bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shared Decision-Making Measures: A Systematic Review
Authors: Ahmad Muayyad , Abu Tabar Nazih , Othman Elham H. , Abdelrahim Zakaria 
Published: March 2020

Background and Objectives:
This review used the recent COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) rating system, which gives the reader the ability to find appropriate instruments in a simple way. Shared decision-making (SDM) is part of health professionals', nurses', and patients' interaction about fundamental and special nursing care issues. The objective of this study was to critically appraise instruments that measure SDM in health care–related decisions according to the COSMIN criteria.

Methods:
This review was reported in accordance with the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guideline. A thorough search identified SMD measures via PubMed, Cochrane Library, MEDLINE, EBSCO Host, Ovid journals, SAGE journals, and Google Scholar search engine through November 2018 and updated on March 24, 2019. A rating system with “very good,” “adequate,” “doubtful,” or “inadequate” for COSMIN was used.

Results:
The 17 instruments reported in this review are varied in the measured perspectives; observer-based viewpoint, patient questionnaires, provider questionnaires, and physician questionnaires, or even mixed perspectives. Only one instrument (OPTION 12 Scale) received an excellent rating across all 5 COSMIN validity rating sections in content, structural, and criterion validity.

Conclusion:
Most of the instruments scored poorly on the COSMIN checklist. Despite the vast number of instruments measuring SDM, researchers must undertake critical appraisal before selecting an acceptable instrument that meets the specific research goal, as well as the quality requirements.
Fully Automated Segmentation of Connective Tissue Compartments for CT-Based Body Composition Analysis
Authors: Nowak Sebastian , Faron Anton , Luetkens Julian A. , Geißler Helena L. , Praktiknjo Michael , Block Wolfgang , Thomas Daniel , Sprinkart Alois M. 
Published: March 2020

Objective
Body composition comprises prognostic information in patients with various malignancies and can be opportunistically determined from routine computed tomography (CT) scans. However, accurate assessment of patients with alterations, for example, due to ascites or anasarca, and accurate identification of intermuscular fat remain challenging. In this study, we aimed to develop a fully automated and highly accurate segmentation tool for connective tissue compartments from abdominal CT scans using the open-source Convolutional Neural Network (CNN) DeepMedic.

Materials and Methods
In this retrospective study, a CNN was developed using data of 1143 consecutive patients undergoing either preinterventional CT for transcatheter aortic valve implantation (TAVI) (82%) or diagnostic CT for liver cirrhosis with portosystemic shunting (PTSS) (18%). All analyses were performed on single-slice images at the L3/L4 level. The data were subdivided into subsets of training (70%), validation (15%), and test data (15%), balanced for TAVI and PTSS patients. To demonstrate the generalizability of the applied method with respect to nonspecific clinical routine data, the model with the highest performance in TAVI and PTSS patients was further tested on 100 randomly selected patients who underwent CT for routine diagnostic purposes at a hospital of maximum care, including critically ill patients. The applicability of the method to native CT examinations was additionally tested on 50 patients.

Results
Compared with the ground truth of the test data, the presented method achieved highly accurate segmentation results (subcutaneous adipose tissue [SAT], Dice score [DSC]: 0.98 ± 0.01; visceral adipose tissue [VAT], DSC: 0.96 ± 0.04; skeletal muscles [SM], DSC: 0.95 ± 0.02) and showed excellent generalizability on the routine CT diagnostic patients (SAT, DSC: 0.97 ± 0.04; VAT, DSC: 0.95 ± 0.05; SM, DSC: 0.95 ± 0.04) and also on native CT scans (SAT, DSC: 0.99 ± 0.01; VAT, DSC: 0.97 ± 0.03; SM, DSC: 0.97 ± 0.02).

