bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mortality patterns in candidemia: Insights from a multispecies analysis using a global research network
Authors: Thompson III George R , Chastain Daniel B , Ferraz Carolina , Alhayek Soubhi , Salinas Jorge L , Sillau Stefan , Stenehjem Edward A , Henao-Martínez Andrés F 
Published: December 2024

Abstract
Understanding the impact of different Candida species on patient outcomes is crucial for effective management and treatment strategies. This study aims to comprehensively analyze the association between Candida species and mortality in documented candidemia. We queried TriNetX, a global research network database, to identify patients diagnosed with candidemia through polymerase chain reaction from 2020 to 2023. The primary outcome was mortality in candidemia patients, categorized by Candida species at 90 days and 1 year. The time to death was assessed using Kaplan–Meier plots. Cox proportional hazard (PH) models were also used for comparative analysis, unadjusted and adjusted for demographic and comorbidity covariates. We captured 1234 candidemia episodes during the study period. The 90-day and 1-year mortality rates for the various Candida species were as follows: C. tropicalis (33.9% and 35.6%), C. glabrata (28.3% and 34%), multispecies (27.7% and 36.4%), C. parapsilosis (25.8% and 31.8%), C. krusei (21.4% and 28.6%), C. albicans (21.1% and 23.9%), and C. auris (13.3% and 15.9%). The unadjusted Kaplan–Meier Survival analysis showed that multispecies candidemia, followed by C. tropicalis, had the lowest survival. The adjusted multivariable Cox PH model found that C.albicans, C. glabrata, C. parapsilosis, C. tropicalis, and multispecies candidemia had significantly higher mortality rates than C. auris. Age and a higher Charlson comorbidity index value emerged as independent predictors of increased mortality. Among patients with candidemia, we found an overall 1-year mortality of 28%. Multispecies candidemia, C. tropicalis, older age, and a higher comorbidity burden were associated with the highest mortality rates.
Detection and characterization of giant planets with Gaia astrometry
Authors: Wallace A L , Casey A R , Brown A G A , Castro-Ginard A 
Published: December 2024

ABSTRACT
Astrometric observations with Gaia are expected to play a valuable role in future exoplanet surveys. With current data from Gaia’s third data release (DR3), we are sensitive to periods from less than 1 yr to more than 4 yr but, unlike radial velocity (R.V.) are not as restricted by the orbital inclination of a potential planet. The presence and potential properties of a companion affect the primary’s renormalized unit weight error (RUWE) making this a valuable quantity in the search for exoplanets. Using this value and the fitted astrometric tracks from Gaia, we use Bayesian inference to constrain the mass and orbital parameters of companions in known systems. Combining this with R.V. measurements, we show it is possible to independently measure mass and inclination and suggest HD 66141 b is a possible brown dwarf with maximum mass 23.9$^{+7.2}_{-6.4}$ $\mathrm{ M}_{\mathrm{J}}$. We show how this method may be applied to directly imaged planets in the future, using $\beta$-Pictoris c as an example but note that the host star is bright and active, making it difficult to draw clear conclusions. We show how the next Gaia data release, which will include epoch astrometry, will allow us to accurately constrain orbital parameters from astrometric data alone, revolutionizing future searches for exoplanets. Combining predicted observational limits on planet mass with theoretical distributions, we estimate the probability that a star with a given RUWE will host a detectable planet, which will be highly valuable in planning future surveys.
SN 2023tsz: a helium-interaction-driven supernova in a very low-mass galaxy
Authors: Warwick B , Lyman J , Pursiainen M , Coppejans D L , Galbany L , Jones G T , Killestein T L , Kumar A , Oates S R , Ackley K , Anderson J P , Aryan A , Breton R P , Chen T W , Clark P , Dhillon V S , Dyer M J , Gal-Yam A , Galloway D K , Gutiérrez C P , Gromadzki M , Inserra C , Jiménez-Ibarra F , Kelsey L , Kotak R , Kravtsov T , Kuncarayakti H , Magee M R , Matilainen K , Mattila S , Müller-Bravo T E , Nicholl M , Noysena K , Nuttall L K , O’Brien P , O’Neill D , Pallé E , Pessi T , Petrushevska T , Pignata G , Pollacco D , Ragosta F , Ramsay G , Sahu A , Sahu D K , Singh A , Sollerman J , Stanway E , Starling R , Steeghs D , Teja R S , Ulaczyk K 
Published: December 2024

