bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perceptions, attitudes, and challenges regarding continuing professional development among Ethiopian Medical Laboratory professionals: A mixed-method study
Authors: Negussie Adugna , Sisay Abay , Shibabaw Agumas , Kebede Edosa , Tesfaye Firehiwot , Kedida Gizachew , Deneke Nadew , Teklu Takele , Cheneke Waqtola 
Published: February 2024

AbstractBackgroundMedical laboratory professionals play vital role in healthcare. The growing demand for quality laboratory services and emerging technologies underscore the crucial need for Continuing Professional Development (CPD). However, there is limited information on CPD programs in Ethiopia. Thus, this study aimed to assess medical laboratory professionals’ perceptions, attitudes, and challenges towards CPD and improve engagement to enhance diagnostic service quality.Methodsthis cross-sectional study enrolled 228 medical laboratory professionals in Ethiopia from July to October 2023. Using a mixed-methods approach that combined quantitative data from an online survey and qualitative data from interviews. SPSS version 28 was used for data analysis.Resultsthe average age of the study participants was 32.6 ±6.4 (SD) years, the majority were men (88.6%), and 44.3% have worked for more than ten years. Of the participants, 51% never had CPD training. About three-fourth of the participants perceived CPD as essential to their professional career. About 45.2% of the study participants perceived that the purpose of CPD course is to renew their license and gain knowledge and skills that are not covered in basic training. While the majority of participants had good attitudes towards CPD, about 10% of them stated that it is not important in their career growth. The majority of the study participants were not in support of the decentralized CPD system. A notable problem with finance, insufficient manpower, unsupportive employers, a lack of awareness by regulatory bodies, inadequate access to training close to their working area, were identified as significant challenges of the CPD program.Conclusionthe study highlights the perception that CPD is crucial for enhanced laboratory practices and career advancement. The study highlights the need for targeted strategies to address the identified problems and increase the engagement of medical laboratory professionals in the CPD program.
Variability in drought gene expression datasets highlight the need for community standardization
Authors: VanBuren Robert , Nguyen Annie , Marks Rose A. , Mercado Catherine , Pardo Anna , Pardo Jeremy , Schuster Jenny , Aubin Brian St. , Wilson Mckena Lipham , Rhee Seung Y. 
Published: February 2024

AbstractPhysiologically relevant drought stress is difficult to apply consistently, and the heterogeneity in experimental design, growth conditions, and sampling schemes make it challenging to compare water deficit studies in plants. Here, we re-analyzed hundreds of drought gene expression experiments across diverse model and crop species and quantified the variability across studies. We found that drought studies are surprisingly uncomparable, even when accounting for differences in genotype, environment, drought severity, and method of drying. Many studies, including most Arabidopsis work, lack high-quality phenotypic and physiological datasets to accompany gene expression, making it impossible to assess the severity or in some cases the occurrence of water deficit stress events. From these datasets, we developed supervised learning classifiers that can accurately predict if RNA-seq samples have experienced a physiologically relevant drought stress, and suggest this can be used as a quality control for future studies. Together, our analyses highlight the need for more community standardization, and the importance of paired physiology data to quantify stress severity for reproducibility and future data analyses.
Genomic and phylogenetic features of thePicobirnaviridaesuggest microbial rather than animal hosts
Authors: Sadiq Sabrina , Holmes Edward C. , Mahar Jackie E. 
Published: February 2024