Conclusions
Fully automated determination of body composition based on CT can be performed with excellent results using the open-source CNN DeepMedic. The trained model is made usable for research by a deployable and sharable application.
Time–energy uncertainty principle for irreversible heat engines
Authors: Hanel Rudolf , Jizba Petr 
Published: March 2020

Even though irreversibility is one of the major hallmarks of any real-life process, an actual understanding of irreversible processes remains still mostly semi-empirical. In this paper, we formulate a thermodynamic uncertainty principle for irreversible heat engines operating with an ideal gas as a working medium. In particular, we show that the time needed to run through such an irreversible cycle multiplied by the irreversible work lost in the cycle is bounded from below by an irreducible and process-dependent constant that has the dimension of an action. The constant in question depends on a typical scale of the process and becomes comparable to Planck’s constant at the length scale of the order Bohr radius, i.e. the scale that corresponds to the smallest distance on which the ideal gas paradigm realistically applies.
This article is part of the theme issue ‘Fundamental aspects of nonequilibrium thermodynamics’.
Phenomenological quantum thermodynamics resource theory for closed bipartite Schottky systems
Authors: Muschik Wolfgang 
Published: March 2020

How to introduce thermodynamics to quantum mechanics? From numerous possibilities of solving this task, the simple choice is here: the conventional von Neumann equation deals with a density operator whose probability weights are time-independent. Because there is no reason apart from the reversible quantum mechanics that these weights have to be time-independent, this constraint is waived, which allows one to introduce thermodynamical concepts to quantum mechanics. This procedure is similar to that of Lindblad’s equation, but different in principle. But beyond this simple starting point, the applied thermodynamical concepts of discrete systems may perform a ‘source theory’ for other versions of phenomenological quantum thermodynamics.This article is part of the theme issue ‘Fundamental aspects of nonequilibrium thermodynamics’.
Nonequilibrium thermodynamics: emergent and fundamental
Authors: Ván P. 
Published: March 2020

How can we derive the evolution equations of dissipative systems? What is the relation between the different approaches? How much do we understand the fundamental aspects of a second law based framework? Is there a hierarchy of dissipative and ideal theories at all? How far can we reach with the new methods of nonequilibrium thermodynamics?
This article is part of the theme issue ‘Fundamental aspects of nonequilibrium thermodynamics’.
Prevalence and Factors Associated with Depression and Anxiety of Hospitalized Patients with COVID-19
Authors: Kong Xiangyu , Zheng Kailian , Tang Min , Kong Fanyang , Zhou Jiahuan , Diao Le , Wu Shouxin , Jiao Piqi , Su Tong , Dong Yuchao 
Published: March 2020

AbstractObjectiveThe 2019 coronavirus disease (COVID-19) epidemic has raised international concern. Mental health is becoming an issue that cannot be ignored in our fight against it. This study aimed to explore the prevalence and factors linked to anxiety and depression in hospitalized patients with COVID-19.MethodsA total of 144 patients diagnosed with COVID-19 were included in this study. We assessed depression and anxiety symptoms using the Hospital Anxiety and Depression Scale (HADS), and social support using the Perceived Social Support Scale (PSSS) among patients at admission. Multivariate linear regression analyses were performed to identify factors associated with symptoms of anxiety and depression.ResultsOf the 144 participants, 34.72% and 28.47% patients with COVID-19 had symptoms of anxiety or depression, respectively. The bivariate correlations showed that less social support was correlated with more anxious (r=-0.196, p<0.05) and depressive (r=-0.360,p<0.05) symptoms among patients with COVID-19. The multiple linear regression analysis showed that gender (β=1.446, p=0.034), age (β=0.074, p=0.003), oxygen saturation (β =-2.140, p=0.049), and social support (β =-1.545, p=0.017) were associated with anxiety for COVID-19 patients. Moreover, age (β=0.084, p=0.001), family infection with SARS-CoV-2 (β =1.515, p=0.027) and social support (β =-2.236, p<0.001) were the factors associated with depression.ConclusionHospitalized patients with COVID-19 presented features of anxiety and depression. Mental concern and appropriate intervention are essential parts of clinical care for those who are at risk.
Disruption of the topological associated domain at Xp21.2 is related to gonadal dysgenesis: A general mechanism of pathogenesis
Authors: dos Santos Ana Paula , Meinel Jakob A. , Cruz Piveta Cristiane dos Santos , de Andrade Juliana Gabriel Ribeiro , Fabbri-Scallet Helena , Gil-da-Silva-Lopes Vera Lúcia , Guerra-Júnior Gil , Künstner Axel , Kaiser Frank J. , Holterhus Paul-Martin , Hiort Olaf , Busch Hauke , Maciel-Guerra Andréa Trevas , de Mello Maricilda Palandi , Werner Ralf 
Published: March 2020

