bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comparison of Methods for Disease Progression Prediction Through a GoDARTS Study
Authors: Nielsen Agnes Martine , Nielsen Rikke Linnemann , Donnelly Louise , Zhou Kaixin , Dahl Anders , Gupta Ramneek , Ersbøll Bjarne , Pearson Ewan , Clemmensen Line 
Published: March 2020

Abstract
Background: In recent years, a variety of new machine learning methods are being employed in prediction of disease progression, e.g. random forest or neural networks, but how do they compare to and are they direct substitutes for the more traditional statistical methods like the Cox proportional hazards model? In this paper, we compare three of the most commonly used approaches to model prediction of disease progression. We consider a type 2 diabetes case from a cohort-based population in Tayside, UK. In this study, the time until a patient goes onto insulin treatment is of interest; in particular discriminating between slow and fast progression. This means that we are both interested in the results as a raw time-to-insulin prediction but also in a dichotomized outcome making the prediction a classification.Methods: Three different methods for prediction are considered: A Cox proportional hazards model, random forest for survival data and a neural network on the dichotomized outcome. The performance is evaluated using survival performance measures (concordance indices and the integrated Brier score) and using the accuracy, sensitivity, specificity, and Matthews correlation.coefficient for the corresponding classification problems.Results: We found no improvement when using the conditional inference forest over the Cox model. The neural network out performed the conditional inference forest in the classification problem. We discuss the limitations of the three approaches and where they each excel in terms of prediction performance, interpretation, and how they handle data imbalance.
Putting together the pieces of the puzzle – Part II - Assessing harbour porpoise (Phocoena phocoena) carcasses potentially subjected to grey seal (Halichoerus grypus) predation
Authors: Neer Abbo van , Gross Stephanie , Kesselring Tina , Grilo Miguel L. , Ludes-Wehrmeister Eva , Roncon Giulia , Siebert Ursula 
Published: March 2020

Abstract
The authors have requested that this preprint be removed from Research Square.
Virtual Reality Therapy in Long Term Care Resident Older Adults With Dementia: A Case Series
Authors: Sultana Munira , Campbell Karen , Jennings Morgan , Montero-Odasso Manuel , Orange Joseph. B. , Knowlton Jill , George Armin St. , Bryant Dianne 
Published: March 2020

Abstract
BACKGROUND: Behavioural and psychological symptoms of dementia (BPSD) worsens as dementia progresses, intensifies caregiver distress and consequent institutionalization. We wanted to evaluate 1) feasibility of Virtual Reality (VR) as cognitive stimulation therapy for BPSD in a Long-Term Care (LTC) home, 2) participants’ tolerance for the therapy, 3) facilitators and barriers to implementing VR therapy, 4) sensitivity to change of the participants’ BPSD to VR therapy, and 5) longitudinal construct validity of BPSD measuring tools. METHODS: A single site (Henley Place at London, Ontario) case series with a convenience sample (24 older adult residents with moderate to severe dementia). Intervention was 30 minutes of VR therapy with Broomx©, five days a week for two weeks. The change in BPSD was measured with Cornell Scale for Depression in Dementia (CSDD), Cohen-Mansfield Agitation Inventory (CMAI) scale, Dementia Observation System (DOS) scale, and proportion of night-time sleep. We validated selected tools with Global Rating of Change (GRC) scale. RESULTS: Implementing VR therapy was possible at Henley Place (recruitment rate=40%, the adherence rate=21%, and the attrition=0%) and participants could tolerate it. No emergency transfers or one-to-one staff use were recorded during the intervention period. CONCLUSION: VR therapy can be implemented in a LTC home. TRIAL REGISTRATION: The study was not registered as clinical trial. We obtained ethics approval from ADVARRA Canada Ethics Board before recruiting participants for the study.
Integrated analysis reveals the prognostic significance of pyrimidine metabolic rate limiting enzymes in patients with lung adenocarcinoma
Authors: Wang Haiwei , Wang Xinrui , Xu Liangpu , Zhang Ji , Cao Hua 
Published: March 2020