ABSTRACT
SN 2023tsz is a Type Ibn supernova (SN Ibn), an uncommon subtype of stripped-envelope core-collapse supernovae (SNe), discovered in an extremely low-mass host. SNe Ibn are characterized by narrow helium emission lines in their spectra and are believed to originate from the collapse of massive Wolf–Rayet (WR) stars, though their progenitor systems still remain poorly understood. In terms of energetics and spectrophotometric evolution, SN 2023tsz is largely a typical example of the class, although line profile asymmetries in the nebular phase are seen, which may indicate the presence of dust formation or unshocked circumstellar material. Intriguingly, SN 2023tsz is located in an extraordinarily low-mass host galaxy that is in the second percentile for stripped-envelope SN host masses and star formation rates (SFRs). The host has a radius of 1.0 kpc, a g-band absolute magnitude of $-12.72 \pm 0.05$, and an estimated metallicity of $\log (Z_{*}/{\rm Z}_{\odot }) \approx -1.6$. The SFR and metallicity of the host galaxy raise questions about the progenitor of SN 2023tsz. The low SFR suggests that a star with sufficient mass to evolve into a WR would be uncommon in this galaxy. Further, the very low metallicity is a challenge for single stellar evolution to enable H and He stripping of the progenitor and produce an SN Ibn explosion. The host galaxy of SN 2023tsz adds another piece to the ongoing puzzle of SNe Ibn progenitors, and demonstrates that they can occur in hosts too faint to be observed in contemporary sky surveys at a more typical SN Ibn redshift.
Structural plasticity of the coiled–coil interactions in human SFPQ
Authors: Koning Heidar J , Lai Jia Y , Marshall Andrew C , Stroeher Elke , Monahan Gavin , Pullakhandam Anuradha , Knott Gavin J , Ryan Timothy M , Fox Archa H , Whitten Andrew , Lee Mihwa , Bond Charles S 
Published: December 2024

Abstract
The proteins SFPQ (splicing Factor Proline/Glutamine rich) and NONO (non-POU domain-containing octamer-binding protein) are mammalian members of the Drosophila Behaviour/Human Splicing (DBHS) protein family, which share 76% sequence identity in their conserved 320 amino acid DBHS domain. SFPQ and NONO are involved in all steps of post-transcriptional regulation and are primarily located in mammalian paraspeckles: liquid phase-separated, ribonucleoprotein sub-nuclear bodies templated by NEAT1 long non-coding RNA. A combination of structured and low-complexity regions provide polyvalent interaction interfaces that facilitate homo- and heterodimerisation, polymerisation, interactions with oligonucleotides, mRNA, long non-coding RNA, and liquid phase-separation, all of which have been implicated in cellular homeostasis and neurological diseases including neuroblastoma. The strength and competition of these interaction modes define the ability of DBHS proteins to dissociate from paraspeckles to fulfil functional roles throughout the nucleus or the cytoplasm. In this study, we define and dissect the coiled–coil interactions which promote the polymerisation of DBHS proteins, using a crystal structure of an SFPQ/NONO heterodimer which reveals a flexible coiled–coil interaction interface which differs from previous studies. We support this through extensive solution small-angle X-ray scattering experiments using a panel of SFPQ/NONO heterodimer variants which are capable of tetramerisation to varying extents. The QM mutant displayed a negligible amount of tetramerisation (quadruple loss of function coiled-coil mutant L535A/L539A/L546A/M549A), the Charged Single Alpha Helix (ΔCSAH) variant displayed a dimer-tetramer equilibrium interaction, and the disulfide-forming variant displayed constitutive tetramerisation (R542C which mimics the pathological Drosophila nonAdiss allele). We demonstrate that newly characterised coiled–coil interfaces play a role in the polymerisation of DBHS proteins in addition to the previously described canonical coiled–coil interface. The detail of these interactions provides insight into a process critical for the assembly of paraspeckles as well as the behaviour of SFPQ as a transcription factor, and general multipurpose auxiliary protein with functions essential to mammalian life. Our understanding of the coiled coil behaviour of SFPQ also enhances the explanatory power of mutations (often disease-associated) observed in the DBHS family, potentially allowing for the development of future medical options such as targeted gene therapy.
PRMT1-mediated methylation regulates MLL2 stability and gene expression
Authors: An Dongju , Kim Jihyun , Moon Byul , Kim Hyoungmin , Nguyen Hoa , Park Sunghu , Lee J Eugene , Kim Jung-Ae , Kim Jaehoon 
Published: December 2024

