bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fault diagnosis of rolling bearings under variable operating conditions based on improved graph neural networks
Authors: Chang Guochao , Liu Chang , Fan Bingbing , He Feifei , Liu Tao 
Published: November 2024

Abstract
To address the issues of low diagnostic accuracy, insufficient generalization, and poor robustness in traditional fault diagnosis methods across different equipment and varying operating conditions. This paper proposes an improved graph neural network-based fault diagnosis method for rolling bearings to enhance model performance under complex conditions. First, the optimized wavelet transform coefficient features are used as nodes, and by exploring the correlations between features, node adjacency relationships are constructed. The associations between fault modes and feature node graphs under different conditions are studied, and a fault feature graph sample set based on subgraph structures is built, providing data for the subsequent graph neural network learning. Then, a multi-head attention mechanism (MHGAT) and multi-scale feature adaptive perception pooling (MSF-ASAP) are integrated to construct a multi-head graph attention mechanism model based on multi-scale feature adaptive perception pooling (MSM-GAT). MHGAT enhances the model’s ability to perceive global information by learning different features from multiple perspectives and dimensions, thus improving the model’s generalization. MSF-ASAP adaptively selects and aggregates multi-scale information, enabling the model to effectively extract key features across various operating conditions and resist noise interference. And this approach enhances adaptability to local information changes, thereby improving the model’s robustness under varying conditions and noisy environments. Experimental results under multiple and continuously varying conditions demonstrate that the proposed method outperforms traditional methods in terms of diagnostic accuracy and robustness. Notably, it exhibits excellent generalization when identifying unknown conditions, achieving over 95% accuracy in recognizing new conditions and maintaining over 92.5% accuracy in noisy environments.
The political economy of gender mainstreaming in energy access in Sierra Leone
Authors: Appiah Sarah , Plutshack Victoria , Agradi Mawunyo , Klug Thomas W , Nunoo Isaac , Saparapa Rajah 
Published: November 2024

Abstract
In 2017, the Economic Community of West African States launched its Policy for Gender Mainstreaming in Energy Access with each member state tasked to create a National Action Plan (NAP). This study explores the case of Sierra Leone to understand how stakeholders have influenced the NAP process, and what that might mean for implementation. Using the Actors, Objectives, Context framework with interview data from key gender and energy actors, we find elements that make Sierra Leone’s NAP unique, such as addressing systematic barriers, explicitly promoting solar energy and heavily relying on civil society for implementation. The study finds that a policy focus on gender reflects both a push from international donor organisations and the national efforts of civil society. Sierra Leone’s NAP reflects the tension between the high priority of gender politics at the national and international level and more immediate interest from the Ministry of Energy and government actors on economic development. It affirms the uneasy co-existence of the liberal and liberating view of women in international development with some evidence that the liberal view prevails. Still, despite the government’s focus on economic development, poor engagement with the private sector and cultural barriers are likely to hamper the inclusion of women into the energy industry.
Introduction: The Governance Model
Authors: He Xin 
Published: November 2024

Abstract
The introduction of this book challenges the conventional wisdom of the judicial independence and rights-based approaches to understanding the Chinese court system. Instead, the book proposes a governance model that views the courts as agents of the state, with two primary functions—policy implementation and legitimacy enhancement. Through an exploration of the different policies that the courts are responsible for enforcing, and the approaches they use to enhance their legitimacy and that of the state, the book sheds new light on the evolution of the Chinese court system. This governance model is distinct from the dualism and order-maintenance theses which have been used to understand the Chinese legal system in the past.
Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases
Authors: Choi Hwisoo , Kim Hyeonkyu , Chung Hoebin , Lee Dong-Sung , Kim Junil 
Published: November 2024

