bluuebunny/crossref_metadata_2025_split huggingface dataset:
Update on Covid-19: vaccines, timing of transplant after COVID-19 infection and use of positive donors
Authors: Boutin Catherine-Audrey , Alamri Maha , Ison Michael G. 
Published: February 2023

Purpose of review
SARS-CoV-2 resulted in a global pandemic that had a chilling effect on transplantation early in the pandemic and continues to result in significant morbidity and mortality of transplant recipients. Over the past 2.5 years, our understanding of the clinical utility of vaccination and mAbs to prevent COVID-19 in solid organ transplant (SOT) recipients has been studied. Likewise, approach to donors and candidates with SARS-CoV-2 has been better understood. This review will attempt to summarize our current understanding of these important COVID-19 topics.

Recent findings
Vaccination against SARS-CoV-2 is effective in reducing the risk of severe disease and death among transplant patients. Unfortunately, humoral and, to a lesser extent, cellular immune response to existing COVID-19 vaccines is reduced in SOT recipients compared with healthy controls. Additional doses of vaccine are required to optimize protection of this population and still may be insufficient in those who are highly immunosuppressed, those receiving belatacept, rituximab and other B-cell active mAbs. Until recently, mAbs were options for the prevention of SARS-CoV-2 but are markedly less effective with recent omicron variants. SARS-CoV-2-infected donors can generally be used for nonlung, nonsmall bowel transplants unless they have died of acute severe COVID-19 or COVID-19-associated clotting disorders.

Summary
Our transplant recipients require a three-dose mRNA or adenovirus-vector and one dose of mRNA vaccine to be optimally protected initially; they then need to receive a bivalent booster 2+ months after completing their initial series. Most nonlung, nonsmall bowel donors with SARS-CoV-2 can be utilized as organ donors.
Local administration of vancomycin powder in orthopaedic fracture surgery: current practice and trends
Authors: Marchand Lucas S. , Sprague Sheila , O'Hara Nathan N. , Li Chuan Silvia , O'Toole Robert V. , Joshi Manjari , Viskontas Darius , Romeo Nicholas , Hymes Robert A. , Obremskey William T. , Higgins Thomas F. , Potter Gorden D. , Bergin Patrick F. , Gage Mark , Gary Joshua L. , Bhandari Mohit , Slobogean Gerard P. ,   PREP-IT Investigators
Published: February 2023

Abstract

Objectives:
Surgical site infections in orthopaedic trauma are a significant problem with meaningful patient and health care system–level consequences. Direct application of antibiotics to the surgical field has many potential benefits in reducing surgical site infections. However, to date, the data regarding the local administration of antibiotics have been mixed. This study reports on the variability of prophylactic vancomycin powder use in orthopaedic trauma cases across 28 centers.

Methods:
Intrawound topical antibiotic powder use was prospectively collected within three multicenter fracture fixation trials. Fracture location, Gustilo classification, recruiting center, and surgeon information were collected. Differences in practice patterns across recruiting center and injury characteristics were tested using chi-square statistic and logistic regression. Additional stratified analyses by recruiting center and individual surgeon were performed.

Results:
A total of 4941 fractures were treated, and vancomycin powder was used in 1547 patients (31%) overall. Local administration of vancomycin powder was more frequent in open fractures 38.8% (738/1901) compared with closed fractures 26.6% (809/3040) (P < 0.001). However, the severity of the open fracture type did not affect the rate at which vancomycin powder was used (P = 0.11). Vancomycin powder use varied substantially across the clinical sites (P < 0.001). At the surgeon level, 75.0% used vancomycin powder in less than one-quarter of their cases.

Conclusions:
Prophylactic intrawound vancomycin powder remains controversial with varied support throughout the literature. This study demonstrates wide variability in its use across institutions, fracture types, and surgeons. This study highlights the opportunity for increased practice standardization for infection prophylaxis interventions.

