bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterogeneity ofCandidabloodstream isolates in an academic medical center and affiliated hospitals
Authors: Scott Nancy E. , Wash Elizabeth , Zajac Christopher , Erayil Serin E. , Kline Susan E. , Selmecki Anna 
Published: February 2025

ABSTRACTInvasiveCandidabloodstream infections (candidemia) are a deadly global health threat. RareCandidaspecies are increasingly important causes of candidemia and phenotypic data, including patterns of antifungal drug resistance, is limited. There is geographic variation in the distribution ofCandidaspecies and frequency of antifungal drug resistance, which means that collecting and reporting regional data can have significant clinical value. Here, we report the first survey of species distribution, frequency of antifungal drug resistance, and phenotypic variability ofCandidabloodstream isolates from an academic medical center and 5 affiliated hospitals in the Minneapolis-Saint Paul region of Minnesota, collected during an 18-month period from 2019 to 2021. We collected 288 isolates spanning 11 species from 119 patients.C. albicanswas the most frequently recovered species, followed byC. glabrataandC. parapsilosis, with 10% of cases representing additional, rare species. We performed antifungal drug susceptibility for the three major drug classes and, concerningly, we identified fluconazole, micafungin and multidrug resistance rates inC. glabratathat were ∼ 2 times higher than that reported in other regions of the United States. We report some of the first phenotypic data in rare non-albicans Candidaspecies. Through analysis of serial isolates from individual patients, we identified clinically relevant within-patient differences of MIC values in multiple drug classes. Our results provide valuable clinical data relevant to antifungal stewardship efforts and highlight important areas of future research, including within-patient dynamics of infection and the mechanisms of drug resistance in rareCandidaspecies.
PET imaging of an antisense oligonucleotide in the living non-human primate brain using click chemistry
Authors: Cook Brendon E. , Pickel Thomas C. , Nag Sangram , Bolduc Philippe N. , Beshr Rouaa , Morén Anton Forsberg , Muste Cathy , Boscutti Giulia , Jiang Di , Yuan Long , Datta Prodip , Ochniewicz Piotr , Meynaq Yasir Khani , Tang Sac-Pham , Plisson Christophe , Amatruda Mario , Zhang Qize , DuBois Jonathan M. , Delavari Armin , Klein Stephanie K. , Polyak Ildiko , Shoroye Adebowale , Girmay Sara , Halldin Christer , Martarello Laurent , Peterson Emily A. , Kaliszczak Maciej 
Published: February 2025

AbstractDetermination of a drug’s biodistribution is critical to ensure it reaches the target tissue of interest. This is particularly challenging in the brain where invasive sampling methods may not be possible. Here, a pretargeted imaging methodology is disclosed that utilizes bioorthogonal click chemistry to determine the distribution of an antisense oligonucleotide in the living brain following intrathecal dosing. A novel PET tracer, [18F]BIO-687, bearing a click-reactivetrans-cyclooctene (TCO) was discovered and tested in conjunction with a Malat1 antisense oligonucleotide (ASO) conjugated with a methyltetrazine (MeTz). PET imaging in rats demonstrated that the tracer possesses good kinetic properties for CNS imaging and can react to form a covalent linkage with high specificity to the MeTz-conjugated-ASOin vivo. Further, the amount of tracer reacted by cycloaddition with the Tz was determined to be dependent on the concentration of ASO-MeTz in tissue, as determined through comparison of the imaging signal with the LC-MS of the tissue homogenate. The system was evaluated in cynomolgus monkeys, with PET imaging showing favorable tracer kinetics and specific binding to the ASOin vivo. These results demonstrate that the tracer [18F]BIO-687 can image intrathecally-delivered ASO distribution in the brain, and future studies should leverage this technology to evaluate ASO distribution in human subjects to study distribution.One Sentence SummaryDistribution of an intrathecally administered antisense oligonucleotide can be imaged using a pretargeted approach in the living brains of non-human primates.
Systems acclimation to osmotic stress in zygnematophyte cells
Authors: Zegers Jaccoline M.S. , Pfeifer Lukas , Darienko Tatyana , Schmitt Kerstin , Dorsch Craig A. , Kunz Cäcilia F. , Braus Gerhard H. , Classen Birgit , Valerius Oliver , de Vries Jan 
Published: February 2025

