controversial. Therefore, it is clinically significant to conduct pair-wise and network meta-analyses to assess such resection methods.MethodsWe searched PubMed, Embase, and the Cochrane library for randomized controlled trials (RCTs). Only studies that involved the resection of polyps &lt;10 mm were included. Outcomes included the complete resection rate, polyp retrieval rate, procedure-related complications, and procedure times.ResultsOverall, 23 RCTs (5,352 patients) were identified. In meta-analysis compared CSP versus HSP for polyps &lt;10 mm, CSP showed lower complete resection rate than HSP although with no statistically significant difference [odds ratio (OR): 0.77, 95% confidence interval (CI): 0.56–1.06]. CSP showed a lower risk of major post-polypectomy complications compared to HSP (OR: 0.28, 95% CI: 0.11–0.73). In the network meta-analysis for 4–10 mm non-pedunculated polyps, HSP, and endoscopic mucosal resection (EMR) showed a higher complete resection rate than CSP (OR: 2.7, 95% CI: 1.3–9.2 vs. OR: 2.6, 95% CI: 1.0–10) but a significantly longer time than CSP (WMD: 16.55 s, 95% CI [7.48 s, 25.25 s], p &lt; 0.001), (WMD: 48.00 s, 95% CI [16.54 s, 79.46 s], p = 0.003). Underwater CSP ranked third for complete resection with no complications.ConclusionFor &lt;10 mm polyps, CSP is safer than HSP, especially for patients taking antithrombotic drugs. For 4–10 mm non-pedunculated polyps, HSP, and EMR have higher complete resection rates than CSP.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/, identifier CRD42022315575.
Corrective surgery for nipple depression in patients with plasmacytic mastitis – A single-center experience
Authors: Xu Yajun , Da Bu , Zhao Fengxia , Gao Mingjuan , Xue Lihua , Zheng Hao , Shi Hongzhi , Hou Lihua , Miao Shan , Liu Xinwei , Wang Yajing , Xu Hong 
Published: April 2023

BackgroundPlasma cell mastitis (PCM) is a complex breast disease in the clinic. Currently, there are no unified diagnostic criteria for the disease and no standard treatment methods. The effects of hormone, Conventional Chinese medicine and other treatments are uncertain, with long treatment duration and notable side effects. Surgery is the preferred treatment, but the recurrence rate after conventional surgery is very high, which may be related to depression of the nipple. This study aimed to evaluate the efficacy of a novel corrective procedure in patients with cellular mastitis and depressed nipples.MethodsPatients with PCM who received surgical treatment in the Third Medical Center of PLA General Hospital from January 1996 to January 2018 were retrospectively analyzed. According to the presence or absence of nipple depression before surgery, the patients were divided into the nipple depression group and the non-nipple depression group. In the nipple depression group, patients were subdivided into a novel corrective surgery group (“one” suture or half pocket suture) and a conventional corrective surgery group (oil yarn traction valgus correction of nipple depression). Demographic, clinical, therapeutic, and postoperative relapse data were collected and analyzed.ResultsCompared with the patients in the non-nipple depression group, patients in the nipple depression group had a significantly higher recurrence risk after surgery (HR = 2.129 95% CI: 1.110–4.083, p = 0.023). Patients who underwent novel corrective surgery had a significantly lower recurrence risk than those who underwent conventional corrective surgery (HR = 0.363 95% CI: 0.150–0.880, p = 0.025). In addition, the novel corrective surgery significantly reduced the postoperative recurrence risk (HR = 0.088 95% CI: 0.009–0.886, p = 0.037).ConclusionHow to correct nipple depression is a critical factor for postoperative recurrence of PCM, and this novel corrective surgery for nipple depression can effectively reduce the postoperative recurrence rate in patients with nipple depression.
Tell me if you prefer bovine or poultry sectors and I’ll tell you who you are: Characterization of Salmonella enterica subsp. enterica serovar Mbandaka in France
Authors: De Sousa Violante Madeleine , Michel Valérie , Romero Karol , Bonifait Laetitia , Baugé Louise , Perrin-Guyomard Agnès , Feurer Carole , Radomski Nicolas , Mallet Ludovic , Mistou Michel-Yves , Cadel-Six Sabrina 
Published: April 2023

