bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding the genomic landscape of chromatin-associated biomolecular condensates
Authors: Yu Zhaowei , Wang Qi , Zhang Qichen , Tian Yawen , Yan Guo , Zhu Jidong , Zhu Guangya , Zhang Yong 
Published: August 2024

AbstractBiomolecular condensates play a significant role in chromatin activities, primarily by concentrating and compartmentalizing proteins and/or nucleic acids. However, their genomic landscapes and compositions remain largely unexplored due to a lack of dedicated computational tools for systematic identification in vivo. To address this, we develop CondSigDetector, a computational framework designed to detect condensate-like chromatin-associated protein co-occupancy signatures (CondSigs), to predict genomic loci and component proteins of distinct chromatin-associated biomolecular condensates. Applying this framework to mouse embryonic stem cells (mESC) and human K562 cells enable us to depict the high-resolution genomic landscape of chromatin-associated biomolecular condensates, and uncover both known and potentially unknown biomolecular condensates. Multi-omics analysis and experimental validation further verify the condensation properties of CondSigs. Additionally, our investigation sheds light on the impact of chromatin-associated biomolecular condensates on chromatin activities. Collectively, CondSigDetector provides an approach to decode the genomic landscape of chromatin-associated condensates, facilitating a deeper understanding of their biological functions and underlying mechanisms in cells.
Characterisation of hydraulic properties of commercial gas diffusion layers: Toray, SGL, MGL, woven carbon cloth
Authors: Aquah Grace Esu-Ejemot , Niblett Daniel , Shokri Javad , Niasar Vahid 
Published: August 2024

AbstractThis study utilises computational fluid dynamics simulations with the OpenFOAM computational framework to investigate and compare the in-plane and through-plane permeability properties of four different gas diffusion layers (GDLs). Also the through-plane water and air relative permeability values and water saturations at different rates were simulated. Permeability analysis enhances our understanding of fluid flow, ways to decrease pressure loss in the GDL, and methods to enhance oxygen concentration at the catalyst layer interface through convection. The analysis reveals that the investigated GDL materials have spatial heterogeneity of porosity and permeability, especially in the Sigracet SGL 25 BA GDL. However, the porosity and permeability of the Toray TGP-H 060 and AvCarb 370 MGL GDLs exhibit less variations. The two-phase flow studies on GDL saturation show that at the same water injection flowrate, the AvCarb 370 MGL GDL has the largest remaining water saturation, with Sigracet SGL 25 BA GDL being the less saturated GDL among the four investigated GDLs. The compression from the ribs significantly affected the in-plane permeabilities of both Toray TGP-H 060 and especially impacted Sigracet SGL 25 BA GDL. This impact was expected as the pore size distribution varied significantly in the areas under the ribs versus the channel.
Development and performance evaluation of fully automated deep learning-based models for myocardial segmentation on T1 mapping MRI data
Authors: Manzke Mathias , Iseke Simon , Böttcher Benjamin , Klemenz Ann-Christin , Weber Marc-André , Meinel Felix G. 
Published: August 2024

AbstractTo develop a deep learning-based model capable of segmenting the left ventricular (LV) myocardium on native T1 maps from cardiac MRI in both long-axis and short-axis orientations. Models were trained on native myocardial T1 maps from 50 healthy volunteers and 75 patients using manual segmentation as the reference standard. Based on a U-Net architecture, we systematically optimized the model design using two different training metrics (Sørensen-Dice coefficient = DSC and Intersection-over-Union = IOU), two different activation functions (ReLU and LeakyReLU) and various numbers of training epochs. Training with DSC metric and a ReLU activation function over 35 epochs achieved the highest overall performance (mean error in T1 10.6 ± 17.9 ms, mean DSC 0.88 ± 0.07). Limits of agreement between model results and ground truth were from -35.5 to + 36.1 ms. This was superior to the agreement between two human raters (-34.7 to + 59.1 ms). Segmentation was as accurate for long-axis views (mean error T1: 6.77 ± 8.3 ms, mean DSC: 0.89 ± 0.03) as for short-axis images (mean error ΔT1: 11.6 ± 19.7 ms, mean DSC: 0.88 ± 0.08). Fully automated segmentation and quantitative analysis of native myocardial T1 maps is possible in both long-axis and short-axis orientations with very high accuracy.
Evaluation of prostate cancer detection using micro-ultrasound versus MRI through co-registration to whole-mount pathology
Authors: Pensa Jake , Brisbane Wayne , Kinnaird Adam , Kuppermann David , Hughes Griffith , Ushko Derrick , Priester Alan , Gonzalez Samantha , Reiter Robert , Chin Arnold , Sisk Anthony , Felker Ely , Marks Leonard , Geoghegan Rory 
Published: August 2024