ABSTRACTZygnematophytes are the closest algal relatives of land plants. They hold key information to infer how the earliest land plants overcame the barrage of terrestrial stressors, prime of which is osmotic stress. Here, we applied two osmotic stressors on a unicellular and a multicellular representative of zygnematophytes and studied their response over a 25-hour time course generating 130, 60, and 30 of transcriptomic, proteomic, and metabolomic samples combined with photophysiology, sugar analysis, immunocytochemical glycoprotein analysis, and microscopy. Our data highlight a shared protein chassis that shows divergent responses with the same outcome: successful acclimation to osmotic challenges. We establish a model of how the algal sisters of land plants can overcome a prime stressor in the terrestrial habitat and highlight components of the plant terrestrialization toolkit.
Noradrenaline and Acetylcholine shape Functional Connectivity organization of NREM substages: an empirical and simulation study
Authors: Lehue Fernando , Coronel-Oliveros Carlos , Medel Vicente , Liebe Thomas , Kaufmann Jörn , Orellana Sebastián , Becerra Diego , Tagliazucchi Enzo , Orio Patricio 
Published: February 2025

AbstractSleep onset is characterized by a departure from arousal, and can be separated into well-differentiated stages: NREM (which encompasses three substages: N1, N2 and N3) and REM (Rapid Eye Movement). Awake brain dynamics are maintained by various wake-promoting mechanisms, particularly the neuromodulators Acetylcholine (ACh) and Noradrenaline (NA), whose levels naturally decrease during the transition to sleep. The combined influence of these neurotransmitters on brain connectivity during sleep remains unclear, as previous models have examined them mostly in isolation or only in deep sleep. In this study, we employ a Whole Brain model to investigate how changes in brain neurochemistry during NREM sleep, specifically involving ACh and NA, affect the Functional Connectivity (FC) of the brain. Using a Wilson-Cowan whole brain model informed by an empirical connectome and a heterogeneous receptivity map of neuromodulators, we explore these dynamics. Initial FC analysis reveals distinct connectivity changes: a decrease in Locus Coeruleus (LC) connectivity with the cortex during N2 and N3, and a decrease in Basal Forebrain (BF) connectivity with the cortex during N3. Additionally, compared to Wakefulness (W), there is a transition to a more integrated state in N1 and a more segregated state in N3. We adjust the coupling and input-output slope of the Whole Brain model for ACh and NA, based on BF or LC priors, to show that region-specific neurotransmitter distribution is key to explaining their effects on FC. This work enhances our understanding of neurotransmitters’ roles in modulating sleep stages and their significant contribution to brain state transitions between different states of consciousness, both in health and disease.
Epigenome and transcriptome changes inKMT2D-related Kabuki syndrome Type 1 iPSCs, neuronal progenitors and cortical neurons
Authors: Cuvertino S. , Martirosian E. , Cheng P. , Garner T. , Donaldson I. J. , Jackson A. , Stevens A. , Sharrocks A. D. , Kimber S. J. , Banka S. 
Published: February 2025

