bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora
Authors: Munro Catriona , Zapata Felipe , Howison Mark , Siebert Stefan , Dunn Casey W 
Published: January 2022

Abstract
Siphonophores are complex colonial animals, consisting of asexually produced bodies (zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. We examine gene expression within species, conduct classical analyses examining expression patterns between species, and introduce species branch filtering, which allows us to examine the evolution of expression across species in a phylogenetic framework. Within and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression. Our findings show that patterns of gene expression have the potential to define zooids in colonial organisms. Traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.
Biomarkers of dietary patterns: a systematic review of randomized controlled trials
Authors: Liang Shuang , Nasir Reeja F , Bell-Anderson Kim S , Toniutti Clémence A , O’Leary Fiona M , Skilton Michael R 
Published: January 2022

Abstract

Context
Most methods for assessing dietary intake have considerable measurement error. Dietary biomarkers are objective tools for dietary assessment. Dietary biomarkers of dietary patterns have not been well described, despite modern dietary guidelines endorsing dietary patterns.

Objective
This systematic review sought to describe the dietary biomarkers commonly used to assess dietary patterns, and the novel biomarkers of dietary patterns identified by exploratory studies.

Data Sources
MEDLINE, Embase, Cochrane Central, PreMEDLINE, and CINAHL databases were searched.

Data Extraction
Data extraction and bias assessment were undertaken in duplicate.

Data Analysis
A qualitative approach was applied, without statistical analysis.

Conclusion
In controlled settings, dietary biomarkers of single nutrients or of individual foods or food groups are commonly used to assess compliance with dietary patterns. However, currently, there are no dietary biomarkers or biomarker profiles that are able to identify the specific dietary pattern that has been consumed by an individual. Future work should seek to validate novel dietary biomarkers and biomarker profiles that are indicative of specific dietary patterns and their characteristics. A dietary biomarker panel consisting of multiple biomarkers is almost certainly necessary to capture the complexity of dietary patterns.

Systematic Review Registration
PROSPERO registration no. CRD42019129839.
lncRNA7 and lncRNA2 modulate cell wall defense genes to regulate cotton resistance to Verticillium wilt
Authors: Zhang Lin , Liu Jinlei , Cheng Jieru , Sun Quan , Zhang Yu , Liu Jinggao , Li Huimin , Zhang Zhen , Wang Ping , Cai Chaowei , Chu Zongyan , Zhang Xiao , Yuan Youlu , Shi Yuzhen , Cai Yingfan 
Published: January 2022

Abstract
In plants, long noncoding RNAs (lncRNAs) regulate disease resistance against fungi and other pathogens. However, the specific mechanism behind this regulation remains unclear. In this study, we identified disease resistance-related lncRNAs as well as their regulating genes and assessed their functions by infection of cotton (Gossypium) chromosome segment substitution lines with Verticillium dahliae. Our results demonstrated that lncRNA7 and its regulating gene Pectin methylesterase inhibitor 13 (GbPMEI13) positively regulated disease resistance via the silencing approach, while ectopic overexpression of GbPMEI13 in Arabidopsis (Arabidopsis thaliana) promoted growth and enhanced resistance to V. dahliae. In contrast, lncRNA2 and its regulating gene Polygalacturonase 12 (GbPG12) negatively regulated resistance to V. dahliae. We further found that fungal disease-related agents, including the pectin-derived oligogalacturonide (OG), could downregulate the expression of lncRNA2 and GbPG12, leading to pectin accumulation. Conversely, OG upregulated the expression of lncRNA7, which encodes a plant peptide phytosulfokine (PSK-α), which was confirmed by lncRNA7 overexpression and Ultra Performance Liquid Chromatography Tandem Mass Spectrometry (UPLC-MS) experiments. We showed that PSK-α promoted 3-Indoleacetic acid (IAA) accumulation and activated GbPMEI13 expression through Auxin Response Factor 5. Since it is an inhibitor of pectin methylesterase (PME), GbPMEI13 promotes pectin methylation and therefore increases the resistance to V. dahliae. Consistently, we also demonstrated that GbPMEI13 inhibits the mycelial growth and spore germination of V. dahliae in vitro. In this study, we demonstrated that lncRNA7, lncRNA2, and their regulating genes modulate cell wall defense against V. dahliae via auxin-mediated signaling, providing a strategy for cotton breeding.
Affective Dysregulation Precedes Emergence of Psychosis-Like Experiences in a Community Sample of Young Adults
Authors: Bornheimer Lindsay A , Martz Meghan E , Suzuki Takakuni , Tso Ivy F , Burton Cynthia Z , Li Verdugo Juliann , Grove Tyler , Heitzeg Mary M , Taylor Stephan F 
Published: January 2022

