bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis
Authors: Ding Xiaobao , Zhang Lin , Fan Ming , Li Lihua 
Published: January 2025

AbstractBreast cancer prognosis is complicated by tumor heterogeneity. Traditional methods focus on cancer-specific gene signatures, but cross-cancer strategies that provide deeper insights into tumor homogeneity are rarely used. Immunotherapy, particularly immune checkpoint inhibitors, results from variable responses across cancers, offering valuable prognostic insights. We introduced a network-based transfer (NBT) of pan-cancer immunotherapy responses to enhance breast cancer prognosis using node embedding and heat diffusion algorithms, identifying gene signatures netNE and netHD. Our results showed that netHD and netNE outperformed seven established breast cancer signatures in prognostic metrics, with netHD excelling. All nine gene signatures were grouped into three clusters, with netHD and netNE enriching the immune-related interferon-gamma pathway. Stratifying TCGA patients into two groups based on netHD revealed significant immunological differences and variations in 20 of 50 cancer hallmarks, emphasizing immune-related markers. This approach leverages pan-cancer insights to enhance breast cancer prognosis, facilitating insight transfer and improving tumor homogeneity understanding.Abstract graph of network-based insights translating pan-cancer immunotherapy responses to breast cancer prognosis. This abstract graph illustrates the conceptual framework for transferring immunotherapy response insights from pan-cancer studies to breast cancer prognosis. It highlights the integration of PPI networks to bridge genetic data and clinical phenotypes. The network-based method facilitates the identification of prognostic gene signatures in breast cancer by leveraging immunotherapy response information, providing a novel perspective on tumor homogeneity and its implications for clinical outcomes.
Autologous macrophage therapy for liver cirrhosis: a phase 2 open-label randomized controlled trial
Authors: Brennan Paul N. , MacMillan Mark , Manship Thomas , Moroni Francesca , Glover Alison , Troland Debbie , MacPherson Iain , Graham Catriona , Aird Rhona , Semple Scott I. K. , Morris David M. , Fraser Alasdair R. , Pass Chloe , McGowan Neil W. A. , Turner Marc L. , Manson Lynn , Lachlan Neil J. , Dillon John F. , Kilpatrick Alastair M. , Campbell John D. M. , Fallowfield Jonathan A. , Forbes Stuart J. 
Published: January 2025

Abstract
Cirrhosis is a major cause of morbidity and mortality; however, there are no approved therapies except orthotopic liver transplantation. Preclinical studies showed that bone-marrow-derived macrophage injections reduce inflammation, resolve fibrosis and stimulate liver regeneration. In a multicenter, open-label, parallel-group, phase 2 randomized controlled trial (ISRCTN10368050) in n = 51 adult patients with compensated cirrhosis and Model for End-Stage Liver Disease (MELD) score ≥10 and ≤17, we evaluated the efficacy of autologous monocyte-derived macrophage therapy (n = 27) compared to standard medical care (n = 24). The primary endpoint was the difference in baseline to day 90 change in MELD score (ΔMELD) between treatment and control groups (ΔΔMELD). Secondary endpoints included adverse clinical outcomes, non-invasive fibrosis biomarkers and health-related quality of life (HRQoL) at 90 d, 180 d and 360 d. The ΔΔMELD between day 0 and day 90 in the treatment group compared to controls was −0.87 (95% confidence interval: −1.79, 0.0; P = 0.06); therefore, the primary endpoint was not met. During 360-d follow-up, five of 24 participants in the control group developed a total of 10 severe adverse events, four of which were liver related, and three deaths (two liver related), whereas no liver-related severe adverse events or deaths occurred in the treatment group. Although no differences were observed in biomarkers or HRQoL, exploratory analysis showed anti-inflammatory serum cytokine profiles after macrophage infusion. This study reinforces the safety and potential efficacy of macrophage therapy in cirrhosis, supporting further investigation.
Predictive value of an unsupervised web-based assessment of the neuropsychological function
Authors: Werrmann Michelle , Gür-Tok Yesim , Eid Michael , Niedeggen Michael 
Published: January 2025

