bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring PBP2a resistance in MRSA by comparison between molecular covalent docking and non-covalent docking
Authors: Cao Ye-Qiang , Shi Yi-Feng
Published: February 2025

Background and objectives

The presence of penicillin-binding protein 2a (PBP2a) is the cause of Methicillin-resistantStaphylococcus aureus(MRSA), which is important nosocomial pathogens worldwide and now are also of growing importance in community-acquired infection. The PBP2a resistance depends upon a supplementary peptidoglycan transpeptidase, which continues to function when normal PBPs have been inactivated by beta-lactam antibiotics. Analysis and quantitative study of the molecular interactions of PBP2a against β-lactam antibiotics are required, as they support explaining and enhance understanding of the structure-activity relationship of antibiotic resistance.

Methods

Bioinformatics and computational methods have been highly effective tools for β-lactams targeting PBPs to tackle the urgent threat of antimicrobial resistance. Regarding β-lactam antibiotics targeting PBP2a and PBPs, we applied different docking programs to illustrate inhibition mode, MM/GBSA to estimate the binding free energies, and molecular dynamic simulation to validate and analyze the molecular interactions.

Results

Based on β-lactam antibiotics targeting PBPs as covalent inhibitors, covalent docking was employed to provide explicit models of PBP2a against susceptible β-lactam antibiotics. The simultaneous use of non-covalent docking enhances our comprehensive comprehension of the resistance of PBP 2a, which resulted from the lack of covalent linked to β-lactam antibiotics. The selected antibiotics strongly interact with PBP2a, revealing the essential amino acid residues and binding affinity for inhibition. MD simulations were performed for the ligand-bound state of PBP-2a to explain their interaction and conformational changes. These findings are also strongly supported by root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF) and Hydrogen bond analysis of the protein-ligand complex.

Conclusions

Our research offers extensive knowledge of the PBP2a-lactam interactions for the ability of known antibiotics to combat MRSA. The simulation results indicating stability and accuracy provide valuable insights for the advancement of pharmaceutical interventions against infectious diseases

Abstract Figure

Figure abstract:

The interaction of Methicillin with PBP2a of MRSA.

The protein is shown as a cartoon model, and the covalent binding of the ligand and serine active site is shown as a stick model.
Bilayer-forming lipids enhance archaeal monolayer membrane stability
Authors: Saracco M. , Schaeffer P. , Tourte M. , Albers S.-V. , Louis Y. , Peters J. , Demé B. , Fontanay S. , Oger P.
Published: February 2025

Archaeal membranes exhibit remarkable stability under extreme environmental conditions, a feature attributed to their unique lipid composition. While it is widely accepted that tetraether lipids confer structural integrity by forming monolayers, the role of bilayer-forming diether lipids in membrane stability remains unclear. Here, we demonstrate that the incorporation of diethers into archaeal-like lipid assemblies enhances membrane organization and adaptability under thermal stress. Using neutron diffraction, we show that membranes composed of mixed diethers and tetraethers exhibit greater structural order and stability compared to pure lipid systems. Contrary to expectations, monolayer-forming tetraethers alone display increased variability in lamellar spacing under fluctuating temperature and humidity, whereas mixed lipid membranes maintain a consistent architecture. Furthermore, neutron scattering length density profiles reveal an unexpected density feature at the bilayer midplane, challenging conventional models of archaeal monolayer organization. These findings suggest that molecular diversity of lipid molecules, rather than tetraether dominance, plays a critical role in membrane auto assembly, stability and adaptability. Our results provide new insights into archaeal membrane adaptation strategies, with implications for the development of bioinspired, robust synthetic membranes for industrial and biomedical applications.
Summing the parts: Improving population estimates using a state-space multispecies production model
Authors: Regular Paul M. , Koen-Alonso Mariano , Morgan M. Joanne , Pepin Pierre , Rideout Rick M.
Published: February 2025

Carrying capacity is a fundamental concept in ecology that has inspired the development and application of a broad range of population models. In the context of fisheries science, production models have been employed globally to calculate carrying capacity and guide the sustainable use of fish populations. Production models have, however, been criticized for failing to account for species interactions and environmental effects. We aim to fill some of these gaps by introducing a novel state-space multispecies production model. We apply our extended model to commercially important demersal fish species off the east coast of Canada to assess its ability to reveal species interactions and the relative impacts of fishing and environmental effects. Our results indicate that accounting for species interactions increases the accuracy of biomass estimates for species within a community. The model also revealed strongly correlated process deviations, unrelated to fishing or density-dependent effects, which unexpectidly indicates that widespread collapses were primarily driven by a common environmental driver rather than fishing. Such inferences indicate that this may be a promising avenue for producing more holistic and accurate assessments for multiple species with relatively minimal data requirements (time-series of landings and fisheries-independent indices). Finally, this approach may serve as a stepping stone towards an ecosystem-based approach to fisheries management.
Influence of Hypoxia on a Biomaterial Model of the Bone Marrow Perivascular Niche
Authors: Thompson Gunnar B , Barnhouse Victoria R , Bierman Sydney K , Harley Brendan
Published: February 2025

