bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probabilistic physics-integrated neural differentiable modeling for isothermal chemical vapor infiltration process
Authors: Akhare Deepak , Chen Zeping , Gulotty Richard , Luo Tengfei , Wang Jian-Xun 
Published: June 2024

AbstractChemical vapor infiltration (CVI) is a widely adopted manufacturing technique used in producing carbon-carbon and carbon-silicon carbide composites. These materials are especially valued in the aerospace and automotive industries for their robust strength and lightweight characteristics. The densification process during CVI critically influences the final performance, quality, and consistency of these composite materials. Experimentally optimizing the CVI processes is challenging due to the long experimental time and large optimization space. To address these challenges, this work takes a modeling-centric approach. Due to the complexities and limited experimental data of the isothermal CVI densification process, we have developed a data-driven predictive model using the physics-integrated neural differentiable (PiNDiff) modeling framework. An uncertainty quantification feature has been embedded within the PiNDiff method, bolstering the model’s reliability and robustness. Through comprehensive numerical experiments involving both synthetic and real-world manufacturing data, the proposed method showcases its capability in modeling densification during the CVI process. This research highlights the potential of the PiNDiff framework as an instrumental tool for advancing our understanding, simulation, and optimization of the CVI manufacturing process, particularly when faced with sparse data and an incomplete description of the underlying physics.
Spaceflight on the ISS changed the skeletal muscle proteome of two astronauts
Authors: Murgia Marta , Rittweger Jörn , Reggiani Carlo , Bottinelli Roberto , Mann Matthias , Schiaffino Stefano , Narici Marco V. 
Published: June 2024

AbstractSkeletal muscle undergoes atrophy and loss of force during long space missions, when astronauts are persistently exposed to altered gravity and increased ionizing radiation. We previously carried out mass spectrometry-based proteomics from skeletal muscle biopsies of two astronauts, taken before and after a mission on the International Space Station. The experiments were part of an effort to find similarities between spaceflight and bed rest, a ground-based model of unloading, focused on proteins located at the costameres. We here extend the data analysis of the astronaut dataset and show compartment-resolved changes in the mitochondrial proteome, remodeling of the extracellular matrix and of the antioxidant response. The astronauts differed in their level of onboard physical exercise, which correlated with their respective preservation of muscle mass and force at landing in previous analyses. We show that the mitochondrial proteome downregulation during spaceflight, particularly the inner membrane and matrix, was dramatic for both astronauts. The expression of autophagy regulators and reactive oxygen species scavengers, however, showed partially opposite expression trends in the two subjects, possibly correlating with their level of onboard exercise. As mitochondria are primarily affected in many different tissues during spaceflight, we hypothesize that reactive oxygen species (ROS) rather than mechanical unloading per se could be the primary cause of skeletal muscle mitochondrial damage in space. Onboard physical exercise might have a strong direct effect on the prevention of muscle atrophy through mechanotransduction and a subsidiary effect on mitochondrial quality control, possibly through upregulation of autophagy and anti-oxidant responses.
An emission-state-switching radio transient with a 54-minute period
Authors: Caleb M. , Lenc E. , Kaplan D. L. , Murphy T. , Men Y. P. , Shannon R. M. , Ferrario L. , Rajwade K. M. , Clarke T. E. , Giacintucci S. , Hurley-Walker N. , Hyman S. D. , Lower M. E. , McSweeney Sam , Ravi V. , Barr E. D. , Buchner S. , Flynn C. M. L. , Hessels J. W. T. , Kramer M. , Pritchard J. , Stappers B. W. 
Published: June 2024

AbstractLong-period radio transients are an emerging class of extreme astrophysical events of which only three are known. These objects emit highly polarized, coherent pulses of typically a few tens of seconds duration, and minutes to approximately hour-long periods. Although magnetic white dwarfs and magnetars, either isolated or in binary systems, have been invoked to explain these objects, a consensus has not emerged. Here we report on the discovery of ASKAP J193505.1+214841.0 (henceforth ASKAP J1935+2148) with a period of 53.8 minutes showing 3 distinct emission states—a bright pulse state with highly linearly polarized pulses with widths of 10–50 seconds; a weak pulse state that is about 26 times fainter than the bright state with highly circularly polarized pulses of widths of approximately 370 milliseconds; and a quiescent or quenched state with no pulses. The first two states have been observed to progressively evolve over the course of 8 months with the quenched state interspersed between them suggesting physical changes in the region producing the emission. A constraint on the radius of the source for the observed period rules out an isolated magnetic white-dwarf origin. Unlike other long-period sources, ASKAP 1935+2148 shows marked variations in emission modes reminiscent of neutron stars. However, its radio properties challenge our current understanding of neutron-star emission and evolution.
Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts
Authors: Mitchell Jessica H. , Freedman Adam H. , Delaney Jennifer A. , Girguis Peter R. 
Published: June 2024

