bluuebunny/crossref_metadata_2025 huggingface dataset:
Cryo-EM structures of the MnmE-MnmG complex reveal large conformational changes and provide new insights into the mechanism of tRNA modification
Authors: Maes Laila , Martin Ella , Bickel David , Claeys Siemen , Vranken Wim , Fislage Marcus , Galicia Christian , Versées Wim
Published: December 2024

MnmE and MnmG form a conserved protein complex responsible for the addition of a 5-carboxymethylaminomethyl (cmnm5) group onto the wobble uridine of several tRNAs. Within this complex, both proteins collaborate intensively to catalyze a tRNA modification reaction that involves glycine as a substrate in addition to three different cofactors, with FAD and NADH binding to MnmG and methylenetetrahydrofolate (5,10-CH2-THF) to MnmE. Without structures of the MnmEG complex it remained enigmatic how these substrates and co-factors can be brought together in a concerted manner. Prior SAXS data suggested that the MnmE (α2) and MnmG (β2) homodimers can adopt either an α2β2or α4β2complex, depending on the nucleotide state of MnmE. Here, we report the cryo-EM structures of the MnmEG complex in the α2β2and α4β2oligomeric states. These structures reveal that MnmE undergoes large conformational changes upon interaction with MnmG, resulting in an asymmetric MnmE dimer. In particular, the functionally important C-terminal helix of MnmE relocates from the 5,10-CH2-THF binding pocket of MnmE to the FAD binding pocket of MnmG, thus suggesting a mechanism for the transfer of an activated methylene group from one active site to the other. Together, these findings provide crucial new insights into the MnmEG-catalyzed reaction.

Graphical abstract
Highly sensitive reverse transcription loop-mediated isothermal amplification for detecting and identifying groundnut ringspot and tomato spotted wilt orthotospoviruses
Authors: de Breuil Soledad , López Salvador , Dottori Carolina , Nome Claudia , Adkins Scott
Published: December 2024

Orthotospovirus arachianuli(groundnut ringspot virus, GRSV) andOrthotospovirus tomatomaculae(tomato spotted wilt virus, TSWV) represent a threat to several agricultural crops worldwide. The management of the diseases they cause is particularly challenging due to their wide host range and transmission by thrips vectors. Accurate diagnosis and early detection are crucial, especially considering the limitations of conventional serological and molecular methods. This study introduces reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a reliable alternative for detecting and identifying GRSV and TSWV in tomato, pepper, and peanut plants. The designed primer sets specifically targeted and amplified fragments of the viral RNA S segment. RT-LAMP reactions produced negative results in the healthy plants and exhibited no cross-reactivity with closely related orthotospoviruses or viruses from other genera. Compared to RT-PCR, RT-LAMP exhibited superior sensitivity, detecting viral RNA at concentrations 100 times lower. Field testing on symptomatic plants further confirmed the effectiveness of this technique. Overall, this study highlights RT-LAMP as a rapid, species-specific, and highly sensitive tool for the early detection of GRSV and TSWV in economically important crops, offering a promising solution for improved disease management.
Efficient synthesis of arabinosyl nucleosides via active site engineering of theLeishmania mexicanapurine 2′-deoxyribosyltranferase
Authors: Cecchini Davide A. , Acosta Javier , Saiz-Álvarez Laura P. , Ortega Carmen , Kaminski Pierre Alexandre , Fernández-Lucas Jesús , Hidalgo Aurelio
Published: December 2024

Even though 2′-deoxyribosyltransferases (NDTs) have emerged as promising and eco-friendly catalysts for synthesizing different 2’-deoxynucleoside analogs, their limited activity towards substrates featuring modifications at the 2′ -C and 3′ -C positions of the ribose moiety significantly restrict their potential application in the pharmaceutical industry. Herein we report two engineered variants fromLeishmania mexicanapurine deoxyribosyltransferase (LmPDT) with the highest reported arabinosyltransferase activity for an NDT, achieved through a semi-rational design approach. The resulting variants,LmPDTN56L andLmPDTN56C, display up to 13.5- and 30-fold enhanced activity on the synthesis of vidarabine compared to the wild-type enzyme. Moreover, thermal unfolding and thermal challenge experiments revealed that the improvement in arabinosyl transferase activity did not result in a stability trade-off, withTmvalues similar to the wild-type enzyme and similar activity retention at 40 °C. After biochemical characterization, the optimal reaction parameters for variantLmPDTN56C were determined to be pH 6 and a temperature interval from 30 to 45 °C. Interestingly, under optimal operational conditions (40 °C, 50 mM MES buffer pH 6) the initial 30-fold enhancement observed forLmPDTN56C escalated to a remarkable 40-fold improvement. This comprehensive study elucidates the potential of the engineeredLmPDT variants for efficient and tailored biocatalytic synthesis of arabinosyl nucleosides, paving the way for enhanced applications in nucleoside analog production.
Sortase A-mediated farnesylation of Cdc42in vitro
Authors: Tschirpke Sophie , Hettema Nynke M. , Spitzbarth Benjamin , Eelkema Rienk , Laan Liedewij
Published: December 2024

