bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplexing PCR allows the identification of within‐species genetic diversity in ancient eDNA
Authors: Lammers Y. , Taberlet P. , Coissac E. , Elliott L. D. , Merkel M. F. , Pitelkova I. ,   PhyloAlps Consortium,   PhyloNorway Consortium, Alsos I. G. 
Published: January 2024

AbstractSedimentary ancient DNA (sedaDNA) has rarely been used to obtain population‐level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population‐level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages in present‐day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primer sets to target these. Initial multiplex PCR testing resulted in a final set of 38 primer sets. These primer sets were used to analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primer sets could be recovered from the sedaDNA data. For each sample on average 28.1 primer sets, representing 34.15 sequence variants, were recovered. All sediment samples were dominated by a single lineage, except three Alpine samples which had co‐occurrence of two different lineages. Furthermore, lineage turnover was observed in the Alps and northern Norway, suggesting that present‐day phylogeographical studies may overlook past genetic patterns. Multiplexing primer is a promising tool for generating population‐level genetic information from sedaDNA. The relatively simple method, combined with high sensitivity, provides a scalable method which will allow researchers to track populations through time and space using environmental DNA.
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods
Authors: Porto Diego S. , Uyeda Josef , Mikó István , Tarasov Sergei 
Published: January 2024

Abstract

Reconstructing ancestral states for discrete characters is essential for understanding trait evolution in organisms. However, most existing methods are limited to individual characters and often overlook the hierarchical and interactive nature of traits. Recent advances in phylogenetics now offer the possibility of integrating knowledge from anatomy ontologies to reconstruct multiple discrete character histories. Nonetheless, practical applications that fully harness the potential of these new approaches are still lacking.

This paper introduces ontophylo, an R package that extends the PARAMO pipeline to address these limitations. Ontophylo enables the reconstruction of phenotypic entities composed of amalgamated characters, such as anatomical regions or entire phenomes. It offers three new applications: (1) reconstruction of evolutionary rates of amalgamated characters using phylogenetic non‐homogeneous Poisson process (pNHPP) that allows modelling rate variation across tree branches and time; (2) reconstruction of morphospace dynamics; and (3) visualization of evolutionary rates on vector images of organisms. Ontophylo incorporates ontological knowledge to facilitate these applications.

Benchmarking confirms the accuracy of pNHPP in estimating character rates under different evolutionary scenarios, and example applications demonstrate the utility of ontophylo in studying morphological evolution in Hymenoptera using simulated data.

Ontophylo can be easily integrated with other ontology‐oriented and general‐purpose R packages and offers new opportunities to examine morphological evolution on a phenomic scale using new and legacy data.
Automated‐detection of risky alcohol use prior to surgery using natural language processing
Authors: Vydiswaran V. G. Vinod , Strayhorn Asher , Weber Katherine , Stevens Haley , Mellinger Jessica , Winder G. Scott , Fernandez Anne C. 
Published: January 2024

AbstractBackgroundPreoperative risky alcohol use is one of the most common surgical risk factors. Accurate and early identification of risky alcohol use could enhance surgical safety. Artificial Intelligence‐based approaches, such as natural language processing (NLP), provide an innovative method to identify alcohol‐related risks from patients' electronic health records (EHR) before surgery.MethodsClinical notes (n = 53,629) from pre‐operative patients in a tertiary care facility were analyzed for evidence of risky alcohol use and alcohol use disorder. One hundred of these records were reviewed by experts and labeled for comparison. A rule‐based NLP model was built, and we assessed the clinical notes for the entire population. Additionally, we assessed each record for the presence or absence of alcohol‐related International Classification of Diseases (ICD) diagnosis codes as an additional comparator.ResultsNLP correctly identified 87% of the human‐labeled patients classified with risky alcohol use. In contrast, diagnosis codes alone correctly identified only 29% of these patients. In terms of specificity, NLP correctly identified 84% of the non‐risky cohort, while diagnosis codes correctly identified 90% of this cohort. In the analysis of the full dataset, the NLP‐based approach identified three times more patients with risky alcohol use than ICD codes.ConclusionsNLP, an artificial intelligence‐based approach, efficiently and accurately identifies alcohol‐related risk in patients' EHRs. This approach could supplement other alcohol screening tools to identify patients in need of intervention, treatment, and/or postoperative withdrawal prophylaxis. Alcohol‐related ICD diagnosis had limited utility relative to NLP, which extracts richer information within clinical notes to classify patients.
Corporate investors and the housing affordability crisis: Having wall street as your landlord
Authors: Camp Yeakey Carol 
Published: January 2024

