bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-energy gamma-ray emission powered by a young protostar: the case of S255 NIRS 3
Authors: de Oña Wilhelmi Emma , López-Coto Rubén , Su Yang 
Published: May 2023

ABSTRACT
Evidence of efficient acceleration of cosmic rays in massive young stellar objects has been recently reported. Among these massive protostars, S255 NIRS 3, for which extreme flaring events associated with radio jets have been detected, is one of the best objects to test this hypothesis. We search for gamma-ray emission associated with this object in Fermi-LAT data and inspect the gas content in different molecular lines using the MWISP survey. A GeV source dubbed 4FGL J0613.1+1749c lies on top of the MYSO region, where two filamentary ∼10 pc CO structures extend along the same direction of the subparsec radio jets. We investigate the spectrum, morphology, and light curve of the gamma-ray source and compare it with the theoretical emission expected from hadronic and leptonic populations accelerated in the radio jets. We argue that the gamma-ray source could be powered by particles accelerated in the S255 NIRS 3 jets, radiating via bremsstrahlung or proton–proton interaction, and with a synchrotron component shinning in radio from primary or secondary electrons in the case of a leptonic or hadronic population.
XQR-30: The ultimate XSHOOTER quasar sample at the reionization epoch
Authors: D’Odorico Valentina , Bañados E , Becker G D , Bischetti M , Bosman S E I , Cupani G , Davies R , Farina E P , Ferrara A , Feruglio C , Mazzucchelli C , Ryan-Weber E , Schindler J-T , Sodini A , Venemans B P , Walter F , Chen H , Lai S , Zhu Y , Bian F , Campo S , Carniani S , Cristiani S , Davies F , Decarli R , Drake A , Eilers A-C , Fan X , Gaikwad P , Gallerani S , Greig B , Haehnelt M G , Hennawi J , Keating L , Kulkarni G , Mesinger A , Meyer R A , Neeleman M , Onoue M , Pallottini A , Qin Y , Rojas-Ruiz S , Satyavolu S , Sebastian A , Tripodi R , Wang F , Wolfson M , Yang J , Zanchettin M V 
Published: May 2023

ABSTRACT
The final phase of the reionization process can be probed by rest-frame UV absorption spectra of quasars at z ≳ 6, shedding light on the properties of the diffuse intergalactic medium within the first Gyr of the Universe. The ESO Large Programme ‘XQR-30: the ultimate XSHOOTER legacy survey of quasars at z ≃ 5.8–6.6’ dedicated ∼250 h of observations at the VLT to create a homogeneous and high-quality sample of spectra of 30 luminous quasars at z ∼ 6, covering the rest wavelength range from the Lyman limit to beyond the Mg ii emission. Twelve quasar spectra of similar quality from the XSHOOTER archive were added to form the enlarged XQR-30 sample, corresponding to a total of ∼350 h of on-source exposure time. The median effective resolving power of the 42 spectra is R ≃ 11 400 and 9800 in the VIS and NIR arm, respectively. The signal-to-noise ratio per 10 km s−1 pixel ranges from ∼11 to 114 at λ ≃ 1285 Å rest frame, with a median value of ∼29. We describe the observations, data reduction, and analysis of the spectra, together with some first results based on the E-XQR-30 sample. New photometry in the H and K bands are provided for the XQR-30 quasars, together with composite spectra whose characteristics reflect the large absolute magnitudes of the sample. The composite and the reduced spectra are released to the community through a public repository, and will enable a range of studies addressing outstanding questions regarding the first Gyr of the Universe.
Identification of molecular clouds in emission maps: a comparison between methods in the 13CO/C18O (J = 3–2) Heterodyne Inner Milky Way Plane Survey
Authors: Rani Raffaele , Moore Toby J T , Eden David J , Rigby Andrew J , Duarte-Cabral Ana , Lee Yueh-Ning 
Published: May 2023