Abstract
Background: Reprogramming of metabolism is illustrated in many types of cancer and is associated with the clinical outcomes of cancer patients. However, the prognostic significance of pyrimidine metabolism signaling pathway in patients with lung adenocarcinoma (LUAD) is unclear.Methods: Using the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets, we determined the prognostic significance of pyrimidine metabolic rate limiting enzymes in patients with lung cancer. The enrichment of pyrimidine metabolism signaling pathway was analyzed by gene set enrichment analysis (GSEA). The expression profiles of pyrimidine metabolic rate limiting enzymes were identified from Affymetrix gene expression data and RNA-seq data. The Kaplan-Meier Plotter was used to identify the prognostic significance of the pyrimidine metabolic rate limiting enzymes. Spearman’s correlation and multivariate cox regression were used to determine the correlation efficiency of pyrimidine metabolic rate limiting enzymes.Results: The pyrimidine metabolism signaling pathway is significantly enriched in LUAD tissues, but not in lung squamous cell carcinoma (LUSC) tissues. Compared with normal lung tissues, the pyrimidine metabolic rate limiting enzymes are highly expressed in lung tumor tissues. Furthermore, the high expression levels of pyrimidine metabolic rate limiting enzymes are associated with unfavorable prognosis in patients with LUAD. Moreover, we demonstrate that the hypo-DNA methylation, DNA amplification and TP53 mutation are contributing to the high expression levels of pyrimidine metabolic rate limiting enzymes in cancer cells. Finally, we reveal the significant connections between the pyrimidine metabolic rate limiting enzymes. Comprehensively, the pyrimidine metabolic rate limiting enzymes are highly expressed in patients with bladder cancer, breast cancer, colon cancer, liver cancer and stomach cancer. And the high expression levels of pyrimidine metabolic rate limiting enzymes are associated with unfavorable prognosis in patients with liver cancer. Conclusions: Pyrimidine metabolism signaling pathway is associated with the development of lung adenocarcinoma. Pyrimidine metabolic rate limiting enzymes CAD, DTYMK, RRM1, RRM2, TK1, TYMS, UCK2, NR5C2 and TK2 have significant prognostic effects in patients with lung adenocarcinoma.
Assessment of Common Mental Disorders among Visitors to Traditional Healers: a Mixed Study in North Ethiopia
Authors: Mossie Tilahun Belete , Tesfay Kenfe 
Published: March 2020

Abstract
Background: People with common mental disorders have instability, poor self-care, social withdrawal, poor communication with others and frequent somatic pains. Seeking help from traditional healers which offer Prayer and treatment with holy water have been strategies reported by several studies particularly in developing world.Purpose : to assess perceived causes, associated factors and prevalence of common mental disorders among visitors to traditional healers in Mekelle town, North Ethiopia.Methods and subjects: We used a mixed study design; a quantitative study on 380 subjects and a qualitative study among fifteen subjects. We used Self-reported questionnaire (SRQ 20) to screen common mental disorders. Also perceived causes of mental illness and psycho-social stressful situations were assessed using a semi structured tool and in-depth interview. We analyzed data using Statistical Package for Social Sciences software, windows 25. Findings in the qualitative study were triangulated with the quantitative finding.Result: the prevalence of common mental disorders was 38.7% (95% CI; 33.7, 43.6). Factors independently associated with common mental disorders were being a woman (AOR= 1.68 (95% CI; 1.04, 2.72)), low level of education (AOR=3.2 (95% CI; 1.28, 6.91)), a conflict in the family (AOR= 3.82 (95% CI; 1.89, 7.68)) and traditional belief about the cause of mental illness (AOR= 2.33 (95% CI; 1.43, 3.79)). Experience of poor/no religious rituals, evil spirit, personal sin and will of God were the top traditional causes of common mental disorders.Conclusion : prevalence of common mental disorders was higher among the visitors as compared to prior studies. This refers the importance of establishing a link between traditional healers and modern treatment of mental illness with special attention to women, low socio-economic class and people with poor family dynamics.
Psychological suffering, medicalization and women: a perspective of Institutional Ethnography
Authors: Medeiros Luciana Fernandes , Veras Renata Meira , Costa Loyanne Monyk Torres , Araujo Gisely da Costa , Oliveira Isabelly Cristina Soares 
Published: March 2020

