bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic heterogeneity shapes the transcriptional landscape of regional microglia
Authors: Margetts Alexander V. , Vilca Samara J. , Bourgain-Guglielmetti Florence , Tuesta Luis M. 
Published: August 2024

AbstractMicroglia, the innate immune cells in the central nervous system, exhibit distinct transcriptional profiles across brain regions that are important for facilitating their specialized function. There has been recent interest in identifying the epigenetic modifications associated with these distinct transcriptional profiles, as these may improve our understanding of the underlying mechanisms governing the functional specialization of microglia. One obstacle to achieving this goal is the large number of microglia required to obtain a genome-wide profile for a single histone modification. Given the cellular and regional heterogeneity of the brain, this would require pooling many samples which would impede biological applications that are limited by numbers of available animals. To overcome this obstacle, we have adapted a method of chromatin profiling known as Cleavage Under Targets and Tagmentation (CUT&Tag-Direct) to profile histone modifications associated with regional differences in gene expression throughout the brain reward system. Consistent with previous studies, we find that transcriptional profiles of microglia vary by brain region. However, here we report that these regional differences also exhibit transcriptional network signatures specific to each region. Additionally, we find that these region-dependent network signatures are associated with differential deposition of H3K27ac and H3K7me3, and while the H3K27me3 landscape is remarkably stable across brain regions, the H3K27ac landscape is most consistent with the anatomical location of microglia which explain their distinct transcriptional profiles. Altogether, these findings underscore the established role of H3K27me3 in cell fate determination and support the active role of H3K27ac in the dynamic regulation of microglial gene expression. In this study, we report a molecular and computational framework that can be applied to improve our understanding of the role of epigenetic regulation in microglia in both health and disease, using as few as 2,500 cells per histone mark.Figure 1.Pipeline of tissue processing and data analysis for the characterization of the microglial transcriptome and epigenome on a regional scale.
Iso-Seq enables discovery of novel isoform variants in human retina at single cell resolution
Authors: Wang Luozixian , Urrutia-Cabrera Daniel , Hung Sandy Shen-Chi , Hewitt Alex W. , Lukowski Samuel W. , Foord Careen , Wang Peng-Yuan , Tilgner Hagen , Wong Raymond C.B. 
Published: August 2024

AbstractRecent single cell transcriptomic profiling of the human retina provided important insights into the genetic signals in heterogeneous retinal cell populations that enable vision. However, conventional single cell RNAseq with 3’ short-read sequencing is not suitable to identify isoform variants. Here we utilized Iso-Seq with full-length sequencing to profile the human retina at single cell resolution for isoform discovery. We generated a retina transcriptome dataset consisting of 25,302 nuclei from three donor retina, and detected 49,710 known transcripts and 241,949 novel transcripts across major retinal cell types. We surveyed the use of alternative promoters to drive transcript variant expression, and showed that 1-8% of genes utilized multiple promoters across major retinal cell types. Also, our results enabled gene expression profiling of novel transcript variants for inherited retinal disease (IRD) genes, and identified differential usage of exon splicing in major retinal cell types. Altogether, we generated a human retina transcriptome dataset at single cell resolution with full-length sequencing. Our study highlighted the potential of Iso-Seq to map the isoform diversity in the human retina, providing an expanded view of the complex transcriptomic landscape in the retina.
Forecasting hotspots of grassland suitability under climate change for restoration
Authors: Rana Santosh Kumar , Lindstrom Jessica , Lehrer Melissa A. , Ahlering Marissa , Hamilton Jill 
Published: August 2024

