bluuebunny/crossref_metadata_2025 huggingface dataset:
The cellular state space of AML unveils novelNPM1subtypes with distinct clinical outcomes and immune evasion properties
Authors: Lilljebjörn Henrik , Peña-Martínez Pablo , Thorsson Hanna , Henningsson Rasmus , Rissler Marianne , Landberg Niklas , Puente-Moncada Noelia , von Palffy Sofia , Rissler Vendela , Stanek Petr , Desponds Jonathan , Zhong Xiangfu , Juliusson Gunnar , Lazarevic Vladimir , Lehmann Sören , Fontes Magnus , Ågerstam Helena , Sandén Carl , Orsmark-Pietras Christina , Fioretos Thoas
Published: February 2025

Acute myeloid leukemia (AML) is a genetically and cellularly heterogeneous disease. We characterized 120 AMLs using genomic and transcriptomic analyses, including single-cell RNA sequencing. Our results reveal an extensive cellular heterogeneity that distorts the bulk transcriptomic profiles. Selective examination of the transcriptional signatures of >90,000 immature AML cells identified four main clusters, thereby extending current genomic classification of AML. Notably,NPM1mutated AML could be stratified into two novel, clinically relevant classes, withNPM1classIassociated with downregulation of MHC class II and excellent survival following hematopoietic stem cell transplantation (HSCT).NPM1classIIwas instead associated with resistance to allogeneic T cells in anex vivoco culture assay, and importantly, dismal survival following HSCT. These findings provide new insights into the cellular state space of AML, define new diagnostic entities, and highlight potential therapeutic intervention points.

Key Points

The bulk transcriptional profiles of AML are mainly driven by a diverse set of cellular signatures.

Single cell RNA-sequencing of the most common AML subtypes reveals marked heterogeneity extending beyond current genomic classification schemes.

NPM1-mutated AML can be divided into two new classes, with distinct immune evasion mechanisms and survival after transplantation.
ClusterApp to visualize, organize, and navigate metabolomics data
Authors: Hansel Vinicius , Karunarathne Pothuvilage , Borelli Tiago Cabral , Quinn Robert , da Silva Ricardo R.
Published: February 2025

Background

Clustering analysis is a foundational step in exploratory data analysis workflows, with dimensionality reduction methods commonly used to visualize multidimensional data in lower-dimensional spaces and infer sample clustering. Principal Component Analysis (PCA) is widely applied in metabolomics but is often suboptimal for clustering visualization. Metabolomics data often require specialized manipulations such as blank removal, quality control adjustments, and data transformations that demand efficient visualization tools. However, the lack of user-friendly tools for clustering without computational expertise presents a challenge for metabolomics researchers. ClusterApp addresses this gap as a web application that performs Principal Coordinate Analysis (PCoA), expanding clustering alternatives in metabolomics. Built on a QIIME 2 Docker image, it enables PCoA computation and Emperor plot visualization. The app supports data input from GNPS, GNPS2, or user-provided spreadsheets. Freely available, ClusterApp can be locally installed as a Docker image or integrated into Jupyter notebooks, offering accessibility and flexibility to diverse users.

Results

To demonstrate the data preprocessing techniques available in ClusterApp, we analyzed two Liquid Chromatography coupled to Tandem Mass Spectrometry (LC-MS/MS) metabolomics datasets: one exploring metabolomic differences in mouse tissue samples and another investigating coral life history stages. Among the dissimilarity measures available, the Bray-Curtis measure effectively highlighted key metabolomic variations and patterns across both datasets. Targeted filtering significantly enhanced data reliability by retaining biologically relevant features, 10,617 in the coral dataset and 7,341 in the mouse dataset while eliminating noise. The combination of Total Ion Current (TIC) normalization and auto-scaling improved clustering resolution, revealing distinct separations in tissue types and life stages. ClusterApp’s flexible features, such as customizable blank removal and group selection, provided tailored analyses, enhancing visualization and interpretation of metabolomic profiles.

Conclusion

ClusterApp addresses the need for accessible, dynamic tools for exploratory data analysis in metabolomics. By coupling data transformation capabilities with PCoA on multiple dissimilarity matrices, it provides a versatile solution for clustering analysis. Its web interface and Docker-based deployment offer flexibility, accommodating a wide range of use cases through graphical or programmatic interactions. ClusterApp empowers researchers to uncover meaningful patterns and relationships in metabolomics data without requiring cumbersome data manipulation or advanced bioinformatics expertise.
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs
Authors: Ghaffaari Ali , Schönhuth Alexander , Marschall Tobias
Published: February 2025

Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based reference structures render the operation considerably more involved. Given the sheer number of such queries in a typical read mapping experiment, an efficient algorithm for answering distance queries is crucial. In this paper, we introduce DiVerG, a compact data structure as well as a fast and scalable algorithm, for constructing distance indexes for general sequence graphs on multi-core CPU and many-core GPU architectures. DiVerG is based on PairG [26], but overcomes the limitations of PairG by exploiting the extensive potential for improvements in terms of scalability and space efficiency. As a consequence, DiVerG can process substantially larger datasets, such as whole human genomes, which are unmanageable by PairG. DiVerG offers faster index construction time and consistently faster query time with gains proportional to the size of the underlying compact data structure. We demonstrate that our method performs favorably on multiple real datasets at various scales. DiVerG achieves superior performance over PairG; e.g. resulting to 2.5–4x speed-up in query time, 44–340x smaller index size, and 3–50x faster construction time for the genome graph of the MHC region, as a particularly variable region of the human genome.

