bluuebunny/crossref_metadata_2025_split huggingface dataset:
Critical Evaluation of Sphingolipids Detection by MALDI-MSI
Authors: Chen Bo , Pathak Ranjana , Subekti Albar , Cheng Xiaolu , Singh Sukhjit , Ostermeyer-Fay Anne G. , Hannun Yusuf A. , Luberto Chiara , Canals Daniel 
Published: February 2025

ABSTRACTThe increasing interest in the role of sphingolipids in (patho)physiology has led to the demand for visualization of these lipids within tissue samples (both from animal models and patient specimens) using techniques such as matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). While increasingly adopted, detection of sphingolipids with MALDI-MSI is challenging due to: i) the significant structural variations of sphingolipid molecules, ii) the potential breakdown of the more complex molecules into structurally simpler species which may confound the analysis, and iii) the great difference in levels among sphingolipid classes and subspecies, with the low-abundant ones often being close to the detection limit. In this study, we adopted a multi-pronged approach to establish a robust pipeline for the detection of sphingolipids by MALDI-MSI and to establish best practices and limitations of this technology. First, we evaluated the more commonly adopted methods [2,5-Dihydroxyacetophenon (DHA) or 2,5-Dihydroxybenzoic acid (DHB) matrix in positive ion mode and 1,5-Diaminonaphthalene (DAN) matrix in negative ion mode] using MALDI-MS on reference standards. These standards were used at ratios similar to their relative levels in biological samples to evaluate signal artifacts originating from fragmentation of more complex sphingolipids and impacting low level species. Next, by applying the most appropriate protocol for each sphingolipid class, MALDI-MSI signals were validated in cell culture by modulating specific sphingolipid species using sphingolipid enzymes and inhibitors. Finally, the optimized parameters were utilized on breast cancer tissue from the PyMT mouse model.We report the optimal signal for sphingomyelin (SM) and, for the first time, Sph in DHB positive ion mode (in cells and PyMT tissue), and the validated detection of ceramides and glycosphingolipids in DAN negative ion mode. We document the extensive fragmentation of SM into sphingosine-1-phosphate (S1P) and even more so into ceramide-1-phosphate (C1P) using DAN in negative ion mode and its effect in generating an artifactual C1P tissue signal; we also report the lack of detectable signal for S1P and C1P in biological samples (cells and tissue) using the more suitable DHB positive ion mode protocol.
CryoEM-enabled visual proteomics revealsde novostructures of oligomeric protein complexes fromAzotobacter vinelandii
Authors: Warmack Rebeccah A. , Maggiolo Ailiena O. , Shen Yuanbo , Zhang Tianzheng 
Published: February 2025

AbstractSingle particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging visual proteomics, we interrogate structures isolated from a complex cellular milieu by cryoEM to identify and classify molecular structures and complexesde novo. That approach determines the identity of six distinct oligomeric protein complexes from partially purified extracts ofAzotobacter vinelandiiusing both anaerobic and aerobic cryoEM. Identification of the first unknown species, phosphoglucoisomerase (Pgi1), is achieved by comparing three automated model building programs: CryoID, DeepTracer, and ModelAngelo with or withouta prioriproteomics data. All three programs identify the Pgi1 protein, revealed to be in a new decameric state, as well as additional globular structures identified as glutamine synthetase (GlnA) and bacterioferritin (Bfr). Large filamentous assemblies are observed in tomograms reconstructed from cryoFIB milled lamellae of nitrogen-fixingA. vinelandii. Enrichment of these species from the cells by centrifugation allows for structure determination of three distinct filament types by helical reconstruction methods: the Type 6 Secretion System non-contractile sheath tube (TssC), a novel filamentous form of the soluble pyridine transhydrogenase (SthA), and the flagellar filament (FliC). The multimeric states of Pgi1 and SthA stand out in contrast to known crystallographic structures and offer a new structural framework from which to evaluate their activities. Overall, by allowing the study of near-native oligomeric protein states, cryoEM-enabled visual proteomics reveals novel structures that correspond to relevant species observedin situ.Abstract Figure
Systematic Investigation of Double Emulsion Dewetting Dynamics for the Droplet Microfluidic Production of Giant Unilamellar Vesicles (GUVs) under Biocompatible Conditions
Authors: Jing Wenyang , Noh Heewon , Tan Timothy J. C. , Wu Nicholas C. , Han Hee-Sun 
Published: February 2025

