bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling bus-based substitution capabilities for metro systems using bipartite graphs
Authors: Kopsidas Athanasios , Kepaptsoglou Konstantinos 
Published: January 2024

Abstract
A disruption of metro services can have a negative impact in the performance of a city’s transportation system and hinder mobility needs of travellers. Investigating the vulnerability of metro systems is required for planning mitigation actions, such as bus substitution services. This study develops a model, which consists of a bipartite graph and its projection to represent the bus substitution capabilities for metro networks. The proposed methodology effectively identifies significant substitution elements (bus lines), evaluates the robustness of alternative options in terms of both connectedness and connectivity, and suggests effective strategies for enhancing bus line capacity to improve network robustness. By applying the methodology to a real-world metro network, valuable insights are gained regarding important bus lines and substitution robustness. Study findings suggest that approaches based on the weighted degree exhibit the greatest effectiveness when it comes to connectivity and the overall efficiency of the network. These findings can assist public transport operators in proactively managing disruptions and improving their services.
Towards a semi-local random walk technique through multilayer social networks to improve link prediction
Authors: Chen Suxia , Zhang Jiachen , Zhang Guijie , Rezaeipanah Amin 
Published: January 2024

AbstractThe rapid expansion of social networks has generated a growing need for scalable algorithms capable of effectively predicting links. Link prediction is a crucial area of study within complex networks research. Link prediction aims to predict future connections between nodes from the current snapshot of the network and plays a vital role in estimating the growth of social networks. This article introduces an improved approach to link prediction in social networks by exploiting an extended version of local random walk as semi-local random walk (SLRW) for multilayer social networks. Here, taking into account the connectivity and structural similarity of the involved nodes, we propose the SLRW method to acquire nodes sequence with the highest similarity. Also, SLRW metric includes a distributed technique to identify the nearest neighbours by considering the extended neighbourhood concept. To ensure optimal performance, we conduct extensive studies on various hyperparameters of the proposed metric. The experimental results conducted on different datasets demonstrate that the proposed metric achieves improvements in the field of link prediction compared to the state-of-the-art baselines.
Ecto-CD38-NADase inhibition modulates cardiac metabolism and protects mice against doxorubicin-induced cardiotoxicity
Authors: Peclat Thais R , Agorrody Guillermo , Colman Laura , Kashyap Sonu , Zeidler Julianna D , Chini Claudia C S , Warner Gina M , Thompson Katie L , Dalvi Pranjali , Beckedorff Felipe , Ebtehaj Sanam , Herrmann Joerg , van Schooten Wim , Chini Eduardo Nunes 
Published: January 2024

Abstract

Aims
Doxorubicin (DXR) is a chemotherapeutic agent that causes dose-dependent cardiotoxicity. Recently, it has been proposed that the NADase CD38 may play a role in doxorubicin-induced cardiotoxicity (DIC). CD38 is the main NAD+-catabolizing enzyme in mammalian tissues. Interestingly, in the heart, CD38 is mostly expressed as an ecto-enzyme that can be targeted by specific inhibitory antibodies. The goal of the present study is to characterize the role of CD38 ecto-enzymatic activity in cardiac metabolism and the development of DIC.

Methods and results
Using both a transgenic animal model and a non-cytotoxic enzymatic anti-CD38 antibody, we investigated the role of CD38 and its ecto-NADase activity in DIC in pre-clinical models. First, we observed that DIC was prevented in the CD38 catalytically inactive (CD38-CI) transgenic mice. Both left ventricular systolic function and exercise capacity were decreased in wild-type but not in CD38-CI mice treated with DXR. Second, blocking CD38-NADase activity with the specific antibody 68 (Ab68) likewise protected mice against DIC and decreased DXR-related mortality by 50%. A reduction of DXR-induced mitochondrial dysfunction, energy deficiency, and inflammation gene expression were identified as the main mechanisms mediating the protective effects.