Cdc42, a Rho-family GTPase, plays a pivotal role in establishing polarity inSaccharomyces cerevisiaeby accumulating on the membrane at the site of bud emergence. Cdc42’s ability to bind to membranes, mediated by prenylation, is essential for its function. Prenylation involves either the post-translational addition of a 15-carbon farnesyl group or a 20-carbon geranylgeranyl group to Cdc42’s C-terminus. One of the mayor challenges in studying the biophysical and biochemical interactions of Cdc42 at the polarity spotin vitrois obtaining prenylated Cdc42, due to labor-intensive and not easily reproducible traditional methods. Here, we present a streamlined, Sortase A-based approach to farnesylate Cdc42in vitro. This method leveragesE. coli-expressed Cdc42 with a Sortase A recognition motif, facilitating efficient and accessible farnesylation and purification using a purification tag-based strategy. The farnesylated Cdc42 retains functionality, as evidenced by GTP-dependent membrane binding, making it suitable for further biophysical and biochemical investigations. Additionally, our method can be easily adapted to yield geranyl-geranylated Cdc42.
Computer-guided design of Z domain peptides with improved inhibition of VEGF
Authors: Geist Carsten , Useini Abibe , Kazimir Aleksandr , Kuempfel Richy , Meiler Jens , Lamers Christina , Kalkhof Stefan , Kuenze Georg
Published: December 2024

Computational protein design is becoming increasingly helpful in the development of new protein therapeutics with enhanced efficacy, specificity, and minimal side effects, for precise modulation of biological pathways. In vascular biology, the interaction between vascular endothelial growth factor A (VEGFA) and its receptors (VEGFR1-R3) is a pivotal process underlying blood vessel growth. Dysregulation of this pathway contributes to diseases such as cancer and diabetic retinopathy. Existing VEGFA inhibitors are effective but have limitations, driving interest in peptide-based therapeutics. Peptide inhibitors offer advantages, including reduced toxicity, improved formulation flexibility, and enhanced stability. This study leverages computational tools, particularly ProteinMPNN and Rosetta, to design optimized peptide-based VEGFA inhibitors. Building on the existing peptide templates mini-Z-1 and Z-1-2, new sequences were computationally predicted and experimentally validated. A novel peptide with improved affinity (KD = 6.2 µM) compared to mini-Z-1 (KD = 9.3 µM) was found, requiring only one round of design and testing. The integration of ProteinMPNN and Rosetta enabled a rapid and cost-effective pipeline for designing potent VEGFA inhibitors, underscoring the potential of computational peptide design in developing next-generation therapeutics targeting angiogenesis-dependent diseases.
Protection againstN. gonorrhoeaeinduced by OMV-based Meningococcal Vaccines are associated with cross-species directed humoral and cellular immune responses
Authors: Zhu Weiyan , Waltmann Andreea , Little Marguerite B. , Connolly Kristie L. , Matthias Kathryn A. , Thomas Keena S. , Gray Mary C. , Sikora Aleksandra E. , Criss Alison K. , Bash Margaret C. , Macintyre Andrew N. , Jerse Ann E. , Duncan Joseph A.
Published: December 2024

Limited protective immunologic responses to naturalN. gonorrhoeaeinfection and a lack of knowledge about mechanisms of protection have hampered development of an effective vaccine. Recent studies in humans and mice have found meningococcal outer membrane vesicle-containing vaccines (OMV) induce cross species immune responses against gonococci and are associated with protection. The exact mechanisms or how humoral and cellular immunity are related to protection, remain unclear. To study this, we immunized mice with two meningococcal OMV-containing vaccines known to accelerate clearance ofN. gonorrhoeae, 4CMenB and OMV from an engineeredN. meningitidisstrain lacking major surface antigens PorA, PorB, and Rmp (MC58 ΔABR). We assessed serologic and cellular immune signatures associated with these immunizations and assessed bacterial clearance in the mice using a vaginal/cervical gonococcal infection model. Mice immunized with 4CMenB or MC58 ΔABR demonstrated shortened courses of recovery of vaginalN. gonorrhoeaecompared to control mice immunized with alum alone. Vaccination with 4CMenB or MC58ΔABR OMV elicited serum and vaginal cross-reactive anti-Ng-OMV antibody responses that were augmented after vaginal challenge withN. gonorrhoeae. Further, splenocytes in 4CMenB and MC58 ΔABR immunized mice exhibited elevated cytokine production after restimulation with heterologousN. gonorrhoeaeOMV when compared to splenocytes from Alum immunized mice. We further tested for correlations between bacterial burden and the measured anti-gonococcal immune responses within each vaccination group and found different immunologic parameters associated with reduced bacterial burden for each vaccine. Our findings suggest the cross-protection against gonococcal infection induced by different meningococcal OMV vaccines is likely multifactorial and mediated by different humoral and cellular immune responses induced by these two vaccines.
Sequence Composition Dictates Condensate Miscibility
Authors: Pei Gaofeng , Wang Xinxin , Geng Danqian , Chen Zhuo , Xu Weifan , Li Tingting , Li Pilong
Published: December 2024