Abstract
Background Recent years have seen a growing psychological suffer in women attended in primary health care in developing countries. This paper aims to analyze the psychological suffering in a small city in northeastern Brazil and its relationship with medicalization from the perspective of Institutional Ethnography (IE).Methods We applied 202 SRQ-20 questionnaires in the first research step. In the second step, four women were interviewed in the primary health care service.Results The results demonstrated a high number of primary health care users in psychological suffering (47.02%). The data also point to a significant prevalence of women in psychological suffering, the use of medicines and the struggles in dealing with the difficulties of everyday life.Conclusions The medicalization of psychological suffering appeared several times in this study through the invisibility of these sufferings under the blanket of biomedical and medicalizing discourse. Those facts can affect contemporary women and the contradictions of being a woman in a capitalist and patriarchal society.
Converting DICOM to STL for 3D Printing: A Process, and Software Package Comparison
Authors: KAMIO Takashi , SUZUKI Madoka , ASAUMI Rieko , KAWAI Taisuke 
Published: March 2020

Abstract
Background : Extracting and three-dimensional (3D) printing an organ in a region of interest in DICOM images typically calls for segmentation in support of 3D printing as a first step. Next, the DICOM images are converted to STL data. After primary and secondary processing, including noise removal and hole correction, the STL data can be 3D printed. The quality of the 3D model is directly related to the quality of the STL data. This study focuses and reports on conversion performance for nine software packages. Methods : Multi-detector row CT scanning was performed on a dry human mandible with two 10-mm-diameter bearing balls as a phantom. The DICOM images file was then converted to a STL file using nine different commercial/open-source software packages. Once the STL models were constructed, the data properties and the size and volume of each were measured and differences across the software packages were noted. Additionally, to evaluate differences between the shapes of the STL models by software package, each pair of STL models was superimposed, with observed differences between their shapes characterized as shape error. Further, deformation caused by reduction in the number of triangles was evaluated. Results : The data size and the number of triangles were different across all software packages. The constructed ball STL model expanded in the X-, Y-, and Z-axis directions, with the length in the Z-axis direction (body axis direction) being slightly longer than other directions. There were no significant differences in shape error across software packages for the mandible STL model. No shape change was observed relative to reduction in the number of triangles. Conclusions : Statistically, no significant differences were found across software packages for size and volume. However, different characteristics of each software package were noticeable, such as different effects in the thin cortical bone area, likely due to the partial volume effect, which may reflect differences in image binarization algorithms. Although the shape of the STL model differs slightly depending on the software, our results indicate that shape error in 3D printing for clinical use in oral and maxillofacial surgery remains within acceptable limits.
Flipping the Paradigm: A Qualitative Exploration of Research Translation Centres in the UK and Australia
Authors: Robinson Tracy , Skouteris Helen , Burns Prue , Melder Angela , Bailey Cate , Croft Charlotte , Spyridonidis Dimitrios , Teede Helena 
Published: March 2020

Abstract
Background: Over the past decade Research Translation Centres have been established in many countries. These Centres (sometimes referred to as Academic Health Science Centres) were established to accelerate the generation and translation of new evidence that is responsive to health service and community priorities. This effectively ‘flips’ the traditional research and education paradigms because it requires active participation and continuous engagement with stakeholders (especially service users, the community and frontline clinicians). Although investment and expectations of RCTs are high, the literature confirms a need to better understand the processes RTCs use to mobilise knowledge, build workforce capacity and co-produce research with patients and the public to ensure population impact and drive healthcare improvement is needed. Methods: Semi structured interviews were conducted with selected leaders and members from RTCs in the UK and Australia. Convenience sampling was utilised based on geography, accessibility and availability. In addition, a snowballing approach was employed with further participants identified by RTC leaders and advisors from Public and Patient initiatives in the UK. Interviews were conducted face to face or via videoconferencing and were recorded, transcribed verbatim and analysed using a reflexive and inductive approach described by Braun and Clarke (2???). This involved re-reading and coding transcripts to generate initial themes. This inductive approach was used to identify patterns and common threads that were subsequently reviewed by two researchers to ensure consistentcy of themes. Results: A total of 41 participants, 22 from the UK and 19 from Australia were interviewed. Five major themes emerged including (1) dissonant metrics, (2) Different models of leadership (3) Public-Patient Involvement and research co-production (4) Workforce development (5) Barriers to collaboration. Conclusions: Participants identified the need for performance measures that capture community impact. Better aligned success metrics, enhanced leadership, strategies to partner with patients and the public, enhanced workforce development and strategies to enhance collaboration were all identified as crucial for RTCs to succeed.
Management of intraoperative acetabular fracture in primary total hip arthroplasty
Authors: Li Juncheng , Ji Quanbo , Ni Ming , Zheng Qingyuan , Sun Jinyang , Zhang Guoqiang 
Published: March 2020

