bluuebunny/crossref_metadata_2025_split huggingface dataset:
A triple functional sensing chip for rapid detection of pathogenicListeria monocytogenes
Authors: Zhang Yachao , Wang Huimin , Xiao Sa , Wang Xia , Xu Ping 
Published: October 2020

AbstractHere a triple functional sensing chip was created forL. monocytogenesdetection by integrating three biomarkers (Listeriolysin O (LLO) at protein level,hlygene at genetic level, and acetoin at metabolic level). Liposome encapsulated catechol was used for LLO detection via LLO pore-forming ability.hlygene was specifically captured by using a thiolated capture probe on nanoporous gold (NPG). As an electroactive label, methylene blue was embedded in double-stranded structures to generate an electrochemical signal forhlydetection. Combined with the electrocatalysis of NADH by NPG, the acetoin detection was achieved by measuring the consumption of NADH as a cofactor under acetoin reductase catalysis. Importantly, theL. monocytogenesdetection results obtained by detecting three biomarkers using the chip can be mutually verified, which reduces the probability of false positives based on a single marker. Moreover, the detection time was reduced to about 90 min, making it a rapid and reliable tool forL. monocytogenesdetection.
Following the footprints of variability during filopodia growth
Authors: Senra Daniela , Páez Alejandra , Gueron Geraldine , Bruno Luciana , Guisoni Nara 
Published: October 2020

AbstractFilopodia are actin-built finger-like dynamic structures that protrude from the cell cortex. These structures can sense the environment and play key roles in migration and cell-cell interactions. The growth-retraction cycle of filopodia is a complex process exquisitely regulated by intra- and extra-cellular cues, whose nature remains elusive. Filopodia present wide variation in length, lifetime and growth rate. Here, we investigate the features of filopodia patterns in fixed prostate cancer cells by confocal microscopy. Analysis of almost a thousand filopodia suggests the presence of two different populations: one characterized by a narrow distribution of lengths and the other with a much more variable pattern with very long filopodia. We explore a stochastic model of filopodia growth which takes into account diffusion and reactions involving actin and the regulatory proteins formin and capping, and retrograde flow. Interestingly, we found an inverse dependence between the filopodial length and the retrograde velocity. This result led us to propose that variations in the retrograde velocity could explain the experimental lengths observed for these tumor cells. In this sense, one population involves a wider range of retrograde velocities than the other population, and also includes low values of this velocity. It has been hypothesized that cells would be able to regulate retrograde flow as a mechanism to control filopodia length. Thus, we propound that the experimental filopodia pattern is the result of differential retrograde velocities originated from heterogeneous signaling due to cell-substrate interactions or prior cell-cell contacts.
Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre
Authors: Ashhurst Thomas Myles , Marsh-Wakefield Felix , Putri Givanna Haryono , Spiteri Alanna Gabrielle , Shinko Diana , Read Mark Norman , Smith Adrian Lloyd , King Nicholas Jonathan Cole 
Published: October 2020

ABSTRACTAs the size and complexity of high-dimensional cytometry data continue to expand, comprehensive, scalable, and methodical computational analysis approaches are essential. Yet, contemporary clustering and dimensionality reduction tools alone are insufficient to analyze or reproduce analyses across large numbers of samples, batches, or experiments. Moreover, approaches that allow for the integration of data across batches or experiments are not well incorporated into computational toolkits to allow for streamlined workflows. Here we present Spectre, an R package that enables comprehensive end-to-end integration and analysis of high-dimensional cytometry data from different batches or experiments. Spectre streamlines the analytical stages of raw data pre-processing, batch alignment, data integration, clustering, dimensionality reduction, visualization and population labelling, as well as quantitative and statistical analysis. Critically, the fundamental data structures used within Spectre, along with the implementation of machine learning classifiers, allow for the scalable analysis of very large high-dimensional datasets, generated by flow cytometry, mass cytometry (CyTOF), or spectral cytometry. Using open and flexible data structures, Spectre can also be used to analyze data generated by single-cell RNA sequencing (scRNAseq) or high-dimensional imaging technologies, such as Imaging Mass Cytometry (IMC). The simple, clear, and modular design of analysis workflows allow these tools to be used by bioinformaticians and laboratory scientists alike. Spectre is available as an R package or Docker container. R code is available on Github (https://github.com/immunedynamics/spectre).
Computational response modeling reveals context dependent Akt activity in luminal breast cancer cells
Authors: Erdem Cemal , Lee Adrian V. , Taylor D. Lansing , Lezon Timothy R. 
Published: October 2020

