bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Convalescent Plasma Therapy in Hospitalized Patients With Severe COVID-19
Authors: Walsh Thomas L. , Shively Nathan R. , Carr Dustin R. , Bremmer Derek N. , Hoffmann Chas , Jacobs Max W. , Santelices Linda , Anderson Michael , Rutman Sarah , Wilson Nicole , Thomas Aaron , Schorr Rebecca , Hobart Emily , Kosoglow Molly , Ogbebor Osakpolor , Moffa Matthew A. 
Published: November 2022

Background
Convalescent plasma (CP) is often administered to hospitalized patients with COVID-19, but the impact on clinical outcomes has varied across different patient populations.

Methods
A retrospective, propensity score–matched controlled study was conducted to compare outcomes of hospitalized patients with nonmechanically ventilated severe COVID-19 who received CP within 36 hours of hospital admission with those who did not receive CP during their hospitalization. A combination of propensity score matching and Mahalanobis distance matching was used.

Results
One hundred forty-three patients were originally in the treatment group, and 94 were able to be matched to control patients who did not receive CP during their hospital stay. Receipt of early CP was not associated with significant differences in clinical outcomes. Overall 30-day mortality was 12.8% in the CP group and 14.9% in the non-CP group (P = 0.67). No significant differences were observed between the early CP group and the non-CP group for 30-day readmissions (12.8% vs 9.6%; P = 0.47), subsequent transfer to an intensive care unit (2.1% vs 2.1%; P = 1.0), and subsequent progression to noninvasive ventilation after 36 hours from admission (12.8% vs 5.3%; P = 0.07). Receipt of early CP was associated with increased need for mechanical ventilation after 36 hours from admission (12.8% vs 3.2%; P = 0.013).

Conclusions
Receipt of early CP for hospitalized patients with severe COVID-19 but not requiring mechanical ventilation was not associated with improvements in clinical status or mortality compared with matched patients who did not receive CP.
Implementing an intravenous ketamine protocol for acute pain in the medical-surgical setting
Authors: Hunter Oluwatobi O. , Lu Alan , Fretwell Deborah , Mariano Edward R. 
Published: November 2022

ABSTRACT
A subanesthetic intravenous ketamine infusion is a safe and effective acute pain management modality for moderate to severely painful surgical procedures and may be useful in patients who are at increased risk for opioid-related adverse events. Despite its safety profile, intravenous ketamine is often restricted to the intensive care unit, which results in decreased patient access to this effective therapy. For clinicians who wish to implement an intravenous ketamine protocol in the medical-surgical setting, there are few resources available. In this brief report, we present our ketamine infusion protocol for acute pain and the clinical and financial outcomes 1 year after implementation. In our experience, ketamine infusions on the medical-surgical ward are safe and cost-effective when an established acute pain service protocol is followed. Nurse practitioners play an essential role in increasing patient access to intravenous ketamine infusions and leading change by collaborating with stakeholders to develop a protocol, training nurses and interdisciplinary team members, and providing ongoing support to nursing staff.
Uncollimated gamma camera measurements at two metres to the patient provide a practical and statistically robust method for SeHCAT retention calculation
Authors: Willson Tamar , Meades Richard 
Published: November 2022

[75Se]tauroselcholic acid (SeHCAT) retention studies may be performed using a collimated or uncollimated (intrinsic) gamma camera, with trade-offs between counting sensitivity, collision risk, and stray source influence. In this work, we evaluate the uncertainty in SeHCAT studies performed in ‘outer room’ mode, where the patient sits or stands two metres away from the uncollimated camera face.
768 SeHCAT studies performed at the Royal Free Hospital were analysed retrospectively, and in all cases, the absolute uncertainty was found to be well within the clinically acceptable limit of ±1 percentage point at 15% retention.
The mean counting sensitivity was found to be 1.64 cps/kBq, which is higher than collimated counting but lower than uncollimated counting with the patient on the couch. Seeing as the outer room method does not require patients to transfer onto the couch it may provide savings in setup time which may offset the necessarily longer acquisition time. Because the patient does not come into close proximity to the unprotected camera face the risk of collision is also reduced.
Spectra from a SeHCAT capsule in a water-filled torso phantom were used to examine the potential impact of modifying the energy windows. We recommend adopting a wide central photopeak and downscatter window (160–296 keV) plus a lower photopeak window (111–159 keV), which may provide significant improvements in sensitivity. This improved sensitivity could be used to reduce the acquisition time, which is of particular interest in the context of increasing numbers of referrals for SeHCAT retention tests.
Risk Factors for Readmission Following Febrile Neutropenia in Pediatric Oncology Patients
Authors: McCormick Meghan , Richardson Troy , Rapkin Louis , Kalpatthi Ram 
Published: November 2022

