bluuebunny/crossref_metadata_2025 huggingface dataset:
An anterior hypothalamic circuit gates stress vulnerability
Authors: Pennington Zachary T , LaBanca Alexa R , Abdel-Raheim Shereen D , Bacon Madeline E , Mahmoud Afra N , Sompolpong Patlapa , Baggetta Austin M , Zaki Yosif , Ko BumJin , Dong Zhe , Smith Alexander CW , Kenny Paul J , Cai Denise Jade
Published: October 2024

Prior adversity increases susceptibility to subsequent stressful events, but the causal underlying changes in brain circuitry are poorly understood. We harnessed unbiased whole-brain activity mapping to identify circuits that are functionally remodeled by prior adversity. This revealed that the anterior hypothalamic nucleus (AHN) displays heightened stress reactivity in previously stressed mice. This was accompanied by increased functional connectivity between the AHN and a threat-related limbic network. Using in vivo Miniscope imaging, we found that neuronal activity in the AHN encodes stressor valence. Moreover, stimulating AHN neurons enhanced, and inhibiting their activity mitigated, reactivity to stressful events. Lastly, silencing amygdala inputs to the AHN abolished the ability of prior adversity to increase stress sensitivity. These findings define a key role of the AHN in gating stress vulnerability by scaling valence signals from the amygdala.
Should I stay or should I go? Generalized marginal value theorem with temporal discounting
Authors: Zylberberg Joel
Published: October 2024

Consider a person in an environment containing patchy rewards. Under what circumstances should they stay in a given reward patch or leave that patch to seek out a new one? In a landmark 1976 study, Charnov derived the action policy that maximizes the expected rate at which this person gathers rewards. This result is called the Marginal Value Theorem (MVT), and decades of study have shown that humans’ and other animals’ behaviors qualitatively follow MVT, but with notable and systematic deviations. These deviations have been hypothesized to arise from the fact that MVT does not incorporate temporal discounting whereas humans and other animals tend to value current rewards more than future ones. Rigorously testing that hypothesis has been challenging because there is no mathematical theory that determines optimal patch foraging decision policies for agents who use temporal discounting. To fill this knowledge gap, I derived the optimal patch foraging policy for agents who exponentially discount future rewards and studied how that optimal policy depends upon their temporal discount rate, and upon the structure of their environment. Notably there are conditions under which the optimal policy with temporal discounting is to leaveearlierthan is predicted by MVT (under-staying), while under other conditions the optimal policy is to stay longer than is predicted by MVT (over-staying). The theory presented here delineates when each situation arises and may help to interpret the otherwise-puzzling ways in which human and animal behaviors deviate from MVT.
Mechanisms and purpose of lowered action potential firing threshold in fast-spiking interneurons in the human neocortex
Authors: Bakos Emoke , Tiszlavicz Ádám , Szegedi Viktor , Douida Abdennour , Furdan Szabina , Welter Daphne , Landry Jonathan , Bende Balazs , Hutoczki Gabor , Barzo Pal , Tamas Gabor , Benes Vladimir , Szucs Attila , Lamsa Karri
Published: October 2024

The mammalian brain exhibits various interspecies differences. Microanatomical and molecular differences in homologous neurons between species are best characterized in the neocortical mantle, but the purpose of these differences remains poorly understood. We performed whole-cell microelectrode recordings and microanatomical and molecular analyses of human fast-spiking parvalbumin (pvalb)-expressing interneurons in neocortical tissue resected during brain surgery. Fast-spiking interneurons exhibited a lower action potential (AP) firing threshold in humans than in mice. Compared with mouse neurons, human neurons displayed an elongated axon initial segment (AIS), and the human AIS was deficient in low-voltage activated inhibitory Kv1 potassium channels. Contrarily, Kv1 ion channels were prominent in mouse neurons. Computational fast-spiking interneuron model simulations revealed that human-type AIS lowers the AP threshold and shortens the time lag for AP generation. Thus, human AIS supports fast in–fast out electrical circuit function in human pvalb neurons, which have electrically slow membrane potential kinetics in somata.

Teaser

Fast-spiking neurons in the human neocortex have structural and molecular adaptations in the axon to shorten IN-OUT delay
A complete approach for circRNA therapeutics from purification to lyophilized delivery using novel ionizable lipids
Authors: Broset Esther , Lampaya Verónica , Larraga Ana , Navarro Víctor , López Alexandre , de Miguel Diego , Peña Álvaro , Martínez-Oliván Juan , Casabona Diego
Published: October 2024

