bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treatment of Distal Forearm Fractures in Children
Authors: Sinikumpu J.-J. , Nietosvaara Y. 
Published: December 2020

Background and Aims: Distal forearm is the most common fracture location in the growing skeleton. The aim of this article is to describe the current practice of these fractures. Materials and Methods: Case series accompanied by experts’ opinion. Results and Conclusion: Most of these injuries are benign incomplete distal metaphyseal torus fractures best treated with a dorsal below elbow splint for 2–3 weeks with no follow-up. Completely displaced metaphyseal fractures in prepubertal children can be either immobilized in bayonet position after axial alignment or fixed with K-wires after reduction. Complete fractures of distal metaphysis in adolescents should heal in near anatomic alignment because remodeling is uncertain. We advocate reduction of most greenstick and complete fractures at the distal metaphyseal diaphyseal junction and radiographic follow-up to monitor fracture alignment. Physeal fractures in adolescents and intra-articular fractures in children of all ages should be anatomically reduced. We perform most of our osteosyntheses with K-wires.
The meaning of autonomy when living with dementia: A Q-method investigation
Authors: Wolfe Sarah E , Greenhill Beth , Butchard Sarah , Day Jennie 
Published: December 2020

Background and Aims Sensitivity to the rights of people with dementia is a key principle cited in the World Health Organisation’s global action plan on dementia. Some critics question whether rights-based approaches embody loose and ill-defined ideas incapable of bringing about meaningful change. Exercising the right to autonomy is considered a core problem for people living with dementia. The tradition of individual sovereignty dominates ideas about autonomy, although the person as an individual is not a cross-culturally universal concept. This study explored the viewpoints of people with dementia and family carers regarding the meaning of autonomy with a view to informing rights-based practice. Methods Twenty participants, people living with dementia and family carers, each conducted a Q-sort of statements regarding the meaning of autonomy. A by-person factor analysis was used to identify patterns in how the range of statements about autonomy were ranked. Results Three factors emerged: retaining independence and self-expression, accepting dependence but being included and opportunity for connection. There was some agreement across these different views regarding the importance of being given time to think before making decisions and being kept active. Conclusions This study highlights the need for a person-centred approach to supporting people with dementia to claim their rights and the importance of adopting a stance of curiosity and critical thinking in rights-based training and professional practice. The findings suggest a variety of meaningful stories of autonomy and the possibility of further developing existing rights-based frameworks for dementia care.
Complementary and Alternative Medicine Use in Breast Cancer Patients at a Medical Center in Taiwan: A Cross-Sectional Study
Authors: Chin Chieh-Ying , Chen Yung-Hsiang , Wu Shin-Chung , Liu Chien-Ting , Lee Yun-Fang , Tsai Ming-Yen 
Published: December 2020

Background Complementary and alternative medicine (CAM) is becoming more common in medical practice, but little is known about the concurrent use of CAM and conventional treatment. Therefore, the aim was to investigate the types of CAM used and their prevalence in a regional patient cohort with breast cancer (BC). Methods BC patients were interviewed with a structured questionnaire survey on the use of CAM in southern Taiwan at an Integrative Breast Cancer Center (IBCC). The National Centre for Complementary and Integrative Health (NCCIH) classification was used to group responses. Over a period of 8 months, all patients receiving treatment for cancer at the IBCC were approached. Results A total of 106 BC patients completed the survey (response rate: 79.7%). The prevalence of CAM use was 82.4%. Patients who were employed, were receiving radiotherapy and hormone therapy, and had cancer for a longer duration were more likely to use CAM ( P < .05). Multivariate analysis identified employment as an independent predictor of CAM use (OR = 6.92; 95% CI = 1.33-36.15). Dietary supplementation (n = 69, 82.1%) was the type of CAM most frequently used, followed by exercise (n = 48, 57.1%) and traditional Chinese medicine (n = 29, 34.5%). The main reason for using CAM was to ameliorate the side effects of conventional therapies. Almost half (46.4%) of these CAM users did not disclose that they were using it in medical consultations with their physicians. Most chose to use CAM due to recommendations from family and friends. Conclusion A large portion of BC patients at the IBCC undergoing anti-cancer treatment courses used CAM, but less than half discussed it with their physicians. Given the high prevalence of CAM, it would be justifiable to direct further resources toward this service so that cancer patients can benefit from a holistic approach to their treatment.
Systematic Review of Sleep Quality Before and After Arthroscopic Rotator Cuff Repair: Are Improvements Experienced and Maintained?
Authors: Kunze Kyle N. , Movasagghi Kamran , Rossi David M. , Polce Evan M. , Cohn Matthew R. , Karhade Aditya V. , Chahla Jorge 
Published: December 2020

