bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimicrobial Resistance in Enterobacterales, Acinetobacter spp. and Pseudomonas aeruginosa Isolates From Bloodstream Infections in Australian Children, 2013–2021
Authors: Williams Anita , Coombs Geoffrey W , Bell Jan M , Daley Denise A , Mowlaboccus Shakeel , Bryant Penelope A , Campbell Anita J , Cooley Louise , Iredell Jon , Irwin Adam D , Kesson Alison , McMullan Brendan , Warner Morgyn S , Williams Phoebe C M , Blyth Christopher C 
Published: October 2024

Abstract

Background
Gram-negative bloodstream infections are associated with significant morbidity and mortality in children. Increasing antimicrobial resistance (AMR) is reported globally, yet efforts to track pediatric AMR at a national level over time are lacking.

Methods
The Australian Group on Antimicrobial Resistance (AGAR) surveillance program captures clinical and microbiological data of isolates detected in blood cultures across Australia. EUCAST 2022 was used for MIC interpretation and the AMR package in R for data analysis.

Results
Over a 9-year period, there were 3145 bloodstream infections with 3266 gram-negative isolates reported in hospitalized children aged &lt;18 years; 21.0% were from neonates. The median length of stay was 9 days, and 30-day all-cause mortality was 5.2%. A greater odds of death was observed in those with a multi-drug resistant organism (aOR: 2.1, 95% CI: 1.3, 3.3, p: 0.001). Escherichia coli (44.5%) and Klebsiella pneumoniae complex (12.6%) were the two most frequently reported organisms. Overall resistance in Enterobacterales to gentamicin/tobramycin was 11.6%, to ceftazidime/ceftriaxone was 12.9%, and 13.2% to ciprofloxacin. Resistance increased over time. Of the 201 Pseudomonas aeruginosa isolates reported, 19.7% were resistant to piperacillin-tazobactam, 13.1% resistant to cefepime/ceftazidime, and 9.8% to ciprofloxacin. Of 108 Acinetobacter spp. isolates, one was resistant to meropenem, and two were resistant to ciprofloxacin. Resistance did not increase over time.

Conclusions
AMR in gram-negative organisms causing bloodstream infections in Australian children is increasing, which should be considered when updating guidelines and empiric treatment regimens. Ongoing pediatric-specific national surveillance with pediatric reporting must remain a priority to strengthen antimicrobial stewardship and infection control programs.
Detection of Ophidiomyces and Nannizziopsis spp. in the dermal lesions of free-roaming native snakes in Taiwan
Authors: Lai Wei-Yin , Yang Chun-Kai , Sun Pei-Lun , Li Wen-Ta , Liu Xuan-Rui , Chen Chiao-Wen , Yu Pin-Huan 
Published: October 2024

Abstract
Chrysosporium-related fungi refers to an assemblage of fungi belonging to the Nannizziopsis, Ophidiomyces, and Paranannizziopsis genera. Chrysosporium-related fungi infection results in various skin lesions, such as necrosis and ulcers, in both captive and free-roaming reptiles. To update the prevalence of ophidiomycosis in Taiwan, which was first detected in 2019, we conducted a large-scale ecological survey of free-roaming native snakes with skin lesions in Taiwan. To the best of our knowledge, this is the first study on Chrysosporium-related fungi prevalence in Southeast Asia. Fungal samples collected from the skin lesions of snakes were cultured and subjected to morphological, histopathological, and molecular analyses. We examined 2382 free-roaming snakes representing 42 snake species; among them, 132 (5.54%) had skin lesions. Ten (0.42%) snakes, representing four species, tested positive for Ophidiomyces (five snakes, four species) or a possibly novel Nannizziopsis species (five snakes, three species). The infected snakes were generally healthy, with mild clinical signs. The low prevalence rate, mild clinical signs, and broad pathogen/host range suggest that Ophidiomyces and Nannizziopsis are endemic to Southeast Asia. The newly reported presence of Nannizziopsis in free-roaming snakes suggests the need for modifying the currently used surveillance strategy.
Spatio-spectral-temporal modelling of two young pulsar wind nebulae
Authors: Kundu A , Joshi Jagdish C , Venter C , Engelbrecht N E , Zhang W , Torres Diego F , Sushch I , Tanaka Shuta J 
Published: October 2024

