bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gender Minorities in Simulation: A Mixed Methods Study of Medical School Standardized Patient Programs in the United States and Canada
Authors: Bohnert Carrie A. , Combs Ryan M. , Noonan Emily J. , Weathers Aaron E. , Weingartner Laura A. 
Published: December 2020

Purpose
A provider's ability to translate knowledge about transgender health to affirming patient care is key to addressing disparities. However, standardized patient (SP) programs have little published guidance for gender-affirming care or addressing disparities experienced by transgender and nonbinary patients.

Method
Between 2018 and 2019, we invited all 208 accredited US and Canadian medical schools to participate in a study to determine how gender minorities are represented in SP encounters. Responding programs (n = 59, response rate = 28%) that represented patients with diverse gender identities were invited to complete semistructured interviews about SP case content, impact, and barriers to this work. Discussions were analyzed using a modified grounded theory method.

Results
Fifty nine of 208 eligible programs (response rate = 28.3%) completed our survey and 24 completed interviews. More than half of programs used gender minority SPs (n = 35, 59.3%). More than half of the programs also reported portraying gender minority cases (n = 31, 52.5%). Interviewees described how effective SP simulation required purposeful case development, engaging subject matter experts with lived experience, and ensuring psychological safety of gender minority SPs. Barriers included recruitment, fear of disrespecting gender minority communities, and transphobia. Engaging gender minorities throughout case development, training, and implementation of SP encounters was perceived to reduce bias and stereotyping, but respondents unanimously desired guidance on best practices on SP methodology regarding gender identity.

Conclusions
Many programs have established or are developing SP activities that portray gender minority patients. Effective SP simulation hinges on authenticity, but the decisions around case development and casting vary. Specifically, programs lack consensus about who should portray gender minority patients. This research suggests that input from gender minority communities both to inform best practices at the macro level and in an ongoing advisory capacity at the program level will be essential to teach gender-affirming care.
Implementation of Simulation Training During the COVID-19 Pandemic
Authors: Pan Di , Rajwani Kapil 
Published: December 2020

Summary Statement
Simulation played a critical role in our institution's response to the COVID-19 pandemic in New York City. With the rapid influx of critically ill patients, resource limitations, and presented safety concerns, simulation became a vital tool that provided solutions to the many challenges we faced. In this article, we describe how simulation training was deployed at our institution throughout the course of the pandemic, which included the period of our medical surge. Simulation helped refine protocols, facilitate practice changes, uncover safety gaps, and train redeployed healthcare workers in unfamiliar roles. We also discuss the obstacles we encountered with implementing simulations during the pandemic, the measures we took to adapt to our limitations, and the simulation strategies and end products that were derived from these adaptations.
Source Imaging of Triphasic Waves and Other Encephalopathies
Authors: Zafar Muhammad S. , Rahman Shareena A. , Ehrenberg Joshua Andrew , Kaplan Peter W. 
Published: December 2020

Purpose:
Triphasic waves (TWs) are defined as high-amplitude positive waveforms with preceding and after-going negative waves, typically seen in medically ill patients. TWs manifest in similar clinical presentations as other EEG encephalopathies; however, electrographically, they appear different. To better understand the difference, the authors used two different source localization software programs to find a reproducible and unique signature for TW.

Methods:
EEGs performed at Johns Hopkins Hospital and Duke University Hospital were retrospectively analyzed. EEG samples of TW, Delta, Theta-Delta, and Frontal Intermittent Rhythmic Delta Activity were selected. The authors did source localization via Commercial Curry 8 and open-source Brainstorm software. A minimum of 10 stereotypical waveforms per subject were selected. The authors used the Boundary Element Method for the head model, which was derived from the Montreal Neurological Institute averaged imaging data set. Dipole and current density analyses were performed.

Results:
Twenty-eight patients were selected (10 TW, 4 Frontal Intermittent Rhythmic Delta Activity, 6 Theta-Delta, and 8 Delta). The findings suggest the activation of anterior frontal and midline structures for TW. Frontal Intermittent Rhythmic Delta Activity had a similar localization but without a moving dipole. In comparison, the Delta and Delta-Theta appeared to have a more diffuse origin.