Level of Evidence:
Prognostic—III.
The Ratio of Clavicle Length to Head Circumference
Authors: Huang Shu-Jing , Huang Mei , Liu Xian-Lan , Hong Long-Cheng , Su Yu-Qing , Lin Yan-Ting , Wang Yan-Qing , Lin Jin-Rong , Zhang Xiao-Dong , Zhou Ying , Su Yi-Ming 
Published: February 2023

Abstract
We aimed to plot the growth curve of the fetal clavicle, identify gestational date-independent parameters. Using 2-dimensional ultrasonography, we obtained the clavicle lengths (CLs) from 601 normal fetuses between 12 and 40 gestational age (GA). The CL/fetal growth parameters ratio was calculated. Moreover, 27 cases of fetal growth restriction (FGR) and 9 cases of small for GA (SGA) were detected. In normal fetuses, the mean CL (mm) = −68.2 + 29.80 × ln(GA) ± Z × (1.07 + 0.02 × GA). A linear relationship was detected between CL and head circumference (HC), biparietal diameter, abdominal circumference and femoral length with R
2 values of 0.973, 0.970, 0.962, and 0.972, respectively. The CL/HC ratio (mean value 0.130) showed no significant correlation with GA. Clavicle lengths in the FGR group significantly decreased compared with the SGA group (P < 0.01). This study determined a reference range of fetal CL in a Chinese population. Furthermore, the CL/HC ratio, which is independent of GA, is a novel parameter for the evaluation of the fetal clavicle.
OUTCOMES FOLLOWING ZONE 3 AND ZONE 1 AORTIC OCCLUSION FOR THE TREATMENT OF BLUNT PELVIC INJURIES
Authors: Cralley Alexis L. , Moore Ernest E. , Dubose Joseph , Brenner Megan L. , Schaid Terry R. , DeBot Margot , Cohen Mitchell , Silliman Christopher , Fox Charles , Sauaia Angela 
Published: February 2023

ABSTRACT

Background: A 2021 report of the Aortic Occlusion for Resuscitation in Trauma and Acute Care Surgery multicenter registry described the outcomes of patients treated with Zone 3 resuscitative endovascular balloon occlusion of the aorta (REBOA zone 3). Our study builds upon that report, testing the hypothesis that REBOA zone 3 is associated with better outcomes than REBOA Zone 1 in the immediate treatment of severe, blunt pelvic injuries. Methods: We included adults who underwent aortic occlusion (AO) via REBOA zone 1 or REBOA Zone 3 in the emergency department for severe, blunt pelvic injuries [Abbreviated Injury Score ≥ 3 or pelvic packing/embolization/first 24 hours] in institutions with >10 REBOAs. Adjustment for confounders was accomplished with a Cox proportional hazards model for survival, generalized estimating equations for intensive care unit (ICU)-free days (IFD) and ventilation-free days (VFD) > 0 days, and mixed linear models for continuous outcomes (Glasgow Coma Scale [GCS], Glasgow Outcome Scale [GOS]), accounting for facility clustering. Results: Of 109 eligible patients, 66 (60.6%) underwent REBOA Zone 3 and 43 (39.4%) REBOA Zone 1. There were no differences in demographics, but compared with REBOA Zone 3, REBOA Zone 1 patients were more likely to be admitted to high volume centers and be more severely injured. These patients did not differ in systolic blood pressure (SBP), cardiopulmonary resuscitation in the prehospital/hospital settings, SBP at the start of AO, time to AO start, likelihood of achieving hemodynamic stability or requirement of a second AO. After controlling for confounders, compared with REBOA Zone 3, REBOA Zone 1 was associated with a significantly higher mortality (adjusted hazard ratio, 1.51; 95% confidence interval [CI], 1.04–2.19), but there were no differences in VFD > 0 (adjusted relative risk, 0.66; 95% CI, 0.33–1.31), IFD > 0 (adjusted relative risk, 0.78; 95% CI, 0.39–1.57), discharge GCS (adjusted difference, −1.16; 95% CI, −4.2 to 1.90) or discharge GOS (adjusted difference, −0.67; 95% CI −1.9 to 0.63). Conclusions: This study suggests that compared with REBOA Zone 1, REBOA Zone 3 provides superior survival and is not inferior regarding other adverse outcomes in patients with severe blunt pelvic injuries.
Using human genetics to validate complement C3 as a drug target in periodontitis
Authors: Alayash Zoheir , Baumeister Sebastian-Edgar , Holtfreter Birte , Kocher Thomas , Baurecht Hansjörg , Ehmke Benjamin , Nolde Michael , Reckelkamm Stefan Lars 
Published: February 2023

