bluuebunny/crossref_metadata_2025 huggingface dataset:
Decoding the molecular mechanism of selective autophagy of glycogen mediated by autophagy receptor STBD1
Authors: Zhang Yuchao , Sun Yishan , Shi Jungang , Xu Peng , Wang Yingli , Liu Jianping , Gong Xinyu , Wang Yaru , Tang Yubin , Liu Haobo , Zhou Xindi , Lin Zhiqiao , Baba Otto , Morita Tsuyoshi , Yu Biao , Pan Lifeng
Published: September 2024

Autophagy of glycogen (glycophagy) is crucial for the maintenance of cellular glucose homeostasis and physiology in mammals. STBD1 can serve as an autophagy receptor to mediate glycophagy by specifically recognizing glycogen and relevant key autophagic factors, but with poorly understood mechanisms. Here, we systematically characterize the interactions of STBD1 with glycogen and related saccharides, and determine the crystal structure of the STBD1 CBM20 domain with maltotetraose, uncovering a unique binding mode involving two different oligosaccharide-binding sites adopted by STBD1 CBM20 for recognizing glycogen. In addition, we demonstrate that the LC3-interacting region (LIR) motif of STBD1 can selectively bind to six mammalian ATG8 family members. We elucidate the detailed molecular mechanism underlying the selective interactions of STBD1 with ATG8 family proteins by solving the STBD1 LIR/GABARAPL1 complex structure. Importantly, our cell-based assays reveal that both the STBD1 LIR/GABARAPL1 interaction and the intact two oligosaccharide binding sites of STBD1 CBM20 are essential for the effective association of STBD1, GABARAPL1, and glycogen in cells. Finally, through mass spectrometry, biochemical, and structural modeling analyses, we unveil that STBD1 can directly bind to the Claw domain of RB1CC1 through its LIR, thereby recruiting the key autophagy initiation factor RB1CC1. In all, our findings provide mechanistic insights into the recognitions of glycogen, ATG8 family proteins, and RB1CC1 by STBD1 and shed light on the potential working mechanism of STBD1-mediated glycophagy.
Static neutral black holes in Kalb-Ramond gravity
Authors: Liu Wentao , Wu Di , Wang Jieci
Published: September 2024

The Kalb-Ramond (KR) gravity theory, a modified gravity theory that nonminimally couples a KR field with a nonzero vacuum expectation value for the gravitational field, can spontaneously break the Lorentz symmetry of gravity. In a recent work, Yang et al. [http://dx.doi.org/10.1103/PhysRevD.108.124004
Phys. Rev. D
108 (2023) 124004] successfully derived Schwarzschild-like black hole solutions both with and without a nonzero cosmological constant within the framework of KR gravity. However, their analysis did not address the more general case of static, neutral, spherically symmetric black holes. In this paper, we fill this gap by resolving the field equations to construct more general static, neutral, spherically symmetric black hole solutions both with and without a nonzero cosmological constant. Our black hole solutions are shown to obey the first law and the Bekenstein-Smarr mass formulas of black hole thermodynamics. Moreover, we demonstrate that our static neutral spherically symmetric AdS black hole does not always satisfy the reverse isoperimetric inequality (RII), as the isoperimetric ratio can be larger or smaller than unity depending on the placement of the solution parameters within the parameter space. This behavior contrasts with the above-mentioned Schwarzschild-like AdS black hole in the KR gravity theory, which always obeys the RII. Significantly, the present more general static, neutral, spherically symmetric AdS black hole is the first example of a static AdS black hole that can violate the RII.
Development, characterization and production of a novel water-based liquid scintillator based on the Surfactant TRITON™ X-100
Authors: Steiger Hans Th.J. , Böhles Manuel , Stock Matthias Raphael , Wurm Michael , Dörflinger David , Fahrendholz Ulrike , Mpoukouvalas Anastasia , Oberauer Lothar , Steiger Andreas , Zundel Dorina
Published: September 2024

Water-based Liquid Scintillator (WbLS) is a novel detector
medium for particle physics experiments. Applications range from the
use as hybrid Cherenkov/scintillation target in low-energy and
accelerator neutrino experiments to large-volume neutron vetoes for
dark matter detectors. Here we present a WbLS based on well-known
components (the surfactant Triton-X, the fluor PPO and vitamin C for
long-term stability), with which a new recipe was developed and the
result subjected to a thorough characterization of its
properties. In addition, based on neutron scattering data we are
able to demonstrate that the pulse shape discrimination capabilities
of this particular LS are comparable to all-organic LAB based
scintillators.
Theoretical study of hydrogen adsorption on quaternary alloy Ti-Zr-V-Hf non-evaporable getter surface applied in vacuum system of particle accelerators
Authors: Yigit Kaan , Wang Jie , Sun Qiuyu , Si Qingyu , Wang Ziwei , Qin Yanyang , Su Yaqiong , Wang Sheng
Published: September 2024

