bluuebunny/crossref_metadata_2025_split huggingface dataset:
What did we learn from our first arthroscopic Trillat procedures? Results, complications and failures in a series of 100 anterior shoulder stabilizations
Authors: Labattut Ludovic , Chauvet Thomas , Colombi Romain , Baulot Emmanuel , Martz Pierre 
Published: February 2021

Objectives: Arthroscopic adaptation of the Trillat procedure has become a part of the armamentarium for anterior shoulder instability. As the first team to have described a surgical technique, we present the results of our first 100 patients. Methods: This is a cohort study on a prospective database, descriptive of patients who had undergone surgery for chronic anterior shoulder instability between March 2011 the date our technique was developed, and October 2019. Patients were clinically and radiologically evaluated preoperatively (standard radiographs, CT scan) and postoperatively (standard radiographs) at 1, 3, 6 and 12 months and by CT scan 6 months postoperatively to evaluate the consolidation of the coracoid fracture and subscapularis muscle trophicity. Functional results were evaluated by Constant, SSV, Walch/Duplay and Rowe scores and recurrences of accidents due to instability and complications were collated. Results: 100 patients, mean follow-up of 25 months (6-96), mean age, 29 years (15-73), 71% sportspeople, mean age at first episode, 20 years (7-59), 20% hyperlaxity. 67% notches, 22% bony Bankart, 15% glenoid wear and 2% rotator cuff tear. The surgical technique was identical, there were 3 operators, average operating time was 50 min (26-145), 70% were ambulatory, there were 13 fractures and no conversion to an open technique. At the last follow-up there were 3 recurrences of luxation and 4 recurrences of subluxation and in 4 cases failure to recover muscle tone was noted. 95% of the sportspersons resumed their activity, 81% at the previous level. One year postoperatively, the Walsh-Duplay score was 88 (40-100) and the Rowe score was 92 (40-100). There were 4 cases of pseudoarthrosis, 3 of which were due to a technical defect, 2 coracoid fractures, 1 case of resolving sepsis and no neurological complications. There was no damage to the subscapularis. 97% of the patients were satisfied or very satisfied. Conclusion: This is the largest available series on the arthroscopic Trillat procedure. The results are identical to those in the preliminary series and as good as those for the reference techniques. Failures and complications were few and often the result of technical errors. The recovery of muscle tone in the limb on which surgery was performed seemed to influence the effectiveness of stabilization.
Complete and partial repair of massive rotator cuff tears provide sustainable long term improvement in clinical scores
Authors: Besnard Marion , Freychet Benjamin , Clechet Julien , Carrillon Yannick , Godenèche Arnaud 
Published: February 2021

Objectives: The aim was to report results of arthroscopic repair of 86 massive cuff tears and decided to assess whether or not clinical scores were maintained 5 years later. Methods: Of the initial series of 86 shoulders, 2 patients died, 16 were lost to follow-up and 4 had a repeat surgery. Therefore, it was possible to reevaluate 64 patients. Repairs were complete in 44 cases and partial in 20 cases. Seventeen shoulders were pseudoparalytic. Tears with fatty degeneration at stage 4 or higher according to the Goutallier classification were not eligible for repair. Preoperatively, the Constant Score (CS), shoulder strength, location of the tear, tendon retraction and degree of fatty infiltration were assessed. Patients were assessed at 8.1±0.6 years [7.1-9.3] using absolute and age- and sex-adjusted CS, the subjective shoulder value (SSV) and the simple shoulder test (SST). Results: The absolute CS was 80.0±11.7 at the first follow-up (at 2-5 years) and decreased to 76.7±10.2 at the last follow-up (at 7-10 years) (p<0.001). The adjusted CS was 99.7±15.9 at the first follow-up and remained at 98.8±15.9 at the last follow-up (ns.). In terms of the other criteria, strength decreased over time (p<0.001) but pain, SSV and SST remained the same. Partial repairs had less strength at the first and last follow-up (p<0.05). Pseudoparalytic shoulders had a lower absolute and adjusted CS at the last follow-up (p<0.05) but the improvement in CS was greater (p=0.014). Conclusion: Partial and complete arthroscopic repair provide good long-term results in patients with massive rotator cuff tears, regardless of the location of the tear, the degree of fat infiltration (I to III according to the Goutallier classification) and even in case of a pseudoparalytic shoulder.
Training and deploying a deep learning model for endoscopic severity grading in ulcerative colitis using multicenter clinical trial data
Authors: Gutierrez Becker Benjamin , Arcadu Filippo , Thalhammer Andreas , Gamez Serna Citlalli , Feehan Owen , Drawnel Faye , Oh Young S. , Prunotto Marco 
Published: February 2021