AbstractGiven the importance of housing affordability to one's social class standing, one's ability to afford decent, secure housing is not only important on an individual level, but impacts intergenerational im/mobility as well. The purpose of this research is threefold. First, it examines the recent trend in bulk housing purchases by corporate investors who turn those purchases into single family rental properties. In so doing, it discusses the implications for the population in general, but for marginalized population in perticular, that is, persons of color and those inthe lower socioeconomic strata of society. Second, this research examines a closely related housing phenomenon, condominium deconversion, where corporate investors purchase privately owned condominiums in bulk who turn them into rental units. Third, summary analysis and suggestions for future research as well as legislative and policy proposals to offset housing affordability conclude this research.
Prickle1‐driven basement membrane deposition of the iPSC‐derived embryoid bodies is separable from the establishment of apicobasal polarity
Authors: Guo Dianlei , Liu Sikai , Zhang Jiao , Gu Xinyu , Shi Lei , Su Yingchun , Xu Shujuan , Ju Rong , Wei Yanhong , Liu Chunqiao 
Published: January 2024

AbstractBasement membrane (BM) component deposition is closely linked to the establishment of cell polarity. Previously, we showed that Prickle1 is crucial for BM deposition and cell polarity events in tear duct elongation. To gain a deeper understanding of the intimate relationship between BM formation and cell polarity, we generated induced pluripotent stem cells (iPSCs)‐derived embryoid bodies (EBs) with a basement membrane separating the visceral endoderm (VE) and inner EB cell mass. We found that Prickle1 was highly expressed in VE of the normal EBs, and the Prickle1 mutant EBs displayed severely impaired BM. Notably, the formation of the basement membrane appeared to rely on the proper microtubule network of the VE cells, which was disrupted in the Prickle1 mutant EBs. Moreover, disruption of vesicle trafficking in the VE hindered BM secretion. Furthermore, reintroducing Prickle1 in the mutant EBs completely rescued BM formation but not the apicobasal cell polarity of the VE. Our data, in conjunction with studies by others, highlight the conserved role of Prickle1 in directing the secretion of BM components of the VE cells during embryonic germ layer differentiation, even in the absence of established general polarity machinery. Our study introduces a novel system based on iPSCs‐derived EBs for investigating cellular and molecular events associated with cell polarity.
Osteoarthritis of the coxofemoral joint in 24 horses: Evaluation of radiography, ultrasonography, intra‐articular anaesthesia, treatment and outcome
Authors: Sauer Fay J. , Hellige Maren , Beineke Andreas , Geburek Florian 
Published: January 2024

