bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA methylation signatures of duplicate gene evolution in angiosperms
Authors: Kenchanmane Raju Sunil K , Ledford Marshall , Niederhuth Chad E 
Published: April 2023

AbstractGene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomic approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole-genome duplicates were typically enriched for CG-only gene body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was a characteristic of more recent single-gene duplicates. Core angiosperm gene families were differentiated into those which preferentially retain paralogs and “duplication-resistant” families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence–absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.
Uptake of glucose from the rhizosphere, mediated by apple MdHT1.2, regulates carbohydrate allocation
Authors: Tian Xiaocheng , Zou Hui , Xiao Qian , Xin Haijun , Zhu Lingcheng , Li Yuxing , Ma Baiquan , Cui Ningbo , Ruan Yong-Ling , Ma Fengwang , Li Mingjun 
Published: April 2023

Abstract
Plant roots can absorb sugars from the rhizosphere, which reduces the consumption of carbon derived from photosynthesis. However, the underlying mechanisms that roots use to control sugar absorption from soil are poorly understood. Here, we identified an apple (Malus × domestica Borkh.) hexose transporter, MdHT1.2, that functions on the root epidermis to absorb glucose (Glc) from the rhizosphere. Based on RNA-seq data, MdHT1.2 showed the highest expression level among 29 MdHT genes in apple roots. Biochemical analyses demonstrated that MdHT1.2 was mainly expressed in the epidermal cells of fine roots, and its protein was located on the plasma membrane. The roots of transgenic apple and Solanum lycopersicum lines overexpressing MdHT1.2 had an increased capability to absorb Glc when fed with [13C]-labeled Glc or 2-NBDG, whereas silencing MdHT1.2 in apple showed the opposite results. Further studies established that MdHT1.2-mediated Glc absorption from the rhizosphere changed the carbon assimilate allocation between apple shoot and root, which regulated plant growth. Additionally, a grafting experiment in tomato confirmed that increasing the Glc uptake capacity in the root overexpressing MdHT1.2 could facilitate carbohydrate partitioning to the fruit. Collectively, our study demonstrated that MdHT1.2 functions on the root epidermis to absorb rhizospheric Glc, which regulates the carbohydrate allocation for plant growth and fruit sugar accumulation.
Functional specialization of expanded orange carotenoid protein paralogs in subaerial Nostoc species
Authors: Yang Yi-Wen , Liu Ke , Huang Da , Yu Chen , Chen Si-Zhuo , Chen Min , Qiu Bao-Sheng 
Published: April 2023

Abstract
Orange carotenoid protein (OCP) is a photoactive protein that participates in the photoprotection of cyanobacteria. There are 2 full-length OCP proteins, 4 N-terminal paralogs (helical carotenoid protein [HCP]), and 1 C-terminal domain-like carotenoid protein (CCP) found in Nostoc flagelliforme, a desert cyanobacterium. All HCPs (HCP1 to 3 and HCP6) from N. flagelliforme demonstrated their excellent singlet oxygen quenching activities, in which HCP2 was the strongest singlet oxygen quencher compared with others. Two OCPs, OCPx1 and OCPx2, were not involved in singlet oxygen scavenging; instead, they functioned as phycobilisome fluorescence quenchers. The fast-acting OCPx1 showed more effective photoactivation and stronger phycobilisome fluorescence quenching compared with OCPx2, which behaved differently from all reported OCP paralogs. The resolved crystal structure and mutant analysis revealed that Trp111 and Met125 play essential roles in OCPx2, which is dominant and long acting. The resolved crystal structure of OCPx2 is maintained in a monomer state and showed more flexible regulation in energy quenching activities compared with the packed oligomer of OCPx1. The recombinant apo-CCP obtained the carotenoid pigment from holo-HCPs and holo-OCPx1 of N. flagelliforme. No such carotenoid transferring processes were observed between apo-CCP and holo-OCPx2. The close phylogenetic relationship of OCP paralogs from subaerial Nostoc species indicates an adaptive evolution toward development of photoprotection: protecting cellular metabolism against singlet oxygen damage using HCPs and against excess energy captured by active phycobilisomes using 2 different working modes of OCPx.
Risk factors for common mental disorders in young refugees from Iran, Somalia and Syria to Sweden
Authors: Yang Lijun , Mittendorfer-Rutz Ellenor , Amin Ridwanul , Helgesson Magnus 
Published: April 2023

Abstract

Background
Our primary aim was to determine sociodemographic and health-related risk factors for diagnosed common mental disorders (CMDs) among young refugees in Sweden.

Methods
All young adult refugees from Iran, Somalia and Syria (n = 7192), who were residents in Sweden in 2009, were followed from 2010 to 2013 regarding diagnosed CMDs. Cox regression models were used to compute hazard ratios (HRs) of CMDs with 95% confidence intervals (CIs).