AbstractNeuropsychological assessment has to consider the subjective and objective functional deficits of help-seeking individuals in several cognitive domains. Due to time constraints in clinical practice, several web-based approaches have been developed. The current study examined whether functional deficits in the mnestic and attentive domain can be predicted based on an unsupervised self-administered online assessment neuropsychological online screening (NOS): This screening includes self-reports and psychometric memory tests (face-name association, visual short-term memory). Data of help-seeking individuals (n = 213, mean age: 48.2 years) running an extensive in-person assessment were analyzed. A functional deficit in at least one cognitive domain was detected in 48 individuals. This classification was supported by the preceding online screening (sensitivity = 0.75, specificity = 0.80), and a linear regression model identified two significant predictors (free recall performance, form discrimination in visual short-term memory). The predictive quality was enhanced for individuals with selective deficits in the mnestic domain (n = 23: sensitivity = 0.78 and specificity = 0.78) as compared to the attentive domain (n = 25: sensitivity = 0.68 and specificity = 0.75). Our results show that a neuropsychological in-person assessment cannot be replaced by an unsupervised self-administered online test. However, a specific pattern of results in the online test might indicate the necessity of an extensive assessment in help-seeking individuals.
Hybridization and diversity of the genus Vandenboschia in Korea insights from morphological, cytological, and genotype analyses
Authors: Park Sang Hee , Kim Jung Sung , Kim Hyoung Tae 
Published: January 2025

Abstract
The genus Vandenboschia exhibits significant diversity, driven by complex hybridization events and varying ploidy levels in the natural habitats of Korea, leads to misidentifications that obscure its true distribution and classification. To address this issue, the present study employed morphological, cytological, and genotype analyses to clarify the taxonomical circumscription and distribution patterns of the Vandenboschia radicans complex in Korea. The V. radicans complex in the genus refers to V. radicans and its closely related species and exhibits significant morphological variation, making classification challenging. Previous molecular studies have revealed that it consists of several non-hybrid and hybrid species among them. Through the present study, comprehensive sampling from Jeju and Ulleung Islands identified five distinct taxa from the V. radicans complex: two non-hybrid species (Vandenboschia kalamocarpa and Vandenboschia nipponica), and three hybrids (Vandenboschia × stenosiphon, Vandenboschia × quelpaertensis, and Vandenboschia kalamocarpa × Vandenboschia nipponica × Vandenboschia striata). Notably, hybrids exhibited broader geographic distributions compared to non-hybrid species, which were confined to specific microhabitats. While overlapping morphological traits among the species complicate identification without genetic analysis, rhizome diameter and the width-to-length ratio of the involucre can serve as key morphological traits for distinguishing members of the Vandenboschia radicans complex in Korea. Additionally, cleaved amplified polymorphic sequence (CAPS) markers and cloning techniques were employed for species identification, particularly when morphological traits were inconclusive. These findings highlight the need to integrate genetic tools with traditional taxonomic methods to resolve complex species relationships within Vandenboschia in Korea and emphasize the importance of conservation efforts for geographically restricted and genetically distinct populations.
The genomic architecture of circulating cytokine levels points to drug targets for immune-related diseases
Authors: Konieczny Marek J. , Omarov Murad , Zhang Lanyue , Malik Rainer , Richardson Tom G. , Baumeister Sebastian-Edgar , Bernhagen Jürgen , Dichgans Martin , Georgakis Marios K. 
Published: January 2025

