bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring the ICM velocity structure in the Ophiuchus cluster
Authors: Gatuzz Efrain , Sanders J S , Dennerl K , Liu A , Fabian A C , Pinto C , Eckert D , Russell H , Tamura T , Walker S A , ZuHone J 
Published: April 2023

ABSTRACT
We have found evidence of bulk velocities following active galactic nucleus (AGN) bubbles in the Virgo cluster and galaxy motions in the Centaurus cluster. In order to increase the sample and improve our understanding of the intracluster medium (ICM), we present the results of a detailed mapping of the Ophiuchus cluster with XMM–Newton to measure bulk flows through very accurate Fe-K measurements. To measure the gas velocities, we use a novel EPIC-pn energy-scale calibration, which uses the Cu Kα instrumental line as reference for the line emission. We created 2D spectral maps for the velocity, metallicity, temperature, density, entropy, and pressure with a spatial resolution of 0.25 arcmin (∼26 kpc). The ICM velocities in the central regions where AGN feedback is most important are similar to the velocity of the brightest cluster galaxy. We have found a large interface region where the velocity changes abruptly from blueshifted to redshifted gas that follows a sharp surface brightness discontinuity. We also found that the metallicities and temperatures do not change as we move outwards from the giant radio fossil previously identified in radio observations of the cluster. Finally, we have found a contribution from the kinetic component of $\lt 25{{\ \rm per\ cent}}$ to the total energy budget for large distances.
On the anticorrelation between pericentric distance and inner dark matter density of Milky Way’s dwarf spheroidal galaxies
Authors: Cardona-Barrero Salvador , Battaglia Giuseppina , Nipoti Carlo , Di Cintio Arianna 
Published: April 2023

ABSTRACT
An anticorrelation between the central density of the dark matter (DM) halo (ρ150, DM) and the pericentric distances (rp) of the Milky Way’s (MW’s) dwarf spheroidal galaxies (dSphs) has been reported in the literature. The existence and origin of such anticorrelation are, however, controversial, one possibility being that only the densest dSphs can survive the tidal field towards the centre of our Galaxy. In this work, we place particular emphasis on quantifying the statistical significance of such anticorrelation, by using available literature data in order to explore its robustness under different assumptions on the MW gravitational potential, and for various derivations of ρ150 and rp. We consider models in which the MW is isolated and has low ($8.8\times 10^{11}\, {\rm M}_{\odot }$ ) and high ($1.6\times 10^{12}\, {\rm M}_{\odot }$ ) halo masses, respectively, as well as configurations in which the MW’s potential is perturbed by a Large Magellanic Cloud (LMC) infall. We find that, while data generally support models in which the dSphs’ central DM density decreases as a function of their pericentric radius, this anticorrelation is statistically significant at 3σ level only in ${\sim} 12~{{ \rm per\ cent}}$ of the combinations of ρ150 and rp explored. Moreover, including the impact of the LMC’s infall on to the MW weakens or even washes away this anticorrelation, with respect to models in which the MW is isolated. Our results suggest that the strength and existence of such anticorrelation are still debatable: exploring it with high-resolution simulations including baryonic physics and different DM flavours will help us to understand its emergence.
Spectroscopic and photometric studies on four solar-type short-period contact binaries in the triple stellar systems
Authors: Yang Yuangui , Michel Raúl , Yuan Huiyu , Wang Shuang , Tamayo Francisco 
Published: April 2023

