bluuebunny/crossref_metadata_2025_split huggingface dataset:
An empirical formula of bottom friction coefficient with a dependence on the current speed for the tidal models
Authors: Dong Yakang , Jiang Jinglu , Liu Xiujuan , Wang Daosheng , Zhang Jicai 
Published: October 2023

Tides are of great importance for ocean mixing and nearshore ocean engineering. Bottom friction is a major factor in tidal dissipation and is usually parameterized by the bottom friction coefficient (BFC). BFC is a critical parameter in numerical tidal models and is known to vary with time and space, as calculated with measured data. However, it is difficult to accurately adjust the spatially-temporally varying BFC in numerical tidal models. Based on the relationship between the spatially-temporally varying BFC estimated by adjoint data assimilation and the simultaneously simulated current speed, an empirical formula of BFC with a dependence on the current speed is proposed. This new empirical formula of BFC is compared with several traditional empirical formulas, including the constant BFC, the Chezy-Manning BFC, and two depth-dependent BFCs. When the four principal tidal constituents (M2, S2, K1, and O1) in the Bohai, Yellow and East China Seas (BYECS) are simulated, the mean vector error between the simulated results obtained using the current speed-dependent BFC and the TOPEX/Poseidon satellite altimetry data (the tidal gauge data) is 8.81 cm (10.62 cm), which is decreased by up to 8.1% (18.2%) compared with those using the several commonly used empirical formulas of BFC. Furthermore, in the sensitivity experiments where only the M2 tide in the BYECS, the M2, S2, K1, and O1 tides in the Bohai and Yellow Sea (BYS), and the M2, S2, K1, and O1 tides in the South China Sea (SCS) are simulated, the errors between the simulated results obtained by using current speed-dependent BFC and the tidal gauge data are less than those using the other empirical formulas of BFC, further demonstrating the superiority of the current speed-dependent BFC proposed in this study. From numerical model experiments, the current speed-dependent BFC can adequately reflect the spatial and temporal variations of BFC and improve the simulation accuracy of tides, thus having a broad application scope.
Prevalence of diagnostically-discrepant Clostridioides difficile clinical specimens: insights from longitudinal surveillance
Authors: Anwar Farhan , Clark Marielle , Lindsey Jason , Claus-Walker Rachel , Mansoor Asad , Nguyen Evy , Billy Justin , Lainhart William , Shehab Kareem , Viswanathan V. K. , Vedantam Gayatri 
Published: October 2023

BackgroundClostridioides difficile Infection (CDI) is a healthcare-associated diarrheal disease prevalent worldwide. A common diagnostic algorithm relies on a two-step protocol that employs stool enzyme immunoassays (EIAs) to detect the pathogen, and its toxins, respectively. Active CDI is deemed less likely when the Toxin EIA result is negative, even if the pathogen-specific EIA is positive for C. difficile. We recently reported, however, that low-toxin-producing C. difficile strains recovered from Toxin-negative (‘discrepant’) clinical stool specimens can be fully pathogenic, and cause lethality in a rodent CDI model. To document frequency of discrepant CDI specimens, and evaluate C. difficile strain diversity, we performed longitudinal surveillance at a Southern Arizona tertiary-care hospital.MethodsDiarrheic stool specimens from patients with clinical suspicion of CDI were obtained over an eight-year period (2015–2022) from all inpatient and outpatient Units of a &gt; 600-bed Medical Center in Southern Arizona. Clinical laboratory EIA testing identified C. difficile-containing specimens, and classified them as Toxin-positive or Toxin-negative. C. difficile isolates recovered from the stool specimens were DNA fingerprinted using an international phylogenetic lineage assignment system (“ribotyping”). For select isolates, toxin abundance in stationary phase supernatants of pure cultures was quantified via EIA.ResultsOf 8,910 diarrheic specimens that underwent diagnostic testing, 1733 (19.4%) harbored C. difficile. Our major findings were that: (1) C. difficile prevalence and phylogenetic diversity was stable over the 8-year period; (2) toxigenic C. difficile was recovered from 69% of clinically Tox-neg (‘discrepant’) specimens; (3) the six most prevalent USA ribotypes were recovered in significant proportions (&gt;60%) from Tox-neg specimens; and (4) toxin–producing C. difficile recovered from discrepant specimens produced less toxin than strains of the same ribotype isolated from non-discrepant specimens.ConclusionOur study highlights the dominance of Toxin EIA-negative CDI specimens in a clinical setting and the high frequency of known virulent ribotypes in these specimens. Therefore, a careful reevaluation of the clinical relevance of diagnostically-discrepant specimens particularly in the context of missed CDI diagnoses and C. difficile persistence, is warranted.
Identification and characterization of a novel 6′-N-aminoglycoside acetyltransferase AAC(6′)-Va from a clinical isolate of Aeromonas hydrophila
Authors: Zhang Guozhi , Zhang Lei , Sha Yuning , Chen Qiaoying , Lin Naru , Zhao Jingxuan , Zhang Yuan , Ji Yongan , Jiang Weiyan , Zhang Xueya , Li Qiaoling , Lu Junwan , Lin Xi , Li Kewei , Zhang Hailin , Bao Qiyu , Lu Jun , Hu Yunliang , Zhu Tingting 
Published: October 2023