Hematopoietic stem cell (HSC) fate is shaped by distinct microenvironments termed niches within the bone marrow. Quiescence, expansion, and differentiation are directly and indirectly regulated by complex combinations of cell secretomes, cell-cell interactions, mechanical signals, and metabolic factors including oxygen tension. The perivascular environment in the bone marrow has been implicated in guiding HSC fate. However, bone marrow presents an environment which is hypoxic (~1-4% O2) relative to traditional cell culture conditions, and the study of hypoxia in vitro is complicated by the speed with which normoxic conditions during HSC isolation induce differentiation. There is a unique opportunity to use engineered models of the bone marrow to investigate the impact of defined hypoxia on HSC fate. Here, we examine the coordinated impact of oxygen tension and the perivascular secretome upon murine hematopoietic stem and progenitor cells (HSPCs) in vitro. Our findings highlight the importance of mitigating oxygen shock during cell isolation in engineered marrow models. We report a shift toward the Lineage- phenotype with hypoxic culture, expansion of HSPCs in response to perivascular niche conditioned medium, and enhanced HSPC maintenance in a hydrogel model of bone marrow in hypoxic culture when oxygen shock is mitigated during isolation using cyclosporin A.
Targeting tGLI1, a novel mediator of tumor therapeutic resistance, using Ketoconazole sensitizes glioblastoma to CDK4/6 therapy and Chemoradiation
Authors: Yu Yang , Arrigo Austin , Chandra Ankush , Zhuang Chuling , Najjar Mariana K , Khan Munazza S , Zhu Dongqin , Dono Antonio , Strowd Roy E , Tandon Nitin , Zhu Jay-Jiguang , Hsu Sigmund H , Esquenazi Yoshua , Chan Michael , Lo Hui-Wen
Published: February 2025

Glioblastoma (GBM) remains the most aggressive primary brain tumor in adults, with no effective treatments. While cyclin-dependent kinase 4/6 inhibitors (CDK4/6is) show clinical promise in some cancers, they have not significantly improved survival in GBM patients. This lack of response is attributed to the treatment-resistant glioma stem cell (GSC) population. We previously identified truncated glioma-associated oncogene homolog 1 (tGLI1) as a novel transcription factor promoting GSCs; however, its role in CDK4/6i resistance has never been investigated in any cancer type. Here, we found positive correlations between tGLI1 and CDK4/6 therapeutic resistance in patient datasets and in vitro studies. Pharmacological inhibition of tGLI1 using FDA-approved ketoconazole (KCZ), a tGLI1-specific inhibitor, sensitized GBM and GSCs to CDK4/6is. KCZ+CDK4/6i combination therapy demonstrated synergistic anti-proliferative effects, significantly inhibiting GBM stemness and cell cycle progression while increasing apoptosis. The combination was more efficacious than monotherapies in two orthotopic GBM mouse models. tGLI1 promoted GBM resistance to radiation therapy and temozolomide, while KCZ potentiated effects of these treatments. Collectively, we report for the first time that tGLI1 is a novel mediator of GBM resistance to CDK4/6is, and KCZ sensitizes GBM to CDK4/6is, thereby supporting future clinical utility of novel KCZ+CDK4/6i combinatorial therapy for GBM patients.
Economical Method to Construct a Prism-based TIRF Setup on an Existing Confocal Microscope to Perform smFRET Experiments
Authors: Agarwala Pratibha , Sasmal Dibyendu K.
Published: February 2025

Total internal reflection fluorescence (TIRF) microscopy enables observation of complex bio-assemblies and macromolecular dynamics in high spatial-temporal resolution at single-molecule level in real-time. With TIRF illumination, fluorophores near a sample substrate are excited by an evanescent field, thereby circumventing the axial diffraction limit of light. Prism-based TIRF (p-TIRF) microscopes are comparatively easy to use. They may be readily adjusted to meet the requirements of a broad range of experimental applications, such as to examine of macromolecular complexes, to study of the behaviour of vesicles and small organelles, the study of protein-DNA complexes at the single-molecule level. These experiments can give unique insights into the mechanisms driving the molecular interactions that underline many fundamental activities within the cell by providing information on fluctuation distributions and unusual events. Here, we report a detailed method to build a p-TIRF setup inexpensively using an existing confocal microscope where the same light source can be used for both systems. Furthermore, we provide a brief overview that aims to give the readers a stepwise tutorial protocol for building, assembling, aligning, and preparing the specimen to conduct single-molecule fluorescence resonance energy transfer (smFRET) experiments using a custom-built p-TIRF setup. We believe that this article will be of assistance to labs that already have a confocal microscope and want to perform TIRF experiments for potential future applications.

Research Highlight

We report here a simple and cost-effective method to build a prism-based TIRF setup on a laser scanning confocal microscope. The setup is affordable, and users can use both confocal and TIRF modes in the same setup with the same light source and optical components.