AbstractGiant unilamellar vesicles (GUVs) embody biomimetic membranes with compartmentalization that serve not only as simplified models to better understand complex biochemical and biophysical processes, but also as a chassis for the bottom-up assembly of synthetic cells. Recently, double emulsion droplet microfluidics has proven to be a promising platform for their production, offering greater throughput, control, and reproducibility over traditional methods. However, the interplay of parameters—particularly under biocompatible conditions—that influence the complex multiphase fluid dynamics of the dewetting process underlying GUV production has not been thoroughly studied, limiting the democratization of the approach. In this study, we systematically investigate how lipid composition and concentration, aqueous phase conditions, droplet confinement, and fluid dynamics effects promote or impede the dewetting process. We show that the prevalent use of high concentrations of glycerol and P188 are unnecessary, and the altered dewetting dynamics with restricted surfactant usage can be tuned by adjusting chip dimensions and multi-phase compositions. Guided by these findings, we achieved robust, high throughput production of monodisperse GUVs using 0.1% P188 and no glycerol with salts. Our results improve the reliability and accessibility of droplet-microfluidics GUV platforms to catalyze advances in biophysics, synthetic biology, and drug discovery.
Structural variation, selection, and diversification of theNPIPgene family from the human pangenome
Authors: Dishuck Philip C. , Munson Katherine M. , Lewis Alexandra P. , Dougherty Max L. , Underwood Jason G. , Harvey William T. , Hsieh PingHsun , Pastinen Tomi , Eichler Evan E. 
Published: February 2025

ABSTRACTTheNPIP(nuclear pore interacting protein) gene family has expanded to high copy number in humans and African apes where it has been subject to an excess of amino acid replacement consistent with positive selection (1). Due to the limitations of short-read sequencing,NPIPhuman genetic diversity has been poorly understood. Using highly accurate assemblies generated from long-read sequencing as part of the human pangenome, we completely characterize 169 human haplotypes (4,665NPIPparalogs and alleles). Of the 28NPIPparalogs, just three (NPIPB2,B11, andB14) are fixed at a single copy, and only a single locus,B2, shows no structural variation. FourNPIPparalogs map to large segmental duplication blocks that mediate polymorphic inversions (355 kbp–1.6 Mbp) corresponding to microdeletions associated with developmental delay and autism. Haplotype-based tests of positive selection and selective sweeps identify two paralogs,B9andB15, within the top percentile for both tests. Using full-length cDNA data from 101 tissue/cell types, we construct paralog-specific gene models and show that 56% (31/55 most abundant isoforms) have not been previously described in RefSeq. We define six distinct translation start sites and other protein structural features that distinguish paralogs, including a variable number tandem repeat that encodes a beta helix of variable size that emerged ∼3.1 million years ago in human evolution. Among the 28NPIPparalogs, we identify distinct tissue and developmental patterns of expression with only a few maintaining the ancestral testis-enriched expression. A subset of paralogs (NPIPA1,A5,A6-9,B3-5, andB12/B13) show increased brain expression. Our results suggest ongoing positive selection in the human population and rapid diversification ofNPIPgene models.
Oscillatory impact of Transcranial Magnetic Stimulation at very weak-intensity on the primary motor cortex: A TMS-EEG study in the human brain
Authors: Corominas-Teruel Xavier , Bracco Martina , Lohof Anne , Sherrard Rachel , Colomina Maria Teresa , Mahon Severine , Charpier Stéphane , Valero-Cabré Antoni 
Published: February 2025

