bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding functional brain reorganisation for naturalistic piano playing in novice pianists
Authors: Olszewska Alicja M. , Gaca Maciej , Droździel Dawid , Widlarz Agnieszka , Herman Aleksandra M. , Marchewka Artur 
Published: January 2024

AbstractLearning to play the piano is a unique complex task, integrating multiple sensory modalities and higher-order cognitive functions. Longitudinal neuroimaging studies on adult novice musicians show training-related functional changes in music perception tasks. The reorganisation of brain activity while actually playing an instrument was studied only on a very short time-frame of a single fMRI session, and longer interventions have not yet been performed. Thus, our aim was to investigate the dynamic complexity of functional brain reorganisation while playing the piano within the first half year of musical training.We scanned twenty-four novice keyboard learners (female, 18-23yo) using fMRI while they played increasingly complex musical pieces after 1, 6, 13 and 26 weeks of training.Playing music evoked responses bilaterally in the auditory, inferior frontal and supplementary motor areas, and the left sensorimotor cortex. The effect of training over time, however, invoked widespread changes encompassing the right sensorimotor cortex, cerebellum, superior parietal cortex, anterior insula and hippocampus, among others. As the training progressed, the activation of these regions decreased while playing music. Post-hoc analysis revealed region-specific time-courses for independent auditory and motor regions of interest. These results suggest that while the primary sensory, motor and frontal regions are associated with playing music, the training decreases the involvement of higher-order cognitive control and integrative regions, and basal ganglia. Moreover, training might affect distinct brain regions in different ways, providing evidence in favour of the dynamic nature of brain plasticity.Significance statementMastering the piano is a unique process requiring a collaboration of multiple brain regions. However, associated brain activation changes are not well understood. Using functional MRI, we showed that playing the piano activated brain areas associated with movement and auditory processing. However, as the novice pianists progressed through their training, the activation of other brain regions, involved in memory retrieval, auditory-motor integration, or the processing of musical syntax, was gradually reduced. Our findings suggest that musical training is an optimisation process, with higher-order cognitive networks being activated more strongly at the beginning and their activity decreasing with increased proficiency.
Do organisms need an impact factor? Citations of key biological resources including model organisms reveal usage patterns and impact
Authors: Piekniewska Agata , Anderson Nathan , Roelandse Martijn , Lloyd K. C. Kent , Korf Ian , Voss S. Randal , de Castro Giovanni , Magnani Diogo M. , Varga Zoltan , James-Zorn Christina , Horb Marko , Grethe Jeffery S. , Bandrowski Anita 
Published: January 2024

AbstractResearch resources like transgenic animals and antibodies are the workhorses of biomedicine, enabling investigators to relatively easily study specific disease conditions. As key biological resources, transgenic animals and antibodies are often validated, maintained, and distributed from university based stock centers. As these centers heavily rely largely on grant funding, it is critical that they are cited by investigators so that usage can be tracked. However, unlike systems for tracking the impact of papers, the conventions and systems for tracking key resource usage and impact lag behind. Previous studies have shown that about 50% of the resources are not findable, making the studies they are supporting irreproducible, but also makes tracking resources difficult. The RRID project is filling this gap by working with journals and resource providers to improve citation practices and to track the usage of these key resources. Here, we reviewed 10 years of citation practices for five university based stock centers, characterizing each reference into two broad categories: findable (authors could use the RRID, stock number, or full name) and not findable (authors could use a nickname or a common name that is not unique to the resource). The data revealed that when stock centers asked their communities to cite resources by RRID, in addition to helping stock centers more easily track resource usage by increasing the number of RRID papers, authors shifted from citing resources predominantly by nickname (∼50% of the time) to citing them by one of the findable categories (∼85%) in a matter of several years. In the case of one stock center, the MMRRC, the improvement in findability is also associated with improvements in the adherence to NIH rigor criteria, as determined by a significant increase in the Rigor and Transparency Index for studies using MMRRC mice. From this data, it was not possible to determine whether outreach to authors or changes to stock center websites drove better citation practices, but findability of research resources and rigor adherence was improved.
Selective manipulation of the host RNA-polymerase transcription fidelity increases phenotypic mutations in an insectParvovirus
Authors: Labadie Thomas , Cambray Guillaume 
Published: January 2024