ABSTRACTKabuki syndrome type 1 (KS1) is a neurodevelopmental disorder caused by loss-of-function variants inKMT2Dwhich encodes a H3K4 methyltransferase. The mechanisms underlying neurodevelopmental problems in KS1 are still largely unknown. Here, we track the epigenome and transcriptome across three stages of neuronal differentiation using patient-derived induced pluripotent stem cells (iPSCs) to gain insights into the disease mechanism of KS1. In KS1 iPSCs we detected significantly lower levels of functionalKMT2Dtranscript and KMT2D protein, and lower global H3K4me1 and H3K4me2 levels. We identify loss of thousands of H3K4me1 peaks in iPSCs, neuronal progenitors (NPs) and early cortical neurons (CNs) in KS1. We show that the number of lost peaks increase as differentiation progresses. We also identify hundreds of differentially expressed genes (DEGs) in iPSCs, NPs and CNs in KS1. In contrast with the epigenomic changes, the number of DEGs decrease as differentiation progresses. Our analysis reveals significant enrichment of differentially downregulated genes in areas containing putative enhancer regions with H3K4me1 loss. We also identify a set of distinct transcription factor binding sites in differentially methylated regions and a set of DEGs related to KS1 phenotypes. We find that genes regulated by SUZ12, a subunit of Polycomb Repressive complex 2, are over-represented in KS1 DEGs at early stages of differentiation. In conclusion, we present a disease-relevant human cellular model for KS1 that provides mechanistic insights for the disorder and could be used for high throughput drug screening for KS1.
The diversity of cellular systems involved in carbonate precipitation byEscherichia coli
Authors: Jennings Matthew E. , Breley George J. , Blackwell Reilly S. , Drabik Anna , Gisser Kathleen R. , Kainrad Joe , Ligman Victoria , Proctor Jaycie , Deshler Rose , O’Hart Brian A. , Rivera Arlyn , Centrella Lorelei , Bonn Sara , Chaudhry Bisma , Barton Hazel A. 
Published: February 2025

AbstractClimate change is increasing the need to limit levels of anthropogenic CO2released into the atmosphere. One approach being investigated is to generate products based on microbially induced carbonate precipitation (MICP), which can trap CO2as CaCO3. We recently identified a novel MICP pathway in bacteria that is initiated by Ca2+toxicity in cells, causing extracellular CO2to be trapped as CO2-byEscherichia coli,although the yield of precipitated CaCO remained low (in the milligram range). In this work, we used theE. coliKeio gene knock-out library to identify 54 genes involved in MICP inE. coli,which could be broadly characterized into four groups: central metabolism, iron metabolism, cell architecture, and transport. The role of central metabolism appears to be crucial in maintaining alkaline conditions surrounding the cell that promote CaCO3precipitation. The role of iron metabolism was less clear, although the results suggest that growth rate influences the initiation of MICP. While the impact of repeating polymeric structures on cell surfaces promoting MICP is well established, our results suggest that other structural features may play a role, including fimbriae and flagella. Finally, the results confirmed that Ca2+transport is central to MICP under calcium stress. The results further suggest that the ZntB efflux pump may play a previously unidentified role in Ca2+transport inE. coli.By overexpressing some of these genes, our work suggests that there are several previously unidentified cellular mechanisms that could serve as a target for enhanced MICP inE. coli.By incorporating these processes into MICP pathways inE. coli,it may be possible to increase the volume of CO2fixed using this pathway and yield potentially new products that can replace CO2intensive products, such as precipitated calcium carbonates (PCCs) for industry.
Museum genomics reveals temporal genetic stasis and global genetic diversity inArabidopsis thaliana
Authors: Lopez Lua , Lang Patricia L. M. , Marciniak Stephanie , Kistler Logan , Latorre Sergio M. , Haile Asnake , Vasquez Cerda Eleanna , Gamba Diana , Xu Yuxing , Woods Patrick , Yifru Mistire , Kerby Jeffrey , McKay John K. , Oakley Christopher G. , Ågren Jon , Wondimu Tigist , Bulafu Collins , Perry George H. , Burbano Hernán A. , Lasky Jesse R. 
Published: February 2025

AbstractGlobal patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift, environmental change (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections ofArabidopsis thalianaand combined these with published genomes. We sought a broader view of genomic diversity across the species, and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterized diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.
Serial Dependence Predicts Generalization in Perceptual Learning
Authors: Pinchuk-Yacobi Noga , Sagi Dov , Bonneh Yoram S. 
Published: February 2025

