bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interoperability Assessment of Emergency Department Processes Based on Multicriteria Decision-Making Methods
Authors: Laus Fernanda Wanka , Pegoraro Fábio , Loures Eduardo de Freitas Rocha , Santos Eduardo Alves Portela 
Published: February 2022

AbstractIt is noticeable that, because of the amount and quality of information exchanged and the criticality of the decisions guided by them, hospitals are considered as some of the most complex organizations in modern society. Evidencing it, emergency departments in hospitals are examples of such complex environments that need perfect integration among systems, people, departments, and data. The processes behind the Emergency Department (ED) routine cause a set of critical and time-dependent decision-making, which must consider several criteria related to organizational and clinical attributes. Based on the literature and worldwide initiatives related to managing complex organizations, an ED can be interpreted through the enterprise interoperability (EI) lens, a concept related to the capability of different systems to work collaboratively within and throughout the organization. Thus, this paper proposes a framework focusing on interoperability assessment in ED processes, where different actors need to interoperate. The proposed framework for Enterprise Interoperability Assessment (EIA) is based on multicriteria decision analysis (MCDA) methods, considering organizational and clinical attributes of the ED. The Analytic Hierarchy Process (AHP) and Preference Ranking Organization Method for Enrichment Evaluation II (PROMETHEE II), in an integrated approach, were elected as the most appropriate multicriteria methods to support, respectively, diagnostic (interoperability assessment) and decisional (interoperability improvements) processes in this background. Last, to validate the framework proposed, a case study was carried out at a stroke unit in a University Hospital (UH) in the south of Brazil. The outcome inferred that the UH achieved the intermediate level of enterprise interoperability in stroke treatment, and Business and Information Technology concerns were found to be the priorities, which deserved greater efforts, to enhance interoperability.
Effectiveness of Covid-19 vaccines against symptomatic and asymptomatic SARS-CoV-2 infections in an urgent care setting
Authors: Rane Madhura S. , Robertson McKaylee , Kulkarni Sarah , Frogel Daniel , Gainus Chris , Nash Denis 
Published: February 2022

AbstractBackgroundIt is critical to monitor changes in vaccine effectiveness against COVID-19 outcomes for various vaccine products in different population subgroups.MethodsWe conducted a retrospective study in patients ≥12 years who underwent testing for the SARS-CoV-2 virus from April 1 - October 25, 2021 at urgent care centers in the New York City metropolitan area. Patients self-reported vaccination status at the time of testing. We used a test-negative design to estimate vaccine effectiveness (VE) by comparing odds of a positive test for SARS-CoV-2 infection among vaccinated (n=484,468), partially vaccinated (n=107,573), and unvaccinated (n=466,452) patients, adjusted for demographic factors and calendar time.ResultsVE against symptomatic infection after 2 doses of mRNA vaccines was 96% (95% Confidence Interval [CI]: 95%, 97%) in the pre-delta period and reduced to 79% (95% CI: 77%, 81%) in the delta period. In the delta period, VE for 12–15-year-olds (85%; [95% CI: 81%, 89%]) was higher compared to older age groups (<65% for all other age groups). VE estimates did not differ by sex, race/ethnicity, and comorbidity. VE against symptomatic infection was the highest for individuals with a prior infection followed by full vaccination. VE against symptomatic infection after the mRNA-1273 vaccine (83% [95% CI: 81%, 84%]) was higher compared to the BNT162b2 vaccine (76% [95% CI: 74%, 78%]) in the delta period. VE after the single-dose Ad26.COV2.S vaccine was the lowest compared to other vaccines (29% [95% CI: 26%, 32%]) in the delta period.ConclusionsVE against infection after two doses of the mRNA vaccine was high initially, but significantly reduced against the delta variant for all three FDA-approved vaccines.
LARisk: An R package for lifetime attributable risk from radiation exposure
Authors: Lee Juhee , Kim Young Min , Park Yeongwoo , Jang Eunjin , Yoo Jinkyung , Seo Songwon , Cha Eun Shil , Lee Won Jin 
Published: February 2022

