bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unusually Rapid Isomerization of Aspartic Acid in Tau
Authors: Shoff Thomas A. , Van Orman Brielle , Onwudiwe Vivian C. , Genereux Joseph C. , Julian Ryan R. 
Published: December 2024

AbstractSpontaneous chemical modifications in long-lived proteins can potentially change protein structure in ways that impact proteostasis and cellular health. For example, isomerization of aspartic acid interferes with protein turnover and is anticorrelated with cognitive acuity in Alzheimer’s disease. However, few isomerization rates have been determined for Asp residues in intact proteins. To remedy this deficiency, we used protein extracts from SH-SY5Y neuroblastoma cells as a source of a complex, brain-relevant proteome with no baseline isomerization. Cell lysates were agedin vitroto generate isomers, and extracted proteins were analyzed by data-independent acquisition (DIA) liquid chromatography-mass spectrometry (LC-MS). Although no Asp isomers were detected at Day 0, isomerization increased across time and was quantifiable for 105 proteins by Day 50. Data analysis revealed that isomerization rate is influenced by both primary sequence and secondary structure, suggesting that steric hindrance and backbone rigidity modulate isomerization. Additionally, we examined lysates extracted under gentle conditions to preserve protein complexes and found that protein-protein interactions often slow isomerization. Base catalysis was explored as a means to accelerate Asp isomerization due to findings of accelerated asparagine deamidation. However, no substantial rate enhancement was found for isomerization, suggesting fundamental differences in acid-base chemistry. With an enhanced understanding of Asp isomerization in proteins in general, we next sought to better understand Asp isomerization in tau.In vitroaging of monomeric and aggregated recombinant tau revealed that tau isomerizes significantly faster than any similar protein within our dataset, which is likely related to its correlation with cognition in Alzheimer’s disease.Abstract Figure
Optimized navigator-based correction of breathing-induced B0field fluctuations in multi-echo gradient-echo imaging of the spinal cord
Authors: Beghini Laura , Büeler Silvan , Liechti Martina D. , Jaffray Alexander , David Gergely , Vannesjo S. Johanna 
Published: December 2024

AbstractPurposeMulti-echo gradient-echo (ME-GRE) imaging in the spinal cord is susceptible to breathing-induced B0field fluctuations due to the proximity of the lungs, leading to ghosting artifacts. A navigator readout can be used to monitor the fluctuations; however, standard navigator processing often fails in the spinal cord. Here, we introduce navigator processing tailored specifically for spinal cord imaging.MethodsME-GRE data covering all spinal cord regions were acquired in six healthy volunteers during free breathing at 3T. Centerline navigator readouts and respiratory belt recordings were collected during the acquisitions. The navigator processing included a Fast Fourier Transform and subsequent interval selection targeting the spinal cord, as well as SNR-weighted averaging over samples and coils on the complex data. Furthermore, a phase unwrapping algorithm making use of the belt recordings was developed. Imaging data were corrected by phase demodulation before image reconstruction.ResultsB0field fluctuations and ghosting artifacts were largest in the lower cervical and upper lumbosacral cord (∼5 Hz std), close to the edges of the lungs. Image reconstruction based on optimized navigator correction improved visual image quality and quantitative metrics (SNR, CNR, ghosting) in all regions of the spinal cord. The improvement was largest in regions with large field fluctuations (group-averaged increase in SNR/CNR of up to 29%/37% in single-echo images).ConclusionsOptimized navigator-based correction can reduce ghosting artifacts and increase SNR/CNR in anatomical ME-GRE of the spinal cord. The enhanced image quality and ease of implementation across sites makes the technique attractive for clinical and scientific applications.
De novodesign of potent CRISPR-Cas13 inhibitors
Authors: Taveneau Cyntia , Chai Her Xiang , D’Silva Jovita , Bamert Rebecca S. , Hayes Brooke K. , Calvert Roland W. , Curwen Daniel J. , Munder Fabian , Martin Lisandra L. , Barr Jeremy J. , Grinter Rhys , Knott Gavin J. 
Published: December 2024