ABSTRACTIn the dynamic dance of evolution, organisms are often faced with fluctuating environments to which adaptation through selection of traditional heritable genetic mutations can be limiting. In this study, we unveil a refined mechanism of non-heritable variability in a virus with a compact DNA genome. We discovered that the genome of theJunona cœniadensovirus (JcDV) experiences a 10-fold lower transcription fidelity than the rest of the host’s transcriptome, despite the shared transcription machinery. We found that the virus’ capsid proteins interact with the host’s RNA Polymerase II, and further show that truncating these proteins through early stop codons largely restore the transcriptional fidelity of viral genes. These observations suggest a potential mechanism for the selective manipulation of transcription accuracy. We also pinpoint specific sequence contexts that may provide other knobs to finely control the local transcription fidelity. We estimate that this lower transcriptional fidelity results in more than 7% of the viral proteome bearing at least one non-synonymous mutation. The production of non-heritable functional diversity by hijacking the transcriptional machinery might be a refined strategy to enhance short term adaptation within the complex and ever-changing host-parasite interface, and might be shared by other genetic parasites. Our findings shed light on a virus-specific transcription fidelity control mechanism, expanding our understanding of adaptive strategies in biological entities.
Crosstalk interactions between transcription factors ERRα and PPARα assist PPARα-mediated gene expression
Authors: Desmet Sofie J. , Thommis Jonathan , Vanderhaeghen Tineke , Vandenboorn Edmee M. F. , Li Yunkun , Timmermans Steven , Fijalkowska Daria , Ratman Dariusz , Van Hamme Evelien , De Cauwer Lode , Staels Bart , Brunsveld Luc , Peelman Frank , Libert Claude , Tavernier Jan , De Bosscher Karolien 
Published: January 2024

AbstractThe peroxisome proliferator-activated receptor α (PPARα) is a crucial transcription factor governing genes associated with fatty acid β-oxidation. How various interacting proteins modulate PPARα’s transcriptional function remains incompletely understood. Employing an unbiased mammalian protein-protein interaction trap with liganded PPARα as bait, we identified an interaction with the orphan nuclear receptor estrogen-related receptor α (ERRα). Random mutagenesis scanning of PPARα’s ligand-binding domain and coregulator profiling experiments implicated bridging coregulators, whilein vitrostudies suggested a trimeric interaction involving RXRα. The PPARα·ERRα interaction, dependent on three C-terminal residues within ERRα’s helix 12, was reinforced by PGC1α and serum deprivation. Pharmacological inhibition of ERRα reduced its interaction with ligand-activated PPARα, revealing a transcriptome indicative of ERRα functioning as a transcriptional repressor on prototypical PPARα target genes. Intriguingly, ERRα exhibited opposite behavior on other PPARα targets, including the isolated PDK4 enhancer. Chromatin immunoprecipitation analyses demonstrated PPARα ligand-dependent recruitment of ERRα onto specific chromatin regions where PPARα binds in mouse livers. These findings highlight intricate transcriptional crosstalk mechanisms between PPARα and ERRα, suggesting a multi-layered regulatory network fine-tuning PPARα’s activity as a nutrient-sensing transcription factor.
Biomechanical properties of defence vibrations produced by bees
Authors: Vallejo-Marin Mario , Field David L. , Fornoni Juan , Montesinos Daniel , Dominguez Cesar A. , Hernandez Ivan , Vallejo Gillian C. , Woodrow Charlie , Barajas Ricardo Ayala , Jafferis Noah 
Published: January 2024

