bluuebunny/crossref_metadata_2025_split huggingface dataset:
A functional analysis of omic network embedding spaces reveals key altered functions in cancer
Authors: Doria-Belenguer Sergio , Xenos Alexandros , Ceddia Gaia , Malod-Dognin Noël , Pržulj Nataša 
Published: April 2023

Abstract

Motivation
Advances in omics technologies have revolutionized cancer research by producing massive datasets. Common approaches to deciphering these complex data are by embedding algorithms of molecular interaction networks. These algorithms find a low-dimensional space in which similarities between the network nodes are best preserved. Currently available embedding approaches mine the gene embeddings directly to uncover new cancer-related knowledge. However, these gene-centric approaches produce incomplete knowledge, since they do not account for the functional implications of genomic alterations. We propose a new, function-centric perspective and approach, to complement the knowledge obtained from omic data.

Results
We introduce our Functional Mapping Matrix (FMM) to explore the functional organization of different tissue-specific and species-specific embedding spaces generated by a Non-negative Matrix Tri-Factorization algorithm. Also, we use our FMM to define the optimal dimensionality of these molecular interaction network embedding spaces. For this optimal dimensionality, we compare the FMMs of the most prevalent cancers in human to FMMs of their corresponding control tissues. We find that cancer alters the positions in the embedding space of cancer-related functions, while it keeps the positions of the noncancer-related ones. We exploit this spacial ‘movement’ to predict novel cancer-related functions. Finally, we predict novel cancer-related genes that the currently available methods for gene-centric analyses cannot identify; we validate these predictions by literature curation and retrospective analyses of patient survival data.

Availability and implementation
Data and source code can be accessed at https://github.com/gaiac/FMM.
Did the Prison Industrial Complex Deliver on Its Promise? Prison Proliferation and Employment in Rural America
Authors: Zhang Yiwen 
Published: April 2023

AbstractTwo concurrent phenomena emerged in rural America in the 1970s: job losses due to deindustrialization and prison proliferation relating to mass incarceration. While supporters of the prison industrial complex promised an economic lifeline for rural America, opponents questioned the economic benefits of prison openings. Using county fixed-effects models and data covering 1960–2000, this study reveals a null association between prison openings and total rural employment. While prison proliferation marginally increased government employment, it simultaneously had a negative impact on private employment. Specifically, prison openings were associated with decreased employment in manufacturing, finance and recreational services; and had no impact on jobs in construction, wholesale, and local retail sales. Thus, the promises of employment growth relating to prisons were, overall, not kept.
Moderate-to-Severe Diarrhea and Stunting Among Children Younger Than 5 Years: Findings From the Vaccine Impact on Diarrhea in Africa (VIDA) Study
Authors: Nasrin Dilruba , Liang Yuanyuan , Powell Helen , Casanova Ines Gonzalez , Sow Samba O , Hossain M Jahangir , Omore Richard , Sanogo Doh , Tamboura Boubou , Zaman Syed M A , Antonio Martin , Jones Joquina Chiquita M , Awuor Alex O , Kasumba Irene N , Ochieng John B , Badji Henry , Verani Jennifer R , Widdowson Marc-Alain , Roose Anna , Jamka Leslie P , Tennant Sharon M , Ramakrishnan Usha , Kotloff Karen L 
Published: April 2023

Abstract

Background
Stunting affects &gt;20% of children &lt;5 years old worldwide and disproportionately impacts underserved communities. The Vaccine Impact on Diarrhea in Africa (VIDA) Study examined the association between an episode of moderate-to-severe diarrhea (MSD) and the risk of subsequent stunting in children &lt;5 years living in 3 sub-Saharan African countries.

Methods
In this prospective, matched, case-control study among children &lt;5 years, data were collected over 36 months from 2 groups. “Children with MSD” visited a health center within 7 days of illness onset experiencing ≥3 loose stools/day plus sunken eyes, poor skin turgor, dysentery, intravenous rehydration, or hospitalization. “Children without MSD” were enrolled from the community within 14 days of the index MSD child; they were diarrhea-free during the previous 7 days and were matched to the index case by age, sex, and residence. Using generalized linear mixed-effects models, we estimated the effect of an MSD episode on odds of being stunted, defined as height-for-age z-scores &lt;−2, at a follow-up visit 2–3 months post-enrollment.

Results
The proportion of stunting at enrollment was similar when 4603 children with MSD and 5976 children without MSD were compared (21.8% vs 21.3%; P = .504). Among children not stunted at enrollment, those with MSD had 30% higher odds of being stunted at follow-up than children without MSD after controlling for age, sex, study site, and socioeconomic status (adjusted OR: 1.30; 95% CI: 1.05–1.62: P = .018).

