bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors associated with timely COVID-19 vaccination in a population-based cohort of patients with cancer
Authors: Powis Melanie , Sutradhar Rinku , Patrikar Aditi , Cheung Matthew , Gong Inna , Vijenthira Abi , Hicks Lisa K , Wilton Drew , Krzyzanowska Monika K , Singh Simron 
Published: November 2022

Abstract

Background
In many jurisdictions, cancer patients were prioritized for COVID-19 vaccination because of increased risk of infection and death. To understand sociodemographic disparities that affected timely receipt of COVID-19 vaccination among cancer patients, we undertook a population-based study in Ontario, Canada.

Methods
Patients older than 18 years and diagnosed with cancer January 2010 to September 2020 were identified using administrative data; vaccination administration was captured between approval (December 2020) up to February 2022. Factors associated with time to vaccination were evaluated using multivariable Cox proportional hazards regression.

Results
The cohort consisted of 356 535 patients, the majority of whom had solid tumor cancers (85.9%) and were not on active treatment (74.1%); 86.8% had received at least 2 doses. The rate of vaccination was 25% lower in recent (hazard ratio [HR] = 0.74, 95% confidence interval [CI] = 0.72 to 0.76) and nonrecent immigrants (HR = 0.80, 95% CI = 0.79 to 0.81). A greater proportion of unvaccinated patients were from neighborhoods with a high concentration of new immigrants or self-reported members of racialized groups (26.0% vs 21.3%, standardized difference = 0.111, P &lt; .001), residential instability (27.1% vs 23.0%, standardized difference = 0.094, P &lt; .001), or material deprivation (22.1% vs 16.8%, standardized difference = 0.134, P &lt; .001) and low socioeconomic status (20.9% vs 16.0%, standardized difference = 0.041, P &lt; .001). The rate of vaccination was 20% lower in patients from neighborhoods with the lowest socioeconomic status (HR = 0.82, 95% CI = 0.81 to 0.84) and highest material deprivation (HR = 0.80, 95% CI = 0.78 to 0.81) relative to those in more advantaged neighborhoods.

Conclusions
Despite funding of vaccines and prioritization of high-risk populations, marginalized patients were less likely to be vaccinated. Differences are likely due to the interplay between systemic barriers to access and cultural or social influences affecting uptake.
Functional variation in the non-coding genome: molecular implications for food security
Authors: Gullotta Giorgio , Korte Arthur , Marquardt Sebastian 
Published: November 2022

Abstract
The growing world population, in combination with the anticipated effects of climate change, is pressuring food security. Plants display an impressive arsenal of cellular mechanisms conferring resilience to adverse environmental conditions, and humans rely on these mechanisms for stable food production. The elucidation of the molecular basis of the mechanisms used by plants to achieve resilience promises knowledge-based approaches to enhance food security. DNA sequence polymorphisms can reveal genomic regions that are linked to beneficial traits of plants. However, our ability to interpret how a given DNA sequence polymorphism confers a fitness advantage at the molecular level often remains poor. A key factor is that these polymorphisms largely localize to the enigmatic non-coding genome. Here, we review the functional impact of sequence variations in the non-coding genome on plant biology in the context of crop breeding and agricultural traits. We focus on examples of non-coding with particularly convincing functional support. Our survey combines findings that are consistent with the view that the non-coding genome contributes to cellular mechanisms assisting many plant traits. Understanding how DNA sequence polymorphisms in the non-coding genome shape plant traits at the molecular level offers a largely unexplored reservoir of solutions to address future challenges in plant growth and resilience.
Spread of Sporothrix spp. through respiratory droplets from infected cats: A potential route of transmission
Authors: de Andrade Galliano Daros Bastos Fernanda , Raimundo Cognialli Regielly Caroline , Rodrigues de Farias Marconi , dos Santos Monti Fabiana , Wu Karen , Queiroz-Telles Flávio 
Published: November 2022

Abstract
Cases of cat-transmitted sporotrichosis in Brazil have increased in recent years. We collected respiratory secretions expelled while sneezing from 28 cats diagnosed with sporotrichosis. We identified the presence of Sporothrix spp. in respiratory droplets expelled in the sneeze of infected cats. The results raise concerns about a new transmission route for cat-transmitted sporotrichosis. Physicians who diagnose and treat human cases of sporotrichosis should be aware of this potential new transmission method to improve clinical suspicion. Approximately half of patients with granulomatous conjunctival sporotrichosis did not report experiencing traumatic injury from cats.
Adaptive optics and VLBA imaging observations of recoiling supermassive black hole candidates
Authors: Kim D-C , Kim Minjin , Yoon Ilsang , Momjian E , Kim Ji Hoon , Letai J , Evans A S 
Published: November 2022

