bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Color Categorization in the Brain Revealed by Frequency-tagging-based EEG
Authors: Sun Mengdan , Gao Xiaoqing 
Published: August 2022

ABSTRACTThe origin of color categories has been debated extensively. Historically, linguistic relativists claim that color categories are shaped by the language we speak and that color terms subsequently affect our perception of color, while universalists postulate that color categories are independent of language and formed based on perceptual mechanisms. A recent hypothesis suggests that the original fine-grained color space in the visual cortex may be transformed into categorical encoding due to top-down modulation. To test the nature of color categorization, our study adopted a sensitive frequency-tagging-based EEG paradigm where the color stimuli were presented sequentially at a fast speed of 10 Hz (SOA: 100 ms) to probe fast, implicit processing of color categories. This SOA was supposed to disrupt top-down feedbacks in visual processing. We showed that EEG responses to cross-category oddball colors at the frequency where the oddball stimuli were presented was significantly larger than the responses to within-category oddball colors. This finding suggested that the brain encodes color categories automatically when top-down feedbacks from frontoparietal areas are blocked. Our study supports the view that the categorical processing of color emerges at the early perceptual stage.
Laminar VASO fMRI in focal hand dystonia patients
Authors: Huber Laurentius (Renzo) , Kassavetis Panagiotis , Gulban Omer Faruk , Hallett Mark , Horovitz Silvina G 
Published: August 2022

AbstractFocal Hand Dystonia (FHD) is a disabling movement disorder characterized by involuntary movements, cramps and spasms. It is associated with pathological neural microcircuits in the cortical somatosensory system. While invasive preclinical modalities allow researchers to probe specific neural microcircuits of cortical layers and columns, conventional functional magnetic resonance imaging (fMRI) cannot resolve such small neural computational units. In this study, we take advantage of recent developments in ultra-high-field MRI hardware and MR-sequences to capture altered digit representations and laminar processing in FHD patients. We aim to characterize the capability and challenges of layer-specific imaging and analysis tools in resolving laminar and columnar structures in clinical research setups.We scanned N=4 affected and N=5 unaffected hemispheres at 7T and found consistent results of altered neural microcircuitry in FHD patients: a) In affected hemispheres of FHD patients, we found a breakdown of ordered finger representation in the primary somatosensory cortex, as suggested from previous low-resolution fMRI. b) In affected primary motor cortices of FHD patients, we furthermore found increased fMRI activity in superficial cortico-cortical neural input layers (II/III), compared to relatively weaker activity in the cortico-spinal output layers (Vb/VI).Overall, we show that layer-fMRI acquisition and analysis tools are applicable to address clinically-driven neuroscience research questions about altered computational mechanisms at the spatial scales that were previously only accessible in animal models. We believe that this study paves the way for easier translation of preclinical work into clinical research in focal hand dystonia and beyond.
TSNAdb v2.0: the updated version of tumor-specific neoantigen database
Authors: Wu Jingcheng , Chen Wenfan , Zhou Yuxuan , Chi Ying , Hua Xiansheng , Wu Jian , Gu Xun , Chen Shuqing , Zhou Zhan 
Published: August 2022

ABSTRACTTumor neoantigens have been well-acknowledged as ideal targets for tumor immunotherapy in recent years. With the deepening of research on neoantigen-based tumor immunotherapy, comprehensive neoantigen databases are urgently needed to meet the growing demand for clinical studies. We have built the Tumor-Specific NeoAntigen Database (TSNAdb v1.0) previously, which has attracted wide attention. In this study, we provide an updated version of the Tumor-Specific NeoAntigen Database (TSNAdb v2.0) with several new features including 1) taking stricter criteria for neoantigen identification. 2) providing predicted neoantigens derived from three types of somatic mutations. 3) collecting experimentally validated neoantigens and classifying them according to the evidence. TSNAdb v2.0 is freely available at https://pgx.zju.edu.cn/tsnadb/.
Artificial immune cell,AI-cell, a new tool to predict interferon production by peripheral blood monocytes in response to nucleic acid nanoparticles
Authors: Chandler Morgan , Jain Sankalp , Halman Justin , Hong Enping , Dobrovolskaia Marina A. , Zakharov Alexey V. , Afonin Kirill A. 
Published: August 2022

