bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cognitive exertion affects the appraisal of one’s own and other people’s pain
Authors: Riontino Laura , Fournier Raphael , Lapteva Alexandra , Silvestrini Nicolas , Schwartz Sophie , Corradi-Dell’Acqua Corrado 
Published: June 2022

AbstractCorrectly evaluating others’ pain is a crucial prosocial ability, especially relevant for the healthcare system. In clinical settings, caregivers assess their patients’ pain under high workload and fatigue, often while dealing with competing information/tasks. However, the effect played by such cognitive strain in the appraisal of others’ pain remains unclear. Following embodied accounts that posit a shared representational code between self and others’ states, it could be hypothesized that the representation of people’s pain might be influenced by cognitive exertion similarly to first-hand experiences.Fifty participants underwent one of two demanding tasks, involving either working memory (Experiment 1: N-Back task) or cognitive interference (Experiment 2: Stroop task). After each task, participants were exposed to painful laser stimulations at three intensity levels (low, medium, high), or video-clips of patients experiencing three intensity levels of pain (low, medium, high). Participants rated the intensity of each pain event on a visual analogue scale.We found that the two tasks influenced rating of both one’s own and others’ pain, by decreasing the sensitivity to medium and high events. This was observed either when comparing the demanding condition to a control (Stroop), or when modelling linearly the difficulty/performance of each depleting task (N-Back).We provide converging evidence that cognitive exertion affects the subsequent appraisal of one’s own and likewise others’ pain. Healthcare personnel should be aware that high workload might alter their cognitive abilities.Perspectivethis research shows that cognitive effort aftereffects impact negatively the assessment of of medium/high pain in others, reminiscently to what was observed in first-hand experiences. Healthcare professionals should be aware that high workload and severe cognitive fatigue could affect their diagnostic skills.
Effects of Oxygen Plasma Treatment on Parylene C and Parylene N Membrane Biocompatibility for Tissue Barrier Models
Authors: Gholizadeh Shayan , Lincoln Daniela M. , Allahyari Zahra , Widom Louis P. , Carter Robert N. , Gaborski Thomas R. 
Published: June 2022

ABSTRACTPorous membranes are integral components of in vitro tissue barrier and co-culture models and their interaction with cells and tissues directly affects the performance and credibility of these models. Plasma-treated Parylene C and Parylene N are two biocompatible Parylene variants with perceived potential for use in these models but their biocompatibility and biological interactions at their interface with cells are not well understood. Here, we use a simple approach for benchtop oxygen plasma treatment and investigate the changes in cell spreading and extracellular matrix deposition as well as the changes in material surface properties. Our results support the previous findings on the persistent effects of plasma treatment on Parylene biocompatibility while showing a more pronounced improvement for Parylene C over Parylene N. It is observed that although both increased surface roughness and persistent increases in oxygen species govern the plasma-driven improvement, the changes in oxygen concentration at the interface are the dominant factor. Overall, the results of this study provide a clear picture of potential mechanisms of plasma-induced changes in synthetic polymers which have implications for their use in in vitro model systems and other BioMEMS applications.
Metamorphosis of memory circuits in Drosophila reveal a strategy for evolving a larval brain
Authors: Truman James W. , Price Jacquelyn , Miyares Rosa L. , Lee Tzumin 
Published: June 2022

AbstractInsects like Drosophila produce a second brain adapted to the form and behavior of a larva. Neurons for both larval and adult brains are produced by the same stem cells (neuroblasts) but the larva possesses only the earliest born neurons produced from each. To understand how a functional larval brain is made from this reduced set of neurons, we examined the origins and metamorphic fates of the neurons of the larval and adult mushroom body circuits. The adult mushroom body core is built sequentially of γ Kenyon cells, that form a medial lobe, followed by α’β’, and αβ Kenyon cells that form additional medial lobes and two vertical lobes. Extrinsic input (MBINs) and output (MBONs) neurons divide this core into computational compartments. The larval mushroom body contains only γ neurons. Its medial lobe compartments are roughly homologous to those of the adult and same MBONs are used for both. The larval vertical lobe, however, is an analogous “facsimile” that uses a larval-specific branch on the γ neurons to make up for the missing α’β’, and αβ neurons. The extrinsic cells for the facsimile are early-born neurons that trans-differentiate to serve a mushroom body function in the larva and then shift to other brain circuits in the adult. These findings are discussed in the context of the evolution of a larval brain in insects with complete metamorphosis.
Molecular insights into human Shieldin complex assembly and recruitment to DSBs
Authors: Susvirkar Vivek , Faesen Alex C. 
Published: June 2022

