bluuebunny/crossref_metadata_2025_split huggingface dataset:
The phylodynamics of SARS-CoV-2 during 2020 in Finland — Disappearance and re-emergence of introduced strains.
Authors: Nguyen Phuoc Truong , Kant Ravi , Broeck Frederik Van den , Suvanto Maija T. , Alburkat Hussein , Virtanen Jenni , Ahvenainen Ella , Castren Robert , Hong Samuel L. , Baele Guy , Ahava Maarit J. , Jarva Hanna , Jokiranta Suvi Tuulia , Kallio-Kokko Hannimari , Kekäläinen Eliisa , Kirjavainen Vesa , Kortela Elisa , Kurkela Satu , Lappalainen Maija , Liimatainen Hanna , Suchard Marc A. , Hannula Sari , Ellonen Pekka , Sironen Tarja , Lemey Philippe , Vapalahti Olli , Smura Teemu 
Published: July 2021

Abstract

Finland has had a low incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infections as compared to most European countries. Here we report the origins and turnover of SARS-CoV-2 lineages circulating in Finland in 2020. SARS-CoV-2 introduced to Finland in January 2020 and spread rapidly across southern Finland during spring. We observed rapid turnover among Finnish lineages during this period. Clade 20C became the most prevalent among sequenced cases and was replaced by other strains in fall 2020. Bayesian phylogeographic reconstructions suggested 42 independent introductions into Finland during spring 2020, mainly from Italy, Austria, and Spain, which might have been the source for a third of cases. The investigations of the original introductions of SARS-CoV-2 to Finland during the early stages of the pandemic and of the subsequent lineage dynamics could be utilized to assess the role of transboundary movements and effects of early intervention and public health measures.
Increasing the efficiency of multy-variant calculations of electromagnetic field distribution in matrix of a polygradient separator
Authors: Jasim Jasim Mohmed Jasim , Shvedchykova Iryna , Panasiuk Igor , Romanchenko Julia , Melkonova Inna 
Published: July 2021

An approach is proposed to carry out multivariate calculations of the magnetic field distribution in the working gaps of a plate polygradient matrix of an electromagnetic separator, based on a combination of the advantages of two- and three-dimensional computer modeling. Two-dimensional geometric models of computational domains are developed, which differ in the geometric dimensions of the plate matrix elements and working air gaps. To determine the vector magnetic potential at the boundaries of two-dimensional computational domains, a computational 3D experiment is carried out. For this, three variants of the electromagnetic separator are selected, which differ in the size of the working air gaps of the polygradient matrices. For them, three-dimensional computer models are built, the spatial distribution of the magnetic field in the working intervals of the electromagnetic separator matrix and the obtained numerical values of the vector magnetic potential at the boundaries of the computational domains are investigated. The determination of the values of the vector magnetic potential for all other models is carried out by interpolation. The obtained values of the vector magnetic potential are used to set the boundary conditions in a computational 2D experiment. An approach to the choice of a rational version of a lamellar matrix is substantiated, which provides a solution to the problem according to the criterion of the effective area of the working area. Using the method of simple enumeration, a variant of the structure of a polygradient matrix with rational geometric parameters is selected. The productivity of the electromagnetic separator with rational geometric parameters of the matrix increased by 3–5 % with the same efficiency of extraction of ferromagnetic inclusions in comparison with the basic version of the device
Comparison between some meteorological elements measured by ECMWF and Earth stations in different regions in Iraq
Authors: A. Basheer Rajaa , AL-Rijabo Dr. Waleed I. 
Published: July 2021