Conclusion
NAD+-preserving strategies by inactivation of CD38 via a genetic or a pharmacological-based approach improve cardiac energetics and reduce cardiac inflammation and dysfunction otherwise seen in an acute DXR cardiotoxicity model.
Radiographic complicated and uncomplicated descending aortic dissections: aortic morphological differences by CT angiography and risk factor analysis
Authors: Berger Tim , Maier Annika , Kletzer Joseph , Schlett Christopher L , Kondov Stoyan , Czerny Martin , Rylski Bartosz , Kreibich Maximilian 
Published: January 2024

Abstract

Aims
To identify radiographic differences between patients with uncomplicated and complicated descending aortic dissections.

Methods and results
Between April 2009 and July 2021, 209 patients with acute descending aortic dissections were analysed as complicated (malperfusion, rupture, diameter progress, and diameter ≥ 55 mm) or uncomplicated. Detailed CTA measurements (slice thickness ≤ 3 mm) were taken in multiplanar reconstruction. A composite endpoint (early aortic failure) was defined as reoperation, diameter progression, and early mortality. Seventy-seven patients were female (36.8%) [complicated n = 27 (36.5%); uncomplicated n = 50 (37.0%) P = 1.00]. Seventy-four (35%) patients were categorized as morphologically complicated, and 135 (65%) as uncomplicated. In patients with complicated dissections, the dissection extended more frequently to the aortic bifurcation (P = 0.044), the coeliac trunk (P = 0.003), the superior mesenteric artery (P = 0.007), and both iliac arteries (P &lt; 0.001) originated less frequently from the true lumen. The length of the most proximal communication (entry) in type B aortic dissection was longer, 14.0 mm [12.0 mm; 27.0 mm] vs. 6.0 mm [4,0 mm; 13.0 mm] in complicated cases (P = 0.005). Identified risk factors for adverse aortic events were connective tissue disease [HR 8.0 (1.9–33.7 95% CI HR)], length of the aortic arch [HR 4.7 (1.5–15.1 95% CI HR)], a false lumen diameter &gt; 19.38 mm [HR 3.389 (1.1–10.2 95% CI HR)], and origin of the inferior mesenteric artery from the false lumen [HR 4.2 (1.0–5.5 95% CI HR)].

Conclusion
We identified significant morphological differences and predictors for adverse events in patients presenting complicated and uncomplicated descending dissections. Our morphological findings will help guide future aortic therapies, taking a tailored patient approach.
Mortality Risk Information, Survival Expectations and Sexual Behaviours
Authors: Ciancio Alberto , Delavande Adeline , Kohler Hans-Peter , Kohler Iliana V 
Published: January 2024

Abstract
We investigate the impact of a randomised information intervention about population-level mortality on health investment and subjective health expectations. Our focus is on risky sex in a high-HIV-prevalence environment. Treated individuals are less likely to engage in risky sexual practices one year after the intervention, with, for example, an 8% increase in abstinence. We collected detailed data on individuals’ subjective expectations about their own and population survival, as well as other important health outcomes. Our findings emphasise the significance of integrating subjective expectation data in field experiments to identify the pathways that lead to behavioural change.
Collateral Damage: The Legacy of the Secret War in Laos
Authors: Riaño Juan Felipe , Valencia Caicedo Felipe 
Published: January 2024

Abstract
We investigate the long-term impact of conflict on economic development, focusing on the US ‘Secret War’ in Laos (1964–73). Our study employs multiple empirical strategies and data on bombing campaigns, satellite imagery, and development indicators to demonstrate that regions heavily bombed during this period experienced lower economic development almost fifty years after the conflict officially ended. A one-standard-deviation increase in bombing intensity is associated with a 7.1% decrease in GDP per capita. We demonstrate the persistent effects of bombing campaigns on human capital accumulation, structural transformation and migration patterns, stressing the role of unexploded ordnance contamination as the primary mechanism of transmission of these effects.
John Sheppard (c.1514–1558/59) at Oxford and the Chapel Royal: exculpation and clarification
Authors: Bowers Roger 
Published: January 2024

