bluuebunny/crossref_metadata_2025_split huggingface dataset:
Framework for converting mechanistic network models to probabilistic models
Authors: Goyal Ravi , De Gruttola Victor , Onnela Jukka-Pekka 
Published: October 2023

AbstractThere are two prominent paradigms for the modelling of networks: in the first, referred to as the mechanistic approach, one specifies a set of domain-specific mechanistic rules that are used to grow or evolve the network over time; in the second, referred to as the probabilistic approach, one describes a model that specifies the likelihood of observing a given network. Mechanistic models (models developed based on the mechanistic approach) are appealing because they capture scientific processes that are believed to be responsible for network generation; however, they do not easily lend themselves to the use of inferential techniques when compared with probabilistic models. We introduce a general framework for converting a mechanistic network model (MNM) to a probabilistic network model (PNM). The proposed framework makes it possible to identify the essential network properties and their joint probability distribution for some MNMs; doing so makes it possible to address questions such as whether two different mechanistic models generate networks with identical distributions of properties, or whether a network property, such as clustering, is over- or under-represented in the networks generated by the model of interest compared with a reference model. The proposed framework is intended to bridge some of the gap that currently exists between the formulation and representation of mechanistic and PNMs. We also highlight limitations of PNMs that need to be addressed in order to close this gap.
Anorectal Manometry in Patients With Fecal Incontinence After Ileal Pouch–Anal Anastomosis for Ulcerative Colitis: A Cohort Study
Authors: Young Sigrid , Lee Briton , Smukalla Scott , Axelrad Jordan , Chang Shannon 
Published: October 2023

Abstract

Background
Fecal incontinence commonly occurs in patients with ulcerative colitis and ileal pouch–anal anastomosis. There is a paucity of manometric data in pouch patients. We aimed to better define manometric parameters in pouch patients with fecal incontinence.

Methods
We compared clinical and manometric variables in ulcerative colitis patients with pouch and fecal incontinence to ulcerative colitis patients with pouch without fecal incontinence and to non-ulcerative colitis patients with fecal incontinence. Manometric data for the 3 cohorts were compared to established normative data. An independent-samples t-test was performed for continuous variables, and chi-square test was used for categorical variables. Logistic regression was performed to identify predictors of incontinence in pouch patients (P &lt; .05).

Results
Among 26 pouch patients with fecal incontinence (73% female), 26 pouch patients without fecal incontinence (35% female), and 84 patients with fecal incontinence without ulcerative colitis (68% female), there were no differences in anorectal pressures between patients with fecal incontinence. Lower pressures were observed in pouch patients with fecal incontinence compared to those without fecal incontinence. Resting pressure was similar between pouch patients with fecal incontinence and healthy controls (60.9 ± 36.1 mmHg vs. 66.9 ± 3.2 mmHg, P = .40). Female sex (P = .019) and defecatory disorders (P = .033) each independently predicted fecal incontinence in pouch patients.

Conclusions
Pouch patients with fecal incontinence have lower anorectal pressures compared to pouch patients without incontinence, though have similar pressures to non-ulcerative colitis patients with fecal incontinence. Pouch patients with fecal incontinence have similar resting pressures as healthy controls. Distinct manometric normative values for pouch patients are needed.
Is Occupation a Risk Factor for Developing Inflammatory Bowel Disease? A Case–Control Study
Authors: Mauriz-Barreiro Violeta , Ruano-Raviña Alberto , Ferreiro-Iglesias Rocío , Bastón-Rey Iria , Calviño-Suárez Cristina , Nieto-García Laura , Porto-Silva Sol , Martínez-Seara Xurxo , Domínguez-Munoz J Enrique , Barreiro-de Acosta Manuel 
Published: October 2023

Abstract

Background and aims
The role of occupation is uncertain in the onset of inflammatory bowel diseases. The aim of this study is to identify if there is a role of occupation in these diseases.

Materials and methods
A case–control study with incident cases with inflammatory bowel diseases was designed. Cases and controls were recruited simultaneously and controls followed a sex and age frequency matching with cases. A detailed questionnaire was completed by all the participants. To analyze the results, a logistic regression was used. A subgroup analysis was performed for each inflammatory bowel disease.

