bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing 2D visual encoding of 3D spatial connectivity
Authors: Baldi Benedetta F. , Vuong Jenny , O’Donoghue Seán I. 
Published: January 2024

Introduction: When visualizing complex data, the layout method chosen can greatly affect the ability to identify outliers, spot incorrect modeling assumptions, or recognize unexpected patterns. Additionally, visual layout can play a crucial role in communicating results to peers.Methods: In this paper, we compared the effectiveness of three visual layouts—the adjacency matrix, a half-matrix layout, and a circular layout—for visualizing spatial connectivity data, e.g., contacts derived from chromatin conformation capture experiments. To assess these visual layouts, we conducted a study comprising 150 participants from Amazon’s Mechanical Turk, as well as a second expert study comprising 30 biomedical research scientists.Results: The Mechanical Turk study found that the circular layout was the most accurate and intuitive, while the expert study found that the circular and half-matrix layouts were more accurate than the matrix layout.Discussion: We concluded that the circular layout may be a good default choice for visualizing smaller datasets with relatively few spatial contacts, while, for larger datasets, the half- matrix layout may be a better choice. Our results also demonstrated how crowdsourcing methods could be used to determine which visual layouts are best for addressing specific data challenges in bioinformatics.
Assessment of the challenges influencing the adoption of smart building technologies
Authors: Baharetha Saleh , Soliman Ashraf M. , Hassanain Mohammad A. , Alshibani Adel , Ezz Mohamed Salah 
Published: January 2024

Introduction: Over the past few decades, there has been an increasing focus on Smart Building Projects (SBP) and the technologies associated with them. Numerous studies have been conducted globally to define smart building technologies (SBT), identify challenges, and explore areas for improvement. This study aims to examine the concept and terminology of SBT and the expertise and experience of participants in SBP in the Arab Gulf countries, specifically Saudi Arabia. The study also investigates the challenges faced by SBT throughout its life cycle.Methods: To identify and assess the challenges affecting the adoption of smart building technologies. This approach included a literature review, pilot-testing, and a questionnaire survey. The survey targeted a sample of 90 architects/engineers, managers, and contractors.Results: A total of 55 challenges were identified and categorized into four groups, corresponding to the key phases of the project life cycle. These phases include the programming and feasibility analysis phase, design phase, installation and commissioning phase, and operation and maintenance phase. The findings of this research expand the body of knowledge by providing architects/engineers, managers, and contractors in the architecture, engineering, construction, and facility management (AEC/FM) industry with insights into the influential challenges related to the adoption of SBT. In conclusion, this study sheds light on the concept and terminology of smart building technologies and explores the challenges faced by SBT during its life cycle. By identifying and categorizing these challenges, the study provides valuable information to AEC/FM practitioners, enabling them to overcome obstacles and improve the adoption of SBT.
Invasive Streptococcus suis isolated in Spain contain a highly promiscuous and dynamic resistome
Authors: Uruén Cristina , Gimeno Jorge , Sanz Marina , Fraile Lorenzo , Marín Clara M. , Arenas Jesús 
Published: January 2024