ABSTRACTNucleic acid nanoparticles, or NANPs, are rationally designed to communicate with the human immune system and can offer innovative therapeutic strategies to overcome the limitations of traditional nucleic acid therapies. Each set of NANPs is unique in their architectural parameters and physicochemical properties, which together with the type of delivery vehicles determine the kind and the magnitude of their immune response. Currently, there are no predictive tools that would reliably guide NANPs’ design to the desired immunological outcome, a step crucial for the success of personalized therapies. Through a systematic approach investigating physicochemical and immunological profiles of a comprehensive panel of various NANPs, our research team has developed a computational model based on the transformer architecture able to predict the immune activities of NANPsviaconstruction of so-called artificial immune cell, orAI-cell. TheAI-cellwill aid addressing in timely manner the current critical public health challenges related to overdose and safety criteria of nucleic acid therapies and promote the development of novel biomedical tools.
Cortical dynamics of speech feedback control in non-fluent Primary Progressive Aphasia
Authors: Kothare Hardik , Ranasinghe Kamalini G. , Hinkley Leighton B. , Mizuiri Danielle , Licata Abigail , Lauricella Michael , Honma Susanne , Borghesani Valentina , Dale Corby , Shwe Wendy , Welch Ariane , Miller Zachary , Gorno-Tempini Maria Luisa , Houde John F. , Nagarajan Srikantan S. 
Published: August 2022

AbstractPrimary Progressive Aphasia (PPA) is a clinical syndrome in which patients progressively lose speech and language abilities. The non-fluent variant of PPA (nfvPPA) is characterised by impaired motor speech and agrammatism. To date, no study in nfvPPA patients has either examined speech motor control behaviour or imaged the speech motor control network during vocal production. Here, we did this using a novel structure-function imaging approach integrating magnetoencephalographic imaging of neural oscillations with voxel-based morphometry (VBM). We examined task-induced non-phase-locked neural oscillatory activity during a vocal motor control task, where participants were prompted to phonate the vowel /□/ for ∼2.4s while the pitch of their auditory feedback was shifted either up or down by 100 cents for a period of 400ms mid-utterance. Participants were 18 nfvPPA patients (14 female, mean age = 67.79 ± 8.02 years) and 17 controls (13 female, mean age = 64.81 ± 5.76 years). Patients showed a smaller compensation response to pitch perturbation than controls (p < 0.05). Task-induced neural oscillations across five frequency bands were reconstructed in source space for each subject during pitch feedback perturbation. Patients exhibited reduced task-induced alpha-band (8-12Hz) neural activity unrelated to their atrophy patterns, in the right temporal lobe and the right temporoparietal junction (p < 0.01) from 250ms to 750ms after pitch perturbation onset. Patients also showed increased task-induced beta-band (12-30Hz) activity also unrelated to cortical atrophy in the left dorsal sensorimotor cortex, left premotor cortex and the left supplementary motor area (p < 0.01) from 50ms to 150ms after pitch perturbation onset. Reduced average alpha-band power at the peak voxel in the temporoparietal cluster in the right hemisphere could predict speech motor impairment in patients (β = 3.41, F = 8.31, p = 0.0128) whereas increased average beta-band power at the peak voxel in the left dorsal sensorimotor cluster could not (β = -1.75, F = 1.72, p = 0.2123). Collectively, these results suggest significant disruption in sensorimotor integration during vocal production in nfvPPA patients which occurs unrelated to patterns of atrophy. These findings highlight how multimodal structure-function imaging in PPA enhances our understanding of its pathophysiological sequelae.
The spectral underpinnings of pathogen spread on animal networks
Authors: Fountain-Jones Nicholas M. , Silk Mathew , Appaw Raima Carol , Hamede Rodrigo , Rushmore Julie , VanderWaal Kimberly , Craft Meggan E , Carver Scott , Charleston Michael 
Published: August 2022