Numerous biomolecular condensates coexist within cells, yet the mechanisms governing their mixing and demixing remain elusive. To investigate how the amino acid composition of intrinsically disordered regions (IDRs) affects condensate coexistence, we paired and tested 28 IDRs in 378 different combinations. Our results reveal that IDRs enriched in serine or aromatic amino acids tend to form miscible condensates. Conversely, IDRs with high charge levels form immiscible condensates, even when the serine levels are artificially boosted. Additionally, phosphorylation acts as a switch, modulating condensate miscibility. We also observed that the miscibility between transcription factor condensates and Pol II condensates profoundly influences transcription. We engineered transcription factors by increasing serine content, enhancing both their miscibility with Pol II and their transcriptional activity. However, introducing high levels of charge had the opposite effect. These findings shed light on the fundamental mechanisms controlling condensate miscibility and offer insights for designing specific functional condensates.
Renovating the Barnes maze for mouse models of Dementia with STARR FIELD: A 4-day protocol that probes learning rate, retention and cognitive flexibility
Authors: Bertolli Aimee , Halhouli Oday , Liu-Martínez Yiming , Blaine Brianna , Thangavel Ramasamy , Zhang Qiang , Emmons Eric , Narayanan Nandakumar S. , Gumusoglu Serena B , Geerling Joel C. , Aldridge Georgina M
Published: December 2024

Land-based mazes that require spatial cues to identify the location of a hiding-place are a low-stress method to evaluate learning rate and memory retention in mice. One version, the Barnes maze, allows quantification of naturalistic exploratory behaviors not evident in water-based tasks. As the task relies on innate behaviors, it does not require overtraining, making it more feasible to examine early learning and non-memory executive functions that are characteristic of some non-amnestic dementias. However, because it is difficult to hide odor cues in the traditional version of the maze, learning rate during individual trials can be difficult to interpret. We designed and tested the use of 3D-printed escape shuttles that can be made in duplicate, as well as a docking tunnel that allows mice to self-exit the maze to improve reproducibility and limit experimenter influence. In combination with maze turning and escape tunnel caps, we show our shuttles mitigate the possibility of undesired cues. We then compare use of our 4-day protocol across several mouse models of cognitive impairment. We demonstrate an additional stage, the STARR protocol (Spatial Training and Rapid Reversal), to better challenge executive functions such as working memory and behavioral flexibility. We examine commonly used outcome measures across mice with and without access to spatial cues, as well as across mouse models of cognitive impairment to demonstrate the use of our 4-day protocol. Overall, this protocol provides detailed instructions to build and perform a robust spatial maze that can help expand the range of deficits identified. Our findings will aid in interpretation of traditional protocols, as well as provide an updated method to screen for both amnestic and non-amnestic cognitive changes.
Hypocretin Receptor 1 Blockade Early in Abstinence Prevents Incubation of Cocaine Seeking and Normalizes Dopamine Transmission
Authors: Clark Philip J. , Migovich Volodar M. , Das Sanjay , Xi Wei , Kortagere Sandhya , España Rodrigo A.
Published: December 2024

Abstinence from cocaine use has been shown to elicit a progressive intensification or incubation of cocaine craving/seeking that is posited to contribute to propensity for relapse. While the mechanisms underlying incubation of cocaine seeking remain elusive, considerable evidence suggests that abstinence from cocaine promotes mesolimbic dopamine adaptations that contribute to exaggerated cocaine seeking. Consequently, preventing these dopamine adaptations may reduce incubation of cocaine seeking and thereby reduce the likelihood of relapse. In the present studies, we first examined if incubation of cocaine seeking was associated with aberrant dopamine transmission in the nucleus accumbens after seven days of abstinence from intermittent access to cocaine. Given the extensive evidence that hypocretins/orexins regulate motivation for cocaine, we then examined to what extent hypocretin receptor 1 antagonism on the first day of abstinence prevented incubation of cocaine seeking and dopamine adaptations later in abstinence. Results indicated that abstinence from intermittent access to cocaine engendered robust incubation of cocaine seeking in both female and male rats. We also observed aberrant dopamine transmission, but only in rats that displayed incubation of cocaine seeking. Further, we showed that a single injection of the hypocretin receptor 1 antagonist, RTIOX-276, on the first day of abstinence prevented incubation of cocaine seeking and aberrant dopamine transmission. These findings suggest that hypocretin receptor 1 antagonism may serve as a viable therapeutic for reducing cocaine craving/seeking, thus reducing the likelihood of relapse.
Circadian Activity Predicts Breeding Phenology in the Asian Burying Beetle Nicrophorus nepalensis
Authors: Chen Hao , Rubenstein Dustin R. , Mai Guan-Shuo , Chang Chung-Fan , Shen Sheng-Feng
Published: December 2024

Climate change continues to alter breeding phenology in a range of plant and animal species across the globe. Traditional methods for assessing when organisms reproduce often rely on time-intensive field observations or destructive sampling, creating an urgent need for efficient, non-invasive approaches to assess reproductive timing. Here, we examined three populations of the Asian burying beetleNicrophorus nepalensisfrom subtropical Okinawa (500 m) and Taiwan mountains (1100-3200 m) that were reared under contrasting photoperiods in order to develop a predictive framework linking circadian activity to breeding phenology. Using automated activity monitors, we quantified adult circadian rhythms and employed machine learning to predict breeding phenology (seasonal versus year-round breeders) from behavior alone. Our model achieved 95% accuracy under long-day conditions using just three behavioural features, and notably, maintained 76% accuracy under short-day conditions when both types are reproductively active, revealing persistent behavioural differences between breeding strategies. These results demonstrate how integrating behavioural monitoring with machine learning can provide both a rapid, scalable method for tracking population responses to climate change and novel insights into species’ adaptive responses to shifting seasonal cues across different elevational gradients in their native range.
Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes
Authors: Magri Marta S. , Voronov Danila , Foley Saoirse , Martínez-García Pedro Manuel , Franke Martin , Cary Gregory A. , Santos-Pereira José M. , Cuomo Claudia , Fernández-Moreno Manuel , Gil-Galvez Alejandro , Acemel Rafael D. , Paganos Periklis , Ku Carolyn , Ranđelović Jovana , Rusciano Maria Lorenza , Firbas Panos N. , Gómez-Skarmeta José Luis , Hinman Veronica F. , Arnone Maria Ina , Maeso Ignacio
Published: December 2024