AbstractCRISPR-Cas systems are transformative tools for gene editing which can be tuned or controlled by anti-CRISPRs (Acrs) - phage derived inhibitors that regulate CRISPR-Cas activity. However, Acrs that are capable of inhibiting biotechnologically relevant CRISPR systems are relatively rare and challenging to discover. To overcome this limitation, we describe a highly successful, rapid, and generalisable approach that leveragesde novoprotein design to develop new-to-nature proteins for controlling CRISPR-Cas activity. Using CRISPR-Cas13 as a representative example, we demonstrate that AI-designed anti-CRISPRs (AIcrs) are capable of highly potent and specific inhibition of CRISPR-Cas13 proteins. We present a comprehensive workflow for design validation and demonstrate AIcrs functionality in controlling CRISPR-Cas13 activity in bacteria. The ability to design bespoke inhibitors of Cas effectors will contribute to the ongoing development of CRISPR-Cas tools in diverse applications across research, medicine, agriculture, and microbiology.
Unambiguous assignment of kinked beta sheets leads to insights into molecular grammar of reversibility in biomolecular condensates
Authors: Roy Irawati , Appadurai Rajeswari , Srivastavava Anand 
Published: December 2024

AbstractKinked-βsheets are short peptide motifs that appear as distortions inβ-strands and often mediate formation of reversible amyloid fibrils in prion-like proteins. Standard methods for assigning secondary structures cannot distinguish these esoteric motifs. Here, we provide a supervised machine learning based structural quantification map to unambiguously characterize Kinked-βsheets from coordinate data. We find that these motifs, although deviating from standardβ-strand region of the Ramachandran plot, scatter around the allowed regions. We also demonstrate the applicability of our technique in wresting out LARKS, which are kinkedβ-strands with designated sequence. Additionally, from our exhaustive simulation generated conformations, we create a repository of potential kinked peptide-segments that can be used as a screening-library for assigning beta-kinks in unresolved coordinate dataset. Overall, our map for Kinked-βprovides a robust framework for detailed structural and kinetics investigation of these important motifs in prion-like proteins that lead to formation of amyloid fibrils.
Rad52 Acts as an Assembly Chaperone to Form and Stabilize Rad51 Filaments Through a Large C-Terminus 85-Residue Segment
Authors: Ma Emilie , Lakhal Fadma , Litsardaki Eleni , Ruault Myriam , Audin Maxime , Levrier Natacha , Navarro Emilie , Garnier Mickaël , Maloisel Laurent , Depagne Jordane , Brocas Clémentine , Thureau Aurelien , Busso Didier , Veaute Xavier , Guerois Raphaël , Taddei Angela , Ochsenbein Françoise , Coïc Eric 
Published: December 2024

AbstractHomologous recombination (HR) is essential for the repair of DNA double-strand breaks and the restart of stalled replication forks. A critical step in HR is the formation of Rad51 nucleofilaments, which perform homology search and strand invasion of a homologous DNA sequence required for repair synthesis. In the yeastSaccharomyces cerevisiae, Rad52 facilitates Rad51 nucleofilament formation by mediating Rad51 loading onto ssDNA and counteracting the dissociation of Rad51 filaments by the DNA translocase Srs2. The molecular basis of these two Rad52 functions remains unclear. Our integrative structural analyses of the Rad51-Rad52 interaction, combining NMR, SAXS, and modeling, reveal that an 85-residue segment of Rad52, conserved in fungi, folds upon binding to a broad surface of a Rad51 monomer. Notably, it includes an FxxA motif conserved in the BRC repeats of BRCA2 and at the Rad51-Rad51 interface. This binding mode was validated through an extensive set of mutations. Usingin vivoassays and a functional fluorescent GFP-Rad51 fusion protein, we demonstrated that this entire segment is critical for Rad51 filament formation. These findings highlight how Rad52 functions as an assembly chaperone, preventing Rad51 oligomerization, promoting nucleation of Rad51 nucleofilaments on ssDNA, and protecting Rad51 filaments from destabilization by Srs2.
Leucine zipper-based SAIM imaging identifies therapeutic agents to disrupt the cancer cell glycocalyx for enhanced immunotherapy
Authors: Park Sangwoo , Paek Justin H. , Colville Marshall J. , Huang Ling-Ting , Struzyk Audrey P. , Womack Sydney J. , Neelamegham Sriram , Reesink Heidi L. , Paszek Matthew J. 
Published: December 2024

