bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stromal vascular fraction in the treatment of myositis
Authors: Gandolfi S. , Pileyre B. , Drouot L. , Dubus I. , Auquit-Auckbur I. , Martinet J. 
Published: September 2023

AbstractMuscle regeneration is a physiological process that converts satellite cells into mature myotubes under the influence of an inflammatory environment progressively replaced by an anti-inflammatory environment, with precise crosstalk between immune and muscular cells. If the succession of these phases is disturbed, the immune system can sometimes become auto-reactive, leading to chronic muscular inflammatory diseases, such as myositis. The triggers of these autoimmune myopathies remain mostly unknown, but the main mechanisms of pathogenesis are partially understood. They involve chronic inflammation, which could be associated with an auto-reactive immune response, and gradually with a decrease in the regenerative capacities of the muscle, leading to its degeneration, fibrosis and vascular architecture deterioration. Immunosuppressive treatments can block the first part of the process, but sometimes muscle remains weakened, or even still deteriorates, due to the exhaustion of its capacities. For patients refractory to immunosuppressive therapies, mesenchymal stem cells have shown interesting effects but their use is limited by their availability. Stromal vascular fraction, which can easily be extracted from adipose tissue, has shown good tolerance and possible therapeutic benefits in several degenerative and autoimmune diseases. However, despite the increasing use of stromal vascular fraction, the therapeutically active components within this heterogeneous cellular product are ill-defined and the mechanisms by which this therapy might be active remain insufficiently understood. We review herein the current knowledge on the mechanisms of action of stromal vascular fraction and hypothesise on how it could potentially respond to some of the unmet treatment needs of refractory myositis.
Cross-species analysis of SHH medulloblastoma models reveals significant inhibitory effects of trametinib on tumor progression
Authors: Borlase Stephanie , DeCarlo Alexandria , Coudière-Morrison Ludivine , Liang Lisa , Porter Christopher J. , Ramaswamy Vijay , Werbowetski-Ogilvie Tamra E. 
Published: September 2023

AbstractSonic Hedgehog (SHH) medulloblastomas (MBs) exhibit an intermediate prognosis and extensive intertumoral heterogeneity. While SHH pathway antagonists are effective in post-pubertal patients, younger patients exhibit significant side effects, and tumors that harbor mutations in downstream SHH pathway genes will be drug resistant. Thus, novel targeted therapies are needed. Here, we performed preclinical testing of the potent MEK inhibitor (MEKi) trametinib on tumor properties across 2 human and 3 mouse SHH MB models in vitro and in 3 orthotopic MB xenograft models in vivo. Trametinib significantly reduces tumorsphere size, stem/progenitor cell proliferation, viability, and migration. RNA-sequencing on human and mouse trametinib treated cells corroborated these findings with decreased expression of cell cycle, stem cell pathways and SHH-pathway related genes concomitant with increases in genes associated with cell death and ciliopathies. Importantly, trametinib also decreases tumor growth and increases survival in vivo. Cell cycle related E2F target gene sets are significantly enriched for genes that are commonly downregulated in both trametinib treated tumorspheres and primary xenografts. However, IL6/JAK STAT3 and TNFα/NFκB signaling gene sets are specifically upregulated following trametinib treatment in vivo indicative of compensatory molecular changes following long-term MEK inhibition. Our study reveals a novel role for trametinib in effectively attenuating SHH MB tumor progression and warrants further investigation of this potent MEK1/2 inhibitor either alone or in combination with other targeted therapies for the treatment of SHH MB exhibiting elevated MAPK pathway activity.
Integrated meta-omics approaches reveal Saccharopolyspora as the core functional genus in huangjiu fermentations
Authors: Liu Shuangping , Zhang Zhi-Feng , Mao Jieqi , Zhou Zhilei , Zhang Jing , Shen Caihong , Wang Songtao , Marco Maria L. , Mao Jian 
Published: September 2023