Graphical Abstract
Forecasting protein evolution by integrating birth-death population models with structurally constrained substitution models
Authors: Ferreiro David , Gonzalez-Vazquez Luis Daniel , Prado-Comesana Ana , Arenas Miguel
Published: February 2025

Evolutionary studies in population genetics and ecology were mainly focused on predicting and understanding past evolutionary events. Recently, however, a growing trend explores the prediction of evolutionary trajectories toward the future promoted by its wide variety of applications. In this context, we introduce a forecasting protein evolution method that integrates birth-death population models with substitution models that consider selection on protein folding stability. In contrast to traditional population genetics methods that usually make the unrealistic assumption of simulating molecular evolution separately from the evolutionary history, the present method combines both processes to simultaneously model forward-in-time birth-death evolutionary trajectories and protein evolution under structurally constrained substitution models that outperformed traditional empirical substitution models. We implemented the method into a freely available computer framework. We evaluated the accuracy of the predictions with several monitored viral proteins of broad interest. Overall, the method showed acceptable errors in predicting the folding stability of the forecasted protein variants but, expectedly, the errors grew up in the prediction of the corresponding sequences. We conclude that forecasting protein evolution is feasible in certain evolutionary scenarios and provide suggestions to enhance its accuracy by improving the underlying models of evolution.
Prevalence of mental health illness in Nigeria: protocol for a systematic review and meta-analysis
Authors: Abubakar Aminu Kende , Yisa Mohammed Nakodi , Olukorode Sarah Oreoluwa , Musa Jolaade , Oyadiran Oluwafemi Temitayo , Okusanya Temitayo Rebecca , Ogunlade Samuel , Kuyebi Moshood Abiodun , Olofin Daniel , Omotayo Moshood Olanrewaju , Abioye Ajibola Ibraheem
Published: February 2025

Background

Mental health disorders pose a major public health challenge worldwide, with one in eight individuals affected, particularly by anxiety and depression. In Nigeria, mental health issues are similarly prevalent, yet access to mental healthcare remains limited. Recent policy initiatives have increased governmental interest, but mental health research in Nigeria remains limited and fragmented.

Methods

This protocol outlines a systematic review and meta-analysis methodology to quantify the prevalence of mental health disorders in Nigeria. The review follows the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) and Joanna Briggs Institute (JBI) guidelines and includes cross-sectional studies, surveys, and cohort studies providing prevalence data on mental disorders diagnosed by healthcare professionals or identified via validated screening tools in the country. Data sources include PubMed/Medline, EMBASE, and African Journals Online (AJOL), covering publications up to April 2024. Study selection, data extraction, and quality assessment will be conducted independently by multiple reviewers. A random-effects meta-analysis model will be used to synthesize data, with sensitivity and subgroup analyses to explore heterogeneity.

Discussion

This systematic review and meta-analysis provides an estimate of the prevalence of mental health disorders in Nigeria, informing future public health policy and resource allocation. These findings will contribute significantly to understanding mental health in Nigeria and support the development of effective strategies and policies.

Systematic review registration: This protocol is registered with PROSPERO (CRD42024559090).
Children with spinal muscular atrophy treated with disease-modifying therapies, do they attain neutral vertical head and trunk control?
Authors: Sakanaka Tania Emi , Butler Penelope , Kulshrestha Richa , Willis Tracey , Loram Ian
Published: February 2025

Aim: To investigate whether children with various spinal muscular atrophy (SMA) subtypes treated with disease-modifying therapies (DMT) obtain neutral vertical (NV) head and trunk control, and how this relates to motor function. Method: In this observational cross-sectional study, a convenience sample of 21 children diagnosed with SMA (6y1m (4y), 10 female) was tested with Segmental Assessment of Trunk Control (SATCo) and functional assessments. A linear mixed-effects model (LME) was used for statistical analysis. Results: SATCo scores were measurably different between condition (types of SMA), F=4.96, p<.05, and control type (static, active, and reactive control), F=6.40, p<.05. The interaction condition*control type was also significant, F=3.14, p<.05. No child with SMA1 demonstrated NV head control and there was no relationship between SATCo scores and motor function. Four children with SMA2 and SMA3 demonstrated NV head static control, and one demonstrated NV mid-thoracic static control. Interpretation: The results indicate that children with SMA treated with DMTs acquire very little or no unsupported NV head/trunk control. SATCo was shown to be sensitive to differences in trunk control in different types of SMA revealing potential as an outcome measure for therapeutic interventions or treatment effectiveness. Further studies are needed to clarify this potential.
The Net Clinical Benefit of Fondaparinux vs LMWH in Chinese Non-ST-Segment Elevation Acute Coronary Syndrome Patients: the REFOCAS Nonrandomized Controlled Trial
Authors: Li Dandan , Tuo Xiaodan , Yu Yani , Ma Genshan , Gao Chuanyu , Mao Wei , Qu Peng , Liu Limin , Shang Zhuo , Yin Xunli , Wang Guozhen , Liu Aifen , Chen Yundai
Published: February 2025

Background and aims

In Chinese patients with non-ST-segment elevation acute coronary syndrome (NSTE-ACS), it is essential to evaluate the net clinical benefit (NCB) of fondaparinux compared to low molecular weight heparin (LMWH) in NSTE-ACS patients with varying bleeding and ischemic risks.

Methods

This multicenter, prospective, open-label, real-world study enrolled 8066 adult patients undergoing non-emergency percutaneous coronary intervention (PCI) at 88 hospitals from July 2019 to July 2021. Patients received fondaparinux (2.5 mg/d) or LMWH (1 mg/kg, twice/day) were followed up within 6 months. The GRACE and CRUSADE scores were used to stratify the included patients. The primary outcome was the incidence of NCB event (all-cause death, reinfarction, nonfatal stroke, or BARC≥ type 2 bleeding) at 30 days.