Abstract
Background Intraoperative acetabular fracture(IAF)is a rare complication of primary total hip arthroplasty(THA). Previous report have locked a sufficiently large number of subjects to allow for an analysis of the causes and appropriate treatment of this problem. Methods Between 2015 to 2018, 4,888 primary THA were enrolled. We retrospectively reviewed the records in our Total Joint Registry Database and found that 24 patients (24 hips) had sustained IFAs .24 patients(16 females and 8males)were all treated with posterolateral approach using uncemented components. 20 patients underwent supplemental screw fixation, of which 2 patients were treated with plate fixation. 2 Patients femoral head was used as a graft. In 4 patients, the acetabular component was judged to be stable despite the fracture and no additional treatment was performed All patients were evaluated clinically with Harris Hip Scores (HHS) and radiographically with serial X-rays which follow up for a mean period of 34.0±12.6 months. We evaluated the anatomic location, cause, treatment, and outcome of the fractures. Results The fracture rate associated with uncemented components was 0.49%. In 17(70.8%) of the these patients, the fracture was noted during impaction of the real acetabular component.6 patients with Ankylosing Spondylitis had fracture 4 in anterior wall,1 in anterior column because of patient with hip joint fusion need to pre-osteotomy before dislocation .The HHS score increased from 30.8±9.7 preoperatively to 90.2±4.2 postoperatively. All the latest x-ray showed that the fracture did not move, and there is no translucent line formed in the acetabular cup bone interface.Conclusion IAFs are rare complications of THA, and most commonly occur during the implantation of the acetabular components. It is necessary to prevent the occurrence of fractures as much as possible even if the fractures are found during the operation. It should be noted that patients with ankylosing spondylitis involving hip joints during THA surgery must be careful to prevent IAFs during dislocation and pre-osteotomy.
Clinical course and outcome of novel coronavirus COVID-19 infection in 107 patients discharged from the Wuhan hospital
Authors: Wang Dawei , Yin Yimei , Hu Chang , Liu Xing , Zhang Xingguo , Zhou Shuliang , Jian Mingzhi , Xu Haibo , Prowly John , Hu Bo , Li Yirong , Peng Zhi-Yong 
Published: March 2020