The implementation is available at:https://github.com/cartoonist/diverg
Sidechain conditioning and modeling for full-atom protein sequence design with FAMPNN
Authors: Shuai Richard W. , Widatalla Talal , Huang Po-Ssu , Hie Brian L.
Published: February 2025

Leading deep learning-based methods for fixed-backbone protein sequence design do not model protein sidechain conformation during sequence generation despite the large role the three-dimensional arrangement of sidechain atoms play in protein conformation, stability, and overall protein function. Instead, these models implicitly reason about crucial sidechain interactions based on backbone geometry and known amino acid sequence labels. To address this, we present FAMPNN (Full-Atom MPNN), a sequence design method that explicitly models both sequence identity and sidechain conformation for each residue, where the per-token distribution of a residue’s discrete amino acid identity and its continuous sidechain conformation are learned with a combined categorical cross-entropy and diffusion loss objective. We demonstrate that learning these distributions jointly is a highly synergistic task that both improves sequence recovery while achieving state-of-the-art sidechain packing. Furthermore, benefits from explicit full-atom modeling generalize from sequence recovery to practical protein design applications, such as zero-shot prediction of experimental binding and stability measurements.
Mesenchymal Stem Cell-Derived Extracellular Vesicles Mitigate Immune Cell Activation in an In Vitro Model of Post-Resuscitation Inflammation
Authors: Rolland Tyler J , Zahra Sumbule , Cucinotta Daniel , Young Rebeccah , Weil Brian
Published: February 2025

Background

Systemic inflammation is a well-established component of post-cardiac arrest syndrome (PCAS), a condition responsible for significant morbidity and mortality in patients who are initially resuscitated from sudden cardiac arrest. Mesenchymal stem cell-derived extracellular vesicles (MSC-EVs) have emerged as promising immunomodulatory agents in various inflammatory conditions, including after ischemia-reperfusion injury (IRI). Here, we investigated the therapeutic potential of MSC-EVs in porcine peripheral blood mononuclear cells (PBMCs) stimulated with lipopolysaccharide (LPS) or mitochondrial DNA (mtDNA) to mimic immune cell activation in PCAS.

Methods

PBMCs were isolated from healthy pigs (Sus scrofa), culturedin vitro, stimulated with LPS or mtDNA, and treated with a range of MSC-EV concentrations. Flow cytometry, quantitative PCR, ELISA, and ROS/RNS measurements were performed to assess PBMC activation.

Results

MSC-EV treatment reduced LPS-induced inflammatory granulocyte activation and selectively modulated cytokine transcripts, including IFNα, IL-1β, and TNF-α, in a concentration-dependent manner. Similar immunosuppressive effects were observed in mtDNA-stimulated PBMCs, where MSC-EVs attenuated dendritic cell activation and inflammatory cytokine release. Furthermore, higher concentrations of MSC-EVs significantly decreased ROS/RNS production in both LPS- and mtDNA-challenged PBMCs.

Conclusions

MSC-EVs exhibit potent immunomodulatory properties against LPS- and mtDNA-induced activation of porcine PBMCs, highlighting their broad capacity to modulate immune responses and mitigate oxidative stress induced by pro-inflammatory stimuli that are relevant to PCAS. These findings provide further support for the administration of MSCs, or MSC-EVs themselves, as a potential therapeutic intervention to target immune activation in PCAS and other disorders characterized by an acute systemic inflammatory state.
Identification of pyroptosis-related diagnostic model relate to immune infiltration in osteoarthritis
Authors: Xiao Meimei , Qiu Yue , Meng Jinzhi , Jiang Cancai , Chen Yanming , Yao Jun
Published: February 2025

Background

Osteoarthritis (OA) is a common chronic diseases which were associated with aging and progressive joint dysfunction. Pyroptosis, a novel mode of cell death. The effect of pyroptosis on osteoarthritis (OA) progression is still in the exploratory stage, and the specific mechanism is unclear.

Methods

OA data sets were obtained from the GEO databases website. Bioinformatics analysis was conducted to identify pyroptosis-related genes (PRGs), construct a pyroptosis-related diagnostic model, and identify subtypes. We established the random forest (RF) model as well as a nomogram of differentially expressed PRGs. The association between immunity and pyroptosis was comprehensively explored. Finally, the expression levels of 3 OA characteristic genes were verified by qRT-PCR and immunohistochemistry.