AbstractThe lifetime radiation associated risk of cancer incidence has been of interest at least seventy years after atomic bombings of Hiroshima and Nagasaki in 1945. Since most of radiation epidemiological studies are retrospective, it is important to assess the potential magnitude of radiation-related cancer risk. The R-package so-call LARisk implements to easily calculate lifetime attributable risks (LAR) of radiation associated cancer incidence presenting bootstrap-based confidence intervals of the estimated risks. The main characteristics of the LARisk package are to flexibly compute the LAR-associated risks, effectively summarize large data, and promptly update domain-knowledge such as new regression coefficients for excess relative risk or excess absolute risk models, population information, etc. The manuscript provides a complete guide for usage of the LARisk package, which will enable to contribute the prospective studies in radiation epidemiology.
Knowledge, Attitude, and Practices of Health Professionals Working in A Major Health Care System Regarding Social Determinants of Health (SDOH) and Community Health Workers (CHW’s)
Authors: Khan Muhammad Nausherwan , Azhar Erum , Zain Areeba , Bowman Meredith Root , Ahmed Natasha Tahir , Khan Muhammad Arslan , Caswell Leigh , Waheed Abdul 
Published: February 2022

AbstractIntroductionSocial Determinants of Health (SDOH) play a key role in impacting the health outcomes of any population. Community Health Workers (CHW’s) play an important role in health promotion, disease prevention, and management of chronic illnesses. This study aims at exploring the knowledge, attitude, and practices of health care professionals towards CHWs to fully integrate in them for mitigation of SDOH.Materials and MethodsA cross-sectional study utilizing an anonymous survey questionnaire across 4 clinical sites was carried out from June 2016 to November 2017 in a major healthcare system (Presbyterian) in Albuquerque, New Mexico. Descriptive statistics (means, standard deviations, and proportions) were collected. Categorical variables were analyzed using Chi-squared and Fisher’s exact test; a p-value of <0.05 was considered statistically significant, using SAS 9.4 statistical software.ResultsAlmost half of the health professionals had no knowledge about the social determinants of health. Almost a quarter of the health professionals did not know the role of CHWs in healthcare, however, 100% of the respondents across all clinic and practice locations and regardless of their role or scope of the practice believed that greater involvement of CHWs would improve patient outcomes.ConclusionThere is a knowledge deficit among health care providers about the social determinants of health (SDOH).More educational and teaching opportunities on SDOH and CHWs to all health professionals should be provided to all health professionals so the clinical team can help manage SDOH in addition to providing clinical care.
Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome
Authors: Zhu Xiaopeng , Zhang Yang , Wang Yuchuan , Tian Dechao , Belmont Andrew S. , Swedlow Jason R. , Ma Jian 
Published: February 2022

AbstractWe introduce Nucleome Browser (http://www.nucleome.org), an interactive, multimodal data visualization and exploration platform for 4D Nucleome research. Our tool effectively integrates heterogeneous datasets (e.g., genomics, imaging, 3D genome structure models, and single-cell data) and external data portals by a new adaptive communication mechanism. Nucleome Browser provides a scalable solution for integrating massive amounts of 4D Nucleome data to navigate multiscale nuclear structure and function in a wide range of biological contexts, enabling hypothesis generation and data sharing with the broad community.
Novel feature selection methods for construction of accurate epigenetic clocks
Authors: Li Adam , Kane Alice E , Mueller Amber , English Brad , Arena Anthony , Vera Daniel , Sinclair David A 
Published: February 2022

