bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the use of supplementary materials to improve genomic variant discovery
Authors: Pasche Emilie , Mottaz Anaïs , Gobeill Julien , Michel Pierre-André , Caucheteur Déborah , Naderi Nona , Ruch Patrick 
Published: April 2023

AbstractThe curation of genomic variants requires collecting evidence not only in variant knowledge bases but also in the literature. However, some variants result in no match when searched in the scientific literature. Indeed, it has been reported that a significant subset of information related to genomic variants are not reported in the full text, but only in the supplementary materials associated with a publication. In the study, we present an evaluation of the use of supplementary data (SD) to improve the retrieval of relevant scientific publications for variant curation. Our experiments show that searching SD enables to significantly increase the volume of documents retrieved for a variant, thus reducing by ∼63% the number of variants for which no match is found in the scientific literature. SD thus represent a paramount source of information for curating variants of unknown significance and should receive more attention by global research infrastructures, which maintain literature search engines.Database URL https://www.expasy.org/resources/variomes
Spoken Sentence Complexity and Grammar Use in Children with CIs
Authors: Socher Michaela , Ingo Elisabeth 
Published: April 2023

Abstract
This study investigated if the language profiles of prelingually deaf children with bilateral cochlear implants (CIs) and children with typical hearing (TH) matched on their quantitative score on clinical spoken expressive language tasks differed in terms of sentence complexity, sentence length, and severity of grammatical errors. No significant differences were found between the groups in terms of (1) proportion of simple, conjoined, and complex sentences; (2) mean length of utterance based on words and syllables; and (3) proportion of local and global grammatical errors. The results indicate that the quantitative scores on the clinical spoken expressive language tasks are related to similar spoken language profiles in children with CIs and children with TH. These findings suggest that these tests can be used for meaningful comparisons of expressive spoken language skills. However, more studies are needed on the real-life expressive language skills of children with CIs, as clinical tests often rely on one specific modality (in this study: spoken language) and might therefore not accurately represent the language skills of the children.
Frailty prevalence and efficient screening in primary care-based memory clinics
Authors: Lee Linda , Jones Aaron , Patel Tejal , Hillier Loretta M , Heckman George A , Costa Andrew P 
Published: April 2023

Abstract

Background
Little is known about the prevalence of frailty among patients with memory concerns attending a primary care-based memory clinic.

Objective
This study aims to describe the prevalence of frailty among patients attending a primary care-based memory clinic and to determine if prevalence rates differ based on the screening tool that is used.

Methods
We conducted a retrospective medical record review for all consecutive patients assessed in a primary care-based memory clinic over 8 months. Frailty was measured in 258 patients using the Fried frailty criteria, which relies on physical measures, and the Clinical Frailty Scale (CFS), which relies on functional status. Weighted kappa statistics were calculated to compare the Fried frailty and the CFS.

Results
The prevalence of frailty was 16% by Fried criteria and 48% by the CFS. Agreement between Fried frailty and CFS was fair for CFS 5+ (kappa = 0.22; 95% confidence interval: 0.13, 0.32) and moderate for CFS 6+ (kappa = 0.47; 0.34, 0.61). Dual-trait measures of hand grip strength with gait speed were found to be a valid proxy for Fried frailty phenotype.

Conclusions
Among primary care patients with memory concerns, frailty prevalence rates differed based on the measure used. Screening for frailty in this population using measures relying on physical performance may be a more efficient approach for persons already at risk of further health instability from cognitive impairment. Our findings demonstrate how measure selection should be based on the objectives and context in which frailty screening occurs.
Assessing the longitudinal effects of the continuation and discontinuation of the school-located influenza vaccination programme on parental vaccine hesitancy in Hong Kong
Authors: Dong Meihong , Ip Dennis Kai Ming , Yuan Jiehu , So Hau Chi , Cowling Benjamin J , Liao Qiuyan 
Published: April 2023

Abstract

Background
School-located influenza vaccination programme (SIVP) can effectively promote childhood seasonal influenza vaccination (SIV). However, the longitudinal effects of continuation and discontinuation of the SIVP on parents’ vaccine hesitancy remained unknown.