Results
A total of 141 patients with incident inflammatory bowel disease (80 ulcerative colitis, 55 Crohn’s disease, and 6 unclassified colitis) and 114 controls were included. There were no statistically significant differences in type of work, working hours, contact with animals, or physical activity at work between inflammatory bowel disease patients and controls. After stratifying results according to type of IBD, there were no statistically significant differences either.

Conclusions
There seems to be no risk for inflammatory bowel disease onset regarding the type of work, working hours, contact with animals, or sedentariness.
Imaging in patients with cardiovascular implantable electronic devices: part 1—imaging before and during device implantation. A clinical consensus statement of the European Association of Cardiovascular Imaging (EACVI) and the European Heart Rhythm Association (EHRA) of the ESC
Authors: Stankovic Ivan , Voigt Jens-Uwe , Burri Haran , Muraru Denisa , Sade Leyla Elif , Haugaa Kristina Hermann , Lumens Joost , Biffi Mauro , Dacher Jean-Nicolas , Marsan Nina Ajmone , Bakelants Elise , Manisty Charlotte , Dweck Marc R , Smiseth Otto A , Donal Erwan ,   Reviewers: This document was reviewed by members of the 2020-2022 EACVI Scientific Documents Committee:, Andreini Daniele , Bäck Magnus , Bertrand Philippe B , Keenan Niall , Neglia Danilo ,   by the 2020–2022 EACVI President:, Cosyns Bernard 
Published: October 2023

Abstract
More than 500 000 cardiovascular implantable electronic devices (CIEDs) are implanted in the European Society of Cardiology countries each year. The role of cardiovascular imaging in patients being considered for CIED is distinctly different from imaging in CIED recipients. In the former group, imaging can help identify specific or potentially reversible causes of heart block, the underlying tissue characteristics associated with malignant arrhythmias, and the mechanical consequences of conduction delays and can also aid challenging lead placements. On the other hand, cardiovascular imaging is required in CIED recipients for standard indications and to assess the response to device implantation, to diagnose immediate and delayed complications after implantation, and to guide device optimization. The present clinical consensus statement (Part 1) from the European Association of Cardiovascular Imaging, in collaboration with the European Heart Rhythm Association, provides comprehensive, up-to-date, and evidence-based guidance to cardiologists, cardiac imagers, and pacing specialists regarding the use of imaging in patients undergoing implantation of conventional pacemakers, cardioverter defibrillators, and resynchronization therapy devices. The document summarizes the existing evidence regarding the use of imaging in patient selection and during the implantation procedure and also underlines gaps in evidence in the field. The role of imaging after CIED implantation is discussed in the second document (Part 2).
The impact of genetic background during laboratory evolution of Pseudomonas aeruginosa in a cystic fibrosis-like environment
Authors: Filipow Nicole , Mallon Samantha , Shewaramani Sonal , Kassen Rees , Wong Alex 
Published: October 2023

Abstract
Genetic background has the potential to influence both the tempo and trajectory of adaptive change: Different genotypes of a given species may adopt varied solutions to the same environmental challenge, or they may approach the same solution at different rates. Laboratory selection has been widely used to experimentally examine the evolutionary consequences of variation in genetic background, although largely using genotypes differing by only a few mutations. Here, we leverage natural variation in the bacterium Pseudomonas aeruginosa to investigate whether different adaptive solutions are accessible from distant points of departure on an adaptive landscape. We evolved 17 diverse genotypes in a laboratory medium that partially mimics the lung sputum of cystic fibrosis patients, and we measured changes in 10 phenotypes as well as in fitness. Using phylogenetically informed analyses, we found that genetic background impacted the tempo, but not the trajectory, of phenotypic evolution: Different starting genotypes converged toward similar phenotypes, but at varying rates. Our findings add to a growing body of evidence supporting widespread diminishing return epistasis during adaptation. The importance of genetic background toward the trajectory of adaptation remains inconsistent across experimental systems and conditions.
Transcriptome analysis reveals molecular signature and cell-type difference of Homo sapiens endothelial-to-mesenchymal transition
Authors: Bronson Ronald , Lyu Junfang , Xiong Jianhua 
Published: October 2023

