bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of precise and approximated building height: Estimation from number of building storeys and spatial variations in the Tokyo metropolitan region
Authors: Usui Hiroyuki 
Published: August 2022

Precise building height is indispensable for evaluating variability in building heights. However, relevant data are not always available. Conventionally, building height is approximated as the product of the number of building storeys and floor height, called approximated building height. However, there is no consensus on how floor height, a key determinant of approximated building height, should be set. In Japan, increasingly precise building height data are becoming available as an open 3D urban model. This provides the motivation for answering the following research questions, in the context of the Tokyo metropolitan region: (1) What is the difference between approximated and precise building height? (2) How should we set floor height to minimise the difference between approximated and precise building height? The results show that (1) the average difference is −3.46 m if floor height, c, is 5 m, −0.87 m if c is 4 m and 1.71 m if c is 3 m; (2) c = 4 can effectively estimate building height from the number of storeys; and (3) the greatest difference between approximated and precise building height is spatially clustered where commercial zones and industrial zones are allocated, with their degree being dependent on how floor height is set. Furthermore, it is found that (1) in commercial zones and industrial districts, the optimal floor height, defined as the optimal solution which minimises the sum of squared differences between approximated and precise building height, is greater than 4 m; (2) in mid/high rise residential districts, the optimal floor height ranges from 3 to 3.4 m; and (3) in low-rise residential districts, the optimal floor height ranges from 3.5 to 3.9 m. The findings of this paper can help urban planners find the optimal floor height in each district and understand spatial variations in building and floor heights.
Avoid or seek light – a randomized crossover fMRI study investigating opposing treatment strategies for photophobia in migraine
Authors: Matt Eva , Aslan Tuna , Amini Ahmad , Sariçiçek Kardelen , Seidel Stefan , Martin Paul , Wöber Christian , Beisteiner Roland 
Published: August 2022

Abstract
Background
Photophobia, the aberrantly increased sensitivity to light, is a common symptom in migraine patients and light discomfort is frequently found as a trigger for migraine attacks. In behavioral studies, planned exposure to light was found to reduce headache in migraine patients with photophobia, potentially by increasing habituation to this migraine trigger. Here, we aimed to elucidate neurophysiological mechanisms of light exposure versus light deprivation in migraine patients using functional magnetic resonance imaging (fMRI).

Methods
Ten migraine patients (9 female, age = 28.70 ± 8.18 years) and 11 healthy controls (9 female, age = 23.73 ± 2.24 years) spent one hour on 7 consecutive days exposed to flashing light (Flash) or darkness (Dark) using a crossover design with a wash-out period of 3 months. Study participants kept a diary including items on interictal and ictal photophobia, presence and severity of headache 7 days before, during and 7 days after the interventions. One week before and one day after both interventions, fMRI using flickering light in a block design was applied. Functional activation was analyzed at whole-brain level and habituation of the visual cortex (V1) was modeled with the initial amplitude estimate and the corrected habituation slope.

Results
Mean interictal photophobia decreased after both interventions, but differences relative to the baseline did not survive correction for multiple comparisons. At baseline, flickering light induced activation in V1 was higher in the patients compared to the controls, but activation normalized after the Flash and the Dark interventions. V1 habituation indices correlated with headache frequency, headache severity and ictal photophobia. In the Flash condition, the individual change of headache frequency relative to the baseline corresponded almost perfectly to the change of the habituation slope compared to the baseline.

Conclusions
On average, light exposure did not lead to symptom relief, potentially due to the short duration of the intervention and the high variability of the patients’ responses to the intervention. However, the strong relationship between visual cortex habituation and headache symptoms and its modulation by light exposure might shed light on the neurophysiological basis of exposure treatment effects.

Trial registration
NCT05369910 (05/06/2022, retrospectively registered).
Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research
Authors: Mashanov Vladimir , Machado Denis Jacob , Reid Robert , Brouwer Cory , Kofsky Janice , Janies Daniel A. 
Published: August 2022

Abstract
Background
Echinoderms are established models in experimental and developmental biology, however genomic resources are still lacking for many species. Here, we present the draft genome of Ophioderma brevispinum, an emerging model organism in the field of regenerative biology. This new genomic resource provides a reference for experimental studies of regenerative mechanisms.

