bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of anti-lymphocyte IgM autoantibodies driving complement activation in COVID-19 patients
Authors: Pérez-Díez Ainhoa , Liu Xiangdong , Calderon Stephanie , Bennett Ashlynn , Lisco Andrea , Kellog Anela , Galindo Frances , Memoli Matthew J. , Rocco Joseph M. , Epling Brian P. , Laidlaw Elizabeth , Sneller Mike C. , Manion Maura , Wortmann Glenn W. , Poon Rita , Kumar Princy , Sereti Irini 
Published: April 2024

IntroductionCOVID-19 patients can develop autoantibodies against a variety of secreted and membrane proteins, including some expressed on lymphocytes. However, it is unclear what proportion of patients might develop anti-lymphocyte antibodies (ALAb) and what functional relevance they might have.MethodsWe evaluated the presence and lytic function of ALAb in the sera of a cohort of 85 COVID-19 patients (68 unvaccinated and 17 vaccinated) assigned to mild (N=63), or moderate/severe disease (N=22) groups. Thirty-seven patients were followed-up after recovery. We also analyzed in vivo complement deposition on COVID-19 patients’ lymphocytes and examined its correlation with lymphocyte numbers during acute disease.ResultsCompared with healthy donors (HD), patients had an increased prevalence of IgM ALAb, which was significantly higher in moderate/severe disease patients and persisted after recovery. Sera from IgM ALAb+ patients exhibited complement-dependent cytotoxicity (CDC) against HD lymphocytes. Complement protein C3b deposition on patients’ CD4 T cells was inversely correlated with CD4 T cell numbers. This correlation was stronger in moderate/severe disease patients.DiscussionIgM ALAb and complement activation against lymphocytes may contribute to the acute lymphopenia observed in COVID-19 patients.
Identification of extracellular matrix-related biomarkers in colon adenocarcinoma by bioinformatics and experimental validation
Authors: Yin Yongkui , Yang Xiaojie , Cheng Zhengyi , Wang Hui , Lei Jun , Wang Dan , Wang Peiwen , Li Biao , Mi Jing , Yuan Qi 
Published: April 2024

BackgroundsExtracellular matrix (ECM) is an important component of tumor microenvironment, and its abnormal expression promotes tumor formation, progression and metastasis.MethodsWeighted gene co-expression network analysis (WGCNA) was used to identify ECM-related hub genes based on The Cancer Genome Atlas (TCGA) colon adenocarcinoma (COAD) data. COAD clinical samples were used to verify the expression of potential biomarkers in tumor tissues, and siRNA was used to explore the role of potential biomarkers in cell proliferation and epithelial−mesenchymal transition (EMT).ResultsThree potential biomarkers (LEP, NGF and PCOLCE2) related to prognosis of COAD patients were identified and used to construct ERGPI. Immunohistochemical analysis of clinical samples showed that the three potential biomarkers were highly expressed in tumor tissues of COAD patients. Knockdown of LEP, NGF or PCOLCE2 inhibited COAD cell proliferation and EMT. Dictamnine inhibited tumor cell growth by binding to these three potential biomarkers based on molecular docking and transplanted tumor model.ConclusionThe three biomarkers can provide new ideas for the diagnosis and targeted therapy of COAD patients.
Deep learning–assisted biodiversity assessment in deep-sea benthic megafauna communities: a case study in the context of polymetallic nodule mining
Authors: Cuvelier Daphne , Zurowietz Martin , Nattkemper Tim W. 
Published: April 2024

IntroductionTechnological developments have facilitated the collection of large amounts of imagery from isolated deep-sea ecosystems such as abyssal nodule fields. Application of imagery as a monitoring tool in these areas of interest for deep-sea exploitation is extremely valuable. However, in order to collect a comprehensive number of species observations, thousands of images need to be analysed, especially if a high diversity is combined with low abundances such is the case in the abyssal nodule fields. As the visual interpretation of large volumes of imagery and the manual extraction of quantitative information is time-consuming and error-prone, computational detection tools may play a key role to lessen this burden. Yet, there is still no established workflow for efficient marine image analysis using deep learning–based computer vision systems for the task of fauna detection and classification.MethodsIn this case study, a dataset of 2100 images from the deep-sea polymetallic nodule fields of the eastern Clarion-Clipperton Fracture zone from the SO268 expedition (2019) was selected to investigate the potential of machine learning–assisted marine image annotation workflows. The Machine Learning Assisted Image Annotation method (MAIA), provided by the BIIGLE system, was applied to different set-ups trained with manually annotated fauna data. The results computed with the different set-ups were compared to those obtained by trained marine biologists regarding accuracy (i.e. recall and precision) and time.ResultsOur results show that MAIA can be applied for a general object (i.e. species) detection with satisfactory accuracy (90.1% recall and 13.4% precision), when considered as one intermediate step in a comprehensive annotation workflow. We also investigated the performance for different volumes of training data, MAIA performance tuned for individual morphological groups and the impact of sediment coverage in the training data.DiscussionWe conclude that: a) steps must be taken to enable computer vision scientists to access more image data from the CCZ to improve the system’s performance and b) computational species detection in combination with a posteriori filtering by marine biologists has a higher efficiency than fully manual analyses.
The impact of spiritual care on the psychological health and quality of life of adults with heart failure: a systematic review of randomized trials
Authors: Zhang Guangwei , Zhang Qiyu , Li Fan 
Published: April 2024

