bluuebunny/crossref_metadata_2025_split huggingface dataset:
Size specific dose estimation in pediatric CT: preliminary study and conversion factors
Authors: Zhang Jian , Zhang Xiaojun 
Published: April 2024

Abstract
The objective of this paper is to compare the differences between volumetric CT dose index (CTDIVOL) and size-specific dose estimate (SSDEWED) based on water equivalent diameter (WED) in radiation dose measurement, and explore a new method for fast calculation of SSDEWED. The imaging data of 1238 cases of head, 1152 cases of chest and 976 cases of abdominopelvic were analyzed retrospectively, and they were divided into five age groups: ≤ 0.5, 0.5 ~ ≤ 1, 1 ~ ≤ 5, 5 ~ ≤ 10 and 10 ~ ≤ 15 years according to age. The area of interest (AR), CT value (CTR), lateral diameter (LAT) and anteroposterior diameter (AP) of the median cross-sectional image of the standard scanning range and the SSDEWED were manually calculated, and a t-test was used to compare the differences between CTDIVOL and SSDEWED in different age groups. Pearson analyzed the correlations between DE and age, DE and WED, f and age, and counted the means of conversion factors in each age group, and analyze the error ratios between SSDE calculated based on the mean age group conversion factors and actual measured SSDE. The CTDIVOL in head was (9.41 ± 1.42) mGy and the SSDEWED was (8.25 ± 0.70) mGy: the difference was statistically significant (t = 55.04, P &lt; 0.001); the CTDIVOL of chest was (2.68 ± 0.91) mGy and the SSDEWED was (5.16 ± 1.16) mGy, with a statistically significant difference (t = −218.78, P &lt; 0.001); the CTDIVOL of abdominopelvic was (3.09 ± 1.58) mGy and the SSDEWED was (5.89 ± 2.19) mGy: the difference was also statistically significant (t = −112.28, P &lt; 0.001). The CTDIVOL was larger than the SSDEWED in the head except for the ≤ 0.5 year subgroup, and CTDIVOL was smaller than SSDEWED within each subgroup in chest and abdominopelvic. There were strong negative correlations between f and age (head: r = −0.81; chest: r = −0.89; abdominopelvic: r = −0.86; P &lt; 0.001). The mean values of f at each examination region were 0.81 ~ 1.01 for head, 1.65 ~ 2.34 for chest and 1.71 ~ 2.35 for abdominopelvic region. The SSDEWED could be accurately estimated using the mean f of each age subgroup. SSDEWED can more accurately measure the radiation dose of children. For children of different ages and examination regions, the SSDEWED conversion factors based on age subgroup can be quickly adjusted and improve the accuracy of radiation dose estimation.
Partial ionization of plasma in solar prominences
Authors: Heinzel Petr , Gunár Stanislav , Jejčič Sonja 
Published: April 2024

The plasma in cool cores of solar prominences is partially ionized and its ionization degree, in general, depends on the actual kinetic temperature and density of the plasma and the ions considered. However, we demonstrate that under typical prominence conditions, the dominant mechanism contributing to partial ionization is photoionization by radiation diffusing through the plasma. This mechanism strongly depends on the radiation illuminating prominences from the surrounding solar atmosphere. The understanding of the partial ionization of prominence plasma thus requires a complex solution of the non-LTE radiative-transfer problem. In this paper, we discuss the ionization of hydrogen, helium and some other important species. We also demonstrate the role of non-equilibrium ionization.
This article is part of the theme issue ‘Partially ionized plasma of the solar atmosphere: recent advances and future pathways’.
Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats
Authors: Yang Hong , Zhang Cheng , Kim Woonghee , Shi Mengnan , Kiliclioglu Metin , Bayram Cemil , Bolat Ismail , Tozlu Özlem Özdemir , Baba Cem , Yuksel Nursena , Yildirim Serkan , Iqbal Shazia , Sebhaoui Jihad , Hacımuftuoglu Ahmet , Uhlen Mathias , Boren Jan , Turkez Hasan , Mardinoglu Adil 
Published: April 2024