Background: Poor sleep quality is prevalent among patients with rotator cuff tears (RCTs) and negatively influences the potential for healing and quality of life. However, there is a paucity of literature describing the magnitude and timing of changes in sleep quality after arthroscopic rotator cuff repair (RCR). Purpose: (1) To evaluate the prevalence of poor sleep quality in patients undergoing arthroscopic RCR and (2) to determine the timing and magnitude of changes in sleep quality after RCR. Study Design: Systematic review; Level of evidence, 4. Methods: PubMed, OVID/Medline, and Cochrane databases were queried in January 2020 for literature investigating the prevalence of poor sleep quality in patients with RCTs or changes in sleep quality after arthroscopic RCR. Data pertaining to study characteristics, risk of bias, sleep quality assessments, and clinical outcomes were extracted. A qualitative analysis of the prevalence of poor sleep quality and changes in sleep quality was performed. Results: A total of 8 studies (1034 patients) were included. The mean Pittsburgh Sleep Quality Index (PSQI) ranged from 5.2 to 15.0 preoperatively among all studies, while the frequency of patients experiencing poor sleep quality ranged from 40.8% to 89.0% in 4 studies. Four studies reported the mean PSQI at a minimum of 6 months postoperatively, which ranged from 4.2 to 7.1. Four studies did not report the PSQI score or the proportion of patients who experienced poor postoperative sleep quality. One study evaluated the PSQI at 12 months postoperatively, which decreased to 4.2 from 5.8 at 6 months. One study evaluated the PSQI at 24 months postoperatively, which decreased to 5.5 from 6.2 at 6 months. Conclusion: Patients with RCTs have a high prevalence of poor sleep quality. Consistent improvements in sleep quality are observed in the 6 months after arthroscopic RCR, but there is limited evidence based on the available data to characterize changes in sleep quality beyond this time. More evidence is needed to characterize changes in sleep quality beyond 6 months and how these changes are perceived by this patient population.
The City as Museum: Guwahati’s Biodiversity Heritage as an Urban Opportunity
Authors: Pasari Mudita 
Published: December 2020

Between the dialectic of nature and human intervention, we often discover ourselves being stuck between extremes. To see human intervention as either completely good or bad is a reductionist view which the author challenges through her work. She accepts that concepts like climate change are slow processes, invisible in short time spans, hence difficult to grasp by humans. Her work strives to bring observation of change through positive reinforcement of small human actions which can have a beneficial ecological impact. Using this method to encourage seeing as a tool to believing, the author has developed a relatability model which has proved effective in her work, so far. In this article, she presents the model in the context of a pilot project conducted in Guwahati, Assam. The project documents a few endangered and common animal species in the city, hoping to highlight the coexistence of these as a form of natural heritage.
Impacts of Inflammation‐Based Prognostic Scores on Survival in Patients With Hypopharyngeal Squamous Cell Carcinoma
Authors: Iuchi Hiroyuki , Kyutoku Takayuki , Ito Kotoko , Matsumoto Hayato , Ohori Junichiro , Yamashita Masaru 
Published: December 2020

