bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Clinical, Economic, and Humanistic Outcomes Between Blood Collection Approaches: A Systematic Literature Review
Authors: Perry Cathy , Alsbrooks Kimberly , Mares Alicia , Hoerauf Klaus 
Published: October 2023

ABSTRACT

Background:
A systematic literature review was performed to understand the prevalence, advantages, and disadvantages of blood collection using different approaches (direct venipuncture or vascular access devices), and interventions used to mitigate the disadvantages.

Methods:
The review included a broad range of study designs and outcomes. Database searches (Embase, MEDLINE, Cochrane library, and Centre for Reviews and Dissemination) were conducted in March 2021 and supplemented by hand searching.

Results:
One hundred forty-one publications were included. The data indicate that blood sampling from vascular access devices is common in emergency departments, trauma centers, and intensive care units. Studies showed that hemolysis and sample contamination place a considerable economic burden on hospitals. Significant cost savings could be made through enforcing strict aseptic technique, or using the initial specimen diversion technique.

Conclusions:
Hemolysis and sample contamination are far from inevitable in vascular access device-collected or venipuncture samples; both can be reduced through adherence to strict blood sampling protocols and utilization of the initial specimen diversion technique. Needle-free blood collection devices offer further hope for reducing hemolysis. No publication focused on the difficult venous access population; insertion success rates are likely to be lower (and the benefits of vascular access devices higher) in these patients.
Patient and Provider Decision Making About HIV Postexposure Prophylaxis Following Sexual Violence: A Qualitative Analysis
Authors: Anderson Jocelyn C. , Boakye Michelle D. S. , Draughon Moret Jessica 
Published: October 2023

Abstract
To explore patient and health care provider HIV postexposure prophylaxis (PEP) decision making following sexual assault, semistructured interviews regarding HIV PEP provision with 15 patients and 10 health care providers were conducted. A qualitative, descriptive, thematic analysis approach was used. Four themes were derived: (a) medical concerns; (b) emotional, trauma, and support factors; (c) daily medication management; and (d) ensuring access to HIV PEP. How participants described these themes and the importance placed on factors within each theme varied between the two groups. Altering provider communication so that HIV PEP discussions better align with patient decision-making factors (e.g., trauma and ability to take in information, how to manage side effects) could facilitate improvement in HIV PEP decision making following sexual assault for patients. High-level policy changes would improve HIV PEP access for sexual assault patients without necessitating the extraordinary efforts individual providers currently undertake.
Medium-term Outcomes in Pediatric Heart Transplant Recipients Managed Using a Steroid Avoidance Immune Suppression Protocol
Authors: Hartje-Dunn Christina , Blume Elizabeth D. , Bastardi Heather , Daly Kevin P. , Fynn-Thompson Francis , Gauvreau Kimberlee , Singh Tajinder P. 
Published: October 2023

Background.
Short-term outcomes using steroid avoidance immune suppression are encouraging in pediatric heart transplant (HT) recipients at low risk of antibody-mediated rejection. We assessed medium-term outcomes in pediatric HT recipients initiated on a steroid avoidance protocol at our institution using surveillance biopsies.

Methods.
All primary HT recipients during 2006–2020 who did not have a donor-specific antibody were eligible for immune suppression consisting of 5-d Thymoglobulin/steroid induction followed by a tacrolimus-based, steroid-free regimen. We assessed freedom from graft failure (death or retransplant), acute rejection, posttransplant lymphoproliferative disease, and cardiac allograft vasculopathy.

Results.
Overall, 150 of 181 primary HT recipients were eligible for steroid avoidance regimen. Their median age was 8.7 y, 41% had congenital heart disease, 23% were sensitized, and 35% were on a mechanical support. The median follow-up was 6.1 y. Eleven patients (8%) were on maintenance steroids at discharge and 13% at 1 y. Graft survival was 94% at 1 y and 87% at 5 y. Freedom from rejection was 73% at 1 y and 64% at 5 y. Freedom from posttransplant lymphoproliferative disease was 96% at 1 y and 95% at 5 y. Freedom from moderate cardiac allograft vasculopathy was 94% at 5 y. Eight patients developed diabetes. Estimated glomerular filtration rate was <60 mL/min/1.73 m2 in 5% of the cohort at 5 y.