Circular RNA (circRNA) has gained significant attention as a potential therapeutic tool due to its remarkable stability and resistance to degradation by exonucleases. However, scalable and efficient methods for purification and delivery remain critical challenges that must be addressed. In this study, we developed and evaluated an optimized affinity chromatography method using Oligo(dT) columns for the purification of circRNA, achieving high yield and purity comparing with high-performance liquid chromatography. Additionally, we investigated thein vivoefficacy of circRNA-Oligo(dT) encapsulated in lipid nanoparticles (LNPs) formulated with emerging STAAR ionizable lipids, including CP-LC-0867 and CP-LC-0729. Our results showed that LNPs formulated with CP-LC-0867 consistently produced higher protein expression compared to SM-102, with sustained luciferase activity observed over a 14-day period. Furthermore, we assessed the lyophilization potential of LNP-circRNA-Oligo(dT) using CP-LC-0729 to extend shelf life and eliminate the need for ultra-low temperature storage. Remarkably, the lyophilized LNPs exhibited no significant differences in protein expression compared to their non-lyophilized counterparts, demonstrating that lyophilization is a viable strategy for extending the storage and transport of circRNA therapies. These findings underscore the potential of optimized new ionizable lipids, improved purification strategies, and lyophilization techniques to enhance the scalability, stability, and practical application of circRNA therapies.
On reconstruction of cortical functional maps using subject-specific geometric and connectome eigenmodes
Authors: Olsen Anders S. , Mansour L. Sina , Pang James C. , Zalesky Andrew , Van De Ville Dimitri , Behjat Hamid
Published: October 2024

Understanding the interplay between human brain structure and function is crucial to discern neural dynamics. This study explores the relation between brain structure and macroscale functional activity using subject-specific structural connectome eigenmodes, complementing prior work that focused on group-level models and geometry. Leveraging data from the Human Connectome Project, we assess accuracy in reconstructing various functional MRI-based cortical maps using individualised eigenmodes, specifically, across a range of connectome construction parameters. Our results show only minor differences in performance between surface geometric eigenmodes, a local neighborhood graph, a highly smoothed null model, and individual and group-level connectomes at modest smoothing and density levels. Furthermore, our results suggest that spatially smooth eigenmodes best explain functional data. The absence of improvement of individual connectomes and surface geometry over smoothed null models calls for further methodological innovation to better quantify and understand the degree to which brain structure constrains brain function.
Coordinated conformational changes in the Tad pilus ATPase CpaF facilitate a rotary mechanism of catalysis
Authors: Yen Ian Y. , Whitfield Gregory B. , Rubinstein John L. , Burrows Lori L. , Brun Yves V. , Howell P. Lynne
Published: October 2024

The type IV pilus family uses PilT-like ATPases to rapidly assemble and disassemble pilin subunits. Among them, the tight adherence (Tad) pilus performs both functions using a single bifunctional ATPase, CpaF. How ATP catalysis by CpaF facilitates both assembly and disassembly of the Tad pilus remains unclear. Here, we determined electron cryo-microscopy structures of CpaF in three distinct conformations and nucleotide occupancies. Packing unit analyses revealed differences in nucleotide coordination in the active sites, as well as synchronized domain movements during the catalytic cycle. Alphafold3 modeling demonstrated that CpaF and other motors within the type IV filament superfamily use a similar binding interface to engage their respective platform proteins. From these data, we propose that CpaF employs a clockwise, rotary mechanism of catalysis, which couples chemical energy to mechanical force during the biogenesis of Tad pili, a process broadly applicable to other single motor systems.
Rapid adaptation and increased genetic parallelism in experimental metapopulations ofPseudomonas aeruginosa
Authors: Chakraborty Partha Pratim , Kassen Rees
Published: October 2024

Natural populations are often spatially structured, meaning they are best described as metapopulations composed of subpopulations connected by migration. We know little about how the topology of connections in metapopulations impacts adaptive evolution. Topologies that concentrate dispersing individuals through a central hub can accelerate adaptation above that of a well-mixed system in some models, however empirical support is lacking. We provide evidence to support this claim and show acceleration is accompanied by high rates of parallel evolution resulting from a reduced probability that rare beneficial mutations are stochastically lost. Our results suggest metapopulation topology can be a potent force driving evolutionary dynamics and patterns of genomic repeatability in structured landscapes such as those involving the spread of pathogens or invasive species.
Screening Envelope Genes Across Primate Genomes Reveals Evolution and Diversity Patterns of Endogenous Retroviruses
Authors: Chabukswar Saili , Grandi Nicole , Soddu Elena , Lin Liang-Tzung , Tramontano Enzo
Published: October 2024