Abstract
Recent advancements in single-cell technologies, including single-cell RNA sequencing (scRNA-seq) and Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq), have greatly improved our insight into the epigenomic landscapes across various biological contexts and diseases. This paper reviews key computational tools and machine learning approaches that integrate scRNA-seq and scATAC-seq data to facilitate the alignment of transcriptomic data with chromatin accessibility profiles. Applying these integrated single-cell technologies in neurodegenerative diseases, such as Alzheimer’s disease and Parkinson's disease, reveals how changes in chromatin accessibility and gene expression can illuminate pathogenic mechanisms and identify potential therapeutic targets. Despite facing challenges like data sparsity and computational demands, ongoing enhancements in scATAC-seq and scRNA-seq technologies, along with better analytical methods, continue to expand their applications. These advancements promise to revolutionize our approach to medical research and clinical diagnostics, offering a comprehensive view of cellular function and disease pathology.
ADTGP: correcting single-cell antibody sequencing data using Gaussian process regression
Authors: Liu Alex C H , Chan Steven M 
Published: November 2024

Abstract

Summary
We present ADTGP, an R package that uses Gaussian process regression to correct droplet-specific technical noise in single-cell protein sequencing data. ADTGP improves the interpretability of the data by modeling the distribution of protein expression, conditioned on equal isotype control counts across cells. ADTGP is written in R and needs only the protein raw counts, isotype control raw counts, and a design matrix to run.

Availability and implementation
ADTGP can be installed from https://github.com/northNomad/ADTGP. It depends on Stan and the R package ‘cmdstanr’.
Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell
Authors: van den Broek Remco L , Bello Xabier , Küpper Rebecca V , van Westen Gerard J P , Jespers Willem , Gutiérrez-de-Terán Hugo 
Published: November 2024

Abstract

Summary
Memprot.GPCR-ModSim leverages our previous web-based protocol, which was limited to class-A G protein-coupled receptors, to become the first one-stop web server for the modelling and simulation of any membrane protein system. Motivated by the exponential growth of experimental structures and the breakthrough of deep-learning-based structural modelling, the server accepts as input either a membrane-protein sequence, in which case it reports the associated AlphaFold model, or a 3D (experimental, modelled) structure, including quaternary complexes with associated proteins and/or ligands of any kind. In both cases, the molecular dynamics (MD) protocol produces a membrane-embedded, solvated, and equilibrated system, ready to be used as a starting point for further MD simulations, including ligand-binding free energy calculations.

Availability and implementation
Memprot.GPCR-ModSim web server is publicly available at https://memprot.gpcr-modsim.org/. The standalone modules for 3D modelling (PyModSim) or membrane embedding and MD equilibration (PyMemDyn) are available under CC BY-NC 4.0 license terms at the GitHub repository https://github.com/GPCR-ModSim/.
Effects of left ventrolateral prefrontal stimulation on forming and maintaining deep and shallow episodic traces
Authors: Peng Nan , Wu Wei , Della Sala Sergio , Hoffman Paul 
Published: November 2024

Abstract
The levels-of-processing framework, proposing that deep encoding enhances retention, plays a crucial role in episodic memory research. Neuroimaging evidence highlights that increased activity of the left ventrolateral prefrontal cortex during deep encoding predicts subsequent memory success. However, cognitive mechanisms underlying this region’s involvement in establishing and consolidating deep and shallow traces remain unclear. In this preregistered study, we investigated whether repetitive transcranial magnetic stimulation over the left ventrolateral prefrontal cortex versus the vertex differentially modulates the formation and maintenance of deep and shallow traces. Trains of 20 Hz online repetitive transcranial magnetic stimulation were delivered over the left ventrolateral prefrontal cortex or vertex during tasks involving pleasantness (deep) and alphabetical order (shallow) judgments of words. Following encoding, two recognition tests assessed immediate and 24-h delayed recognition of words. Compared to the vertex control, ventrolateral prefrontal stimulation selectively disrupted the formation of episodic memory under deep encoding conditions, evidenced by increased response time at encoding and reduced immediate recognition in the deep but not shallow condition. Notably, forgetting rates across the 24-h delay were similar for disrupted deep, intact deep, and shallow items, implying that the rate of trace decay is independent of the strength of trace formation. The constant trace decay indicates that distinct mechanisms are involved in establishing and maintaining episodic traces.
Developmental encoding of natural sounds in the mouse auditory cortex
Authors: Zucca Stefano , La Rosa Chiara , Fellin Tommaso , Peretto Paolo , Bovetti Serena 
Published: November 2024