AbstractIdentification of the core functional microorganisms in food fermentations is necessary to understand the ecological and functional processes for making those foods. Wheat qu, which provides liquefaction and saccharifying power, and affects the flavor quality, is a key ingredient in ancient alcoholic huangjiu fermentation, while core microbiota of them still remains indistinct. In this study, metagenomics, metabolomics, microbial isolation and co-fermentation were used to investigate huangjiu. Although Aspergillus is usually regarded as core microorganism in wheat qu to initiate huangjiu fermentations, our metagenomic analysis showed that bacteria Saccharopolyspora are predominant in wheat qu and responsible for breakdown of starch and cellulose. Metabolic network and correlation analysis showed that Saccharopolyspora rectivirgula, Saccharopolyspora erythraea, and Saccharopolyspora hirsuta made the greatest contributions to huangjiu’s metabolites, consisting of alcohols (phenylethanol, isoamylol and isobutanol), esters, amino acids (Pro, Arg, Glu and Ala) and organic acids (lactate, tartrate, acetate and citrate). S. hirsuta J2 isolated from wheat qu had the highest amylase, glucoamylase and protease activities. Co-fermentations of S. hirsuta J2 with S. cerevisiae HJ resulted in a higher fermentation rate and alcohol content, and huangjiu flavors were more similar to that of traditional huangjiu compared to co-fermentations of Aspergillus or Lactiplantibacillus with S. cerevisiae HJ. Genome of S. hirsuta J2 contained genes encoding biogenic amine degradation enzymes. By S. hirsuta J2 inoculation, biogenic amine content was reduced by 45%, 43% and 62% in huangjiu, sausage and soy sauce, respectively. These findings show the utility of Saccharopolyspora as a key functional organism in fermented food products.
Endogenous tenocyte activation underlies the regenerative capacity of the adult zebrafish tendon
Authors: Tsai Stephanie L. , Villaseñor Steffany , Shah Rishita R. , Galloway Jenna L. 
Published: September 2023

AbstractTendons are essential, frequently injured connective tissues that transmit forces from muscle to bone. Their unique highly ordered, matrix-rich structure is critical for proper function. While adult mammalian tendons heal after acute injuries, endogenous tendon cells, or tenocytes, fail to respond appropriately, resulting in the formation of disorganized fibrovascular scar tissue with impaired function and increased propensity for re-injury. Here, we show that, unlike mammals, adult zebrafish tenocytes activate upon injury and fully regenerate the tendon. Using a full tear injury model in the adult zebrafish craniofacial tendon, we defined the hallmark stages and cellular basis of tendon regeneration through multiphoton imaging, lineage tracing, and transmission electron microscopy approaches. Remarkably, we observe that zebrafish tendons regenerate and restore normal collagen matrix ultrastructure by 6 months post-injury (mpi). Tendon regeneration progresses in three main phases: inflammation within 24 h post-injury (hpi), cellular proliferation and formation of a cellular bridge between the severed tendon ends at 3–5 days post-injury (dpi), and re-differentiation and matrix remodeling beginning from 5 dpi to 6 mpi. Importantly, we demonstrate that pre-existing tenocytes are the main cellular source of regeneration, proliferating and migrating upon injury to ultimately bridge the tendon ends. Finally, we show that TGF-β signaling is required for tenocyte recruitment and bridge formation. Collectively, our work debuts and aptly positions the adult zebrafish tendon as an invaluable comparative system to elucidate regenerative mechanisms that may inspire new therapeutic strategies.
A large-scale LC-MS dataset of murine liver proteome from time course of heavy water metabolic labeling
Authors: Deberneh Henock M. , Abdelrahman Doaa R. , Verma Sunil K. , Linares Jennifer J. , Murton Andrew J. , Russell William K. , Kuyumcu-Martinez Muge N. , Miller Benjamin F. , Sadygov Rovshan G. 
Published: September 2023

AbstractMetabolic stable isotope labeling with heavy water followed by liquid chromatography coupled with mass spectrometry (LC-MS) is a powerful tool for in vivo protein turnover studies. Several algorithms and tools have been developed to determine the turnover rates of peptides and proteins from time-course stable isotope labeling experiments. The availability of benchmark mass spectrometry data is crucial to compare and validate the effectiveness of newly developed techniques and algorithms. In this work, we report a heavy water-labeled LC-MS dataset from the murine liver for protein turnover rate analysis. The dataset contains eighteen mass spectral data with their corresponding database search results from nine different labeling durations and quantification outputs from d2ome+ software. The dataset also contains eight mass spectral data from two-dimensional fractionation experiments on unlabeled samples.
Robertsonian fusion triggers recombination suppression on sex chromosomes in Coleonyx geckos
Authors: Lisachov Artem , Tishakova Katerina , Romanenko Svetlana , Lisachova Lada , Davletshina Guzel , Prokopov Dmitry , Kratochvíl Lukáš , O`Brien Patricia , Ferguson-Smith Malcolm , Borodin Pavel , Trifonov Vladimir 
Published: September 2023