ABSTRACTAberrant signaling through insulin (Ins) and insulin-like growth factor I (IGF1) receptors contributes to the risk and advancement of many cancer types by activating cell survival cascades. Mechanistic computational modeling of such pathways provides insights into each component’s role in the cell response. In previous computational models, the two receptors were treated as indistinguishable, missing the opportunity to delineate their distinct roles in cancer progression. Here, a dual receptor (IGF1R & InsR) computational model elucidated new experimental hypotheses on how differential early responses emerge. Complementary to our previous findings, the model suggested that the regulation of insulin receptor substrate (IRS) is critical in inducing differential MAPK and Akt activation. As predicted, perturbing ribosomal protein S6 kinase (RPS6K) kinase activity led to an increased Akt activation with insulin stimulation compared to IGF1 stimulation. Being able to discern differential downstream signaling, we can explore improved anti-IGF1R cancer therapies by eliminating emergence of compensation mechanisms, without disrupting InsR signaling.ImplicationsThe study shows, both experimentally and through computational models, that IGF1 and insulin receptor signaling pathways respond differently to RPS6K inhibition.
Unified neural dynamics of decisions and actions in the cerebral cortex and basal ganglia
Authors: Thura David , Cabana Jean-François , Feghaly Albert , Cisek Paul 
Published: October 2020

AbstractSeveral theoretical models suggest that deciding about actions and executing them are not completely distinct neural mechanisms but instead two modes of an integrated dynamical system. Here, we investigate this proposal by examining how neural activity unfolds during a dynamic decision-making task within the high-dimensional space defined by the activity of cells in monkey dorsal premotor (PMd), primary motor (M1), and dorsolateral prefrontal cortex (dlPFC) as well as the external and internal segments of the globus pallidus (GPe, GPi). Dimensionality reduction shows that the four strongest components of neural activity are functionally interpretable, reflecting a state transition between deliberation and commitment, the transformation of sensory evidence into a choice, and the baseline and slope of the rising urgency to decide. Analysis of the contribution of each population to these components shows differences between regions but no distinct clusters within each region. During deliberation, cortical activity unfolds on a two-dimensional “decision manifold” defined by sensory evidence and urgency, and falls off this manifold at the moment of commitment into a choice-dependent trajectory leading to movement initiation. The structure of the manifold varies between regions: In PMd it is curved, in M1 it is nearly perfectly flat, and in dlPFC it is almost entirely confined to the sensory evidence dimension. In contrast, pallidal activity during deliberation is primarily defined by urgency. We suggest that these findings reveal the distinct dynamics of different regions, supporting a unified recurrent attractor model of action selection and execution.
Learning to leverage salient regions in neuro-oncology using Deep Learning
Authors: Grigis A. , Alentorn A. , Frouin V. 
Published: October 2020

AbstractDeveloping an automatic tumor detector for MRI medical images is a major challenge in neuro-oncology. The availability of such a tool would be a valuable assistance for the radiologists. Numerous works have tried to segment the tumor tissues, others have attempted to localize the tumor globally. In this work we focus on this second class of methods and we compare two drastically different strategies. The first one is an assumption-free anomaly detector build over a Variational Auto-Encoder (VAE), and the second one is a VGG classifier that embed Attention-Gated (AG) units to focus on the target structures at almost no additional computational cost. This comparison is first conducted on the publicly available BraTS glioma dataset for which published performance results can serve as reference, and extended as such (ie., without transfer learning) to two internal image datasets, namely Primary Central Nervous System Lymphoma (PCNSL) and Metastasis. The results demonstrate that the VAE and AG-VGG strategies can be used, up to a certain extent, to localize brain tumors.
Mass mortality of foundation species on rocky shores: another reason why monitoring programs are relevant
Authors: Mendez María M. , Livore Juan P. , Márquez Federico , bigatti Gregorio 
Published: October 2020