Abstract
Mice communicate through high-frequency ultrasonic vocalizations, which are crucial for social interactions such as courtship and aggression. Although ultrasonic vocalization representation has been found in adult brain areas along the auditory pathway, including the auditory cortex, no evidence is available on the neuronal representation of ultrasonic vocalizations early in life. Using in vivo two-photon calcium imaging, we analyzed auditory cortex layer 2/3 neuronal responses to USVs, pure tones (4 to 90 kHz), and high-frequency modulated sweeps from postnatal day 12 (P12) to P21. We found that ACx neurons are tuned to respond to ultrasonic vocalization syllables as early as P12 to P13, with an increasing number of responsive cells as the mouse age. By P14, while pure tone responses showed a frequency preference, no syllable preference was observed. Additionally, at P14, USVs, pure tones, and modulated sweeps activate clusters of largely nonoverlapping responsive neurons. Finally, we show that while cell correlation decreases with increasing processing of peripheral auditory stimuli, neurons responding to the same stimulus maintain highly correlated spontaneous activity after circuits have attained mature organization, forming neuronal subnetworks sharing similar functional properties.
Acute coronary syndrome as the initial manifestation of infective endocarditis in an apparently normal native valve: a case report
Authors: Lozano Pineda Felipe , Navarro Navajas Alberto , Senior Juan Manuel 
Published: November 2024

Abstract

Background
Acute coronary syndrome is a rare complication of infectious endocarditis. We present the case of a patient with a bicuspid aortic valve who presented an acute ST elevation myocardial infarction (STEMI) of the inferior wall secondary to vegetation that generated obstruction of the ostium of the right coronary artery (RCA).

Case summary
A 54-year-old patient with only a history of smoking was admitted for chest pain. An acute STEMI in the inferior wall was documented; he underwent an emergent coronary angiography, which showed a mass that obstructed the ostium of the RCA that did not allow its channelling. An angiotomography of the aorta was performed, where dissection was ruled out and the presence of a mass in the right coronary sinus that protruded towards the ostium of the coronary artery was confirmed. In the extension studies, a bicuspid aortic valve and thrombosis in the right brachial artery and in the infrarenal abdominal aorta were documented.

Discussion
The case was taken to a medical meeting and given the embolic and mechanical compromise; it was decided to perform surgery where a mass that invaded the proximal segment of the RCA was resected. The histopathological study documented findings of vegetation; the cultures were positive for Staphylococcus epidermidis, and he finally received antibiotic and anticoagulation treatment.
The ecomorphological radiation of phyllostomid bats
Authors: Santana Sharlene E , Sadier Alexa , Mello Marco A R 
Published: November 2024

Abstract
Neotropical leaf-nosed bats (family Phyllostomidae) underwent an impressive adaptive radiation characterized primarily by the diversification of dietary strategies in tandem with functional morphological diversification of their craniodental and sensory systems. In this perspective, we integrate information from extensive research across multiple fields to outline the interplay between extrinsic and intrinsic drivers of the phyllostomid adaptive radiation and the resulting ecomorphological diversity of the clade. We begin by exploring the relationship between phyllostomids and their environments, focusing on the ecogeographical drivers of their radiation. Then, we detail current knowledge about the role of genes and development in enabling morphological diversification of the group. Finally, we describe the breathtaking ecomorphological diversification of phyllostomids, trying to unveil functional connections underlying their diverse dietary niches.
Evaluating the impact of redox potential on the growth capacity of anaerobic gut fungi
Authors: England Emma E , Pratt Carrie J , Elshahed Mostafa S , Youssef Noha H 
Published: November 2024