AbstractPredicting what factors promote or protect populations from infectious disease is a fundamental epidemiological challenge. Social networks, where nodes represent hosts and edges represent direct or indirect contacts between them, are important in quantifying these aspects of infectious disease dynamics. However, how network structure and epidemic parameters interact in empirical networks to promote or protect animal populations from infectious disease remains a challenge. Here we draw on advances in spectral graph theory and machine learning to build predictive models of pathogen spread on a large collection of empirical networks from across the animal kingdom. We show that the spectral features of an animal network are powerful predictors of pathogen spread for a variety of hosts and pathogens and can be a valuable proxy for the vulnerability of animal networks to pathogen spread. We validate our findings using interpretable machine learning techniques and provide a flexible web application for animal health practitioners to assess the vulnerability of a particular network to pathogen spread.
Iron accumulation drives fibrosis, senescence, and the senescence-associated secretory phenotype
Authors: Maus Mate , López-Polo Vanessa , Lafarga Miguel , Aguilera Mònica , Lama Eugenia De , Meyer Kathleen , Manonelles Anna , Sola Anna , Martinez Cecilia Lopez , López-Alonso Ines , Hernandez-Gonzales Fernanda , Chaib Selim , Rovira Miguel , Sanchez Mayka , Faner Rosa , Agusti Alvar , Prats Neus , Albaiceta Guillermo , Cruzado Josep M. , Serrano Manuel 
Published: August 2022

ABSTRACTFibrogenesis is part of a normal protective response to tissue injury that can become irreversible and progressive, leading to fatal diseases. Senescent cells are a main driver of fibrotic diseases through their secretome, known as senescence-associated secretory phenotype (SASP). However, the mechanisms involved in the conversion of damaged cells into senescent cells remain incompletely understood. Here, we report that multiple types of fibrotic diseases in mice and humans are characterized by the accumulation of iron. We show that vascular and hemolytic injuries, through the release of iron, are efficient in triggering senescence and fibrosis. Interestingly, the accumulation of iron is an intrinsic property of senescent cells that does not require an abnormal surge in extracellular iron. Upon damage, cells initiate an iron accumulation response with abundant ferritin-bound iron within lysosomes and high levels of labile iron, the latter being a main driver of senescence-associated ROS and SASP. Finally, we demonstrate that detection of iron by magnetic resonance imaging (MRI) is a powerful non-invasive method to assess fibrotic burden in the kidneys of mice and patients with renal fibrosis. Our findings establish a central role for iron accumulation in senescence and fibrogenesis.
NEMO- and RelA-dependent NF-κB Signaling Promotes Small Cell Lung Cancer
Authors: Koerner Lioba , Yang Tsun-Po , Schmiel Marcel , Peifer Martin , Buettner Reinhard , Pasparakis Manolis 
Published: August 2022

AbstractSmall cell lung cancer (SCLC) is an aggressive type of lung cancer driven by combined loss of the tumor suppressors RB1 and TP53. SCLC is highly metastatic and despite good initial response to chemotherapy patients usually relapse, resulting in poor survival. Therefore, better understanding of the mechanisms driving SCLC pathogenesis is required to identify new therapeutic targets. Here we identified a critical role of the IKK/NF-κB signaling pathway in SCLC development. Using a relevant mouse model of SCLC, we found that ablation of NEMO/IKKγ, the regulatory subunit of the IKK complex that is essential for activation of canonical NF-κB signaling, strongly delayed the onset and growth of SCLC resulting in considerably prolonged survival. In addition, ablation of the main NF-κB family member p65/RelA also delayed the onset and growth of SCLC and prolonged survival, albeit to a lesser extent than NEMO. Interestingly, constitutive activation of IKK/NF-κB signaling within the tumor cells did not exacerbate the pathogenesis of SCLC, suggesting that endogenous NF-κB levels are sufficient to fully support tumor development. Moreover, TNFR1 deficiency did not affect the development of SCLC, showing that TNF signaling does not play an important role in this tumor type. Taken together, our results revealed that IKK/NF-κB signaling plays an important role in promoting SCLC, identifying the IKK/NF-κB pathway as a promising therapeutic target.
Mapping the Macrostructure and Microstructure of the in vivo Human Hippocampus using Diffusion MRI
Authors: Karat Bradley G. , DeKraker Jordan , Hussain Uzair , Köhler Stefan , Khan Ali R. 
Published: August 2022