AbstractDuplications of dosage sensitive sex-locus Xp21.2 including NR0B1 have been linked to 46,XY gonadal dysgenesis (GD) and their effects are attributed merely to increase gene dosage of NR0B1 (DAX1). Here we present a general mechanism how deletions, duplications, triplications or inversions with or without NR0B1 at Xp21.2 can lead to partial or complete GD by disrupting the cognate topological associated domain (TAD) in the vincinity of NR0B1. Our model is supported by three unrelated patients: two showing a 287kb overlapping duplication at the Xp21.2 locus upstream of NR0B1 containing CXorf21 and GK and one patient having a large new triplication of Xp21.2 as the most likely cause of GD. Whole Genome sequencing uncovered the exact structural rearrangements of the duplications and the triplication. Comparison with a previously published deletion upstream of NR0B1 revealed a common 35kb overlap between the deletion, our newly reported NR0B1 upstream duplications and the triplication as well as all other copy number variations (CNVs) at Xp21.2 reported so far. This overlap contains a strong CCCTC-binding factor (CTCF) binding site representing one boundary of the NR0B1 TAD. All three CNVs at Xp21.2 most likely disrupt this TAD boundary, which isolates NR0B1 from CXorf21 and GK and putatively results in GK and CXorf21 enhancer adoption and ensuing ectopic NR0B1 expression. As a result, the patients’ transcriptomes developed an intermediate expression pattern with both ovarian and testicular features and greatly reduced expression of spermatogenesis-related genes. This model not only allows better diagnosis of GD displaying CNVs at Xp21.2, but also gives deeper insight how spatiotemporal activation of developmental genes can be disrupted by reorganized TADs also in other rare diseases.
Framing the potential of public frameshift peptides as immunotherapy targets in colon cancer
Authors: Spaanderman Ide T. , Peters Fleur S. , Jongejan Aldo , Redeker Egbert J.W. , Punt Cornelis J.A. , Bins Adriaan D. 
Published: March 2020

AbstractApproximately 15% of Colon Cancers are Microsatellite Instable (MSI). Frameshift Peptides (FPs) formed in MSI Colon Cancer are potential targets for immunotherapeutic strategies. Here we comprehensively characterize the mutational landscape of 71 MSI Colon Cancer patients from the cancer genome atlas (TCGA-COAD). We confirm that the mutations in MSI Colon Cancers are frequently frameshift deletions (23% in MSI; 1% in microsatellite stable), We find that these mutations cluster at specific locations in the genome which are mutated in up to 41% of the patients. We filter these for an adequate variant allele frequency, a sufficient mean mRNA level and the formation of a Super Neo Open Reading Frame (SNORF). Finally, we check the influence of Nonsense Mediated Decay by comparing RNA and DNA sequencing results. Thereby we identify a set of 20 NMD-escaping Public FPs (PFPs) that cover over 90% of MSI Colon Cancer patients and 3 out of 4 Lynch patients in the TCGA-COAD. This underlines the potential for PFP directed immunotherapy, both in a therapeutic and a prophylactic setting.
Task-related motor response inflates confidence
Authors: Siedlecka Marta , Paulewicz Borysław , Koculak Marcin 
Published: March 2020

AbstractStudies on confidence in decision-making tasks have repeatedly shown correlations between confidence and the characteristics of motor responses. Here, we show the results of two experiments in which we manipulated the type of motor response that precedes confidence rating. Participants decided which box, left or right, contained more dots and then reported their confidence in this decision. In Experiment 1, prior to confidence rating, participants were required to follow a motor cue. Cued-response type was manipulated in two dimensions: task-compatibility (the relation between response set and task-relevant decision alternatives), and stimulus-congruence (spatial correspondence between response key and the location of the stimulus that should be chosen). In Experiment 2, a decision-related response set was randomly varied in each trial, being either vertical (task incompatible) or horizontal (task-compatible, spatially congruent and incongruent). The main results showed that choice confidence increased following task-compatible responses, i.e. responses related to the alternatives of the choice in which confidence was reported. Moreover, confidence was higher in these conditions, independently of response accuracy and spatial congruence with the ‘correct’ stimuli. We interpret these results as suggesting that action appropriate in the context of a given task is an indicator of successful completion of the decision-related process. Such an action, even a spurious one, inflates decisional confidence.
Comparative performance of four nucleic acid amplification tests for SARS-CoV-2 virus
Authors: Xiong Yujuan , Li Zhen-Zhen , Zhuang Qi-Zhen , Chao Yan , Li Fei , Ge Yi-Yuan , Wang Yi , Ke Pei-Feng , Huang Xian-Zhang 
Published: March 2020