IntroductionStreptococcus suis is a major pathogen for swine and human. Here we aimed to know the rates of antimicrobial resistance (AMR) in invasive S. suis isolates recovered along Spain between 2016 – 2021 and elucidate their genetic origin.MethodsAntibiotic susceptibility testing was performed for 116 isolates of different genetic backgrounds and geographic origins against 18 antibiotics of 9 families. The association between AMR and genotypes and the origin of the isolates were statistically analyzed using Pearson´s chi-square test and the likelihood ratio. The antimicrobial resistant genes were identified by whole genome sequencing analysis and PCR screenings.ResultsHigh AMR rates (&gt;80%) were detected for tetracyclines, spectinomycin, lincosamides, and marbofloxacin, medium (20-40%) for sulphonamides/trimethoprim, tiamulin, penicillin G, and enrofloxacin, and low (&lt; 20%) for florfenicol, and four additional β-lactams. The occurrence of multidrug resistance was observed in 90% of isolates. For certain antibiotics (penicillin G, enrofloxacin, marbofloxacin, tilmicosin, and erythromycin), AMR was significantly associated with particular sequence types (STs), geographic regions, age of pigs, and time course. Whole genome sequencing comparisons and PCR screenings identified 23 AMR genes, of which 19 were previously reported in S. suis (aph(3’)-IIIa, sat4, aadE, spw, aac(6’)-Ie-aph(2’’)-Ia, fexA, optrA, erm(B), mef(A/E), mrs(D), mph(C), lnu(B), lsa(E), vga(F), tet(M), tet(O), tet(O/W/32/O), tet(W)), and 4 were novel (aph(2’’)-IIIa, apmA, erm(47), tet(T)). These AMR genes explained the AMR to spectinomycin, macrolides, lincosamides, tiamulin, and tetracyclines. Several genes were located on mobile genetic elements which showed a variable organization and composition. As AMR gene homologs were identified in many human and animal pathogens, the resistome of S. suis has a different phylogenetic origin. Moreover, AMR to penicillin G, fluoroquinolones, and trimethoprim related to mutations in genes coding for target enzymes (pbp1a, pbp2b, pbp2x, mraY, gyrA, parC, and dhfr). Bioinformatic analysis estimated traits of recombination on target genes, also indicative of gene transfer events.ConclusionsOur work evidences that S. suis is a major contributor to AMR dissemination across veterinary and human pathogens. Therefore, control of AMR in S. suis should be considered from a One Health approach in regions with high pig production to properly tackle the issue of antimicrobial drug resistance.
Epidemiology of atherosclerotic cardiovascular disease in polygenic hypercholesterolemia with or without high lipoprotein(a) levels
Authors: Vinci Pierandrea , Fiotti Nicola , Panizon Emiliano , Tosoni Letizia Maria , Cerrato Carla , Pellicori Federica , Pirulli Alessia , Altamura Nicola , Schincariol Paolo , Di Girolamo Filippo Giorgio , Biolo Gianni 
Published: January 2024

Background and aimsEpidemiology of atherosclerotic cardiovascular disease might be different in patients with polygenic hypercholesterolemia plus high levels (≥30 mg/dl) of Lp(a) (H-Lpa) than in those with polygenic hypercholesterolemia alone (H-LDL). We compared the incidence of peripheral artery disease (PAD), coronary artery disease (CAD), and cerebrovascular disease (CVD) in patients with H-Lpa and in those with H-LDL.MethodsRetrospective analysis of demographics, risk factors, vascular events, therapy, and lipid profile in outpatient clinical data. Inclusion criteria was adult age, diagnosis of polygenic hypercholesterolemia, and both indication and availability for Lp(a) measurement.ResultsMedical records of 258 patients with H-Lpa and 290 H-LDL were reviewed for occurrence of vascular events. The median duration of follow-up was 10 years (IQR 3–16). In spite of a similar reduction of LDL cholesterol, vascular events occurred more frequently, and approximately 7 years earlier (P = 0.024) in patients with H-Lpa than in H-LDL (HR 1.96 1.21–3.17, P = 0.006). The difference was around 10 years for acute events (TIA, Stroke, acute coronary events) and one year for chronic ones (P = 0.023 and 0.525, respectively). Occurrence of acute CAD was higher in H-Lpa men (HR 3.1, 95% CI 1.2–7.9, P = 0.007) while, among women, PAD was observed exclusively in H-Lpa subjects with smoking habits (P = 0.009).ConclusionsPatients with high Lp(a) levels suffer from a larger and earlier burden of the disease compared to those with polygenic hypercholesterolemia alone. These patients are at higher risk of CAD if they are men, and of PAD if they are women.
Associations between post-acute sequelae of SARS-CoV-2, COVID-19 vaccination and HIV infection: a United States cohort study
Authors: Yendewa George A. , Perez Jaime Abraham , Patil Nirav , McComsey Grace A. 
Published: January 2024