Non-evaporable getter (NEG) films are extensively employed
in particle accelerators to attain and sustain ultra-high vacuum
(UHV) and extremely high vacuum (XHV) conditions. This study
primarily focused on studying the adsorption characteristics of the
main residual gas-H2 molecules in the vacuum system on the
Ti-Zr-V-Hf (110) NEG surface. To carry out this analysis, we
employed the first-principles Density Functional Theory (DFT). The
adsorption energies of 23 distinct adsorption sites, and
particularly the electronic structure of the adsorption sites with
the highest absolute adsorption energies (Zr, Ti-V, Hf-V, and
Ti-Hf-V), were analyzed by partial density of states (PDOS) and
Mulliken charge and bond overlap population calculations. The
results of our investigation revealed that the order of
effectiveness of adsorption sites is as follows:
bridge > hollow > top. Based on the adsorption energy results,
it can be inferred that there are strong chemical interactions
between H atoms and Ti-Zr-V-Hf (110) surface metal atoms at Zr,
Ti-V, Hf-V, and Ti-Hf-V adsorption sites. The results of PDOS
calculations also indicate that there is strong hybridization
between the H2 molecule and the Ti-Zr-V-Hf (110) surface at
each studied adsorption site, demonstrating the formation of strong
chemical bonds between them. The Mulliken charge and bond overlap
population and electron density difference analyses show significant
changes in charge distribution between H atoms and Ti-Zr-V-Hf (110)
surface metal atoms before and after H2 adsorption at each
studied adsorption site, suggesting the occurrence of
chemisorption. Additionally, covalent bonds are formed between H
atoms and Ti-Zr-V-Hf (110) surface metal atoms at these sites. This
study uncovered specific adsorption sites where the H2 molecule
interacts most efficiently on the Ti-Zr-V-Hf (110) surface and where
high-energy bonds are formed. These findings can provide a potential
pathway to improve the adsorption efficiency of quaternary
Ti-Zr-V-Hf NEG films.
Quandles as pre-Lie skew braces, set-theoretic Hopf algebras & universalR-matrices
Authors: Doikou Anastasia , Rybołowicz Bernard , Stefanelli Paola
Published: September 2024

We present connections between left non-degenerate solutions of the set-theoretic braid equation and left shelves using Drinfel’d homomorphisms. We generalize the notion of affine quandle, by using heap endomorphisms and metahomomorphisms, and identify the underlying Yang–Baxter algebra for solutions of the braid equation associated to a given quandle. We introduce the notion of the pre-Lie skew brace and identify certain affine quandles that give rise to pre-Lie skew braces. Generalisations of the braiding of a group, associated to set-theoretic solutions of the braid equation are also presented. These generalized structures encode part of the underlying Hopf algebra. We then introduce the quasi-triangular (quasi) Hopf algebras and universalR-matrices for rack and set-theoretic algebras. Generic set-theoretic solutions coming from heap endomorphisms are also identified.
Degenerations of Hodge structure
Authors: Robles Colleen
Published: September 2024

Two interesting questions in algebraic geometry are: (i) how can a smooth projective variety degenerate? and (ii) given two such degenerations, when can we say that one is “more singular/degenerate” than the other? Schmid’s Nilpotent Orbit Theorem yields Hodge-theoretic analogs of these questions, and the Hodge-theoretic answers in turn provide insight into the motivating algebro-geometric questions, sometimes with applications to the study of moduli. Recently the Hodge-theoretic questions have been completely answered. This is an expository survey of that work.
A primer for unstable motivic homotopy theory
Authors: Antieau Benjamin , Elmanto Elden
Published: September 2024

In this expository article, we give the foundations, basic facts, and first examples of unstable motivic homotopy theory with a view towards the approach of Asok-Fasel to the classification of vector bundles on smooth complex affine varieties. Our focus is on making these techniques more accessible to algebraic geometers.
Ax–Kochen–Ershov principles for finitely ramified henselian fields
Authors: Anscombe Sylvy , Dittmann Philip , Jahnke Franziska
Published: September 2024

We study the model theory of finitely ramified henselian valued fields of fixed initial ramification, obtaining versions of the Ax–Kochen–Ershov principle as follows. We identify the induced structure on the residue field and show that once the residue field is endowed with this structure, the theory of the valued field is determined by the theories of the enriched residue field and the value group. Similarly, we show that the existential theory of the valued field is determined by the positive existential theory of the enriched residue field. We also prove that an embedding of finitely ramified henselian valued fields is existentially closed as soon as the induced embeddings of value group and residue field are existentially closed. This last result requires no enrichment of the residue field, in analogy to the corresponding result for model completeness, which holds by results of Ershov and Ziegler.
Conclusion
Authors: Toska Silvana
Published: September 2024

This concluding chapter summarizes the book’s findings and their implications for theory and practice in world politics. It returns to the generalizing ethos of the book by zooming out again from the Arab uprisings to show that the emotional and cognitive mechanisms are applicable across other cases of diffusion of revolt. It briefly refers to events in 1848 and discusses the failures of the Iranian revolution of 1979 and the Green Revolution of 2009 to diffuse as further evidence of the generalizability of the theory and its mechanisms. It concludes by briefly evaluating efforts by major powers to either prevent or aid the diffusion of revolt and argues that these interventions would likely be more effective if they were based on the theory that is proposed and tested in this book.
Blast phase of chronic myeloid leukemia presenting as early T-cell precursor acute lymphoblastic leukemia
Authors: E Shuyu , Xu Jie , Wang Sa A , Tang Guilin , Jabbour Elias J , Li Shaoying , You M James , Medeiros L Jeffrey , Yin C Cameron
Published: September 2024

Objectives

The blasts in most cases of chronic myeloid leukemia blast phase (CML-BP) have a myeloid or precursor-B immunophenotype, with only a small subset having T-cell or natural killer–cell lineage. Patients with CML-BP having early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) are extremely rare.