ABSTRACT
We reported new spectroscopy and photometry for four short-period binaries, which were acquired by several small telescopes in China from 2020 to 2022. From new spectrum and Large Sky Area Multiobject Fiber Spectroscopic Telescope data, we determined their spectral types of G8V for PZ UMa, G7 for MM Com, and V0685 Peg and G3 for V1055 Her. When compared to the Transiting Exoplanet Survey Satellite (TESS) light curve (LC) with a 2-min cadence, the difference between two light maxima for V1055 Her displays a 29.7-d oscillation. Utilizing the Wilson–Devinney program, we deduced 10 photometric solutions from our new and TESS data. Four binaries are W-type ones with variable O’Connell effects. For LC2022.1 (MM Com) and LC2022.9 (V1055 Her), Δmmax=Max.I–Max.II is as large as $15{{\ \rm per\ cent}}$ of variable light amplitude, which may be attributed to the spot’s migration and evolution. From the mass-luminosity diagram, the more massive components aref somewhat evolved main-sequence stars, whereas the less massive ones are overluminous as a result of energy exchange. Based on all eclipse timing residuals, the orbital period variations are preferably described by the light-travel time effects via the presence of additional companions. Their modulation periods range from 10 to 20 yr for four binaries, corresponding the companion’s mass ranging from M3 = 0.11 to 0.34 M⊙. Therefore, four solar-type short-period contact binaries (i.e. MM Com, PZ UMa, V0685 Peg, and V1055 Her) may be triple stellar systems.
Deletion of the mRNA stability factor ELAVL1 (HuR) in pancreatic cancer cells disrupts the tumor microenvironment integrity
Authors: McCarthy Grace A , Di Niro Roberto , Finan Jennifer M , Jain Aditi , Guo Yifei , Wyatt Cory R , Guimaraes Alexander R , Waugh Trent A , Keith Dove , Morgan Terry K , Sears Rosalie C , Brody Jonathan R 
Published: April 2023

Abstract
Stromal cells promote extensive fibrosis in pancreatic ductal adenocarcinoma (PDAC), which is associated with poor prognosis and therapeutic resistance. We report here for the first time that loss of the RNA-binding protein human antigen R (HuR, ELAVL1) in PDAC cells leads to reprogramming of the tumor microenvironment. In multiple in vivo models, CRISPR deletion of ELAVL1 in PDAC cells resulted in a decrease of collagen deposition, accompanied by a decrease of stromal markers (i.e. podoplanin, α-smooth muscle actin, desmin). RNA-sequencing data showed that HuR plays a role in cell–cell communication. Accordingly, cytokine arrays identified that HuR regulates the secretion of signaling molecules involved in stromal activation and extracellular matrix organization [i.e. platelet-derived growth factor AA (PDGFAA) and pentraxin 3]. Ribonucleoprotein immunoprecipitation analysis and transcription inhibition studies validated PDGFA mRNA as a novel HuR target. These data suggest that tumor-intrinsic HuR supports extrinsic activation of the stroma to produce collagen and desmoplasia through regulating signaling molecules (e.g. PDGFAA). HuR-deficient PDAC in vivo tumors with an altered tumor microenvironment are more sensitive to the standard of care gemcitabine, as compared to HuR-proficient tumors. Taken together, we identified a novel role of tumor-intrinsic HuR in its ability to modify the surrounding tumor microenvironment and regulate PDGFAA.
HiTAIC: hierarchical tumor artificial intelligence classifier traces tissue of origin and tumor type in primary and metastasized tumors using DNA methylation
Authors: Zhang Ze , Lu Yunrui , Vosoughi Soroush , Levy Joshua J , Christensen Brock C , Salas Lucas A 
Published: April 2023

Abstract
Human cancers are heterogenous by their cell composition and origination site. Cancer metastasis generates the conundrum of the unknown origin of migrated tumor cells. Tracing tissue of origin and tumor type in primary and metastasized cancer is vital for clinical significance. DNA methylation alterations play a crucial role in carcinogenesis and mark cell fate differentiation, thus can be used to trace tumor tissue of origin. In this study, we employed a novel tumor-type-specific hierarchical model using genome-scale DNA methylation data to develop a multilayer perceptron model, HiTAIC, to trace tissue of origin and tumor type in 27 cancers from 23 tissue sites in data from 7735 tumors with high resolution, accuracy, and specificity. In tracing primary cancer origin, HiTAIC accuracy was 99% in the test set and 93% in the external validation data set. Metastatic cancers were identified with a 96% accuracy in the external data set. HiTAIC is a user-friendly web-based application through https://sites.dartmouth.edu/salaslabhitaic/. In conclusion, we developed HiTAIC, a DNA methylation-based algorithm, to trace tumor tissue of origin in primary and metastasized cancers. The high accuracy and resolution of tumor tracing using HiTAIC holds promise for clinical assistance in identifying cancer of unknown origin.
Stem-like signatures in human meningioma cells are under the control of CXCL11/CXCL12 chemokine activity
Authors: Barbieri Federica , Bajetto Adriana , Dellacasagrande Irene , Solari Agnese , Würth Roberto , Fernandez Virginia , Rancati Silvia , Ceresa Davide , Appolloni Irene , De Luca Giuseppa , Dono Mariella , Nozza Paolo , Schiapparelli Piero , Gambaro Monica , Fiaschi Pietro , Gaggero Gabriele , Costanzo Nicolò , Thellung Stefano , Malatesta Paolo , Pagano Aldo , Zona Gianluigi , De Pietri Tonelli Davide , Florio Tullio 
Published: April 2023