ABSTRACTThe RNA virus familyPicobirnaviridaehas traditionally been associated with the gastrointestinal systems of terrestrial mammals and birds, with the majority of viruses detected in animal stool samples. Metatranscriptomic studies of vertebrates, invertebrates, microbial communities, and environmental samples have resulted in an enormous expansion of the genomic and phylogenetic diversity of this family. Yet picobirnaviruses remain poorly classified, with only one genus and three species formally ratified by the International Committee of Virus Taxonomy. Additionally, an inability to culture picobirnaviruses in a laboratory setting or isolate them in animal tissue samples, combined with the presence of bacterial genetic motifs in their genomes, suggests these viruses may represent RNA bacteriophage rather than being associated with animal infection. Utilising a data set of 2,286 picobirnaviruses sourced from mammals, birds, reptiles, fish, invertebrates, microbial communities, and environmental samples, we identified seven consistent phylogenetic clusters likely representing picobirnavirus genera that we tentatively nameAlpha-, Beta-, Gamma-, Delta-, Epsilon-, Zeta-,andEtapicobirnavirus. A statistical analysis of topological congruence between virus-host phylogenies revealed more frequent cross-species transmission than any other RNA virus family. In addition, bacterial ribosomal binding site motifs were more enriched in picobirnavirus genomes than in the two groups of established RNA bacteriophage – theLeviviricetesandCystoviridae. Overall, our findings support the hypothesis that thePicobirnaviridaehave bacterial hosts and provide a lower-level taxonomic classification for this highly diverse and ubiquitous family of RNA viruses.
Human-AI Collaboration in Large Language Model-Assisted Brain MRI Differential Diagnosis: A Usability Study
Authors: Kim Su Hwan , Schramm Severin , Berberich Cornelius , Rosenkranz Enrike , Schmitzer Lena , Serguen Kerem , Klenk Christopher , Lenhart Nicolas , Zimmer Claus , Wiestler Benedikt , Hedderich Dennis M. 
Published: February 2024

AbstractBackgroundPrior studies have shown the potential of large language models (LLMs) to support in differential diagnosis in radiology. However, the interaction of human users with LLMs in this context has not been evaluated.PurposeTo investigate the impact of human-LLM collaboration on accuracy and efficiency of brain MRI differential diagnosis.MethodsIn this retrospective study, twenty brain MRI cases with a challenging but definitive diagnosis were selected and randomized into two groups. Six inexperienced radiology residents were instructed to determine the three most likely differential diagnoses for each of these cases via conventional internet search or utilizing an LLM-based search engine (© Perplexity AI, powered by GPT-4). Accuracy of suggested differential diagnoses was analyzed using the chi-square test and Mann-Whitney U test. Interpretation times were analyzed using the student’s t-test. Benefits and challenges in human-LLM interaction were derived from observations and participant feedback.ResultsLLM-assisted brain MRI differential diagnosis yielded superior accuracy (38/59 [LLM-assisted] vs 25/59 [conventional] correct diagnoses, p = 0.03). No difference in interpretation time (8.12 +/- 3.22 min [LLM-assisted] vs 7.96 +/- 2.65 min [conventional], p = 0.76) or level of confidence (median of 2.5 [LLM-assisted] vs 3.0 [conventional], p = 0.96) was observed. Several challenges related to human errors and technical limitations were identified.ConclusionHuman-LLM collaboration has the potential to improve brain MRI differential diagnosis. Yet, several challenges must be addressed to ensure effective adoption and user acceptance.
Clinical evaluation of the Roche distributed SD Biosensor SARS-CoV-2 & Flu A/B Rapid Antigen Test amongst mild symptomatic people during the 2022/2023 winter season
Authors: Iglὁi Zsὁfia , Velzing Jans , Koopmans Marion , Molenkamp Richard 
Published: February 2024

