bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viral Kinetics in Sylvatic Yellow Fever Cases
Authors: Avelino-Silva Vivian I , Thomazella Mateus Vailant , Marmorato Mariana Prado , Correia Carolina A , Dias Juliana Z C , Maestri Alvino , Cerqueira Natalia B , Moreira Carlos H V , Buccheri Renata , Félix Alvina C , Zanella Luiz G F A B E , Costa Priscilla R , Kallás Esper G 
Published: November 2022

Abstract

Background
Yellow fever is a mosquito-borne zoonotic disease caused by yellow fever virus (YFV). Between 2017 and 2019, more than 504 human cases and 176 deaths were confirmed in the outskirts of São Paulo city. Throughout this outbreak, studies suggested a potential association between YFV viremia and mortality.

Methods
Viral ribonucleic acid was measured using reverse-transcription quantitative polymerase chain reaction in plasma samples collected at up to 5 time points, between 3 and 120 days after symptoms onset.

Results
Eighty-four patients with confirmed YFV infection were included. Most were males, median age was 42, and 30 (36%) died. Deceased patients were older than survivors (P = .003) and had a higher viremia across all time points (P = .0006). Mean values of viremia had a positive, statistically significant correlation with peak values of neutrophils, indirect bilirubin, aspartate transaminase, international normalized ratio, and creatinine. Finally, a Cox proportional hazards model adjusted for age and laboratory variables showed that viremia is independently associated with death, with a mean 1.84-fold increase (84%) in the hazard of death (P &lt; .001) for each unit increase in mean log10 viremia.

Conclusions
Our results raise the importance of monitoring YFV viremia and suggest a potential benefit of antiviral drugs or neutralizing monoclonal antibodies early in the course of this infection to improve disease outcomes.
Portal venous gas accompanied by gallbladder torsion: a case report
Authors: Tohma Takayuki , Kobe Yoshiro , Yoshida Mitsuhiko , Ushio Masaya 
Published: November 2022

Abstract
Portal venous gas (PVG) generally suggests critically ill conditions such as severe bowel ischemia. We herein report a rare case of gallbladder torsion with PVG. An 88-year-old woman complained of right hypogastric pain. Ultrasonography (US) showed diffuse wall thickening of her gallbladder and mobile echogenic foci moving inside the portal venous branches. Computed tomography showed a thickened wall of the gallbladder with poor enhancement and tiny pockets of air in the portal venous branches (segments 4 and 5). There was no evidence of other visceral ischemia. She was diagnosed with necrotic cholecystitis and immediately underwent an emergency operation. We found a gangrenous gallbladder with 180° clockwise rotation along the longitudinal axis and performed cholecystectomy. We confirmed the disappearance of PVG with US after the operation. Her postoperative course was uneventful. Gallbladder diseases can produce PVG, and US might be a useful diagnostic modality to evaluate changes in PVG.
Virulence is one of the mechanisms of vulvovaginal candidiasis recurrence, rather than drug resistance
Authors: Li Xinzheng , Chen Shi , Lyu Xiangcai , Tian Jiyun 
Published: November 2022

Abstract
To explore the mechanism of vulvovaginal candidiasis (VVC) recurrence. A total of 127 strains of Candida albicans (C. albicans) were collected, including 58, 40, and 29 strains from the recurrent vulvovaginal candidiasis (RVVC), VVC, and asymptomatic carrier (AC), respectively. The strains’ virulence such as in vivo hypha formation rate, germ tube formation rate, biofilm formation ability, and sensitivity to five common antifungals were detected. The in vivo hypha formation rates of C. albicans from the RVVC (55.2%) and VVC (40.0%) were significantly higher than that from the AC (0%) (P &lt; .001). The median germ tube formation rate of the RVVC was 88.2%, which was higher than that of the VVC and AC (59.9% and 65.6%), respectively (P &lt; .001). The median absorbance of the biofilm formation test for strains in the RVVC was 0.380, considerably higher than that in the VVC and AC (0.246 and 0.254) (P &lt; .001). The drug sensitivity rate of the strains to 5-fluorocytosine and itraconazole and the ratio of strains sensitive to all the five antifungals in the VVC group were lower than those in the RVVC and AC groups. In conclusion, the virulence of strains from the RVVC is stronger than that of strains from the VVC and AC, the antifungal resistance rate of strains from the RVVC group is lower than that of strains from the VVC group. So, it is suitable to argue that the strains’ virulence is one of the mechanisms for the relapse of RVVC, rather than its antifungal resistance.
Star formation time-scale in the molecular filament WB 673
Authors: Ryabukhina O L , Kirsanova M S , Henkel C , Wiebe D S 
Published: November 2022