Methods
A two-wave longitudinal study recruited adult parents who had at least one child attending a kindergarten or primary school using random-digital-dialled telephone interviews. Generalized estimating equation and structural equation modelling were used to examine the impact of changes in schools’ SIVP participation status on parents’ vaccine-related attitudes, and childhood SIV acceptance over 2 years in Hong Kong.

Results
Children’s SIV uptake varied by the schools’ SIVP participation status. The highest SIV uptake was found in schools that consistently participated in SIVP (Consistent participation group) (2018/2019: 85.0%; 2019/2020: 83.0%) but lowest in the Consistent non-Participation group (2018/2019: 45.0%; 2019/2020: 39.0%). SIV uptake increased in the Late Initiation group but declined in the Discontinuation group. An increasing trend of parental vaccine-hesitant attitudes was observed in the Consistent non-Participation group.

Conclusions
Initiation and continuation of the SIVP can reduce parental vaccine hesitancy to achieve a high childhood SIV uptake. Conversely, discontinuation of the SIVP or persistent resistance to the implementation of SIVP can increase parental vaccine hesitancy and reduce childhood SIV uptake.
Neural and behavioral signatures of the multidimensionality of manipulable object processing
Authors: Almeida J. , Fracasso A. , Kristensen S. , Valério D. , Bergström F. , Chakravarthi R. , Tal Z. , Walbrin J. 
Published: April 2023

AbstractUnderstanding how we recognize everyday objects requires unravelling the variables that govern the way we think about objects and the way in which our representations are organized neurally. A major hypothesis is that the organization of object knowledge follows key object-related dimensions, analogously to how sensory information is organized in the brain. Here, we explored, behaviorally and neurally, the multidimensionality of object processing. We focused on within-domain object information as a proxy for the kinds of object decision tasks we typically engage in our daily lives – e.g., identifying a knife from other types of manipulable objects such as spoons, axes or screwdrivers. To do so, we extracted object-related dimensions from subjective human judgments on a set of objects from a particular object domain – i.e., manipulable objects. We demonstrated that the extracted dimensions are cognitively interpretable – i.e., participants are able to label them; are cognitively relevant for manipulable object processing – i.e., categorization decisions are guided by these dimensions; and are important for the neural organization of knowledge – i.e., they are good predictors of the neural signals elicited by manipulable objects. This shows that multidimensionality is a hallmark of the organization of object knowledge in the brain.
Angular head velocity cells within brainstem nuclei projecting to the head direction circuit
Authors: Graham Jalina A. , Dumont Julie R. , Winter Shawn S. , Brown Joel E. , LaChance Patrick A. , Amon Carly C. , Farnes Kara B. , Morris Ashlyn J. , Streltzov Nicholas A. , Taube Jeffrey S. 
Published: April 2023

