bluuebunny/crossref_metadata_2025 huggingface dataset:
Haplotype editing with CRISPR/Cas9 as a therapeutic approach for dominant-negative missense mutations inNEFL
Authors: Dua Poorvi H. , Simon Bazilco M. J. , Marley Chiara B.E. , Feliciano Carissa M. , Watry Hannah L. , Steury Dylan , Abraham Abin , Gilbertson Erin N. , Ramey Grace D. , Capra John A. , Conklin Bruce R. , Judge Luke M.
Published: December 2024

Inactivation of disease alleles by allele-specific editing is a promising approach to treat dominant-negative genetic disorders, provided the causative gene is haplo-sufficient. We previously edited a dominantNEFLmissense mutation with inactivating frameshifts and rescued disease-relevant phenotypes in induced pluripotent stem cell (iPSC)-derived motor neurons. However, a multitude of differentNEFLmissense mutations cause disease. Here, we addressed this challenge by targeting common single-nucleotide polymorphisms in cis withNEFLdisease mutations for gene excision. We validated this haplotype editing approach for two different missense mutations and demonstrated its therapeutic potential in iPSC-motor neurons. Surprisingly, our analysis revealed that gene inversion, a frequent byproduct of excision editing, failed to reliably disrupt mutant allele expression. We deployed alternative strategies and novel molecular assays to increase therapeutic editing outcomes while maintaining specificity for the mutant allele. Finally, population genetics analysis demonstrated the power of haplotype editing to enable therapeutic development for the greatest number of patients. Our data serve as an important case study for many dominant genetic disorders amenable to this approach.
Genome-mining algorithm to identify identical repetitive sequences for sensitive and specific diagnostic assays for infectious diseases
Authors: Rajeswari Kalepu , Poojary Raksha , Padiwal Shruptha , Krishna Rajesh Muliyar , Satyamoorthy Kapaettu , Paul Bobby
Published: December 2024

Nucleic acid amplification-based approaches are extensively used as the first line of choice for infectious diseases. However, the success rates of DNA amplification or hybridization techniques are highly dependent on short primer or probe sequences. A pair of primers that can bind at multiple loci across the genome and randomly amplify multiple copies increases the analytical sensitivity of the currently used diagnostic assays. Herein, we developed a novel genome mining algorithm to identify short identical repeat sequences (IRSs) dispersed across the genome, which can amplify multiple nonhomologous regions of variable sizes via three potential priming combinations. Using this algorithm, we analysed the genomes of five pathogens, namely, gammaherpesvirus, vaccinia virus,Mycobacterium tuberculosis, Plasmodium falciparum, andPhytophthora palmivora, and identified short identical sequences that were repeated at multiple loci.In silicoPCR revealed that these identical repeat sequences can amplify multiple copies with different amplicon sizes in these five species. We further performed a polymerase chain reaction assay with short identical repeat pairs identified fromM. tuberculosis. Very interestingly, the amplification yielded multiple copies for individual IRSs and even more copies, as in a pair of IRSs. These results indicate that the IRS-based approach can detect pathogens during disease progression in the case of low-concentration DNA. The genome mining algorithm can be used as a translation technology platform for developing highly sensitive varieties of PCR, microarray, loop-mediated isothermal amplification, fluorescencein situhybridization, and DNA-DNA hybridization-based diagnostic assays.
Cancer Histone Mutations Impact Binding and DNA Repair Processes, Leading to Increased Mutagenesis
Authors: Espiritu Daniel , Sheng Yiru , Peng Yunhui , Ostroverkhova Daria , Li Shuxiang , Landsman David , Aristizabal Maria , Panchenko Anna R.
Published: December 2024

Histones are key epigenetic factors for regulating the accessibility and compaction of eukaryotic genomes, affecting the replication, repair, and expression of DNA. Recent studies have demonstrated that histone missense mutations can perturb normal histone function, promoting the development of phenotypically distinguishable cancers. However, most histone mutations observed in cancer patients remain enigmatic in their potential to promote cancer development. To assess the oncogenic potential of histone missense mutations, we have gathered whole-exome sequencing data for the tumors of over 12,000 patients. Overall, histone mutations occurred in about 16% of cancer patients, although specific cancer types showed substantially higher rates. Using a combination of genomic, structural, and biophysical analyses, we found several predominant modes of action, where cancer missense mutations in histones affected acidic patches and protein binding interfaces in a cancer-specific manner and targeted interaction sites with specific DNA repair proteins. Consistent with this finding, we observed a high tumour mutational burden in patients with histone mutations affecting interactions of DNA repair proteins. We also identified potential cancer driver mutations in several histone genes, including histone H4-a highly conserved histone without previously documented driver mutations.
Antimitotic chemotherapy promotes tumor NF-kB secretory phenotype and immunosuppressive CXCR2+ neutrophils chemotaxis in triple-negative breast cancers
Authors: Chocteau Florian , Gautier Fabien , Josso Vanessa , Douillard Elise , Juin Philippe , Barillé-Nion Sophie
Published: December 2024