Conclusions
Children &lt;5 years in sub-Saharan Africa without stunting experienced an increased likelihood of stunting during 2–3 months following an episode of MSD. Strategies for control of early childhood diarrhea should be integrated into programs intended to reduce childhood stunting.
Stunting Following Moderate-to-Severe Diarrhea Among Children Aged &lt;5 Years in Africa Before and After Rotavirus Vaccine Introduction: A Comparison of the Global Enteric Multicenter Study and the Vaccine Impact on Diarrhea in Africa (VIDA) Study
Authors: Nasrin Dilruba , Liang Yuanyuan , Verani Jennifer R , Powell Helen , Sow Samba O , Omore Richard , Hossain M Jahangir , Doh Sanogo , Zaman Syed M A , Jones Joquina Chiquita M , Awuor Alex O , Kasumba Irene N , Tennant Sharon M , Ramakrishnan Usha , Kotloff Karen L 
Published: April 2023

Abstract

Background
Studies conducted before rotavirus vaccine introduction found that moderate-to-severe diarrhea (MSD) in children aged &lt;5 years was associated with stunting at follow-up. It is unknown whether the reduction in rotavirus-associated MSD following vaccine introduction decreased the risk of stunting.

Methods
The Global Enteric Multicenter Study (GEMS) and the Vaccine Impact on Diarrhea in Africa (VIDA) study, two comparable matched case-control studies, were conducted during 2007–2011 and 2015–2018, respectively. We analyzed data from 3 African sites where rotavirus vaccine was introduced after GEMS and before starting VIDA. Children with acute MSD (&lt;7 days onset) were enrolled from a health center and children without MSD (diarrhea-free for ≥7 days) were enrolled at home within 14 days of the index MSD case. The odds of being stunted at a follow-up visit 2–3 months after enrollment for an episode of MSD was compared between GEMS and VIDA using mixed-effects logistic regression models controlling for age, sex, study site, and socioeconomic status.

Results
We analyzed data from 8808 children from GEMS and 10 579 from VIDA. Among those who were not stunted at enrollment in GEMS, 8.6% with MSD and 6.4% without MSD became stunted during the follow-up period. In VIDA, 8.0% with MSD and 5.5% children without MSD developed stunting. An episode of MSD was associated with higher odds of being stunted at follow-up compared with children without MSD in both studies (adjusted odds ratio [aOR], 1.31; 95% confidence interval [CI]: 1.04–1.64 in GEMS and aOR, 1.30; 95% CI: 1.04–1.61 in VIDA). However, the magnitude of association was not significantly different between GEMS and VIDA (P = .965).

Conclusions
The association of MSD with subsequent stunting among children aged &lt;5 years in sub-Saharan Africa did not change after rotavirus vaccine introduction. Focused strategies are needed for prevention of specific diarrheal pathogens that cause childhood stunting.
Antibiotic-Prescribing Practices for Management of Childhood Diarrhea in 3 Sub-Saharan African Countries: Findings From the Vaccine Impact on Diarrhea in Africa (VIDA) Study, 2015–2018
Authors: Awuor Alex O , Ogwel Billy , Powell Helen , Verani Jennifer R , Sow Samba O , Hossain M Jahangir , Ochieng John B , Juma Jane , Jamka Leslie P , Roose Anna , Doh Sanogo , Deichsel Emily L , Onwuchekwa Uma , Keita Adama Mamby , Antonio Martin , Jones Joquina Chiquita M , Zaman Syed M A , Badji Henry , Kasumba Irene N , Nasrin Dilruba , Platts-Mills James A , Houpt Eric R , Berendes David M , Sugerman Ciara E , Widdowson Marc-Alain , Tennant Sharon M , Mintz Eric D , Omore Richard , Kotloff Karen L 
Published: April 2023

