bluuebunny/crossref_metadata_2025_split huggingface dataset:
Healthcare Equity in Epilepsy Surgery: Equivalent Outcomes Between NAEC-IV Public Safety-Net and Tertiary Academic Centers in a Major Metropolitan Area
Authors: Lam Jordan , Mehta Vivek , Russin Jonathan , Millett David , Shaw Susan , Liu Lauren , Lee Brian , Kalayjian Laura , Armacost Michelle , Gong Hui , Heck Christi , Lee Darrin , Liu Charles 
Published: November 2024

AbstractAccess to and delivery of quality surgical epilepsy care remains a challenge in both safety-net and private hospital systems. Underserved populations are more likely to utilize safety-net hospital systems, but there are few data on epilepsy surgery outcomes in this setting. We aimed to analyze and compare surgical epilepsy care in a safety-net versus private hospital system. We prospectively collected evaluation and treatment data in patients undergoing resective surgery for epilepsy at a safety-net hospital system and a collaborating private hospital system between 2010-2017. Seizure characteristics, pre-surgical evaluation, perioperative complications, and seizure outcomes were prospectively recorded. Data from 102 patients in the safety-net and 145 patients in the private hospital system were analyzed. There were higher proportions of African American (p=.02) and Hispanic patients (p= .03) in the safety-net hospital system. There was no difference in mean time from epilepsy onset to surgery between groups (p=.54). The presurgical evaluation was equivalent (p>.18), except for more frequent use of magnetoencephalography in the private system (p=.02). Seizure freedom outcomes were excellent, and complication rates were low with no significant differences between groups (p=.95 and p>.22, respectively). However, patients from safety-net hospital systems were more likely to be lost to follow up (p=.04). Quality and equitable surgical epilepsy care can be delivered in a safety-net hospital system despite the higher-minority demographics and intrinsic factors of safety-net hospitals. Partnership of safety-net hospital systems with established comprehensive epilepsy centers and the expansion of these services is essential for healthcare equity in modern epilepsy care.
Diagnostic Accuracy of Artificial Intelligence in Classifying HER2 Status in Breast Cancer Immunohistochemistry Slides and Implications for HER2-Low Cases: A Systematic Review and Meta-Analysis
Authors: Arruda Navarro Albuquerque Daniel , Trotta Vianna Matheus , Alencar Fernandes Sampaio Luana , Vasiliu Andrei , Cunha Neves Filho Eduardo Henrique 
Published: November 2024

AbstractBreast cancer with overexpression of the Human Epidermal Growth Factor Receptor 2 (HER2) accounts for 15-20% of cases and is associated with poor outcomes. Although trastuzumab-deruxtecan (T-DXd) has traditionally demonstrated survival benefits in metastatic HER2-positive patients, the DESTINY-Breast04 trial expanded its effectiveness to those with immunohistochemistry (IHC) scores of 1+, and 2+ with negative in situ hybridisation, a subset of patients that has since been termed “HER2-low”. Accurate differentiation of HER2 scores has now become crucial. However, visual IHC scoring is labour-intensive and prone to high interobserver variability. AI has emerged as a promising tool in diagnostic medicine, particularly within histopathology. This study assesses AI’s ability to identify patients eligible for T-DXd and its performance in accurately classifying HER2 scores. Electronic searches were conducted in MEDLINE, EMBASE, Scopus, and Web of Science up to May 2024. Eligibility criteria were limited to studies evaluating the performance of AI compared to pathologists in classifying HER2 utilising IHC slides. Metaanalysis was performed using the bivariate random-effects model to estimate pooled sensitivity, specificity, concordance, and area under the curve (AUC). To explore sources of heterogeneity, subgroup analysis and meta-regression were performed. Risk of bias was assessed using QUADAS-AI tool. We analysed 25 contingency tables across thirteen included publications, showing excellent AI accuracy in predicting T-DXd eligibility, with a pooled sensitivity of 0.97 [95%CI 0.96-0.98], specificity of 0.82 [95%CI 0.73-0.88], and AUC of 0.98 [95%CI 0.96-0.99]. In the individual scores analysis, AI performed better particularly in scores 2+ and 3+. Substantial heterogeneity was observed, and meta-regression revealed better performance with deep learning and patch-based analysis, while performance declined in externally validated and those utilising commercially available algorithms. Our findings indicate that AI holds promising potential in accurately identifying HER2-low patients and excels in distinguishing 2+ and 3+ scores. Upcoming validation studies should focus on enhancing AI’s precision in the 0-1+ range and improving the reporting of clinical and pre-analytical data to standardise samples characteristics, ensuring models are more comparable to each other. This review highlights that deep learning advancements are driving automation, requiring pathologists to adapt and integrate this technology into their workflow.
Evaluation of DNA-poli: study protocol of a randomised controlled trial to assess a digital platform for family cascade genetic testing and predictive genetic counselling
Authors: van Lingen Marlies N. , Meulenkamp Janine V. , Siemelink Marten A. , Beinema Tessa C. , Klaassen Randy , Heylen Dirk K.J. , van Tintelen J. Peter , van den Heuvel Lieke M. 
Published: November 2024