ABSTRACTBackgroundVery weak transcranial magnetic stimulation (TMS, 10 mT, ∼0.05-10 V/m) has been explored in animal models showcasing potential for effective neuromodulation. However, the physiological effects of these type of pulsed fields remain rather unexplored in humans.ObjectiveWe here aimed to characterize the neural effects of very weak TMS pulsed fields (∼6V/m, ∼6% of the resting motor threshold, rMT) and explore their ability to evoke and/or modulate local oscillatory activity generated on human primary motor regions.MethodsNeuronavigated TMS was employed in a cohort of healthy participants (n=18) to deliversingle pulsesandshort burstsofrhythmic(20 Hz) TMS at very weak intensity and at conventional levels (here referred as high intensity) usually employed in human applications (∼113V/m, ∼77% rMT), to the left primary motor cortex (M1). In parallel, their potential to evoke brain activity such as Transcranial Evoked Potentials (TEPs), and to entrain or modulate local ongoing oscillations was explored with scalp EEG recordings.ResultsBoth, single TMS pulses and 4-pulse rhythmic TMS beta (20 Hz) bursts delivered at conventional intensity elicited consistent Transcranial Evoked Potentials (TEPs) and beta-synchronized Event Related Spectral Perturbations (ERSP) around the left M1 area. Most interestingly, very-weak-intensity TMS modulated in this same area oscillatory activity at a mu-alpha frequency (7-13 Hz) only for rhythmic TMS bursts time-locked to -the troughs of the local ongoing beta oscillations.ConclusionsOur data provide first time support for the modulation of oscillatory signals with TMS delivered at an unprecedentedly weak intensity on the human primary motor cortex. This evidence enriches current knowledge on the impact of weak pulsed magnetic fields in humans, paving the way for future neurotherapeutics with a new generation of portable and autonomous low-intensity multichannel TMS devices.HIGHLIGHTSVery weak-intensity 20Hz TMS rhythmic patterns evoked significant mu-alpha central activity (7-13Hz) when bursts were aligned with the troughs of local ongoing beta oscillatory activity.Conventional high-intensity single pulse and 20Hz TMS patterns elicited consistent TMS evoked potentials (TEP) and beta-synchronized local changes of Event Related Spectral Perturbations (ERSPs) in the left M1.Fulfilling established criteria of TMS entrainment, the effects driven by high-intensity stimulation on M1 were TMS pattern- and oscillation-phase-dependent. Differences featured by very weak vs. conventional intensity TMS on entrained oscillatory activity suggests these two modalities operate on distinct physiological mechanisms.
Setting new boundaries of 16S rRNA gene identity for prokaryotic taxonomy
Authors: Hackmann Timothy J. 
Published: February 2025

ABSTRACTThe 16S ribosomal RNA (rRNA) gene is frequently sequenced to classify prokaryotes and identify new taxa. If sequences from two strains share less than ∼99% identity, the strains are usually classified as different species. Classification thresholds for genera and other ranks have also been proposed, but they are based on dated datasets. Here we update these thresholds by determining sequence identity of the 16S rRNA gene for nearly 18,000 type strains. This represents 86.5% of all strains validly published, and it involved making more than 161 million pairwise sequence alignments. In 90% of all cases, sequences from the same species shared a minimum of 97.2 to 100% identity. The corresponding values for genus were 90.3 to 99.0%, 79.6 to 94.1% for family, 73.1 to 90.1% for order, 72.2 to 86.3% for class, and 69.7 to 83.6% for phylum. We propose these values serve as thresholds for classifying new prokaryotic taxa. A major change from previous guidelines is recognizing that these boundaries overlap. This overlap has already been observed for relative evolutionary divergence, a metric correlated with 16S rRNA gene identity. Together with other metrics, 16S rRNA gene identity allows classification of prokaryotes from species to phylum.
Solubilization of Membrane Proteins using designed protein WRAPS
Authors: Mihaljević Ljubica , Kim David E. , Eisenach Helen E. , Bandawane Pooja D. , Borst Andrew J. , Courbet Alexis , Bettin Everton , Liu Qiushi , Weidle Connor , Majumder Sagardip , Li Xinting , Lamb Mila , Azcárraga Murray Analisa Nicole , Ravichandran Rashmi , Williams Elizabeth C. , Hu Shuyuan , Stuart Lynda , Grillová Linda , Thomson Nicholas R. , Chang Pengxiang , Caimano Melissa J. , Hawley Kelly L. , King Neil P. , Baker David 
Published: February 2025

