bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multilamellar organelle for chemosymbiosis in an aplacophoran mollusc adapted to anoxic cold seep sediment
Authors: Li Yunlong , Chen Chong , Liu Xu , Li Menggong , Zhou Haiyun , Wang Hui , Zheng Xiaoshan , He Xing , Liu Shanshan , Qiu Jian-Wen , Qian Pei-Yuan , Sun Jin 
Published: January 2025

AbstractSymbiosis with chemoautotrophic bacteria has evolved in many animal lineages inhabiting reducing habitats such as hydrothermal vents, allowing these holobionts to thrive in dark biospheres1. In certain instances, the symbionts have become intracellular, residing within specialised bacteriocytes2. The integration of microbial symbionts with eukaryotic cells vary across known animals; however, no specialised organelle dedicated to chemosynthesis has been identified yet2. Here, we report a mode of symbiosis where sulphur-oxidising bacteria cultured within spherical multilamellar compartments (~12 μm) in the cold-seep aplacophoran molluscChaetoderma shenloong. This organelle, which we name ‘dracosphera’, is ubiquitous within the hypertrophied and intricately reticulate digestive gland ofC. shenloong, which has otherwise lost most of its gut. Given that the symbionts are strictly anaerobic and the host resides in anoxic sediments tens of centimetres below the surface, the dracosphera may serve to minimise oxygen diffusion to the bacteria, akin to mechanisms observed in microbial diazotrophs3or termite hindguts4, as supported by our genomic and spatial transcriptomic analyses. Hypoxic conditions have been known to induce radical adaptations in meiofauna, exemplified by the acquisition of hydrogenosomes5. Our discovery of similarly exceptional adaptations inC. shenloongprovides new insights into the evolution of such organelles also in larger animals.
Cleaner wrasse failed in early testing stages of both visual and spatial Working Memory paradigms
Authors: Bonin Leonore , Manrique Héctor M. , Bshary Redouan 
Published: January 2025

AbstractWorking memory (WM), an attention-based short-term storage system responsible for the manipulation and integration of past knowledge with present information for goal-directed behavior, is a key executive function and a principal predictor of general intelligence. As WM has not been a major research topic in animal behavior, we first summarize key ideas from the social sciences for interested colleagues. Given that past methodological inconsistencies have led to mixed results and conclusions across various species, we designed experiments that incorporate the critical components of WM, facilitating cross-species comparisons and accounting for potential ecological influences. We present such experiments on WM in an ectothermic vertebrate, the cleaner wrasse (Labroides dimidiatus), which faces environmental challenges potentially requiring complex cognitive adaptations. Overcoming several experimental challenges, we consistently obtained negative results across multiple experimental paradigms. Our negative results using experiments specifically designed to test WM call into question previous studies that used other experiments and reported positive WM findings in other fish species. If the negative results in specific WM tests were to be confirmed in other ectotherm vertebrates, the absence of WM may turn out to be a key factor underlying the significant encephalization gap between ectotherm and endotherm vertebrate species.
Investigation of Bile Salt Hydrolase Activity in Human Gut Bacteria Reveals Production of Conjugated Secondary Bile Acids
Authors: Lucas Lauren N. , Mallikarjun Jillella , Cattaneo Lea E. , Gangwar Bhavana , Zhang Qijun , Kerby Robert L. , Stevenson David , Rey Federico E. , Amador-Noguez Daniel 
Published: January 2025