BackgroundHeart failure (HF) brings not only physical pain but also psychological distress. This systematic review investigated the influence of spiritual care on the psychological well-being and quality of life in adults with HF.MethodsWe conducted a systematic literature review following PRISMA guidelines, searching seven electronic databases for relevant randomized controlled studies without language or temporal restrictions. The studies were assessed for quality using the Cochrane Bias Risk tool.ResultsA total of 13 studies (882 participants) were reviewed, investigating interventions such as religion, meditation, mental health, cognitive interventions, and spiritual support. Key factors influencing the effectiveness of spiritual care implementation included integration into routine care, respect for diversity, patient engagement, intervention quality, and alignment with patient beliefs. The majority of the studies indicated that spiritual care has a potentially beneficial impact on the mental health and quality of life of patients with HF.ConclusionThe findings provide valuable insights for healthcare professionals, highlighting the importance of adopting a spiritual care approach to healthcare for this population.
The effect of supplementing with Saccharomyces boulardii on bismuth quadruple therapy for eradicating Helicobacter pylori: a systematic review and meta-analysis of randomized controlled trials
Authors: Chen Yin , Teng Tao , Su Yu , Chen Wen-Zhong 
Published: April 2024

Background and objectiveIt remains uncertain if the addition of Saccharomyces boulardii (S. boulardii) to bismuth quadruple therapy (BQT) recommended in the current guidelines can enhance the Helicobacter pylori (H. pylori) eradication rate and decrease the incidence of adverse events. We therefore conducted a meta-analysis of randomized controlled trials (RCTs) to address this issue.MethodsWe performed comprehensive searches in PubMed, Embase, Web of Science, and Cochrane library databases from the inception of the databases through to November 1, 2023. A meta-analysis was conducted to determine the pooled relative risk (RR) with 95% confidence intervals (CI) using a random-effects model. We utilized the revised Cochrane Risk of Bias Tool to assess the risk of bias of included studies.ResultsA total of six RCTs (1,404 patients) included in this meta-analysis. The results of the intention-to-treat analysis showed that the combination of S. boulardii with BQT had a higher eradication rate than BQT alone (87.0% versus 83.3%), with a pooled RR of 1.05 (95% CI: 1.00–1.10, p = 0.03). In the per-protocol analysis, however, there was no statistical significance between the two groups in the eradication rate (93.7% versus 91.0%, RR = 1.03, 95% CI: 1.00–1.06, p = 0.07). The combination of S. boulardii and BQT had a significantly lower rate of overall adverse events (22% vs. 39%, RR = 0.56, 95% CI: 0.44–0.70, p &lt; 0.00001), diarrhea (7.9% vs. 25.7%, RR = 0.29, 95% CI: 0.17–0.48, p &lt; 0.00001), constipation (2.9% vs. 8.4%, RR = 0.35, 95% CI: 0.14–0.88, p = 0.03) and abdominal distention (4.9% vs. 12.7%, RR = 0.41, 95% CI: 0.23–0.72, p = 0.002) than BQT alone. For the assessment of risk of bias, five studies were deemed to have some concerns, while one study was judged to have a low risk.ConclusionCurrent evidence suggests that supplementation with S. boulardii in BQT may not have a major effect on the H. pylori eradication rate, but significantly reduces the incidence of overall adverse events, diarrhea, abdominal distention and constipation. Combining S. Boulardii with BQT can help alleviate symptoms, potentially improving patient adherence.Systematic review registrationhttps://osf.io/n9z7c.
Antimicrobial stewardship program for gastrointestinal surgeries at a Vietnamese tertiary hospital
Authors: Pham Hong Tham , Mai-Phan Tuong-Anh , Nguyen Anh Dung , Nguyen Van-Quang-Huy , Tran Minh-Hoang 
Published: April 2024