Integrated approaches that help understand how tumors, as immune-surveilled ecosystems, respond to chemotherapy are crucial for developing effective antitumor treatments. We previously showed, in immunodeficient context, that antimitotic chemotherapy induced cGAS/STING pathway amplifying antitumor response through a paracrine IFN-1 secretome. We herein studied tumor progression and response to treatment using an immunocompetent murine model. scRNAseq analysis revealed that paclitaxel treatment altered tumor cell phenotypes, favoring tumor cells with a gene expression signature indicative of active NF-κB pathway with secretory phenotype. Treatment coincidently reduced IFN-I signature cells during tumor progression. The resulting secretory shift correlated with neutrophil recruitment to the tumor, particularly CXCR2+ neutrophils, thereby contributing to an immunosuppressive microenvironment. Pharmacological inhibition of CXCR2 receptor by navarixin reactivated antitumor immunity, enhancing NK cell infiltration and tumor cytotoxicity. Navarixin combination with paclitaxel significantly reduced tumor volume and metastasis. Targeting the NF-κB-driven secretory phenotype, in particular through neutrophil modulation, holds promise for improving TNBC treatment outcomes.
Sensory expectations shape neural population dynamics in motor circuits
Authors: Michaels Jonathan A. , Kashefi Mehrdad , Zheng Jack , Codol Olivier , Weiler Jeffrey , Kersten Rhonda , Gribble Paul L. , Diedrichsen Jörn , Pruszynski J. Andrew
Published: December 2024

The neural basis of movement preparation has been extensively studied during self-initiated actions where motor cortical activity during preparation shows a lawful relationship to the parameters of the subsequent action1,2. However, movements are regularly triggered and constantly corrected based on sensory inputs caused by disturbances to the body or environment. Since such disturbances are often predictable and since preparing for disturbances would make movements better, we hypothesized that expectations about sensory inputs also influence preparatory activity in motor circuits. Here we show that when humans and monkeys are probabilistically cued about the direction of a future mechanical perturbation, they incorporate sensory expectations into their movement preparation and improve their corrective responses. Using high-density neural recordings, we establish that sensory expectations are widespread across the brain, including the motor cortical areas involved in preparing self-initiated actions. The geometry of these preparatory signals in the neural population state is simple, scaling directly with the probability of each perturbation direction. After perturbation onset, a condition-independent perturbation signal shifts the neural state leading to rapid responses that initially reflect sensory expectations. Based on neural networks coupled to a biomechanical model of the arm3, we show that this neural geometry emerges through training, but only when the incoming sensory information indicating perturbation direction coincides with – or is preceded by – a condition-independent signal indicating that a perturbation has occurred. Thus, motor circuit dynamics are shaped by future sensory inputs, providing clear empirical support for the idea that movement is governed by the sophisticated manipulation of sensory feedback4.
Identification of neuron-glia signaling feedback in human schizophrenia using patient-derived, mix-and-match forebrain assembloids
Authors: Kim Eunjee , Kim Yunhee , Hong Soojung , Kim Inha , Lee Juhee , Lee Kwanghwan , An Myungmo , Kim Sung-Yon , Kim Sanguk , Shin Kunyoo
Published: December 2024

Although abnormal activities across multiple cell types are believed to contribute to the development of various neurodevelopmental disorders, current brain organoid technologies fall short in accurately modeling the dynamic cellular interactions in the human brain. Recently, we developed a cellular reconstitution technology to create human forebrain assembloids with enhanced cellular diversity, representing dynamic interactions between neurons and glial cells. Here, we created patient-derived, mix-and-match forebrain assembloids, in which neurons, astrocytes, and microglia from both healthy individuals and schizophrenia patients were reconstituted in a combinatorial manner, and identified aberrant cellular interactions between neurons and glial cells in human schizophrenia. At the early stage, schizophrenia forebrain assembloids showed premature neurogenesis induced by the abnormal proliferation and differentiation of neural progenitor cells. Integrated modular analysis of gene expression in post-mortem schizophrenia brain tissue and brain assembloids found increased expression of tumor protein p53 (TP53) and nuclear factor of activated T-cells 4 (NFATC4), which functioned as master transcriptional regulators to epigenetically reprogram the transcriptome involved in the cellular dynamics of neuronal progenitor cells, leading to premature neurogenesis. At the later stage, we observed weakened structures of laminar organization of the cortical layers in forebrain assembloids and identified the neuron-dependent transcriptional plasticity of glial cells and their altered signaling feedback with neurons, in which neuronal urocortin (UCN) and protein tyrosine phosphatase receptor type F (PTPRF) elicited the expression of Wnt family member 11 (WNT11) and thrombospondin 4 (THBS4) in astrocytes and microglia, respectively. These aberrant signaling axes altered the neuronal transcriptome associated with neuronal response to various stimuli and synthetic processes of biomolecules, resulting in reduced synapse connectivity. Thus, we elucidated developmental stage-specific, multifactorial mechanisms by which dynamic cellular interplay among neural progenitor cells, neurons, and glial cells contribute to the development of the human schizophrenia brain. Our study further demonstrated the potential and applicability of patient-derived forebrain assembloid technology to advance our understanding of the pathogenesis of various neurodevelopmental disorders.
The Role of Cytonemes and Diffusive Transport in the Establishment of Morphogen Gradients
Authors: Stotsky Jay , Othmer Hans G.
Published: December 2024