AbstractThe Shieldin complex represses end resection at DNA double-strand breaks (DSBs) and thereby serves as a pro-non homologous end joining (NHEJ) factor in the G1 phase of the cell cycle. Its components SHLD1, SHLD2, SHLD3 and REV7 are recruited in a hierarchical fashion. SHLD3 and REV7 localize first to DSBs, while the subsequently recruited SHLD2 is the only known DNA binding protein in the complex. The molecular details of the initial recruitment of SHLD3 and REV7, and the subsequent assembly of Shieldin on DSBs are unclear. Here, we report the identification of a promiscuous DNA binding domain in the C-terminal half of SHLD3. At the N-terminus, SHLD3 interacts with a dimer of REV7 molecules. We show that the interaction between SHLD3 and the first REV7 is remarkably slow, which is likely due to the substantial activation energy required to remodel mobile structural elements within the REV7 molecule to allow for binding to SHLD3. In contrast, the interaction between SHLD3 and SHLD2 with a second REV7 molecule is fast and does not require structural remodelling. Overall, these results provide insights into the rate-limiting step of the molecular assembly and recruitment of Shieldin complex at DNA DSBs.
Triangulation fails when neither linguistic, genetic, nor archaeological data support the Transeurasian narrative
Authors: Tian Zheng , Tao Yuxin , Zhu Kongyang , Jacques Guillaume , Ryder Robin J. , de la Fuente José Andrés Alonso , Antonov Anton , Xia Ziyang , Zhang Yuxuan , Ji Xiaoyan , Ren Xiaoying , He Guanglin , Guo Jianxin , Wang Rui , Yang Xiaomin , Zhao Jing , Xu Dan , Gray Russell D. , Zhang Menghan , Wen Shaoqing , Wang Chuan-Chao , Pellard Thomas 
Published: June 2022

Robbeets et al.1 argue that the dispersal of the so-called “Transeurasian” languages, a highly disputed language superfamily comprising the Turkic, Mongolian, Tungusic, Koreanic, and Japonic language families, was driven by Neolithic farmers in the West Liao River region of China. They adduce evidence from linguistics, archaeology, and genetics to support their claim. An admirable feature of the Robbeets et al.’s paper is that all their datasets can be accessed. However, a closer investigation of all three types of evidence reveals fundamental problems with each of them. Robbeets et al.’s analysis of the linguistic data does not conform to the minimal standards required by traditional scholarship in historical linguistics and contradicts their own stated sound correspondence principles. A reanalysis of the genetic data finds that they do not conclusively support the farming-driven dispersal of Turkic, Mongolian, and Tungusic, nor the two-wave spread of farming to Korea. Their archaeological data contain little phylogenetic signal, and we failed to reproduce the results supporting their core hypotheses about migrations.Given the severe problems we identify in all three parts of the “triangulation” process, we conclude that there is neither conclusive evidence for a Transeurasian language family nor for associating the five different language families with the spread of Neolithic farmers from the West Liao River region.
Viscoelastic Notch Signaling Hydrogel Induces Liver Bile Duct Organoid Growth and Morphogenesis
Authors: Rizwan Muhammad , Ling Christopher , Guo Chengyu , Liu Tracy , Jiang Jia-Xin , Bear Christine E , Ogawa Shinichiro , Shoichet Molly S. 
Published: June 2022