Abstract
The interplay between multiple transcription factors precisely regulates eukaryotic transcription. Here, we report that the protein methyltransferases, MLL2/KMT2B and PRMT1, interact directly and act collectively to regulate gene expression. PRMT1 binds to the N-terminal region of MLL2, considered an intrinsically disordered region, and methylates multiple arginine residues within its RGG/RG motifs. Notably, overexpression of PRMT1 decreased poly-ubiquitylation of MLL2, whereas mutations on methylation sites in MLL2 increased MLL2 poly-ubiquitylation, suggesting that PRMT1-mediated methylation stabilizes MLL2. MLL2 and PRMT1 cooperatively stimulated the expression of a chromosomal reporter gene in a PRMT1-mediated, MLL2-methylation-dependent manner. RNA-seq analysis found that MLL2 and PRMT1 jointly regulate the expression of genes involved in cell membrane and extracellular matrix functions, and depletion of either resulted in impaired cell migration and invasion. Our study provides evidence that PRMT1-mediated MLL2 methylation regulates MLL2 protein stability and the expression of their target genes.
Mining single-cell data for cell type–disease associations
Authors: Chen Kevin G , Farley Kathryn O , Lassmann Timo 
Published: December 2024

Abstract
A robust understanding of the cellular mechanisms underlying diseases sets the foundation for the effective design of drugs and other interventions. The wealth of existing single-cell atlases offers the opportunity to uncover high-resolution information on expression patterns across various cell types and time points. To better understand the associations between cell types and diseases, we leveraged previously developed tools to construct a standardized analysis pipeline and systematically explored associations across four single-cell datasets, spanning a range of tissue types, cell types and developmental time periods. We utilized a set of existing tools to identify co-expression modules and temporal patterns per cell type and then investigated these modules for known disease and phenotype enrichments. Our pipeline reveals known and novel putative cell type–disease associations across all investigated datasets. In addition, we found that automatically discovered gene co-expression modules and temporal clusters are enriched for drug targets, suggesting that our analysis could be used to identify novel therapeutic targets.
GRAViTy-V2: a grounded viral taxonomy application
Authors: Mayne Richard , Aiewsakun Pakorn , Turner Dann , Adriaenssens Evelien M , Simmonds Peter 
Published: December 2024

Abstract
Taxonomic classification of viruses is essential for understanding their evolution. Genomic classification of viruses at higher taxonomic ranks, such as order or phylum, is typically based on alignment and comparison of amino acid sequence motifs in conserved genes. Classification at lower taxonomic ranks, such as genus or species, is usually based on nucleotide sequence identities between genomic sequences. Building on our whole-genome analytical classification framework, we here describe Genome Relationships Applied to Viral Taxonomy Version 2 (GRAViTy-V2), which encompasses a greatly expanded range of features and numerous optimisations, packaged as an application that may be used as a general-purpose virus classification tool. Using 28 datasets derived from the ICTV 2022 taxonomy proposals, GRAViTy-V2 output was compared against human expert-curated classifications used for assignments in the 2023 round of ICTV taxonomy changes. GRAViTy-V2 produced taxonomies equivalent to manually-curated versions down to the family level and in almost all cases, to genus and species levels. The majority of discrepant results arose from errors in coding sequence annotations in INDSC records, or from inclusion of incomplete genome sequences in the analysis. Analysis times ranged from 1-506 min (median 3.59) on datasets with 17-1004 genomes and mean genome length of 3000–1 000 000 bases.
Infiltrative classical monocyte-derived and SPP1 lipid-associated macrophages mediate inflammation and fibrosis in ANCA-associated glomerulonephritis
Authors: Vegting Yosta , Jongejan Aldo , Neele Annette E , Claessen Nike , Sela Gal , Prange Koen H M , Kers Jesper , Roelofs Joris J T H , van der Heijden Joost W , de Boer Onno J , Remmerswaal Ester B M , Vogt Liffert , Bemelman Frederike J , de Winther Menno P J , Moerland Perry D , Hilhorst Marc L 
Published: December 2024

ABSTRACT

Background
Kidney macrophage infiltration is a histological hallmark of vasculitic lesions and is strongly linked to disease activity in anti-neutrophil cytoplasmic antibodies (ANCA)-associated glomerulonephritis (AGN). The precise mechanisms by which kidney macrophages influence local inflammation and long-term damage remain largely unknown.