AbstractThe classical hypothesis proposes that the lack of recombination on sex chromosomes arises due to selection for linkage between a sex-determining locus and sexually antagonistic loci, primarily facilitated by inversions. However, cessation of recombination on sex chromosomes could be attributed also to neutral processes, connected with other chromosome rearrangements or can reflect sex-specific recombination patterns existing already before sex chromosome differentiation. Three Coleonyx gecko species share a complex X1X1X2X2/X1X2Y system of sex chromosomes evolved via a fusion of the Y chromosome with an autosome. We analyzed synaptonemal complexes and sequenced flow-sorted sex chromosomes to investigate the effect of chromosomal rearrangement on recombination and differentiation of these sex chromosomes. The gecko sex chromosomes evolved from syntenic regions that were also co-opted also for sex chromosomes in other reptiles. We showed that in male geckos, recombination is less prevalent in the proximal regions of chromosomes and is even further drastically reduced around the centromere of the neo-Y chromosome. We highlight that pre-existing recombination patterns and Robertsonian fusions can be responsible for the cessation of recombination on sex chromosomes and that such processes can be largely neutral.
Intermediate LET-like effect in distal part of proton Bragg peak revealed by track-ends imaging during super-Fricke radiolysis
Authors: Audouin J. , Hofverberg P. , Ngono-Ravache Y. , Desorgher L. , Baldacchino G. 
Published: September 2023

AbstractUpstream of the efficiency of proton or carbon ion beams in cancer therapy, and to optimize hadrontherapy results, we analysed the chemistry of Fricke solutions in track-end of 64-MeV protons and 1.14-GeV carbon ions. An original optical setup is designed to determine the primary track-segment yields along the last millimetres of the ion track with a sub-millimetre resolution. The Fe3+-yield falls in the Bragg peak to (4.9 ± 0.4) × 10–7 mol/J and 1.9 × 10–7 mol/J, under protons and carbon ions respectively. Beyond the Bragg peak, a yield recovery is observed over 1 mm for proton beams. It is attributed to the intermediate-LET of protons in this region where their energy decreases and energy distribution becomes broader, in relation with the longitudinal straggling of the beam. Consequently to this LET decrease in the distal part of the Bragg peak, Fe3+-yield increases. For the first time, this signature is highlighted at the chemical level under proton irradiation. Nevertheless, this phenomenon is not identified for carbon ion beams since their straggling is lower. It would need a greater spatial resolution to be observed.
Oxidative stress induces mitochondrial iron overload and ferroptotic cell death
Authors: Chen Yi , Guo Xiaoyun , Zeng Yachang , Mo Xiaoliang , Hong Siqi , He Hui , Li Jing , Fatima Sulail , Liu Qinghang 
Published: September 2023

AbstractOxidative stress has been shown to induce cell death in a wide range of human diseases including cardiac ischemia/reperfusion injury, drug induced cardiotoxicity, and heart failure. However, the mechanism of cell death induced by oxidative stress remains incompletely understood. Here we provide new evidence that oxidative stress primarily induces ferroptosis, but not apoptosis, necroptosis, or mitochondria-mediated necrosis, in cardiomyocytes. Intriguingly, oxidative stress induced by organic oxidants such as tert-butyl hydroperoxide (tBHP) and cumene hydroperoxide (CHP), but not hydrogen peroxide (H2O2), promoted glutathione depletion and glutathione peroxidase 4 (GPX4) degradation in cardiomyocytes, leading to increased lipid peroxidation. Moreover, elevated oxidative stress is also linked to labile iron overload through downregulation of the transcription suppressor BTB and CNC homology 1 (Bach1), upregulation of heme oxygenase 1 (HO-1) expression, and enhanced iron release via heme degradation. Strikingly, oxidative stress also promoted HO-1 translocation to mitochondria, leading to mitochondrial iron overload and lipid reactive oxygen species (ROS) accumulation. Targeted inhibition of mitochondrial iron overload or ROS accumulation, by overexpressing mitochondrial ferritin (FTMT) or mitochondrial catalase (mCAT), respectively, markedly inhibited oxidative stress-induced ferroptosis. The levels of mitochondrial iron and lipid peroxides were also markedly increased in cardiomyocytes subjected to simulated ischemia and reperfusion (sI/R) or the chemotherapeutic agent doxorubicin (DOX). Overexpressing FTMT or mCAT effectively prevented cardiomyocyte death induced by sI/R or DOX. Taken together, oxidative stress induced by organic oxidants but not H2O2 primarily triggers ferroptotic cell death in cardiomyocyte through GPX4 and Bach1/HO-1 dependent mechanisms. Our results also reveal mitochondrial iron overload via HO-1 mitochondrial translocation as a key mechanism as well as a potential molecular target for oxidative stress-induced ferroptosis in cardiomyocytes.
Reservoir computing using self-sustained oscillations in a locally connected neural network
Authors: Kawai Yuji , Park Jihoon , Asada Minoru 
Published: September 2023