Spatial distributions of morphogens provide positional information in developing systems, but how the distributions are established and maintained remains an open problem. Transport by diffusion has been the traditional mechanism, but recent experimental work has shown that cells can also communicate by filopodia-like structures called cytonemes that make direct cell-to-cell contacts. Here we investigate the roles each may play individually in a complex tissue and how they can jointly establish a reliable spatial distribution of a morphogen. To this end, we formulate models that capture fundamental aspects of various cytoneme-based transport mechanisms. In simple cases, exact solutions are attainable, and in more complex cases, we discuss results of numerical simulations.
Fbxo42 promotes the degradation of Ataxin-2 granules to trigger terminal Xbp1 signaling
Authors: Santos Cristiana C , Schweizer Nadine , Cairrão Fátima , Ramirez Juanma , Osinalde Nerea , Yang Ming , Gaspar Catarina J , Rasheva Vanya I , Hensel Zach , Adrain Colin , Cordeiro Tiago N , Voigt Franka , Gameiro Paulo A , Mayor Ugo , Domingos Pedro M
Published: December 2024

The Unfolded Protein Response (UPR) is composed by homeostatic signaling pathways that are activated by the accumulation of misfolded proteins in the Endoplasmic Reticulum (ER), a condition known as ER stress. Prolonged ER stress and activation of the UPR causes cell death, by mechanisms that remain poorly understood. Here, we report that regulation of Ataxin-2 by Fbxo42 is a crucial step during UPR-induced cell death. From a genetic screen inDrosophila, we identified loss of function mutations inFbxo42that suppress cell death and retinal degeneration induced by the overexpression of Xbp1spliced, an important mediator of the UPR. We identified the RNA binding protein Ataxin-2 as a substrate of Fbxo42, which, as part of a Skp-A/Cullin-1 complex, promotes the ubiquitylation and degradation of Ataxin-2. Upon ER-stress, the mRNA of Xbp1 is not immediately translated but instead it is sequestered and stabilized in Ataxin-2 granules, until the Fbxo42 recruitment to these granules promotes the degradation of Ataxin-2, allowing the translation of Xbp1 mRNA at later stages of UPR activation. Our results identify Fbxo42-mediated degradation of Ataxin-2 as a key mechanism regulating the levels of Xbp1 mRNA and protein, to trigger cell death during the terminal stages of UPR activation.
Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics
Authors: Park Jonghan , Prokopchuk Galina , Popchock Andrew R. , Hao Jingzhou , Liao Ting-Wei , Yan Sophia , Hedman Dylan J. , Larson Joshua D. , Walther Brandon K. , Becker Nicole A. , Basu Aakash , Maher L. James , Wheeler Richard J. , Asbury Charles L. , Biggins Sue , Lukeš Julius , Ha Taekjip
Published: December 2024

Connections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence. Further, the model predicts intrinsic bending direction in 3D space. Using this tool, we aimed to probe mechanical selection - that is, the evolutionary selection of DNA sequence based on its mechanical properties - in diverse circumstances. First, we found that the intrinsic bend direction of DNA sequences correlated with the observed bending in known protein-DNA complex structures, suggesting that many proteins co-evolved with their DNA partners to capture DNA in its intrinsically preferred bent conformation. We then applied our model to large-scale yeast population genetics data and showed that centromere DNA element II, whose consensus sequence is unknown, leaving its sequence-specific role unclear, is under mechanical selection to increase the stability of inner-kinetochore structure and to facilitate centromeric histone recruitment. Finally,in silicoevolution under strong mechanical selection discovered hallucinated sequences with cyclizability values so extreme that they required experimental validation, yet, found in nature in the densely packed mitochondrial(mt) DNA ofNamystynia karyoxenos, an ocean-dwelling protist with extreme mitochondrial gene fragmentation. The need to transmit an extraordinarily large amount of mtDNA, estimated to be > 600 Mb, in combination with the absence of mtDNA compaction proteins may have pushed mechanical selection to the extreme. Similarly extreme DNA mechanics are observed in bird microchromosomes, although the functional consequence is not yet clear. The discovery of eccentric DNA mechanics in unrelated unicellular and multicellular eukaryotes suggests that we can predict extreme natural biology which can arise through strong selection. Our methods offer a way to study the biological functions of DNA mechanics in any genome and to engineer DNA sequences with desired mechanical properties.
In vivomultiplex imaging of dynamic neurochemical networks with designed far-red dopamine sensors
Authors: Zheng Yu , Cai Ruyi , Wang Kui , Zhang Junwei , Zhuo Yizhou , Dong Hui , Zhang Yuqi , Wang Yifan , Deng Fei , Ji En , Cui Yiwen , Fang Shilin , Zhang Xinxin , Zhang Kecheng , Wang Jinxu , Li Guochuan , Miao Xiaolei , Wang Zhenghua , Yang Yuqing , Li Shaochuang , Grimm Jonathan , Johnsson Kai , Schreiter Eric , Lavis Luke , Chen Zhixing , Mu Yu , Li Yulong
Published: December 2024