Abstract
Anaerobic gut fungi (AGF, Neocallimastigomycota) inhabit the alimentary tract of herbivores. Although strict anaerobes, studies have suggested their capacity to retain viability after various durations of air exposure. It is currently unclear whether AGF can actively grow, and not merely survive, in redox potentials (Eh) higher than those encountered in the herbivorous gut. We evaluated the growth of two AGF strains (Orpinomyces joyonii and Testudinimyces gracilis) at various Eh levels, achieved by manipulating the concentrations of reductant (cysteine hydrochloride) in culture media. Both strains exhibited robust and sustainable growth at negative Eh (−50 mV or below). However, growth in the absence of cysteine hydrochloride (Eh value around +50 mV) was possible only for O. joyonii and only for one subcultivation. The capacity to grow at +50 mV was further confirmed in four additional taxa (Pecoramyces ruminatium, Anaeromyces mucronatus, Aklioshbmyces papillarum, and Piromyces communis), while two (Aestipascuomyces dupliciliberans and Capellomyces foraminis) failed to grow under these conditions. Our results establish the ability of AGF to grow at redox potential values higher than those encountered in their natural habitats. Such capability could contribute to efficient AGF dispersal and horizontal transmission between hosts, and could have important implications for industrial applications of AGF.
Chromosome-level reference genome for the Jonah crab, Cancer borealis
Authors: Polinski Jennifer M , O’Donnell Timothy P , Bodnar Andrea G 
Published: November 2024

Abstract
The Jonah crab, Cancer borealis, is integral to marine ecosystems and supports a rapidly growing commercial fishery in the northwest Atlantic Ocean. This species also has a long history as a model for neuroscience that has expanded our understanding of central pattern generators, neuromodulation, synaptic plasticity, and the connectivity of neural circuits. Here, we present a highly contiguous reference genome for the Jonah crab that will provide an essential resource to advance fisheries, conservation, and biomedical research. Using a combination of PacBio long-read sequencing and Omni-C scaffolding, we generated a final genome assembly spanning 691 Mb covering 51 chromosome-length scaffolds and 106 additional contigs. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis indicated a high-quality assembly with a completeness score of 90.8%. Repeat annotation identified 1,649 repeat families making up 48.27% of the Jonah crab genome. Gene model predictions annotated 24,830 protein coding genes with a 92.3% BUSCO score. Gene family evolution analysis revealed the expansion of gene families associated with nervous system function, and targeted analysis revealed an extensive repertoire of neural genes. The Jonah crab genome will not only provide a resource for neuroscience research but will also serve as a foundation to investigate adaptation to stress and population structure to support sustainable fisheries management during this time of rapidly changing environmental conditions in the northwest Atlantic Ocean.
Detection and annotation of unique regions in mammalian genomes
Authors: Vieira Mourato Beatriz , Haubold Bernhard 
Published: November 2024

Abstract
Long unique genomic regions have been reported to be highly enriched for developmental genes in mice and humans. In this paper, we identify unique genomic regions using an efficient method based on fast string matching. We quantify the resource consumption and accuracy of this method before applying it to the genomes of 18 mammals. We annotate their unique regions (URs) of at least 10 kb and find that they are strongly enriched for developmental genes across the board. We then investigated the subset of URs that lack annotations, which we call “anonymous.” The longest anonymous UR in the Tasmanian devil spanned 83 kb and contained the gene encoding inositol polyphosphate-5-phosphatase A, which is an essential part of intracellular signaling. This discovery of an essential gene in a UR implies that URs might be given priority when annotating mammalian genomes. Our documented pipeline for annotating URs in any mammalian genome is available from the repository github.com/evolbioinf/auger; the additional data for this study are available from the dataverse at doi.org/10.17617/3.4IKQAG.
Measuring hospital inpatient Procedure Access Inequality in the United States
Authors: Bergman Alon , David Guy , Nathan Ashwin , Giri Jay , Ryan Michael , Chikermane Soumya , Thompson Christin , Clancy Seth , Gunnarsson Candace 
Published: November 2024

