bluuebunny/crossref_metadata_2025_split huggingface dataset:
Verification of Immunity to Measles in Adults
Authors: Smith Eleanor E.A. , Atmar Robert L. , Giordano Thomas P. , Kulkarni Prathit A. 
Published: January 2025

Abstract
Recently, there have been several measles outbreaks reported in the United States and globally. Declining rates of childhood vaccination and potential lack of complete coverage in the adult population could impact population levels of immunity against measles over the next decade and beyond. Therefore, it is important for primary care clinicians and others who provide vaccinations to verify the status of immunity to measles as part of routine clinical care for adult patients. Self-reported receipt of “childhood vaccinations” might not reflect actual receipt of the currently licensed live-virus measles, mumps, and rubella vaccine, depending upon an adult patient's age and childhood location. Most adult patients who do not have evidence of immunity to measles should receive measles, mumps, and rubella vaccination, as per longstanding recommendations from the Advisory Committee on Immunization Practices.
Nursing Initiation of Rapid Electroencephalography Point-of-Care Monitoring: Lessons From the Pioneer Summit
Authors: Bader Mary Kay , Mayer Stephan A. , Dorriz Parshaw J. , Desai Masoom , Kaplan Matthew , Torbey Michel T. , Olson DaiWai M. , Vespa Paul M. ,   the participants of the Pioneer Summit
Published: January 2025

ABSTRACT

BACKGROUND: Status epilepticus is an emergency, and applying electroencephalography (EEG) monitoring is an important part of diagnosing and treating seizure. The use of rapidly applied limited array continuous EEG (rapid EEG) has become technologically feasible in recent years. Nurse-led protocols using rapid EEG as a point-of-care monitor are increasingly being adopted. METHODS: A virtual summit meeting of nurses and physicians was convened to discuss various technological and practical aspects of rapid EEG, including the use of nurse-led protocols using rapid EEG. After oral presentations, participants responded to a survey indicating their level of agreement with key position statements. RESULTS: From the 52 participants who participated in the 2-hour summit, there was a strong agreement with the statement “Bedside nurses can start point-of-care EEG with automated seizure alert software to provide more informed care,” with a median Likert score of 5 (completely agree) and an interquartile range of 4 to 5. CONCLUSION: Using rapid EEG to monitor for seizure is a valid and valuable method that falls within the nursing domain. Nurse-driven protocols may provide the opportunity to enhance patient care through early identification of seizures.
Histological differences among thrombi in thrombotic diseases
Authors: Yamashita Atsushi , Gi Toshihiro , Sato Yuichiro 
Published: January 2025

Purpose of review
This review aims to summarize the histological differences among thrombi in acute myocardial infarction, ischemic stroke, venous thromboembolism, and amniotic fluid embolism, a newly identified thrombosis.

Recent findings
Acute coronary thrombi have a small size, are enriched in platelets and fibrin, and show the presence of fibrin and von Willebrand factor, but not collagen, at plaque rupture sites. Symptomatic deep vein thrombi are large and exhibit various phases of time-dependent histological changes. Cancer-associated venous thromboemboli contain invasive cancer cells that penetrate the vascular walls, and small cancer cell aggregates are observed within the thrombi. The thrombus composition in atherosclerotic and cardioembolic ischemic strokes varies from case to case, while the thrombi in cancer-associated ischemic stroke are rich in platelets and fibrin. A pathological study on amniotic fluid embolism identified uterine vein thrombi and massive platelet-rich microthrombi in the lungs.

Summary
Atherothrombus formation is induced by plaque disruption and may occlude a narrow lumen within a short time. Venous thrombi may grow to a large size in a multistage or chronic manner. Cancer cells can directly contribute to venous thrombus formation. The thrombus formation in amniotic fluid embolism may explain the occurrence of consumptive coagulopathy and cardiopulmonary collapse.
Should We Transplant Candidates With a Positive SARS-CoV-2 RT-PCR Test?
Authors: Benotmane Ilies , Kasriel Nathan , Masset Christophe , Michard Baptiste , Malvezzi Paolo , Giguet Baptiste , Tinel Claire , Conti Filomena , Von Tokarski Florent , Ursic-Bedoya José , Matignon Marie , Flahault Adrien , Mohamadou Inna , Lebossé Fanny , Kamar Nassim , Maanaoui Mehdi , Kounis Ilias , Poulain Coralie , Hilleret Marie-Noëlle , Anglicheau Dany , Lacaille Florence , Bouvier Nicolas , Golbin Léonard , Duveau Agnès , Caillard Sophie , Couzi Lionel , Kaminski Hannah , Dumortier Jérôme 
Published: January 2025

Background.
It remains unclear whether physicians should accept transplantation offers for candidates with a positive SARS-CoV-2 reverse transcription polymerase chain reaction test due to the potential risk of severe infection after initiating immunosuppressive therapy.