ABSTRACT
Recent observations of a few young pulsar wind nebulae (PWNe) have revealed their morphologies in some detail. Given the availability of spatio-spectral-temporal data, we use our multi-zone (1D) leptonic emission code to model the PWNe associated with G29.7$-$0.3 (Kes 75) and G21.5$-$0.9 (G21.5), and obtain (by-eye) constraints on additional model parameters compared to spectral-only modelling. Kes 75 is a Galactic composite supernova remnant (SNR) with an embedded pulsar, PSR J1846$-$0258. X-ray studies reveal rapid expansion of Kes 75 over the past two decades. PWN G21.5 is also a composite SNR, powered by PSR J1833$-$1034. For Kes 75, we study a sudden plasma bulk speed increase that may be due to the magnetar-like outbursts of the central pulsar. An increase of a few per cent in this speed does not result in any significant change in the model outputs. For G21.5, we investigate different diffusion coefficients and pulsar spin-down braking indices. We can reproduce the broad-band spectra and X-ray surface brightness profiles for both PWNe, and the expansion rate, flux over different epochs, and X-ray photon index versus epoch and central radius for Kes 75 quite well. The latter three features are also investigated for G21.5. Despite obtaining reasonable fits overall, some discrepancies remain, pointing to further model revision. We find similar values to overlapping parameters between our 1D code and those of an independent 0D dynamical code (tide). Future work will incorporate spatial data from various energy wavebands to improve model constraints.
Characterizing the features of the low-amplitude peaks in delta Scuti stars with TESS
Authors: Barceló Forteza S , Pascual-Granado J , Suárez J C , García Hernández A , Mirouh G M , Lares-Martiz M 
Published: October 2024

ABSTRACT
The presence of low-amplitude peaks over the noise in the power spectra of $\delta$ Scuti stars is frequently disregarded. These seemingly insignificant peaks, collectively referred to as grass, might contain valuable information about the origin of these stars and the reasons behind the occurrence or absence of a plateau. It is crucial to systematically parametrize the grass phenomenon throughout a comprehensive sample that covers the entire $\delta$ Scuti star parameter range. Thus, we conduct a quantitative study of long-duration, high-duty-cycle Transiting Exoplanet Survey Satellite light curves, leading to improved detection methods for plateaus and a deeper understanding of their nature. This approach minimizes the impact of unresolved peaks caused by mode variations over time. Additionally, we present appropriate analysis techniques to mitigate window effects and identify and eliminate spurious peaks. We demonstrate here that the grass can be effectively parametrized based on peak density. With such parametrization two distinct regimes are found: the sparse grass regime, characterized by low peak density and the absence of a plateau in the power spectra, and the dense grass regime, characterized by high peak densities and the presence of an observable plateau. Our study is the first rigorous quantification of the emergence of such a plateau in the power spectra of $\delta$ Scuti stars. Since the grass might be related with fractality, mode variability, and stellar rotation rate, its parametrization opens a new way to analyse these stars.
Joining the dots: high redshift black holes
Authors: King Andrew 
Published: October 2024

ABSTRACT
A recent paper suggested that emission from the central supermassive black holes in high-redshift galaxies must be tightly collimated by the effects of partly expelling a super-Eddington mass supply. I show here that this idea predicts that these galaxies should produce very little detectable rest-frame X-ray emission, appear Compton thick, and show no easily detectable sign of outflows. All of these properties agree with current observations. To produce these effects, the mass supply to the black holes should exceed the Eddington rate by factors ${\sim} 50{\!-\!}100$, which appears in line with conditions during the early growth of the holes. I note that theoretical derivations of the ratio of black hole mass to host galaxy stellar mass already predict that this should increase significantly at high redshift, in line with recent observations.
ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner
Authors: Wunderlich Tim Marius , Deshpande Chandrika , Paasche Lena W , Friedrich Tobias , Diegmüller Felix , Haddad Elias , Kreienbaum Carlotta , Naseer Haniya , Stebel Sophie E , Daus Nadine , Leers Jörg , Lan Jie , Trinh Van Tuan , Vázquez Olalla , Butter Falk , Bartkuhn Marek , Mackay Joel P , Hake Sandra B 
Published: October 2024