Conclusions.
Pediatric HT recipients at low risk of antibody-mediated rejection have excellent medium-term survival and relatively low incidence of posttransplant morbidities when managed using a steroid avoidance immune suppression protocol.
Public but ineffective: Fatality inquiries into childhood deaths in Alberta
Authors: Verbeke Mary-Claire , Mitchell Ian 
Published: September 2023

ABSTRACTIntroductionChild Death Review (CDR) processes are public efforts to review a child’s death to understand how and why children die, to improve child health and to prevent future deaths. In 2013, the Canadian Paediatric Society made specific recommendations to establish structured and comprehensive CDR systems in each province and territory. In Alberta, there is no comprehensive CDR process but there are some components. The most public and probably the most expensive component is the public fatality inquiry. A new notification policy adopted after in June 2017 appears to be of limited value for child death prevention.MethodsWe examined all Alberta fatality inquiry reports from January 1, 1995 to April 15, 2023 concerning children aged 0-17 years (n=133) to determine whether the fatality inquiry system might be effective in preventing future similar deaths.ResultsRecommendations made by judges in a fatality inquiry were not always followed by action, and hence inquiry recommendations have been largely ineffective. Fatality inquiry recommendations were sometimes untimely, and therefore had little chance of being effective. There is an increasing trend from 1995 (case 1) to 2023 (case 133) in the time taken to initiate a child fatality inquiry review.Discussion and ConclusionInformation and recommendations from fatality inquiries into Alberta childhood deaths tend to be delayed and not followed by action. A comprehensive CDR process is required in Alberta. With system changes, public fatality inquiries could be an effective part of the child death prevention process.
Measuring Hemoglobin A1C with Frozen Packed Cell and Frozen Whole Blood Samples in an Epidemiologic Study: The Reasons for Geographic and Racial Differences in Stroke (REGARDS) Study
Authors: Mukaz Debora Kamin , Tison Stephanie , Long D. Leann , Carson April P. , Hunt Kelly J. , Judd Suzanne E. , Cushman Mary 
Published: September 2023

ABSTRACTIntroductionHemoglobin A1c (HbA1c) measurement in epidemiology studies could be increased if reliability of measurements in frozen stored samples was known. In the REasons for Geographic and Racial Differences in Stroke, a longitudinal study of 30,239 Black and White U.S. adults, we investigated reliability of HbA1c measurements for two types of samples stored at -80°C for up to 14 years.MethodsAmong 917 participants without diabetes, HbA1c was measured in 2017 in frozen packed cells from the first visit (2003-07) and in frozen whole blood samples from the second visit (2013-16). To study reliability, associations between HbA1c and glycemia-related characteristics were examined.ResultsEach 10mg/dL greater fasting glucose was associated with 0.08% (95%CI: 0.05-0.11%) greater HbA1c in frozen packed cells (visit 1) and 0.10% (95%CI: 0.08-0.12%) greater HbA1c in whole blood (visit 2). HbA1c was also similarly higher with both methods with increasing age, gender, systolic blood pressure, body mass index, high-density lipoprotein, triglycerides, C-reactive protein, and hemoglobin. Using both methods, ≤3.5% were classified with diabetes based on HbA1c ≥6.5%.ConclusionsIn REGARDS participants without diabetes, HbA1c measurement appeared reliable in frozen packed cells or whole blood under long-term storage, suggesting acceptability for study of the epidemiology of HbA1c.
Nanotope: A Graph Neural Network-Based Model for Nanobody paratope prediction
Authors: Meng Xiangpeng , Li Shangru , Li Rui , Huang Bingding , Wang Xin 
Published: September 2023