AbstractBackgroundFew case reports describe equine coxofemoral joint osteoarthritis (CFJOA).ObjectivesTo evaluate diagnostic findings and outcome of horses with CFJOA and to provide a score facilitating radiographic assessment.Study designRetrospective case series.MethodsHistory, clinical signs, ultrasonographic, radiographic and intra‐articular anaesthesia findings, treatments, outcome, and necropsy results of horses with CFJOA presented between 2002 and 2023 were collated. Radiographic findings were categorised to develop a radiographic score which was applied by two masked examiners. Intra‐ and inter‐observer reliability was determined using weighted Cohen's kappa (Cκ) and the correlation between radiographic and ultrasound findings via Spearman correlation coefficient.ResultsThe study included 24 horses (median age 14 years). Most of them (20/24) were chronically lame. Frequent clinical signs included unilateral gluteal muscle atrophy (18/21), lengthening of the stride of the affected limb (13/19) and locomotion on three tracks (13/20). Both imaging modalities enabled evaluation of periarticular osteophytes (correlation coefficient r = 0.64; p = 0.003). Additionally, radiography allowed detection of irregular joint spaces, subchondral bone opacity changes and femoral head flattening/tapering. Inter‐observer (Cκ = 0.846) and intra‐observer (Cκ = 0.853 and Cκ = 0.842) agreement was excellent. If treated, mostly intra‐articular corticosteroids were administered (16/18). Nine horses were euthanised immediately or during follow‐up examination. Post‐mortem, the Ligamentum capitis ossis femoris was commonly found ruptured. All surviving horses remained lame.Main limitationsRetrospective analysis of clinical records and subjective outcome assessment based on owner follow‐up with potential recall bias. Due to overall disease severity, associations between different grades of clinical findings, radiographic abnormalities and outcome could not be evaluated.ConclusionsTypical clinical signs may indicate CFJOA. Standardised evaluation of ventrodorsal radiographs allows a comprehensive diagnosis. Postmortem findings suggest joint instability as a possible causative factor that may contribute to the poor prognosis and resistance to medical therapy of the disorder.
Effect of telephone‐assisted smoking cessation programme on the self‐efficacy, recurrence in patients with bladder cancer: A study protocol
Authors: Özdemir İrem Nur , Kılınç İşleyen Eda , Danacıoğlu Yavuz Onur 
Published: January 2024

AbstractThe aim of this study protocol is to examine the effect of telephone‐assisted smoking cessation programme based on the information motivation behavioural skills model on the self‐efficacy, smoking behaviour, tumour recurrence and progression in patients diagnosed with non‐muscle‐invasive bladder cancer. A single‐center, single‐blind, parallel‐group, randomized control trial. The intervention group will receive telephone‐assisted smoking cessation programme, while no intervention will be applied to the control group. Face‐to‐face smoking cessation training will be provided for the information component of the programme, motivational interview will be conducted via WhatsApp for its motivation component. Motivational interviews will be undertaken in total of six sessions organized at two‐week intervals. The patients' chronic disease management self‐efficacy, smoking behaviour will be evaluated at the third, sixth, 12th months. Tumour recurrence, progression will be followed up by cystoscopy at the third, 12th months. This is a randomized controlled study protocol, results are not available at the time of the submission. All results will be reported on the completion of this study. This study protocol, will involve the implementation of comprehensive smoking cessation programme that is much needed for the target population around the world. It is expected that the use of this programme will increase the self‐efficacy of smokers with bladder cancer, decrease their smoking behaviour and amount of smoking, eliminate tumour recurrence. Smoking is the most important, modifiable risk factor for bladder cancer. In this study, it is expected that the implementation of telephone‐assisted smoking cessation programme based on the information–motivation–behavioural skills model will increase self‐efficacy in cancer management and decrease smoking behaviour, tumour recurrence in patients diagnosed with bladder cancer. In the literature, there is no smoking cessation programme based on this model intended for patients diagnosed with bladder cancer.
The rich heterogeneous dial‐a‐ride problem with trip time prediction
Authors: Portell Laura , Ramalhinho Helena 
Published: January 2024

AbstractThe dial‐a‐ride problem (DARP) involves designing vehicle routes to fulfill the door‐to‐door transportation requests of users where the goal is to minimize costs while satisfying transportation requests. In this paper, we introduce the rich heterogeneous DARP, which extends the generalized heterogeneous DARP to consider a fleet of buses and taxis, multiple depots, time windows at pickup and delivery locations, maximum ride and waiting times, and the possibility of an accompanying person. Our approach is based on a real service in Barcelona, and we also consider the variation in trip duration based on the time of day and day of the week. A predictive model is developed using machine learning techniques to estimate trip durations accurately. We apply our proposal to the daily door‐to‐door transportation of people with reduced mobility in Barcelona and demonstrate its superiority in terms of costs and quality of service by using the Gurobi optimizer. Additionally, we provide an analysis of the consequences of varying certain features on the costs and quality of service.
Remote area nurses' experiences of workplace safety in very remote primary health clinics: A qualitative study
Authors: Wright Laura K. , Jatrana Santosh , Lindsay David 
Published: January 2024