SUMMARYRecent visual experiences systematically bias current perceptual reports, a phenomenon known as serial dependence. This study examines how serial dependence interacts with perceptual learning, specifically focusing on its role in learning generalization. We reanalyzed data from 50 observers who practiced the texture discrimination task (TDT) under three conditions designed to modulate learning generalization: consistent target location, alternating two target locations, and mixed with targetless trials (Harris et al., 2012); over 200,000 trials. Our analysis revealed substantial report biases toward the orientation of targets from previous trials, extending up to 10 trials back, much longer than previously reported. These biases, when accumulated across consistent trial sequences, nearly overshadowed responses to the current target. Remarkably, although TDT thresholds improved by 40% over the 8 days of training, the biases persisted despite the randomization of target orientations, with trial history being irrelevant to the current trial. The effect was most pronounced when current targets had low visibility, prior targets were highly visible, and prior targets appeared at the same location as the current target. Training conditions that facilitated learning generalization exhibited stronger and longer serial dependence effects from distant trial histories compared to conditions promoting specific learning. Across observers, stronger serial dependence from distant history was associated with greater learning transfer, suggesting that distant memory traces are essential for efficient learning. We propose that these extended memory traces integrate information across multiple trials to create a generalized learning template, preventing overfitting to specific stimuli thus enhancing learning transfer. In contrast, strong adaptation in the consistent target location condition disrupts these traces, thereby limiting generalization.
Long non-coding RNA BCAR4 is required for efficient influenza A virus replication
Authors: Cao Yi , Chin Alex W.H. , Gu Haogao , Li Mengting , Poon Leo L.M. 
Published: February 2025

AbstractLong non-coding RNAs (lncRNAs) regulate diverse biological processes, including influenza A virus (IAV) infection. However, the understanding of lncRNAs in IAV infection is limited. By using both bioinformatic analyses and virological assays, we showed that lncRNABCAR4expression can be highly induced by infection of multiple different IAV subtypes.BCAR4was required for the propagation of IAV infection. Genetic inactivation ofBCAR4inhibited IAV growth. Investigation of the IAV infection cycle revealed a suppressed IAV viral RNA transcription and replication, and attenuated viral protein synthesis in theBCAR4-deficient cells.BCAR4potentially interacted with cellular splicing-associated proteins and the activation ofBCAR4was associated with influenza viralNSsegment. These findings suggest the important role of lncRNABCAR4in regulation of IAV infection.ImportanceLong non-coding RNAs (lncRNAs) serve as critical regulators in the biological processes of influenza A virus (IAV) infection. However, how lncRNAs engage IAV infection remains unclear. Here we showBCAR4as highly universally induced lncRNA in infection of multiple different IAV subtypes. Deletion ofBCAR4reduced IAV multiplication. In the IAV infection cycle,BCAR4deficiency decreased IAV viral RNA transcription, replication and viral protein biosynthesis.BCAR4was potentially binding to the host RNA splicing associated protein, and the IAV viral NS segment is required for the activation ofBCAR4. Our results highlight important regulation ofBCAR4in IAV infection.
Fluctuations in arousal reflect latent state transitions that facilitate behavioral optimization
Authors: Li Tiantian , Marble Harrison , Chen Timothy , Razmi Niloufar , Nassar Matthew R 
Published: February 2025

AbstractPeople are often faced with surprising events that defy expectations. Such events elicit transient activity in the locus coeruleus/norepinephrine system and elevation of peripheral arousal markers including pupil dilation and the EEG P300, but the function of these signals remains unclear. We propose that they reflect latent state transitions that dynamically control the mental context governing learning and perception. We tested and confirmed five preregistered predictions of this theory using EEG and pupil measurements collected from people performing a color prediction and reproduction task. Task latent state transitions elicited pupil dilation and amplified event-related potentials including the P300. These EEG and pupil measures related to behavioral signatures of latent state updating, including reduced bias and bidirectional adjustment of learning, both across trials and individuals. Our findings support the theory that LC/NE-linked arousal systems optimize behavior by signaling environmental transitions to facilitate rapid adjustments of mental context.
Representing spatial futures in the age of social media: unpacking the case of The Line
Authors: Alaily-Mattar Nadia , Jones Paul 
Published: February 2025