Abstract
The received biography available for the English composer John Sheppard (c.1514 – late 1558 or early 1559) is amenable to clarification at a number of points. He was employed as Master of the Choristers at Magdalen College, Oxford, for just a single spell, September 1543 to early 1548. The available evidence suggests that he proceeded thence directly to admission to the Chapel Royal. He had no further contact with Magdalen College; an instance of kidnap and confinement perpetrated in 1555 that is commonly attributed to him was instead committed by one Richard Sheparde/Sheper/Sheprey, a fellow of the college. Despite being only an imperfect draft, his ‘will’ of 1 December 1558 reveals much about his family circumstances at Westminster. He died between 1 December 1558 and 31 January 1559; the actual date must be reconcilable with expectation of his attendance at Queen Elizabeth’s coronation on 15 January 1559, as recorded on a list compiled not earlier than 15 December 1558.
Area-level excess mortality in times of COVID-19 in Switzerland: geographical, socioeconomic and political determinants
Authors: Riou Julien , Panczak Radoslaw , Konstantinoudis Garyfallos , Egger Matthias 
Published: January 2024

Abstract
The coronavirus disease 2019 (COVID-19)-related excess mortality in Switzerland is well documented, but no study examined mortality at the small-area level. We analysed excess mortality in 2020 for 2141 Swiss municipalities using a Bayesian spatiotemporal model fitted to 2011–19 data. Areas most affected included the Ticino, the Romandie and the Northeast. Rural areas, municipalities within cross-border labour markets, of lower socioeconomic position and with less support for control measures in the popular vote on the COVID-19 Act had greater excess mortality. Particularly vulnerable municipalities require special efforts to mitigate the impact of pandemics.
Construction of an economical xylose-utilizing Saccharomyces cerevisiae and its ethanol fermentation
Authors: Li Fan , Bai Wenxin , Zhang Yuan , Zhang Zijian , Zhang Deguo , Shen Naidong , Yuan Jingwei , Zhao Guomiao , Wang Xiaoyan 
Published: January 2024

Abstract
Traditional industrial Saccharomyces cerevisiae could not metabolize xylose due to the lack of a specific enzyme system for the reaction from xylose to xylulose. This study aims to metabolically remould industrial S. cerevisiae for the purpose of utilizing both glucose and xylose with high efficiency. Heterologous gene xylA from Piromyces and homologous genes related to xylose utilization were selected to construct expression cassettes and integrated into genome. The engineered strain was domesticated with industrial material under optimizing conditions subsequently to further improve xylose utilization rates. The resulting S. cerevisiae strain ABX0928-0630 exhibits a rapid growth rate and possesses near 100% xylose utilization efficiency to produce ethanol with industrial material. Pilot-scale fermentation indicated the predominant feature of ABX0928-0630 for industrial application, with ethanol yield of 0.48 g/g sugars after 48 hours and volumetric xylose consumption rate of 0.87 g/l/h during the first 24 hours. Transcriptome analysis during the modification and domestication process revealed a significant increase in the expression level of pathways associated with sugar metabolism and sugar sensing. Meanwhile, genes related to glycerol lipid metabolism exhibited a pattern of initial increase followed by a subsequent decrease, providing a valuable reference for the construction of efficient xylose-fermenting strains.
Modeling basal area yield using simultaneous equation systems incorporating uncertainty estimators
Authors: Sandoval Simón , Montes Cristián R , Bullock Bronson P 
Published: January 2024