Abstract

Background
Meningiomas are mainly benign brain tumors, although about 20% of histologically benign cases are clinically aggressive and recur after resection. We hypothesize that meningioma brain invasiveness and recurrence may be related to the presence of cancer stem cells and their high responsiveness to the CXCL12-CXCR4/CXCR7 chemokine axis. The aim of this study was to isolate meningioma stem cells from human samples, characterize them for biological features related to malignant behavior, and to identify the role of CXCR4/CXCR7 in these processes.

Methods
Meningioma stem cells were isolated from patient-derived primary cultures in stem cell-permissive conditions, and characterized for phenotype, self-renewal, proliferation and migration rates, vasculogenic mimicry (VM), and in vivo tumorigenesis, in comparison with differentiated meningioma cells and stem-like cells isolated from normal meninges. These cell populations were challenged with CXCL12 and CXCL11 and receptor antagonists to define the chemokine role in stem cell-related functions.

Results
Stem-like cells isolated from meningioma cultures display higher proliferation and migration rates, and VM, as compared to meningioma non-stem cells or cells isolated from normal meninges and were the only tumorigenic population in vivo. In meningioma cells, these stem-like functions were under the control of the CXCR4/CXCR7 chemokine axis.

Conclusions
We report a role for CXCL11 and CXCL12 in the control of malignant features in stem-like cells isolated from human meningioma, providing a possible basis for the aggressive clinical behavior observed in subsets of these tumors. CXCR4/CXCR7 antagonists might represent a useful approach for meningioma at high risk of recurrence and malignant progression.
Predicting methylation class from diffusely infiltrating adult gliomas using multimodality MRI data
Authors: Alom Zahangir , Tran Quynh T , Bag Asim K , Lucas John T , Orr Brent A 
Published: April 2023

Abstract

Background
Radiogenomic studies of adult-type diffuse gliomas have used magnetic resonance imaging (MRI) data to infer tumor attributes, including abnormalities such as IDH-mutation status and 1p19q deletion. This approach is effective but does not generalize to tumor types that lack highly recurrent alterations. Tumors have intrinsic DNA methylation patterns and can be grouped into stable methylation classes even when lacking recurrent mutations or copy number changes. The purpose of this study was to prove the principle that a tumor’s DNA-methylation class could be used as a predictive feature for radiogenomic modeling.

Methods
Using a custom DNA methylation-based classification model, molecular classes were assigned to diffuse gliomas in The Cancer Genome Atlas (TCGA) dataset. We then constructed and validated machine learning models to predict a tumor’s methylation family or subclass from matched multisequence MRI data using either extracted radiomic features or directly from MRI images.

Results
For models using extracted radiomic features, we demonstrated top accuracies above 90% for predicting IDH-glioma and GBM-IDHwt methylation families, IDH-mutant tumor methylation subclasses, or GBM-IDHwt molecular subclasses. Classification models utilizing MRI images directly demonstrated average accuracies of 80.6% for predicting methylation families, compared to 87.2% and 89.0% for differentiating IDH-mutated astrocytomas from oligodendrogliomas and glioblastoma molecular subclasses, respectively.

Conclusions
These findings demonstrate that MRI-based machine learning models can effectively predict the methylation class of brain tumors. Given appropriate datasets, this approach could generalize to most brain tumor types, expanding the number and types of tumors that could be used to develop radiomic or radiogenomic models.
Diffuse leptomeningeal glioneuronal tumor in a child masquerading as an intramedullary spinal pilocytic astrocytoma
Authors: Madsen Peter J , Hollawell Madison L , Santi Mariarita , Surrey Lea F , Vossough Arastoo , Orr Brent A , Hill-Kayser Christine , Tucker Alexander M , Storm Phillip B , Foster Jessica B 
Published: April 2023