Conclusions:
Source analysis of TW via two different software suggests the anterior midline location of TW with anterior to posterior propagation. These findings correlate with the previous hypotheses of TW origin. Retrospective analysis, low number of recording electrodes, and difficult analysis of slow waves limit the interpretation of these results. Nonetheless, this article opens the prospect of future studies in this field.
Kineobactrum salinum sp. nov., isolated from marine sediment
Authors: Kim Minji , Cha In-Tae , Lee Ki-Eun , Lee Byoung-Hee , Park Soo-Je 
Published: December 2020

Strain M2T, isolated from marine sediment collected at Jeju Island, was an aerobic, Gram-stain-negative, oxidase- and catalase-positive, motile, rod-shaped bacterium that formed circular, raised, yellow colonies. Strain M2T grew at 15–42 °C, pH 5.5–9.0 and with 1–9 % (w/v) NaCl. Phylogenetic analysis based on its 16S rRNA gene sequences indicated that strain M2T was closely related to

Kineobactrum sediminis

F02T (98.0 % sequence similarity). Ubiquinone-8 was determined to be the sole respiratory quinone. Summed feature 3 (C16 : 1
ω6c/C16 : 1
ω7c) and summed feature 8 (C18 : 1
ω7c/C18 : 1
ω6c) were identified as the predominant fatty acids. The DNA G+C content and digital DNA–DNA relatedness between strain M2T and

K. sediminis

F02T were 60.7 mol% and 19.5 %, respectively. Phosphatidylglycerol and phosphatidylethanolamine were identified as the major polar lipids. Thus, polyphasic characterization revealed that strain M2T represents a novel species in the genus

Kineobactrum

, for which the name Kineobactrum salinum sp. nov. is proposed. The type strain is M2T (=KCTC 72815T=VTCC 910108T).
COVID-19 Trends in Florida K-12 Schools, August 10 – November 14, 2020
Authors: Jones Rebekah D. 
Published: December 2020

AbstractData collected from 38 states from August 3 – November 15, 2020 showed more than 250,000 confirmed student and staff cases of SARS-CoV-2 in K-12 schools1. Yet, analysis of COVID-19 case data in USA schools has been extremely limited2,3. To date, no large-scale or state-wide analyses by school level and grade has been published, opening a wide gap in understanding COVID-19 in American schools. A large-scale assessment of available data and trends could provide a baseline for understanding the virus in the K-12 learning environment and dispel misconceptions about the prevalence of COVID-19 in schools.Table of Contents SummaryUsing the most comprehensive database of K-12 COVID-19 case data in the country, Florida provides clues for understanding student and staff cases in schools.What’s known on this subjectFlorida schools began reopening to in-person instruction in August have reported more than 18,000 student and staff cases of COVID-19 as of November 14, 2020. Incidence of COVID-19 cases in K-12 students and staff is of urgent public health concern.What this study addsCOVID-19 cases reported in Florida schools were most influenced by community case rates, district mask policies, and percent of students attending face-to-face. Student case rates were highest in high schools (12.5 per 1,000).
TAPER: Pinpointing errors in multiple sequence alignments despite varying rates of evolution
Authors: Zhang Chao , Zhao Yiming , Braun Edward L , Mirarab Siavash 
Published: December 2020

AbstractErroneous data can creep into sequence datasets for reasons ranging from contamination to annotation and alignment mistakes. These errorscanreduce the accuracy of downstream analyses such as tree inference andwilldiminish the confidence of the community in the results even when they do not impact the analysis. As datasets keep getting larger, it has become difficult to visually check for errors, and thus, automatic error detection methods are needed more than ever before. Alignment masking methods, which are widely used, completely remove entire aligned sites. Therefore, theymayreduce signal as much as or more than they reduce the noise. An alternative is designing targeted methods that look for errors in small species-specific stretches of the alignment by detecting outliers. Crucially, such a method should attempt to distinguish the real heterogeneity, which includes signal, from errors. This type of error filtering is surprisingly under-explored. In this paper, we introduce TAPER, an automatic algorithm that looks for small stretches of error in sequence alignments. Our results show that TAPER removes very little data yet finds much of the error and cleans up the alignments.
Impact of COVID-19 restrictions on pre-school children’s eating, activity and sleep behaviours: a qualitative study
Authors: Clarke JL , Kipping R , Chambers S , Willis K , Taylor H , Brophy R , Hannam K , Simpson SA , Langford R 
Published: December 2020