AbstractAn animal’s perceived sense of orientation depends upon the head direction (HD) system found in several limbic structures and depends upon an intact peripheral vestibular labyrinth. However, how the vestibular system influences the generation, maintenance, and updating of the HD signal remains poorly understood. Anatomical and lesion studies point towards three key brainstem nuclei as being potential critical components in generating the HD signal: nucleus prepositus hypoglossi (NPH), supragenual nucleus (SGN), and dorsal paragigantocellularis reticular nuclei (PGRNd). Collectively, these nuclei are situated between the vestibular nuclei and the dorsal tegmental and lateral mammillary nuclei, which are thought to serve as the origin of the HD signal. To test this hypothesis, extracellular recordings were made in these areas while rats either freely foraged in a cylindrical environment or were restrained and rotated passively. During foraging, a large subset of cells in all three nuclei exhibited activity that correlated with changes in the rat’s angular head velocity (AHV). Two fundamental types of AHV cells were observed: 1) symmetrical AHV cells increased or decreased their neural firing with increases in AHV regardless of the direction of rotation; 2) asymmetrical AHV cells responded differentially to clockwise (CW) and counter-clockwise (CCW) head rotations. When rats were passively rotated, some AHV cells remained sensitive to AHV whereas others had attenuated firing. In addition, a large number of AHV cells were modulated by linear head velocity. These results indicate the types of information conveyed in the ascending vestibular pathways that are responsible for generating the HD signal.Significance StatementExtracellular recording of brainstem nuclei (nucleus prepositus hypoglossi, supragenual nucleus, and dorsal paragigantocellularis reticular nucleus) that project to the head direction circuit identified different types of angular head velocity (AHV) cells while rats freely foraged in a cylindrical environment. The firing of many cells was also modulated by linear velocity. When rats were restrained and passively rotated some cells remained sensitive to AHV, whereas others had attenuated firing. These brainstem nuclei provide critical information about the rotational movement of the rat’s head in the azimuthal plane.
Interactions between environmental sensitivity and gut microbiota are associated with biomarkers of stress-related psychiatric symptoms
Authors: Iimura Shuhei , Takasugi Satoshi , Yasuda Miyabi , Saito Yoshie , Morifuji Masashi 
Published: April 2023

AbstractBackgroundHumans vary in their sensitivity to stressful and supportive environments and experiences. Such individual differences in environmental sensitivity are associated with mechanisms of stress-related psychiatric symptoms. In recent years, researchers have focused on bidirectional interactions in the brain-gut-microbiota axis as a neurophysiological pathway contributing to the mechanisms of stress-related psychiatric symptoms, and evidence is rapidly accumulating.MethodsData on environmental sensitivity, gut microbiota, gut permeability (lipopolysaccharide-binding protein; LBP) and inflammation (C-reactive protein; CRP) were collected from 90 adults (50% female;Mage= 42.1;SDage= 10.0). Environmental sensitivity was measured using a self-report questionnaire. Study participants’ feces were analyzed, and observed operational taxonomic units for richness, Shannon’s index for evenness, and phylogenetic diversity for biodiversity were evaluated as indicators of gut microbiota. In addition, participants’ serum was analyzed for CRP and LBP. We investigated whether the interaction between environmental sensitivity and gut microbiota is associated with biomarkers of inflammation and gut permeability.ResultsThe interaction between environmental sensitivity and gut microbiota (excluding the Shannon’s index) explained the levels of these biomarkers. Individuals with high environmental sensitivity displayed higher levels of CRP and LBP, when the richness and diversity of the gut microbiota was low. However, even highly susceptible individuals had lower levels of CRP and LBP, when the richness and diversity of the gut microbiota was high.ConclusionsOur study indicates that high environmental sensitivity can be a risk factor for inflammation and gut permeability, when the gut microbiota diversity is low, suggesting a brain-gut-microbiota axis interaction.
Cue Disparity and Visual Selective Attention in Praying Mantises
Authors: Robert Théo , Ting Tan Yi , Ganot Dune , Loh Yi Jie , Nityananda Vivek 
Published: April 2023

SummaryResearch on insect selective attention has typically investigated it using stimuli in a single plane. The importance of cues to depth, such as stereoscopic disparity, is less well understood. Recent findings on the neurobiology of mantis stereopsis demonstrated centrifugal neuronal connections from the central brain to peripheral optic areas, suggesting the possibility of attentional modulation. To test this, we investigated whether the disparity of a prior cue influences mantis tracking of 3D targets. We fitted mantises with 3D glasses and presented them with a cue, followed by two 3D stimuli – a high contrast target and a distractor with different contrasts. The cue appeared either on the side of the target or the distractor. We varied the disparity of the cue and measured the influence of the cue on the probability of head saccades to the target. Our results show that, compared to the uncued condition, cues with a crossed or an uncrossed disparity reduced head saccades to a single target when presented on the opposite side of the screen. These effects were not seen for cues with zero disparity. The effects of cues of different disparities did not themselves differ significantly, but crossed and uncrossed disparity cues had a stronger effect than zero disparity cues. Our results show that mantis selective attention is influenced by the presence and position of prior cues with a potential influence of cue disparity. This adds further evidence for the complexity of attention-like processes in insects.
Spectrally and temporally resolved estimation of neural signal diversity
Authors: Mediano Pedro A.M. , Rosas Fernando E. , Luppi Andrea I. , Noreika Valdas , Seth Anil K. , Carhart-Harris Robin L. , Barnett Lionel , Bor Daniel 
Published: April 2023

