bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association Between Arterial Stiffness and Measures of Autonomic Dysfunction in People With Chronic Kidney Disease
Authors: Davies Rachelle , Wiebe Natasha , Brotto Andrew , Stickland Michael K. , Braam Branko , Thompson Stephanie 
Published: November 2023

Background: Autonomic nervous system (ANS) dysfunction and vascular stiffness increase cardiovascular risk in people with chronic kidney disease (CKD). Chronic elevations in sympathetic activity can lead to increased arterial stiffness; however, the relationship between these variables is unknown in CKD. Objective: To explore the association between measures of autonomic function and arterial stiffness in patients with moderate-to-severe CKD. Methods: This study was a prespecified secondary analysis of a randomized controlled trial. This included the following measures: 24-hour ambulatory blood pressure (BP), carotid-femoral and carotid-radial pulse wave velocity (PWV), and postexercise heart rate recovery (HRR). We used mixed effect linear regression models with Bayesian information criteria (BIC) to assess the contribution of ANS measurements. Results: Forty-four patients were included in the analysis. Mean carotid-femoral and carotid-radial PWV were 7.12 m/s (95% CI 6.13, 8.12) and 8.51 m/s (7.90, 9.11), respectively. Mean systolic dipping, calculated as percentage change in mean systolic readings from day to night, was 10.0% (95% CI 7.79, 12.18). Systolic dipping was independently associated with carotid-radial PWV, MD −0.09 m/s (95% CI −0.15, −0.02) and had the lowest BIC. Conclusions: Systolic dipping was associated with carotid-radial PWV in people with moderate-to-severe CKD; however, there was no association with carotid-femoral PWV. Systolic dipping may be a feasible surrogate of ANS function, as the association with carotid-radial PWV was consistent with the minimal clinically important difference (MCID). Future studies are needed to define the relationship between ANS function, arterial stiffness, and CV events over time in people with CKD.
Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts
Authors: Pettersen Jakob P. , Castillo Sandra , Jouhten Paula , Almaas Eivind 
Published: November 2023

Abstract
Background
Use of alternative non-Saccharomyces yeasts in wine and beer brewing has gained more attention the recent years. This is both due to the desire to obtain a wider variety of flavours in the product and to reduce the final alcohol content. Given the metabolic differences between the yeast species, we wanted to account for some of the differences by using in silico models.

Results
We created and studied genome-scale metabolic models of five different non-Saccharomyces species using an automated processes. These were: Metschnikowia pulcherrima, Lachancea thermotolerans, Hanseniaspora osmophila, Torulaspora delbrueckii and Kluyveromyces lactis. Using the models, we predicted that M. pulcherrima, when compared to the other species, conducts more respiration and thus produces less fermentation products, a finding which agrees with experimental data. Complex I of the electron transport chain was to be present in M. pulcherrima, but absent in the others. The predicted importance of Complex I was diminished when we incorporated constraints on the amount of enzymatic protein, as this shifts the metabolism towards fermentation.

Conclusions
Our results suggest that Complex I in the electron transport chain is a key differentiator between Metschnikowia pulcherrima and the other yeasts considered. Yet, more annotations and experimental data have the potential to improve model quality in order to increase fidelity and confidence in these results. Further experiments should be conducted to confirm the in vivo effect of Complex I in M. pulcherrima and its respiratory metabolism.
Probable human origin of the SARS-CoV-2 polybasic furin cleavage motif
Authors: Romeu Antonio R. 
Published: November 2023

Abstract
Background
The key evolutionary step leading to the pandemic virus was the acquisition of the PRRA furin cleavage motif at the spike glycoprotein S1/S2 junction by a progenitor of SARS-CoV-2. Two of its features draw attention: (i) it is absent in other known lineage B beta-coronaviruses, including the newly discovered coronaviruses in bats from Laos and Vietnam, which are the closest known relatives of the covid virus; and, (ii) it introduced the pair of arginine codons (CGG-CGG), whose usage is extremely rare in coronaviruses. With an occurrence rate of only 3%, the arginine CGG codon is considered a minority in SARS CoV-2. On the other hand, Laos and Vietnam bat coronaviruses contain receptor-binding domains that are almost identical to that of SARS-CoV-2 and can therefore infect human cells despite the absence of the furin cleavage motif.