Methods

We report the clinicopathologic, immunophenotypic, and molecular genetic features and outcome of 3 patients with CML-BP who had ETP-ALL, with a review of the literature.

Results

Only patient 1 had a history of chronic myeloid leukemia chronic phase. Fluorescence in situ hybridization revealed BCR::ABL1 rearrangement in cells with round nuclei (blasts) and cells with segmented nuclei (neutrophils) in cases 2 and 3, supporting a diagnosis of CML-BP rather than de novo Ph+ ETP-ALL. The blasts were positive for cytoplasmic CD3, CD7, CD33, and CD117; were negative for CD1a and CD8; and had dim CD5 expression in 2 cases. Next-generation sequencing showed a TET2 mutation in case 1 and BCOR, RUNX1, and STAG2 mutations in case 3. All patients received chemotherapy and tyrosine kinase inhibitors. Patients 2 and 3 died 33 days and 39 days, respectively, after diagnosis. Patient 1 received stem cell transplantation and was alive 14 months after blast phase.

Conclusions

Patients with CML-BP may have ETP-ALL. These patients usually have an aggressive clinical course, requiring intensive therapy, and may benefit from stem cell transplantation.
Human microbiome: Impact of newly approved treatments on C. difficile infection
Authors: Bland Christopher M , Love Bryan L , Jones Bruce M
Published: September 2024

Purpose

The primary purposes of this review are to provide a brief overview of the microbiome, discuss the most relevant outcome data and key characteristics of each live microbiome agent, and pose questions for consideration going forward as these agents are integrated into clinical practice.

The management of Clostridiodes difficile infection (CDI) remains a difficult clinical conundrum, with recurrent CDI occurring in 15% to 35% of patients and causing significant morbidity and decreased quality of life. For patients with frequent CDI recurrences, fecal microbiota transplantation (FMT) has been demonstrated to have significant benefit but also significant risks, and FMT is not approved by the US Food and Drug Administration (FDA) for that indication. FDA has established a new therapeutic class for agents known as live biotherapeutic products (LBPs) that offer significant advantages over FMT, including standardized screening, testing, and manufacturing as well as known quantities of organisms contained within. Two new live microbiome products within this class were recently approved by FDA for prevention of CDI recurrences in adult patients following treatment for recurrent CDI with standard antimicrobial therapy. Both agents had demonstrated efficacy in registry trials in preventing CDI recurrence but differ significantly in a number of characteristics, such as route of administration. Cost as well as logistics are current obstacles to use of these therapies.

Conclusion

Live microbiome therapy is a promising solution for patients with recurrent CDI. Future studies should provide further evidence within yet-to-be-evaluated populations not included in registry studies. This along with real-world evidence will inform future use and clinical guideline placement.
Exploring combination treatment options for persistent methicillin-susceptible Staphylococcus aureus bacteremia
Authors: Al Shaikhli Hiba , Akins Ronda L , Stover Kayla R , Barber Katie E
Published: September 2024

Purpose

This review explores the management of persistent methicillin-susceptible Staphylococcus aureus bacteremia (SAB), emphasizing the importance of timely intervention due to SAB’s association with metastatic dissemination, relapse, and mortality.

The literature analysis first delves into risk factors for persistent SAB, highlighting the need for effective treatment strategies. The subsequent focus is on combination strategies for persistent SAB. Daptomycin, ertapenem, ceftaroline, fosfomycin, rifampin, and gentamicin are explored as adjuncts to cefazolin or antistaphylococcal penicillins. Daptomycin combination therapy is assessed through in vivo and clinical studies, indicating potential benefits, especially with higher-risk sources of infection. Ertapenem combination therapy has been demonstrated to have a synergistic effect with cefazolin, presenting a viable salvage option. Rifampin’s ability to penetrate biofilm is examined, with discussion of inconclusive evidence on mortality benefits. The review also considers stewardship implications, discussing concerns such as resistance emergence, adverse events, and increased costs associated with combination therapy. Mathematical models suggest combination therapy as an effective approach to prevent resistance. Adverse events vary with each combination, and duration of therapy remains diverse across studies in the absence of well-established dosing guidelines.

Conclusion

The review provides a thorough exploration of the literature on treatment of persistent SAB, underscoring the need for evidence-based guidelines, further studies, and clinical judgment in tailoring treatment strategies. The multifaceted analysis contributes valuable insights for clinicians managing this challenging condition.
Evaluating AI Models: Performance Validation Using Formal Multiple-Choice Questions in Neuropsychology
Authors: García-Rudolph Alejandro , Sanchez-Pinsach David , Opisso Eloy
Published: September 2024

High-quality and accessible education is crucial for advancing neuropsychology. A recent study identified key barriers to board certification in clinical neuropsychology, such as time constraints and insufficient specialized knowledge. To address these challenges, this study explored the capabilities of advanced Artificial Intelligence (AI) language models, GPT-3.5 (free-version) and GPT-4.0 (under-subscription version), by evaluating their performance on 300 American Board of Professional Psychology in Clinical Neuropsychology-like questions. The results indicate that GPT-4.0 achieved a higher accuracy rate of 80.0% compared to GPT-3.5’s 65.7%. In the “Assessment” category, GPT-4.0 demonstrated a notable improvement with an accuracy rate of 73.4% compared to GPT-3.5’s 58.6% (p = 0.012).