AbstractBees use thoracic vibrations produced by their indirect flight muscles for powering wingbeats in flight, but also during mating, pollination, defence, and nest building. Previous work on non-flight vibrations has mostly focused on acoustic (airborne vibrations) and spectral properties (frequency domain). However, mechanical properties such as the vibration’s acceleration amplitude are important in some behaviours, e.g., during buzz pollination, where higher amplitude vibrations remove more pollen from flowers. Bee vibrations have been studied in only a handful of species and we know very little about how they vary among species. Here, we conduct the largest survey to date of the biomechanical properties of non-flight bee buzzes. We focus on defence buzzes as they can be induced experimentally and provide a common currency to compare among taxa. We analysed 15,000 buzzes produced by 306 individuals in 65 species and six families from Mexico, Scotland, and Australia. We found a strong association between body size and the acceleration amplitude of bee buzzes. Comparison of genera that buzz-pollinate and those that do not suggests that buzz-pollinating bees produce vibrations with higher acceleration amplitude. We found no relationship between bee size and the fundamental frequency of defence buzzes. Although our results suggest that body size is a major determinant of the amplitude of non-flight vibrations, we also observed considerable variation in vibration properties among bees of equivalent size and even within individuals. Both morphology and behaviour thus affect the biomechanical properties of non-flight buzzes.Summary statementAnalyses across 65 bee taxa in three continents indicates that body size is a major determinant of the acceleration amplitude but not the oscillation frequency of non-flight thoracic vibrations.
Simultaneous, cortex-wide and cellular-resolution neuronal population dynamics reveal an unbounded scaling of dimensionality with neuron number
Authors: Manley Jason , Demas Jeffrey , Kim Hyewon , Martínez Traub Francisca , Vaziri Alipasha 
Published: January 2024

SUMMARYThe brain’s remarkable properties arise from collective activity of millions of neurons. Widespread application of dimensionality reduction to multi-neuron recordings implies that neural dynamics can be approximated by low-dimensional “latent” signals reflecting neural computations. However, what would be the biological utility of such a redundant and metabolically costly encoding scheme and what is the appropriate resolution and scale of neural recording to understand brain function? Imaging the activity of one million neurons at cellular resolution and near-simultaneously across mouse cortex, we demonstrate an unbounded scaling of dimensionality with neuron number. While half of the neural variance lies within sixteen behavior-related dimensions, we find this unbounded scaling of dimensionality to correspond to an ever-increasing number of internal variables without immediate behavioral correlates. The activity patterns underlying these higher dimensions are fine-grained and cortex-wide, highlighting that large-scale recording is required to uncover the full neural substrates of internal and potentially cognitive processes.
Bacterial ADP-heptose initiates a revival stem cell program in the intestinal epithelium
Authors: Goyal Shawn , Guo Cynthia X. , Ranger Adrienne , Tsang Derek K. , Singh Ojas , Harrigan Caitlin F. , Zaslaver Olga , Rost Hannes L. , Gaisano Herbert Y. , Yuzwa Scott A. , Gao Nan , Wrana Jeffrey L. , Philpott Dana J. , Gray-Owen Scott D. , Girardin Stephen E. 
Published: January 2024