AbstractBackgroundIn spring 2020, the COVID-19 lockdown placed unprecedented restrictions on the behaviour and movements of the UK population. Citizens were ordered to ‘stay at home’, only allowed to leave their houses to buy essential supplies, attend medical appointments or exercise once a day. This qualitative study explored how ‘lockdown’ and its subsequent easing changed young children’s everyday activities, eating and sleep habits to gain insight into the impact for health and wellbeing.MethodsIn summer 2020 we interviewed 20 parents of children due to start school in September 2020 (aged 3-5 years) by phone or video call to explore their experiences of lockdown and its easing. We recruited participants through nurseries and local Facebook community groups in the South West and West Midlands of England. Half the sample were from Black, Asian or Minority Ethnic backgrounds and half lived in the most deprived quintile. We analysed interviews using thematic analysis.ResultsChildren’s activity, screen time, eating, and sleep routines had some level of disruption. Parents reported children ate more snacks during lockdown, but also spent more time preparing meals and eating as a family. Most parents reported a reduction in their children’s physical activity and an increase in screen time, which some linked to difficulties in getting their child to sleep. Parents sometimes expressed guilt about changes in activity, screen time and snacking over lockdown. Most felt these changes would be temporary with no lasting impact, though others worried about re-establishing healthy routines.ConclusionsThe spring COVID-19 lockdown negatively impacted on pre-school children’s eating, activity and sleep routines. While some positive changes were reported, there were wide-spread reports of lack of routines, habits and boundaries which, at least in the short-term, were likely to have been detrimental for child health and development. Guidance and support for families during times of COVID-19 restrictions could be valuable to help them maintain healthy activity, eating, screen-time and sleeping routines to protect child health and ensure unhealthy habits are not adopted.
Does living close to petrochemical complex increase the adverse psychological effects of COVID-19 lockdown?
Authors: Vicens Paloma , Heredia Luis , Bustamante Edgar , Pérez Yolanda , Domingo José L. , Torrente Margarita 
Published: December 2020

ABSTRACTThe petrochemical industry has made possible the economic development of many local communities, increasing the employment opportunities and generating a complex network of secondary industries closely related to those. However, it is known that petrochemical industries emit air pollutants, which are related to different negative effects on mental health. In addition, many people around the world are being exposed to highly stressful situations derived from the COVID-19 pandemic and the lockdown adopted by the national and regional governments. The present study was aimed at analysing the possible differential effects on different psychological outcomes (stress, anxiety, depression and emotional regulation strategies) derived from the COVID-19 pandemic and the consequent lockdown in individuals living near an important petrochemical complex and subjects living in other areas, non-exposed to the characteristic environmental pollutants emitted by this kind of complexes. The sample was composed by 1607 subjects which respond a questionnaire developed ad hoc about the confinement conditions, the Perceived Stress Scale (PSS), the Hospital Anxiety and Depression Scale (HADS), the Barratt Impulsivity Scale (BIS) and the Emotional Regulation Questionnaire (ERQ). The results indicated that people living closer to petrochemical complexes reported greater risk perception. However, no significant relationships between psychological variables and proximity to the focus were detected when compared people living near to or far away from a chemical/petrochemical complex. Regarding the adverse psychological effects of the first lockdown due to COVID-19 on the general population in Catalonia, we can conclude that the lockdown conditions included in this survey were mainly related to changes in the impulsivity levels of participants. However, we can also suggest that the economic effects are going to be harder than those initially detected in this study. More studies are necessary to corroborate our results.Author ContributionsConceptualization: Paloma Vicens, Luis Heredia, José L. Domingo, Margarita TorrenteFunding Acquisition: José L. DomingoData Curation and Formal Analysis: Paloma Vicens, Luis Heredia, Edgar Bustamante, Yolanda Pérez, Margarita TorrenteMethodology: Paloma Vicens, Luis Heredia, Margarita TorrenteWriting-original draft: Paloma Vicens, Luis HerediaWriting- review and editing: Paloma Vicens, Luis Heredia, Yolanda Pérez, José L. Domingo, Margarita Torrente
Is the end near? When the different countries will surmount COVID-19 pandemic: new approach applying physical, mathematical and game theory models
Authors: García de Alcañíz J. G. , López-Rodas V. , Costas E. 
Published: December 2020

