bluuebunny/crossref_metadata_2025_split huggingface dataset:
FocAn: automated 3D analysis of DNA repair foci in image stacks acquired by confocal fluorescence microscopy
Authors: Memmel Simon , Sisario Dmitri , Zimmermann Heiko , Sauer Markus , Sukhorukov Vladimir L. , Djuzenova Cholpon S. , Flentje Michael 
Published: January 2020

Abstract
Background
Phosphorylated histone H2AX, also known as γH2AX, forms μm-sized nuclear foci at the sites of DNA double-strand breaks (DSBs) induced by ionizing radiation and other agents. Due to their specificity and sensitivity, γH2AX immunoassays have become the gold standard for studying DSB induction and repair. One of these assays relies on the immunofluorescent staining of γH2AX followed by microscopic imaging and foci counting. During the last years, semi- and fully automated image analysis, capable of fast detection and quantification of γH2AX foci in large datasets of fluorescence images, are gradually replacing the traditional method of manual foci counting. A major drawback of the non-commercial software for foci counting (available so far) is that they are restricted to 2D-image data. In practice, these algorithms are useful for counting the foci located close to the midsection plane of the nucleus, while the out-of-plane foci are neglected.

Results
To overcome the limitations of 2D foci counting, we present a freely available ImageJ-based plugin (FocAn) for automated 3D analysis of γH2AX foci in z-image stacks acquired by confocal fluorescence microscopy. The image-stack processing algorithm implemented in FocAn is capable of automatic 3D recognition of individual cell nuclei and γH2AX foci, as well as evaluation of the total foci number per cell nucleus. The FocAn algorithm consists of two parts: nucleus identification and foci detection, each employing specific sequences of auto local thresholding in combination with watershed segmentation techniques. We validated the FocAn algorithm using fluorescence-labeled γH2AX in two glioblastoma cell lines, irradiated with 2 Gy and given up to 24 h post-irradiation for repair. We found that the data obtained with FocAn agreed well with those obtained with an already available software (FoCo) and manual counting. Moreover, FocAn was capable of identifying overlapping foci in 3D space, which ensured accurate foci counting even at high DSB density of up to ~ 200 DSB/nucleus.

Conclusions
FocAn is freely available an open-source 3D foci analyzer. The user-friendly algorithm FocAn requires little supervision and can automatically count the amount of DNA-DSBs, i.e. fluorescence-labeled γH2AX foci, in 3D image stacks acquired by laser-scanning microscopes without additional nuclei staining.
Gene expression identifies metabolic and functional differences between intramuscular and subcutaneous adipocytes in cattle
Authors: Hudson Nicholas J. , Reverter Antonio , Griffiths William J. , Yutuc Eylan , Wang Yuqin , Jeanes Angela , McWilliam Sean , Pethick David W. , Greenwood Paul L. 
Published: January 2020

Abstract
Background
This study used a genome-wide screen of gene expression to better understand the metabolic and functional differences between commercially valuable intramuscular fat (IMF) and commercially wasteful subcutaneous (SC) fat depots in Bos taurus beef cattle.

Results
We confirmed many findings previously made at the biochemical level and made new discoveries. The fundamental lipogenic machinery, such as ACACA and FASN encoding the rate limiting Acetyl CoA carboxylase and Fatty Acid synthase were expressed at 1.6–1.8 fold lower levels in IMF, consistent with previous findings. The FA elongation pathway including the rate limiting ELOVL6 was also coordinately downregulated in IMF compared to SC as expected. A 2-fold lower expression in IMF of ACSS2 encoding Acetyl Coenzyme A synthetase is consistent with utilisation of less acetate for lipogenesis in IMF compared to SC as previously determined using radioisotope incorporation. Reduced saturation of fat in the SC depot is reflected by 2.4 fold higher expression of the SCD gene encoding the Δ9 desaturase enzyme. Surprisingly, CH25H encoding the cholesterol 25 hydroxylase enzyme was ~ 36 fold upregulated in IMF compared to SC. Moreover, its expression in whole muscle tissue appears representative of the proportional representation of bovine marbling adipocytes. This suite of observations prompted quantification of a set of oxysterols (oxidised forms of cholesterol) in the plasma of 8 cattle exhibiting varying IMF. Using Liquid Chromatography-Mass Spectrometry (LC-MS) we found the levels of several oxysterols were significantly associated with multiple marbling measurements across the musculature, but (with just one exception) no other carcass phenotypes.