AbstractMicro-ultrasound has recently been introduced as a low-cost alternative to multi-parametric MRI for imaging prostate cancer. Early clinical studies have demonstrated promising results; however, robust validation via comparison with whole-mount pathology has yet to be achieved. Due to micro-ultrasound probe design and tissue deformation during scanning, it is difficult to accurately correlate micro-ultrasound imaging planes with ground truth whole-mount pathology slides. In this study, we developed a multi-step methodology to co-register micro-ultrasound and MRI to whole-mount pathology. The three-step process had a registration error of 3.90 ± 0.11 mm and consists of: (1) micro-ultrasound image reconstruction, (2) 3D landmark registration of micro-ultrasound to MRI, and (3) 2D capsule registration of MRI to whole-mount pathology. This process was then used in a preliminary reader study to compare the diagnostic accuracy of micro-ultrasound and MRI in 15 patients who underwent radical prostatectomy for prostate cancer. Micro-ultrasound was found to have equivalent performance to retrospective MRI review for index lesion detection (91.7% vs. 80%), while demonstrating an increased detection of tumor extent (52.5% vs. 36.7%) with similar false positive regions-of-interest (38.3% vs. 40.8%). Prospective MRI review had reduced detection of index lesions (73.3%) and tumor extent (18.9%) but improved false positive regions-of-interest (22.7%) relative to micro-ultrasound and retrospective MRI. Further evaluation is needed with a larger sample size.
Orange maker: a CRISPR/Cas9-mediated genome editing and screening project to generate orange-eyed DarkJedi GAL4 lines by undergraduate students
Authors: Park Hee Su , Gross Anna C. , Oh Seungjae , Kim Nam Chul 
Published: August 2024

AbstractOne of the greatest strengths of Drosophila genetics is its easily observable and selectable phenotypic markers. The mini-white marker has been widely used as a transgenic marker for Drosophila transgenesis. Flies carrying a mini-white construct can exhibit various eye colors ranging from pale orange to intense red, depending on the insertion site and gene dosage. Because the two copies of the mini-white marker show a stronger orange color, this is often used for selecting progenies carrying two transgenes together in a single chromosome after chromosomal recombination. However, some GAL4 lines available in the fly community originally have very strong red eyes. Without employing another marker, such as GFP, generating a recombinant chromosome with the strong red-eyed GAL4 and a desired UAS-transgene construct may be difficult. Therefore, we decided to change the red eyes of GAL4 lines to orange color. To change the eye color of the fly, we tested the CRISPR/Cas9 method with a guide RNA targeting the white gene with OK371-GAL4 and elav-GAL4. After a simple screening, we have successfully obtained multiple lines of orange-eyed OK371-GAL4 and elav-GAL4 that still maintain their original expression patterns. All of these simple experiments were performed by undergraduate students, allowing them to learn about a variety of different genetic experiments and genome editing while contributing to the fly research community by creating fruit fly lines that will be used in real-world research.
Divergent venom effectors correlate with ecological niche in neuropteran predators
Authors: Fischer Maike Laura , Schmidtberg Henrike , Tidswell Olivia , Weiss Benjamin , Dersch Ludwig , Lüddecke Tim , Wielsch Natalie , Kaltenpoth Martin , Vilcinskas Andreas , Vogel Heiko 
Published: August 2024