Results

Seven differentially expressed PRGs (CASP3, GPX4, NOD1, TIRAP, SCAF11, CASP4, and CASP9) were obtained by differential analysis to establish RF models, and three important OA genes (CASP9, TIRAP, and SCAF11) were obtained. ROC curve proved that the established model had high diagnostic accuracy. Based on the above three important PRGs, a high-precision nomogram model is constructed. Two PRG models are determined by consensus clustering method. The enrichment degree of immune cells in cluster A was higher than that in cluster B, suggesting that cluster A might be related to the occurrence and development of OA. GPX4 was found to be positively correlated with higher immune infiltration. Finally, the expression levels of 3 OA characteristic genes were verified by qRT-PCR and immunohistochemistry.

Conclusion

We constructed an effective prognostic model according to PRGs in OA and integrated explored the association between pyroptosis and immunity-related elements. This article provides a strong point for investigating directed immunotherapy methods with novelty for OA.
The interplay of climate change, urbanization, and species traits shapes European butterfly population trends
Authors: Colom Pau , Tejeda Ashley , Bonelli Simona , Fontaine Benoît , Kuussaari Mikko , Maes Dirk , Mestdagh Xavier , Munguira Miguel L. , Musche Martin , Pettersson Lars B. , Roy David , Rüdisser Johannes , Šašić Martina , Schmucki Reto , Stefanescu Constanti , Titeux Nicolas , Settele Josef , van Swaay Chris , Gordillo Javier , Melero Yolanda
Published: February 2025

Species populations naturally fluctuate, yet long-term trend analysis can reveal patterns of success, decline, or stability under global change pressures. While responses to climate change are well-documented, its synergy with another major global driver, urbanization, remains understudied. Here, we analyzed long-term monitoring data from over 8,400 populations of 145 butterfly species across Europe, representing a high diversity of species traits, to assess population trends in response to climate change and urbanization. We examined how population responses vary between urban and rural contexts, providing insights into the influence of site-specific conditions. Climate warming was associated with population declines, which were more pronounced in urban areas. The effect of precipitation varied between environments: increases in precipitation generally benefited populations in rural areas but had detrimental effects in urban ones. Aridity consistently drove population declines across environments, with slightly stronger effects in urban areas. Species with colder climatic niches declined the most in response to warming, increased aridity, and reduced precipitation, while trophic specialists were particularly vulnerable to aridity and precipitation changes in urban environments. Although increasing urbanization did not explain overall population trends, its effects became evident when considering species traits, with certain traits being more vulnerable to urbanization. Specifically, species with narrow climatic niches declined the most in response to urbanization in rural areas, while those and larger body sizes decline the most in urban environments. Our findings highlight the complex interplay between environmental change, landscape context, and species traits in shaping biodiversity outcomes. Importantly, our results suggest that urbanization generally amplifies the impact of climate change on insect population trends.
Regioselectively Acetylated Silybin Derivatives and their Cytotoxic Activity in Liver Cancer Cells
Authors: Van Chien Tran , Phuong Thao Tran Thi , Anh Nguyen The , Van Loc Tran , Garrett Michelle D. , Nga Nguyen Thi , Thao Do Thi , Serpell Christopher J. , Van Sung Tran
Published: February 2025

Natural products continue to serve as a valuable source of starting points for therapeutic agents. Six silybin derivatives have been synthesized and testedin vitrofor their cytotoxic effect on the human hepatocellular carcinoma line HepG2 using the MTT assay. Results indicate that the 3,5,7,20,23-penta-O-acetyl-2,3-dehydrosilybin possesses a stronger cytotoxic effect than that of the parent silybin by a factor of 12. This compound was further evaluated for its cytotoxic activity on Hep3B, Huh7, and Huh7R hepatocellular carcinoma cell lines, giving similar potencies, arresting the cell cycle at S phase and causing apoptosis. These results illustrate the potential of silybin derivatives as therapeutics against liver cancer.
Commonly used compositional data analysis implementations are not advantageous in microbial differential abundance analyses benchmarked against biological ground truth
Authors: Gamboa-Tuz Samuel D. , Ramos Marcel , Franzosa Eric , Huttenhower Curtis , Segata Nicola , Oh Sehyun , Waldron Levi
Published: February 2025

Previous benchmarking of differential abundance (DA) analysis methods in microbiome studies have employed synthetic data, simulations, and “real data” examples, but to the best of our knowledge, none have yet employed experimental data with known “ground truth” differential abundance. A key debate in the field centers on whether compositional methods are necessary for DA analysis, which is challenging to answer due to the lack of ground truth data. To address this gap, we created the Bioconductor data packageMicrobiomeBenchmarkData, featuring three microbiome datasets with established biological ground truths: 1) diverse oral microbiomes from supragingival and subgingival plaques, expected to favor aerobic and anaerobic bacteria, respectively, 2) low-diversity microbiomes from healthy vaginas and bacterial vaginosis, conditions that have been well-characterized through cell culture and microscopy, and 3) a spike-in dataset with constant, known absolute abundances of three bacteria. We benchmarked 17 DA approaches and demonstrated that compositional DA methods are not beneficial but rather lack sensitivity, show increased variability in constant-abundance spike-ins, and, most surprisingly, more frequently produce paradoxical results with DA in the wrong direction for the low-diversity microbiome. Conversely, commonly used methods in microbiome literature, such asLEfSe, the Wilcoxon test, and RNA-seq-derived methods, performed best. We conclude that researchers continue using widely adopted non-parametric or RNA-seq DA methods and that further development of compositional methods includes benchmarking against datasets with known biological ground truth.
Delayed transplantation of neural stem cells improves initial graft survival following stroke
Authors: Weber Rebecca Z , Rentsch Nora H , Buil Beatriz Achón , Nih Lina R. , Tackenberg Christian , Rust Ruslan
Published: February 2025