Results

A total of 5430 patients received fondaparinux and 2636 received LMWH. The NCB outcome occurred in 136 patients (2.5%) receiving fondaparinux and in 110 patients (4.2%) receiving LMWH [HR=0.594 (95% CI: 0.462, 0.764), p<0.001]. The 30-day incidence of BARC≥2 bleeding was significantly lower in the fondaparinux group compared with the LMWH group [68 (1.3%) vs. 66 (2.5%), HR=0.498 (95% CI: 0.355, 0.699), p<0.001].Among patients with lower risk, defined by GRACE score≤140 and CRUSADE scores≤40, fondaparinux significantly reduced the incidence of MACE and BARC ≥ 2 bleeding. Fondaparinux decreased the risk of BARC≥2 bleeding across different risk groups, with absolute risk reductions (ARD) of -0.9% for CRUSADE score≤40, -3.0% for CRUSADE score>40, -1.2% for GRACE score≤140, and -1.7% for GRACE score>140, indicating a more pronounced protective effect in individuals at high bleeding risk.

Conclusions

In Chinese patients with NSTE-ACS, fondaparinux effectively diminished the incidence of the NCB event of 30 days compared with LMWH. Additionally, fondaparinux exhibited superior safety than LMWH in patients with high bleeding risk, consistently outperformed LMWH in terms of efficacy and safety in the low-risk group as well.
NOR1and Mitophagy: An Insight into Sertoli Cell Function Regulating Spermatogenesis
Authors: Pradhan Bhola Shankar , Das Deepyaman , Sarkar Hironmoy , Bhattacharya Indrashis , Majumdar Subeer S
Published: February 2025

The development and differentiation of germ cell (Gc) is supported by the Sertoli cel (Sc). We previously reported that a developmental switch in Sc around 12 days of age onwards in rats. During the process of differentiation of Sc, the differential expression of mitophagy-related genes and its role in male fertility is poorly understood. To address this gap, we evaluated the microarray dataset GSE48795 to identify 12 mitophagy-related hub genes -Egfr, Bcl2, Ccl2, Mmp2, Igf1, Fgf7, Apoe, Fos, Cxcl12, Ocln, Dcn,andSnca. We identifyNOR1as a potential mitophagy-related gene of interest due to its strong regulatory association with two hub genes Bcl2 and Fos. To determine the importance of our analysis of finding key mitophagy-related genes, we generated a transgenic rat model with Sc-specific knockdown ofNOR1during puberty. Adult male transgenic rats were found to be infertile due to impaired spermatogenesis, indicating a critical role forNOR1in Sc function. These findings suggest that mitophagy-related genes may play an important role in the differentiation of Sc and thereby, regulate male fertility.
Unveiling the Cellular and Molecular Mechanisms of Diabetic Retinopathy with Human Retinal Organoids
Authors: Polesovska Lada , Trmacova Simona , Celiker Canan , Hruba Eva , Gambin Francisco Molina , Matuskova Veronika , Beli Eleni , Barta Tomas
Published: February 2025

Diabetic retinopathy (DR) is a leading cause of vision impairment worldwide, driven by chronic hyperglycaemia and its complex metabolic consequences. While animal models have been widely used to study DR, they often fail to replicate the physiology of human retina. To address this limitation, we employed human retinal organoids as a model to study the effects of hyperglycaemia across various stages of retinal differentiation. Early-stage organoids demonstrated resilience to high glucose levels, maintaining normal morphology, viability, and gene expression. However, advanced-stage organoids displayed significant disruptions, including the downregulation of outer segment-specific genes, which impaired photoreceptor maturation, and a noticeable shortening of photoreceptor outer segments. Transcriptomic analysis revealed substantial changes in pathways related vision including G protein-coupled receptor signalling pathway, response to light stimulus, and visual perception. While photoreceptors were particularly vulnerable, other retinal cell types, including bipolar cells, ganglion cells, and Muller glia, showed greater resilience. Additionally, glial activation, evidenced by increased expression of astrocyte markers, suggested an adaptive response to hyperglycaemia. To validate our findings, we compared our dataset with publicly available transcriptomic datasets from human retinas with DR, confirming key overlaps in pathways related to photoreceptor dysfunction, gliogenesis, and oxidative stress responses. These results establish human retinal organoids as an effective and relevant model for studying the molecular mechanisms of neurodegeneration associated with DR progression.
Historic mine waste contains diverse microbial communities that reflect waste type and geochemistry
Authors: Best Mackenzie B. , Kazemi Motlagh Zohreh , McLemore Virginia T. , Jones Daniel S.
Published: February 2025

