bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of photobiomodulation to control pain after placement of elastomeric spacers: a randomized controlled study protocol
Authors: Pascuali Moya Luis Eduardo , Consolandich Cirisola Rolf Wilhem , García Olazabal María Victoria , Bruno Laura Hermida , Safi Federico Todeschini , Piriz Trindade Lucia , Longo Priscila Larcher , Chavantes Maria Cristina , Navarro Ricardo Scarparo , Duran Cinthya Cosme Gutierrez , Fernandes Kristianne Porta Santos , Mesquita Ferrari Raquel Agnelli , Bussadori Sandra Kalil , Motta Lara Jansiski , Horliana Anna Carolina Ratto Tempestini 
Published: October 2023

ABSTRACTRecent studies have shown that photobiomodulation (FBM) can modulate pain after the placement of elastomeric separators, however, to date, there is no ideal protocol for its application. Therefore, the objective of this study will be to evaluate the effect of photobiomodulation on pain control 24 hours after the placement of elastomeric separators using the visual analog scale (VAS). Twenty-five participants between 13 and 30 years old with the need for the placement of orthodontic bands in the lower first molars bilaterally will be included, which establishes a sample of fifty molars (right and left). Elastomeric separators will be placed on the mesial and distal surfaces of the right and left molars. The study groups will be G1 (experimental) - elastomeric separators + FBM (diode laser, 808nm, 100mw power, with 4 J, 3 points per vestibular and 3 points per palatal, single session) and G2-(control)-elastomeric separators + FBM simulation. Treatment will be randomized to the right molar and the opposite treatment will be applied to the left side. The patient and the evaluator will be blinded to the intervention performed. The primary outcome variable will be spontaneous pain assessed 24 hours after the placement of elastomeric separators measured with the VAS scale. Secondary outcome variables will be pain during mastication (measured with the VAS scale) at 72h after the placement, count of the number of analgesics (paracetamol), and local temperature (measured with a digital thermometer). To assess the impact of oral health on quality of life. of the participant, the OHIP-14 questionnaire will be applied. All the outcomes will be evaluated at baseline, 24 and 72 hours after the placement of elastomeric separators. If the data are normal, they will be submitted to the ANOVA – one-way test. Data will be presented as means ± SD and the p-value will be set to < 0.05.
Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes
Authors: Latrille T. , Bastian M. , Gaboriau T. , Salamin N. 
Published: October 2023

AbstractTo quantify selection acting on a trait, methods have been developed using either within or between-species variation. However, methods using within-species variation do not integrate the changes at the macro-evolutionary scale. Conversely, current methods using between-species variation usually discard within-species variation, thus not accounting for processes at the micro-evolutionary scale. The main goal of this study is to define a neutrality index for a quantitative trait, by combining within- and between-species variation. This neutrality index integrates nucleotide polymorphism and divergence for normalizing trait variation. As such, it does not require estimation of population size nor of time of speciation for normalization. Our index can be used to seek deviation from the null model of neutral evolution, and test for diversifying selection. Applied to brain mass and body mass at the mammalian scale, we show that brain mass is under diversifying selection. Finally, we show that our test is not sensitive to the assumption that population sizes, mutation rates and generation time are constant across the phylogeny, and automatically adjust for it.
MAP1B Regulates Cortical Neuron Interstitial Axon Branching Through the Tubulin Tyrosination Cycle
Authors: Ziak Jakub , Dorskind Joelle , Trigg Brian , Sudarsanam Sriram , Hand Randal , Kolodkin Alex L. 
Published: October 2023