Neurochemical signals like dopamine (DA) play a crucial role in a variety of brain functions through intricate interactions with other neuromodulators and intracellular signaling pathways. However, studying these complex networks has been hindered by the challenge of detecting multiple neurochemicalsin vivosimultaneously. To overcome this limitation, we developed a single-protein chemigenetic DA sensor, HaloDA1.0, which combines a cpHaloTag-chemical dye approach with the G protein-coupled receptor activation-based (GRAB) strategy, providing high sensitivity for DA, sub-second response kinetics, and an extensive spectral range from far-red to near-infrared. When used together with existing green and red fluorescent neuromodulator sensors, Ca2+indicators, cAMP sensors, and optogenetic tools, HaloDA1.0 provides high versatility for multiplex imaging in cultured neurons, brain slices, and behaving animals, facilitating in-depth studies of dynamic neurochemical networks.
Introgression and divergence in a young species group
Authors: Satokangas I. , Martin SH. , Seifert B. , Puukko T. , Helanterä H. , Kulmuni J.
Published: December 2024

The process of speciation concerns often not only pairs of species but rather groups of diverging and interacting taxa, as highlighted by recent research. Hence, to understand the evolution of species’ diversity and their persistence, it is crucial to understand how gene flow and evolution of reproductive isolation shape groups of closely related species. Using resequencing data, we disentangle here genomic patterns of divergence and introgression in fiveFormica rufagroup wood ant species that are at the early stage of speciation. We first revise earlier mitochondrial phylogenies with a nuclear genomic tree, and demonstrate then introgression that is in line with observations of their current day natural hybridisation. Investigating the genome-wide differentiation and divergence we find correlations between population genetic parameters of divergence, differentiation, and diversity, that are in line with theoretical expectations for young species. Despite previously found evidence for polygenic species barriers, our data lacks the genome-wide correlation between differentiation and divergence that would be expected under a model of polygenic barriers. The likely explanation for this lack is the dominating effect of ancestral diversity at these early stages of speciation. As hybridisation has led to both deleterious and adaptive consequences within the group, we examined the signatures of introgression. We find no strong positive correlation between introgression and recombination, suggesting introgression does not have a predominantly deleterious effect. We also infer low diversity in the genomic regions with high proportions of introgression, consistent with the idea that selection has locally favoured introgression. This could be due to sharing of adaptive alleles or reduction of genetic load in the receiving species. Interestingly, gene flow in this group could potentially cross multiple species boundaries even in the absence of direct interbreeding between all the species. We discuss the long-term benefits and costs of introgression in young species, including the effect of environmental fluctuations and multi-species introgression.
Proteostasis Signatures in Human Diseases
Authors: Lim Christine M , Vendruscolo Michele
Published: December 2024

The protein homeostasis (proteostasis) system maintains the proteome in a healthy state. Although this system has been comprehensively mapped, its perturbations in disease remain incompletely characterised. To address this problem, here we define the proteostasis signatures, which represent the characteristic patterns of change in the proteostasis system associated with disease. We performed a large-scale, pandisease analysis across 32 human diseases spanning 7 disease types. We first identified unique proteostasis perturbations in specific disease states. We then uncovered distinctive signatures differentiating disease types, pointing to a range of proteostasis mechanisms in disease development. Next, we tracked the temporal evolution of proteostasis signatures, revealing shifts in proteostasis disruption over the course of disease progression. Finally, we demonstrated how smoking, a major risk factor of many diseases, impairs proteostasis in a manner similar to disease, potentially creating a predisposed environment for disease onset. These results illustrate the opportunities offered by the study of human diseases from the perspective of proteostasis signatures.
Tryptophan metabolite atlas uncovers organ, age, and sex-specific variations
Authors: Perez-Castro Lizbeth , Nawas Afshan F. , Kilgore Jessica A. , Garcia Roy , Lafita-Navarro M.Carmen , Acosta Paul H. , Nogueira Pedro A. S. , Williams Noelle S. , Conacci-Sorrell Maralice
Published: December 2024

Although tryptophan (Trp) is the largest and most structurally complex amino acid, it is the least abundant in the proteome. Its distinct indole ring and high carbon content enable it to generate various biologically active metabolites such as serotonin, kynurenine (Kyn), and indole-3-pyruvate (I3P). Dysregulation of Trp metabolism has been implicated in diseases ranging from depression to cancer. Investigating Trp and its metabolites in healthy tissues offers pathways to target disease-associated disruptions selectively, while preserving essential functions. In this study, we comprehensively mapped Trp metabolites across the Kyn, serotonin, and I3P pathways, as well as the microbiome-derived metabolite tryptamine, in C57BL/6 mice. Our comprehensive analysis covered 12 peripheral organs, the central nervous system, and serum in both male and female mice at three life stages: young (3 weeks), adult (54 weeks), and aged (74 weeks). We found significant tissue-, sex-, and age-specific variations in Trp metabolism, with notably higher levels of the oncometabolites I3P and Kyn in aging males. These findings emphasize the value of organ-specific analysis of Trp metabolism for understanding its role in disease progression and identifying targeted therapeutic opportunities.