Results
We report a de novo nuclear genome assembly for the brittle star O. brevispinum and annotation facilitated by the transcriptome assembly. The final assembly is 2.68 Gb in length and contains 146,703 predicted protein-coding gene models. We also report a mitochondrial genome for this species, which is 15,831 bp in length, and contains 13 protein-coding, 22 tRNAs, and 2 rRNAs genes, respectively. In addition, 29 genes of the Notch signaling pathway are identified to illustrate the practical utility of the assembly for studies of regeneration.

Conclusions
The sequenced and annotated genome of O. brevispinum presented here provides the first such resource for an ophiuroid model species. Considering the remarkable regenerative capacity of this species, this genome will be an essential resource in future research efforts on molecular mechanisms regulating regeneration.
Assessment of DNA methylation in porcine immune cells reveals novel regulatory elements associated with cell-specific gene expression and immune capacity traits
Authors: Corbett Ryan J. , Luttman Andrea M. , Herrera-Uribe Juber , Liu Haibo , Raney Nancy E. , Grabowski Jenna M. , Loving Crystal L. , Tuggle Christopher K. , Ernst Catherine W. 
Published: August 2022

Abstract
Background
Genetics studies in the porcine immune system have enhanced selection practices for disease resistance phenotypes and increased the efficacy of porcine models in biomedical research; however limited functional annotation of the porcine immunome has hindered progress on both fronts. Among epigenetic mechanisms that regulate gene expression, DNA methylation is the most ubiquitous modification made to the DNA molecule and influences transcription factor binding as well as gene and phenotype expression. Human and mouse DNA methylation studies have improved mapping of regulatory elements in these species, but comparable studies in the pig have been limited in scope.

Results
We performed whole-genome bisulfite sequencing to assess DNA methylation patterns in nine pig immune cell populations: CD21+ and CD21− B cells, four T cell fractions (CD4+, CD8+, CD8+CD4+, and SWC6γδ+), natural killer and myeloid cells, and neutrophils. We identified 54,391 cell differentially methylated regions (cDMRs), and clustering by cDMR methylation rate grouped samples by cell lineage. 32,737 cDMRs were classified as cell lowly methylated regions (cLMRs) in at least one cell type, and cLMRs were broadly enriched in genes and regions of intermediate CpG density. We observed strong correlations between differential methylation and expression across immune cell populations, with cell-specific low methylation disproportionately impacting genes exhibiting enriched gene expression in the same cell type. Motif analysis of cLMRs revealed cell type-specific enrichment of transcription factor binding motifs, indicating that cell-specific methylation patterns may influence accessibility by trans-acting factors. Lastly, cDMRs were enriched for immune capacity GWAS SNPs, and many such overlaps occurred within genes known to influence immune cell development and function (CD8B, NDRG1).

Conclusion
Our DNA methylation data improve functional annotation of the porcine genome through characterization of epigenomic regulatory patterns that contribute to immune cell identity and function, and increase the potential for identifying mechanistic links between genotype and phenotype.
Effects of berberine hydrochloride on immune response in the crab Charybdis japonica
Authors: Gao Tian-heng , Han Ming-ming , Zhou Hui , Zhu Chen-xi , Yang Ying , Zuraini Zakaria , Guo Yan-Xia , Jiang Qi-chen 
Published: August 2022