ABSTRACTRegulation of directed axon guidance and branching during development is essential for the generation of neuronal networks. However, the molecular mechanisms that underlie interstitial axon branching in the mammalian brain remain unresolved. Here, we investigate interstitial axon branchingin vivousing an approach for precise labeling of layer 2/3 callosal projection neurons (CPNs), allowing for quantitative analysis of axonal morphology at high acuity and also manipulation of gene expression in well-defined temporal windows. We find that the GSK3β serine/threonine kinase promotes interstitial axon branching in layer 2/3 CPNs by releasing MAP1B-mediated inhibition of axon branching. Further, we find that the tubulin tyrosination cycle is a key downstream component of GSK3β/MAP1B signaling. We propose that MAP1B functions as a brake on axon branching that can be released by GSK3β activation, regulating the tubulin code and thereby playing an integral role in sculpting cortical neuron axon morphology.HIGHLIGHTS- GSK3β activation induces excessive interstitial axon branching in excitatory cortical neurons- MAP1B, acting as a brake, is a downstream effector of GSK3β-mediated axon branching- MAP1B inhibition of axon branching is released by GSK3β phosphorylation- GSK3β/MAP1B regulation of interstitial axon branching is through modification of the tubulin code
The nutrient sensor CRTC & Sarcalumenin / Thinman represent a new pathway in cardiac hypertrophy
Authors: Dondi Cristiana , Vogler Georg , Gupta Anjali , Walls Stanley M. , Kervadec Anaïs , Romero Michaela R. , Diop Soda B. , Goode Jason , Thomas John B. , Colas Alexandre R. , Bodmer Rolf , Montminy Marc , Ocorr Karen 
Published: October 2023

ABSTRACTObesity and type 2 diabetes are at epidemic levels and a significant proportion of these patients are diagnosed with left ventricular hypertrophy.CREBRegulatedTranscriptionCo-activator (CRTC) is a key regulator of metabolism in mammalian hepatocytes, where it is activated by calcineurin (CaN) to increase expression of gluconeogenic genes. CaN is known its role in pathological cardiac hypertrophy, however, a role for CRTC in the heart has not been identified. InDrosophila,CRTCnull mutants have little body fat and exhibit severe cardiac restriction, myofibrillar disorganization, cardiac fibrosis and tachycardia, all hallmarks of heart disease. Cardiac-specific knockdown ofCRTC, or its coactivatorCREBb, mimicked the reduced body fat and heart defects ofCRTCnull mutants. Comparative gene expression inCRTCloss- or gain-of-function fly hearts revealed contra-regulation of genes involved in glucose, fatty acid, and amino acid metabolism, suggesting thatCRTCalso acts as a metabolic switch in the heart. Among the contra-regulated genes with conserved CREB binding sites, we identified the fly ortholog ofSarcalumenin,which is a Ca2+-binding protein in the sarcoplasmic reticulum. Cardiac knockdown recapitulated the loss of CRTC cardiac restriction and fibrotic phenotypes, suggesting it is a downstream effector ofCRTCwe namedthinman(tmn). Importantly, cardiac overexpression of either CaN orCRTCin flies caused hypertrophy that was reversed in aCRTCmutant background, suggesting CRTC mediates hypertrophy downstream of CaN, perhaps as an alternative to NFAT. CRTC novel role in the heart is likely conserved in vertebrates as knockdown in zebrafish also caused cardiac restriction, as in fl ies. These data suggest that CRTC is involved in myocardial cell maintenance and that CaN-CRTC- Sarcalumenin/tmnsignaling represents a novel and conserved pathway underlying cardiac hypertrophy.
WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows
Authors: Bouyssié David , Altıner Pınar , Capella-Gutierrez Salvador , Fernández José M. , Hagemeijer Yanick Paco , Horvatovich Peter , Hubálek Martin , Levander Fredrik , Mauri Pierluigi , Palmblad Magnus , Raffelsberger Wolfgang , Rodríguez-Navas Laura , Di Silvestre Dario , Kunkli Balázs Tibor , Uszkoreit Julian , Vandenbrouck Yves , Vizcaíno Juan Antonio , Winkelhardt Dirk , Schwämmle Veit 
Published: October 2023