Introduction: The Mayo Clinic Endoscopic Subscore is a commonly used grading system to assess the severity of ulcerative colitis. Correctly grading colonoscopies using the Mayo Clinic Endoscopic Subscore is a challenging task, with suboptimal rates of interrater and intrarater variability observed even among experienced and sufficiently trained experts. In recent years, several machine learning algorithms have been proposed in an effort to improve the standardization and reproducibility of Mayo Clinic Endoscopic Subscore grading. Methods: Here we propose an end-to-end fully automated system based on deep learning to predict a binary version of the Mayo Clinic Endoscopic Subscore directly from raw colonoscopy videos. Differently from previous studies, the proposed method mimics the assessment done in practice by a gastroenterologist, that is, traversing the whole colonoscopy video, identifying visually informative regions and computing an overall Mayo Clinic Endoscopic Subscore. The proposed deep learning–based system has been trained and deployed on raw colonoscopies using Mayo Clinic Endoscopic Subscore ground truth provided only at the colon section level, without manually selecting frames driving the severity scoring of ulcerative colitis. Results and Conclusion: Our evaluation on 1672 endoscopic videos obtained from a multisite data set obtained from the etrolizumab Phase II Eucalyptus and Phase III Hickory and Laurel clinical trials, show that our proposed methodology can grade endoscopic videos with a high degree of accuracy and robustness (Area Under the Receiver Operating Characteristic Curve = 0.84 for Mayo Clinic Endoscopic Subscore ⩾ 1, 0.85 for Mayo Clinic Endoscopic Subscore ⩾ 2 and 0.85 for Mayo Clinic Endoscopic Subscore ⩾ 3) and reduced amounts of manual annotation. Plain language summary Patient, caregiver and provider thoughts on educational materials about prescribing and medication safety Artificial intelligence can be used to automatically assess full endoscopic videos and estimate the severity of ulcerative colitis. In this work, we present an artificial intelligence algorithm for the automatic grading of ulcerative colitis in full endoscopic videos. Our artificial intelligence models were trained and evaluated on a large and diverse set of colonoscopy videos obtained from concluded clinical trials. We demonstrate not only that artificial intelligence is able to accurately grade full endoscopic videos, but also that using diverse data sets obtained from multiple sites is critical to train robust AI models that could potentially be deployed on real-world data.
A neutrophil activation signature predicts critical illness and mortality in COVID-19
Authors: Meizlish Matthew L. , Pine Alexander B. , Bishai Jason D. , Goshua George , Nadelmann Emily R. , Simonov Michael , Chang C-Hong , Zhang Hanming , Shallow Marcus , Bahel Parveen , Owusu Kent , Yamamoto Yu , Arora Tanima , Atri Deepak S. , Patel Amisha , Gbyli Rana , Kwan Jennifer , Won Christine H. , Dela Cruz Charles , Price Christina , Koff Jonathan , King Brett A. , Rinder Henry M. , Wilson F. Perry , Hwa John , Halene Stephanie , Damsky William , van Dijk David , Lee Alfred I. , Chun Hyung J. 
Published: February 2021

