bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-invasive real-time access to the output of the spinal cord via a wrist wearable interface
Authors: Mendez Irene , Barsakcioglu Deren Y. , Vujaklija Ivan , Wetmore Daniel Z. , Farina Dario 
Published: April 2021

ABSTRACTDespite the promising features of neural interfaces, their trade-off between information transfer and invasiveness has limited translation and viability outside research settings. Here, we present a non-invasive neural interface that provides access to spinal motoneuron activities from a sensor band at the wrist. The interface decodes electric signals present at the tendon endings of the forearm muscles by using a model of signal generation and deconvolution. First, we evaluated the reliability of the interface to detect motoneuron firings, and thereafter we used the decoded neural activity for the prediction of finger movements in offline and real-time conditions. The results showed that motoneuron activity decoded from the wrist accurately predicted individual and combined finger commands and therefore allowed for highly accurate real-time control. These findings demonstrate the feasibility of a wearable, non-invasive, neural interface at the wrist for precise real-time control based on the output of the spinal cord.
Prior Pro-inflammatory Polarization Changes the Macrophage Response to IL-4
Authors: O’Brien Erin M. , Spiller Kara L. 
Published: April 2021

AbstractTissue repair is largely regulated by diverse macrophage populations whose functions are timing- and context-dependent. The early phase of healing is dominated by pro-inflammatory macrophages, also known as M1, followed by the emergence of a distinct and diverse population that is collectively referred to as M2. The extent of the diversity of the M2 population is unknown. M2 macrophages may originate directly from circulating monocytes or from phenotypic switching of pre-existing M1 macrophages within the site of injury. The differences between these groups have not been investigated, but have major implications for understanding and treating pathologies characterized by deficient M2 activation, such as chronic wounds, which also exhibit diminished M1 macrophage behavior. This study investigated the influence of prior M1 activation on human macrophage polarization to an M2 phenotype in response to IL-4 treatment in vitro. Compared to unactivated (M0) macrophages, M1 macrophages upregulated several receptors that promote the M2 phenotype, including the primary receptor for IL-4. M1 activation also changed the macrophage response to treatment with IL-4, generating an M2-like phenotype with a distinct gene and protein expression signature compared to M2 macrophages prepared directly from M0 macrophages. Functionally, compared to M0-derived M2 macrophages, M1-derived M2 macrophages demonstrated increased migratory response to SDF-1α, and conditioned media from these macrophages promoted increased recruitment of endothelial cells in transwell assays. Together, these findings indicate the importance of prior M1 activation in regulating subsequent M2 behavior, and suggest that augmentation of M1 behavior may be a therapeutic target in dysfunctional tissue repair.Summary sentenceM1 macrophages that are switched to an M2 phenotype exhibit a distinct functional phenotype compared to M2 macrophages derived directly from unactivated (M0) macrophages.
Pre-Stimulus Alpha-Band Phase Gates Afferent Visual Cortex Responses
Authors: Dou Wei , Morrow Audrey , Iemi Luca , Samaha Jason 
Published: April 2021

SummaryThe neurogenesis of alpha-band (8-13 Hz) activity has been characterized across many different animal experiments. However, the functional role that alpha oscillations play in perception and behavior has largely been attributed to two contrasting hypotheses, with human evidence in favor of either (or both or neither) remaining sparse. On the one hand, alpha generators have been observed in relay sectors of the visual thalamus and are postulated to phasically inhibit afferent visual input in a feedforward manner1–4. On the other hand, evidence also suggests that the direction of influence of alpha activity propagates backwards along the visual hierarchy, reflecting a feedback influence upon the visual cortex5–9. The primary source of human evidence regarding the role of alpha phase in visual processing has been on perceptual reports10–16, which could be modulated either by feedforward or feedback alpha activity. Thus, although these two hypotheses are not mutually exclusive, human evidence clearly supporting either one is lacking. Here, we present human subjects with large, high-contrast visual stimuli that elicit robust C1 event-related potentials (ERP), which peak between 70-80 milliseconds post-stimulus and are thought to reflect afferent primary visual cortex (V1) input17–20. We find that the phase of ongoing alpha oscillations modulates the global field power (GFP) of the EEG during this first volley of stimulus processing (the C1 time-window). On the standard assumption21–23that this early activity reflects postsynaptic potentials being relayed to visual cortex from the thalamus, our results suggest that alpha phase gates visual responses during the first feed-forward sweep of processing.
The determinants of subjective sleep depth: insights from a high-density-EEG study with serial awakenings
Authors: Stephan Aurélie , Lecci Sandro , Cataldi Jacinthe , Siclari Francesca 
Published: April 2021

