bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correction of Cupping Artifacts in Axial Cone-Beam Computed Tomography Images by Using Image Processing Algorithms
Authors: Razi Tahmineh , Manaf Nader Vahdani , Yadekar Morteza , Razi Sedigheh , Gheibi Shiva 
Published: November 2019

Objectives: One of the most important problems of cone-beam computed tomography (CBCT) imaging technique is the presence of dense objects, such as implants, amalgam fillings, and metal veneers, which result in beam-hardening artifacts. With an increase in the application of CBCT images and considering the problems in relation to cupping artifacts, some algorithms have been presented to reduce these artifacts. The aim was to present an algorithm to eliminate cupping artifacts from axial and other reconstructed CBCT images. Materials and Methods: We used CBCT images of NewTom VG imaging system (Verona, Italy, at Dentistry Faculty, Medical Sciences University, Tabriz, Iran) in which every image has a resolution of 366 × 320 in DICOM format. 50 images of patients with cupping artifacts were selected. Using Sobel edge detector and nonlinear gamma correction coefficient, the difference was calculated between the density of axial images in the main image and the image resulting from nonlinear gamma correction at the exact location of the radiopaque dental materials detected by Sobel. The points at which this density difference was out of a definite limit were treated as image artifacts and were eliminated from the main image by the inpainting method. Results: The resultant axial images, for producing reconstructed cross-sectional, panoramic images without cupping artifacts, were imported into NTT viewer V5.6 and utilized. Conclusions: With comparison, acquired images observed that the offering algorithm is practical and effective for reducing the cupping artifacts and preserving the quality of the reconstructed images. This algorithm does not need any additional equipment.
‘This is what we’ve always wanted’: Perspectives on young autistic people’s transition from special school to mainstream satellite classes
Authors: Croydon Abigail , Remington Anna , Kenny Lorcan , Pellicano Elizabeth 
Published: November 2019

Background & aims According to parents, teachers and policymakers alike, including autistic children and young people in mainstream schools is notoriously difficult – especially so for the significant minority of young people on the autism spectrum with additional intellectual, communication and behavioural needs. The current study sought to understand the perceived impact of one particular, emerging model of education, in which selected students from special schools are transferred to dedicated ‘satellite’ classes in local, mainstream partner schools, while continuing to receive the tailored curriculum and specialist teaching of the originating school. Methods We conducted interviews with London-based young autistic people ( n = 19), their parents/carers and teachers to understand their experiences of transitioning from specialist to satellite mainstream provision. Results Participants overwhelmingly welcomed the prospect of transition and its perceived benefits in the short and longer term. Young people and families celebrated achieving access to ‘more normal places and things’, ‘seeing what others are doing’, and greater autonomy, without losing the trusted expert support of their former special school. Young people also felt a deep sense of belonging to their new mainstream school, despite only being minimally included in regular mainstream classes and activities. Teachers were equally positive and felt that their students had responded to higher expectations in their new mainstream schools, reportedly resulting in better behavioural regulation and more sustained attention in the classroom. Conclusions The strikingly positive evaluations provided by all participants suggest that this satellite model of education might have advantages for young autistic people with additional intellectual disability, when appropriate support extends across transition and beyond. Implications These findings shed light on the experiences of an under-researched group of autistic students and a specific model of education – following a needs-based perspective on inclusion – that seeks to extend their participation in local schools. Future research should examine the potential effects of satellite classrooms on the knowledge of, and attitudes toward, autism in non-autistic mainstream peers.
Short- and Long-Term Effects on Knowledge, Skills, and Attitudes About a Sonography Training Concept for Medical Students
Authors: Vennemann Sabrina , Holzmann-Littig Christopher , Marten-Mittag Birgitt , Vo Cong Minh , Berberat Pascal , Stock Konrad 
Published: November 2019

Objectives: Worldwide medical schools that provide sonography training appear to be very heterogeneous in their offerings. A medical school has developed a training program with limited resources, which used a peer teaching method, to provide sonography training. The implemented courses consist of a voluntary laboratory practical and a required didactic seminar. Methods: To analyze this concept, the effects on knowledge, skills, and attitudes were examined by using surveys, multiple-choice tests, and practical tests. Results: The teaching concept demonstrated a positive effect on theoretical knowledge, practical skills, and attitudes. Nevertheless, some practical skills such as conducting gallbladder sonography deteriorated over the time of the study. Discussion: The peer-teaching approach with well-trained students as instructors and tutorials in smaller groups appeared to be a key element for success. This cohort study underlines the need to provide both theoretical and practical mandatory training. Conclusion: Peer teaching may be a cost-effective way to teach sonography skills to medical students during their training.
Differential DNA methylation in bronchial biopsies between persistent asthma and asthma in remission
Authors: Vermeulen Cornelis J. , Xu Cheng-Jian , Vonk Judith M. , ten Hacken Nick H.T. , Timens Wim , Heijink Irene H. , Nawijn Martijn C. , Boekhoudt Jeunard , van Oosterhout Antoon J. , Affleck Karen , Weckmann Markus , Koppelman Gerard H. , van den Berge Maarten 
Published: November 2019