AbstractThrough biochemical transformation of host-derived bile acids (BAs), gut bacteria mediate host-microbe crosstalk and sit at the interface of nutrition, the microbiome, and disease. BAs play a crucial role in human health by facilitating the absorption of dietary lipophilic nutrients, interacting with hormone receptors to regulate host physiology, and shaping gut microbiota composition through antimicrobial activity. Bile acid deconjugation by bacterial bile salt hydrolase (BSH) has long been recognized as the first necessary BA modification required before further transformations can occur. Here, we show that BSH activity is common among human gut bacterial isolates spanning seven major phyla. We observed variation in both the extent and the specificity of deconjugation of BAs among the tested taxa. Unexpectedly, we discovered that certain strains were capable of directly dehydrogenating conjugated BAs via hydroxysteroid dehydrogenases (HSD) to produce conjugated secondary BAs. These results challenge the prevailing notion that deconjugation is a prerequisite for further BA modifications and lay a foundation for new hypotheses regarding how bacteria act individually or in concert to diversify the BA pool and influence host physiology.
Validation of Structure Tensor Analysis for Orientation Estimation in Brain Tissue Microscopy
Authors: Gray Bryson , Smith Andrew , MacKenzie-Graham Allan , Shattuck David W. , Tward Daniel 
Published: January 2025

AbstractAccurate localization of white matter pathways using diffusion MRI is critical to investigating brain connectivity, but the accuracy of current methods is not thoroughly understood. A fruitful approach to validating accuracy is to consider microscopy data that have been co-registered with MRI of post mortem samples. In this setting, structure tensor analysis is a standard approach to computing local orientations for validation. However, structure tensor analysis itself has not been well-validated and is subject to uncertainty in its angular resolution, and selectivity to specific spatial scales. In this work, we conducted a simulation study to investigate the accuracy of using structure tensors to estimate the orientations of fibers arranged in configurations with and without crossings. We examined a range of simulated conditions, with a focus on investigating the method’s behavior on images with anisotropic resolution, which is particularly common in microscopy data acquisition. We also analyzed 2D and 3D optical microscopy data. Our results show that parameter choice in structure tensor analysis has relatively little effect on accuracy for estimating single orientations, although accuracy decreases with anisotropy. On the other hand, when estimating the orientations of crossing fibers, the choice of parameters becomes critical, and poor choices result in orientation estimates that are essentially random. This work provides a set of recommendations for researchers seeking to apply structure tensor analysis effectively in the study of axonal orientations in brain imaging data and quantifies the method’s limitations, particularly in the case of anisotropic data.HighlightsStructure tensor estimates of homogeneous orientations are robust to parameter choiceAccuracy in crossing-fiber regions is highly sensitive to parameter choiceImage anisotropy has a large effect on accuracy in 3D imagesSimulations provide guidelines for choosing parameters based on image characteristics
Gaze dynamics prior to navigation support hierarchical planning
Authors: Gordon Jeremy , Chuang John , Pezzulo Giovanni 
Published: January 2025

AbstractThe task of planning future actions in the context of an uncertain world results in massive state spaces that preclude exhaustive search and other strategies explored in the domains of both human decision-making and computational agents. One plausible solution to this dimensionality explosion is to decompose the task into subgoals that match the information geometry of the task at hand. However, how individuals identify a productive hierarchy, and perceive and select subgoals suitable to planning, is not well understood. To investigate this topic, we designed a virtual-reality based behavioral experiment which collected eye movements during a pre-navigation planning phase. By capturing gaze dynamics correlated with the simulative processes used in planning, we were able to identify the spatiotemporal evolution of visual search under uncertainty. Our results highlight gaze dynamics indicative of a search process that exhibits hierarchical structure. These include a decreasing trend seen in gaze distance from origin and a broad to narrow shift (with reducing saccade distances and longer fixation durations) as plans are established. In line with prior work, critical tiles to which landscape connectivity is most sensitive were the strongest predictors of visual attention. We also find that deeper planning was correlated with success only on the most complex maps (e.g. those with a larger number of information-nodes, higher branching factor, and more forks, according to an info-graphical map analysis). This study highlights the role of embodied visual search during planning, and the skill-dependence of the specific subgoals and hierarchical decomposition used which unlocked successful performance.
Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration
Authors: Dhillon-Richardson Rekha M. , Haugan Alexandra K. , Lyons Luke W. , McKenna Joseph K. , Bronner Marianne E. , Martik Megan L. 
Published: January 2025