AbstractPathologic immune hyperactivation is emerging as a key feature of critical illness in COVID-19, but the mechanisms involved remain poorly understood. We carried out proteomic profiling of plasma from cross-sectional and longitudinal cohorts of hospitalized patients with COVID-19 and analyzed clinical data from our health system database of more than 3300 patients. Using a machine learning algorithm, we identified a prominent signature of neutrophil activation, including resistin, lipocalin-2, hepatocyte growth factor, interleukin-8, and granulocyte colony-stimulating factor, which were the strongest predictors of critical illness. Evidence of neutrophil activation was present on the first day of hospitalization in patients who would only later require transfer to the intensive care unit, thus preceding the onset of critical illness and predicting increased mortality. In the health system database, early elevations in developing and mature neutrophil counts also predicted higher mortality rates. Altogether, these data suggest a central role for neutrophil activation in the pathogenesis of severe COVID-19 and identify molecular markers that distinguish patients at risk of future clinical decompensation.
Development and validation of a framework for the assessment of school curricula on the presence of evolutionary concepts (FACE)
Authors: Sá-Pinto Xana , Realdon Giulia , Torkar Gregor , Sousa Bruno , Georgiou Martha , Jeffries Alex , Korfiatis Konstantinos , Paolucci Silvia , Pessoa Patrícia , Rocha Joana , Stasinakis Panagiotis K. , Cavadas Bento , Crottini Angelica , Gnidovec Tanja , Nogueira Teresa , Papadopoulou Penelope , Piccoli Costanza , Barstad Johan , Dufour Heloise D. , Pejchinovska Milena , Pobric Alma , Cvetković Dragana , Mavrikaki Evangelia 
Published: February 2021

AbstractEvolution is a key concept of biology, fundamental to understand the world and address important societal problems, but research studies show that it is still not widely understood and accepted. Several factors are known to influence evolution acceptance and understanding, but little information is available regarding the impacts of the curriculum on these aspects. Very few curricula have been examined to assess the coverage of biological evolution. The available studies do not allow comparative analyses, due to the different methodologies employed by the authors. However, such an analysis would be useful for research purposes and for the development of appropriate educational policies to address the problem of a lack of evolution acceptance in some countries. In this paper we describe the steps through which we developed a valid and reliable instrument for curricula analysis known as FACE: “Framework to Assess the Coverage of biological Evolution by school curricula.” This framework was developed based on the “Understanding Evolution Conceptual Framework” (UECF). After an initial pilot study, our framework was reformulated based on identified issues and experts’ opinions. To generate validity and reliability evidence in support of the framework, it was applied to four European countries’ curricula. For each country, a team of a minimum of two national and two foreign coders worked independently to assess the curriculum using this framework for content analysis. Reliability evidence was estimated using Krippendorf's alpha and resulted in appropriate values for coding the examined curricula. Some issues that coders faced during the analysis were discussed and, to ensure better reliability for future researchers, additional guidelines and one extra category were included in the framework. The final version of the framework includes six categories and 34 subcategories. FACE is a useful tool for the analysis and the comparison of curricula and school textbooks regarding the coverage of evolution, and such results can guide curricula development.
The prevalence of psychological distress during pregnancy in Miyagi Prefecture for 3 years after the Great Eas t Japan Earthquake
Authors:   Japan Environment and Children’s Study (JECS) Group, Tanoue Kaou , Watanabe Zen , Nishigori Hidekazu , Iwama Noriyuki , Satoh Michihiro , Murakami Takahisa , Tanaka Kousuke , Sasaki Satomi , Sakurai Kasumi , Ishikuro Mami , Obara Taku , Saito Masatoshi , Sugawara Junichi , Tatsuta Nozomi , Kuriyama Shinichi , Arima Takahiro , Nakai Kunihiko , Yaegashi Nobuo , Metoki Hirohito 
Published: February 2021

Abstract
Background
To examine changes in psychological distress prevalence among pregnant women in Miyagi Prefecture, which was directly affected by the Great East Japan Earthquake and tsunami, and compare it with the other, less damaged areas of Japan.

Methods
This study was conducted in conjunction with the Japan Environment and Children`s Study. We examined 76,152 pregnant women including 8270 in Miyagi Regional Center and 67,882 in 13 other regional centers from the all-birth fixed data of the Japan Environment and Children’s Study. We then compared the prevalence and risk of distress in women in Miyagi Regional Center and women in the 13 regional centers for 3 years after the disaster.

Results
Women in the Miyagi Regional Center suffered more psychological distress than those in the 13 regional centers: OR 1.38 (95% CI, 1.03–1.87) to 1.92 (95% CI, 1.42–2.60). Additionally, women in the inland area had a consistently higher prevalence of psychological distress compared to those from the 13 regional centers: OR 1.67 (95% CI, 1.18–2.38) to 2.19 (95% CI, 1.60–2.99).