Conclusions
These data build on our molecular understanding of ruminant fat depot biology and suggest oxysterols represent a promising circulating biomarker for cattle marbling.
De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism
Authors: Hui Wen-Kai , Zhao Fei-Yan , Wang Jing-Yan , Chen Xiao-Yang , Li Jue-Wei , Zhong Yu , Li Hong-Yun , Zheng Jun-Xing , Zhang Liang-Zhen , Que Qing-Min , Wu Ai-Min , Gong Wei 
Published: January 2020

Abstract
Background
Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species.

Results
Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage).

Conclusions
The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.
Deconstructing the genetic architecture of iron deficiency chlorosis in soybean using genome-wide approaches
Authors: Assefa Teshale , Zhang Jiaoping , Chowda-Reddy R. V. , Moran Lauter Adrienne N. , Singh Arti , O’Rourke Jamie A. , Graham Michelle A. , Singh Asheesh K. 
Published: January 2020

Abstract
Background
Iron (Fe) is an essential micronutrient for plant growth and development. Iron deficiency chlorosis (IDC), caused by calcareous soils or high soil pH, can limit iron availability, negatively affecting soybean (Glycine max) yield. This study leverages genome-wide association study (GWAS) and a genome-wide epistatic study (GWES) with previous gene expression studies to identify regions of the soybean genome important in iron deficiency tolerance.

Results
A GWAS and a GWES were performed using 460 diverse soybean PI lines from 27 countries, in field and hydroponic iron stress conditions, using more than 36,000 single nucleotide polymorphism (SNP) markers. Combining this approach with available RNA-sequencing data identified significant markers, genomic regions, and novel genes associated with or responding to iron deficiency. Sixty-nine genomic regions associated with IDC tolerance were identified across 19 chromosomes via the GWAS, including the major-effect quantitative trait locus (QTL) on chromosome Gm03. Cluster analysis of significant SNPs in this region deconstructed this historically prominent QTL into four distinct linkage blocks, enabling the identification of multiple candidate genes for iron chlorosis tolerance. The complementary GWES identified SNPs in this region interacting with nine other genomic regions, providing the first evidence of epistatic interactions impacting iron deficiency tolerance.

Conclusions
This study demonstrates that integrating cutting edge genome wide association (GWA), genome wide epistasis (GWE), and gene expression studies is a powerful strategy to identify novel iron tolerance QTL and candidate loci from diverse germplasm. Crops, unlike model species, have undergone selection for thousands of years, constraining and/or enhancing stress responses. Leveraging genomics-enabled approaches to study these adaptations is essential for future crop improvement.
Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum
Authors: Chen Dong-Hong , Qiu Han-Lin , Huang Yong , Zhang Lei , Si Jin-Ping 
Published: January 2020

Abstract
Background
Dendrobium catenatum, as a precious Chinese herbal medicine, is an epiphytic orchid plant, which grows on the trunks and cliffs and often faces up to diverse environmental stresses. SET DOMAIN GROUP (SDG) proteins act as histone lysine methyltransferases, which are involved in pleiotropic developmental events and stress responses through modifying chromatin structure and regulating gene transcription, but their roles in D. catenatum are unknown.