Abstract
Geographic disparities in access to inpatient procedures are a significant issue within the US healthcare system. This study introduces the Procedure Access Inequality (PAI) index, a standardized metric to quantify these disparities while adjusting for disease prevalence. Using data from the Healthcare Cost and Utilization Project State Inpatient Databases, we analyzed inpatient procedure data from 18 states between 2016 and 2019. The PAI index reveals notable variability in access inequality across different procedures, with minimally invasive and newer procedures exhibiting higher inequality. Key findings indicate that procedures such as skin grafts and minimally invasive gastrectomy have the highest PAI scores, while cesarean sections and percutaneous coronary interventions have the lowest. The study highlights that higher inequality is associated with greater market concentration and in particular, fewer hospitals offering these procedures. These findings emphasize the need for targeted policy interventions to address procedural access disparities to promote more equitable healthcare delivery across the United States.
Development of a Rapid, Culture-Free, Universal Microbial Identification System Using Internal Transcribed Spacer Targeting Primers
Authors: Asthana Vishwaratn , Nieves Erika Martínez , Bugga Pallavi , Smith Clara , Dunn Tim , Narayanasamy Satish , Dickson Robert P , VanEpps J Scott 
Published: November 2024

Abstract
The indiscriminate administration of broad-spectrum antibiotics is a primary contributor to the increasing prevalence of antibiotic resistance. Unfortunately, culture, the gold standard for bacterial identification is a time intensive process. Due to this extended diagnostic period, broad-spectrum antibiotics are generally prescribed to prevent poor outcomes. To overcome the deficits of culture-based methods, we have developed a rapid universal bacterial identification system. The platform uses a unique universal polymerase chain reaction primer set that targets the internal transcribed spacer regions between conserved bacterial genes, creating a distinguishable amplicon signature for every bacterial species. Bioinformatic simulation demonstrates that nearly every bacteria in a set of 45 commonly isolated pathogenic species can be uniquely identified using this approach. We experimentally confirmed these predictions on a representative set of pathogenic bacterial species. We further showed that the system can determine the corresponding concentration of each pathogen. Finally, we validated performance in clinical urinary tract infection samples.
Resistance profiles of carbapenemase-producing Enterobacterales in a large centre in England: are we already losing cefiderocol?
Authors: Baltas Ioannis , Patel Trupti , Soares Ana Lima 
Published: November 2024

Abstract

Background
Carbapenemase-producing Enterobacterales (CPE) pose difficult therapeutic challenges. We aimed to characterize antimicrobial resistance profiles of CPE in our centre.

Methods
All non-duplicate CPE isolates between 1 August 2020 and 31 August 2023 in a large teaching trust in England were retrospectively studied. Cefiderocol antimicrobial susceptibility testing (AST) was performed using disc diffusion, ceftazidime/avibactam using disc diffusion and gradient diffusion, and ceftazidime/avibactam aztreonam synergy using the double disc diffusion method. EUCAST version 14.0 breakpoints were used.

Results
A total of 158 CPE from 136 patients were isolated. Most patients were colonized with CPE, but only 16.9% had active infections. Thirty-day all-cause mortality was 10.3%, increasing to 13% for patients with infections and to 18.2% for bacteraemias. OXA-48 was the most prevalent carbapenemase (48.1%), followed by NDM (38%). All isolates exhibited MDR profiles, with high levels of resistance to meropenem (41.1%). Resistance to cefiderocol was found in 69.7% of NDM-producing isolates, with a further 18.2% in the area of technical uncertainty. Ceftazidime/avibactam and aztreonam synergy was seen in 87.5% of isolates, whereas colistin and fosfomycin susceptibility remained high (98.1% and 97.2%, respectively). All OXA-48-producing isolates were susceptible to ceftazidime/avibactam, and 15.3% were resistant to cefiderocol. No patients had been exposed to cefiderocol beforehand, whereas three had been exposed to ceftazidime/avibactam. The most common risk factor for CPE isolation was travel and receiving healthcare abroad, especially in Asia.

Conclusions
We found high rates of resistance to cefiderocol in CPE isolates without prior cefiderocol exposure. Our results prohibit empirical use of cefiderocol for the treatment of CPE infections in our setting.