AbstractCholangiocyte organoids can be used to model liver biliary disease; however, both a defined matrix in which to emulate cholangiocyte self-assembly and the mechano-transduction pathways involved therein remain elusive. We designed a series of defined viscoelastic hyaluronan hydrogels in which to culture primary cholangiocytes and found that by mimicking the stress relaxation rate of liver tissue, we could induce cholangiocyte organoid growth and significantly increase expression of Yes-associated protein (YAP) target genes. Strikingly, inhibition of matrix metalloproteinases (MMPs) did not significantly affect organoid growth in 3D culture, suggesting that mechanical remodeling of the viscoelastic microenvironment – and not MMP-mediated degradation – is key to cholangiocyte organoid growth. By immobilizing jagged1 to the hyaluronan, stress relaxing hydrogel, self-assembled bile duct structures formed in organoid culture, indicating the synergistic effects of Notch signaling and viscoelasticity. By uncovering critical roles of hydrogel viscoelasticity, YAP signaling and Notch activation, we controlled cholangiocyte organogenesis, thereby paving the way for their use in disease modeling and/or transplantation.
Innate and adaptive immune basis of mental health effect on Alzheimer’s disease progression
Authors: Feng Yilin , Fan Jiaqi , Cheng Yifan , Dai Qionghai , Ma Shaohua 
Published: June 2022

AbstractMental health has long been suspected to be highly associated with neurodegenerative disease, but it lacks experimental evidence to elaborate the link and immunological mechanism between them. In this work, we studied the progression of Alzheimer’s disease (AD) and its associated immune activity by using the transgenic mice under negative (depression) and positive (environmental enrichment, EE) mental health intervention. The tissue pathology, resident and peripheral immunity and behavioral characteristics were investigated. The transgenic mice undergoing depression treatment was featured with aggravated AD pathology, elevated activation of microglia in the brains, more abundance of Treg cells and cytotoxic T cells, and higher ratios of central memory T cells to effector memory T (TCM-to-TEM) cells in the peripheral blood and spleens. The EE treated mice were featured with alleviated AD pathology, reduced activation of microglia, less amounts of Treg and cytotoxic T cells and lower ratios of TCM-to-TEM cells. This study may provide strategies for immunity regulation and mental health intervention that benefit AD therapy.Significance statementMental health is suspected to regulate AD progression, but its validation in histology examination and the regulatory mechanism remains unclear. Here, we prove that both innate and adaptive immunity are playing important roles and mental health-immunity-AD progression forms a triad. More active microglia, Treg, and cytotoxic T cells, and higher TCM-to-TEM feature negative mental health and severer AD progress, and vice versa. The findings in adaptive immunity and the triad may inspire AD regulation.
Invasive genetic rescue: Dispersal following repeated culling reinforces the genetic diversity of an invasive mammal
Authors: Synnott Rebecca , Shuttleworth Craig , Everest David J. , Stevenson-Holt Claire , O’Reilly Catherine , McDevitt Allan D. , O’Meara Denise B 
Published: June 2022

AbstractSince its introduction from the United States in 1876 the invasive North American Eastern grey squirrel (Sciurus carolinensis) has contributed to the decline of the native Eurasian red squirrel (Sciurus vulgaris) in Britain. Consequently, grey squirrel populations are often subjected to extensive control efforts in order to reduce local abundance and prevent spread, particularly within habitats containing red squirrels. Grey squirrel removal from the island of Anglesey off the coast of north Wales began in 1998 and was completed in 2013. A parallel successful red squirrel reinforcement translocation project also took place. The narrow sea-channel, road and rail bridge connection has meant that the adjacent mainland grey squirrel population has been controlled in subsequent years to reduce the probability of re-invasion. The aim of this study was to assess the overall impact of repeated culling efforts carried out between 2011 and 2020 on the genetic diversity of the grey squirrel population in north Wales to inform future adaptive management plans. Using a combination of mitochondrial DNA (mtDNA) and microsatellite DNA analysis, we found high genetic diversity in both marker types, with six diverse mtDNA haplotypes found and relatively high levels of nuclear genetic diversity, even after repeated culling efforts. Our results suggest that ongoing culling efforts may not adequately reduce genetic diversity to a level where it contributes to a long-term population decline.
Masked target visibility is selectively impaired by 20 Hz transcranial alternating current stimulation
Authors: Ilkson Yayla , de la Fuente Alethia , Tagliazucchi Enzo , Pallavicini Carla 
Published: June 2022