Despite the growing abundance of sequenced animal genomes, we only have detailed knowledge of regulatory organization for a handful of lineages, particularly flies and vertebrates. These two groups of taxa show contrasting trends in the molecular mechanisms of 3D chromatin organization and long-term evolutionary dynamics of cis-regulatory element (CREs) conservation. To help us identify shared versus derived features that could be responsible for the evolution of these different regulatory architectures in animals, we studied the evolution and organization of the regulatory genome of echinoderms, a lineage whose phylogenetic position and relatively slow molecular evolution has proven particularly useful for evolutionary studies. First, using PacBio and HiC data, we generated new reference genome assemblies for two species belonging to two different echinoderm classes: the purple sea urchinStrongylocentrotus purpuratusand the bat sea starPatiria miniata. Second, we characterized their 3D chromatin architecture, identifying TAD-like domains in echinoderms that, like in flies, do not seem to be associated with CTCF motif orientation. Third, we systematically profiled CREs during sea star and sea urchin development using ATAC-seq, comparing their regulatory logic and dynamics over multiple developmental stages. Finally, we investigated sea urchin and sea star CRE evolution across multiple evolutionary distances and timescales, from closely related species to other echinoderm classes and deuterostome lineages. This showed the presence of several thousand elements conserved for hundreds of millions of years, revealing a vertebrate-like pattern of CRE evolution that probably constitutes an ancestral property of the regulatory evolution of animals.
Gene mobility elements mediate cell type specific genome organization and radial gene movementin vivo
Authors: Lucas Tanguy , Wang Lin-Ing , Glass-Klaiber Juniper , Quiroz Elvis , Patra Sofiya , Molotkova Natalia , Kohwi Minoree
Published: December 2024

ABSTRACT

Understanding the level of genome organization that governs gene regulation remains a challenge despite advancements in chromatin profiling techniques. Cell type specific chromatin architectures may be obscured by averaging heterogeneous cell populations. Here we took a reductionist perspective, starting with the relocation of thehunchbackgene to the nuclear lamina inDrosophilaneuroblasts. We previously found that this event terminates competence to produce early-born neurons and is mediated by an intronic 250 base-pair element, which we term gene mobility element (GME). Here we found over 800 putative GMEs globally that are chromatin accessible and are Polycomb (PcG) target sites. GMEs appear to be distinct from PcG response elements, however, which are largely chromatin inaccessible in neuroblasts. Performingin situHi-C of purified neuroblasts, we found that GMEs form megabase-scale chromatin interactions, spanning multiple topologically associated domain borders, preferentially contacting other GMEs. These interactions are cell type and stage-specific. Notably, GMEs undergo developmentally- timed mobilization to/from the neuroblast nuclear lamina, and domain swapping a GFP reporter transgene intron with a GME relocates the transgene to the nuclear lamina in embryos. We propose that GMEs constitute a genome organizational framework and mediate gene-to-lamina mobilization during progenitor competence state transitionsin vivo.
Sex-and Stress-Dependent Plasticity of a Corticotropin Releasing Hormone / GABA Projection from the Basolateral Amygdala to Nucleus Accumbens that Mediates Reward Behaviors
Authors: Taniguchi Lara , Goodpaster Caitlin , De Carvalho Gregory Bello , Birnie Matthew T , Chen Yuncai , Chen Lulu , Baram Tallie Z , DeNardo Laura A
Published: December 2024

Background: Motivated behaviors are executed by refined brain circuits. Early-life adversity (ELA) is a risk for human affective disorders involving dysregulated reward behaviors. In mice, ELA causes anhedonia-like behaviors in males and augmented reward motivation in females, indicating sex-dependent disruption of reward circuit operations. We recently identified a corticotropin-releasing hormone (CRH) expressing GABAergic projection from basolateral amygdala (BLA) to nucleus accumbens (NAc) that governs reward-seeking deficits in adult ELA males, but not females. Methods: To probe the sex-specific role of this projection in reward behaviors, adult male and female CRH-Cre mice raised in control or ELA conditions received excitatory or inhibitory Cre-dependent DREADDs in BLA, and then clozapine N-oxide or vehicle to NAc medial shell during reward behaviors. We determined the cell identity of the projection using immunostaining and electrophysiology. Using tissue clearing, light sheet fluorescence microscopy and deep learning pipelines, we mapped brain-wide BLA CRH+ axonal projections to uncover sex differences in innervation. Results: Chemogenetic manipulations in male mice demonstrated inhibitory effects of the CRH+ BLA-NAc projection on reward behaviors, whereas neither excitation nor inhibition influenced female behaviors. Molecular and electrophysiological cell-identities of the projection did not vary by sex. By contrast, comprehensive whole-brain mapping uncovered significant differences in NAc innervation patterns that were both sex and ELA-dependent, as well as selective changes of innervation of other brain regions. Conclusions: The CRH/GABA BLA-NAc projection that influences reward behaviors in males differs structurally and functionally in females, uncovering potential mechanisms for the profound sex-specific impacts of ELA on reward behaviors.
TTF2 promotes replisome eviction from stalled forks in mitosis
Authors: Can Geylani , Shyian Maksym , Krishnamoorthy Archana , Lim Yang , Wu R. Alex , Zaher Manal S. , Raschle Markus , Walter Johannes C. , Pellman David S.
Published: December 2024