AbstractAimEvidence from a phase IIa trial showed that a complement C3-targeted drug reduced gingival inflammation in patients with gingivitis. We investigated the therapeutic effect of genetically proxied C3 inhibition on periodontitis using drug target Mendelian randomization (MR).Materials and methodsWe used multiple ‘cis’ instruments from the vicinity of the encoding loci of C3 that are associated with serum C3. We selected three independent single nucleotide polymorphisms (rs141552034, rs145406915, rs11569479) from a genome-wide association study (GWAS) of 5,368 European descent individuals. We extracted association statistics from a GWAS of 17,353 clinical periodontitis cases and 28,210 European controls. Wald ratios were combined using inverse-variance weighted meta-analysis.ResultsMR analysis revealed that the inhibition of C3 reduces the risk of periodontitis (Odds ratio 0.91 per 1 standard deviation reduction in C3; 95% Confidence Interval 0.87–0.96, P-value=0.0003).ConclusionsFindings from MR analysis showed that C3 blockade protects against periodontitis.Clinical relevanceScientific rationale for studyMounting evidence suggests that the complement system is dysregulated in periodontitis. First human randomized clinical trials demonstrated promising effects mediated via the blockade of C3, a key factor of the complement system. Results from drug target MR analysis can provide compelling evidence to predict the efficacy of pharmacological C3 blockage in future clinical trials in periodontitis patients.Principle findingsGenetically proxied C3 inhibition reduced periodontitis risk.Practical implicationsOur MR analysis provides genetic evidence that C3-targeted drugs might be an efficient adjunct therapy in periodontitis.
A third vaccine dose equalizes the levels of effectiveness and immunogenicity of heterologous or homologous COVID-19 vaccine regimens
Authors: Guibert Nicolas , Trepat Kylian , Pozzetto Bruno , Josset Laurence , Fassier Jean-Baptiste , Allatif Omran , Saker Kahina , Brengel-Pesce Karen , Walzer Thierry , Vanhems Philippe , Trouillet-Assant Sophie 
Published: February 2023

AbstractBackgroungTo cope with the persistence of the Covid-19 epidemic and the decrease in antibody levels following vaccination, a third dose of vaccine has been recommended in the general population. However, several vaccine regimens had been used initially, and the heterologous ChadOx1-S/BNT162b2 regimen had shown better efficacy and immunogenicity than the homologous BNT162b2/BNT162b2 regimen.AimWe wanted to determine if this benefit was retained after the third dose.MethodsWe combined an observational study of SARS-COV-2 infections among vaccinated healthcare workers at the University-Hospital of Lyon, France, with an analysis of immunological parameters before and after the third mRNA vaccine dose.ResultsFollowing the second vaccine dose, heterologous vaccination regimens were more protective against infection than homologous regimens, but this was no longer the case after the third dose. RBD-specific IgG levels and serum neutralization capacity against different SARS-CoV-2 variants were higher after the third dose than after the second dose in the homologous regimen group, but not in the heterologous group.ConclusionThe advantage conferred by heterologous vaccination is lost after the third dose both in terms of protection and immunogenicity. Immunological measurements suggest that heterologous vaccination induces maximal immunity after the second dose, whereas the third dose is required to reach the same level in individuals with a homologous regimen.
Relationship between adherence to the 2019 Canada’s Food Guide recommendations on healthy food choices and nutrient intakes in older adults
Authors: Brassard Didier , Chevalier Stéphanie 
Published: February 2023

