bluuebunny/crossref_metadata_2025_split huggingface dataset:
Galaxy Spectra neural Network (GaSNet). II. Using deep learning for spectral classification and redshift predictions
Authors: Zhong Fucheng , Napolitano Nicola R , Heneka Caroline , Li Rui , Bauer Franz Erik , Bouche Nicolas , Comparat Johan , Kim Young-Lo , Krogager Jens-Kristian , Longhetti Marcella , Loveday Jonathan , Roukema Boudewijn F , Rouse Benedict L , Salvato Mara , Tortora Crescenzo , Assef Roberto J , Cassarà Letizia P , Costantin Luca , Croom Scott M , Davies Luke J M , Fritz Alexander , Guiglion Guillaume , Humphrey Andrew , Pompei Emanuela , Ricci Claudio , Sifón Cristóbal , Tempel Elmo , Zafar Tayyaba 
Published: June 2024

ABSTRACT
The size and complexity reached by the large sky spectroscopic surveys require efficient, accurate, and flexible automated tools for data analysis and science exploitation. We present the Galaxy Spectra Network/GaSNet-II, a supervised multinetwork deep learning tool for spectra classification and redshift prediction. GaSNet-II can be trained to identify a customized number of classes and optimize the redshift predictions. Redshift errors are determined via an ensemble/pseudo-Monte Carlo test obtained by randomizing the weights of the network-of-networks structure. As a demonstration of the capability of GaSNet-II, we use 260k Sloan Digital Sky Survey spectra from Data Release 16, separated into 13 classes including 140k galactic, and 120k extragalactic objects. GaSNet-II achieves 92.4 per cent average classification accuracy over the 13 classes and mean redshift errors of approximately 0.23 per cent for galaxies and 2.1 per cent for quasars. We further train/test the pipeline on a sample of 200k 4MOST (4-metre Multi-Object Spectroscopic Telescope) mock spectra and 21k publicly released DESI (Dark Energy Spectroscopic Instrument) spectra. On 4MOST mock data, we reach 93.4 per cent accuracy in 10-class classification and mean redshift error of 0.55 per cent for galaxies and 0.3 per cent for active galactic nuclei. On DESI data, we reach 96 per cent accuracy in (star/galaxy/quasar only) classification and mean redshift error of 2.8 per cent for galaxies and 4.8 per cent for quasars, despite the small sample size available. GaSNet-II can process ∼40k spectra in less than one minute, on a normal Desktop GPU. This makes the pipeline particularly suitable for real-time analyses and feedback loops for optimization of Stage-IV survey observations.
Revealing asymmetry on mid-plane of protoplanetary disc through modelling of axisymmetric emission: methodology
Authors: Aizawa Masataka , Muto Takayuki , Momose Munetake 
Published: June 2024

ABSTRACT
This study proposes an analytical framework for deriving the surface brightness profile and geometry of a geometrically thin axisymmetric disc from interferometric observation of continuum emission. Such precise modelling facilitates the exploration of faint non-axisymmetric structures, such as spirals and circumplanetary discs. As a demonstration, we simulate interferometric observations of geometrically thin axisymmetric discs. The proposed method can reasonably recover the injected axisymmetric structures, whereas Gaussian fitting of the same data yielded larger errors in disc orientation estimation. To further test the applicability of the method, it was applied to the mock data for $m=1,2$ spirals and a point source, which are embedded in a bright axisymmetric structure. The injected non-axisymmetric structures were reasonably recovered except for the innermost parts, and the disc geometric parameter estimations were better than Gasussian fitting. The method was then applied to the real data of Elias 20 and AS 209, and it adequately subtracted the axisymmetric component, notably in Elias 20, where substantial residuals remained without our method. We also applied our method to continuum data of PDS 70 to demonstrate the effectiveness of the method. We successfully recovered emission from PDS 70 c consistently with previous studies, and also tentatively discovered new substructures. The current formulation can be applied to any data for disc continuum emission, and aids in the search of spirals and circumplanetary discs, whose detection is still limited.
What determines the boundaries of H2O maser emission in an X-ray illuminated gas disc?
Authors: Kuo C Y , Gao F , Braatz J A , Pesce D W , Humphreys E M L , Reid M J , Impellizzeri C M V , Henkel C , Wagner J , Wu C E 
Published: June 2024