The aim of this paper is to validate the data of three meteorological elements Air Temperature (Ta) , Relative Humidity (RH), Wind Speed (WS) from the European Center For-Medium Range Weather Forecasting (ECMWF) , against ground stations data using several Models at six stations well distributed in Iraq (Mosul, Kirkuk, Baghdad, Kut, Nasiriya, and Basra).
Due to the difficulties which experienced by the ground climate stations in Iraq from a shortage of devices and equipment for measuring the various climatic elements, which led to a huge shortage of data throughout time for political, economic and natural disasters. It is found that researchers can adopt the data of satellite stations to monitor the climate because let’s found that there is a highly significance Correlations between the data of these stations and the data of the ground stations for climate monitoring
Five Mathematical Models were used for that [Linear Models, Quadratic Models, Exponential Models, Logarithmic Models, and Power Models]. The performance of these models were evaluated by comparing the calculated (Ta, RH, WS) from earth stations.
Those mathematical correlations help to be able to calculate the ground data in state of there is no ground climate stations data.
Several statistical tests Correlation Coefficient (R), Coefficient of Determination (R2), Root Mean Square Error (RMSE), Mean Absolute Error (MAE) were used to control the validation and goodness of these Models.
The R2 obtained from these Models were very high in all stations. This means that, there is a highly significance Correlations between (Ta, RH, WS) estimated and [Ta, RH, WS] measured in all station
Duration on ART, Alcohol Use and HIV Stage May Predict Risky Sexual Behavior in a Resource-limited Environment: A Cross-sectional Study
Authors: New-Aaron Moses , Kingi Happiness , Meza Jane L. , Goedert Martha H. , Kibusi Stephen M , Mkhoi Mkhoi L. , Mayengo Caroline Damian , Charles James , Shabani Siraji , New-Aaron Temitope O. , Sumba Samwel , Cheney Anlan 
Published: July 2021

Background:
The intention of antiretroviral therapy (ART) and regular clinic visits are
to engender safe sex attitudes among HIV-infected individuals. However, this may not be the case
due to the perceived therapeutic benefits of ART and may result in exposure to drug-resistant HIV
strains.

Objective:
We aimed to determine the prevalence and predict the factors associated with risky sexual
behaviors among ART users in a resource-limited environment.

Methods:
Two hundred and ninety-one sexually active ART-users aged 18-50 years and seeking
care at the HIV clinic in Dodoma, Tanzania, participated in this study. The outcome variables modeled
in a logistic regression were condom use, multiple sex partners, casual sex partners, and payment
for sex. The predictors included in the models were the patients' socio-demographic characteristics.
In addition, a new variable, sexual risk scores, was generated by culminating all the outcome
variables. Finally, a multiple Poisson regression with the socio-demographic variables of the
participants was used to model the sexual risk scores.

Results:
Patients reported inconsistent/no condom use (44%), payment for sex (4%), casual sex encounters
(13%), multiple sex partners (21%), and STD symptoms (15%). While having a casual
sexual partner was significantly associated with age group in a Pearson Chi-square (p=0.0147), participants
≤35 years old were less likely to have single-sex partners than older participants (AOR:
0.188, 95 C.I: 0.042-0.849). Meanwhile, the likelihood of condom use was higher among participants
with no HIV-infected family members (AOR= 2.409, 95% C.I:1.236,4.697) and among participants
who had single-sex partners (AOR= 2.721, 95% C.I.: 1.115,6.640); these participants were
less likely to report STD symptoms (AOR=0.265, 95% C.I.: 0.081-0.865). Adjusted analysis
showed that estimated mean sexual risk scores significantly increased (mean, λ=1.61, 95%
C.I:1.0817-2.4063) for recent ART recipients (within 1-3 years vs. ≥8 years). However, sexual risk
scores of participants with HIV stage 3 were 38.8% lower than participants at stage 4 (95% C.I.:
0.3910-0.9558), and non-alcohol drinkers had an adjusted mean sexual risk score of 29% lower
than participants who were alcohol drinkers (95% C.I.: 0.5102-0.9879).