ObjectiveTo investigate the predictive accuracies of the modified Glasgow Prognostic Score (mGPS), neutrophil‐lymphocyte ratio (NLR), and platelet‐lymphocyte ratio (PLR) as prognostic factors for patients with hypopharyngeal squamous cell carcinoma (HSCC).Study DesignRetrospective study.SettingUniversity hospital.MethodsThe records of 106 patients who were histologically diagnosed with HSCC between January 2007 and December 2017 were reviewed. mGPS, NLR, and PLR were analyzed; univariate and multivariate analyses were performed to evaluate the prognosis of overall survival (OS).ResultsThe overall 5‐year survival rates of patients with mGPS0, mGPS1, and mGPS2 were 82.0%, 41.9%, and 13.5%, respectively. The overall 5‐year survival rates of patients with low and high NLRs and with low and high PLRs were 83.8%, 46.2%, 57.0%, and 59.1%, respectively. mGPS (P <. 001) and NLR (P <. 05) were independently associated with OS, whereas PLR was not. For stage IV HSCC, only mGPS was independently associated with OS (P =. 004).ConclusionmGPS is an excellent prognostic factor for patients with HSCC.
COVID-19—The Pandemic of the 21st Century and Correlation With Cardiovascular System—A Single Center Experience
Authors: Modi Ranjan , Khetrapal Shaan , Modi Sunil , Singh Abhishek Vikram , Mishra Nikesh 
Published: December 2020

Objective: To analyze the data of the cardiac comorbidities, investigational modalities, laboratory parameters, and outcomes of patients with COVID-19 related to cardiovascular system hospitalized in our center. Methods: Confirmed cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) COVID-19 infection by positive result on polymerase chain reaction testing of a nasopharyngeal sample, who were admitted to Indraprastha Apollo Hospital, Delhi, were included in the study. Demographics, baseline comorbidities, and test results related to cardiovascular diseases were collected and analyzed. Results: The study included 1012 patients, admitted in our institute with a COVID-19 positive report. The mean age of the patients was 54.6 ± 6.8 years. The male to female ratio was 1.7:1. The demographic characteristics included diabetes in 38%, hypertensives 45%, history of coronary artery disease 22%, and chronic kidney disease 30%. A total of 426 patients were all treated on HCQS. A total of 7 patients were primigravida with full term pregnancy. The patients were also stratified according to age and demographic characteristics were noted. The total number deceased were 41 with 971 patients making complete recovery. The results showed no change in QTc interval in survivors and nonsurvivors. D-dimer, ferritin, and LDH were raised in all nonsurvivors compared to survivors. Even thrombocytopenia and low albumin levels were noted in nonsurvivors. Conclusions: The study revealed no significant change in QTc interval in survivors and nonsurvivors on HCQS. Critically ill patients showed the trends of being underweight, low albumin levels, thrombocytopenia, raised D-dimer, lactate dehydrogenase (LDH), and ferritin levels. Further studies on larger numbers are needed to confirm these findings.
Dependency parsing of biomedical text with BERT
Authors: Kanerva Jenna , Ginter Filip , Pyysalo Sampo 
Published: December 2020

AbstractBackground: Syntactic analysis, or parsing, is a key task in natural language processing and a required component for many text mining approaches. In recent years, Universal Dependencies (UD) has emerged as the leading formalism for dependency parsing. While a number of recent tasks centering on UD have substantially advanced the state of the art in multilingual parsing, there has been only little study of parsing texts from specialized domains such as biomedicine.Methods: We explore the application of state-of-the-art neural dependency parsing methods to biomedical text using the recently introduced CRAFT-SA shared task dataset. The CRAFT-SA task broadly follows the UD representation and recent UD task conventions, allowing us to fine-tune the UD-compatible Turku Neural Parser and UDify neural parsers to the task. We further evaluate the effect of transfer learning using a broad selection of BERT models, including several models pre-trained specifically for biomedical text processing.Results: We find that recently introduced neural parsing technology is capable of generating highly accurate analyses of biomedical text, substantially improving on the best performance reported in the original CRAFT-SA shared task. We also find that initialization using a deep transfer learning model pre-trained on in-domain texts is key to maximizing the performance of the parsing methods.
An automated protocol for modelling peptide substrates to proteases
Authors: Ochoa Rodrigo , Magnitov Mikhail , Laskowski Roman A. , Cossio Pilar , Thornton Janet M. 
Published: December 2020

Abstract
Background
Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promiscuity which can also be essential. Databases compiling specificity matrices derived from experimental assays have provided valuable insights into protease substrate recognition. Despite this, there are still gaps in our knowledge of the structural determinants. Here, we compile a set of protease crystal structures with bound peptide-like ligands to create a protocol for modelling substrates bound to protease structures, and for studying observables associated to the binding recognition.