AbstractThe development of therapies and vaccines targeting integral membrane proteins has been complicated by their extensive hydrophobic surfaces, which can make production and structural characterization difficult. Here we describe a general deep learning-based design approach for solubilizing native membrane proteins while preserving their sequence, fold, and function using genetically encodedde novoprotein WRAPs (Water-solubleRFdiffusedAmphipathicProteins) that surround the lipid-interacting hydrophobic surfaces, rendering them stable and water-soluble without the need for detergents. We design WRAPs for both beta-barrel outer membrane and helical multi-pass transmembrane proteins, and show that the solubilized proteins retain the binding and enzymatic functions of the native targets with enhanced stability. Syphilis vaccine development has been hindered by difficulties in characterizing and producing the outer membrane protein antigens; we generated soluble versions of fourTreponema pallidumouter membrane beta barrels which are potential syphilis vaccine antigens. A 4.0 Å cryo-EM map of WRAPed TP0698 is closely consistent with the design model. WRAPs should be broadly useful for facilitating biochemical and structural characterization of integral membrane proteins, enabling therapeutic discovery by screening against purified soluble targets, and generating antigenically intact immunogens for vaccine development.
High-Dimensional Quantum Key Distribution by a Spin-Orbit Microlaser
Authors: Zhang Yichi , Zhao Haoqi , Wu Tianwei , Gao Zihe , Ge Li , Feng Liang 
Published: February 2025

Quantum key distribution offers a promising avenue for establishing secure communication networks. However, its performance is significantly hampered by the conventional two-level information carriers (i.e., qubits) due to their limited information capacity and noise resilience. A fundamental approach to overcoming these limitations involves the adoption of high-dimensional qudits. Practical qudit platforms require robust propagation, outstanding controllability, and extreme compactness, to which integrated photonics provides a promising solution. Here, we achieved, for the first time, microlaser-enabled high-dimensional quantum communication through leveraging spin-orbit photon qudits, where the dynamical generation and manipulation of these multi-degrees-of-freedom complex quantum state are realized by a non-Hermitian-physics-driven integrated microlaser quantum transmitter. Such a microlaser photon manipulation, as a novel route towards high-dimensional quantum state generation, promises high energy efficiency, along with fast, compact, and precise qudit state reconfigurability. The four spin-orbit eigenstates emitted by the microlaser possess the same spatial-temporal structures, ensuring homogeneity between all qudit states used for key distribution, which effectively eliminates propagation dephasing and walk-off problems, thereby delivering the high-dimensional spin-orbit secret key generation to construct a robust quantum link. The demonstrated long-term system stability showcases the practical potential of the microlaser quantum transmitter, providing a critical step towards compact, high-information-capacity quantum communication networks.

Published by the American Physical Society
2025
Representations of foreign nationals in Japanese disaster risk reduction policy: increasing alignment with a “whole community” discourse
Authors: Cadwell Patrick 
Published: February 2025

PurposeThis article examines how foreign nationals have been represented in the disaster risk reduction (DRR) policy discourse in Japan in recent decades and analyses the consequences these representations have had for foreign nationals’ DRR there.Design/methodology/approachThe article reports on a monolingual, corpus-based, critical discourse analysis of 23 years of White Papers on Disaster Management in Japan to assess the discourse representations of foreign nationals in the policy texts over three chronological periods: 2001–2008, 2009–2016 and 2017–2023.FindingsThe article finds that the way the Government of Japan has communicated to stakeholders about foreign nationals through its policy has increasingly included them into a “whole community” discourse of DRR. This is significant because research has shown that foreign nationals have long gone un- or under-recognised in relevant DRR policies and have been insufficiently considered at local levels. If they are now better represented in policy as local community members, there is hope that their risk of negative consequences in times of disaster will truly be reduced.Originality/valueThis contribution is novel in that it addresses a nexus between discourse, policy communication and a social problem of inclusion and engagement of foreign nationals in DRR that has not been published elsewhere, but that nonetheless engages with ongoing academic conversations about inclusivity, vulnerability and community-based DRR approaches.
Application of artificial intelligence in demand planning for supply chains: a systematic literature review
Authors: Walter Arne , Ahsan Kamrul , Rahman Shams 
Published: February 2025