The “Assessment” category, which comprised 128 questions and exhibited the highest error rate by both AI models, was analyzed. A thematic analysis of the 26 incorrectly answered questions revealed 8 main themes and 17 specific codes, highlighting significant gaps in areas such as “Neurodegenerative Diseases” and “Neuropsychological Testing and Interpretation.”
Beyond the Face: Double-Sided Renaissance Portraits and the Craft of Thought
Authors: Wijnands Clim
Published: September 2024

This essay investigates how touching and handling Renaissance portraits could serve as a memory technique. It analyses three paintings that solicited physical interaction: Giovanni Bellini’s Portrait of Giovanni Andrea Probi (once the lid of a chest); and two double-sided panels, Previtali’s Portrait of a Man; and Boltraffio’s Portrait of Girolamo Casio. The notion that memory resided in a (physical or symbolic) place in the back of the head was widespread in sixteenth-century Italy, and the backsides of double-sided portraits can be identified with such memory spaces. By bringing the portraits into dialogue with sixteenth-century texts on memory and art theory, I argue that they reflect the idea that memory and painting were sister arts. Critically adding to Carruthers’s notion of the craft of thought, I interpret the beholder’s physical interaction with portraits as a technique for shaping thoughts, making associations and forging links between beholders and portraits through the moving body.
Federated unsupervised random forest for privacy-preserving patient stratification
Authors: Pfeifer Bastian , Sirocchi Christel , Bloice Marcus D , Kreuzthaler Markus , Urschler Martin
Published: September 2024

Motivation

In the realm of precision medicine, effective patient stratification and disease subtyping demand innovative methodologies tailored for multi-omics data. Clustering techniques applied to multi-omics data have become instrumental in identifying distinct subgroups of patients, enabling a finer-grained understanding of disease variability. Meanwhile, clinical datasets are often small and must be aggregated from multiple hospitals. Online data sharing, however, is seen as a significant challenge due to privacy concerns, potentially impeding big data’s role in medical advancements using machine learning. This work establishes a powerful framework for advancing precision medicine through unsupervised random forest-based clustering in combination with federated computing.

Results

We introduce a novel multi-omics clustering approach utilizing unsupervised random forests. The unsupervised nature of the random forest enables the determination of cluster-specific feature importance, unraveling key molecular contributors to distinct patient groups. Our methodology is designed for federated execution, a crucial aspect in the medical domain where privacy concerns are paramount. We have validated our approach on machine learning benchmark datasets as well as on cancer data from The Cancer Genome Atlas. Our method is competitive with the state-of-the-art in terms of disease subtyping, but at the same time substantially improves the cluster interpretability. Experiments indicate that local clustering performance can be improved through federated computing.

Availability and implementation

The proposed methods are available as an R-package (https://github.com/pievos101/uRF)
Scalable CNN-based classification of selective sweeps using derived allele frequencies
Authors: van den Belt Sjoerd , Zhao Hanqing , Alachiotis Nikolaos
Published: September 2024

Motivation

Selective sweeps can successfully be distinguished from neutral genetic data using summary statistics and likelihood-based methods that analyze single nucleotide polymorphisms (SNPs). However, these methods are sensitive to confounding factors, such as severe population bottlenecks and old migration. By virtue of machine learning, and specifically convolutional neural networks (CNNs), new accurate classification models that are robust to confounding factors have been recently proposed. However, such methods are more computationally expensive than summary-statistic-based ones, yielding them impractical for processing large-scale genomic data. Moreover, SNP data are frequently preprocessed to improve classification accuracy, further exacerbating the long analysis times.

Results

To this end, we propose a 1D CNN-based model, dubbed FAST-NN, that does not require any preprocessing while using only derived allele frequencies instead of summary statistics or raw SNP data, thereby yielding a sample-size-invariant, scalable solution. We evaluated several data fusion approaches to account for the variance of the density of genetic diversity across genomic regions (a selective sweep signature), and performed an extensive neural architecture search based on a state-of-the-art reference network architecture (SweepNet). The resulting model, FAST-NN, outperforms the reference architecture by up to 12% inference accuracy over all challenging evolutionary scenarios with confounding factors that were evaluated. Moreover, FAST-NN is between 30× and 259× faster on a single CPU core, and between 2.0× and 6.2× faster on a GPU, when processing sample sizes between 128 and 1000 samples. Our work paves the way for the practical use of CNNs in large-scale selective sweep detection.

Availability and implementation

https://github.com/SjoerdvandenBelt/FAST-NN
Multi-task deep latent spaces for cancer survival and drug sensitivity prediction
Authors: Rintala Teemu J , Napolitano Francesco , Fortino Vittorio
Published: September 2024

Motivation

Cancer is a very heterogeneous disease that can be difficult to treat without addressing the specific mechanisms driving tumour progression in a given patient. High-throughput screening and sequencing data from cancer cell-lines has driven many developments in drug development, however, there are important aspects crucial to precision medicine that are often overlooked, namely the inherent differences between tumours in patients and the cell-lines used to model them in vitro. Recent developments in transfer learning methods for patient and cell-line data have shown progress in translating results from cell-lines to individual patients in silico. However, transfer learning can be forceful and there is a risk that clinically relevant patterns in the omics profiles of patients are lost in the process.

