bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel technique for arterial reconstruction in simultaneous pancreas-kidney transplantation, a randomized clinical trial
Authors: Karar Hassan , Shafiekhani Mojtaba , Mahmoudi Mohamad Mahdi , Azadeh Nazanin , Shamsaeefar Alireza , Nazari Sahar Sohrabi , Jafari Mehran , Ashrafzadeh Kiarash , Esmaeili Maryam , Nikeghbalian Saman , Nikoupour Hamed 
Published: October 2023

Abstract
Introduction
Simultaneous pancreas kidney (SPK) transplantation is an invaluable procedure to enhance the quality of life of insulin-dependent patients with advanced renal disease. The creation of vascular anastomoses of the donor’s pancreas vessels to the recipient’s, is of utmost importance to predict the graft outcome and surgical complications. In the study we introduce a novel technique for arterial reconstruction during SPK transplantation.

Methods
Conventionally, during the SPK transplantation, a so-called Y-graft is anastomosed between donor’s superior mesenteric and splenic artery to the recipient’s right iliac artery. In the study we adopted a new technique by preparing an extra extension using the donor’s carotid artery, to be anastomosed to the Y-graft and the iliac artery. In this non-blinded randomized clinical trial we compared the surgical complications and early outcomes between the 2 groups of patients with the traditional and new arterial reconstruction techniques during 3 months after transplantation.

Results
Thirty adult patients were included in the study. The incidence of pancreatitis, vascular thrombosis and surgical site infection was lower in the new Y-graft and extension technique, which was not statistically significant. However, the calculated Cohen’s d index showed the medium effect of new Y-graft and extension technique on complication after SPK transplantations.

Conclusion
The post-operative complications tend to be lower in the novel arterial reconstruction technique, however a study on a larger patient group is encouraged to confirm our primary results.

Trial registration
The study was registered at the Iranian Registry of Clinical Trials on 12/05/2022; IRCT 20210625051701N2; (http://www.irct.ir/).
Probiotic potential and safety analysis of lactic acid bacteria isolated from Ethiopian traditional fermented foods and beverages
Authors: Amenu Desalegn , Bacha Ketema 
Published: October 2023

Abstract
Background
Probiotics are live microorganisms that effectively combat foodborne pathogens, promoting intestinal health when consumed in sufficient amounts. This study evaluated the probiotic potential and safety of lactic acid bacteria isolated from selected Ethiopian traditional fermented foods and beverages (Kotcho, Bulla, Ergo, Cabbage-Shamita, Borde, and Bukuri). To assess the isolates’ probiotic activity, tolerance, and survival rate under various stressful conditions, including low pH, intestinal inhibitory substances, salt concentration, bile salt, and simulated gastric/intestinal juice. The isolates were also tested for antagonistic activities against common bacterial and fungal pathogens (Staphylococcus aureus, Salmonella Typhimurium, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Candida albicans) and safety (auto-aggregation, co-aggregation, cell source hydrophobicity, hemolytic activity, DNase, and antibiotic susceptibility). The best probiotic lactic acid bacteria (LAB) were characterized to species level following standard MALDI TOF/mass spectrometry analysis.

Results
A total of 125 potentially probiotic LAB were isolated of which 17 (13.60%) isolates survived low pH (2, 2.5, and 3), bile salt (0.3%), intestinal inhibitory chemicals (phenol, bile, low acidity, pepsin, and pancreas), and simulated gastro-intestinal settings with near 60–94% survival rate. In addition, 11 best LAB isolates were further screened based on additional screening including their antimicrobial efficacy, preservative efficiency, bacteriocin production besides resistance to low acid and bile salts, and survival potential under simulated gastrointestinal conditions. All 11 LAB isolates were resistant to ampicillin, vancomycin, gentamicin, kanamycin, clindamycin, and chloramphenicol, while they were susceptible to streptomycin and tetracycline. The MALDI TOF mass spectrometry analysis result of efficient probiotic LAB grouped them under the genus Pediococcus, Enterococcus, and Lactococcus including Pediococcus pentosaceus, Enterococcus faecium, Lactococcus lactis, and Pediococcus acidilactici.