ABSTRACT
High precision mapping of H$_{2}$O megamaser emission from active galaxies has revealed more than a dozen Keplerian H$_{2}$O maser discs, which enable a $\sim$4 per cent uncertainty estimate of the Hubble constant as well as providing accurate masses for the central black holes. These discs often have well-defined inner and outer boundaries of maser emission on sub-parsec scales. In order to better understand the physical conditions that determine the inner and outer radii of a maser disc, we examine the distributions of gas density and X-ray heating rate in a warped molecular disc described by a power-law surface density profile. For a suitable choice of the disc mass, we find that the outer radius $R_{\rm out}$ of the maser disc predicted from our model can match the observed value, with $R_{\rm out}$ mainly determined by the maximum heating rate or the minimum density for efficient maser action, depending on the combination of the Eddington ratio, black hole mass, and disc mass. Our analysis also indicates that the inner radius for maser action is comparable to the dust sublimation radius, suggesting that dust may play a role in determining the inner radius of a maser disc. Finally, our model predicts that H$_{2}$O gigamaser discs could exist at the centres of high-z quasars, with disc sizes of $\gtrsim 10-30$ pc.
Metal factories in the early Universe
Authors: Eales Stephen , Gomez Haley , Dunne Loretta , Dye Simon , Smith Matthew W L 
Published: June 2024

ABSTRACT
We have estimated the mass of metals in the molecular gas in 13 dusty star-forming galaxies at $z \sim 4$ in which the gas, based on previous observations, lies in a cold rotating disc. We estimated the metal masses using either the submillimetre line or continuum emission from three tracers of the overall metal content – carbon atoms, carbon monoxide molecules, and dust grains – using the first simultaneous calibration of all three tracers. We obtain very similar mass estimates from the different tracers, which are similar to the entire metal content of a present-day massive early-type galaxy. We used the dynamical masses of these galaxies to estimate an upper limit on the mass of the molecular gas in each galaxy, allowing us to estimate a lower limit on the metal abundance of the gas, finding values for many of the galaxies well above the solar value. We show that the high metal masses and metal abundances are what is expected shortly after the formation of a galaxy for a top-heavy IMF. We suggest a scenario for galaxy evolution in which massive galaxies reach a high metal abundance during their formation phase, which is then gradually reduced by dry mergers with lower mass galaxies. We show that the metals in the outflows from high-redshift dusty star-forming galaxies can quantitatively explain the long-standing puzzle that such a large fraction of the metals in galaxy clusters ($\simeq$0.75) is in the intracluster gas rather than in the galaxies themselves.
CANUCS: UV and ionizing properties of dwarf star-forming galaxies at z ~ 5–7
Authors: Harshan Anishya , Bradač Maruša , Abraham Roberto , Asada Yoshihisa , Brammer Gabriel , Desprez Guillaume , Iyer Karthiek , Martis Nicholas S , Matharu Jasleen , Mowla Lamiya , Muzzin Adam , Noirot Gaël , Rihtaršič Gregor , Sarrouh Ghassan T E , Sawicki Marcin , Strait Victoria , Willott Chris J 
Published: June 2024