When cells enter mitosis with under-replicated DNA, sister chromosome segregation is compromised, which can lead to massive genome instability. The replisome-associated E3 ubiquitin ligase TRAIP mitigates this threat by ubiquitylating the CMG helicase in mitosis, leading to disassembly of stalled replisomes, fork cleavage, and restoration of chromosome structure by alternative end-joining. Here, we show that replisome disassembly requires TRAIP phosphorylation by the mitotic Cyclin B-CDK1 kinase, as well as TTF2, a SWI/SNF ATPase previously implicated in the eviction of RNA polymerase from mitotic chromosomes. We find that TTF2 tethers TRAIP to replisomes using an N-terminal Zinc finger that binds to phosphorylated TRAIP and an adjacent TTF2 peptide that contacts the CMG-associated leading strand DNA polymerase ε. This TRAIP-TTF2-pol ε bridge, which forms independently of the TTF2 ATPase domain, is essential to promote CMG unloading and stalled fork breakage. Conversely, RNAPII eviction from mitotic chromosomes requires the ATPase activity of TTF2. We conclude that in mitosis, replisomes undergo a CDK- and TTF2-dependent structural reorganization that underlies the cellular response to incompletely replicated DNA.
A tool to automate assessment of regional brain atrophy in mouse models of neurodegenerative disease
Authors: Moldenhauer Samuel , Potluri Nalini , Xie Yuanyun , Southwell Amber L
Published: December 2024

As life expectancy rises, so too does the prevalence of neurodegenerative diseases. Neurodegeneration causes progressive regional brain atrophy, typically initiating prior to symptom onset. Researchers measure the impact of potential treatments on atrophy in mouse models to assess their effectiveness. This is important because treatments designed to combat neuropathology are more likely to modify the disease, per contra to symptom management. Magnetic resonance imaging, while accurate in measurement of brain region structure volumes, is prohibitively expensive. Conversely, stereological volume assessment, the process of estimating the volume of individual 3D brain regions from imaged 2D brain sections, is more commonly used. This involves manually tracing brain region(s) of interest in regularly spaced imaged cross-sections to determine their 2D area, followed by application of the Cavalieri principle to estimate the volume. The pertinent caveats of this approach are the labor-intensive manual tracing process, and potential inaccuracies that arise due to human variation. To overcome these challenges, we have created a Neuropathology Assessment Tool (NAT) to automate regional brain tracing and identification using artificial intelligence (AI) and concepts from topological data analysis. The NAT was validated by comparing manual and NAT analysis of striatal volume in Huntington disease model mice. The NAT detected striatal atrophy with higher efficiency, 93.8% agreement with manual measurements, and lower inter-group variability. The NAT will increase efficiency of preclinical neuropathology assessment, allowing for a greater number of experimental therapies to be tested and facilitating drug discovery intractable neurodegenerative diseases.
Mechanisms of Social Behavior in the Anti-Social Blind Cavefish (Astyanax mexicanus)
Authors: Sekulovski Britney , Miller Noam
Published: December 2024

The evolution of social behavior inAstyanax mexicanus, which exists as a sighted, surface-dwelling morph and a blind, cave-dwelling morph, provides a model for understanding how environmental pressures shape social behaviors. We compared the shoaling behavior of blind and surfaceA. mexicanusto that of zebrafish (Danio rerio), and examined the effects of nutritional state and the neuropeptides isotocin (IT) and arginine vasotocin (AVT) on their social behavior. Blind cavefish not only fail to form shoals, but actively avoid conspecifics, with hunger further diminishing their social cohesion. Administration of low doses of AVT and an IT antagonist partially restored social behavior in blind cavefish, reducing distances between individuals, whereas surface fish exhibited minimal or opposite responses to these hormonal manipulations. Our findings suggest that the loss of schooling behavior in blind cavefish is not a consequence of visual impairment alone, as they remain capable of detecting and responding to others. Instead, this behavior likely reflects an adaptive response to their resource-poor, predator-free cave environment, where shoaling may be disadvantageous. The differing responses to social hormones between the morphs indicate that blind cavefish may have lost the motivation to shoal rather than the ability, highlighting how ecological pressures can shape social behavior.
MortX: A Domain Generalization Benchmark for Mouse Cortex Segmentation and Registration
Authors: Iqbal Asim , Khan Romesa , Gasser Edith M. Schneider , Karayannis Theofanis
Published: December 2024

