bluuebunny/crossref_metadata_2025_split huggingface dataset:
Signaling pathway mechanisms of circadian clock gene Bmal1 regulating bone and cartilage metabolism: a review
Authors: Ze Yiting , Wu Yongyao , Tan Zhen , Li Rui , Li Rong , Gao Wenzhen , Zhao Qing 
Published: January 2025

Abstract
Circadian rhythm is ubiquitous in nature. Circadian clock genes such as Bmal1 and Clock form a multi-level transcription-translation feedback network, and regulate a variety of physiological and pathological processes, including bone and cartilage metabolism. Deletion of the core clock gene Bmal1 leads to pathological bone alterations, while the phenotypes are not consistent. Studies have shown that multiple signaling pathways are involved in the process of Bmal1 regulating bone and cartilage metabolism, but the exact regulatory mechanisms remain unclear. This paper reviews the signaling pathways by which Bmal1 regulates bone/cartilage metabolism, the upstream regulatory factors that control Bmal1, and the current Bmal1 knockout mouse models for research. We hope to provide new insights for the prevention and treatment of bone/cartilage diseases related to circadian rhythms.
PLIN1 suppresses glioma progression through regulating lipid metabolism
Authors: Luo Kui , Zhuang Kai , Wu Hao , Chen Yuanbing , Liu Yi , Yang Fan , Wang Zhifei 
Published: January 2025

Abstract
Glioma is a common and destructive brain tumor, which is highly heterogeneous with poor prognosis. Developing diagnostic and prognostic markers to identify and treat glioma early would significantly improve the therapeutic outcomes. Here, we conducted RNA next-generation sequencing with 33 glioma samples and 15 normal brain samples. We found Perilipin 1 (PLIN1) downregulated in glioma and correlated with poorer outcome. Subsequent experiments revealed that up regulation of PLIN1 led to repressed cell growth and invasion in glioma. Moreover, overexpression of PLIN1 increased lipid accumulation in glioma cells, with increasing expression of lipid biosynthesis related genes and decreasing expression of lipolysis related genes. Mechanically, we revealed that the PI3K/AKT axis could regulate PLIN1 levels in glioma, that inhibition of the activity of PI3K/AKT axis could increase PLIN1 levels in glioma. In conclusion, the dysregulation PI3K/AKT axis led to PLIN1 downregulation and the following tumor proliferation, invasion and lipid metabolism reprogramming in glioma.
NIRS-BIDS: Brain Imaging Data Structure Extended to Near-Infrared Spectroscopy
Authors: Luke Robert , Oostenveld Robert , Cockx Helena , Niso Guiomar , Shader Maureen J , Orihuela-Espina Felipe , Innes-Brown Hamish , Tucker Stephen , Boas David , Yücel Meryem A. , Gau Remi , Salo Taylor , Appelhoff Stefan , Markiewicz Christopher J. , McAlpine David ,   The BIDS Maintainers, Pollonini Luca 
Published: January 2025

Abstract
Functional near-infrared spectroscopy (fNIRS) is an increasingly popular neuroimaging technique that measures cortical hemodynamic activity in a non-invasive and portable fashion. Although the fNIRS community has been successful in disseminating open-source processing tools and a standard file format (SNIRF), reproducible research and sharing of fNIRS data amongst researchers has been hindered by a lack of standards and clarity over how study data should be organized and stored. This problem is not new in neuroimaging, and it became evident years ago with the proliferation of publicly available neuroimaging datasets. To solve this critical issue, the neuroimaging community created the Brain Imaging Data Structure (BIDS) that specifies standards for how datasets should be organized to facilitate sharing and reproducibility of science. Currently, BIDS supports dozens of neuroimaging modalities including MRI, EEG, MEG, PET, and many others. In this paper, we present the extension of BIDS for NIRS data alongside tools that may assist researchers in organizing existing and new data with the goal of promoting public disseminations of fNIRS datasets.
PCMMD: A Novel Dataset of Plasma Cells to Support the Diagnosis of Multiple Myeloma
Authors: L. B. Andrade Caio , Ferreira Marcos V. , M. Alencar Brenno , S. B. Filho Jorge L. , A. Guimaraes Matheus , Porto Cruz Moraes Iarley , S. Lopes Tiago J. , S. dos Santos Allan , M. dos Santos Mariane , C. S. e Silva Maria I. , D. R. P. Rosa Izabela M. , C. de Carvalho Gilson , M. Santos Herbert H. , L. Santos Márcia M. , Meyer Roberto , P. B. Knop Luciana M. , M. Freire Songeli , A. Rios Ricardo , N. Rios Tatiane 
Published: January 2025

