bluuebunny/crossref_metadata_2025_split huggingface dataset:
What competencies do environmental health graduates need to manage social determinants of health?
Authors: Omid Athar , Sepyani Fateme , Yamani Nikoo , Pourzamani Hamidreza , Aghdak Pejman 
Published: December 2021

Abstract
Background
Graduates of environmental health engineering should be able to manage Social Determinants of Health (SDH) and acquire the essential competencies during their studies at university. This study was performed to determine the expected competencies of environmental health graduates in a way to be able to manage environmental and Social Determinants of Health according to their job description.

Methods
This descriptive cross-sectional study was performed using Delphi technique. First, the literature review was done and the Delphi technique was performed in three rounds. The purposeful sampling was used and 50 people were selected among the specialists in the field of environmental health engineering and SDH. Participants answered an open-ended question, for the first round. Then, a questionnaire with 8 areas was designed based on the results of the first round and distributed for the second round. Data analysis was performed using descriptive statistics. The third round was done to reach the agreement on final items.

Results
The agreement on the items of the third round of Delphi was more than 70%. The final results showed eight competency areas under which 29 competencies were defined. Competency areas included expert knowledge, reasoning and planning, advocacy, system-based practice, professionalism, instructional expertise, social and personal skills and, research and self-development. The first three priorities of the required competency areas were expert knowledge (4.46 ± 0.55), professionalism (4.42 ± 0.64), and advocacy (4.32 ± 0.77).

Conclusions
It is necessary that environmental health engineers achieve necessary competencies regarding managing SDH, upon their graduation. It is suggested to integrate these competencies into the curriculum of environmental and health engineering in Iran universities.
Laser lithotripsy using dusting technique (low energy, high frequency) for symptomatic upper urinary tract stones
Authors: Ashmawy A. , Khedr M. , Saad I. R. , Zamel S. , Kassem A. 
Published: December 2021

Abstract
Background
A prospective study to assess the feasibility of stone dusting technique (low energy and high frequency) during laser lithotripsy in symptomatic upper urinary tract |(UUT) stones.

Methods
Sixty patients with symptomatic single or multiple UUT stones less than 3 cm in diameter were included. Patients with coagulation disorders and active UTIs were excluded. All patients were clinically evaluated and underwent non-contrast spiral CT (NCSCT) to detect stone site, size, number, Hounsfield unit. A rigid or flexible ureteroscope was used with stone dusting using the Ho: YAG laser at low-energy and high-frequency (0.5 J & 20 Hz) set. Operative and fluoroscopy time, total energy delivered, type of stent, hospitalization time, complications and its grade, and stone-free rate using NCSCT after 4 weeks were recorded.

Results
The mean stone size ± SD (range) was 1.55 ± 0.55 (0.5–3) cm; out of sixty patients (50 with single stone and 10 with multiple stones), fifty-five patients were stone-free at 4 weeks. Complications had occurred in 11 patients (eight with grade I, one with grade II, and two with grade IIIa) according to Clavien–Dindo grading of surgical complications. Stone size was the only parameter which correlated significantly with stone-free rate. No significant correlation was found between incidence of complications and other parameters (stone size, site, BMI, age and operative time).

Conclusions
Stone dusting technique is feasible, safe and effective in management of UUT stones.
Adipose tissue macrophages in aging-associated adipose tissue function
Authors: Lu Bangchao , Huang Liang , Cao Juan , Li Lingling , Wu Wenhui , Chen Xiaolin , Ding Congzhu 
Published: December 2021

Abstract“Inflammaging” refers to the chronic, low-grade inflammation that characterizes aging. Aging, like obesity, is associated with visceral adiposity and insulin resistance. Adipose tissue macrophages (ATMs) have played a major role in obesity-associated inflammation and insulin resistance. Macrophages are elevated in adipose tissue in aging. However, the changes and also possibly functions of ATMs in aging and aging-related diseases are unclear. In this review, we will summarize recent advances in research on the role of adipose tissue macrophages with aging-associated insulin resistance and discuss their potential therapeutic targets for preventing and treating aging and aging-related diseases.
QuickPIV: Efficient 3D particle image velocimetry software applied to quantifying cellular migration during embryogenesis
Authors: Pereyra Marc , Drusko Armin , Krämer Franziska , Strobl Frederic , Stelzer Ernst H. K. , Matthäus Franziska 
Published: December 2021