AbstractAffective dysregulation (AD) among persons with schizophrenia spectrum disorders, involving the tendency to exhibit sensitivity to minor stress and negative affective states, is an important diagnostic feature and relates to poorer functional and clinical outcomes. Studies of persons with elevated risk for psychosis demonstrate similar AD to those with schizophrenia, and literature suggest a potential influence of AD in the transition from psychosis-like symptoms (PLEs) to disorder. Cross-sectional investigations to date have supported the link between AD and psychosis, and longitudinal studies have mostly yielded mixed findings without demonstration of potential causal relationships between AD and psychosis. This study examined the concurrent and predictive relationships between AD and PLE in a community sample of youth (n = 630) with attention to distinct facets of AD as a latent construct, including low resiliency, low reactive control, and negative emotionality, using structural equation to estimate a longitudinal cross-lagged and autoregressive model across 3 study waves from 15 to 24 years of age. As hypothesized, AD in the mid-teen years predicted subsequent PLE 3 years later. In addition, we found that increasing PLE in the end of the teen years related to a subsequent increase in AD in the early 20s. A cross-sectional relationship between AD and PLE in the mid-teen years was also supported. Findings overall describe important relationships between AD and PLE that appear to vary with developmental stage, implicating various factors to inform approaches for identifying youth who may be at risk for subsequent PLE or other mental health conditions.
The Effects of Organophosphate Esters Used as Flame Retardants and Plasticizers on Granulosa, Leydig, and Spermatogonial Cells Analyzed Using High-Content Imaging
Authors: Wang Xiaotong , Luu Trang , Beal Marc A , Barton-Maclaren Tara S , Robaire Bernard , Hales Barbara F 
Published: January 2022

Abstract
The replacement of regulated brominated flame retardants and plasticizers with organophosphate esters (OPEs) has led to their pervasive presence in the environment and in biological matrices. Further, there is evidence that exposure to some of these chemicals is associated with reproductive toxicity. Using a high-content imaging approach, we assessed the effects of exposure to 9 OPEs on cells related to reproductive function: KGN human granulosa cells, MA-10 mouse Leydig cells, and C18-4 mouse spermatogonial cells. The effects of OPEs were compared with those of 2,2′,4,4′-tetrabromodiphenyl ether (BDE-47), a legacy brominated flame retardant. Alterations in several important cell features, including cell survival, mitochondrial dynamics, oxidative stress, lysosomes, and lipid droplets, were analyzed. Most of the OPEs tested displayed higher cytotoxicity than BDE-47 in all 3 cell lines. Effects on phenotypic parameters were specific for each cell type. Several OPEs increased total mitochondria, decreased lysosomes, increased the total area of lipid droplets, and induced oxidative stress in KGN cells; these endpoints were differentially affected in MA-10 and C18-4 cells. Alterations in cell phenotypes were highly correlated in the 2 steroidogenic cell lines for a few triaryl OPEs. Potency ranking using 2 complementary approaches, Toxicological Prioritization Index analyses and the lowest benchmark concentration/administered equivalent dose method, revealed that while most of the OPEs tested were more potent than BDE-47, others showed little to no effect. We propose that these approaches serve as lines of evidence in a screening strategy to identify the potential for reproductive and endocrine effects of emerging chemicals and assist in regulatory decision-making.
An observational assessment of the safety of mass drug administration for trachoma in Ethiopian children
Authors: Ciciriello Allan M , Addiss David G , Teferi Tesfaye , Emerson Paul M , Hooper P J , Seid Mohammed , Tadesse Girma , Seife Fikre , Sormolo Mohammed-Aman Jemal , Kebede Fikreab , Kiflu Genet , West Sheila K , Alemu Menbere , LaCon Genevieve , Gebre Teshome 
Published: January 2022