Abstract
The evolutionarily conserved histone variant H2A.Z plays a crucial role in various DNA-based processes, but the mechanisms underlying its activity are not completely understood. Recently, we identified the zinc finger (ZF) protein ZNF512B as a protein associated with H2A.Z, HMG20A and PWWP2A. Here, we report that high levels of ZNF512B expression lead to nuclear protein and chromatin aggregation foci that form in a manner that is dependent on the ZF domains of ZNF512B. Notably, we demonstrate ZNF512B binding to the nucleosome remodeling and deacetylase (NuRD) complex. We discover a conserved amino acid sequence within ZNF512B that resembles the NuRD-interaction motif (NIM) previously identified in FOG-1 and other transcriptional regulators. By solving the crystal structure of this motif bound to the NuRD component RBBP4 and by applying several biochemical and biophysical assays, we demonstrate that this internal NIM is both necessary and sufficient for robust and high-affinity NuRD binding. Transcriptome analyses and reporter assays identify ZNF512B as a repressor of gene expression that can act in both NuRD-dependent and -independent ways. Our study might have implications for diseases in which ZNF512B expression is deregulated, such as cancer and neurodegenerative diseases, and hints at the existence of more proteins as potential NuRD interactors.
PIPdb: a comprehensive plasmid sequence resource for tracking the horizontal transfer of pathogenic factors and antimicrobial resistance genes
Authors: Zhu Qianhui , Chen Qi , Gao Shenghan , Li Zhenpeng , Zhou Haijian , Cui Zhigang , Fan Guomei , Liu Xiao , Wu Xinmiao , Ma Juncai , Kan Biao , Hu Songnian , Wu Linhuan , Lu Xin 
Published: October 2024

Abstract
Plasmids, as independent genetic elements, carrying resistance or virulence genes and transfer them among different pathogens, posing a significant threat to human health. Under the ‘One Health’ approach, it is crucial to control the spread of plasmids carrying such genes. To achieve this, a comprehensive characterization of plasmids in pathogens is essential. Here we present the Plasmids in Pathogens Database (PIPdb), a pioneering resource that includes 792 964 plasmid segment clusters (PSCs) derived from 1 009 571 assembled genomes across 450 pathogenic species from 110 genera. To our knowledge, PIPdb is the first database specifically dedicated to plasmids in pathogenic bacteria, offering detailed multi-dimensional metadata such as collection date, geographical origin, ecosystem, host taxonomy, and habitat. PIPdb also provides extensive functional annotations, including plasmid type, insertion sequences, integron, oriT, relaxase, T4CP, virulence factors genes, heavy metal resistance genes and antibiotic resistance genes. The database features a user-friendly interface that facilitates studies on plasmids across diverse host taxa, habitats, and ecosystems, with a focus on those carrying antimicrobial resistance genes (ARGs). We have integrated online tools for plasmid identification and annotation from assembled genomes. Additionally, PIPdb includes a risk-scoring system for identifying potentially high-risk plasmids. The PIPdb web interface is accessible at https://nmdc.cn/pipdb.
The UCSC Genome Browser database: 2025 update
Authors: Perez Gerardo , Barber Galt P , Benet-Pages Anna , Casper Jonathan , Clawson Hiram , Diekhans Mark , Fischer Clay , Gonzalez Jairo Navarro , Hinrichs Angie S , Lee Christopher M , Nassar Luis R , Raney Brian J , Speir Matthew L , van Baren Marijke J , Vaske Charles J , Haussler David , Kent W James , Haeussler Maximilian 
Published: October 2024