Results
Those arriving as unaccompanied refugee minors had a lower risk of being diagnosed with CMDs (HR: 0.7; 95%CI: 0.6–0.9) than those arriving as accompanied refugee minors. A higher risk of being diagnosed with CMDs was also found in female refugees (HR: 1.3; 95%CI: 1.1–1.5) compared with male refugees. In addition, individuals with a low (HR: 1.7; 95%CI: 1.3–2.3) or a medium (HR: 1.4; 95%CI: 1.1–1.8) educational level were found to have a higher risk of being diagnosed with CMDs compared with individuals with a high educational level. Refugees from Iran (HR: 2.3; 95%CI: 1.8–2.9) had a higher risk of a diagnosis of a CMD than refugees from Somalia. Moreover, refugees with a diagnosis of a mental disorder other than a CMD (HR: 4.2; 95%CI: 2.8–6.1), digestive (HR: 1.5; 95%CI: 1.0–2.2) or musculoskeletal diseases (HR: 1.5; 95%CI: 1.0–2.2) had a higher risk of being diagnosed with subsequent CMDs, compared with those with no such disorders.

Conclusions
Pre-existing diagnoses of mental disorders other than CMDs, and digestive and musculoskeletal disorders should be carefully considered in clinical assessments to initiate early interventions to prevent CMDs.
Limited recourse? Is there an alternative statutory approach to priority of liens and payment of trustees’ creditors?
Authors: Holden Richard 
Published: April 2023

Abstract
Equity Trust (Jersey) Limited v Halabi held that successive trustees’ liens rank pari passu, rather than by priority in time. It held this to be the English law, Jersey law being presumed the same unless established otherwise. However, does Jersey law already contain its own provision for pari passu ranking of trustees’ liens and indemnities? This article considers Article 32 of the Trusts (Jersey) Law 1984, as well as similar provisions in Guernsey and the BVI, which appear to have provided for pari passu satisfaction not only of trustees’ creditors, but also trustees’ liens to secure such satisfaction, all along.
Weight of evidence for cross-species conservation of androgen receptor-based biological activity
Authors: Vliet Sara M F , Markey Kristan J , Lynn Scott G , Adetona Anna , Fallacara Dawn , Ceger Patricia , Choksi Neepa , Karmaus Agnes L , Watson AtLee , Ewans Andrew , Daniel Amber B , Hamm Jonathan , Vitense Kelsey , Wolf Kaitlyn A , Thomas Amy , LaLone Carlie A 
Published: April 2023

Abstract
The U.S. Environmental Protection Agency’s Endocrine Disruptor Screening Program (EDSP) is tasked with assessing chemicals for their potential to perturb endocrine pathways, including those controlled by androgen receptor (AR). To address challenges associated with traditional testing strategies, EDSP is considering in vitro high-throughput screening assays to screen and prioritize chemicals more efficiently. The ability of these assays to accurately reflect chemical interactions in nonmammalian species remains uncertain. Therefore, a goal of the EDSP is to evaluate how broadly results can be extrapolated across taxa. To assess the cross-species conservation of AR-modulated pathways, computational analyses and systematic literature review approaches were used to conduct a comprehensive analysis of existing in silico, in vitro, and in vivo data. First, molecular target conservation was assessed across 585 diverse species based on the structural similarity of ARs. These results indicate that ARs are conserved across vertebrates and are predicted to share similarly susceptibility to chemicals that interact with the human AR. Systematic analysis of over 5000 published manuscripts was used to compile in vitro and in vivo cross-species toxicity data. Assessment of in vitro data indicates conservation of responses occurs across vertebrate ARs, with potential differences in sensitivity. Similarly, in vivo data indicate strong conservation of the AR signaling pathways across vertebrate species, although sensitivity may vary. Overall, this study demonstrates a framework for utilizing bioinformatics and existing data to build weight of evidence for cross-species extrapolation and provides a technical basis for extrapolating hAR-based data to prioritize hazard in nonmammalian vertebrate species.
Focus on the Plant Endomembrane System in Molecular Plant-Microbe Interactions
Authors: Burch-Smith Tessa M. , Wang Aiming , Park Eunsook , Jin Hailing , Wang Dong 
Published: April 2023