Abstract

Background
The International Trachoma Initiative (ITI) provides azithromycin for mass drug administration (MDA) to eliminate trachoma as a public health problem. Azithromycin is given as tablets for adults and powder for oral suspension (POS) is recommended for children aged &lt;7 y, children &lt;120 cm in height (regardless of age) or anyone who reports difficulty in swallowing tablets. An observational assessment of MDA for trachoma was conducted to determine the frequency with which children aged 6 mo through 14 y received the recommended dose and form of azithromycin according to current dosing guidelines and to assess risk factors for choking and adverse swallowing events (ASEs).

Methods
MDA was observed in three regions of Ethiopia and data were collected on azithromycin administration and ASEs.

Results
A total of 6477 azithromycin administrations were observed; 97.9% of children received the exact recommended dose. Of children aged 6 mo to &lt;7 y or &lt;120 cm in height, 99.6% received POS. One child experienced choking and 132 (2%) experienced ≥1 ASEs. Factors significantly associated with ASEs included age 6–11 mo or 1–6 y, non-calm demeanor and requiring coaxing prior to drug administration.

Conclusions
There is a high level of adherence to the revised azithromycin dosing guidelines and low incidence of choking and ASEs.
Physician Training for Electrocardiogram Interpretation: A Systematic Review and Meta-Analysis
Authors: Oh So-Young , Cook David A. , Van Gerven Pascal W.M. , Nicholson Joseph , Fairbrother Hilary , Smeenk Frank W.J.M. , Pusic Martin V. 
Published: January 2022

Purpose
Using electrocardiogram (ECG) interpretation as an example of a widely taught diagnostic skill, the authors conducted a systematic review and meta-analysis to demonstrate how research evidence on instruction in diagnosis can be synthesized to facilitate improvement of educational activities (instructional modalities, instructional methods, and interpretation approaches), guide the content and specificity of such activities, and provide direction for research.

Method
The authors searched PubMed/MEDLINE, Embase, Cochrane CENTRAL, PsycInfo, CINAHL, ERIC, and Web of Science databases through February 21, 2020, for empirical investigations of ECG interpretation training enrolling medical students, residents, or practicing physicians. They appraised study quality with the Medical Education Research Study Quality Instrument and pooled standardized mean differences (SMDs) using random effects meta-analysis.

Results
Of 1,002 articles identified, 59 were included (enrolling 17,251 participants). Among 10 studies comparing instructional modalities, 8 compared computer-assisted and face-to-face instruction, with pooled SMD 0.23 (95% CI, 0.09, 0.36) indicating a small, statistically significant difference favoring computer-assisted instruction. Among 19 studies comparing instructional methods, 5 evaluated individual versus group training (pooled SMD −0.35 favoring group study [95% CI, −0.06, −0.63]), 4 evaluated peer-led versus faculty-led instruction (pooled SMD 0.38 favoring peer instruction [95% CI, 0.01, 0.74]), and 4 evaluated contrasting ECG features (e.g., QRS width) from 2 or more diagnostic categories versus routine examination of features within a single ECG or diagnosis (pooled SMD 0.23 not significantly favoring contrasting features [95% CI, −0.30, 0.76]). Eight studies compared ECG interpretation approaches, with pooled SMD 0.92 (95% CI, 0.48, 1.37) indicating a large, statistically significant effect favoring more systematic interpretation approaches.

