bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recommendations for SARS-CoV-2/COVID-19 testing: a scoping review of current guidance
Authors: Arevalo-Rodriguez Ingrid , Seron Pamela , Buitrago-García Diana , Ciapponi Agustin , Muriel Alfonso , Zambrano-Achig Paula , del Campo Rosa , Galán-Montemayor Juan Carlos , Simancas-Racines Daniel , Perez-Molina Jose A , Khan Khalid Saeed , Zamora Javier 
Published: January 2021

BackgroundTesting used in screening, diagnosis and follow-up of COVID-19 has been a subject of debate. Several organisations have developed formal advice about testing for COVID-19 to assist in the control of the disease. We collated, delineated and appraised current worldwide recommendations about the role and applications of tests to control SARS-CoV-2/COVID-19.MethodsWe searched for documents providing recommendations for COVID-19 testing in PubMed, EMBASE, LILACS, the Coronavirus Open Access Project living evidence database and relevant websites such as TRIP database, ECRI Guidelines Trust, the GIN database, from inception to 21 September 2020. Two reviewers applied the eligibility criteria to potentially relevant citations without language or geographical restrictions. We extracted data in duplicate, including assessment of methodological quality using the Appraisal of Guidelines for Research and Evaluation-II tool.ResultsWe included 47 relevant documents and 327 recommendations about testing. Regarding the quality of the documents, we found that the domains with the lowest scores were ‘Editorial independence’ (Median=4%) and ‘Applicability’ (Median=6%). Only six documents obtained at least 50% score for the ‘Rigour of development’ domain. An important number of recommendations focused on the diagnosis of suspected cases (48%) and deisolation measures (11%). The most frequently recommended test was the reverse transcription-PCR (RT-PCR) assay (87 recommendations) and the chest CT (38 recommendations). There were 22 areas of agreement among guidance developers, including the use of RT-PCR for SARS-Cov-2 confirmation, the limited role of bronchoscopy, the use chest CT and chest X-rays for grading severity and the co-assessment for other respiratory pathogens.ConclusionThis first scoping review of recommendations for COVID-19 testing showed many limitations in the methodological quality of included guidance documents that could affect the confidence of clinicians in their implementation. Future guidance documents should incorporate a minimum set of key methodological characteristics to enhance their applicability for decision making.
Effectiveness and cost-effectiveness of TeleStroke consultations to support the care of patients who had a stroke presenting to regional emergency departments in Western Australia: an economic evaluation case study protocol
Authors: Tsou Christina , Robinson Suzanne , Boyd James , Kamath Shruthi , Yeung Justin , Waters Stephanie , Gifford Karen , Jamieson Andrew , Hendrie Delia 
Published: January 2021

IntroductionThe Western Australia (WA) Acute TeleStroke Programme commenced incrementally across regional WA during 2016–2017. Since the introduction of the TeleStroke Programme, there has been monitoring of service outputs, including regional patient access to tertiary stroke specialist advice and reperfusion treatment; however, the impact of consultation with a stroke specialist via telehealth (videoconferencing or telephone) on the effectiveness and cost-effectiveness of stroke care and the drivers of cost-effectiveness has not been systematically evaluated.Methods and analysisThe aim of the case study was to examine the impact of consultation with a stroke specialist via telehealth on the effectiveness and cost-effectiveness of stroke and transient ischaemic attack care using a mixed methods approach. A categorical decision tree model will be constructed in collaboration with clinicians and programme managers. A before and after comparison using state-wide administrative datasets will be used to run the base model. If sample size and statistical power permits, the cases and comparators will be matched by stroke type and presence of CT scan at the initial site of presentation, age category and presenting hospital. The drivers of cost-effectiveness will be explored through stakeholder interviews. Data from the qualitative analysis will be cross-referenced with trends emerging from the quantitative dataset and used to guide the factors to be involved in subgroup and sensitivity analysis.Ethics and disseminationEthics approval for this case study has been granted from the Western Australian Country Health Service Human Research and Ethics Committee (RGS3076). Reciprocal approval has been granted from Curtin University Human Research Ethics Office (HRE2019-0740). Findings will be disseminated publicly through conference presentation and peer-review publications. Interim findings will be released as internal reports to inform the service development.
Authorship inequality: a bibliometric study of the concentration of authorship among a diminishing number of individuals in high-impact medical journals, 2008–2019
Authors: Hart Kamber L , Perlis Roy H 
Published: January 2021