Conclusion:
Researchers should prioritize patients at HIV CTC for education concerning safe sexual
practices for those characterized by alcohol consumption, younger age (less than 35 years old),
HIV stage 4, or commencement of ART within three years.
Data Empowerment of Decision-Makers in an Era of a Pandemic: Intersection of “Classic” and Artificial Intelligence in the Service of Medicine
Authors: Geva Gil A , Ketko Itay , Nitecki Maya , Simon Shoham , Inbar Barr , Toledo Itay , Shapiro Michael , Vaturi Barak , Votta Yoni , Filler Daniel , Yosef Roey , Shpitzer Sagi A , Hir Nabil , Peri Markovich Michal , Shapira Shachar , Fink Noam , Glasberg Elon , Furer Ariel 
Published: July 2021

Background
The COVID-19 outbreak required prompt action by health authorities around the world in response to a novel threat. With enormous amounts of information originating in sources with uncertain degree of validation and accuracy, it is essential to provide executive-level decision-makers with the most actionable, pertinent, and updated data analysis to enable them to adapt their strategy swiftly and competently.

Objective
We report here the origination of a COVID-19 dedicated response in the Israel Defense Forces with the assembly of an operational Data Center for the Campaign against Coronavirus.

Methods
Spearheaded by directors with clinical, operational, and data analytics orientation, a multidisciplinary team utilized existing and newly developed platforms to collect and analyze large amounts of information on an individual level in the context of SARS-CoV-2 contraction and infection.

Results
Nearly 300,000 responses to daily questionnaires were recorded and were merged with other data sets to form a unified data lake. By using basic as well as advanced analytic tools ranging from simple aggregation and display of trends to data science application, we provided commanders and clinicians with access to trusted, accurate, and personalized information and tools that were designed to foster operational changes and mitigate the propagation of the pandemic. The developed tools aided in the in the identification of high-risk individuals for severe disease and resulted in a 30% decline in their attendance to their units. Moreover, the queue for laboratory examination for COVID-19 was optimized using a predictive model and resulted in a high true-positive rate of 20%, which is more than twice as high as the baseline rate (2.28%, 95% CI 1.63%-3.19%).

Conclusions
In times of ambiguity and uncertainty, along with an unprecedented flux of information, health organizations may find multidisciplinary teams working to provide intelligence from diverse and rich data a key factor in providing executives relevant and actionable support for decision-making.
Integrated Smoking Cessation for Smokers With Serious Mental Illness: Protocol for a Convergent Mixed Methods Implementation Evaluation Study
Authors: Schnitzer Kristina , Maravić Melissa Culhane , Arntz Diana , Phillips Nathaniel L , Pachas Gladys , Evins A Eden , Fetters Michael 
Published: July 2021

Background
Tobacco smoking is associated with significant morbidity and premature mortality in individuals with serious mental illness. A 2-year pragmatic clinical trial (PCORI PCS-1504-30472) that enrolled 1100 individuals with serious mental illness in the greater Boston area was conducted to test 2 interventions for tobacco cessation for individuals with serious mental illness: (1) academic detailing, which delivers education to primary care providers and highlights first-line pharmacotherapy for smoking cessation, and (2) provision of community health worker support to smoker participants. Implementing and scaling this intervention in other settings will require the systematic identification of barriers and facilitators, as well as the identification of relevant subgroups, effective and unique components, and setting-specific factors.

Objective
This protocol outlines the proposed mixed methods evaluation of the pragmatic clinical trial to (1) identify barriers and facilitators to effective implementation of the interventions, (2) examine group differences among primary care physicians, and (3) identify barriers that stakeholders such as clinical, payor, and policy leaders would anticipate to impact the implementation of effective components of the intervention.

Methods
Qualitative interviews will be conducted with all study community health workers and selected smoker participants, primary care providers, and other stakeholders. Measures of performance and engagement will guide purposive sampling. The Consolidated Framework for Implementation Research will guide qualitative data collection and analysis in accordance with the following framework approach: (1) familiarization, (2) identifying a thematic framework, (3) indexing, (4) charting, and (5) mapping and interpretation. Joint display analyses will be constructed to analyze and draw conclusions across the quantitative and qualitative data.