Conclusions
Some instructional interventions appear to improve learning in ECG interpretation; however, many evidence-based instructional strategies are insufficiently investigated. The findings may have implications for future research and design of training to improve skills in ECG interpretation and other types of visual diagnosis.
The Optimized Oxford Hip Skeletal Maturity System Proves Resilient to Rotational Variation
Authors: Castillo Tafur Julio C. , Furdock Ryan J. , Sattar Abdus , Liu Raymond W. 
Published: January 2022

Background:The recently described optimized Oxford skeletal maturity system utilizes anteroposterior (AP) hip radiographs to accurately, rapidly, and reliably estimate skeletal maturity. However, in the real-world setting, significant positional variation in AP hip radiographs may influence the accuracy of optimized Oxford skeletal age estimates. We sought to evaluate the consistency of skeletal age estimations using the optimized Oxford system between differently rotated radiographs.Methods:Thirty normal computerized tomography scans of males (15 children, 9 to 15 y) and females (15 children, 8 to 14 y) were obtained retrospectively, converted into 3D reconstructions, and then used to produce simulated hip radiographs in five different rotational positions. The optimized Oxford system was applied to the 150 simulated AP hip radiographs (5 differently rotated views of 30 hips) to produce a skeletal age estimate for each.Results:Rotational position did not have a statistically significant effect on the skeletal age (P=0.84) using 1-way repeated measures analysis of variance. Of the 5 radiographic parameters in the optimized Oxford system, only greater trochanter height showed significant rotational variation after Greenhouse-Geisser correction (F2.58, 74.68=5.98,P<0.001). However, post hoc analyses showed that the greater trochanter height obtained at the most centered position was not different from the other 4 rotational positions (P>0.05 for all).Conclusion:The optimized Oxford skeletal maturity system is resilient to rotational variation. Mildly to moderately rotated radiographs obtained in the modern clinical setting can be used for skeletal age estimation by this method, broadening the clinical usage of this system.Level of Evidence:Level III—diagnostic study.
The Use of Physical Restraints in Italian Intensive Care Units: Results From a Multicenter Observational Study
Authors: Mattiussi Elisa , Piani Tommaso , De Marco Alice , Portolan Camilla , Castriotta Luigi , Danielis Matteo 
Published: January 2022

Background
The use of physical restraints (PRs) varies across countries and clinical settings, with intensive care units having the highest frequency. Although many investigations on the use of PRs have been conducted worldwide, few studies are reported in the Italian context.

Objectives
The aims of this study were to describe PR rates and types and to observe the factors associated with PR use.

Methods
In this observational study, 2 methods were used to collect data: direct observation and review of patients' documentations.

Results
We performed 328 observations on 146 critically ill patients. Physical restraints were applied in 56.7% (n = 186) of these observations. Bilateral wrist ties were used for most PR episodes (n = 135, 72.6%), followed by unilateral wrist ties (12.9%). The most documented reasons were preventing patients from self-extubation (n = 93, 50.0%) and preserving indwelling lines and tubes (n = 60, 32.2%). In the multivariate logistic regression analysis, patients who were cared for during the night shift were almost 4 times more likely to be restrained than patients in the morning shifts (odds ratio, 3.84; P = .001) and patients with endotracheal tube were 3.5 times more likely to be restricted than spontaneously breathing patients (odds ratio, 3.59; P < .001).

Discussions
Physical restraints are commonly used among critically ill patients in Italian intensive care units. There is a need to share the metrics for an efficient and accurate measurement of PR usage and trends and to document the reason for restraints, type of restraints, timeframe, and decision-making criteria.
Amylin: new insight into pathogenesis, diagnosis, and prognosis of non-insulin-dependent diabetes-mellitus-related cardiomyopathy
Authors: Xie Jiaying , Tong Zhoujie , Shen Longfei , Shang Yuanyuan , Li Yulin , Lu Bin , Ma Weixuan , Zhang Wei , Zhong Ming 
Published: January 2022

