bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Candida colonization in intensive care unit patients with and without COVID-19: First prospective cohort study from Turkey
Authors: Çaklovica Küçükkaya Ilvana , Orhun Günseli , Çağatay Arif Atahan , Kalaycı Sadık , Esen Figen , Şahin Fikrettin , Ağaçfidan Ali , Erturan Zayre 
Published: April 2024

Abstract
Candida species are the primary cause of fungal infections in intensive care units (ICUs). Despite the increasing prevalence of Candida-related infections, monitoring the progression of these infections from colonization in COVID-19 ICU patients lacks sufficient information. This study aims prospectively to compare 62 COVID-19 and 60 non-COVID-19 ICU patients from admission to discharge in terms of colonization development, rates, isolated Candida species, risk factors, and Candida infections during hospitalization. A total of 1464 samples were collected at specific time intervals from various body sites [mouth, skin (axilla), rectal, and urine]. All samples were inoculated onto CHROMagar Candida and CHROMagar Candida Plus media, and isolates identified using MALDI-TOF MS. COVID-19 patients exhibited significantly higher colonization rates in oral, rectal, and urine samples compared to non-COVID-19 patients, (p &lt; 0.05). Among the Candida species, non-albicans Candida was more frequently detected in COVID-19 patients, particularly in oral (75.8%–25%; p &lt; 0.001) and rectal regions (74.19% – 46.66%; p &lt; 0.05). Colonization with mixed Candida species was also more prevalent in the oropharyngeal region (p &lt; 0.05). Mechanical ventilation and corticosteroid use emerged as elevated risk factors among COVID-19 patients (p &lt; 0.05). Despite the colonization prevalence, both COVID-19-positive and negative patients exhibited low incidences of Candida infections, with rates of 9.67% (n = 6/62) and 6.67% (n = 3/60), respectively. Consequently, although Candida colonization rates were higher in COVID-19 ICU patients, there was no significant difference in Candida infection development compared to the non-COVID-19 group. However, the elevated rate of non-albicans Candida isolates highlights potential future infections, particularly given their intrinsic resistance in prophylactic or empirical treatments if needed. Additionally, the high rate of mixed colonization emphasizes the importance of using chromogenic media for routine evaluation.
The TELPERION survey for extended emission regions around active galactic nuclei: a strongly interacting and merging galaxy sample
Authors: Keel William C , Moiseev Alexei , Uklein Roman , Smirnova Aleksandrina 
Published: April 2024

ABSTRACT
We present the results of a search for extended emission-line regions (EELRs) ionized by extant or recently faded active galactic nuclei (AGNs), using [O III] narrow-band imaging and spectroscopic follow-up. The sample includes 198 galaxies in 92 strongly interacting or merging galaxy systems in the range of z = 0.009–0.0285. Among these, three systems have EELRs extended beyond 10 kpc in projection from the nucleus detected in previous studies. We identify a single new distant emission region, projected 35 kpc from UGC 5941. Our optical spectrum does not detect He II, but its strong-line ratios put this in the same class as securely characterized EELR clouds. The nucleus of UGC 5941 is dominated by recent star formation, preventing detection of any weak ongoing AGN. Overall counts of distant EELRs in this and the previous TELPERION samples give incidence 2–5 per cent depending on galaxy and AGN selection, 20–50 times higher than the Galaxy Zoo EELR survey with its higher surface-brightness threshold and much larger input sample. AGNs in interacting and merging systems have an increased detection rate of 12 ± 6 per cent, while none are detected around non-interacting AGNs. Some of these AGNs are at luminosity low enough to require additional X-ray or far-infrared information to tell whether the EELR ionization level suggests long-term fading.
A search for intermediate-mass black holes in compact stellar systems through optical emissions from tidal disruption events
Authors: Pomeroy Richard T , Norris Mark A 
Published: April 2024