AbstractBoth influenza and SARS-CoV-2 are seasonal respiratory illnesses with similar symptoms, however distinguishing one from the other can have benefits for the patient and have different implications in various settings.In this study we have evaluated the clinical performance of the Roche distributed SD Biosensor SARS-CoV-2 & Flu A/B Rapid Antigen Test during the 2022/2023 winter season, in a non-hospitalized, mild symptomatic population, comparing results with reverse transcription quantitative polymerase chain reaction (RT-qPCR). Participants also filled in a short questionnaire about their symptom onset, symptoms, vaccination status for both influenza and SARS-CoV-2.We could include 290 people with complete records with female majority (72%, 209/290). Age ranged from 18 years old (minimum age for inclusion) to 71 years (mean age was 40.4 years). From the 290 inclusions 93 tested positive with SARS-CoV-2 PCR, 12 by influenza A and 6 by influenza B PCR. For SARS-CoV-2 overall sensitivity was 72.0% (confidence interval, CI 61.8-80.9%) and specificity 99.5% (CI 97.2-99.9%). SARS-CoV-2 RDT performed best up to and including PCR ct value of 25 (sensitivity 96% CI 85.8-99.5%), but could also detect samples less or equal to PCR ct 33, however with lower sensitivity (sensitivity 80.0% CI 69.6-88.1%). For influenza limited amount of samples were available; the RDT detected influenza A with 58.3% sensitivity (CI 27.7-84.8) and 100% specificity (CI 98.6-100.0%). In case of influenza B the inclusions were too low to calculate sensitivity reliably (2/6, 33.3% CI 4.3-77.7%); specificity was 98.2% (5/274, CI 95.8-99.4%). No cross reaction between SARS-CoV-2 and Flu A/B was experienced.As was shown before, SARS-CoV-2 could be determined with high sensitivity in recent onset and lower than ct 25 samples. In spite of performing the study throughout the influenza season, we had sub optimal inclusions for determining RDT clinical performance; further studies are needed.
Predictors of breast cancer screening among women of reproductive age in Tanzania: Evidence from DHS 2022
Authors: Tibenderana Jovin R. , Kessy Sanun Ally , Mlaponi Dosanto Felix , Mwaitete Ndinagwe Lloyd , Mtenga John Elyas 
Published: February 2024

AbstractBackgroundBreast cancer is a global concern, registering 2.3 million new cases and 685,000 deaths in 2020, with projections reaching 4.4 million cases by 2070. In Tanzania, it’s the second leading cause of cancer-related deaths among women, often diagnosed at advanced stages, leading to poor outcomes. Only 5% of women in the country report undergoing breast cancer screening, the aim study is to determine factors associated with breast cancer screening in Tanzania.MethodsA cross-sectional study among women of reproductive age in Tanzania, utilizing data from the Demographic and Health Surveys (DHS). We used available data on breast cancer screening the DHS. The outcome of the study was breast cancer screening. To find independent variables associated with breast cancer screening, logistic regression was used.ResultsAfter controlling for other factors, the following factors remained significantly associated with breast cancer screening among women of reproductive age; age(AOR=5.33, 95% CI 3.72, 7.63), being wealthy (AOR=2.34, 95% CI 1.61, 3.38), residing in rural(AOR= 0.59, 95% CI 0.46, 0.763), being educated(AOR=2.43, 95% CI 1.60, 3.68), being insured(AOR= 2.40, 95% CI 1.89, 3.06), healthcare facility visits in the past 12 months(AOR=1.43, 95% CI 1.14, 1.78) and living in Northern zone(AOR= 2.43, 95% CI 1.42, 4.15) compared to western zoneConclusionBreast cancer screening is still under-utilized and have shown to be marginalized in women of reproductive age. Policies to address disparities, comprehensive health education and awareness campaigns are instrumental to increase utilization and reduction of burden of breast cancers in Tanzania
The timing of surgical interventions following the implantation of coronary drug-eluting stents in patients undergoing gastrointestinal cancer surgery: A multicenter retrospective cohort study
Authors: Xu Ziyao , Hao Xinyu , Tian Jingyang , Song Qiying , Li Tian , Gao Lei , Wang Xinxin 
Published: February 2024

AbstractBackgroundThe guidelines recommending a minimum deferral of six months for non-cardiac surgeries following drug-eluting stent percutaneous coronary intervention (DES-PCI) do not adequately address the requirements for individuals undergoing gastrointestinal cancer surgery (GCS). We aim to investigate the optimal timing for surgical interventions to maximize patient benefit.MethodsThe study encompassed 2,501 patients treated from January 2017 to December 2021, all of whom underwent GCS within one year after DES-PCI. We conducted an analysis by comparing the occurrence of Major Adverse Cardiovascular Events (MACEs) within 30 days post-surgery at different time points.ResultsThis study enrolled a total of 2501 participants with meticulously recorded data who underwent DES-PCI and subsequently underwent GCS within one year post-implantation. The incidence rate of MACEs is 14.2%, including MI(5.1%), HF(5.8%), IS(3.2%), Cardiac death(0.2%) across all patients in this study. The threshold probability was determined using the Youden Index, resulting in a value of 0.320, corresponding to a “Time of surgery value” of 87. Significant statistical differences were observed in the occurrence rates of MACEs for adjacent time intervals at 30 days (p < 0.001), 90 days (p < 0.009), and 180 days (p < 0.001).ConclusionsThe timing of surgical intervention following DES-PCI significantly influences the occurrence of MACEs at 1 month, 3 months, and 6 months. GCS may be appropriately advanced within the 6-month timeframe, but with the exception of emergency, efforts should be made to defer them beyond the initial month.
The accomplices: Heparan sulfates and N-glycans foster SARS-CoV-2 spike:ACE2 receptor binding and virus priming
Authors: Paiardi Giulia , Ferraz Matheus , Rusnati Marco , Wade Rebecca C. 
Published: February 2024