Mesoscale understanding of human brain development is crucial for understanding neurodevelopmental disorders. By applying AI techniques to analyze high-resolution, multi-modal brain imaging datasets across postnatal ages, researchers can study cortical development at the granular level. We introduce MortX, a benchmark dataset of the developing mouse cortex that captures multiple postnatal stages with annotations for distinct anatomical and functional subregions and layers. MortX features high-resolution imaging data including bright-field and fluorescence-labeled neuronal markers. We developed a standardized cortical atlas of genetic markers and manually registered it to brain section images for ground-truth labeling. The dataset serves as a benchmark for domain generalization in neuroimaging, enabling both classical and deep learning models to be trained on source brains and tested on unseen targets. Our results demonstrate generalized model performance and structural invariance across ages. We open-source MortX as a community resource for mouse brain segmentation and registration, emphasizing domain adaptation. This dataset addresses key challenges in mouse brain imaging and advances machine learning models that will help unravel neurodevelopmental disorders.
Individual uniqueness of connectivity gradients is driven by the complexity of the embedded networks and their dispersion
Authors: Serhan Yvonne , Darawshy Shaymaa , Wei Wei , Margulies Daniel S. , Nenning Karl-Heinz , Ovadia-Caro Smadar
Published: December 2024

Connectivity gradients are widely used to characterize meaningful principles of functional brain organization in health and disease. However, the degree of individual uniqueness and shared common principles is not yet fully understood. Here, we leveraged the Hangzhou test-retest dataset, comprising repeated resting-state fMRI scans over the span of one month, to investigate the balance between individual variation and shared patterns of brain organization. We quantified the short- and long-term stability for the first three connectivity gradients and used connectome fingerprinting to establish the associated individual identification rate. We found that all three connectivity gradients are highly correlated over both short and long time intervals, demonstrating connectome fingerprinting utility. Individual uniqueness was dictated by the complexity of the networks such that heteromodal networks had higher connectome fingerprinting rates than unimodal networks. Importantly, the dispersion of the gradient coefficients associated with canonical functional networks was correlated with identification rates, irrespective of the position along the gradients. Beyond individual uniqueness, between subject similarity was high along the first connectivity gradient, which captures the dissociation between unimodal and heteromodal cortices, and the second connectivity gradient, which differentiates sensory cortices. Our results support the usage of connectivity gradients for the purposes of both group comparisons and prediction of individual behaviours. Our work adds to existing knowledge on the shared versus unique organizational principles and offers insights into the importance of network dispersion to the individual uniqueness it carries.
No pains no gains: understanding the impacts of physician efforts in online reviews on outpatient appointment
Authors: Wu Pengkun , Wang Liuan , Jiang Jiuan , Yu Li
Published: December 2024

Purpose

This study aims to investigate the impact of physician efforts in online reviews on outpatient appointments, while also examining the moderating effect of physician title.

Design/methodology/approach

This study employs the heuristic-systematic model (HSM) to analyze the impact of physician efforts on outpatient appointments. Subsequently, a fixed effect model is employed to examine the research model using an 89-week panel dataset (from April 16, 2018 to December 29, 2019) comprising appointment and online review information pertaining to 8,157 physicians from a prominent online health community in China.

Findings

The findings suggest that physicians with lower professional titles exhibit a significantly higher inclination to enhance heuristic information (e.g. attracting helpful votes) compared to those with higher professional title. All physicians can enhance their outpatient appointments by dedicating efforts towards improving systematic review information, but physician title would weaken the relationship. Moreover, the effect of increasing review volume is considerably more substantial than that of increasing review length, which also surpasses the influence of providing managerial response.

Originality/value

Unlike previous studies that primarily focus on patients’ perspectives, this paper represents one of the pioneering effects to examine physicians’ engagement in online reviews.
Determinants of healthcare workers' job retention during the global health crisis: insights from a national survey in Canada
Authors: Habibov Nazim , Auchynnikava Alena , Lyu Yunhong
Published: December 2024

Purpose

The purpose of this study is to investigate the determinants of job retention intention among healthcare workers (HCWs) in Canada during the COVID-19 pandemic.

Design/methodology/approach

Data are from a large nationally representative cross-sectional survey conducted by the Canadian National Statistics Agency. Ordered logistic regression is estimated to find an association between job retention and its main determinants as gleaned from the literature while controlling for a wide range of pertinent covariates. Odds and standardized odds are reported and discussed.

Findings

The results suggest that worsening working conditions, changes in health and well-being and lack of organizational support weaken intentions regarding job retention. Being employed rather than self-employed and working as a nurse also weakens job retention.

Originality/value

This is the first research on the determinants of intentions regarding job retention in Canada using nationally representative data. It allows us to test and confirm the results of previous studies on a large sample of Canadian HCWs. The paper also discusses the implications of the findings for health management and administration.
Linking leader boundary spanning to task performance and its boundary conditions: a conservation of resources perspective
Authors: Kim Seckyoung Loretta , Mah Sunghyuck , Yoon Seoin , Yun Seokhwa
Published: December 2024

Purpose

Drawing on conservation of resources (COR) theory, this research aims to advance the current understanding of leader boundary spanning by examining its effect on task performance, psychological mechanism and boundary conditions.

Design/methodology/approach

The empirical data were gathered by a paper-and-pencil survey from 155 employee-supervisor dyads working in various industries.

Findings

Our results indicated that leader boundary spanning is positively related to task performance, mediated by employees’ enhanced self-efficacy. Moreover, the results indicated that the positive effect of leader boundary spanning on task performance via enhanced self-efficacy is strengthened when the level of abusive supervision is low or when the level of an employee’s emotional exhaustion is high.

Practical implications

Organizations should find a way to facilitate leaders to engage in boundary spanning behaviors since a leader’s boundary spanning behavior enhances task performance through employee’s self-efficacy. Additionally, it is crucial to establish policies and provide training sessions to reduce the occurrence of abusive supervision in the workplace.