AbstractMost autotrophic organisms possess a single carbon fixation pathway. The chemoautotrophic symbionts of the hydrothermal vent tubeworm Riftia pachyptila, however, possess two functional pathways: the Calvin–Benson–Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycles. How these two pathways are coordinated is unknown. Here we measured net carbon fixation rates, transcriptional/metabolic responses and transcriptional co-expression patterns of Riftia pachyptila endosymbionts by incubating tubeworms collected from the East Pacific Rise at environmental pressures, temperature and geochemistry. Results showed that rTCA and CBB transcriptional patterns varied in response to different geochemical regimes and that each pathway is allied to specific metabolic processes; the rTCA is allied to hydrogenases and dissimilatory nitrate reduction, whereas the CBB is allied to sulfide oxidation and assimilatory nitrate reduction, suggesting distinctive yet complementary roles in metabolic function. Furthermore, our network analysis implicates the rTCA and a group 1e hydrogenase as key players in the physiological response to limitation of sulfide and oxygen. Net carbon fixation rates were also exemplary, and accordingly, we propose that co-activity of CBB and rTCA may be an adaptation for maintaining high carbon fixation rates, conferring a fitness advantage in dynamic vent environments.
Epigenetic inheritance of diet-induced and sperm-borne mitochondrial RNAs
Authors: Tomar A. , Gomez-Velazquez M. , Gerlini R. , Comas-Armangué G. , Makharadze L. , Kolbe T. , Boersma A. , Dahlhoff M. , Burgstaller J. P. , Lassi M. , Darr J. , Toppari J. , Virtanen H. , Kühnapfel A. , Scholz M. , Landgraf K. , Kiess W. , Vogel M. , Gailus-Durner V. , Fuchs H. , Marschall S. , Hrabě de Angelis M. , Kotaja N. , Körner A. , Teperino R. 
Published: June 2024

AbstractSpermatozoa harbour a complex and environment-sensitive pool of small non-coding RNAs (sncRNAs)1, which influences offspring development and adult phenotypes1–7. Whether spermatozoa in the epididymis are directly susceptible to environmental cues is not fully understood8. Here we used two distinct paradigms of preconception acute high-fat diet to dissect epididymal versus testicular contributions to the sperm sncRNA pool and offspring health. We show that epididymal spermatozoa, but not developing germ cells, are sensitive to the environment and identify mitochondrial tRNAs (mt-tRNAs) and their fragments (mt-tsRNAs) as sperm-borne factors. In humans, mt-tsRNAs in spermatozoa correlate with body mass index, and paternal overweight at conception doubles offspring obesity risk and compromises metabolic health. Sperm sncRNA sequencing of mice mutant for genes involved in mitochondrial function, and metabolic phenotyping of their wild-type offspring, suggest that the upregulation of mt-tsRNAs is downstream of mitochondrial dysfunction. Single-embryo transcriptomics of genetically hybrid two-cell embryos demonstrated sperm-to-oocyte transfer of mt-tRNAs at fertilization and suggested their involvement in the control of early-embryo transcription. Our study supports the importance of paternal health at conception for offspring metabolism, shows that mt-tRNAs are diet-induced and sperm-borne and demonstrates, in a physiological setting, father-to-offspring transfer of sperm mitochondrial RNAs at fertilization.
MYCT1 controls environmental sensing in human haematopoietic stem cells
Authors: Aguadé-Gorgorió Júlia , Jami-Alahmadi Yasaman , Calvanese Vincenzo , Kardouh Maya , Fares Iman , Johnson Haley , Rezek Valerie , Ma Feiyang , Magnusson Mattias , Wang Yanling , Shin Juliana E. , Nance Karina J. , Goodridge Helen S. , Liebscher Simone , Schenke-Layland Katja , Crooks Gay M. , Wohlschlegel James A. , Mikkola Hanna K. A. 
Published: June 2024