ABSTRACT
We present the observations of ammonia emission lines toward the interstellar filament WB 673 hosting the dense clumps WB 673, WB 668, S233-IR, and G173.57+2.43. LTE analysis of the lines allows us to estimate gas kinetic temperature (≲30K in all the clumps), number density (7–17 × 103 cm−3), and ammonia column density (≈1–1.5 × 1015 cm−2) in the dense clumps. We find signatures of collapse in WB 673 and presence of compact spatially unresolved dense clumps in S233-IR. We reconstruct 1D density and temperature distributions in the clumps and estimate their ages using astrochemical modelling. Considering CO, CS, NH3, and N2H+ molecules (plus HCN and HNC for WB 673), we find a chemical age of tchem = 1–3 × 105 yrs, providing the best agreement between the simulated and observed column densities in all the clumps. Therefore, we consider tchem as the chemical age of the entire filament. A long preceding low-density stage of gas accumulation in the astrochemical model would break the agreement between the simulated and observed column densities. We suggest that rapid star formation over a ∼105 yrs time-scale take place in the filament.
A systematic comparison of galaxy cluster temperatures measured with NuSTAR and Chandra
Authors: Wallbank A N , Maughan B J , Gastaldello F , Potter C , Wik D R 
Published: November 2022

ABSTRACT
Temperature measurements of galaxy clusters are used to determine their masses, which in turn are used to determine cosmological parameters. However, systematic differences between the temperatures measured by different telescopes imply a significant source of systematic uncertainty on such mass estimates. We perform the first systematic comparison between cluster temperatures measured with Chandra and NuSTAR. This provides a useful contribution to the effort of cross-calibrating cluster temperatures due to the harder response of NuSTAR compared with most other observatories. We measure average temperatures for eight clusters observed with NuSTAR and Chandra. We fit the NuSTAR spectra in a hard (3–10 keV) energy band, and the Chandra spectra in both the hard and a broad (0.6–9 keV) band. We fit a power-law cross-calibration model to the resulting temperatures. At a Chandra temperature of 10 keV, the average NuSTAR temperature was $(10.5\pm 3.7)$ and $(15.7\pm 4.6){{\ \rm per\ cent}}$, lower than Chandra for the broad- and hard-band fits, respectively. We explored the impact of systematics from background modelling and multiphase temperature structure of the clusters, and found that these did not affect our results. Our sample are primarily merging clusters with complex thermal structures so are not ideal calibration targets. However, given the harder response of NuSTAR, it would be expected to measure a higher average temperature than Chandra for a non-isothermal cluster, so we interpret our measurement as a lower limit on the difference in temperatures between NuSTAR and Chandra.
Iterative mean-field approach to the spherical collapse of dark matter haloes
Authors: Shi Xun 
Published: November 2022

ABSTRACT
Gravitational collapse of dark matter overdensities leads to the formation of dark matter haloes which embed galaxies and galaxy clusters. An intriguing feature of dark matter haloes is that their density profiles closely follow a universal form irrespective of the initial condition or the corresponding growth history. This represents a class of dynamical systems with emergent universalities. We propose an ‘iterative mean-field approach’ to compute the solutions of the gravitational collapse dynamics. This approach iteratively searches for the evolution of the interaction field ϕ(t) – in this case the enclosed mass profile M(r, t) – that is consistent with the dynamics, thus that ϕ(t) is the fix-point of the iterative mapping, $\mathcal {H}(\phi) = \phi$. The formalism replaces the N-body interactions with one-body interactions with the coarse-grained interaction field, and thus shares the spirit of the mean-field theory in statistical physics. This ‘iterative mean-field approach’ combines the versatility of numerical simulations and the comprehensiveness of analytical solutions, and is particularly powerful in searching for and understanding intermediate asymptotic states in a wide range of dynamical systems where the solutions can not be obtained through the traditional self-similar analysis.
The buildup of galaxies and their spheroids: The contributions of mergers, disc instabilities, and star formation
Authors: Huško Filip , Lacey Cedric G , Baugh Carlton M 
Published: November 2022