Results
As an application, we modelled a subset of protease–peptide complexes for which experimental cleavage data are available to compare with informational entropies obtained from protease–specificity matrices. The modelled complexes were subjected to conformational sampling using the Backrub method in Rosetta, and multiple observables from the simulations were calculated and compared per peptide position. We found that some of the calculated structural observables, such as the relative accessible surface area and the interaction energy, can help characterize a protease’s substrate recognition, giving insights for the potential prediction of novel substrates by combining additional approaches.

Conclusion
Overall, our approach provides a repository of protease structures with annotated data, and an open source computational protocol to reproduce the modelling and dynamic analysis of the protease–peptide complexes.
Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis
Authors: Gao Shouguo , Wu Zhijie , Feng Xingmin , Kajigaya Sachiko , Wang Xujing , Young Neal S. 
Published: December 2020

Abstract
Background
Presently, there is no comprehensive analysis of the transcription regulation network in hematopoiesis. Comparison of networks arising from gene co-expression across species can facilitate an understanding of the conservation of functional gene modules in hematopoiesis.

Results
We used single-cell RNA sequencing to profile bone marrow from human and mouse, and inferred transcription regulatory networks in each species in order to characterize transcriptional programs governing hematopoietic stem cell differentiation. We designed an algorithm for network reconstruction to conduct comparative transcriptomic analysis of hematopoietic gene co-expression and transcription regulation in human and mouse bone marrow cells. Co-expression network connectivity of hematopoiesis-related genes was found to be well conserved between mouse and human. The co-expression network showed “small-world” and “scale-free” architecture. The gene regulatory network formed a hierarchical structure, and hematopoiesis transcription factors localized to the hierarchy’s middle level.

Conclusions
Transcriptional regulatory networks are well conserved between human and mouse. The hierarchical organization of transcription factors may provide insights into hematopoietic cell lineage commitment, and to signal processing, cell survival and disease initiation.
Deep learning for HGT insertion sites recognition
Authors: Li Chen , Chen Jiaxing , Li Shuai Cheng 
Published: December 2020

Abstract
Background
Horizontal Gene Transfer (HGT) refers to the sharing of genetic materials between distant species that are not in a parent-offspring relationship. The HGT insertion sites are important to understand the HGT mechanisms. Recent studies in main agents of HGT, such as transposon and plasmid, demonstrate that insertion sites usually hold specific sequence features. This motivates us to find a method to infer HGT insertion sites according to sequence features.

Results
In this paper, we propose a deep residual network, DeepHGT, to recognize HGT insertion sites. To train DeepHGT, we extracted about 1.55 million sequence segments as training instances from 262 metagenomic samples, where the ratio between positive instances and negative instances is about 1:1. These segments are randomly partitioned into three subsets: 80% of them as the training set, 10% as the validation set, and the remaining 10% as the test set. The training loss of DeepHGT is 0.4163 and the validation loss is 0.423. On the test set, DeepHGT has achieved the area under curve (AUC) value of 0.8782. Furthermore, in order to further evaluate the generalization of DeepHGT, we constructed an independent test set containing 689,312 sequence segments from another 147 gut metagenomic samples. DeepHGT has achieved the AUC value of 0.8428, which approaches the previous test AUC value. As a comparison, the gradient boosting classifier model implemented in PyFeat achieve an AUC value of 0.694 and 0.686 on the above two test sets, respectively. Furthermore, DeepHGT could learn discriminant sequence features; for example, DeepHGT has learned a sequence pattern of palindromic subsequences as a significantly (P-value=0.0182) local feature. Hence, DeepHGT is a reliable model to recognize the HGT insertion site.