ABSTRACT
We present the results of high-resolution adaptive optics imaging observations of four kinematically identified recoiling supermassive black hole (rSMBH) candidates. Ellipse fitting was carried out to measure the spatial offset between the active galactic nucleus (AGN) and the centre of the host galaxy. Two rSMBH candidates (J1713 + 3523 and J2054 + 0049) are found to be offset AGN. However, the Very Long Baseline Array 1.5 GHz continuum imaging observation and spectral decomposition of the [O iii]5007 line suggest that J1713 + 3523 is a dual AGN and its spatial offset is not due to a recoil event. The spatial offset between the AGN and the centre of the host galaxy in J2054 + 0049 is 0.06 ± 0.01 arcsec (201 ± 22 pc). Spectral decomposition of J2054 + 0049 also suggests that it could be a dual AGN system and the measured spatial offset may not be due to a recoil event.
Absorption lines from magnetically driven winds in X-ray binaries – II. High resolution observational signatures expected from future X-ray observatories
Authors: Chakravorty Susmita , Petrucci Pierre-Olivier , Datta Sudeb Ranjan , Ferreira Jonathan , Wilms Joern , Jacquemin-Ide Jonatan , Clavel Maica , Marcel Gregoire , Rodriguez Jerome , Malzac Julien , Belmont Renaud , Corbel Stephane , Coriat Mickael , Henri Gilles , Parra Maxime 
Published: November 2022

ABSTRACT
In our self-similar, analytical, magnetohydrodynamic (MHD) accretion–ejection solution, the density at the base of the outflow is explicitly dependent on the disc accretion rate – a unique property of this class of solutions. We had earlier found that the ejection index $p \gt \sim 0.1 (\dot{M}_{\rm{acc}} \propto r^p)$ is a key MHD parameter that decides if the flow can cause absorption lines in the high resolution X-ray spectra of black hole binaries. Here, we choose three dense warm solutions with p = 0.1, 0.3, 0.45 and carefully develop a methodology to generate spectra which are convolved with the Athena and XRISM response functions to predict what they will observe seeing through such MHD outflows. In this paper two other external parameters were varied – extent of the disc, $\rm {r_o|_{\rm{max}}} = 10^5, \, 10^6 \, \, \rm {r_G}$, and the angle of the line of sight, i ∼ 10–25°. Resultant absorption lines (H and He-like Fe, Ca, Ar) change in strength and their profiles manifest varying degrees of asymmetry. We checked if (a) the lines and (ii) the line asymmetries are detected, in our suit of synthetic Athena and XRISM spectra. Our analysis shows that Athena should detect the lines and their asymmetries for a standard 100 ks observation of a 100 mCrab source – lines with equivalent width as low as a few eV should be detected if the 6–8 keV counts are larger than 104–105 even for the least favourable simulated cases.
Chromosome maps of globular clusters from wide-field ground-based photometry
Authors: Jang S , Milone A P , Legnardi M V , Marino A F , Mastrobuono-Battisti A , Dondoglio E , Lagioia E P , Casagrande L , Carlos M , Mohandasan A , Cordoni G , Bortolan E , Lee Y-W 
Published: November 2022

