bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcome of Emergency Blood Transfusion in Children Seen at a Tertiary Children's Hospital in Freetown
Authors: Ikhurionan Paul Ehiabhi , Bell Nellie V. T. , Ofovwe Gabriel Egberue 
Published: September 2023

Objective
This study sought to describe the prevalence and clinical outcome after emergency blood transfusion among children presenting with severe anemia in a tertiary children's hospital in Sierra Leone.

Method
This was a retrospective study of 395 children who received emergency blood transfusion at the Ola During Children's Hospital in Freetown. Association between mortality and sociodemographic and clinical factors was assessed using χ2 test. Statistical significance was set at P < 0.05.

Results
Three hundred ninety-five of 4719 children (8.4%) admitted to the emergency room of the Ola During Children's Hospital received emergency blood transfusion within 24 hours of presentation. Twenty-five (6.3%) were excluded because of incomplete data. The median age of the subjects was 24 months (interquartile range, 14–48). There were 191 boys (51.6%) and 179 girls (48.4%), giving a male/female ratio of 1.06:1. The most common indication for emergency transfusion was severe malaria anemia (67.8%). The mean hemoglobin concentration before transfusion was 4.8 g/dL (±1.4 g/dL). A total of 339 children (91.6%) were discharged home, 8 (2.2%) were discharged against medical advice, and 23 children (6.2%) died. The median length of stay on admission was 3 days (interquartile range, 2–5). Children with severe sepsis (P < 0.001) and those with pretransfusion hemoglobin concentration less than 5% (P = 0.047) were significantly more likely to die after transfusion compared with the other categories of patients. In a multivariate regression analysis, none of the factors were independently associated with clinical outcome after blood transfusion in children who received emergency blood transfusion.

Conclusion
The study suggests that emergency blood transfusion in children with severe anemia may improve in-hospital survival.
Reducing Vaccination Disparities During a National Emergency Response: The US Mpox Vaccine Equity Pilot Program
Authors: Bautista Gregorio J. , Madera-Garcia Valerie , Carter Rosalind J. , Schwitters Amee , Byrkit Ramona , Carnes Neal , Prejean Joseph 
Published: September 2023

Context:
In response to the first reported mpox cases in May 2022, the US government implemented plans to bring testing, treatment, and vaccines to communities disproportionately affected by mpox—including the population of men who have sex with men (MSM) and Black/African American and Hispanic/Latino men, 2 subpopulations experiencing vaccination disparities. We describe the development and implementation of the US Mpox Vaccine Equity Pilot Program (MVEPP), characteristics of completed vaccination projects, and challenges that occurred. We also discuss opportunities for reducing vaccination disparities in future outbreaks.

Program:
To address reported vaccination disparities, the US government launched MVEPP in 2 phases. Phase 1 centered around public events attended by large numbers of gay, bisexual, and other MSM, such as Pride festivals. Phase 2 asked health departments to propose mpox vaccination projects specifically aimed at reducing or eliminating racial/ethnic and other demographic disparities in mpox vaccination.

Implementation:
MVEPP received 35 vaccination project proposals. We analyzed data from 22 completed projects that resulted in 25 675 doses of JYNNEOS administered. We note 3 innovative strategies that were implemented in several projects: direct collaboration with organizations providing services to MSM and transgender women; implementation of MVEPP projects in unique nonclinical community settings and at venues frequented by MSM and transgender women; and offering an array of services as part of mpox vaccination projects, rather than offering only mpox vaccination.

Evaluation:
MVEPP highlighted the importance of recognizing and working to eliminate racial/ethnic and other disparities in access to medical countermeasures during a public health emergency. Jurisdictions developed and implemented innovative strategies to bring mpox vaccination and related services to communities disproportionately affected by mpox—including MSM and the subpopulations of Black/African American and Hispanic/Latino MSM. Lessons learned from MVEPP may inform efforts to reduce disparities during future public health responses.
The Effect of Telerehabilitation-Based Exercise and Education on Pain, Function, Strength, Proprioception and Psychosocial Parameters in Patients with Knee Osteoarthritis
Authors: Tümtürk İsmet , Bakırhan Serkan , Özden Fatih , Gültaç Emre , Kılınç Cem Yalın 
Published: September 2023

Abstract

Objective
In middle-aged individuals with early-stage knee osteoarthritis (OA), follow-up with remote rehabilitation methods may provide effective clinical outcomes. The present study aimed to investigate the effect of telerehabilitation (TR) on pain, function, performance, strength, proprioception, and psychosocial parameters in patients with knee OA.