AbstractExcessive consumption of sucrose, in the form of sugar-sweetened beverages, has been implicated in the pathogenesis of metabolic dysfunctionLassociated fatty liver disease (MAFLD) and other related metabolic syndromes. The c-Jun N-terminal kinase (JNK) pathway plays a crucial role in response to dietary stressors, and it was demonstrated that the inhibition of the JNK pathway could potentially be used in the treatment of MAFLD. However, the intricate mechanisms underlying these interventions remain incompletely understood given their multifaceted effects across multiple tissues. In this study, we challenged rats with sucrose-sweetened water and investigated the potential effects of JNK inhibition by employing network analysis based on the transcriptome profiling obtained from hepatic and extrahepatic tissues, including visceral white adipose tissue, skeletal muscle, and brain. Our data demonstrate that JNK inhibition by JNK-IN-5A effectively reduces the circulating triglyceride accumulation and inflammation in rats subjected to sucrose consumption. Coexpression analysis and genome-scale metabolic modelling reveal that sucrose overconsumption primarily induces transcriptional dysfunction related to fatty acid and oxidative metabolism in the liver and adipose tissues, which are largely rectified after JNK inhibition at a clinically relevant dose. Skeletal muscle exhibited minimal transcriptional changes to sucrose overconsumption but underwent substantial metabolic adaptation following the JNK inhibition. Overall, our data provides novel insights into the molecular basis by which JNK inhibition exerts its metabolic effect in the metabolically active tissues. Furthermore, our findings underpin the critical role of extrahepatic metabolism in the development of diet-induced steatosis, offering valuable guidance for future studies focused on JNK-targeting for effective treatment of MAFLD.
Multi-layered apoplastic barrier underlying the ability of Na+exclusion inVigna marina
Authors: Wang Fanmiao , Tanoi Keitaro , Yamauchi Takaki , Naito Ken 
Published: April 2024

SummarySalt tolerance is important to tackle problems of soil salinization and ground water depletion. However, developing salt tolerant crops is facing difficulties due to limited potential in model plants and crop species. Thus, it is important to elucidate how coastal species, such asVigna marina, adapt to saline environments.By comparative transcriptome and histological analyses, this study elucidated one important aspect of howVigna marinaachieves salt exclusion and extraordinary salt tolerance.Under salt stress, genes involved in casparian strip formation were specifically upregulated in JP247202 (V. marina). JP247202 reinforced apoplastic barrier with thick lignification in multiple layers of cells around endodermis. Also, disruption of lignification led to a dramatic increase of shoot Na+accumulation and salt lesion in JP247202. Interestingly, despite the salt-induced apoplastic barrier, JP247202 maintained transport of essential ions including K+, Mg2+, and Ca2+.Our results revealed that lignification of multi-layered cells around endodermis was an important apoplastic barrier to the transport of Na+to shoots in JP247202, while it did not restrict the transport of K+, Mg2+, and Ca2+. This feature, together with the ability of Na+excretion by SOS1, enablesV. marinato thrive in marine beaches.
Visual Analysis of Multi-Omics Data
Authors: Swart Austin , Caspi Ron , Paley Suzanne , Karp Peter D. 
Published: April 2024

AbstractWe present a tool for multi-omics data analysis that enables simultaneous visualization of up to four types of omics data on organism-scale metabolic network diagrams. The tool’s interactive web-based metabolic charts depict the metabolic reactions, pathways, and metabolites of a single organism as described in a metabolic pathway database for that organism; the charts are constructed using automated graphical layout algorithms.The multi-omics visualization facility paints each individual omics dataset onto a different “visual channel” of the metabolic-network diagram. For example, a transcriptomics dataset might be displayed by coloring the reaction arrows within the metabolic chart, while a companion proteomics dataset is displayed as reaction arrow thicknesses, and a complementary metabolomics dataset is displayed as metabolite node colors. Once the network diagrams are painted with omics data, semantic zooming provides more details within the diagram as the user zooms in. Datasets containing multiple time points can be displayed in an animated fashion. The tool will also graph data values for individual reactions or metabolites designated by the user. The user can interactively adjust the mapping from data value ranges to the displayed colors and thicknesses to provide more informative diagrams.
Restoration of retinal regenerative potential of Müller glia by disrupting intercellular Prox1 transfer
Authors: Lee Eun Jung , Kim Museong , Park Sooyeon , Shim Ji Hyeon , Cho Hyun-Ju , Park Jung Ah , Park Kihyun , Lee Dongeun , Kim Jeong Hwan , Jeong Haen , Matsuzaki Fumio , Kim Seon-Young , Kim Jaehoon , Yang Hanseul , Lee Jeong-Soo , Kim Jin Woo 
Published: April 2024

