bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of risk factors of bronchial mucus plugs in children with Mycoplasma pneumoniae pneumonia
Authors: zhang Jiahui , Wang Ting , Ji Wei , Yan Yongdong , Sun Zhichao , Tan Jiahong , Wu Jinfeng , Huang Li , Chen Zhengrong , Li Rongrong 
Published: December 2020

Abstract
Background: Recently, many cases of pneumonia in children with Mycoplasma pneumoniae infection have been shown to have varying degrees of intrabronchial mucus plug formation. The clinical, laboratory, radiological characteristics, and treatment of patients with Mycoplasma infection are analyzed in this study. The risk factors for M. pneumoniae pneumonia (MPP) mucus plug formation in children are explored, and a risk factor scoring system is established.Methods: MPP patients treated with bronchoscopy were retrospectively enrolled in the study from February 2015 to December 2019. The children were divided into a mucus plug group and a control group according to the presence or absence of mucus plug formation. The clinical, laboratory, radiological characteristics, and treatment of the two groups of children were compared. Univariate and multivariate logistic regression models were used to identify the risk factors for MPP mucus plug formation. The receiver operating characteristic (ROC) curve was drawn to evaluate the regression model and establish the MPP mucous plug risk factor scoring system.Results: A univariate analysis showed that the children in the mucous group were older and had a longer fever duration, longer hospital stay, higher fever peak, more cases of wheezing symptoms and allergies, and azithromycin or corticosteroids were administered later. In addition, neutrophil, C-reactive protein (CRP), lactate dehydrogenase (LDH), D-dimer (DD), sputum MP-DNA copy number, and total immunoglobulin A (IgA) levels were higher, while prealbumin (PA) levels were lower. The ROC curve analysis showed that children with MPP had PA ≤144.5 mg/L, had used corticosteroids during the course of the illness of ≥4.5 days, CRP ≥12.27 mg/L, an LDH≥462.65 U/L, and there was a possibility of intra-airway mucus formation. The independent risk factors were scored according to their odds ratio (OR) value. Among the 255 children with MPP, the high-risk group had 44 (83.02%) mucus plugs out of 53; the middle-risk group had 35 (34.3%) mucus plugs out of 102; and the low-risk group had 11 (11%) mucus plugs out of 100.Conclusions: PA levels, timing of corticosteroid use (use in the first few days), CRP levels, and LDH levels were independent risk factors for MPP mucus plug formation. This provides a basis for the early identification of MPP in children combined with mucus plug formation.
Genomic analysis of Helicobacter himalayensis sp. nov. isolated from Marmota himalayana
Authors: Hu Shouhui , Niu Lina , Wu Lei , Zhu Xiaoxue , Cai Yu , Jin Dong , Yan Linlin , Zhao Fan 
Published: December 2020

Abstract
Background: Helicobacter himalayensis was isolated from Marmota himalayana in the Qinghai-Tibet Plateau, China, and is a new non-H. pylori species, with unclear taxonomy, phylogeny, and pathogenicity. Results: A comparative genomic analysis was performed between the H. himalayensis type strain 80(YS1)T and other the genomes of Helicobacter species present in the National Center for Biotechnology Information (NCBI) database to explore the molecular evolution and potential pathogenicity of H. himalayensis. H. himalayensis 80(YS1)T formed a clade with H. cinaedi and H. hepaticus that was phylogenetically distant from H. pylori. The H. himalayensis genome showed extensive collinearity with H. hepaticus and H. cinaedi. However, it also revealed a low degree of genome collinearity with H. pylori. The genome of 80(YS1)T comprised 1,829,936 bp, with a 39.89% GC content, a predicted genomic island, and 1,769 genes. Comparatively, H. himalayensis has more genes for functions in “cell wall/membrane/envelope biogenesis” and “coenzyme transport and metabolism” sub-branches than the other compared helicobacters, and its genome contained 42 virulence factors genes, including that encoding cytolethal distending toxin (CDT). Conclusions: We characterized the H. himalayensis 80(YS1)T genome, its phylogenetic position, and its potential pathogenicity. However, further understanding of the pathogenesis of this potentially pathogenic bacterium is required, which might help to manage H. himalayensis-induced diseases.
Drug-Induced Cell Viability Prediction from LINCS-L1000 through WRFEN-XGBoost Algorithm
Authors: Lu Jiaxing , Chen Ming , Qin Yufang 
Published: December 2020