AbstractEpigenetic clocks allow the accurate prediction of age based on the methylation status of specific CpG sites in a variety of tissues. These predictive models can be used to distinguish the biological age of an organism from its chronological age, and are a powerful tool to measure the effectiveness of aging interventions. There is a growing need for methods to efficiently construct epigenetic clocks. The most common approach is to create clocks using elastic net regression modelling of all measured CpG sites, without first identifying specific features or CpGs of interest. The addition of feature selection approaches provides the opportunity to reduce the cost and time of clock development by decreasing the number of CpG sites included in clocks. Here, we apply both classic feature selection methods and novel combinatorial methods to the development of epigenetic clocks. We perform feature selection on the human whole blood methylation dataset of ∼470,000 CpG features published by Hannum and colleagues (2015). We develop clocks to predict age, using a variety of feature selection approaches, and all clocks have R2 correlation scores of greater than 0.73. The most predictive clock uses 35 CpG sites for a R2 correlation score of 0.87. The five most frequent sites across all clocks are also modelled to build a clock with a R2 correlation score of 0.83. These two clocks are validated on two external datasets where they maintain excellent predictive accuracy and outperform Hannum et al’s model in accuracy of age prediction despite using significantly less CpGs. We also identify the associated gene regulatory regions of these CpG sites, which may be possible targets for future aging studies. These novel feature selection algorithms will lower the number of sites needed to be sequenced to build clocks and allow conventionally expensive aging epigenetic studies to cost a fraction of what it would normally.
An averaging model for analysis and interpretation of high-order genetic interactions
Authors: Katagiri Fumiaki 
Published: February 2022

ABSTRACTWhile combinatorial genetic data collection from biological systems in which quantitative phenotypes are controlled by functional and non-functional alleles of multiple genes (multi-gene systems) is becoming common, a standard analysis method for such data has not been established. A common additive model of the non-functional allele effects contrasted against the functional alleles, based on ANOVA with interaction, has three issues. First, although it is a long tradition in genetics, modeling the effect of the non-functional allele (a null mutant allele) contrasted against that of the functional allele (the wild-type allele) is not suitable for mechanistic understanding of multi-gene systems. Second, an additive model fails in estimation of interactions among more than two genes when the phenotypic response is not linear. Third, interpretation of higher-order interactions defined by an additive model is not intuitive. I propose an averaging model, which is suitable for mechanistic understanding of multi-gene systems: the effect of the functional allele is contrasted against the effect of the non-functional allele for easier mechanistic interpretations; it is stable in estimation of higher-order interactions even when the phenotypic response is not linear; and the higher-order interactions it defines are highly intuitive. Yet, the averaging model is still a general linear model, so model fitting is easy and accurate using common statistical tools.
Multimodal Thrombectomy Device for Treatment of Acute Deep Venous Thrombosis
Authors: Ismail Usama , Rowe Roger A. , Cashin John , Genin Guy M. , Zayed Mohamed 
Published: February 2022

ABSTRACTDeep vein thrombosis (DVT) is a potentially deadly medical condition that is costly to treat and impacts thousands of Americans every year. DVT is characterized by the formation of blood clots within the deep venous system of the body. If a DVT dislodges it can lead to venous thromboembolism (VTE) and pulmonary embolism (PE), both of which can lead to significant morbidity or death. Current treatment options for DVT are limited in both effectiveness and safety, in part because the treatment of the DVT cannot be confined to a defined sequestered treatment zone. We therefore developed and tested a thrombectomy device that enables the sequesteration of a DVT to a defined treatment zone during fragmentation and evacuation. We observed that, compared to a predicate thrombectomy device, the sequestered approach reduced distal DVT embolization during ex vivo thrombectomy. The sequestered approach also facilitated isovolumetric infusion and suction that enabled clearance of the sequestered treatment zone without significantly impacting vein wall diameter. Results suggest that our novel device using sequestered therapy holds promise for the treatment of high risk large-volume DVTs.
SexFindR: A computational workflow to identify young and old sex chromosomes
Authors: Grayson Phil , Wright Alison , Garroway Colin J. , Docker Margaret F. 
Published: February 2022