Results

We present MODAE, a novel deep learning algorithm to integrate omics profiles from cell-lines and patients for the purposes of exploring precision medicine opportunities. MODAE implements patient survival prediction as an additional task in a drug-sensitivity transfer learning schema and aims to balance autoencoding, domain adaptation, drug-sensitivity prediction, and survival prediction objectives in order to better preserve the heterogeneity between patients that is relevant to survival. While burdened with these additional tasks, MODAE performed on par with baseline survival models, but struggled in the drug-sensitivity prediction task. Nevertheless, these preliminary results were promising and show that MODAE provides a novel AI-based method for prioritizing drug treatments for high-risk patients.

Availability and implementation

https://github.com/UEFBiomedicalInformaticsLab/MODAE.
Polyphest: fast polyploid phylogeny estimation
Authors: Yan Zhi , Cao Zhen , Nakhleh Luay
Published: September 2024

Motivation

Despite the widespread occurrence of polyploids across the Tree of Life, especially in the plant kingdom, very few computational methods have been developed to handle the specific complexities introduced by polyploids in phylogeny estimation. Furthermore, methods that are designed to account for polyploidy often disregard incomplete lineage sorting (ILS), a major source of heterogeneous gene histories, or are computationally very demanding. Therefore, there is a great need for efficient and robust methods to accurately reconstruct polyploid phylogenies.

Results

We introduce Polyphest (POLYploid PHylogeny ESTimation), a new method for efficiently and accurately inferring species phylogenies in the presence of both polyploidy and ILS. Polyphest bypasses the need for extensive network space searches by first generating a multilabeled tree based on gene trees, which is then converted into a (uniquely labeled) species phylogeny. We compare the performance of Polyphest to that of two polyploid phylogeny estimation methods, one of which does not account for ILS, namely PADRE, and another that accounts for ILS, namely MPAllopp. Polyphest is more accurate than PADRE and achieves comparable accuracy to MPAllopp, while being significantly faster. We also demonstrate the application of Polyphest to empirical data from the hexaploid bread wheat and confirm the allopolyploid origin of bread wheat along with the closest relatives for each of its subgenomes.

Availability and implementation

Polyphest is available at https://github.com/NakhlehLab/Polyphest.
GGTyper: genotyping complex structural variants using short-read sequencing data
Authors: Mirus Tim , Lohmayer Robert , Döhring Clementine , Halldórsson Bjarni V , Kehr Birte
Published: September 2024

Motivation

Complex structural variants (SVs) are genomic rearrangements that involve multiple segments of DNA. They contribute to human diversity and have been shown to cause Mendelian disease. Nevertheless, our abilities to analyse complex SVs are very limited. As opposed to deletions and other canonical types of SVs, there are no established tools that have explicitly been designed for analysing complex SVs.

Results

Here, we describe a new computational approach that we specifically designed for genotyping complex SVs in short-read sequenced genomes. Given a variant description, our approach computes genotype-specific probability distributions for observing aligned read pairs with a wide range of properties. Subsequently, these distributions can be used to efficiently determine the most likely genotype for any set of aligned read pairs observed in a sequenced genome. In addition, we use these distributions to compute a genotyping difficulty for a given variant, which predicts the amount of data needed to achieve a reliable call. Careful evaluation confirms that our approach outperforms other genotypers by making reliable genotype predictions across both simulated and real data. On up to 7829 human genomes, we achieve high concordance with population-genetic assumptions and expected inheritance patterns. On simulated data, we show that precision correlates well with our prediction of genotyping difficulty. This together with low memory and time requirements makes our approach well-suited for application in biomedical studies involving small to very large numbers of short-read sequenced genomes.

Availability and implementation

Source code is available at https://github.com/kehrlab/Complex-SV-Genotyping.
Graspot: a graph attention network for spatial transcriptomics data integration with optimal transport
Authors: Gao Zizhan , Cao Kai , Wan Lin
Published: September 2024

Spatial transcriptomics (ST) technologies enable the measurement of mRNA expression while simultaneously capturing spot locations. By integrating ST data, the 3D structure of a tissue can be reconstructed, yielding a comprehensive understanding of the tissue’s intricacies. Nevertheless, a computational challenge persists: how to remove batch effects while preserving genuine biological structure variations across ST data. To address this, we introduce Graspot, a graph attention network designed for spatial transcriptomics data integration with unbalanced optimal transport. Graspot adeptly harnesses both gene expression and spatial information to align common structures across multiple ST datasets. It embeds multiple ST datasets into a unified latent space, facilitating the partial alignment of spots from different slices. Demonstrating superior performance compared to existing methods on four real ST datasets, Graspot excels in ST data integration, including tasks that require partial alignment. In particular, Graspot efficiently integrates multiple ST slices and guides coordinate alignment. In addition, Graspot accurately aligns the spatio-temporal transcriptomics data to reconstruct human heart developmental processes.