Neural stem cell therapies hold great promise for improving stroke recovery, but the hostile stroke microenvironment can hinder the initial graft survival. It has long been well documented that the microenvironment evolves over time, making it crucial to identify the optimal transplantation window to maximize therapeutic efficacy. However, it remains uncertain whether acute or delayed local cell transplantations better supports graft viability after stroke. Here, we show that delayed intracerebral transplantation of neural progenitor cells (NPCs) derived from human induced pluripotent cells (iPSCs) at 7 days post stroke significantly enhances graft proliferation and survival, compared to acute transplantation at 1 day post stroke, in a mouse model of large cortical stroke. Usingin vivobioluminescence imaging over a 6-week period post-transplantation, we observe a more than 5-fold increase in bioluminescence signal in mice that received delayed NPC therapy, compared to those that underwent acute NPC transplantation. The increased number of cell grafts in mice receiving delayed NPC transplantation was driven by increased proliferation rates early after transplantation, which subsequently declined to similarly low levels in both groups. Notably, we found that the majority of transplanted NPCs differentiated into neurons after 6 weeks, with no significant differences in the neuron-to-glia ratio between acute and delayed transplantation groups. These findings suggest that delayed NPC transplantation improves early graft survival and proliferation, which could help identify the optimal therapeutic window for maximizing the effectiveness of NPC-based therapies in stroke.
Effects of High-Intensity Interval Training on Physical and Cognitive Function in Middle-Aged Male Mice
Authors: Stephenson Justin C. , Tran Tuan D. , Graber Ted G.
Published: February 2025

Declining functional capacity, both physical and cognitive, is a consequence of aging. However, exercise is a promising intervention to mitigate normal age-related decline. While numerous studies have elucidated the benefits of exercise per se, less well-studied is the effect of high intensity interval training (HIIT) on a middle-aged population. Our primary purpose was to assess the effect of three months of HIIT on physical and cognitive performance in middle-aged (17-month-old) male C57BL/6J mice, compared to sedentary controls. We hypothesized that exercised mice would be resistant to any decline in cognitive and physical ability, both measured pre- and post-intervention. To measure physical function, we used the well-validated CFAB (comprehensive functional assessment battery) scoring system comprised of determinants including voluntary wheel running, inverted cling, grip test, treadmill max speed, and rotarod. We measured cognition with open field, novel object recognition, y-maze, and puzzle box. Further measures of sarcopenia/frailty included body composition (MRI) andin vivocontractile physiology (plantar flexor torque). Training resulted in significant aerobic capacity improvements for the HIIT group, increasing treadmill time by 28%, while the SED group demonstrated a 41.4% decline in treadmill time. However, no significant differences in cognitive function were determined. Contrary to our previous research in other age groups, the current study found a negligible effect of HIIT on body composition. We note that at 17 months old, mice did not experience any evidence of cognitive deterioration in either group over the three-month period, thus explaining the lack of exercise effect. We found that HIIT had less influence on either physical or cognitive function than we expected, which may be because function in this age group is stable. Future work will investigate older adult cognitive response to HITT at ages where there is well-documented cognitive decline.
Reversable Acute Sedation Response of Phosphorothioate Antisense Oligonucleotides Following Local Delivery to the Central Nervous System
Authors: O'Rourke Jacqueline G , Bachmann Gemma , Mazur Curt , Zhou Keming , Platoshyn Oleksandr , Hernandez Mariana Bravo , Klein Stephanie , Nguyen Jonathon , Burel Sebastien , Hoffmaster Christine , Zanardi Tom , Jafar-nejad Paymaan , Marsala Martin , Henry Scott P , Swayze Eric E , Powers Berit , Kordasiewicz Holly B
Published: February 2025

Antisense oligonucleotides (ASOs) locally delivered to the central nervous system (CNS) are being approved as therapies for neurological diseases. After intrathecal injection of some ASOs, transient toxicities have been reported, but considerable inconsistencies remain in classifying them and their underlying mechanisms. Here, we characterize an acute sedation response that can include loss of lower spinal reflexes, hypoactivity, paresis, sedation and ataxia, peaking ~3 hours post-intrathecal injection of some phosphorothioate ASOs and reversing by 24 hours with no sequelae. Acute sedation is distinct from acute activation, which is hyperactivity and muscle cramping that occurs immediately after administering oligonucleotides. Acute sedation translates across species from rodents to non-human primates and is sequence-, dose-, and chemistry dependent. Acute sedation can be mitigated by strategic placement of phosphorothioate backbone linkages in ASOs and by avoiding G-rich sequences. The acute sedation response can be modeled in primary neural cultures, with good predictability of in vivo response. Mechanistically, we demonstrate that acute sedation is caused by high extracellular ASO concentrations inhibiting synaptic transmission, which reverses as ASO is cleared from the extracellular space and taken up into cells. Our results provide a comprehensive framework for quantifying and mitigating acute sedation caused by some phosphorothioate ASOs.
Pneumo-Typer: a high-throughput capsule genotype visualization tool with integrated serotype and sequence type prediction forStreptococcus pneumoniae
Authors: Li Xiangyang , Zhu Yaoyao , Yang Zilin , Li Yanzi , Zhang Guohui , Wang Xiangyu , Zhao Xuan , Huang Yinyan , Zhang Huajie , Li Bingqing , Ma Zhongrui
Published: February 2025