Conclusions
The lack of pre-disaster data in the Japan Environment and Children’s Study made it impossible to compare the incidence of psychological distress before and after the March 2011 Great East Japan Earthquake. However, 3 years after the Great East Japan Earthquake, the prevalence of pregnant women with psychological distress did not improve in Miyagi Regional Center. Further, the prevalence of mental illness in inland areas was consistently higher than that in the 13 regional centers after the disaster.
On the use of whole-genome sequence data for across-breed genomic prediction and fine-scale mapping of QTL
Authors: Meuwissen Theo , van den Berg Irene , Goddard Mike 
Published: February 2021

AbstractBackgroundWhole-genome sequence (WGS) data are increasingly available on large numbers of individuals in animal and plant breeding and in human genetics through second-generation resequencing technologies, 1000 genomes projects, and large-scale genotype imputation from lower marker densities. Here, we present a computationally fast implementation of a variable selection genomic prediction method, that could handle WGS data on more than 35,000 individuals, test its accuracy for across-breed predictions and assess its quantitative trait locus (QTL) mapping precision.MethodsThe Monte Carlo Markov chain (MCMC) variable selection model (Bayes GC) fits simultaneously a genomic best linear unbiased prediction (GBLUP) term, i.e. a polygenic effect whose correlations are described by a genomic relationship matrix (G), and a Bayes C term, i.e. a set of single nucleotide polymorphisms (SNPs) with large effects selected by the model. Computational speed is improved by a Metropolis–Hastings sampling that directs computations to the SNPs, which are, a priori, most likely to be included into the model. Speed is also improved by running many relatively short MCMC chains. Memory requirements are reduced by storing the genotype matrix in binary form. The model was tested on a WGS dataset containing Holstein, Jersey and Australian Red cattle. The data contained 4,809,520 genotypes on 35,549 individuals together with their milk, fat and protein yields, and fat and protein percentage traits.ResultsThe prediction accuracies of the Jersey individuals improved by 1.5% when using across-breed GBLUP compared to within-breed predictions. Using WGS instead of 600 k SNP-chip data yielded on average a 3% accuracy improvement for Australian Red cows. QTL were fine-mapped by locating the SNP with the highest posterior probability of being included in the model. Various QTL known from the literature were rediscovered, and a new SNP affecting milk production was discovered on chromosome 20 at 34.501126 Mb. Due to the high mapping precision, it was clear that many of the discovered QTL were the same across the five dairy traits.ConclusionsAcross-breed Bayes GC genomic prediction improved prediction accuracies compared to GBLUP. The combination of across-breed WGS data and Bayesian genomic prediction proved remarkably effective for the fine-mapping of QTL.
Biomedical articles share annotations with their citation neighbors
Authors: Rodriguez-Esteban Raul 
Published: February 2021

Abstract
Background
Numerous efforts have been poured into annotating the wealth of knowledge contained in biomedical articles. Thanks to such efforts, it is now possible to quantitatively explore relations between these annotations and the citation network at large scale.

Results
With the aid of several large and small annotation databases, this study shows that articles share annotations with their citation neighborhood to the point that the neighborhood’s most common annotations are likely to be those appearing in the article.

Conclusions
These findings posit that an article’s citation neighborhood defines to a large extent the article’s annotated content. Thus, citations should be considered as a foundation for future knowledge management and annotation of biomedical articles.
Identification, characterization and functional analysis of grape (Vitis vinifera L.) mitochondrial transcription termination factor (mTERF) genes in responding to biotic stress and exogenous phytohormone
Authors: Yin Xiangjing , Gao Yu , Song Shiren , Hassani Danial , Lu Jiang 
Published: February 2021

Abstract
Background
Mitochondrial transcription termination factor (mTERF) is a large gene family which plays a significant role during plant growth under various environmental stresses. However, knowledge of mTERF genes in grapevine (Vitis L.) is limited.