Methods
Here, we investigate kidney macrophage diversity using single-cell transcriptome analysis of 25 485 freshly retrieved unfrozen, high-quality kidney CD45+ immune cells from five AGN patients during active disease, a lupus nephritis and a nephrectomy control. Detailed subclustering of myeloid cells was performed to identify disease-specific macrophage subtypes. Next, transcriptome differences between macrophage subsets and disease serotypes were assessed. Findings were validated by immunostainings of an extended cohort of kidney biopsies and flow cytometric analysis of peripheral blood monocytes.

Results
Four main macrophage subsets were identified, including a classical monocyte-derived macrophage (MDM) subset expressing a chemotactic (CXCL2, CXCL3, CXCL8, CCL3) and pro-inflammatory (IL1β, TNF) set of markers and an osteopontin/SPP1+ lipid-associated macrophage (SPP1 LAMs) subtype exhibiting distinctive upregulation of fibrotic genesets. AGN samples revealed a markedly increased proportion of CD163+ macrophages, predominantly composed of classical MDMs, accompanied by resident-like C1Q macrophages, and SPP1 LAMs. An analogous trend was observed in the expansion of peripheral blood classical monocytes during active disease. The proteinase 3 (PR3)-AGN subtype exhibited heightened classical MDM and SPP1 LAM infiltration and markers of acute inflammation, while interferon signaling and markers of chronicity were reduced compared with myeloperoxidase-AGN.

Conclusions
Our findings highlight the expression of inflammatory and fibrotic genes by kidney macrophage subsets in AGN. Classical monocyte dysregulation might contribute to inflammation in the pathogenesis of AGN. Targeting these specific monocyte/macrophage subsets may potentially control the inflammatory cascade and attenuate resulting fibrosis in AGN and kidney disease in general.
Recovery of Mycobacterium tuberculosis Complex Isolates Including Pre–Extensively Drug-Resistant Strains From Cattle at a Slaughterhouse in Chennai, India
Authors: Ramanujam Harini , Refaya Ahmed Kabir , Thiruvengadam Kannan , Pazhanivel Natesan , Kandasamy Devika , Shanmugavel Ashokkumar , Radhakrishnan Ammayappan , Radhika Golla , Ravi Rajkumar , Ravi Neelakandan , Palanisamy Maheswaran , Shanmugam Sivakumar , Stuber Tod P , Kapur Vivek , Palaniyandi Kannan 
Published: December 2024

Abstract

Background
India has the highest global burden of human tuberculosis (TB) and the largest cattle herd with endemic bovine TB (bTB). However, the extent of cross-species transmission and the zoonotic spillover risk, including drug-resistant Mycobacterium tuberculosis complex (MTBC) strains circulating in cattle, remain uncharacterized.

Methods
To address this major knowledge gap, we investigated tissue samples from 500 apparently healthy cattle at a slaughterhouse in Chennai, India. Whole genome sequencing was performed to characterize the isolates.

Results
Sixteen animals (32 per 1000 [95% confidence interval, 16–47]) were MTBC-positive, a rate that is nearly an order of magnitude greater than the reported human TB incidence in the region. Thirteen isolates were identified as Mycobacterium orygis and 3 were M tuberculosis: 1 was a mixed infection of M tuberculosis lineage 1 and M orygis, and the other 2 had pure growth of M tuberculosis lineage 2, in both cases pre–extensively drug-resistant (pre-XDR) with identical resistance patterns and separated by 7 single-nucleotide polymorphisms. The results confirm that bTB in this region is primarily due to M orygis and M tuberculosis, and not Mycobacterium bovis.