Interactions between plants and microbes are ubiquitous. The outcomes of these interactions involve interkingdom communication, with myriad, diverse signals moving between microbes and their potential plant hosts. Years of biochemical, genetic, and molecular biology research have provided an overview of the landscape of the repertoires of effectors and elicitors encoded by microbes that allow them to stimulate and manipulate responses from their potential plant hosts. Similarly, considerable insight into the plant machinery and capacity for responding to microbes has been gained. The advent of new bioinformatics and modeling approaches has greatly contributed to our understanding of how these interactions occur, and it is expected that these tools, coupled with burgeoning genome sequencing data, will eventually allow the prediction of the outcome of these interactions and whether they will result in a relationship that benefits one or both partners. As a complement to these studies, cell biological studies are elucidating how cells in the plant hosts behave in response to microbial signals. Such studies have brought new attention to the indispensable role of the plant endomembrane system in determining the outcome of plant-microbe interactions. This Focus Issue addresses not only how the plant endomembrane acts locally to mediate responses to microbes but, also, the importance of the plant endomembrane beyond the plant cell borders for cross-kingdom effects. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.
Nonopioid Substance Use among Patients Who Recently Initiated Office-based Buprenorphine Treatment
Authors: Dugosh Karen L. , Lent Michelle R. , Burkley S. Brook , Millard Conor M.K. , McKay James R. , Kampman Kyle M. 
Published: April 2023

Objectives
Medications for opioid use disorder (MOUDs) like buprenorphine are a first-line treatment for individuals who have opioid use disorder (OUD); however, these medications are not designed to impact the use of other classes of drugs. This descriptive study provides up-to-date information about nonopioid substance use among patients who recently initiated office-based buprenorphine treatment for OUD using data from 2 ongoing clinical trials.

Methods
The study sample was composed of 257 patients from 6 federally qualified health centers in the mid-Atlantic region who recently (i.e., within the past 28 days) initiated office-based buprenorphine treatment between July 2020 and May 2022. After the screening and informed consent processes, participants completed a urine drug screen and psychosocial interview as a part of the study baseline assessment. Descriptive analyses were performed on urine drug screen results to identify the prevalence and types of substances detected.

Results
More than half of participants provided urine specimens that were positive for nonopioid substances, with marijuana (37%, n = 95), cocaine (22%, n = 56), and benzodiazepines (11%, n = 28) detected with the highest frequencies.

Conclusions
A significant number of participants used nonopioid substances after initiating buprenorphine treatment, suggesting that some patients receiving MOUDs could potentially benefit from adjunctive psychosocial treatment and supports to address their nonopioid substance use.
Hypertension prevalence by degrees of urbanization and altitude in Peru: pooled analysis of 186 906 participants
Authors: Mendoza-Quispe Daniel , Chambergo-Michilot Diego , Moscoso-Porras Miguel , Bernabe-Ortiz Antonio 
Published: April 2023

Objective:
Few studies, using countrywide data, examined how hypertension prevalence varies at diverse degrees of urbanization and altitude. This study examined the association between urbanization and altitude, including the potential interaction between those variables, with hypertension prevalence in Peru.

Methods:
Cross-sectional analysis of the Peruvian Demographic and Health Survey (2014–2019). Hypertension (SBP ≥140 mmHg or DBP ≥90 mmHg or self-reported diagnosis) was the outcome. Exposures were altitude levels, and urbanization assessed with four indicators (urban/rural; type of place of residence; population density level; and population size level).

Results:
Among 186 906 participants (mean age ± standard deviation: 40.6 ± 17.9; 51.1% women), pooled hypertension prevalence was 19% [95% confidence interval (CI) 18.7–19.3], which was higher in urban compared with rural areas (prevalence ratio: 1.09; 95% CI 1.05–1.15). Compared with countryside, hypertension was higher in towns (prevalence ratio: 1.09; 95% CI 1.04–1.15), small cities (prevalence ratio: 1.07; 95% CI 1.02–1.13) and large cities (prevalence ratio: 1.19; 95% CI 1.12–1.27). Compared with least density settings (1–500 inhabitants/km2), hypertension was higher in the highest density (≥10 001 inhabitants/km2) settings (prevalence ratio: 1.12; 95% CI 1.07–1.18). Population size was not associated with hypertension. Compared with low altitude, hypertension was lower above 2500 m (prevalence ratio 0.91; 95% CI 0.87–0.94) and above 3500 m (prevalence ratio 0.89; 95% CI 0.84–0.95). Interaction between exposures had varying patterning.

Conclusion:
Hypertension in Peru is more prevalent at urban than rural areas, especially in large cities and in more densely populated areas above 10 001 inhabitants/km2, and less prevalent at altitudes above 2500 m.
Online calculators for predicting the risk of anastomotic stricture after hepaticojejunostomy for bile duct injury after cholecystectomy: a multicenter retrospective study
Authors: Chen Jiangming , Chen Zixiang , Yan Xiyang , Liu Xiaoliang , Fang Debao , Miao Xiang , Tong Zhong , Wang Xiaoming , Lu Zheng , Hou Hui , Wang Cheng , Geng Xiaoping , Liu Fubao 
Published: April 2023

Background:
Anastomotic stricture is a common underlying cause of long-term morbidity after hepaticojejunostomy (HJ) for bile duct injury (BDI) following cholecystectomy. However, there are no methods for predicting stricture risk. This study was aimed at establishing two online calculators for predicting anastomotic stricture occurrence (ASO) and stricture-free survival (SFS) in this patient population.