ObjectiveAuthorship and number of publications are important criteria used for making decisions about promotions and research funding awards. Given the increase in the number of author positions over the last few decades, this study sought to determine if there had been a shift in the distribution of authorship among those publishing in high-impact academic medical journals over the last 12 years.DesignThis study analysed the distribution of authorship across 312 222 original articles published in 134 medium-impact to high-impact academic medical journals between 1 January 2008 and 31 December 2019. Additionally, this study compared the trends in author distributions across nine medical specialties and a collection of cross-specialty high-impact journal articles.Primary outcome measuresThe distribution of authorship was assessed using the Gini coefficient (GC), a widely used measure of economic inequality.ResultsThe overall GC for all articles sampled across the 12-year study period was 0.49, and the GCs for the first and last authorship positions were 0.30 and 0.44, respectively. Since 2008, there was a significant positive correlation between year and GC for the overall authorship position (r=0.99, p<0.001) the first author position (r=0.75, p=0.007) and the last author position (r=0.85, p<0.001) indicating increasingly uneven distribution in authorship over time. The cross-specialty high-impact journals exhibited the greatest rate of increase in GC over the study period for the first and last author position of any specialty analysed.ConclusionOverall, these data suggest a growing inequality in authorship across authors publishing in high-impact academic medical journals, especially among the highest impact journals. These findings may have implications for processes such as promotions and allocation of research funding that use authorship metrics as key criteria for making decisions.
Movements of selected minnows between the lower Yellowstone River and its tributaries
Authors: Duncan Michael B. , Bramblett Robert G. , Zale Alexander V. 
Published: January 2021

Reduced population connectivity has been implicated as a cause of decreased distributions and abundances of many Great Plains fishes. However, scant empirical evidence quantifying movement and relating the contribution of spatial linkages to population abundances and resilience exists. We used otolith microchemistry analysis to characterize the movements of western silvery minnows (Hybognathus argyritis Girard, 1856), flathead chubs (Platygobio gracilis (Richardson, 1836)), and sand shiners (Notropis stramineus (Cope, 1865)) between the Yellowstone River and its tributaries. Sixty-nine percent of western silvery minnows, 65% of flathead chubs, and 42% of sand shiners moved between the Yellowstone River and tributaries. Mean total number of interchanges was highest among western silvery minnows (4.8 interchanges/mover), intermediate among flathead chubs (4.3 interchanges/mover), and lowest among sand shiners (1.4 interchanges/mover; P < 0.01). Natal movements were rare, but juvenile movements were common and frequent among all three species. Movements between main-stem and tributary habitats are probably prominent facets of the life cycles of other Great Plains minnows. Therefore, connectivity among such habitats should be a high conservation priority to enhance the long-term viability of such fishes.
Design and implementation of a smart home system with two levels of security based on IoT technology
Authors: Murad Mohammed , Bayat Oguz , M. Marhoon Hamzah 
Published: January 2021