AbstractNanobodies are artificial antibodies derived from the immune system of camelid species, obtained through artificial processing and isolation of antigen-binding proteins. Their small molecular size and high specificity endow nanobodies with extensive potential applications in various fields. However, determining nanobody paratopes through experimental methods is both costly and time-consuming, while traditional computational approaches often lack sufficient accuracy. To enhance the prediction accuracy, we propose Nanotope, a structurebased model capable of efficiently and accurately predicting paratopes, utilizing graph neural networks and an antibody pretrained language model. Our approach primarily leverages sequence features obtained from the AntiBERTy antibody pretrained language model and three-dimensional spatial structure features of nanobodies as inputs. Employing one-dimensional convolution, EGConv graph convolution, and GATConv convolution, we predict the probability of nanobody paratopes with a much higher accuracy. Our method significantly improves the prediction of nanobody paratopes and requires only nanobody sequences and structural information, without the need for additional antigen information. Source code is freely available athttps://github.com/WangLabforComputationalBiology/Nanotope
Drug-bacterial membrane interactions: A Tale of two force fields
Authors: Basu Subhadip , Mandal Sandip , Maiti Prabal K. 
Published: September 2023

AbstractTuberculosis (TB), caused byMycobacterium tuberculosis(M.tb), a gram-positive bacteria, is known to infect and kill millions of people worldwide, specifically in poor and developing countries. M.tb has unique characteristics in terms of the presence of an extraordinarily thick cell wall structure, mainly composed of mycolic acid (MA) and arabinogalactan (AG). Between these components, mycolic acid is of particular interest because it exhibits extremely low permeability for most of the drug molecules, thus helping M.tb to survive against medical treatment. Hence, it is extremely useful to study the interactions between drug molecules and mycolic acids in order to better design potential TB medicine. On that premise, the present work aims to computationally model mycolic acid monolayer and probe its permeability against some first-line TB drugs, namely ethambutol, ethionamide, and isoniazid. It is a known fact that such modelling strongly depends on the interaction parameters used. The current study addresses this issue by employing two widely used force fields-GROMOS 54A7-ATB (hereafter GROMOS) united atom force fields and CHARMM36 (hereafter CHARMM) all-atom force fields to collate the drug-mycolic acid interplay. Our findings indicate that both force fields provide consistent results in terms of the mode of drug-monolayer interactions but significantly differ for the monolayer permeability. Mycolic acid monolayer generally exhibited a higher free energy barrier of crossing using CHARMM FF, while GROMOS parameters provide better stability of drug molecules on the monolayer surface, which can be attributed to the greater electrostatic potential at the monolayer-water interface. Both the force field parameters predicted the highest resistance against ethambutol, the most soluble molecule. However, significant differences can be recorded for the other two molecules with the change in the interaction parameter set. In summary, our study provides insight into the dependency ofin silicomodelling of membranes on force field parameters together with the guidelines to investigate the drug-membrane interactions consisting of non-standard lipids/fatty acids.
T cell receptor-centric perspective to multimodal single-cell data analysis
Authors: Mullan Kerry A. , Ha My , Valkiers Sebastiaan , de Vrij Nicky , Ogunjimi Benson , Laukens Kris , Meysman Pieter 
Published: September 2023

AbstractThe T-cell receptor (TCR) carries critical information regarding T-cell functionality. The TCR, despite its importance, is underutilized in single cell transcriptomics, with gene expression (GEx) features solely driving current analysis strategies. Here, we argue for a switch to a TCR-first approach, which would uncover unprecedented insights into T cell and TCR repertoire mechanics. To this end, we curated a large T-cell atlas from 12 prominent human studies, containing in total 500,000 T cells spanning multiple diseases, including melanoma, head-and-neck cancer, T-cell cancer, and lung transplantation. Herein, we identified severe limitations in cell-type annotation using unsupervised approaches and propose a more robust standard using a semi-supervised method or the TCR arrangement. We then showcase the utility of a TCR-first approach through application of the novel STEGO.R tool for the successful identification of hyperexpanded clones to reveal treatment-specific changes. Additionally, a meta-analysis based on neighbor enrichment revealed previously unknown public T-cell clusters with potential antigen-specific properties as well as highlighting additional common TCR arrangements. Therefore, this paradigm shift to a TCR-first with STEGO.R highlights T-cell features often overlooked by conventional GEx-focused methods, and enabled identification of T cell features that have the potential for improvements in immunotherapy and diagnostics.One Sentence SummaryRevamping the interrogation strategies for single-cell data to be centered on T cell receptor (TCR) rather than the generic gene expression improved the capacity to find relevant disease specific TCR.Key PointsThe TCR-first approach captures dynamic T cell features, even within a clonal population.A novel ∼500,000 T-cell atlas to enhance single cell analysis, especially for restricted populations.Novel STEGO.R program and pipeline allows for consistent and reproducible interrogating of scTCR-seq with GEx.
Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails
Authors: Castillo Diego Garcia , Barton Nick , Faria Rui , Larsson Jenny , Stankowski Sean , Butlin Roger , Johannesson Kerstin , Westram Anja Marie 
Published: September 2023