AbstractNeuropteran larvae are fierce predators that use venom to attack and feed on arthropod prey. Neuropterans have adapted to diverse and sometimes extreme habitats, suggesting their venom may have evolved accordingly, but the ecology and evolution of venom deployment in different families is poorly understood. We applied spatial transcriptomics, proteomics, morphological analysis, and bioassays to investigate the venom systems in the antlion Euroleon nostras and the lacewing Chrysoperla carnea, which occupy distinct niches. Although the venom system morphology was similar in both species, we observed remarkable differences at the molecular level. E. nostras produces particularly complex venom secreted from three different glands, indicating functional compartmentalization. Furthermore, E. nostras venom and digestive tissues were devoid of bacteria, strongly suggesting that all venom proteins are of insect origin rather than the products of bacterial symbionts. We identified several toxins exclusive to E. nostras venom, including phospholipase A2 and several undescribed proteins with no homologs in the C. carnea genome. The compositional differences have significant ecological implications because only antlion venom conferred insecticidal activity, indicating its use for the immobilization of large prey. Our results indicate that molecular venom evolution plays a role in the adaptation of antlions to their unique ecological niche.
A novel density‐based representation for point cloud and its ability to facilitate classification
Authors: Xie Xianlin , Tang Xue‐song 
Published: August 2024

AbstractCurrently, in the field of processing 3D point cloud data, two primary representation methods have emerged: point‐based methods and voxel‐based methods. However, the former suffer from significant computational costs and lack the ease of handling exhibited by voxel‐based methods. Conversely, the later often encounter challenges related to information loss resulting from downsampling operations, thereby impeding subsequent tasks. To address these limitations, this article introduces a novel density‐based representation method for voxel partitioning. Additionally, a corresponding network structure is devised to extract features from this specific density representation, thereby facilitating the successful completion of classification tasks. The experiments are implemented on ModelNet40 and MNIST demonstrate that the proposed 3D convolution can achieve the‐state‐of‐the‐art performance based on the voxels.
Les inducteurs émotionnels perçus par des lycéens en EPS : quel impact de cinq formats de jeu en badminton ?
Authors: Visioli Jérôme , Level Julie , Dieu Olivier 
Published: August 2024

L’objectif de cet article est d’identifier et de comparer les inducteurs des émotions positives et négatives ressenties par des élèves du secondaire en EPS dans le cadre de cinq formats de jeu en badminton. Les perceptions de 58 lycéens (24 filles et 34 garçons – Mâge = 15,01, Ec = 0,25) ont été recueillies à l’aide d’un questionnaire basé sur la méthode des incidents critiques (Flanagan, 1954). Les élèves devaient raconter le moment le plus marquant vécu au sein de chaque format, juste après l’avoir pratiqué. L’analyse inductive des incidents critiques recueillis a permis de rendre compte et de comparer l’impact des dispositifs proposés par l’enseignant sur les émotions positives et négatives des élèves. La discussion invite notamment à porter une attention particulière aux émotions des filles et à la sensibilité à l’espace de jeu, mais également à relativiser l’impact du seul format de jeu sur les émotions des élèves. Plus globalement, c’est l’impact émotionnel des formats de jeu en badminton qui est interrogé dans l’optique de la formation des enseignants d’EPS, en lien avec le projet de conception et d’exploitation d’« affective learning design ».
The Year in Cardiology—Practice Changing Trials from European Society of Cardiology Congress 2023
Authors: Pradhan Akshyaya , Tripathi Umesh , Singh Abhishek 
Published: August 2024

AbstractThe European Society of Cardiology annual congress is the premier global platform for dissemination and unraveling major scientific advances in the field of cardiology. Each year a myriad number of scientific ideas are exchanged at this meeting and many major path-breaking clinical trials are presented that have the potential to alter our practice. Last year was not different and more than 30 clinical trials spanning various facets of cardiology were unveiled and discussed—heart failure, lipid lowering, coronary intervention, intracoronary imaging, cardiomyopathies, anticoagulation, atrial fibrillation, antiplatelet therapy, etc. We present a brief summary of 10 major trials which in the view of authors have the potential for impacting daily cardiology practice. In each study, we also attempt to provide a contemporary perspective and the way forward. We aim to provide a glimpse on the major advances in the field of cardiology in the past year.
Introducing the “Parallel European Corpus of Informal Interaction” (PECII)
Authors: Küttner Uwe-A. , Kornfeld Laurenz , Mack Christina , Mondada Lorenza , Rogowska Jowita , Rossi Giovanni , Sorjonen Marja-Leena , Weidner Matylda , Zinken Jörg 
Published: August 2024