Endogenous Retroviruses (ERVs) are integrated into the host DNA as result of ancient germ line infections, majorly by now extinct exogenous retroviruses. Accordingly, vertebrates’ genomes contain thousands of ERV copies, providing “fossil” records for the ancestral retroviral diversity and its evolution within the host. Like exogenous retroviruses, ERV proviral sequence consists ofgag, pro-pol, andenvgenes flanked by long terminal repeats (LTRs). In particular, the characterization ofenvgene changes over time allows both to understand ERVs evolutionary trajectory and to infer their potential role in host physiology, including their pathological involvement. Despite their potential impact on the host, a detailed characterization has been performed for few domesticatedenvgenes, while a comprehensive survey of their abundance and diversity among primates’ genomes is still lacking. The study primarily focused on ERVs’envthat are known to be present in hominoid species, given their well-characterized nature and availability in public databases. Hence using theseenvsequences, we reconstructed 32 Env sequences representing the prototypes of these ancestral proteins in Class I, Class II, and Class III HERVs. These reconstructed Envs were then used for similarity search, phylogenetic analysis, and examination of recombination events occurred within primates’ genomes that were applied to 55 primate species across theCatarrhiniandPlatyrrhiniparvorders. Through such comprehensive pipeline, we reconstituted a phylogenetic distribution of ERV based specifically on theenvgenes, showing that the ERVs have been prevalent and widely distributed across the primate lineage. We observed for the first time the presence of the HML (human mouse mammary tumor virus-like) group in thePlatyrrhiniparvorder, indicating initiation of spread of HML supergroup before the split between New World Monkeys (NWM) and Old World Monkeys (OWM) i.e. even before 40 mya. Importantly, we confirmed interclass and intra-classenvrecombination events confirming the phenomenon of “envsnatching” among primates’ ERVs. As a result, we demonstrate that tracing the diversity patterns of ERVs’envprovides relevant insights into the retroviral evolutionary history of ERVs inCatarrhiniandPlatyrrhiniparvorders. Overall, our findings reveal thatenvrecombination contributes to the diversification of ERVs, thereby broadening our comprehension of retroviral and primate evolution.
Mapping hippocampal-cerebellar functional connectivity across the adult lifespan
Authors: Apasamy Kavishini , Ramnani Narender , Hodgetts Carl J.
Published: October 2024

Although the hippocampus and cerebellum are traditionally considered to support distinct memory systems, evidence from nonhuman species indicates a close bidirectional relationship during learning and navigational behaviour, with the hippocampus projecting to – and receiving input from – several cerebellar regions. However, little is known about the nature and topography of hippocampal-cerebellar connectivity in the human brain. To address this gap, we applied seed-based functional connectivity analyses to resting-state fMRI data from 479 cognitively normal participants, aged 18–88 years. We identified significant functional correlations between the hippocampus and widespread areas of cerebellar cortex, particularly lobules HIV, HV, HVI, HVIIA (Crus I and II), HIX, and HX. Contrasting the left and right hippocampus, we found significant correlations with the contralateral Crus II. We also compared longitudinal subdivisions of the hippocampus, revealing that anterior hippocampus demonstrated stronger connectivity with right Crus II, whereas posterior hippocampus was strongly connected to vermal parts of lobule V. Finally, we found that functional correlations between several hippocampal seeds (left, right, and anterior) and lobules HVI and HV decreased significantly with age. These results provide novel insights into hippocampal-cerebellar functional organisation and the influence of ageing on this system. Further studies are required to establish the role of this connection in learning and memory, as well as its potential vulnerability to neurodegeneration.
Alzheimer’s Disease Patient Brain Extracts Induce Multiple Pathologies in Vascularized Neuroimmune Organoids for Disease Modeling and Drug Discovery
Authors: Ji Yanru , Chen Xiaoling , Joseph Meek Connor , McLean Jenna Lillie , Yang Yang , Yuan Chongli , Rochet Jean-Christophe , Liu Fei , Xu Ranjie
Published: October 2024

Alzheimer’s Disease (AD) is the most common cause of dementia afflicting 55 million individuals worldwide, with limited treatment available. Current AD models mainly focus on familial AD (fAD), which is due to genetic mutations. However, models for studying sporadic AD (sAD), which represents over 95% of AD cases without specific genetic mutations, are severely limited. Moreover, the fundamental species differences between humans and animals might significantly contribute to clinical failures for AD therapeutics that have shown success in animal models, highlighting the urgency to develop more translational human models for studying AD, particularly sAD. In this study, we developed a complex human pluripotent stem cell (hPSC)-based vascularized neuroimmune organoid model, which contains multiple cell types affected in human AD brains, including human neurons, microglia, astrocytes, and blood vessels. Importantly, we demonstrated that brain extracts from individuals with sAD can effectively induce multiple AD pathologies in organoids four weeks post-exposure, including amyloid beta (Aβ) plaques-like aggregates, tau tangles-like aggregates, neuroinflammation, elevated microglial synaptic pruning, synapse/neuronal loss, and impaired neural network. Furthermore, after treatment with Lecanemab, an FDA-approved drug targeting Aβ, AD brain extract exposed organoids showed a significant reduction of amyloid burden. Thus, the neuroimmune organoid model provides a unique opportunity to study AD, particularly sAD under a pathophysiological relevant three-dimensional (3D) human cell environment. It also holds great promise to facilitate AD drug development, particularly for immunotherapies.
Light tunes a novel long-term threat avoidance behavior
Authors: Aranda Marcos L. , Min Eric , Liu Lucy T. , Schipma Anika E. , Schmidt Tiffany M.
Published: October 2024