ABSTRACT
The growing range of automated algorithms for the identification of molecular clouds and clumps in large observational data sets has prompted the need for the direct comparison of these procedures. However, these methods are complex and testing for biases is often problematic: only a few of them have been applied to the same data set or calibrated against a common standard. We compare the Fellwalker method, a widely used watershed algorithm, to the more recent Spectral Clustering for Interstellar Molecular Emission Segmentation (SCIMES). SCIMES overcomes sensitivity and resolution biases that plague many friends-of-friends algorithms by recasting cloud segmentation as a clustering problem. Considering the 13CO/C18O (J = 3–2) Heterodyne Inner Milky Way Plane Survey (CHIMPS) and the CO High-Resolution Survey (COHRS), we investigate how these two different approaches influence the final cloud decomposition. Although the two methods produce largely similar statistical results over the CHIMPS dataset, FW appears prone to oversegmentation, especially in crowded fields where gas envelopes around dense cores are identified as adjacent, distinct objects. FW catalogue also includes a number of fragmented clouds that appear as different objects in a line-of-sight projection. In addition, cross-correlating the physical properties of individual sources between catalogues is complicated by different definitions, numerical implementations, and design choices within each method, which make it very difficult to establish a one-to-one correspondence between the sources.
Synthesis of infrared Stokes spectra in an evolving solar chromospheric jet
Authors: Matsumoto T , Kawabata Y , Katsukawa Y , Iijima H , Quintero Noda C 
Published: May 2023

ABSTRACT
Chromospheric jets are plausible agents of energy and mass transport in the solar chromosphere, although their driving mechanisms have not yet been elucidated. Magnetic field measurements are key for distinguishing the driving mechanisms of chromospheric jets. We performed a full Stokes synthesis in the infrared range with a realistic radiative magnetohydrodynamics simulation that generated a chromospheric jet to predict spectropolarimetric observations from the Sunrise Chromospheric Infrared spectro-Polarimeter (SCIP) onboard the SUNRISE III balloon telescope. The jet was launched by the collision between the transition region and an upflow driven by the ascending motion of the twisted magnetic field at the envelope of the flux tube. This motion is consistent with upwardly propagating non-linear Alfvénic waves. The upflow could be detected as continuous Doppler signals in the Ca ii 849.8 nm line at the envelope where the dark line core intensity and strong linear polarization coexist. The axis of the flux tube was bright in both Fe i 846.8 nm and Ca ii 849.8 nm lines with downflowing plasma inside it. The structure, time evolution, and Stokes signals predicted in our study will improve the physical interpretation of future spectropolarimetric observations with SUNRISE III/SCIP.
The Three Hundred Project: the evolution of physical baryon profiles
Authors: Li Qingyang , Cui Weiguang , Yang Xiaohu , Davé Romeel , Rasia Elena , Borgani Stefano , Massimo Meneghetti , Knebe Alexander , Dolag Klaus , Sayers Jack 
Published: May 2023

ABSTRACT
The distribution of baryons provides a significant way to understand the formation of galaxy clusters by revealing the details of its internal structure and changes over time. In this paper, we present theoretical studies on the scaled profiles of physical properties associated with the baryonic components, including gas density, temperature, metallicity, pressure and entropy as well as stellar mass, metallicity and satellite galaxy number density in galaxy clusters from z = 4 to z = 0 by tracking their progenitors. These mass-complete simulated galaxy clusters are coming from The Three Hundred with two runs: Gizmo-SIMBA and Gadget-X. Through comparisons between the two simulations, and with observed profiles that are generally available at low redshift, we find that (1) the agreements between the two runs and observations are mostly at outer radii r ≳ 0.3r500, in line with the self-similarity assumption. While Gadget-X shows better agreements with the observed gas profiles in the central regions compared to Gizmo-SIMBA; (2) the evolution trends are generally consistent between the two simulations with slightly better consistency at outer radii. In detail, the gas density profile shows less discrepancy than the temperature and entropy profiles at high redshift. The differences in the cluster centre and gas properties imply different behaviours of the AGN models between Gadget-X and Gizmo-SIMBA, with the latter, maybe too strong for this cluster simulation. The high-redshift difference may be caused by the star formation and feedback models or hydrodynamics treatment, which requires observation constraints and understanding.
Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes
Authors: Cleary Alan M , Farmer Andrew D 
Published: May 2023