Design
A randomized controlled study was conducted with 54 participants with knee OA. All patients were randomized into two groups: the home-based telerehabilitation group (TRG) (n = 29) and the home-based paper group (PG) (n = 28). The home exercise program and training were provided with an instruction manual to PG. The same home exercise and education prescriptions were given to individuals in TRG via an online platform. Pain, function, quality of life, physical performance, muscle strength, and proprioception were evaluated at baseline and after eight weeks of intervention. In addition, satisfaction and usability were evaluated at week 8.

Results
TRG demonstrated better improvement in terms of pain, function, quality of life index score, and left extremity proprioception (p < 0.05). TRG was not superior to PG in terms of muscle strength and performance tests (except the Five Times Sit to Stand Test) (p > 0.05).

Conclusions
The home-based TR program was superior to the home-based PG program for pain, function, quality of life, and proprioception in patients with knee OA.
Incidence of Hospital-Acquired Conditions During Pediatric Clinical Research Inpatient Hospitalizations: A Matched Cohort Study
Authors: Milliren Carly E. , Denhoff Erica R. , Hahn Phillip D. , Ozonoff Al 
Published: September 2023

Objectives
In this matched cohort study using data from pediatric hospitals, we compared the incidence of hospital-acquired conditions (HACs) during clinical research hospitalizations to nonresearch hospitalizations.

Methods
Using Pediatric Health Information System data for inpatient discharges January 2017–June 2022, we matched research hospitalizations (identified by International Classification of Diseases, Tenth Revision, diagnosis code) to nonresearch hospitalizations within hospital on age (±3 y), sex, discharge year (±2), and All Patients Refined Diagnosis Related Groups classification, severity of illness (±1), and risk of mortality (±1). We calculated the incidence (per 1000 discharges) and incidence rate (per 10,000 patient days) of HAC identified by International Classification of Diseases, Tenth Revision, codes and compare research versus nonresearch using logistic and Poisson regression, accounting for matching using generalized estimating equations and adjusting for sociodemographic factors and hospital utilization.

Results
We matched 7000 research hospitalizations to 26,447 nonresearch from 28 hospitals. Median age was 6.0 years (interquartile range, 10.6 y). Median length of stay was 4.0 days (interquartile range, 11.0 days) with longer stays among research hospitalizations (P < 0.001). Incidence of HAC among research hospitalizations was 13.1 versus 7.2 per 1000 for nonresearch (P < 0.001) and incidence rate 6.7 versus 4.5 per 10,000 patient days. Adjusting for sociodemographic and clinical factors, research stays had 1.65 times the odds of any HAC (95% confidence interval, 1.27–2.16; P < 0.001) and 1.38 times the incidence rate (95% confidence interval, 1.09–1.75; P = 0.009).

Conclusions
Our findings indicate that pediatric research hospitalizations are more likely to experience HACs compared with nonresearch hospitalizations. These findings have important safety implications for pediatric inpatient clinical research that warrant further study.
Multiomics Data Reveal the Important Role of ANXA2R in T Cell–mediated Rejection After Renal Transplantation
Authors: Zhang Di , Zhang He , Lu Jun , Hu Xiaopeng 
Published: September 2023

Background.
T cell–mediated rejection (TCMR) is a severe issue after renal transplantation, but research on its T cell–receptor (TCR) repertoire is lacking. This study intended to elucidate the TCR repertoire landscape in TCMR and hence identify novel potential targets.

Methods.
A total of 12 multiomics data sets were collected. The TRUST4 algorithm was used to construct and analyze the TCR repertoire in renal allografts with TCMR and stable renal function. Then, novel TCR-related key genes were identified through various criteria and literature research. In bulk transcriptome, cell line, single-cell transcriptome data sets, multiple immune cell infiltration algorithms, and gene set enrichment analysis were used to analyze potential mechanisms of the identified key gene. Twenty-three pathological sections were collected for immunofluorescence staining in the clinical cohort. Finally, the diagnostic and prognostic values of ANXA2R were evaluated in multiple renal transplant data sets.