AUTHOR SUMMARY

Trp metabolism has primarily been studied in cell lines, often leading to generalized assumptions about its role in health and disease. However, how Trp and its metabolites are allocated across tissues, sexes, and life stages has remained poorly understood. This gap is critical, as Trp is the largest amino acid, minimally used for protein synthesis, and largely metabolized in the liver, yet its distribution and metabolism in other tissues are unknown. Misconceptions, such as the idea that all cancers universally increase Kyn production, have contributed to therapeutic failures, highlighting the need for rigorous, tissue-specific studies. Our study systematically quantifies Trp metabolites across organs and tissues in vivo, revealing significant organ-, sex-, and age-specific variations. These findings provide a foundational resource for understanding Trp metabolism in normal physiology and disease, with potential applications in cancer, neurodegeneration, and other metabolic disorders.
Reconstructing superoscillations buried deeply in noise
Authors: White Derek D. , Zhang Shunxing , Šoda Barbara , Kempf Achim , Struppa Daniele C. , Jordan Andrew N. , Howell John C.
Published: December 2024

We utilize a method using frequency combs to construct waves that feature superoscillations—local regions of the wave that exhibit a change in phase that the bandlimits of the wave should not otherwise allow. This method has been shown to create superoscillating regions that mimic any analytic function—even ones well outside the bandlimits—to an arbitrary degree of accuracy. We experimentally demonstrate that these waves are extremely robust against noise, allowing for accurate reconstruction of a superoscillating target function thoroughly buried in noise. We additionally show that such a construction can be easily used to range-resolve a signal well below the commonly accepted fundamental limit.

Published by the American Physical Society
2024
Reentrant polar phase induced by the ferroionic coupling in
Bi1−xSmxFeO3
nanoparticles
Authors: Morozovska Anna N. , Eliseev Eugene A. , Fesych Igor V. , Zagorodniy Yuriy O. , Pylypchuk Oleksandr S. , Leonenko Evgenii V. , Rallev Maxim V. , Yaremkevych Andrii D. , Yurchenko Lesya P. , Demchenko Lesya , Kalinin Sergei V. , Fesenko Olena M.
Published: December 2024

Using the model of four sublattices, the Landau-Ginzburg-Devonshire-Kittel phenomenological approach and the Stephenson-Highland ionic adsorption model for the description of coupled polar and antipolar long-range orders in ferroics, we analytically calculated the phase diagrams and polar properties of Bi1−xSmxFeO3 nanoparticles covered by surface ions with dependence on their size, surface ions density, samarium content x, and temperature. The size effects and ferroionic coupling govern the appearance and stability conditions of the long-range ordered ferroelectric, reentrant ferrielectric, and antiferroelectric phases in Bi1−xSmxFeO3 nanoparticles. Calculated phase diagrams are in qualitative agreement with the x-ray diffraction phase analysis, electron paramagnetic resonance, infrared spectroscopy, and electrophysical measurements of Bi1−xSmxFeO3 nanopowders sintered by the solution combustion method. The combined theoretical-experimental approach allows us to explain the influence of the ferroionic coupling and size effects in Bi1−xSmxFeO3 nanoparticles on their polar properties.

Published by the American Physical Society
2024
Swarm coherence mechanism for jellyfish
Authors: Gengel Erik , Kuplik Zafrir , Angel Dror , Heifetz Eyal
Published: December 2024

We present a model of active Brownian particles for the process of jellyfish swarm formation. The motivation for our analysis is the phenomenon of jellyfish blooming in natural habitats and clustering of jellyfish in laboratory tanks which follow from an interplay of physical and behavioral mechanisms. We reach the conclusion that phase separation at low jellyfish density is induced by behavioral reactions to environmental conditions. Dense regions are then maintained by self-induced stimuli which result in a recruitment process. Our results agree with the biological fact that jellyfish exhibit an extreme sensitivity to stimuli in order to achieve favorable aggregations. Based on our model, we are able to provide a clear terminology for future experimental analysis of jellyfish swarming and we pinpoint potential limitations of tank experiments.

Published by the American Physical Society
2024
Quantum resources for assisted optimal state discrimination
Authors: Jiménez O. , Solís-Prosser M. A. , Delgado A. , Neves L.
Published: December 2024

We revisit the discussion of the quantum resources required to perform optimal unambiguous discrimination between two nonorthogonal quantum states when the protocol is assisted by an auxiliary system (ancilla). Initially, the formulation of the problem led to the assumption that entanglement between the main system and the ancilla was the key resource for the task. However, it was later shown that entanglement is not necessary at all, while quantum dissonance may or may not be required, depending on the relationship between the overlap and the probabilities of the inputs [Zhang, ]. Here, we show that, regardless of this relationship, coherence and purity are required resources for the task and thus more fundamental than dissonance. Coherence is analyzed based on its generalized resource theory, which allowed us to find the scenario that generates the maximal cryptographic randomness gain in the protocol. Purity, on the other hand, is shown to be greater than coherence when both measures are defined via the same distance, including the extreme cases of orthogonal and parallel states, where the latter is zero. Therefore, we conclude that purity is the most fundamental resource for assisted optimal state discrimination.