AbstractIndividuals with retinal degenerative diseases face significant obstacles in restoring normal vision due to the inability to regenerate degenerated retinal cells. While retinal neurons can be regenerated from Müller glia (MG) in cold-blooded vertebrates, this regenerative ability is lacking in mammals, indicating the limited competence of mammalian MG for retinal regeneration. In this study, we elucidate the role of prospero-related homeobox 1 (Prox1) in rendering the mammalian retina incompetent for MG-derived regeneration. Prox1 accumulates in MG in the degenerating human and mouse retinas but not in those in the regenerating zebrafish retina. Strikingly, Prox1 in mouse MG originated from neighboring retinal neurons through intercellular protein transfer. Consequently, inhibition of Prox1 transfer to MG enables the reprogramming of MG into proliferative retinal progenitor cells in injured mouse retinas. Furthermore, we succeeded in regenerating retinal neurons and delaying vision loss in retinitis pigmentosa disease model in mice by adenoassociated viral gene delivery of an anti-Prox1 antibody that sequesters extracellular Prox1 in the mouse retina. Taken together, our findings highlight the therapeutic potential of anti-Prox1 therapy in restoring the regenerative potential of the mammalian retina.
Membrane permeability selection drove the stereochemistry of life
Authors: Goode Olivia , Łapińska Urszula , Glover Georgina , Milner David S. , Santoro Alyson E. , Pagliara Stefano , Richards Thomas A. 
Published: April 2024

AbstractEarly in the evolution of life a proto-metabolic network was encapsulated within a membrane compartment. The permeability characteristics of the membrane determined several key functions of this network by determining which compounds could enter the compartment and which compounds could not. One key feature of known life is the utilisation of right-handed D- ribose and deoxyribose sugars and left-handed L- amino acid stereochemical isomers (enantiomers), however, it is not clear why life adopted this specific chirality. We previously demonstrated that an archaeal and an intermediate membrane mimic, bearing a mixture of bacterial and archaeal lipid characteristics (a ‘hybrid’ membrane), display increased permeability compared to bacterial-like membranes. Here, we investigate if these membranes can drive stereochemical selection on pentose sugars, hexose sugars and amino acids. Using permeability assays of homogenous unilamellar vesicles, we demonstrate that both membranes select for D- ribose and deoxyribose sugars while the hybrid membrane uniquely selects for a reduced alphabet of L- facing amino acids. This repertoire includes alanine, the plausible first L- amino acid utilised. We conclude such compartments could provide stereochemical compound selection thereby demonstrating a solution to the chirality problem during the evolution of life.
Transcriptional regulators ensuring specific gene expression and decision making at high TGFβ doses
Authors: Hartmann Laura , Kristofori Panajot , Li Congxin , Becker Kolja , Hexemer Lorenz , Bohn Stefan , Lenhardt Sonja , Weiss Sylvia , Voss Björn , Loewer Alexander , Legewie Stefan 
Published: April 2024

AbstractTGFβ-signaling regulates cancer progression by controlling cell division, migration and death. These outcomes are mediated by gene expression changes, but the mechanisms of decision making towards specific fates remain unclear. Here, we combine SMAD transcription factor imaging, genome-wide RNA sequencing and morphological assays to quantitatively link signaling, gene expression and fate decisions in mammary epithelial cells. Fitting genome-wide kinetic models to our time-resolved data, we find that the majority of TGFβ target genes can be explained as direct targets of SMAD transcription factors, whereas the remainder show signs of complex regulation, involving delayed regulation and strong amplification at high TGFβ doses. Knockdown experiments followed by global RNA sequencing revealed transcription factors interacting with SMADs in feedforward loops to control delayed and dose-discriminating target genes, thereby reinforcing the specific epithelial-to-mesenchymal transition at high TGFβ doses. We identified early repressors, preventing premature activation, and a late activator, boosting gene expression responses for a sufficiently strong TGFβ stimulus. Taken together, we present a global view of TGFβ-dependent gene regulation and describe specificity mechanisms reinforcing cellular decision making.
Comparative analysis of Pearson and Canonical correlation-based functional connectivity matrices for neuroimaging classification tasks
Authors: Antipushina Ekaterina , Zubrikhina Maria , Kalimullin Ruslan , Kotoyants Nikolay , Sharaev Maxim 
Published: April 2024