<span>Besides the development of technology in recent years, there has been an effective tendency to construct smart cities and homes. Whereas the smart home control system components can be incorporated with the existing home appliances to eliminate the need for human intervention, save electricity, protect homes from accidents as well as the theft, and provide home residents with comfort. This work comprises the utilising of the internet of things (IoT) technology to build the proposed design for the smart home. The proposed design includes many subsystems as well as several types of sensors, such as the passive infrared (PIR) sensor, the gas sensor, the soil moisture sensor, the water level sensor, the temperature sensor, the light dependent resistance (LDR), and the flame sensor. Each sensor will be connected to the Arduino Nano for the data processing purpose, after which the Arduino Nano will be connected to the NodeMCU module via the digital pins to implement the IoT subsystem. The proposed system also includes a smart garage gate based on Bluetooth HC-05 module with a specially programmed android app. </span>
Categorizing and measurement satellite image processing of fire in the forest greece using remote sensing
Authors: Mohammed Ali Abdul Wahhab , Khamees Hussein Thary 
Published: January 2021

This paper has been utilized satellite Sentinel-2A imagery, this satellite is a polar-orbiting, multispectral high-resolution to cover Athens city, Greece that located at latitude (37° 58′ 46″) N, (23° 42′ 58″) E.,the work aims to measurement and study the wildfires natural resourcesbefore and after fire break out that happenedin forests of Athens city in Greece for a year (2007, 2018) and analysis the damage caused by these wildfiresand their impact on environment and soil by categorize the satellite images for the interested region before and after wildfires for a year (2007) and a year (2018) and Discuss techniques that compute the area covered of each class and lessen or limit the rapidly spreading wildfires damage.The categorizing utilizing the moments with (K-Means) grouping algorithm in RS (remote sensing). And the categorizing results show five unique classes (water, trees, buildings without tree, buildings with tree, bare lands) where, it can be notice that the region secured by each class before and after wildfires and the changed pixels for all classes.The experimental resulted of categorizing technique shows that the good performance exactness with a good categorizing and result analysisa bout the harms resulted from the fires in the forest Greece for a years (2007 and 2018).
Le rapport connotation/dénotation à l’épreuve des mythologies de Barthes
Authors: Perusset Alain 
Published: January 2021

La problématique du rapport entre dénotation et connotation, termes introduits en linguistique par Hjelmslev au milieu du siècle passé, resurgit fréquemment dans les débats sémiotiques. Greimas (1968), Rastier (1987), Klinkenberg (1996) et Badir (2014) se sont notamment penchés sur la question, proposant des lectures, si ce n’est opposées, en tout cas à chaque fois éclairantes. Également, les commentateurs de Barthes, tels Eco et Pezzini (1982) ou Zenkine (1997), ont indirectement contribué au débat en considérant les « mythologies » du sémiologue français comme des types de connotations. Or, ainsi que se propose de le montrer cet article, les mythologies s’avèrent non pas ressortir du phénomène de la connotation, mais de la dénotation. Ainsi, l’objectif de ce travail sera d’enrichir la discussion sur ces langages sémiotiques, en contredisant cette croyance selon laquelle les mythologies seraient des formes de connotations, autrement dit, en faisant dialoguer Hjelmslev et Barthes sur la question des significations culturelles.
Graphene oxide nanofilm and chicken embryo extract decrease the invasiveness of HepG2 liver cancer cells
Authors: Sosnowska Malwina , Kutwin Marta , Strojny Barbara , Koczoń Piotr , Szczepaniak Jarosław , Bałaban Jaśmina , Daniluk Karolina , Jaworski Sławomir , Chwalibog André , Bielawski Wiesław , Sawosz Ewa 
Published: January 2021

Abstract
Background
The extracellular matrix (ECM) is a mosaic of various structural and functional proteins that cooperate with the cell, regulate adhesion, and consequently manage its further fate. Liver destruction is accompanied by a disruption of the physicochemical properties of the ECM which deregulates the cell–ECM interaction and can lead to uncontrolled proliferation and neoplastic transformation of cells. Therefore, it can be assumed that ECM modification and restoration of its characteristics for healthy tissue may counteract uncontrolled cell proliferation. The purpose of the presented research model was to optimise the physical characteristics of ECM by introducing a graphene oxide plane/nanofilm (nfGO) and enriching the cell environment with potentially missing proteins by adding a functional protein cocktail (chicken embryo liver extract) and determine the impact of these factors on cell–ECM cooperation and its consequences on adhesion, proliferation, and cell phase, which are factors of the invasiveness of cancer cells.