AbstractCirculating cytokines orchestrate immune reactions and are promising drug targets for immune-mediated and inflammatory diseases. Exploring the genetic architecture of circulating cytokine levels could yield key insights into causal mediators of human disease. Here, we performed genome-wide association studies (GWAS) for 40 circulating cytokines in meta-analyses of 74,783 individuals. We detected 359 significant associations between cytokine levels and variants in 169 independent loci, including 150 trans- and 19 cis-acting loci. Integration with transcriptomic data point to key regulatory mechanisms, such as the buffering function of the Atypical Chemokine Receptor 1 (ACKR1) acting as scavenger for multiple chemokines and the role of tumor necrosis factor receptor-associated factor 1 (TRAFD1) in modulating the cytokine storm triggered by TNF signaling. Applying Mendelian randomization (MR), we detected a network of complex cytokine interconnections with TNF-b, VEGF, and IL-1ra exhibiting pleiotropic downstream effects on multiple cytokines. Drug target cis-MR using 2 independent proteomics datasets paired with colocalization revealed G-CSF/CSF-3 and CXCL9/MIG as potential causal mediators of asthma and Crohn’s disease, respectively, but also a potentially protective role of TNF-b in multiple sclerosis. Our results provide an overview of the genetic architecture of circulating cytokines and could guide the development of targeted immunotherapies.
Emergence of high-mass stars in complex fiber networks (EMERGE)
Authors: Hacar A. , Konietzka R. , Seifried D. , Clark S. E. , Socci A. , Bonanomi F. , Burkert A. , Schisano E. , Kainulainen J. , Smith R. 
Published: January 2025

Context. Identified as parsec-size, gas clumps at the junction of multiple filaments, hub-filament systems (HFS) play a crucial role during the formation of young clusters and high-mass stars. These HFS still appear to be detached from most galactic filaments when compared in the mass–length (M–L) phase space.
Aims. We aim to characterize the early evolution of HFS as part of the filamentary description of the interstellar medium (ISM).
Methods. Combining previous scaling relations with new analytic calculations, we created a toy model to explore the different physical regimes described by the M–L diagram. Despite its simplicity, our model accurately reproduces several observational properties reported for filaments and HFS, such as their expected typical aspect ratio (A), mean surface density (Σ), and gas accretion rate (ṁ). Moreover, this model naturally explains the different mass and length regimes populated by filaments and HFS, respectively.
Results. Our model predicts a dichotomy between filamentary (A ≥ 3) and spheroidal (A < 3) structures connected to the relative importance of their fragmentation, accretion, and collapse timescales. Individual filaments with low accretion rates are dominated by an efficient internal fragmentation. In contrast, the formation of compact HFS at the intersection of filaments triggers a geometric phase-transition, leading to the gravitational collapse of these structures at parsec-scales in ~1–2 Myr. In addition, this process also induces higher accretion rates.
RIS: Regularized imaging spectroscopy for STIX on board Solar Orbiter
Authors: Volpara Anna , Lupoli Alessandro , Filbir Frank , Perracchione Emma , Maria Massone Anna , Piana Michele 
Published: January 2025

Context. The generation of spatially resolved count spectra and of cubes of count maps at different energies via imaging spectroscopy is one of the main goals of solar hard X-ray missions based on Fourier imaging. Thus, so far, for these telescopes, this goal has been realized via the generation of either count maps that are independently reconstructed in the different energy channels or electron flux maps reconstructed via a deconvolution of the approximate forms for the bremsstrahlung cross-section.
Aims. Our aim is to introduce a regularized imaging spectroscopy method (RIS), whereby the regularization implemented in the count space imposes a smoothing constraint across contiguous energy channels, without the need for computing any deconvolution of the bremsstrahlung effect.
Methods. STIX records imaging data, while computing the visibilities in the spatial frequency domain. Our RIS is a sequential scheme in which part of the information coded in the image is reconstructed at a specific energy channel and transferred to the reconstruction process at a contiguous channel via a visibility interpolation computed by means of variably scaled kernels (VSKs).
Results. In the case of STIX visibilities recorded during the November 11, 2022 flaring event, we show that RIS is able to generate hard X-ray maps, whose morphology is seen to smoothly evolve from one energy channel to the contiguous one; accordingly, from these maps, it is possible to infer spatially resolved count spectra characterized by a notable numerical stability. We also show that the performance of this approach is robust with respect to both the image reconstruction method and the count energy channel utilized to trigger the sequential process.
Conclusions. We conclude that RIS is not only an appropriate, but also an effective and necessary approach to constructing image cubes from STIX visibilities that are characterized by smooth behavior across count energies. Thus, it allows for the generation of numerically stable (and, thus, physically reliable) local count spectra.
New stellar bow shocks and bubbles found around runaway stars
Authors: Carretero-Castrillo M. , Benaglia P. , Paredes J. M. , Ribó M. 
Published: January 2025