ABSTRACTIntroductionThe present uptake of predictive genetic counselling among at-risk relatives (ARRs) for cardiogenetic diseases is suboptimal with 40-50% of ARRs being tested after one to three years post- disclosure. Digital technologies are increasingly proposed to improve accessibility, efficiency, and uptake of predictive genetic counselling and, if desired, predictive genetic testing. Therefore, DNA- poli was developed: a digital platform providing family communication support and pre- and post-test genetic counselling for ARRs. The online DNA-poli aims to decrease the threshold for ARRs to seek genetic counselling without compromising the quality of care while increasing the efficiency of genetic care. Here, we describe the study protocol for a randomised controlled trial evaluating DNA- poli in clinical practice.Methods and analysisA non-inferiority multicentre randomised controlled trial with parallel-group design will be conducted. The intervention group using the DNA-poli platform will be compared to a control group receiving regular counselling. Probands with hypertrophic or dilated cardiomyopathy in whom a (likely) pathogenic variant in specific genes with definitive gene-disease validity is identified, will be included like their ARRs and physicians. The primary outcome is the uptake of cardiogenetic counselling six months post-disclosure with an extended follow-up of one year and stakeholders’ experiences. Secondary outcomes are informed decision-making in ARRs, empowerment, and the satisfaction of all stakeholder groups. In addition, the efficiency of consultations and the genetic care process will be analysed. Descriptive and inferential statistics will be performed to analyse data.Ethics and disseminationThis study protocol was exempted from approval by the Medical Ethical Committee NedMec because the Act of Medical Research Involving Human Subject (WMO) was not applicable (no. 23-066/C). Study findings will be shared with stakeholders, published in journals, and will be presented at both international and national conferences.Registration detailsNCT06431425ClinicalTrials.gov
Completion of multi-dose COVID-19 vaccines and the associated factors among adolescents and adults in two urban informal settlements in Nairobi, Kenya
Authors: Ng’oda Maurine , Izudi Jonathan , Otieno Collins , Mwanga Daniel , Sanya Richard E. , Ziraba Abdhalah 
Published: November 2024

ABSTRACTCompletion of vaccine doses is essential for robust immunity and long-term protection against specific diseases. This study aimed to investigate factors associated with the completion of multi-dose COVID-19 vaccines (MDV) among adolescents and adults in two informal urban settlements in Nairobi, Kenya. We analyzed data from the Kenya Multisite Integrated Serosurveillance (KEMIS) project. We defined completion of MDV as receiving an additional COVID-19 vaccine dose between weeks 6 and 8 following the first COVID-19 vaccination shot. We applied the modified Poisson regression model with robust standard errors to determine the factors that were independently associated with the completion of MDV. We analyzed data from 402 individuals aged 14-90 years and found that the completion rate for MDV was 85.3%. In the adjusted analysis, participants aged ≥60 years (adjusted prevalence risk ratio [aPR] 1.30, 95% confidence interval [CI] 1.05-1.60) and those who recommended the COVID-19 vaccine to others (aPR 1.40, 95% CI 1.00-1.96) were significantly more likely to complete MDV. Individuals aged 25-59 years (aPR 1.22, 95% CI 0.99-1.50), those who perceived themselves as being at risk for COVID-19 (aPR 1.09, 95% CI 0.99-1.19), and those who had access to healthcare during the pandemic tended to have a higher completion of MDV. Overall, the MDV completion rate is relatively high, however, public health interventions should endeavor to target those being left behind such as younger individuals and those hesitant about vaccination.
High Temperature and Microbiome Conditions Affect Gene Expression in Soybean
Authors: Van der Laan Liza , Elango Dinakaran , Ferela Antonella , O’Rourke Jamie A. , Singh Asheesh K. 
Published: November 2024