Published by the American Physical Society
2024
Causal influence versus signaling for interacting quantum channels
Authors: Barsse Kathleen , Perinotti Paolo , Tosini Alessandro , Vaglini Leonardo
Published: December 2024

A causal relation between quantum agents, say Alice and Bob, is necessarily mediated by an interaction. Modeling the latter as a reversible quantum channel, an intervention of Alice can have causal influence on Bob's system, modifying correlations between Alice and Bob's systems. Causal influence between quantum systems necessarily allows for signaling. Here we prove a mismatch between causal influence and signaling via direct computation of the two quantities for the Cnot gate. Finally we show a continuity theorem for causal effects of unitary channels: a channel has small causal influence if it allows for small signaling.

Published by the American Physical Society
2024
Existential unforgeability in quantum authentication from quantum physical unclonable functions based on random von Neumann measurement
Authors: Ghosh Soham , Galetsky Vladlen , Julià Farré Pol , Deppe Christian , Ferrara Roberto , Boche Holger
Published: December 2024

Physical unclonable functions (PUFs) leverage inherent, nonclonable physical randomness to generate unique input-output pairs, serving as secure fingerprints for cryptographic protocols like authentication. Quantum PUFs (QPUFs) extend this concept by using quantum states as input-output pairs, offering advantages over classical PUFs, such as challenge reusability via public channels and eliminating the need for trusted parties due to the no-cloning theorem. Recent work introduced a generalized mathematical framework for QPUFs. It was shown that random unitary QPUFs cannot achieve existential unforgeability against quantum polynomial time (QPT) adversaries. Security was possible only with additional uniform randomness. To avoid the cost of external randomness, we propose a novel measurement-based scheme. Here, the randomness naturally arises from quantum measurements. Additionally, we introduce a second model where the QPUF functions as a nonunitary quantum channel, which guarantees existential unforgeability. These are the first models in the literature to demonstrate a high level of provable security. Finally, we show that the quantum phase estimation (QPE) protocol, applied to a Haar random unitary, serves as an approximate implementation of the second type of QPUF by approximating a von Neumann measurement on the unitary's eigenbasis.

Published by the American Physical Society
2024
AlphaFold-guided molecular replacement for solving challenging crystal structures
Authors: Wang Wei , Gong Zhen , Hendrickson Wayne A.
Published: December 2024

Molecular replacement (MR) is highly effective for biomolecular crystal structure determination, increasingly so as the database of known structures has increased. For candidates without recognizable similarity to known structures, however, crystal structure analyses have nearly always required experiments for de novo phase evaluation. Now, with the unprecedented accuracy of AlphaFold predictions of protein structures from amino-acid sequences, an appreciable expansion of the reach of MR for proteins is realized. Here, we sought to automate an AlphaFold-guided MR procedure that tailors predictions to the MR problem at hand. We first optimized the reliability cutoff parameters for residue inclusion as tested in application to a previously MR-intractable problem. We then examined cases where AlphaFold by default predicts a conformation alternative to that of the candidate structure, devising tests for MR solution either from domain-specific predictions or from predictions based on diverse sequence subclusters. We tested subclustering procedures on an enzyme system that entails multiple MR-challenging conformations. The overall process as implemented in Phenix automatically surveys a succession of trials of increasing computational complexity until an MR solution is found or the options are exhausted. Validated MR solutions were found for 92% of one set of 158 challenging problems from the PDB and 93% of those from a second set of 215 challenges. Thus, many crystal structure analyses that previously required experimental phase evaluation can now be solved by AlphaFold-guided MR. In effect, this and related MR approaches are de novo phasing methods.
Perception of AI tool adoption and training: initial validation using GSEM method
Authors: Vázquez-Parra José Carlos , Henao-Rodríguez Carolina , Lis-Gutiérrez Jenny Paola , Palomino-Gámez Sergio , Suárez-Brito Paloma
Published: December 2024

Purpose

This study develops and validates the “Perception of the Adoption and Training in the Use of Artificial Intelligence Tools in the Profession” instrument, designed to measure Latin American university students' attitudes and perceptions regarding AI training in their professional education across diverse fields.

Design/methodology/approach

The instrument was administered to 238 students from various disciplines at a Mexican university. Structural validity and reliability were assessed using a generalized structural equation model (GSEM) with quasi-maximum likelihood (QML) to handle data non-normality and analyze latent construct relationships.