BackgroundAeromonas species have been identified as agents responsible for various diseases in both humans and animals. Multidrug-resistant Aeromonas strains pose a significant public health threat due to their emergence and spread in clinical settings and the environment. The aim of this study was to determine a novel resistance mechanism against aminoglycoside antimicrobials in a clinical isolate.MethodsThe function of aac(6′)-Va was verified by gene cloning and antibiotic susceptibility tests. To explore the in vivo activity of the enzyme, recombinant proteins were expressed, and enzyme kinetics were tested. To determine the molecular background and mechanism of aac(6′)-Va, whole-genome sequencing and bioinformatic analysis were performed.ResultsThe novel aminoglycoside N-acetyltransferase gene aac(6′)-Va confers resistance to several aminoglycosides. Among the antimicrobials tested, ribostamycin showed the highest increase (128-fold) in the minimum inhibitory concentration (MIC) compared with the control strains. According to the MIC results of the cloned aac(6′)-Va, AAC(6′)-Va also showed the highest catalytic efficiency for ribostamycin [kcat/Km ratio = (3.35 ± 0.17) × 104 M−1 s−1]. Sharing the highest amino acid identity of 54.68% with AAC(6′)-VaIc, the novel aminoglycoside N-acetyltransferase constituted a new branch of the AAC(6′) family due to its different resistance profiles. The gene context of aac(6′)-Va and its close relatives was conserved in the genomes of species of the genus Aeromonas.ConclusionThe novel resistance gene aac(6′)-Va confers resistance to several aminoglycosides, especially ribostamycin. Our finding of a novel resistance gene in clinical A. hydrophila will help us develop more effective treatments for this pathogen’s infections.
Colorectal cancer and gut viruses: a visualized analysis based on CiteSpace knowledge graph
Authors: Jian Chu , Jing Zhuang , Yinhang Wu , Jinlong Duan , Yuefen Pan , Quan Qi , Shuwen Han 
Published: October 2023

BackgroundGut microbiome is a complex community of microbes present in the human gut and plays an important role in the occurrence and progression of colorectal cancer (CRC). However, the relationship between virus and CRC has not been fully understood.ObjectiveTo explore the hot spots and research trends in the field of CRC and virus.MethodsBy using the bibliometric analysis tool CiteSpace and based on the articles of the Web of Science Core Collection (WoSCC) database, the country, institution, highly cited literature, keywords and so on were visually analyzed.ResultsA total of 356 research articles on CRC from 2001 to 2023 were thoroughly analyzed. The USA and China have made the largest contribution in the field of virus and CRC. The Helmholtz Association published the most papers. There were relatively few cooperations among institutions from different countries. The results of keyword cluster analysis proved that the literature on the relationship between human cytomegalovirus (CMV) and CRC was the most widely studied aspect in this field. “Gut microbiota,” “inflammatory bowel disease,” “hepatitis b virus,” and “human papillomavirus infection” are the current research hotspots; “oncolytic virus,” “apoptosis,” and “gut microbiome” are the recent research frontiers and should be paid closer attention.ConclusionBy using CiteSpace bibliometric software, the visual analysis reflected the research trends and hot topics of virus and CRC. In addition, the prevalence and mechanism of specific virus on CRC were also reviewed, which provides valuable references for future CRC research.
Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios
Authors: Poirier Simon , Coeuret Gwendoline , Champomier-Vergès Marie-Christine , Desmonts Marie-Hélène , Werner Dalal , Feurer Carole , Frémaux Bastien , Guillou Sandrine , Luong Ngoc-Du Martin , Rué Olivier , Loux Valentin , Zagorec Monique , Chaillou Stéphane ,   on behalf of the ANR Redlosses Consortium Group
Published: October 2023