Abstract●Local species-climate relationships are often considered in restoration management. However, as climate change disrupts species-climate relationships, identifying factors that influence habitat suitability now and into the future for individual species, functional groups, and communities will be increasingly important for restoration. This involves identifying hotspots of community suitability to target seed sourcing and restoration efforts.●Using ensemble species distribution modeling (eSDM), we analyzed 26 grassland species commonly used in restoration to identify bioclimatic variables influencing their distributions. We predicted habitat suitability under current and future (2050) climates and identified hotspots where diverse species and functional group suitability was greatest. These hotspots of habitat suitability were then overlaid with estimates of landscape connectivity and protected status to quantify potential suitability for restoration now and into the future.●Temperature and precipitation during warmer quarters largely influenced grassland species habitat suitability. Hotspots of grassland habitat suitability were identified in Minnesota, North Dakota, and South Dakota, with projected northward shifts under future climate scenarios. Overlaying these hotspots with estimates of landscape connectivity and protected status revealed limited connectivity and protection, highlighting regions to prioritize for restoration and conservation efforts.●Leveraging an understanding of species relationship with climate, this research emphasizes the importance of quantifying connectivity and protected status across aggregated hotspots of species suitability for conservation and restoration. Identifying these hotspots now and into the future can be used to prioritize regions for seed sourcing and restoration, ensuring long-term maintenance of functional ecosystems across grassland communities.
Automated Evaluation of Antibiotic Prescribing Guideline Concordance in Pediatric Sinusitis Clinical Notes
Authors: Weissenbacher Davy , Dutcher Lauren , Boustany Mickael , Cressman Leigh , O’Connor Karen , Hamilton Keith W. , Gerber Jeffrey , Grundmeier Robert , Gonzalez-Hernandez Graciela 
Published: August 2024

BackgroundEnsuring antibiotics are prescribed only when necessary is crucial for maintaining their effectiveness and is a key focus of public health initiatives worldwide. In cases of sinusitis, among the most common reasons for antibiotic prescriptions in children, health-care providers must distinguish between bacterial and viral causes based on clinical signs and symptoms. However, due to the overlap between symptoms of acute sinusitis and viral upper respiratory infections, antibiotics are often over-prescribed.ObjectivesCurrently, there are no electronic health record (EHR)-based methods, such as lab tests or ICD-10 codes, to retroactively assess the appropriateness of these prescriptions, making manual chart reviews the only available method for evaluation, which is time-intensive and not feasible at a large scale. In this study, we propose using natural language processing to automate this assessment.MethodsWe developed, trained, and evaluated generative models to classify the appropriateness of antibiotic prescriptions in 300 clinical notes from pediatric patients with sinusitis seen at a primary care practice in the Children’s Hospital of Philadelphia network. We utilized standard prompt engineering techniques, including few-shot learning and chain-of-thought prompting, to refine an initial prompt. Additionally, we employed Parameter-Efficient Fine-Tuning to train a medium-sized generative model Llama 3 70B-instruct.ResultsWhile parameter-efficient fine-tuning did not enhance performance, the combination of few-shot learning and chain-of-thought prompting proved beneficial. Our best results were achieved using the largest generative model publicly available to date, the Llama 3.1 405B-instruct. On our test set, the model correctly identified 91.4% of the 35 notes where antibiotic prescription was appropriate and 71.4% of the 14 notes where it was not appropriate. However, notes that were insufficiently, vaguely, or ambiguously documented by physicians posed a challenge to our model, as none evaluation sets were accurately classified.ConclusionOur generative model demonstrated strong performance in the challenging task of chart review. This level of performance may be sufficient for deploying the model within the EHR, where it can assist physicians in real-time to prescribe antibiotics in concordance with the guidelines, or for monitoring antibiotic stewardship on a large scale.
The open to closed D-loop conformational switch determines length in filopodia-like actin bundles
Authors: Gadsby Jonathan R , Ioannou Pantelis Savvas , Butler Richard , Mason Julia , Smith Alison , Dobramysl Ulrich , Chin Stacey , Dobson Claire , Gallop Jennifer L 
Published: August 2024