ABSTRACT
We use the GALFORM semi-analytical model of galaxy formation and the Planck-Millennium simulation to investigate the origins of stellar mass in galaxies and their spheroids. We compare the importance of mergers and disc instabilities, as well as the starbursts that they trigger. We find that the fraction of galaxy stellar mass formed ex situ (i.e. through mergers; fex) increases sharply from M* = 1011 M⊙ upwards, reaching 80 per cent at M* = 1011.3 M⊙. The massive end of the fex–M* relation does not evolve with redshift, in disagreement with other models. For low-mass galaxies we find larger ex situ contributions at z = 0 than in other models (7–12 per cent), with a decrease towards higher redshifts. Major mergers contribute roughly half of the ex situ mass, with minor mergers and smooth accretion of satellites both accounting for ≈25 per cent, almost independent of stellar mass and redshift. Mergers dominate in building up high-mass (M*, sph &gt; 1011 M⊙) and low-mass (M*, sph &lt; 108.5 M⊙) spheroids. Disc instabilities and their associated starbursts dominate for intermediate-mass spheroids (108.5 &lt; M*, sph &lt; 1011 M⊙) at z = 0. The mass regime where pseudo-bulges dominate is in agreement with observed pseudo-bulge fractions, but the peak value in the pseudo-bulge fraction predicted by GALFORM is likely too high. Starbursts induced by disc instabilities are the dominant channel for spheroid growth at all redshifts, while merger-induced starbursts are relatively negligible, except at very high redshifts (z &gt; 5).
A PAM-free CRISPR/Cas12a ultra-specific activation mode based on toehold-mediated strand displacement and branch migration
Authors: Wu You , Luo Wang , Weng Zhi , Guo Yongcan , Yu Hongyan , Zhao Rong , Zhang Li , Zhao Jie , Bai Dan , Zhou Xi , Song Lin , Chen Kena , Li Junjie , Yang Yujun , Xie Guoming 
Published: November 2022

AbstractCRISPR (clustered regularly interspaced short palindromic repeats) technology has achieved great breakthroughs in terms of convenience and sensitivity; it is becoming the most promising molecular tool. However, only two CRISPR activation modes (single and double stranded) are available, and they have specificity and universality bottlenecks that limit the application of CRISPR technology in high-precision molecular recognition. Herein, we proposed a novel CRISPR/Cas12a unrestricted activation mode to greatly improve its performance. The new mode totally eliminates the need for a protospacer adjacent motif and accurately activates Cas12a through toehold-mediated strand displacement and branch migration, which is highly universal and ultra-specific. With this mode, we discriminated all mismatch types and detected the EGFR T790M and L858R mutations in very low abundance. Taken together, our activation mode is deeply incorporated with DNA nanotechnology and extensively broadens the application boundaries of CRISPR technology in biomedical and molecular reaction networks.
Estrogen regulates divergent transcriptional and epigenetic cell states in breast cancer
Authors: Ors Aysegul , Chitsazan Alex Daniel , Doe Aaron Reid , Mulqueen Ryan M , Ak Cigdem , Wen Yahong , Haverlack Syber , Handu Mithila , Naldiga Spandana , Saldivar Joshua C , Mohammed Hisham 
Published: November 2022