AbstractProteomics research encompasses a wide array of experimental designs, resulting in diverse datasets varying in structure and properties. This diversity has led to a considerable variety of software solutions for data analysis, each of them using multiple tools with different algorithms for operations like peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. Computational workflows combine these algorithms to facilitate end-to-end analysis, spanning from raw data to detecting differentially regulated proteins. We introduce WOMBAT-P, a versatile platform designed for the automatic benchmarking and comparison of bottom-up label-free proteomics workflows. By standardizing software parameterization and workflow outputs, WOMBAT-P empowers an objective comparison of four commonly utilized data analysis workflows. Furthermore, WOMBAT-P streamlines the processing of public data based on the provided metadata, with an optional specification of 30 parameters. Wombat-P can use Sample and Data Relationship Format for Proteomics (SDRF-Proteomics) as the file input to simply process annotated local or ProteomeXchange deposited datasets. This feature offers a shortcut for data analysis and facilitates comparisons among diverse outputs. Through an examination of experimental ground truth data and a realistic biological dataset, we unveil significant disparities and a low overlap between identified and quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of four workflows (on the same dataset) using a wide range of benchmarking metrics but also provides insights into the capabilities of different software solutions. These metrics support researchers in selecting the most suitable workflow for their specific dataset. The modular architecture of WOMBAT-P promotes extensibility and customization, making it an ideal platform for testing newly developed software tools within a realistic data analysis context.
Biochemical and structural characterization of a Class A β-lactamase fromNocardia cyriacigeorgica
Authors: Feuillard Jérôme , Couston Julie , Benito Yvonne , Hodille Elisabeth , Dumitrescu Oana , Blaise Mickaël 
Published: October 2023

AbstractNocardiaare gram-positive bacteria from the Actinobacteria phylum. SomeNocardiaspecies can infect humans and are usually considered opportunist pathogens as they often infect immunocompromised patients. Albeit, their clinical incidence is low, manyNocardiaspecies are nowadays considered emerging pathogens. Primary sites of infection ofNocardiaare the skin or the lungs but dissemination to other body parts is very frequent. These disseminated infections are very difficult to treat and thus, tackled with multiple classes of antibiotics, on top of the traditional treatment targeting the folate pathway. ß-lactams are often included in the regimen but manyNocardiaspecies present moderate or strong resistance to some of this drug class. Genomic, microbiological, and biochemical studies have reported the presence of class A ß-lactamases (ABL) in a handful ofNocardiaspecies but no structural investigation ofNocardiaß-lactamases has been performed yet. In this study, we report the expression, purification, and preliminary biochemical characterization of the ABL from aNocardia cyriacigeorgica(NCY-1) clinical strain. We describe, as well, the crystallization and the very high-resolution crystal structure of NCY-1. The protein sequence and structural analysis demonstrate that NCY-1 belongs to ß-lactamase of class A1 and attest to its very high conservation with ABL from other human pathogenicNocardia. In addition, the presence of one molecule of citrate tightly bound in the catalytic site of the enzyme is described. This structure may provide a solid basis for future drug development to specifically targetNocardiaspp. ß-lactamases.SynopsisThe crystal structure at high resolution of a class A ß-lactamase from a clinical strain ofNocardia cyriacigeorgicais reported.
Scene-selectivity in CA1/subicular complex: Multivoxel pattern analysis at 7T
Authors: Read Marie-Lucie , Berry Samuel C. , Graham Kim S. , Voets Natalie L. , Zhang Jiaxiang , Aggleton John P. , Lawrence Andrew D. , Hodgetts Carl J. 
Published: October 2023

AbstractPrior univariate functional magnetic resonance imaging (fMRI) studies in humans suggest that the anteromedial subicular complex of the hippocampus is a hub for scene-based cognition. However, it is possible that univariate approaches were not sufficiently sensitive to detect scene-related activity in other subfields that have been implicated in spatial processing (e.g., CA1). Further, as connectivity-based functional gradients in the hippocampus do not respect classical subfield boundary definitions, category sensitivity may be distributed across anatomical subfields. Region-of-interest approaches, therefore, may limit our ability to observe category selectivity across discrete subfield boundaries. To address these issues, we applied searchlight multivariate pattern analysis to 7T fMRI data of healthy adults who undertook a simultaneous visual odd-one-out discrimination task for scene and non-scene (including face) visual stimuli, hypothesising that scene classification would be possible in multiple hippocampal regions within, but not constrained to, anteromedial subicular complex and CA1. Indeed, we found that the scene-selective searchlight map overlapped not only with anteromedial subicular complex (distal subiculum, pre/para subiculum), but also inferior CA1, alongside retrosplenial and parahippocampal cortices. Probabilistic overlap maps revealed gradients of scene category selectivity, with the strongest overlap located in the medial hippocampus, converging with searchlight findings. This was contrasted with gradients of face category selectivity, which had stronger overlap in more lateral hippocampus, supporting ideas of parallel processing streams for these two categories. Our work helps to map the scene, in contrast to, face processing networks within, and connected to, the human hippocampus.
Evolution of research topics and paradigms in plant sciences
Authors: Shiu Shin-Han , Lehti-Shiu Melissa D. 
Published: October 2023