AbstractFilopodia, microspikes and cytonemes are implicated in sensing the environment and in dissemination of morphogens, organelles and pathogens across tissues. Their major structural component is parallel bundles of actin filaments that assemble from the cell membrane. Whilst the length of filopodia is central to their function, it is not known how their lengths are determined by actin bundle dynamics. Here, we identified a set of monoclonal antibodies that lengthen filopodia-like structures formed in a cell-free reconstitution system, and used them to uncover a key molecular switch governing length regulation. Using immunolabelling, enzyme-linked immunosorbent assays, immunoprecipitation and immunoblock experiments, we identified four antibodies that lengthen actin bundles by selectively binding the open DNase 1-binding loop (D-loop) of actin filaments. The antibodies inhibit actin disassembly and their effects can be alleviated by providing additional actin or cofilin. This work indicates that maintaining an open state of the actin filament D-loop is a mechanism of generating the long projections of filopodia-like actin bundles.
The Performance and Potential of Deep Learning for Predicting Species Distributions
Authors: Kellenberger Benjamin , Winner Kevin , Jetz Walter 
Published: August 2024

AbstractSpecies distribution models (SDMs) address the whereabouts of species and are central to ecology. Deep learning (DL) is poised to further elevate the already significant role of SDMs in ecology and conservation, but the potential and limitations of this transformation are still largely unassessed.We evaluate DL SDMs for 2,299 terrestrial vertebrate and invertebrate species at continental scale and 1km resolution in a like-for-like comparison with latest implementation of classic SDMs. We compare two DL methods (a multi-layer perceptron (MLP) on point covariates and a convolutional neural network (CNN) on geospatial patches) against existing SDMs (Maxent and Random Forest). On average, DL models match, but do not surpass, the performance of existing methods. DL performance is substantially weaker for species with narrow geographic ranges, fewer data points, and those assessed as threatened and hence often of greatest conservation concern. Furthermore, information leakage across dataset splits substantially inflates performance metrics, especially of CNNs. We find current DL SDMs to not provide significant gains, instead requiring careful experimental design to avoid biases. However, future advances in DL-supported use of ancillary ecological information have the potential to make DL a viable instrument in the larger SDM toolbox. Realising this opportunity will require a close collaboration between ecology and machine learning disciplines.
Probing
CPV
mixing in the Higgs sector in vector boson fusion at a 1 TeV ILC
Authors: Vukašinović N. , Božović-Jelisavčić I. , Kačarević G. , Smiljanić I. , Vidaković I. 
Published: August 2024

With the current precision of measurements by the ATLAS and CMS experiments, it cannot be excluded that a standard model (SM)-like Higgs boson is a CP violating mixture of CP-even and CP-odd states. We explore this possibility here, assuming Higgs boson production in ZZ-fusion, at 1 TeV ILC, with unpolarized beams. The full simulation of SM background and fast simulation of the signal is performed, simulating 8  ab−1 of data collected with the ILD detector. We demonstrate that the CP mixing angle ΨCP between scalar and pseudoscalar states can be measured with the statistical uncertainty of 3.8 mrad at 68% CL, corresponding to 1.44×10−5 for the CP parameter fCP, for the pure scalar state. This is the first result on sensitivity of an e+e− collider to measure fCP in the Higgs production vertex in vector boson fusion.

Published by the American Physical Society
2024
Antiskyrmions in Ferroelectric Barium Titanate
Authors: Gonçalves Mauro A. P. , Paściak Marek , Hlinka Jiří 
Published: August 2024

Typical magnetic skyrmion is a string of inverted magnetization within a ferromagnet, protected by a sleeve of a vortexlike spin texture, such that its cross-section carries an integer topological charge. Some magnets form antiskyrmions, the antiparticle strings which carry an opposite topological charge. Here we demonstrate that topologically equivalent but purely electric antiskyrmion can exist in a ferroelectric material as well. In particular, our computer experiments reveal that the archetype ferroelectric, barium titanate, can host antiskyrmions at zero field. The polarization pattern around their cores reminds ring windings of decorative knots rather than the typical magnetic antiskyrmion texture. We show that the antiskyrmion of barium titanate has just 2–3 nm in diameter, a hexagonal cross section, and an exotic topological charge with doubled magnitude and opposite sign when compared to the standard skyrmion string.