AbstractThe abnormally thick glycocalyx of cancer cells can provide a physical barrier to immune cell recognition and effective immunotherapy. Here, we demonstrate an optical method based on Scanning Angle Interference Microscopy (SAIM) for the screening of therapeutic agents that can disrupt the glycocalyx layer as a strategy to improve anti-cancer immune responses. We developed a new membrane labeling strategy utilizing leucine zipper pairs to fluorescently mark the glycocalyx layer boundary for precise and robust measurement of glycocalyx thickness with SAIM. Using this platform, we evaluated the effects of glycosylation inhibitors and targeted enzymatic degraders of the glycocalyx, with particular focus on strategies for cholangiocarcinoma (CCA), a highly lethal malignancy with limited therapeutic options. We found that CCA had the highest mean expression of the cancer-associated mucin, MUC1, across all cancers represented in the cancer cell line encyclopedia. Pharmacological inhibitors of mucin-type O-glycosylation and mucin-specific proteases, such as StcE, could dramatically reduce the glycocalyx layer in the YSCCC model of intrahepatic CCA. Motivated by these findings, we engineered Natural Killer (NK) cells tethered with StcE to enhance NK cell-mediated cytotoxicity against CCA. In a CCA xenograft model, these engineered NK cells demonstrated superior anti-tumor efficacy compared to wild-type NK cells, with no observable adverse effects. Our findings not only provide a reliable imaging-based screening platform for evaluating glycocalyx-targeting pharmacological interventions but also offer mechanistic insights into how CCA may avoid immune elimination through fortification of the glycocalyx layer with mucins. Additionally, this work presents a novel therapeutic strategy for mucin-overexpressing cancers, potentially improving immunotherapy efficacy across various cancer types.
Spatiotemporal distribution of the glycoprotein pherophorin II reveals stochastic geometry of the growing ECM ofVolvox carteri
Authors: von der Heyde Benjamin , Srinivasan Anand , Birwa Sumit Kumar , von der Heyde Eva Laura , Höhn Steph S.M.H. , Goldstein Raymond E. , Hallmann Armin 
Published: December 2024

AbstractThe evolution of multicellularity involved the transformation of a simple cell wall of unicellular ancestors into a complex, multifunctional extracellular matrix (ECM). A suitable model organism to study the formation and expansion of an ECM during ontogenesis is the multicellular green algaVolvox carteri, which, along with the related volvocine algae, produces a complex, self-organized ECM composed of multiple substructures. These self-assembled ECMs primarily consist of hydroxyproline-rich glycoproteins, a major component of which is pherophorins. To investigate the geometry of the growing ECM, we fused theyfpgene with the gene for pherophorin II (PhII) inV. carteri. Confocal microscopy reveals PhII:YFP localization at key structures within the ECM, including the boundaries of compartments surrounding each somatic cell and the outer surface of the organism. Image analysis during the life cycle allows the stochastic geometry of those growing compartments to be quantified. We find that their areas and aspect ratios exhibit robust gamma distributions and exhibit a transition from a tight polygonal to a looser acircular packing geometry with stable eccentricity over time, evoking parallels and distinctions with the behavior of hydrated foams. These results provide a quantitative benchmark for addressing a general, open question in biology: How do cells produce structures external to themselves in a robust and accurate manner?
Multivalued dispersion equation for coupling between plasmons and surface optical phonons in a graphene/polar-substrate system
Authors: Kukhtaruk S. M. , Kochelap V. A. 
Published: December 2024

Dispersion equations are a common paradigm of collective excitation physics. However, in some systems, dispersion equations contain multivalued functions and their solutions are ambiguous. As an example, we consider graphene on a polar substrate where Dirac plasmons are coupled with surface optical phonons. The dispersion equation for this system contains square-root singularity. Using the initial value problem resolves this uncertainty and gives a unique solution. Particularly, we found that the lower plasmon-phonon mode, which in terms of dispersion can have a good quality factor, is almost absent in excitation spectra. The physical reason and experimental evidence of the mode collapse are discussed.