AbstractIn the year 2020 COVID-19 pandemic was a global issue that changed mankinds lifestyle. Since then, when we will control the pandemic and recover our normal life has become the paramount question to be answered, and it needs to be solved. One problem is that there are wealthy countries, with very good health care systems and scientific resources while others barely dedicate 100 US $ per citizen per year, rich countries could cooperate at different levels with poorer ones. In such a diverse context classic epidemiology models, excellent for predicting short term evolution of the pandemic at a local level are not as suitable for long term predictions at a global scale specially if the data they use are of questionable accuracy. Alternatively, big data and AI approaches have been tried. There is an option that can be more effective. Physics applies predictive models about the duration of an event based on analysing the dynamics of the time evolution of the event itself. These models can be used alongside with probabilistic and game theory models that consider different degrees of cooperation. By means of the physics Delta-targument and a game theory model (cooperate versus defector) we calculate when different countries may control COVID-19 pandemic. In a non-cooperate model, those countries with more resources and best manage the pandemic will have it under control between May and September 2021, whereas those with no resources will suffer the pandemic until at least October 2023. On the other hand, a strong cooperative model will allow that the majority could control the COVID-19 pandemic between October 2021 and November 2022.
Transcriptional Landscape of Hepatocellular Carcinoma Reveals that Patient Ethnic-Origin Influences Patterns of Expression
Authors: Zayas Rachel , Sisson Artemio , Kuhnsman Ariana , Nagalo Bolni Marius , Roberts Lewis R. , Buetow Kenneth 
Published: December 2020

AbstractThe global incidence of hepatocellular carcinoma (HCC) has increased threefold in the last 30 years. In the United States, individuals with ancestry from Asia, Africa and Latin America have a significantly higher risk of developing HCC. However, the molecular mechanisms by which HCC disparities occur remain mostly understudied. Herein, we employed advanced bioinformatics analysis tools to identify genomic drivers that could explain the differences seen among HCC patients of distinct ethnicities (geographic origins). Data from TCGA and open-source software tools HiSTAT, StringTie, and Ballgown were used to map next-generation sequencing (NGS) reads from DNA and RNA, assemble transcripts, and quantify gene abundance. Differential genes/transcripts were mapped to known biomarkers and targets of systemic HCC therapeutics. Four overlapping transcripts were identified between each ethnicity group: FCN2, FCN3, COLEC10, and GDF2. However, we also found that multiple genes are expressed in an ethnicity-specific manner. Our models also revealed that both current and emerging biomarkers fail to capture heterogeneity between patients of different ethnicities. Finally, we have determined that first-line treatment, such as Sorafenib, may be better suited for Asian patients, while Lenvatinib may exhibit better efficacy for Caucasian patients. In conclusion, we have outlined that the pathways involved in early hepatocarcinogenesis may occur in an ethnicity-specific manner and that these distinct phenotypes should be taken into account for biomarker and therapeutic development.
Spatiotemporal analysis of glioma heterogeneity reveals Col1A1 as an actionable target to disrupt tumor mesenchymal differentiation, invasion and malignancy
Authors: Comba Andrea , Faisal Syed M. , Dunn Patrick J. , Argento Anna E. , Hollon Todd C. , Al-Holou Wajd N. , Varela Maria Luisa , Zamler Daniel B. , Quass Gunnar L , Apostolides Pierre F. , Abel Clifford , Brown Christine E. , Kish Phillip E. , Kahana Alon , Kleer Celina G. , Motsch Sebastien , Castro Maria G , Lowenstein Pedro R. 
Published: December 2020