Waste rock and tailings left behind by historic mining operations can contain substantial critical mineral resources. However, over the decades and centuries since these deposits were emplaced, microbial communities developed that can catalyze rock weathering and elemental cycling, which could have impacted the economic resources but also might be harnessed for future biomining or other metal recovery efforts. Here we combined cell counting, rRNA gene and transcript sequencing, and whole rock geochemistry to compare the composition and abundance of microbial communities from five inactive mine sites in South-Central New Mexico that contain critical minerals. While acidic seeps and adits at the sites contained organisms commonly found in acid rock drainage and bioleaching operations, these organisms were only present at very low abundance in the waste rock and tailings, which were instead dominated by bacteria and archaea that mostly represent inorganic nitrogen- and organic carbon-oxidizing populations. Generally, rRNA transcript libraries contained many of the same organisms as rRNA gene libraries, indicating that most of these microbial populations are active. Differences among total and active communities correspond to waste rock geochemistry, including concentrations of sulfur, iron, and other variables such as copper, lead, and rare earth elements. Nevertheless, many of the rRNA gene and transcript sequences in these deposits were from groups without cultured representatives, and these unknown microorganisms are likely important for biogeochemical cycling over the long lifetime of these waste deposits. We also discuss recommendations for microbiological assessment of similar large historic mine waste deposits.

IMPORTANCE

New Mexico has a long history of mining, with hundreds of mining districts across the state, many of which contain inactive operations with historic tailings and waste rock. Because metallurgical processing was in its infancy when most of these mines were active, they contain substantial metal resources in tailings and waste rock that could be used to support domestic demand for critical minerals. We found that microbial communities associated with these deposits do not represent typical bioleaching communities, and instead are dominated by taxa not typically associated with mine wastes. However, the deposits do contain rare iron and sulfur-cycling taxa that could catalyze metal mobilization, as well as active populations of novel microorganisms that are likely important for biogeochemical cycling. These mine waste-associated microbial communities could represent important resources for bioremediation and other biotechnological applications to recover valuable elements from these and other historic mine waste deposits.
Physiologic recovery ofMycobacterium tuberculosisfrom drug injury: A molecular study of post antibiotic effect in mice
Authors: Hendrix Jo , Mubarak Reem Al , Bateman Adeline , Massoudi Lisa M. , Rossmassler Karen , Kaya Firat , Zimmerman Matthew D. , Wynn Elizabeth A. , Voskuil Martin I. , Robertson Gregory T. , Moore Camille M. , Walter Nicholas D.
Published: February 2025

Post-antibiotic effect (PAE) describes the delayed recovery of bacteria following antibiotic exposure. PAE is thought to underlie tuberculosis (TB) treatment forgiveness,i.e.the capacity of regimens to tolerate non-adherence. The basis of PAE inMycobacterium tuberculosis(Mtb) remains poorly understood, partly because PAE has conventionally been measured based on change inMtbburdenin vitrorather than change inMtbphysiologyin vivo. We investigatedMtbphysiologic recovery in the BALB/c mouse model following sub-curative 2- and 4-week durations of the standard isoniazid, rifampin, pyrazinamide, ethambutol (HRZE) treatment. Measurement of rRNA synthesis via the RS ratio® and the entire transcriptome via SEARCH-TB elucidated the dynamics of physiologic recovery.

Mtbburden did not increase over 28 days of drug-free post-treatment recovery, indicating prolonged PAEin vivo.The RS ratio indicated thatMtbribosomal RNA synthesis resumed within four days of treatment interruption. However, transcriptional changes indicative of metabolic reactivation were delayed for over two weeks. Processes critical for replication, including expression of genes involved in protein and cell wall synthesis, remained suppressed throughout 28 days post-treatment. Longer treatment induced more extensive physiologic perturbation and was associated with slower and less complete recovery.

Expression of processes that are typically induced by environmental stress (e.g., DosR regulon, universal stress proteins, and heat shock proteins) exhibited the reverse, decreasing during drug treatment and rising during recovery.

These findings provide a new basis for understanding PAE based on drug-induced injury and physiologic recovery. Following relatively short durations of HRZE, physiologic recovery ofMtbwas a slow, sequential and incomplete processin vivo.Our observation that longer treatment resulted in even slower recovery suggests thatMtbmay progressively lose capacity to recover. This work establishes a tractable experimental framework for quantifying the forgiveness of new TB treatment regimensin vivo.
Reorganization of motor functions within visuomotor networks subsequent to somatosensory cortical damage
Authors: Liu Yuqi , Halfen Elizabeth J. , Yau Jeffrey M. , Fischer-Baum Simon , Kohler Peter , Faseyitan Olufunsho , Coslett H. Branch , Medina Jared
Published: February 2025

Somatosensory inputs are critical to motor control. Animal studies have shown that primary somatosensory lesions cause sensorimotor deficits along with disrupted organization in primary motor cortex (M1). How does damage in primary somatosensory cortex (S1) influence motor networks in humans? Using fMRI, we examined two individuals with extensive damage to left somatosensory cortex, but primarily intact motor cortex and preserved motor abilities. Given left S1 damage, tactile detection and localization were impaired for the contralesional hand in both individuals. When moving the contralesional hand, LS, with near complete damage to the S1 hand area, showed increased activation in ipsilesional putamen and deactivation in contralesional cerebellum relative to age-matched controls. These findings demonstrate influences of S1 damage to subcortical sensorimotor areas that are distant from the lesion site, and a potential reweighting of the motor network with increased action selection in putamen and inhibition of sensory prediction in cerebellum in the face of sensory loss. In contrast, RF, who had a small island of spared S1 in the hand area, showed greater activation in contralesional S1 for movement versus rest. This same region was also activated by pure somatosensory stimulation in a second experiment, suggesting that the spared S1 area in RF still subserves sensorimotor processing. Finally, the right middle occipital gyrus was more strongly activated in both individuals compared with controls, suggesting a potential reliance on visual imagery in the face of degraded sensory feedback.
Beam-based identification of magnetic field errors in a synchrotron using deep Lie map networks
Authors: Caliari Conrad , Oeftiger Adrian , Boine-Frankenheim Oliver
Published: February 2025