Results.
Allografts with TCMR showed significantly increased clonotype and specific clonal expansion. ANXA2R was found to be a novel key gene for TCMR and showed strong positive connections with the TCR complex and lymphocyte cells, especially CD8+ T cells. Immunofluorescence staining confirmed the existence of ANXA2R+ CD8+ T cells, with their percentage significantly elevated in TCMR compared with stable renal function. Finally, both mRNA and protein levels of ANXA2R showed promising diagnostic and prognostic value for renal transplant recipients.

Conclusions.

ANXA2R, identified as a novel TCR-related gene, had critical roles in clinicopathology, diagnosis, and prognosis in renal transplantation, which offered promising potential therapeutic targets.
Response of siliceous marine organisms to the Permian-Triassic climate crisis based on new findings from central Spitsbergen, Svalbard
Authors: Foster W.J. , Asatryan G. , Rauzi S. , Botting J. , Buchwald S. , Lazarus D. , Isson T. , Renaudie J. , Kiessling W. 
Published: September 2023

AbstractSiliceous marine ecosystems play a critical role on the Earth’s climate system through its influence on organic carbon burial and rates of marine authigenic clay formation (i.e. reverse weathering). The ecological demise of silicifying organisms associated with the Permian-Triassic mass extinction is postulated to have elevated rates of marine authigenic clay formation, resulting in a prolonged greenhouse climate during the Early Triassic. Yet, our understanding of the response of siliceous marine organisms during this critical interval is poor. Whilst radiolarians experienced the strongest diversity loss in their evolutionary history and perhaps also the greatest population decline of silica-secreting organisms during this event, only a small number of Griesbachian (post-extinction) localities that record siliceous organisms are known. Here, we report newly discovered latest Changhsingian to early Griesbachian (Clarkina meishanensis-Hindeodus parvusZone) radiolarians and siliceous sponge spicules from Svalbard. This fauna documents the survival of a low-diversity radiolarian assemblage alongside stem-group hexactinellid sponges making this the first described account of post-extinction silica-secreting organisms from the Permian/Triassic boundary in a shallow marine shelf environment and a mid-northern palaeolatitudinal setting. Our findings indicate that latitudinal diversity gradients for silica-secreting organisms following the mass extinction were significantly altered, and that silica productivity was restricted to high latitude and deep water thermal refugia. This result has potential to further shape our understanding of changes to marine porewater and seawater dissolved silica levels and in turn rates of reverse weathering, with implications for our understanding of carbon cycle dynamics during this interval. This also suggests that the export of organic carbon to the deep ocean was not as severely impacted at non-equatorial latitudes.Key PointsWe document the first occurrence of siliceous sponge spicules and radiolarians (biogenic silica) from a mid-northern paleolatitude following the mass extinction eventHoldover radiolarian species show poleward range shiftsThe ecological composition and the restriction to shallow water oxygenated facies suggests a shallow mid-latitude refuge for siliceous marine organismsThis result has potential to further shape our understanding of changes to marine dissolved silica levels and in turn rates of reverse weathering, with implications for our understanding of Permian-Triassic carbon cycle dynamics.
Estimation of inbreeding and kinship coefficients via latent identity-by-descent states
Authors: Guan Yongtao , Levy Daniel 
Published: September 2023

AbstractEstimating the individual inbreeding coefficient and pairwise kinship is an important problem in human genetics (e.g., in disease mapping) and in animal and plant genetics (e.g., inbreeding design). Existing methods such as sample correlation-based genetic relationship matrix, KING, and UKin are either biased, or not able to estimate inbreeding coefficients, or produce a large proportion of negative estimates that are difficult to interpret. This limitation of existing methods is partly due to failure to explicitly model inbreeding. Since all humans are inbred to various degrees by virtue of shared ancestries, it is prudent to account for inbreeding when inferring kinship between individuals. We present “Kindred”, an approach that estimates inbreeding and kinship by modeling latent identity-by-descent states that accounts for all possible allele sharing – including inbreeding – between two individuals. Through simulation, we demonstrate the high accuracy and, more importantly, non-negativity of kinship estimates by Kindred. By selecting a subset of SNPs that are similar in allele frequencies across different populations, Kindred can accurately estimate kinship between admixed samples. Finally, we demonstrate that the realized kinship matrix estimated by Kindred is effective in reducing genomic control values via linear mixed model in genome-wide association studies, and it also produces sensible heritability estimates. Kindred is freely available athttp://www.haplotype.org.
Individual and spatial determinants of mortality during the Covid-19 pandemic: The case of Belgium in 2020
Authors: Bourguignon Mélanie , Bertrand Aurélie , Damiens Joan , Doignon Yoann , Eggerickx Thierry , Plavsic Audrey , Sanderson Jean-Paul 
Published: September 2023