Streptococcus pneumoniaeremains a significant global pathogen, with capsule-based vaccines targeting only a subset of over 100 serotypes. Accurate serotyping is critical for evaluating vaccine impact and optimizing capsule formulations. While whole-genome sequencing (WGS)-based methods achieve high serotyping accuracy, they often struggle to identify serotype variants with altered capsule loci that may evade vaccine-induced immunity. Here, we present Pneumo-Typer, a high-throughput tool for capsule genotype (CapT) visualization, enabling rapid identification of isolates with capsular gene variations, including mutations and horizontal gene transfer. In addition, Pneumo-Typer integrates serotype and sequence type (ST) prediction, achieving 98.44% accuracy in predicting 93 serotypes across 17,683 genomes. Our analysis reveals substantial serotypes linked to multiple STs and CapTs, with STs and CapTs demonstrating relative evolutionary independence and limited CapT variation during ST expansion. Within multi-serotype serogroups, we observe striking CapT diversity, providing insights into the evolutionary dynamics of serogroup formation. These findings underscore the utility of Pneumo-Typer for epidemiological surveillance and vaccine design, contributing to efforts to mitigate the global burden of S. pneumoniae.
Deciphering population-level response under spatial drug heterogeneity on microhabitat structures
Authors: Hu Zhijian , Wood Kevin
Published: February 2025

Bacteria and cancer cells live in a spatially heterogeneous environment, where migration shapes the microhabitat structures critical for colonization and metastasis. The interplay between growth, migration, and microhabitat structure complicates the prediction of population responses to drugs, such as clearance or sustained growth, posing a longstanding challenge. Here, we disentangle growth-migration dynamics and identify that population decline is determined by two decoupled terms: a spatial growth variation term and a microhabitat structure term. Notably, the microhabitat structure term can be interpreted as a dynamic-related centrality measure. For fixed spatial drug arrangements, we show that interpreting these centralities reveals how different network structures, even with identical edge densities, microhabitat numbers, and spatial heterogeneity, can lead to distinct population-level responses. Increasing edge density shifts the population response from growth to clearance, supporting an inversed centrality-connectivity relationship, and mirroring the effects of higher migration rates. Furthermore, we derive a sufficient condition for robust population decline across various spatial growth rate arrangements, regardless of spatial-temporal fluctuations induced by drugs. Additionally, we demonstrate that varying the maximum growth-to-death ratio, determined by drug-bacteria interactions, can lead to distinct population decline profiles and a minimal decline phase emerges. These findings address key challenges in predicting population-level responses and provide insights into divergent clinical outcomes under identical drug dosages. This work may offer a new method of interpreting treatment dynamics and potential approaches for optimizing spatially explicit drug dosing strategies.
Evidence of functional connectivity disruptions between auditory and non-auditory regions in adolescents living with HIV
Authors: Madzime Joanah , Jankiewicz Marcin , Meintjes Ernesta M. , Torre Peter , Laughton Barbara , Holmes Martha J.
Published: February 2025

Children living with perinatally acquired HIV (CPHIV) demonstrate hearing impairments and language processing delays even in the presence of combination antiretroviral therapy (cART). Even though efficient processing of sound relies on the proper function of both the peripheral and central auditory auditory systems (PAS; CAS), investigations on the effect of HIV on the auditory system have predominantly focused on the PAS. Additionally, language processing requires the efficient interaction between CAS brain regions and non-auditory regions. Investigating the functional connectivity (FC) within the CAS and between the CAS and non-auditory regions may reveal the influence of HIV on regions involved in auditory function.

Within a Bayesian stastical framework, we used resting-state functional magnetic resonance imaging (RS-fMRI) to map FC in the CAS as well as between CAS regions and non-auditory regions of 11-year-old CPHIV. Graph theory was used to investigate the regional effects of HIV on functional brain network properties. Finally we explored the relationships between FC and neurocognitive outcomes relating to auditory and language processing. We hypothesized that CPHIV would show disruptions in FC between CAS regions as well as between CAS and non-auditroy regions. Secondly, we hypothesized that in CPHIV, regional brain network properties would be altered compared to their uninfected peers (CHUU). Finally we hypothesized that FC and functional network regional outcomes would be related to neurocognitive outcomes.