Abstract
The UCSC Genome Browser (https://genome.ucsc.edu) is a widely utilized web-based tool for visualization and analysis of genomic data, encompassing over 4000 assemblies from diverse organisms. Since its release in 2001, it has become an essential resource for genomics and bioinformatics research. Annotation data available on Genome Browser includes both internally created and maintained tracks as well as custom tracks and track hubs provided by the research community. This last year's updates include over 25 new annotation tracks such as the gnomAD 4.1 track on the human GRCh38/hg38 assembly, the addition of three new public hubs, and significant expansions to the Genome Archive[GenArk) system for interacting with the enormous variety of assemblies. We have also made improvements to our interface, including updates to the browser graphic page, such as a new popup dialog feature that now displays item details without requiring navigation away from the main Genome Browser page. GenePred tracks have been upgraded with right-click options for zooming and precise navigation, along with enhanced mouseOver functions. Additional improvements include a new grouping feature for track hubs and hub description info links. A new tutorial focusing on Clinical Genetics has also been added to the UCSC Genome Browser.
Out-of-pocket costs for patients diagnosed with high-grade glioma and their carers
Authors: Newton Jade C , Halkett Georgia K B , Wright Cameron , O.’Connor Moira , Nowak Anna K , Moorin Rachael 
Published: October 2024

Abstract

Background
This study aimed to describe the out-of-pocket costs incurred by patients diagnosed with high-grade glioma (HGG) and their carers in the standard care arm of the Care-IS trial in the 6 to 8 months following their diagnosis.

Methods
Carers completed monthly cost surveys detailing the out-of-pocket costs incurred by patients and carers over a 6-month period. Seventy carers reported out-of-pocket costs at baseline (within 2 months following patient diagnosis), and a maximum of 50% of participants reported costs in any subsequent month. Costs were adjusted to 2023 AUD and reported as medians with an interquartile range. Demographic factors were assessed to determine if any were significantly associated with being in the first or fourth quartile of total out-of-pocket costs at baseline.

Results
Median monthly costs for patient-carer dyads were highest at baseline ($535[IQR:$170–$930]), and 2 months post-recruitment ($314 [IQR:$150–$772]). The largest contributors to patient-carer costs were patient health service use and patient medications. Patient and carer health service use and medication costs varied over time. The median health service use and medication out-of-pocket costs for patients and carers were mostly below $100 per month; however, there was a large variance in the upper 75th percentile for these cost categories. No factors were significantly associated with higher baseline out-of-pocket costs.

Conclusions
A HGG diagnosis has a significant and sustained financial impact on people who are diagnosed and their carers. Patients experience significant additional costs relating to their diagnosis and travel to receive care, and their carers also continue to experience sustained costs whilst managing the additional tasks associated with informal caregiving.
Noted, but not decisive. A cross-disciplinary analysis of metrics usage in Polish evaluative cultures
Authors: Remisiewicz Łukasz 
Published: October 2024

Abstract
Metrics-based reasoning patterns diffuse from core to periphery as peripheral and semi-peripheral countries adopt Western evaluation standards as formal categories or cultural scripts. While these scripts are applied across disciplines, each field maintains its own traditional criteria for scientific assessment. Consequently, scholars navigate between internalized and externally imposed evaluative frameworks when writing reviews. This study examines how metrics-based reasoning diffuses differently across disciplines through evaluative practices, with metrics being transformed and interpreted within the context of each field's unique evaluative culture. To compare diffusion patterns, this article analyzes 174 negative habilitation reviews across four Polish disciplines: art history, mathematics, materials engineering, and sociology. Despite uniform policy incentives, reviewers employed diverse criteria when assessing publication records. Materials engineering exhibited the most extensive use and emphasis on metrics, while art history relied minimally on indicators. Crucially, metrics were never the sole basis for negative conclusions but were consistently accompanied by additional forms of reasoning.
Designing Pension Plans According to Consumption-Savings Theory
Authors: Schlafmann Kathrin , Setty Ofer , Vestman Roine 
Published: October 2024

Abstract
We derive optimal characteristics of contribution rates into defined contribution pension plans based on consumption-savings theory. Contribution rates should increase with age and decrease with the balance-to-income ratio. Using Swedish registry data, we show that on average, individuals save according to those principles. However, almost half of the population behaves hand-to-mouth and does not undo the mandated constant contribution rates. In a quantitative model, designing contribution rates to follow the principles implies a 1.8% welfare gain and less dispersed replacement rates, while maintaining the same average replacement rate. Results are robust to various sources of model misspecification, including temptation preferences.
Impressions about harm are formed rapidly and then refined, modulated by serotonin
Authors: Moutoussis Michael , Barnby Joe , Durand Anais , Croal Megan , Dilley Laura , Rutledge Robb B , Mason Liam 
Published: October 2024