Context. Runaway stars with peculiar high velocities can generate stellar bow shocks. Only a few bow shocks show clear radio emission.
Aims. Our goal is to identify and characterize new stellar bow shocks around O and Be runaway stars in the infrared (IR), as well as to study their possible radio emission and nature.
Methods. Our input data is a catalog of O and Be runaways compiled using Gaia DR3. We used WISE IR images to search for bow shock structures around these runaways, Gaia DR3 data to determine the actual motion of the runaway stars corrected for interstellar medium (ISM) motion caused by Galactic rotation, and archival radio data to search for emission signatures. We finally explored the radio detectability of these sources under thermal and nonthermal scenarios.
Results. We found nine new stellar bow shock candidates, three new bubble candidates, and one intermediate structure candidate. One of them is an in situ bow shock candidate. We also found 17 already known bow shocks in our sample, though we discarded one, and 62 miscellaneous sources showing some IR emission around the runaways. We geometrically characterized the sources in IR using the WISE-4 band and estimated the ISM density at the bow shock positions, obtaining median values of ∼6 and ∼4 cm−3 using 2D and 3D peculiar velocities, respectively. Most of the new discovered bow shocks come from new runaway discoveries. Within our samples we found that ∼24% of the O-type runaway stars show bow shocks, while this decreases to ∼3% for Be-type runaway stars. Two bow shocks present radio emission but not as clear counterparts, and two others show hints of radio emission. The physical scenarios indicate that two sources could still be compatible with nonthermal radio emission.
Conclusions. The new sample of O and Be runaway stars allowed us to discover both new stellar bow shocks and bubbles. Their geometrical characterization can be used to assess the physical scenario of the radio emission. Deeper radio observations are needed to unveil a population of radio-detected bow shocks, and the physical scenarios occurring in these sources.
GA-NIFS: A galaxy-wide outflow in a Compton-thick mini-broad-absorption-line quasar at z = 3.5 probed in emission and absorption
Authors: Perna Michele , Arribas Santiago , Ji Xihan , Marconcini Cosimo , Lamperti Isabella , Bertola Elena , Circosta Chiara , D’Eugenio Francesco , Übler Hannah , Böker Torsten , Maiolino Roberto , Bunker Andrew J. , Carniani Stefano , Charlot Stéphane , Willott Chris J. , Cresci Giovanni , Marconi Alessandro , Parlanti Eleonora , Rodríguez Del Pino Bruno , Scholtz Jan , Venturi Giacomo 
Published: January 2025