Our investigation revealed lower FC of the primary auditory cortex (PAC) in CPHIV as well as disruptions in FC between CAS regions (including the PAC) and non-auditry regions including hippocampal sub-regions, the lingual gyri and basal ganglia. Functional network analysis reavealed lower nodal degree and efficiency in CAS regions including the cochlear nucleus/superior olivary complex (CN/SOC) and the inferior colliculus (IC). We also report associations between the nodal efficiency of middle temporal and superior frontal regions and delayed recall, a neurocognitive marker of working memory, present in CHUU but not in CPHIV.

Our results demonstrate FC alterations in the PAC and between CAS regions and non-auditory regions involved in limbic, visual and motor processing, as well as disruptions to the regional properties of the CAS regions as part of the functional brain network. These results provide insight into the state of the CAS FC in the presence of HIV and its possible role in the hearing and language impairments seen in this population.
Phosphorylation-State Modulated Binding of HSP70: Structural Insights and Compensatory Protein Engineering
Authors: Stewart Mariah , Paththamperuma Chathura , McCann Colleen , Cottingim Kelsey , Zhang Huaqun , DelVecchio Rian , Peng Ivy , Fennimore Erica , Nix Jay C. , Saeed Morcos N , George Kathleen , Makaroff Katherine , Colie Meagan , Paulakonis Ethan , Almeida Michael F. , Afolayan Adeleye J , Brown Nicholas G , Page Richard C. , Schisler Jonathan C
Published: February 2025

Protein quality control is crucial for cellular homeostasis, involving the heat shock response, the ubiquitin-proteasome system, and the autophagy-lysosome pathway. Central to these systems are the chaperone homologs heat shock protein 70 (HSP70) and heat shock cognate 70 (HSC70), which manage protein folding and degradation. This study investigated the impact of the C-terminal phosphorylation of HSP70 on its interaction with the co-chaperone CHIP (C-terminus of HSC70 interacting protein), an E3 ligase that ubiquitinates protein substrates for degradation. Using both cell-free and cell-based approaches, including X-ray crystallography, biolayer interferometry, and live cell biocomplementation assays, we demonstrate that phosphorylation at HSP70 T636 reduces CHIP’s binding affinity, shifting the preference toward other co-chaperones like HOP. Structural analysis reveals that phosphorylation disrupts key hydrogen bonds, altering binding dynamics. We engineered a CHIP variant (CHIP-G132N) to restore binding affinity to phosphorylated HSP70. While CHIP-G132N effectively restored binding without additional functional domains, its effectiveness was diminished in full-length phosphomimetic constructs in cell-free and in-cell assays, suggesting that additional interactions may influence binding. Functional assays indicate that phosphorylation of HSP70 affects its stability and degradation, with implications for diseases such as cancer and neurodegeneration. Our findings highlight the complexity of chaperone-co-chaperone interactions and underscore the importance of post-translational modifications in regulating protein quality control mechanisms. By elucidating the molecular details of HSP70 and CHIP interactions, our study provides a foundation for developing therapeutic interventions for diseases characterized by proteostasis imbalance.
In vivodirected evolution of an ultra-fast RuBisCO from a semi-anaerobic environment imparts oxygen resistance
Authors: McDonald Julie L. , Shapiro Nathan P. , Whitney Spencer M. , Wilson Robert H. , Shoulders Matthew D.
Published: February 2025

Carbon dioxide assimilation by the enzyme Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (RuBisCO) underpins biomass accumulation in photosynthetic bacteria and eukaryotes. Despite its pivotal role, RuBisCO has a slow carboxylation rate () and is competitively inhibited by oxygen. These traits impose limitations on photosynthetic efficiency, making RuBisCO a compelling target for improvement. Interest in RuBisCO fromGallionellaceaebacteria, which comprise a dimer or hexamer of large subunits, arises from their nearly 5-fold higherthan the average RuBisCO enzyme. Here, a comprehensive kinetic analysis of aGallionellaceaeRuBisCO (GWS1B) reveals the fastest CO2fixation rate measured for this enzyme (25.8 s−1), and exposes an extreme sensitivity to oxygen inhibition, consistent with its evolution under semi-anaerobic environments. We used a novelin vivomutagenesis-mediated screening pipeline to evolve GWS1B over six rounds under oxygenic selection, identifying three catalytic point mutants with improved ambient carboxylation efficiency; Thr-29-Ala (T29A), Glu-40-Lys (E40K) and Arg-337-Cys (R337C). Full kinetic characterization showed that each substitution enhanced the CO2affinity of GWS1B under oxygenic conditions while simultaneously subduing oxygen affinity, leading to 24% (E40K), 9% (T29A) and 7% (R337C) enhancements in carboxylation efficiency under ambient O2. By contrast, under the near anaerobic natural environment ofGallionellaceae, the carboxylation efficiency of each mutant was impaired ∼16%. These findings demonstrate the efficacy of artificial directed evolution to access novel regions of catalytic space in RuBisCO, and a capacity for rapid evolution of kinetic traits in response to environmental change.