AbstractBerberine hydrochloride is the main effective component of Coptis spp. used in Chinese herbal medicine and its underlying molecular mechanisms, responsible for inducing effects in crustacean species, are not fully understood. In this study, the molecular response of the crab Charybdis japonica to berberine hydrochloride exposure was studied using transcriptome sequencing. The survival rate, gene expression and activities of several immune enzymes were measured after berberine hydrochloride treatments, with or without injection of the pathogenic bacterium Aeromonas hydrophila. A total of 962 differentially expressed genes (464 up-regulated and 498 down-regulated) were observed during exposure to 100 mg/L of berberine hydrochloride and in the control group after 48 h. Enrichment analysis revealed that these genes are involved in metabolism, cellular processes, signal transduction and immune functions, indicating that exposure to berberine hydrochloride activated the immune complement system. This bioactive compound simultaneously activated fibrinogen beta (FGB), fibrinogen alpha (FGA), alpha-2-macroglobulin (A2M), kininogen (KNG), fibrinogen gamma chain (FGB), alpha-2-HS-glycoprotein (AHSG), caspase-8 (CASP8), cathepsin L (CTSL), adenylate cyclase 3 (Adcy3) and MMP1. Its action could significantly increase the survival rate of the crabs injected with A. hydrophila and promote the activity of LZM, Caspas8, FGA, ACP and AKP in the hepatopancreas. When A. hydrophila was added, the neutralization of 300 mg/L berberine hydrochloride maximized the activities of Caspas8, LZM, ACP and AKP. Our results provide a new understanding of the potential effects of berberine hydrochloride on the immune system mechanisms in crustaceans.
Homocysteine is related to enlarged perivascular spaces in the brainstem in patients with isolated pontine infarction
Authors: Fu Yunting , Yun Wenwei , Zhang Zhixiang , Ma Yi , Xiao Lulu , Zhang Min , Zhu Wusheng 
Published: August 2022

Abstract
Background
Homocysteine is correlated with several imaging features of cerebral small vessel disease including white matter hyperintensities, lacunes, and enlarged perivascular spaces (EPVS) in the basal ganglia. However, little is known about EPVS in the brainstem. This study aimed to investigate the correlation between serum total homocysteine (tHcy) and EPVS in the brainstem in patients with acute isolated pontine infarction.

Methods
Consecutive patients with isolated pontine infarction were retrospectively enrolled. Clinical characteristics and laboratory tests including tHcy were recorded. Imaging markers of cerebral small vessel disease including EPVS in the basal ganglia (BG-EPVS), EPVS in the centrum semiovale, and EPVS in the midbrain or pons (brainstem-EPVS) were assessed using conventional magnetic resonance imaging. The relation between tHcy and EPVS of different parts in the brain was analyzed using univariate and multivariate regression model.

Results
A total of 227 patients were included (mean age 67.10 ± 9.38 years, male sex 58.6%). The frequencies of brainstem-EPVS and moderate to severe BG-EPVS accounted for 40.1% (91/227) and 40.5% (92/227) respectively. After controlling for confounding factors, multivariate logistic regression analyses showed that tHcy was an independent risk factor for both moderate to severe BG-EPVS (P = 0.003, P for trend < 0.001) and the presence of brainstem-EPVS (P < 0.001, P for trend < 0.001) in a dose-dependent manner. Furthermore, multivariate linear regression model indicated that the presence of brainstem-EPVS (β = 0.264, 95% confidence interval = 0.143-0.402, P < 0.001) and the severity of BG-EPVS (β = 0.162, 95% confidence interval = 0.024-0.197, P = 0.013) were positively associated with serum tHcy.

Conclusions
Serum tHcy is correlated with brainstem-EPVS and BG-EPVS dose-dependently. This study may support a contributing role for homocysteine in the pathophysiology of EPVS in the brainstem and the basal ganglia.
COVID-19 vaccine adoption and hesitancy among older Veterans
Authors: Wyte-Lake Tamar , Levy Cari , Hovsepian Sona , Mudoh Yvonne , Schmitz Cheryl , Dobalian Aram 
Published: August 2022

Abstract
Background
Older adults are particularly at risk for severe illness or death from COVID-19. Accordingly, the Veterans Health Administration (VA) has prioritized this population group in its COVID-19 vaccination strategy. This study examines the receptivity of Veterans enrolled in the VA’s Geriatric Patient Aligned Care Team (GeriPACT) to receiving the COVID-19 vaccine. GeriPACT is an outpatient primary care program that utilizes multi-disciplinary teams to provide health services to older Veterans.

Methods
We conducted semistructured interviews with 42 GeriPACT-enrolled Veterans from five states. Participants were asked to identify barriers to vaccine acceptance. We gathered data from January-March 2021 and analyzed them using qualitative methods.