Methods.
A multicenter observational study was conducted in 19 French solid organ transplantation units. Patients on the waiting list for liver or kidney transplants who had a positive SARS-CoV-2 reverse transcription polymerase chain reaction nasopharyngeal swab at the time of transplantation were recorded.

Results.
Sixty-five patients were included. The recipients were predominantly men (n = 40; 62%) with a mean age of 55.4 y (SD = 16.5). On the day of transplantation, 2 patients exhibited symptoms compatible with COVID-19. The majority of patients (n = 55; 85%) underwent thoracic imaging, with only 3 patients showing imaging results compatible with COVID-19. Ten patients (28%) had a cycle threshold value <30. Anti–SARS-CoV-2 spike protein serology within 3 mo before transplantation was available for 36 patients; only 2 patients were seronegative. Due to COVID-19, physicians adapted the immunosuppressive therapy for 16 patients (25%). Specific antiviral therapy was used for 15 patients (23%), primarily remdesivir (n = 12). Overall, the majority of patients did not receive any adjustment of immunosuppressive therapy or antiviral treatment (n = 36; 55%). The outcomes were generally favorable even for patients with the lowest cycle threshold values, indicating a high viral load. Four patients died during follow-up, although none of these deaths were attributable to COVID-19.

Conclusions.
Transplantation appears to be safe for patients who are asymptomatic or have mild symptoms, reassuring thoracic imaging, and a history of anti–SARS-CoV-2 infection and/or immunization.
Beyond the Neck: When Is Thoracic Operation Needed for Thyroidectomy?
Authors: Wang Rongzhi , Song Zhixing , Balachandra Sanjana , Gillis Andrea , Fazendin Jessica , Lindeman Brenessa , Wei Benjamin , Chen Herbert 
Published: January 2025

Background:
Although most patients with intrathoracic thyroid glands can undergo thyroidectomy via a cervical incision, some cases necessitate intraoperative thoracic surgery assistance. This study aims to identify computed tomography(CT) findings that predict the need for thoracic surgery assistance during thyroidectomy.

Methods:
We reviewed administrative data at our institution(2012-2023), encompassing 7370 thyroidectomies, to identify patients who underwent thyroidectomy for intrathoracic thyroid glands, defined as thyroid glands that extended below the sternal notch. Detailed CT analysis was conducted, including measurements of intrathoracic thyroid dimensions, shape, extension to posterior mediastinum, and relation to thoracic inlet. Receiver operating characteristic(ROC) curve analysis and multivariable regression analysis were performed to identify the most accurate independent predictors of the need for intraoperative thoracic surgery assistance.

Results:
Among 255 patients with intrathoracic thyroid glands, 34(13.3%) required intraoperative thoracic surgery assistance. Patients needing thoracic assistance had significantly larger intrathoracic thyroid glands in anteroposterior, craniocaudal, and horizontal dimensions compared to those without. Additionally, their thyroid glands were more likely to enlarge below the sternal notch or extend into the posterior mediastinum ROC curve indicated that distance from inferior border of thyroid gland to sternal notch (Area Under Curve(AUC)=0.94) is a better predictor than distance to aortic arch (AUC=0.91) or sternal angle (AUC=0.91). Thresholds of distance to sternal notch≥5.3cm, anteroposterior dimension≥5.2cm, and horizontal dimension≥5.3cm provided 80% sensitivity and ≥70% specificity for predicting the need for thoracic assistance. Multivariable regression analysis identified thyroid increasing in size below sternal notch, distance to sternal notch≥5.3cm, and horizontal dimension≥5.3cm as independent predictors for intraoperative thoracic assistance.