Abstract
Endothelial-to-mesenchymal transition (EndoMT), a specific form of epithelial-to-mesenchymal transition, drives a growing number of human (Homo sapiens) pathological conditions. This emerging knowledge opens a path to discovering novel therapeutic targets for many EndoMT-associated disorders. Here, we constructed an atlas of the endothelial-cell transcriptome and demonstrated EndoMT-induced global changes in transcriptional gene expression. Our gene ontology analyses showed that EndoMT could be a specific checkpoint for leukocyte chemotaxis, adhesion, and transendothelial migration. We also identified distinct gene expression signatures underlying EndoMT across arterial, venous, and microvascular endothelial cells. We performed protein–protein interaction network analyses, identifying a class of highly connected hub genes in endothelial cells from different vascular beds. Moreover, we found that the short-chain fatty acid acetate strongly inhibits the transcriptional program of EndoMT in endothelial cells from different vascular beds across tissues. Our results reveal the molecular signature and cell-type difference of EndoMT across distinct tissue- and vascular-bed-specific endothelial cells, providing a powerful discovery tool and resource value. These results suggest that therapeutically manipulating the endothelial transcriptome could treat an increasing number of EndoMT-associated pathological conditions.
Chromosome-Level Genome Assembly for the Angiosperm Silene conica
Authors: Fields Peter D , Weber Melody M , Waneka Gus , Broz Amanda K , Sloan Daniel B 
Published: October 2023

Abstract
The angiosperm genus Silene has been the subject of extensive study in the field of ecology and evolution, but the availability of high-quality reference genome sequences has been limited for this group. Here, we report a chromosome-level assembly for the genome of Silene conica based on Pacific Bioscience HiFi, Hi-C, and Bionano technologies. The assembly produced 10 scaffolds (1 per chromosome) with a total length of 862 Mb and only ∼1% gap content. These results confirm previous observations that S. conica and its relatives have a reduced base chromosome number relative to the genus's ancestral state of 12. Silene conica has an exceptionally large mitochondrial genome (&gt;11 Mb), predominantly consisting of sequence of unknown origins. Analysis of shared sequence content suggests that it is unlikely that transfer of nuclear DNA is the primary driver of this mitochondrial genome expansion. More generally, this assembly should provide a valuable resource for future genomic studies in Silene, including comparative analyses with related species that recently evolved sex chromosomes.
Critical view on oligo(dT)-based RNA-seq: bias arising, modeling, and mitigating
Authors: Su Qiang , Wang Jun , Kang Kang , Niu Yanqin , Li Shujin , Gou Deming 
Published: October 2023

Abstract
The precise biological interpretation of oligo(dT)-based RNA sequencing (RNA-seq) datasets, particularly in single-cell RNA-seq (scRNA-seq), is invaluable for understanding complex biological systems. However, the presence of biases can lead to misleading results in downstream analysis. This study has now identified two additional biases that are not accounted for in established bias models: poly(A)-tail length bias and fixed-position GC-content bias. These biases have a significant negative impact on the overall quality of oligo(dT)-based RNA-seq data. To address these biases, we have developed a universal bias-mitigating method based on the lower-affinity binding of short and nonanchored oligo(dT) primers to poly(A) tails. This method significantly reduces poly(A) length bias and completely eliminates fixed-position GC bias. Furthermore, the use of short oligo(dT) with impartial binding behavior toward the diverse poly(A) tails renders RNA-seq with more reliable measurements. The findings of this study are particularly beneficial for scRNA-seq datasets, where accurate benchmarking is critical.
Educational Influences on Late-Life Health: Genetic Propensity and Attained Education
Authors: Ericsson Malin , Finch Brian , Karlsson Ida K , Gatz Margaret , Reynolds Chandra A , Pedersen Nancy L , Mosing Miriam A 
Published: October 2023

Abstract

Objectives
The educational gradient in late-life health is well established. Despite this, there are still ambiguities concerning the role of underlying confounding by genetic influences and gene-environment (GE) interplay. Here, we investigate the role of educational factors (attained and genetic propensities) on health and mortality in late life using genetic propensity for educational attainment (as measured by a genome-wide polygenic score, PGSEdu) and attained education.

