bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined SPT and FCS methods reveal a mechanism of RNAP II oversampling in cell nuclei
Authors: Fournier Marie , Leclerc Pierre , Leray Aymeric , Champelovier Dorian , Agbazahou Florence , Dahmani Fatima , Bidaux Gabriel , Furlan Alessandro , Héliot Laurent 
Published: September 2023

AbstractGene expression orchestration is a key question in fundamental and applied research. Different models for transcription regulation were proposed, yet the dynamic regulation of RNA polymerase II (RNAP II) activity remains a matter of debate. To improve our knowledge of this topic, we investigated RNAP II motility in eukaryotic cells by combining single particle tracking (SPT) and fluorescence correlation spectroscopy (FCS) techniques, to take advantage of their different sensitivities in order to analyze together slow and fast molecular movements. Thanks to calibrated samples, we developed a benchmark for quantitative analysis of molecular dynamics, to eliminate the main potential instrumental biases. We applied this workflow to study the diffusion of RPB1, the catalytic subunit of RNAP II. By a cross-analysis of FCS and SPT, we could highlight different RPB1 motility states and identifyed a stationary state, a slow diffusion state, and two different modes of subdiffusion. Interestingly, our analysis also unveiled the oversampling by RPB1 of nuclear subdomains. Based on these data, we propose a novel model of spatio-temporal transcription regulation. Altogether, our results highlight the importance of combining microscopy approaches at different time scales to get a full insight into the real complexity of molecular kinetics in cells.
Impact of hand osteoarthritis in women on maximal forces in six different grasp types
Authors: Gracia-Ibáñez Verónica , Jarque-Bou Néstor J. , Bayarri-Porcar Vicente , Roda-Sales Alba , Granell Pablo , Vergara Margarita , Sancho-Bru Joaquín L. 
Published: September 2023

AbstractThis work aims to: (1) Provide maximal hand force data on six different grasp types for healthy subjects; (2) detect grasp types with maximal force significantly affected by hand osteoarthritis (HOA) in women; (3) look for predictors to detect HOA from the maximal forces using discriminant analyses. Thirty-three healthy subjects (37 ± 17 years, 17 women, 16 men) and 30 HOA patients (72 ± 9 years, all women) participated in the experiment. Participants were asked to exert their maximal force while performing six different grasp types 3 times. Two MANOVAs were conducted to detect if force depended on gender in healthy participants and if force significantly diminished in women with HOA. Finally, a linear discriminant analysis for detecting HOA was performed using forces of the grasp types that were significantly affected by HOA. Gender-disaggregated statistics are provided for healthy participants. Significant differences are obtained for all grasp types per gender. The women with HOA exerted significantly lower force values (p < 0.001) for all the grasp types than healthy ones. The discriminant analysis revealed that oblique grasp was the most significant one for detecting HOA. A discrimination equation was obtained with a specificity of 88.2% and a sensitivity of 83.3%. This work provides grip force data on six grasp types for healthy participants and for women with HOA. HOA women present reduced strength in all grasps due to pathology. Three of these grasps are a novelty. Oblique grasp strength may suffice to discriminate a patient with HOA, which might help non-invasive HOA detection.
Video action recognition collaborative learning with dynamics via PSO-ConvNet Transformer
Authors: Nguyen Huu Phong , Ribeiro Bernardete 
Published: September 2023