AbstractCoronavirus disease 2019 (COVID-19) can be screened and diagnosed through the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction. SARS-CoV-2 nucleic acid amplification tests (NAATs) have been rapidly developed and quickly applied to clinical testing during the pandemic. However, studies evaluating the performance of these NAAT assays are limited. We evaluated the performance of four NAATs, which were marked by the Conformité Européenne and widely used in China during the pandemic. Results showed that the analytical sensitivity of the four assays was significantly lower than that claimed by the NAAT manufacturers. The limit of detection (LOD) of Daan, Sansure, and Hybribio NAATs was 3000 copies/mL, whereas the LOD of Bioperfectus NAATs was 4000 copies/mL. The results of the consistency test using 46 samples showed that Daan, Sansure, and Hybribio NAATs could detect the samples with a specificity of 100% (30/30) and a sensitivity of 100% (16 /16), whereas Bioperfectus NAAT detected the samples with a specificity of 100% (30/30) and a sensitivity 81.25% (13/16). The sensitivity of Bioperfectus NAAT was lower than that of the three other NAATs; this finding was consistent with the result that Bioperfectus NAAT had a higher LOD than the three other kinds of NAATs. The four above mentioned reagents presented high specificity; however, for the detection of the samples with low virus concentration, Bioperfectus reagent had the risk of missing detection. Therefore, the LOD should be considered in the selection of SARS-CoV-2 NAATs.
Mining Twitter to Assess the Determinants of Health Behavior towards Palliative Care in the United States
Authors: Zhao Yunpeng , Zhang Hansi , Huo Jinhai , Guo Yi , Wu Yonghui , Prosperi Mattia , Bian Jiang 
Published: March 2020

AbstractPalliative care is a specialized service with proven efficacy in improving patients’ quality-of-life. Nevertheless, lack of awareness and misunderstanding limits its adoption. Research is urgently needed to understand the determinants (e.g., knowledge) related to its adoption. Traditionally, these determinants are measured with questionnaires. In this study, we explored Twitter to reveal these determinants guided by the Integrated Behavioral Model. A secondary goal is to assess the feasibility of extracting user demographics from Twitter data—a significant shortcoming in existing studies that limits our ability to explore more fine-grained research questions (e.g., gender difference). Thus, we collected, preprocessed, and geocoded palliative care-related tweets from 2013 to 2019 and then built classifiers to:1) categorize tweets into promotional vs. consumer discussions, and 2) extract user gender. Using topic modeling, we explored whether the topics learned from tweets are comparable to responses of palliative care-related questions in the Health Information National Trends Survey.
Clinical features and outcomes of 197 adult discharged patients with COVID-19 in Yichang, Hubei
Authors: Zhou Fating , Yu Xiaogang , Tong Xiaowei , Zhang Rong 
Published: March 2020

AbstractPurposeTo investigate the epidemiology and clinical features of discharged adult patients with coronavirus infection disease 2019 (COVID-19) in Yichang.MethodThe retrospective study recruited 197 cases of COVID-19 discharged from Yichang Central People’s Hospital and Yichang Third People’s Hospital from Jan 17 to Feb 26, 2020. All cases were confirmed by real-time RT-PCR or chest computer tomography (CT). The survivors were followed up until March 4,2020. Clinical data, including demographic characteristic, presentation, underlying illness, exposure history, laboratory examination, radiology and prognosis were enrolled and analyzed by SPSS 19.0 software.ResultsThere were 197 adult discharged patients with COVID-19 in this study. Statistical analysis indicated that the average age was 55.94 years, and female patients were 99(50.3%).Those patients mainly resided in urban with exposure history in 2 weeks, while 7 medical staffs were infected. Fever (77.6%%), cough (43.6%) and weakness (14.7%) were the common symptoms. Leukocytes were mainly normal or decreased in 185 patients (92.9%), both lymphocytes and eosinophils were below normal range, the ratios were 56.9% and 50.3%, respectively. On the contrary, lactate dehydrogenases raised in 65 patients. C-reactive protein (72.4%) elevated in the most of patients. The sensitivity of RT-PCR was 63.5%. Chest CT indicated that bilateral patchy shadows (69.0%) were the most common imaging manifestations.169(85.8%) patients recovered and transferred to a designated hospital for observation, and the others (14.2%) turned worst and died of acute respiratory failure.ConclusionCOVID-19 infection with highly contagious have become a life-threaten public healthy problem, the sensitivity of RT-PCR was limited. Chest CT scan was recommended for the suspected patients. Furthermore, lymphocytopenia and eosinophils declining without leukocytes increasing may be considered as a useful evidence for the diagnosis.
Descriptive and prognostic value of a computational model of metastasis in high-risk neuroblastoma
Authors: Benzekry Sébastien , Sentis Coline , Coze Carole , Tessonnier Laëtitia , André Nicolas 
Published: March 2020