Animals must constantly scan their environment for imminent threats to their safety. However, they must also integrate their past experiences across long timescales to assess the potential recurrence of new threats. Though visual inputs are critical for the detection of environmental danger, whether and how visual information shapes an animal’s assessment of whether a new threat is likely to reappear in a given context is unknown. Using a novel behavioral assessment of long-term threat avoidance behavior, we find that animals will avoid a familiar location where they previously experienced a single exposure to an innately threatening visual stimulus. This avoidance behavior is highly sensitive and lasts for multiple days. Intriguingly, we find that the melanopsin-expressing, intrinsically photosensitive retinal ganglion cells tune this behavior via a perihabenular-nucleus accumbens circuit distinct from the canonical visual threat detection circuits. These findings define a specific retinal cell type driving a new long-term threat avoidance behavior driven by prior visual experience.
Reductions ofGrin2ain adolescent dopamine neurons confers aberrant salience and related psychosis phenotype
Authors: Kielhold Michelle L. , Jacobs David S. , Torrado-Pacheco Alejandro , Lebowitz Joseph J. , Langdon Angela J. , Williams John T. , Zweifel Larry S. , Moghaddam Bita
Published: October 2024

Psychosis is a hallmark of schizophrenia. It typically emerges in late adolescence and is associated with dopamine abnormalities and aberrant salience. Most genes associated with schizophrenia risk involve ubiquitous targets that may not explain delayed emergence of dopaminergic disruptions. This includesGRIN2A,the gene encoding the GluN2A subunit of the NMDA receptor. Both common and rare variants ofGRIN2Aare considered genetic risk factors for schizophrenia diagnosis. We find thatGrin2aknockout in dopamine neurons during adolescence is sufficient to produce a behavioral phenotype that mirrors aspects of psychosis. These include disruptions in effort optimization, salience attribution, and ability to utilize feedback to guide behavior. We also find a selective effect of this manipulation on dopamine release during prediction error signaling. These data provide mechanistic insight into how variants ofGRIN2Amay lead to the latent presentation of aberrant salience and abnormalities in dopamine dynamics. This etiologically relevant model may aid future discovery of course altering treatments for schizophrenia.
CRISPR-enabled control of gene expression sets the isotopic composition of microbial methane
Authors: Gropp Jonathan , Bill Markus , Lloyd Max K. , Stein Rebekah , Nayak Dipti D. , Stolper Daniel A.
Published: October 2024

The stable isotopic composition of biogenic methane varies substantially in the environment and is routinely used to fingerprint its source. However, the underlying cause of this variation is debated. Here, we experimentally manipulate the growth rate of the model methanogen,Methanosarcina acetivorans, using CRISPR mutagenesis to generate a tunable version of the key and final enzyme in methanogenesis, methyl-coenzyme M reductase (MCR). We demonstrate that the carbon and hydrogen isotopic composition of methane change as a function of MCR expression and growth rate. Using an isotope enabled metabolic model we show that these changes stem from a substrate-independent increase in reversibility of methanogenic enzymes. Overall, these data provide a novel framework for calibrating growth coupled changes in the isotopic composition of biogenic methane.
Mu opioid receptor expression by nucleus accumbens inhibitory interneurons promotes affiliative social behavior
Authors: Toddes Carlee , Lefevre Emilia M. , Retzlaff Cassandra L. , Zugschwert Lauryn , Khan Sameer , Myhre Erin , Gauthier Elysia A. , Fernandez de Velasco Ezequiel Marron , Kieffer Brigitte L. , Rothwell Patrick E.
Published: October 2024

Mu opioid receptors in the nucleus accumbens regulate motivated behavior, including pursuit of natural rewards like social interaction as well as exogenous opioids. We used a suite of genetic and viral strategies to conditionally delete mu opioid receptor expression from all major neuron types in the nucleus accumbens. We pinpoint inhibitory interneurons as an essential site of mu opioid receptor expression for typical social behavior, independent from exogenous opioid sensitivity.
A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities
Authors: Eisfeldt Jesper , Ameur Adam , Lenner Felix , Ten Berk de Boer Esmee , Ek Marlene , Wincent Josephine , Vaz Raquel , Ottosson Jesper , Jonson Tord , Ivarsson Sofie , Thunström Sofia , Topa Alexandra , Stenberg Simon , Rohlin Anna , Sandestig Anna , Nordling Margareta , Palmebäck Pia , Burstedt Magnus , Nordin Frida , Stattin Eva-Lena , Sobol Maria , Baliakas Panagiotis , Bondeson Marie-Louise , Höijer Ida , Saether Kristine Bilgrav , Lovmar Lovisa , Ehrencrona Hans , Melin Malin , Feuk Lars , Lindstrand Anna
Published: October 2024