ABSTRACTThe intestinal epithelium has an exceptional capacity to repair following injury, and recent evidence has suggested that YAP-dependent signaling was crucial for the expansion ofClu+revival stem cells (revSCs) with fetal-like characteristics, which are essential for epithelial regeneration. However, neither the mechanism underlying where these revSCs emerge from nor the nature of the physiological cues that induce this revSC program, are clearly identified. Here, we first demonstrate thatAlpk1andTifa, which encode the proteins essential for the detection of the bacterial metabolite ADP-heptose (ADP-Hep), were expressed by the stem cell pool in the intestinal epithelium. Treatment of intestinal organoids with ADP-Hep not only induced acute NF-κB pro-inflammatory signaling but also TNF-dependent apoptosis within the crypt, causing blunted proliferation and acute disruption of the crypt architecture, while also triggering induction of a revSC program. To identify the molecular underpinnings of this process, we performed single-cell RNA-seq analysis of ADP-Hep-treated organoids as well as lineage-tracing experiments. Our data reveal that ADP-Hep induced the specific ablation of the homeostatic intestinal stem cell (ISC) pool. Removal of ADP-Hep resulted in the rapid recovery of ISCs through dedifferentiation of Paneth cells, which transiently acquired revSC features and expressed nuclear YAP. Moreover, lineage tracing fromLyz1+Paneth cells showed that ADP-Hep triggered Paneth cell de-differentiation towards pluripotent and proliferative cells in organoids.In vivo, revSC emergence in response to irradiation-induced injury was severely blunted inTifa-deficient mice, suggesting that efficient epithelial regeneration in this model required detection of microbiota-derived ADP-Hep by the ALPK1-TIFA pathway. Together, our work reveals that Paneth cells can serve as the cell of origin for revSC induction in the physiological context of microbial stimulation, and that the transient loss ofAlpk1-expressing ISCs is the initiating event for this regenerative process.
Biochemical and Structural Characterization of Fapy•dG Replication by Human DNA Polymerase β
Authors: Gao Shijun , Oden Peyton N. , Ryan Benjamin J. , Yang Haozhe , Freudenthal Bret D. , Greenberg Marc M. 
Published: January 2024

ABSTRACTN6-(2-deoxy-α,β-D-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamido-pyrimidine (Fapy•dG) is formed from a common intermediate and in comparable amounts to the well-studied mutagenic DNA lesion 8-oxo-7,8-dihydro-2’-deoxyguanosine (8-OxodGuo). Fapy•dG preferentially gives rise to G → T transversions and G → A transitions. However, the molecular basis by which Fapy•dG is processed by DNA polymerases during this mutagenic process remains poorly understood. To address this we investigated how DNA polymerase β (Pol β), a model mammalian polymerase, bypasses a templating Fapy•dG, inserts Fapy•dGTP, and extends from Fapy•dG at the primer terminus. When Fapy•dG is present in the template, Pol β incorporates TMP less efficiently than either dCMP or dAMP. Kinetic analysis revealed that Fapy•dGTP is a poor substrate but is incorporated ∼3-times more efficiently opposite dA than dC. Extension from Fapy•dG at the 3’-terminus of a nascent primer is inefficient due to the primer terminus being poorly positioned for catalysis. Together these data indicate that mutagenic bypass of Fapy•dG is likely to be the source of the mutagenic effects of the lesion and not Fapy•dGTP. These experiments increase our understanding of the promutagenic effects of Fapy•dG.
biobank.cy: The Biobank of Cyprus past, present and future
Authors: Loizidou Eleni M. , Kyratzi Maria , Tsiarli Maria A. , Kakouri Andrea C. , Charalambidou Georgia , Antoniou Stella , Pieri Stylianos , Veloudi Panagiota , Mayrhofer Michaela Th. , Wutte Andrea , Kozera Lukasz , Habermann Jens , Muller Heimo , Zatloukal Kurt , Sargsyan Karine , Michaelides Alexandros , Papaioannou Maria , Schizas Christos , Malatras Apostolos , Papagregoriou Gregory , Deltas Constantinos 
Published: January 2024