AbstractIt has been proposed that both conscious and unconscious perception are associated with a feedforward sweep of oscillatory activity in the gamma band (>40 Hz), while conscious perception also requires recurrent feedback via beta band (~20 Hz) oscillations. To investigate the causal relationship between these oscillations and (un)conscious visual perception, we assessed the effect of transcranial alternating current stimulation (tACS) in the gamma (40 Hz) and beta (20 Hz) bands on the objective and subjective visibility of targets in a metacontrast backward masking task. We expected that 40hz-tACS would affect both the correct categorization of the target (i.e. objective visibility) and the reports of conscious perception (i.e. subjective visibility). Moreover, we expected that 20Hz-tACS would selectively affect the subjective visibility. Our results showed that target visibility was selectively compromised by 20Hz-tACS but, in contrast to our hypothesis, this effect was specific to objective visibility. Although the power of local beta oscillations increased after 20Hz-tACS, inter-areal beta synchrony could have nevertheless been impaired, a possibility that should be investigated in the future by means of source reconstructed high density electroencephalography recordings. In summary, we provided evidence supporting that 20Hz-tACS is capable of modulating target visibility, suggesting a possible a causal link between synchrony in this frequency band and visual perception. Future studies could build upon this result by investigating other forms of stimulation and other model organisms, further contributing to our knowledge of how conscious access causally depends on brain oscillations.
Effects of Aversive Classical Conditioning on Pupil Dilation and Microsaccades
Authors: Friedl W.M. , Keil Andreas 
Published: June 2022

AbstractUnintentional shifts of gaze and the modulation of pupil size are both highly automated processes that serve to regulate the initial influx of visual information. The present work investigated these mechanisms as they came to differentially respond to initially unthreatening stimuli following aversive conditioning. The classical conditioning experimental paradigm employed simple grating stimuli (Gabor patches) shown individually at various (5) on-screen locations, one of which was paired with a noxious auditory unconditioned stimulus (US). Aversively paired Gabor patches elicited an attenuated initial constriction of the pupil (pupillary light response; PLR) along with more rapid re-dilation compared to otherwise identical but unpaired gratings. Modulation of both the PLR and the rate of re-dilation following conditioning showed pronounced individual differences. Rapid eye movements away from fixation (microsaccades) were suppressed for the aversively associated compared to unassociated stimulus locations at several post-stimulus latencies. Mutual information between pupil dilation and microsaccade rate, meanwhile, did not differ between the aversively associated and unassociated visual on-screen locations. Together, these results suggest that measures of pupil diameter and microsaccade rate supply complementary information on early-stage processes of associative learning through experience.
Starvation Decreases Immunity and Immune Regulatory Factor NF-κB in the Starlet Sea Anemone Nematostella vectensis
Authors: Carrión Pablo J. Aguirre , Desai Niharika , Brennan Joseph J. , Fifer James E. , Davies Sarah W. , Gilmore Thomas D. 
Published: June 2022

AbstractLack of proper nutrition (malnutrition) or the complete absence of all food (starvation) have important consequences on the physiology of all organisms. In many cases, nutritional status affects immunity, but, for the most part, the relationship between nutrition and immunity has been limited to studies in vertebrates and terrestrial invertebrates. Herein, we describe a positive correlation between nutrition and immunity in the sea anemone Nematostella vectensis. Gene expression profiling of adult fed and starved anemones showed downregulation of many genes involved in nutrient metabolism and cellular respiration, as well as immune-related genes, in starved animals. Starved adult anemones also had reduced protein levels and DNA-binding activity of immunity-related transcription factor NF-κB. Starved juvenile anemones had increased sensitivity to bacterial infection and also had lower NF-κB protein levels, as compared to fed controls. Weighted Gene Correlation Network Analysis (WGCNA) revealed significantly correlated gene networks that were inversely associated with starvation. Based on the WGCNA and a reporter gene assay, we identified TRAF3 as a likely NF-κB target gene in N. vectensis. Overall, these experiments demonstrate a correlation between nutrition and immunity in a basal marine metazoan, and the results have implications for the survival of marine organisms as they encounter changing environments.Significance StatementAdequate nutrition is required to sustain proper biological function. One factor threatening many marine organisms, as a result of modern day anthropogenic environmental changes, is nutrient availability. Here, we characterize transcriptional changes following food deprivation in the cnidarian model sea anemone Nematostella vectensis. We show that starvation is correlated with decreased expression of genes associated with nutrient metabolism and immunity, among others. Moreover, starvation reduces the level of expression and activity of immune regulatory transcription factor NF-κB and causes anemones to have increased susceptibility to bacterial infection. These results demonstrate that this basal organism responds at the transcriptional level to the absence of food, and that, in addition to changes in metabolic factors, starvation leads to a reduction in immunity.
Diffusion on PCA-UMAP manifold captures a well-balance of local, global, and continuum structure to denoise single-cell RNA sequencing data
Authors: Padron-Manrique Cristian , Vázquez-Jiménez Aarón , Esquivel-Hernandez Diego Armando , Martinez Lopez Yoscelina Estrella , Neri-Rosario Daniel , Sánchez-Castañeda Jean Paul , Giron-Villalobos David , Resendis-Antonio Osbaldo 
Published: June 2022