Abstract
The Genome Context Viewer is a web application for identifying, aligning, and visualizing genomic regions based on their micro and macrosyntenic structures. By using functional elements such as gene annotations as the unit of search and comparison, the Genome Context Viewer can compute and display relationships between regions across many assemblies from federated data sources in real-time, enabling users to rapidly explore multiple annotated genomes and identify divergence and structural events that can help provide insight into evolutionary mechanisms associated with functional consequences. In this work, we introduce version 2 of the Genome Context Viewer and highlight new features that enhance usability, performance, and ease of deployment.
Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires
Authors: Zong Fanjie , Long Chenyu , Hu Wanxin , Chen Shuang , Dai Wentao , Xiao Zhi-Xiong , Cao Yang 
Published: May 2023

Abstract
The utilization of high-throughput sequencing (HTS) for B-cell receptor (BCR) immune repertoire analysis has become widespread in the fields of adaptive immunity and antibody drug development. However, the sheer volume of sequences generated by these experiments presents a challenge in data processing. Specifically, multiple sequence alignment (MSA), a critical aspect of BCR analysis, remains inadequate for handling massive BCR sequencing data and lacks the ability to provide immunoglobulin-specific information. To address this gap, we introduce Abalign, a standalone program specifically designed for ultrafast MSA of BCR/antibody sequences. Benchmark tests demonstrate that Abalign achieves comparable or even better accuracy than state-of-the-art MSA tools, and shows remarkable advantages in terms of speed and memory consumption, reducing the time required for high-throughput analysis from weeks to hours. In addition to its alignment capabilities, Abalign offers a broad range of BCR analysis features, including extracting BCRs, constructing lineage trees, assigning VJ genes, analyzing clonotypes, profiling mutations, and comparing BCR immune repertoires. With its user-friendly graphic interface, Abalign can be easily run on personal computers instead of computing clusters. Overall, Abalign is an easy-to-use and effective tool that enables researchers to analyze massive BCR/antibody sequences, leading to new discoveries in the field of immunoinformatics. The software is freely available at http://cao.labshare.cn/abalign/.
UMSBP2 is chromatin remodeler that functions in regulation of gene expression and suppression of antigenic variation in trypanosomes
Authors: Soni Awakash , Klebanov-Akopyan Olga , Erben Esteban , Plaschkes Inbar , Benyamini Hadar , Mitesser Vera , Harel Amnon , Yamin Katereena , Onn Itay , Shlomai Joseph 
Published: May 2023

Abstract
Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.
Home-based exercise in patients on maintenance dialysis: a systematic review and meta-analysis of randomized clinical trials
Authors: Battaglia Yuri , Amicone Maria , Mantovani Alessandro , Combe Christian , Mitra Sandip , Basile Carlo ,   EuDial Working Group of ERA
Published: May 2023

ABSTRACT

Background
The impact of home-based exercise on physical performance and quality of life (QoL) in patients on maintenance dialysis has not yet been fully established.

Methods
We searched four large electronic databases to identify randomized controlled trials (RCTs) reporting the impact of home-based exercise interventions vs. usual care or intradialytic exercise interventions, on physical performance and QoL in patients on dialysis. The meta-analysis was performed using fixed effects modeling.

Results
We included 12 unique RCTs involving 791 patients of various ages on maintenance dialysis. Home-based exercise interventions were associated with an improvement of walking speed at the 6 Minutes Walking Test [6MWT; nine RCTs; pooled weighted mean differences (WMD): 33.7 m, 95% confidence interval (CI) 22.8–44.5; P &lt; 0.001; I2 = 0%) and in aerobic capacity as assessed by the peak oxygen consumption (VO2 peak; 3 RCTs; pooled WMD: 2.04 ml/kg/min, 95% CI 0.25–3.83; P = 0.03; I2 = 0%). They were also associated with improved QoL, as assessed by the Short Form (36) Health (SF-36) score. Stratifying the RCTs by control groups, no significant difference was found between home-based exercise and intradialytic exercise interventions. Funnel plots did not reveal any significant publication bias.