Results
Based on these data, the aim of this work is to provide a detailed sequence analysis between the SARS-CoV-2 S gene insert encoding PRRA and the human mRNA transcripts. The result showed a 100% match to several mRNA transcripts. The set of human genes whose mRNAs match this S gene insert are ubiquitous and highly expressed, e.g., the ATPase F1 (ATP5F1) and the ubiquitin specific peptidase 21 (USP21) genes; or specific genes of target organs or tissues of the SARS-CoV-2 infection (e.g., MEMO1, SALL3, TRIM17, CWC15, CCDC187, FAM71E2, GAB4, PRDM13). Results suggest that a recombination between the genome of a SARS-CoV-2 progenitor and human mRNA transcripts could be the origin of the S gene 12-nucleotide insert encoding the S protein PRRA motif.

Conclusions
The hypothesis of probable human origin of the SARS-CoV-2 polybasic furin cleavage motif is supported by: (i) the nature of human genes whose mRNA sequence 100% match the S gene insert; (ii) the synonymous base substitution in the arginine codons (CGG-CGG); and (iii) further spike glycoprotein PRRA-like insertions suggesting that the acquisition of PRRA may not have been a single recombination event.
Identification of plasmids in avian-associated Escherichia coli using nanopore and illumina sequencing
Authors: Sanderson Haley , McCarthy Madeline C. , Nnajide Chinenye R. , Sparrow Jessica , Rubin Joseph E. , Dillon Jo-Anne R. , White Aaron P. 
Published: November 2023

Abstract
Background
Avian pathogenic Escherichia coli (APEC) are the causative agents of colibacillosis in chickens, a disease which has significant economic impact on the poultry industry. Large plasmids detected in APEC are known to contribute to strain diversity for pathogenicity and antimicrobial resistance, but there could be other plasmids that are missed in standard analysis. In this study, we determined the impact of sequencing and assembly factors for the detection of plasmids in an E. coli whole genome sequencing project.

Results
Hybrid assembly (Illumina and Nanopore) combined with plasmid DNA extractions allowed for detection of the greatest number of plasmids in E. coli, as detected by MOB-suite software. In total, 79 plasmids were identified in 19 E. coli isolates. Hybrid assemblies were robust and consistent in quality regardless of sequencing kit used or if long reads were filtered or not. In contrast, long read only assemblies were more variable and influenced by sequencing and assembly parameters. Plasmid DNA extractions allowed for the detection of physically smaller plasmids, but when averaged over 19 isolates did not significantly change the overall number of plasmids detected.

Conclusions
Hybrid assembly can be reliably used to detect plasmids in E. coli, especially if researchers are focused on large plasmids containing antimicrobial resistance genes and virulence factors. If the goal is comprehensive detection of all plasmids, particularly if smaller sized vectors are desired for biotechnology applications, the addition of plasmid DNA extractions to hybrid assemblies is prudent. Long read sequencing is sufficient to detect many plasmids in E. coli, however, it is more prone to errors when expanded to analyze a large number of isolates.
Development and evaluation of an anesthesia module for electronic medical records in the operating room: an applied developmental study
Authors: Jokar Marjan , Sahmeddini Mohammad Ali , Zand Farid , Rezaee Rita , Bashiri Azadeh 
Published: November 2023

AbstractDeveloping an anesthesia module in the operating room is one of the significant steps toward the implementation of electronic medical records (EMR) in health care centers. This study aimed to develop and evaluate the web based-anesthesia module of an electronic medical record Sciences, in the operating room of the Namazi Medical Training Center of Shiraz University of Medical Iran. This developmental and applied study was conducted in steps including determining the functional and non-functional requirements, designing and implementing the anesthesia module, and usability evaluation. 3 anesthesiologists, 3 anesthesiologist assistants, and 12 anesthetist nurses were included in the study as a research community. React.js, Node.js programming language to program this module, Mongo dB database, and Windows server for data management and USE standard questionnaire were used. In the anesthesia module, software quality features were determined as functional requirements and non-functional requirements included 286 data elements in 25 categories (demographic information, surgery information, laboratory results, patient graphs, consults, consent letter, physical examinations, medication history, family disease records, social record, past medical history, type of anesthesia, anesthesia induction method, airway management, monitoring, anesthesia chart, blood and fluids, blood gases, tourniquets and warmers, accessories, positions, neuromuscular reversal, transfer the patient from the operating room, complications of anesthesia and, seal/ signature). Also, after implementing the anesthesia module, results of the usability evaluation showed that 69.1% of the users agreed with the use of this module in the operating room and considered it user-friendly.
Advanced lung cancer inflammation index combined with geriatric nutritional risk index predict all-cause mortality in heart failure patients
Authors: Shi Tao , Wang Yan , Peng Yunzhu , Wang Meifen , Zhou Yanji , Gu Wenyi , Li Yanyan , Zou Jie , Zhu Na , Chen Lixing 
Published: November 2023