AbstractAlthough it is well established that the SARS-CoV-2 spike glycoprotein binds to the host cell ACE2 receptor to initiate infection, far less is known about the tissue tropism and host cell susceptibility to the virus. Differential expression across different cell types of heparan sulfate (HS) proteoglycans, with variably sulfated glycosaminoglycans (GAGs), and their synergistic interactions with host and viral N-glycans may contribute to tissue tropism and host cell susceptibility. Nevertheless, their contribution remains unclear since HS and N-glycans evade experimental characterization. We, therefore, carried out microsecond-long all-atom molecular dynamics simulations, followed by random acceleration molecular dynamics simulations, of the fully glycosylated spike:ACE2 complex with and without highly sulfated GAG chains bound. By considering the model GAGs as surrogates for the highly sulfated HS expressed in lung cells, we identified key novel cell entry mechanisms of spike SARS-CoV-2. We find that HS promotes structural and energetic stabilization of the active conformation of the spike receptor binding domain (RBD) and reorientation of ACE2 toward the N-terminal domain in the same spike subunit as the RBD. Spike and ACE2 N-glycans exert synergistic effects, promoting better packing, strengthening the protein:protein interaction, and prolonging the residence time of the complex. ACE2 and HS binding trigger rearrangement of the S2’ functional protease cleavage site through allosteric interdomain communication. These results thus show that HS has a multifaceted role in facilitating SARS-CoV-2 infection and they provide a mechanistic basis for the development of novel GAG derivatives with anti-SARS-CoV-2 potential.Significance StatementA key to blocking SARS-CoV-2 infection is to understand why it infects some cell types more than others. Heparan sulfate (HS) proteoglycans are differentially expressed on the surface of host cells and, with ACE2 receptors, provide an entry route for SARS-CoV-2. Here, we used computer simulations to investigate how highly sulfated glycosaminoglycans, a model for HS expressed in lungs, impact the interaction between virus spike and host ACE2. The simulations indicate that HS, together with host and spike N-glycans, stabilizes the spike:ACE2 complex and triggers structural changes, including host protease cleavage, contributing to the SARS-CoV-2 infection mechanism. This study lays the basis for a better understanding of the cell-specificity of SARS-CoV-2 infection and for developing strategies for inhibiting SARS-CoV-2 infection.
Feature and space-based interference with functionally active and passive items in working memory
Authors: Wilhelm Sophia A. , Weng Yuanyuan , Borst Jelmer P. , Havekes Robbert , Akyürek Elkan G. 
Published: February 2024