AbstractUnderstanding how the structural organization of neural networks influences their computational capabilities is of great interest to both machine learning and neuroscience communities. In our previous work, we introduced a novel learning system, called the reservoir of basal dynamics (reBASICS), which features a modular neural architecture (small-sized random neural networks) capable of reducing chaoticity of neural activity and of producing stable self-sustained limit cycle activities. The integration of these limit cycles is achieved by linear summation of their weights, and arbitrary time series are learned by modulating these weights. Despite its excellent learning performance, interpreting a modular structure of isolated small networks as a brain network has posed a significant challenge. Here, we investigate how local connectivity, a well-known characteristic of brain networks, contributes to reducing neural system chaoticity and generates self-sustained limit cycles based on empirical experiments. Moreover, we present the learning performance of the locally connected reBASICS in two tasks: a motor timing task and a learning task of the Lorenz time series. Although its performance was inferior to that of modular reBASICS, locally connected reBASICS could learn a time series of tens of seconds while the time constant of neural units was ten milliseconds. This work indicates that the locality of connectivity in neural networks may contribute to generation of stable self-sustained oscillations to learn arbitrary long-term time series, as well as the economy of wiring cost.
Loss of Grin2a causes a transient delay in the electrophysiological maturation of hippocampal parvalbumin interneurons
Authors: Camp Chad R. , Vlachos Anna , Klöckner Chiara , Krey Ilona , Banke Tue G. , Shariatzadeh Nima , Ruggiero Sarah M. , Galer Peter , Park Kristen L. , Caccavano Adam , Kimmel Sarah , Yuan Xiaoqing , Yuan Hongjie , Helbig Ingo , Benke Tim A. , Lemke Johannes R. , Pelkey Kenneth A. , McBain Chris J. , Traynelis Stephen F. 
Published: September 2023

AbstractN-methyl-D-aspartate receptors (NMDARs) are ligand-gated ionotropic glutamate receptors that mediate a calcium-permeable component to fast excitatory neurotransmission. NMDARs are heterotetrameric assemblies of two obligate GluN1 subunits (GRIN1) and two GluN2 subunits (GRIN2A-GRIN2D). Sequencing data shows that 43% (297/679) of all currently known NMDAR disease-associated genetic variants are within the GRIN2A gene, which encodes the GluN2A subunit. Here, we show that unlike missense GRIN2A variants, individuals affected with disease-associated null GRIN2A variants demonstrate a transient period of seizure susceptibility that begins during infancy and diminishes near adolescence. We show increased circuit excitability and CA1 pyramidal cell output in juvenile mice of both Grin2a+/− and Grin2a−/− mice. These alterations in somatic spiking are not due to global upregulation of most Grin genes (including Grin2b). Deeper evaluation of the developing CA1 circuit led us to uncover age- and Grin2a gene dosing-dependent transient delays in the electrophysiological maturation programs of parvalbumin (PV) interneurons. We report that Grin2a+/+ mice reach PV cell electrophysiological maturation between the neonatal and juvenile neurodevelopmental timepoints, with Grin2a+/− mice not reaching PV cell electrophysiological maturation until preadolescence, and Grin2a−/− mice not reaching PV cell electrophysiological maturation until adulthood. Overall, these data may represent a molecular mechanism describing the transient nature of seizure susceptibility in disease-associated null GRIN2A patients.
Organic photothermal cocrystal with high stability for efficient solar-driven water evaporation
Authors: Jiang Mengjia , Su Yi , Li Shuyu , Fu Siyao , Wang Lingsong , Khan Darya , Sun Yajing , Sun Lingjie , Zhang Xiaotao , Hu Wenping 
Published: September 2023