ABSTRACT
Intermediate-mass black holes (IMBHs) are expected to exist in globular clusters (GCs) and compact stellar systems (CSSs) in general, but none have been conclusively detected. Tidal disruption events (TDEs), where a star is tidally disrupted by the gravitational field of a black hole, have been observed to occur around the supermassive black holes (SMBHs) found at the centres of galaxies, and should also arise around IMBHs, especially in the dense stellar cores of CSSs. However, to date none have been observed in such environments. Using data from the Zwicky Transient Facility, we search for TDEs associated with CSSs, but none are found. This non-detection allows us to set an upper limit on the TDE rate in CSSs of $n_\text{TDE,Total}\lessapprox 10^{-7} \, \mathrm{ CSS}^{-1}\, \text{yr}^{-1}$, which is 2 dex below the observed TDE rate involving SMBHs interacting with 1 M⊙ main-sequence stars in the nuclei of massive galaxies. We also consider ultracompact dwarfs (UCDs) formed through a tidal stripping process in the surveyed volume. On the assumption that these CSSs contain SMBHs and TDE rates are comparable to current observed optical rates in galactic nuclei ($\approx 3.2 \times 10^{-5}\, \text{gal}^{-1}\, \text{yr}^{-1}$), we determine an upper limit for the number of UCDs formed through a tidal stripping process in the surveyed volume to be NGC,Strip &lt; 1.4 × 104, which we estimate represents $\lt 6~{{\ \rm per\ cent}}$ of the population of GCs &gt;106 M⊙.
Effective mass function of radio meteoroids as a modulating factor in determining atmospheric scale height
Authors: Sarkar Emranul , Ulich Thomas , Lester Mark 
Published: April 2024

ABSTRACT
A long-standing problem in meteor science has been the persistent presence of bias in the measured value of atmospheric scale heights obtained from radio meteor echoes. A common practice of fitting a linear function for bias correction follows the assumption that the systematic bias is devoid of seasonal asymmetry. This would be true if the mass and the velocity distribution of meteoroids remain invariant, both spatially and temporally. But so far no such convincing evidence has been published. On the contrary, fundamental arguments suggest that a universal mass function of radio meteoroids is counterintuitive. This parameter cannot remain invariant due to the intrinsic variability in the meteor response function resulting from the Earth’s motion on the plane of ecliptic. In this paper, we show that an inverse relation exists between the width of meteor height distribution, expressed in unit of atmospheric scale height, and the exponent of the mass function. The overall mean of this exponent for the Sodankylä radar is $1.91 \pm 0.02$, modulated by a seasonal variation from the mean of the order of $\sim \pm 0.1$. The stated inverse relation is applied to correct for the effect of mass distribution on the height distribution. Allowing for variable mass correction effectively removes the non-linear bias in the measured scale heights in the meteor ionization region.
Multiple time-step reversible N-body integrators for close encounters in planetary systems
Authors: Hernandez David M , Dehnen Walter 
Published: April 2024

ABSTRACT
We present new ‘almost’ time-reversible integrators for solution of planetary systems consisting of ‘planets’ and a dominant mass (‘star’). The algorithms can be considered adaptive generalizations of the Wisdom–Holman method, in which all pairs of planets can be assigned time-steps. These time-steps, along with the global time-step, can be adapted time-reversibly, often at no appreciable additional compute cost, without sacrificing any of the long-term error benefits of the Wisdom–Holman method. The method can also be considered a simpler and more flexible version of the symba symplectic code. We perform tests on several challenging problems with close encounters and find the reversible algorithms are up to 2.6 times faster than a code based on symba. The codes presented here are available on Github. We also find adapting a global time-step reversibly and discretely must be done in block-synchronized manner or similar.
Structure-functional characterization of Lactococcus AbiA phage defense system
Authors: Gapińska Marta , Zajko Weronika , Skowronek Krzysztof , Figiel Małgorzata , Krawczyk Paweł S , Egorov Artyom A , Dziembowski Andrzej , Johansson Marcus J O , Nowotny Marcin 
Published: April 2024