Findings

Results show high internal consistency and validity, with strong correlations between items and constructs of “attitude” and “perception of AI training value.” The study found significant relationships between understanding AI tools and the perceived value of AI training, as well as between this perception and attitudes toward incorporating AI in professional training.

Practical implications

The instrument helps institutions identify student attitudes and training needs related to AI, enabling tailored curricula and training programs that foster positive AI acceptance, thus preparing students for modern technological challenges.

Originality/value

This study offers a validated instrument tailored to the Latin American context, addressing a gap in measuring student perceptions of AI in professional training. It serves as a diagnostic tool for educators and policymakers in designing AI-integrated pedagogical strategies that align with student needs.
Digital leadership and its impact on agility, innovation and resilience: a qualitative study of the UAE media industry
Authors: Albannai Najla Abdullah Ahmed , Raziq Muhammad Mustafa , Malik Mehreen , Abrar Ayesha
Published: December 2024

Purpose

To explore the role of digital leadership in fostering strategic agility, innovation adaptivity, organizational agility and resilience in the context of digital transformation.

Design/methodology/approach

Following an interpretive case study approach and using a thematic data analysis technique, we conducted 20 in-depth interviews with digital leaders from five different media firms across the UAE.

Findings

The findings reveal that digital leaders are central to developing and executing digital strategies that enhance organizational agility and competitive edge, particularly in firms’ digital transformation. Digital leaders catalyze innovation and adaptability, ensuring the organization’s readiness for technological and market shifts. Moreover, digital leaders are instrumental in fostering an environment that promotes continuous learning, technological integration and a culture of change, which drives organizational agility and resilience.

Originality/value

The originality of this study lies in its focused examination of digital leadership within the UAE’s media sector, offering new insights into how digital leadership drives strategic agility, innovation adaptivity, organizational agility and resilience in a regionally specific digital transformation context. Our findings contribute to the broader academic and practical understanding of digital transformation in the media industry.
Promoting water accounting implementation processes: an argumentation-based Fuzzy-DEMATEL approach
Authors: Behzadian Fatah , Abdoli Mohammadreza
Published: December 2024

Purpose

This paper’s purpose is to contribute to the financial management knowledge literature by presenting the framework of water accounting factors and evaluation of its identified factors through an argumentation-based Fuzzy-DEMATEL approach.

Design/methodology/approach

This study adopted mixed, inductive and deductive approaches to develop a water accounting framework, validate its practicability and verify its effectiveness in selected firms listed on the Tehran Stock Exchange (TSE). In developing the framework and implementation procedure, the study employed an exploratory data collection (qualitative) approach to review the phenomenon of water accounting factors. Then, in this study’s second phase, Fuzzy-DEMATEL is used to evaluate the areas identified in the presented framework. In this study, Fuzzy-Delphi is also used to verify the reliability of the core components so that it is possible to generalize the factors to the Fuzzy-DEMATEL process.

Findings

The results obtained from the process of ground theory indicate the identification of 3 categories, 6 core components and 29 propositional themes, which are considered to constitute the framework of water accounting. Besides was determined in the quantitative phase that the optimal water consumption efficiency is considered the most effective component of implementing water accounting in capital market firms.

Originality/value

This research is one of the few studies in the field of water accounting framework and Fuzzy evaluation of its functions in the capital market. Because prior research has only described the importance of financial functions and sustainability in the form of a case study, this study seeks to achieve a framework for the implementation of water accounting. Also, through the evaluation of Fuzzy-DEMATEL, this study tries to develop the strategic functions of firms in managing water consumption. The originality of this study is, firstly, the identification of the driving fields of the water accounting, and secondly, the study follows the Fuzzy-Delphi and Fuzzy-DEMATEL of the factors identified in the TSE. Both implications raised in this section show the knowledge-enhancing and practical capacities of the study.
Marketing contracts and technical efficiency of citrus production
Authors: Zhang Hepei , Ma Wanglin
Published: December 2024

Purpose

This study examines the impacts of marketing contracts (written contracts, verbal contracts and no contracts) on technical efficiency, taking citrus production in Jiangxi Province, China, as an example.

Design/methodology/approach

We first use a stochastic production frontier (SPF) model to calculate the technical efficiency scores of citrus production at the individual level. Then, we use a multinomial endogenous switching regression (MESR) model, which mitigates selection bias issues arising from observed and unobserved factors, to estimate the treatment effects of marketing contract choices on technical efficiency. Data used in this study were collected from a survey of citrus farmers conducted between October and November 2022 in Jiangxi Province, China.

Findings

The SPF model estimates show that the mean technical efficiency score of citrus production is 0.616, ranging between 0.021 and 0.894. The MESR model estimates reveal that the technical efficiency scores for written and oral contract users are 18.3 and 10.5% higher, respectively, compared to citrus farmers with no marketing contracts. Additionally, the average technical efficiency score for written contract users exceeds that of oral contract users by 2.5%. We also find that farmers with higher household incomes and less farming experience were more likely to use written contracts. At the same time, those endowed with better education, larger farm sizes and better production conditions were more likely to use verbal contracts.