ABSTRACTDuring vertebrate development, the heart primarily arises from mesoderm, with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here, by integrating bulk and single cell RNA-seq with ATAC-seq, we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factorsegr1, sox9a, tfap2aandets1. Notably, we show that cells expressing the canonical neural crest genesox10are essential for proper cardiac regeneration in adult zebrafish. Furthermore, expression of all transcription factors from the migratory cardiac crest gene subcircuit are reactivated after injury at the wound edge. Together, our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination, with key factors reactivated during regeneration.SIGNIFICANCEMany common human congenital heart defects are linked to problems that arise during cardiac neural crest development. Here, we use the zebrafish, which has the remarkable ability to regenerate their adult heart, to understand the genetic programs that control cardiac development and adult repair. We discover a set of genes that control the development of the cardiac neural crest and find that these genes are reactivated after heart injury in the adult zebrafish. Unlike the zebrafish, human hearts have a very limited ability to regenerate after injury. Our findings in zebrafish can provide insight to potential clinical interventions for congenital heart defects and adult heart damage.
The medial prefrontal cortex encodes procedural rules as sequential neuronal activity dynamics
Authors: Ohno Shuntaro , Nomoto Masanori , Inokuchi Kaoru 
Published: January 2025

SummaryThe prefrontal cortex plays a crucial role in procedural rule learning; however, the specific neuronal mechanism through which it represents rules is unknown. We hypothesized that sequential neuronal activities in the prefrontal cortex encode these rules. To investigate this, we recorded neuronal activities in the medial prefrontal cortex of mice during rule learning using Ca2+imaging. We utilized a method based on convolutional negative matrix factorization, iSeq, to automatically detect temporal neuronal sequences in the recorded data. As rule learning advanced, these neuronal sequences began to encode critical information for rule execution. In mice that had mastered the rule, the dynamics of neuronal sequences could predict success and failure of reward acquisition. Furthermore, the composition of cell populations within the neuronal sequences was rearranged throughout the learning process. These findings suggest that as animals learn a rule, the medial prefrontal cortex continually updates its neuronal sequences to assign significance to behavioral actions crucial for reward acquisition.
Repopulation of the brain with microglia-like cells following intraperitoneal bone marrow cell transfer in microglia-deficient mice
Authors: Taylor Isis , Patkar Omkar L. , Liu Yajun , Jacquelin Sebastien , Ranpura Ginell , Carter-Cusack Dylan , Ewing Adam , Kurniawan Nyoman D. , Li Mosi , Vasoya Deepali , He Xin , Dando Owen R. , Kind Peter , Hardingham Giles E. , Bradford Barry M. , Mabbott Neil A. , LeFevre Lucas , Pridans Clare , Summers Kim M. , Irvine Katharine M. , Hume David A. 
Published: January 2025

AbstractGerm-line deletion of a conserved enhancer (the Fms intrinsic regulatory element, FIRE) in the mouseCsf1rlocus causes congenital absence of microglia. Homozygous FIRE deletion on a C57BL/6J background leads to perinatal lethality and hydrocephalus (HC) in surviving pups. We developed a congenic C57BL/6J line with defined regions of non-C57BL/6J genomic DNA, increased postnatal viability and reduced incidence of HC. Both perinatal lethality and HC were eliminated in F2 mice following outcross of the congenic line to CBA/J or BALBc/J backgrounds. To assess the impacts of microglial deficiency in postnatal neurodevelopment we analyzed deep total RNA-seq data from multiple brain regions of wild-type andCsf1rΔFIRE/ΔFIREmice. Aside from the loss of microglial-specific transcripts, we found no significant alterations in relative abundance of any cell-type or region-specific transcriptomic signature. Transcripts associated with endosome/lysosome function, which are enriched in microglia, were not affected, suggesting compensatory expression by other cell types. On the C57BL/6J x CBA/J F2 background, congenital absence of microglia did not affect motor activity, behavior or myelination up to 7 months of age but was associated with astrocytosis and calcification in the thalamus. In the congenic C57BL/6JCsf1rΔFIRE/ΔFIREmouse line, intraperitoneal transfer of wild-type bone marrow cells (BMT) at weaning led to complete repopulation of the brain with microglia-like cells without giving rise to monocytic intermediates. Our results suggest novel strategies for treatment of microglial deficiency.
The ratio of Wnt signaling activity to Sox2 transcription factor levels predicts neuromesodermal fate potential
Authors: Morabito Robert D. , Tatarakis David , Swick Ryan , Stettnisch Samantha , Schilling Thomas F. , Horsfield Julia A. , Martin Benjamin L. 
Published: January 2025