Conclusions:
Thyroid glands extending≥5.3cm below sternal notch, enlarging below sternal notch, or having a horizontal dimension≥5.3cm warrant preoperative thoracic surgery consultation for potential intraoperative assistance.
Conformal Prediction and Venn-ABERS Calibration for Reliable Machine Learning-Based Prediction of Bacterial Infection Focus
Authors: Schmidt Jacob Bahnsen , Nielsen Karen Leth , Strunin Dmytro , Kirkby Nikolai Søren , Thomassen Jesper Qvist , Rasmussen Steen Christian , Frikke-Schmidt Ruth , Hertz Frederik Boëtius , Engsig-Karup Allan Peter 
Published: January 2025

AbstractFinding the focus of bacterial infections can be challenging, especially for hospitalised patients. Conventional microbiological diagnostic methods are either time consuming, expensive, or difficult to interpret due to contamination. The aim of this study was to apply machine learning (ML) to reliably predict the focus of bacterial infections. This study utilised a dataset including samples from 10,153 patients, collected from November 1, 2019 to June 3, 2023 at Rigshospitalet, Denmark. The dataset contains microbiological findings, biochemical data, and vital parameters. The dataset was analysed using ML. The ML-outputs were calibrated using Venn-ABERS calibration and model uncertainty was addressed using conformal risk control. The best performing model was the XGBoost model achieving an AUC of 0.93 ± 0.051 (mean ± SD.). Combining the model with methods from the conformal prediction framework achieves predictive capabilities that surpasses similar studies, while also accounting for model uncertainty by providing statistically robust uncertainty estimates.
Test-Retest Reliability of Assessment of Work Performance for Thai Homeless People
Authors: Chatthong Winai , Thanapet Uthaikan , Ammawat Watthanaree , Rueankam Maliwan , Khemthong Supalak 
Published: January 2025

AbstractPurposeThis study aims to conduct test-retest reliability of the AWP – Thai version. Internal consistency has been tested after completing an approval process of forward-backward translation and achieving good content validity. Under the shortage of mental workforce, vocational rehabilitation (VR) has been trained to enhance supported employment in homeless people with mental illness (MI). The Assessment of Work Performance (AWP) is required for Thai translation to classify the quality of job skills in one pilot setting at Nonthaburi’s destitute home.MethodsTwo weeks were set for test-retest reliability of the AWP collecting a group of participants (n = 59). Intraclass Correlation Coefficient (ICC) was calculated at the 95% confidential level with an F-test of true value.ResultsModerate to good test-retest reliability of the AWP is addressed for all participants and separation of those participants into four groups of job selection: rug hooking, cleaning food table, sweeping the leaves, and community gardening. However, a cautious interpretation of ICC provides accurate implications of the AWP in both clinical utility and the VR program evaluation.ConclusionsThe AWP is a performance-based tool that can be an observable process in participatory work routines. Motor, process, and interactive communication skills are essential components connected to a practical solution to enhance the VR to the social welfare system.
Heterozygosity at a conserved candidate sex determination locus is associated with female development in the clonal raider ant
Authors: Lacy Kip D. , Lee Jina , Rozen-Gagnon Kathryn , Wang Wei , Carroll Thomas S. , Kronauer Daniel J.C. 
Published: January 2025

AbstractSex determination is a developmental switch that triggers sex-specific developmental programs. This switch is “flipped” by the expression of genes that promote male- or female-specific development. Many lineages have evolved sex chromosomes that act as primary signals for sex determination. However, haplodiploidy (males are haploid and females are diploid), which occurs in ca. 12% of animal species, is incompatible with sex chromosomes. Haplodiploid taxa must, therefore, rely on other strategies for sex determination. One mechanism, “complementary sex determination” (CSD), uses heterozygosity as a proxy for diploidy. In CSD, heterozygosity at a sex determination locus triggers female development, while hemizygosity or homozygosity permits male development. CSD loci have been mapped in honeybees and two ant species, but we know little about their evolutionary history. Here, we investigate sex determination in the clonal raider ant,Ooceraea biroi. We identified a 46kb candidate CSD locus at which all females are heterozygous, but diploid males are homozygous for either allele. As expected for CSD loci, the candidate locus has more alleles than most other loci, resulting in a peak of nucleotide diversity. This peak negligibly affects the amino acid sequences of protein-coding genes, suggesting that heterozygosity of a non-coding genomic sequence triggers female development. This locus is distinct from the CSD locus in honeybees but homologous to a CSD locus mapped in two distantly related ant species, implying that this molecular mechanism has been conserved since a common ancestor that lived approximately 112 million years ago.
OxLDL-targeted Chimeric Antigen Receptor T Regulatory Cells Reduce Atherosclerotic Plaque Development
Authors: Schwab Robert D. , Hong Seok-Jae Albert , Bi Xin , Degaramo David A. , Faruqi Aisha , Brookens Shawna K. , Keane John T. , Liu Fang , Musunuru Kiran , Rader Daniel J. , Posey Avery D. 
Published: January 2025