AbstractContextThe year 2020 was marked by the Covid-19 pandemic. In Belgium, it led to a doubling in deaths, mainly grouped into two periods. This article aims to compare the relative importance of predictors and individual and spatial determinants of mortality during these two waves to an equivalent non-pandemic period and to identify whether and to what extent the pandemic has altered the sociodemographic patterns of conventional mortality.MethodsThe analyses relate to all-cause mortality during the two waves of Covid-19 and their equivalent in 2019. They are based on matching individual and exhaustive data from the Belgian National Register with tax and population census data. A multi-level approach was adopted combining individual and spatial determinants.ResultsMortality patterns during the pandemic are very similar to those observed outside the pandemic. As in 2019, age, sex, and household composition significantly determine the individual risk of dying, with a higher risk of death among the oldest people, men, and residents of collective households. However, their risk of death increases during the Covid period, especially in the 65–79 age group. Spatial information is no more significant in 2020 than in 2019. However, a higher risk of death is observed when the local excess mortality index or the proportions of isolated or disadvantaged people increase.ConclusionsWhile the Covid pandemic did not fundamentally alter conventional mortality patterns, it did amplify some of the pre-existing differences in mortality.
Correlation of myeloid-derived suppressor cell expansion with upregulated transposable elements in severe COVID-19 unveiled in single-cell RNA sequencing reanalysis
Authors: Farahmandnejad Mitra , Mosaddeghi Pouria , Dorvash Mohammadreza , Sakhteman Amirhossein , Faridi Pouya , Negahdaripour Manica 
Published: September 2023

AbstractSome studies investigated the potential role of transposable elements (TEs) in COVID-19 pathogenesis and complications. However, to the best of our knowledge, there is no study to examine the possible association of TEs expression in cell functions and its potential role in COVID-19 immune response at the single-cell level.In this study, we reanalyzed single-cell RNA seq data of bronchoalveolar lavage (BAL) samples obtained from six severe COVID-19 patients and three healthy donors to assess the probable correlation of TE expression with the immune responses induced by the SARS-CoV-2 virus in COVID-19 patients.Our findings indicated that the expansion of myeloid-derived suppressor cells (MDSCs) may be a characteristic feature of COVID-19. Additionally, a significant increase in TEs expression in MDSCs was observed. This upregulation of TEs in COVID-19 may be linked to the adaptability of these cells in response to their microenvironments. Furthermore, it appears that the identification of overexpressed TEs by Pattern recognition receptors (PRRs) in MDSCs may enhance the suppressive capacity of these cells. Thus, this study emphasizes the crucial role of TEs in the functionality of MDSCs during COVID-19.
Axon guidance during CNS regeneration is required for specific brain innervation
Authors: Delpech Céline , Schaeffer Julia , Vilallongue Noemie , Benadjal Amin , Blot Beatrice , Excoffier Blandine , Plissonnier Elise , Albert Floriane , Paccard Antoine , Zagar Yvrick , Castellani Valérie , Belin Stephane , Chédotal Alain , Nawabi Homaira 
Published: September 2023

AbstractReconstruction of functional neuronal circuits in the mature brain remains a big challenge in the field of central nervous system (CNS) repair. Despite achievement of robust, long-distance regeneration through modulation of specific neuronal intrinsic growth properties, functional recovery is still limited due to major guidance defects of regenerating axons. Using co-activation of mTOR, JAK/STAT and c-myc pathways in retinal ganglion cells (RGC), we highlight that regenerating axons avoid the suprachiasmatic nucleus (SCN) due to repulsive mechanisms. We show that Slit/Robo guidance signaling is responsible for this reinnervation failure. In vivo suppression of this repulsive signaling allows regenerating axons to enter the SCN. The newly formed circuit is associated with functional behavioral recovery. Our results provide evidence that axon guidance mechanisms are required in the context of mature neuronal circuit repair.
Neutralization Escape by SARS-CoV-2 Omicron Subvariant BA.2.86
Authors: Lasrado Ninaad , Collier Ai-ris Y. , Hachmann Nicole P. , Miller Jessica , Rowe Marjorie , Schonberg Eleanor D. , Rodrigues Stefanie L. , LaPiana Austin , Patio Robert C. , Anand Trisha , Fisher Jana , Mazurek Camille , Guan Ruoran , Wagh Kshitij , Theiler James , Korber Bette , Barouch Dan H. 
Published: September 2023