AbstractPredicting the outcomes of adaptation is a major goal of evolutionary biology. When temporal changes in the environment mirror spatial gradients, it opens up the potential for predicting the course of adaptive evolution over time based on patterns of spatial genetic and phenotypic variation. We assessed this approach in a 30-year transplant experiment in the marine snailLittorina saxatilis. In 1992, snails were transplanted from a predation-dominated environment to one dominated by wave action. Based on spatial patterns, we predicted transitions in shell size and morphology, allele frequencies at positions throughout the genome, and chromosomal rearrangement frequencies. Observed changes closely agreed with predictions. Hence, transformation can be both dramatic and rapid, and predicted from knowledge of the phenotypic and genetic variation among populations.
Pre-clinical Evaluation of Biomarkers for Early Detection of Nephrotoxicity Following Alpha-particle Radioligand Therapy
Authors: Li Mengshi , Robles-Planells Claudia , Liu Dijie , Graves Stephen A. , Vasquez-Martinez Gabriela , Mayoral-Andrade Gabriel , Lee Dongyoul , Rastogi Prerna , Marks Brenna M. , Sagastume Edwin A. , Weiss Robert M. , Linn-Peirano Sarah C. , Johnson Frances L. , Schultz Michael K. , Zepeda-Orozco Diana 
Published: September 2023

AbstractPurposeCancer treatment with alpha-emitter-based radioligand therapies (α-RLTs) demonstrates promising tumor responses. Radiolabeled peptides are filtered through glomeruli, followed by potential reabsorption of a fraction by proximal tubules, which may cause acute kidney injury (AKI) and chronic kidney disease (CKD). Because tubular cells are considered the primary site of radiopeptides’ renal reabsorption and potential injury, the current use of kidney biomarkers of glomerular functional loss limits the evaluation of possible nephrotoxicity and its early detection. This study aimed to investigate whether urinary secretion of tubular injury biomarkers could be used as additional non-invasive sensitive diagnostic tool to identify unrecognizable tubular damage and risk of long-term α-RLTs nephrotoxicity.MethodsA bifunctional cyclic peptide, melanocortin ligand-1(MC1L), labeled with [203Pb]Pb-MC1L, was used for [212Pb]Pb-MC1L biodistribution and absorbed dose measurements in CD-1 Elite mice. Mice were treated with [212Pb]Pb-MC1L in a dose escalation study up to levels of radioactivity intended to induce kidney injury. The approach enabled prospective kidney functional and injury biomarker evaluation and late kidney histological analysis to validate these biomarkers.ResultsBiodistribution analysis identified [212Pb]Pb-MC1L reabsorption in kidneys with a dose deposition of 2.8, 8.9, and 20 Gy for 0.9, 3.0, and 6.7 MBq injected [212Pb]Pb-MC1L doses, respectively. As expected, mice receiving 6.7 MBq had significant weight loss and CKD evidence based on serum creatinine, cystatin C, and kidney histological alterations 28 weeks after treatment. A dose-dependent urinary Neutrophil gelatinase-associated lipocalin (NGAL, tubular injury biomarker) urinary excretion the day after [212Pb]Pb-MC1L treatment highly correlated with the severity of late tubulointerstitial injury and histological findings.Conclusionurine NGAL secretion could be a potential early diagnostic tool to identify unrecognized tubular damage and predict long-term α-RLT-related nephrotoxicity.
Anticipatory brain activity depends on the sensory modality of the expected stimulus: insights from single-trial analyses
Authors: Hoxha Isabelle , Chevallier Sylvain , Delorme Arnaud , Amorim Michel-Ange 
Published: September 2023

