bluuebunny/crossref_metadata_2025_split huggingface dataset:
Body-wandering reveals an embodied dimension of thought with distinct affective and neural signatures
Authors: Banellis Leah , Nikolova Niia , Brændholdt Malthe , Vejlø Melina , Fardo Francesca , Smallwood Jonathan , Allen Micah G. 
Published: October 2024

AbstractHumans often engage in self-generated thoughts when unoccupied by external events, a phenomenon commonly known as mind-wandering. Previous research has predominantly focused on the cognitive aspects of mind-wandering, overlooking the potential embodied or interoceptive components that contribute to our ongoing thought patterns. In this study, we addressed this gap by exploring “body-wandering“—thoughts related to internal bodily sensations such as breathing, heartbeat, and gastrointestinal functions. To assess body-wandering, we applied a retrospective multi-dimensional interoceptive experience sampling approach in 536 healthy participants concurrently with resting-state functional brain imaging. Our findings revealed that body-wandering is distinct from cognitively focused thoughts, underscoring the unique role of embodied processes in ongoing experience. Embodied thought patterns were associated with increased negative affect, heightened physiological arousal, and reduced ADHD symptoms. In contrast, cognitive-focused thoughts were linked to decreased negative affect, lower arousal, and higher depression symptoms. Notably, body-wandering corresponded with a unique neural signature involving increased connectivity between somatomotor, interoceptive, and thalamocortical brain networks. These results emphasise the importance of incorporating embodied processes into theoretical models of mind-wandering and suggest that individual differences in body-wandering significantly impact emotional states and mental health.Significance statementContemporary cognitive neuroscience recognizes the role of internally generated states known as mind-wandering. However, research has predominantly taken a cognitive perspective, overlooking the embodied influences on conscious experience. Our study addresses this gap by demonstrating the unique contribution of body-related and interoceptive thoughts to waking cognition. This “body-wandering” was associated with increased negative affect, heightened physiological arousal, and reduced ADHD symptoms, along with a distinct neural signature involving interoceptive, somatomotor, and subcortical networks. Conversely, cognitive mind-wandering was linked to decreased negative affect, lower arousal, and increased depressive symptoms. Incorporating embodied processes into models of mind-wandering provides a more comprehensive theoretical framework and reveals how these experiences influence our emotional state and mental health.
LncRAnalyzer: Uncovering Long Non-Coding RNAs and Exploring Gene Co-expression Patterns in Sorghum Genomics
Authors: Nikhil Shinde , Mohideen Habeeb Shaikh , Sella Raja Natesan 
Published: October 2024

AbstractSorghum (Sorghum bicolor L. Moench) is a versatile crop with significant phenotypic and genetic diversity. Despite the availability of multiple re-sequenced sorghum genomes, non-coding regions remain underexplored. Long non-coding RNAs (lncRNAs), a major class of non-coding RNAs, with low expression levels, complex expression patterns, and can be identified using RNA-seq. However, distinguishing lncRNAs from protein-coding genes is challenging due to their low abundance and tissue-specific expressions. This study developed an automated pipeline for identifying lncRNAs and Novel Protein Coding Transcripts (NPCTs) using RNA-seq datasets. Using a dual sorghum reference genome scheme, we identified 8770 lncRNAs in BTX642 (33.35% cultivar-specific) and 8869 lncRNAs in RTX430 (30.72% cultivar-specific). Some lncRNAs were linked to pre- and post-flowering drought tolerance in RTX430 and BTX642, respectively. The NPCTs encoded elements such as RE-1, TNT, Zinc finger (zf) protein, FAR1 related, and Xylan glucosyltransferase suggesting their involvement in drought-specific phenotype development. Target predictions for lncRNAs revealed both cis- and trans-regulated genes were associated with peroxidase, glutathione S-transferase, and MYB TFs during drought, emphasizing their role in drought tolerance. Differentially expressed lncRNAs in leaf and root tissues (p-value < 0.05, |log2fold| > 2), revealed that the most abundant lncRNAs during drought regulate TFs such as C2H2-GATA, DUF domain, and WD-40. Downstream gene co-expression analysis showed time point-specific lncRNA interactions with TFs, highlighting their roles in drought response in sorghum. Our developed pipeline LncRAnalyzer identified lncRNAs and NPCTs, and integrated them into gene co-expression networks provided deeper insights into drought tolerance in sorghum.
Differential Sensitivity of Midline Patterning to Mitosis during and after Primitive Streak Extension
Authors: Zhao Zhiling , Asai Rieko , Mikawa Takashi 
Published: October 2024