Results
The 3-year cluster-randomized trial has concluded, and the analysis of primary outcomes is underway. Results from the pragmatic trial and this mixed methods implementation evaluation will be used to help disseminate, scale, and expand a systems intervention.

Conclusions
The results of this mixed methods implementation evaluation will inform strategies for dissemination and solutions to potential barriers to the implementation of interventions from a smoking cessation trial for individuals with serious mental illness.

International Registered Report Identifier (IRRID)
DERR1-10.2196/25390
Radiation Oncologists’ Perceptions of Adopting an Artificial Intelligence–Assisted Contouring Technology: Model Development and Questionnaire Study
Authors: Zhai Huiwen , Yang Xin , Xue Jiaolong , Lavender Christopher , Ye Tiantian , Li Ji-Bin , Xu Lanyang , Lin Li , Cao Weiwei , Sun Ying 
Published: July 2021

Background
An artificial intelligence (AI)–assisted contouring system benefits radiation oncologists by saving time and improving treatment accuracy. Yet, there is much hope and fear surrounding such technologies, and this fear can manifest as resistance from health care professionals, which can lead to the failure of AI projects.

Objective
The objective of this study was to develop and test a model for investigating the factors that drive radiation oncologists’ acceptance of AI contouring technology in a Chinese context.

Methods
A model of AI-assisted contouring technology acceptance was developed based on the Unified Theory of Acceptance and Use of Technology (UTAUT) model by adding the variables of perceived risk and resistance that were proposed in this study. The model included 8 constructs with 29 questionnaire items. A total of 307 respondents completed the questionnaires. Structural equation modeling was conducted to evaluate the model’s path effects, significance, and fitness.

Results
The overall fitness indices for the model were evaluated and showed that the model was a good fit to the data. Behavioral intention was significantly affected by performance expectancy (β=.155; P=.01), social influence (β=.365; P<.001), and facilitating conditions (β=.459; P<.001). Effort expectancy (β=.055; P=.45), perceived risk (β=−.048; P=.35), and resistance bias (β=−.020; P=.63) did not significantly affect behavioral intention.

Conclusions
The physicians’ overall perceptions of an AI-assisted technology for radiation contouring were high. Technology resistance among Chinese radiation oncologists was low and not related to behavioral intention. Not all of the factors in the Venkatesh UTAUT model applied to AI technology adoption among physicians in a Chinese context.
Predicting Patient Deterioration: A Review of Tools in the Digital Hospital Setting
Authors: Mann Kay D , Good Norm M , Fatehi Farhad , Khanna Sankalp , Campbell Victoria , Conway Roger , Sullivan Clair , Staib Andrew , Joyce Christopher , Cook David 
Published: July 2021

Background
Early warning tools identify patients at risk of deterioration in hospitals. Electronic medical records in hospitals offer real-time data and the opportunity to automate early warning tools and provide real-time, dynamic risk estimates.

Objective
This review describes published studies on the development, validation, and implementation of tools for predicting patient deterioration in general wards in hospitals.

Methods
An electronic database search of peer reviewed journal papers from 2008-2020 identified studies reporting the use of tools and algorithms for predicting patient deterioration, defined by unplanned transfer to the intensive care unit, cardiac arrest, or death. Studies conducted solely in intensive care units, emergency departments, or single diagnosis patient groups were excluded.

Results
A total of 46 publications were eligible for inclusion. These publications were heterogeneous in design, setting, and outcome measures. Most studies were retrospective studies using cohort data to develop, validate, or statistically evaluate prediction tools. The tools consisted of early warning, screening, or scoring systems based on physiologic data, as well as more complex algorithms developed to better represent real-time data, deal with complexities of longitudinal data, and warn of deterioration risk earlier. Only a few studies detailed the results of the implementation of deterioration warning tools.