Conclusion
Ethiopian traditional fermented foods and beverages are good sources of promising probiotic lactic acid bacteria. These isolates could serve as potential starter cultures and bio-preservative for the enhancement of the shelf life of foods. This study established the groundwork for the selection of excellent probiotics for the development and application of LAB for antibacterial action, starter culture production, and preservation activities.
The pseudoenzyme ADPRHL1 affects cardiac function by regulating the ROCK pathway
Authors: Tian Lei , Guo Tianwei , Wu Fujian , Bai Rui , Ai Sinan , Wang Hongyue , Song Yuanxiu , Zhu Min , Jiang Youxu , Ma Shuhong , Zhuang Xiaofeng , Guo Shuzhen 
Published: October 2023

Abstract
Background
Pseudoenzymes, catalytically deficient variants of active enzymes, have a wide range of regulatory functions. ADP-ribosylhydrolase-like 1 (ADPRHL1), a pseudoenzyme belonging to a small group of ADP-ribosylhydrolase enzymes that lacks the amino acid residues necessary for catalytic activity, may have a significant role in heart development based on accumulating evidence. However, the specific function of ADPRHL1 in this process has not been elucidated. To investigate the role of ADPRHL1 in the heart, we generated the first in vitro human embryonic stem cell model with an ADPRHL1 knockout.

Method
Using the CRISPR/Cas9 system, we generated ADPRHL1 knockout in the human embryonic stem cell (hESC) H9 line. The cells were differentiated into cardiomyocytes using a chemically defined and xeno-free method. We employed confocal laser microscopy to detect calcium transients and microelectrode array (MEA) to assess the electrophysiological activity of ADPRHL1 deficiency cardiomyocytes. Additionally, we investigated the cellular mechanism of ADPRHL1 by Bulk RNA sequencing and western blot.

Results
The results indicate that the absence of ADPRHL1 in cardiomyocytes led to adhered abnormally, as well as perturbations in calcium transients and electrophysiological activity. We also revealed that disruption of focal adhesion formation in these cardiomyocytes was due to an excessive upregulation of the ROCK–myosin II pathway. Notably, inhibition of ROCK and myosin II effectively restores focal adhesions in ADPRHL1-deficient cardiomyocytes and improved electrical conduction and calcium activity.

Conclusions
Our findings demonstrate that ADPRHL1 plays a critical role in maintaining the proper function of cardiomyocytes by regulating the ROCK–myosin II pathway, suggesting that it may serve as a potential drug target for the treatment of ADPRHL1-related diseases.
Regulation of self-renewal and senescence in primitive mesenchymal stem cells by Wnt and TGFβ signaling
Authors: Mazzella Matteo , Walker Keegan , Cormier Christina , Kapanowski Michael , Ishmakej Albi , Saifee Azeem , Govind Yashvardhan , Chaudhry G. Rasul 
Published: October 2023

Abstract
Background
The therapeutic application of multipotent mesenchymal stem cells (MSCs) encounters significant challenges, primarily stemming from their inadequate growth and limited self-renewal capabilities. Additionally, as MSCs are propagated, their ability to self-renew declines, and the exact cellular and molecular changes responsible for this are poorly understood. This study aims to uncover the complex molecular mechanisms that govern the self-renewal of primitive (p) MSCs.

Methods
We grew pMSCs using two types of medium, fetal bovine serum (FM) and xeno-free (XM), at both low passage (LP, P3) and high passage (HP, P20). To evaluate LP and HP pMSCs, we examined their physical characteristics, cell surface markers, growth rate, colony-forming ability, BrdU assays for proliferation, telomerase activity, and potential to differentiate into three lineages. Moreover, we conducted RNA-seq to analyze their transcriptome and MNase-seq analysis to investigate nucleosome occupancies.