AbstractGlobal concern around substantial losses of biodiversity has led to the development of a number of large-scale long-term monitoring programs. In the past few decades, networks were established to obtain appropriate data on the spatial and temporal variation of marine species on rocky shores. Recently, the Marine Biodiversity Observation Network Pole to Pole of the Americas program (MBON P2P) was established and is coordinating biodiversity surveys along coastal areas throughout the continent. In this context, the goal of this paper was to demonstrate whether the proposed MBON P2P sampling protocol is capable of detecting rapid declines in cover of foundation species on Patagonian rocky shores. Changes in mussel beds cover were studied on monitored sites in northern Patagonia. Concurrently, long-term mussel bed dynamics were assessed based on existing data. Results showed that a mussel mortality event could be detected with this methodology. It took less than a year for mussel cover to drop from 90 to almost 0% despite the fact that significant changes in mussel bed cover were not registered in the previous 20 years at the study area. Therefore, yearly monitoring is needed, as a minimum, in order to timely perceive this kind of process. Real-time detection offers the opportunity of properly understanding the causes that lead to the loss of key community components such as these foundation species. Furthermore, it would provide early warning to decision makers enhancing the chances of conservation of natural environments and their key ecosystem services.
Single-cell secretion analysis reveals a dual role for IL-10 in restraining and resolving the TLR4-induced inflammatory response
Authors: Alexander Amanda F. , Forbes Hannah , Miller-Jensen Kathryn 
Published: October 2020

AbstractFollowing TLR4 stimulation of macrophages, negative feedback mediated by the anti-inflammatory cytokine IL-10 limits the inflammatory response. However, extensive cell-to-cell variability in TLR4-stimulated cytokine secretion raises questions about how negative feedback is robustly implemented. To explore this, we characterized the TLR4-stimulated secretion program in primary murine macrophages using a single-cell microwell assay that enabled evaluation of functional autocrine IL-10 signaling. High-dimensional analysis of single-cell data revealed three distinct tiers of TLR4-induced proinflammatory activation based on levels of cytokine secretion. Surprisingly, while IL-10 inhibits TLR4-induced activation in the highest tier, it also contributes to the TLR4-induced activation threshold by regulating which cells transition from non-secreting to secreting states. This role for IL-10 in restraining TLR4 inflammatory activation is largely mediated by intermediate IFN-β signaling, while TNF-a likely mediates response resolution by IL-10. Thus, cell-to-cell variability in cytokine regulatory motifs provides a means to tailor the TLR4-induced inflammatory response.
Mapping the Antibody Repertoires in Ferrets with Repeated Influenza A/H3 Infections: Is Original Antigenic Sin Really “Sinful”?
Authors: Einav Tal , Kosikova Martina , Radvak Peter , Kuo Yuan-Chia , Kwon Hyung Joon , Xie Hang 
Published: October 2020

AbstractThe influenza-specific antibody repertoire is continuously reshaped by infection and vaccination. The host immune response to contemporary viruses can be redirected to preferentially boost antibodies specific for viruses encountered early in life, a phenomenon called original antigenic sin (OAS) that is suggested to be responsible for diminished vaccine effectiveness after repeated vaccination. In this study, we used a new computational tool called Neutralization Map to determine the hemagglutination inhibition profiles of individual antibodies within ferret antisera elicited by repeated influenza A/H3 infections. Our results suggest that repeated infections continuously reshape the ferret antibody repertoire, but that a broadly neutralizing antibody signature can nevertheless be induced irrespective of OAS. Overall, our study offers a new way to visualize how immune history shapes individual antibodies within a repertoire, which may help inform future vaccine design.
The mechanism of motor inhibition by microtubule-associated proteins
Authors: Ferro Luke S , Eshun-Wilson Lisa , Gölcük Mert , Fernandes Jonathan , Huijben Teun , Gerber Eva , Jack Amanda , Costa Katelyn , Gür Mert , Fang Qianglin , Nogales Eva , Yildiz Ahmet 
Published: October 2020