Clinical genetic laboratories often require a comprehensive analysis of chromosomal rearrangements/structural variants (SVs), from large events like translocations and inversions to supernumerary ring/marker chromosomes and small deletions or duplications. Understanding the complexity of these events and their clinical consequences requires pinpointing breakpoint junctions and resolving the derivative chromosome structure. This task often surpasses the capabilities of short-read sequencing technologies. In contrast, long-read sequencing techniques present a compelling alternative for clinical diagnostics. Here, Genomic Medicine Sweden—Rare Diseases has explored the utility of HiFi Revio long-read genome sequencing (lrGS) for digital karyotyping of SVs nationwide. The 16 samples from 13 families were collected from all Swedish healthcare regions. Prior investigations had identified 16 SVs, ranging from simple to complex rearrangements, including inversions, translocations, and copy number variants. We have established a national pipeline and a shared variant database for variant calling and filtering. Using lrGS, 14 of the 16 known SVs are detected. Of these, 13 are mapped at nucleotide resolution, and one complex rearrangement is only visible by read depth. Two Chromosome 21 rearrangements, one mosaic, remain undetected. Average read lengths are 8.3–18.8 kb with coverage exceeding 20× for all samples. De novo assembly results in a limited number of phased contigs per individual (N50 6–86 Mb), enabling direct characterization of the chromosomal rearrangements. In a national pilot study, we demonstrate the utility of HiFi Revio lrGS for analyzing chromosomal rearrangements. Based on our results, we propose a 5-year plan to expand lrGS use for rare disease diagnostics in Sweden.
Measurement of differential collisional excitation cross sections for the
Kα
emission of He-like oxygen
Authors: Grilo Filipe , Shah Chintan , Marques José , Santos José Paulo , Crespo López-Urrutia José R. , Amaro Pedro
Published: October 2024

We measure the energy-differential cross sections for collisional excitation of the soft x-ray electric-dipole Kα (x+y+w) emission from He-like oxygen (O ), using an electron beam ion trap. Values near their excitation thresholds were extracted from the observed emissivity by rapidly cycling the energy of the exciting electron beam. This allows us to subtract time-dependent contributions of the forbidden z-line emission to the multiplet. We develop a time-dependent collisional-radiative model to further demonstrate the method and predict all spectral features. We then compare the extracted x+y+w cross sections with calculations based on distorted-wave and R-matrix methods from the literature and our own predictions using the . All R-matrix results are validated by our measurements of direct and resonant excitation, supporting the use of such state-of-the-art codes for astrophysical and plasma physics diagnostics.

Published by the American Physical Society
2024
Toward UV models of kinetic mixing and portal matter. VI. A more complex dark matter sector?
Authors: Rizzo Thomas G.
Published: October 2024

Portal matter (PM), having both Standard Model (SM) and dark sector charges, can induce kinetic mixing between the U(1)D dark photon and the SM gauge fields at the 1-loop level offering an attractive mechanism by which light (≲1  GeV) thermal dark matter (DM) can interact with visible matter and obtain its observed relic density. In doing so, if the DM is fermionic, the CMB and other astrophysical observations inform us that it must be Majorana/pseudo-Dirac in nature to avoid velocity/temperature-independent s-wave annihilation to SM final states. How does this idea fit into a more UV-complete picture also including the SM interactions? There are some reasons to believe that at least a first step along this path may not lie too far away in energy due to the renormalization group equations running of the dark gauge coupling, which for a significant range of parameters, becomes nonperturbative at/before the ∼10’s of TeV energy range. This implies that U(1)D must become embedded in an asymptotically free, non-Abelian group, GD, before this can occur. The breaking of this larger group then produces the masses for the PM and the additional gauge fields associated with GD then can lead to new interactions between the SM and the dark sector. Following several bottom-up approaches, we have examined a set of distinctive and testable phenomenological features associated with this general setup, based upon a number of simplifying assumptions. Clearly, it behooves us to explore the impact of these specific assumptions on these predictions for the array of possible experimental tests of this class of models. In most past analyses it has been assumed that DM is a vectorlike, complex singlet under the group GD. If this assumption is relaxed, the dark sector must be augmented by additional fermion(s) and the associated scalar fields needed to break the gauge symmetries while generating the needed Majorana-like mass terms for the DM. In this paper, we analyze the simplest extension of this kind wherein the DM lies in a vectorlike doublet of GD, which we take to have the structure SU(2)I×U(1)YI as in earlier work, leading to new phenomenological implications. We find, for example, that given the current LHC search constraints on the masses of heavy gauge bosons, the production of these new dark states with large rates is unlikely to occur at colliders unless they are produced singly in gg fusion or their pair production cross sections are resonantly enhanced. We also find that an additional mechanism arises to generate hierarchal neutrino masses in such a setup.