Originality/value

Farmers seeking marketing contracts for product sales need to adjust their production behaviour in advance to meet the product attributes required by market buyers. However, little is known about whether marketing contract users are more efficient in farm production than non-users. This study provides the first attempt to investigate the associations between different types of marketing contracts and technical efficiency.
Classification and fault diagnosis of power transformers with dissolved gas analysis using improved clustering methods
Authors: Kianimehr Nasser , Zeinoddini-Meymand Hamed , Shahnia Farhad
Published: December 2024

Purpose

Power transformers are vital components of an electrical network. A defective transformer can cause instability and blackouts in parts of the network. An accurate classification of different transformer faults results in a relatively accurate fault diagnosis and timely corrective actions. It is possible to increase productivity and reduce costs by using fault detection of power transformers through the analysis of gases dissolved in oil. The proposed technique is a suitable tool to help the utilities and engineers in charge of preventive maintenance by reducing the costs of different fault diagnosis tests for power transformers.

Design/methodology/approach

In this paper, the IEC 60599 standard along with clustering and classification methods are used to classify power transformer’s fault types. K-means and Fuzzy C-means clustering methods are used for clustering, and the support vector machine (SVM) method is used for classification of different types of faults in ‎power ‎transformers. The performance of K-means and SVM methods is improved by using the Grasshopper Optimization Algorithm (GOA). The efficiency of the proposed methods is evaluated using real field data of power transformers. The purpose of this study is to propose hybrid methods including K-means-GOA clustering and SVM-GOA classification for accurate fault diagnosis. These methods have been used for the first time in fault diagnosis determination of power transformers through gas analysis. The Silhouette criteria is used in this paper to compare the efficiency of different clustering methods.

Findings

Simulation results of the paper are based on the gas chromatography data related to 266 different real power transformers. They show the high accuracy and high-performance speed of intelligent clustering and classification methods compared to conventional ones. This analysis would be helpful in performing the required maintenance check and plan for repairs.

Originality/value

The applicability and efficiency of the proposed hybrid K-means-GOA and SVM-GOA models are verified for transformer fault detection using the experimental diverse data set including 266 set of real field test parameters of power transformers.
A reflection on governance, ethics and intellectual boundary enforcement in academic journals
Authors: Ozkazanc-Pan Banu
Published: December 2024

Purpose

This paper critiques practices related to governance, ethics and intellectual boundary enforcement in critically oriented academic journals in the aftermath of mass resignations from the leading feminist journal, Gender, Work & Organization. In doing so, the paper highlights problematic issues that undermine inclusive academic publishing in regard to non-White, non-Western and/or early-career academics. It calls upon scholars to address the lack of inclusion and transparency in these journals and offers suggestions to be undertaken by all academic editors to remedy the situation.

Design/methodology/approach

Based on the author’s experiences as joint editor-in-chief at Gender, Work & Organization, the paper offers a viewpoint of exclusion issues and problematic behaviors within academic publishing through a first-hand perspective and critical analysis of practices.

Findings

Three issues are found to impact inclusion in academic publishing. First, there is a lack of transparency in how editorships and board seats are allocated in many critically oriented academic journals. Alongside these governance issues, potential conflicts of interest related to prolific “cartel” or networked publishing among scholars create ethical challenges. Finally, boundary enforcement of intellectual contributions results in narrowly defined academic communities that replicate racialized exclusionary practices.

Originality/value

This paper is a reflexive praxis that calls out the need for academics to engage in good governance practices in journal management and foster ethical approaches in the publishing process. It also calls upon scholars and editors to reflect upon their practices in enforcing intellectual boundaries for the purpose of keeping particular ideas and people out of networks and consequently, out of academic communities.
Determining the antecedents of digital transformation and performance: the roles of social capital, open social innovation, absorptive capacity and government support
Authors: Tran Dien Van , Nguyen Phuong Van , Nguyen Sam Thi Ngoc , Huynh Thang Nam , Ma Khanh Van
Published: December 2024

Purpose

Open social innovation has become a critical practice for firms competing in volatile markets. Simultaneously, the rise of digital technologies has opened opportunities across sectors, making digital transformation a key driver of corporate change. This study examines the impact of internal and external factors, such as social capital, absorptive capacity and government support, in facilitating open social innovation and digital transformation activities, which may ultimately enhance business performance.

Design/methodology/approach

Data were collected through a questionnaire survey distributed to management members across various enterprises in a wide range of industries in Vietnam. A total of 289 valid responses were obtained, and the research hypotheses were tested using partial least squares structural equation modeling.

Findings

First, open social innovation positively influences digital transformation, with absorptive capacity mediating this relationship. Second, social capital directly affects open social innovation and indirectly impacts digital transformation through open social innovation. Third, digital transformation directly enhances business performance, while absorptive capacity indirectly influences business performance through digital transformation. Finally, government support directly impacts business performance and indirectly influences digital transformation via open social innovation.

Originality/value

By integrating social capital theory and the resource-based view, this research significantly advances the understanding of the complex relationships among government support, social capital, open social innovation, digital transformation, absorptive capacity and business performance.