SUMMARYMicrotubule (MT)-associated proteins (MAPs) regulate intracellular transport by selectively recruiting or excluding kinesin and dynein motors from MTs. We used single-molecule and cryo-electron imaging to determine the mechanism of MAP-motor interactionsin vitro. Unexpectedly, we found that the regulatory role of a MAP cannot be predicted based on whether it overlaps with the motor binding site or forms liquid condensates on the MT. Although the MT binding domain (MTBD) of MAP7 overlaps with the kinesin-1 binding site, tethering of kinesin-1 by the MAP7 projection domain supersedes this inhibition and results in biphasic regulation of kinesin-1 motility. Conversely, the MTBD of tau inhibits dynein motility without overlapping with the dynein binding site or by forming tau islands on the MT. Our results indicate that MAPs sort intracellular cargos moving in both directions, as neither dynein nor kinesin can walk on a MAP-coated MT without favorably interacting with that MAP.HIGHLIGHTSMAP7 binds to a novel site and can coexist with tau on the MT.Kinesin-1 motility is biphasically regulated by MAP7 accumulation on the microtubule.MT decoration of MAPs inhibits motors even when they do not block the motor binding site.Motors need to interact with a MAP to walk on MAP-decorated MTs
Distributed Phase Oscillatory Excitation Efficiently Produces Attractors Using Spike Timing Dependent Plasticity
Authors: Wong Eric C. 
Published: October 2020

ABSTRACTThe brain is thought to represent information in the form of activity in distributed groups of neurons known as attractors, but it is not clear how attractors are formed or used in processing. We show here that in a randomly connected network of simulated spiking neurons, periodic stimulation of neurons with distributed phase offsets, along with standard spike timing dependent plasticity (STDP), efficiently creates distributed attractors. These attractors may have a consistent ordered firing pattern, or become disordered, depending on the conditions. We also show that when two such attractors are stimulated in sequence, the same STDP mechanism can create a directed association between them, forming the basis of an associative network. We find that for an STDP time constant of 20ms, the dependence of the efficiency of attractor creation on the driving frequency has a broad peak centered around 8Hz. Upon restimulation, the attractors selfoscillate, but with an oscillation frequency that is higher than the driving frequency, ranging from 10-100Hz.
A Transgenic System for Targeted Ablation of Reproductive and Maternal-Effect genes
Authors: Bertho Sylvain , Kaufman Odelya , Lee KathyAnn , Santos-Ledo Adrian , Dellal Daniel , Marlow Florence L. 
Published: October 2020

AbstractMaternally provided gene products regulate the earliest events of embryonic life, including formation of the oocyte that will develop into an egg, and eventually an embryo. Forward genetic screens have provided invaluable insights into the molecular regulation of embryonic development, including essential contributions of some genes whose products must be provided to the transcriptionally silent early embryo for normal embryogenesis, maternal-effect genes. However, other maternal-effect genes are not accessible due to their essential zygotic functions during embryonic development. Identifying these regulators is essential to fill the large gaps in our understanding of the mechanisms and molecular pathways contributing to fertility and maternally regulated developmental processes. To identify these maternal factors, it is necessary to bypass the earlier requirement for these genes so that their potential later functions can be investigated. Here we report reverse genetic systems to identify genes with essential roles in reproductive and maternal-effect processes, as proof of principal and to assess the efficiency and robustness of mutagenesis we used these transgenic systems to disrupt two genes with known maternal-effect functions,kif5Baandbucky ball.Summary StatementWe report reverse genetic systems to identify essential regulators of reproductive and maternal-effect processes, as proof of principal we used these transgenic systems to disrupt genes with known maternal-effect functions.
Transient light-activated gene expression in Chinese hamster ovary cells
Authors: Minami Shiaki A. , Shah Priya S. 
Published: October 2020