Approximately 40% of asthmatics experience remission of asthma symptoms. A better understanding of biological pathways leading to asthma remission may provide insight into new therapeutic targets for asthma. As an important mechanism of gene regulation, investigation of DNA methylation provides a promising approach. Our objective was to identify differences in epigenome wide DNA methylation levels in bronchial biopsies between subjects with asthma remission and subjects with persistent asthma or healthy controls.We analysed differential DNA methylation in bronchial biopsies from 26 subjects with persistent asthma, 39 remission subjects and 70 healthy controls, using the limma package. The comb-p tool was used to identify differentially methylated regions. DNA methylation of CpG-sites was associated to expression of nearby genes from the same biopsies to understand function.Four CpG-sites and 42 regions were differentially methylated between persistent asthma and remission. DNA methylation at two sites was correlatedinciswith gene expression atACKR2andDGKQ. Between remission subjects and healthy controls 1163 CpG-sites and 328 regions were differentially methylated. DNA methylation was associated with expression of a set of genes expressed in ciliated epithelium.CpGs differentially methylated between remission and persistent asthma identify genetic loci associated with resolution of inflammation and airway responsiveness. Despite the absence of symptoms, remission subjects have a DNA methylation profile that is distinct from that of healthy controls, partly due to changes in cellular composition, with a higher gene expression signal related to ciliated epithelium in remissionversushealthy controls.
Hecaton: reliably detecting copy number variation in plant genomes using short read sequencing data
Authors: Wijfjes Raúl Y. , Smit Sandra , de Ridder Dick 
Published: November 2019

Abstract

Background
Copy number variation (CNV) is thought to actively contribute to adaptive evolution of plant species. While many computational algorithms are available to detect copy number variation from whole genome sequencing datasets, the typical complexity of plant data likely introduces false positive calls.

Results
To enable reliable and comprehensive detection of CNV in plant genomes, we developed Hecaton, a novel computational workflow tailored to plants, that integrates calls from multiple state-of-the-art algorithms through a machine-learning approach. In this paper, we demonstrate that Hecaton outperforms current methods when applied to short read sequencing data of Arabidopsis thaliana, rice, maize, and tomato. Moreover, it correctly detects dispersed duplications, a type of CNV commonly found in plant species, in contrast to several state-of-the-art tools that erroneously represent this type of CNV as overlapping deletions and tandem duplications. Finally, Hecaton scales well in terms of memory usage and running time when applied to short read datasets of domesticated and wild tomato accessions.

Conclusions
Hecaton provides a robust method to detect CNV in plants. We expect it to be of immediate interest to both applied and fundamental research on the relationship between genotype and phenotype in plants.
Integrative analysis of transcriptomic data related to the liver of laying hens: from physiological basics to newly identified functions
Authors: Gloux Audrey , Duclos Michel J. , Brionne Aurélien , Bourin Marie , Nys Yves , Réhault-Godbert Sophie 
Published: November 2019

AbstractBackgroundAt sexual maturity, the liver of laying hens undergoes many metabolic changes to support vitellogenesis. In published transcriptomic approaches, hundreds of genes were reported to be overexpressed in laying hens and functional gene annotation using gene ontology tools have essentially revealed an enrichment in lipid and protein metabolisms. We reanalyzed some data from a previously published article comparing 38-week old versus 10-week old hens to give a more integrative view of the functions stimulated in the liver at sexual maturity and to move beyond current physiological knowledge. Functions were defined based on information available in Uniprot database and published literature.ResultsOf the 516 genes previously shown to be overexpressed in the liver of laying hens, 475 were intracellular (1.23–50.72 fold changes), while only 36 were predicted to be secreted (1.35–66.93 fold changes) and 5 had no related information on their cellular location. Besides lipogenesis and protein metabolism, we demonstrated that the liver of laying hens overexpresses several clock genes (which supports the circadian control of liver metabolic functions) and was likely to be involved in a liver/brain/liver circuit (neurotransmitter transport), in thyroid and steroid hormones metabolisms. Many genes were associated with anatomical structure development, organ homeostasis but also regulation of blood pressure. As expected, several secreted proteins are incorporated in yolky follicles but we also evidenced that some proteins are likely participating in fertilization (ZP1, MFGE8, LINC00954, OVOCH1) and in thyroid hormone maturation (CPQ). We also proposed that secreted proteins (PHOSPHO1, FGF23, BMP7 but also vitamin-binding proteins) may contribute to the development of peripheral organs including the formation of medullar bones to provide labile calcium for eggshell formation. Thirteen genes are uniquely found in chicken/bird but not in human species, which strengthens that some of these genes may be specifically related to avian reproduction.ConclusionsThis study gives additional hypotheses on some molecular actors and mechanisms that are involved in basic physiological function of the liver at sexual maturity of hen. It also revealed some additional functions that accompany reproductive capacities of laying hens, and that are usually underestimated when using classical gene ontology approaches.
Analysis of pooled genome sequences from Djallonke and Sahelian sheep of Ghana reveals co-localisation of regions of reduced heterozygosity with candidate genes for disease resistance and adaptation to a tropical environment
Authors: Yaro M. , Munyard K. A. , Morgan E. , Allcock R. J. N. , Stear M. J. , Groth D. M. 
Published: November 2019