Published by the American Physical Society
2024
Cosmic stability of dark matter from Pauli blocking
Authors: Batell Brian , Yin Wen
Published: October 2024

Why does dark matter (DM) live longer than the age of the Universe? Here we study a novel sub-eV scalar DM candidate whose stability is due to the Pauli exclusion of its fermionic decay products. We analyze the stability of the DM condensate against decays, scatterings (i.e., evaporation), and parametric resonance, delineating the viable parameter regions in which DM is cosmologically stable. In a minimal scenario in which the scalar DM decays to a pair of new exotic fermions, we find that scattering can populate an interacting thermal dark sector component to energies far above the DM mass. This self-interacting dark radiation may potentially alleviate the Hubble tensions. Furthermore, our scenario can be probed through precise measurements of the halo-mass function or the masses of dwarf spheroidal galaxies since scattering prevents the DM from becoming too dense. On the other hand, if the lightest neutrino stabilizes the DM, the cosmic neutrino background (CνB) can be significantly altered from the Lambda cold dark matter prediction and thus be probed in the future by CνB detection experiments.

Published by the American Physical Society
2024
Study of gluon GPDs in exclusive
J/ψ
production in electron-proton scattering
Authors: Goloskokov S. V. , Xie Ya-Ping , Chen Xurong
Published: October 2024

Exclusive photoproduction of heavy J/ψ meson is performed within the handbag factorization method. The general parton distributions (GPDs) for gluons, which are an essential ingredient here, are constructed using double distribution (DD) representation. The calculated cross section for few sets of gluon GPDs Hg describe fine J/ψ production experimental data from HERA to LHC energies. Based on this approach we estimate J/ψ spin asymmetries determined by Eg and H˜g. The GPDs factorization approach can be employed to analyze heavy vector meson production in electron-proton scattering. Investigations of this reactions at future electron-ion colliders in USA and China can give essential information on gluon GPDs.

Published by the American Physical Society
2024
Confinement in the Transverse Field Ising Model on the Heavy Hex Lattice
Authors: Tindall Joseph , Sels Dries
Published: October 2024

Inspired by a recent quantum computing experiment [Y. Kim , ], we study the emergence of confinement in the transverse field Ising model on a decorated hexagonal lattice. Using an infinite tensor network state optimized with belief propagation we show how a quench from a broken symmetry state leads to striking nonthermal behavior underpinned by persistent oscillations and saturation of the entanglement entropy. We explain this phenomenon by constructing a minimal model based on the confinement of elementary excitations. Our model is in excellent agreement with our numerical results. For quenches to larger values of the transverse field and/or from nonsymmetry broken states, our numerical results display the expected signatures of thermalization: a linear growth of entanglement entropy in time, propagation of correlations, and the saturation of observables to their thermal averages. These results provide a physical explanation for the unexpected classical simulability of the quantum dynamics.

Published by the American Physical Society
2024
The smearing function for a multi-slit very small angle neutron scattering instrument
Authors: Han Zehua , Ma Changli , Zhu Hong , Cui Tengfei , Zuo Taisen , Cheng He
Published: October 2024

Besides traditional pinhole geometry, the multi-slit very small angle neutron scattering instrument (MS-VSANS) at the China Spallation Neutron Source also utilizes a multi-slit collimation system to focus neutrons. Using the special focusing structures, the minimum scattering vector magnitude (q) can reach 0.00028 Å−1. The special structures also lead to a significantly different smearing function. By comparing the results of theoretical calculations with experimental data, we have validated the feasibility of a smearing method based on a mature theory for slit smearing. We use the weight-averaged intensity of neutron wavelength as a representative to evaluate the effect from a broad wavelength distribution, concentrating on the effect from the geometry of the multi-slit structures and the detector. The consistency of the theoretical calculation of the smearing function with experimental VSANS scattering profiles for a series of polystyrene standards of different diameters proves the feasibility of the smearing method. This marks the inaugural use of real experimental data from an instrument employing a multi-slit collimation system.
Integrating machine learning interatomic potentials with hybrid reverse Monte Carlo structure refinements in RMCProfile
Authors: Cuillier Paul , Tucker Matthew G. , Zhang Yuanpeng
Published: October 2024