Originality/value

This study gives insights into the current literature by uncovering whether, how and under what circumstances boundary spanning leaders exert influences on task performance via employees’ self-efficacy. Our results showed that the positive effect of leader boundary spanning is likely to be strengthened when boundary spanners do not abuse their employees or when employees are in need of additional resources.
Gut Microbiota and Metabolite Profiles Associated With Functional Constipation Severity
Authors: Wang Jiwei , He Jixin , Liu Dandan , Zhang Tao , Wu Yin , Xie Ming
Published: December 2024

Functional constipation (FC) is a common digestive disorder that affects patients' quality of life and is closely associated with intestinal tumors. This study used a cross‐sectional design to assess the changes of intestinal flora and metabolites in different severities of FC patients through 16S rRNA sequencing and metabolomics analysis. Results showed that patients with severe FC had significantly higher clinical and anxiety scores compared to those in the mild and moderate groups. The species richness of intestinal microorganisms in the severe FC group was also significantly higher, and obvious differences in the flora composition existed. Specifically, the Bacteroidota was more abundant in the severe FC group, which was a characteristic feature distinguishing severe FC. Metabolomic analyses also revealed metabolite differences among patients with mild‐to‐moderate and severe FC, with the severe FC group showing increased enrichment in L‐isoleucine biosynthesis and glycolysis metabolic pathways. The short‐chain fatty acid–targeted metabolome suggested that a decrease in butyric acid might be related to worsening constipation. This study suggests that specific flora and metabolic pathways could serve as potential diagnostic and therapeutic targets, thereby contributing to the development of new diagnostic and therapeutic approaches to improve the quality of life and therapeutic outcomes for FC patients.
RpoB H481Y Rifampicin Resistance Mutation‐Associated Oxidative Stress Sensitivity Reduces the Virulence of Staphylococcus aureus
Authors: Kano Tomonori , Ishikawa Kazuya , Imai Lina , Furuta Kazuyuki , Kaito Chikara
Published: December 2024

In this study, we have established a Staphylococcus aureus RpoB H481Y mutant strain and demonstrated that it is sensitive to menadione or hydrogen peroxide‐induced oxidative stress and exhibits reduced virulence against a silkworm infection model. Furthermore, the reduced virulence of the RpoB H481Y mutant was abrogated in the presence of N‐acetylcysteine, a reactive oxygen species scavenger. These results suggest that oxidative stress sensitivity caused by the RpoB H481Y rifampicin resistance mutation attenuates the virulence of S. aureus.
Industry Image Perceptions and Organizational Attractiveness: Results of an International Survey
Authors: Davies Samuel , Nguyen Thanh , Stoermer Sebastian , Froese Fabian Jintae , Budhwar Pawan
Published: December 2024

Extending the research on corporate brand image and recruitment, this study investigates the influence of industry image on organizational attractiveness in a cross–national context. Drawing from signaling theory and the application of the instrumental‐symbolic image framework, we apply an experimental vignette design in the renewable energy industry (REI) and the oil and gas exploration and production industry (OGI) with potential job applicants in France, Germany, and the United Kingdom. We conceptualize national context as collective signaling environments. Results from 550 respondents indicate that the REI and OGI differ in most of the instrumental and symbolic image dimensions. The instrumental image dimension of pay and the three symbolic image dimensions of sincerity, innovativeness, and prestige predict organizational attractiveness. Moreover, sincerity, innovativeness, and prestige carry a mediating effect in the link between industry affiliation and organizational attractiveness. Findings also demonstrate that image perceptions of the REI and OGI vary across countries such that the already more favorable image perceptions regarding the REI are for the most part even more pronounced in France. Implications for theory and tailored recommendations for practice are provided.
Long‐term quality of life in patients with bladder cancer following radical cystectomy
Authors: Akdemir Emine , Stuiver Martijn M. , van de Kamp Maaike W. , der Hulst Jolanda Bloos ‐ van , Mertens Laura S. , Hendricksen Kees , van Harten Wim H. , May Anne M. , Sweegers Maike G.
Published: December 2024

Objectives

To investigate changes in quality of life (QoL) up to 8 years after radical cystectomy (RC) and compare QoL after RC with a gender‐ and age‐matched Dutch normative population. Furthermore, we aimed to identify patient characteristics associated with QoL and QoL trajectories after RC.

Patients and Methods

Patients with bladder cancer were invited to complete QoL questionnaires at 3‐month intervals in the first year and yearly thereafter. Follow‐up data were available for a maximum of 8 years. We used linear mixed‐effect models to investigate changes in QoL subscales (physical functioning [PF], emotional functioning [EF], and QoL summary score [QoL‐sum]) over time, and to identify potential demographic and clinical correlates of QoL and QoL trajectories (i.e., interaction with time).

Results

Data from 278 patients was included. Post‐RC EF scores increased from 83.7 (95% confidence interval [CI] 81.7–85.6) to levels comparable to the normative population (90.1) 8 years after RC. PF (post‐RC: 82.4, 95% CI 78.5–86.3) and QoL‐sum (post‐RC: 88.2, 95% CI 85.2–91.2) remained lower compared to the normative population (88.9 and 91.4, respectively) 8 years after RC. Compared to patients with an American Society of Anesthesiologists (ASA) score of 1 at diagnosis, those with ASA score 2 or ASA score 3 had significant lower post‐RC PF (mean difference (MD) = −8 and −22, respectively; P < 0.001), EF (MD = −1 and −11; P = 0.5 and P < 0.01) and QoL‐sum (MD = −2 and −9; P = 0.2 and P < 0.01). In addition, patients with a higher ASA score had a worse QoL‐sum trajectory (Pinteraction = 0.01). Older patients had a worse PF trajectory (Pinteraction < 0.01) but higher post‐RC EF (P < 0.01).