AbstractRecognizing human actions in video sequences, known as Human Action Recognition (HAR), is a challenging task in pattern recognition. While Convolutional Neural Networks (ConvNets) have shown remarkable success in image recognition, they are not always directly applicable to HAR, as temporal features are critical for accurate classification. In this paper, we propose a novel dynamic PSO-ConvNet model for learning actions in videos, building on our recent work in image recognition. Our approach leverages a framework where the weight vector of each neural network represents the position of a particle in phase space, and particles share their current weight vectors and gradient estimates of the Loss function. To extend our approach to video, we integrate ConvNets with state-of-the-art temporal methods such as Transformer and Recurrent Neural Networks. Our experimental results on the UCF-101 dataset demonstrate substantial improvements of up to 9% in accuracy, which confirms the effectiveness of our proposed method. In addition, we conducted experiments on larger and more variety of datasets including Kinetics-400 and HMDB-51 and obtained preference for Collaborative Learning in comparison with Non-Collaborative Learning (Individual Learning). Overall, our dynamic PSO-ConvNet model provides a promising direction for improving HAR by better capturing the spatio-temporal dynamics of human actions in videos. The code is available athttps://github.com/leonlha/Video-Action-Recognition-Collaborative-Learning-with-Dynamics-via-PSO-ConvNet-Transformer.
Identification of non-ischaemic fibrosis in male veteran endurance athletes, mechanisms and association with premature ventricular beats
Authors: Farooq Maryum , Brown Louise A. E. , Fitzpatrick Andrew , Broadbent David A. , Wahab Ali , Klassen Joel R. L. , Farley Jonathan , Saunderson Christopher E. D. , Das Arka , Craven Thomas , Dall’Armellina Erica , Levelt Eylem , Xue Hui , Kellman Peter , Greenwood John P. , Plein Sven , Swoboda Peter P. 
Published: September 2023

AbstractLeft ventricular fibrosis can be identified by late gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) in some veteran athletes. We aimed to investigate prevalence of ventricular fibrosis in veteran athletes and associations with cardiac arrhythmia. 50 asymptomatic male endurance athletes were recruited. They underwent CMR imaging including volumetric analysis, bright blood (BB) and dark blood (DB) LGE, motion corrected (MOCO) quantitative stress and rest perfusion and T1/T2/extracellular volume mapping. Athletes underwent 12-lead electrocardiogram (ECG) and 24-h ECG. Myocardial fibrosis was identified in 24/50 (48%) athletes. All fibrosis was mid-myocardial in the basal-lateral left ventricular wall. Blood pressure was reduced in athletes without fibrosis compared to controls, but not athletes with fibrosis. Fibrotic areas had longer T2 time (44 ± 4 vs. 40 ± 2 ms, p < 0.0001) and lower rest myocardial blood flow (MBF, 0.5 ± 0.1 vs. 0.6 ± 0.1 ml/g/min, p < 0.0001). On 24-h ECG, athletes with fibrosis had greater burden of premature ventricular beats (0.3 ± 0.6 vs. 0.05 ± 0.2%, p = 0.03), with higher prevalence of ventricular couplets and triplets (33 vs. 8%, p = 0.02). In veteran endurance athletes, myocardial fibrosis is common and associated with an increased burden of ventricular ectopy. Possible mechanisms include inflammation and blood pressure. Further studies are needed to establish whether fibrosis increases risk of malignant arrhythmic events.
68Ga-bisphosphonates for the imaging of extraosseous calcification by positron emission tomography
Authors: Keeling George P. , Baark Friedrich , Katsamenis Orestis L. , Xue Jing , Blower Philip J. , Bertazzo Sergio , T. M. de Rosales Rafael 
Published: September 2023

AbstractRadiolabelled bisphosphonates (BPs) and [18F]NaF (18F-fluoride) are the two types of radiotracers available to image calcium mineral (e.g. bone), yet only [18F]NaF has been widely explored for the non-invasive molecular imaging of extraosseous calcification (EC) using positron emission tomography (PET) imaging. These two radiotracers bind calcium mineral deposits via different mechanisms, with BPs chelating to calcium ions and thus being non-selective, and [18F]NaF being selective for hydroxyapatite (HAp) which is the main component of bone mineral. Considering that the composition of EC has been reported to include a diverse range of non-HAp calcium minerals, we hypothesised that BPs may be more sensitive for imaging EC due to their ability to bind to both HAp and non-HAp deposits. We report a comparison between the 68Ga-labelled BP tracer [68Ga]Ga-THP-Pam and [18F]NaF for PET imaging in a rat model of EC that develops macro- and microcalcifications in several organs. Macrocalcifications were identified using preclinical computed tomography (CT) and microcalcifications were identified using µCT-based 3D X-ray histology (XRH) on isolated organs ex vivo. The morphological and mineral analysis of individual calcified deposits was performed using scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX). PET imaging and ex vivo analysis results demonstrated that while both radiotracers behave similarly for bone imaging, the BP-based radiotracer [68Ga]Ga-THP-Pam was able to detect EC more sensitively in several organs in which the mineral composition departs from that of HAp. Our results strongly suggest that BP-based PET radiotracers such as [68Ga]Ga-THP-Pam may have a particular advantage for the sensitive imaging and early detection of EC by being able to detect a wider array of relevant calcium minerals in vivo than [18F]NaF, and should be evaluated clinically for this purpose.
Microplastics influence on herbicides removal and biosurfactants production by a Bacillus sp. strain active against Fusarium culmorum
Authors: Walaszczyk Aleksandra , Jasińska Anna , Bernat Przemysław , Płaza Grażyna , Paraszkiewicz Katarzyna 
Published: September 2023