AbstractBackgroundMidline establishment is a fundamental process during early embryogenesis forBilaterians. Midline patterning in nonamniotes can occur without mitosis, through Planar Cell Polarity (PCP) signaling. By contrast, amniotes utilize both cell proliferation and PCP signaling for patterning early midline landmark, the primitive streak (PS). This study examined their roles for midline patterning at post PS-extension.ResultsIn contrast to PS extension stages, embryos under mitotic arrest during the post PS-extension preserved notochord (NC) extension and Hensen’s node (HN)/PS regression judged by both morphology and marker genes, although they became shorter, and laterality was lost. Remarkably, no or background level of expression was detected for the majority of PCP core components in the NC-HN-PS area at post PS-extension stages, except for robustly detectedprickle-1. Morpholino knockdown of Prickle-1 showed little influence on midline patterning, except for suppressed embryonic growth. Lastly, associated with mitotic arrest-induced size reduction, midline tissue cells displayed hypertrophy.ConclusionThus, the study has identified at least two distinct mitosis sensitivity phases during early midline pattering: One is PS extension that requires both mitosis and PCP, and the other is mitotic arrest-resistant midline patterning with little influence by PCP at post PS-extension stages.
Identifying the Fusarium species involved in foot rot disease of faba beans in the UK using a combined molecular and microbiological approach
Authors: Attar Basem , Kitson James J. N. , Cuff Jordan P. , Howard Becky , Lages Ana , Gomez Dina , Boonham Neil 
Published: October 2024

AbstractFoot rot is a devastating disease of faba bean crops globally, including in the United Kingdom, the world’s third largest producer. To identify the causal agents, we have sampled foot rot-affected plants and soils from faba bean crops across England. We isolated organisms associated with foot rot disease in culture and assessed pathogenicityin vivoto evaluate the infectivity of the isolates on faba bean. We identified the pathogenic isolates using DNA barcoding of the Internal Transcribed Spacer (ITS) and Translation Elongation Factor one α (TEF1α) molecular markers. A total of 113 clonal isolates were obtained from infected plants and soil samples across England. Of these, 60 were pathogenic, inducing mild to severe symptoms on faba bean. Sequencing of the ITS andTEF1α loci and comparison against sequence databases (Genbank and Fusarium_ID) enabled the identification of pathogenic isolates, in decreasing order of frequency, asFusarium oxysporum(26.6 %),F. vanettenii(25%),F. redolens(15 %),F. solani(11.6%),F. culmorum(8.3 %),F. avenaceum(6.7 %),F. equiseti(1.7 %),F. clavum(1.7 %),Clonostachys rosea(1.7%) andAlternaria alternata(1.7%).F. oxysporum, F. redolensandF. avenaceuminduced the most severe symptoms, whilstF. solaniinduced the least severe symptoms. Determining the most prevalent causal agents of foot rot in UK faba beans will facilitate targeted disease monitoring and intervention for enhanced productivity.
A type I 3’ UTR-derived sRNA is involved in heme metabolism and virulence inStaphylococcus aureus
Authors: Silard Chloé , Germain-Amiot Noëlla , Poirette Pierre , Legros Julie , Duraõ Gabriella , Martinais Sophie , Mirouze Nicolas , Augagneur Yoann 
Published: October 2024

