bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glioblastoma cells use an integrin- and CD44-mediated motor-clutch mode of migration in brain tissue
Authors: Anderson Sarah M , Kelly Marcus , Odde David J. 
Published: October 2023

SummaryGlioblastoma (GBM) is an aggressive malignant brain tumor with 2-year survival rates of 6.7% [1], [2]. One key characteristic of the disease is the ability of glioblastoma cells to migrate rapidly and spread throughout healthy brain tissue[3], [4]. To develop treatments that effectively target cell migration, it is important to understand the fundamental mechanism driving cell migration in brain tissue. Here we utilized confocal imaging to measure traction dynamics and migration speeds of glioblastoma cells in mouse organotypic brain slices to identify the mode of cell migration. Through imaging cell-vasculature interactions and utilizing drugs, antibodies, and genetic modifications to target motors and clutches, we find that glioblastoma cell migration is most consistent with a motor-clutch mechanism to migrate through brain tissueex vivo, and that both integrins and CD44, as well as myosin motors, play an important role in constituting the adhesive clutch.
scBoolSeq: Linking scRNA-Seq Statistics and Boolean Dynamics
Authors: Maganã López Gustavo , Calzone Laurence , Zinovyev Andrei , Paulevé Loïc 
Published: October 2023

AbstractBoolean networks are largely employed to model the qualitative dynamics of cell fate processes by describing the change of binary activation states of genes and transcription factors with time. Being able to bridge such qualitative states with quantitative measurements of gene expressions in cells, as scRNA-Seq, is a cornerstone for data-driven model construction and validation. On one hand, scRNA-Seq binarisation is a key step for inferring and validating Boolean models. On the other hand, the generation of synthetic scRNA-Seq data from baseline Boolean models provides an important asset to benchmark inference methods. However, linking characteristics of scRNA-Seq datasets, including dropout events, with Boolean states is a challenging task.We presentscBoolSeq, a method for the bidirectional linking of scRNA-Seq data and Boolean activation state of genes. Given a reference scRNA-Seq dataset,scBoolSeqcomputes statistical criteria to classify the empirical gene pseudocount distributions as either unimodal, bimodal, or zero-inflated, and fit a probabilistic model of dropouts, with gene-dependent parameters. From these learnt distributions,scBoolSeqcan perform both binarisation of scRNA-Seq datasets, and generate synthetic scRNA-Seq datasets from Boolean trajectories, as issued from Boolean networks, using biased sampling and dropout simulation. We present a case study demonstrating the application ofscBoolSeq’s binarisation scheme in data-driven model inference. Furthermore, we compare synthetic scRNA-Seq data generated byscBoolSeqwith BoolODE from the same Boolean Network model. The comparison shows that our method better reproduces the statistics of real scRNA-Seq datasets, such as the mean-variance and mean-dropout relationships while exhibiting clearly defined trajectories in a two-dimensional projection of the data.Author summaryThe qualitative and logical modeling of cell dynamics has brought precious insight on gene regulatory mechanisms that drive cellular differentiation and fate decisions by predicting cellular trajectories and mutations for their control. However, the design and validation of these models is impeded by the quantitative nature of experimental measurements of cellular states. In this paper, we provide and assess a new methodology,scBoolSeqfor bridging single-cell level pseudocounts of RNA transcripts with Boolean classification of gene activity levels. Our method, implemented as a Python package, enables both tobinarisescRNA-Seq data in order to match quantitative measurements with states of logicals models, and to generate synthetic data from Boolean trajectories in order to benchmark inference methods. We show thatscBoolSeqaccurately captures main statistical features of scRNA-Seq data, including measurement dropouts, improving significantly the state of the art. Overall, scBoolSeq brings a statistically-grounded method for enabling the inference and validation of qualitative models from scRNA-Seq data.
Unlocking the Role of sMyBP-C: A Key Player in Skeletal Muscle Development and Growth
Authors: Song Taejeong , McNamara James W. , Baby Akhil , Ma Weikang , Landim-Vieira Maicon , Natesan Sankar , Pinto Jose Renato , Lorenz John N. , Irving Thomas C. , Sadayappan Sakthivel 
Published: October 2023