AbstractBackgroundFollowing Canada’s food guide (CFG) recommendations should ensure adequate nutrient intakes. Older adults have increased needs for certain nutrients and nutrient density; the extent to which adherence to CFG recommendations can help reduce inadequate nutrient intakes is unknown.ObjectiveOur aim was to assess the relationship between adherence to CFG recommendations on healthy food choices and intake of key nutrients in adults 65 years and older from the Canadian Community Health Survey (CCHS) 2015 - Nutrition.MethodsSecondary analysis of data from 4,093 older adults of the CCHS 2015 - Nutrition (mean age, 73.6 years, 54% females). Dietary intakes were measured using an interviewer-administered 24-hour dietary recall including one repeat in a subsample (42%). The National Cancer Institute multivariate method was used to estimate usual (i.e., long-term) dietary intakes. Adherence to CFG recommendations was measured using the Healthy Eating Food Index (HEFI)-2019 score. Simple linear and logistic regression models estimated the effect of increased HEFI-2019 score on usual nutrient intakes and the prevalence of inadequate nutrient intakes (i.e., below the estimated average requirements), respectively.ResultsCompared with the prevalence of inadequate intakes at median HEFI-2019 score (46.4/80 points), a higher HEFI-2019 (+11 points) was associated with reductions in the prevalence of inadequate intakes of magnesium, vitamin B6, and protein (-19.8% [95%CI: -30.8, -8.9], -12.7% [95%CI: -22.5, -3.0], and -4.7% [95%CI: -9.4, -0.1], respectively). In contrast, data for higher HEFI-2019 scores were compatible with increased prevalence of inadequate intakes of folate, vitamin D, and calcium (4.0% [95%CI: -8.4, 16.3], 2.6% [95%CI: 1.1, 4.0], and 2.3% [95%CI: -3.0, 7.5], respectively).ConclusionsBased on dietary intakes of Canadian older adults in 2015, increasing the degree of adherence to CFG recommendations on healthy food choices may reduce nutrient intake inadequacy for most key nutrients except folate, vitamin D and calcium.
Interpreting biologically informed neural networks for enhanced biomarker discovery and pathway analysis
Authors: Hartman Erik , Scott Aaron , Malmström Lars , Malmström Johan 
Published: February 2023

AbstractThe advent of novel methods in mass spectrometry-based proteomics allows for the identification of biomarkers and biological pathways which are crucial for the understanding of complex diseases. However, contemporary analytical methods often omit essential information, such as protein abundance and protein co-regulation, and therefore miss crucial relationships in the data. Here, we introduce a generalized workflow that incorporates proteins, their abundances, and associated pathways into a deep learning-based methodology to improve biomarker identification and pathway analysis through the creation and interpretation of biologically informed neural networks (BINNs). We successfully employ BINNs to differentiate between two subphenotypes of septic acute kidney injury (AKI) and COVID-19 from the plasma proteome and utilize feature attribution-methods to introspect the networks to identify which proteins and pathways are important for distinguishing between subphenotypes. Compared to existing methods, BINNs achieved the highest predictive accuracy and revealed that metabolic processes were key to differentiating between septic AKI subphenotypes, while the immune system was more important to the classification of COVID-19 subphenotypes. The methodology behind creating, interpreting, and visualizing BINNs were implemented in a free and open source Python-package:https://github.com/InfectionMedicineProteomics/BINN.
Communicating the benefits of quitting smoking on mental health increases motivation to quit in people with anxiety and/or depression: A randomized trial of two health messages
Authors: Steinberg Marc L. , Rosen Rachel L. , Ganz Ollie , Wackowski Olivia A. , Jeong Michelle , Delnevo Cristine D. 
Published: February 2023

ABSTRACTBackgroundAlthough smoking rates have declined over time, this decline has not been observed among those with mental health concerns. It is therefore important to develop effective messaging to support quitting in this population.MethodsWe conducted an online experiment with 419 adults who smoke cigarettes daily. Participants with, or without a lifetime history of anxiety and/or depression were randomized to view a message focused on the benefits of quitting smoking on mental or physical health. Participants then reported motivation to quit smoking, mental health concerns about quitting, and perceived effectiveness of the message.ResultsParticipants with a lifetime history of anxiety and/or depression who saw the message focused on the benefits of quitting smoking on mental health reported greater motivation to quit than when they saw a message focused on the benefits to physical health. This was not replicated when examining current symptoms instead of lifetime history. Pre-existing beliefs that smoking improves one’s mood were greater in those experiencing current symptoms and in those with a lifetime history of anxiety and/or depression. There was no main or interaction (message type X mental health status) effect of message type received on mental health related concerns about quitting.ConclusionsThis study is one of the first to evaluate a smoking cessation message with content specifically targeted to those with mental health concerns about quitting smoking. Additional work is needed to determine how to best target those with mental health concerns with messages focused on the benefits of quitting on mental health.ImplicationsThese data can begin to inform regulatory efforts to address tobacco use in those with comorbid anxiety and/or depression by providing information on how to effectively communicate the benefits of quitting smoking on mental health.
An SEIDR Model for the Early Spread of COVID-19
Authors: Cao Tingrui 
Published: February 2023