AbstractPerceptual anticipation is known to impact the reaction time of decisions. While anticipatory patterns have been identified in human brain activity, the single-trial neural signature of anticipation remains unexplored. Similarly, past studies have underlined an effect of pre-stimulus alpha-band activity on reaction times. Still, it remains unknown whether this activity is stimulus-specific or rather acts as a general indicator of readiness. This study aimed to determine whether human participants expected a visual or an auditory stimulus at the single-trial level in both cued and uncued trials. We show that pre-stimulus brain activity entails information about the expected upcoming stimulus, and that the information content can be extracted from single-trial brain activity. Behavioral analyses helped uncover the link between correct anticipation and shifts in decision strategy, and additionally validated the classification of uncued trials. This understanding of single-trial stimulus-specific neural signatures of anticipation can significantly impact cognitive neuroscience, human-computer interaction, and neuroergonomics research, enabling the development of real-time systems capable of predicting and adapting to an individual’s anticipated stimuli, thereby enhancing task performance and user experience in diverse applications ranging from adaptive interfaces to clinical interventions.Novelty and SignificanceWith a focus on uncovering single-trial neural signatures of anticipation, this study aims to explore the specificity of pre-stimulus brain activity to expected visual or auditory stimuli in both cued and uncued trials, i.e. whether participants are informed about the upcoming stimulus or not. Our research seeks to contribute to the fundamental understanding of human cognition by elucidating the informational content embedded in anticipatory brain patterns. The insights gained hold promise in advancing fields like cognitive neuroscience and human-computer interaction, paving the way for innovative applications in adaptive interface design, real-time systems, and personalized interventions.
Nuclear corepressors NCOR1 and NCOR2 entrain thymocyte signaling, selection, and emigration
Authors: David Natalie A. , Lee Robin D. , LaRue Rebecca S. , Joo Sookyong , Farrar Michael A. 
Published: September 2023

AbstractT cell development proceeds via discrete stages that require both gene induction and gene repression. Transcription factors direct gene repression by associating with corepressor complexes containing chromatin-remodeling enzymes; the corepressors NCOR1 and NCOR2 recruit histone deacetylases to these complexes to silence transcription of target genes. Earlier work identified the importance of NCOR1 in promoting the survival of positively-selected thymocytes. Here, we used flow cytometry and single-cell RNA sequencing to identify a broader role for NCOR1 and NCOR2 in regulating thymocyte development. UsingCd4-cremice, we found that conditional deletion of NCOR2 had no effect on thymocyte development, whereas conditional deletion of NCOR1 had a modest effect. In contrast,Cd4-crexNcor1f/fxNcor2f/fmice exhibited a significant block in thymocyte development at the DP to SP transition. Combined NCOR1/2 deletion resulted in increased signaling through the T cell receptor, ultimately resulting in elevated BIM expression and increased negative selection. The NF-κB, NUR77, and MAPK signaling pathways were also upregulated in the absence of NCOR1/2, contributing to altered CD4/CD8 lineage commitment, TCR rearrangement, and thymocyte emigration. Taken together, our data identify multiple critical roles for the combined action of NCOR1 and NCOR2 over the course of thymocyte development.
Auditory attention detection in cocktail-party: A microstate study
Authors: Roushan Hossein , Bakhshalipour Gavgani Sahar , Geravanchizadeh Masoud 
Published: September 2023

AbstractHealthy human brain can easily attend to one auditory stimulus and filter out the other stimuli, described in the terms of “selective auditory attention” or referred to as the cocktail party phenomenon. This paper proposes a new real-time mapping-based selective auditory attention detection (SAAD) system using only EEG signals. In the proposed system, several quasi-stable maps, called EEG microstates, are extracted. After the optimization of the microstates topographies, the temporal dynamics of the microstates are used for the classification of auditory attention direction. The evaluation results obtained in different listening conditions (i.e., dichotic and spatial hearing) show that the use of an integrated set of 6 microstate topographies best describes the data and provides better classification performance. Due to the nature of EEG microstates in reflecting the fundamentals of brain information processing, this study provides an appropriate way of reaching the underlying mechanism of selective attention. The proposed system based on microstates can effectively detect the attention direction in dynamic scenarios, where the listener’s attention might be switched in seconds, making the model suitable for real-time applications. Furthermore, the proposed auditory attention detection system is advantageous in the sense that the detection of attention is performed without using speech signals.