ABSTRACTIntra-tumoral heterogeneity and diffuse infiltration are hallmarks of glioblastoma that challenge treatment efficacy. However, the mechanisms that set up both tumor heterogeneity and invasion remain poorly understood. Herein, we present a comprehensive spatiotemporal study that aligns distinctive intra-tumoral histopathological structures, oncostreams, with dynamic properties and a unique, actionable, spatial transcriptomic signature. Oncostreams are dynamic multicellular fascicles of spindle-like and aligned cells with mesenchymal properties, detected usingex vivoexplants andin vivointravital imaging. Their density correlates with tumor aggressiveness in genetically engineered mouse glioma models, and high-grade human gliomas. Oncostreams facilitate the intra-tumoral distribution of tumoral and non-tumoral cells, and the invasion of the normal brain. These fascicles are defined by a specific molecular signature that regulates their organization and function. Oncostreams structure and function depend on overexpression of COL1A1. COL1A1 is a central gene in the dynamic organization of glioma mesenchymal transformation, and a powerful regulator of glioma malignant behavior. Inhibition of COL1A1 eliminated oncostreams, reprogramed the malignant histopathological phenotype, reduced expression of the mesenchymal associated genes, induced changes in the tumor microenvironment and prolonged animal survival. Oncostreams represent a novel pathological marker of potential value for diagnosis, prognosis, and treatment.
Species-resolved sequencing of low-biomass microbiomes by 2bRAD-M
Authors: Sun Zheng , Huang Shi , Zhu Pengfei , Tzehau Lam , Zhao Helen , Lv Jia , Zhang Rongchao , Zhou Lisha , Niu Qianya , Wang Xiuping , Zhang Meng , Jing Gongchao , Bao Zhenmin , Liu Jiquan , Wang Shi , Xu Jian 
Published: December 2020

AbstractMicrobiome samples with low microbial biomass or severe DNA degradation remain challenging for amplicon-based (e.g., 16S/18S-rRNA) or whole-metagenome sequencing (WMS) approaches. Here, we introduce 2bRAD-M, a highly reduced and cost-effective metagenome-sequencing strategy which only sequences ~1% of metagenome and can simultaneously produce species-level bacterial, archaeal, and fungal profiles for low-biomass and highly degraded samples. For mock communities, 2bRAD-M can accurately generate species-level taxonomic profiles for otherwise hard-to-sequence samples with (i) low biomass of merely 1 pg of total DNA, (ii) high host DNA contamination (99%), and (iii) severely fragmented DNA (50-bp) from degraded samples. Tests of 2bRAD-M on stool, skin and environment-surface samples deliver successful reconstruction of comprehensive, high-resolution microbial profiles with agreement across 16S-rRNA, WMS and existing literature. In addition, it enables microbial profiling in formalin-fixed paraffin-embedded (FFPE) cervical tissue samples which were recalcitrant to conventional approaches due to the low amount and heavy degradation of microbial DNA, and discriminated healthy tissue, pre-invasive cancer and invasive cancer via species-level microbial profiles with 91.1% accuracy. Therefore, 2bRAD-M greatly expands the reach of microbiome sequencing.
New self-identities evolve via point mutation in an invertebrate allorecognition gene
Authors: Huene Aidan , Chen Traci , Nicotra Matthew L. 
Published: December 2020

SummaryMany organisms use genetic self-recognition systems to distinguish themselves from other members of their species. To understand how new self-identities evolve, we studied Allorecognition 2 (Alr2), a self-recognition gene from the colonial cnidarian,Hydractinia symbiolongicarpus.Alr2encodes a highly polymorphic transmembrane protein that discriminates self from non-self by selectively binding across cell membranes to other Alr2 proteins with identical or very similar sequences. Here, we show that new Alr2 proteins evolve by amino acid substitutions that immediately create isoforms with entirely novel binding specificities, or through intermediates with relaxed binding specificities. Our results also suggest a topology for homophilic interactions between Alr2 proteins. These results provide direct evidence for the generation and maintenance of functional variation at an allorecognition locus and reveal that one-component and two-component self-recognition systems evolve via different mechanisms.