Context. Studying the distribution and properties of ionised gas in outflows driven by active galactic nuclei (AGN) is crucial for understanding the feedback mechanisms at play in extragalactic environments. These outflows provide key insights into the regulation of star formation and the growth of supermassive black holes.
Aims. In this study, we explore the connection between ionised outflows traced by rest-frame ultra-violet (UV) absorption and optical emission lines in GS133, a Compton thick AGN at z = 3.47. We combine observations from the James Webb Space Telescope (JWST) NIRSpec Integral Field Spectrograph (IFS) with archival Very Large Telescope (VLT) VIMOS long-slit spectroscopic data, as part of the ‘Galaxy Assembly with NIRSpec IFS’ (GA-NIFS) project.
Methods. We performed a multi-component kinematic decomposition of the UV and optical line profiles to derive the physical properties of the absorbing and emitting gas in GS133.
Results. Our kinematic decomposition reveals two distinct components in the optical emission lines. The first component likely traces a rotating disc with a dynamical mass of 2 × 1010 M⊙. The second component corresponds to a galaxy-wide, bi-conical outflow, with a velocity of ∼ ± 1000 km s−1 and an extension of ∼3 kpc. The UV absorption lines show two outflow components, with bulk velocities vout ∼ −900 km s−1 and ∼ − 1900 km s−1, respectively. This characterises GS133 as a mini-broad absorption line (mini-BAL) system. Balmer absorption lines with similar velocities are tentatively detected in the NIRSpec spectrum. Both photoionisation models and outflow energetics suggest that the ejected absorbing gas is located at 1–10 kpc from the AGN. We use 3D gas kinematic modelling to infer the orientation of the [O III] bi-conical outflow, and find that a portion of the emitting gas resides along our line of sight, suggesting that [O III] and absorbing gas clouds are partially mixed in the outflow. The derived mass-loading factor (i.e. the mass outflow rate divided by the star formation rate) of 1–10, and the kinetic coupling efficiency (i.e. the kinetic power divided by LAGN) of 0.1–1% suggest that the outflow in GS133 provides significant feedback on galactic scales.
Liver damage and immune responses
Authors: Hackstein Carl-Philipp 
Published: January 2025

AbstractChronic liver disease (CLD) has massive systemic repercussions including major impacts on the body’s immune system. Abnormalities in phenotype, function and numbers of various immune cell subsets have been established by a large number of clinical and pre-clinical studies. The loss of essential immune functions renders CLD-patients exceptionally susceptible to bacterial and viral infections and also impairs the efficacy of vaccination. Consequently, infections represent a major clinical issue causing significant morbidity and mortality in these patients. Mechanistically, the immune dysfunction associated with CLD results from the increased translocation of bacteria and bacterial cues from the intestine. These trigger a signaling axis around the cytokines IFN I and IL-10 in hepatic myeloid cells, which aside from impairing the function of the myeloid cells themselves, also has notable negative impacts on the functionality of other immune cells. T cells in CLD-patients and -models are especially affected by this signaling axis and display a variety of quantitative and qualitative defects. Due to the high clinical relevance, understanding the mechanisms underlaying CED-associated immune dysfunction is of critical importance to discover and develop new therapeutic targets.
Tissue Determinants of Antiviral Immunity in the Liver
Authors: Wohlleber Dirk , Knolle Percy A. 
Published: January 2025

AbstractThe liver is an organ bearing important metabolic and immune functions. Hepatocytes are the main metabolically active cells of the liver and are the target of infection by hepatotropic viruses. Virus-specific CD8 T cells are essential for the control of hepatocyte infection with hepatotropic viruses but may be subject to local regulation of their effector function. Here, we review our current knowledge of the tissue determinants of antiviral immunity in the liver. Liver Sinusoidal Endothelial Cells (LSECs) not only allow through their fenestrations the access of circulating virus-specific CD8 T cells to engage in direct contact with infected hepatocytes without the need for extravasation but also cross-present viral antigens released from infected hepatocytes to these CD8 T cells. Two important features of LSECs and hepatocytes contribute to antiviral immune surveillance and liver failure. First, CD8 T cell immunity targeting LSECs leads to widespread endothelial cell death and results in sinusoidal microcirculation failure, causing fulminant viral hepatitis, whereas immune-mediated loss of hepatocytes is rapidly compensated by the regenerative capacity of the liver. Second, virus-infected hepatocytes support clearance of infection by responding to TNF, which is released from virus-specific CD8 T cells, with the selective induction of apoptosis. This increased sensitivity for TNF-induced death is caused by reduced mitochondrial resilience in virus-infected hepatocytes and may assist antiviral immunity in preferential targeting of virus-infected hepatocytes. Thus, hepatocytes and LSECs actively contribute to the outcome of antiviral CD8 T cell immunity in the liver. The knowledge of the mechanisms determining CD8 T cell control of hepatotropic viral infection will help to improve strategies to increase antiviral immune surveillance.