Methods
By utilizing genetically informative twin data from the Swedish Twin Registry (n = 14,570), we investigated influences of the educational measures, familial confounding as well as the possible presence of passive GE correlation on both objective and subjective indicators of late-life health, that is, the Frailty Index, Multimorbidity, Self-rated health, cardiovascular disease, and all-cause mortality.

Results
Using between-within models to adjust for shared familial factors, we found that the relationship between educational level and health and mortality later in life persisted despite controlling for familial confounding. PGSEdu and attained education both uniquely predicted late-life health and mortality, even when mutually adjusted. Between-within models of PGSEdu on the health outcomes in dizygotic twins showed weak evidence for passive GE correlation (prGE) in the education-health relationship.

Discussion
Both genetic propensity to education and attained education are (partly) independently associated with health in late life. These results lend further support for a causal education-health relationship but also raise the importance of genetic contributions and GE interplay.
Obesity, Sarcopenia and Myosteatosis: Impact on Clinical Outcomes in the Operative Management of Crohn’s Disease
Authors: Donnelly Mark , Driever Dorothee , Ryan Éanna J , Elliott Jessie A , Finnegan John , McNamara Deirdre , Murphy Ian , Conlon Kevin C , Neary Paul C , Kavanagh Dara O , O’Riordan James M 
Published: October 2023

Abstract

Background
Obesity, sarcopenia, and myosteatosis in inflammatory bowel disease may confer negative outcomes, but their prevalence and impact among patients with Crohn’s disease (CD) have not been systematically studied. The aim of this study was to assess nutritional status and body composition among patients undergoing resectional surgery for CD and determine impact on operative outcomes.

Methods
Consecutive patients with CD undergoing resection from 2000 to 2018 were studied. Total, subcutaneous, and visceral fat areas and lean tissue area (LTA) and intramuscular adipose tissue (IMAT) were determined preoperatively by computed tomography at L3 using SliceOmatic (Tomovision, Canada). Univariable and multivariable linear, logistic, and Cox proportional hazards regression were performed.

Results
One hundred twenty-four consecutive patients were studied (ileocolonic disease 53%, n = 62, biologic therapy 34.4% n = 43). Mean fat mass was 22.7 kg, with visceral obesity evident in 23.9% (n = 27). Increased fat stores were associated with reduced risk of emergency presentation but increased corticosteroid use (β 9.09, standard error 3.49; P = .011). Mean LBM was 9.9 kg. Sarcopenia and myosteatosis were associated with impaired baseline nutritional markers. Myosteatosis markers IMAT (P = .002) and muscle attenuation (P = .0003) were associated with increased grade of complication. On multivariable analysis, IMAT was independently associated with increased postoperative morbidity (odds ratio [OR], 1.08; 95% confidence interval (CI), 1.01-1.16; P = .037) and comprehensive complications index (P = .029). Measures of adiposity were not associated with overall morbidity; however, increased visceral fat area independently predicted venous thromboembolism (OR, 1.02; 95% CI, 1.00-1.05; P = .028), and TFA was associated with increased wound infection (OR, 1.00; 95% CI, 1.00-1.01; P = .042) on multivariable analysis.

Conclusion
Myosteatosis is associated with nutritional impairment and predicts increased overall postoperative morbidity following resection for CD. Despite its association with specific increased postoperative risks, increased adiposity does not increase overall morbidity, reflecting preservation of nutritional status and relatively more quiescent disease phenotype. Impaired muscle mass and function represent an appealing target for patient optimization to improve outcomes in the surgical management of CD.
Get Fit: Muscle Health for Crohn’s Disease Surgical Outcome Optimization
Authors: Massironi Sara , Sileri Pierpaolo , Danese Silvio 
Published: October 2023

Lay Summary
Muscular health, encompassing sarcopenia and myosteatosis, has a pivotal role in optimizing surgical outcomes in patients with Crohn’s disease. A comprehensive approach is advocated for improving patient well-being after surgery.
Longitudinal Trends in Pregnancy Outcomes Among Women With Inflammatory Bowel Disease in the Era of Biologics: A 20-Year Nationwide Analysis
Authors: Prakash Preeti , Dua Anoushka , Blumenfeld Yair , Chen Po-Hung , Parian Alyssa M , Limketkai Berkeley N 
Published: October 2023

Abstract

Background
Many women with inflammatory bowel disease (IBD) are diagnosed by their reproductive years. Prior literature suggests that women with IBD may be at increased risk of adverse pregnancy outcomes. Biologics have revolutionized IBD treatment, and current evidence favors continuation during pregnancy. We sought to examine trends in pregnancy outcomes over 20 years with the evolution of IBD treatment.