Abstract
Multiple Myeloma (MM) is a cytogenetically heterogeneous clonal plasma cell proliferative disease whose diagnosis is supported by analyses on histological slides of bone marrow aspirate. In summary, experts use a labor-intensive methodology to compute the ratio between plasma cells and non-plasma cells. Therefore, the key aspect of the methodology is identifying these cells, which relies on the experts’ attention and experience. In this work, we present a valuable dataset comprising more than 5,000 plasma and non-plasma cells, labeled by experts, along with some patient diagnostics. We also share a Deep Neural Network model, as a benchmark, trained to identify and count plasma and non-plasma cells automatically. The contributions of this work are two-fold: (i) the labeled cells can be used to train new practitioners and support continuing medical education; and (ii) the design of new methods to identify such cells, improving the results presented by our benchmark. We emphasize that our work supports the diagnosis of MM in practical scenarios and paves new ways to advance the state-of-the-art.
Tailoring and characterization of bioactive graft material for alveolar bone preservation and regeneration in fresh extraction sockets of dog model
Authors: Hamdy Ayat , Saad Manal , ElBackly Rania , Nouh Samir , Jain Himanshu , Marei Mona 
Published: January 2025

Abstract
The objective of this study was to tailor an osteoinductive scaffold for alveolar bone regeneration and around immediately placed implants in extraction sockets of dogs. Tailored amorphous multiporous bioactive glass (TAMP -BG) was prepared and characterized for bioactivity and response of human alveolar bone marrow mesenchymal stem cells (hABMSCs). Extraction sockets of twenty-two male mongrel dogs received TAMP-BG in the right side around implant in the distal socket of the mandibular fourth premolar (P4), while the adjacent empty mesial socket of the same tooth was filled with the same graft. Autologous bone chips were used in the left side. Animals were euthanized at 1, 2, 4, 8 &12 weeks for histological and SEM analyses. SEM/EDX, FTIR and XRD analyses displayed formation of a bioactive hydroxycarbonated apatite layer. TAMP-BG significantly increased proliferation and migration of hABMSCs. Histologically, at the 1st week, advanced bone healing was shown in TAMP-BG group. At four weeks bone density was significantly higher forTAMP-BG (92.71% ± 1.71) versus control (62.92% ± 2.02) (P = 0.0001).At eight weeks, significant increase in width of buccal plate and height of lingual bony plate was observedfor TAMP-BG grafted implant.The socket orifice width significantly decreased for autologous bone from 1 to 12 weeks (P < 0.001), while it significantly increased for TAMP-BG (P = 0.03). We conclude that TAMP-BG can provide a preservative dynamic microenvironment following extraction up to three months which can be attributed to its unique physico-chemical characteristics.
Orbital angular momentum light interacted with double quantum dot-metal nanoparticle hybrid structure under spontaneous coherence
Authors: Abdulmahdi Mohanad Ahmed , Al-Khursan Amin Habbeb 
Published: January 2025