AbstractMachine learning (ML) methodologies offer significant potential for addressing the intricate challenges inherent in the analysis of neuroimaging data within the realm of neurological research. Nonetheless, the effective application of these techniques is markedly contingent upon the particular task and dataset under examination, and the absence of standardized methodologies poses impediments to cross-study result comparisons. This study contributes substantively to the collective endeavor by conducting a comprehensive evaluation and comparative analysis of ML models in the context of predicting schizophrenia and autism spectrum disorder (ASD) utilizing distinct functional Magnetic Resonance Imaging (fMRI) datasets. In this research, we introduce Canonical Correlation Analysis (CCA) as an innovative modality to augment the classification of these multifaceted neurological conditions. By elucidating the efficacy of CCA in ameliorating classification accuracy within the framework of Support Vector Machines (SVM), our study endeavors to propel the domain of neuroimaging and deepen our understanding of these intricate neurological disorders.
A proposed workflow to analyze bacterial transcripts in RNAseq from blood extracellular vesicles of people with Multiple Sclerosis
Authors: Ascensión Alex M. , Gorostidi-Aicua Miriam , Otaegui-Chivite Ane , Alberro Ainhoa , Bravo-Miana Rocio del Carmen , Castillo-Trivino Tamara , Moles Laura , Otaegui David 
Published: April 2024

AbstractMotivationThe taxonomical characterisation of bacterial species derived from genetic material blood, including reads derived from bacterial extracellular vesicles (bEVs) poses certain challenges, such as the proper discrimination of “true” reads from contaminating reads. This is a common issue in taxa profiling and can lead to the false discovery of species that are present in the sample. To avoid such biases a careful approximation to taxa profiling is necessary.ResultsIn this work we propose a workflow to analyze the presence of bacterial transcripts as indicative of putative bEVs circulating in the blood of people with MS (pwMS). The workflow includes several reference mapping steps against the host genome and a consensus selection of genera based on different taxa profilers. The consensus selection is performed with a flagging system that removes species with low abundance or with high variation across profilers. Additionally, the inclusion of biological samples from known cultured species as well as the generation of artificial reads constitute two key aspects of this workflow.AvailabilityThe workflow is available at the following repository:https://github.com/NanoNeuro/EV_taxprofiling.Contactdavidangel.otaeguibichot@osakidetza.eus
Single cell sequencing of zebrafish kidney marrows reveals AHR2-dependent endogenous regulation of hematopoiesis
Authors: Dasgupta Subham , Goodale Britton , Tanguay Robyn 
Published: April 2024

AbstractThe aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates a wide range of biological and toxicological responses. While largely studied in ligand-activated toxicant responses, AHR also plays important roles in endogenous physiological processes. We leveraged single cell sequencing and an AHR2 knockout zebrafish line to investigate the role of AHR2 in regulating hematopoiesis (production and differentiation of red and white blood cells from hematopoietic stem cells). Our objectives were to determine if absence of AHR2-1) alters proportions of immune cell populations and/or 2) impacts gene expression within individual immune cell types. We dissected kidney marrow (organ of hematopoiesis in zebrafish) from adult wildtype and AHR2 knockout zebrafish (N=3/genotype), isolated single cells and sequenced ∼ 5000 cells/sample (10X Genomics). We identified 14 cell clusters representing the expected major blood (erythrocytes, thrombocytes), immune (B cells, macrophages, lymphoid cells, granulocytes, etc), progenitors and kidney cell populations. We focused our analyses only on the progenitor and mature immune cell types. While there were no genotype-specific differences in proportion of individual cell types, gene expression differences were observed within several cell types. For known genes, such asrrm2, changes were up to 2000-fold, signifying their importance in AHR2-hematopoesis interaction. Several of the known genes are also identified as markers of carcinoma cells for an array of cancer types. However, many of the dysregulated genes are poorly annotated, limiting our ability to examine biological processes and pathways dysregulated on AHR2 mutation. Nevertheless, our study indicates that AHR2 plays an important endogenous role in hematopoiesis. Future work will focus on better characterizing anatomy of dysregulated genes and their functions in hematopoiesis.
Genome Report: Pseudomolecule-scale genome assemblies ofDrepanocaryum sewerzowiiandMarmoritis complanata
Authors: Smit Samuel J. , Whitehead Caragh , James Sally R. , Jeffares Daniel C. , Godden Grant , Peng Deli , Sun Hang , Lichman Benjamin R. 
Published: April 2024