Results
In this study, we identified 44 SDG proteins from D. catenatum genome. Subsequently, comprehensive analyses related to gene structure, protein domain organization, and phylogenetic relationship were performed to evaluate these D. catenatum SDG (DcSDG) proteins, along with the well-investigated homologs from the model plants Arabidopsis thaliana and Oryza sativa as well as the newly characterized 42 SDG proteins from a closely related orchid plant Phalaenopsis equestris. We showed DcSDG proteins can be grouped into eight distinct classes (I~VII and M), mostly consistent with the previous description. Based on the catalytic substrates of the reported SDG members mainly in Arabidopsis, Class I (E(z)-Like) is predicted to account for the deposition of H3K27me2/3, Class II (Ash-like) for H3K36me, Class III (Trx/ATX-like) for H3K4me2/3, Class M (ATXR3/7) for H3K4me, Class IV (Su (var)-like) for H3K27me1, Class V (Suv-like) for H3K9me, as well as class VI (S-ET) and class VII (RBCMT) for methylation of both histone and non-histone proteins. RNA-seq derived expression profiling showed that DcSDG proteins usually displayed wide but distinguished expressions in different tissues and organs. Finally, environmental stresses examination showed the expressions of DcASHR3, DcSUVR3, DcATXR4, DcATXR5b, and DcSDG49 are closely associated with drought-recovery treatment, the expression of DcSUVH5a, DcATXR5a and DcSUVR14a are significantly influenced by low temperature, and even 61% DcSDG genes are in response to heat shock.

Conclusions
This study systematically identifies and classifies SDG genes in orchid plant D. catenatum, indicates their functional divergence during the evolution, and discovers their broad roles in the developmental programs and stress responses. These results provide constructive clues for further functional investigation and epigenetic mechanism dissection of SET-containing proteins in orchids.
Flow-controlled ventilation (FCV) improves regional ventilation in obese patients – a randomized controlled crossover trial
Authors: Weber Jonas , Straka Leonie , Borgmann Silke , Schmidt Johannes , Wirth Steffen , Schumann Stefan 
Published: January 2020

AbstractBackgroundIn obese patients, high closing capacity and low functional residual capacity increase the risk for expiratory alveolar collapse. Constant expiratory flow, as provided by the new flow-controlled ventilation (FCV) mode, was shown to improve lung recruitment. We hypothesized that lung aeration and respiratory mechanics improve in obese patients during FCV.MethodsWe compared FCV and volume-controlled (VCV) ventilation in 23 obese patients in a randomized crossover setting. Starting with baseline measurements, ventilation settings were kept identical except for the ventilation mode related differences (VCV: inspiration to expiration ratio 1:2 with passive expiration, FCV: inspiration to expiration ratio 1:1 with active, linearized expiration). Primary endpoint of the study was the change of end-expiratory lung volume compared to baseline ventilation. Secondary endpoints were the change of mean lung volume, respiratory mechanics and hemodynamic variables.ResultsThe loss of end-expiratory lung volume and mean lung volume compared to baseline was lower during FCV compared to VCV (end-expiratory lung volume: FCV, − 126 ± 207 ml; VCV, − 316 ± 254 ml;p < 0.001, mean lung volume: FCV, − 108.2 ± 198.6 ml; VCV, − 315.8 ± 252.1 ml;p < 0.001) and at comparable plateau pressure (baseline, 19.6 ± 3.7; VCV, 20.2 ± 3.4; FCV, 20.2 ± 3.8 cmH2O;p = 0.441), mean tracheal pressure was higher (baseline, 13.1 ± 1.1; VCV, 12.9 ± 1.2; FCV, 14.8 ± 2.2 cmH2O;p < 0.001). All other respiratory and hemodynamic variables were comparable between the ventilation modes.ConclusionsThis study demonstrates that, compared to VCV, FCV improves regional ventilation distribution of the lung at comparable PEEP, tidal volume, PPlatand ventilation frequency. The increase in end-expiratory lung volume during FCV was probably caused by the increased mean tracheal pressure which can be attributed to the linearized expiratory pressure decline.Trial registrationGerman Clinical Trials Register:DRKS00014925. Registered 12 July 2018.
Prevalence and multivariable factors associated with inadvertent intraoperative hypothermia in video-assisted thoracoscopic surgery: a single-center retrospective study
Authors: Li Yinan , Liang Hansheng , Feng Yi 
Published: January 2020

Abstract
Background
Inadvertent intraoperative hypothermia increases the risk of adverse events, but its related risk factors have not been defined in video-assisted thoracoscopic surgery (VATS). This study aimed at analyzing the prevalence and factors related to inadvertent intraoperative hypothermia in adults undergoing elective VATS under general anesthesia.