IntroductionIn north-western France, Salmonella enterica susp. enterica serovar Mbandaka (S. Mbandaka) is most frequently isolated from bovine and dairy samples. While this serovar most often results in asymptomatic carriage, for a number of years it has caused episodes of abortions, which have serious economic consequences for the sector. Interestingly, this serovar is also isolated from Gallus gallus in the same geographic zone. Despite its prevalence in bovines in north-western France, S. Mbandaka has not been broadly studied at the genomic level, and its prevalence and host adaptation are still not fully understood.MethodsIn this study, we analyzed the genomic diversity of 304 strains of S. Mbandaka isolated from the bovine and poultry sectors in this area over a period of 5 years. A phylogenetic analysis was carried out and two approaches were followed to identify conserved genes and mutations related to host associations. The first approach targeted the genes compiled in the MEGARESv2, Resfinder, VFDB and SPI databases. Plasmid and phage contents were also investigated. The second approach refers to an in-house algorithm developed for this study that computes sensitivity, specificity, and accuracy of accessory genes and core variants according to predefined genomes groups.Results and discussionAll the analyzed strains belong to the multi-locus sequence type profile ST413, and the phylogenomic analysis revealed main clustering by host (bovine and poultry), emphasizing the circulation of 12 different major clones, of which seven circulate in poultry and five in the bovine sector in France and a likely food production chain adaptation of these clones. All strains present resistance determinants including heavy metals and biocides that could explain the ability of this serovar to survive and persist in the environment, within herds, and in food processing plants. To explore the wild animal contribution to the spread of this serovar in north-western France, we retrieved S. Mbandaka genomes isolated from wild birds from EnteroBase and included them in the phylogenomic analysis together with our collection. Lastly, screening of accessory genes and major variants allowed us to identify conserved specific mutations characteristic of each major cluster. These mutations could be used to design useful probes for food safety surveillance.
Non-targeted metabolomics of moldy wheat by ultra-performance liquid chromatography – quadrupole time-of-flight mass spectrometry
Authors: Gao Boyan , Lu Weiying , Jin Mengchu , Chen Yumei 
Published: April 2023

IntroductionAs one of the staple foods for the world’s major populations, the safety of wheat is critical in ensuring people’s wellbeing. However, mildew is one of the prevalent safety issues that threatens the quality of wheat during growth, production, and storage. Due to the complex nature of the microbial metabolites, the rapid identification of moldy wheat is challenging.MethodsIn this research, identification of moldy wheat samples was studied using ultra-performance liquid chromatography - quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) coupled with chemometrics. The non-targeted PCA model for identifying moldy wheat from normal wheat was established by using previously established compounds database of authentic wheat samples. The partial least squares-discriminant analysis (PLS-DA) was performed.Results and discussionBy optimizing the model parameters, correct discrimination of the moldy wheat as low as 5% (w/w) adulteration level could be achieved. Differential biomarkers unique to moldy wheat were also extracted to identify between the moldy and authentic wheat samples. The results demonstrated that the chemical information of wheat combined with the existing PCA model could efficiently discriminate between the constructed moldy wheat samples. The study offered an effective method toward screening wheat safety.
Gut microbiota from sigma-1 receptor knockout mice induces depression-like behaviors and modulates the cAMP/CREB/BDNF signaling pathway
Authors: Li Jia-Hao , Liu Jia-Li , Li Xiu-Wen , Liu Yi , Yang Jian-Zheng , Chen Li-Jian , Zhang Kai-Kai , Xie Xiao-Li , Wang Qi 
Published: April 2023

IntroductionDepression is a common mental disorder that affects approximately 350 million people worldwide. Much remains unknown about the molecular mechanisms underlying this complex disorder. Sigma-1 receptor (Sig-1R) is expressed at high levels in the central nervous system. Increasing evidence has demonstrated a close association between the Sig-1R and depression. Recently, research has suggested that the gut microbiota may play a crucial role in the development of depression.MethodsMale Sig-1R knockout (Sig-1R KO) and wild-type (WT) mice were used for this study. All transgenic mice were of a pure C57BL/6J background. Mice received a daily gavage of vancomycin (100 mg/kg), neomycin sulfate (200 mg/kg), metronidazole (200 mg/kg), and ampicillin (200 mg/kg) for one week to deplete gut microbiota. Fecal microbiota transplantation (FMT) was conducted to assess the effects of gut microbiota. Depression-like behaviors was evaluated by tail suspension test (TST), forced swimming test (FST) and sucrose preference test (SPT). Gut microbiota was analyzed by 16s rRNA and hippocampal transcriptome changes were assessed by RNA-seq.ResultsWe found that Sig-1R knockout induced depression-like behaviors in mice, including a significant reduction in immobility time and an increase in latency to immobility in the FST and TST, which was reversed upon clearance of gut microbiota with antibiotic treatment. Sig-1R knockout significantly altered the composition of the gut microbiota. At the genus level, the abundance of Alistipes, Alloprevotella, and Lleibacterium decreased significantly. Gut microbiota dysfunction and depression-like phenotypes in Sig-1R knockout mice could be reproduced through FMT experiments. Additionally, hippocampal RNA sequencing identified multiple KEGG pathways that are associated with depression. We also discovered that the cAMP/CREB/BDNF signaling pathway is inhibited in the Sig-1R KO group along with lower expression of neurotrophic factors including CTNF, TGF-α and NGF. Fecal bacteria transplantation from Sig-1R KO mice also inhibited cAMP/CREB/BDNF signaling pathway.DiscussionIn our study, we found that the gut-brain axis may be a potential mechanism through which Sig-1R regulates depression-like behaviors. Our study provides new insights into the mechanisms by which Sig-1R regulates depression and further supports the concept of the gut-brain axis.
New insights into the epidemiology of Listeria monocytogenes – A cross-sectoral retrospective genomic analysis in the Netherlands (2010–2020)
Authors: Coipan Claudia E. , Friesema Ingrid H. M. , van Hoek Angela H. A. M. , van den Bosch Tijs , van den Beld Maaike , Kuiling Sjoerd , Gras Lapo Mughini , Bergval Indra , Bosch Thijs , Wullings Bart , van der Voort Menno , Franz Eelco 
Published: April 2023