Abstract
Background
This study was undertaken to explore the predictive value of the advanced lung cancer inflammation index (ALI) combined with the geriatric nutritional risk index (GNRI) for all-cause mortality in patients with heart failure (HF).

Methods and results
We enrolled 1123 patients with HF admitted to our cardiology department from January 2017 to October 2021. Patients were divided into four groups, according to the median ALI and GNRI. From the analysis of the relationship between the ALI and GNRI, we concluded that there was a mild positive linear correlation (r = 0.348, p < 0.001) and no interaction (p = 0.140) between the ALI and GNRI. Kaplan‒Meier analysis showed that the cumulative incidence of all-cause mortality in patients with HF was highest in Group 1 (log-rank χ2 126.244, p < 0.001). Multivariate Cox proportional hazards analysis revealed that ALI and GNRI were independent predictors of all-cause mortality in HF patients (ALI: HR 0.407, 95% CI 0.296–0.560, p < 0.001; GNRI: HR 0.967, 95% CI 0.954–0.980, p < 0.001). The area under the curve (AUC) for ALI combined with GNRI was 0.711 (p < 0.001), according to the time-dependent ROC curve.

Conclusion
ALI and GNRI were independent predictors of all-cause mortality in HF patients. Patients with HF had the highest risk of all-cause mortality when the ALI was < 24.60 and the GNRI was < 94.41. ALI combined with the GNRI has good predictive value for the prognosis of HF patients.
Diagnosing Fabry nephropathy: the challenge of multiple kidney disease
Authors: Esposito Pasquale , Caputo Carmela , Repetto Monica , Somaschini Alberto , Pietro Bellone , Colomba Paolo , Zizzo Carmela , Parodi Angelica , Zanetti Valentina , Canepa Marco , Eustachi Virginia , Sanguineri Francesca , Mandich Paola , Viazzi Francesca 
Published: November 2023

AbstractFabry disease (FD) is an X-linked inherited lysosomal disorder due to a deficiency of the enzyme alpha-galactosidase A (α-gla) due to mutations in the GLA gene. These mutations result in plasma and lysosome accumulation of glycosphingolipids, leading to progressive organ damage and reduced life expectancy. Due to the availability of specific disease-modifying treatments, proper and timely diagnosis and therapy are essential to prevent irreversible complications. However, diagnosis of FD is often delayed because of the wide clinical heterogeneity of the disease and multiple organ involvement developing in variable temporal sequences. This observation is also valid for renal involvement, which may manifest with non-specific signs, such as proteinuria and chronic kidney disease, which are also common in many other nephropathies. Moreover, an additional confounding factor is the possibility of the coexistence of FD with other kidney disorders. Thus, suspecting and diagnosing FD nephropathy in patients with signs of kidney disease may be challenging for the clinical nephrologist. Herein, also through the presentation of a unique case of co-occurrence of autosomal dominant polycystic kidney disease and FD, we review the available literature on cases of coexistence of FD and other renal diseases and discuss the implications of these conditions. Moreover, we highlight the clinical, laboratory, and histological elements that may suggest clinical suspicion and address a proper diagnosis of Fabry nephropathy.
The trajectory of a range of commonly captured symptoms with standard care in people with kidney failure receiving haemodialysis: consideration for clinical trial design
Authors: Hnynn Si Pann Ei , Hernández-Alava Mónica , Dunn Louese , Wilkie Martin , Fotheringham James 
Published: November 2023

Abstract
Background
Despite the recognized high symptom prevalence in haemodialysis population, how these symptoms change over time and its implications for clinical practice and research is poorly understood.