Abstract
Diffuse leptomeningeal glioneuronal tumor (DLGNT) occurs predominantly in children and is typically characterized by diffuse leptomeningeal lesions throughout the neuroaxis with focal segments of parenchymal involvement. Recent reports have identified cases without diffuse leptomeningeal involvement that retain classic glioneuronal features on histology. In this report, we present a case of a 4-year-old boy with a large cystic-solid intramedullary spinal cord lesion that on surgical biopsy revealed a biphasic astrocytic tumor with sparsely distributed eosinophilic granular bodies and Rosenthal fibers. Next-generation sequencing revealed a KIAA1549-BRAF fusion, 1p/19q codeletion, and lack of an IDH1 mutation. Methylation profiling demonstrated a calibrated class score of 0.98 for DLGNT and copy number loss of 1p. Despite the morphologic similarities to pilocytic astrocytoma and the lack of oligodendroglial/neuronal components or leptomeningeal dissemination, the molecular profile was definitive in classifying the tumor as DLGNT. This case highlights the importance of molecular and genetic testing in the characterization of pediatric central nervous system tumors.
Persistence of Human Immunodeficiency Virus–Associated Cerebral Toxoplasmosis Lesions in Successfully Treated Patients Receiving Combination Antiretroviral Therapy
Authors: Coleman Benjamin , Smith Bryan R , Kapoor Rama , Proschan Michael A , Sereti Irini , Hammoud Dima A , Kovacs Joseph A 
Published: April 2023

Abstract

Background
Toxoplasmic encephalitis (TE) is a life-threatening complication of people with human immunodeficiency virus (PWH) with severe immunodeficiency, especially those with a CD4+ T-cell count &lt;100 cells/µL. Following a clinical response to anti-Toxoplasma therapy, and immune reconstitution after initiation of combination antiretroviral therapy (ART), anti-Toxoplasma therapy can be discontinued with a low risk of relapse.

Methods
To better understand the evolution of magnetic resonance imaging (MRI)–defined TE lesions in PWH receiving ART, we undertook a retrospective study of PWH initially seen at the National Institutes of Health between 2001 and 2012, who had at least 2 serial MRI scans. Lesion size and change over time were calculated and correlated with clinical parameters.

Results
Among 24 PWH with TE and serial MRI scans, only 4 had complete clearance of lesions at the last MRI (follow-up, 0.09–5.8 years). Of 10 PWH off all anti-Toxoplasma therapy (median, 3.2 years after TE diagnosis), 6 had persistent MRI enhancement. In contrast, all 5 PWH seen in a pre–ART era study who were followed for &gt;6 months had complete clearance of lesions. TE lesion area at diagnosis was associated with the absolute change in area (P &lt; .0001).

Conclusions
Contrast enhancement can persist even when TE has been successfully treated and anti-Toxoplasma therapy has been stopped, highlighting the need to consider diagnostic alternatives in successfully treated patients with immune reconstitution presenting with new neurologic symptoms.
Hormone-regulated expansins: Expression, localization, and cell wall biomechanics in Arabidopsis root growth
Authors: Samalova Marketa , Melnikava Alesia , Elsayad Kareem , Peaucelle Alexis , Gahurova Evelina , Gumulec Jaromir , Spyroglou Ioannis , Zemlyanskaya Elena V , Ubogoeva Elena V , Balkova Darina , Demko Martin , Blavet Nicolas , Alexiou Panagiotis , Benes Vladimir , Mouille Gregory , Hejatko Jan 
Published: April 2023