Abstract
This work studies the generation of the orbital angular momentum (OAM) beam in the double quantum dot-metal nanoparticle (DQD-MNP) system under the application of the OAM beam. First, an analytical model is derived to attain the relations of probe and generated fields as a distance function in the DQD-MNP system under OAM applied field and spontaneously generated coherence (SGC) components. The calculation here is of material property; it differs from others by calculating energy states of the DQDs and the computation of the transition momenta between quantum dot (QD)-QD and QD-wetting layer (WL) transitions. The orthogonalized plane wave (OPW) calculates QD-WL transitions and their momenta. The momentum calculation is essential to specify the Rabi frequency of the input field. Such characteristics are not used in earlier models. The results show that SGC is vital in increasing the generated field. The signal field generated in the DQD-MNP system doubles that from the DQD system alone. So, the DQD-MNP system is preferred to the DQD system. The generated field in the DQD-MNP for the strong coupling DQD-MNP system is higher than that for the weak coupling. Increasing the distance separating the DQD-MNP reduces the generated field. Higher OAM number reduce the generated field at a long distance in the device. The model is then extended to study the effect of incoherent pumping (
$$\:{R}_{inc}$$
) and the relations are modified to cover this part. The results show that
$$\:{R}_{inc}$$
reduces the generated field. While the results that compare the weak and strong coupling appear for the first, others compare well to the literature.
A novel uORF regulates folliculin to promote cell growth and lysosomal biogenesis during cardiac stress
Authors: Bencun Maja , Spreyer Laura , Boileau Etienne , Eschenbach Jessica , Frey Norbert , Dieterich Christoph , Völkers Mirko 
Published: January 2025

Abstract
Pathological cardiac remodeling is a maladaptive response that leads to changes in the size, structure, and function of the heart. These changes occur due to an acute or chronic stress on the heart and involve a complex interplay of hemodynamic, neurohormonal and molecular factors. As a critical regulator of cell growth, protein synthesis and autophagy mechanistic target of rapamycin complex 1 (mTORC1) is an important mediator of pathological cardiac remodeling. The tumor suppressor folliculin (FLCN) is part of the network regulating non-canonical mTORC1 activity. FLCN activates mTORC1 by functioning as a guanosine triphosphatase activating protein (GAP). Our work has identified a regulatory upstream open reading frame (uORF) localized in the 5′UTR of the FLCN mRNA. These small genetic elements are important regulators of protein expression. They are particularly important for the regulation of stress-responsive protein synthesis. We have studied the relevance of the FLCN uORF in the regulation of FLCN translation. We show that FLCN downregulation through the uORF is linked to cardiomyocyte growth and increased lysosomal activity. In summary, we have identified uORF-mediated control of RNA translation as another layer of regulation in the complex molecular network controlling cardiomyocyte hypertrophy.
Investigation of corrosion and water absorption of biomass natural coir fiber/hBN reinforced epoxy hybrid composites using different optimisation approaches
Authors: Kirubakaran Ramraji , Pitchumani Shenbaga Velu , Tom Sanju , Nagaraj R. Ashwin , Salin P. , Natchimuthu Harish Kumar , Gopalan Venkatachalam , Vinayagamurthy G. 
Published: January 2025

Abstract
Agricultural waste or agro-waste, including natural fibers and particles from various crop parts, is increasingly recognized as a significant contributor to environmental issues. However, from a circular economy perspective, these materials present an opportunity to be repurposed into new, eco-friendly products. The present study, specifically focuses on understanding the effect of different factors, such as the particulate loading and the size (coir and hBN − 1 to 5 wt%; Coir Powder size (100–200 μm) of the particles on composite’s corrosion rates and water absorption properties. These hybrid particulate composites (HPC) are fabricated using the hand layup process. The study uses a Box-Behnken Design (BBD-L15), a statistical experimental design tool that facilitates the effective investigation of many input parameters and their interactions, to comprehensively investigate these impacts. In addition, the study utilizes four metaheuristic algorithms—the Dragonfly Algorithm (DFO), the Salp Swarm Algorithm (SSA), Teaching Learning Optimization (TLO) and Particle Swarm Optimization (PSO)—alongside regression equations to predict the optimal characteristics of the composite material. To determine the best-performing algorithm, a comparison is made using Deng’s method. The findings indicate that the composite with a higher weight% of hBN particulates exhibits reduced water absorption and corrosion rates. A larger Deng’s Value often indicates better performance. Based on its higher Deng’s Value, the SSO algorithm outperforms other algorithms in minimizing both corrosion resistance (CR) and water absorption (WA). The Deng’s Value for SSO reached a maximum of 0.68, while the other algorithms show comparable but lower performance.
Post-processing methods for delay embedding and feature scaling of reservoir computers
Authors: Jaurigue Jonnel , Robertson Joshua , Hurtado Antonio , Jaurigue Lina , Lüdge Kathy 
Published: January 2025