AbstractCardiovascular disease caused by atherosclerosis is responsible for 18 million deaths annually, highlighting a significant need for new medical therapies, especially for patients ineligible for surgical interventions. Atherosclerosis is driven by the accumulation of low-density lipoprotein (LDL) and the formation of foam cells, accompanied by oxidative stress and the deposition of oxidized LDL (OxLDL), a pro-inflammatory molecule. Lowering LDL is the mainstay of current medical treatment in addition to blood pressure control and lifestyle changes, but to date, specifically targeting the inflammatory pathways contributing to plaque development without significant systemic side effects has not been feasible. Over the past decade, chimeric antigen receptor (CAR) T cells have treated cancer and restored immune imbalance in autoimmune diseases in patients and resolved cardiac fibrosis in preclinical models. Using an inducible T regulatory cell (Treg) platform, we created an anti-OxLDL-specific CAR Treg therapy that exerts cell- and cytokine-mediated immunosuppression to reduce macrophage-foam cell formation in vitro. Murine anti-OxLDL CAR Tregs inhibited 80% of atherosclerotic plaque formation in immunocompetent mouse models of hyperlipidemia and atherosclerosis. These studies illustrate the potential of anti-OxLDL CAR Tregs to mitigate the inflammation and plaque deposition associated with OxLDL, potentially offering a new therapeutic option for atherosclerosis.
Microbes under climatic refugia: Self-stabilizing subcommunity rank dynamics in large-river deltaic estuaries
Authors: Liu Huaiqiang , Zhong Zhenghua , Xu Juan , Qu Liping , Liu Haijun , Zheng Fengfeng , Zhang Chuanlun , Xie Wei 
Published: January 2025

AbstractMicroorganisms, akin to macroorganisms, can be sheltered by climatic refugia, overlooked for optimism about microbial extinction. By categorizing microbial communities into ecologically distinct subcommunities, we conducted a two-year survey of large-river deltaic estuaries (LDEs) which are regarded as refugial hotspots, and established rank hierarchies to monitor temporal changes. We found that, consistent with macroecology, LDEs harbor distinct microbial community structures, with the abundance distribution of subcommunities exhibiting resilience against environmental perturbations, persisting on an annual cycle. In particular, while the evenness of subcommunity rank abundance curves fluctuates frequently, shifts in rank order are less dynamic but, once initiated, have a more pronounced impact on subsequent rank dynamics. Our results suggest that the microbial subcommunity rank structure in LDEs is both persistent and robust, aligning with classic patterns of species abundance distributions. This study emphasizes that, despite differences in their roles, the stable functioning of microbial rank systems is also fundamental to the refugial capacity of ecosystems and should be given equal importance.
Rprot-Vec: A deep learning approach for fast protein structure similarity calculation
Authors: Zhang Yichuan , Zhang Wen 
Published: January 2025

AbstractThe prediction of structural similarity and homology detection of protein sequences has always been a very challenging and valuable research. Based on protein structure similarity, rapid and accurate detection of homologous proteins can infer the functions of newly discovered or unannotated proteins. If we can use a method to quickly predict the structural similarity between two proteins, we can achieve the task of homologous detection of protein sequences. By using this method with partially known protein structures, we can quickly infer the functions of more unknown proteins. In this article, we propose an enhanced model Rprot-vec (Rapid Protein Vector) based on deep learning, which improves existing methods. It can quickly calculate the structural similarity of proteins and perform protein homology detection using only protein sequences. Meanwhile, our model can also be used to simulate proteins to accomplish more downstream tasks related to proteins. Our model performs well within the very important TM-score range, with an accurate similarity prediction rate of 65.3% for homologous proteins. In addition, for all protein pairs within the TM-score range, the average prediction error is 0.0561, indicating good performance. The superiority of our model can be demonstrated from various aspects. In addition, we have also supplemented the dataset in this field, providing data support for future researchers studying this field simultaneously.Contactzhangyichuan09@gmail.comSupplementary informationhttps://github.com/SuperZyccc/RProt-vec/
Multi-species integration, alignment and annotation of single-cell RNA-seq data with CAMEX
Authors: Guo Zhen-Hao , Huang De-Shuang , Zhang Shihua 
Published: January 2025