Abstract

Background
The Djallonke sheep is well adapted to harsh environmental conditions, and is relatively resistant to Haemonchosis and resilient to animal trypanosomiasis. The larger Sahelian sheep, which cohabit the same region, is less well adapted to these disease challenges. Haemonchosis and Trypanosomiasis collectively cost the worldwide animal industry billions of dollars in production losses annually.

Results
Here, we separately sequenced and then pooled according to breed the genomes from five unrelated individuals from each of the Djallonke and Sahelian sheep breeds (sourced from Ghana), at greater than 22-fold combined coverage for each breed. A total of approximately 404 million (97%) and 343 million (97%) sequence reads from the Djallonke and Sahelian breeds respectively, were successfully mapped to the sheep reference genome Oar v3.1. We identified approximately 11.1 million and 10.9 million single nucleotide polymorphisms (SNPs) in the Djallonke and Sahelian breeds, with approximately 15 and 16% respectively of these not previously reported in sheep. Multiple regions of reduced heterozygosity were also found; 70 co-localised within genomic regions harbouring genes that mediate disease resistance, immune response and adaptation in sheep or cattle. Thirty- three of the regions of reduced heterozygosity co-localised with previously reported genes for resistance to haemonchosis and trypanosomiasis.

Conclusions
Our analyses suggest that these regions of reduced heterozygosity may be signatures of selection for these economically important diseases.
Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.)
Authors: Qiu Lihang , Chen Rongfa , Fan Yegeng , Huang Xing , Luo Hanmin , Xiong Faqian , Liu Junxian , Zhang Ronghua , Lei Jingchao , Zhou Huiwen , Wu Jianming , Li Yangrui 
Published: November 2019

Abstract

Background
Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied.

Results
Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane.

Conclusions
The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.
Routine frailty assessment predicts postoperative complications in elderly patients across surgical disciplines – a retrospective observational study
Authors: Birkelbach Oliver , Mörgeli Rudolf , Spies Claudia , Olbert Maria , Weiss Björn , Brauner Maximilian , Neuner Bruno , Francis Roland C. E. , Treskatsch Sascha , Balzer Felix 
Published: November 2019

Abstract

Background
Frailty is a frequent and underdiagnosed functional syndrome involving reduced physiological reserves and an increased vulnerability against stressors, with severe individual and socioeconomic consequences. A routine frailty assessment was implemented at our preoperative anaesthesia clinic to identify patients at risk.

Objective
This study examines the relationship between frailty status and the incidence of in-hospital postoperative complications in elderly surgical patients across several surgical disciplines.

Design
Retrospective observational analysis.

Setting
Single center, major tertiary care university hospital. Data collection took place between June 2016 and March 2017.

Patients
Patients 65 years old or older were evaluated for frailty using Fried’s 5-point frailty assessment prior to elective non-cardiac surgery. Patients were classified into non-frail (0 criteria, reference group), pre-frail (1–2 positive criteria) and frail (3–5 positive criteria) groups.

Main outcome measures
The incidence of postoperative complications was assessed until discharge from the hospital, using the roster from the National VA Surgical Quality Improvement Program. Propensity score matching and logistic regression analysis were performed.

Results
From 1186 elderly patients, 46.9% were classified as pre-frail (n = 556), and 11.4% as frail (n = 135). The rate of complications were significantly higher in the pre-frail (34.7%) and frail groups (47.4%), as compared to the non-frail group (27.5%). Similarly, length of stay (non-frail: 5.0 [3.0;7.0], pre-frail: 7.0 [3.0;9.0], frail 8.0 [4.5;12.0]; p < 0.001) and discharges to care facilities (non-frail:1.6%, pre-frail: 7.4%, frail: 17.8%); p < 0.001) were significantly associated with frailty status. After propensity score matching and logistic regression analysis, the risk for developing postoperative complications was approximately two-fold for pre-frail (OR 1.78; 95% CI 1.04–3.05) and frail (OR 2.08; 95% CI 1.21–3.60) patients.