AbstractBackgroundThe Cyprus Biobank collects biosamples, medical and lifestyle information with the aim of reaching 16,500 Cypriots aged ≥18-years, by year 2027, as part of a multitasked EU funded project. Volunteers are both from the general population and from disease cohorts of focused research projects, who amongst others will contribute to canvas the architecture of the Cyprus human genome and study the healthy and morbid anatomy of Cypriots. The Cyprus Biobank is a research infrastructure pillar of the biobank.cy Center of Excellence in Biobanking and Biomedical Research.MethodsWithin 3-years (November 2019-October 2022), 1348 participants of the general population who represent a subset of the Cyprus Biobank recruited individuals, were enrolled in the pilot study. The study did not include individuals from separate disease-specific cohorts. Extensive information was collected from each participant, including biochemistry, complete blood count, physiological, anthropometric, socio-demographic, diet, and lifestyle characteristics. Prevalent health conditions along with medication use and family history were recorded, including 58 biomarkers based on blood and urine samples. With a systematic recruitment campaign, the Biobank is continuously increasing the number of individuals in the general population cohort and is developing separate disease cohorts of the Cypriot population.ResultsThe pilot study enrolled 579 men and 769 women, aged between 18-85 years (median 48-years). The enrollment takes 40 minutes on average, including the collection of biological samples and phenotypic information. More than half (n=733, 55%) of the participants are educated to college level or above. Statistically significant differences were found between men and women regarding their education level (p<0.001), marital status (p=0.01) and employment status (p<0.001) but not their age (p=0.29). The most prevalent medical conditions recorded are hypertension (17.2%), osteoporosis (6.9%) and diabetes (6.0%).ConclusionsThe Cyprus biobanking pilot study has successfully collected extensive baseline information from enrolled participants. The Biobank will comprise a rich data resource used to examine the major risk factors leading to public health burdens and develop strategies for disease prevention.
A treasure trove of 1,034 actinomycete genomes
Authors: Jørgensen Tue Sparholt , Mohite Omkar , Sterndorff Eva B , Alvarez-Arevalo Maria , Blin Kai , Booth Thomas J , Charusanti Pep , Faurdal David , Hansen Troels Ø , Nuhamunada Matin , Mourched Anna-Sophie , Palsson Bernhard Ø , Weber Tilmann 
Published: January 2024

AbstractFilamentous Actinobacteria, previously Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences from more than 1,000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera and 389 species, including 244 likely novel species. All genomes are from filamentous isolates of the class Actinomycetia from the NBC culture collection. The largest genus isStreptomyceswith 886 genomes including 742 complete assemblies. We use this data to show that analysis of complete genomes can bring biological understanding not previously derived from more fragmented sequences or less systematic datasets. We document the central and structured location of core genes and distal location of specialized metabolite biosynthetic gene clusters and duplicate core genes on the linearStreptomyceschromosome, and analyze the content and length of the terminal inverted repeats which are characteristic forStreptomyces. We then analyze the diversity of trans-AT polyketide synthase biosynthetic gene clusters, which encodes the machinery of a biotechnologically highly interesting compound class. These insights have both ecological and biotechnological implications in understanding the importance of high quality genomic resources and the complex role synteny plays in Actinomycetia biology.
An intracranial dissection of human escape circuits
Authors: Zhang Haoming , Cheng Jiayu , Hu Keyu , Wang Fengpeng , Qi Song , Liu Quanying , Yao Yi , Mobbs Dean , Wu Haiyan 
Published: January 2024

AbstractPredators attack at different spatiotemporal scales, spurring prey to elicit escape responses that range from simple motor reactions and strategic planning that involve more complex cognitive processes. Recent work in humans suggests that escape relies on two distinct circuits: the reactive and cognitive fear circuits. However, the specific involvement of these two circuits in different stages of human escaping remains poorly characterized. In this study, we recorded intracranial electroencephalography (iEEG) from epilepsy patients while they performed a modified flight initiation distance (FID) task. We found brain regions in the cognitive fear circuit, including the ventromedial prefrontal cortex and hippocampus, encoded the threat level during the information processing stage. The actual escaping stage, especially under rapid attack, prominently activated areas within the reactive fear circuit, including the midcingulate cortex and amygdala. Furthermore, we observed a negative correlation between the high gamma activity (HGA) of the amygdala and the HGA of the vmPFC and HPC under rapid attacks. This indicates that the amygdala may suppress the activity of the cognitive fear circuit under rapid attacks, enabling the organism to react quickly to ensure survival under the imminent threat. These findings highlight the distinct roles of the reactive and cognitive fear circuits in human escaping and provide accounts for the importance of fear in human survival decisions.