We report on the recovery of both linear and nonlinear optics in a hadron synchrotron using the novel deep Lie map network (DLMN) approach. The DLMN enables the construction of a detailed accelerator model by integrating charged particle dynamics with machine learning methods within a data-driven framework. The primary observable is the centroid motion over a limited number of turns, captured by beam position monitors. The DLMN generates an updated description of the accelerator in terms of magnetic multipole components, which can be directly utilized in established accelerator physics tools and tracking codes for further analysis. In this study, the DLMN approach is employed to recover a linear optics model, including gradient errors, from a single measured trajectory. Nonlinear optics, including sextupole errors, are recovered using three measured trajectories. We assess the validity of these results by comparison with the linear optics from closed orbits algorithm and through estimates of resonance driving terms. Additionally, we illustrate an application of the deep Lie map network and the predicted synchrotron optics by comparing measured and simulated tune scans.

Published by the American Physical Society
2025
Net-proton fluctuations influenced by baryon stopping and quark deconfinement
Authors: Savchuk Oleh
Published: February 2025

Preliminary data from the Beam-Energy Scan II measurements by the STAR Collaboration at the Relativistic Heavy Ion Collider suggest a dip in the fourth-to-second-order cumulant ratio when plotted vs beam energy. At the same energy range where the structure appears, a transition from hadrons to quarks is expected, the deconfinement transition. In this paper, the role of quark deconfinement in establishing fluctuaitions in the early stages of the collision is considered. Two models are compared: one with stopping occurring on a baryon-by-baryon basis, and a second where stopping proceeds through quark degrees of freedom. In the latter model, the fluctuation of baryon number is significantly reduced and this signal is found to survive recombination into hadrons and the subsequent diffusion. The transformation from baryon to quark stopping thus produces a dip in the fourth-to-second-order cumulant ratio when plotted vs beam energy, consistent with observations.

Published by the American Physical Society
2025
Analysis of the data on differential cross sections and spin density matrix elements for
γp→ρ0p
Authors: Wang Ai-Chao , Wei Neng-Chang , Huang Fei
Published: February 2025

The newly published data on spin density matrix elements from the GlueX Collaboration, along with the previously released differential cross-section data from the CLAS Collaboration and the other two experiments for the γp→ρ0p reaction, are systematically investigated using an effective Lagrangian approach within the tree-level Born approximation. The model combines contributions from t-channel meson exchanges (π, η, and f2), s-channel nucleon (N) and nucleon resonance (N*) exchanges, u-channel N exchange, and a generalized contact term to construct the scattering amplitudes. Regge propagators are employed for t-channel amplitudes to incorporate the contributions from mesons with various spins lying on the same trajectories. The analysis shows that the background contributions, dominated by the f2-trajectory exchange, provide a satisfactory description of the data in the high-energy and forward-angle regions. The inclusion of specific nucleon resonances, such as N(2100)1/2+, N(2060)5/2−, or Δ(2000)5/2+, significantly improves the description of the differential cross-section data at near-perpendicular scattering angles in the low-energy region. Predictions of photon beam and target nucleon asymmetries are provided, offering valuable insights to discriminate reaction mechanisms when corresponding data become available in the future.

Published by the American Physical Society
2025
Magnetic Lyddane-Sachs-Teller Relation
Authors: Rindert Viktor , Darakchieva Vanya , Sarkar Tapati , Schubert Mathias
Published: February 2025

We describe a magnetic relation in analogy to the well-known dielectric Lyddane-Sachs-Teller relation [R. H. Lyddane , ]. This magnetic relation follows directly from the model equations for nuclear induction due to fast oscillating electromagnetic fields [F. Bloch, ] and relates the static permeability with the product over all ratios of antiresonance and resonance frequencies associated with all magnetic excitations within a given specimen. The magnetic relation differs significantly from its dielectric analog where the static properties are related to ratios of the squares of resonance frequencies. We demonstrate the validity of the magnetic Lyddane-Sachs-Teller relation using optical magnetization data from terahertz electron magnetic resonance spectroscopic ellipsometry measurements in the presence of an external magnetic field on an iron-doped semiconductor crystal of gallium nitride.