AbstractNeuromesodermal progenitors (NMPs) are a vertebrate cell type that contribute descendants to both the spinal cord and the mesoderm. The undifferentiated bipotential NMP state is maintained when both Wnt signaling is active and Sox2 is present. We used transgenic reporter lines to live-image both Wnt activity and Sox2 levels in NMPs and observed a unique cellular ratio in NMPs compared to NMP-derived mesoderm or neural tissue. We used this unique signature to identify the previously unknown anatomical position of a progenitor population that gives rise to the midline tissues of the floor plate of the spinal cord and the mesodermal notochord. Thus, quantification of the active Wnt signaling to Sox2 ratio can be used to predict and identify cells with neuromesodermal potential. We also developed the auxin inducible degron 2 system for use in zebrafish to test the temporal role that Sox2 plays during midline formation. We found ectopic Sox2 in the presence of Wnt activity holds cells in the undifferentiated floor plate/notochord progenitor state, and that degradation of the ectopic Sox2 is required for cells to adopt a notochord fate.
High Prevalence and Genotypic Diversity of PersistentChlamydia trachomatisInfections Among South African Adolescent Girls and Young Women: A Tale of Two Cities
Authors: Dabee Smritee , Barnabas Shaun , Versteeg Bart , Kullin Brian , Jaumdally Shameem Z. , Gamieldien Hoyam , Mkhize Nonhlanhla , Muller Etienne , Maseko Venessa , Gill Katherine , Martin Darren P. , Gray Glenda , Bekker Linda-Gail , Lewis David A. , Jaspan Heather B. , Bruisten Sylvia M. , Passmore Jo-Ann S. 
Published: January 2025

AbstractChlamydia trachomatis(CT) is the most common sexually transmitted bacterial infection globally, significantly affecting adolescent girls and young women (AGYW) in South Africa. This study investigated CT prevalence and genotypic diversity among 298 AGYW from Cape Town and Johannesburg, revealing an overall prevalence of 29.5%. Prevalence was higher in Cape Town (41.6%) compared to Johannesburg (17.4%; p<0.0001). Genetic analysis identified 34 sequence types, including 15 novel variants. Longitudinal data highlighted frequent reinfections or persistent infections despite treatment. These findings underscore the importance of addressing CT’s genetic diversity for improved reproductive health strategies and vaccine development.
LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development
Authors: Adami Anita , Garza Raquel , Gerdes Patricia , Johansson Pia A. , Dorazehi Fereshteh , Koutounidou Symela , Castilla-Vallmanya Laura , Atacho Diahann A.M. , Sharma Yogita , Johansson Jenny G. , Tam Oliver , Kirkeby Agnete , Barker Roger A. , Gale-Hammell Molly , Douse Christopher H. , Jakobsson Johan 
Published: January 2025