Abstract
Breast cancers are known to be driven by the transcription factor estrogen receptor and its ligand estrogen. While the receptor's cis-binding elements are known to vary between tumors, heterogeneity of hormone signaling at a single-cell level is unknown. In this study, we systematically tracked estrogen response across time at a single-cell level in multiple cell line and organoid models. To accurately model these changes, we developed a computational tool (TITAN) that quantifies signaling gradients in single-cell datasets. Using this approach, we found that gene expression response to estrogen is non-uniform, with distinct cell groups expressing divergent transcriptional networks. Pathway analysis suggested the two most distinct signatures are driven separately by ER and FOXM1. We observed that FOXM1 was indeed activated by phosphorylation upon estrogen stimulation and silencing of FOXM1 attenuated the relevant gene signature. Analysis of scRNA-seq data from patient samples confirmed the existence of these divergent cell groups, with the FOXM1 signature predominantly found in ER negative cells. Further, multi-omic single-cell experiments indicated that the different cell groups have distinct chromatin accessibility states. Our results provide a comprehensive insight into ER biology at the single-cell level and potential therapeutic strategies to mitigate resistance to therapy.
The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain
Authors: Ament Seth A , Adkins Ricky S , Carter Robert , Chrysostomou Elena , Colantuoni Carlo , Crabtree Jonathan , Creasy Heather H , Degatano Kylee , Felix Victor , Gandt Peter , Garden Gwenn A , Giglio Michelle , Herb Brian R , Khajouei Farzaneh , Kiernan Elizabeth , McCracken Carrie , McDaniel Kennedy , Nadendla Suvarna , Nickel Lance , Olley Dustin , Orvis Joshua , Receveur Joseph P , Schor Mike , Sonthalia Shreyash , Tickle Timothy L , Way Jessica , Hertzano Ronna , Mahurkar Anup A , White Owen R 
Published: November 2022

Abstract
Scalable technologies to sequence the transcriptomes and epigenomes of single cells are transforming our understanding of cell types and cell states. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative Cell Census Network (BICCN) is applying these technologies at unprecedented scale to map the cell types in the mammalian brain. In an effort to increase data FAIRness (Findable, Accessible, Interoperable, Reusable), the NIH has established repositories to make data generated by the BICCN and related BRAIN Initiative projects accessible to the broader research community. Here, we describe the Neuroscience Multi-Omic Archive (NeMO Archive; nemoarchive.org), which serves as the primary repository for genomics data from the BRAIN Initiative. Working closely with other BRAIN Initiative researchers, we have organized these data into a continually expanding, curated repository, which contains transcriptomic and epigenomic data from over 50 million brain cells, including single-cell genomic data from all of the major regions of the adult and prenatal human and mouse brains, as well as substantial single-cell genomic data from non-human primates. We make available several tools for accessing these data, including a searchable web portal, a cloud-computing interface for large-scale data processing (implemented on Terra, terra.bio), and a visualization and analysis platform, NeMO Analytics (nemoanalytics.org).
MethBank 4.0: an updated database of DNA methylation across a variety of species
Authors: Zhang Mochen , Zong Wenting , Zou Dong , Wang Guoliang , Zhao Wei , Yang Fei , Wu Song , Zhang Xinran , Guo Xutong , Ma Yingke , Xiong Zhuang , Zhang Zhang , Bao Yiming , Li Rujiao 
Published: November 2022

Abstract
DNA methylation, as the most intensively studied epigenetic mark, regulates gene expression in numerous biological processes including development, aging, and disease. With the rapid accumulation of whole-genome bisulfite sequencing data, integrating, archiving, analyzing, and visualizing those data becomes critical. Since its first publication in 2015, MethBank has been continuously updated to include more DNA methylomes across more diverse species. Here, we present MethBank 4.0 (https://ngdc.cncb.ac.cn/methbank/), which reports an increase of 309% in data volume, with 1449 single-base resolution methylomes of 23 species, covering 236 tissues/cell lines and 15 biological contexts. Value-added information, such as more rigorous quality evaluation, more standardized metadata, and comprehensive downstream annotations have been integrated in the new version. Moreover, expert-curated knowledge modules of featured differentially methylated genes associated with biological contexts and methylation analysis tools have been incorporated as new components of MethBank. In addition, MethBank 4.0 is equipped with a series of new web interfaces to browse, search, and visualize DNA methylation profiles and related information. With all these improvements, we believe the updated MethBank 4.0 will serve as a fundamental resource to provide a wide range of data services for the global research community.
HGD: an integrated homologous gene database across multiple species
Authors: Duan Guangya , Wu Gangao , Chen Xiaoning , Tian Dongmei , Li Zhaohua , Sun Yanling , Du Zhenglin , Hao Lili , Song Shuhui , Gao Yuan , Xiao Jingfa , Zhang Zhang , Bao Yiming , Tang Bixia , Zhao Wenming 
Published: November 2022