BackgroundPeople with HIV (PWH) are at higher risk of complications from acute COVID-19, but their risk of subsequent post-acute sequelae of SARS-CoV2 (PASC) remains unclear. Although vaccination is protective of PASC among survivors in the general population, its effectiveness in PWH has not been explored.MethodsWe used the TriNetX health research database to identify patients with and without HIV aged ≥18 years with confirmed SARS-CoV-2 between January 1, 2020 and July 20, 2023. We employed 1:1 propensity score matching to balance HIV and non-HIV cohorts based on demographics and key comorbidities. The primary outcomes accessed odds of PASC and mortality and secondary outcomes assessed odds of PASC and mortality by vaccination status. PASC was defined as new-onset conditions ≥ 28 days after COVID-19 diagnosis. We reported odd ratios (OR) of outcomes with 95% confidence intervals (CI), with statistical significance set at p &lt; 0.05.ResultsOf 3,029,340 people with confirmed SARS-CoV-2 infection, 0.5% (n=13,214) were PWH, with 7.5% of PWH (n=989) vaccinated. After 28 days post-COVID-19, PWH had higher odds of mortality compared with their non-HIV counterparts (OR 1.22, 95% CI 1.06-1.40) and developing new-onset HTN (OR 1.18, 95% CI 1.03-1.36), heart disease (OR 1.35 95% CI 1.18-1.54), malignancy (OR 1.49, 95% CI 1.22-1.81), and mental disorders (OR 1.62, 95% CI 1.42-1.85). Furthermore, vaccinated PWH had significantly lower odds of death (OR 0.63, 95% CI 0.42-0.93) and new-onset PASC outcomes: DM (OR 0.65, 95% CI 0.43-0.99), heart disease (OR 0.58, 95% CI 0.4-0.85), mental disorders (OR 0.66, 95% CI 0.43-1.00), fatigue (OR 0.82, 95% CI 0.67-0.98), respiratory (OR 0.82, 95% CI 0.70-0.95) and gastrointestinal symptoms (OR 0.78, 95% CI 0.67-0.90).ConclusionHIV-positive status increased PASC odds, while COVID-19 vaccination reduced PASC and all-cause mortality risks in PWH.
Cross-protection induced by highly conserved human B, CD4+, and CD8+ T-cell epitopes-based vaccine against severe infection, disease, and death caused by multiple SARS-CoV-2 variants of concern
Authors: Prakash Swayam , Dhanushkodi Nisha R. , Zayou Latifa , Ibraim Izabela Coimbra , Quadiri Afshana , Coulon Pierre Gregoire , Tifrea Delia F. , Suzer Berfin , Shaik Amin Mohammed , Chilukuri Amruth , Edwards Robert A. , Singer Mahmoud , Vahed Hawa , Nesburn Anthony B. , Kuppermann Baruch D. , Ulmer Jeffrey B. , Gil Daniel , Jones Trevor M. , BenMohamed Lbachir 
Published: January 2024

BackgroundThe coronavirus disease 2019 (COVID-19) pandemic has created one of the largest global health crises in almost a century. Although the current rate of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has decreased significantly, the long-term outlook of COVID-19 remains a serious cause of morbidity and mortality worldwide, with the mortality rate still substantially surpassing even that recorded for influenza viruses. The continued emergence of SARS-CoV-2 variants of concern (VOCs), including multiple heavily mutated Omicron sub-variants, has prolonged the COVID-19 pandemic and underscores the urgent need for a next-generation vaccine that will protect from multiple SARS-CoV-2 VOCs.MethodsWe designed a multi-epitope-based coronavirus vaccine that incorporated B, CD4+, and CD8+ T- cell epitopes conserved among all known SARS-CoV-2 VOCs and selectively recognized by CD8+ and CD4+ T-cells from asymptomatic COVID-19 patients irrespective of VOC infection. The safety, immunogenicity, and cross-protective immunity of this pan-variant SARS-CoV-2 vaccine were studied against six VOCs using an innovative triple transgenic h-ACE-2-HLA-A2/DR mouse model.ResultsThe pan-variant SARS-CoV-2 vaccine (i) is safe , (ii) induces high frequencies of lung-resident functional CD8+ and CD4+ TEM and TRM cells , and (iii) provides robust protection against morbidity and virus replication. COVID-19-related lung pathology and death were caused by six SARS-CoV-2 VOCs: Alpha (B.1.1.7), Beta (B.1.351), Gamma or P1 (B.1.1.28.1), Delta (lineage B.1.617.2), and Omicron (B.1.1.529).ConclusionA multi-epitope pan-variant SARS-CoV-2 vaccine bearing conserved human B- and T- cell epitopes from structural and non-structural SARS-CoV-2 antigens induced cross-protective immunity that facilitated virus clearance, and reduced morbidity, COVID-19-related lung pathology, and death caused by multiple SARS-CoV-2 VOCs.
Features of severe asthma response to anti-IL5/IL5r therapies: identikit of clinical remission
Authors: Carpagnano Giovanna Elisiana , Portacci Andrea , Nolasco Santi , Detoraki Aikaterini , Vatrella Alessandro , Calabrese Cecilia , Pelaia Corrado , Montagnolo Francesca , Scioscia Giulia , Valenti Giuseppe , D’Amato Maria , Caiaffa Maria Filomena , Triggiani Massimo , Scichilone Nicola , Crimi Claudia 
Published: January 2024