Significance

Given RuBisCO’s crucial role in carbon dioxide assimilation, addressing its slow carboxylation rate and oxygen inhibition is a significant challenge. Utilizing the fastest known, yet highly oxygen-sensitive, RuBisCO from the bacteriaGallionellaceae, we applied a novelin vivodirected evolution pipeline inEscherichia colito discover mutations that specifically enhance carboxylation efficiency under ambient oxygen, a condition distinct fromGallionellaceae’snatural semi-anaerobic environment. Our findings underscore the potential of directed evolution to unlock new catalytic capabilities for RuBisCO, with implications for both fundamental research and practical agricultural applications.
Biological function and mechanism offlpLgene in regulating pathogenicity ofAeromonas hydrophila
Authors: Jiao Hanyang , Liu Kemei , Liao Ziyi , Naseer Adeeba , Ye Hua , Xu Hao , Li Yun , Yu Yongyao , Mei HuiQing , Wu Ronghua
Published: February 2025

Aeromonas hydrophilais human-animal commensal bacterium that seriously threatens the development of aquaculture and human health. Type IV pili (T4P) are essential for bacterial physiological function. The relationship between the molecular mechanism offlpLgene affiliated to T4P and the pathogenicity is still unclear. In the research,A. hydrophilawith a genetically stable deletion offlpLgene (ΔflpL) was constructed. The median lethal dose of ΔflpLfor Crucian carp was 4.87 times higher compared to wild-type strain, suggesting that ΔflpLsignificantly reduced pathogenicity. The attenuation may be attributed to a reduced capacity for biofilm formation and downregulation of the expression levels of virulence-related genes in ΔflpL. Meanwhile, the significant increase in swimming capacity and adhesion can be related to the upregulation offlpC, tapM, tapBandtapPgenes. In conclusion,flpLgene plays essential role in the pathogenicity, adhesion, motility, and capacity for biofilm formation inA. hydrophila. The research aims to clarify the pathogenesis ofA. hydrophila, and lay the foundation for developing live attenuated vaccines through the targeted modificationflpLgene.
A comparison of short- and long-read whole genome sequencing for microbial pathogen epidemiology
Authors: Schiffer Andrea M. , Rahman Arafat , Sutton Wendy , Putnam Melodie L. , Weisberg Alexandra J.
Published: February 2025

Whole genome sequencing provides the highest resolution for characterizing pathogen evolution, epidemiology, and diagnostics. Genome assemblies contain information on the identity and potential phenotypes of a pathogen. Likewise, variant calling can inform on transmission patterns and evolutionary relationships. Recent improvements in Oxford Nanopore long-read sequencing have made its use attractive for genomic epidemiology. However, the accuracy and optimal strategy for analysis of Nanopore reads remains to be determined. We compared the use of Illumina short reads and Oxford Nanopore long reads for genome assembly and variant calling of phytopathogenic bacteria. We generated short- and long-read datasets for diverse phytopathogenicAgrobacteriumstrains. We then analyzed these data using multiple pipelines designed for either short or long reads and compared the results. We found that assemblies made from long reads were more complete than those made from short-read data and contained few sequence errors. Variant calling pipelines differed in their ability to accurately call variants and infer genotypes from long reads. Results suggest that computationally fragmenting long reads can improve the accuracy of variant calling in population-level studies. Using fragmented long reads, pipelines designed for short reads were more accurate at recovering genotypes than pipelines designed for long reads. Further, short- and long-read datasets can be analyzed together with the same pipelines. These findings show that Oxford Nanopore sequencing is accurate and can be sufficient for microbial pathogen genomics and epidemiology. Ultimately, this enhances the ability of researchers and clinicians to understand and mitigate the spread of pathogens.
Key drivers affecting safety intervention success: evidence from Thai construction industry
Authors: Kurakaew Nuanan , Hadikusumo Bonaventura
Published: February 2025

Purpose

Safety interventions are a crucial component of organizational strategy, which are aimed at mitigating factors that compromise workplace safety. In the construction industry, these interventions are vital owing to the high-risk nature of construction activities. For developing effective safety interventions, the underlying factors that drive the need for these interventions must be understood. This study identifies and analyzes the critical factors driving safety interventions in Thai construction projects, focusing on both situational and organizational factors.

Design/methodology/approach

A survey conducted with a questionnaire among medium- to large-sized building contractors in Bangkok and nearby areas garnered 98 project responses. To validate the constructs of reasons for safety interventions and identify critical safety practices, the data were analyzed using confirmatory factor analysis and structural equation modeling.

Findings

The results indicate that organizational factors, positively influenced by situational factors, have a direct effect on safety interventions. Successful safety interventions can be obtained by focusing on five key organizational factors: safety as a core value, continuous improvement plans, leadership and management support, safety strategies and policies and safety committees.

Originality/value

These results provide valuable insights for construction site management, providing guidance on improving safety interventions via the effective utilization of these critical factors.
Exploring the dynamics of student learning behavior in higher education: an expanded theory of reasoned action approach
Authors: Bhojak Nimesh P. , Momin Mohammadali , Joshi Brijeshkumar H.
Published: February 2025

Purpose

This research aims to enhance the model of student learning behavior by expanding the traditional theory of reasoned action (TRA) to incorporate variables such as student mental well-being (SMW), attitude, subjective norms (SNB), perceived behavioral control (PBC) and climate change concerns. The study examines students’ intentions as a mediator variable and student area as a moderator variable in student learning behaviors.