AbstractBackgroundDespite antibiotic prescription being recommended for dysentery and suspected cholera only, diarrhea still triggers unwarranted antibiotic prescription. We evaluated antibiotic-prescribing practices and their predictors among children aged 2–59 months in the Vaccine Impact on Diarrhea in Africa (VIDA) Study performed in The Gambia, Mali, and Kenya.MethodsVIDA was a prospective case-control study (May 2015–July 2018) among children presenting for care with moderate-to-severe diarrhea (MSD). We defined inappropriate antibiotic use as prescription or use of antibiotics when not indicated by World Health Organization (WHO) guidelines. We used logistic regression to assess factors associated with antibiotic prescription for MSD cases who had no indication for an antibiotic, at each site.ResultsVIDA enrolled 4840 cases. Among 1757 (36.3%) who had no apparent indication for antibiotic treatment, 1358 (77.3%) were prescribed antibiotics. In The Gambia, children who presented with a cough (adjusted odds ratio [aOR]: 2.05; 95% confidence interval [95% CI]: 1.21–3.48) were more likely to be prescribed an antibiotic. In Mali, those who presented with dry mouth (aOR: 3.16; 95% CI: 1.02–9.73) were more likely to be prescribed antibiotics. In Kenya, those who presented with a cough (aOR: 2.18; 95% CI: 1.01–4.70), decreased skin turgor (aOR: 2.06; 95% CI: 1.02–4.16), and were very thirsty (aOR: 4.15; 95% CI: 1.78–9.68) were more likely to be prescribed antibiotics.ConclusionsAntibiotic prescription was associated with signs and symptoms inconsistent with WHO guidelines, suggesting the need for antibiotic stewardship and clinician awareness of diarrhea case-management recommendations in these settings.
Epidemiology of Enteroaggregative, Enteropathogenic, and Shiga Toxin–ProducingEscherichia coliAmong Children Aged &lt;5 Years in 3 Countries in Africa, 2015–2018: Vaccine Impact on Diarrhea in Africa (VIDA) Study
Authors: Ochieng John B , Powell Helen , Sugerman Ciara E , Omore Richard , Ogwel Billy , Juma Jane , Awuor Alex O , Sow Samba O , Sanogo Doh , Onwuchekwa Uma , Keita Adama Mamby , Traoré Awa , Badji Henry , Hossain M Jahangir , Jones Joquina Chiquita M , Kasumba Irene N , Nasrin Dilruba , Roose Anna , Liang Yuanyuan , Jamka Leslie P , Antonio Martin , Platts-Mills James A , Liu Jie , Houpt Eric R , Mintz Eric D , Hunsperger Elizabeth , Onyango Clayton O , Strockbine Nancy , Widdowson Marc-Alain , Verani Jennifer R , Tennant Sharon M , Kotloff Karen L 
Published: April 2023

AbstractBackgroundTo address knowledge gaps regarding diarrheagenic Escherichia coli (DEC) in Africa, we assessed the clinical and epidemiological features of enteroaggregative E. coli (EAEC), enteropathogenic E. coli (EPEC), and Shiga toxin–producing E. coli (STEC) positive children with moderate-to-severe diarrhea (MSD) in Mali, The Gambia, and Kenya.MethodsBetween May 2015 and July 2018, children aged 0–59 months with medically attended MSD and matched controls without diarrhea were enrolled. Stools were tested conventionally using culture and multiplex polymerase chain reaction (PCR), and by quantitative PCR (qPCR). We assessed DEC detection by site, age, clinical characteristics, and enteric coinfection.ResultsAmong 4840 children with MSD and 6213 matched controls enrolled, 4836 cases and 1 control per case were tested using qPCR. Of the DEC detected with TAC, 61.1% were EAEC, 25.3% atypical EPEC (aEPEC), 22.4% typical EPEC (tEPEC), and 7.2% STEC. Detection was higher in controls than in MSD cases for EAEC (63.9% vs 58.3%, P &lt; .01), aEPEC (27.3% vs 23.3%, P &lt; .01), and STEC (9.3% vs 5.1%, P &lt; .01). EAEC and tEPEC were more frequent in children aged &lt;23 months, aEPEC was similar across age strata, and STEC increased with age. No association between nutritional status at follow-up and DEC pathotypes was found. DEC coinfection with Shigella/enteroinvasive E. coli was more common among cases (P &lt; .01).ConclusionsNo significant association was detected between EAEC, tEPEC, aEPEC, or STEC and MSD using either conventional assay or TAC. Genomic analysis may provide a better definition of the virulence factors associated with diarrheal disease.
Clinical and Epidemiologic Features of Cryptosporidium-Associated Diarrheal Disease Among Young Children Living in Sub-Saharan Africa: The Vaccine Impact on Diarrhea in Africa (VIDA) Study
Authors: Hossain M Jahangir , Powell Helen , Sow Samba O , Omore Richard , Roose Anna , Jones Joquina Chiquita M , Zaman Syed M A , Badji Henry , Sarwar Golam , Kasumba Irene N , Onwuchekwa Uma , Doh Sanogo , Awuor Alex O , Ochieng John B , Verani Jennifer R , Liu Jie , Tennant Sharon M , Nasrin Dilruba , Jamka Leslie P , Liang Yuanyuan , Howie Stephen R C , Antonio Martin , Houpt Eric R , Kotloff Karen L 
Published: April 2023

Abstract

Background
As part of the Vaccine Impact on Diarrhea in Africa (VIDA) Study, we examined the prevalence, clinical presentation, and seasonality of Cryptosporidium in children to understand its relative burden after the introduction of rotavirus vaccine.