Abstract
Background
The technical development of imaging techniques in life sciences has enabled the three-dimensional recording of living samples at increasing temporal resolutions. Dynamic 3D data sets of developing organisms allow for time-resolved quantitative analyses of morphogenetic changes in three dimensions, but require efficient and automatable analysis pipelines to tackle the resulting Terabytes of image data. Particle image velocimetry (PIV) is a robust and segmentation-free technique that is suitable for quantifying collective cellular migration on data sets with different labeling schemes. This paper presents the implementation of an efficient 3D PIV package using the Julia programming language—quickPIV. Our software is focused on optimizing CPU performance and ensuring the robustness of the PIV analyses on biological data.

Results
QuickPIV is three times faster than the Python implementation hosted in openPIV, both in 2D and 3D. Our software is also faster than the fastest 2D PIV package in openPIV, written in C++. The accuracy evaluation of our software on synthetic data agrees with the expected accuracies described in the literature. Additionally, by applying quickPIV to three data sets of the embryogenesis of Tribolium castaneum, we obtained vector fields that recapitulate the migration movements of gastrulation, both in nuclear and actin-labeled embryos. We show normalized squared error cross-correlation to be especially accurate in detecting translations in non-segmentable biological image data.

Conclusions
The presented software addresses the need for a fast and open-source 3D PIV package in biological research. Currently, quickPIV offers efficient 2D and 3D PIV analyses featuring zero-normalized and normalized squared error cross-correlations, sub-pixel/voxel approximation, and multi-pass. Post-processing options include filtering and averaging of the resulting vector fields, extraction of velocity, divergence and collectiveness maps, simulation of pseudo-trajectories, and unit conversion. In addition, our software includes functions to visualize the 3D vector fields in Paraview.
Comparative transcriptomic analysis of gonadal development and renewal in the ovoviviparous black rockfish (Sebastes schlegelii)
Authors: Li Jianshuang , Lyu Likang , Wen Haishen , Li Yun , Wang Xiaojie , Zhang Ying , Yao Yijia , Qi Xin 
Published: December 2021

Abstract
Background
The black rockfish (Sebastes schlegelii) has an ovoviviparous reproductive pattern and long-term sperm storage, resulting in asynchronous gonadal development between the sexes. However, the comprehensive understanding of gonadal development in black rockfish has not yet been achieved. Here, we studied gonadal development and germ cell renewal using histology and RNA-seq.

Results
In this study, RNA-seq was performed on testes and ovaries to characterize key pathways and genes that are active during development and gamete maturation in black rockfish. Differentially expressed genes (DEGs) were identified and annotated in 4 comparisons (F_III vs. F_IV, F_IV vs. F_V, M_III vs. M_IV and M_IV vs. M_V). Based on analysis of DEGs enriched in the testis, 11 and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were mapped to the M_III vs. M_IV group and the M_IV vs. M_V group, respectively. DEGs in ovarian development were also classified into 10 groups according to their biological functions. The expression patterns of the selected genes determined by qPCR were significantly correlated with the RNA-Seq results, supporting the reliability and accuracy of the RNA-Seq analysis. E2 levels showed down regulation from previtellogenesis to mature stage in female and T level showed down regulation from spermatogenesis to regressed stage in the male.

Conclusions
The categories “intercellular interaction and cytoskeleton”, “molecule amplification” and “repair in the cell cycle” were revealed to be crucial in testis development and spermatogenesis, as was the biosynthesis of a series of metabolites. Our results provide comprehensive insight into black rockfish gonadal development and provide a basis for further study of reproductive physiology and molecular biology in ovoviviparity teleosts.
Establishing community-wide DNA barcode references for conserving mangrove forests in China
Authors: Mao Xiaomeng , Xie Wei , Li Xinnian , Shi Suhua , Guo Zixiao 
Published: December 2021

Abstract
Background
Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering ‘blue carbon’. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country’s coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. DNA barcoding technology may help protect mangrove ecosystems by providing rapid species identification.