AbstractSkeletal muscle is the largest organ in the body, responsible for gross movement and metabolic regulation. Recently, variants in theMYBPC1gene have been implicated in a variety of developmental muscle diseases, such as distal arthrogryposis. HowMYBPC1variants cause disease is not well understood. Here, through a collection of novel gene-edited mouse models, we define a critical role for slow myosin binding protein-C (sMyBP-C), encoded byMYBPC1, across muscle development, growth, and maintenance during prenatal, perinatal, postnatal and adult stages. Specifically,Mybpc1knockout mice exhibited early postnatal lethality and impaired skeletal muscle formation and structure, skeletal deformity, and respiratory failure. Moreover, a conditional knockout ofMybpc1in perinatal, postnatal and adult stages demonstrates impaired postnatal muscle growth and function secondary to disrupted actomyosin interaction and sarcomere structural integrity. These findings confirm the essential role of sMyBP-C in skeletal muscle and reveal specific functions in both prenatal embryonic musculoskeletal development and postnatal muscle growth and function.
Hyperbolic graph embedding of MEG brain networks to study brain alterations in individuals with subjective cognitive decline
Authors: Baker Cole , Suárez-Méndez Isabel , Smith Grace , Marsh Elisabeth B. , Funke Michael , Mosher John C. , Maestú Fernando , Xu Mengjia , Pantazis Dimitrios 
Published: October 2023

AbstractAn expansive area of research focuses on discerning patterns of alterations in functional brain networks from the early stages of Alzheimer’s disease, even at the subjective cognitive decline (SCD) stage. Here, we developed a novel hyperbolic MEG brain network embedding framework for transforming high-dimensional complex MEG brain networks into lower-dimensional hyperbolic representations. Using this model, we computed hyperbolic embeddings of the MEG brain networks of two distinct participant groups: individuals with SCD and healthy controls. We demonstrated that these embeddings preserve both local and global geometric information, presenting reduced distortion compared to rival models, even when brain networks are mapped into low-dimensional spaces. In addition, our findings showed that the hyperbolic embeddings encompass unique SCD-related information that improves the discriminatory power above and beyond that of connectivity features alone. Notably, we introduced a unique metric—the radius of the node embeddings—which effectively proxies the hierarchical organization of the brain. Using this metric, we identified subtle hierarchy organizational differences between the two participant groups, suggesting increased hierarchy in the dorsal attention, frontoparietal, and ventral attention subnetworks among the SCD group. Last, we assessed the correlation between these hierarchical variations and cognitive assessment scores, revealing associations with diminished performance across multiple cognitive evaluations in the SCD group. Overall, this study presents the first evaluation of hyperbolic embeddings of MEG brain networks, offering novel insights into brain organization, cognitive decline, and potential diagnostic avenues of Alzheimer’s disease.
New races with wider virulence indicate local evolution ofPuccinia striiformisf. sp.triticiin South America
Authors: Riella V. , Rodriguez-Algaba J. , García R. , Pereira F. , Silva P. , Hovmøller M.S. , Germán S. 
Published: October 2023

AbstractWheat yellow (stripe) rust, caused byPuccinia striiformisf. sp.tritici(Pst), is one of the most devastating diseases of wheat worldwide.Pstpopulations are composed of multiple genetic groups, each carrying one or more races characterized by different avirulence/virulence combinations. Since the severe epidemics in 2017, yellow rust has become the most economically important wheat foliar disease in Uruguay. Evolution of virulence was investigated based on genotyping and race typing of a representative set of 27Pstisolates collected from wheat fields in Uruguay between 2017 and 2021. Three genetic groups were identified, i.e.,PstS7,PstS10andPstS13, the latter being the most prevalent. Two races previously reported in Europe, Warrior (PstS7) and Benchmark (PstS10), were detected in four and two isolates, respectively. A third race known as Triticale2015 (PstS13), first detected in Europe in 2015 and in Argentina in 2017, was detected at several locations. Additional virulence toYr3, Yr17,Yr25,Yr27orYr32was detected in three new race variants withinPstS13. The identification of these new races, which have not been reported outside South America, provides strong evidence of the local evolution of virulence inPstduring the recent epidemic years.
Structure of the human heparan-α-glucosaminideN-acetyltransferase (HGSNAT)
Authors: Navratna Vikas , Kumar Arvind , Rana Jaimin K. , Mosalaganti Shyamal 
Published: October 2023