AbstractThe amounts of anthropogenic pollutants, e.g., microplastics (MPs) and pesticides, in terrestrial and aquatic ecosystems have been increasing. The aim of this study was to assess the influence of MPs on the removal of herbicides (metolachlor, MET; 2,4-dichlorophenoxyacetic acid, 2,4-D) and the production of biosurfactants (surfactin and iturin) by Bacillus sp. Kol L6 active against Fusarium culmorum. The results showed that Kol L6 eliminated 40–55% MET and 2,4-D from liquid cultures, but this process was inhibited in the presence of MPs. Although the pollutants did not strongly limit the production of surfactin, iturin secretion was found to decrease by more than 70% in the presence of all three pollutants. Interestingly, the strongest modification in the profile of iturin homologues was calculated for the cultures containing MET + MP and 2,4-D + MET + MP. The bacteria significantly limited the growth of the phytopathogenic F. culmorum DSM1094F in the presence of individual pollutants and their two-component mixtures. However, in the presence of all three tested pollutants, the growth of the fungus was limited only partially (by no more than 40%). The presented results are a starting point for further research on bacteria-fungi-plants interactions in the soil environment in the presence of multiple pollutants.
SCH23390 and a humanized anti-cocaine mAb decrease the latency to cocaine-induced reinstatement of lever pressing behavior in rats that self-administer cocaine
Authors: Zinani Dakota B. , Desai Jhanvi N. , Norman Andrew B. 
Published: September 2023

AbstractIn rats that self-administer cocaine, the latency to the reinstatement of lever pressing behavior induced by a single dose of cocaine is due to the time taken for cocaine levels to fall to the satiety threshold. The D1 dopamine receptor antagonist SCH23390, and the recombinant humanized anti-cocaine mAb h2E2 increase the cocaine satiety threshold and would be expected to alter the latency to reinstatement. Male rats acquired cocaine self-administration behavior on an FR1 schedule. These rats received a single injection of cocaine (12 µmol/kg i.v.) after an i.v. injection of SCH23390 or an infusion of h2E2 or vehicle. The latency to, and the duration of, lever pressing was measured but the presses had no consequence. SCH23390 decreased the latency to lever pressing consistent with dose-dependent increases in satiety threshold. The duration of lever pressing behavior was inversely proportional to the SCH23390 dose suggesting that SCH23390 also increased the cocaine compulsion zone. The mAb h2E2 also produced a similar decrease in latency to responding that gradually reversed over 2 weeks. SCH23390 and h2E2 had an additive effect on the decreased latency to cocaine-induced lever pressing. The single cocaine dose reinstatement paradigm within the context of the compulsion zone theory is a useful pharmacological bioassay system to explore potential pharmacotherapies for relapse prevention in cocaine use disorder.
Assessing the impact of turbulent kinetic energy boundary conditions on turbulent flow simulations using computational fluid dynamics
Authors: Jung Eui Cheol , Lee Gyu-Han , Shim Eun Bo , Ha Hojin 
Published: September 2023