ABSTRACT
Hubble Space Telescope (HST) photometry is providing an extensive analysis of globular clusters (GCs). In particular, the pseudo-two-colour diagram dubbed 'chromosome map (ChM)’ allowed to detect and characterize their multiple populations with unprecedented detail. The main limitation of these studies is the small field of view of HST, which makes it challenging to investigate some important aspects of the multiple populations, such as their spatial distributions and the internal kinematics in the outermost cluster regions. To overcome this limitation, we analyse state-of-art wide-field photometry of 43 GCs obtained from ground-based facilities. We derived high-resolution reddening maps and corrected the photometry for differential reddening when needed. We use photometry in the U, B, and I bands to introduce the ΔcU, B, I versus ΔB, I ChM of red-giant branch (RGB) and asymptotic-giant branch stars. We demonstrate that this ChM, which is built with wide-band ground-based photometry, is an efficient tool to identify first- and second-generation stars (1G and 2G) over a wide field of view. To illustrate its potential, we derive the radial distribution of multiple populations in NGC 288 and infer their chemical composition. We present the ChMs of RGB stars in 29 GCs and detect a significant degree of variety. The fraction of 1G and 2G stars, the number of subpopulations, and the extension of the ChMs significantly change from one cluster to another. Moreover, the metal-poor and metal-rich stars of Type II GCs define distinct sequences in the ChM. We confirm the presence of extended 1G sequences.
Extending optical flare models to the UV: results from comparing of TESS and GALEX flare observations for M Dwarfs
Authors: Jackman James A G , Shkolnik Evgenya L , Million Chase , Fleming Scott , Richey-Yowell Tyler , Loyd R O Parke 
Published: November 2022

ABSTRACT
The ultraviolet (UV) emission of stellar flares may have a pivotal role in the habitability of rocky exoplanets around low-mass stars. Previous studies have used white-light observations to calibrate empirical models which describe the optical and UV flare emission. However, the accuracy of the UV predictions of models has previously not been tested. We combined TESS optical and GALEX UV observations to test the UV predictions of empirical flare models calibrated using optical flare rates of M stars. We find that the canonical 9000-K black-body model used by flare studies underestimates the GALEX near-ultraviolet (NUV) energies of field age M stars by up to a factor of 6.5 ± 0.7 and the GALEX far-ultraviolet energies of fully convective field age M stars by 30.6 ± 10.0. We calculated energy correction factors that can be used to bring the UV predictions of flare models closer in line with observations. We calculated pseudo-continuum flare temperatures that describe both the white-light and GALEX NUV emission. We measured a temperature of 10 700 K for flares from fully convective M stars after accounting for the contribution from UV line emission. We also applied our correction factors to the results of previous studies of the role of flares in abiogenesis. Our results show that M stars do not need to be as active as previously thought in order to provide the NUV flux required for prebiotic chemistry, however, we note that flares will also provide more FUV flux than previously modelled.
Stellar age determination in the mass–luminosity plane
Authors: Higgins Erin R , Vink Jorick S 
Published: November 2022

ABSTRACT
The ages of stars have historically relied on isochrone fitting of standardized grids of models. While these stellar models have provided key constraints on observational samples of massive stars, they inherit many systematic uncertainties, mainly in the internal mixing mechanisms applied throughout the grid, fundamentally undermining the isochrone method. In this work, we utilize the mass–lumiosity (M–L) plane of Higgins & Vink as a method of determining stellar age, with mixing-corrected models applying a calibrated core overshooting αov and rotation rate to fit the observational data. We provide multiple test-beds to showcase our new method, while also providing comparisons to the commonly used isochrone method, highlighting the dominant systematic errors. We reproduce the evolution of individual O stars, and analyse the wider sample of O and B supergiants from the VLT-FLAMES Tarantula Survey, providing dedicated models with estimates for αov, Ω/Ωcrit, and ultimately stellar ages. The M–L plane highlights a large discrepancy in the spectroscopic masses of the O supergiant sample. Furthermore the M–L plane also demonstrates that the evolutionary masses of the B supergiant sample are inappropriate. Finally, we utilize detached eclipsing binaries, VFTS 642 and VFTS 500, and present their ages resulting from their precise dynamical masses, offering an opportunity to constrain their interior mixing. For the near-TAMS system, VFTS 500, we find that both components require a large amount of core overshooting (αov ≃ 0.5), implying an extended main-sequence width. We hence infer that the vast majority of B supergiants are still burning hydrogen in their cores.
Multiwavelength periodicity search in a sample of γ-ray bright blazars
Authors: Otero-Santos J , Peñil P , Acosta-Pulido J A , Becerra González J , Raiteri C M , Carnerero M I , Villata M 
Published: November 2022