Febrile neutropenia is the most common reason for admission from the emergency department for pediatric oncology patients. We identified pediatric inpatients age 1 to 21 years with an International Classification of Diseases, Ninth Revision (ICD-9) diagnosis code of malignancy and either fever with neutropenia or fever alone over a 6-year period (2007-2012) using the PHIS+ database. We evaluated factors associated with readmission within 7 days after index hospitalization. There were 4029 index hospitalizations among 2349 patients in 6 hospitals, 294 encounters (7.3%) were followed by readmission within 7 days. Factors associated with increased odds of readmission included being in the lowest quartile for median household income (odds ratio [OR]=1.64, P=0.009), diagnosis of acute lymphoblastic leukemia (OR=1.37, P=0.016), lack of anerobic coverage during index hospitalization (OR=1.48, P=0.026), and absolute neutrophil count <200 cells/μL at discharge from index hospitalizations (OR=1.55, P=0.008). Patients who required readmission had a longer median length of stay and greater hospitalization costs during the index hospitalization. There was a trend towards increasing hospitalization rates for febrile neutropenia over time. While absolute neutrophil count is incorporated into many risk stratification strategies for fever management, further work should focus on addressing socioeconomic factors which may impact readmission rates.
Uterine Inflammatory Myofibroblastic Tumors
Authors: Ladwig Nicholas R. , Bean Gregory R. , Pekmezci Melike , Boscardin John , Joseph Nancy M. , Therrien Nicole , Sangoi Ankur R. , Piening Brian , Rajamanickam Venkatesh , Galvin Matthew , Bernard Brady , Zaloudek Charles , Rabban Joseph T. , Garg Karuna , Umetsu Sarah E. 
Published: November 2022

Inflammatory myofibroblastic tumor (IMT) of the uterus is a rare mesenchymal tumor with largely benign behavior; however, a small subset demonstrate aggressive behavior. While clinicopathologic features have been previously associated with aggressive behavior, these reports are based on small series, and these features are imperfect predictors of clinical behavior. IMTs are most commonly driven by ALK fusions, with additional pathogenic molecular alterations being reported only in rare examples of extrauterine IMTs. In this study, a series of 11 uterine IMTs, 5 of which demonstrated aggressive behavior, were evaluated for clinicopathologic variables and additionally subjected to capture-based next-generation sequencing with or without whole-transcriptome RNA sequencing. In the 6 IMTs without aggressive behavior, ALK fusions were the sole pathogenic alteration. In contrast, all 5 aggressive IMTs harbored pathogenic molecular alterations and numerous copy number changes in addition to ALK fusions, with the majority of the additional alterations present in the primary tumors. We combined our series with cases previously reported in the literature and performed statistical analyses to propose a novel clinicopathologic risk stratification score assigning 1 point each for: age above 45 years, size≥5 cm,≥4 mitotic figures per 10 high-power field, and infiltrative borders. No tumors with 0 points had an aggressive outcome, while 21% of tumors with 1 to 2 points and all tumors with ≥3 points had aggressive outcomes. We propose a 2-step classification model that first uses the clinicopathologic risk stratification score to identify low-risk and high-risk tumors, and recommend molecular testing to further classify intermediate-risk tumors.
Family Caregiver Comorbidities in Lewy Body Dementia Versus Alzheimer Disease and Associated Disorders
Authors: Fleisher Jori E. , Moshkovich Anna , Levin Melissa , Akram Faizan , Hess Serena P. , Suresh Madhuvanthi , Bentley Cintra D. , Manak Thomas , Mattke Maraline , Miller Allegra , Pennsyl Claire E. , Pierce Carmen M. , Voss Margaret , Taylor Angela , Schroeder Karlin , Chodosh Joshua 
Published: November 2022