Abstract
Background In December 2019, Coronavirus Disease 2019 (COVID-19) outbreak was reported from Wuhan, China. Information on the clinical progress and prognosis of COVID-19 was not thoroughly described. We described the clinical courses and prognosis in COVID-19 patients. Methods Retrospective case series of COVID-19 patients from Zhongnan Hospital of Wuhan University in Wuhan, and Xi-shui Hospital, Hubei Province, China, up to February 10, 2020. Epidemiological, demographic and clinical data were collected. Clinical progress of survivors and non-survivors were compared. Risk factors for death were analyzed. Results A total of 107 discharged patients with COVID-19 were enrolled. The clinical progression of COVID-19 presented as a tri-phasic pattern. Week 1 after illness onset was characterized by fever, cough, dyspnea, lymphopenia and radiological multilobar pulmonary infiltrates. In severe cases, thrombocytopenia, acute kidney injury, acute myocardial injury or adult respiratory distress syndrome were observed. During week 2, in mild cases, fever, cough and systemic symptoms began to resolve and platelet count rose to normal range, but lymphopenia persisted. In severe cases, leukocytosis, neutrophilia and deteriorating multi-organ dysfunction were dominant. By week 3, mild cases had clinically resolved except for lymphopenia. However, severe cases showed persistent lymphopenia, severe acute respiratory dyspnea syndrome , refractory shock, anuric acute kidney injury, coagulopathy, thrombocytopenia and death. Older age and male sex were independent risk factors for poor outcome of the illness. Conclusions A period of 7–13 days after illness onset is the critical stage in COVID-19 progression. Age and male gender were independent risk factors for death of COVID-19.
Smokers who have not tried alternative nicotine products: a 2019 survey of adults in Great Britain
Authors: Simonavicius Erikas , McNeill Ann , Cheeseman Hazel , Arnott Deborah , Brose Leonie S. 
Published: March 2020

Abstract
Aims: Switching from smoking to using nicotine replacement therapy (NRT), electronic cigarettes (e‑cigarettes) or heated tobacco products can reduce tobacco-related health risks. However, not all smokers in Great Britain have tried these products, which is a missed opportunity for harm reduction. This study aims to identify and describe smokers who have never tried alternative nicotine products. Methods: Study analysed cross-sectional survey data of smokers ( n =1777) from a representative adult sample from Great Britain. The online survey was run in March 2019. The proportion of smokers who had never used alternative nicotine products was measured. A multivariate logistic regression assessed the association between never using alternative nicotine products and smokers’ sociodemographic and smoking characteristics and motivation to stop smoking. Results: One in four smokers (27.8%, 95% CI: 25.8%–29.9%) had never tried NRT, e-cigarettes or heated tobacco products. These smokers were more commonly from Black and Minority than White ethnic groups (AOR=1.55; 95% CI: 1.02–2.31), were more likely to smoke up to 10 versus more cigarettes per day (AOR=1.52; 95% CI: 1.14–2.03) and reported low versus moderate or high motivation to stop smoking (AOR=1.79; 95% CI: 1.20–2.74). Conclusion: Light smokers, those unmotivated to stop and smokers from Black and Minority ethnic groups are less likely to have ever tried alternative nicotine products. Different approaches are needed to facilitate harm reduction and smoking cessation among these groups of smokers.
Outpatient treatment in low-risk pulmonary embolism patients receiving direct acting oral anticoagulants is associated with cost savings.
Authors: Ghazvinian Raein , Elf Johan , Gottsäter Anders , Löfvendahl Sofie , Holst Jan 
Published: March 2020

Abstract
Background Direct oral anticoagulants (DOAC) are first line treatment for pulmonary embolism (PE). Treatment of acute PE is traditionally hospital based and associated with high costs, in spite of recent guidelines suggesting outpatient treatment for low-risk patients. The aims of this study were to evaluate potential cost savings with outpatient DOAC treatment of patients with low risk PE compared to DOAC treatment of low risk PE patients in hospital. Methods A retrospective comparatory multicenter cohort study in patients with low risk PE (simplified pulmonary severity index [sPESI]) ≤ 1 admitted to the eight hospitals in Sweden´s southernmost healthcare region during 2013-2015, and treated with DOAC. Local criteria guiding outpatient treatment had been used, and sPESI was calculated retrospectively. Health care costs were analysed in the 223 (44%) patients treated as outpatients and the 287 (56%) treated in hospital. Results Total cost per patient was 7334 EUR in the inpatient group, and 2088 EUR in the outpatient group (p<0.001). In multivariate analysis, type of treatment (in- or outpatient, p=<0.001) and sPESI group (0 or 1, p=<0.001) were significantly associated with total cost below or above median, whereas age (p=0.565) and gender (p=0.177) was not. Total cost for inpatients was higher (p<0.001) compared to outpatients in subgroups with sPESI 0 and 1. Conclusion Better adherence to current guidelines recommending outpatient treatment with DOAC in patients with low risk PE would potentially lead to significant savings in healthcare expenditure.