SummaryWhat accounts for the feeling of being deeply asleep? Standard sleep recordings only incompletely reflect subjective aspects of sleep and some individuals with so-called sleep misperception frequently feel awake although sleep recordings indicate clear-cut sleep. To identify the determinants of the subjective perception of sleep, we performed 787 awakenings in 20 good sleepers and 10 individuals with sleep misperception and interviewed them about their subjective sleep depth while they underwent high-density EEG sleep recordings. Surprisingly, in good sleepers, sleep was subjectively lightest in the first two hours of Non-rapid eye movement (NREM) sleep, generally considered the ‘deepest’ sleep, and deepest in rapid eye movement (REM) sleep. Compared to good sleepers, sleep misperceptors felt more frequently awake during sleep and reported lighter REM sleep. At the EEG level, spatially widespread high-frequency power was inversely related to subjective sleep depth in NREM sleep in both groups and in REM sleep in misperceptors. Subjective sleep depth positively correlated with dream-like qualities of reports of mental activity. These findings challenge the widely held notion that slow wave sleep best accounts for feeling deeply asleep. Instead, they indicate that subjective sleep depth is inversely related to a neurophysiological process that predominates in early NREM sleep, becomes quiescent in REM sleep and is reflected in high-frequency EEG-activity. In sleep misperceptors, this process is more frequently active, more spatially widespread, and abnormally persists into REM sleep. These findings help identify the neuromodulatory systems involved in subjective sleep depth and are relevant for studies aiming to improve subjective sleep quality.
Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples
Authors:   SEQC2 Oncopanel Sequencing Working Group, Zhang Yifan , Blomquist Thomas M. , Kusko Rebecca , Stetson Daniel , Zhang Zhihong , Yin Lihui , Sebra Robert , Gong Binsheng , LoCoco Jennifer S. , Mittal Vinay K. , Novoradovskaya Natalia , Yeo Ji-Youn , Dominiak Nicole , Hipp Jennifer , Raymond Amelia , Qiu Fujun , Arib Hanane , Smith Melissa L. , Brock Jay E. , Farkas Daniel H. , Craig Daniel J. , Crawford Erin L. , Li Dan , Morrison Tom , Tom Nikola , Xiao Wenzhong , Yang Mary , Mason Christopher E. , Richmond Todd A. , Jones Wendell , Johann Donald J. , Shi Leming , Tong Weida , Willey James C. , Xu Joshua 
Published: April 2021

AbstractClinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targeted therapy. To understand the technical error due to FFPE processing, a robustly characterized normal cell line was used to create FFPE samples with four different pre-tissue processing formalin fixation times. A total of 96 FFPE sections were then distributed to different laboratories for targeted sequencing analysis by four oncopanels, and variants resulting from technical error were identified. Tissue sections that failed more frequently showed low cellularity, lower than recommended library preparation DNA input, or target sequencing depth. Importantly, sections from block surfaces were more likely to show FFPE-specific errors, akin to “edge effects” seen in histology, and the depth of formalin damage was related to fixation time. To assure reliable results, we recommend avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence.
Metabolic function in aging retina and retinal pigment epithelium remains robust despite vision loss
Authors: Tsantilas Kristine A. , Cleghorn Whitney M. , Bisbach Celia M. , Whitson Jeremy A. , Hass Daniel T. , Robbings Brian M. , Sadilek Martin , Linton Jonathan D. , Rountree Austin M. , Valencia Ana P. , Sweetwyne Mariya T. , Campbell Matthew D. , Zhang Huiliang , Jankowski Connor S.R. , Sweet Ian R. , Marcinek David J. , Rabinovitch Peter S. , Hurley James B. 
Published: April 2021