Methods
Using the National Inpatient Sample, IBD and non-IBD obstetric hospitalizations were identified between 1998 and 2018 using International Classification of Diseases 9 and 10 codes. Outcomes of interest included cesarean delivery, gestational diabetes, preeclampsia/eclampsia, premature rupture of membranes (PROM), preterm delivery, fetal growth restriction (FGR), fetal distress, and stillbirth. Stratified by Crohn’s disease (CD), ulcerative colitis (UC), and non-IBD deliveries, temporal trends and multivariable logistic regression were analyzed.

Results
There were 48 986 CD patients, 30 998 UC patients, and 69 963,805 non-IBD patients. Between 1998 and 2018, CD deliveries increased from 3.3 to 12.9 per 10 000 deliveries (P &lt; 0.001) and UC deliveries increased from 2.3 to 8.6 per 10 000 deliveries (P &lt; 0.001). Cesarean deliveries, gestational diabetes, preeclampsia/eclampsia, PROM, FGR, and fetal distress increased over time for IBD and non-IBD women, while preterm deliveries decreased (P &lt; 0.001). Multivariable analyses demonstrated that IBD patients had higher risk of cesarean delivery, preeclampsia/eclampsia, PROM, and preterm delivery compared with non-IBD patients.

Conclusion
Over a 20-year period, live deliveries amongst women with IBD have increased. Trends in pregnancy outcomes have followed a similar trajectory in patients with and without IBD. However, there is still demonstrable risk of adverse pregnancy outcomes in patients with IBD.
Enteric Infection at Flare of Inflammatory Bowel Disease Impacts Outcomes at 2 Years
Authors: Dimopoulos-Verma Abhishek , Hong Soonwook , Axelrad Jordan E 
Published: October 2023

Abstract

Background
Outcomes of inflammatory bowel disease (IBD) following flare complicated by enteric infection (EI) are limited by follow-up duration and insufficient assessment of the role of non-Clostridioides difficile pathogens. We compared 2-year IBD outcomes following flare with and without EI.

Methods
We performed a retrospective cohort study of adults evaluated with stool PCR testing for IBD flare. Subjects were stratified by presence of EI at flare and were matched for age, sex, and date to those without EI. The primary outcome was a composite of steroid-dependent IBD, colectomy, and/or IBD therapy class change/dose escalation at 2 years. Additional analyses were performed by dividing the EI group into C. difficile infection (CDI) and non-CDI EI, and further subdividing non-CDI EI into E. coli subtypes and other non-CDI EI.

Results
We identified 137 matched subjects, of whom 62 (45%) had EI (40 [29%] CDI; 17 [12%] E. coli). Enteric infection at flare was independently associated with the primary outcome (adjusted odds ratio, 4.14; 95% confidence interval [CI], 1.62-11.5). After dividing EI into CDI and non-CDI EI, only CDI at flare was independently associated with the primary outcome (adjusted odds ratio, 4.04; 95% CI, 1.46-12.6). After separating E. coli subtypes from non-CDI EI, E. coli infection and CDI at flare were both independently associated with the primary outcome; other EI was not.

Conclusions
Enteric infection at flare—specifically with CDI—is associated with worse IBD outcomes at 2 years. The relationship between E. coli subtypes at flare and subsequent IBD outcomes requires further investigation.
Statelessness and Nationality Matters in the context of Migration between Northern Africa and Spain
Authors: Remi Njiki Michel 
Published: October 2023

Abstract
This article explores the problems linked with the determination of nationality and the condition of statelessness in a complex setting characterized by undocumented migration, such as the transit zone around the Strait of Gibraltar, between North Africa and the southern borders of Spain. The States immediately concerned are Morocco and Spain, although the situation affects many other neighbouring States in North Africa. The study suggests that without a precise mechanism to separate regimes between ordinary migrants and migrants who need international protection, such States fail to fulfil their international obligations regarding stateless persons and other undocumented migrants.