Conclusions
Our systematic review and meta-analysis showed that home-based exercise interventions for 3–6 months were associated with significant improvements in physical performance in patients on maintenance dialysis. However, further RCTs with a longer follow-up should be conducted to assess the safety, adherence, feasibility, and effects on QoL of home-based exercise programs in dialysis patients.
Plant polygalacturonase structures specify enzyme dynamics and processivities to fine-tune cell wall pectins
Authors: Safran Josip , Tabi Wafae , Ung Vanessa , Lemaire Adrien , Habrylo Olivier , Bouckaert Julie , Rouffle Maxime , Voxeur Aline , Pongrac Paula , Bassard Solène , Molinié Roland , Fontaine Jean-Xavier , Pilard Serge , Pau-Roblot Corinne , Bonnin Estelle , Larsen Danaé Sonja , Morel-Rouhier Mélanie , Girardet Jean-Michel , Lefebvre Valérie , Sénéchal Fabien , Mercadante Davide , Pelloux Jérôme 
Published: May 2023

Abstract
Polygalacturonases (PGs) fine-tune pectins to modulate cell wall chemistry and mechanics, impacting plant development. The large number of PGs encoded in plant genomes leads to questions on the diversity and specificity of distinct isozymes. Herein, we report the crystal structures of 2 Arabidopsis thaliana PGs, POLYGALACTURONASE LATERAL ROOT (PGLR), and ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE2 (ADPG2), which are coexpressed during root development. We first determined the amino acid variations and steric clashes that explain the absence of inhibition of the plant PGs by endogenous PG-inhibiting proteins (PGIPs). Although their beta helix folds are highly similar, PGLR and ADPG2 subsites in the substrate binding groove are occupied by divergent amino acids. By combining molecular dynamic simulations, analysis of enzyme kinetics, and hydrolysis products, we showed that these structural differences translated into distinct enzyme–substrate dynamics and enzyme processivities: ADPG2 showed greater substrate fluctuations with hydrolysis products, oligogalacturonides (OGs), with a degree of polymerization (DP) of ≤4, while the DP of OGs generated by PGLR was between 5 and 9. Using the Arabidopsis root as a developmental model, exogenous application of purified enzymes showed that the highly processive ADPG2 had major effects on both root cell elongation and cell adhesion. This work highlights the importance of PG processivity on pectin degradation regulating plant development.
Cajal bodies: Evolutionarily conserved nuclear biomolecular condensates with properties unique to plants
Authors: Taliansky Michael E , Love Andrew J , Kołowerzo-Lubnau Agnieszka , Smoliński Dariusz Jan 
Published: May 2023

AbstractProper orchestration of the thousands of biochemical processes that are essential to the life of every cell requires highly organized cellular compartmentalization of dedicated microenvironments. There are 2 ways to create this intracellular segregation to optimize cellular function. One way is to create specific organelles, enclosed spaces bounded by lipid membranes that regulate macromolecular flux in and out of the compartment. A second way is via membraneless biomolecular condensates that form due to to liquid-liquid phase separation. Although research on these membraneless condensates has historically been performed using animal and fungal systems, recent studies have explored basic principles governing the assembly, properties, and functions of membraneless compartments in plants. In this review, we discuss how phase separation is involved in a variety of key processes occurring in Cajal bodies (CBs), a type of biomolecular condensate found in nuclei. These processes include RNA metabolism, formation of ribonucleoproteins involved in transcription, RNA splicing, ribosome biogenesis, and telomere maintenance. Besides these primary roles of CBs, we discuss unique plant-specific functions of CBs in RNA-based regulatory pathways such as nonsense-mediated mRNA decay, mRNA retention, and RNA silencing. Finally, we summarize recent progress and discuss the functions of CBs in responses to pathogen attacks and abiotic stresses, responses that may be regulated via mechanisms governed by polyADP-ribosylation. Thus, plant CBs are emerging as highly complex and multifunctional biomolecular condensates that are involved in a surprisingly diverse range of molecular mechanisms that we are just beginning to appreciate.
Bicarbonate activation of the monomeric photosystem II-PsbS/Psb27 complex
Authors: Fantuzzi Andrea , Haniewicz Patrycja , Farci Domenica , Loi M Cecilia , Park Keunha , Büchel Claudia , Bochtler Matthias , Rutherford A William , Piano Dario 
Published: May 2023