AbstractThe hippocampus is classically divided into mesoscopic subfields which contain varying microstructure that contribute to their unique functional roles. It has been challenging to characterize this microstructure with current MR based neuroimaging techniques. In this work, we used diffusion MRI and a novel surface-based approach in the hippocampus which revealed distinct microstructural distributions of neurite density and dispersion, T1w/T2w ratio as a proxy for myelin content, fractional anisotropy, and mean diffusivity. We used the Neurite Orientation Dispersion and Density Imaging (NODDI) model optimized for gray matter diffusivity to characterize neurite density and dispersion. We found that neurite dispersion was highest in the Cornu Ammonis (CA) 1 and subiculum subfields which likely captures the large heterogeneity of tangential and radial fibers, such as the Schaffer collaterals, perforant path, and pyramidal neurons. Neurite density and T1w/T2w were highest in the subiculum and CA3 and lowest in CA1, which may reflect known myeloarchitecture differences between these subfields. Using a simple logistic regression model, we showed that neurite density, dispersion, and T1w/T2w measures provided good separability across the subfields, suggesting that they may be sensitive to the known variability in subfield cyto- and myeloarchitecture. We report macrostructural measures of gyrification, thickness, and curvature that were in line with ex vivo descriptions of hippocampal anatomy. We employed a multivariate orthogonal projective non-negative matrix factorization (OPNNMF) approach to capture co-varying regions of macro- and microstructure across the hippocampus. The clusters were highly variable along the medial-lateral (proximal-distal) direction, likely reflecting known differences in morphology, cytoarchitectonic profiles, and connectivity. Finally, we show that by examining the main direction of diffusion relative to canonical hippocampal axes, we could identify regions with stereotyped microstructural orientations that may map onto specific fiber pathways, such as the Schaffer collaterals, perforant path, fimbria, and alveus. These results highlight the value of combining in vivo diffusion MRI with computational approaches for capturing hippocampal microstructure, which may provide useful features for understanding cognition and for diagnosis of disease states.
12S Gene Metabarcoding with DNA Standard Quantifies Marine Bony Fish Environmental DNA, Identifies Threshold for Reproducible Amplification, and Overcomes Distortion Due to Non-Fish Vertebrate DNA
Authors: Stoeckle Mark Y. , Ausubel Jesse H. , Coogan Michael 
Published: August 2022

ABSTRACTSingle-species PCR assays accurately measure eDNA concentration. Here we test whether multi-species PCR, i.e., metabarcoding, with an internal standard can quantify eDNA of marine bony fish. Replicate amplifications with Riaz 12S gene primers were spiked with known amounts of a non-fish vertebrate DNA standard, indexed separately, and sequenced on an Illumina MiSeq. Fish eDNA copies were calculated by comparing fish and standard reads. Relative reads were directly proportional to relative DNA copies, with average and maximum variance between replicates of about 1.3- and 2.0-fold, respectively. There was an apparent threshold for consistent amplification of about 10 eDNA copies per PCR reaction. The internal DNA standard corrected for distortion of read counts due to non-fish vertebrate DNA. To assess potential amplification bias among species, we compared reads obtained with Riaz 12S primers to those with modified MiFish primers. Our results provide evidence that Riaz 12S gene metabarcoding with an internal DNA standard quantifies marine bony fish eDNA over a range of about 10 to 5,000 copies per reaction, without indication of significant PCR bias among teleost species. In mid-Atlantic coastal samples, eDNA rarity was the main limitation to reproducible detection and quantification, and this was partly overcome by increasing the amount of a DNA sample amplified. Our findings support incorporating a DNA standard in 12S metabarcoding to help quantify eDNA abundance for marine bony fish species.
The managerial role and psychosocial factors of job satisfaction: a cross-sectional study among Wittyfit’s users
Authors: Colin-Chevalier Rémi , Pereira Bruno , Dewavrin Samuel , Cornet Thomas , Żak Marek , Benson Amanda Clare , Dutheil Frédéric 
Published: August 2022