ABSTRACT
We present the results of a long-term periodicity search in a sample of γ-ray blazars within a multiwavelength context. These blazars have been selected from the Steward Observatory sample as part of its optical monitoring program between 2008 and 2018. We study 15 sources with a temporal coverage in their optical total and polarized emission sufficiently large (&gt;9 yr) to perform a reliable long-term periodicity analysis. We collect data from several observatories to extend the coverage, enabling the search of longer periods. In addition, data are also gathered in the high-energy (E &gt; 100 MeV) γ-ray band from the Fermi Large Area Telescope; and in the 15 GHz radio band from the Owens Valley Radio Observatory. We identify 5 promising candidates to host quasi-periodic emission, AO 0235+164, PKS 1222+216, Mrk 501, BL Lacertae, and 1ES 2344+514 with periods in one or more bands and statistical significances ∼3σ after trial factor correction. AO 0235+164 shows a period of ∼8.2 yr in the R band; PKS 1222+216 has a quasi-periodic modulation in its total and polarized optical emission of ∼1.6 yr; Mrk 501 displays a ∼5 yr quasi-periodicity in optical and radio wavelengths; BL Lacertae presents a period of ∼1.8 yr in its polarized emission; and 1ES 2344 + 514 shows a hint of a ∼5.5 yr period in its optical R band. We interpret these results in the framework of the most common models and scenarios, namely the presence of a binary supermassive black hole system; or geometrical effects like helical or precessing jets.
Feasibility and applicability of locomotive syndrome risk test in elderly patients who underwent total knee arthroplasty
Authors: Ogata Toru , Yamada Keiko , Miura Hiromasa , Hino Kazunori , Kutsuna Tatsuhiko , Watamori Kunihiko , Kinoshita Tomofumi , Ishibashi Yasuyuki , Yamamoto Yuji , Sasaki Tomoyuki , Matsuda Shuichi , Kuriyama Shinichi , Watanabe Mutsumi , Tomita Tetsuya , Tamaki Masashi , Ishibashi Teruya , Okazaki Ken , Mizu-uchi Hideki , Ishibashi Shojiro , Ma Yuan , Ito Yoichi M , Nakamura Kozo , Tanaka Sakae 
Published: November 2022

ABSTRACT

Objectives
The concept of locomotive syndrome (LS) and its evaluation method, the LS risk test, have been applied in an integrated manner to capture the decline in mobility resulting from musculoskeletal disorders. The purpose of this study was to evaluate the impact of total knee arthroplasty (TKA) in the elderly with knee osteoarthritis, a common disorder found in LS.

Methods
A total of 111 patients were registered prior to TKA and postoperatively followed up for 1 year. Three components of the LS risk test (the two-step test, stand-up test, and Geriatric Locomotive Function Scale-25) were assessed pre- and postoperatively.

Results
After surgery, all three components of the test showed significant improvements from the baseline. The ratio of Stage 3 LS patients (progressed stage of decrease in mobility) reduced from 82.3% to 33.9% postoperatively. There was no significant difference in the degree of change in the scores between the younger (60–74 years) and older (≥75 years) age groups.

Conclusions
We found that TKA has a major impact in preventing the progression of LS in patients with knee osteoarthritis. The LS risk test is a feasible tool for the longitudinal evaluation of patients with musculoskeletal diseases of varying severity and with multiple symptoms.
HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses
Authors: Shi Xiaoying , Yu Zhiguang , Ren Pengfei , Dong Xin , Ding Xuanxin , Song Jiaming , Zhang Jing , Li Taiwen , Wang Chenfei 
Published: November 2022

Abstract
Understanding gene expression patterns across different human cell types is crucial for investigating mechanisms of cell type differentiation, disease occurrence and progression. The recent development of single-cell RNA-seq (scRNA-seq) technologies significantly boosted the characterization of cell type heterogeneities in different human tissues. However, the huge number of datasets in the public domain also posed challenges in data integration and reuse. We present Human Universal Single Cell Hub (HUSCH, http://husch.comp-genomics.org), an atlas-scale curated database that integrates single-cell transcriptomic profiles of nearly 3 million cells from 185 high-quality human scRNA-seq datasets from 45 different tissues. All the data in HUSCH were uniformly processed and annotated with a standard workflow. In the single dataset module, HUSCH provides interactive gene expression visualization, differentially expressed genes, functional analyses, transcription regulators and cell–cell interaction analyses for each cell type cluster. Besides, HUSCH integrated different datasets in the single tissue module and performs data integration, batch correction, and cell type harmonization. This allows a comprehensive visualization and analysis of gene expression within each tissue based on single-cell datasets from multiple sources and platforms. HUSCH is a flexible and comprehensive data portal that enables searching, visualizing, analyzing, and downloading single-cell gene expression for the human tissue atlas.
ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers
Authors: Wu Song , Huang Yue , Zhang Mochen , Gong Zheng , Wang Guoliang , Zheng Xinchang , Zong Wenting , Zhao Wei , Xing Peiqi , Li Rujiao , Liu Zhaoqi , Bao Yiming 
Published: November 2022