ABSTRACTThe continued evolution of SARS-CoV-2 may lead to evasion of vaccine immunity and natural immunity. A highly mutated Omicron variant BA.2.86 has recently been identified with over 30 amino acid changes in Spike compared with BA.2 and XBB.1.5. As of September 4, 2023, BA.2.86 has been identified in 37 sequences from 10 countries, which is likely an underestimate due to limited surveillance. The ability of BA.2.86 to evade NAbs compared with other currently circulating Omicron variants remains unknown. Our data show that NAb responses to BA.2.86 were lower than to BA.2 but were comparable or slightly higher than to the current circulating recombinant variants XBB.1.5, XBB.1.16, EG.5, EG.5.1, and FL.1.5.1.
Hopanoid lipids promote soybean-Bradyrhizobiumsymbiosis
Authors: Pan Huiqiao , Shim Ashley , Lubin Matthew B. , Belin Brittany J. 
Published: September 2023

ABSTRACTThe symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promoteBradyrhizobiumsymbioses with tropical legumes. To characterize hopanoids inBradyrhizobiumsymbiosis with soybean, the most economically significantBradyrhizobiumhost, we validated a recently published cumate-inducible hopanoid mutant ofBradyrhizobium diazoefficiensUSDA110, Pcu-shc::Δshc. GC-MS analysis showed that this strain does not produce hopanoids without cumate induction, and under this condition, is impaired in growth in rich medium and under osmotic, temperature, and pH stress.In planta, Pcu-shc::Δshcis an inefficient soybean symbiont with significantly lower rates of nitrogen fixation and low survival within host tissue. RNA-seq revealed that hopanoid loss reduces expression of flagellar motility and chemotaxis-related genes, further confirmed by swim plate assays, and enhances expression of genes related to nitrogen metabolism and protein secretion. These results suggest that hopanoids provide a significant fitness advantage toB. diazoefficiensin legume hosts and provide a foundation for future mechanistic studies of hopanoid function in protein secretion and motility.IMPORTANCEA major problem for global sustainability is feeding our exponentially growing human population while available arable land is decreasing, especially in areas with the greatest population growth. Harnessing the power of plant-beneficial microbes has gained attention as a potential solution, including the increasing our reliance on the symbioses of leguminous plants and nitrogen-fixing rhizobia. This study examines the role of hopanoid lipids in the symbiosis betweenBradyrhizobium diazoefficiensUSDA110, an important commercial inoculant strain, and its economically important host soybean. Our research extends our knowledge of the functions of bacterial lipids in symbiosis to an agricultural context, which may one day help improve the practical applications of plant-beneficial microbes in agriculture.
Genomics-based timely detection of Dengue Virus type I genotypes I and V in Uruguay
Authors: Morel Noelia , Giovanetti Marta , Fonseca Vagner , Burgueño Analía , Lima Mauricio , Castro Emerson , R. Guimarães Natália , Iani Felipe C. M. , Bormida Victoria , Cortinas Maria Noel , Ramas Viviana , Coppola Leticia , Bento Ana I. , Rosewell Alexander , Franco Leticia , Rico Jairo Mendez , Lourenço José , Alcantara Luiz Carlos Junior , Chiparelli Hector 
Published: September 2023

AbstractWe report the first whole-genome sequences of Dengue Virus type I genotypes I and V from Uruguay, including the first cases ever reported in the country. Through timely genomic analysis, identification of these genotypes was possible, aiding in timely public health responses and intervention strategies to mitigate the impact of dengue outbreaks.Article Summary LineGenomic Analysis for identification of Dengue virus serotype 1 genotypes I and V in Uruguay: an early detection approach