Abstract
Reservoir computing is a machine learning method that is well-suited for complex time series prediction tasks. Both delay embedding and the projection of input data into a higher-dimensional space play important roles in enabling accurate predictions. We establish simple post-processing methods that train on past node states at uniformly or randomly-delayed timeshifts. These methods improve reservoir computer prediction performance through increased feature dimension and/or better delay embedding. Here we introduce the multi-random-timeshifting method that randomly recalls previous states of reservoir nodes. The use of multi-random-timeshifting allows for smaller reservoirs while maintaining large feature dimensions, is computationally cheap to optimise, and is our preferred post-processing method. For experimentalists, all our post-processing methods can be translated to readout data sampled from physical reservoirs, which we demonstrate using readout data from an experimentally-realised laser reservoir system.
Exposomics: a review of methodologies, applications, and future directions in molecular medicine
Authors: Wan Melissa , Simonin Elisabeth M , Johnson Mary Margaret , Zhang Xinyue , Lin Xiangping , Gao Peng , Patel Chirag J , Yousuf Aroub , Snyder Michael P , Hong Xiumei , Wang Xiaobin , Sampath Vanitha , Nadeau Kari C 
Published: January 2025

Abstract
The exposome is the measure of all the exposures of an individual in a lifetime and how those exposures relate to health. Exposomics is the emerging field of research to measure and study the totality of the exposome. Exposomics can assist with molecular medicine by furthering our understanding of how the exposome influences cellular and molecular processes such as gene expression, epigenetic modifications, metabolic pathways, and immune responses. These molecular alterations can aid as biomarkers for the diagnosis, disease prediction, early detection, and treatment and offering new avenues for personalized medicine. Advances in high throughput omics and other technologies as well as increased computational analytics is enabling comprehensive measurement and sophisticated analysis of the exposome to elucidate their cumulative and combined impacts on health, which can enable individuals, communities, and policymakers to create programs, policies, and protections that promote healthier environments and people. This review provides an overview of the potential role of exposomics in molecular medicine, covering its history, methodologies, current research and applications, and future directions.
Multi-spacecraft observations of the decay phase of solar energetic particle events
Authors: Hyndman R. A. , Dalla S. , Laitinen T. , Hutchinson A. , Cohen C. M. S. , Wimmer-Schweingruber R. F. 
Published: January 2025

Context. The parameters of solar energetic particle (SEP) event profiles such as the onset time and peak time have been researched extensively to obtain information on the acceleration and transport of SEPs. The corotation of particle-filled magnetic flux tubes with the Sun is generally thought to play a minor role in determining intensity profiles. However recent simulations have suggested that corotation affects the SEP decay phases and depends on the location of the observer with respect to the active region associated with the event.
Aims. We aim to determine whether signatures of corotation are present in observations of the decay phases of SEP events, and we study the dependence of the parameters of the decay phase on the properties of the flares and coronal mass ejections associated with the events.
Methods. We analysed multi-spacecraft observations of SEP intensity profiles from 11 events between 2020 and 2022 using data from Solar Orbiter, PSP, STEREO-A, and SOHO. We determined the decay-time constant, τ, in three energy channels; electrons ∼ 1 MeV, protons ∼ 25 MeV, and protons ∼ 60 MeV. We studied the dependence of τ on the longitudinal separation, Δϕ, between the source of the active region and the spacecraft magnetic footpoint on the Sun.
Results. Individual events show a tendency for the decay-time constant to decrease with increasing Δϕ. This agrees with test particle simulations. The magnitude of the event as measured through the intensity of the associated flare and SEP peak flux affects the measured τ values and likely is the cause of the observed large inter-event variability together with the varying solar wind and the conditions in the interplanetary magnetic field.
Conclusions. We conclude that corotation affects decay phase of an SEP event and should be included in future simulations and interpretations of these events.
The impact of interplanetary magnetic field intensity on the Martian ionosphere
Authors: Song Yihui , Li Yun , Lu Haoyu , Cao Jinbin , Li Shibang 
Published: January 2025