AbstractAlternative splicing (AS) is a fundamental process that governs almost all aspects of cellular functions, and dysregulation in this process has been implicated in tumor initiation, progression and treatment resistance. With accumulating studies of carcinogenic mis-splicing in cancers, there is an urgent demand to integrate cancer-associated splicing changes to better understand their internal cross-talks and functional consequences from a global view. However, a resource of key functional AS events in human cancers is still lacking. To fill the gap, we developed ASCancer Atlas (https://ngdc.cncb.ac.cn/ascancer), a comprehensive knowledgebase of aberrant splicing in human cancers. Compared to extant databases, ASCancer Atlas features a high-confidence collection of 2006 cancer-associated splicing events experimentally proved to promote tumorigenesis, a systematic splicing regulatory network, and a suit of multi-scale online analysis tools. For each event, we manually curated the functional axis including upstream splicing regulators, splicing event annotations, downstream oncogenic effects, and possible therapeutic strategies. ASCancer Atlas also houses about 2 million computationally putative splicing events. Additionally, a user-friendly web interface was built to enable users to easily browse, search, visualize, analyze, and download all splicing events. Overall, ASCancer Atlas provides a unique resource to study the functional roles of splicing dysregulation in human cancers.
GenomicKB: a knowledge graph for the human genome
Authors: Feng Fan , Tang Feitong , Gao Yijia , Zhu Dongyu , Li Tianjun , Yang Shuyuan , Yao Yuan , Huang Yuanhao , Liu Jie 
Published: November 2022

AbstractGenomic Knowledgebase (GenomicKB) is a graph database for researchers to explore and investigate human genome, epigenome, transcriptome, and 4D nucleome with simple and efficient queries. The database uses a knowledge graph to consolidate genomic datasets and annotations from over 30 consortia and portals, including 347 million genomic entities, 1.36 billion relations, and 3.9 billion entity and relation properties. GenomicKB is equipped with a web-based query system (https://gkb.dcmb.med.umich.edu/) which allows users to query the knowledge graph with customized graph patterns and specific constraints on entities and relations. Compared with traditional tabular-structured data stored in separate data portals, GenomicKB emphasizes the relations among genomic entities, intuitively connects isolated data matrices, and supports efficient queries for scientific discoveries. GenomicKB transforms complicated analysis among multiple genomic entities and relations into coding-free queries, and facilitates data-driven genomic discoveries in the future.
AsgeneDB: a curated orthology arsenic metabolism gene database and computational tool for metagenome annotation
Authors: Song Xinwei , Li Yiqun , Stirling Erinne , Zhao Kankan , Wang Binhao , Zhu Yongguan , Luo Yongming , Xu Jianming , Ma Bin 
Published: November 2022

Abstract
Arsenic (As) is the most ubiquitous toxic metalloid in nature. Microbe-mediated As metabolism plays an important role in global As biogeochemical processes, greatly changing its toxicity and bioavailability. While metagenomic sequencing may advance our understanding of the As metabolism capacity of microbial communities in different environments, accurate metagenomic profiling of As metabolism remains challenging due to low coverage and inaccurate definitions of As metabolism gene families in public orthology databases. Here we developed a manually curated As metabolism gene database (AsgeneDB) comprising 400 242 representative sequences from 59 As metabolism gene families, which are affiliated with 1653 microbial genera from 46 phyla. AsgeneDB achieved 100% annotation sensitivity and 99.96% annotation accuracy for an artificial gene dataset. We then applied AsgeneDB for functional and taxonomic profiling of As metabolism in metagenomes from various habitats (freshwater, hot spring, marine sediment and soil). The results showed that AsgeneDB substantially improved the mapping ratio of short reads in metagenomes from various environments. Compared with other databases, AsgeneDB provides more accurate, more comprehensive and faster analysis of As metabolic genes. In addition, we developed an R package, Asgene, to facilitate the analysis of metagenome sequencing data. Therefore, AsgeneDB and the associated Asgene package will greatly promote the study of As metabolism in microbial communities in various environments.