BackgroundThe use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics.MethodsOur strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers.ResultsOur results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism.ConclusionWe conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.
Bayesian workflow for the investigation of hierarchical classification models from tau-PET and structural MRI data across the Alzheimer’s disease spectrum
Authors: Belasso Clyde J. , Cai Zhengchen , Bezgin Gleb , Pascoal Tharick , Stevenson Jenna , Rahmouni Nesrine , Tissot Cécile , Lussier Firoza , Rosa-Neto Pedro , Soucy Jean-Paul , Rivaz Hassan , Benali Habib 
Published: October 2023

BackgroundAlzheimer’s disease (AD) diagnosis in its early stages remains difficult with current diagnostic approaches. Though tau neurofibrillary tangles (NFTs) generally follow the stereotypical pattern described by the Braak staging scheme, the network degeneration hypothesis (NDH) has suggested that NFTs spread selectively along functional networks of the brain. To evaluate this, we implemented a Bayesian workflow to develop hierarchical multinomial logistic regression models with increasing levels of complexity of the brain from tau-PET and structural MRI data to investigate whether it is beneficial to incorporate network-level information into an ROI-based predictive model for the presence/absence of AD.MethodsThis study included data from the Translational Biomarkers in Aging and Dementia (TRIAD) longitudinal cohort from McGill University’s Research Centre for Studies in Aging (MCSA). Baseline and 1 year follow-up structural MRI and [18F]MK-6240 tau-PET scans were acquired for 72 cognitive normal (CN), 23 mild cognitive impairment (MCI), and 18 Alzheimer’s disease dementia subjects. We constructed the four following hierarchical Bayesian models in order of increasing complexity: (Model 1) a complete-pooling model with observations, (Model 2) a partial-pooling model with observations clustered within ROIs, (Model 3) a partial-pooling model with observations clustered within functional networks, and (Model 4) a partial-pooling model with observations clustered within ROIs that are also clustered within functional brain networks. We then investigated which of the models had better predictive performance given tau-PET or structural MRI data as an input, in the form of a relative annualized rate of change.ResultsThe Bayesian leave-one-out cross-validation (LOO-CV) estimate of the expected log pointwise predictive density (ELPD) results indicated that models 3 and 4 were substantially better than other models for both tau-PET and structural MRI inputs. For tau-PET data, model 3 was slightly better than 4 with an absolute difference in ELPD of 3.10 ± 1.30. For structural MRI data, model 4 was considerably better than other models with an absolute difference in ELPD of 29.83 ± 7.55 relative to model 3, the second-best model.ConclusionOur results suggest that representing the data generating process in terms of a hierarchical model that encompasses both ROI-level and network-level heterogeneity leads to better predictive ability for both tau-PET and structural MRI inputs over all other model iterations.
Predictive value of admission red cell distribution width-to-platelet ratio for 30-day death in patients with spontaneous intracerebral hemorrhage: an analysis of the MIMIC database
Authors: Liang Hanbai , Liu Ping , Guo Lei , Feng Jie , Yin Cheng , Zhao Dongdong , Chen Longyi 
Published: October 2023