AbstractPurposeCharacterize how metabolic function in the murine retina and retinal pigment epithelium-choroid-sclera (eyecup) complex is impacted by natural aging.MethodsWe examined scotopic and photopic visual function of young (3-6 months) and aged (23-26 months) C57Bl/6J mice using electroretinograms (ERGs). Metabolic changes in retina and eyecup explants were characterized by measuring uptake and usage of U-13C-glucose or U-13C-glutamine at different timepoints by gas chromatography-mass spectrometry (GC-MS), measuring oxygen consumption rate (OCR) using a perifusion apparatus, and determining ATP levels with a bioluminescence assay.ResultsScotopic and photopic ERG responses declined in aged mice. Glucose metabolism, glutamine metabolism, OCR, and ATP pools in retinal explants were mostly unaffected by the age of the mouse. In eyecups, glutamine usage in the Krebs Cycle decreased while glucose metabolism, OCR, and ATP pools remained stable.ConclusionsTheex vivoapproach in our study to examine aging glucose and glutamine metabolism in retina and RPE showed negligible impact of age on retina and an impairment of glutamine anaplerosis in eyecups. The surprising metabolic stability of these tissuesex vivosuggests age-related metabolic alterations in these tissues may not be intrinsic. Future experiments should focus on determining whether external factors including nutrient supply, oxygen availability, or other structural changes influence ocular metabolismin vivo.
A general approach for stabilizing nanobodies for intracellular expression
Authors: Dingus John , Tang Jonathan C.Y. , Cepko Constance 
Published: April 2021

AbstractConventional antibodies and their derived fragments are difficult to deploy against intracellular targets in live cells, due to their bulk and structural complexity. Nanobodies provide an alternative modality, with well documented examples of intracellular expression. Despite their promise as intracellular reagents, there has not been a systematic study of nanobody intracellular expression. Here, we examined intracellular expression of 75 nanobodies from the Protein Data Bank. Surprisingly, a majority of nanobodies were unstable in cells, illustrated by aggregation and clearance. Using comparative analysis and framework mutagenesis, we developed a general approach that stabilized a great majority of originally intracellularly unstable nanobodies, without compromising target-binding function. Additionally, we identified distinct sequence features impacting nanobody intracellular stability, and demonstrated mutationally stabilized nanobody expression in vivo, in the murine retina and inE. coli. This work will allow for standardized nanobody engineering for intracellular applications, potentiating a growing field of intracellular interrogation and intervention.
Genetically Engineered DENV Produces Antigenically Distinct Mature Particles
Authors: Tse Longping V. , Meganck Rita M. , Dong Stephanie , Adams Lily E. , White Laura J. , de Silva Aravinda M. , Baric Ralph S. 
Published: April 2021

AbstractMaturation of Dengue viruses (DENV) alters the structure, immunity and infectivity of the virion and highly mature particles represent the dominant formin vivo. The production of highly mature virions principally relies on the structure and function of the viral premature protein (prM) and its cleavage by the host protease furin. We developed a reliable clonal cell line which produces single-round mature DENVs without the need for DENV reverse genetics. More importantly, using protein engineering coupled with natural and directed evolution of the prM cleavage site, we engineered genetically stable mature DENVs without comprising viral yield and independent of cell, host, or passage. Using these complementary strategies to regulate maturation, we demonstrate that the resulting mature DENVs are antigenically distinct from their isogenic immature forms. Given the clinical importance of mature DENVs in immunity, our strategy provides a reliable strategy for the production of stable, high-titer mature candidate DENV live virus vaccines, genetically stabilized viruses for DENV maturation and immunity studies, and models for maturation-regulated experimental evolution in mammalian and invertebrate cells. Our data from directed-evolution across host species reveals distinct maturation-dependent selective pressures between mammalian and insect cells, which sheds light on the divergent evolutionary relationship of DENVs between its host and vector.
Caspar, an adapter for VAP and TER94 delays progression of disease by regulating glial inflammation in aDrosophilamodel of ALS8
Authors: Tendulkar Shweta , Hegde Sushmitha , Thulasidharan Aparna , Garg Lovleen , Kaduskar Bhagyashree , Ratnaparkhi Anuradha , Ratnaparkhi Girish S 
Published: April 2021