IntroductionClinical remission (CliR) achievement has been recognized as a new potential outcome in severe asthma. Nevertheless, we still lack a detailed profile of what features could better identify patients undergoing clinical remission. In this study, we aim to address this issue, tracing a possible identikit of patients fulfilling remission criteria.MethodsWe enrolled 266 patients with severe eosinophilic asthma (SEA) treated with a 12-month course of anti-IL5/IL5 receptor (IL5r) monoclonal antibodies. Patients with no exacerbation, OCS withdrawal, ACT ≥ 20 and FEV1 ≥ 80% after 1 year of biologic treatment were classified as in clinical remission.Results30.5% of the enrolled patients achieved remission after biologic administration. CliR group showed a lower number of baseline asthma exacerbations and better lung function parameters, with a trend for higher ACT scores and a less frequent history of a positive skin prick test. CliR achievement was unlikely in presence of a higher BMI, a positive skin prick test, an increased number of asthma exacerbations before biologic treatment, anti-muscarinic administration, and a previous diagnosis of EGPA, bronchiectasis or osteoporosis. In contrast, a better lung function, an increased blood eosinophilic count, the presence of chronic rhinosinusitis with nasal polyps and a more frequent use of reliever therapy predicts remission development. Changes in exacerbations number, OCS use, ACT scores and FEV1% between remittent and non-remittent patients arise at specific follow up timepoints and are positively associated with CliR achievement.Discussionanti-IL5/IL5r biologics can induce CliR in a proportion of patients with SEA. Patients achieving remission demonstrate specific clinical, functional and inflammatory features, as well as a specific moment of improvement in all the CliR items.
Mononuclear cell composition and activation in blood and mucosal tissue of eosinophilic esophagitis
Authors: Gruden Eva , Kienzl Melanie , Ristic Dusica , Kindler Oliver , Kaspret David Markus , Schmid Sophie Theresa , Kargl Julia , Sturm Eva , Doyle Alfred D. , Wright Benjamin L. , Baumann-Durchschein Franziska , Konrad Julia , Blesl Andreas , Schlager Hansjörg , Schicho Rudolf 
Published: January 2024

IntroductionEosinophilic esophagitis (EoE) is a chronic, inflammatory, antigen-driven disease of the esophagus. Tissue EoE pathology has previously been extensively characterized by novel transcriptomics and proteomic platforms, however the majority of surface marker determination and screening has been performed in blood due to mucosal tissue size limitations. While eosinophils, CD4+ T cells, mast cells and natural killer (NK) T cells were previously investigated in the context of EoE, an accurate picture of the composition of peripheral blood mononuclear cells (PBMC) and their activation is missing.MethodsIn this study, we aimed to comprehensively analyze the composition of peripheral blood mononuclear cells and their activation using surface marker measurements with multicolor flow cytometry simultaneously in both blood and mucosal tissue of patients with active EoE, inactive EoE, patients with gastroesophageal reflux disease (GERD) and controls. Moreover, we set out to validate our data in co-cultures of PBMC with human primary esophageal epithelial cells and in a novel inducible mouse model of eosinophilic esophagitis, characterized by extensive IL-33 secretion in the esophagus.ResultsOur results indicate that specific PBMC populations are enriched, and that they alter their surface expression of activation markers in mucosal tissue of active EoE. In particular, we observed upregulation of the immunomodulatory molecule CD38 on CD4+ T cells and on myeloid cells in biopsies of active EoE. Moreover, we observed significant upregulation of PD-1 on CD4+ and myeloid cells, which was even more prominent after corticosteroid treatment. With co-culture experiments we could demonstrate that direct cell contact is needed for PD-1 upregulation on CD4+ T cells. Finally, we validated our findings of PD-1 and CD38 upregulation in an inducible mouse model of EoE.DiscussionHerein we show significant alterations in the PBMC activation profile of patients with active EoE in comparison to inactive EoE, GERD and controls, which could have potential implications for treatment. To our knowledge, this study is the first of its kind expanding the multi-color flow cytometry approach in different patient groups using in vitro and in vivo translational models.
Early immune factors associated with the development of post-acute sequelae of SARS-CoV-2 infection in hospitalized and non-hospitalized individuals
Authors: Leung Jacqueline M. , Wu Michelle J. , Kheradpour Pouya , Chen Chen , Drake Katherine A. , Tong Gary , Ridaura Vanessa K. , Zisser Howard C. , Conrad William A. , Hudson Natalia , Allen Jared , Welberry Christopher , Parsy-Kowalska Celine , Macdonald Isabel , Tapson Victor F. , Moy James N. , deFilippi Christopher R. , Rosas Ivan O. , Basit Mujeeb , Krishnan Jerry A. , Parthasarathy Sairam , Prabhakar Bellur S. , Salvatore Mirella , Kim Charles C. 
Published: January 2024

BackgroundInfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can lead to post-acute sequelae of SARS-CoV-2 (PASC) that can persist for weeks to years following initial viral infection. Clinical manifestations of PASC are heterogeneous and often involve multiple organs. While many hypotheses have been made on the mechanisms of PASC and its associated symptoms, the acute biological drivers of PASC are still unknown.MethodsWe enrolled 494 patients with COVID-19 at their initial presentation to a hospital or clinic and followed them longitudinally to determine their development of PASC. From 341 patients, we conducted multi-omic profiling on peripheral blood samples collected shortly after study enrollment to investigate early immune signatures associated with the development of PASC.ResultsDuring the first week of COVID-19, we observed a large number of differences in the immune profile of individuals who were hospitalized for COVID-19 compared to those individuals with COVID-19 who were not hospitalized. Differences between individuals who did or did not later develop PASC were, in comparison, more limited, but included significant differences in autoantibodies and in epigenetic and transcriptional signatures in double-negative 1 B cells, in particular.ConclusionsWe found that early immune indicators of incident PASC were nuanced, with significant molecular signals manifesting predominantly in double-negative B cells, compared with the robust differences associated with hospitalization during acute COVID-19. The emerging acute differences in B cell phenotypes, especially in double-negative 1 B cells, in PASC patients highlight a potentially important role of these cells in the development of PASC.
Assessment of preparedness and proficiency in basic and advanced life support among nursing professionals: a cross-sectional study
Authors: Izquierdo-Condoy Juan S. , Arias Rodríguez Fabián D. , Duque-Sánchez Erick , Alegría N. Nicolás , Rojas Cadena Marlon , Naranjo-Lara Patricio , Mendoza Alexander Puglla , Jima-Sanmartín Jackson , Casanova Dayana Andrade , García Balbina , Giraldo Natalia Castaño 
Published: January 2024

BackgroundCardiac diseases are among the leading causes of death worldwide, including sudden cardiac arrest in particular. Nursing professionals are often the first to encounter these scenarios in various settings. Adequate preparation and competent knowledge among nurses significantly impact survival rates positively.AimTo describe the state of knowledge about Basic and Advanced Life Support guidelines among Ecuadorian nursing professionals.MethodologyA nationwide, descriptive, cross-sectional study was conducted from February to April 2023 among Ecuadorian nursing professionals. Participants were invited through official social media groups such as WhatsApp and Facebook. The study utilized a self-administered online questionnaire to evaluate theoretical knowledge of Basic Life Support (BLS) and Advanced Life Support (ALS). Knowledge scores were assigned based on the number of correct answers on the tests. T-tests and one-way ANOVA were used to examine relationships between knowledge scores and demographic and academic training variables.ResultsA total of 217 nursing professionals participated in the study. The majority of the participants were female (77.4%) and held a university degree (79.9%). Among them, only 44.7% claimed to have obtained a BLS training certificate at least once, and 19.4% had ALS certification. The overall BLS knowledge score (4.8/10 ± 1.8 points) was higher than the ALS score (4.3/10 ± 1.8 points). Participants who had obtained BLS certification and those who used evidence-based summaries as a source of extracurricular training achieved higher BLS and ALS knowledge scores.ConclusionEcuadorian nursing professionals in this study exhibited a significant deficiency in theoretical knowledge of BLS and ALS. Formal training and preparation positively impact life support knowledge. Support and inclusion of Ecuadorian nurses in training and academic preparation programs beginning at the undergraduate level are essential for promoting life support knowledge and improving outcomes.