Abstract
Bacterial reverse transcriptases (RTs) are a large and diverse enzyme family. AbiA, AbiK and Abi-P2 are abortive infection system (Abi) RTs that mediate defense against bacteriophages. What sets Abi RTs apart from other RT enzymes is their ability to synthesize long DNA products of random sequences in a template- and primer-independent manner. Structures of AbiK and Abi-P2 representatives have recently been determined, but there are no structural data available for AbiA. Here, we report the crystal structure of Lactococcus AbiA polymerase in complex with a single-stranded polymerization product. AbiA comprises three domains: an RT-like domain, a helical domain that is typical for Abi polymerases, and a higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain that is common for many antiviral proteins. AbiA forms a dimer that distinguishes it from AbiK and Abi-P2, which form trimers/hexamers. We show the DNA polymerase activity of AbiA in an in vitro assay and demonstrate that it requires the presence of the HEPN domain which is enzymatically inactive. We validate our biochemical and structural results in vivo through bacteriophage infection assays. Finally, our in vivo results suggest that AbiA-mediated phage defense may not rely on AbiA-mediated cell death.
ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response
Authors: Bakr Ali , Corte Giuditta Della , Veselinov Olivera , Kelekçi Simge , Chen Mei-Ju May , Lin Yu-Yu , Sigismondo Gianluca , Iacovone Marika , Cross Alice , Syed Rabail , Jeong Yunhee , Sollier Etienne , Liu Chun- Shan , Lutsik Pavlo , Krijgsveld Jeroen , Weichenhan Dieter , Plass Christoph , Popanda Odilia , Schmezer Peter 
Published: April 2024

Abstract
AT-rich interaction domain protein 1A (ARID1A), a SWI/SNF chromatin remodeling complex subunit, is frequently mutated across various cancer entities. Loss of ARID1A leads to DNA repair defects. Here, we show that ARID1A plays epigenetic roles to promote both DNA double-strand breaks (DSBs) repair pathways, non-homologous end-joining (NHEJ) and homologous recombination (HR). ARID1A is accumulated at DSBs after DNA damage and regulates chromatin loops formation by recruiting RAD21 and CTCF to DSBs. Simultaneously, ARID1A facilitates transcription silencing at DSBs in transcriptionally active chromatin by recruiting HDAC1 and RSF1 to control the distribution of activating histone marks, chromatin accessibility, and eviction of RNAPII. ARID1A depletion resulted in enhanced accumulation of micronuclei, activation of cGAS-STING pathway, and an increased expression of immunomodulatory cytokines upon ionizing radiation. Furthermore, low ARID1A expression in cancer patients receiving radiotherapy was associated with higher infiltration of several immune cells. The high mutation rate of ARID1A in various cancer types highlights its clinical relevance as a promising biomarker that correlates with the level of immune regulatory cytokines and estimates the levels of tumor-infiltrating immune cells, which can predict the response to the combination of radio- and immunotherapy.
DeepLoc 2.1: multi-label membrane protein type prediction using protein language models
Authors: Ødum Marius Thrane , Teufel Felix , Thumuluri Vineet , Almagro Armenteros José Juan , Johansen Alexander Rosenberg , Winther Ole , Nielsen Henrik 
Published: April 2024

Abstract
DeepLoc 2.0 is a popular web server for the prediction of protein subcellular localization and sorting signals. Here, we introduce DeepLoc 2.1, which additionally classifies the input proteins into the membrane protein types Transmembrane, Peripheral, Lipid-anchored and Soluble. Leveraging pre-trained transformer-based protein language models, the server utilizes a three-stage architecture for sequence-based, multi-label predictions. Comparative evaluations with other established tools on a test set of 4933 eukaryotic protein sequences, constructed following stringent homology partitioning, demonstrate state-of-the-art performance. Notably, DeepLoc 2.1 outperforms existing models, with the larger ProtT5 model exhibiting a marginal advantage over the ESM-1B model. The web server is available at https://services.healthtech.dtu.dk/services/DeepLoc-2.1.
Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation
Authors: Mas-Ponte David , Supek Fran 
Published: April 2024