AbstractSex chromosomes have evolved frequently across the tree of life, and have been a source of fascination for decades due to their unique evolutionary trajectories. They are hypothesised to be important drivers in a broad spectrum of biological processes and are the focus of a rich body of evolutionary theory. Whole-genome sequencing provides exciting opportunities to test these theories through contrasts between independently evolved sex chromosomes across the full spectrum of their evolutionary lifecycles. However, identifying sex chromosomes, particularly nascent ones, is challenging, often requiring specific combinations of methodologies. This is a major barrier to progress in the field and can result in discrepancies between studies that apply different approaches. Currently, no single pipeline exists to integrate data across these methods in a statistical framework to identify sex chromosomes at all ages and levels of sequence divergence. To address this, we present SexFindR, a comprehensive workflow to improve robustness and transparency in identifying sex-linked sequences. We validate our approach using publicly available data from five species that span the continuum of sex chromosome divergence, from homomorphic sex chromosomes with only a single SNP that determines sex, to heteromorphic sex chromosomes with extensive degeneration. Next, we apply SexFindR to our large-scale population genomics dataset for sea lamprey, a jawless vertebrate whose sex determination system remains a mystery despite decades of research. We decisively show that sea lamprey do not harbour sex-linked sequences in their somatic genome, leaving open the possibility that sex is determined environmentally or within the germline genome.
Cryptic Genes for Interbacterial Antagonism distinguish Rickettsia species Infecting Blacklegged Tick from other Rickettsia pathogens
Authors: Verhoeve Victoria I. , Fauntleroy Tyesha D. , Risteen Riley G. , Driscoll Timothy P. , Gillespie Joseph J. 
Published: February 2022

AbstractBackgroundGenus Rickettsia (Alphaproteobacteria: Rickettsiales) encompasses numerous obligate intracellular species with predominantly ciliate and arthropod hosts. Notable species are pathogens transmitted to mammals by blood-feeding arthropods. Mammalian pathogenicity evolved from basal, non-pathogenic host-associations; however, some non-pathogens are closely related to pathogens. One such species, Rickettsia buchneri, is prevalent in the blacklegged tick, Ixodes scapularis. While I. scapularis transmits several pathogens to humans, it does not transmit Rickettsia pathogens. We hypothesize that R. buchneri established a mutualism with I. scapularis, blocking tick superinfection with Rickettsia pathogens.MethodsTo improve estimates for assessing R. buchneri infection frequency in blacklegged tick populations, we used comparative genomics to identify an R. buchneri gene (REIS_1424) not present in other Rickettsia species present throughout the I. scapularis geographic range. Bioinformatic and phylogenomics approaches were employed to propose a function for the hypothetical protein (263 aa) encoded by REIS_1424.ResultsREIS_1424 has few analogs in other Rickettsiales genomes and greatest similarity to non-Proteobacteria proteins. This cohort of proteins varies greatly in size and domain composition, possessing characteristics of Recombination hotspot (Rhs) and contact dependent growth inhibition (CDI) toxins, with similarity limited to proximal C-termini (∼145 aa). This domain was named CDI-like/Rhs-like CT toxin (CRCT). As such proteins are often found as toxin-antidote (TA) modules, we interrogated REIS_1423 (151 aa) as a putative antidote. Indeed, REIS_1423 is similar to proteins encoded upstream of CRCT domain-containing proteins. Accordingly, we named these proteins CDI-like/Rhs-like C-terminal toxin antidotes (CRCA). R. buchneri expressed both REIS_1423 and REIS_1424 in tick cell culture, and PCR assays showed specificity for R. buchneri over other rickettsiae and utility for positive detection in three tick populations. Finally, phylogenomics analyses uncovered divergent CRCT/CRCA modules in varying states of conservation; however, only R. buchneri and related Tamurae/Ixodes Group rickettsiae carry complete TA modules.ConclusionWe hypothesize that Rickettsia CRCT/CRCA modules circulate in the Rickettsia mobile gene pool, arming rickettsiae for battle over arthropod colonization. While its functional significance remains to be tested, R. buchneri CRCT/CRCA serves as a marker to positively identify infection and begin deciphering the role this endosymbiont plays in the biology of the blacklegged tick.
Clinical severity of COVID-19 patients admitted to hospitals during the Omicron wave in South Africa
Authors: Jassat Waasila , Abdool Karim Salim S , Mudara Caroline , Welch Richard , Ozougwu Lovelyn , Groome Michelle J. , Govender Nevashan , von Gottberg Anne , Wolter Nicole , Wolmarans Milani , Rousseau Petro ,   DATCOV author group, Blumberg Lucille , Cohen Cheryl 
Published: February 2022