Abstract
Over the last three decades, many growth and yield systems developed for the southeast USA have incorporated methods to create a compatible basal area (BA) prediction and projection equation. This technique allows practitioners to calibrate BA models using both measurements at a given arbitrary age, as well as the increment in BA when time series panel data are available. As a result, model parameters for either prediction or projection alternatives are compatible. One caveat of this methodology is that pairs of observations used to project forward have the same weight as observations from a single measurement age, regardless of the projection time interval. To address this problem, we introduce a variance–covariance structure giving different weights to predictions with variable intervals. To test this approach, prediction and projection equations were fitted simultaneously using an ad hoc matrix structure. We tested three different error structures in fitting models with (i) homoscedastic errors described by a single parameter (Method 1); (ii) heteroscedastic errors described with a weighting factor ${w}_t$ (Method 2); and (iii) errors including both prediction ($\overset{\smile }{\varepsilon }$) and projection errors ($\tilde{\varepsilon}$) in the weighting factor ${w}_t$ (Method 3). A rotation-age dataset covering nine sites, each including four blocks with four silvicultural treatments per block, was used for model calibration and validation, including explicit terms for each treatment. Fitting using an error structure which incorporated the combined error term ($\overset{\smile }{\varepsilon }$ and $\tilde{\varepsilon}$) into the weighting factor ${w}_t$ (Method 3), generated better results according to the root mean square error with respect to the other two methods evaluated. Also, the system of equations that incorporated silvicultural treatments as dummy variables generated lower root mean square error (RMSE) and Akaike’s index values (AIC) in all methods. Our results show a substantial improvement over the current prediction-projection approach, resulting in consistent estimators for BA.
SlWRKY80-mediated jasmonic acid pathway positively regulates tomato resistance to saline–alkali stress by enhancing spermidine content and stabilizing Na+/K+ homeostasis
Authors: Shang Chunyu , Liu Xiaoyan , Chen Guo , Zheng Hao , Khan Abid , Li Guobin , Hu Xiaohui 
Published: January 2024

Abstract
Saline–alkali is an important abiotic stressor influencing tomato production. Exogenous methyl jasmonate (MeJA) is well known to increase tomato resistance to a variety of stresses, although its exact mechanism is yet unknown. In this study we confirmed that 22.5 μmol/l MeJA could significantly improve the saline–alkali stress resistance of tomato. Saline–alkali (300 mM) stress increased the endogenous MeJA and jasmonic acid (JA) contents of tomato by 18.8 and 13.4%, respectively. Exogenous application of 22.5 μmol/l MeJA increased the endogenous MeJA and JA contents in tomato by 15.2 and 15.9%, respectively. Furthermore, we found an important transcription factor, SlWRKY80, which responded to MeJA, and constructed its overexpressing and knockout lines through genetic transformation. It was found that SlWRKY80 actively regulated tomato resistance to saline–alkali stress, and the spraying of exogenous MeJA (22.5 μmol/l) reduced the sensitivity of SlWRKY80 knockout lines to saline–alkali stress. The SlWRKY80 protein directly combines with the promoter of SlSPDS2 and SlNHX4 to positively regulate the transcription of SlSPDS2 and SlNHX4, thereby promoting the synthesis of spermidine and Na+/K+ homeostasis, actively regulating saline–alkali stress. The augmentation of JA content led to a notable reduction of 70.6% in the expression of SlJAZ1, and the release of the SlWRKY80 protein interacting with SlJAZ1. In conclusion, we revealed the mechanism of exogenous MeJA in tomato stress resistance through multiple metabolic pathways, elucidated that exogenous MeJA further promotes spermidine synthesis and Na+/K+ homeostasis by activating the expression of SlWRKY80, which provides a new theoretical basis for the study of the JA stress resistance mechanism and the production of tomato.
Risk of Common Neurological Disorders in Adult Patients with Inflammatory Bowel Disease: A Systematic Review and Meta-analysis
Authors: Zamani Mohammad , Ebrahimtabar Forough , Alizadeh-Tabari Shaghayegh , Kasner Scott E , Elkind Mitchell S V , Ananthakrishnan Ashwin N , Choden Tenzin , Rubin David T , Malekzadeh Reza 
Published: January 2024

Abstract

Background
Several studies investigated the risks of neurological conditions in patients with inflammatory bowel disease (IBD), with some variability in findings. We aimed to perform a systematic review and meta-analysis of available evidence to elucidate the association between IBD and the risks of common neurological disorders.

Methods
We conducted a literature search through Embase, PubMed, Scopus, and ProQuest databases from inception to June 30, 2023, to identify cohort studies assessing the risk of developing stroke, all-cause dementia, Parkinson’s disease (PD), multiple sclerosis (MS), seizure/epilepsy, and peripheral neuropathy in adult IBD patients compared with non-IBD population. We combined hazard ratios (HRs) with 95% confidence intervals (CIs) to compute pooled estimates using a random-effects model.