ABSTRACT
The epoch of reionization (EoR) progressed through the emission of ionizing photons from galaxies to their local intergalactic medium. In this work, we characterize the dwarf star-forming galaxies as candidates for the source of ionizing photons that drove EoR. We investigate the ionizing properties and star formation histories of star-forming dwarf galaxies at the last stages of EoR at $4.8\lt z \lt 7$ using observations from the CAnadian NIRISS Unbiased Cluster Survey (CANUCS). The magnification due to gravitational lensing allows us to probe large dynamic ranges in stellar mass ($2\times 10^{6}\le {M}_*/{\rm M}_\odot \le 5\times 10^{9}$) and ultraviolet (UV) magnitudes ($-22.68\le M_{\rm UV}\le =-15.95$). We find a median UV slope $\beta _{1500}\,$ of $-2. 56\pm 0.23$ and the production efficiency of ionizing photons $\log$$\xi _{\rm {ion}}\,$$=25.39\pm 0.6$ for the full sample ($4.8\lt z \lt 7$) with a median stellar mass of $6.3\pm 0.5\times 10^{7} \, {\rm M}_\odot$. We find both $\beta _{1500}\,$ and $\xi _{\rm {ion}}\,$ are marginally correlated with the stellar mass of the galaxy, indicating a possible greater contribution of dwarf galaxies to the reionization of the Universe. We find that on average, galaxies in our sample are experiencing a recent rise/burst of star formation which translates to a higher scatter in $\xi _{\rm {ion}}\,$ and a large scatter in H$\alpha$ equivalent widths (EWs). Finally, we investigate the trends of H$\alpha$ and [O iii] + H$\beta$ EWs with UV magnitude and find $M_{\rm UV}$ is correlated between H$\alpha$ but not with [O iii] + H$\beta$ EWs indicating low metallicities and recent burst in the UV faint galaxies.
PHACTboost: A Phylogeny-Aware Pathogenicity Predictor for Missense Mutations via Boosting
Authors: Dereli Onur , Kuru Nurdan , Akkoyun Emrah , Bircan Aylin , Tastan Oznur , Adebali Ogün 
Published: June 2024

Abstract
Most algorithms that are used to predict the effects of variants rely on evolutionary conservation. However, a majority of such techniques compute evolutionary conservation by solely using the alignment of multiple sequences while overlooking the evolutionary context of substitution events. We had introduced PHACT, a scoring-based pathogenicity predictor for missense mutations that can leverage phylogenetic trees, in our previous study. By building on this foundation, we now propose PHACTboost, a gradient boosting tree–based classifier that combines PHACT scores with information from multiple sequence alignments, phylogenetic trees, and ancestral reconstruction. By learning from data, PHACTboost outperforms PHACT. Furthermore, the results of comprehensive experiments on carefully constructed sets of variants demonstrated that PHACTboost can outperform 40 prevalent pathogenicity predictors reported in the dbNSFP, including conventional tools, metapredictors, and deep learning–based approaches as well as more recent tools such as AlphaMissense, EVE, and CPT-1. The superiority of PHACTboost over these methods was particularly evident in case of hard variants for which different pathogenicity predictors offered conflicting results. We provide predictions of 215 million amino acid alterations over 20,191 proteins. PHACTboost is available at https://github.com/CompGenomeLab/PHACTboost. PHACTboost can improve our understanding of genetic diseases and facilitate more accurate diagnoses.
Soma-germline communication drives sex maintenance in the Drosophila testis
Authors: Zhang Rui , Shi Peiyu , Xu Shuyang , Ming Zhe , Liu Zicong , He Yuanyuan , Dai Junbiao , Matunis Erika , Xu Jin , Ma Qing 
Published: June 2024

ABSTRACT
In adult gonads, disruption of somatic sexual identity leads to defective gametogenesis and infertility. However, the underlying mechanisms by which somatic signals regulate germline cells to achieve proper gametogenesis remain unclear. In our previous study, we introduced the chinmoSex Transformation (chinmoST) mutant Drosophila testis phenotype as a valuable model for investigating the mechanisms underlying sex maintenance. In chinmoST testes, depletion of the Janus Kinase-Signal Transducer and Activator of Transcription downstream effector Chinmo from somatic cyst stem cells (CySCs) feminizes somatic cyst cells and arrests germline differentiation. Here, we use single-cell RNA sequencing to uncover chinmoST-specific cell populations and their transcriptomic changes during sex transformation. Comparative analysis of intercellular communication networks between wild-type and chinmoST testes revealed disruptions in several soma-germline signaling pathways in chinmoST testes. Notably, the insulin signaling pathway exhibited significant enhancement in germline stem cells (GSCs). Chinmo cleavage under targets and tagmentation (CUT&Tag) assay revealed that Chinmo directly regulates two male sex determination factors, doublesex (dsx) and fruitless (fru), as well as Ecdysone-inducible gene L2 (ImpL2), a negative regulator of the insulin signaling pathway. Further genetic manipulations confirmed that the impaired gametogenesis observed in chinmoST testes was partly contributed by dysregulation of the insulin signaling pathway. In summary, our study demonstrates that somatic sex maintenance promotes normal spermatogenesis through Chinmo-mediated conserved sex determination and the insulin signaling pathway. Our work offers new insights into the complex mechanisms of somatic stem cell sex maintenance and soma-germline communication at the single-cell level. Additionally, our discoveries highlight the potential significance of stem cell sex instability as a novel mechanism contributing to testicular tumorigenesis.
The Microbiological Characteristics of Acinetobacter Baumannii Associated With Early Mortality in Patients With Bloodstream Infection
Authors: Lee Chan Mi , Choi Yunsang , Choi Seong Jin , Moon Song Mi , Kim Eu Suk , Kim Hong Bin , Ham Sin Young , Park Jeong Su , Yeom Jinki , Song Kyoung-Ho 
Published: June 2024