A novel photothermal conversion cocrystal of TMBZ-TCNB exhibiting 59.46% photothermal efficiency under 808 nm laser radiation. The TMBZ-TCNB-PU interfacial evaporator shows an evaporation efficiency of 63.49% under 1 kW m−2 radiation.
A model for the infrared-radio correlation of main sequence galaxies at gigahertz frequencies and its variation with redshift and stellar mass
Authors: Schober J. , Sargent M. T. , Klessen R. S. , Schleicher D. R. G. 
Published: September 2023

Context. The infrared-radio correlation (IRRC) of star-forming galaxies can be used to estimate their star formation rate (SFR) based on the radio continuum luminosity at MHz–GHz frequencies. For its practical application in future deep radio surveys, it is crucial to know whether the IRRC persists at high redshift z.
Aims. Previous works have reported that the 1.4 GHz IRRC correlation of star-forming galaxies is nearly z-invariant up to z ≈ 4, but depends strongly on the stellar mass M⋆. This should be taken into account for SFR calibrations based on radio luminosity.
Methods. To understand the physical cause behind the M⋆ dependence of the IRRC and its properties at higher z, we constructed a phenomenological model for galactic radio emission. Our model is based on a dynamo-generated magnetic field and a steady-state cosmic ray population. It includes a number of free parameters that determine the galaxy properties. To reduce the overall number of model parameters, we also employed observed scaling relations.
Results. We find that the resulting spread of the infrared-to-radio luminosity ratio, q(z, M⋆), with respect to M⋆ is mostly determined by the scaling of the galactic radius with M⋆, while the absolute value of the q(z, M⋆) curves decreases with more efficient conversion of supernova energy to magnetic fields and cosmic rays. Additionally, decreasing the slope of the cosmic ray injection spectrum, αCR, results in higher radio luminosity, decreasing the absolute values of the q(z, M⋆) curves. Within the uncertainty range of our model, the observed dependence of the IRRC on M⋆ and z can be reproduced when the efficiency of supernova-driven turbulence is 5%, 10% of the kinetic energy is converted into magnetic energy, and αCR ≈ 3.0.
Conclusions. For galaxies with intermediate to high (M⋆ ≈ 109.5 − 1011 M⊙) stellar masses, our model results in an IRRC that is nearly independent of z. For galaxies with lower masses (M⋆ ≈ 108.5 M⊙), we find that the IR-to-radio flux ratio increases with increasing redshift. This matches the observational data in that mass bin which, however, only extends to z ≈ 1.5. The increase in the IR-to-radio flux ratio for low-mass galaxies at z ≳ 1.5 that is predicted by our model could be tested with future deep radio observations.
CRIRES-POP: A library of high resolution spectra in the near-infrared
Authors: Zendel M. , Lebzelter T. , Nicholls C. P. 
Published: September 2023

Context. High-resolution spectra in the near-infrared (NIR) are an important tool for the detailed study of stellar atmospheres. The accurate identification of elements and molecules in these spectra can be used to determine chemical abundances and physical conditions in the photosphere of the observed star. Such identifications require precise line positions and strengths of both atomic and molecular features.
Aims. This work focusses on the full identification of absorption lines in the NIR spectrum of the K-giant 10 Leo, including previously unidentified lines. The large number and complexity of the observed absorption lines require a deep search for potential spectral signatures to enable an unambiguous assignment to specific elements or molecular species. We aim to improve the published line lists of metals, some of which are determined by model calculations only, and many of which presently lack the completeness and accuracy of line parameters.
Methods. The CRIRES-POP project provided high-resolution, high signal-to-noise ratio (S/N) spectra of several bright stars in the 1–5 μm range. For the K-giant 10 Leo, a spectrum corrected for telluric absorption and with precise wavelength calibration is available. This has been analysed by comparison with model spectra and up-to-date line lists.
Results. We identified lines of 29 elements and eight molecular species. While the positions of many known lines could be confirmed, about 6% of all lines detected in 10 Leo could not be attributed to any known feature. For CO and its isotopologues, molecular constants could be derived and several additional lines identified. We report major inconsistencies for some prominent lines. In addition, abundances for several key elements in 10 Leo are provided.