Results
To investigate this potential, 898 plant specimens were collected from 33 major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers rbcL, trnH-psbA, matK, and one nuclear marker ITS2 were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity, and phylogenetic monophyly, we propose that a single marker, ITS2, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, rbcL or trnH-psbA can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances.

Conclusion
We suggest using ITS2 to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.
Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte
Authors: Chen Zhengjie , Tang Dengguo , Hu Kun , Zhang Lei , Yin Yong , Ni Jixing , Li Peng , Wang Le , Rong Tingzhao , Liu Jian 
Published: December 2021

AbstractBackgroundTeosinte ear bears single spikelet, whereas maize ear bears paired spikelets, doubling the number of grains in each cupulate during maize domestication. In the past 20 years, genetic analysis of single vs. paired spikelets (PEDS) has been stagnant. A better understanding of genetic basis of PEDS could help fine mapping of quantitative trait loci (QTL) and cloning of genes.ResultsIn this study, the advanced mapping populations (BC3F2and BC4F2) of maize × teosinte were developed by phenotypic recurrent selection. Four genomic regions associated with PEDS were detected using QTL-seq, located on 194.64–299.52 Mb, 0–162.80 Mb, 12.82–97.17 Mb, and 125.06–157.01 Mb of chromosomes 1, 3, 6, and 8, respectively. Five QTL for PEDS were identified in the regions of QTL-seq using traditional QTL mapping. Each QTL explained 1.12–38.05% of the phenotypic variance (PVE); notably, QTLqPEDS3.1with the average PVE of 35.29% was identified in all tests. Moreover, 14 epistatic QTL were detected, with the total PVE of 47.57–66.81% in each test. The QTLqPEDS3.1overlapped with, or was close to, one locus of 7 epistatic QTL. Near-isogenic lines (NILs) of QTLqPEDS1.1,qPEDS3.1,qPEDS6.1, andqPEDS8.1were constructed. All individuals of NIL-qPEDS6.1(MT1) and NIL-qPEDS8.1(MT1) showed paired spikelets (PEDS = 0), but the flowering time was 7 days shorter in the NIL-qPEDS8.1(MT1). The ratio of plants with PEDS > 0 was low (1/18 to 3/18) in the NIL-qPEDS1.1(MT1) and NIL-qPEDS3.1(MT1), maybe due to the epistatic effect.ConclusionOur results suggested that major QTL, minor QTL, epistasis and photoperiod were associated with the variation of PEDS, which help us better understand the genetic basis of PEDS and provide a genetic resource for fine mapping of QTL.
Genome-wide identification and analysis of Oleosin gene family in four cotton species and its involvement in oil accumulation and germination
Authors: Yuan Yanchao , Cao Xinzhe , Zhang Haijun , Liu Chunying , Zhang Yuxi , Song Xian-Liang , Gai Shupeng 
Published: December 2021

Abstract
Background
Cotton is not only a major textile fiber crop but also a vital oilseed, industrial, and forage crop. Oleosins are the structural proteins of oil bodies, influencing their size and the oil content in seeds. In addition, the degradation of oleosins is involved in the mobilization of lipid and oil bodies during seed germination. However, comprehensive identification and the systematic analysis of the Oleosin gene (OLEOs) family have not been conducted in cotton.

Results
An in-depth analysis has enabled us to identify 25 and 24 OLEOs in tetraploid cotton species G. hirsutum and G. barbadense, respectively, while 12 and 13 OLEOs were identified in diploid species G. arboreum and G. raimondii, respectively. The 74 OLEOs were further clustered into three lineages according to the phylogenetic tree. Synteny analysis revealed that most of the OLEOs were conserved and that WGD or segmental duplications might drive their expansion. The transmembrane helices in GhOLEO proteins were predicted, and three transmembrane models were summarized, in which two were newly proposed. A total of 24 candidate miRNAs targeting GhOLEOs were predicted. Three highly expressed oil-related OLEOs, GH_A07G0501 (SL), GH_D10G0941 (SH), and GH_D01G1686 (U), were cloned, and their subcellular localization and function were analyzed. Their overexpression in Arabidopsis increased seed oil content and decreased seed germination rates.