Conclusions

Directly after RC, patients have lower PF, EF and QoL‐sum, compared to a normative population. Notably, EF recovers to normative levels over a period of 8 years after RC. Clinicians are encouraged to administer supportive care interventions to enhance the QoL for patients undergoing RC, especially targeting older patients and those with higher ASA scores.
Systematic drug screening and target analysis identify digitoxin as a potential therapy for uveal melanoma
Authors: Liu Huilin , Huang Chao , Liu Zhenni , Li Yuhan , Zhu Yanan , Gao Min , Chen Jing , Zhang Hui , Xiao Zhengtao , Zhao Wei
Published: December 2024

Background and Purpose

Cardiac glycosides (CGs), traditionally prescribed for heart failure and arrhythmias, show anticancer potential. However, their mechanisms for preferential inhibition of tumour tissue and constituent malignant cells are not fully elucidated. This study aims to elucidate the therapeutic benefits of CGs in targeting specific tumours and dissect their multi‐targeting mechanisms that confer their cytotoxicity against malignant cells.

Experimental Approach

We designed an integrated workflow to identify therapeutic CGs with high toxicity to certain cancers, investigating their multi‐target effects, assessing their toxicity to malignant cells and analysing the prognostic relevance of CGs' target genes. The computational findings were confirmed through gene knockdown, cell viability assays, reactive oxygen species (ROS) measurements and so forth.

Key Results

CGs modulate multiple genes crucial for ion homeostasis, oxidative stress and apoptosis, with a particularly strong inhibitory effects on uveal melanoma (UVM). Notably, digitoxin suppresses UVM cell proliferation and induces ROS levels by simultaneously targeting STAT3 and KLF5. Single‐cell transcriptomic analysis revealed that malignant cells are likely more vulnerable to CGs due to their higher expression of CG target genes compared with surrounding cells in the UVM microenvironment.

Conclusions and Implications

Given UVM's limited options, our study highlights the potential of digitoxin as a promising novel therapeutic agent for this aggressive and rare ocular cancer. Our comprehensive approach is effective in identifying the potent, cancer‐specific therapeutic agents from herbal plants.
Enhancing logistics through a vehicle routing problem with deliveries, pickups, and backhauls
Authors: Santos Maria João , Jorge Diana , Bonomi Valentina , Ramos Tânia , Póvoa Ana
Published: December 2024

Today, logistics activities are driven by the pressing need to simultaneously increase efficiency, reduce costs, and promote sustainability. In our research, we tackle this challenge by adapting a general vehicle routing problem with deliveries and pickups to accommodate different types of customers. Customers requiring both delivery and pickup services are mandatory, while those needing only a pickup service (backhaul customers) are optional and are only visited if profitable. A mixed‐integer linear programming model is formulated to minimize fuel consumption. This model can address various scenarios, such as allowing mandatory customers to be served with combined or separate delivery or pickup visits, and visiting optional customers either during or only after mandatory customer visits. An adaptive large neighborhood search is developed to solve instances adapted from the literature as well as to solve a real‐case study of a beverage distributor. The results show the effectiveness of our approach, demonstrating the potential to utilize the available capacity on vehicles returning to the depot to create profitable and environmentally friendly routes, and so enhancing efficient, cost‐effective, and sustainable logistics activities.
Evaluating performance and quality of a fast multi‐contrast scan in routine brain MRI
Authors: Milshteyn Eugene , Griffin Harry , Chang Yi Shuen , Shaikh Ibraheem , Sprenger Tim , Skare Stefan , Maclellan Christopher J. , Soman Salil
Published: December 2024

Background and Purpose

Neuromix is a fast, motion robust multi‐contrast sequence capable of providing all diagnostic contrasts in ∼3.5 minutes. However, more evaluation is needed across the various contrasts compared to gold standard, optimized sequences routinely used in the clinic. The goal of this study was to prospectively determine how NeuroMix performs in the clinical setting compared to routine clinical MRI.

Methods

NeuroMix and routine clinical MRI sequences were acquired on a 3 Tesla clinical scanner for 39 patients clinically indicated for brain MRI. Three radiologists were asked to assess the diagnostic confidence of NeuroMix compared to the routine MRI using a series of questions. Signal‐to‐noise and contrast‐to‐noise ratios (SNR and CNR) were assessed for NeuroMix. Fleiss’ free‐marginal multirater kappa was calculated for the qualitative assessment performed by the radiologists.

Results

Radiologists were comfortable substituting or reading some of the NeuroMix sequences in place of the corresponding conventional sequence for some contrasts, including diffusion‐weighted imaging, single‐shot T2, and susceptibility‐weighted imaging. The image quality, SNR, and CNR allowed the radiologists to visualize anatomy and pathology on NeuroMix images. There was no significant difference between coefficient of variation for the apparent diffusion coefficient maps (p = .084).

Conclusions

Analysis revealed both positives and some pitfalls of NeuroMix. However, these results indicate Neuromix as having the capability to be a backup sequence in case artifacts are present in routine sequences, or potentially a replacement for some contrasts altogether.