Abstract

Background
Despite rapid deaths resulting from Acinetobacter baumannii bacteremia, the clinical impact of the microbiological characteristics of A baumannii strains on early mortality (EM) is unclear. We aimed to identify the microbiological characteristics of A baumannii strains associated with EM.

Methods
Clinical information and isolates from patients with A baumannii bacteremia from January 2015 to December 2021 were collected. EM was defined as death within 3 days of the initial positive blood culture, whereas late mortality meant death within 5–30 days. The microbiological characteristics of A baumannii were analyzed using multilocus sequence typing, polymerase chain reactions, and a Galleria mellonella in vivo infection model.

Results
Among 130 patients, 69 (53.1%) died within 30 days and EM occurred in 38 (55.1% of 30-day deaths). Sequence type 191 (ST191) strain was more prevalent in patients with EM than in 30-day survivors (31.6% vs 6.6%). Regarding virulence genes, bfmS was more frequent (92.1% vs 47.5%), whereas bauA was less frequent (13.2% vs 52.5%) in patients with EM than in 30-day survivors. Higher clinical severity, pneumonia, and ST191 infection were identified as independent risk factors for EM. In the G mellonella infection model, ST191, bfmS+, and bauA– isolates showed higher virulence than non-ST191, bfmS–, and bauA+ isolates, respectively.

Conclusions
ST191 and bfmS were more frequently found in the EM group. ST191 infection was also an independent risk factor for EM and highly virulent in the in vivo model. Tailored infection control measures based on these characteristics are necessary for A baumannii bacteremia management.
Predictors of response to immunotherapy in colorectal cancer
Authors: González-Montero Jaime , Rojas Carlos I , Burotto Mauricio 
Published: June 2024

Abstract
Colorectal cancer (CRC) is a major cause of cancer-related deaths globally. While treatment advancements have improved survival rates, primarily through targeted therapies based on KRAS, NRAS, and BRAF mutations, personalized treatment strategies for CRC remain limited. Immunotherapy, mainly immune checkpoint blockade, has shown efficacy in various cancers but is effective in only a small subset of patients with CRC with deficient mismatch repair (dMMR) proteins or high microsatellite instability (MSI). Recent research has challenged the notion that CRC is immunologically inert, revealing subsets with high immunogenicity and diverse lymphocytic infiltration. Identifying precise biomarkers beyond dMMR and MSI is crucial to expanding immunotherapy benefits. Hence, exploration has extended to various biomarker sources, such as the tumor microenvironment, genomic markers, and gut microbiota. Recent studies have introduced a novel classification system, consensus molecular subtypes, that aids in identifying patients with CRC with an immunogenic profile. These findings underscore the necessity of moving beyond single biomarkers and toward a comprehensive understanding of the immunological landscape in CRC, facilitating the development of more effective, personalized therapies.
Charting the evolutionary path of the SUMO modification system in plants reveals molecular hardwiring of development to stress adaptation
Authors: Ghosh Srayan , Mellado Sanchez Macarena , Sue-Ob Kawinnat , Roy Dipan , Jones Andrew , Blazquez Miguel A , Sadanandom Ari 
Published: June 2024