ABSTRACTAmyotrophic Lateral Sclerosis (ALS) is a fatal, late onset, progressive motor neurodegenerative disorder. We have been studying cellular and molecular mechanisms involved in ALS using a vesicle-associated membrane protein-associated protein B (VAPB/ALS8)Drosophilamodel, which mimics many systemic aspects of the human disease. Here, we show that the ER resident VAPB interacts with Caspar, an ortholog of human fas associated factor 1 (FAF1). Caspar, in turn, interacts with transitional endoplasmic reticulum ATPase (TER94), a fly ortholog of ALS14 (VCP/p97, Valosin-containing protein), via its UBX domain and poly-ubiqutinated proteins with its UBA domain. Caspar overexpression in the glia extends lifespan and also slows the progression of motor dysfunction in the ALS8 model, a phenomenon that we ascribe to its ability to restrain age-dependant inflammation, modulated by Relish/NFκB signalling.We hypothesize that Caspar is a key molecule in the pathogenesis of ALS. Caspar connects the plasma membrane (PM) localized immune signalosome to the ER based VAPB degradative machinery, presumably at PM:ER contact sites. The Caspar:TER94:VAPB complex appears to be a strong candidate for regulating both protein homeostasis and NFκB signalling. These, in turn, regulate glial inflammation and determine progression of disease. Our study projects human FAF1 as an important protein target to alleviate the progression of motor neuron disease.
Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp3 Papain-like Protease
Authors: Lim Chew Theng , Tan Kang Wei , Wu Mary , Ulferts Rachel , Armstrong Lee A. , Ozono Eiko , Drury Lucy S. , Milligan Jennifer C. , Zeisner Theresa U. , Zeng Jingkun , Weissmann Florian , Canal Berta , Bineva-Todd Ganka , Howell Michael , O’Reilly Nicola , Beale Rupert , Kulathu Yogesh , Labib Karim , Diffley John F.X 
Published: April 2021

SummaryThe COVID-19 pandemic has emerged as the biggest life-threatening disease of this century. Whilst vaccination should provide a long-term solution, this is pitted against the constant threat of mutations in the virus rendering the current vaccines less effective. Consequently, small molecule antiviral agents would be extremely useful to complement the vaccination program. The causative agent of COVID-19 is a novel coronavirus, SARS-CoV-2, which encodes at least nine enzymatic activities that all have drug targeting potential. The papain-like protease (PLpro) contained in the nsp3 protein generates viral non-structural proteins from a polyprotein precursor, and cleaves ubiquitin and ISG protein conjugates. Here we describe the expression and purification of PLpro. We developed a protease assay that was used to screen a custom chemical library from which we identified Dihydrotanshinone I and Ro 08-2750 as compounds that inhibit PLpro in protease and isopeptidase assays and also inhibit viral replication in cell culture-based assays.
Identification of SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of the nsp14 RNA Cap Methyltransferase
Authors: Basu Souradeep , Mak Tiffany , Ulferts Rachel , Wu Mary , Deegan Tom , Fujisawa Ryo , Tan Kang Wei , Lim Chew Theng , Basier Clovis , Canal Berta , Curran Joseph F. , Drury Lucy , McClure Allison W. , Roberts Emma L. , Weissmann Florian , Zeisner Theresa U. , Beale Rupert , Cowling Victoria H. , Howell Michael , Labib Karim , Diffley John F.X. 
Published: April 2021

SummaryThe COVID-19 pandemic has presented itself as one of the most critical public health challenges of the century, with SARS-CoV-2 being the third member of theCoronaviridaefamily to cause fatal disease in humans. There is currently only one antiviral compound, remdesivir, that can be used for the treatment of COVID-19. In order to identify additional potential therapeutics, we investigated the enzymatic proteins encoded in the SARS-CoV-2 genome. In this study, we focussed on the viral RNA cap methyltransferases, which play a key role in enabling viral protein translation and facilitating viral escape from the immune system. We expressed and purified both the guanine-N7 methyltransferase nsp14, and the nsp16 2’-O-methyltransferase with its activating cofactor, nsp10. We performed anin vitrohigh-throughput screen for inhibitors of nsp14 using a custom compound library of over 5,000 pharmaceutical compounds that have previously been characterised in either clinical or basic research. We identified 4 compounds as potential inhibitors of nsp14, all of which also show antiviral capacity in a cell based model of SARS-CoV-2 infection. Three of the 4 compounds also exhibited synergistic effects on viral replication with remdesivir.
Consolidation of human skill linked to waking hippocampo-neocortical replay
Authors: Buch ER , Claudino L , Quentin R , Bönstrup M , Cohen LG 
Published: April 2021