AbstractQuantifying the complexity of neural activity has provided fundamental insights into cognition, consciousness, and clinical conditions. However, the most widely used approach to estimate the complexity of neural dynamics, Lempel-Ziv complexity (LZ), has fundamental limitations that substantially restrict its domain of applicability. In this article we leverage the information-theoretic foundations of LZ to overcome these limitations by introducing a complexity estimator based on state-space models —which we dubComplexity via State-space Entropy Rate(CSER). While having a performance equivalent to LZ in discriminating states of consciousness, CSER boasts two crucial advantages: 1) CSER offers a principled decomposition into spectral components, which allows us to rigorously investigate the relationship between complexity and spectral power; and 2) CSER provides a temporal resolution two orders of magnitude better than LZ, which allows complexity analyses of e.g. event-locked neural signals. As a proof of principle, we use MEG, EEG and ECoG datasets of humans and monkeys to show that CSER identifies the gamma band as the main driver of complexity changes across states of consciousness; and reveals early entropy increases thatprecedethe standard ERP in an auditory mismatch negativity paradigm by approximately 20ms. Overall, by overcoming the main limitations of LZ and substantially extending its range of applicability, CSER opens the door to novel investigations on the fine-grained spectral and temporal structure of the signal complexity associated with cognitive processes and conscious states.
Identification and Characterisation of Proteins Binding to a G-Quadruplex Origin G-rich Repeated Element in Mammalian Cells
Authors: Hutchins James R. A. , Peiffer Isabelle , Urbach Serge , Mergny Jean-Louis , Marin Philippe , Maiorano Domenico , Méchali Marcel 
Published: April 2023

AbstractIn metazoan cells, replication of genomic DNA initiates from thousands of discrete chromosomal loci known as origins. Proteins such as the Origin Recognition Complex (ORCs) associate with origins, but this does not show clear sequence specificity for DNA binding. Genome-wide origin mapping studies have shown that the region surrounding the replication initiation site contains motifs such as the Origin G-rich Repeated Element (OGRE), proximal to the majority of origins. Here, using an approach coupling DNA affinity purification to quantitative proteomics, we identified proteins that interact specifically with an OGRE. Three of the top-scoring interactors, Dhx36, Pura and Tial1, were selected for further study. We show that Dhx36 and Tial1 localise to the nucleus and their knockdown decreased cells in S-phase resulting in their accumulation in the G1phase of the cell cycle. Altogether these results indicate that these OGRE-binding factors may play roles in DNA synthesis in mammalian cells.
Optical polarization evolution and transmission in multi-Ranvier-node axonal myelin-sheath waveguides
Authors: Frede Emily , Zadeh-Haghighi Hadi , Simon Christoph 
Published: April 2023

ABSTRACTIn neuroscience, it is of interest to consider all possible modes of information transfer between neurons in order to fully understand processing in the brain. It has been suggested that photonic communication may be possible along axonal connections, especially through the myelin sheath as a waveguide, due to its high refractive index. There is already a good deal of theoretical and experimental evidence for light guidance in the myelin sheath; however, the question of how the polarization of light is transmitted remains largely unexplored. It is presently unclear whether polarization-encoded information could be preserved within the myelin sheath. We simulate guided mode propagation through a myelinated axon structure with multiple Ranvier nodes. This allows both to observe polarization change and to test the assumption of exponentiated transmission loss through multiple Ranvier nodes for guided light in myelin sheath waveguides. We find that the polarization can be well preserved through multiple nodes and that transmission losses through multiple nodes are approximately multiplicative. These results provide an important context for the hypothesis of neural information transmission facilitated by biophotons, strengthening the possibility of both classical and quantum photonic communication within the brain.
Spatiotemporal patterns of cortical microstructural maturation in children and adolescents with diffusion MRI
Authors: Lynch Kirsten M. , Cabeen Ryan P. , Toga Arthur W. 
Published: April 2023