Methods
This was a retrospective study using data from the Peking University People’s Hospital from January through December, 2018. Data were collected on age, sex, height, weight, American Society of Anesthesiologists physical status, the duration of preparation and surgery, timing of surgery, surgery types, anesthesia types, intraoperative core temperature and the length of stay (LOS) in the hospital from the electronic database in our center. Patients were covered with a cotton blanket preoperatively and the surgical draping during the operation. A circulation-water warming mattress set to 38 °C were placed under the body of the patients. Inadvertent intraoperative hypothermia was identified as a core temperature monitored in nasopharynx < 36 °C. Multivariate logistic regression analysis was used to identify independent risk factors of hypothermia.

Results
We found that 72.7% (95% CI 70.5 to 75.0%) of 1467 adult patients who underwent VATS suffered hypothermia during surgery. The factors associated with inadvertent intraoperative hypothermia included age (OR = 1.23, 95% CI 1.11 to 1.36, p < 0.001), BMI (OR = 1.83, 95% CI 1.43 to 2.35, p < 0.001), the duration of preparation (OR = 1.01, 95% CI 1.00 to 1.02, p = 0.014), the duration of surgery (OR = 2.10, 95% CI 1.63 to 2.70, p < 0.001), timing of surgery (OR = 1.64, 95% CI 1.28 to 2.12, p < 0.001), ambient temperature in the operating room (OR = 0.67, 95% CI 0.53 to 0.85, p = 0.001) and general anesthesia combined with paravertebral block after induction of anesthesia (OR = 2.30, 95% CI 1.31 to 4.03, p = 0.004). The average LOS in the hospital in the hypothermia group and the normothemic group was 9 days and 8 days, respectively (p < 0.001).

Conclusions
We highlight the high prevalence of inadvertent intraoperative hypothermia during elective VATS and identify key risk factors including age, duration of surgery more than 2 h, surgery in the morning and general anesthesia combined with paravertebral block (PVB) after intubation. We also find that hypothermia did prolong the LOS in the hospital.
Health mediators as members of multidisciplinary group practice: lessons learned from a primary health care model programme in Hungary
Authors: Kósa Karolina , Katona Cintia , Papp Magor , Fürjes Gergely , Sándor János , Bíró Klára , Ádány Róza 
Published: January 2020

Abstract
Background
A Model Programme of primary care group practices was implemented in Hungary between 2013 and 2017 – where virtually all GPs had worked in single practices – aiming to increase preventive service uptake and reduce inequalities based on a bilateral agreement between the Swiss and Hungarian governments. Group practices employed a wide variety of health professionals as well as support workers called health mediators. Employment of the latter was based on two decades of European experience of health mediators who specifically facilitate access to and use of health services in Roma minority groups. Health mediators had been recruited from local communities, received training on the job, and were tasked to increase uptake of new preventive services provided by the group practices by personal contacts in the local minority populace. The paper describes the contribution of the work of health mediators to the uptake of two new services provided by group practices.

Methods
Quantitative analysis of depersonalized administrative data mandatorily reported to the Management of the Programme during 43 months of operation was carried out on the employment of health mediators and their contribution to the uptake of two new preventive services (health status assessment and community health promoting programmes).

Results
80% of all clients registered with the GPs participated at health status assessment by invitation that was 1.3–1.7 times higher than participation at the most successful national screening programmes in the past 15 years. Both the number of mediator work minutes per client and participation rate at health status assessment, as well as total work time of mediators and participants at community health events showed high correlation. Twice as many Roma minority patients were motivated for service use by health mediators compared to all patients. The very high participation rate reflects the wide impact of health mediators who probably reached not only Roma minority, but vulnerable population groups in general.