Abstract
Local mutation rates in human are highly heterogeneous, with known variability at the scale of megabase-sized chromosomal domains, and, on the other extreme, at the scale of oligonucleotides. The intermediate, kilobase-scale heterogeneity in mutation risk is less well characterized. Here, by analyzing thousands of somatic genomes, we studied mutation risk gradients along gene bodies, representing a genomic scale spanning roughly 1–10 kb, hypothesizing that different mutational mechanisms are differently distributed across gene segments. The main heterogeneity concerns several kilobases at the transcription start site and further downstream into 5′ ends of gene bodies; these are commonly hypomutated with several mutational signatures, most prominently the ubiquitous C &gt; T changes at CpG dinucleotides. The width and shape of this mutational coldspot at 5′ gene ends is variable across genes, and corresponds to variable interval of lowered DNA methylation depending on gene activity level and regulation. Such hypomutated loci, at 5′ gene ends or elsewhere, correspond to DNA hypomethylation that can associate with various landmarks, including intragenic enhancers, Polycomb-marked regions, or chromatin loop anchor points. Tissue-specific DNA hypomethylation begets tissue-specific local hypomutation. Of note, direction of mutation risk is inverted for AID/APOBEC3 cytosine deaminase activity, whose signatures are enriched in hypomethylated regions.
MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation
Authors: Pang Zhiqiang , Lu Yao , Zhou Guangyan , Hui Fiona , Xu Lei , Viau Charles , Spigelman Aliya F , MacDonald Patrick E , Wishart David S , Li Shuzhao , Xia Jianguo 
Published: April 2024

Abstract
We introduce MetaboAnalyst version 6.0 as a unified platform for processing, analyzing, and interpreting data from targeted as well as untargeted metabolomics studies using liquid chromatography - mass spectrometry (LC–MS). The two main objectives in developing version 6.0 are to support tandem MS (MS2) data processing and annotation, as well as to support the analysis of data from exposomics studies and related experiments. Key features of MetaboAnalyst 6.0 include: (i) a significantly enhanced Spectra Processing module with support for MS2 data and the asari algorithm; (ii) a MS2 Peak Annotation module based on comprehensive MS2 reference databases with fragment-level annotation; (iii) a new Statistical Analysis module dedicated for handling complex study design with multiple factors or phenotypic descriptors; (iv) a Causal Analysis module for estimating metabolite - phenotype causal relations based on two-sample Mendelian randomization, and (v) a Dose-Response Analysis module for benchmark dose calculations. In addition, we have also improved MetaboAnalyst's visualization functions, updated its compound database and metabolite sets, and significantly expanded its pathway analysis support to around 130 species. MetaboAnalyst 6.0 is freely available at https://www.metaboanalyst.ca.
Assembly of SARS-CoV-2 nucleocapsid protein with nucleic acid
Authors: Zhao Huaying , Syed Abdullah M , Khalid Mir M , Nguyen Ai , Ciling Alison , Wu Di , Yau Wai-Ming , Srinivasan Sanjana , Esposito Dominic , Doudna Jennifer A , Piszczek Grzegorz , Ott Melanie , Schuck Peter 
Published: April 2024