Conclusions
The detection of pre-XDR M tuberculosis in cattle highlights a potential public health concern, since controlling human TB alone may be insufficient without addressing bovine TB. Overall, our findings underscore an urgent need for targeted interventions to mitigate zoonotic tuberculosis transmission in regions where bTB is endemic.
Ideas of Closure
Authors: Caplin William E. 
Published: December 2024

Abstract
This chapter surveys general concepts of closure in everyday life, gestalt psychology, and literature, especially poetry. Important for the latter are the concepts of terminal modification, a significant change in the final lines of a poem, as well as formal circularity, created by bringing back the opening lines of a poem to conclude it. The chapter shows how these ideas resonate in discussions on closure by music theorists. Some of their formulations are relatively abstract, while others are more pertinent to the topic of cadential closure specifically. Leonard Meyer discusses how closure is created foremost by syntactical parameters (harmony, melody, meter); Kofi Agawu differentiates between closure and ending; Robert Hatten proposes a notion of dramatic closure; Patrick McCreless relates musical closure to a more general sense of narrative closure; Mark Anson-Cartwright offers three definitions of musical closure, all of which characterize it as expressing differing modes of ending and finality.
Cadential Deviations
Authors: Caplin William E. 
Published: December 2024

Abstract
This chapter investigates how promised cadences may fail to be realized by means of cadential deviations. Three deviation types—deceptive cadence, evaded cadence, and abandoned cadence—are associated with authentic cadences, whereas an implied half cadence may bring in its place various kinds of dominant arrival. Each deviation type is defined by how its harmonic content and grouping structure disrupt the norms of genuine cadential closure. The deviations normally involve processes that loosen the formal organization. Especially typical is how a cadential deviation functions as a way station on the road to an eventual perfect authentic cadence, thus helping to defer that cadence in time and making its arrival a strongly articulated rhetorical event. Dominant arrivals are shown to be manifest by a variety of harmonic means, as well as by how they often appear in a manner that seems premature to the actual closing of various thematic processes.
Cadential Expansion
Authors: Caplin William E. 
Published: December 2024

Abstract
This chapter examines various techniques for cadential expansion from both morphological and form-functional perspectives. Whereas a simple, relatively compact cadence typically lasts one or two measures, a cadence supported by an expanded cadential progression (ECP) occupies four or more measures and supports one or more phrases of a theme. In that the means of expansion are essentially harmonic, the chapter treats, in turn, how the initial tonic, pre-dominant, and dominant harmonies of a cadence can undergo significant lengthening, often accompanied by extensive chromaticism. It assesses as well the extent to which the theory of cadential melody introduced in Chapter 3 is applicable to ECPs, especially in the context of highly embellished melodic lines. The chapter considers how cadential deviations work in connection with phrase expansion techniques and concludes by analyzing some remarkable expanded cadences in Beethoven’s symphonic oeuvre.
Mappings
Authors: Müller Ulrich , de la Flor Gemma 
Published: December 2024

Abstract
A mapping which maps parallel straight lines onto parallel straight lines is an affine mapping. It is represented by a set of equations that relate the coordinates of an initial point with the coordinates of its image point. For a concise notation, the equations are recorded as matrix—column pairs (W,w). An isometry is an affine mapping that leaves distances and angles unchanged. If, in addition, the object is mapped onto itself, it is a symmetry operation and it is a crystallogtaphic symmetry operation if the object is a crystal. The set of all symmetry operations of a crystal is its space group. Changes of the coordinate system entail changes of the coordinates that are calculated by equations similar to those of affine mappings.
Group theory
Authors: Müller Ulrich , de la Flor Gemma 
Published: December 2024

Abstract
A group is set of elements that fulfils the group axioms. A subset that also fulfils the axioms is a subgroup. According to certain rules, the elements of a group can be decomposed to a subgroup and i −1 cosets; i is the index of the subgroup. Two subgroups of a symmetry group G are conjugate if they are transformed one to another by some other symmetry operation of the same group G. If a symmetry group G acts on a point (or atom) X, it yields a set of symmetry-equivalent points called the orbit of X under G.
Conjugate subgroups and normalizers of space groups
Authors: Müller Ulrich , de la Flor Gemma 
Published: December 2024

Abstract
Conjugate subgroups of space groups together form a conjugacy class. Conjugate maximal subgroups of space groups show either orientational conjugation or translational conjugation. In a group—subgroup pair G &gt; H, the normalizer of H in G is the group of all elements of G that map H onto itself. The Euclidean normalizer of a space group is a supergroup of the space group that maps all symmetry elements of the space group onto equal symmetry elements; it exhibits the ‘symmetry of the symmetry’. Subgroups on a par belong to different conjugacy classes, have the same lattice dimensions and the same space-group type.