Abstract
Background: Predicting the drug response of the cancer diseases through the cellular perturbation signatures under the action of specific compounds is very important in personalized medicine. In the process of testing drug responses to the cancer, traditional experimental methods have been greatly hampered by the cost and sample size. At present, the public availability of large amounts of gene expression data makes it a challenging task to use machine learning methods to predict the drug sensitivity. Results: In this study, we introduced the WRFEN-XGBoost cell viability prediction algorithm based on LINCS-L1000 cell signatures. We integrated the LINCS-L1000, CTRP and Achilles datasets and adopted a weighted fusion algorithm based on random forest and elastic net for key gene selection. Then the FEBPSO algorithm was introduced into XGBoost learning algorithm to predict the cell viability induced by the drugs. The proposed method was compared with some new methods, and it was found that our model achieved good results with 0.83 Pearson correlation. At the same time, we completed the drug sensitivity validation on the NCI60 and CCLE datasets, which further demonstrated the effectiveness of our method. Conclusions: The results showed that our method was conducive to the elucidation of disease mechanisms and the exploration of new therapies, which greatly promoted the progress of clinical medicine.
Trends in the use of health services and their relationship with multimorbidity in Brazil, 1998–2013
Authors: de Souza Ana Sara Semeão , Braga Jose Ueleres 
Published: December 2020

Abstract
Background: Chronic non-communicable diseases (NCDs) are the leading cause of multimorbidity. Access to effective and equitable health services that meet NCDs’ needs is still limited in many countries. This constitutes the main barrier to coping with NCDs, especially in minimising the suffering of those who are already sick. The present study aimed to identify the relationship between multimorbidity and the use of different health services in Brazil from 1998 to 2013. Methods: This is a panel study using data from the health supplement of the National Household Sample Survey of 1998, 2003 and 2008 and data from the National Health Survey carried out in 2013. Three health service utilization outcomes were considered: 1. search for health services in the last 15 days (excluding dental services), 2. medical consultation in the previous 12 months and 3. hospitalisations over the last 12 months. Multimorbidity was assessed by counting the number of morbidities from a list of 10 morbidities. Poisson regression models stratified by sex were used to estimate the crude and adjusted prevalence ratios and their respective 95% confidence intervals for each outcome of health service use and multimorbidity, per year. Results: There was an increase in the prevalence of demand for health services and medical consultations in the last 12 months between 1998 and 2013, regardless of the multimorbidity classification. The prevalence of hospitalisations has decreased over the study period and increased twofold in individuals with multimorbidity. Having multimorbidity increased the use of health services for the three outcomes under the study, being more expressive among men. Conclusions: This study found that individuals with multimorbidity have higher levels of use of health services. Better understand the multimorbidity epidemiology and the associated impacts on the use and costs of health services can increase the quality of care provided to these patients and reduce rising health care costs.
Why do healthcare professionals fail to escalate as per the Early Warning System (EWS) protocol? A qualitative evidence synthesis of the barriers and facilitators of escalation
Authors: Neill Sinead M O , Clyne Barbara , Bell Miriam , Casey Avilene , Leen Brendan , Smith Susan M , Ryan Mairin , O’Neill Michelle 
Published: December 2020