AbstractComputational fluid dynamics has been widely used to study hemodynamics, but accurately determining boundary conditions for turbulent blood flow remains challenging. This study aims to investigate the effect of patient-specific turbulence boundary conditions on the accuracy of turbulent flow simulation. Using a stenosis model with 50% severity in diameter, the post-stenosis turbulence flow region was simulated with different planes to obtain inlet boundary conditions and simulate downstream flows. The errors of simulated flow fields obtained with turbulence kinetic energy (TKE) boundary data and arbitrary turbulence intensity were compared. Additionally, the study tested various TKE data resolutions and noise levels to simulate experimental environments. The mean absolute error of velocity and TKE was investigated with various turbulence intensities and TKE mapping. While voxel size and signal-to-noise ratio of the TKE data affected the results, simulation with SNR > 5 and voxel size < 10% resulted in better accuracy than simulations with turbulence intensities. The simulation with appropriate TKE boundary data resulted in a more accurate velocity and turbulence field than those with arbitrary turbulence intensity boundary conditions. The study demonstrated the potential improvement of turbulent blood flow simulation with patient-specific turbulence boundary conditions, which can be obtained from recent measurement techniques.
OCT-based deep-learning models for the identification of retinal key signs
Authors: Leandro Inferrera , Lorenzo Borsatti , Aleksandar Miladinovic , Dario Marangoni , Rosa Giglio , Agostino Accardo , Daniele Tognetto 
Published: September 2023

AbstractA new system based on binary Deep Learning (DL) convolutional neural networks has been developed to recognize specific retinal abnormality signs on Optical Coherence Tomography (OCT) images useful for clinical practice. Images from the local hospital database were retrospectively selected from 2017 to 2022. Images were labeled by two retinal specialists and included central fovea cross-section OCTs. Nine models were developed using the Visual Geometry Group 16 architecture to distinguish healthy versus abnormal retinas and to identify eight different retinal abnormality signs. A total of 21,500 OCT images were screened, and 10,770 central fovea cross-section OCTs were included in the study. The system achieved high accuracy in identifying healthy retinas and specific pathological signs, ranging from 93 to 99%. Accurately detecting abnormal retinal signs from OCT images is crucial for patient care. This study aimed to identify specific signs related to retinal pathologies, aiding ophthalmologists in diagnosis. The high-accuracy system identified healthy retinas and pathological signs, making it a useful diagnostic aid. Labelled OCT images remain a challenge, but our approach reduces dataset creation time and shows DL models’ potential to improve ocular pathology diagnosis and clinical decision-making.
Anti-proliferative activity, molecular genetics, docking analysis, and computational calculations of uracil cellulosic aldehyde derivatives
Authors: Fahim Asmaa M. , Dacrory Sawsan , Elsayed Ghada H. 
Published: September 2023

AbstractIn this study, the oxidation of microcrystalline cellulose using NaIO4 to yield the corresponding cellulose aldehyde utilized microwave irradiation as a green tool, the obtained cellulosic aldehyde was confirmed through spectral analysis and it has an active site to react with the synthesized uracil acetamide to afford the corresponding arylidene cellulosic MDAU(4), the latter compound which can easily due to presence of active CH=group behind a cyano group react with nitrogen nucleophile’s and cyclized with hydrazine hydrate to give pyrazole cellulosic MDPA(5). The spectral analysis of the obtained cellulosic derivatives was confirmed with FT-IR, NMR, and SEM. Additionally, a neutral red uptake analysis has been used to investigate the cytotoxic activity of the cellulosic compounds MDAC(2), MDAU(4), and MDAP(5) against the cancer cells A549 and Caco2. After 48 h, Compound MDAU(4) had a stronger inhibitory effect on the growth of A549 and Caco2, compared to control cells. Then, using QRT-PCR, the expression levels of the genes β-Catenin, c-Myc, Cyclin D1, and MMP7 in A549 cells were examined. By reducing the expression levels of the Wnt signaling cascade genes (β-Catenin, c-Myc, Cyclin D1, and MMP7) when administered to A549 cells, compound MDAU(4) was shown in this investigation to be a viable candidate compared to lung cancer. Additionally, docking simulation was used to explore the uracil cellulosic heterocycles attached to different proteins, and computational investigations of these compounds looked at how well their physical characteristics matched the outcomes of their experiments.
Association of workplace bullying and burnout with nurses’ suicidal ideation in Bangladesh
Authors: Kabir Humayun , Chowdhury Saifur Rahman , Roy Anjan Kumar , Chowdhury Samiul Amin , Islam Md. Nazrul , Chomon Rifat Jahan , Akter Masuda , Hossain Ahmed 
Published: September 2023