Abstract
Co-secretion with insulin, highly amyloidogenic human amylin is considered to contribute to the initiation and progression of diabetic heart complications, despite other situations such as hypertension and atherosclerosis. In response to insulin resistance, hyperinsulinemia, and consequently hyperamylinemia, is common in prediabetic patients, where highly concentrated amylin is prone to form amylin oligomers, which further assemble into fibrils and amyloids with high β-sheet content. The infusion and deposition of oligomeric amylin in myocytes cause a series of consequences, including cytosolic Ca2+ dysregulation, calmodulin activation, myocyte hypertrophy, and ventricular stiffness, eventually leading to heart failure. In this review, we present the latest reports of amylin-related heart complications, provide new insights, and state the underlying pathogenesis, diagnosis, possible treatment, and prevention of diabetic cardiomyopathy.
Cost Utility of Schlemm’s Canal Microstent Injection With Cataract Surgery for Open-angle Glaucoma in the US Medicare System
Authors: Atik Alp , Rhodes Lindsay A. , Samuels Brian C. , Mennemeyer Stephen T. , Girkin Christopher A. 
Published: January 2022

Précis:
Hydrus microstent (HMS) implantation at the time of cataract surgery appears to be cost-effective in mild-to-moderate glaucoma. However, long-term follow-up is essential for a full assessment of device performance, safety and cost-effectiveness.

Purpose:
The aim was to assess the societal cost-utility to the US Medicare system of implanting HMS with cataract surgery versus cataract surgery alone in patients with open-angle glaucoma.

Patients:
Markov model cohort of patients with mild-to-moderate open-angle glaucoma and visually significant cataract.

Methods:
Patients received HMS during cataract surgery versus cataract surgery alone, in a deterministic model over a 2-year horizon using TreeAge software. Both arms received additional ocular hypotensive agents to control intraocular pressure. Treatment effect of HMS was measured as mean number of ocular hypotensive medications and intraocular pressure, which directly impacted transition probabilities. Health states included the Hodapp-Parrish-Anderson glaucoma stages (mild, moderate, advanced, blind) and death. One-way sensitivity and probabilistic sensitivity analyses were conducted on device efficacy and longer time horizons.

Results:
At 2 years, HMS with cataract surgery in mild glaucoma had an incremental cost-utility ratio of USD 38,346.43 per utility gained, compared with cataract surgery alone. Probabilistic sensitivity analysis was cost-effective in 61.4% of iterations for HMS+cataract surgery. The probability of side-effects with eye drops, utility decrement with side-effects, cost of the HMS and real-world efficacy rate had the greatest impact on model outcomes. HMS must be 85.60% as effective as published data to maintain cost-effectiveness at a willingness-to-pay threshold of USD 50,000. The incremental cost-utility ratio of HMS with cataract surgery in moderate glaucoma was USD 42,895.38.

Conclusions:
HMS implantation during cataract surgery appears to be cost-effective for patients with mild-to-moderate glaucoma. Nevertheless, more long-term safety and efficacy data are required.
Restricted use of copy and paste in electronic health records potentially improves healthcare quality
Authors: Cheng Chun-Gu , Wu Ding-Chung , Lu Jui-Cheng , Yu Chia-Peng , Lin Hong-Ling , Wang Mei-Chuen , Cheng Chun-An 
Published: January 2022

Abstract
The copy-and-paste feature is commonly used for clinical documentation, and a policy is needed to reduce overdocumentation. We aimed to determine if the restricted use of copy and paste by doctors could improve inpatient healthcare quality.
Clinical documentation in an inpatient dataset compiled from 2016 to 2018 was used. Copied-and-pasted text was detected in word templates using natural language programming with a threshold of 70%. The prevalence of copying and pasting after the policy introduction was accessed by segmented regression for trend analysis. The rate of readmission for the same disease within 14 days was assessed to evaluate inpatient healthcare quality, and the completion of discharge summary notes within 3 days was assessed to determine the timeliness of note completion. The relationships between these factors were used cross-correlation to detect lag effect. Poisson regression was performed to identify the relative effect of the copy and paste restriction policy on the 14-day readmission rate or the discharge note completion rate within 3 days.
The prevalence of copying and pasting initially decreased, then increased, and then flatly decreased. The cross-correlation results showed a significant correlation between the prevalence of copied-and-pasted text and the 14-day readmission rate (P < .001) and a relative risk of 1.105 (P < .005), with a one-month lag. The discharge note completion rate initially decreased and not affected long term after restriction policy.
Appropriate policies to restrict the use of copying and pasting can lead to improvements in inpatient healthcare quality. Prospective research with cost analysis is needed.