Abstract
Expansins facilitate cell expansion by mediating pH-dependent cell wall (CW) loosening. However, the role of expansins in controlling CW biomechanical properties in specific tissues and organs remains elusive. We monitored hormonal responsiveness and spatial specificity of expression and localization of expansins predicted to be the direct targets of cytokinin signaling in Arabidopsis (Arabidopsis thaliana). We found EXPANSIN1 (EXPA1) homogenously distributed throughout the CW of columella/lateral root cap, while EXPA10 and EXPA14 localized predominantly at 3-cell boundaries in the epidermis/cortex in various root zones. EXPA15 revealed cell-type-specific combination of homogenous vs. 3-cell boundaries localization. By comparing Brillouin frequency shift and AFM-measured Young's modulus, we demonstrated Brillouin light scattering (BLS) as a tool suitable for non-invasive in vivo quantitative assessment of CW viscoelasticity. Using both BLS and AFM, we showed that EXPA1 overexpression upregulated CW stiffness in the root transition zone (TZ). The dexamethasone-controlled EXPA1 overexpression induced fast changes in the transcription of numerous CW-associated genes, including several EXPAs and XYLOGLUCAN:XYLOGLUCOSYL TRANSFERASEs (XTHs), and associated with rapid pectin methylesterification determined by in situ Fourier-transform infrared spectroscopy in the root TZ. The EXPA1-induced CW remodeling is associated with the shortening of the root apical meristem, leading to root growth arrest. Based on our results, we propose that expansins control root growth by a delicate orchestration of CW biomechanical properties, possibly regulating both CW loosening and CW remodeling.
Prognostic value of automated assessment of interstitial lung disease on CT in systemic sclerosis
Authors: Le Gall Aëlle , Hoang-Thi Trieu-Nghi , Porcher Raphaël , Dunogué Bertrand , Berezné Alice , Guillevin Loïc , Le Guern Véronique , Cohen Pascal , Chaigne Benjamin , London Jonathan , Groh Matthieu , Paule Romain , Chassagnon Guillaume , Vakalopoulou Maria , Dinh-Xuan Anh-Tuan , Revel Marie Pierre , Mouthon Luc , Régent Alexis 
Published: April 2023

Abstract

Objective
Stratifying the risk of death in SSc-related interstitial lung disease (SSc-ILD) is a challenging issue. The extent of lung fibrosis on high-resolution CT (HRCT) is often assessed by a visual semiquantitative method that lacks reliability. We aimed to assess the potential prognostic value of a deep-learning–based algorithm enabling automated quantification of ILD on HRCT in patients with SSc.

Methods
We correlated the extent of ILD with the occurrence of death during follow-up, and evaluated the additional value of ILD extent in predicting death based on a prognostic model including well-known risk factors in SSc.

Results
We included 318 patients with SSc, among whom 196 had ILD; the median follow-up was 94 months (interquartile range 73–111). The mortality rate was 1.6% at 2 years and 26.3% at 10 years. For each 1% increase in the baseline ILD extent (up to 30% of the lung), the risk of death at 10 years was increased by 4% (hazard ratio 1.04, 95% CI 1.01, 1.07, P = 0.004). We constructed a risk prediction model that showed good discrimination for 10-year mortality (c index 0.789). Adding the automated quantification of ILD significantly improved the model for 10-year survival prediction (P = 0.007). Its discrimination was only marginally improved, but it improved prediction of 2-year mortality (difference in time-dependent area under the curve 0.043, 95% CI 0.002, 0.084, P = 0.040).

Conclusion
The deep-learning–based, computer-aided quantification of ILD extent on HRCT provides an effective tool for risk stratification in SSc. It might help identify patients at short-term risk of death.
Life stress and suicidality mediated by insomnia and depressive symptoms in adolescents: a three-wave longitudinal study
Authors: Liu Xianchen , Yang Yanyun , Liu Zhen-Zhen , Jia Cun-Xian 
Published: April 2023

Abstract

Study Objectives
Little empirical work has investigated the associations between life stress (LS), insomnia, depression, and suicidality in multi-wave longitudinal studies. With three waves of data collection 1-year apart, this longitudinal study with a large sample of adolescents examined the predicting effects of LS on suicidality 1-year later and 2 years later and the mediating roles of insomnia and depression in the LS-suicidality link.

Methods
A total of 6995 adolescents (mean age = 14.86 years, 51.4% male) participated in a three-wave longitudinal study of behavior and health in Shandong, China. A self-administered structured questionnaire and standardized scales were used to assess suicidality (including suicidal thought [ST], suicide plan [SP], and suicide attempt [SA]), LS, insomnia, and depression in 2015 (T1), 1-year later (T2), and 2 years later (T3). Mediation effects were examined with path models.

Results
The overall prevalence rates of past-year suicidality were 13.4% at T1, 10.0% at T2, and 9.5% at T3, respectively. The prevalence rates of suicidality across T1–T3 significantly increased with elevated levels of baseline LS, insomnia, and depression (p &lt; .001). Path models indicated that the relationship between baseline LS and suicidal ideation (i.e., ST/SP) 2 years later was significantly mediated by both insomnia and depression. Depression was also a significant mediator between LS and SA.

Conclusions
LS is a significant predictor of suicidality 1–2 years later in adolescents. Depression mediates the association between LS and suicidal ideation and suicide attempt while insomnia appears to be a mediator for suicidal ideation rather than suicide attempt.