Published by the American Physical Society
2024
Correlation of structural and magnetic properties of
RFeO3
(
R=Dy,Lu
)
Authors: Biswas Banani , Naumov Pavel , Motti Federico , Hautle Patrick , Bartkowiak Marek , Pomjakushina Ekaterina V. , Stuhr Uwe , Fuchs Dirk , Lippert Thomas , Schneider Christof W. 
Published: August 2024

In orthoferrites the rare-earth (R) ion has a big impact on structural and magnetic properties; in particular, the ionic size influences the octahedral tilt and the R3+−Fe3+ interaction modifies properties like the spin reorientation. Growth-induced strain in thin films is another means to modify materials properties since the sign of strain affects the bond length and therefore directly the orbital interaction. Our study focuses on epitaxially grown (010)-oriented DyFeO3 and LuFeO3 thin films, thereby investigating the impact of compressive lattice strain on the magnetically active Dy3+ and magnetically inactive Lu3+ compared to uniaxially strained single-crystal DyFeO3. The DyFeO3 films exhibits a shift of more than 20 K in spin-reorientation temperatures, maintain the antiferromagnetic Γ4 phase of the Fe lattice below the spin reorientation, and show double-step hysteresis loops for both in-plane directions between 5 and 390 K. This is the signature of an Fe-spin-induced ferromagnetic Dy3+ lattice above the Néel temperature of the Dy. The observed shift in the film spin reorientation temperatures vs lattice strain is in good agreement with isostatic single-crystal neutron diffraction experiments with a rate of 2 K/kbar.

Published by the American Physical Society
2024
Dicarbonyl[10,10-dimethyl-5,15-bis(pentafluorophenyl)biladiene]ruthenium(II): discovery of the first ruthenium tetrapyrrole cis-dicarbonyl complex by X-ray and electron diffraction
Authors: Pham Trong-Nhan , Shirley Hunter , Merkelbach Johannes , Gurung Kshitij , Palatinus Lukáš , Yap Glenn P. A. , Rosenthal Joel 
Published: August 2024

Dicarbonyl[10,10-dimethyl-5,15-bis(pentafluorophenyl)biladiene]ruthenium(II), [Ru(C33H16F10N4)(CO)2] or Ru(CO)2[DMBil1], is the first reported ruthenium(II) cis-dicarbonyl tetrapyrrole complex. The neutral complex sports two carbonyls and an oligotetrapyrrolic biladiene ligand. Notably, the biladiene adopts a coordination geometry that is well distorted from square planar and much more closely approximates a seesaw arrangement. Accordingly, Ru(CO)2[DMBil1] is not only the first ruthenium cis-dicarbonyl with a tetrapyrrole ligand, but also the first metal biladiene complex in which the tetrapyrrole does not adopt a (pseudo-)square-planar coordination geometry. Ru(CO)2[DMBil1] is weakly luminescent, displaying λem = 552 nm upon excitation at λex = 500 nm, supports two reversible 1 e− reductions at −1.45 and −1.73 V (versus Fc+/Fc), and has significant absorption features at 481 and 531 nm, suggesting suitability for photocatalytic and photosensitization applications. While the structure of Ru(CO)2[DMBil1] was initially determined by X-ray diffraction, a traditionally acceptable quality structure could not be obtained (despite multiple attempts) because of consistently poor crystal quality. An independent structure obtained from electron diffraction experiments corroborates the structure of this unusual biladiene complex.
Examining the integration of ERP and BI in the industrial sector and its impact on decision-making processes in KSA
Authors: Jaradat Zaid , AL-Hawamleh Ahmad , Hamdan Allam 
Published: August 2024

Purpose
The Kingdom of Saudi Arabia’s dedicated pursuit of technological modernization positions it as a forefront leader in integrating advanced systems, aligning smoothly with the ambitious goals outlined in Vision 2030. The purpose of this study is to investigate the influence of integrating enterprise resource planning (ERP) and business intelligence (BI) systems on decision-making processes within the industrial sector of Saudi Arabia.