Methods
Prevalent haemodialysis patients in the SHAREHD trial reported 17 POS-S Renal symptoms (none, mild, moderate, severe and overwhelming) at baseline, 6, 12 and 18 months. To assess the prevalence change at population level in people reporting moderate or worse symptoms at baseline, the absolute change in prevalence was estimated using multi-level mixed effects probit regression adjusting for age, sex, time on haemodialysis and Charlson Comorbidity Score. To assess changes at individual level, the proportion of people changing their symptom score every 6 months was estimated.

Results
Five hundred fifty-two participants completed 1725 questionnaires at four timepoints. Across all 17 symptoms with moderate or worse symptom severity at baseline, the majority of the change in symptom prevalence at population level occurred in the ‘severe’ category. The absolute improvement in prevalence of the ‘severe’ category was ≤ 20% over 18 months in eleven of the seventeen symptoms despite a large degree of relatively balanced movement of individuals in and out of severe category every six months. Examples include depression, skin changes and drowsiness, which had larger proportion (75–80%) moving in and out of severe category each 6 months period but < 5% difference between movement in and out of severe category resulting in relatively static prevalence over time. Meanwhile, larger changes in prevalence of > 20% were observed in six symptoms, driven by a 9 to 18% difference between movement in and movement out of severe category. All symptoms had > 50% of people in severe group changing severity within 6 months.

Conclusions
Changes in the severity of existing symptoms under standard care were frequent, often occurring within six months. Certain symptoms exhibited clinically meaningful shifts at both the population and individual levels. This highlighted the need to consider improvements in symptom severity when determining sample size and statistical power for trials. By accounting for potential symptom improvements with routine care, researchers can design trials capable of robustly detecting genuine treatment effects, distinguishing them from spontaneous changes associated with standard haemodialysis.
Economic burden of in-hospital AKI: a one-year analysis of the nationwide French hospital discharge database
Authors: Monard Céline , Rimmelé Thomas , Blanc Esther , Goguillot Mélanie , Bénard Stève , Textoris Julien 
Published: November 2023

Abstract
Background
Although Acute Kidney Injury (AKI) incidence is increasing worldwide, data investigating its cost are lacking. This population-wide study aimed to describe the characteristics and costs of hospital stays with, and without AKI, and to estimate the AKI-associated increases in costs and length of stay (LOS) in three subgroups (major open visceral surgery (MOV), cardiovascular surgery with extracorporeal circulation (CVEC), and sepsis).

Methods
All hospital stays that occurred in France in 2018 were included. Stay and patient characteristics were collected in the French hospital discharge database and described. Medical conditions were identified using the 10th International Classification of Diseases and the medical acts classification. In each subgroup, the adjusted increase in cost and LOS associated with AKI was estimated using a generalized linear model with gamma distribution and a log link function.

Results
26,917,832 hospital stays, of which 415,067 (1.5%) with AKI, were included. AKI was associated with 83,553 (19.8%), 7,165 (17.9%), and 15,387 (9.2%) of the stays with sepsis, CVEC, and MOV, respectively. Compared to stays without AKI, stays with AKI were more expensive (median [IQR] €4,719[€2,963-€7782] vs. €735[€383-€1,805]) and longer (median [IQR] 9[4–16] vs. 0[0–2] days). AKI was associated with a mean [95%CI] increase in hospitalization cost of 70% [69;72], 48% [45;50], and 68% [65;70] in the sepsis, CVEC, and MOV groups respectively, after adjustment.

Conclusion
This study confirms the major economic burden of in-hospital AKI in a developed country. Interventions to prevent AKI are urgently needed and their cost should be balanced with AKI-related costs.
The association between trimethylamine N-oxide levels and ischemic stroke occurrence: a meta-analysis and Mendelian randomization study
Authors: Hu Xinhua , Ren Haiyan , Cao Yuan 
Published: November 2023

Abstract
Background
Trimethylamine-N-oxide (TMAO), an intestinal microbiota-derived choline metabolite, has been found to be associated with ischemic stroke (IS) in more and more studies. However, the causal role of TMAO on IS occurrence remains perplexing.

Methods
We comprehensively screened the related clinical studies on PubMed, Web of Science, and Embase. Case-control and cohort studies that reported the TMAO levels of both IS patients and healthy controls were included, and the risk of bias was assessed according to the criteria by the Centre for Evidence-Based Medicine in Oxford, UK. A meta-analysis of the retrieved publications was performed with a random-effect model to analyze the connection between TMAO levels and IS events. Besides, a Mendelian randomization (MR) analysis was performed to study the causal effect of TMAO on IS, with pooled data of TMAO and IS obtained from genome-wide association studies (GWAS). The following methods were used: MR-Egger, weighted median, inverse-variance weighted, simple mode, and weighted mode. The study has been registered in INPLASY (Registration number: INPLASY2023100027).