AbstractThe processes that govern human haematopoietic stem cell (HSC) self-renewal and engraftment are poorly understood and challenging to recapitulate in culture to reliably expand functional HSCs1–3. Here we identify MYC target 1 (MYCT1; also known as MTLC) as a crucial human HSC regulator that moderates endocytosis and environmental sensing in HSCs. MYCT1 is selectively expressed in undifferentiated human haematopoietic stem and progenitor cells (HSPCs) and endothelial cells but becomes markedly downregulated during HSC culture. Lentivirus-mediated knockdown of MYCT1 prevented human fetal liver and cord blood (CB) HSPC expansion and engraftment. By contrast, restoring MYCT1 expression improved the expansion and engraftment of cultured CB HSPCs. Single-cell RNA sequencing of human CB HSPCs in which MYCT1 was knocked down or overexpressed revealed that MYCT1 governs important regulatory programmes and cellular properties essential for HSC stemness, such as ETS factor expression and low mitochondrial activity. MYCT1 is localized in the endosomal membrane in HSPCs and interacts with vesicle trafficking regulators and signalling machinery. MYCT1 loss in HSPCs led to excessive endocytosis and hyperactive signalling responses, whereas restoring MYCT1 expression balanced culture-induced endocytosis and dysregulated signalling. Moreover, sorting cultured CB HSPCs on the basis of lowest endocytosis rate identified HSPCs with preserved MYCT1 expression and MYCT1-regulated HSC stemness programmes. Our work identifies MYCT1-moderated endocytosis and environmental sensing as essential regulatory mechanisms required to preserve human HSC stemness. Our data also pinpoint silencing of MYCT1 as a cell-culture-induced vulnerability that compromises human HSC expansion.
Genome-wide meta-analyses of restless legs syndrome yield insights into genetic architecture, disease biology and risk prediction
Authors: Schormair Barbara , Zhao Chen , Bell Steven , Didriksen Maria , Nawaz Muhammad S. , Schandra Nathalie , Stefani Ambra , Högl Birgit , Dauvilliers Yves , Bachmann Cornelius G. , Kemlink David , Sonka Karel , Paulus Walter , Trenkwalder Claudia , Oertel Wolfgang H. , Hornyak Magdolna , Teder-Laving Maris , Metspalu Andres , Hadjigeorgiou Georgios M. , Polo Olli , Fietze Ingo , Ross Owen A. , Wszolek Zbigniew K. , Ibrahim Abubaker , Bergmann Melanie , Kittke Volker , Harrer Philip , Dowsett Joseph , Chenini Sofiene , Ostrowski Sisse Rye , Sørensen Erik , Erikstrup Christian , Pedersen Ole B. , Topholm Bruun Mie , Nielsen Kaspar R. , Butterworth Adam S. , Soranzo Nicole , Ouwehand Willem H. , Roberts David J. , Danesh John , Burchell Brendan , Furlotte Nicholas A. , Nandakumar Priyanka ,   23andMe Research Team,   D.E.S.I.R. study group, Bonnefond Amélie , Potier Louis , Earley Christopher J. , Ondo William G. , Xiong Lan , Desautels Alex , Perola Markus , Vodicka Pavel , Dina Christian , Stoll Monika , Franke Andre , Lieb Wolfgang , Stewart Alexandre F. R. , Shah Svati H. , Gieger Christian , Peters Annette , Rye David B. , Rouleau Guy A. , Berger Klaus , Stefansson Hreinn , Ullum Henrik , Stefansson Kari , Hinds David A. , Di Angelantonio Emanuele , Oexle Konrad , Winkelmann Juliane 
Published: June 2024