Results
When grown in FM, pMSCs underwent changes in their cellular morphology, becoming larger and elongated. This was accompanied by a decrease in the expression of CD90 and CD49f, as well as a reduction in CFE, proliferation rate, and telomerase activity. In addition, these cells showed an increased tendency to differentiate into the adipogenic lineage. However, when grown in XM, pMSCs maintained their self-renewal capacity and ability to differentiate into multiple lineages while preserving their fibroblastoid morphology. Transcriptomic analysis showed an upregulation of genes associated with self-renewal, cell cycle regulation, and DNA replication in XM-cultured pMSCs, while senescence-related genes were upregulated in FM-cultured cells. Further analysis demonstrated differential nucleosomal occupancies in self-renewal and senescence-related genes for pMSCs grown in XM and FM, respectively. These findings were confirmed by qRT-PCR analysis, which revealed alterations in the expression of genes related to self-renewal, cell cycle regulation, DNA replication, differentiation, and senescence. To understand the underlying mechanisms, we investigated the involvement of Wnt and TGFβ signaling pathways by modulating them with agonists and antagonists. This experimental manipulation led to the upregulation and downregulation of self-renewal genes in pMSCs, providing further insights into the signaling pathways governing the self-renewal and senescence of pMSCs.

Conclusion
Our study shows that the self-renewal potential of pMSCs is associated with the Wnt pathway, while senescence is linked to TGFβ.
The augmented value of using clinical notes in semi-automated surveillance of deep surgical site infections after colorectal surgery
Authors: Verberk Janneke D.M. , van der Werff Suzanne D. , Weegar Rebecka , Henriksson Aron , Richir Milan C. , Buchli Christian , van Mourik Maaike S.M. , Nauclér Pontus 
Published: October 2023

Abstract
Background
In patients who underwent colorectal surgery, an existing semi-automated surveillance algorithm based on structured data achieves high sensitivity in detecting deep surgical site infections (SSI), however, generates a significant number of false positives. The inclusion of unstructured, clinical narratives to the algorithm may decrease the number of patients requiring manual chart review. The aim of this study was to investigate the performance of this semi-automated surveillance algorithm augmented with a natural language processing (NLP) component to improve positive predictive value (PPV) and thus workload reduction (WR).

Methods
Retrospective, observational cohort study in patients who underwent colorectal surgery from January 1, 2015, through September 30, 2020. NLP was used to detect keyword counts in clinical notes. Several NLP-algorithms were developed with different count input types and classifiers, and added as component to the original semi-automated algorithm. Traditional manual surveillance was compared with the NLP-augmented surveillance algorithms and sensitivity, specificity, PPV and WR were calculated.

Results
From the NLP-augmented models, the decision tree models with discretized counts or binary counts had the best performance (sensitivity 95.1% (95%CI 83.5–99.4%), WR 60.9%) and improved PPV and WR by only 2.6% and 3.6%, respectively, compared to the original algorithm.

Conclusions
The addition of an NLP component to the existing algorithm had modest effect on WR (decrease of 1.4–12.5%), at the cost of sensitivity. For future implementation it will be a trade-off between optimal case-finding techniques versus practical considerations such as acceptability and availability of resources.
The role of short-chain fatty acids (SCFAs) in regulating stress responses, eating behavior, and nutritional state in anorexia nervosa: protocol for a randomized controlled trial
Authors: Quagebeur Robin , Dalile Boushra , Raes Jeroen , Van Oudenhove Lukas , Verbeke Kristin , Vrieze Elske 
Published: October 2023

Abstract
Objective
This protocol proposes investigating the effects of short-chain fatty acids (SCFAs)—namely acetate, propionate, and butyrate—as mediators of microbiota-gut-brain interactions on the acute stress response, eating behavior, and nutritional state in malnourished patients with anorexia nervosa (AN). SCFAs are produced by bacterial fermentation of dietary fiber in the gut and have recently been proposed as crucial mediators of the gut microbiota's effects on the host. Emerging evidence suggests that SCFAs impact human psychobiology through endocrine, neural, and immune pathways and may regulate stress responses and eating behavior.

Method
We will conduct a randomized, triple-blind, placebo-controlled trial in 92 patients with AN. Patients will receive either a placebo or a mixture of SCFAs (acetate propionate, butyrate) using pH-dependent colon-delivery capsules for six weeks. This clinical trial is an add-on to the standard inpatient psychotherapeutic program focusing on nutritional rehabilitation.