Results
In total, 22 cohort studies were included, of which 9 studies reported 7074 stroke events in 202 460 IBD patients, 5 studies reported 3783 all-cause dementia diagnoses in 109 602 IBD patients, 7 studies reported 932 PD diagnoses in 354 792 IBD patients, and 1 study reported 6 MS events in 35 581 IBD patients. We observed increased risks of incident stroke (pooled HR = 1.19; 95% CI, 1.06-1.31), all-cause dementia (pooled HR = 1.22; 95% CI, 1.05-1.38), PD (pooled HR = 1.39; 95% CI, 1.20-1.58), and MS (HR = 2.89; 95% CI, 1.02-8.42). No eligible studies were found on peripheral neuropathy and seizure/epilepsy.

Conclusions
Inflammatory bowel disease may be modestly associated with increased risks of stroke, all-cause dementia, and PD. Further longitudinal studies are warranted to investigate potential links with MS, seizure/epilepsy, and peripheral neuropathy, as well as their clinical significance.
THE MODULATORY EFFECT OF PREBIOTIC INULIN-TYPE FRUCTANS ON THE MICROBIOME PROFILE OF CHILDREN WITH INFLAMMATORY BOWEL DISEASE: A DOUBLE-BLIND RANDOMIZED CONTROLLED TRIAL
Authors: Breton Jessica , Tanes Ceylan , Kyle Bittinger , Kachelries Kelly , Crisci Melissa , Compher Charlene , Baldassano Robert , Albenberg Lindsey 
Published: January 2024

Abstract

OBJECTIVE
The intestinal microbiota plays a pivotal role in the inflammation associated with inflammatory bowel disease (IBD) through their interaction with the mucosal immune system. Prebiotic interventions using inulin-type fructans increase faecal and mucosal bifidobacteria as well as butyrate producing bacteria in healthy volunteers. The aim of this study was to assess the effect of a two-month oligofructose-enriched inulin (OI) supplementation on the microbiome composition, metabolome of children with IBD with subclinical disease activity.

DESIGN
We performed a single-center, double-blind, placebo-controlled trial at the Children’s Hospital of Philadelphia. Participants included children, 6–21 years old, with subclinical active colonic IBD as defined by a fecal calprotectin level between 50 and 500 μg/g and clinical remission. Participants were randomly assigned 1:1 to consume prebiotic OI or maltodextrin placebo for 8 weeks. Fecal and rectal swabs samples were collected at baseline, week 4, 8 and 16 for fecal calprotectin, microbiome profiling (shotgun metagenomic sequencing) and matching metabolomics (liquid chromatography tandem mass spectrometry).

RESULTS
The study randomized 68 patients, and 59 were included in the efficacy analyses. The global fecal and mucosal microbiome composition was significantly altered by prebiotic intake and specific inulin-induced increase in relative abundance of Bifidobacterium and Anaerostipes in the fecal samples were identified at week 4 (Figure 1). Two months after discontinuation of OI, the microbial composition of both groups returned to baseline levels. Fecal metabolite profiles were not altered during the 8-week intervention. A negative correlation was observed between calprotectin levels and the relative abundance of Bifidobacterium [q=0.08] and butyrate producer Anaerostipes [q=0.017] (Figure 2). Outcome analysis of inulin-induced change in calprotectin level during the intervention is pending.

CONCLUSIONS
Dietary intervention with prebiotic OI causes short term alterations in the microbiome of children with IBD characterized by an enrichment of Bifidobacterium and butyrate producer Anaerostipes. These results open new perspectives for development of microbiome-targeted dietary interventions in pediatric IBD.
JB received the Crohn’s and Colitis Foundation Career Development Award # 693867 for this study.

Figure 1 Selective effect of prebiotic supplementation on microbiome composition

Figure 2 Correlation between calprotectin level and inulin-induced microbiome shift
A negative correlation between fecal calprotectin level and inulin-induced change in relative abundance of Bifidobacterium [q= 0.08] and Anaerostipes [q=0.017] was observed during the 8-week intervention.