AbstractRestless legs syndrome (RLS) affects up to 10% of older adults. Their healthcare is impeded by delayed diagnosis and insufficient treatment. To advance disease prediction and find new entry points for therapy, we performed meta-analyses of genome-wide association studies in 116,647 individuals with RLS (cases) and 1,546,466 controls of European ancestry. The pooled analysis increased the number of risk loci eightfold to 164, including three on chromosome X. Sex-specific meta-analyses revealed largely overlapping genetic predispositions of the sexes (rg = 0.96). Locus annotation prioritized druggable genes such as glutamate receptors 1 and 4, and Mendelian randomization indicated RLS as a causal risk factor for diabetes. Machine learning approaches combining genetic and nongenetic information performed best in risk prediction (area under the curve (AUC) = 0.82–0.91). In summary, we identified targets for drug development and repurposing, prioritized potential causal relationships between RLS and relevant comorbidities and risk factors for follow-up and provided evidence that nonlinear interactions are likely relevant to RLS risk prediction.
CD40 ligand antagonist dazodalibep in Sjögren’s disease: a randomized, double-blinded, placebo-controlled, phase 2 trial
Authors: St. Clair E. William , Baer Alan N. , Ng Wan-Fai , Noaiseh Ghaith , Baldini Chiara , Tarrant Teresa K. , Papas Athena , Devauchelle-Pensec Valerie , Wang Liangwei , Xu Wenjing , Pham Tuyet-Hang , Sikora Keith , Rees William A. , Alevizos Ilias 
Published: June 2024

AbstractSjögren’s disease (SjD) is a chronic, systemic autoimmune disease with no approved disease-modifying therapies. Dazodalibep (DAZ), a novel nonantibody fusion protein, is a CD40 ligand antagonist that blocks costimulatory signals between T and B cells and antigen-presenting cells, and therefore may suppress the wide spectrum of cellular and humoral responses that drive autoimmunity in SjD. This study was a phase 2, randomized, double-blinded, placebo (PBO)-controlled trial of DAZ with a crossover stage in two distinct populations of participants with SjD. Population 1 had moderate-to-severe systemic disease activity and population 2 had an unacceptable symptom burden and limited systemic organ involvement. All participants had a diagnosis of SjD, with 21.6% and 10.1% having an associated connective tissue disease (rheumatoid arthritis or systemic lupus erythematosus) in populations 1 and 2, respectively. The remaining participants would be considered as having primary Sjögren’s syndrome. The primary endpoint for population 1 (n = 74) was the change from baseline in the European League Against Rheumatism Sjögren’s Syndrome Disease Activity Index at day 169. The primary endpoint for population 2 (n = 109) was the change from baseline in the European League Against Rheumatism Sjögren’s Syndrome Patient Reported Index at day 169. The primary endpoints (least squares mean ± standard error) were achieved with statistical significance for both population 1 (DAZ, −6.3 ± 0.6; PBO, −4.1 ± 0.6; P = 0.0167) and population 2 (DAZ, −1.8 ± 0.2; PBO, −0.5 ± 0.2; P = 0.0002). DAZ was generally safe and well tolerated. Among the most frequently reported adverse events were COVID-19, diarrhea, headache, nasopharyngitis, upper respiratory tract infection, arthralgia, constipation and urinary tract infection. In summary, DAZ appears to be a potential new therapy for SjD and its efficacy implies an important role for the CD40/CD40 ligand pathway in its pathogenesis. ClinicalTrials.gov identifier: NCT04129164.
A global dataset for assessing nitrogen-related plant traits using drone imagery in major field crop species
Authors: Castilho Diogo , Tedesco Danilo , Hernandez Carlos , Madari Beata Emoke , Ciampitti Ignacio 
Published: June 2024

AbstractEnhancing rapid phenotyping for key plant traits, such as biomass and nitrogen content, is critical for effectively monitoring crop growth and maximizing yield. Studies have explored the relationship between vegetation indices (VIs) and plant traits using drone imagery. However, there is a gap in the literature regarding data availability, accessible datasets. Based on this context, we conducted a systematic review to retrieve relevant data worldwide on the state of the art in drone-based plant trait assessment. The final dataset consists of 41 peer-reviewed papers with 11,189 observations for 11 major crop species distributed across 13 countries. It focuses on the association of plant traits with VIs at different growth/phenological stages. This dataset provides foundational knowledge on the key VIs to focus for phenotyping key plant traits. In addition, future updates to this dataset may include new open datasets. Our goal is to continually update this dataset, encourage collaboration and data inclusion, and thereby facilitate a more rapid advance of phenotyping for critical plant traits to increase yield gains over time.
In silico intravascular optical coherence tomography (IVOCT) for quality assured imaging with reduced intervention
Authors: Zhuo Haoyu , Huang Xianchen , Xiao Jie 
Published: June 2024