ABSTRACTBackgroundClinical severity of patients hospitalised with SARS-CoV-2 infection during the Omicron (fourth) wave was assessed and compared to trends in the D614G (first), Beta (second), and Delta (third) waves in South Africa.MethodsWeekly incidence of 30 laboratory-confirmed SARS-CoV-2 cases/100,000 population defined the start and end of each wave. Hospital admission data were collected through an active national COVID-19-specific surveillance programme. Disease severity was compared across waves by post-imputation random effect multivariable logistic regression models. Severe disease was defined as one or more of acute respiratory distress, supplemental oxygen, mechanical ventilation, intensive-care admission or death.Results335,219 laboratory-confirmed SARS-CoV-2 admissions were analysed, constituting 10.4% of 3,216,179 cases recorded during the 4 waves. In the Omicron wave, 8.3% of cases were admitted to hospital (52,038/629,617) compared to 12.9% (71,411/553,530) in the D614G, 12.6% (91,843/726,772) in the Beta and 10.0% (131,083/1,306,260) in the Delta waves (p<0.001). During the Omicron wave, 33.6% of admissions experienced severe disease compared to 52.3%, 63.4% and 63.0% in the D614G, Beta and Delta waves (p<0.001). The in-hospital case fatality ratio during the Omicron wave was 10.7%, compared to 21.5%, 28.8% and 26.4% in the D614G, Beta and Delta waves (p<0.001). Compared to the Omicron wave, patients had more severe clinical presentations in the D614G (adjusted odds ratio [aOR] 2.07; 95% confidence interval [CI] 2.01-2.13), Beta (aOR 3.59; CI: 3.49-3.70) and Delta (aOR 3.47: CI: 3.38-3.57) waves.ConclusionThe trend of increasing cases and admissions across South Africa’s first three waves shifted in Omicron fourth wave, with a higher and quicker peak but fewer admitted patients, who experienced less clinically severe illness and had a lower case-fatality ratio. Omicron marked a change in the SARS-CoV-2 epidemic curve, clinical profile and deaths in South Africa. Extrapolations to other populations should factor in differing vaccination and prior infection levels.
Impact of BNT162b2 mRNA Vaccination on the Development of Short and Long-term Vaccine-Related Adverse Events in Inflammatory Bowel Disease: A Multi-Center Prospective Study
Authors: Shehab Mohammad , Alrashed Fatema , Abdullah Israa , Alfadhli Ahmad , Ali Hamad , Abu-Farha Mohamed , Channanath Arshad , Abubaker Jehad , Al-Mulla Fahd 
Published: February 2022

AbstractIntroductionSARS-CoV-2 vaccination has been effective in protecting against severe COVID-19 infections and related mortality. It is recommended for all individuals including patients with inflammatory bowel disease (IBD). However, safety data is lacking in this group of patients. Therefore, we aim to evaluate the short- and long-term vaccine related adverse events (AEs) in patients with IBD.MethodThis is a prospective, observational cohort study investigating short- and long-term AEs related to BNT162b2 vaccine in patients with IBD (study group) after first and second dose compared to healthy participants (study group). Patients were recruited at the time of attendance to clinic or infusion rooms. Short term (<3 weeks) localized and systemic AEs were assessed via questionnaire. Follow-up phone-based survey was made to collect data on long term (up to 24 weeks) AEs.ResultsA total of 408 patients answered the questionnaires, 204 patients in each group, the study and control group. No serious adverse events were reported in either the study nor the control group after the first or the second dose. Participants in the control group reported more frequent pain at the injection site than those in the study group after the first dose (58 (57%) vs 38 (37%) respectively, P-value= 0.005). After the second dose, tiredness was reported more frequently in the control group [49 (48%)] compared to the study group [25 (24%), (P-value<0.001)]. At 20-24 weeks post vaccination, 386 out of 408 (94.6%) patients were willing to participate in the follow-up phone based questionnaire (196 (96.1%) in the study group vs 190 (93.1%) in the control group). In both groups, none of the patients reported local, systemic or severe adverse events (0 out of 386) at week 20-244 post second dose.ConclusionThe BNT162b2 vaccine is safe in patients with IBD. No severe or long-term adverse events were reported in our study. The frequency of local and systemic adverse events after the second dose was generally higher among healthy participants compared to patients with IBD. Further studies including a larger cohort with longer follow-up duration are needed to assess for possible rare adverse events.