AimPrognostic assessment plays an important role in the effective management of patients with spontaneous intracerebral hemorrhage (ICH). The study aimed to investigate whether elevated red cell distribution width-to-platelet ratio (RPR) at admission was related to 30-day death in patients with spontaneous intracerebral hemorrhage (ICH).MethodsThis retrospective cohort study included 2,823 adult patients with ICH from the Multiparameter Intelligent Monitoring in Intensive Care (MIMIC) III and IV databases between 2001 and 2019. The Cox proportional hazard model was utilized to evaluate the relationship between RPR levels and 30-day death risk. The area under receiver-operating characteristic curve (AUC) was used to assess the predictive ability of RPR for 30-day death in patients with ICH.ResultsAt the end of the 30-day follow-up, 799 (28.30%) patients died, and the median RPR level was 0.066 (0.053, 0.087). After adjusting for confounders, the tertile 3 of RPR levels [hazard ratio (HR) = 1.37, 95% confidence interval (CI): 1.15–1.64] were associated with a higher risk of 30-day death in patients with ICH compared with tertile 1. In the stratified analyses, elevated RPR levels were found to be associated with an increased risk of 30-day death in patients aged &lt;65 years (HR = 1.77, 95%CI: 1.29–2.43), aged ≥65 years (HR = 1.30, 95%CI: 1.05–1.61), with Glasgow Coma Score (GCS) &lt;14 (HR = 1.65, 95%CI: 1.27–2.14), with Charlson comorbidity index (CCI) ≥4 (HR = 1.45, 95%CI: 1.17–1.80), with (HR = 1.66, 95%CI: 1.13–2.43) or without sepsis (HR = 1.32, 95%CI: 1.08–1.61), and female patients (HR = 1.75, 95%CI: 1.35–2.26) but not in male patients (P = 0.139) and patients with GCS ≥14 (P = 0.058) or CCI &lt;4 (P = 0.188). The AUC for RPR to predict 30-day death in patients with ICH was 0.795 (95%CI: 0.763–0.828) in the testing set, indicating a good predictive ability.ConclusionElevated RPR levels were correlated with an increased risk of 30-day death in patients with ICH, and RPP levels showed good predictive ability for 30-day death.
Examination of betahistine bioavailability in combination with the monoamine oxidase B inhibitor, selegiline, in humans—a non-randomized, single-sequence, two-period titration, open label single-center phase 1 study (PK-BeST)
Authors: Strupp Michael , Churchill Grant C. , Naumann Ivonne , Mansmann Ulrich , Al Tawil Amani , Golentsova Anastasia , Goldschagg Nicolina 
Published: October 2023

BackgroundBetahistine was registered in Europe in the 1970s and approved in more than 80 countries as a first-line treatment for Menière's disease. It has been administered to more than 150 million patients. However, according to a Cochrane systematic review of betahistine and recent meta-analyses, there is insufficient evidence to say whether betahistine has any effect in the currently approved dosages of up to 48 mg/d. A combination with the monoamine oxidase B (MAO-B) inhibitor, selegiline, may increase the bioavailability of betahistine to levels similar to the well-established combination of L-DOPA with carbidopa or benserazide in the treatment of Parkinson's disease. We investigated the effect of selegiline on betahistine pharmacokinetics and the safety of the combination in humans.MethodsIn an investigator-initiated prospective, non-randomized, single-sequence, two-period titration, open label single-center phase 1 study, 15 healthy volunteers received three single oral dosages of betahistine (24, 48, and 96 mg in this sequence with at least 2 days' washout period) without and with selegiline (5 mg/d with a loading period of 7 days). Betahistine serum concentrations were measured over a period of 240 min at eight time points (area under the curve, AUC0-240 min). This trial is registered with EudraCT (2019-002610-39) and ClinicalTrials.gov.FindingsIn all three single betahistine dosages, selegiline increased the betahistine bioavailability about 80- to 100-fold. For instance, the mean (±SD) of the area under curve for betahistine 48 mg alone was 0.64 (+/-0.47) h*ng/mL and for betahistine plus selegiline 53.28 (+/-37.49) h*ng/mL. The half-life time of around 30 min was largely unaffected, except for the 24 mg betahistine dosage. In total, 14 mild adverse events were documented.InterpretationThis phase 1 trial shows that the MAO-B inhibitor selegiline increases betahistine bioavailability by a factor of about 80 to 100. No safety concerns were detected. Whether the increased bioavailability has an impact on the preventive treatment of Menière's disease, acute vestibular syndrome, or post-BPPV residual dizziness has to be evaluated in placebo-controlled trials.Clinical trial registrationhttps://clinicaltrials.gov/study/NCT05938517?intr=betahistine%20and%20selegiline&amp;rank=1, identifier: NCT05938517.
Case Report: Primary endodermal sinus tumor on the abdominal wall near the right liver: a diagnostic pitfall
Authors: Chen Shuo , Chen Feng , Xu Xiao 
Published: October 2023