Conclusions
The preoperative frailty assessment of elderly patients identified pre-frail and frail subgroups to have the highest rate of postoperative complications, regardless of age, surgical discipline, and surgical risk. Significantly increased length of hospitalisation and discharges to care facilities were also observed. Implementation of routine frailty assessments appear to be an effective tool in identifying patients with increased risk. Now future studies are needed to investigate whether patients benefit from optimization of patient counselling, process planning, and risk reduction protocols based on the application of risk stratification.
Predictors of mortality and validation of burn mortality prognostic scores in a Malaysian burns intensive care unit
Authors: Lip Henry Tan Chor , Idris Mohamad Azim Md. , Imran Farrah-Hani , Azmah Tuan Nur’ , Huei Tan Jih , Thomas Mathew 
Published: November 2019

Abstract

Background
Majority burn mortality prognostic scores were developed and validated in western populations. The primary objective of this study was to evaluate and identify possible risk factors which may be used to predict burns mortality in a local Malaysian burns intensive care unit. The secondary objective was to validate the five well known burn prognostic scores (Baux score, Abbreviated Burn Severity Index (ABSI) score, Ryan score, Belgium Outcome Burn Injury (BOBI) score and revised Baux score) to predict burn mortality prediction.

Methods
Patients that were treated at the Hospital Sultan Ismail’s Burns Intensive Care (BICU) unit for acute burn injuries between 1 January 2010 to 31 December 2017 were included. Risk factors to predict in-patient burn mortality were gender, age, mechanism of injury, total body surface area burn (TBSA), inhalational injury, mechanical ventilation, presence of tracheotomy, time from of burn injury to BICU admission and initial centre of first emergency treatment was administered. These variables were analysed using univariate and multivariate analysis for the outcomes of death. All patients were scored retrospectively using the five-burn mortality prognostic scores. Predictive ability for burn mortality was analysed using the area under receiver operating curve (AUROC).

Results
A total of 525 patients (372 males and 153 females) with mean age of 34.5 ± 14.6 years were included. There were 463 survivors and 62 deaths (11.8% mortality rate). The outcome of the primary objective showed that amongst the burn mortality risk factors that remained after multivariate analysis were older age (p = 0.004), wider TBSA burn (p < 0.001) and presence of mechanical ventilation (p < 0.001). Outcome of secondary objective showed good AUROC value for the prediction of burn death for all five burn prediction scores (Baux score; AUROC:0.9, ABSI score; AUROC:0.92, Ryan score; AUROC:0.87, BOBI score; AUROC:0.91 and revised Baux score; AUROC:0.94). The revised Baux score had the best AUROC value of 0.94 to predict burns mortality.

Conclusion
Current study evaluated and identified older age, total body surface area burns, and mechanical ventilation as significant predictors of burn mortality. In addition, the revised Baux score was the most accurate burn mortality risk score to predict mortality in a Malaysian burn’s population.
Different mechanisms of two anti-anthrax protective antigen antibodies and function comparison between them
Authors: Xiong Siping , Zhou Tingting , Zheng Feng , Liang Xudong , Cao Yongping , Wang Chunhui , Feng Zhengqin , Tang Qi , Zhu Jin 
Published: November 2019

Abstract

Background
Bacillus anthracis causes a highly lethal infectious disease primarily due to toxin-mediated injury. Antibiotics are no longer effective to treat the accumulation of anthrax toxin, thereby new strategies of antibody treatment are essential. Two anti- anthrax protective antigen (PA) antibodies, hmPA6 and PA21, have been reported by our lab previously.

Methods
The mechanisms of the two antibodies were elucidated by Electrophoresis, Competitive Enzyme-linked immune sorbent assay, Western blot analysis and immunoprecipitation test, and in vitro, in vivo (F344 rats) treatment test. The epitopes of the two antibodies were proved by Western blot and Enzyme-linked immune sorbent assay with different domains of PA.

Results
In this study, we compared affinity and neutralization of these two antibodies. PA21 was better in protecting cells and rats, whereas hmPA6 had higher affinity. Furthermore, the neutralization mechanisms of the two antibodies and their recognition domains of PA were studied. The results showed that hmPA6 recognized domain IV, thus PA could not bind to cell receptors. Conversely, PA21 recognized domain II, thereby limiting heptamer oligomerization of PA63 in cells.

Conclusions
Our studies elucidated the mechanisms and epitopes of hmPA6 and PA21. The present investigation can advance future use of the two antibodies in anthrax treatment or prophylaxis, and potentially as a combination treatment as the antibodies target different epitopes.