BackgroundAntimicrobial Stewardship Programs (ASP) have been applied widely in high-resource countries to prevent surgical site infections (SSI). Evidence favoring ASP interventions (ASPi) in gastrointestinal surgeries from low and middle-income countries has been limited, especially in antimicrobial prophylaxis. We aimed to investigate this gap at a Vietnamese tertiary hospital.MethodsWe conducted a retrospective cohort study on patients undergoing clean-contaminated surgeries in 2015 who received standard of care (SoC) or SoC + ASPi. Primary outcome was 30-day SSI incidence. Secondary outcomes included length of stay (LoS) after surgery (days), cost of antibiotics, and cost of treatment (USD). Results were controlled for multiplicity and reported with treatment effect and 95% confidence interval (95%CI). A predictive model was built and cross-validated to detect patients at high risk of SSI.ResultsWe included 395 patients for analysis (48.1% being female, mean age 49.4 years). Compared to patients receiving SoC, those with SoC + ASPi had a lower incidence of 30-day SSI (−8.8, 95%CI: −16.0 to −1.6, p = 0.042), shorter LoS after surgery (−1.1 days, 95%CI: −1.8 to −0.4, p = 0.004), and lower cost of antibiotics (−37.3 USD, 95%CI: −59.8 to −14.8, p = 0.012) and treatment (−191.1 USD, 95%CI: −348.4 to −33.8, p = 0.042). We estimated that by detecting patients at high risk of SSI with the predictive model and providing prophylactic measures, we could save 398120.7 USD per 1,000 cases of SSI.ConclusionWe found that ASPi were associated with a reduction in risks of SSI, hospital stays, and cost of antibiotics/treatment in a Vietnamese tertiary hospital.
Utilization of a Meningitis/Encephalitis PCR panel at the University Hospital Basel – a retrospective study to develop a diagnostic decision rule
Authors: Erba Andrea , Franzeck Fabian C. , Hinic Vladimira , Egli Adrian , Osthoff Michael 
Published: April 2024

BackgroundThe Biofire® FilmArray® Meningitis/Encephalitis (ME) PCR panel covers 14 viral, bacterial, and fungal pathogens and has been implemented in many institutions worldwide. Post-marketing studies indicate a reduced sensitivity and overutilization underscoring the need for a more targeted usage. The aim of our study is to describe the utilization of the ME panel and to develop a diagnostic-stewardship based decision rule.MaterialsAdult patients, who underwent CSF analysis with the ME panel between August 2016 and June 2021 at the University Hospital Basel, were included. Demographic, clinical, microbiological, and laboratory data were extracted from the electronic health record. Factors associated with a positive ME panel result were identified, and a decision rule was developed to potentially optimize the diagnostic yield and reduce the number of unnecessary tests.Results1,236 adult patients received at least one panel in the observed period, of whom 106 panels tested positive (8.6%). The most frequently observed pathogens were Varicella Zoster Virus (VZV, 27%), Streptococcus pneumoniae (19%), Enterovirus (16%), Herpes simplex Virus 1/2 (16%), and Human Herpesvirus 6 (HHV-6, 13%). Fever, vomiting, headache, and photophobia were more frequently present in test positive patients as were significantly higher CSF leukocytes and protein concentrations. When simulating a decision rule based on CSF leukocytes and protein concentration, only 35% of all patients would have qualified for a ME panel tests, thereby increasing the positivity rate to 22.7%. 10 of 106 positive ME panels would have been missed, only involving HHV-6 and VZV (6 and 4 cases, respectively). As these subjects were either severely immunocompromised or had clinical features of shingles we propose extending the testing algorithm by including those criteria.ConclusionThe ME panel positivity rate at our institution was similar as previously published. Our results highlight the need for diagnostic-stewardship interventions when utilizing this assay by implementing a stepwise approach based on a limited number of clinical and laboratory features. This decision rule may improve the pretest probability of a positive test result, increase the quality of test utilization, and reduce costs.
Target-controlled infusion of remimazolam effect-site concentration for total intravenous anesthesia in patients undergoing minimal invasive surgeries
Authors: Chon Jin Young , Seo Kwon Hui , Lee Jaesang , Lee Subin 
Published: April 2024