Structure refinement with reverse Monte Carlo (RMC) is a powerful tool for interpreting experimental diffraction data. To ensure that the under-constrained RMC algorithm yields reasonable results, the hybrid RMC approach applies interatomic potentials to obtain solutions that are both physically sensible and in agreement with experiment. To expand the range of materials that can be studied with hybrid RMC, we have implemented a new interatomic potential constraint in RMCProfile that grants flexibility to apply potentials supported by the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular dynamics code. This includes machine learning interatomic potentials, which provide a pathway to applying hybrid RMC to materials without currently available interatomic potentials. To this end, we present a methodology to use RMC to train machine learning interatomic potentials for hybrid RMC applications.
Crystal structure of a bacterial photoactivated adenylate cyclase determined by serial femtosecond and serial synchrotron crystallography
Authors: Kapetanaki Sofia M. , Coquelle Nicolas , von Stetten David , Byrdin Martin , Rios-Santacruz Ronald , Bean Richard , Bielecki Johan , Boudjelida Mohamed , Fekete Zsuzsana , Grime Geoffrey W. , Han Huijong , Hatton Caitlin , Kantamneni Sravya , Kharitonov Konstantin , Kim Chan , Kloos Marco , Koua Faisal H. M. , de Diego Martinez Iñaki , Melo Diogo , Rane Lukas , Round Adam , Round Ekaterina , Sarma Abhisakh , Schubert Robin , Schulz Joachim , Sikorski Marcin , Vakili Mohammad , Valerio Joana , Vitas Jovana , de Wijn Raphael , Wrona Agnieszka , Zala Ninon , Pearson Arwen , Dörner Katerina , Schirò Giorgio , Garman Elspeth F. , Lukács András , Weik Martin
Published: October 2024

OaPAC is a recently discovered blue-light-using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata that uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report crystal structures of the enzyme in the absence of its natural substrate determined from room-temperature serial crystallography data collected at both an X-ray free-electron laser and a synchrotron, and we compare these structures with cryo-macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6W mutation in the BLUF domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side chain of the critical Gln48 residue. These studies pave the way for picosecond–millisecond time-resolved serial crystallography experiments at X-ray free-electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well studied picosecond–millisecond spectroscopic intermediates.
Supply chain resilience in the construction industry: a bibliometric review on operations management practices from Industry 4.0 to Industry 5.0
Authors: Bello Jummai Okikiola , Stephen Seyi , Adetoro Pelumi , Mogaji Iseoluwa Joanna
Published: October 2024

Purpose

The purpose of this research was to conduct a comprehensive bibliometric analysis to explore supply chain resilience and operations management practices in the construction industry, with a particular focus on the transition from Industry 4.0 to Industry 5.0. The study addressed a significant gap in the literature regarding the impact of these advanced technologies on the construction sector’s ability to anticipate, respond to and recover from disruptions.

Design/methodology/approach

The methodology employed a bibliometric analysis using the Scopus database to identify key trends, influential publications and emerging research areas using keywords such as “supply chain”, “operations management”, “Industry 4.0”, “Industry 5.0” and “construction”. This approach allowed for a quantitative evaluation of existing literature, offering insights into the intellectual structure of the field.

Findings

The findings revealed that while Industry 4.0 technologies, such as IoT and AI, have enhanced the construction industry’s supply chain visibility and efficiency, the shift towards the Industry 5.0 paradigm introduces a human-centric approach that further strengthens resilience through collaboration and sustainability.

Practical implications

The study’s practical implications suggest to both industry and academia that embracing Industry 5.0 principles could significantly enhance the construction industry’s resilience, enabling it to withstand disruptions better and maintain project quality, timelines, and budgets in an increasingly complex global environment.

Originality/value

This research examines the shift from Industry 4.0 to Industry 5.0 within construction supply chains, offering a novel perspective on integrating these technologies.
Can a zoom class be dialogic? An examination of a virtual English methods class
Authors: Reynolds Todd
Published: October 2024

Purpose

Synchronous virtual classes are becoming more common as universities expand access. However, instructors can feel hesitant as they move to a new style of teaching, especially if they are not sure their chosen pedagogy will work with virtual instruction. The purpose of this dialogic analysis is to examine the experiences of a dialogic teacher in a synchronous virtual English methods course.

Design/methodology/approach

The 75-min methods class met on Zoom twice a week. Class sessions were recorded. Dialogic analysis was used to analyze moments of whole-class discussion to explain what kinds of discussions happened and determine to what extent the class functioned as a dialogic class.

Findings

Overall, there was more student voice than teacher voice, and students spent over a third of the class in small group discussions. Even though the teacher still took over, and controlled discussions, the overall class maintained dialogic teaching principles. Despite this, the professor felt displaced for three reasons. In addition, some ideas for increasing the dialogic nature of the class are mentioned.

Originality/value

Synchronous virtual teaching will continue to grow, but as instructors move to that format, they can examine whether their pedagogies match the format. This paper explored one professor’s pedagogy of dialogic teaching and its compatibility with synchronous virtual teaching. This method of self-analysis could work with any pedagogy and could help instructors be successful in a new format.
Impact of biogas adoption on household energy use and livelihood improvement in Kenya: an overview on a roadmap toward sustainability
Authors: Kimutai Stephen Kibet , Kimutai Isaiah Kipkorir , Manirambona Egide
Published: October 2024

Purpose

This study assesses the impact of biogas adoption on household energy use and livelihood improvement. Also, this study aims to clarify the benefits of biogas adoption as a pathway to sustainable household energy.

Design/methodology/approach

The study explored the benefits of adopting biogas uptake. Fourteen sustainability indicators were identified, validated and categorized.