Background:
Family caregivers of people living with dementia have high caregiver strain and poor health consequences. Limited research exists on Lewy body dementia (LBD) caregivers and their specific comorbidities. This study aimed to (1) identify the prevalence of self-reported comorbidities among LBD caregivers and (2) contextualize these findings with historical data on caregivers of persons living with Alzheimer disease and associated disorders (ADADs).

Methods:
In a national, online survey, LBD family caregivers completed the Self-Administered Comorbidity Questionnaire and we compared these findings with extant literature on ADAD caregiver comorbidities.

Results:
Among 217 LBD caregivers, 84.3% were female, 39.1% were 64 years old or younger, and 66.8% had >2 years of caregiving experience. Caregivers self-identified as current (83.9%) or former (16.1%) caregivers. The most frequent comorbidities were hypertension (38.2%), depression (35.0%), back pain (34.1%), and arthritis (27.7%). LBD caregivers, particularly younger caregivers, had a higher prevalence of depression compared with ADAD caregivers and older adult populations, and back pain prevalence nearly equivalent to spinal cord injury caregivers.

Conclusions:
Our study is the first to illustrate and contextualize specific comorbidities among LBD caregivers. Understanding the causality and impact of these conditions will be critical in designing effective interventions to improve the lives of families affected by LBD.
eccDNA Atlas: a comprehensive resource of eccDNA catalog
Authors: Zhong Tengwei , Wang Wenqing , Liu Houyan , Zeng Maolin , Zhao Xinyu , Guo Zhiyun 
Published: November 2022

AbstractExtrachromosomal circular DNA (eccDNA) represents a large category of nonmitochondrial and nonplasmid circular extrachromosomal DNA playing an indispensable role in various aspects such as tumorigenesis, immune responses, liquid biopsy, etc. However, characteristic and functions of eccDNA are fragmented, hiding behind abundant literatures and massive whole-genome sequencing (WGS) data, which have not been sufficiently used for identification of eccDNAs. Therefore, establishing an integrated repository portal is essential for identifying and analyzing eccDNAs. Here, we developed eccDNA Atlas (http://lcbb.swjtu.edu.cn/eccDNAatlas), a user-friendly database of eccDNAs that aims to provide a high-quality and integrated resource for browsing, searching and analyzing eccDNAs from multiple species. eccDNA Atlas currently containing 630,434 eccDNAs and 7,774 ecDNAs manually curated from literatures and 1,105 ecDNAs predicted by AmpliconArchitect based on WGS data involved in 66 diseases, 57 tissue and 319 cell lines. The content of each eccDNA entry included multiple aspects such as sequence, disease, function, characteristic, validation strategies, etc. Furthermore, abundant annotations and analyzing utilities were provided to explore existed eccDNAs in eccDNA Atlas or user-defined eccDNAs including oncogenes, typical enhancers, super enhancers, gene expression, survival, and genome visualization. Based on these resources, eccDNA Atlas will significantly improve our understanding of eccDNAs and serve as an important catalyst for future research of eccDNAs.
Urban ecological connectivity as a planning tool for different animal species
Authors: Kirk Holly , Soanes Kylie , Amati Marco , Bekessy Sarah , Harrison Lee , Parris Kirsten , Ramalho Cristina , van der Ree Rodney , Threlfall Caragh 
Published: November 2022