SummaryThe introduction of rest intervals interspersed with practice strengthens wakeful consolidation of skill. The mechanisms by which the brain binds discrete action representations into consolidated, highly temporally-resolved skill sequences during waking rest are not known. To address this question, we recorded magnetoencephalography (MEG) during acquisition and rapid consolidation of a sequential motor skill. We report the presence of highly prominent, fast waking neural replay during the same rest periods in which rapid consolidation occurs. The observed replay was temporally compressed by approximately 20x relative to the acquired skill, occurred in both forward and reverse directions, was selective for the trained sequence and predicted the magnitude of skill consolidation. Replay representations extended beyond the hippocampus and entrorhinal cortex to the contralateral sensorimotor cortex. These results document the presence of robust hippocampo-neocortical replay supporting rapid wakeful consolidation of skill.
Comparable environmental stability and disinfection profiles of the currently circulating SARS-CoV-2 variants of concern B.1.1.7 and B.1.351
Authors: Meister Toni Luise , Fortmann Jil , Todt Daniel , Heinen Natalie , Ludwig Alfred , Brueggemann Yannick , Elsner Carina , Dittmer Ulf , Pfaender Stephanie , Steinmann Eike 
Published: April 2021

AbstractThe emergence of novel SARS-CoV-2 B.1.1.7 and B.1.351 variants of concern with increased transmission dynamics has raised questions regarding stability and disinfection of these viruses. In this study, we analyzed surface stability and disinfection of the currently circulating SARS-CoV-2 variants B.1.1.7 and B.1.351 compared to the wildtype. Treatment with heat, soap and ethanol revealed similar inactivation profiles indicative of a comparable susceptibility towards disinfection. Furthermore, we observed comparable surface stability on steel, silver, copper and face masks. Overall, our data support the application of currently recommended hygiene concepts to minimize the risk of B.1.1.7 and B.1.351 transmission.
APOE ε4allele advances the age-dependent decline of amyloid β clearance in the human cortex
Authors: Saito Atsushi , Kageyama Yusuke , Pletnikova Olga , Rudow Gay L. , An Yang , Irie Yumi , Kita Akiko , Miki Kunio , Li Ling , Southall Pamela , Irie Kazuhiro , Troncoso Juan C. 
Published: April 2021

AbstractIntroductionOur previous study indicated that the pericapillary clearance of amyloid β (Aβ) declines with age inAPOE 3/3subjects. Here, we examine whether theAPOEε4allele has an impact on this age-related decline.MethodsWe examined 69 autopsy brains ofAPOEε3/ε4orAPOEε3/ε3individuals (30-65 years) for the immunohistochemical localization of intracellular, extracellular, and pericapillary Aβ in the cerebral cortex.ResultsInAPOEε3/ε4individuals, the percentage of Aβ positive pericapillary spaces began to decrease (p=0.030), and the number of extracellular Aβ particles increased in the early 30s (p=0.0008). Those average values were significantly lower (p<0.0001) and higher (p<0.0001), respectively, compared toAPOEε3/ε3individuals.DiscussionOur observations indicate thatAPOEε4allele advances by one decade at the onset of age-related decline in Aβ glymphatic clearance. This finding supports early clinical intervention and stratification by APOE genotype to prevent Aβ deposition and AD progression.
CLCd and CLCf act redundantly at the TGN/EE and prevent acidification of the Golgi stack
Authors: Scholl Stefan , Hilmer Stefan , Krebs Melanie , Schumacher Karin 
Published: April 2021

AbstractThe trans-Golgi network/early endosome (TGN/EE) serves as the central hub in which exo- and endocytic trafficking pathways converge and specificity of cargo routing needs to be achieved. Acidification is a hallmark of the TGN/EE and is maintained by the vacuolar H+-ATPase (V-ATPase) with support of proton-coupled antiporters. We show here that CLCd and CLCf, two distantly related members of the Arabidopsis chloride channel (CLC)-family that colocalize in the TGN/EE act redundantly and are essential for male gametophyte development. Combining an inducible knock-down approach and in vivo pH-measurements, we show here that reduced CLC-activity does not affect pH in the TGN/EE but causes accumulation of the V-ATPase in trans-Golgi cisternae leading to their hyper-acidification. Taken together, our results show that CLC-mediated anion transport into the TGN/EE is essential and affects spatio-temporal aspects of TGN/EE-maturation as well as its functional separation from the Golgi stack.