AbstractFunctionally active and passive states in working memory have been related to different neural mechanisms. Memoranda in active states might be maintained by persistent neural firing, whereas memoranda in passive states might be maintained through short-term synaptic plasticity. We reasoned that this might make these items differentially susceptible to interference during maintenance, in particular that passively maintained items might be more robust. To test this hypothesis, we gave our participants a working memory task in which one item was prioritised (active) by always probing it first, while the other item was deprioritised (passive) by always probing it second. In two experiments, on half the trials, we presented an interfering task during memory maintenance, in which the stimuli matched either the feature dimension of the memory items (colour or orientation), or their spatial location. Whether the interfering task appeared on a given trial was unpredictable. Finally, we conducted a third experiment where participants were given prior knowledge of the interference condition. We found that both active and passive memory items were affected by interference to a similar extent, with overall performance being closely matched in all experiments. We further investigated precision and probability of target response parameters from the standard mixture model, which also showed no differences between states. We conclude that active and passive items, although potentially stored in different neuronal states, do not show differential susceptibility to interference.Public significance statementThe ability to briefly remember information is critical to human cognition. Our so-called working memory is nevertheless rather limited, able to hold only a few items at any one time, and prone to forgetting when we are briefly distracted. Yet, there is reason to believe that not all information in working memory is equally vulnerable. Items that are more passively stored, because they will only be required after some time, might be more resilient to interference. Items that are stored actively, for more immediate recall, might be more easily disrupted. Here, we investigated the effect of an interference task on the retention of both active and passive items in working memory. Our results showed that active and passive items are equally affected by interference, suggesting that resilience in working memory does not depend on the functional state of the items therein.
Single-cell and spatial transcriptomics of the avian embryo tailbud
Authors: Mok GF , Turner S , Smith E , Mincarelli L , Lister A , Lipscombe J , Uzun V , Haerty W , Macaulay IC , Münsterberg A 
Published: February 2024

AbstractVertebrate body axis formation initiates during gastrulation and continues within the tail bud at the posterior end of the embryo. Major structures in the trunk are paired somites, which generate the musculoskeletal system, the spinal cord - forming part of the central nervous system, and the notochord, with important patterning functions. The specification of these different cell lineages by key signalling pathways and transcription factors is essential, however, a global map of cell types and expressed genes in the avian trunk is missing. Here we use single-cell RNA sequencing and RNA tomography to generate a molecular map of the emerging trunk and tailbud in the chick embryo. Single cell RNA-sequencing (scRNA-seq) identifies discrete cell lineages including somites, neural tube, neural crest, lateral plate mesoderm, ectoderm, endothelial and blood progenitors. In addition, high-throughput RNA-seq of sequential tissue sections provides a spatially resolved, genome-wide expression dataset for the avian tailbud and emerging body, comparable to other model systems. Combining the single-cell and spatial datasets, we identify spatially restricted genes, focusing on somites and early myoblasts. Thus, this high-resolution transcriptome map incorporating cell types in the embryonic trunk can expose molecular pathways involved in body axis development.
NEAT1 promotes genome stability via m6A methylation-dependent regulation of CHD4
Authors: Mamontova Victoria , Trifault Barbara , Gribling-Burrer Anne-Sophie , Bohn Patrick , Preckwinkel Pit , Schmitz Werner , Gallant Peter , Papadopoulos Dimitrios , Eilers Martin , Gutschner Tony , Smyth Redmond P. , Burger Kaspar 
Published: February 2024

ABSTRACTLong non-coding (lnc)RNA emerge as regulators of genome stability. The nuclear enriched abundant transcript 1 (NEAT1) locus encodes two lncRNA isoforms that modulate gene expression, growth and proliferation in mammals. Interestingly, NEAT1 transcripts are overexpressed in many tumours and induced by DNA damage, suggesting a genome-protective function. However, the precise role of NEAT1 in the DNA damage response (DDR) is unclear. Here, we investigate the expression, modification levels, localization and structure of NEAT1 in response to DNA double-strand breaks (DSBs) induced by the topoisomerase-II inhibitor etoposide or the locus-specific endonuclease AsiSI. We find that induction of DSBs increases both the levels and N6-methyladenosine (m6A) marks on NEAT1, which promotes alterations in NEAT1 secondary structure and accumulation of hyper-methylated NEAT1 at a subset of promoter-associated DSBs to facilitate efficient DSB signalling. The depletion of NEAT1, in turn, delays the response to DSBs and triggers elevated DNA damage. The genome-protective role of NEAT1 is mediated by the RNA methyltransferase 3 (METTL3) and involves spreading of the chromodomain helicase DNA binding protein 4 (CHD4) upon release from NEAT1. Together, we describe a novel RNA-dependent DDR pathway that couples NEAT1 to the recognition and repair of DSBs.