AbstractSuicidal ideation is a complex phenomenon influenced by several predisposing, contextual, and mediating factors that seem more common among healthcare workers, especially nurses. We investigated the association of bullying and burnout with suicidal ideation among Bangladeshi nurses and identified the associated factors. We conducted a cross-sectional study among 1264 nurses in Bangladesh between February 2021 and July 2021. We applied a modified Poisson regression model with robust error variance to determine the association of bullying and burnout with suicidal ideation. Among 1264 nurses, the female was 882 (70.02%), and the mean age was 28.41 (SD = 5.54) years. The prevalence of high levels of suicidal ideation was 13.26%. In the Poison regression model, high risk bullying (RR = 6.22, 95% CI 3.13–12.38), targeted to bullying (RR = 7.61, 95% CI 3.53–16.38), and burnout (RR = 8.95, 95% CI 2.84–28.20) were found to be significantly associated with suicidal ideation. Furthermore, we found significant interaction between workplace bullying and burnout with suicidal ideation (p < 0.05). The high prevalence of bullying, burnout, suicidal ideation, and their association indicate an unsafe workplace for the nurses. Initiatives are needed to make a favorable work environment to improve nurses' overall mental health and reduce suicide ideation.
Tannic acid-mediated synthesis of flower-like mesoporous MnO2 nanostructures as T1–T2 dual-modal MRI contrast agents and dual-enzyme mimetic agents
Authors: Sorouri Farzaneh , Gholibegloo Elham , Mortezazadeh Tohid , Kiani Sahar , Foroumadi Alireza , Firoozpour Loghman , Khoobi Mehdi 
Published: September 2023

AbstractThis study introduces a simple method for preparing a new generation of MnO2 nanomaterials (MNMs) using tannic acid as a template. Two shapes of MnO2 NMs, flower-like M1-MnO2 and near-spherical M2-MnO2, were prepared and compared as dual-active nanozymes and contrast agents in magnetic resonance imaging (MRI). Various parameters, including the crystallinity, morphology, magnetic saturation (Ms), surface functionality, surface area, and porosity of the MNMs were investigated. Flower-like M1-MnO2 NMs were biocompatible and exhibited pH-sensitive oxidase and peroxidase mimetic activity, more potent than near-spherical M2-MnO2. Furthermore, the signal intensity and r1 relaxivity strongly depended on the crystallinity, morphology, pore size, and specific surface area of the synthesized MNMs. Our findings suggest that flower-like M1-MnO2 NM with acceptable dual-enzyme mimetic (oxidase-like and peroxidase-like) and T1 MRI contrast activities could be employed as a promising theranostic system for future purposes.
Proteomic and functional characterisation of extracellular vesicles from collagen VI deficient human fibroblasts reveals a role in cell motility
Authors: Badosa Carmen , Roldán Mónica , Fernández-Irigoyen Joaquín , Santamaria Enrique , Jimenez-Mallebrera Cecilia 
Published: September 2023

AbstractExtracellular vesicles (EVs) are key mediators of cell-to-cell communication. Their content reflects the state of diseased cells representing a window into disease progression. Collagen-VI Related Muscular Dystrophy (COL6-RD) is a multi-systemic disease involving different cell types. The role of EVs in this disease has not been explored. We compared by quantitative proteomics the protein cargo of EVs released from fibroblasts from patients with COL6-RD and controls. Isolated EVs contained a significant proportion of the most frequently reported proteins in EVs according to Exocarta and Vesiclepedia. We identified 67 differentially abundant proteins associated with vesicle transport and exocytosis, actin remodelling and the cytoskeleton, hemostasis and oxidative stress. Treatment of control fibroblasts with EVs from either patient or healthy fibroblasts altered significantly the motility of cells on a cell migration assay highlighting the functional relevance of EVs. In parallel, we analysed the secretome from the same cells and found a distinctly different set of 48 differentially abundant proteins related to extracellular matrix organisation and remodelling, growth factor response, RNA metabolism and the proteasome. The EVs and secretome sets of proteins only shared two identifiers indicating that the sorting of proteins towards EVs or the secretory pathway is tightly regulated for different functions.