Methods:
The clinicopathological characteristics and follow-up information of patients who underwent HJ for BDI after cholecystectomy from a multi-institutional database were reviewed. Univariate and multivariate analyses of the risk factors of ASO and SFS were performed in the training cohort. Two nomogram-based online calculators were developed and validated by internal bootstrapping resamples (n=1000) and an external cohort.

Results:
Among 220 screened patients, 41 (18.64%) experienced anastomotic strictures after a median follow-up of 110.7 months. Using multivariate analysis, four variables, including previous repair, sepsis, HJ phase, and bile duct fistula, were identified as independent risk factors associated with both ASO and SFS. Two nomogram models and their corresponding online calculators were subsequently developed. In the training cohort, the novel calculators achieved concordance indices (C-indices) of 0.841 and 0.763 in predicting ASO and SFS, respectively, much higher than those of the above variables. The predictive accuracy of the resulting models was also good in the internal (C-indices: 0.867 and 0.821) and external (C-indices: 0.852 and 0.823) validation cohorts.

Conclusions:
The two easy-to-use online calculators demonstrated optimal predictive performance for identifying patients at high risk for ASO and with dismal SFS. The estimation of individual risks will help guide decision-making and long-term personalized surveillance.
START-Play Physical Therapy Intervention Indirectly Impacts Cognition Through Changes in Early Motor-Based Problem-Solving Skills
Authors: Koziol Natalie A. , Kretch Kari S. , Harbourne Regina T. , Lobo Michele A. , McCoy Sarah W. , Molinini Rebecca , Hsu Lin-Ya , Babik Iryna , Cunha Andrea Baraldi , Willett Sandra L. , Bovaird James A. , Dusing Stacey C. 
Published: April 2023

Purpose:
This study tested whether the Sitting Together and Reaching to Play (START-Play) physical therapy intervention indirectly impacts cognition through changes in perceptual-motor skills in infants with motor delays.

Methods:
Participants were 50 infants with motor delays randomly assigned to START-Play plus Usual Care Early Intervention (UC-EI) or UC-EI only. Infants' perceptual-motor and cognitive skills were assessed at baseline and 1.5, 3, 6, and 12 months post-baseline.

Results:
Short-term changes in sitting, fine motor skills, and motor-based problem-solving, but not reaching, predicted long-term changes in cognition. START-Play indirectly impacted cognition through motor-based problem-solving but not sitting, reaching, or fine motor skills.

Conclusions:
This study provided preliminary evidence that early physical therapy interventions that blend activities across developmental domains and are supported by an enriched social context can place infants on more optimal developmental trajectories.
Pediatric GI Health Care Professionals’ Perceptions of and Engagement With Psychosocial Providers in Pediatric IBD Care
Authors: David Jennie G. , Sejkora Ellen , Michel Hilary K. , Mackner Laura ,   ImproveCareNow Learning Health System
Published: April 2023

Objectives:
Multidisciplinary care is recommended for optimal pediatric inflammatory bowel disease (IBD) care, including psychosocial providers (eg, psychologists). However, health care professionals’ (HCPs) perceptions of and engagement with psychosocial providers in pediatric IBD is lacking.

Methods:
Cross-sectional REDCap surveys were completed by HCPs (eg, gastroenterologists) across American ImproveCareNow (ICN) centers. Demographics and self-reported perceptions of and engagement with psychosocial providers were collected. Data were analyzed at participant and site levels through descriptives, frequencies, an independent t test, and exploratory analyses of variance.

Results:
A total of 101 participants from 52% of ICN sites participated. Participants were 88% gastrointestinal physicians, 49% identifying as female, 94% non-Hispanic, and 76% Caucasian. Of ICN sites, 75% and 94% of sites reported outpatient and inpatient psychosocial care, respectively. Participants referred for various clinical reasons to psychosocial providers (eg, illness adjustment). At the participant level, 92% of HCPs reported psychosocial care was very important and 64% reported their clinical thresholds shifted to engage psychosocial providers earlier in care. Barriers to psychosocial care included limited psychosocial providers (92%), psychosocial providers availability (87%), and IBD patients’ lack of openness to psychosocial care (85%). One-way analyses of variance by HCP length of experiences were not statistically significant on perceived understanding of psychosocial providers or perceived changes in clinical threshold over time.

Conclusion:
HCPs overall reported positive perceptions of and frequent engagement with psychosocial providers in pediatric IBD. Limited psychosocial providers and other notable barriers are discussed. Future work should continue interprofessional education of HCPs and trainees and efforts to improve access to psychosocial care in pediatric IBD.