Abstract
Background: Early warning systems (EWSs) are used to assist clinical judgment in the detection of acute deterioration to avoid or reduce adverse events including unanticipated cardiopulmonary arrest, admission to the intensive care unit and death. Sometimes healthcare professionals (HCPs) do not trigger the alarm and escalate for help according to the EWS protocol and it is unclear why this is the case. The aim of this qualitative evidence synthesis was to answer the question ‘why do HCPs fail to escalate care according to EWS protocols?’ The findings will inform the update of the National Clinical Effectiveness Committee (NCEC) National Clinical Guideline No. 1 Irish National Early Warning System (INEWS). Methods: A systematic search of the published and grey literature was conducted (until February 2018). Data extraction and quality appraisal were conducted by two reviewers independently using standardised data extraction forms and quality appraisal tools. A thematic synthesis was conducted by two reviewers of the qualitative studies included and categorized into the barriers and facilitators of escalation. GRADE CERQual was used to assess the certainty of the evidence.Results: Eighteen studies incorporating a variety of HCPs across seven countries were included. The barriers and facilitators to the escalation of care according to EWS protocols were developed into five overarching themes: Governance, Rapid Response Team (RRT) Response, Professional Boundaries, Clinical Experience, and EWS parameters. Barriers to escalation included: Lack of Standardisation, Resources, Lack of accountability, RRT behaviours, Fear, Hierarchy, Increased Conflict, Over confidence, Lack of confidence, and Patient variability. Facilitators included: Accountability, Standardisation, Resources, RRT behaviours, Expertise, Additional support, License to escalate, Bridge across boundaries, Clinical confidence, Empowerement, Clinical judgment, and a tool for detecting deterioration. These are all individual yet inter-related barriers and facilitators to escalation. Conclusions: The findings of this qualitative evidence synthesis provide insight into the real world experience of HCPs when using EWSs. This in turn has the potential to inform policy-makers and HCPs as well as hospital management about emergency response system-related issues in practice and the changes needed to address barriers and facilitators and improve patient safety and quality of care.
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
Authors: Yamawaki Tracy M , Lu Daniel R , Ellwanger Daniel C , Bhatt Dev , Manzanillo Paolo , Zhou Hong , Yoon Oh-Kyu , Homann Oliver , Wang Songli , Arias Vanessa , Li Chi-Ming Kevin 
Published: December 2020

Abstract
Background: Elucidation of immune populations with single-cell RNA-seq has greatly benefited the field of immunology by deepening the characterization of immune heterogeneity and leading to the discovery of new subtypes. However, single-cell methods inherently suffer from limitations in the recovery of complete transcriptomes due to the prevalence of cellular and transcriptional dropout events. This issue is often compounded by limited sample availability and limited prior knowledge of heterogeneity, which can confound data interpretation. Results: Here, we systematically benchmarked seven high-throughput single-cell RNA-seq methods. We prepared 21 libraries under identical conditions of a defined mixture of two human and two murine lymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes. We evaluate methods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expression signatures for each cell type. We observed higher mRNA detection sensitivity with the 10x Genomics 5’ v1 and 3’ v3 methods. We demonstrate that these methods have fewer drop-out events which facilitates the identification of differentially-expressed genes and improves the concordance of single-cell profiles to immune bulk RNA-seq signatures.Conclusion: Overall, our characterization of immune cell mixtures provides useful metrics, which can guide selection of a high-throughput single-cell RNA-seq method for profiling more complex immune-cell heterogeneity usually found in vivo.
Evidence of coupled oscillator to wave packet dynamics in human brain
Authors: Pal Mayukha , . Neeraj , Panigrahi Prasanta 
Published: December 2020