AbstractHeat stress is increasingly a problem in global agriculture production, both in increasing occurrences and extended durations. Understanding the molecular mechanisms of the soybean heat stress response is essential for breeding heat tolerant soybeans. Plant associated microbiomes are known to mitigate adverse effects from abiotic stress. Soybean heat stress studies have primarily focused on response to short periods of stress, and how soybean responds on a transcriptional level to a soil microbiome is poorly understood. We hypothesize a soil microbiome may help soybean survive long-term heat stress exposure. We used RNA-seq to measure the transcriptional responses in four soybean exposed to two temperature regimes and grown in two soil microbiome conditions. We identified unique responses to temperature based on the soil microbiome conditions and to the different genotypes, with fewer changes across genotypes in response to a soil microbiome. Our findings provide insights on the interaction of soil microbiome with heat stress response in soybean and identify gene targets to further study the soybean heat stress tolerance with applications to develop improved varieties.
EEG connectome-based predictive modeling of nonverbal intelligence level in healthy subjects
Authors: Pashkov Anton , Dakhtin Ivan , Feklicheva Inna , Shmotina Julia , Hassan Mahmoud 
Published: November 2024

AbstractIntelligence is increasingly recognized as a critical factor in successful behavioral and emotional regulation. Neuroimaging techniques coupled with machine learning algorithms have proven to be valuable tools for uncovering the neural foundations of individual cognitive abilities. Nevertheless, current electroencephalograph (EEG) studies primarily focus on classification tasks to predict the intelligence category of subjects (e.g., high, medium, or low intelligence), rather than providing quantitative intelligence level forecasts. Furthermore, the outcomes obtained are significantly impacted by the specific data processing pipeline chosen, which could potentially compromise result generalizability. In this study, we implemented a connectome-based predictive modeling approach on high-density resting state EEG data from healthy participants to predict their nonverbal intelligence level. This method was applied to three independently collected datasets (N = 255) with different functional connectivity methods, parcellation atlases, threshold p-values and curve fitting orders used to ensure the reliability of the findings. We found that the prediction accuracy expressed in terms of R² varied significantly depending on the processing pipeline configuration, ranging from negative R2values up to 0.27. The most consistent results across datasets were found in the alpha frequency band. Furthermore, we employed a computational lesioning approach to identify the valuable edges that made the most significant contribution to predicting intelligence. This analysis highlighted the crucial role of frontal and parietal regions in complex cognitive computations. Overall, these findings support and expand upon previous research, underscoring the close relationship between alpha rhythm characteristics and cognitive functions and emphasizing the critical consideration of method selection in result evaluation.
Potassium ferric oxalate nanoparticles prevent human blood clotting and thrombosis in a mouse model
Authors: Yenurkar Devyani , Choudhary Ankit , Shrivastava Anoushka , Pragya  , Mandal Snehasish , Soni Priyanshu , Pradhan Lipi , Singh Ankur , Sarkar Arnab , Mukherjee Sudip 
Published: November 2024

AbstractBlood clot creates occlusion in the veins and arteries, which leads to pernicious effects. Here, the anticoagulation properties of potassium ferric oxalate nanoparticles (KFeOx-NPs) in human blood were demonstrated for blood clot management. The mechanism involves the chelation of calcium ions from the blood by the oxalate present in the KFeOx-NPs. Various commercial assays were used to determine the clotting time for the KFeOx-NPs and identified the hindrance in activating factor XII in the intrinsic pathway. We used animal models to show toxicity and biodistribution profiles and determined the safety and efficacy. Intravenously injected KFeOx-NPs increased clotting time and thrombosis prevention in a mouse model confirmed by ultrasound and the power Doppler images. Coating catheters with KFeOx-NPs prevents clot formation with reduced protein attachment when incubated with blood, enhancing blood flow properties. In biological applications, KFeOx-NPs may improve the long-term prevention of blood clot formation and enhance the efficiency of medical devices.TOCPVP-stabilized novel potassium ferric oxalate nanoparticles were synthesized for the application of blood clot management and thrombosis prevention.
A high-resolution analysis of arrestin2 interactions responsible for CCR5 endocytosis
Authors: Petrovic Ivana , Desai Samit , Isaikina Polina , Abiko Layara Akemi , Spang Anne , Grzesiek Stephan 
Published: November 2024