AbstractAimTo explore Remote Area Nurses' experiences of the implementation of workplace health and safety policies and risk mitigation strategies in Australian very remote primary health clinics.DesignThis qualitative study used online semi‐structured interviews, with participants purposively sampled to maximize variation in work location and service type. Data were analysed using a reflexive thematic analysis approach. Coding was carried out inductively, with NVivo 12 aiding data management.SettingThe interviews were conducted from 24 Februrary 2021 to 06 March 2021 with Remote Area Nurses from very remote primary health clinics in Australia.ParticipantsFifteen Remote Area Nurses participated in the study.ResultsThematic analysis revealed varied approaches to workplace safety among the different health services and regions. While the spread of ‘never alone’ policies in many clinics addressed one of the significant risks faced by Remote Area Nurses, gaps remained even for hazards specifically highlighted in existing work health and safety legislation. Meaningful collaboration with staff and the community, local orientation, preparation for the role and providing quality care were protective factors for staff safety. Understaffing, unsafe infrastructure and inadequate equipment were common concerns among Remote Area Nurses.ConclusionHealth services need to prioritize workplace safety and take a continuous quality improvement approach to its implementation. This will include ensuring safety strategies are appropriate for the local context, improving infrastructure maintenance, and establishing sustainable second responder systems such as a pool of drivers with local knowledge.Implications for the ProfessionPoor personal safety contributes to burnout and high turnover of staff. Nurses' insights into the barriers and enablers of current workplace safety strategies will aid policymakers and employers in future improvements.Reporting MethodCOREQ reporting guidelines were followed.PIPE StatementA panel of six Remote Area Nurses collaborated in the development of this project.
The parent perspective on paediatric delirium and an associated care bundle: A qualitative study
Authors: Stenkjaer Rikke Louise , Egerod Ingrid , Moszkowicz Mala , Collet Marie Oxenbøll , Weis Janne , Ista Erwin , Greisen Gorm , Herling Suzanne Forsyth 
Published: January 2024

AbstractAimsTo explore how parents experienced their child with delirium and how parents viewed our delirium management bundle.DesignWe conducted a qualitative exploratory descriptive study using semi‐structured individual or dyad interviews.MethodsTwelve semi‐structured interviews with 16 parents of 12 critically ill children diagnosed with delirium in a paediatric intensive care unit were conducted from October 2022 to January 2023 and analysed through a reflexive thematic analysis.FindingsWe generated five themes: (1) knowing that something is very wrong, (2) observing manifest changes in the child, (3) experiencing fear of long‐term consequences, (4) adding insight to the bundle, and (5) family engagement.ConclusionThe parents in our study were able to observe subtle and manifest changes in their child with delirium. This caused fear of lasting impact. The parents regarded most of the interventions in the delirium management bundle as relevant but needed individualization in the application. The parents requested more information regarding delirium and a higher level of parent engagement in the care of their child during delirium.ImpactThis paper contributes to understanding how parents might experience delirium in their critically ill child, how our delirium management bundle was received by the parents, and their suggestions for improvement. Our study deals with critically ill children with delirium, their parents, and staff working to prevent and manage paediatric delirium (PD) in the paediatric intensive care unit.Reporting MethodThe consolidated criteria for reporting qualitative research guidelines were used to ensure the transparency of our reporting.Patient or Public ContributionNo patient or public contribution to the research design.What does this Paper Contribute to the Wider Global Community?

‐ It increases awareness of the parent's perspective on PD in critically ill children.

‐ It shows how PD might affect parents, causing negative emotions such as distress, frustration, and fear of permanent damage.