Abstract
Clear evidence of oscillator dynamics to wave packet collapse and revival in the brain EEG signals is demonstrated for the first time, with distinct differences in healthy individuals and epileptic patients. The low frequency components exhibit single oscillator type behavior in a phase-space description, with the potentials as coordinates and their instantaneous changes as the corresponding velocities. The closed paths reveal periodic motion, well described by one linear oscillator or possibly coupled ones with limit cycle dynamics and synchronization at the macroscopic level. The epileptic patients reveal dynamical features of bi-stability, originating from non-linearity, a prominent feature in the signals from the epileptogenic zone and much enhanced during the periods of seizure. Analogy from the phase-space of oscillator dynamics reveals dominance of potential energy in the signals from the epileptogenic zone, as also in the patients during occurrence of seizure. The acceleration, arising from the change of velocity, is found to be particularly strong in epileptic patients, when the phase space shows bi-stability and bursty behavior. Wave behavior with characteristics of superposition emerges in the frequency range corresponding to the observed unstable periodic orbits, that appear at the boundary of alpha and beta waves of 8-14Hz, centered at 10Hz. A modulated carrier wave is observed for all subjects at 18Hz, higher in width for patients. Coherent wave dynamics, with interference playing a key role in the wave packet collapse and revival, is observed starting from 18Hz, with the coherence getting significantly enhanced around 40-45Hz. Mechanism of intra frequency energy transfer is shown to be neutral turbulence.
Experiment and fitting calculation of migration critical velocity of small-sized sediment particles erosion in rainwater pipeline
Authors: Liu Cuiyun , Chen Yanzhi , Yang Yuting , Zhou Jingqin , Wang Yiyang , Zhou Jie , Zhang Xiaohua 
Published: December 2020

Abstract
The migration critical velocity of small-sized sediment particles was investigated through experiments under different particle sizes, pipe wall roughness, and sediment thickness. Such experiments were carried out to simulate the erosion process of small-sized sediment particles in a rainwater pipeline during rainfall. The mathematical models were established via quadratic fitting to calculate the critical velocity of migration. Results showed that small particles had powerful cohesive force, and aggregates had strong erosion resistance. So, for the small-sized particles (in the range of 0.33–0.83 mm), the smaller the particle size, the larger the critical velocity. When the pipe wall roughness was large, the ‘starting’ particle resistance was high. A large flow dynamic was needed to overcome such resistance. Thus, the critical velocity was great. The critical velocity was also large when the sediment thickness was large. The difference rate between the critical velocity calculated by mathematical models and the measured value was within the range of −3.60% to 5.33% and had good consistency. Under the research conditions, the critical velocity ranges of the four commonly used pipes; namely, plexiglass, steel/PVC, galvanized/clay, and cast iron pipes, were calculated.
IL-8 and MCP-1 Impact on Tau Phosphorylation and Phosphatase Activity
Authors: Vaz Margarida , Domingues Catarina , Trindade Dário , Barra Cátia , Oliveira Joana M. , Rosa Ilka M. , da Cruz e Silva Odete A.B. , Henriques Ana G. 
Published: December 2020

Background:
Chronic inflammation is a feature of Alzheimer´s disease (AD), resulting in
excessive production of inflammatory mediators that can lead to neuroinflammation, contributing to
alterations in Aβ production and deposition as Senile Plaques (SPs), and to neurofibrillary tangles
(NFTs) formation, due to hyperphosphorylated Tau protein.

Objective:
This work addressed the impact of the interleukin-8 (IL-8) and monocyte chemoattractant
protein-1 (MCP-1), two chemokines, on Tau phosphorylation; and also evaluated the chemokines’ levels
in plasma using samples from a regional cohort.

Methods:
Human neuronal SH-SY5Y cells exposed to IL-8 and MCP-1 chemokines were monitored for
their protein and phosphorylated protein levels by western blotting analysis. A serine/threonine protein
phosphatase (PPs) activity assay was employed to monitor PPs activity. Subsequently, flow cytometry
was used to monitor chemokines levels in plasma samples from individuals with cognitive deficits.

Results:
Chemokines’ exposure resulted only in minor cytotoxicity effects on SH-SY5Y, and in
increased Tau phosphorylation, particularly at the S396 residue. Tau phosphorylation correlated with
PPs inhibition and was consistent with GSK3β phosphorylation-mediated inhibition. Subsequent analysis
of plasma from individuals with cognitive deficits showed that IL-8 levels were decreased.