Findings

Adopting biogas technology provides numerous benefits, including better air quality, reduced deforestation and lower greenhouse gas emissions. Households can replace up to 4.5 tons of wood fuel, cutting CO2 emissions by around 6.75 tons annually. This shift saves approximately US$25 (Ksh.3223) monthly and frees up 45.5 h per week, enabling families to pursue additional income-generating activities. Biogas also produces digestate, a natural fertilizer that improves soil fertility, water retention and reduces erosion while minimizing the need for chemical fertilizers. Integrating biogas in livestock housing reduces odors, pathogens and methane emissions.

Research limitations/implications

The findings demonstrate numerous social, economic and environmental implications of biogas use.

Social implications

Health benefits include lower exposure to smoke and particulate matter, particularly benefiting women and children by reducing respiratory issues, improving lighting and enhancing educational opportunities. Biogas further improves hygiene, promotes cleanliness, strengthens energy security and alleviates energy poverty. In addition, the construction, operation and maintenance of biogas systems create jobs, and the use of digestate enhances agricultural productivity.

Originality/value

This study provides a unique and thorough analysis of the benefits of biogas, offering valuable insights and outlining a sustainable approach.
Two birds, one stone: minimum wage and child labor
Authors: Özmen Mustafa Utku , Turan Belgi
Published: October 2024

Purpose

This paper investigates the impact of quasi-exogenous and substantial increases in the minimum wage on child labor outcomes in Türkiye. The study aims to provide empirical evidence on how minimum wage policies affect child labor outcomes in a developing country context, with a focus on gender and age differences. It seeks to understand whether minimum wage increases lead to a reduction in child labor and whether the impact is different for various demographic groups.

Design/methodology/approach

The research employs a difference-in-differences methodology using data from the 2012 and 2019 Child Labor Force Survey in Türkiye. The treatment group consists of children from households with minimum wage earners, while the control group comprises children from other households. Various labor market outcomes are analyzed, and robustness checks are performed.

Findings

Our findings indicate that while the overall effect of minimum wage increases on child labor is statistically insignificant, there are notable heterogeneous impacts across different demographic groups and employment sectors. Specifically, we observe a significant reduction in the employment probability of girls under the age of 15 and unpaid family workers. Additionally, the likelihood of younger children being wage earners decreases, and the minimum wage increase reduces employment in the agriculture and services sectors for certain subgroups. The impact is also more limited for children in single-adult-worker households.

Social implications

These results underscore the varying effects of minimum wage policies on child labor and highlight the importance of considering demographic and sectoral differences in policy formulation. Policymakers should complement such policies with income-generating programs and targeted education initiatives to address child labor issues more comprehensively and sustainably.

Originality/value

This study fills a critical gap in the limited international literature on the causal effects of minimum wage policies on child labor incidence. One notable exception, Menon and van der Meulen Rodgers (2018) have explored the impact of minimum wage on child labor in India using regional variation, our study uniquely analyzes the effects at the household level in Türkiye. This approach provides valuable insights into how minimum wage changes affect child labor outcomes in a developing economy context with a high prevalence of minimum wage earners. It also contributes to the broader economic understanding of child labor and household income dynamics.
From struggle to strain: effects of financial distress on household vulnerability to poverty
Authors: Islam Khan , Chowdhury Murshed
Published: October 2024

Purpose

This study explores the impact of financial distress on household vulnerability to poverty in Canada. Previous studies primarily focus on assessing financial stress using one or two indicators, such as mortgage and non-mortgage debt. Moreover, there is limited discussion on the association between financial distress and poverty dynamics. Households that are currently non-poor may become poor in the next period and vice versa. Our objective is to explore the presence of financial stress, poverty dynamics and their associations in Canada.

Design/methodology/approach

We construct a Financial Distress Index utilizing five important financial indicators and employ Polychoric Principal Component Analysis (PPCA). Our index is rescaled to a bounded range of 0.1–1, where higher numbers reflect more financial stress. Additionally, we develop a vulnerability to poverty matrix based on households' socioeconomic characteristics. We employ both fractional probit and a dichotomous probit model to examine how financial distress and other factors could influence poverty dynamics in Canada.

Findings

Our quantitative analysis suggests that among Canadian households, higher financial distress raises the risk of falling into poverty or remaining below the poverty threshold in the future. A one-unit increase in financial distress corresponds to a 17% higher likelihood of vulnerability to poverty. Additionally, age, gender, education, family size, family type, employment, source of income, assets and type of assets are significant predictors of vulnerability to poverty in Canada. Interestingly, the relationship between education and vulnerability to poverty is not linear.

Originality/value

The literature examining the link between financial stress and poverty is scant for developed countries, and Canada is no exception. However, our study uniquely contributes to the literature by developing a Financial Distress Index and measuring its influence on poverty dynamics in Canada.

Peer review

The peer review history for this article is available at https://publons.com/publon/10.1108/IJSE-12-2023-0977.