ABSTRACTStaphylococcus aureusis a pathogen responsible for a wide array of superficial to life-threatening infections. To efficiently adapt to environmental cues, a complex regulatory network is needed, involving among others regulatory RNAs (sRNAs). Here, we studied Srn_9342, an sRNA transcribed into two isoforms of different lengths and known to interact with RNAIII, leading to a modulation of δ-hemolysin production. We showed that the two isoforms are oppositely expressed in a growth phase-dependent manner. Then, we demonstrated using transcriptional fusions and various chromosomally recombinant strains that Srn_9342 is a type I 3’UTR-derived sRNA whose the expression of the long form (Srn_9342L) is SigB-dependent. Using aΔsrn_9342mutant, we monitored the transcript level of various RNA partners previously identified by MAPS and showed that thehemQmRNA level, encoding a protein involved in heme biosynthesis and reported to participate in small colony variant (SCV) phenotype, increased in the mutant.In silicoandin vitrobiochemical investigations showed that a 5’ region of Srn_9342 bindshemQleading to a repression of the HemQ protein level whereas the overexpression of Srn_9342 induced an SCV phenotype which was partially relieved by the addition of hemin. Finally, we report that the deletion ofsrn_9342significantly increased the virulence of the pathogen in aGalleria mellonellamodel. Taking together, these data uncovered a novel type I 3’ UTR-derived sRNA regulating the heme biosynthesis pathway and implicated in virulence and SCV formation inS. aureus.
The E3 Ubiquitin Ligase Trip12 attenuates Wnt9a/Fzd9b signaling during hematopoietic stem cell development
Authors: Ensing Jessica , Ide Amber D. , Gilliland Carla , Tsurho Visakuo , Caza Isabella , Stratman Amber N. , Lanning Nathan J. , Grainger Stephanie 
Published: October 2024

AbstractWnt signaling is essential for both the development and homeostasis of diverse cellular lineages, including hematopoietic stem cells. Organism-wide, Wnt signals are tightly regulated, as overactivation of the pathway can lead to tumorigenesis. Although numerous Wnt ligands and Frizzled (Fzd) receptors exist, how particular Wnt/Fzd pairings are established and how their signals are regulated is poorly understood. We have previously identified the requirements of the cognate pairing of Wnt9a and Fzd9b for early hematopoietic stem cell proliferation. However, the specific signals governing activation, but equally important, the molecular mechanisms required to turn the signal ‘off,’ are unknown. Here, we show that the E3 ubiquitin ligase Trip12 (thyroid hormone receptor interactor 12) is specifically required to ubiquitinate the third intracellular loop of Fzd9b at K437, targeting it for lysosomal degradation. In contrast to other ubiquitin ligases described to regulate the cell surface availability of multiple Fzds broadly, our data indicate that Trip12 is selective for Fzd9b. We further demonstrate that this occurs through ubiquitination at K437 of Fzd9b in the third intracellular loop, ultimately leading to a decrease in Fzd9b receptor availability and in Wnt9a/Fzd9b signaling that impacts hematopoietic stem cell proliferation in zebrafish. Our results point to specific mechanisms driving the availability of different Fzd receptors. Determining how particular Fzd abundance is regulated at the membrane will be critical to developing specific therapies for human intervention.One sentence summaryTrip12 ubiquitinates Fzd9b
Cellular and molecular mechanisms that shape the development and evolution of tail vertebral proportion in mice and jerboas
Authors: Weber Ceri J. , Weitzel Alexander J. , Liu Alexander Y. , Gacasan Erica G. , Sah Robert L. , Cooper Kimberly L. 
Published: October 2024

ABSTRACTDespite the functional importance of the vertebral skeleton, little is known about how individual vertebrae elongate or achieve disproportionate lengths as in the giraffe neck. Rodent tails are an abundantly diverse and more tractable system to understand mechanisms of vertebral growth and proportion. In many rodents, disproportionately long mid-tail vertebrae form a ‘crescendo-decrescendo’ of lengths in the tail series. In bipedal jerboas, these vertebrae grow exceptionally long such that the adult tail is 1.5x the length of a mouse tail, relative to body length, with four fewer vertebrae. How do vertebrae with the same regional identity elongate differently from their neighbors to establish and diversify adult proportion? Here, we find that vertebral lengths are largely determined by differences in growth cartilage height and the number of cells progressing through endochondral ossification. Hypertrophic chondrocyte size, a major contributor to differential elongation in mammal limb bones, differs only in the longest jerboa mid-tail vertebrae where they are exceptionally large. To uncover candidate molecular mechanisms of disproportionate vertebral growth, we performed intersectional RNA-Seq of mouse and jerboa tail vertebrae with similar and disproportionate elongation rates. Many regulators of posterior axial identity and endochondral elongation are disproportionately differentially expressed in jerboa vertebrae. Among these, the inhibitory natriuretic peptide receptor C (NPR3) appears in multiple studies of rodent and human skeletal proportion suggesting it refines local growth rates broadly in the skeleton and broadly in mammals. Consistent with this hypothesis, NPR3 loss of function mice have abnormal tail and limb proportions. Therefore, in addition to genetic components of the complex process of vertebral evolution, these studies reveal fundamental mechanisms of skeletal growth and proportion.
Chronic activation of corticospinal tract neurons after pyramidotomy injury enhances neither behavioral recovery nor axonal sprouting
Authors: Wang Zimei , Brannigan Matthew , Friedrich Logan , Blackmore Murray G. 
Published: October 2024