AbstractNeocortical maturation is a dynamic process that proceeds in a hierarchical manner; however, the spatiotemporal organization of cortical microstructure with diffusion MRI has yet to be fully defined. This study characterized cortical microstructural maturation using diffusion MRI (fwe-DTI and NODDI multi-compartment modeling) in a cohort of 637 children and adolescents between 8 and 21 years of age. We found spatially heterogeneous developmental patterns broadly demarcated into functional domains where NODDI metrics increased and fwe-DTI metrics decreased with age. Using non-negative matrix factorization, we found cortical regions that correspond to lower-order sensory regions mature earlier than higher-order association regions. Our findings corroborate previous histological and neuroimaging studies that show spatially-varying patterns of cortical maturation that may reflect unique developmental processes of cytoarchitectonically-determined regional patterns of change.
RIF1 regulates replication origin activity and early replication timing in B cells
Authors: Malzl Daniel , Peycheva Mihaela , Rahjouei Ali , Gnan Stefano , Klein Kyle N. , Nazarova Mariia , Schoeberl Ursula E. , Gilbert David M. , Buonomo Sara C. B. , Virgilio Michela Di , Neumann Tobias , Pavri Rushad 
Published: April 2023

ABSTRACTThe mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin, regulates early origin firing and promotes early replication. RIF1 has a minor role in gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal new layers of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.
Vasopressin regulates social play behavior in sex-specific ways through glutamate modulation in the lateral septum
Authors: Bredewold Remco , Washington Catherine , Veenema Alexa H. 
Published: April 2023

ABSTRACTSocial play is a highly rewarding behavior that is essential for the development of social skills. Social play is impaired in children diagnosed with autism, a disorder with a strong sex bias in prevalence. We recently showed that the arginine vasopressin (AVP) system in the lateral septum (LS) regulates social play behavior sex-specifically in juvenile rats: Administration of a AVP 1a receptor (V1aR) antagonist increased social play behavior in males and decreased it in females. Here, we demonstrate that glutamate, but not GABA, is involved in the sex-specific regulation of social play by the LS-AVP system. First, males show higher extracellular glutamate concentrations in the LS than females while they show similar extracellular GABA concentrations. This resulted in a baseline sex difference in excitatory/inhibitory balance, which was eliminated by V1aR antagonist administration into the LS: V1aR antagonist increased extracellular glutamate release in females but not in males. Second, administration of the glutamate receptor agonist L-glutamic acid into the LS prevented the V1aR antagonist-induced increase in social play behavior in males while mimicking the V1aR antagonist-induced decrease in social play behavior in females. Third, administration of the glutamate receptor antagonists AP-5 and CNQX into the LS prevented the V1aR antagonist-induced decrease in social play behavior in females. Last, both sexes showed increases in extracellular LS-GABA release upon V1aR antagonist administration into the LS and decreases in social play behavior upon administration of the GABA-A receptor agonist muscimol into the LS, suggesting that GABA is not involved in the sex-specific regulation of social play by the LS-AVP system. Finally, to start identifying the cellular mechanism mediating the sex-specific effects of the LS-AVP system on LS-glutamate, we determined the presence of potential sex differences in the type of LS cells expressing V1aR. However, no sex differences were found in the percentage of Avpr1a+ LS cells expressing markers for either GABAergic neurons, somatostatin-expressing neurons, calbindin 1-expressing neurons, or astrocytes. In conclusion, these findings demonstrate that the LS-AVP system regulates social play sex-specifically via differential local glutamatergic neurotransmission in male and female juvenile rats. Further research is required to uncover the underlying cellular mechanism.