AbstractBackgroundJob satisfaction is an emerging indicator for measuring workers’ occupational well-being, however this has been poorly studied in those with managerial roles.ObjectiveWe aimed to explore job satisfaction in workers and to determine and assess psychosocial factors that may influence this relationship.MethodsData from Wittyfit’s users were collected between January 2018 and February 2020. Volunteers anonymously provided socio-demographic data and responses to questionnaires about their levels of job satisfaction and psychosocial feelings (ambiance, meaning, organization, recognition, values, work-life balance).Results10,484 employees (40.9% of women) and 836 managers (33.9% of women), i.e. 11,320 workers with median age of 45 years and seniority of median 10 years of service, were included in the study. Job satisfaction of workers was higher in managers than employees (mean ± SD 68.1 ± 20.4 vs 57.8 ± 24.2, p < .001), as were their feelings about ambiance (71.2 ± 20.9 vs 66.1 ± 24.2), meaning (66.9 ± 21.8 vs 56.1 ± 23.1), organization (55.3 ± 23.6 vs 46.6 ± 24.6), recognition (62.8 ± 23.9 vs 48.3 ± 26.7) and values (66.3 ± 21.7 vs 56.5 ± 23.1) (p < .001). There was no difference in work-life balance (58.1 ± 23.9 vs 59.2 ± 23.4, p = 0.2). All psychosocial factors had an impact on job satisfaction for both managers and employees (p < .001). High job satisfaction was more prevalent in workers who were managers than in employees (84.6 vs 68.8%, p < .001). Even though the managerial position was the most influential factor of job satisfaction (OR = 2.65, 95% CI 2.18 to 3.23, p < .001), other socio-demographic variables such as age (0.87, 0.79 to 0.95, p = 0.002) and seniority (0.71, 0.65 to 0.79, p < .001) also had an influence, although three times less.ConclusionsManagers seem to have higher job satisfaction and psychosocial feelings about their work than employees. Psychosocial factors, many which are modifiable, as well as socio-demographic factors such as age and seniority, may influence job satisfaction among workers.Trial registrationClinicaltrials.gov: NCT02596737.
Contribution of the eye and ofopn4xafunction to circadian photoentrainment in the diurnal zebrafish
Authors: Chaigne Clair , Sapède Dora , Cousin Xavier , Sanchou Laurent , Blader Patrick , Cau Elise 
Published: August 2022

AbstractThe eye is instrumental for controlling circadian rhythms in mice and human. Here, we address the conservation of this function in the zebrafish, a diurnal vertebrate. Using lakritz (lak) mutant larvae, which lack retinal ganglion cells (RGCs), we show that while a functional eye contributes to masking, it is largely dispensable for the establishment of circadian rhythms of locomotor activity. Furthermore, the eye is dispensable for the induction of a phase delay following a pulse of white light at CT 16 but contributes to the induction of a phase advance upon a pulse of white light at CT21. Melanopsin photopigments are important mediators of photoentrainment, as shown in nocturnal mammals. One of the zebrafish melanopsin genes,opn4xa, is expressed in RGCs but also in photosensitive projection neurons in the pineal gland. Pinealopn4xa+ projection neurons function in a LIGHT ON manner in contrast to other projection neurons which function in a LIGHT OFF mode. We generated anopn4xamutant in which the pineal LIGHT ON response is impaired. This mutation has no effect on masking and circadian rhythms of locomotor activity, or for the induction of phase shifts, but slightly modifies period length when larvae are subjected to constant light. Finally, analysis ofopn4xa;lakdouble mutant larvae did not reveal redundancy between the function of the eye andopn4xain the pineal for the control of phase shifts after light pulses. Our results support the idea that the eye is not the sole mediator of light influences on circadian rhythms of locomotor activity and highlight differences in the circadian system and photoentrainment of behaviour between different animal models.Author summaryExperiments performed in mice have established a crucial role for the eye in general and melanopsin expressing cells in particular in the control of circadian rhythms most notably during photoentrainment, by which circadian rhythms adapt to a changing light environment. In marked contrast to this, we show that in zebrafish the eye and photosensitivity dependent on one of the melanopsin genes,opn4xa, which is expressed in both the eye and the pineal gland, are largely dispensable for correct circadian rhythms. These results provide insight that the light sensors orchestrating circadian rhythms of locomotor activity are different between animal models supporting that vertebrates might employ different molecular/cellular circuits for photoentrainment of behaviour depending on their phylogeny and/or temporal niche.