PurposeThis paper is concerned with materials developed to represent and communicate state-commissioned spatial experiments on social media. Our objective is to reveal what such materials can do, even before – or whether–the projects they represent are built. Such materials can constitute an intervention in the way political territory is created, shared and made sense of.Design/methodology/approachWe use empirical research of The Line, a new city set to be built in the Kingdom of Saudi Arabia (KSA), to explore this contention. Our research data is the publicly available visual, textual and audio-visual materials commissioned by The Line’s delivery company to be disseminated on digital platforms. Our methodological approach to these materials is a qualitative content analysis.FindingsThe materials do not provide a clear sense of fundamental elements of what The Line as an architectural project actually is. Rather the materials foreground three main tropes that disrupt existing notions of nature, space and temporality. Such disruptions propagate KSA’s official story of transformation as drafted in its Vision 2030. They lead us to understand The Line as a radical experiment to rework the Saudi territory and therefore reflecting the power of the state.Originality/valueExploring critically the ways in which material projects are embedded in predominantly visual digital cultural forms that imply architecture – and are compounded by affordances of social media – can illuminate much about how designed environments can be mobilized vis-a-vis political imaginaries.
Analysis of air-gap field modulation effect on torque contribution of 6-slot 4-pole high-speed permanent magnet machine
Authors: Li Kai , Wang Chen 
Published: February 2025

Purpose
This paper aims to investigate and analyze the air-gap field modulation (AGFM) effect on torque contribution in a 6-slot/4-pole high-speed permanent magnet (HSPM) machine. To further illustrate the torque generation mechanism, the torque contribution is quantified using the Maxwell stress tensor (MST) method.

Design/methodology/approach
First, a simplified permanent magnet (PM) magnetomotive force model is established to identify the effective main-order working field harmonics. Then, the MST method is used to determine the average torque contributions of the effective main-order working field harmonics. Finally, the influences of various stator and rotor parameters on the AGFM effect are analyzed and optimized to enhance the torque density.

Findings
Apart from the fundamental harmonics, the AGFM harmonics contribute non-negligible average torque on the HSPM machine, and the optimized machine has higher torque density. Finally, a prototype of the 10 kW HSPM machine is manufactured and experimented with to validate the effectiveness of the theoretical analysis.

Originality/value
In this paper, the torque generation mechanism of the HSPM machine is investigated and analyzed. Meanwhile, the AGFM effect of the HSPM machine with different design parameters is analyzed and optimized to enhance the torque density.
Is reactive corporate social responsibility such a bad idea? It depends on your positioning
Authors: Baghi Ilaria , Antonetti Paolo 
Published: February 2025

Purpose
Following a crisis, stakeholders tend to appreciate costly organizational responses that attempt to reverse the harm caused by the organization. The deployment of reactive corporate social responsibility (CSR), defined as a CSR initiative explicitly promoted to make amends for a negative event, can thus be an effective crisis response strategy. However, existing studies suggest that this strategy could backfire, as it increases stakeholders’ skepticism regarding an organization’s motives to engage in CSR when this is only done under external pressure. Applying attribution theory, the purpose of this paper is to demonstrate that the effectiveness of reactive CSR as a crisis response strategy depends on the positioning of the brand promoting it.

Design/methodology/approach
The authors use three between-subject experiments to test our hypotheses. In Studies 1 and 3, they consider a fictitious crisis scenario with a fictitious brand, and in Study 2, they test their hypotheses using existing brands involved in a fictitious crisis.

Findings
Compared to a purely verbal response (an apology), reactive CSR improves consumers’ responses when implemented by a brand positioned to focus on CSR rather than on performance. This effect is mediated by perceived brand benevolence: a brand focused on CSR is seen as more benevolent when proposing reactive CSR initiatives than a brand with a performance positioning. The effect holds even when the CSR positioning is not aligned with the reactive CSR domain. For a brand with a performance positioning, a costlier reactive CSR strategy is no more effective than an apology.

Originality/value
The study extends their understanding of how information on brand positioning influences reactive CSR in response to a crisis. Their analysis clarifies the circumstances under which reactive CSR can be an effective crisis response.