AbstractDegradation of heparan sulfate (HS), a glycosaminoglycan (GAG) comprised of repeating units ofN-acetylglucosamine and glucuronic acid, begins in the cytosol and is completed in the lysosomes. Acetylation of the terminal non-reducing amino group of α-D-glucosamine of HS is essential for its complete breakdown into monosaccharides and free sulfate. Heparan-α-glucosaminideN-acetyltransferase (HGSNAT), a resident of the lysosomal membrane, catalyzes this essential acetylation reaction by accepting and transferring the acetyl group from cytosolic acetyl-CoA to terminal α-D-glucosamine of HS in the lysosomal lumen. Mutation-induced dysfunction in HGSNAT causes abnormal accumulation of HS within the lysosomes and leads to an autosomal recessive neurodegenerative lysosomal storage disorder called mucopolysaccharidosis IIIC (MPS IIIC). There are no approved drugs or treatment strategies to cure or manage the symptoms of, MPS IIIC. Here, we use cryo-electron microscopy (cryo-EM) to determine a high-resolution structure of the HGSNAT-acetyl-CoA complex, the first step in HGSNAT catalyzed acetyltransferase reaction. In addition, we map the known MPS IIIC mutations onto the structure and elucidate the molecular basis for mutation-induced HGSNAT dysfunction.
Helium optically pumped magnetometers can detect epileptic abnormalities as well as SQUIDs as shown by intracerebral recordings
Authors: Badier Jean-Michel , Schwartz Denis , Bénar Christian-George , Kanzari Khoubeib , Daligault Sébastien , Romain Rudy , Mitryukovskiy Sergey , Fourcault William , Josselin Vincent , Prado Matthieu Le , Jung Julien , Palacios-Laloy Augustin , Carron Romain , Bartolomei Fabrice , Labyt Etienne , Bonini Francesca 
Published: October 2023

AbstractSQUID-based magnetoencephalography has been shown to improve the diagnosis and surgical treatment decision for presurgical evaluation of drug-resistant epilepsy. Still, its use remains limited due to several constraints such as cost, fixed helmet size and obligation of immobility. A new generation of sensors, the optically pumped magnetometers (OPMs), could overcome these limitations. In this study, we validate the ability of innovative Helium-based OPM (4He-OPM) sensors to record epileptic brain activity thanks to simultaneous recordings with intracerebral EEG (stereotactic EEG, SEEG). We recorded simultaneous SQUIDs-SEEG and 4He-OPM-SEEG signals in one patient during two sessions. We show that epileptic activities on intracerebral EEG can be recorded by OPMs with a better signal-to noise ratio than classical SQUIDs. The OPM sensors open new venues for the widespread application of magnetoencephalography in the management of epilepsy and other neurological diseases and fundamental neuroscience.Significance StatementWe performed a simultaneous recording of Helium-based Optically Pumped Magnetometers (OPM) and intracerebral EEG and validate for the first time OPM results with signals recorded directly within the brain. We demonstrate that epileptic abnormalities seen on intracerebral electrodes are detected by OPMs with a better signal-to noise ratio than classical magnetoencephalography. This represents a significant step towards the validation of OPM-based recordings for epilepsy diagnosis and for clinical and neuroscience research.
A Protocol Describing A Scoping Review to Characterise ICU Admission Criteria
Authors: Soares James , Andersen Chris 
Published: October 2023