ABSTRACTModulation of neural activity is a promising strategy to influence the growth of axons and improve behavioral recovery after damage to the central nervous system. The benefits of neuromodulation likely depend on optimization across multiple input parameters. Here we used a chemogenetic approach to achieve continuous, long-term elevation of neural activity in murine corticospinal tract (CST) neurons. To specifically target CST neurons, AAV2-retro-DIO-hM3Dq-mCherry or matched mCherry control was injected to the cervical spinal cord of adult Emx1-Cre transgenic mice. Pilot studies verified efficient transgene expression in CST neurons and effective elevation of neural activity as assessed by cFos immunohistochemistry. In subsequent experiments mice were administered either DIO-hM3Dq-mCherry or control DIO-mCherry, were pre-trained on a pellet retrieval task, and then received unilateral pyramidotomy injury to selectively ablate the right CST. Mice then received continual clozapine via drinking water and weekly testing on the pellet retrieval task, followed by cortical injection of a viral tracer to assess cross-midline sprouting by the spared CST. After sacrifice at eight weeks post-injury immunohistochemistry for cFos verified elevated CST activity in hM3Dq-treated animals and immunohistochemistry for PKC-gamma verified unilateral ablation of the CST in all animals. Despite the chronic elevation of CST activity, however, both groups showed similar levels of cross-midline CST sprouting and similar success in the pellet retrieval task. These data indicate that continuous, long-term elevation of activity that is targeted specifically to CST neurons does not affect compensatory sprouting or directed forelimb movements.
Quantitative Resolving Cell Fate in the Early Embryogenesis ofCaenorhabditis elegans
Authors: Xiong Ruiqi , Su Yang , Yao Mengchao , Liu Zefei , Lu Jie , Chen Yong-Cong , Ao Ping 
Published: October 2024

AbstractThe nematodeCaenorhabditis elegansexhibits an invariant cell lineage during its development where the gene-molecular network that regulates the development is crucial for the biological process. While there are many molecular cell atlases describing the phenomena and key molecules involved in cell transformation, the underlying mechanisms from a systems biology perspective have received less attention. Based on an endogenous molecular-cellular theory that relates the molecular mechanisms to biological phenotypes, we constructed a model of core endogenous network to describe the early stages of embryonic development of the nematode. Different cell types and intermediate cell states during development from zygotes to founder cells correspond to the steady states of the network as a nonlinear stochastic dynamical system. Connections between steady states form a topological landscape that encompasses known developmental lineage trajectories. By regulating the expression of agents in the network, we quantitatively simulated the effects of the Wnt and Notch signaling pathway on cell fate transitions and predicted the possible trajectories of transdifferentiation of the AB cell across the lineage. The success of the current study may help advance our understanding of the fundamental principles of developmental biology and cell fate determination, offering an effective tool for quantitative analysis of cellular processes.
Spatiotemporal dynamics of primary and motile cilia throughout lung development
Authors: Spurgin Stephen , Nguimtsop Ange Michelle , Chaudhry Fatima N. , Michki Sylvia N. , Salvador Jocelynda , Iruela-Arispe M. Luisa , Zepp Jarod A. , Mukhopadhyay Saikat , Cleaver Ondine 
Published: October 2024