AbstractIn the clinical application of intravascular optical coherence tomography (IVOCT), it is necessary to flush opaque blood during image acquisition. However, there are no specific standards for how to perform low-dose but effective flushing. In this study, computational fluid dynamics (CFD) and optical models were integrated to numerically simulate the complete process of IVOCT, which includes blood flushing with normal saline followed by image acquisition. Moreover, an intermittent injection scheme was proposed, and its advantages over the conventionally adopted scheme of continuous injection were verified. The results show that intermittent injection can significantly reduce the dosage of normal saline (reduced by 44.4%) with only a slight sacrifice of image quality (reduced by 8.7%, but still acceptable). The developed model and key findings in this work can help surgeons practice optimized IVOCT operations and potentially lead to improved designs of the IVOCT equipment.
An interpretable ensemble structure with a non-iterative training algorithm to improve the predictive accuracy of healthcare data analysis
Authors: Izonin Ivan , Tkachenko Roman , Yemets Kyrylo , Havryliuk Myroslav 
Published: June 2024

AbstractThe modern development of healthcare is characterized by a set of large volumes of tabular data for monitoring and diagnosing the patient's condition. In addition, modern methods of data engineering allow the synthesizing of a large number of features from an image or signals, which are presented in tabular form. The possibility of high-precision and high-speed processing of such large volumes of medical data requires the use of artificial intelligence tools. A linear machine learning model cannot accurately analyze such data, and traditional bagging, boosting, or stacking ensembles typically require significant computing power and time to implement. In this paper, the authors proposed a method for the analysis of large sets of medical data, based on a designed linear ensemble method with a non-iterative learning algorithm. The basic node of the new ensemble is an extended-input SGTM neural-like structure, which provides high-speed data processing at each level of the ensemble. Increasing prediction accuracy is ensured by dividing the large dataset into parts, the analysis of which is carried out in each node of the ensemble structure and taking into account the output signal from the previous level of the ensemble as an additional attribute on the next one. Such a design of a new ensemble structure provides both a significant increase in the prediction accuracy for large sets of medical data analysis and a significant reduction in the duration of the training procedure. Experimental studies on a large medical dataset, as well as a comparison with existing machine learning methods, confirmed the high efficiency of using the developed ensemble structure when solving the prediction task.
Discrete element modeling and experimental study of biomechanical properties of cotton stalks in machine-harvested film-stalk mixtures
Authors: Zhang Jia , Xie Jianhua , Du Yakun , Li Yuanze , Yue Yong , Cao Silin 
Published: June 2024

AbstractTo address the current problems of low accuracy and poor reliability of the discrete element model of cotton stalks, as well as the difficulty of guiding the design and optimization of the equipment through simulations, the discrete element modeling and physical-mechanical tests of cotton stalks in machine harvested film-stalk mixtures are carried out. The peak tensile force $$F_{\rm j}^{\max }$$

F

j

max

, the peak pressure $$F_{\rm y}^{\max }$$

F

y

max

, the peak bending force $$F_{\rm w}^{\max }$$

F

w

max

, the peak shear force $$F_{\rm j}^{\max }$$

F

j

max

, and the force-displacement (F–x) curves of cotton stalks are obtained from the physical tests. The discrete element model of double-layer cotton stalks based on the flat-joint model is established with the PFC$$^{\rm 3D}$$

3
D

software. The $$F_{\rm y}^{\max }$$

F

y

max

is taken as the response value, and the microscopic parameters of the cotton stalk model are used as the test factors, then the Plackett–Burman test, the steepest climb test, and the Box–Behnken test are sequentially designed using Design-Expert software. The second-order regression model describing the relationship between the $$F_{\rm y}^{\max }$$

F

y

max

and the microscopic parameters is established. The optimal parameter combinations of the microscopic parameters are obtained, and then they are utilized to construct the compression, bending, and shear models of cotton stalks and to carry out the validation tests. The results confirm that the established discrete element model could accurately characterize the biomechanical properties of cotton stalks and that the parameter calibration method is reasonable, which could provide a reference for the discrete element modeling of cotton stalks and other stalks, and also offer a theoretical basis for the research of the crushing and separation mechanism of the film-stalk mixtures and the development of the equipment.