BackgroundAlthough pharmacokinetic and pharmacodynamic models of remimazolam have been developed, their clinical application remains limited. This study aimed to administer a target-controlled infusion (TCI) of remimazolam at the effect-site concentration (Ce) in patients undergoing general anesthesia and to investigate the relationship of the remimazolam Ce with sedative effects and with recovery from general anesthesia.MethodsFifty patients aged 20–75 years, scheduled for minimally invasive surgery under general anesthesia for less than 2 h, were enrolled. Anesthesia was induced and maintained using Schüttler’s model for effect-site TCI of remimazolam. During induction, the remimazolam Ce was increased stepwise, and sedation levels were assessed using the Modified Observer’s Assessment of Alertness/Sedation (MOAA/S) scale and bispectral index (BIS). Following attainment of MOAA/S scale 1, continuous infusion of remifentanil was commenced, and rocuronium (0.6 mg/kg) was administered for endotracheal intubation. The target Ce of remimazolam and the remifentanil infusion rate were adjusted to maintain a BIS between 40 and 70 and a heart rate within 20% of the baseline value. Approximately 5 min before surgery completion, the target Ce of remimazolam was reduced by 20–30%, and anesthetic infusion ceased at the end of surgery. Nonlinear mixed-effects modeling was employed to develop pharmacodynamic models for each sedation level as well as emergence from anesthesia.ResultsThe remimazolam Ces associated with 50% probability (Ce50) of reaching MOAA/S scale ≤4, 3, 2, and 1 were 0.302, 0.397, 0.483, and 0.654 μg/mL, respectively. The Ce50 values for recovery of responsiveness (ROR) and endotracheal extubation were 0.368 and 0.345 μg/mL, respectively. The prediction probabilities of Ce and BIS for detecting changes in sedation level were 0.797 and 0.756, respectively. The sedation scale significantly correlated with remimazolam Ce (r = −0.793, P &lt; 0.0001) and BIS (r = 0.914, P &lt; 0.0001). Age significantly correlated with Ce at MOAA/S1 and ROR.ConclusionEffect-site TCI of remimazolam was successfully performed in patients undergoing general anesthesia. The remimazolam Ce significantly correlated with sedation depth. The Ce50 for MOAA/S scale ≤1 and ROR were determined to be 0.654 and 0.368 μg/mL, respectively.
The relationship between gastric microbiome features and responses to neoadjuvant chemotherapy in gastric cancer
Authors: Zhang Peng , Xu Jianfei , Zhou Yanbing 
Published: April 2024

BackgroundEmerging evidence demonstrates that the gastrointestinal microbiome has the potential to be a biomarker in neoadjuvant chemoradiotherapy for colorectal cancer (CRC). Yet studies on the impact of the gastric microbiome (GM) on the response to neoadjuvant chemotherapy (NACT) are still scarce.MethodsForty-eight patients with gastric cancer participated in this retrospective study, and 16S rRNA sequencing was performed to evaluate formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens and fresh-frozen tissues.ResultsIn this study, 16 bacterial taxa at different levels, including Bacillus, Anaerococcus, and Chloroflexi, were identified to be enriched before NACT in response (R) patients in group FFPE. In contrast, 6 bacterial taxa, such as Haemophilus, Veillonellaceae (Veillonella), etc. were enriched after NACT, in which we reported for the first time that the phylum Chloroflexi was enriched before NACT in R patients. Thirty-one bacterial taxa of Coriobacteriaceae, Ruminococcaceae, Veillonellaceae, and Lachnospiraceae were identified in group mucosa as being enriched in R patients. In comparison, 4 bacterial taxa dominated by the phylum Proteobacteria were enriched in NR patients. Notably, the family Veillonellaceae was found in both tissue samples, and the metabolic pathways, including the citrate cycle (TCA cycle) and various amino acids, including alanine, were found to be potentially predictive in both sample species.ConclusionThere are differences in the features of the GM for different NACT response results. The causal relationship deserves to be confirmed by further investigations.
Neisseria gonorrhea in Ethiopia, prevalence among STI suspected patients and its antimicrobial susceptibility: a systematic review and meta-analysis
Authors: Gobezie Mengistie Yirsaw , Tesfaye Nuhamin Alemayehu , Solomon Tewodros , Demessie Mulat Belete , Kassa Tesfaye Dessale , Wendie Teklehaimanot Fentie , Alemayehu Ermiyas , Hassen Minimize 
Published: April 2024