AbstractSingle-cell transcriptomics (scRNA-seq) is becoming a technology that is transforming biological discovery in many fields of medicine. Despite its impact in many areas, scRNASeq is technologically and experimentally limited by the inefficient transcript capture and the high rise of noise sources. For that reason, imputation methods were designed to denoise and recover missing values. Many imputation methods (e.g., neighbor averaging or graph diffusion) rely on k nearest neighbor graph construction derived from a mathematical space as a low-dimensional manifold. Nevertheless, the construction of mathematical spaces could be misleading the representation of densities of the distinct cell phenotypes due to the negative effects of the curse of dimensionality. In this work, we demonstrated that the imputation of data through diffusion approach on PCA space favor over-smoothing when increases the dimension of PCA and the diffusion parameters, such k-NN (k-nearest neighbors) and t (value of the exponentiation of the Markov matrix) parameters. In this case, the diffusion on PCA space distorts the cell neighborhood captured in the Markovian matrix creating an artifact by connecting densities of distinct cell phenotypes, even though these are not related phenotypically. In this situation, over-smoothing of data is due to the fact of shared information among spurious cell neighbors. Therefore, it can not account for more information on the variability (from principal components) or nearest neighbors for a well construction of a cell-neighborhood. To solve above mentioned issues, we propose a new approach called sc-PHENIX( single cell-PHEnotype recovery by Non-linear Imputation of gene eXpression) which uses PCA-UMAP initialization for revealing new insights into the recovered gene expression that are masked by diffusion on PCA space. sc-PHENIX is an open free algorithm whose code and some examples are shown at https://github.com/resendislab/sc-PHENIX.
Glioma-BioDP: Database for Visualization of Molecular Profiles to Improve Prognosis of Brain Cancer
Authors: Das Shaoli , Deng Xiang , Kaur Harpreet , Wilson Evan , Camphausen Kevin , Shankavaram Uma 
Published: June 2022

AbstractCancer researchers often seek user-friendly interactive tools for validation, exploration, analysis, and visualization of molecular profiles in cancer patient samples. To aid researchers working on both low-and high-grade gliomas, we developed Glioma-BioDP, a web tool for exploration and visualization of RNA and protein expression profiles of interest in these tumor types. Glioma-BioDP is an extended version of our earlier published tool GBM-BioDP. In this version we have included expression data from both the low-and high-grade glioma patient samples from The Cancer Genome Atlas and enabled querying by mRNA, microRNA, and protein level expression data from Illumina HiSeq and RPPA platforms respectively. Glioma-BioDP enables users to explore the association of genes, proteins, and miRNA expression with molecular and/or histological subtypes of gliomas, surgical resection status and survival. The prognostic significance and visualization of the selected expression profiles can be explored using interactive utilities provided. This tool also enables potential validation and generation of new hypotheses of novel therapies impacting gliomas that aid in personalization of treatment for optimum outcomes.AvailabilityGlioma-BioDP web tool with user manual is available from: https://glioma-biodp.nci.nih.gov Contact: uma@mail.nih.gov