AbstractClathrin-mediated endocytosis (CME) is crucial for regulating G protein-coupled receptors (GPCRs) via phosphorylation-dependent arrestin interactions. The interplay between receptor phosphorylation and arrestin coupling to the CME machinery has only been explored for a few GPCRs. Here we have investigated the CME of the chemokine receptor CCR5 induced by native and engineered CCL5 ligands. Upon CCL5 agonist stimulation, arrestin2 translocates to CCR5 at the plasma membrane forming a long-lived CCR5-arrestin2 complex that is internalized but does not reach the lysosomes. Solution NMR revealed that arrestin2 interacts weakly with clathrin through a single binding site, independent of arrestin2 activation by phosphorylated CCR5 C-terminal tail peptides. In contrast, the arrestin2-AP2 interaction is stronger and requires arrestin2 activation depending quantitatively on the CCR5 C-terminal tail phosphorylation. Thein vitroresults are corroborated by cellular assays, which establish a crucial role of the arrestin2 interaction with AP2, but not with clathrin for CCR5 internalization. These findings give insights how receptor phosphorylation regulates arrestin-mediated GPCR internalization.
Analyses of transposable elements in arbuscular mycorrhizal fungi support evolutionary parallels with filamentous plant pathogens
Authors: Oliveira Jordana I. N. , Lane Catrina , Mugambi Ken , Yildirir Gokalp , Nicol Ariane M. , Kokkoris Vasilis , Banchini Claudia , Dadej Kasia , Dettman Jeremy , Stefani Franck , Corradi Nicolas 
Published: November 2024

AbstractTransposable elements (TEs) are repetitive DNA sequences that excise or create copies that are inserted elsewhere in the genome. Their expansion shapes genome variability and evolution by impacting gene expression and rearrangement rates. Arbuscular mycorrhizal fungi (AMF) are beneficial plant symbionts with large, TE-rich genomes, and recent findings showed these elements vary significantly in abundance, evolution, and regulation among model AMF strains. Here, we aimed to obtain a more comprehensive understanding of TE function and evolution in AMF by investigating assembled genomes from representatives of all known families. We uncovered multiple, family-specific bursts of insertions in different species, indicating variable past and ongoing TE activity contributing to the diversification of AMF lineages. We also found that TEs are preferentially located within and around candidate effectors/secreted proteins, as well as in proximity to promoters. Altogether, these findings support the role of TEs in promoting the diversity in proteins involved in molecular dialogues with hosts and, more generally, in driving gene regulation. The mechanisms of TEs evolution we observed in these prominent plant symbionts bear striking similarities to those of many filamentous plant pathogens.
PreciCE: Precision engineering of cell fates via data-driven multi-gene control of transcriptional networks
Authors: Magnusson Jens P. , Roohani Yusuf , Stauber Daniel , Situ Yinglin , de Castroviejo Teba Paloma Ruiz , Sandberg Rickard , Leskovec Jure , Qi Lei S. 
Published: November 2024

AbstractThe directed differentiation of stem cells into specific cell types is critical for regenerative medicine and cell-based applications. However, current methods for cell fate control are inefficient, imprecise, and rely on laborious trial-and-error. To address these limitations, we present a method for data-driven multi-gene modulation of transcriptional networks. We develop bidirectional CRISPR-based tools based on dCas12a, Cas13d, and dCas9 for simultaneously activating and repressing many genes. Due to the vast combinatorial complexity of multi-gene regulation, we introduce a machine learning-based computational algorithm that uses single-cell RNA sequencing data to predict multi-gene perturbation sets for converting a starting cell type into a desired target cell type. By combining these technologies, we establish a unified workflow for data-driven cell fate engineering and demonstrate its efficacy in controlling early stem cell differentiation while suppressing alternative lineages through logic-based cell fate operations. This approach represents a significant advancement in the use of synthetic biology to engineer cell identity.
Extracting doubly excited state lifetimes in helium directly in the time domain with attosecond noncollinear four-wave-mixing spectroscopy
Authors: Rupprecht Patrick , Puskar Nicolette G. , Neumark Daniel M. , Leone Stephen R. 
Published: November 2024