Conclusions
Despite relative progress in the development of algorithms to predict patient deterioration, the literature has not shown that the deployment or implementation of such algorithms is reproducibly associated with improvements in patient outcomes. Further work is needed to realize the potential of automated predictions and update dynamic risk estimates as part of an operational early warning system for inpatient deterioration.
An Augmented Reality Device for Remote Supervision of Ultrasound Examinations in International Exercise Science Projects: Usability Study
Authors: Rigamonti Lia , Secchi Matteo , Lawrence Jimmy B , Labianca Luca , Wolfarth Bernd , Peters Harm , Bonaventura Klaus , Back David Alexander 
Published: July 2021

Background
Support for long-distance research and clinical collaborations is in high demand and has increased owing to COVID-19–related restrictions on travel and social contact. New digital approaches are required for remote scientific exchange.

Objective
This study aims to analyze the options of using an augmented reality device for remote supervision of exercise science examinations.

Methods
A mobile ultrasound examination of the diameter and intima-media thickness of the femoral and carotid arteries was remotely supervised using a head-mounted augmented reality device. All participants were provided with a link to a YouTube video of the technique in advance. In part 1, 8 international experts from the fields of engineering and sports science were remotely connected to the study setting. Internet connection speed was noted, and a structured interview was conducted. In part 2, 2 remote supervisors evaluated 8 physicians performing an examination on a healthy human subject. The results were recorded, and an evaluation was conducted using a 25-item questionnaire.

Results
In part 1, the remote experts were connected over a mean distance of 1587 km to the examination site. Overall transmission quality was good (mean upload speed: 28.7 Mbps, mean download speed: 97.3 Mbps, mean ping: 21.6 milliseconds). In the interview, participants indicated that the main potential benefits would be to the fields of education, movement analysis, and supervision. Challenges regarding internet connection stability and previous training with the devices used were reported. In part 2, physicians’ examinations showed good interrater correlation (interclass correlation coefficient: 0.84). Participants valued the experienced setting as highly positive.

Conclusions
The study showed the good feasibility of the chosen design and a highly positive attitude of all participants toward this digital approach. Head-mounted augmented reality devices are generally recommended for collaborative research projects with physical examination–based research questions.
Patient Portals to Support Palliative and End-of-Life Care: Scoping Review
Authors: Ingle M Pilar , Valdovinos Cristina , Ford Kelsey L , Zhou Shou , Bull Sheana , Gornail Starlynne , Zhang Xuhong , Moore Susan , Portz Jennifer 
Published: July 2021

Background
Although patient portals are widely used for health promotion, little is known about the use of palliative care and end-of-life (PCEOL) portal tools available for patients and caregivers.

Objective
This study aims to identify and assess the user perspectives of PCEOL portal tools available to patients and caregivers described and evaluated in the literature.

Methods
We performed a scoping review of the academic literature directed by the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) extension for Scoping Review and searched three databases. Sources were included if they reported the development or testing of a feature, resource, tool, or intervention; focused on at least one PCEOL domain defined by the National Coalition for Hospice and Palliative Care; targeted adults with serious illness or caregivers; and were offered via a patient portal tethered to an electronic medical record. We independently screened the titles and abstracts (n=796) for eligibility. Full-text (84/796, 10.6%) sources were reviewed. We abstracted descriptions of the portal tool name, content, targeted population, and reported user acceptability for each tool from included sources (n=19).

Results
In total, 19 articles describing 12 tools were included, addressing the following PCEOL domains: ethical or legal (n=5), physical (n=5), and psychological or psychiatric (n=2). No tools for bereavement or hospice care were identified. Studies have reported high acceptability of tools among users; however, few sources commented on usability among older adults.

Conclusions
PCEOL patient portal tools are understudied. As medical care increasingly moves toward virtual platforms, future research should investigate the usability and acceptability of PCEOL patient portal resources and evaluate their impact on health outcomes.