AbstractHigh Risk Neuroblastoma (HRNB) is the second most frequent solid tumor in children. Prognosis remains poor despite multimodal therapies. Mathematical models have been developed to describe metastasis, but their prognosis value has yet to be determined and none exists in neuroblastoma.We established such a model for HRNB relying on two coefficients: α(growth) and μ (dissemination). The model was calibrated using diagnosis values of primary tumor size, lactate dehydrogenase circulating levels (LDH) and the meta-iodo-benzyl-guanidine (mIBG) SIOPEN score from nuclear imaging, using data from 49 metastatic patients treated according to the European HR_NBL1 protocol.The model was able to accurately describe the data for both total tumor mass (LDH, R2 > 0.99) and number of visible metastasis (SIOPEN, R2 = 0.96). Statistical analysis revealed significant association of LDH with overall survival (OS, p=0.0268). However, clinical variables alone were not able to generate a Cox-based model with sufficient prognosis ability (p=0.507). The parameter μ was found to be independent of the clinical variables and positively significantly associated with OS (p = 0.0175 in multivariate analysis). Critically, addition of this novel computational biomarker to the clinical data drastically improved the performances of predictive algorithms, with a concordance index in cross-validation going from 0.755 to 0.827. The resulting signature had significant prognosis ability of OS (p=0.0353).Mechanistic modeling was able to describe pathophysiological data of metastatic HRNB and outperformed the predictive value of clinical variables. The physiological substrate underlying these results has yet to be explored, and results should be confirmed in a larger cohort.SignificanceA mechanistic mathematical model of metastasis in high risk neuroblastoma is able to describe clinical data and provides a numerical biomarker with superior predictive power of overall survival than clinical data alone.
Health Worker Practices, Facilitators and Barriers towards the Intensified Case-Finding Tuberculosis Screening Tool in Uganda
Authors: Kakinda Michael , Matovu Joseph K. B , Obuku Ekwaro A. 
Published: March 2020

AbstractIntroductionAlthough the Tuberculosis (TB) Intensified Case Finding (ICF) tool was introduced in 2011, only 15.7% of the estimated 35 million people living with HIV were screened for TB in 2013. We explored the facilitators, barriers and health care workers’ practices regarding use of the ICF tool in TB screening.MethodsWe conducted a qualitative study in Jinja, eastern Uganda. We purposively sampled eight (4 private and 4 Government) health facilities (HFs) with the guidance of the District TB and Leprosy Supervisor (DTLS). At each health facility, three health care workers (in-charge TB clinic, a TB focal person & one laboratory technician (total: 24 participants in 8 HFs) were interviewed using a key informant interview guide. Data were collected on how TB was screened and diagnosed in general and when using the ICF tool in particular. Data were audio-recorded, transcribed in verbatim, coded and analyzed using a thematic framework.ResultsThe ICF tool was available in all the 8 HFs; however, only half (12/24) the health workers interviewed at these facilities had ever used it for screening TB. The facilitators to ICF use were all levels of health cadres could use it, with simple, close-ended questions and clear, simple instructions. However, several barriers were identified as hindering the use of the ICF tool. The barriers to the use of the ICF tool are segmented according to the Health System building blocks, Leadership and Governance Barriers (concurrent use of other tools, lack of detailed training), Health Workforce Barriers (Lack of awareness of about the tool, perceived increased workload) and Health Information Management System Barriers (Stock-outs of the ICF tools).DiscussionThe ICF tool was found to be simple and easy to use; however, its use remained low due to a variety of perceived barriers by health workers. There is a need to increase the health care workers’ awareness about the ICF tool to improve its utilization in TB screening.