Availability and implementation

Graspot software is available at https://github.com/zhan009/Graspot.
Establishing the size and configuration of the imaging support workforce: a census of national workforce data in England
Authors: Nightingale Julie , Etty Sarah , Snaith Beverley , Sevens Trudy , Appleyard Rob , Kelly Shona
Published: September 2024

Objectives

The imaging support workforce is a key enabler to unlock imaging capacity and capability, yet no evidence exists of the workforce size and configuration. This research provides the first comprehensive analysis of workforce data to explore the deployment of the support workforce within National Health Service (NHS) imaging services in England.

Methods

Using a census methodology, an anonymised Electronic Staff Record (ESR) data set extracted in December 2022 was analysed to identify support workers and their employment bandings at NHS Trust, regional and national (England) level. Support workforce proportions, median values and Spearman’s Rank correlations were calculated.

Results

Analysis of 137 NHS Trusts, comprising 100% of Acute Trusts (n = 124) and Specialist Trusts with imaging services (n = 13), identified that the support workforce (pay bands 2-4) constitutes 23.6% of the imaging staff base. Ranking Trusts into three categories based on the proportion of support workers in their imaging establishment, median values ranged from 30.7% (high), to 22.2% (medium) and 10.5% (low). Two opposing deployment models of Band 2 and Band 3 support workers were identified.

Conclusions

Comprising almost one quarter of the imaging establishment, models of deployment at Bands 2 and 3 are highly variable. Assistant practitioners (Band 4) are under-utilised, providing an opportunity to introduce innovations to address workforce demands.

Advances in knowledge

This census is the first to provide evidence of the size and structure of the support workforce, the first step in enabling effective workforce transformation. Further research is required to explain the two opposing deployment models.
Attract and kill trees? No simple solution for Anoplophora glabripennis (Coleoptera: Cerambycidae) control
Authors: Sun Zuo-Xiang , Sun Hui-Quan , Zhong Qiu-Mei , Shao Peng-Peng , Su Zhi , Wang Zhuo , Liu Yu-Ting , Wei Jian-Rong
Published: September 2024

Anoplophora glabripennis (Motschulsky), the Asian longhorned beetle, is a serious wood-boring pest of hardwood trees. There have been records that suggest Elaeagnus angustifolia L. (Elaeagnaceae) might be an “attract and kill” tree species for A. glabripennis, i.e., a tree that is attractive to A. glabripennis adults but kills their oviposited eggs. To evaluate the possibility of E. angustifolia as a control measure for A. glabripennis, we carried out a series of behavioral experiments in the laboratory and in the field. Results showed that: (i) A. glabripennis females preferred E. angustifolia branches and leaves over poplar tree species evaluated; the weight of feces from both female and male A. glabripennis feeding on E. angustifolia was significantly higher than from those feeding on Populus deltoides ‘Shalinyang’ or Populus alba. L. var. pyramidalis; (ii) the average lifespan of females and males feeding on E. angustifolia was significantly longer than those feeding on other host trees evaluated; (iii) in the laboratory oviposition choice experiment, there were significantly fewer egg notch grooves on E. angustifolia than on P. deltoides ‘Shalinyang‘, and those made in E. angustifolia were without eggs; (iv) in the field, the number of egg notch grooves on E. angustifolia was 43.6 ± 18.1 per stem, but the number of eggs laid was only 14.4 ± 6.4 per stem; and (v) Field surveys of existing mixed forests showed that when E. angustifolia was planted with P. alba. var. pyramidalis or Populus simonii × (Populus pyramidalis + Salix matsudana) ‘Poparis’ in the mixed forest, both poplar varieties suffered greater infestation than E. angustifolia. Therefore, E. angustifolia is not a suitable attract and kill tree to be extensively planted in mixed forests for control of A. glabripennis.
Rethinking AI: bias in speech-recognition chatbots for ELT
Authors: Jeon Jaeho , Lee Seongyong , Coronel-Molina Serafín M
Published: September 2024

Artificial intelligence (AI) technologies, particularly chatbots with speech-recognition, are gaining attention as tools for ELT. However, this frontline development in contemporary ELT seems to stand in stark contrast to the multilingual effort, another innovative trend, as chatbots’ speech recognition capabilities are primarily attuned to native English speaker pronunciation. Addressing this concern, this study adopted a Global Englishes (GE) perspective and examined students’ attitudes toward English after their use of a speech-recognition chatbot. Text-mining analysis of reflection papers from 38 students and thematic analysis of interviews with seven students revealed that the chatbot hindered the incorporation of diverse English use into ELT and students expressed a conception of English not as a language in flux but rather as a subject with specific content to be mastered. The findings are discussed concerning GE, AI ethics, and computer-assisted language learning, and implications for future chatbot use in ELT are provided.
Age structure and age heaping: solving Ireland’s post-famine digit preference puzzle
Authors: Colvin Christopher L , Henderson Stuart , Mclaughlin Eoin
Published: September 2024