ABSTRACTIntroductionEffectively identifying deteriorated patients is vital to the development and validation of automated systems designed to predict clinical deterioration. Existing outcome measures used for this purpose have significant limitations. Published criteria for admission to high acuity inpatient areas may represent markers of patient deterioration and could inform the development of alternate outcome measures.ObjectivesThis is a protocol for a scoping review which aims to characterise published criteria for admission of adult inpatients to high acuity inpatient areas including intensive care units.Data sourcesElectronic databasesPubMedandProQuest EBook Centralwill be searched to identify papers published from 1999 to date of search. Publications of interest are those which describe prescriptive criteria for admission of adult inpatients to a clinical area with a higher level of care than a general hospital ward.Charting methodsData will be extracted from each publication using a standardised data-charting form.Data synthesisAdmission criteria characteristics from included publications will be summarised and presented in text and summary table form.
Complementary, Alternative, and Integrative Medicine Researchers’ Practices and Perceived Barriers Related to Open Science: An International, Cross-Sectional Survey
Authors: Ng Jeremy Y. , Santoro Lucas J. , Cobey Kelly D. , Steel Amie , Cramer Holger , Moher David 
Published: October 2023

AbstractIntroduction and ObjectiveOpen science (OS) aims to make the dissemination of knowledge and the research process transparent and accessible to everyone. With the increasing popularity of complementary, alternative, and integrative medicine (CAIM), our objective was to assess practices and perceived barriers towards OS among CAIM researchers.MethodsWe conducted an anonymous online survey of researchers who published in journals listed in Scopus containing the words “complementary”, “alternative”, or “integrative” medicine in their names. We emailed 6040 researchers our purpose-built electronic survey after extracting their email address from one of their publications in our sample of journals. We questioned their familiarity with different OS concepts, along with their experiences and challenges engaging in these practices over the last 12 months.ResultsThe survey was completed by 392 researchers (6.5% response rate, 97.1% completion rate). Most respondents were CAIM researchers familiar with the overall concept of OS, indicated by those actively publishing open access (OA) (n=244, 76.0%), registering a study protocol (n=148, 48.0%), and using reporting guidelines (n=181, 59.0%) in the past 12 months. Preprinting, sharing raw data, and sharing study materials were less popular. A lack of funding was reported as the greatest barrier to publishing OA by most respondents (n=252, 79.0%), and that additional funding is the most significant incentive in applying more OS practices to their research (n=229,72.2%). With respect to preprinting barriers, 36.3% (n=110) participants believed there are potential harms in sharing non-peer-reviewed work and 37.0% (n=112) feared preprinting would reduce the likelihood of their manuscript being accepted by a journal. Respondents were also concerned about intellectual property control regarding sharing data (n=94, 31.7%) and research study materials (n=80, 28.7%).ConclusionsAlthough many participants were familiar with and practiced aspects of OS, many reported facing barriers relating to lack of funding to enable OS and perceived risks of revealing research ideas and data prior to publication. Future research should explore interventions, such as increasing CAIM researchers’ funding and educational resources to implement OS practices.
Geometrically-aggregated training samples: Leveraging summary statistics to enable healthcare data democratization
Authors: Yang Jenny , Thakur Anshul , Soltan Andrew A. S. , Clifton David A. 
Published: October 2023

AbstractHealthcare data is highly sensitive and confidential, with strict regulations and laws to protect patient privacy and security. However, these regulations impede the access of healthcare data to a wider AI research community. As a result, AI healthcare research is often dominated by organisations with access to larger datasets or limited to silo-based development, where models are trained and evaluated on a limited population. Taking inspiration from the non-sensitive nature of the summary statistics (mean, variance, etc.) of healthcare data, this paper proposesgeometrically-aggregated training samples (GATS)where each training sample is a convex combination of multiple patients’ characteristics. Thus, mappings from patients to any constructed sample are highly convoluted, preserving patient privacy. We demonstrate that these “summary training units” provide effective training on different tabular and time-series datasets (CURIAL, UCI Adult, and eICU), and indeed behave as a summary of the original training datasets. This approach takes important steps towards data accessibility and democratization.
An infectious disease model with asymptomatic transmission and waning immunity
Authors: Rong Sophia Y. , Li Alice X. , Gao Shasha , Wang Chunmei 
Published: October 2023