Hypotheses
We hypothesize that colonic SCFAs delivery will modulate neuroendocrine, cardiovascular, and subjective responses to an acute laboratory psychosocial stress task. As secondary outcome measures, we will assess alterations in restrictive eating behavior and nutritional status, as reflected by changes in body mass index. Additionally, we will explore changes in microbiota composition, gastrointestinal symptoms, eating disorder psychopathology, and related comorbidities.

Discussion
The findings of this study would enhance our understanding of how gut microbiota-affiliated metabolites, particularly SCFAs, impact the stress response and eating behavior of individuals with AN. It has the potential to provide essential insights into the complex interplay between the gut, stress system, and eating behavior and facilitate new therapeutic targets for stress-related psychiatric disorders.
This protocol is prospectively registered with ClinicalTrials.gov, with trial registration number NCT06064201.
Intratumoral and peritumoral MRI-based radiomics prediction of histopathological grade in soft tissue sarcomas: a two-center study
Authors: Zhang Liyuan , Yang Yang , Wang Ting , Chen Xi , Tang Mingyue , Deng Junnan , Cai Zhen , Cui Wei 
Published: October 2023

Abstract
Objectives
This study aims to develop a model based on intratumoral and peritumoral radiomics from fat-suppressed T2-weighted(FS-T2WI) images to predict the histopathological grade of soft tissue sarcoma (STS).

Methods
This retrospective study included 160 patients with STS from two centers, of which 82 were low-grade and 78were high-grade. Radiomics features were extracted and selected from the region of tumor mass volume (TMV) and peritumoral tumor volume (PTV) respectively. The TMV, PTV, and combined(TM-PTV) radiomics models were established in the training cohort (n = 111)for the prediction of histopathological grade. Finally, a radiomics nomogram was constructed by combining the TM-PTV radiomics signature (Rad-score) and the selected clinical-MRI predictor. The ROC and calibration curves were used to determine the performance of the TMV, PTV, and TM-PTV models in the training and validation cohort (n = 49). The decision curve analysis (DCA) and calibration curves were used to investigate the clinical usefulness and calibration of the nomogram, respectively.

Results
The TMV model, PTV model, and TM-PTV model had AUCs of 0.835, 0.879, and 0.917 in the training cohort and 0.811, 0.756, 0.896 in the validation cohort. The nomogram, including the TM-PTV signatures and peritumoral hyperintensity, achieved good calibration and discrimination with a C-index of 0.948 (95% CI, 0.906 to 0.990) in the training cohort and 0.921 (95% CI, 0.840 to 0.995) in the validation cohort. Decision curve analysis demonstrated the clinical usefulness of the nomogram.

Conclusion
The proposed model based on intratumoral and peritumoral radiomics showed good performance in distinguishing low-grade from high-grade STSs.
Safety design study for energy harvesters
Authors: Gaidai Oleg , Yakimov Vladimir , Wang Fang , Xing Yihan , Zhang Fuxi 
Published: October 2023

AbstractModern offshore and onshore green energy engineering includes energy harvesting—as a result, extensive experimental investigations, as well as safety and reliability analysis are crucial for design and engineering. For this study, several wind-tunnel experiments under realistic in situ wind speed conditions have been conducted to examine the performance of galloping energy harvester. Next, a novel structural reliability approach is presented here that is especially well suited for multi-dimensional energy harvesting systems that have been either numerically simulated or analog observed during the representative time lapse, yielding an ergodic system time record. As demonstrated in this study, the advocated methodology may be used for risk assessment of dynamic system structural damage or failure. Furthermore, traditional reliability methodologies dealing with time series do not easily cope with the system’s high dimensionality, along with nonlinear cross-correlations between the system’s components. This study’s objective was to assess state-of-the-art reliability method, allowing efficient extraction of relevant statistical information, even from a limited underlying dataset. The methodology described in this study aims to assist designers when assessing nonlinear multidimensional dynamic energy harvesting system’s failure and hazard risks.
The association between macronutrient intakes and coronavirus disease 2019 (COVID-19) in an Iranian population: applying a dynamical system model
Authors: Hafezi Somayeh Ghiasi , Seifi Najmeh , Bahari Hossein , Mohammadi Maryam , Ghasemabadi Atena , ferns Gordon A. , Farkhani Ehsan Mosa , Ghayour-mobarhan Majid 
Published: October 2023