The quality of age reporting in Ireland worsened in the years after the 1845–1852 Great Irish Famine, even as measures of educational attainment improved. We show how Ireland’s age structure partly accounts for this seemingly conflicting pattern. Specifically, we argue that a greater propensity to emigrate typified the youngest segment (23–32-year-olds) used in conventional indices of age heaping. Any quantification of age heaping patterns must therefore be interpreted considering an older underlying population which is inherently more likely to heap. We demonstrate how age heaping indices can adjust for such demographic change by introducing age standardization.
Genomic Diversity Illuminates the Environmental Adaptation of Drosophila suzukii
Authors: Feng Siyuan , DeGrey Samuel P , Guédot Christelle , Schoville Sean D , Pool John E
Published: September 2024

Biological invasions carry substantial practical and scientific importance and represent natural evolutionary experiments on contemporary timescales. Here, we investigated genomic diversity and environmental adaptation of the crop pest Drosophila suzukii using whole-genome sequencing data and environmental metadata for 29 population samples from its native and invasive range. Through a multifaceted analysis of this population genomic data, we increase our understanding of the D. suzukii genome, its diversity and its evolution, and we identify an appropriate genotype–environment association pipeline for our dataset. Using this approach, we detect genetic signals of local adaptation associated with nine distinct environmental factors related to altitude, wind speed, precipitation, temperature, and human land use. We uncover unique functional signatures for each environmental variable, such as the prevalence of cuticular genes associated with annual precipitation. We also infer biological commonalities in the adaptation to diverse selective pressures, particularly in terms of the apparent contribution of nervous system evolution to enriched processes (ranging from neuron development to circadian behavior) and to top genes associated with all nine environmental variables. Our findings therefore depict a finer-scale adaptive landscape underlying the rapid invasion success of this agronomically important species.
A Systematic Review and Meta-Analysis of the Association Between Physical Capability, Social Support, Loneliness, Depression, Anxiety, and Life Satisfaction in Older Adults
Authors: Sulandari Santi , Coats Rachel O , Miller Amy , Hodkinson Alexander , Johnson Judith
Published: September 2024

Background and Objectives

Physical capability, social support, loneliness, depression, and anxiety predict life satisfaction in older adults. Currently, no systematic review and meta-analysis have been conducted to investigate the strength of these associations globally. Therefore, this study quantified the strength of these associations.

Research Design and Methods

A systematic literature search was conducted using MEDLINE, EMBASE, APA PsycINFO, Web of Science, and Scopus. We included observational studies assessing the association between physical capability, social support, loneliness, depression, and anxiety with life satisfaction in adults aged 65+.

Results

In total, 10,552 articles were identified, of which 78 studies in 164,478 participants were included in the systematic review and 57 were included in the meta-analysis. Greater life satisfaction was significantly associated with greater physical capabilities (odds ratio [OR] = 2.64; 95% confidence interval [CI]: 2.01–3.45; p < .001, k = 35, n = 33,732), higher social support (OR = 3.27; 95% CI: 2.59–4.13, k = 20 studies, n = 13,228), reduced loneliness (OR = 3.30; 95% CI: 2.53–4.30, k = 11, n = 33,638), depression (OR = 4.76; 95% CI: 3.10–7.32, k = 24, n = 64,097), and anxiety (OR = 5.10; 95% CI: 2.21–11.78, k = 5, n = 43,368). The strength of associations did not vary between Western and Eastern countries, year of publication, or quality. Gender was a moderator: Loneliness was more strongly associated with life satisfaction in females. Age was also a moderator; the association between social support and life satisfaction weakened with increasing age.

Discussion and Implications

Improving the physical capabilities of older individuals, fostering social support, and alleviating feelings of loneliness, depression, and anxiety may help build life satisfaction in older individuals, which policy-makers and healthcare professionals should prioritize when implementing strategies.
Investigation in yeast of novel variants in mitochondrial aminoacyl-tRNA synthetases WARS2, NARS2, and RARS2 genes associated with mitochondrial diseases
Authors: Figuccia Sonia , Izzo Rossella , Legati Andrea , Nasca Alessia , Goffrini Paola , Ghezzi Daniele , Ceccatelli Berti Camilla
Published: September 2024

Aminoacyl-transfer RiboNucleic Acid synthetases (ARSs) are essential enzymes that catalyze the attachment of each amino acid to their cognate tRNAs. Mitochondrial ARSs (mtARSs), which ensure protein synthesis within the mitochondria, are encoded by nuclear genes and imported into the organelle after translation in the cytosol. The extensive use of next generation sequencing (NGS) has resulted in an increasing number of variants in mtARS genes being identified and associated with mitochondrial diseases. The similarities between yeast and human mitochondrial translation machineries make yeast a good model to quickly and efficiently evaluate the effect of variants in mtARS genes. Genetic screening of patients with a clinical suspicion of mitochondrial disorders through a customized gene panel of known disease-genes, including all genes encoding mtARSs, led to the identification of missense variants in WARS2, NARS2 and RARS2. Most of them were classified as Variant of Uncertain Significance. We exploited yeast models to assess the functional consequences of the variants found in these genes encoding mitochondrial tryptophanyl-tRNA, asparaginyl-tRNA, and arginyl-tRNA synthetases, respectively. Mitochondrial phenotypes such as oxidative growth, oxygen consumption rate, Cox2 steady-state level and mitochondrial protein synthesis were analyzed in yeast strains deleted in MSW1, SLM5, and MSR1 (the yeast orthologues of WARS2, NARS2 and RARS2, respectively), and expressing the wild type or the mutant alleles. Pathogenicity was confirmed for most variants, leading to their reclassification as Likely Pathogenic. Moreover, the beneficial effects observed after asparagine and arginine supplementation in the growth medium suggest them as a potential therapeutic approach.
Thermal comfort in different building forms and operation conditions—case study of Ningbo dental treatment rooms
Authors: Ma Siyu , Lu Hanyue , Deng Wu , Lu Jun , Zhou Tongyu , Zhang Huayan
Published: September 2024