Results
Eight cohort or case-control studies covering 2444 cases and 1707 controls were identified. The pooled data indicated that the IS patients tended to have higher TMAO levels compared with the controls (mean difference: 1.97 μM; 95% confidence interval [CI]: 0.87, 3.07; P = 0.0005), while distinctive heterogeneity (I2 = 96%, P < 0.00001) was observed. Sub-group analysis revealed that the heterogeneity of the studies might be derived from the studies themselves. However, no causal effect of TMAO on IS was observed (P > 0.05) in the Mendelian randomization analysis of this study.

Conclusion
We confirmed that IS patients tend to have higher TMAO levels than healthy individuals, while our findings of MR analysis did not support the causal role of TMAO in IS occurrence. Therefore, more studies are required for a better understanding of the relationship between TMAO levels and IS onset.
Stratified analysis of clinical pregnancy outcomes of sequential embryo transfer in frozen embryo transfer cycles based on different factors: a retrospective study
Authors: Li Jialing , Ji Jing , Guo Hua , Wang Feimiao , Fu Yunxing , Hu Rong 
Published: November 2023

Abstract
Objective
To explore the effect of sequential embryo transfer (ET) on the pregnancy outcome of frozen-thawed embryo transfer (FET) cycle and the indications of sequential transfer.

Methods
A total of 1440 FET cycles were enrolled in this retrospective study, of which 1080 patients received conventional ET and 360 patients received sequential ET. Further stratified analysis was performed according to the number of previous failed cycles, the number of embryos transferred and the stage of blastocyst (day 5 or 6, denoted D5 or D6) transferred. Comparison of pregnancy rates, implantation rate, miscarriage rate and multiple pregnancy rate among the groups of patients.

Results
The clinical pregnancy rate and implantation rate of the sequential ET group were higher than those of the conventional ET group (P < 0.01); however, there was no statistical difference in multiple pregnancy rate and miscarriage rate (P > 0.05). In sequential transfer, the number of transferred embryos (2 or 3) and the stage of transferred blastocysts (D5 or D6) had no effect on clinical pregnancy rate, implantation rate, multiple pregnancy rate and miscarriage rate (P > 0.05). In patients with three or more previous failure cycles, the sequential ET group showed higher clinical pregnancy rate and implantation rate (P > 0.05).

Conclusions
Compared with conventional ET in FET cycle, sequential ET strategy could significantly improve the clinical pregnancy rate and implantation rate. In sequential transfer, patients with three embryos transferred don’t have higher pregnancy rate and implantation rate. Besides, sequential transfer is more suitable for patients with repeated implantation failures (RIF), and increase the utilization rate of D6 blastocysts.
Investigate the relationship between the microbiota awareness in first trimester and high risk pregnancy in Turkish women: cross-sectional study
Authors: Cömert Tuğba Küçükkasap , Karadeniz Sinan , Akpınar Funda 
Published: November 2023

AbstractBackgroundIt is suggested that pregnancy risks may be related to microbial dysbiosis, and it is known that knowledge on this subject is reflected in behaviors. The purpose of this study was to investigate whether microbiota awareness in the first trimester of pregnancy is associated with pregnancy-related risks.MethodsWithin the scope of the study, the microbiota awareness scale was administered to 426 individuals in the first trimester of pregnancy, and information on any diagnosis related to high-risk pregnancy, gestational age, birth weight, and birth height of the newborn was obtained from their file records.ResultsThe mean total microbiota awareness score of individuals was 61.38 ± 11.00 (26.00–91.00). The microbiota awareness score (56.85 ± 11.65) was found to be lower in individuals diagnosed with high-risk pregnancy (p < 0.05) than in healthy subjects (63.64 ± 9.94). Moreover, in individuals with high-risk pregnancies, a positive correlation was found between the microbiota awareness score and newborn birth weight and height (p < 0.05).ConclusionThe poor microbiota awareness level in pregnant women is associated with high-risk pregnancy and neonatal growth status.