Conclusion
DeepHGT is the first deep learning model that can accurately recognize HGT insertion sites on genomes according to the sequence pattern.
Adjunctive air-polishing with erythritol in nonsurgical periodontal therapy: a randomized clinical trial
Authors: Jentsch Holger F. R. , Flechsig Christian , Kette Benjamin , Eick Sigrun 
Published: December 2020

Abstract
Background
This study was aimed to investigate if the adjunctive use of erythritol air-polishing powder applied with the nozzle-system during subgingival instrumentation (SI) has an effect on the outcome of non-surgical periodontal treatment in patients with moderate to severe periodontitis.

Methods
Fourty-two individuals with periodontitis received nonsurgical periodontal therapy by SI without (controls, n = 21) and with adjunctive air-polishing using nozzle + erythritol powder (test, n = 21). They were analyzed for the clinical variables BOP (primary outcome at six months), probing depth (PD), attachment level, four selected microorganisms and two biomarkers at baseline, before SI as well as three and six months after SI. Statistical analysis included nonparametric tests for intra- and intergroup comparisons.

Results
In both groups, the clinical variables PD, attachment level and BOP significantly improved three and six months after SI. The number of sites with PD ≥ 5 mm was significantly lower in the test group than in the control group after six months. At six months versus baseline, there were significant reductions of Tannerella forsythia and Treponema denticola counts as well as lower levels of MMP-8 in the test group.

Conclusions
Subgingival instrumentation with adjunctive erythritol air-polishing powder does not reduce BOP. But it may add beneficial effects like reducing the probing depth measured as number of residual periodontal pocket with PD ≥ 5 mm when compared with subgingival instrumentation only.

Clinical relevance
The adjunctive use of erythritol air-polishing powder applied with the nozzle-system during SI may improve the clinical outcome of SI and may reduce the need for periodontal surgery.
Trial registration The study was retrospectively registered in the German register of clinical trials, DRKS00015239 on 6th August 2018, https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL.
Mental health symptoms in a cohort of hospital healthcare workers following the first peak of the COVID-19 pandemic in the UK
Authors: Wanigasooriya Kasun , Palimar Priyanka , Naumann David N. , Ismail Khalida , Fellows Jodie L. , Logan Peter , Thompson Christopher V. , Bermingham Helen , Beggs Andrew D. , Ismail Tariq 
Published: December 2020

Background
The coronavirus disease 2019 (COVID-19) pandemic is likely to lead to a significant increase in mental health disorders among healthcare workers (HCW).

Aims
We evaluated the rates of anxiety, depressive and post-traumatic stress disorder (PTSD) symptoms in a population of HCW in the UK.

Method
An electronic survey was conducted between the 5 June 2020 and 31 July 2020 of all hospital HCW in the West Midlands, UK using clinically validated questionnaires: the 4-item Patient Health Questionnaire(PHQ-4) and the Impact of Event Scale-Revised (IES-R). Univariate analyses and adjusted logistic regression analyses were performed to estimate the strengths in associations between 24 independent variables and anxiety, depressive or PTSD symptoms.

Results
There were 2638 eligible participants who completed the survey (female: 79.5%, median age: 42 years, interquartile range: 32–51). The rates of clinically significant symptoms of anxiety, depression and PTSD were 34.3%, 31.2% and 24.5%, respectively. In adjusted analysis a history of mental health conditions was associated with clinically significant symptoms of anxiety (odds ratio (OR) = 2.3, 95% CI 1.9–2.7, P < 0.001), depression (OR = 2.5, 95% CI 2.1–3.0, P < 0.001) and PTSD (OR = 2.1, 95% CI 1.7–2.5, P < 0.001). The availability of adequate personal protective equipment (PPE), well-being support and lower exposure to moral dilemmas at work demonstrated significant negative associations with these symptoms (P ≤ 0.001).

Conclusions
We report higher rates of clinically significant mental health symptoms among hospital HCW following the initial COVID-19 pandemic peak in the UK. Those with a history of mental health conditions were most at risk. Adequate PPE availability, access to well-being support and reduced exposure to moral dilemmas may protect hospital HCW from mental health symptoms.