The helium atom, with one nucleus and two electrons, is a prototypical system to study quantum many-body dynamics. Doubly excited states, or quantum states in which both electrons are excited by one photon, showcase electronic-correlation mediated effects. In this paper, the natural lifetimes of the doubly excited 1Po2snp Rydberg series and the 1Se2p2 dark state in helium in the 60–65 eV region are measured directly in the time domain with extreme-ultraviolet/near-infrared noncollinear attosecond four-wave-mixing (FWM) spectroscopy. The measured lifetimes agree with lifetimes deduced from spectral linewidths and theoretical predictions, and the roles of specific decay mechanisms are considered. While complex spectral line shapes in the form of Fano resonances are common in absorption spectroscopy of autoionizing states, the background-free and thus homodyned character of noncollinear FWM results exclusively in Lorentzian spectral features in the absence of strong-field effects. The onset of strong-field effects that would affect the extraction of accurate natural lifetimes in helium by FWM is determined to be approximately 0.3 Rabi cycles. This study provides a systematic understanding of the FWM parameters necessary to enable accurate lifetime extractions, which can be utilized in more complex quantum systems in the future.

Published by the American Physical Society
2024
Absolute frequency measurements on the
5s5p3P0 → 5s6d3D1
transition in strontium
Authors: Zhang S. , Tiwari B. S. , Ganesh S. , Singh Y. , Flambaum V. V. 
Published: November 2024

We report the first absolute frequency measurements for the 5s5p3P0→5s6d3D1 transition at 394 nm for all the stable strontium isotopes by utilizing repumping induced spectroscopy in a magneto-optical trap. Absolute transition frequency is measured to be 760524409251(25) kHz for Sr88. With reference to Sr88, the isotope shifts are measured to be 91052(35), 54600(33), and 51641(28) kHz for Sr84, Sr86, and Sr87, respectively. We calculate the hyperfine constants A and B for the fermionic isotope Sr87 at kHz level. Furthermore, we perform King plot analysis by combining isotope shifts on the 689-nm transition to our data.

Published by the American Physical Society
2024
Understanding beneficiary evaluative capacity within nonprofit organisations through an immanent perspective
Authors: Kingston Kylie L , Luke Belinda , Vinnari Eija 
Published: November 2024

PurposeThe purpose of this research was to seek a more refined understanding of the ways beneficiaries are evaluating nonprofit organisations (NPO), from the beneficiaries’ perspectives. Understanding evaluation from beneficiaries’ perspectives is not only important theoretically, but also for enabling evaluation processes to authentically contribute toward enhanced downward accountability.Design/methodology/approachTheorisation of immanent evaluation (Deleuze, 1998), the ontological view that there is no form imposed from outside or above but instead an articulation from within, was drawn upon to direct attention toward understanding beneficiaries’ inherent productive evaluative capacity and agency. This theorisation enabled a different way of observing and understanding beneficiary evaluation within a qualitative case study conducted in an Australian NPO. Data was sourced from interviews, observations and document analysis.FindingsFindings suggest beneficiaries largely viewed the NPO’s evaluation processes to be unsatisfactory toward meeting their needs in relation to meaningful engagement. However, beneficiaries’ evaluative capacity was noted to include their own evaluation criteria and evaluative expressions indicating the production of an evaluative account. Here beneficiaries’ evaluative expressions are representations of events of evaluation, initiated by them. Findings enable a more refined understanding of beneficiaries’ engagement in evaluation, moving beyond traditional considerations of participative evaluation, and illustrating beneficiaries’ agency and active role in the production of evaluation.Originality/valueThis research furthers understandings of downward accountability and participative evaluation by detailing how beneficiaries’ evaluative capacity is part of an NPO’s evaluative environment, and as such, conceives of an immanent theory of beneficiary evaluation. Findings highlight how evaluation, as a mechanism of downward accountability, functions from beneficiaries’ perspectives and the type of organisational environment capable of enabling and better supporting beneficiary engagement.