Abstract
This article introduces the Parallel European Corpus of Informal Interaction
(PECII), a multi-language video-corpus of social interactions in a range of informal settings and activity-contexts.
After describing the basic motivation for its compilation, the design principles that underlie its composition and the
data it contains, we illustrate PECII’s usefulness for comparative Interactional Linguistic (IL) and Conversation
Analytic (CA) research. We do this by offering an analytic sketch of the practices people use to initiate turns that
interfere with and seek to rectify another’s (problematic) behavior, focusing on their variability across languages
and settings/activity-contexts. By maximizing the comparability of interactional data, PECII not only promotes the enhancement of cross-linguistic research in IL, it also opens up new avenues for
exploring “cross-situational” variability (so-called “situation design”).
Requesting in shop encounters
Authors: Mondada Lorenza 
Published: August 2024

Abstract
The chapter offers a systematic study of requests in shop encounters. Considering
their detailed formats, constituted through the specific assembling of diverse resources including speakers’ turn,
gaze, gestures, and body postures that I call multimodal Gestalts, it identifies different types of requests and their sequential implicativeness.
The chapter shows how these multimodal formats are methodically bound to the categorization of speakers/customers, their epistemic and sensorial relations to the product, and as a consequence,
to the response of the seller, the service they offer,
and the progressivity of the encounter. In this sense, multimodal Gestalts are crucial for understanding the systematic accountability of the action and its sequential
organization, as well as the social-institutional features of the situated activity in which this action is embedded.
The study contributes to IL research by demonstrating
how linguistic and embodied resources are deeply and systematically intertwined, and showing the necessity to go
beyond talk for understanding the variation and indexicality of social actions.
Shadow and gravitational weak lensing for quantum improved charged black hole in plasma*
Authors: Alloqulov Mirzabek , Atamurotov Farruh , Abdujabbarov Ahmadjon , Ahmedov Bobomurat , Juraeva Nozima 
Published: August 2024

Abstract
We investigated the shadow and weak gravitational lensing for the quantum-improved charged black hole (BH). First, the photon motion and BH shadow were studied in a plasma medium. It can be seen from our analysis that the radius of the photon sphere of the quantum-improved charged BH and size of the BH shadow decrease under the influence of the plasma parameter

. Furthermore, the gravitational weak lensing is considered for the quantum-improved charged BH, and we have obtained the deflection angle of light rays around a compact object for uniform and non-uniform plasma cases. It is shown that the value of the deflection angle for uniform plasma increases with increasing plasma parameter, and vice versa for non-uniform plasma. It has been also indicated that under the influence of the plasma parameter

and BH charge

, the values of the deflection angles for the two cases decrease. Finally, we investigated the magnification of image brightness using the deflection angle of the light rays around the quantum-improved charged BH.
Scissors vibration and its collective rotation in a microscopic investigation*
Authors: Chen 陈 Fang-Qi 芳祁 
Published: August 2024

Abstract
The intrinsic vibrational motion and the rotational behavior of the scissors mode in well deformed nuclei are investigated with an angular-momentum-projected approach, which is interpreted as a generator-coordinate-method with the generator coordinates corresponding to the degrees of freedom of interest. The picture of the intrinsic and rotational motion of the scissors mode is illustrated from the collective wave function within the framework of the generator-coordinate-method. The harmonicity of the scissors vibration is found to arise naturally from the present model but can be disturbed by the Coriolis effect as spin increases. The odd and even spin members of the rotational band based on the scissors mode rotate about different axes perpendicular to each other, leading to the flipping moment of inertia and the consequent splitting behavior that has been suggested previously.
Long-term Speckle Interferometric Monitoring of Binary Systems: 2007–2023 Positional Measurements and Orbits of Seven Objects
Authors: Mitrofanova Arina , Dyachenko Vladimir , Beskakotov Anatoly , Balega Yuri , Maksimov Alexander , Rastegaev Denis 
Published: August 2024