Results
Experiments were performed with non-cancer HS-5 cells and liver cancer cells HepG2 and C3A. The cells were divided into four groups: (1) control, (2) cultured on nfGO, (3) cultured with the addition of chicken embryo liver extract (CELE) and (4) cultured on the nfGO with the addition of CELE. CELE contained 1735 proteins; the top 57 of these proteins have been presented. The use of nfGO as well as CELE and nfGO + CELE reduced the proliferation of HepG2 cancer cells to the greatest extent; this is in contrast to non-cancer cells and also to C3A cancer cells. Furthermore, the combined use of the CELE protein cocktail and GO substrate effectively resulted in a decrease in the population of HepG2 cells in the G0/G1 phase and an increase of the population in G2/M. Molecular analysis of HepG2 cancer cells also showed an increase in the expression of genes responsible for adhesion such as focal adhesion kinase (fak), e-cadherin, and n-cadherin and a decrease in β-catenin, which is considered a proto-oncogene.

Conclusions
Studies have shown that both the GO surface structure on which the cells are grown as well as the presence of a multi-component natural cocktail of regulatory proteins, can modify the expression of integrins, increase adhesion and, as a consequence, proliferation and the cell cycle—entering the resting phase. For the first time, it has been documented that hepatic cancer cells of the HepG2 line under the influence of stimuli derived from mimic ECM (graphene oxide) in interaction with a unique protein complex derived from chicken liver embryo decreased of the invasiveness of cancer cells.
Curcumin-enriched Gemini surfactant nanoparticles exhibited tumoricidal effects on human 3D spheroid HT-29 cells in vitro
Authors: Zibaei Zohre , Babaei Esmaeil , Rezaie Nezhad Zamani Arezoo , Rahbarghazi Reza , Azeez Hewa Jalal 
Published: January 2021

Abstract
Background
Here, we examined the tumoricidal effect of Gemini surfactant nanoparticles enriched with curcumin on 3D spheroid HT-29 cells. The delivery of curcumin and other phytocompounds to the tumor niche is an important challenge.

Methods
Spheroid HT-29 cells were generated by using a conventional hanging drop method and exposed to different concentrations of Gemini-curcumin nanoparticles. The changes in spheroid integrity and cell viability were evaluated by measuring the spheroid diameter and LDH release, respectively. The uptake of Gemini-curcumin nanoparticles was detected by flow cytometry assay. Flow cytometric of Rhodamine 123 efflux was also performed. Migration capacity was analyzed using a Transwell insert assay. By using real-time PCR analysis and Western blotting, we studied the expression level of MMP-2, -9, Vimentin, and E-cadherin genes.

Results
Gemini-curcumin nanoparticles had the potential to disintegrate spheroids and decrease central density compared to the control group (p < 0.05). These changes coincided with enhanced LDH release by the increase of nanoparticle concentration (p < 0.05). Data highlighted the ability of cells to uptake synthetic nanoparticles in a dose-dependent manner. We found reduced Rhodamine 123 efflux in treated HT-29 spheroid cells compared to the control (p < 0.05). Nanoparticles significantly decreased the metastasis and epithelial-mesenchymal transition (EMT) rate by the suppression of MMP-2 and MMP-9, Vimentin, and induction of E-cadherin (p < 0.05).

Conclusion
Our data confirmed that Gemini curcumin has the potential to suppress cell proliferation and inhibit metastasis in 3D spheroid HT-29 cells in vitro.
recoup: flexible and versatile signal visualization from next generation sequencing
Authors: Moulos Panagiotis 
Published: January 2021

Abstract
Background
The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlying signal generated to answer important qualitative and quantitative biological questions. As a result, the need for novel software able to reliably produce quick, comprehensive, and easily repeatable genomic signal visualizations in a user-friendly manner is rapidly re-emerging.