AbstractSingle-cell RNA-seq (scRNA-seq) data from multiple species present remarkable opportunities to explore cellular origins and evolution. However, integrating and annotating scRNA-seq data across different species remains challenging due to the variations in sequencing techniques, ambiguity of homologous relationships, and limited biological knowledge. To tackle the above challenges, we introduce CAMEX, a heterogeneous Graph Neural Network (GNN) tool that leverages many-to-many homologous relationships for multi-species integration, alignment, and annotation of scRNA-seq data from multiple species. Notably, CAMEX outperforms state-of-the-art methods integration on various cross-species benchmarking datasets (ranging from one to eleven species). Besides, CAMEX facilitates the alignment of diverse species across different developmental stages, significantly enhancing our understanding of organ and organism origins. Furthermore, CAMEX enables the detection of species-specific cell types and marker genes through cell and gene embedding. In short, CAMEX holds the potential to provide invaluable insights into how evolutionary forces operate across different species at single-cell resolution.
A highly efficient CRISPR-Cas9-based gene editing system in oat (Avena sativa)
Authors: Mehtab-Singh  , Kaye Cali , Kaur Rajvinder , Singh Jaswinder 
Published: January 2025

AbstractCultivated oat (Avena sativa) is an emerging cereal for healthy lives owing to its unique characteristics, such as high β-glucan and oil content, distinctive fatty acid composition, and gluten-free nature. The recent unravelling of the 12.5 Gb hexaploid oat genome underlined breeding barriers caused by ancestral translocations and inversions, leading to recombination suppression and pseudo-linkage further hindering conventional trait introgression. Over the past decade, the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system has been extensively used for crop improvement and functional genomics in all other cereals except oats. Its large repetitive genome with three sub-genomes, lack of efficient transformation, recalcitrant nature, and complex molecular screening due to gene redundancy have been major obstacles to gene editing success in oat. We report the first successful CRISPR-Cas9-based gene editing in oat in three genes —AsTLP8, AsVRN3andAsVRN3Dwith gene-editing efficiency of up to 41.1%. The gene-edited plants for all the genes carried deletions and/or one base insertion. Further analysis ofVRN3T1and T2mutants revealed bent leaves in heterozygous knockouts (AACCdD), while an extended vegetative growth phase was seen in the T1homozygous and biallelic mutants (aaccdd), accentuating the important role ofVRN3in oat development. We are confident that this highly efficient oat gene editing system will pave the way for a deeper molecular understanding of this healthy cereal, deciphering oat’s functional genomics, and creating genetic diversity at the cold spots of recombination in oat.
SARS-CoV-2 cellular coinfection is limited by superinfection exclusion
Authors: Sims Anna , Weir Daniel J. , Cole Sarah J. , Hutchinson Edward 
Published: January 2025

AbstractThe coinfection of individual cells is a requirement for exchange between two or more virus genomes, which is a major mechanism driving virus evolution. Coinfection is restricted by a mechanism known as superinfection exclusion (SIE), which prohibits the infection of a previously infected cell by a related virus after a period of time. SIE regulates coinfection for many different viruses, but its relevance to the infection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was unknown. In this study, we investigated this using a pair of SARS-CoV-2 variant viruses encoding distinct fluorescent reporter proteins. We show for the first time that SARS-CoV-2 coinfection of individual cells is limited temporally by SIE. We defined the kinetics of the onset of SIE for SARS-CoV-2 in this system, showing that the potential for coinfection starts to diminish within the first hour of primary infection, and then falls exponentially as the time between the two infection events is increased. We then asked how these kinetics would affect the potential for coinfection with viruses during a spreading infection. We used plaque assays to model the localised spread of SARS-CoV-2 observed in infected tissue, and showed that the kinetics of SIE restrict coinfection, and therefore sites of possible genetic exchange, to a small interface of infected cells between spreading viral infections. This indicates that SIE, by reducing the likelihood of coinfection of cells, likely reduces the opportunities for genetic exchange between different strains of SARS-CoV-2 and therefore is an underappreciated factor in shaping SARS-CoV-2 evolution.