Abstract
The results of seventeen years of speckle interferometric monitoring of seven objects (Chara 122Aa, GJ 3010, HIP 1987, GJ 3076, HIP 11253, HIP 11352, and HIP 14929) are presented. Observational data were obtained at the 6 m Big Telescope Alt-azimuthal Special Astrophysical Observatory of the Russian Academy of Science (BTA SAO RAS) from 2007 to the present. Analysis of previously published and new measurements made it possible to construct completely new orbits for Chara 122Aa, HIP 11253, and HIP 14929. The orbit of GJ 3076 cannot be constructed accurately due to the large influence of the weights assigned to the measurements. The resulting orbital solutions are classified based on a grading scheme suggested by W.I. Hartkopf, B.D. Mason and C.E. Worley; most orbits are “definitive” (Grade 1). The mass sums and masses of components calculated by two independent methods using Hipparcos and Gaia DR2 and DR3 parallaxes were compared for the objects under study.
Frequency tunable non-invasive microwave blood glucose sensor based on negative impedance circuit
Authors: Peng Jinyang , Yong Jinglei , He Xingli , Li Lingfeng , Li Peng , Zhang Yun Jing 
Published: August 2024

Abstract
This article proposes a frequency adjustable non-invasive blood glucose microwave sensor based on negative impedance circuit. Firstly, this article establishes a skin-blood-skin human tissue model for the detection of non-invasive microwave sensors. Compared to traditional passive microwave blood glucose sensors, this design uses a negative impedance compensation circuit (NIC), greatly increasing microwave penetration and improving its detection sensitivity. In addition, this design achieves the goal of adjustable operating frequency by adding an additional dielectric layer at the detection end. This function is of great significance for microwave non-invasive blood glucose sensors. On the one hand, it can adjust to the optimal operating frequency band according to the characteristics of blood glucose changes; On the other hand, it is possible to measure changes in blood glucose concentration at multiple frequency points, thereby increasing the accuracy of detection. The relevant results show that adjusting the frequency band can reach 1–4 GHz, and the specific method of frequency adjustment is provided in the article; Meanwhile, four initial frequency points were selected in the article, at which the results show that the sensitivity reaches 1.356 × 10−3, 3.142 × 10−3, 2.071 × 10−3, 1.903 × 10−3. The above results demonstrate the superiority of our design, and blood glucose sensors based on this principle are expected to break through the limitations of current blood glucose sensors.
A high-performance digital polymerase chain reaction chip integrated with nanorods-decorated microchannel plate
Authors: Li Guangyang , Xu Xuefeng , Xue Lingyue , Xu Mingzhu , Hu Sixing , Xiang Anli , Yang Xi , Cao Zhen 
Published: August 2024

Abstract
In this paper, we report on a digital PCR chip integrated with microchannel plate (MCP) for the quantification of DNA molecules. MCP, a highly porous glass membrane, is employed here as microreactors. The density of the microreactors reaches up to 1600 mm−2 with a total number of 40,000 chambers each in 100 pL volumes embedded in a 5 × 5 mm2 MCP, which is 100 times larger than that of the conventional microfabricated chips. In addition, the MCP is functionalized with ZnO nanorods to enhance the fluorescence signal. The dynamic range is noted as 105 and the detection limit of λDNA is determined to be 1.4 copies/μL.
Cost-effective scanning digital microscopic system for wide field-of-view and high-resolution biomedical imaging
Authors: Lin Siru , Lv Zhihang , Huang Xiwei 
Published: August 2024

Abstract
Microscopes serve as indispensable tools for exploring the microcosm and conducting biological detection. However, traditional microscopes fail to balance the field of view and resolution, limiting wide-field imaging capabilities. Here, we propose a low-cost, wide-field, high-resolution digital microscopy imaging system, providing high-quality and versatile microscopy tools for budget-constrained laboratories. The design of this system is based on the low-cost mechanical scanning and positioning platform provided by a computer numerical control (CNC) router architecture. The use of a transmitted light structure ensures uniform field illumination for both bright-field and fluorescence microscopy. Utilizing a 20× objective lens, this microscopy system achieves clear imaging of 1μm particles and rapidly acquires hundreds of microscopic images for subsequent stitching, thus achieving high-resolution wide-field imaging in both bright-field and fluorescence modes. The system integrates the advantages of wide-field, high-resolution imaging, and high-throughput image acquisition, providing a cost-effective solution for wide-field microscopy.