Design/methodology/approach

A structured questionnaire was administered to 610 higher education students in Gujarat, exploring variables related to student characteristics, mental well-being, attitudes, SNB, PBC, Climate change concerns (CML), change concerns and intentions to study. Data analysis involved descriptive statistics, exploratory factor analysis and structural equation modeling with mediation and moderation analyses using SPSS 22 and AMOS 26.

Findings

The empirical findings support the hypothesized relationships within the expanded model, indicating significant contributions of SMW, attitude, SNB, PBC and CML to forming solid intentions to pursue education. Additionally, the study reveals a positive association between intention and subsequent learning behavior moderated by the student residence area.

Research limitations/implications

The study confirms the proposed relationships within the expanded model, with SMW significantly influencing students’ academic intentions. Factors like attitude, SNB and climate change are crucial in shaping educational pursuits. The research enriches educational psychology by detailing the complex influences on student learning behavior, offering insights for enhancing educational strategies and outcomes as the academic environment evolves.

Originality/value

This research offers an innovative approach by expanding the traditional TRA to explore the influences on student learning behavior in education comprehensively. Integrating variables such as SMW, attitude and CML provides a nuanced understanding, contributing to theoretical development and practical educational implications.
Smart living services’ factors and influences on subjective well-being and intention to use
Authors: Lu Hsiao-Han , Huang Wei-Jen
Published: February 2025

Purpose

This study aims to examine the effects of network externalities and diffusion of innovation on users’ perceived usefulness and perceived enjoyment, and in turn subjective well-being and intention to use in the smart living context.

Design/methodology/approach

To explore different types of smart living services, the data collected come from surveying 512 users of smart home services and 570 users of smart living apps. Structural equation modeling is used to analyze the data, and post hoc interviews are conducted to provide insights into our conceptual model of smart living services.

Findings

Compatibility and perceived service complementarity are the most influential determinants of users’ perceived usefulness and perceived enjoyment toward smart living services. Perceived usefulness has a greater impact on users’ intention to use and their subjective well-being than perceived enjoyment. Interestingly, perceived enjoyment exerts a stronger influence on subjective well-being than on intention to use.

Originality/value

This study is one of the first to provide empirical evidence in the context of smart living services, contributing to transformative service literature by extending the understanding of technology use and its influence on user well-being into a less explored service context. This study also advances users’ intention to use and subjective well-being of technology adoption in the service context by integrating perspectives from network externalities and diffusion of innovation.
Stakeholder activities in PCAOB audit standard setting: a manual content analysis of comment letter submissions
Authors: Yang Xiaoshuai , Zhang Joseph H.
Published: February 2025

Purpose

The purpose of this study is to analyze comment letters on Docket 034, which proposes reforms to audit reports, to shed light on the actions of various stakeholder groups in the Public Company Accounting Oversight Board (PCAOB)’s standard-setting process. The study identifies stakeholder groups, examines the timing of their involvement, and evaluates their arguments and lobbying efforts to influence regulatory outcomes.

Design/methodology/approach

This paper examines stakeholders’ behaviors in submitting comment letters during the PCAOB’s public consultation period for its rulemaking and their influence on regulatory outcomes. Stakeholder participation in the PCAOB’s rulemaking process is analyzed through a content analysis of 489 comment letters submitted to PCAOB’s Docket 034, using manual content analysis. Stakeholder groups are identified, including accounting professionals, financial statement preparers, financial statement users, regulators and academics. Argument strategies, such as economic, conceptual or a combination of both approaches, are also identified.

Findings

This paper finds that accounting professionals and preparers submit more comment letters than the other stakeholder groups. There is a significant association between stakeholder groups and their lobbying position across issues. Preparers take negative positions on all issues except independence, whereas users support all issues. There is also a significant association between stakeholder groups and their argument strategies, and the significant differences lie in preparers and accounting professionals. Preparers primarily rely on economic arguments, such as costs or time. At the same time, accounting professionals use economic and conceptual arguments (such as violating the FASB conceptual framework) to justify their positions.

Originality/value

To the best of the authors’ knowledge, this is the first study to examine lobbying in the PCAOB’s due process, including all stakeholder groups. The PCAOB’s audit standard-setting process and public consultation via the online docket system promote transparency and the effectiveness of public participation. This study analyzes the nature and impact of stakeholder participation in this due process. Understanding lobbying in an audit standard setting enables the PCAOB and stakeholder groups to work more efficiently on regulatory reforms. This assessment of lobbying efforts in the USA complements and enriches the growing body of literature on lobbying efforts and audit policy reforms across countries. Second, by extending the current literature, this study examines the complexities of lobbying through a detailed content analysis of comment letters. This approach provides insights into the properties of lobbying about stakeholder groups, the scope of lobbying, argument strategies, opinions and consultation periods.