Published by the American Physical Society
2024
Measuring kinetic inductance and superfluid stiffness of two-dimensional superconductors using high-quality transmission-line resonators
Authors: Kreidel Mary , Chu Xuanjing , Balgley Jesse , Antony Abhinandan , Verma Nishchhal , Ingham Julian , Ranzani Leonardo , Queiroz Raquel , Westervelt Robert M. , Hone James , Fong Kin Chung 
Published: December 2024

The discovery of van der Waals superconductors in recent years has generated a lot of excitement for their potentially novel pairing mechanisms. However, their typical atomic-scale thickness and micrometer-scale lateral dimensions impose severe challenges to investigations of pairing symmetry by conventional methods. We demonstrate an improved technique that employs high-quality-factor superconducting resonators to measure the kinetic inductance—up to one part per million—and loss of a van der Waals superconductor. We analyze the equivalent circuit model to extract the kinetic inductance, superfluid stiffness, penetration depth, and ratio of imaginary and real parts of the complex conductivity. We validate the technique by measuring aluminum and finding excellent agreement in both the zero-temperature superconducting gap as well as the complex conductivity data when compared with BCS theory. We then demonstrate the utility of the technique by measuring the kinetic inductance of multilayered niobium diselenide and discuss the limits to the accuracy of our technique when the transition temperature of the sample, NbSe2 at 7.06 K, approaches our Nb probe resonator at 8.59 K. Our method will be useful for practitioners in the growing fields of superconducting physics, materials science, and quantum sensing, as a means of characterizing superconducting circuit components and studying pairing mechanisms of the novel superconducting states which arise in layered two-dimensional materials and heterostructures.

Published by the American Physical Society
2024
Climate change sentiment, ESG practices and firm value: international insights
Authors: Bagh Tanveer , Bouri Elie , Khan Muhammad Asif 
Published: December 2024

PurposeThis study investigates the effect of climate change sentiments (CCS) on firm value (FV) and how environmental, social and governance (ESG) practices moderate this effect.Design/methodology/approachHigh-dimensional fixed effects and a two-stage generalized method of moments are applied to data on 6,059 publicly traded firms from 2006 to 2022.FindingsThere is a significant negative effect of CCS on FV, specifically on growth option value (GOV) and Tobin’s Q (TQR), which intensifies during crisis periods. ESG practices, however, moderate this relationship positively, especially for firms with higher GOV and TQR, enhancing their resilience to climate risks. External shocks accelerate sustainability-driven strategies in firms with higher CCS exposure. In developed countries, firms show a stronger sensitivity to CCS due to stronger institutional environments and investor pressure, while firms in developing countries exhibit a weaker sensitivity.Practical implicationsThe results underline the necessity for corporate managers to proactively manage climate-related risks and integrate robust ESG strategies to sustain and enhance FV. Analysts, risk managers and investors should consider a company’s exposure to CCS and its ESG performance when assessing risk profiles. Policymakers are encouraged to implement stronger regulatory frameworks and incentives promoting corporate transparency and accountability in managing climate-related risks.Originality/valueThis study unfolds novel evidence, linking psychological research and the traditional basic modified model through an examination of the effect of CCS on FV using an international sample. It highlights the critical role of ESG practices in mitigating the adverse effects of CCS on FV, providing valuable insights for businesses, investors and policymakers.
A numerical approach to a two-phase free boundary problem with MPC material in a finite domain
Authors: Jain Lipi , Joshi Jaya , Rajeev  
Published: December 2024

Purpose
The main purpose of this paper is given below: To present a mathematical model of a two-phase Stefan problem including a moving phase change material and variable thermophysical properties. To find a numerical solution of the problem to discuss the dependence of considered phase change problem on variable thermal conductivity, variable specific heat and Peclet number.