AbstractBackgroundChinese hamster ovary (CHO) cells are widely used for industrial production of biopharmaceuticals. Many genetic, chemical, and environmental approaches have been developed to modulate cellular pathways to improve titers. However, these methods are often irreversible or have off-target effects. Development of techniques which are precise, tunable, and reversible will facilitate temporal regulation of target pathways to maximize titers. In this study, we investigate the use of optogenetics in CHO cells. The light-activated CRISPR-dCas9 effector (LACE) system was first transiently transfected to express eGFP in a light-inducible manner. Then, a stable system was tested using lentiviral transduction.ResultsTransient transfections resulted in increasing eGFP expression as a function of LED intensity, and activation for 48 hours yielded up to 4-fold increased eGFP expression compared to cells kept in the dark. Fluorescence decreased once the LACE system was deactivated, and a half-life of 14.9 hours was calculated, which is in agreement with values reported in the literature. In cells stably expressing the LACE system, eGFP expression was confirmed, but there was no significant increase in expression following light activation.ConclusionsTaken together, these results suggest that optogenetics can regulate CHO cell cultures, but development of stable cell lines requires optimized expression levels of the LACE components to maintain high dynamic range.
ATAC-seq with unique molecular identifiers improves quantification and footprinting
Authors: Zhu Tao , Liao Keyan , Zhou Rongfang , Xia Chunjiao , Xie Weibo 
Published: October 2020

AbstractATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) provides an efficient way to analyze nucleosome-free regions and has been applied widely to identify transcription factor footprints. Both applications rely on the accurate quantification of insertion events of the hyperactive transposase Tn5. However, due to the presence of the PCR amplification, it is impossible to accurately distinguish independently generated identical Tn5 insertion events from PCR duplicates using the standard ATAC-seq technique. Removing PCR duplicates based on mapping coordinates introduces an increasing bias towards highly accessible chromatin regions. To overcome this limitation, we establish a UMI-ATAC-seq technique by incorporating unique molecular identifiers (UMIs) into standard ATAC-seq procedures. In our study, UMI-ATAC-seq can rescue about 20% of reads that are mistaken as PCR duplicates in standard ATAC-seq, which helps identify an additional 50% or more of footprints. We demonstrate that UMI-ATAC-seq could more accurately quantify chromatin accessibility and significantly improve the sensitivity of identifying transcription factor footprints. An analytic pipeline is developed to facilitate the application of UMI-ATAC-seq, and it is available athttps://github.com/tzhu-bio/UMI-ATAC-seq.
Specificities of modeling membrane proteins using multi-template homology modeling
Authors: Leman Julia Koehler , Bonneau Richard 
Published: October 2020

AbstractStructures of membrane proteins are challenging to determine experimentally and currently represent only about 2% of the structures in the ProteinDataBank. Because of this disparity, methods for modeling membrane proteins are fewer and of lower quality than those for modeling soluble proteins. However, better expression, crystallization, and cryo-EM techniques have prompted a recent increase in experimental structures of membrane proteins, which can act as templates to predict the structure of closely related proteins through homology modeling. Because homology modeling relies on a structural template, it is easier and more accurate than fold recognition methods orde novomodeling, which are used when the sequence similarity between the query sequence and the sequence of related proteins in structural databases is below 25%. In homology modeling, a query sequence is mapped onto the coordinates of a single template and refined. With the increase in available templates, several templates often cover overlapping segments of the query sequence. Multi-template modeling can be used to identify the best template for local segments and join them into a single model. Here we provide a protocol for modeling membrane proteins from multiple templates in the Rosetta software suite. This approach takes advantage of several integrated frameworks, namely RosettaScripts, RosettaCM, and RosettaMP with the membrane scoring function.