Results
In this research, a comprehensive analysis of grape mTERF (VvmTERF) genes, including chromosome locations, phylogeny, protein motifs, gene structures, gene duplications, synteny analysis and expression profiles, was conducted. As a result, a total of 25 mTERF genes were identified from the grape genome, which are distributed on 13 chromosomes with diverse densities and segmental duplication events. The grape mTERF gene family is classified into nine clades based on phylogenetic analysis and structural characteristics. These VvmTERF genes showed differential expression patterns in response to multiple phytohormone treatments and biotic stresses, including treatments with abscisic acid and methyl jasmonate, and inoculation of Plasmopara viticola and Erysiphe necator.

Conclusions
These research findings, as the first of its kind in grapevine, will provide useful information for future development of new stress tolerant grape cultivars through genetic manipulation of VvmTERF genes.
The eukaryotic MEP-pathway genes are evolutionarily conserved and originated from Chlaymidia and cyanobacteria
Authors: Zeng Liping , Dehesh Katayoon 
Published: February 2021

Abstract
Background
Isoprenoids are the most ancient and essential class of metabolites produced in all organisms, either via mevalonate (MVA)-and/or methylerythritol phosphate (MEP)-pathways. The MEP-pathway is present in all plastid-bearing organisms and most eubacteria. However, no comprehensive study reveals the origination and evolutionary characteristics of MEP-pathway genes in eukaryotes.

Results
Here, detailed bioinformatics analyses of the MEP-pathway provide an in-depth understanding the evolutionary history of this indispensable biochemical route, and offer a basis for the co-existence of the cytosolic MVA- and plastidial MEP-pathway in plants given the established exchange of the end products between the two isoprenoid-biosynthesis pathways. Here, phylogenetic analyses establish the contributions of both cyanobacteria and Chlamydiae sequences to the plant’s MEP-pathway genes. Moreover, Phylogenetic and inter-species syntenic block analyses demonstrate that six of the seven MEP-pathway genes have predominantly remained as single-copy in land plants in spite of multiple whole-genome duplication events (WGDs). Substitution rate and domain studies display the evolutionary conservation of these genes, reinforced by their high expression levels. Distinct phenotypic variation among plants with reduced expression levels of individual MEP-pathway genes confirm the indispensable function of each nuclear-encoded plastid-targeted MEP-pathway enzyme in plant growth and development.

Conclusion
Collectively, these findings reveal the polyphyletic origin and restrict conservation of MEP-pathway genes, and reinforce the potential function of the individual enzymes beyond production of the isoprenoids intermediates.
Global transcriptional profiling between inbred parents and hybrids provides comprehensive insights into ear-length heterosis of maize (Zea mays)
Authors: Zhang Xiangge , Ma Chenchen , Wang Xiaoqing , Wu Mingbo , Shao Jingkuan , Huang Li , Yuan Liang , Fu Zhiyuan , Li Weihua , Zhang Xuehai , Guo Zhanyong , Tang Jihua 
Published: February 2021

AbstractBackgroundMaize (Zea mays) ear length, which is an important yield component, exhibits strong heterosis. Understanding the potential molecular mechanisms of ear-length heterosis is critical for efficient yield-related breeding.ResultsHere, a joint netted pattern, including six parent-hybrid triplets, was designed on the basis of two maize lines harboring long (T121 line) and short (T126 line) ears. Global transcriptional profiling of young ears (containing meristem) was performed. Multiple comparative analyses revealed that 874 differentially expressed genes are mainly responsible for the ear-length variation between T121 and T126 lines. Among them, four key genes,Zm00001d049958,Zm00001d027359,Zm00001d048502andZm00001d052138, were identified as being related to meristem development, which corroborated their roles in the superior additive genetic effects on ear length in T121 line. Non-additive expression patterns were used to identify candidate genes related to ear-length heterosis. A non-additively expressed gene (Zm00001d050649) was associated with the timing of meristematic phase transition and was determined to be the homolog of tomatoSELF PRUNING, which assistsSINGLE FLOWER TRUSSin driving yield-related heterosis, indicating thatZm00001d050649is a potential contributor to drive heterotic effect on ear length.ConclusionOur results suggest that inbred parents provide genetic and heterotic effects on the ear lengths of their corresponding F1hybrids through two independent pathways. These findings provide comprehensive insights into the transcriptional regulation of ear length and improve the understanding of ear-length heterosis in maize.