Design/methodology/approach
In this paper, a numerical solution of the problem is obtained using the front-fixing method in tandem with the explicit finite difference scheme. The authors have also discussed the consistency and stability of proposed numerical scheme.

Findings
In this study, it is observed that the considered scheme is an efficient tool that provides sufficiently accurate results for exploring the behaviors of moving interface (free boundary) and temperature profile for a nonclassical two-phase free boundary problem. In this study, the authors have observed that the parameters α1 and α2 influence the temperature profiles of the liquid region and the solid region. It is also found that the free boundary propagates faster when the authors increase the parameter α1 or decrease the parameter α2.

Originality/value
From the literature, it is seen that most of the two-phase problems with free boundary in an infinite domain are considered by the authors with constant thermophysical properties. Because it is possible to establish an analytical solution of two-phase problems with free boundary in case of an infinite domain. Moreover, a two-phase problem in a finite domain involving moving phase change material with the unidirectional speed is not considered. Therefore, the authors have considered a two-phase free boundary problem with variable thermal coefficients.
Decoding business analytics: discovering the hidden core through a novel taxonomy
Authors: Dinulescu Catalin C. , Alshare Khaled , Prybutok Victor 
Published: December 2024

PurposeThis study develops a comprehensive taxonomy of the business analytics (BA) discipline, uncovering its intellectual core and revealing its evolution over the past 12 years.Design/methodology/approachUsing stakeholder-driven identity formation theory, this study explores how organizational identity emerges through stakeholder negotiations. It investigates how top scholarly journals shape the BA discipline’s image and influence perceptions. High-quality articles from top journals listed by the Australian Business Deans Council are analyzed using latent Dirichlet allocation (LDA), a natural language processing and topic modeling method.FindingsThe study outlines key research areas identified as analytics methods, marketing, finance, operations and decision support analytics, along with 12 subareas. An analysis of the top 100 topics reveals prevalent research themes, showcasing the breadth of BA. A 12-year time-series review shows initial growth followed by maturation across most areas, except for decision support analytics, which maintained steady growth. These findings provide empirical evidence of BA’s development as a distinct discipline, highlighting its interdisciplinary nature and evolving research focus.Originality/valueThis study presents the first comprehensive, data-driven taxonomy of BA research, distilling the intellectual core into five key areas and 12 subareas, while identifying 100 supporting themes. It extends the stakeholders’ approach to identity development theory in the context of BA, providing empirical support for discussions on the field’s identity and diversity. The findings offer valuable insights for scholars, industries, managers and professionals, guiding curriculum development, research directions and practical applications of BA.
RegTech advancements-a comprehensive review of its evolution, challenges, and implications for financial regulation and compliance
Authors: El Khoury Rim , Alshater Muneer M. , Joshipura Mayank 
Published: December 2024

Purpose
This study aims to assess the current state and impact of the RegTech industry on financial regulation and compliance by providing a comprehensive overview of its evolution and identifying key challenges and opportunities.

Design/methodology/approach
A hybrid review approach was employed, involving a detailed bibliometric analysis of 89 scholarly articles and a content analysis of 47 key studies, covering the period from 2010 to 2023.

Findings
The research identifies critical trends and challenges within the RegTech industry, focusing on the roles of regulatory bodies and technological innovations. It explores four major themes: (1) RegTech applications in FinTech, financial services and banking regulations; (2) RegTech’s role in compliance management and fraud prevention; (3) the impact of digital transformation, governance and regulations; and (4) the integration of Big Data, AI, ML and blockchain in regulatory systems.

Practical implications
This study provides a comprehensive framework for understanding the complicated applications of RegTech, highlighting its potential to enhance compliance efficiency, mitigate risks and foster innovation within the financial sector. The insights provided are valuable for policymakers and financial institutions aiming to develop more robust regulatory frameworks and practices.

Originality/value
This study uniquely integrates bibliometric and content analysis to provide an up-to-date and nuanced overview of RegTech, focusing on recent advancements in AI, ML and blockchain technologies. It not only maps current trends but also identifies research gaps and offers new directions for future research.