AbstractScientific advances due to conceptual or technological innovations can be revealed by examining how research topics have evolved. But such topical evolution is difficult to uncover and quantify because of the large body of literature and the needs of expert knowledge from a wide range of areas in any field. Here we used machine learning and language models to classify plant science citations into topics representing interconnected, evolving subfields. The changes in prevalence of topical records over the last 50 years reflect major research paradigm shifts and recent radiation of new topics, as well as turnovers of model species and vastly different plant science research trajectories among countries. Our approaches readily summarize the topical diversity and evolution of a scientific field with hundreds of thousands of relevant papers, and they can be applied broadly to other fields.Significance statementChanges in scientific paradigms are foundational for the advancement of science, but such changes are difficult to summarize, quantify, and illustrate. These challenges are exacerbated by the rapid, exponential growth of literature. Applying a combination of machine learning and language modeling to hundreds of thousands of published abstracts, we demonstrate that a scientific field (i.e., plant science) can be summarized as interconnected subfields evolving from one another. We also reveal insights into major research trends and the rise and decline in the use of model organisms in different countries. Our study demonstrates how artificial intelligence and language models can be broadly applied to understand scientific advances that inform science policy and funding decisions.
Evolution of olfactory sensitivity, preferences and behavioral responses in Mexican cavefish: fish personality matters
Authors: Blin Maryline , Valay Louis , Kuratko Manon , Pavie Marie , Rétaux Sylvie 
Published: October 2023

AbstractAnimals are adapted to their natural habitats and lifestyles. Their brains perceive the external worldviatheir sensory systems, compute information together with that of internal states and autonomous activity, and generate appropriate behavioral outputs. However, how do these processes evolve across evolution? Here, focusing on the sense of olfaction, we have studied the evolution in olfactory sensitivity, preferences and behavioral responses to six different food-related amino acid odors in the two eco-morphs of the fishAstyanax mexicanus. To this end, we have developed a high-throughput behavioral setup and pipeline of quantitative and qualitative behavior analysis, and we have tested 489 six-week-oldAstyanaxlarvae. The blind, dark-adapted morphs of the species showed markedly distinct basal swimming patterns and behavioral responses to odors, higher olfactory sensitivity and a strong preference for alanine, as compared to their river-dwelling eyed conspecifics. In addition, we discovered that fish have an individual “swimming personality”, and that this personality influences their capability to respond efficiently to odors and find the source. Importantly, the personality traits that favored significant responses to odors were different in surface fish and cavefish. Moreover, the responses displayed by second-generation cave x surface F2 hybrids suggested that olfactory-driven behavior and olfactory sensitivity is a quantitative genetic trait. Our findings show that olfactory processing has rapidly evolved in cavefish at several levels: detection threshold, odor preference, and foraging behavior strategy. Cavefish is therefore an outstanding model to understand the genetic, molecular and neurophysiological basis of sensory specialization in response to environmental change.
Identity and Nature of Neural Stem Cells in the Adult Human Subventricular Zone
Authors: Baig Salma , Nadaf Javad , Allache Redouane , Le Phuong U. , Luo Michael , Djedid Annisa , Safisamghabadi Maryam , Prat Alex , Antel Jack , Guiot Marie-Christine , Petrecca Kevin 
Published: October 2023

ABSTRACTThe existence of neural stem cells (NSCs) in adult human brain neurogenic regions remains unresolved. To address this, we created a cell atlas of the adult human subventricular zone (SVZ) derived from fresh neurosurgical samples using single-cell transcriptomics. We discovered 2 adult radial glia (RG)-like populations, aRG1 and aRG2. aRG1 shared features with fetal early RG (eRG) and aRG2 were transcriptomically similar to fetal outer RG (oRG). We also captured early neuronal and oligodendrocytic NSC states. We found that the biological programs driven by their transcriptomes support their roles as early-lineage NSCs. Finally, we show that these NSCs have the potential to transition between states and along lineage trajectories. These data reveal that multipotent NSCs reside in the adult human SVZ.
Activity-Dependent Alternative Splicing of Adhesion-GPCR Latrophilin-3 Controls Synapse Formation
Authors: Wang Shuai , DeLeon Chelsea , Roth Bryan , Südhof Thomas C. 
Published: October 2023