Results
recoup is a Bioconductor package for quick, flexible, versatile, and accurate visualization of genomic coverage profiles generated from Next Generation Sequencing data. Coupled with a database of precalculated genomic regions for multiple organisms, recoup offers processing mechanisms for quick, efficient, and multi-level data interrogation with minimal effort, while at the same time creating publication-quality visualizations. Special focus is given on plot reusability, reproducibility, and real-time exploration and formatting options, operations rarely supported in similar visualization tools in a profound way. recoup was assessed using several qualitative user metrics and found to balance the tradeoff between important package features, including speed, visualization quality, overall friendliness, and the reusability of the results with minimal additional calculations.

Conclusion
While some existing solutions for the comprehensive visualization of NGS data signal offer satisfying results, they are often compromised regarding issues such as effortless tracking of processing and preparation steps under a common computational environment, visualization quality and user friendliness. recoup is a unique package presenting a balanced tradeoff for a combination of assessment criteria while remaining fast and friendly.
Examination of hydrogen cross-feeders using a colonic microbiota model
Authors: Smith Nick W. , Shorten Paul R. , Altermann Eric , Roy Nicole C. , McNabb Warren C. 
Published: January 2021

Abstract
Background
Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing.

Results
An existing mathematical model for microbial community growth and metabolism was combined with models for each of the three hydrogenotrophic functional groups. The model was further developed for application to the colonic environment via inclusion of responsive pH, host metabolite absorption and the inclusion of host mucins. Predictions of the model, using two existing metabolic parameter sets, were compared to experimental faecal culture datasets. Model accuracy varied between experiments and measured variables and was most successful in predicting the growth of high relative abundance functional groups, such as the Bacteroides, and short chain fatty acid (SCFA) production. Two versions of the colonic model were developed: one representing the colon with sequential compartments and one utilising a continuous spatial representation. When applied to the colonic environment, the model predicted pH dynamics within the ranges measured in vivo and SCFA ratios comparable to those in the literature. The continuous version of the model simulated relative abundances of microbial functional groups comparable to measured values, but predictions were sensitive to the metabolic parameter values used for each functional group. Sulphate availability was found to strongly influence hydrogenotroph activity in the continuous version of the model, correlating positively with SRB and sulphide concentration and negatively with methanogen concentration, but had no effect in the compartmentalised model version.

Conclusions
Although the model predictions compared well to only some experimental measurements, the important features of the colon environment included make it a novel and useful contribution to modelling the colonic microbiota.
Cell-specific characterization of the placental methylome
Authors: Yuan Victor , Hui Desmond , Yin Yifan , Peñaherrera Maria S. , Beristain Alexander G. , Robinson Wendy P. 
Published: January 2021

Abstract
Background
DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epigenetically distinct cell populations. Here, we present the first methylome-wide analysis of first trimester (n = 9) and term (n = 19) human placental samples of four cell populations: trophoblasts, Hofbauer cells, endothelial cells, and stromal cells, using the Illumina EPIC methylation array, which quantifies DNAm at > 850,000 CpGs.

Results
The most distinct DNAm profiles were those of placental trophoblasts, which are central to many pregnancy-essential functions, and Hofbauer cells, which are a rare fetal-derived macrophage population. Cell-specific DNAm occurs at functionally-relevant genes, including genes associated with placental development and preeclampsia. Known placental-specific methylation marks, such as those associated with genomic imprinting, repetitive element hypomethylation, and placental partially methylated domains, were found to be more pronounced in trophoblasts and often absent in Hofbauer cells. Lastly, we characterize the cell composition and cell-specific DNAm dynamics across gestation.

Conclusions
Our results provide a comprehensive analysis of DNAm in human placental cell types from first trimester and term pregnancies. This data will serve as a useful DNAm reference for future placental studies, and we provide access to this data via download from GEO (GSE159526), through interactive exploration from the web browser (https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/), and through the R package planet, which allows estimation of cell composition directly from placental DNAm data.