Abstract
Attributing motives to others is a crucial aspect of mentalizing, can be biased by prejudice, and is affected by common psychiatric disorders. It is therefore important to understand in depth the mechanisms underpinning it. Toward improving models of mentalizing motives, we hypothesized that people quickly infer whether other’s motives are likely beneficial or detrimental, then refine their judgment (classify-refine). To test this, we used a modified Dictator game, a game theoretic task, where participants judged the likelihood of intent to harm vs. self-interest in economic decisions. Toward testing the role of serotonin in judgments of intent to harm, we delivered the task in a week-long, placebo vs. citalopram study. Computational model comparison provided clear evidence for the superiority of classify-refine models over traditional ones, strongly supporting the central hypothesis. Further, while citalopram helped refine attributions about motives through learning, it did not induce more positive initial inferences about others’ motives. Finally, model comparison indicated a minimal role for racial bias within economic decisions for the large majority of our sample. Overall, these results support a proposal that classify-refine social cognition is adaptive, although relevant mechanisms of serotonergic antidepressant action will need to be studied over longer time spans.
High-throughput solutions in tumor organoids: from culture to drug screening
Authors: Zuo Jianing , Fang Yanhua , Wang Ruoyu , Liang Shanshan 
Published: October 2024

Abstract
Tumor organoids have emerged as an ideal in vitro model for patient-derived tissues, as they recapitulate the characteristics of the source tumor tissue to a certain extent, offering the potential for personalized tumor therapy and demonstrating significant promise in pharmaceutical research and development. However, establishing and applying this model involves multiple labor-intensive and time-consuming experimental steps and lacks standardized protocols and uniform identification criteria. Thus, high-throughput solutions are essential for the widespread adoption of tumor organoid models. This review provides a comprehensive overview of current high-throughput solutions across the entire workflow of tumor organoids, from sampling and culture to drug screening. Furthermore, we explore various technologies that can control and optimize single-cell preparation, organoid culture, and drug screening with the ultimate goal of ensuring the automation and high efficiency of the culture system and identifying more effective tumor therapeutics.
Motor, mood, and memory impairments persist during remission periods in chronic colitis and are influenced by neuroinflammation and sex
Authors: Sotelo‐Parrilla Gema , Ruiz‐Calero Alejandro , García‐Miranda Pablo , Calonge María L. , Vázquez‐Carretero María D. , Peral María J. 
Published: October 2024

AbstractUlcerative colitis is a chronic pathology characterized by relapsing–remitting phases of intestinal inflammation. Additionally, some patients develop neuropsychiatric disorders, such as depression and anxiety, or cognitive deficits. We aimed to investigate whether the development of chronic colitis elicits memory, locomotion, and mood impairments. It further examined whether these impairments are influenced by the relapsing–remitting phases of the colitis or by sex. Here, we used a chronic colitis model in male and female rats, induced with sodium dextran sulfate, mirroring the phases of human ulcerative colitis. Our results revealed that the severity of colitis was slightly higher in males than females. Chronic colitis triggered motor and short‐term memory deficits and induced anxiety‐ and depression‐like behaviors that remained throughout the development of the disease. There are also sex differences under control or inflammatory conditions. Therefore, in both situations, females compared to males displayed: (i) slightly lower locomotion, (ii) increased anxiety‐like behaviors, (iii) similar depression‐like behaviors, and (iv) similar short‐term memory deficit. Additionally, under control conditions, the mRNA levels of IL‐1β, IL‐6, and TNF‐α were higher in the female hippocampus. In both sexes, when chronic colitis was established, the neuroinflammation was evidenced by increased mRNA levels of these three cytokines in the hippocampus and in the motor and prefrontal cortices. Interestingly, this neuroinflammation was slightly greater in males. In summary, we show that the development of chronic colitis caused persistent behavioral abnormalities, highlighting sex differences, and that could be a consequence, at least in part, of the increase in IL‐1β, IL‐6, and TNF‐α in the brain.