AbstractIn this article, we conduct a literature review on the history and mathematical modeling of infectious diseases and COVID-19. Next, some simple epidemic dynamic models and the basic reproductive number theory are introduced. We propose a SEIDR model for COVID-19 and provide the solution methods for the basic reproduction number, parameters, and dynamic model. Finally, we simulate the early stages of the COVID-19 epidemic in Argentina, Indonesia, Mexico, and South Africa with the SEIDR model.
OME-Zarr: a cloud-optimized bioimaging file format with international community support
Authors: Moore Josh , Basurto-Lozada Daniela , Besson Sébastien , Bogovic John , Bragantini Jordão , Brown Eva M. , Burel Jean-Marie , Casas Moreno Xavier , de Medeiros Gustavo , Diel Erin E. , Gault David , Ghosh Satrajit S. , Gold Ilan , Halchenko Yaroslav O. , Hartley Matthew , Horsfall Dave , Keller Mark S. , Kittisopikul Mark , Kovacs Gabor , Küpcü Yoldaş Aybüke , Kyoda Koji , le Tournoulx de la Villegeorges Albane , Li Tong , Liberali Prisca , Lindner Dominik , Linkert Melissa , Lüthi Joel , Maitin-Shepard Jeremy , Manz Trevor , Marconato Luca , McCormick Matthew , Lange Merlin , Mohamed Khaled , Moore William , Norlin Nils , Ouyang Wei , Özdemir Bugra , Palla Giovanni , Pape Constantin , Pelkmans Lucas , Pietzsch Tobias , Preibisch Stephan , Prete Martin , Rzepka Norman , Samee Sameeul , Schaub Nicholas , Sidky Hythem , Solak Ahmet Can , Stirling David R. , Striebel Jonathan , Tischer Christian , Toloudis Daniel , Virshup Isaac , Walczysko Petr , Watson Alan M. , Weisbart Erin , Wong Frances , Yamauchi Kevin A. , Bayraktar Omer , Cimini Beth A. , Gehlenborg Nils , Haniffa Muzlifah , Hotaling Nathan , Onami Shuichi , Royer Loic A. , Saalfeld Stephan , Stegle Oliver , Theis Fabian J. , Swedlow Jason R. 
Published: February 2023

AbstractA growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself – OME-Zarr – along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain — the file format that underlies so many personal, institutional, and global data management and analysis tasks.
Active mesh and neural network pipeline for cell aggregate segmentation
Authors: Smith Matthew B. , Sparks Hugh , Almagro Jorge , Chaigne Agathe , Behrens Axel , Dunsby Chris , Salbreux Guillaume 
Published: February 2023

AbstractSegmenting cells within cellular aggregates in 3D is a growing challenge in cell biology, due to improvements in capacity and accuracy of microscopy techniques. Here we describe a pipeline to segment images of cell aggregates in 3D. The pipeline combines neural network segmentations with active meshes. We apply our segmentation method to cultured mouse mammary duct organoids imaged over 24 hours with oblique plane microscopy, a high-throughput light-sheet fluorescence microscopy technique. We show that our method can also be applied to images of mouse embryonic stem cells imaged with a spinning disc microscope. We segment individual cells based on nuclei and cell membrane fluorescent markers, and track cells over time. We describe metrics to quantify the quality of the automated segmentation. Our segmentation pipeline involves a Fiji plugin which implement active meshes deformation and allows a user to create training data, automatically obtain segmentation meshes from original image data or neural network prediction, and manually curate segmentation data to identify and correct mistakes. Our active meshes-based approach facilitates segmentation postprocessing, correction, and integration with neural network prediction.Statement of significanceIn vitro culture of organ-like structures derived from stem cells, so-called organoids, allows to image tissue morphogenetic processes with high temporal and spatial resolution. Three-dimensional segmentation of cell shape in timelapse movies of these developing organoids is however a significant challenge. In this work, we propose an image analysis pipeline for cell aggregates that combines deep learning with active contour segmentations. This combination offers a flexible and efficient way to segment three-dimensional cell images, which we illustrate with by segmenting datasets of growing mammary gland organoids and mouse embryonic stem cells.