Conclusion
The future of general practices lays in multidisciplinary teams in which health mediators recruited from the serviced communities can be valuable members, especially in deprived areas.
Poor oral health and mortality in geriatric patients admitted to an acute hospital: an observational study
Authors: Maeda Keisuke , Mori Naoharu 
Published: January 2020

Abstract
Background
Poor oral health at hospital admission is a potential higher mortality risk predictor. We aimed to determine in-hospital mortality by assessing poor oral health using a validated tool.

Methods
A retrospective observational study was conducted in an acute care hospital, and 624 consecutive geriatric patients were included. Patients were divided into three groups according to oral health, stratified by the Oral Health Assessment Tool (OHAT) scores. Nutritional status, daily living activities, cognitive impairment, and comorbidities were collected as covariates. Univariate and multivariate analyses were performed to identify the relationship between oral health and survival.

Results
The mean age was 83.8 ± 7.9 years, and 41% were males. Groups with an OHAT score equivalent to 0, 1–2, and ≥ 3 comprised 213, 206, and 205 patients, and 11 (5.2%), 13 (6.3%), and 37 (18.0%) of those patients died in the hospital, respectively. Patients in the OHAT score ≥ 3 group had higher mortality than those in the other groups (log-rank test: p = 0.012 for the OHAT = 0 group; p = 0.010 for the OHAT = 1–2 group after Bonferroni corrections). Patients in the OHAT score ≥ 3 group continued to have poor survival even after adjusting for confounders in the Cox’s regression analysis (hazard ratio: 2.514, 95% confidence interval: 1.220–5.183, p = 0.012).

Conclusion
In geriatric patients, poor oral health at hospital admission was an independent in-hospital mortality predictor. Future studies on oral care intervention stratified by oral health conditions are warranted.
Schistosoma and Strongyloides screening in migrants initiating HIV Care in Canada: a cross sectional study
Authors: McLellan Jessica , Gill M. John , Vaughan Stephen , Meatherall Bonnie 
Published: January 2020

AbstractBackgroundFollowing migration fromSchistosomaandStrongyloidesendemic to non-endemic regions, people remain at high risk for adverse sequelae from these chronic infections. HIV co-infected persons are particularly vulnerable to the serious and potentially fatal consequences of untreated helminth infection. While general screening guidelines exist for parasitic infection screening in immigrant populations, they remain silent on HIV positive populations. This study assessed the seroprevalence, epidemiology and laboratory characteristics of these two parasitic infections in a non-endemic setting in an immigrant/refugee HIV positive community.MethodsBetween February 2015 and 2018 individuals born outside of Canada receiving care at the centralized HIV clinic serving southern Alberta, Canada were screened by serology and direct stool analysis for schistosomiasis and strongyloidiasis. Canadian born persons with travel-based exposure risk factors were also screened. Epidemiologic and laboratory values were analyzed using bivariate logistic regression. We assessed the screening utility of serology, direct stool analysis, eosinophilia and hematuria.Results253 HIV positive participants were screened. The prevalence of positive serology forSchistosomaandStrongyloideswas 19.9 and 4.4%, respectively. Age between 40 and 50 years (OR 2.50, 95% CI 1.13–5.50), refugee status (3.55, 1.72–7.33), country of origin within Africa (6.15, 2.44–18.60), eosinophilia (3.56, 1.25–10.16) and CD4 count < 200 cells/mm3(2.46, 1.02–5.92) were associated with positiveSchistosomaserology. Eosinophilia (11.31, 2.03–58.94) was associated with positiveStrongyloidesserology. NoSchistosomaorStrongyloidesparasites were identified by direct stool microscopy. Eosinophilia had poor sensitivity for identification of positive serology. Hematuria was not associated with positiveSchistosomaserology.ConclusionPositiveSchistosomaandStrongyloidesserology was common in this migrant HIV positive population receiving HIV care in Southern Alberta. This supports the value of routine parasitic screening as part of standard HIV care in non-endemic areas. Given the high morbidity and mortality in this relatively immunosuppressed population, especially forStrongyloidesinfection, screening should include both serologic and direct parasitological tests. Eosinophilia and hematuria should not be used forSchistosomaandStrongyloidesserologic screening in HIV positive migrants in non-endemic settings.