Results
Both White and African American GeriPACT Veterans had minimal vaccine hesitancy towards the COVID-19 vaccine. On-line registration and ineligibility of a spouse/caregiver for vaccination were primary barriers to early vaccination.

Conclusions
As the first wave of early adopters of the COVID-19 vaccination effort nears completion, targeted strategies are needed to understand and respond to vaccine hesitancy to lower the risk of subsequent waves of infections. The 2021 SAVE LIVES Act, begins to address identified vaccination barriers by permitting vaccination of Veteran spouses and caregivers, but consideration must be given to creating alternatives to on-line registration and allowing spouses and caregivers to register for appointments together.
Environmental and personal factors for osteoporosis or osteopenia from a large health check-up database: a retrospective cohort study in Taiwan
Authors: Chung Ping-Chen , Chan Ta-Chien 
Published: August 2022

Abstract
Background
Osteoporosis is an important public health issue in aging societies because of its associated morbidity, mortality, and decreased quality of life. The study aims to identify the association of low bone mineral density, including osteoporosis and osteopenia, with environmental and personal factors.

Methods
The data of participants aged ≥ 20 years with multiple visits were obtained from a health check-up database in Taiwan from 2008 to 2016. Multivariable logistic regressions were performed to identify the selected factors associated with low bone mineral density for multiple visit data.

Results
A total of 194,910 participants with 359,943 visits were included in this study. The prevalence of low bone mineral density (BMD) in the study population was 10.6% (n = 20.615). Older women, ever and current smokers (odds ratio (OR) = 1.04 [95% confidence interval (CI) = 1.01, 1.08]), or participants who were underweight (OR = 1.72 [1.64, 1.81]), consumed a vegetarian diet (OR = 1.32 [1.25, 1.39]), or had higher triglyceride levels (OR = 1.04 [1.01, 1.06]) were significantly associated with a higher risk of low BMD. Participants who had higher educational years (OR = 0.43 [0.41, 0.46]), higher physical activity (OR = 0.93 [0.89, 0.97]), appropriate sleep duration and better quality (OR = 0.98 [0.97, 0.99]), dairy intake (≥ 1 slice of yogurt or cheese/week, OR = 0.97 [0.95, 0.99]), higher uric acid (OR = 0.93 [0.91, 0.95]), higher walkability (OR = 0.997 [0.995,0.999]), and higher solar radiation exposure (OR = 0.997 [0.97,0.99]) were significantly associated with a lower risk of low BMD.

Conclusion
Interventions in different directions, such as having better health behaviors, increasing sun exposure, and residing in a highly walkable environment, are beneficial for reducing the risk of low BMD.
Acceptance and experience of digital dental technology, burnout, job satisfaction, and turnover intention for Taiwanese dental technicians
Authors: Teng Tang-Yun , Wu Ju-Hui , Lee Chen-Yi 
Published: August 2022

Abstract
Background
Digital dental technology (DDT) has progressed and been introduced to Taiwan in the recent years, gradually changing the industry ecology. Many studies have demonstrated that DDT is more accurate and faster than conventional dental technology. However, there is a paucity of research exploring dental technicians’ perspectives on digital dental techniques, and their burnout, job satisfaction, and turnover intention.

Methods
This cross-sectional survey with convenience sampling was conducted at the conference venue of the Taiwan Association of Dental Technology to investigate the perspectives of dental technicians. We used the snowballing method in this study; two sampling methods were adopted, a convenience sampling of dental technicians to complete a survey, followed by asking the survey participants of the convenience sample to invite their colleagues to participate in the online survey. The survey questionnaire included questions on demographics, work-related information, acceptance and experiences of dental technicians toward DDT, occupational burnout, job satisfaction, and turnover intention. Regression models were used to determine the predictors of job satisfaction and determinants of turnover intention.

Results
In total, 341 valid questionnaires were obtained. Overall, the participants reported long working hours (95.5%), positive score on the DDT acceptance scale, moderate job satisfaction, higher personal burnout, and work burnout, along with lower over-commitment. Among them, 32.9% and 28.2% reported the intention to leave their organization and profession, respectively. The stepwise multiple regression model revealed that higher work burnout decreased job satisfaction, while higher DDT acceptance and position as employer increased job satisfaction. The binary logistic regression models revealed that geographical area of workplace, work burnout, and job satisfaction were significant predictors of turnover intentions.