AbstractInfectious diseases present persistent challenges to global public health, demanding a comprehensive understanding of their dynamics to develop effective prevention and control strategies. The presence of asymptomatic carriers, individuals capable of transmitting pathogens without displaying symptoms, challenges conventional containment approaches focused on symptomatic cases. Waning immunity, the decline in protective response following natural recovery or vaccination, introduces further complexity to disease dynamics. In this paper, we developed a mathematical model to investigate the interplay between these factors, aiming to inform strategies for the management of infectious diseases. We derived the basic reproduction number for the model and showed that the disease would die out when this number falls below 1. We obtained a formula to estimate the relative contributions of asymptomatic and symptomatic transmission to the basic reproduction number, which remains unchanged when vaccination is included in the model. Through computer simulations with parameter values tailored for COVID-19 and sensitivity analysis, we demonstrated that population susceptibility significantly impacts the timing and magnitude of infection peaks. Populations with lower susceptibility experience delayed and less severe outbreaks. Vaccination was shown to play a crucial role in disease control, with an increased vaccination rate, extended immunity, and heightened vaccine efficacy proving pivotal. However, the effectiveness of these strategies hinges on maintaining a low vaccine escape proportion. Taken together, this study underscores the need for multifaceted, adaptable approaches to infectious disease management, highlighting the central role of vaccination in mitigating disease spread. Further research and validation with disease-specific data will enhance parameter estimates, improve model predictions, and inform evidence-based disease control strategies.
The Long-Term Impacts of Dementia on Preventive Care Utilization and Health Behaviors
Authors: Lin Zhuoer , Chen Xi 
Published: October 2023

AbstractDementia has large impact on individuals’ decision making, independent living, and wellbeing. Identifying early signals of dementia risk may offer people more time to prepare for the future, helping to delay the onset or slow the progression of dementia. Using the 1995-2018 waves of Health and Retirement Study, we offer novel evidence on the impacts of dementia on a rich set of preventive care utilization and health behaviors. Leveraging both within- and between-individual variations in an event study design, we characterize long-term dynamic changes in preventive care and health behaviors relative to the incidence of dementia and find early behavioral indicators of the disorder. We show that relative to the group of people who never develop dementia during the study periods, people with dementia have consistent and escalating declines in the use of cholesterol test, dental visit, prostate test and mammogram around the incidence of dementia. Significant declines are also found in physical activities and social engagement. Importantly, we demonstrate that the behavioral changes can occur up to 6 years before the incidence of dementia; and these patterns are absent in other chronic or acute conditions. The results are robust to sample selection, model specification, and the further control of aging and cohort effects. Overall, our findings highlight the salient impact of dementia risk on preventive care utilization and health behaviors, which may increase individuals’ vulnerability to health shocks. Detecting early signals of dementia and facilitating targeted interventions are thus called for to prevent individuals from adverse behavioral and health consequences.
Evaluation of 2022 Nursing Intake Forms from Massachusetts Jails: Content Analysis and Accuracy Assessment
Authors: Grussing Emily D. , Pickard Bridget , Smyth Emma , Brinkley-Rubinstein Lauren , Wurcel Alysse G. 
Published: October 2023

AbstractThe medical intake process is usually the first clinical interaction that people have after being incarcerated. In many states, the first vital person conducting this assessment is a nurse. In this project, nursing intake forms from Massachusetts jails were analyzed for the offer of 15 different screening and preventative services (e.g., HIV testing). Then, Health Services Administrators (HSAs) at the jails were asked to review and comment on the assessment. The average agreement rate between the project team members and HSAs was 73%. Twelve of the 14 jails had questions about history of HIV or HCV on the nursing intake form. Only 5 facilities discussed PrEP. There is potential to standardize the nursing intake form and therefore medical intake process. This must be done with key stakeholder groups, in particular nurses, to best understand the logistics of the complex medical intake process.