Abstract
SUMO modification is part of the spectrum of Ubiquitin-like (UBL) systems that give rise to proteoform complexity through post-translational modifications (PTMs). Proteoforms are essential modifiers of cell signaling for plant adaptation to changing environments. Exploration of the evolutionary emergence of Ubiquitin-like (UBL) systems unveils their origin from prokaryotes, where it is linked to the mechanisms that enable sulfur uptake into biomolecules. We explore the emergence of the SUMO machinery across the plant lineage from single-cell to land plants. We reveal the evolutionary point at which plants acquired the ability to form SUMO chains through the emergence of SUMO E4 ligases, hinting at its role in facilitating multicellularity. Additionally, we explore the possible mechanism for the neofunctionalization of SUMO proteases through the fusion of conserved catalytic domains with divergent sequences. We highlight the pivotal role of SUMO proteases in plant development and adaptation, offering new insights into target specificity mechanisms of SUMO modification during plant evolution. Correlating the emergence of adaptive traits in the plant lineage with established experimental evidence for SUMO in developmental processes, we propose that SUMO modification has evolved to link developmental processes to adaptive functions in land plants.
The Arabidopsis ARID–HMG DNA-BINDING PROTEIN 15 modulates jasmonic acid signaling by regulating MYC2 during pollen development
Authors: Sachdev Sonal , Biswas Ruby , Roy Adrita , Nandi Ayantika , Roy Vishal , Basu Sabini , Chaudhuri Shubho 
Published: June 2024

Abstract
The intricate process of male gametophyte development in flowering plants is regulated by jasmonic acid (JA) signaling. JA signaling initiates with the activation of the basic helix–loop–helix transcription factor (TF), MYC2, leading to the expression of numerous JA-responsive genes during stamen development and pollen maturation. However, the regulation of JA signaling during different stages of male gametophyte development remains less understood. This study focuses on the characterization of the plant ARID–HMG DNA-BINDING PROTEIN 15 (AtHMGB15) and its role in pollen development in Arabidopsis (Arabidopsis thaliana). Phenotypic characterization of a T-DNA insertion line (athmgb15-4) revealed delayed bolting, shorter siliques, and reduced seed set in mutant plants compared to the wild type. Additionally, AtHMGB15 deletion resulted in defective pollen morphology, delayed pollen germination, aberrant pollen tube growth, and a higher percentage of nonviable pollen grains. Molecular analysis indicated the downregulation of JA biosynthesis and signaling genes in the athmgb15-4 mutant. Quantitative analysis demonstrated that JA and its derivatives were ∼10-fold lower in athmgb15-4 flowers. Exogenous application of methyl jasmonate could restore pollen morphology and germination, suggesting that the low JA content in athmgb15-4 impaired JA signaling during pollen development. Furthermore, our study revealed that AtHMGB15 physically interacts with MYC2 to form a transcription activation complex. This complex promotes the transcription of key JA signaling genes, the R2R3-MYB TFs MYB21 and MYB24, during stamen and pollen development. Collectively, our findings highlight the role of AtHMGB15 as a positive regulator of the JA pathway, controlling the spatiotemporal expression of key regulators involved in Arabidopsis stamen and pollen development.
Reverse social contagion as a mechanism for regulating mass behaviors in highly integrated social systems
Authors: Porfiri Maurizio , De Lellis Pietro , Aung Eighdi , Meneses Santiago , Abaid Nicole , Waters Jane S , Garnier Simon 
Published: June 2024

Abstract
Mass behavior is the rapid adoption of similar conduct by all group members, with potentially catastrophic outcomes such as mass panic. Yet, these negative consequences are rare in integrated social systems such as social insect colonies, thanks to mechanisms of social regulation. Here, we test the hypothesis that behavioral deactivation between active individuals is a powerful social regulator that reduces energetic spending in groups. Borrowing from scaling theories for human settlements and using behavioral data on harvester ants, we derive ties between the hypermetric scaling of the interaction network and the hypometric scaling of activity levels, both relative to the colony size. We use elements of economics theory and metabolic measurements collected with the behavioral data to link activity and metabolic scalings with group size. Our results support the idea that metabolic scaling across social systems is the product of different balances between their social regulation mechanisms.