AbstractCilia are specialized structures found on a variety of mammalian cells, with variable roles in the transduction of mechanical and biological signals (by primary cilia, PC), as well as the generation of fluid flow (by motile cilia). Their critical role in the establishment of a left-right axis in early development is well described, as is the innate immune function of multiciliated upper airway epithelium. By contrast, the dynamics of ciliary status during organogenesis and postnatal development is largely unknown. In this study, we define the progression of ciliary status within the endothelium, epithelium, and mesenchyme of the lung. Remarkably, we find that endothelial cells (ECs) lack PC at all stages of development, except in low numbers in the most proximal portions of the pulmonary arteries. In the lung epithelium, a proximodistal ciliary gradient is established over time, as the uniformly mono-ciliated epithelium transitions into proximal, multiciliated cells, and the distal alveolar epithelium loses its cilia. Mesenchymal cells, interestingly, are uniformly ciliated in early development, but with restriction to PDGFRα+ fibroblasts in the adult alveoli. This dynamic process in multiple cellular populations both challenges prior assertions that PC are found on all cells, and highlights a need to understand their spatiotemporal functions.HighlightsPrimary cilia are found broadly throughout early embryonic tissues.Primary cilia are observed in both epithelial and mesenchymal cells in the early lung.Pulmonary endothelial cells largely do not possess primary cilia during embryonic development.Differential multiciliation and loss of epithelial cilia in a proximal-distal axis.Maintenance of cilia in adult pulmonary PDGFRα+ fibroblasts.
Resting-state functional connectivity changes following audio-tactile speech training
Authors: Cieśla Katarzyna , Wolak Tomasz , Amedi Amir 
Published: October 2024

AbstractUnderstanding speech in background noise is a challenging task, especially if the signal is also distorted. In a series of previous studies we have shown that comprehension can improve if simultaneously to the auditory speech, the person receives speech-extracted low-frequency signals on fingertips. The effect increases after short audio-tactile speech training. Here we use resting-state functional magnetic resonance, measuring spontaneous low-frequency oscillations in the brain while at rest, to assess training-induced changes in functional connectivity. We show enhanced connectivity within a right-hemisphere cluster encompassing the middle temporal motion area (MT), and the extrastriate body area (EBA), and lateral occipital cortex (LOC), which before training is found to be more connected to bilateral dorsal anterior insula. Furthermore, early visual areas are found to switch from increased connectivity with the auditory cortex before, to increased connectivity with an association sensory/multisensory parietal hub, contralateral to the palm receiving vibrotactile inputs, after. Also the right sensorimotor cortex, including finger representations, is more connected internally after training. The results alltogether can be interpreted within two main complementary frameworks. One, speech-specific, relates to the pre-existing brain connectivity for audio-visual speech processing, including early visual, motion and body regions for lip-reading and gesture analysis in difficult acoustic conditions, which the new audio-tactile speech network might be built upon. The other refers to spatial/body awareness and audio-tactile integration, including in the revealed parietal and insular regions. It is possible that an extended training period may be necessary to more effectively strengthen direct connections between the auditory and sensorimotor brain regions, for the utterly novel speech comprehension task. The outcomes of the study can be relevant for both basic neuroscience, as well as development of rehabilitation tools for the hearing impaired population.
What matters in the linkage between value orientations and usage behavior of electric ride hailing service?
Authors: Nguyen Dinh Toan , Le Thi Thu Mai , Nguyen Thi Quynh Mai , Pham Nhat Linh , Ngo Thi Ngoc Anh , Chu Thuy Binh , Dinh Mai Huong 
Published: October 2024

PurposeThis research aims to investigate the relationship between value orientations, attitude, behavioral intention and usage behavior of electric ride hailing service in Vietnam through the moderating role of social influences.Design/methodology/approachIn total, 552 valid questionnaires were collected using the survey questionnaire to analyze the effects of value orientations on attitude toward electric ride hailing and behavioral intention. Besides, this study investigates the mediating effect of attitude toward electric ride hailing and behavioral intention in the relationship with the behavior usage of electric ride hailing service as well as the moderating effect of social influence.FindingsThree types of value orientations stimulate attitude toward electric ride hailing service and behavioral intention. In addition, attitude toward electric ride hailing service and behavioral intention play the mediating role in the effect of value orientations on behavior usage. Specifically, social influence plays a negative moderating role in the linkage between attitude towards and behavioral intention of electric ride hailing service and between intention and the behavior usage.Originality/valueWhile numerous studies have investigated the influence of customers’ value orientations on multiple green purchase behaviors, this study offers new insights into the moderating role of social influence in the linkages between attitude, behavioral intention and usage behavior of electric ride hailing service.