IntroductionListeriosis, caused by infection withListeria monocytogenes(Lm), is a relatively rare but severe disease with one of the highest mortality rates among bacterial foodborne illnesses. A better understanding on the degree ofLmclustering, the temporal distribution of the clusters, and their association with the various food sources is expected to lead to improved source tracing and risk-based sampling.MethodsWe investigated the genomic epidemiology ofLmin the Netherlands between 2010 and 2020 by analyzing whole-genome-sequencing (WGS) data of isolates from listerioss patients and food sources from nationwide integrated surveillance and monitoring. WGS data of 756 patient and 770 food/environmental isolates was assessed using core-genome multi-locus sequence typing (cgMLST) with Hamming distance as measure for pairwise distances. Associations of genotype with the epidemiological variables such as patient’s age and gender, and systematic use of specific drugs were tested by multinomial logistic regressions. Genetic differentiation of theLmwithin and between food categories was calculated based on allele frequencies at the 1701 cgMLST loci in each food category.ResultsWe confirmed previous results that some clonal complexes (CCs) are overrepresented among clinical isolates but could not identify any epidemiological risk factors. The main findings of this study include the observation of a very weak attribution ofLmtypes to food categories and a much better attribution to the producer level. In addition, we identified a high degree of temporal persistence of food, patient and mixed clusters, with more than half of the clusters spanning over more than 1 year and up to 10  years.DiscussionTaken together this would indicate that identifying persistent contamination in food production settings, and producers that process a wide variety of raw food produce, could significantly contribute to lowering theLmdisease burden.
Biocontrol potential and action mechanism of Bacillus amyloliquefaciens DB2 on Bipolaris sorokiniana
Authors: Luan Pengyu , Yi Yanjie , Huang Yifan , Cui Liuqing , Hou Zhipeng , Zhu Lijuan , Ren Xiujuan , Jia Shao , Liu Yang 
Published: April 2023

IntroductionBipolaris sorokiniana is the popular pathogenic fungi fungus which lead to common root rot and leaf spot on wheat. Generally, chemical fungicides are used to control diseases. However, the environmental pollution resulting from fungicides should not be ignored. It is important to study the mode of antagonistic action between biocontrol microbes and plant pathogens to design efficient biocontrol strategies.ResultsAn antagonistic bacterium DB2 was isolated and identified as Bacillus amyloliquefaciens. The inhibition rate of cell-free culture filtrate (CF, 20%, v/v) of DB2 against B. sorokiniana reached 92.67%. Light microscopy and scanning electron microscopy (SEM) showed that the CF significantly altered the mycelial morphology of B. sorokiniana and disrupted cellular integrity. Fluorescence microscopy showed that culture filtrate destroyed mycelial cell membrane integrity, decreased the mitochondrial transmembrane potential, induced reactive oxygen species (ROS) accumulation, and nuclear damage which caused cell death in B. sorokiniana. Moreover, the strain exhibited considerable production of protease and amylase, and showed a significant siderophore and indole-3-acetic acid (IAA) production. In the detached leaves and potted plants control assay, B. amyloliquefacien DB2 had remarkable inhibition activity against B. sorokiniana and the pot control efficacy was 75.22%. Furthermore, DB2 suspension had a significant promotion for wheat seedlings growth.ConclusionB. amyloliquefaciens DB2 can be taken as a potential biocontrol agent to inhibit B. sorokiniana on wheat and promote wheat growth.