Conclusion
We identified OLEO gene family in four cotton species and performed comparative analyses of their relationships, conserved structure, synteny, and gene duplication. The subcellular localization and function of three highly expressed oil-related OLEOs were detected. These results lay the foundation for further functional characterization of OLEOs and improving seed oil content.
A cotransformation system of the unicellular red alga Cyanidioschyzon merolae with blasticidin S deaminase and chloramphenicol acetyltransferase selectable markers
Authors: Fujiwara Takayuki , Hirooka Shunsuke , Miyagishima Shin-ya 
Published: December 2021

Abstract
Background
The unicellular red alga Cyanidioschyzon merolae exhibits a very simple cellular and genomic architecture. In addition, procedures for genetic modifications, such as gene targeting by homologous recombination and inducible/repressible gene expression, have been developed. However, only two markers for selecting transformants, uracil synthase (URA) and chloramphenicol acetyltransferase (CAT), are available in this alga. Therefore, manipulation of two or more different chromosomal loci in the same strain in C. merolae is limited.

Results
This study developed a nuclear targeting and transformant selection system using an antibiotics blasticidin S (BS) and the BS deaminase (BSD) selectable marker by homologous recombination in C. merolae. In addition, this study has succeeded in simultaneously modifying two different chromosomal loci by a single-step cotransformation based on the combination of BSD and CAT selectable markers. A C. merolae strain that expresses mitochondrion-targeted mSCARLET (with the BSD marker) and mVENUS (with the CAT marker) from different chromosomal loci was generated with this procedure.

Conclusions
The newly developed BSD selectable marker enables an additional genetic modification to the already generated C. merolae transformants based on the URA or CAT system. Furthermore, the cotransformation system facilitates multiple genetic modifications. These methods and the simple nature of the C. merolae cellular and genomic architecture will facilitate studies on several phenomena common to photosynthetic eukaryotes.
Cardiovascular risk in patients with and without diabetes presenting with chronic coronary syndrome in 2004–2016
Authors: Jensen Esben Skov , Olesen Kevin Kris Warnakula , Gyldenkerne Christine , Thrane Pernille Gro , Jensen Lisette Okkels , Raungaard Bent , Poulsen Per Løgstrup , Thomsen Reimar Wernich , Maeng Michael 
Published: December 2021

Abstract
Background
It was recently shown that new-onset diabetes patients without previous cardiovascular disease have experienced a markedly reduced risk of adverse cardiovascular events from 1996 to 2011. However, it remains unknown if similar improvements are present following the diagnosis of chronic coronary syndrome. The purpose of this study was to examine the change in cardiovascular risk among diabetes patients with chronic coronary syndrome from 2004 to 2016.

Methods
We included patients with documentation of coronary artery disease by coronary angiography between 2004 and 2016 in Western Denmark. Patients were stratified by year of index coronary angiography (2004–2006, 2007–2009, 2010–2012, and 2013–2016) and followed for two years. The main outcome was major adverse cardiovascular events (MACE) defined as myocardial infarction, ischemic stroke, or death. Analyses were performed separately in patients with and without diabetes. We estimated two-year risk of each outcome and adjusted incidence rate ratios (aIRR) using patients examined in 2004-2006 as reference.

Results
Among 5931 patients with diabetes, two-year MACE risks were 8.4% in 2004–2006, 8.5% in 2007–2009, and then decreased to 6.2% in 2010–2012 and 6.7% in 2013–2016 (2013–2016 vs 2004–2006: aIRR 0.70, 95% CI 0.53–0.93). In comparison, 23,540 patients without diabetes had event rates of 6.3%, 5.2%, 4.2%, and 3.9% for the study intervals (2013–2016 vs 2004–2006: aIRR 0.57, 95% CI 0.48–0.68).