Methods
VIDA was a 3-year, age-stratified, matched case-control study of medically attended acute moderate-to-severe diarrhea (MSD) in children aged 0–59 months residing in censused populations at sites in Kenya, Mali, and The Gambia. Clinical and epidemiologic data were collected at enrollment, and a stool sample was tested for enteropathogens by quantitative PCR. An algorithm was created based on the organism's cycle threshold (Ct) and association with MSD to identify the subset of Cryptosporidium PCR-positive (Ct &lt;35) cases most likely to be attributed to MSD. Clinical outcomes were assessed at 2–3 months after enrollment.

Results
One thousand one hundred six (22.9%) cases of MSD and 873 controls (18.1%) were PCR positive for Cryptosporidium; 465 cases (42.0%) were considered attributable to Cryptosporidium, mostly among children 6–23 months. Cryptosporidium infections peaked in The Gambia and Mali during the rainy season, while in Kenya they did not have clear seasonality. Compared with cases with watery MSD who had a negative PCR for Cryptosporidium, cases with watery MSD attributed to Cryptosporidium were less frequently dehydrated but appeared more severely ill using a modified Vesikari scale (38.1% vs 27.0%; P &lt; 0.001), likely due to higher rates of hospitalization and intravenous fluid administration, higher prevalence of being wasted or very thin very thin (23.4% vs 14.7%; P &lt; 0.001), and having severe acute malnutrition (midupper arm circumference &lt;115 mm, 7.7% vs 2.5%; P &lt; 0.001). On follow-up, Cryptosporidium-attributed cases had more prolonged and persistent episodes (43.2% vs 32.7%; P &lt;0 .001) and linear growth faltering (change in height-for-age z score between enrollment and follow-up: −0.29 vs −0.17; P &lt; 0.001).

Conclusions
The burden of Cryptosporidium remains high among young children in sub-Saharan Africa. Its propensity to cause illness and further impact children longer term by compromising nutritional status early in life calls for special attention to enable appropriate management of clinical and nutritional consequences.
Health Communication Research Informs Inflammatory Bowel Disease Practice and Research: A Narrative Review
Authors: Karimi Neda , Moore Alison Rotha , Lukin Annabelle , Connor Susan J 
Published: April 2023

Abstract

Background
In the absence of targeted empirical evidence on effective clinical communication in inflammatory bowel disease (IBD), a broad overview of existing evidence on effective communication in healthcare and available recommendations for communication in telehealth is provided and mapped onto IBD research and practice.

Methods
A narrative literature review was conducted using Pubmed and Scopus databases and snowballing literature search.

Results
Evidence-based relationship building strategies include communicating emotions, acknowledging and addressing patients’ hesitancy, and ensuring continued support. A particular recommendation regarding telehealth interaction is to avoid long stretches of talk. Effective informational strategies include facilitating and supporting information exchange and considering patients’ preferences in decision-making. In teleconsultations, clinicians should ask direct questions about patients’ emotional state, clarify their understanding of patients’ concerns and check patients’ understanding, address at least one patient-reported outcome when discussing the recommended treatment, and shorten the consultation where possible. Strategies for maximizing effective clinical communication in the spoken communicative mode include using infographics and simple language, and assessing adherence at the beginning of the consultation. For teleconsultations, clinicians are advised to allow patients to explain the reason for their call at the beginning of the teleconsultation, probe additional concerns early and before ending the teleconsultation, and be mindful of technical issues such as voice delays.

Conclusions
Use of question prompt lists, decision aids, micro-lessons, and communication training interventions for clinicians could be beneficial in IBD care. Further research into the implementation of such interventions as well as clinical communication concerns specific to IBD is warranted.
The great deceiver: a case series of ‘double fire’ atrioventricular nodal response
Authors: Leão Sílvia , Luermans Justin , Vernooy Kevin , ter Bekke Rachel , den Uijl Dennis , Linz Dominik , Chaldoupi Sevasti-Maria 
Published: April 2023

Abstract

Background
The ‘double fire’ (DF) atrioventricular (AV) nodal response is a rare mechanism of two ventricular electrical activations following a single atrial beat due to dual AV node physiology. DF AV nodal response is often misdiagnosed and may lead to unnecessary invasive procedures.