The research on indoor thermal comfort has extensively covered office, educational, and residential buildings, but healthcare facilities have been relatively overlooked. This study compared and analyzed the annual dynamic thermal comfort of six dental treatment rooms with different building forms and operation conditions through on-site surveys and EnergyPlus simulations. The results indicated that due to the significant internal heat gain of the dental equipment, treatment rooms with excellent insulation performance may paradoxically experience severe overheating issues during the cooling and free-running seasons. The findings can be used to provide empirical data to support dental treatment spaces design in Ningbo.
Lifeguard Pharmacy: the co-development of a new community pharmacy response service for people in danger from domestic abuse or suicidal ideation
Authors: Barcelos Ana Maria , Latham-Green Tracey , Barnes Rebecca , Gorton Hayley , Gussy Mark , Henderson Claire , Khatri Mahomed , Knapp Peter , Solomon Josie
Published: September 2024

Background

Domestic abuse (DA) and suicidal ideation (SI) are prevalent and often co-occur. Numerous practical and psychosocial barriers inhibit help-seeking, including accessibility and confidentiality concerns. Pharmacies are accessible and may be perceived as a discreet venue for a DA and SI response service.

Objective

To co-develop a community pharmacy response service for people experiencing domestic abuse or suicidal ideation.

Methods

Overall, 36 unique individuals contributed at least once to a series of focus groups, interviews or workshops to co-develop the service components. Participants had lived experience of DA/SI or were professionals from DA/SI support services or pharmacies. Audio recordings and field notes from events were thematically analysed. Specific themes were identified and informed the development of the service components.

Key findings

Participants supported the development of this new service and considered community pharmacies to be an ideal setting. They thought of the service as a lifeline, that would offer hope. Under this main concept of hope, five main themes were identified: Safety, Empathy, Empowerment, Equity, and Discretion. Participants’ practical considerations were incorporated into the service design, including the name choice of “Lifeguard Pharmacy”, the strapline “Bringing Hope to Life”, and the development of a “Client Flowchart” outlining how to welcome a client, arrange for a consultation, and then guide clients out of the pharmacy afterwards.

Conclusions

Overall, the findings supported the development and introduction of this pharmacy-based intervention, which may help overcome barriers to help-seeking for DA or SI due to its sense of hope, accessibility, and discretion.
The Resurgence of Ideology under Xi Jinping and International Relations Scholarship in China
Authors: Mokry Sabine
Published: September 2024

This article examines how the increased emphasis on ideology under Xi Jinping has impacted Chinese IR scholarship published in Chinese- and English-language academic journals, as well as research funding awarded by the National Planning Office for Philosophy and Social Sciences. It finds that ideological concepts featured increasingly prominently in awarded research funding and published scholarship the longer Xi Jinping has been in office. Considerable decreases in thematic diversity were noticeable in funding and publications. The article finds that the resurgence of ideology further exacerbated differences between scholars who are relatively close to the state and scholars who are more distant from the state. Close scholars publish more on ideological concepts, but their scholarship is also characterized by a higher degree of thematic diversity than distant scholars’. Drawing on scholars’ biographical data, publicly available data on research funding, and bibliometric data collected from Chinese- and English-language academic journals, this article offers a systematic account of the status quo of the IR discipline in China. In addition, it offers insights into the conditions for social science scholarship under authoritarian rule by proposing a novel conceptualization and measurement of scholars’ proximity to the state, which could also be applied to other authoritarian settings.
Comprehensive review of noncontact sensing technologies for bridge condition monitoring and assessment
Authors: Tian Yongding , Zhang Junhao , Lyu Yangfeng , Zhang Jian
Published: September 2024

Bridges play a vital role in modern transportation networks. Nevertheless, the degradation of their materials, combined with the effects of natural disasters (e.g. earthquakes, floods, rockfalls, landslides), can result in decreased performance or even collapse. Therefore, monitoring the health of bridges is essential to maintain the safety and integrity of highway and railway systems. Noncontact sensing technologies provide effective solutions for bridge condition monitoring and performance assessment, as they can gather data without direct interaction with the structure. This paper provides a comprehensive review of the latest noncontact sensing technologies employed for bridge condition monitoring, detailing their principles, benefits, drawbacks, and applications. Firstly, the recent advancements in vision sensing technology for detecting defects, measuring deformations, vibrations, cable forces, vehicle loads, pedestrian-induced impact force, and monitoring vessel collision with bridges are summarized; secondly, the laser scanning technology for three-dimensional model reconstruction, full-field deformation measurement, and quality inspection of bridges are examined; thirdly, the use of microwave radar technology for measuring deformations, vibrations, and cable forces in bridges is investigated. Finally, the paper outlines future trends in noncontact sensing technologies for bridge condition monitoring and evaluation. This comprehensive review offers valuable insights for engineers and researchers in the field of civil engineering.