‐ It shows that the parents in our study, in addition to the care bundle, requested more information on delirium and more involvement in the care of their delirious child.
Mapping potential pathways from polygenic liability through brain structure to psychological problems across the transition to adolescence
Authors: Lahey Benjamin B. , Durham E. Leighton , Brislin Sarah J. , Barr Peter B. , Dick Danielle M. , Moore Tyler M. , Pierce Brandon L. , Tong Lin , Reimann Gabrielle E. , Jeong Hee Jung , Dupont Randolph M. , Kaczkurkin Antonia N. 
Published: January 2024

BackgroundWe used a polygenic score for externalizing behavior (extPGS) and structural MRI to examine potential pathways from genetic liability to conduct problems via the brain across the adolescent transition.MethodsThree annual assessments of child conduct problems, attention‐deficit/hyperactivity problems, and internalizing problems were conducted across across 9–13 years of age among 4,475 children of European ancestry in the Adolescent Brain Cognitive DevelopmentSM Study (ABCD Study®).ResultsThe extPGS predicted conduct problems in each wave (R2 = 2.0%–2.9%). Bifactor models revealed that the extPRS predicted variance specific to conduct problems (R2 = 1.7%–2.1%), but also variance that conduct problems shared with other measured problems (R2 = .8%–1.4%). Longitudinally, extPGS predicted levels of specific conduct problems (R2 = 2.0%), but not their slope of change across age. The extPGS was associated with total gray matter volume (TGMV; R2 = .4%) and lower TGMV predicted both specific conduct problems (R2 = 1.7%–2.1%) and the variance common to all problems in each wave (R2 = 1.6%–3.1%). A modest proportion of the polygenic liability specific to conduct problems in each wave was statistically mediated by TGMV.ConclusionsAcross the adolescent transition, the extPGS predicted both variance specific to conduct problems and variance shared by all measured problems. The extPGS also was associated with TGMV, which robustly predicted conduct problems. Statistical mediation analyses suggested the hypothesis that polygenic variation influences individual differences in brain development that are related to the likelihood of conduct problems during the adolescent transition, justifying new research to test this causal hypothesis.
Allergic phenotype identified on allergen testing is associated with proton pump inhibitor nonresponse in eosinophilic esophagitis
Authors: Muftah Mayssan , Hartnett Davis A. , Flanagan Ryan , Redd Walker D. , Jenkins Andrew , Goldin Alison H. , Hsu Blatman Karen , Chan Walter W. 
Published: January 2024

AbstractBackground and AimFood/environmental allergens have been associated with eosinophilic esophagitis (EoE); however, the correlation between allergy profiles and disease responsiveness to proton pump inhibitor (PPI) therapy remains unclear. We aimed to assess the association between food/environmental allergies identified on allergen testing and histologic response to PPI in patients with treatment‐naive EoE.MethodsAdults with newly diagnosed EoE who underwent formal testing for food/environmental allergies at a tertiary center were included. All patients underwent twice‐daily PPI for 8 weeks with subsequent repeat endoscopy and biopsy to assess histologic response. Patients with <15 eosinophils/hpf on post‐PPI mucosal biopsies were classified as responders (PPI‐r‐EoE), while those with ≥15 eosinophils/hpf were nonresponders (PPI‐nr‐EoE).ResultsSixty‐one patients met inclusion criteria (21 PPI‐r‐EoE vs 40 PPI‐nr‐EoE). Demographic, clinical, and endoscopic finding variables were similar between groups. Positive food allergen test was more prevalent among PPI‐nr‐EoE patients (82.5% vs 42.9%, P = 0.003). On multivariable analysis, positive food allergen testing remained an independent predictor for PPI nonresponse (aOR 0.15, CI: 0.04–0.58, P = 0.0006). Positive environmental allergen testing was highly prevalent, with no significant differences between groups (77.5% vs 95.2%, P = 0.14). However, higher number of positive environmental allergens (23.3% [≥5 allergens] vs 73.3% [<5 allergens], P = 0.003) and specific aeroallergens correlated with PPI‐nr‐EoE.ConclusionPositive food allergy testing and increased environmental allergens predicted lower likelihood of histologic response to PPI in EoE. Our findings support an allergic phenotype of EoE that may less likely respond to PPI therapy. Formal allergen testing may play a role in therapy selection and tailored management in EoE.