Design/methodology/approach
Using a quantitative research design, this study uses a bootstrapping approach and partial least squares structural equation modeling to meticulously analyze data collected from Saudi industrial firms.

Findings
The research reveals favorable relationships among infrastructure readiness, data quality, security and access control, user capabilities, user training and the integration of ERP and BI. These positive associations collectively affirm the overarching positive impact of ERP and BI integration on decision-making processes within the industrial sector.

Practical implications
The study underscores the strategic imperative of aligning organizational practices with the identified characteristics to fully unlock the potential benefits of ERP and BI integration in the Saudi Arabian industrial sector.

Originality/value
This study contributes significantly to the existing literature by delving into the integration of ERP and BI in the industrial sector and its nuanced impact on decision-making processes, specifically in the context of the Kingdom of Saudi Arabia – an area that has not been extensively studied.
Customer involvement in co-development: problem-solving and decision-making in new product development
Authors: Dean Tereza , Zhang Haisu , Xiao Yazhen 
Published: August 2024

Purpose
Customers can participate in new product development (NPD) in many ways. Drawing on the knowledge-based view (KBV) and innovation literature, this study aims to contrast two main product development activity types, i.e. problem-solving and decision-making. It proposes customers play distinct roles if they get involved in these activities, which influence NPD outcomes differently. It also explores customer need specificity as a boundary condition for the above-mentioned relationships.

Design/methodology/approach
The authors collected survey data from 308 managers in the innovation domain.

Findings
Customer involvement in problem-solving and decision-making distinctively influences new product innovativeness and development speed. Customer need specificity interacts with the two co-development types differently to impact these NPD outcomes further.

Research limitations/implications
This research extends the KBV and addresses the inconsistent findings in the literature regarding customer involvement as co-developers in innovation. It also provides novel insights into how knowledge characteristics like customer need specificity can direct co-developing activities to generate distinct NPD results.

Practical implications
This paper offers practical implications for firms on how to involve customers in developing innovative new products while managing development speed.

Originality/value
Prior research has yet to distinguish customer responsibilities related to co-development activities. This research fills this gap and offers novel insights that problem-solving and decision-making have opposite impacts on different NPD outcomes. This research demonstrates that finer knowledge about customer involvement responsibilities is needed for critical NPD outcomes.
The nexus between CRM and behavioural loyalty in hotel sector: the mediating role of relationship quality (trust and satisfaction)
Authors: Karim Rashed Al , Rabiul Md Karim , Tahrin Sunehla , Arfat Sayed Mohammed 
Published: August 2024

Purpose
This study aims to examine how hotel customer relationship management (CRM) practices affect tourist behavioural loyalty. This study also investigates the relationship quality (trust and satisfaction) as a mediator between CRM practices and tourist behavioural loyalty in Bangladesh’s hotel sector.

Design/methodology/approach
Data was collected through a survey using a standardized questionnaire that used a five-point Likert scale. A total of 411 respondents were selected using a convenient sampling method. The data was analysed and interpreted using Smart-PLS.

Findings
Relationship quality (both trust and satisfaction) partially mediates the relationship between hotel CRM practices and tourist behavioural loyalty in the hospitality industry.

Practical implications
The Bangladeshi hotel management can use the outcomes of this study to enhance tourist loyalty by implementing and maintaining better CRM features in the hotel.

Originality/value
The unique contribution to the hotel industry of Bangladesh is the role of relationship quality, which includes trust and customer satisfaction, as a mediator between hotel CRM practices and traveller behavioural loyalty.