IntroductionNeisseria gonorrhea (N. gonorrhea) represents a significant causative agent of sexually transmitted infections (STIs), posing considerable global health challenges. Despite the presence of diagnostic tools and empirically guided therapies, the escalating AMR of N. gonorrhea continues to pose a threat. This study aims to assess the prevalence of N. gonorrhea among STI suspected patients in Ethiopia and explore the patterns of AMR to common antimicrobials.MethodsFollowing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we conducted a systematic review and meta-analysis. A thorough search of electronic databases from July 11 to July 24, 2023, identified 10 eligible studies. Data were extracted and analyzed using a random-effects model. Heterogeneity was assessed using the I2 statistic, and publication bias was evaluated through Egger’s regression test and funnel plots.ResultsThe overall pooled prevalence of N. gonorrhea among STI suspected patients in Ethiopia was 20% (95% confidence interval (CI): 8–30, I2 = 99.0%; p-value &lt;0.001). Substantial regional variations were observed, with the highest prevalence in Addis Ababa (55, 95% CI: 45–65) and the lowest in the Southern Nations, Nationalities, and Peoples’ Region (SNNPR) (4, 95% CI: 2–8). The pooled prevalence of AMR to ciprofloxacin, ceftriaxone, azithromycin, benzylpenicillin, tetracycline, and spectinomycin was 37, 9, 10, 79, 93, and 2%, respectively. Significant heterogeneity existed between studies (I2 = 99.0%; p value &lt;0.001). Publication bias, identified through funnel plot examination and Egger’s regression test (p &lt; 0.001), execution of trim and fill analysis resulted in an adjusted pooled prevalence of (6.2, 95% CI: −6.8 to 19.3).ConclusionThe prevalence of N. gonorrhea among STI suspected patients in Ethiopia is alarming, particularly in specific regions. The elevated AMR to ciprofloxacin underscores the immediate need for alternative treatment options and enhanced surveillance systems. Future initiatives should prioritize strengthening laboratory capacities and implementing targeted interventions to curtail N. gonorrhea transmission and prevent the emergence of AMR.Systematic Review Registrationhttps://www.crd.york.ac.uk/prospero, identifier CRD42023459698.
Novel anti-inflammatory effects of the IL-1 receptor in kidney myeloid cells following ischemic AKI
Authors: Chen Yanting , Lu Xiaohan , Whitney Raeann L. , Li Yu , Robson Matthew J. , Blakely Randy D. , Chi Jen-Tsan , Crowley Steven D. , Privratsky Jamie R. 
Published: April 2024

Introduction: Acute kidney injury (AKI) is one of the most common causes of organ failure in critically ill patients. Following AKI, the canonical pro-inflammatory cytokine interleukin-1β (IL-1β) is released predominantly from activated myeloid cells and binds to the interleukin-1 receptor R1 (IL-1R1) on leukocytes and kidney parenchymal cells. IL-1R1 on kidney tubular cells is known to amplify the immune response and exacerbate AKI. However, the specific role of IL-1R1 on myeloid cells during AKI is poorly understood. The objective of the present study was to elucidate the function of myeloid cell IL-1R1 during AKI. As IL-1R1 is known to signal through the pro-inflammatory Toll-like receptor (TLR)/MyD88 pathway, we hypothesized that myeloid cells expressing IL-1R1 would exacerbate AKI.Methods: IL-1R1 was selectively depleted in CD11c+-expressing myeloid cells with CD11cCre+/IL-1R1fl/fl (Myel KO) mice. Myel KO and littermate controls (CD11cCre-/IL-1R1fl/fl–Myel WT) were subjected to kidney ischemia/reperfusion (I/R) injury. Kidney injury was assessed by blood urea nitrogen (BUN), serum creatinine and injury marker neutrophil gelatinase-associated lipocalin (NGAL) protein expression. Renal tubular cells (RTC) were co-cultured with CD11c+ bone marrow-derived dendritic cells (BMDC) from Myel KO and Myel WT mice.Results: Surprisingly, compared to Myel WT mice, Myel KO mice displayed exaggerated I/R-induced kidney injury, as measured by elevated levels of serum creatinine and BUN, and kidney NGAL protein expression. In support of these findings, in vitro co-culture studies showed that RTC co-cultured with Myel KO BMDC (in the presence of IL-1β) exhibited higher mRNA levels of the kidney injury marker NGAL than those co-cultured with Myel WT BMDC. In addition, we observed that IL-1R1 on Myel WT BMDC preferentially augmented the expression of anti-inflammatory cytokine interleukin-1 receptor antagonist (IL-1ra/Il1rn), effects that were largely abrogated in Myel KO BMDC. Furthermore, recombinant IL-1Ra could rescue IL-1β-induced tubular cell injury.Discussion: Our findings suggest a novel function of IL-1R1 is to serve as a critical negative feedback regulator of IL-1 signaling in CD11c+ myeloid cells to dampen inflammation to limit AKI. Our results lend further support for cell-specific, as opposed to global, targeting of immunomodulatory agents.