PurposeDemand planning (DP) is a key element of supply chain management (SCM) and is widely regarded as an important catalyst for improving supply chain performance. Regarding the availability of technology to process large amounts of data, artificial intelligence (AI) has received increasing attention in the DP literature in recent years, but there are no reviews of studies on the application of AI in supply chain DP. Given the importance and value of this research area, we aimed to review the current body of knowledge on the application of AI in DP to improve SCM performance.Design/methodology/approachUsing a systematic literature review approach, we identified 141 peer-reviewed articles and conducted content analysis to examine the body of knowledge on AI in DP in the academic literature published from 2012 to 2023.FindingsWe found that AI in DP is still in its early stages of development. The literature is dominated by modelling studies. We identified three knowledge clusters for AI in DP: AI tools and techniques, AI applications for supply chain functions and the impact of AI on digital SCM. The three knowledge domains are conceptualised in a framework to demonstrate how AI can be deployed in DP to improve SCM performance. However, challenges remain. We identify gaps in the literature that make suggestions for further research in this area.Originality/valueThis study makes a theoretical contribution by identifying the key elements in applying AI in DP for SCM. The proposed conceptual framework can be used to help guide further empirical research and can help companies to implement AI in DP.
Metaverse retailing and the customer experience journey: a case study approach
Authors: Alexander Bethan , Blazquez Marta , Chrimes Courtney 
Published: February 2025

PurposeThis study adopts the customer journey framework to investigate the role of the metaverse in the customer purchase experience. It establishes the effect of the metaverse on the three stages of the customer purchase journey, namely pre-purchase, purchase and post-purchase, in the context of the fashion industry, an early adopter of the metaverse.Design/methodology/approachThe research is a qualitative case study explored through consumer diaries and focus groups. The resultant data are analysed thematically.FindingsMetaverse usage is the most significant at the pre-purchase stage. However, technical problems and other sources of friction negatively impact the customer experience journey, providing insight into the reasons underlying the recent decline of metaverse marketplaces.Originality/valueThis study’s empirical findings have theoretical and practical implications related to metaverse retailing and the customer experience journey. The study benefits metaverse designers and customers and will influence retail strategy choice. Additionally, it contributes two conceptual frameworks to the underdeveloped metaverse retailing field and extends the customer experience journey framework to the metaverse context, thus contributing to the body of knowledge on omnichannel retailing.
The impact of financial distress on capital structure following Egypt's currency flotation: the moderating role of board characteristics and ownership structure
Authors: Balboula Mohamed Zaki , Shemes Mona Ahmed 
Published: February 2025

PurposeThis study examines how financial distress affects the capital structure of Egyptian firms following the 2016 currency flotation, examining the moderating roles of board characteristics and ownership structure.Design/methodology/approachUtilizing data from non-financial companies listed on the Egyptian Stock Exchange from 2017 to 2022, we apply two-stage least squares (2SLS) and propensity score matching (PSM) to address endogeneity and selection bias.FindingsOur findings indicate that financially distressed firms tend to increase their debt burden, but robust governance mechanisms, such as higher board independence, larger boards and strong blockholder and institutional ownership, significantly mitigate this effect. Managerial ownership shows a stabilizing influence during distress, while chief executive officer duality does not significantly impact leverage decisions. These findings underscore how robust corporate governance promotes more conservative capital structure decisions during economic volatility.Research limitations/implicationsOur study focus, country and period could limit the generalizability of our findings to other regions or sectors.Practical implicationsInvestors and policymakers are advised to focus on firms with effective governance structures to mitigate distress-induced leverage increases. Governance reforms that enhance board effectiveness and ownership structure, e.g. increasing board independence requirements and promoting greater institutional investor participation, can further stabilize capital structure during downturns. Managers, in turn, should diversify financing and adopt prudent debt strategies to reduce overreliance on leverage.Originality/valueIn contrast to most studies, this research reverses the lens by exploring how financial distress shapes capital structure decisions in an emerging market context, specifically post-Egypt’s 2016 currency flotation. Employing both 2SLS and PSM to address endogeneity and selection bias, the study highlights the mitigating role of governance mechanisms, which can buffer firms against heightened debt reliance under economic volatility.