AbstractLong interspersed nuclear element 1 (L1) retrotransposons represent a vast source of divergent genetic information. However, mechanistic analysis of whether and how L1s contribute to human developmental programs is lacking, in part due to the challenges associated with specific profiling and manipulation of human L1 expression. Here we show that thousands of hominoid-specific L1 integrants are expressed in human induced pluripotent stem cells and cerebral organoids. The activity of individual L1 promoters is surprisingly divergent and correlates with an active epigenetic state. Efficient on-target CRISPRi silencing of L1s revealed nearly a hundred co-opted L1-derived chimeric transcripts and L1 silencing resulted in changes in neural differentiation programs and reduced cerebral organoid size. Together, these data implicate L1s and L1-derived transcripts in hominoid-specific CNS developmental processes.
Popular movie effects on advanced finance course performance: flipped classroom vs in-class view
Authors: Brahmana Rayenda Khresna , Yau Josephine Tan-Hwang 
Published: January 2025

PurposeInterest in using popular movies in higher education has flourished, but determining their actual impact remains tricky. Some studies suggest these movies can positively affect student satisfaction, yet many criticize this method as ineffective or lazy. Our study compared two ways of using popular movies – watching them in class versus a flipped approach – for an advanced finance module. We aim to examine the best teaching delivery of watching popular movies in an advanced module.Design/methodology/approachThis study compares two teaching methods during movie screenings: a didactic flipped classroom (Group 01) and in-class viewing (Group 02). The sampling frame was final-year finance students from a public university. It was conducted over two academic years and involved 190 students aged 20–23. These students were split into two groups: G01, with 93 students, and G02, with 97 students. The study focused on the movie “Big Short,” chosen for its relevance to the Fixed-Income Securities course (the advanced module).FindingsOur findings indicate both methods led to high student satisfaction, with no significant difference between in-class viewing and the flipped approach. However, the understanding of the advanced module significantly increased overall. Importantly, using popular movies as flipped material resulted in better student grades compared to in-class viewing. This suggests that while using popular movies is a beneficial teaching method, employing a didactic flipped classroom approach yields superior outcomes for students.Practical implicationsThis research offers practical insights for instructors, highlighting the value of utilizing popular movies in advanced education. It suggests incorporating movies as learning materials can enhance student satisfaction, particularly when employed within a flipped classroom framework. Importantly, the study reveals that adopting the flipped classroom approach yields superior academic outcomes compared to traditional in-class viewing. Thus, instructors teaching advanced modules should consider integrating popular movies within flipped classrooms to not only enhance student satisfaction but also improve academic performance.Originality/valueOur research investigates popular movies' efficacy, particularly in advanced finance education. While previous studies have explored using movies to enhance student satisfaction, this study investigates it further by comparing two delivery methods: the didactic flipped classroom and traditional in-class viewing. While both methods effectively increase student satisfaction, the didactic flipped classroom significantly improves academic performance. This highlights the innovative potential of the flipped approach in promoting deeper learning and suggests practical implications for instructors seeking to enhance both satisfaction and academic outcomes in advanced courses.
A new holistic approach to preventing accounting fraud in the non-profit organisation (NPO) sector: some propositions and research agenda
Authors: Nguyen Khanh , Sands John , Trimmer Karen 
Published: January 2025

PurposeThis paper systematically reviewed research on accounting fraud in the non-profit organisation (NPO) sector during 2004–2024 to identify gaps in theory and practice with the aim of producing a new parsimonious global fraud model.Design/methodology/approachThis paper utilised a structured literature review methodology.FindingsWe propose a new holistic approach for the NPO sector worldwide, with two foci of “what may contribute to fraud” and “what may prevent fraud”.Research limitations/implicationsThe future research agenda for the new holistic approach is provided.Practical implicationsThe approach helps donors promote accountability and transparency in the NPO sector worldwide, thereby sustaining the development of this sector.Originality/valueTo the best of the authors’ knowledge, this paper is the first comprehensive worldwide fraud research review, making distinct contributions. Globally, the approach is the first dedicated to the NPO sector, including different stages of fraud occurrence (undetected, suspected, actual/detected and future), and using a multi-disciplinary approach to prevent these stages. The approach is also the first to incorporate individual-level, organisational-level, industry-level and country-level factors into predicting future fraud.