ABSTRACTThe application of ecological theory to urban planning is becoming more important as land managers focus on increasing urban biodiversity as a way to improve human welfare. City authorities must decide not only what types of biodiversity-focused infrastructure should be prioritized, but also where new resources should be positioned and existing resources protected or enhanced. Careful spatial planning can contribute to the successful return and conservation of urban nature by maximizing the contribution of green infrastructure to landscape connectivity. By using ecological connectivity theory as a planning tool, governments can quantify the effect of different interventions on the ease with which wildlife can move across the landscape. Here we outline an approach to a) quantify ecological connectivity for different urban wildlife species and b) use this to test different urban planning scenarios using QGIS. We demonstrate four extensions to the work by Deslaurier et al. (2018) and Spanowicz & Jaeger (2019) which improve the application of this method as a planning tool for local government:A step-by-step method for calculating effective mesh size using the open-source software QGIS.Conversion of the effective mesh size value (meff) to a “probability of connectedness” (Pc, for easier interpretation by local government and comparisons between planning scenarios).Guidance for measuring species-specific connectivity, including how to decide what spatial information should be included and which types of species might be most responsive to connectivity planning.Advice for using the method to measure the outcome of different urban planning scenarios on ecological connectivity.
Changes in Alcohol Consumption during the COVID-19 Pandemic: Evidence from Wisconsin
Authors: Pomazal Rachel , McCulley Laura , Schultz Amy , Stafford Noah , Schowalter Mikayla , Malecki Kristen 
Published: November 2022

AbstractIntroductionThe COVID-19 pandemic increased stress levels broadly in the general population. Patterns of alcohol consumption are known to increase in times of increased stress like natural disasters, disease outbreaks, and economic turmoil. Wisconsin is an important place to study changes in alcohol consumption because it is one of the heaviest-drinking states in the United States. The primary aim of this study is to identify changes in alcohol use at three distinct timepoints during the COVID-19 pandemic in a statewide sample.MethodsAn online survey was sent to 5,502 previous Survey of the Health of Wisconsin (SHOW) participants to ask about a wide range of topics related to COVID-19. The timepoints were taken May through June 2020 (Wave 1), January to February 2021 (Wave 2), and June 2021 (Wave 3) The sample included 1,290, 1,868, and 1,585 participants in each of the three waves respectively. Changes in alcohol consumption (whether they drank more, about the same, or less) were examined by race, age, gender, educational attainment, annual income, anxiety and depression status, remote work status, whether the participant experienced employment changes due to COVID-19, and whether there were children present in the home. Within-wave univariate changes in alcohol consumption were evaluated by demographics using a chi-squared test.ResultsIn all three waves, those with anxiety, a bachelor’s degree or higher, two younger age groups, and those with children in the home were significantly more likely to increase alcohol consumption. Those reporting depression, those in the highest income quartile, and those working remotely were more likely to report increased drinking in the first two surveys, but not in the third survey. Participants reporting changes in employment due to COVID-19 were more likely to increase drinking in the first survey only. Non-white participants were more likely to report decreased drinking in the first survey only.ConclusionsThere may be subpopulations in Wisconsin at higher risk for the negative effects of heavy drinking during the pandemic like those with anxiety, those with children in the home, those with a bachelor’s degree or higher, and those in younger age groups, as these groups had consistently higher alcohol use that did not subside 15 months after lockdowns began.
Mathematical characterization of fractal river networks
Authors: Terui Akira 
Published: November 2022

AbstractCarraro and Altermatt1performed an extensive analysis to study scaling properties of river networks. They concluded that: (1) branching “probability” is better termed as branching “ratio” for real river networks because it is not a probability; (2) branching ratio is a scale-dependent quantity as the value changes across spatial resolutions at which river networks are extracted (expressed as the threshold catchment areaATthat initiates channels or pixel sizel); (3) Optimal Channel Networks most accurately predicted the metapopulation stability and capacity. However, the supporting ground for these conclusions is either seriously flawed or inconclusive due to the improper use of branching probability, scale invariance, dimensions, and units.
RNAin situconformation sequencing reveals novel long-range RNA structures with impact on splicing
Authors: Margasyuk Sergei , Kalinina Marina , Petrova Marina , Skvortsov Dmitry , Cao Changchang , Pervouchine Dmitri D. 
Published: November 2022