BackgroundEndodermal sinus tumors are rare, especially extragonadal endodermal sinus tumors, which often occur in the midline of the brain, neck, chest, and abdomen.Case summaryWe present the case of a 37-year-old woman with a mass on the right edge of the liver. Color Doppler ultrasound, computed tomography, and magnetic resonance imaging examinations were performed before the operation. Given these results and the elevation of alpha-fetoprotein, the diagnosis of hepatocellular carcinoma was made. Postoperative pathological examination indicated an endodermal sinus tumor on the abdominal wall near the right liver. The causes of misdiagnosis were analyzed, and the related literature was reviewed.ConclusionPrimary endodermal sinus tumors on the abdominal wall near the right liver are easily misdiagnosed as hepatocellular carcinoma due to liver compression and elevated alpha-fetoprotein. The key point of differentiation is the wide basal connection between the tumor and the abdominal wall near the liver. In addition, the enhancement mode of endodermal sinus tumors is different from the enhancement pattern of hepatocellular carcinoma.Core tipExtragonadal endodermal sinus tumors often occur in the midline of the body. Here, we present a case of a primary endodermal sinus tumor on the abdominal wall near the right liver for the first time.
3D laparoscopic treatment of bladder cancer with pelvic multi-organ invasion: a case report and literature review
Authors: Chen Zheng , Deng Kaifeng , Sun Luping , Qu Lijun , Chao Xinhui , Rao Jingmin , Hong Caimmei , Zhuo Yumin , Lin Zhichao , Lai Caiyong 
Published: October 2023

IntroductionRadical cystectomy with dissection of pelvic lymph nodes and urethral diversion is the standard surgical treatment for muscle-invasive non-metastatic bladder cancer. In rare cases where patients with bladder cancer without distant metastasis have pelvic multi-organ invasion, the cancer compresses or invades the ureter and, in severe cases, leads to bilateral upper urinary tract obstruction and renal damage. The treatment recommended by guidelines often cannot improve the patients’ clinical symptoms immediately, and patients cannot complete the treatment owing to severe side effects, resulting in poor survival benefits.Case presentationA 69-year-old woman with facial edema was treated at the First Affiliated Hospital of Jinan University. The serum creatinine and potassium values were 1244 umol/L and 5.86 mmol/L, respectively. Pelvic magnetic resonance and abdominal computed tomography revealed that the bladder tumor had infiltrated the uterus, anterior vaginal wall, rectum, right ureter, right fallopian tube, and right ovary and metastasized to multiple pelvic lymph nodes. Tumor invasion of the right ureter resulted in severe hydronephrosis of the right kidney and loss of function and obstructive symptoms in the left kidney. Four days later, the patient’s creatinine level decreased to 98 u mol/L, the general condition significantly improved, and the patient and family members strongly desired surgical treatment of the tumor. Through a comprehensive preoperative discussion, possible intraoperative and postoperative complications were evaluated. Right nephrectomy, right ureterectomy, total pelvic organ resection, extended pelvic lymph node dissection, and bowel and urinary diversion were conducted under 3D laparoscopy-assisted treatment. The patient was followed-up for 1.5 years and showed good tumor control, self-care, and mental status.ConclusionMinimally invasive surgery is a curative option for patients with bladder cancer with pelvic multi-organ invasion without distant metastasis. Surgeons should strictly control the indications for surgery and warn patients about the occurrence of related post-surgical complications.