Abstract
In thylakoid membranes, photosystem II (PSII) monomers from the stromal lamellae contain the subunits PsbS and Psb27 (PSIIm-S/27), while PSII monomers (PSIIm) from granal regions lack these subunits. Here, we have isolated and characterized these 2 types of PSII complexes in tobacco (Nicotiana tabacum). PSIIm-S/27 showed enhanced fluorescence, the near absence of oxygen evolution, and limited and slow electron transfer from QA to QB compared to the near-normal activities in the granal PSIIm. However, when bicarbonate was added to PSIIm-S/27, water splitting and QA to QB electron transfer rates were comparable to those in granal PSIIm. The findings suggest that the binding of PsbS and/or Psb27 inhibits forward electron transfer and lowers the binding affinity for bicarbonate. This can be rationalized in terms of the recently discovered photoprotection role played by bicarbonate binding via the redox tuning of the QA/QA•− couple, which controls the charge recombination route, and this limits chlorophyll triplet-mediated 1O2 formation. These findings suggest that PSIIm-S/27 is an intermediate in the assembly of PSII in which PsbS and/or Psb27 restrict PSII activity while in transit using a bicarbonate-mediated switch and protective mechanism.
Lysine malonylation of DgnsLIPID TRANSFER PROTEIN1 at the K81 site improves cold resistance in chrysanthemum
Authors: Liao Xiaoqin , Zhang Xingsu , Li Xin , Tian Yuchen , Yang Qing , Wang Yongyan , Tang Si , Luo Xuanling , Zhang Fan , Zhang Lei , Jiang Beibei , Liu Qinglin 
Published: May 2023

Abstract
Lysine malonylation (Kmal) is a recently discovered posttranslational modification, and its role in the response to abiotic stress has not been reported in plants. In this study, we isolated a nonspecific lipid transfer protein, DgnsLTP1, from chrysanthemum (Dendranthema grandiflorum var. Jinba). Overexpression and CRISPR-Cas9–mediated gene editing of DgnsLTP1 demonstrated that the protein endows chrysanthemum with cold tolerance. Yeast 2-hybrid, bimolecular fluorescence complementation, luciferase complementation imaging, and coimmunoprecipitation experimental results showed that DgnsLTP1 interacts with a plasma membrane intrinsic protein (PIP) DgPIP. Overexpressing DgPIP boosted the expression of DgGPX (glutathione peroxidase), increased the activity of GPX, and decreased the accumulation of reactive oxygen species (ROS), thereby enhancing the low-temperature stress tolerance of chrysanthemum, while the CRISPR-Cas9–mediated mutant dgpip inhibited this process. Transgenic analyses in chrysanthemum showed that DgnsLTP1 improves the cold resistance of chrysanthemum in a DgPIP-dependent manner. Moreover, Kmal of DgnsLTP1 at the K81 site prevented the degradation of DgPIP in Nicotiana benthamiana and chrysanthemum, further promoted DgGPX expression, enhanced GPX activity, and scavenged excess ROS produced by cold stress, thereby further enhancing the cold resistance of chrysanthemum.
7-UP: Generating in silico CODEX from a small set of immunofluorescence markers
Authors: Wu Eric , Trevino Alexandro E , Wu Zhenqin , Swanson Kyle , Kim Honesty J , D’Angio H Blaize , Preska Ryan , Chiou Aaron E , Charville Gregory W , Dalerba Piero , Duvvuri Umamaheswar , Colevas Alexander D , Levi Jelena , Bedi Nikita , Chang Serena , Sunwoo John , Egloff Ann Marie , Uppaluri Ravindra , Mayer Aaron T , Zou James 
Published: May 2023

Abstract
Multiplex immunofluorescence (mIF) assays multiple protein biomarkers on a single tissue section. Recently, high-plex CODEX (co-detection by indexing) systems enable simultaneous imaging of 40+ protein biomarkers, unlocking more detailed molecular phenotyping, leading to richer insights into cellular interactions and disease. However, high-plex data can be slower and more costly to collect, limiting its applications, especially in clinical settings. We propose a machine learning framework, 7-UP, that can computationally generate in silico 40-plex CODEX at single-cell resolution from a standard 7-plex mIF panel by leveraging cellular morphology. We demonstrate the usefulness of the imputed biomarkers in accurately classifying cell types and predicting patient survival outcomes. Furthermore, 7-UP's imputations generalize well across samples from different clinical sites and cancer types. 7-UP opens the possibility of in silico CODEX, making insights from high-plex mIF more widely available.