AbstractThe Nepetoideae, a subfamily of Lamiaceae (mint family), is rich in aromatic plants, many of which are sought after for their use as flavours and fragrances or for their medicinal properties. Here we present genome assemblies for two species in Nepetiodeae:Drepanocaruym sewerzowiiandMarmoritis complanata. Both assemblies were generated using Oxford Nanopore Q20+ reads with contigs anchored to nine pseudomolecules that resulted in 335 Mb and 305 Mb assemblies, respectively, and BUSCO scores above 95% for both the assembly and annotation. We furthermore provide a species tree for the Lamiaceae using only genome derived gene models, complementing existing transcriptome and marker-based phylogenies.
Copper acquisition is essential for plant colonization and virulence in a root-infecting vascular wilt fungus
Authors: Palos-Fernández Rafael , Aguilar-Pontes María Victoria , Puebla-Planas Gema , Berger Harald , Studt-Reinhold Lena , Strauss Joseph , Di Pietro Antonio , López-Berges Manuel Sánchez 
Published: April 2024

ABSTRACTPhytopathogenic fungi provoke devastating agricultural losses and are difficult to control. How fungal pathogens adapt to the plant environment to cause disease and complete their life cycle on the host remains poorly understood. Here we show that efficient acquisition of copper, mediated by the transcriptional regulator Mac1, is crucial for plant colonization and virulence inFusarium oxysporum,a soilborne ascomycete that causes vascular wilt on more than 150 different crops. RNA-seq and ChIP-seq establish a direct role of Mac1 in activation of copper deficiency response genes, many of which are induced during plant infection. Loss of Mac1 impairs growth ofF. oxysporumunder copper-limiting condition as well as vascular colonization and virulence on tomato plants. Importantly, Mac1-independent overexpression of a copper reductase and a copper transporter restores growth under copper limitation and virulence in themac1null mutant background. These findings establish a key role for copper acquisition in fungal pathogenicity on plants and reveal new ways to protect crops from phytopathogens.
Blind source separation of event-related potentials using a recurrent neural network
Authors: O’Reilly Jamie A. , Sunthornwiriya-Amon Hassapong , Aparprasith Naradith , Kittichalao Pannapa , Chairojwong Pornnaphas , Klai-on Thanabodee , Lannon Edward W. 
Published: April 2024

AbstractEvent-related potentials (ERPs) are a superposition of electric potential differences generated by neurophysiological activity associated with psychophysical events. Spatiotemporal dissociation of these signal sources can supplement conventional ERP analysis and improve source localization. However, results from established source separation methods applied to ERPs can be challenging to interpret. Hence, we have developed a recurrent neural network (RNN) method for blind source separation. The RNN transforms input step pulse signals representing events into corresponding ERP difference waveforms. Source waveforms are obtained from penultimate layer units and scalp maps are obtained from feed-forward output layer weights that project these source waveforms onto EEG electrode amplitudes. An interpretable, sparse source representation is achieved by incorporating L1 regularization of signals obtained from the penultimate layer of the network during training. This RNN method was applied to four ERP difference waveforms (MMN, N170, N400, P3) from the open-access ERP CORE database, and independent component analysis (ICA) was applied to the same data for comparison. The RNN decomposed these ERPs into eleven spatially and temporally separate sources that were less noisy, tended to be more ERP-specific, and were less similar to each other than ICA-derived sources. The RNN sources also had less ambiguity between source waveform amplitude, scalp potential polarity, and equivalent current dipole orientation than ICA sources. In conclusion, the proposed RNN blind source separation method can be effectively applied to grand-average ERP difference waves and holds promise for further development as a computational model of event-related neural signals.