Published by the American Physical Society
2025
Synthesis and characterization of coumarin-derived sulfur analogues using Lawesson's reagent
Authors: Mama Neliswa , Schoeman Stiaan , Myburgh Lisa , Hosten Eric C.
Published: February 2025

The synthesis and characterization of six novel coumarin derivatives containing O and S atoms are described here, namely, ethyl 2-oxo-2H-chromene-3-carboxylate, C12H10O4 (S1a), ethyl 2-sulfanylidene-2H-chromene-3-carboxylate, C12H10O3S (S2a), ethyl 2-sulfanylidene-2H-chromene-3-carbothioate, C12H10O2S2 (S3a), ethyl 8-methoxy-2-oxo-2H-chromene-3-carboxylate, C13H12O5 (S1b), ethyl 8-methoxy-2-sulfanylidene-2H-chromene-3-carboxylate, C13H12O4S (S2b), and ethyl 8-methoxy-2-sulfanylidene-2H-chromene-3-carbothioate, C13H12O3S2 (S3b). Compounds S1a/b were synthesized in good yields following the Knoevenagel condensation method. The thiocarbonyl analogues of these compounds, S2a/b and S3a/b, were obtained using Lawesson's reagent as a thionating compound. The structures of S2a/b and S3a/b were confirmed using FT–IR, 1H and 13C NMR, and UV–Vis spectroscopy, and single-crystal X-ray diffraction. Hirshfeld surface and energy framework analyses show that stacked π–π ring interactions occur for all the structures obtained here, and various hydrogen-bond interactions link the stacks to form three-dimensional energy frameworks.
Unveiling how business process management capabilities foster dynamic decision-making for effectiveness of sustainable digital transformation
Authors: Huy Pham Quang , Phuc Vu Kien
Published: February 2025

Purpose

This research aims at investigating how business process management capabilities (BPMC) impact the effectiveness of sustainable digital transformation (ESDT). Furthermore, it delves into the mediation of dynamic decision-making (DDM) in the relationship between BPMC and ESDT.

Design/methodology/approach

This research employed the hypothetico-deductive technique. The statistical database was generated from sample of 712 respondents from small and medium companies (SMEs) in Vietnam, utilizing convenience and snowball sampling methods. The two-step process utilizing structural equation modeling, supported by SmartPLS version 4.1.0.9 and AMOS 28, was employed to assess the measurement model, while SmartPLS version 4.1.0.9 was used to evaluate the structural model.

Findings

The results of the analysis emphasize significant and positive correlations between the proposed constructs related to significance and effect size. The statistical results indicated that BPMC had a significant and beneficial effect on ESDT. This relationship was partially mediated by DMM.

Practical implications

The salient point emphasized that practitioners should prioritize enhancing focus on BPMC and DDM, as this would significantly facilitate more comprehensive solutions, enabling SMEs to achieve optimal success in sustainable digital transformation. Policymakers and government influencers are urged to concentrate on innovative attributes and ensure a conducive environment for the implementation of innovation by enacting regulations that promote the application of digital technology.

Originality/value

The findings of this study will broaden scholars’ understanding of the influence of BPMC on ESDT. The originality of the research is to provide research directions for advancing studies on the role of DDM in the context of sustainable digital transformation.
Prediction of surrounding rock grade for ultra-deep roadway engineering using BPNN combined with optimal algorithms
Authors: Yu Bingbing , Wang Guohao , Cheng Weixian , Wang Bo , Li Yi , Yang Zhen
Published: February 2025

Purpose

This paper attempts to combine the application of artificial intelligence in predicting and evaluating the classification of surrounding rock grades and provides guidance for subsequent support design and reinforcement support operations.

Design/methodology/approach

This paper discusses the use of BPNN as the primary tool, combined with three swarm bionic optimization algorithms (GA, PSO, GWO), to solve stability evaluation and grade prediction of surrounding rock in ultra-deep roadway excavation.

Findings

Taking the Great Wall ore group as the core and the Shanghaimiao mining area as the extension, the optimal model is applied to the classification of surrounding rock grade in ultra-deep roadway engineering. Prediction results show that the performance of BPNN models is excellent.

Research limitations/implications

Due to the limitations of geological conditions and construction environment in deep coal mines, the period of roadway excavation is too long, resulting in less data collection.

Practical implications

The prediction results can provide guidance for the excavation method, support scheme correction and reinforcement support scheme design of deep coal mine roadway engineering.

Social implications

It provides guidance for deep mining of coal mine (the premise of surrounding rock support stability), so as to ensure the economic and safety benefits of coal enterprises.

Originality/value

The neural network is applied to rock mechanics in a deep site for the first time, which is used to solve the prediction direction of surrounding rock grade evaluation. The index of the input layer is determined by combining the “three high and one disturbance” with the on-site construction situation, which is closer to the actual project. The swarm intelligent bionic algorithms are selected to optimize the hyperparameters of back propagation neural network, so as to improve the accuracy of the models. The classification and evaluation system of surrounding rock for the Great Wall ore group is constructed, which is the core of Shanghaimiao mining area in the northwest of China, guiding the dynamic adjustment of on-site excavation and support operations.
Resilience of Islamic and conventional equity markets in turbulent times
Authors: Jahromi Maria
Published: February 2025

Purpose

The purpose of this study is to examine the resilience of Islamic equities during crisis periods and in times of financial distress and how the industry composition and other characteristics of Islamic financial markets contribute to this resilience.

Design/methodology/approach

This study uses panel regressions, pooled regressions and EGARCH models to analyse the impact of various crisis periods and financial distress on the returns and the volatility of Islamic and conventional equities. The main sample covers 48 Islamic and conventional equity indices from 1996 to 2023.