Abstract
Aims
The possible role of lifestyle including diet on immunity led us to investigate the association between dietary macronutrient intake and COVID-19 in an Iranian population.

Methods
Dietary intakes were recorded in the first phase of the MASHAD cohort study (started in 2007), using a 24-h dietary recall. To determine the COVID-19 incidence, data from all PCR-positive patients in Mashhad were recorded between February 2020 and June 2022. Dietary macronutrients were included in the regression model, adjusting for age and sex. System dynamical models were also applied.

Results
The analysis included 1957 participants, including 193 COVID-19-positive patients. Dietary intakes of non-starch polysaccharides (NSP) and fiber were significantly lower in COVID-19 patients (P < 0.05). After adjusting for age and sex, starch and total sugar were significantly associated with COVID-19 infection ((OR = 1.0008, P = 0.001) and (OR = 1.0006, P = 0.026), respectively). There was also a significant association between dietary fiber intake and hospitalization (OR = 0.99, P = 0.018). In the dynamical system models, dietary intakes of cholesterol, polyunsaturated fatty acids (PUFA), and total sugar above 180.2 mg, 13.11 g, and 79.53 mg, respectively, were associated with an increased susceptibility to COVID-19 infection, while dietary fiber had a protective role.

Conclusion
Dietary intake of starch and total sugars was associated with increased odds of COVID-19, while fiber intake decreased the odds of hospitalization due to COVID-19. The dynamical system models showed that dietary intake of cholesterol, PUFAs, and total sugar was associated with an increased risk of COVID-19, while fiber had a protective role.
Exploring limitations in the induced polarization versus surface conductivity relationship in the case of wetland soils
Authors: Emmanuel Efemena D. , Slater Lee D. , Doro Kennedy O. 
Published: October 2023

Recent induced polarization studies suggest that the real part of surface conductivity ([Formula: see text]) scales linearly with the imaginary conductivity ([Formula: see text] = [Formula: see text]) or normalized chargeability (Mn) for a range of soil types. The coefficients of this relationship l and l_Mn ( l = [Formula: see text]/[Formula: see text] or l_Mn = Mn/[Formula: see text]) allow the separation of the surface and electrolytic conductivities from the bulk conductivity. However, the dependence of these constants on varying soil physicochemical properties, including under unsaturated conditions, is yet to be assessed. Using estimates of [Formula: see text] from 18 undisturbed soil samples from a restored wetland and [Formula: see text] measured over a frequency range of 0.01 Hz to 10 kHz, the [Formula: see text] and [Formula: see text] were compared with the laboratory measurements of soil properties. Also, l and l_Mn were calculated for each soil sample and regressed them against the soil properties. We find an apparent dependence of l on soil texture, bulk density, organic matter, and moisture contents, with coefficients of determination ([Formula: see text]) ranging from 0.5 to 0.65 at low frequencies (e.g., 1 Hz) but not at high frequencies (e.g., 936 Hz). This dependence of l on soil texture results from the insensitivity of [Formula: see text] at low frequency to [Formula: see text] and, by implication, to the soil properties controlling [Formula: see text]. In contrast, l_Mn indicates no correlation with the soil properties because Mn is linearly correlated with [Formula: see text] and correlated with the soil properties controlling [Formula: see text]. Our results call for caution on the application of [Formula: see text] at a single frequency as a proxy of [Formula: see text] because [Formula: see text] is not necessarily correlated with [Formula: see text] across all soil types. Although using l_Mn derived from multifrequency measurements overcomes this limitation, field acquisition of spectral information (e.g., up to 1000 Hz) remains a challenge.