Case summary
We describe a series of three cases with distinct clinical manifestations of DF AV nodal response: Patient 1 remained symptomatic after slow pathway modification for common AV nodal re-entry tachycardia. Patient 2 was misdiagnosed as having junctional bigeminy and developed heart failure with reduced left ventricle ejection fraction. Patient 3 was misdiagnosed as having atrial fibrillation (AF) and underwent two pulmonary vein isolation (PVI) procedures, without clinical improvement. All patients underwent an electrophysiological study (EPS) during which DF AV nodal response was confirmed and treated with radiofrequency ablation of the slow pathway. All patients were afterwards relieved from their symptoms.

Discussion and conclusion
DF AV nodal response is a rare electrophysiological phenomenon which can be clinically misinterpreted as other common arrhythmias, such as premature junctional bigeminy or AF and can contribute to tachycardia induced cardiomyopathy. Typical electrocardiogram- and EPS-derived findings can be indicative for DF AV nodal response. DF AV nodal response can be easily and effectively treated by slow pathway ablation.
Left atrial appendage strain predicts subclinical atrial fibrillation in embolic strokes of undetermined source
Authors: Saberniak Jørg , Skrebelyte-Strøm Loreta , Orstad Eivind Bjørkan , Hilde Janne Mykland , Solberg Magnar Gangås , Rønning Ole Morten , Kjekshus Harald , Steine Kjetil 
Published: April 2023

Abstract

Aims
Left atrial (LA) strain is promising in prediction of clinical atrial fibrillation (AF) in stroke patients. However, prediction of subclinical AF is critical in patients with embolic strokes of undetermined source (ESUS). The aim of this prospective study was to investigate novel LA and left atrial appendage (LAA) strain markers in prediction of subclinical AF in ESUS patients.

Methods and results
A total of 185 patients with ESUS, mean age 68 ± 13years, 33% female, without diagnosed AF, were included. LAA and LA function by conventional echocardiographic parameters and reservoir strain (Sr), conduit strain (Scd), contraction strain (Sct), and mechanical dispersion (MD) of Sr were assessed with transoesophageal and transthoracic echocardiography. Subclinical AF was detected by insertable cardiac monitors during follow-up. LAA strain was impaired in 60 (32%) patients with subclinical AF compared to those with sinus rhythm: LAA-Sr, 19.2 ± 4.5% vs. 25.6 ± 6.5% (P &lt; 0.001); LAA-Scd, −11.0 ± 3.1% vs. −14.4 ± 4.5% (P &lt; 0.001); and LAA-Sct, −7.9 ± 4.0% vs. −11.2 ± 4% (P &lt; 0.001), respectively, while LAA-MD was increased, 34 ± 24 ms vs. 26 ± 20 ms (P = 0.02). However, there was no significant difference in phasic LA strain or LA-MD. By ROC analyses, LAA-Sr was highly significant in prediction of subclinical AF and showed the best AUC of 0.80 (95% CI 0.73–0.87) with a sensitivity of 80% and a specificity of 73% (P &lt; 0.001). LAA-Sr and LAA-MD were both independent and incremental markers of subclinical AF in ESUS patients.

Conclusion
LAA function by strain and mechanical dispersion predicted subclinical AF in ESUS patients. These novel echocardiographic markers may improve risk stratification in ESUS patients.
Embedded racism: Inequitable niche construction as a neglected evolutionary process affecting health
Authors: Ivey Henry Paula , Spence Beaulieu Meredith R , Bradford Angelle , Graves Joseph L 
Published: April 2023

Abstract
Racial health disparities are a pervasive feature of modern experience and structural racism is increasingly recognized as a public health crisis. Yet evolutionary medicine has not adequately addressed the racialization of health and disease, particularly the systematic embedding of social biases in biological processes leading to disparate health outcomes delineated by socially defined race. In contrast to the sheer dominance of medical publications which still assume genetic ‘race’ and omit mention of its social construction, we present an alternative biological framework of racialized health. We explore the unifying evolutionary-ecological principle of niche construction as it offers critical insights on internal and external biological and behavioral feedback processes environments at every level of the organization. We Integrate insights of niche construction theory in the context of human evolutionary and social history and phenotype-genotype modification, exposing the extent to which racism is an evolutionary mismatch underlying inequitable disparities in disease. We then apply ecological models of niche exclusion and exploitation to institutional and interpersonal racial constructions of population and individual health and demonstrate how discriminatory processes of health and harm apply to evolutionarily relevant disease classes and life-history processes in which socially defined race is poorly understood and evaluated. Ultimately, we call for evolutionary and biomedical scholars to recognize the salience of racism as a pathogenic process biasing health outcomes studied across disciplines and to redress the neglect of focus on research and application related to this crucial issue.