Conclusion:
Data shows that both chemokines tested can exert an effect on GSK3β phosphorylation and
modulate PPs activity, potentially resulting in increased Tau phosphorylation and subsequent NFTs formation.
One can deduce that increased chemokines stimulation during chronic inflammation can exacerbate
this event. The work contributes to a better understanding of the mode of action of these chemokines
on AD pathogenesis and opens novel research avenues.
Optimizing an Obesity Treatment Using the Multiphase Optimization Strategy Framework: Protocol for a Randomized Factorial Trial
Authors: Bennett Gary G , Steinberg Dori , Bolton Jamiyla , Gallis John A , Treadway Cayla , Askew Sandy , Kay Melissa C , Pollak Kathryn I , Turner Elizabeth L 
Published: December 2020

Background
Effective weight loss interventions exist, yet few can be scaled up for wide dissemination. Further, none has been fully delivered via text message. We used the multiphase optimization strategy (MOST) to develop multicomponent interventions that consist only of active components, those that have been experimentally determined to impact the chosen outcome.

Objective
The goal of this study is to optimize a standalone text messaging obesity intervention, Charge, using the MOST framework to experimentally determine which text messaging components produce a meaningful contribution to weight change at 6 months.

Methods
We designed a 6-month, weight loss texting intervention based on our interactive obesity treatment approach (iOTA). Participants are randomized to one of 32 experimental conditions to test which standalone text messaging intervention components produce a meaningful contribution to weight change at 6 months.

Results
The project was funded in February 2017; enrollment began in January 2018 and data collection was completed in June 2019. Data analysis is in progress and first results are expected to be submitted for publication in 2021.

Conclusions
Full factorial trials are particularly efficient in terms of cost and logistics when leveraged for standalone digital treatments. Accordingly, MOST has the potential to promote the rapid advancement of digital health treatments. Subject to positive findings, the intervention will be low cost, immediately scalable, and ready for dissemination. This will be of great potential use to the millions of Americans with obesity and the providers who treat them.

Trial Registration
ClinicalTrials.gov NCT03254940; https://clinicaltrials.gov/ct2/show/NCT03254940

International Registered Report Identifier (IRRID)
RR1-10.2196/19506
Use and Control of Artificial Intelligence in Patients Across the Medical Workflow: Single-Center Questionnaire Study of Patient Perspectives
Authors: Lennartz Simon , Dratsch Thomas , Zopfs David , Persigehl Thorsten , Maintz David , Große Hokamp Nils , Pinto dos Santos Daniel 
Published: December 2020

Background
Artificial intelligence (AI) is gaining increasing importance in many medical specialties, yet data on patients’ opinions on the use of AI in medicine are scarce.

Objective
This study aimed to investigate patients’ opinions on the use of AI in different aspects of the medical workflow and the level of control and supervision under which they would deem the application of AI in medicine acceptable.

Methods
Patients scheduled for computed tomography or magnetic resonance imaging voluntarily participated in an anonymized questionnaire between February 10, 2020, and May 24, 2020. Patient information, confidence in physicians vs AI in different clinical tasks, opinions on the control of AI, preference in cases of disagreement between AI and physicians, and acceptance of the use of AI for diagnosing and treating diseases of different severity were recorded.

Results
In total, 229 patients participated. Patients favored physicians over AI for all clinical tasks except for treatment planning based on current scientific evidence. In case of disagreement between physicians and AI regarding diagnosis and treatment planning, most patients preferred the physician’s opinion to AI (96.2% [153/159] vs 3.8% [6/159] and 94.8% [146/154] vs 5.2% [8/154], respectively; P=.001). AI supervised by a physician was considered more acceptable than AI without physician supervision at diagnosis (confidence rating 3.90 [SD 1.20] vs 1.64 [SD 1.03], respectively; P=.001) and therapy (3.77 [SD 1.18] vs 1.57 [SD 0.96], respectively; P=.001).

Conclusions
Patients favored physicians over AI in most clinical tasks and strongly preferred an application of AI with physician supervision. However, patients acknowledged that AI could help physicians integrate the most recent scientific evidence into medical care. Application of AI in medicine should be disclosed and controlled to protect patient interests and meet ethical standards.