Context. The interplanetary magnetic field (IMF) is one of the important external drivers that controls the Martian-induced magnetosphere and ionosphere. Previous studies have shown that the ion escape process is highly influenced by both the direction and intensity of the IMF. The enhanced IMF may decrease the ion escape rate by inducing a stronger magnetosphere that protects the Martian ionosphere, but the mechanisms have not been investigated thoroughly. Further studies are needed to reveal the response of ionospheric heavy ions to IMF variation as well as the underlying physical mechanism.
Aims. This study aims to investigate the influence the IMF strength has on the Martian ionosphere. We adopted a multifluid magnetohydrodynamic model in this study, which can self-consistently simulate the interaction between solar wind and Mars. By comparing different cases, we analyzed the ionospheric structure on the dayside and near nightside as well as the ion transport process. We aim to obtain a deeper understanding of how the IMF intensity variation impacts the Martian ionosphere and the escape of planetary ions.
Methods. A three-dimensional multifluid MHD model was used to simulate the interaction between the upstream solar wind and Mars. Four major species in the Martian ionosphere, H+, O2+, O+, and CO2+, are considered in the model, with the chemical reactions and particle collisions included to calculate ion distribution and ion motions. We analyzed three cases where the IMF strength was set to 1 nT, 3 nT, and 5 nT.
Results. The enhancement of the IMF produces a stronger electromagnetic field in the Martian plasma environment. Both the electric field and magnetic field intensity increase, which provides a shielding effect to the Martian ionosphere, hindering the intrusion of solar wind particles. Thus, less planetary ions are produced by the chemical reactions between the solar wind and the Martian neutral particles, leading to shrinkage of the ionospheric upper boundary. As the IMF strength increases, both the day-to-night plasma transport and the ion outflow decreases. Thus, a more depleted nightside ionosphere is formed, and the tailward ion escape may be weakened, decreasing the global ion escape rate. Moreover, the strong crustal fields in the southern hemisphere enhance the electromagnetic field on the southern dayside, which withstand the penetration of solar wind plasma more effectively, resulting in asymmetry structures in the ionosphere.
Réseaux trophiques et socio-écologiques marins sous pression : étude du cumul d’impacts entre changements climatiques et développement de l’éolien en mer
Authors: Niquil Nathalie , Raoux Aurore , Thermes Maud , Fofack-Garcia Rhoda , Noguès Quentin 
Published: January 2025

À l’ère de l’anthropocène, l’un des plus grands défis de la modélisation trophique appliquée au milieu marin est sa capacité à coupler les multiples effets issus à la fois du changement climatique et des activités anthropiques locales, notamment le développement de l’éolien en mer. L’enjeu majeur est de réaliser des scénarios pour caractériser le cumul d’effets sur le fonctionnement de l’ensemble du système socio-écologique de ce milieu. Si la modélisation du cumul d’impacts sur les réseaux socio-écologiques est encore peu répandue dans le contexte de l’éolien en mer, les données rapportées dans la présente revue montrent que sa pertinence n’en est pas moins avérée pour l’établissement de plans de gestion adaptés. Deux approches de modélisation sont proposées : d’une part une modélisation mathématique quantitative qui permet de simuler l’effet de deux pressions simultanées sur les propriétés du réseau trophique, et d’autre part une modélisation qualitative qui présente l’avantage de reposer sur une démarche participative pour caractériser plus finement les boucles de rétroaction entre systèmes de gouvernance et écologique. Ces méthodes quantitatives et qualitatives de modélisation de scénarios basés sur des analyses de réseaux d’interactions ont été appliquées à la fois au futur parc éolien localisé en face de Courseulles-sur-Mer (Manche-Est) et au site éolien pilote de Groix-Belle-Ile (Atlantique). La perspective de recherche ouverte par ces études met l’accent, à partir du concept de Sato-Umi, sur les scénarios de modélisation qui croisent évolution des réseaux écosystèmes et augmentation de la capacité d’action collective.