Conclusions
Many Taiwanese dental technicians reported turnover intentions and higher burnout. With the trend of digitalization in the dental industry, even though most dental technicians had a positive outlook toward DDT, its influence on job satisfaction appears limited. Retaining good and professional talents required of a dental technician is crucial, especially as Taiwan’s dental care becomes increasingly specialized. Strategies for improving the work environment and occupational health of dental technicians should thus be the focus of future studies.
Griottes: a generalist tool for network generation from segmented tissue images
Authors: Ronteix Gustave , Aristov Andrey , Bonnet Valentin , Sart Sebastien , Sobel Jeremie , Esposito Elric , Baroud Charles N. 
Published: August 2022

AbstractBackgroundMicroscopy techniques and image segmentation algorithms have improved dramatically this decade, leading to an ever increasing amount of biological images and a greater reliance on imaging to investigate biological questions. This has created a need for methods to extract the relevant information on the behaviors of cells and their interactions, while reducing the amount of computing power required to organize this information.ResultsThis task can be performed by using a network representation in which the cells and their properties are encoded in the nodes, while the neighborhood interactions are encoded by the links. Here, we introduce Griottes, an open-source tool to build the “network twin” of 2D and 3D tissues from segmented microscopy images. We show how the library can provide a wide range of biologically relevant metrics on individual cells and their neighborhoods, with the objective of providing multi-scale biological insights. The library’s capacities are demonstrated on different image and data types.ConclusionsThis library is provided as an open-source tool that can be integrated into common image analysis workflows to increase their capacities.
Associations of genetically predicted IL-6 signaling with cardiovascular disease risk across population subgroups
Authors: Georgakis Marios K. , Malik Rainer , Richardson Tom G. , Howson Joanna M. M. , Anderson Christopher D. , Burgess Stephen , Hovingh G. Kees , Dichgans Martin , Gill Dipender 
Published: August 2022

Abstract
Background
Interleukin 6 (IL-6) signaling is being investigated as a therapeutic target for atherosclerotic cardiovascular disease (CVD). While changes in circulating high-sensitivity C-reactive protein (hsCRP) are used as a marker of IL-6 signaling, it is not known whether there is effect heterogeneity in relation to baseline hsCRP levels or other cardiovascular risk factors. The aim of this study was to explore the association of genetically predicted IL-6 signaling with CVD risk across populations stratified by baseline hsCRP levels and cardiovascular risk factors.

Methods
Among 397,060 White British UK Biobank participants without known CVD at baseline, we calculated a genetic risk score for IL-6 receptor (IL-6R)-mediated signaling, composed of 26 variants at the IL6R gene locus. We then applied linear and non-linear Mendelian randomization analyses exploring associations with a combined endpoint of incident coronary artery disease, ischemic stroke, peripheral artery disease, aortic aneurysm, and cardiovascular death stratifying by baseline hsCRP levels and cardiovascular risk factors.

Results
The study participants (median age 59 years, 53.9% females) were followed-up for a median of 8.8 years, over which time a total of 46,033 incident cardiovascular events occurred. Genetically predicted IL-6R-mediated signaling activity was associated with higher CVD risk (hazard ratio per 1-mg/dL increment in absolute hsCRP levels: 1.11, 95% CI: 1.06–1.17). The increase in CVD risk was linearly related to baseline absolute hsCRP levels. There was no evidence of heterogeneity in the association of genetically predicted IL-6R-mediated signaling with CVD risk when stratifying the population by sex, age, body mass index, estimated glomerular filtration rate, or systolic blood pressure, but there was evidence of greater associations in individuals with low-density lipoprotein cholesterol ≥ 160 mg/dL.

Conclusions
Any benefit of inhibiting IL-6 signaling for CVD risk reduction is likely to be proportional to absolute reductions in hsCRP levels. Therapeutic inhibition of IL-6 signaling for CVD risk reduction should therefore prioritize those individuals with the highest baseline levels of hsCRP.