Conclusions
Between 2004 and 2016, the two-year relative risk of MACE decreased by 30% in patients with diabetes and chronic coronary syndrome, but slightly larger absolute and relative reductions were observed in patients without diabetes.
The LUCID study: living with ulcerative colitis; identifying the socioeconomic burden in Europe
Authors: Ruiz-Casas Leonardo , Evans Jonathan , Rose Alison , Pedra Gabriel Ghizzi , Lobo Alan , Finnegan Alan , Hayee Bu , Peyrin-Biroulet Laurent , Sturm Andreas , Burisch Johan , Terry Helen , Avedano Luisa , Tucknott Seb , Fiorino Gionata , Limdi Jimmy 
Published: December 2021

Abstract
Background
Ulcerative colitis (UC) is an inflammatory bowel disease with increasing prevalence worldwide. Current treatment strategies place considerable economic and humanistic burdens on patients. The aim of this study was to determine the socioeconomic burden of UC in adult patients in European countries in a real-world setting.

Methods
In this retrospective, cross-sectional and observational pan-European study, patients with moderate or severe UC were assigned to ARM 1 and patients who had moderate or severe UC but achieved mild or remission status 12 months before index date (or clinical consultation date), were assigned to ARM 2. Clinical and medical resource use data were collected via electronic case report forms, and data on non-medical and indirect costs, and health-related quality of life (HRQoL) were collected via patient and public involvement and engagement (PPIE) questionnaires. Per-patient annual total costs per ARM and per country were calculated using the collated resource use in the last 12 months (between the start of the documentation period and patient consultation or index date) and country specific unit costs. Quality of life was described by arm and by country.

Results
In the physician-reported eCRF population (n = 2966), the mean annual direct medical cost was €4065 in ARM 1 (n = 1835) and €2935 in ARM 2 (n = 1131). In the PPIE population (ARM 1, n = 1001; ARM 2, n = 647), mean annual direct cost was €4526 in ARM 1 and €3057 in ARM 2, mean annual direct non-medical cost was €1162 in ARM 1 and €1002 in ARM 2, mean annual indirect cost was €3098 in ARM 1 and €2309 ARM 2, and mean annual total cost was in €8787 in ARM 1 and €6368 in ARM 2. HRQoL scores showed moderate to high burden of UC in both groups.

Conclusions
The cost and HRQoL burden were high in patients in both ARM 1 and ARM 2 indicating unmet needs in the UC active population.
Physical interventions for people with more advanced dementia – a scoping review
Authors: Hall Abigail J. , Febrey Samantha , Goodwin Victoria A. 
Published: December 2021

Abstract
Background
Dementia is a neuro-degenerative condition resulting in cognitive and physical decline over time. In the early stages of the condition, physical decline may be slow, but in the later stages, it may become more pronounced. Physical interventions may be employed to try and reduce the physical decline that people experience, yet it is unclear what interventions may be effective. The aim of this study was to explore the breadth and quantity of evidence that exists in relation to the delivery of physical interventions for people with advanced dementia.

Methods
We undertook a scoping review in order to map the current literature. All types of study design were included in the search in order to gain a comprehensive scope of the literature. We searched a variety of databases from inception until March 2021, focusing on physical interventions. Double screening and data extraction were employed in order to increase the reliability of the results.

Results
Our review found four studies which focused on physical interventions aimed at improving physical outcomes for people with more advanced dementia. The majority of studies were excluded as their interventions were not specific to people with advanced dementia. The studies that were included incorporated functional activities and, despite small sample sizes, suggested statistically significant improvements in outcomes for people with advanced dementia.

Conclusion
There is currently limited evidence relating to physical rehabilitation interventions for people with more advanced dementia, however, the evidence we presented suggests potential benefits for physical outcomes. Future research should focus on robust research to determine the most effective and cost-effective interventions that meet the needs of this population.