ABSTRACTHow synapses are assembled and specified in brain is incompletely understood. Latrophilin- 3, a postsynaptic adhesion-GPCR, mediates Schaffer-collateral synapse formation in the hippocampus but the mechanisms involved remained unclear. Here we show that Latrophilin-3 organizes synapses by a convergent dual-pathway mechanism by which Latrophilin-3 simultaneously activates GαS/cAMP-signaling and recruits phase-separated postsynaptic protein scaffolds. We found that cell type-specific alternative splicing of Latrophilin-3 controls its G protein coupling mode, resulting in Latrophilin-3 variants that predominantly signal via Gαsand cAMP or via Gα12/13. A CRISPR-mediated genetic switch of Latrophilin-3 alternative splicing from a GαS- to a Gα12/13-coupled mode impaired synaptic connectivity similar to the overall deletion of Latrophilin-3, suggesting that GαS/cAMP- signaling by Latrophilin-3 splice variants mediates synapse formation. Moreover, GαS- but not Gα12/13-coupled splice variants of Latrophilin-3 recruit phase-transitioned postsynaptic protein scaffolds that are clustered by binding of presynaptic Latrophilin-3 ligands. Strikingly, neuronal activity promotes alternative splicing of the synaptogenic variant of Latrophilin-3, thereby enhancing synaptic connectivity. Together, these data suggest that activity- dependent alternative splicing of a key synaptic adhesion molecule controls synapse formation by parallel activation of two convergent pathways, GαS/cAMP signaling and the phase separation of postsynaptic protein scaffolds.
Neuronal activity induces symmetry breaking in neurodegenerative disease spreading
Authors: Alexandersen Christoffer G. , Goriely Alain , Bick Christian 
Published: October 2023

AbstractDynamical systems on networks typically involve several dynamical processes evolving at different timescales. For instance, in Alzheimer’s disease, the spread of toxic protein throughout the brain not only disrupts neuronal activity but is also influenced by neuronal activity itself, establishing a feed-back loop between the fast neuronal activity and the slow protein spreading. Motivated by the case of Alzheimer’s disease, we study the multiple-timescale dynamics of a heterodimer spreading process on an adaptive network of Kuramoto oscillators. Using a minimal two-node model, we establish that heterogeneous oscillatory activity facilitates toxic outbreaks and induces symmetry breaking in the spreading patterns. We then extend the model formulation to larger networks and perform numerical simulations of the slow-fast dynamics on common network motifs and on the brain connectome. The simulations corroborate the findings from the minimal model, underscoring the significance of multiple-timescale dynamics in the modeling of neurodegenerative diseases.
Distinct learning, retention, and generalization in de novo learning
Authors: Gastrock Raphael Q. , ’t Hart Bernard Marius , Henriques Denise Y. P. 
Published: October 2023

AbstractPeople correct for movement errors when acquiring new motor skills (de novo learning) or adapting well-known movements (motor adaptation). These two motor learning types should be distinct, as de novo learning establishes new control policies while adaptation modifies existing ones. Here, we distinguish between these two motor learning types, and assess de novo learning retention and generalization. In study 1, participants train with both 30° visuomotor rotation and mirror reversal perturbations, to compare adaptation and de novo learning respectively. We find no perturbation order effects, and that learning develops with similar rates and comparable asymptotes for both perturbations. Explicit instructions also provide an advantage during early learning in both perturbations. However, mirror reversal learning shows larger inter-participant variability. Furthermore, movement initiation is slower for the mirror perturbation, and we only observe reach aftereffects following rotation training. In study 2, we use a browser-based mirror reversal task to investigate learning retention and generalization to the untrained hand and across the workspace. Learning persists across three or more days, substantially transfers to the untrained hand, and to targets on both sides of the mirror axis. Our results show that behavioral mechanisms underlying motor skill acquisition are distinct from adapting well-known movements.