AbstractOver past years, long-range RNA structure has emerged as a factor that is fundamental to alternative splicing regulation. Since an increasing number of human disorders are now being associated with splicing defects, it is essential to develop methods that assess long-range RNA structure experimentally. RNAin situconformation sequencing (RIC-seq) is the method that recapitulates RNA structure within physiological RNA-protein complexes. In this work, we juxtapose RIC-seq experiments conducted in eight human cell lines with pairs of conserved complementary regions (PCCRs) that were predictedin silico. We show statistically that RIC-seq support strongly correlates with PCCR properties such as equilibrium free energy, presence of compensatory substitutions, and occurrence of A-to-I RNA editing sites and forked eCLIP peaks. Based on these findings, we prioritize PCCRs according to their RIC-seq support and show experimentally using antisense nucleotides and minigene mutagenesis that PCCRs in two disease-associated genes,PHF20L1andCASK, impact alternative splicing. In sum, we demonstrate how RIC-seq experiments can be used to discover functional long-range RNA structures, and particularly those that regulate alternative splicing.
Measures of genetic diversification in somatic tissues at bulk and single cell resolution
Authors: Moeller Marius E. , Père Nathaniel V. Mon , Werner Benjamin , Huang Weini 
Published: November 2022

AbstractIntra-tissue genetic heterogeneity is universal to both healthy and cancerous tissues. It emerges from the stochastic accumulation of somatic mutations throughout development and homeostasis. By combining population genetics theory and genomic information, genetic heterogeneity can be exploited to infer tissue organisation and dynamicsin vivo. However, many basic quantities, for example the dynamics of tissue specific stem cells remain difficult to quantify precisely. Here we show that single cell and bulk sequencing data inform on different aspects of the underlying stochastic processes. Bulk derived variant allele frequency spectra (VAF) show transitions from growing to constant stem cell populations with age in samples of healthy oesophagus epithelium. Single-cell mutational burden distributions allow a sample size independent measure of mutation and proliferation rates. Mutation rates in adult haematopietic stem cells are higher compared to inferences during development, suggesting additional proliferation independent effects. Furthermore, single cell derived VAF spectra contain information on the number of tissue specific stem cells. In haematopiesis, we find approximately 2×105HSCs, if all stem cells divide symmetrically. However, the single cell mutational burden distribution is over-dispersed compared to a model of Poisson distributed random mutations suggesting. A time-associated model of mutation accumulation with a constant rate alone cannot generate such a pattern. At least one additional source of stochasticity would be needed. Possible candidates for these processes may be occasional bursts of stem cell divisions, potentially in response to injury, or non-constant mutation rates either through environmental exposures or cell intrinsic variation.
Assessing the factors that affected the development of cloud-based accounting education and students' academic performance in Oman
Authors: Tawfik Omar Ikbal , Elmaasrawy Hamada Elsaid 
Published: November 2022

PurposeThis study aims to assesses the factors that affected the development of cloud-based accounting education (DCBAE) and students' academic performance at Oman Universities.Design/methodology/approachIn this paper a questionnaire was used to collect data for a sample of students. Partial least squares (PLS) were used to assess the hypotheses and model.FindingsResults indicate that human factors and cultural and social factors have a direct positive effect on the DCBAE and students' academic performance.Practical implicationsThis study is carried out after five semesters since the beginning of the COVID-19 pandemic. Thus, it can help universities (accounting education in particular) in the Sultanate of Oman know the factors that affect the development of accounting education and adopt policies and strategies that depend on cloud computing in education operations, even after the COVID-19 pandemic.Originality/valueThe main contribution of this study is to evaluate the factors that affected the DCBAE and the academic performance of students in the Sultanate of Oman from March 15, 2020 to June 2022, a period that witnessed the application of cloud-based education, either in whole or in part using a questionnaire about the opinions of students.