Findings

Islamic equity indices are more stable than conventional equity indices during various financial crises and the COVID-19 pandemic. These findings also hold for continuous measures of financial distress and a global crisis index. Industry composition contributes substantially to the relative resilience of Islamic equities. Many performance differences reduce or disappear once controlling for industry. There are additional protective factors of Islamic equities including lower leverage and the exclusion of volatile assets.

Practical implications

The findings provide valuable insights for index construction, risk management and diversification strategies in times of financial instability. Diversification across Shari’ah-compliant firms and industries is beneficial.

Originality/value

This study provides a comprehensive analysis of resilience among Islamic equities in turbulent times, covering multiple binary and continuous measures of financial crises and financial distress. Importantly, it considers the role of industry composition and other factors in contributing to their resilience. These results have implications for index construction and for risk management and diversification strategies in turbulent times.
Impact of supplier trust and integrated technology on supply chain resilience for sustainable supply chain in FMCG sector
Authors: Rashid Aamir , Rasheed Rizwana , Rahi Samar , Amirah Noor Aina
Published: February 2025

Purpose

The Fast Moving Consumer Goods (FMCG) sector is a critical component of the global economy, providing consumers with a wide range of products that are consumed daily. However, this sector faces vulnerability during disruptions. Therefore, this research amid to examine the effect of supplier trust and integrated technology on supply chain resilience (SCR) for sustainable supply chains in the FMCG sector.

Design/methodology/approach

Data was collected from 409 respondents from the FMCG sector in the United States. The hypotheses were tested using Structural Equation Modeling through SmartPLS. The study findings found that all the direct and mediating hypotheses were supported.

Findings

The findings suggest that better supplier trust and the use of integrated technology enhance the capability of an organization to better respond to disruptions. It makes the supply chain more resilient. Further, SCR brings sustainable supply chains to the FMCG sector. Similarly, SCR is a significant mediator in the relationships between independent and dependent variables, highlighting the importance of resilient supply chains.

Originality/value

This research contributes to the literature on study variables and the Dynamic Capability View theory, as supplier trust integrated technologies are crucial factors in building resilient supply chains. This research has several managerial implications, including managers’ need to prioritize building trust with suppliers to facilitate increased information sharing. They should invest in integrated technologies to sense, forecast and be proactive in building SCR and, eventually, a sustainable supply chain.
Embracing digital business ecosystem: transforming traditional marketplaces
Authors: Almunawar Mohammad Nabil , Anshari Muhammad , Ordoñez De Pablos Patricia , Fauzi Anas Miftah
Published: February 2025

Purpose

This paper aims to devise a framework for mapping and designing business ecosystems and to demonstrate its effectiveness in crafting digital transformation for traditional marketplaces.

Design/methodology/approach

A digital business ecosystem framework is developed as a Value Exchange Network (VEN) to analyze both the existing marketplace business ecosystem and a prospective digital marketplace ecosystem. The transformation process is divided into four stages. The first stage begins with describing the case and mapping it onto the framework as a business ecosystem depicted in a Value Exchange Network Diagram (VEND). In the second stage, a future or new business ecosystem is designed and represented using VEND. The third stage involves developing guidelines for the digital transformation. Finally, the fourth stage focuses on creating a management tool to operate and expand the new digital business ecosystem.

Findings

Traditional marketplaces in Indonesia face significant threats from hypermarkets, supermarkets, minimarkets and the growing preference of the younger generation for digital marketplaces, especially after the COVID-19 pandemic. Our framework (VEN) offers a structured approach to support traditional marketplaces in undergoing digital transformation through four stages.

Research limitations/implications

This paper showcases the expressive power of our business ecosystem framework. The digital transformation of the traditional marketplace presented here serves as an example application of the framework. However, the framework has yet to be tested in a real-world digital transformation project.

Practical implications

This paper offers direction and guidelines for the digital transformation journey of traditional marketplaces using the VEN framework.

Originality/value

This paper uses an innovative framework for mapping, analyzing and constructing business ecosystems, presenting a four-stage method to outline the digital transformation of traditional marketplaces. The adoption of ecosystem thinking in the pursuit of digitally transforming conventional marketplaces is novel, offering a comprehensive approach to this transformation.
Financial literacy and investment in wine: a two-country study on Generations Y and Z
Authors: Agnoli Lara , Le Fur Eric , Outreville Jean-François
Published: February 2025

Purpose

Financial literacy is crucial in explaining a broader set of investment behaviors. This paper investigates what financial literacy, wine knowledge, risk propensity and wine purchase behavior have in common.

Design/methodology/approach

The analysis is on a questionnaire distributed online to an equal number of young adults from a traditional wine-producing and consuming country (France) and a country less linked to wine by tradition (the UK).

Findings

The analysis shows how financial literacy, financial education and financial risk attitudes impact the attitudes toward wine purchase decisions. Results indicate that participants prefer to drink wine for pleasure rather than for potential financial gain. Significant relationships exist between financial literacy, wine consumption frequency and willingness to store and pay for wine.

Originality/value

These results allow for a better understanding of wine purchasing behavior in light of willingness to pay, invest and store.

Highlights

(1)

Financial literacy has a positive role in influencing wine storage and investments.

(2)

Culture shapes the impact of financial literacy, habits and risk on wine investments.

(3)

Gender and age have a role in influencing wine investments.