Abstract
Homology is fundamental to infer genes’ evolutionary processes and relationships with shared ancestry. Existing homolog gene resources vary in terms of inferring methods, homologous relationship and identifiers, posing inevitable difficulties for choosing and mapping homology results from one to another. Here, we present HGD (Homologous Gene Database, https://ngdc.cncb.ac.cn/hgd), a comprehensive homologs resource integrating multi-species, multi-resources and multi-omics, as a complement to existing resources providing public and one-stop data service. Currently, HGD houses a total of 112 383 644 homologous pairs for 37 species, including 19 animals, 16 plants and 2 microorganisms. Meanwhile, HGD integrates various annotations from public resources, including 16 909 homologs with traits, 276 670 homologs with variants, 398 573 homologs with expression and 536 852 homologs with gene ontology (GO) annotations. HGD provides a wide range of omics gene function annotations to help users gain a deeper understanding of gene function.
CRAMdb: a comprehensive database for composition and roles of microbiome in animals
Authors: Lei Bingbing , Xu Yueren , Lei Yunjiao , Li Cunyuan , Zhou Ping , Wang Limin , Yang Qing , Li Xiaoyue , Li Fulin , Liu Chuyang , Cui Chaowen , Chen Tong , Ni Wei , Hu Shengwei 
Published: November 2022

Abstract
CRAMdb (a database for composition and roles of animal microbiome) is a comprehensive resource of curated and consistently annotated metagenomes for non-human animals. It focuses on the composition and roles of the microbiome in various animal species. The main goal of the CRAMdb is to facilitate the reuse of animal metagenomic data, and enable cross-host and cross-phenotype comparisons. To this end, we consistently annotated microbiomes (including 16S, 18S, ITS and metagenomics sequencing data) of 516 animals from 475 projects spanning 43 phenotype pairs to construct the database that is equipped with 9430 bacteria, 278 archaea, 2216 fungi and 458 viruses. CRAMdb provides two main contents: microbiome composition data, illustrating the landscape of the microbiota (bacteria, archaea, fungi, and viruses) in various animal species, and microbiome association data, revealing the relationships between the microbiota and various phenotypes across different animal species. More importantly, users can quickly compare the composition of the microbiota of interest cross-host or body site and the associated taxa that differ between phenotype pairs cross-host or cross-phenotype. CRAMdb is freely available at (http://www.ehbio.com/CRAMdb).
REBASE: a database for DNA restriction and modification: enzymes, genes and genomes
Authors: Roberts Richard J , Vincze Tamas , Posfai Janos , Macelis Dana 
Published: November 2022

Abstract
REBASE is a comprehensive and extensively curated database of information about the components of restriction-modification (RM) systems. It is fully referenced and provides information about the recognition and cleavage sites for both restriction enzymes and DNA methyltransferases together with their commercial availability, methylation sensitivity, crystal and sequence data. All completely sequenced genomes and select shotgun sequences are analyzed for RM system components. When PacBio sequence data is available, the recognition sequences of many DNA methyltransferases (MTases) can be determined. This has led to an explosive growth in the number of well-characterized MTases in REBASE. The contents of REBASE may be browsed from the web rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email.
SulfAtlas, the sulfatase database: state of the art and new developments
Authors: Stam Mark , Lelièvre Pernelle , Hoebeke Mark , Corre Erwan , Barbeyron Tristan , Michel Gurvan 
Published: November 2022

Abstract
SulfAtlas (https://sulfatlas.sb-roscoff.fr/) is a knowledge-based resource dedicated to a sequence-based classification of sulfatases. Currently four sulfatase families exist (S1–S4) and the largest family (S1, formylglycine-dependent sulfatases) is divided into subfamilies by a phylogenetic approach, each subfamily corresponding to either a single characterized specificity (or few specificities in some cases) or to unknown substrates. Sequences are linked to their biochemical and structural information according to an expert scrutiny of the available literature. Database browsing was initially made possible both through a keyword search engine and a specific sequence similarity (BLAST) server. In this article, we will briefly summarize the experimental progresses in the sulfatase field in the last 6 years. To improve and speed up the (sub)family assignment of sulfatases in (meta)genomic data, we have developed a new, freely-accessible search engine using Hidden Markov model (HMM) for each (sub)family. This new tool (SulfAtlas HMM) is also a key part of the internal pipeline used to regularly update the database. SulfAtlas resource has indeed significantly grown since its creation in 2016, from 4550 sequences to 162 430 sequences in August 2022.