AbstractThe viral genome of SARS-CoV-2 is packaged by the nucleocapsid (N-)protein into ribonucleoprotein particles (RNPs), 38 ± 10 of which are contained in each virion. Their architecture has remained unclear due to the pleomorphism of RNPs, the high flexibility of N-protein intrinsically disordered regions, and highly multivalent interactions between viral RNA and N-protein binding sites in both N-terminal (NTD) and C-terminal domain (CTD). Here we explore critical interaction motifs of RNPs by applying a combination of biophysical techniques to ancestral and mutant proteins binding different nucleic acids in an in vitro assay for RNP formation, and by examining nucleocapsid protein variants in a viral assembly assay. We find that nucleic acid-bound N-protein dimers oligomerize via a recently described protein–protein interface presented by a transient helix in its long disordered linker region between NTD and CTD. The resulting hexameric complexes are stabilized by multivalent protein-nucleic acid interactions that establish crosslinks between dimeric subunits. Assemblies are stabilized by the dimeric CTD of N-protein offering more than one binding site for stem–loop RNA. Our study suggests a model for RNP assembly where N-protein scaffolding at high density on viral RNA is followed by cooperative multimerization through protein–protein interactions in the disordered linker.
RNAhugs web server for customized 3D RNA structure alignment
Authors: Zurkowski Michal , Swiercz Mateusz , Wozny Filip , Antczak Maciej , Szachniuk Marta 
Published: April 2024

Abstract
Alignment of 3D molecular structures involves overlaying their sets of atoms in space in such a way as to minimize the distance between the corresponding atoms. The purpose of this procedure is usually to analyze and assess structural similarity on a global (e.g. evaluating predicted 3D models and clustering structures) or a local level (e.g. searching for common substructures). Although the idea of alignment is simple, combinatorial algorithms that implement it require considerable computational resources, even when processing relatively small structures. In this paper, we introduce RNAhugs, a web server for custom and flexible alignment of 3D RNA structures. Using two efficient heuristics, GEOS and GENS, it finds the longest corresponding fragments within 3D structures that may differ in sizes—given in the PDB or PDBx/mmCIF formats—that manage to align with user-specified accuracy (i.e. with an RMSD not exceeding a cutoff value given as an input parameter). A distinctive advantage of the system lies in its ability to process multi-model files and compare the results of 1–25 alignments in a single task. RNAhugs has an intuitive interface and is publicly available at https://rnahugs.cs.put.poznan.pl/.
Analysis of Candy Tobacco Imitation Products Available Online in the United States
Authors: Bearman Dov S , Sheeran Tadhg J , Kowitt Sarah D , Clark Sonia A , Klein Jonathan D , Goldstein Adam O 
Published: April 2024

Abstract

Introduction
Youth tobacco use remains a critical public health concern, and childhood use of candy tobacco imitation products (CTIP) is associated with cigarette use among youth. However, no research has examined the full extent of CTIP available for purchase in the United States.

Aims and Methods
We conducted a content analysis of CTIP available on English-language, US-based websites. We identified sites that marketed CTIP utilizing Google and candy retail websites, examining each product for product names, the tobacco product being replicated (eg, cigar and cigarette), manufacturer, candy flavor, images, product rating, pack color, and if the product had packaging that may appeal to youth.

Results
We found 66 CTIP available. The most popular CTIP were cigars, with 39 separate products (59%), followed by candy cigarettes—14 products (21%), candy pipes—8 products (12%), and chewing tobacco—5 products (8%). In the 52 products where packaging design was available, 39 (75%) had packaging that may appeal to youth.

Conclusions
CTIP, many of which contain packaging appealing to youth, are widely available for purchase online across the United States. These findings could stimulate policy actions, such as removal of CTIP from popular retail websites, labeling of CTIP as potentially dangerous to youth, or age verification requirements for purchasing CTIP.

Implications
CTIP continues to be sold on the internet despite research indicating candy cigarette product use by youth increases their likelihood of smoking. We conducted research to understand the extent to which CTIP are sold on the internet and whether these products are being marketed to youth. The results provide evidence that some of the largest retail companies in the world continue to sell CTIP, and the majority are sold in packaging that likely appeals to youth. The results suggest that further research into the market for these products is needed, and regulatory measures should be considered to prevent CTIP from leading to youth tobacco use.