bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variant-specific changes in persistent or resurgent Na+current inSCN8A-EIEE13 iPSC-derived neurons
Authors: Tidball Andrew M. , Lopez-Santiago Luis F. , Yuan Yukun , Glenn Trevor W. , Margolis Joshua L. , Walker J. Clayton , Kilbane Emma G. , Isom Lori L. , Parent Jack M 
Published: January 2020

AbstractMissense variants in the voltage-gated sodium channel (VGSC) gene,SCN8A, are linked to early-infantile epileptic encephalopathy type 13 (EIEE13). EIEE13 patients exhibit a wide spectrum of intractable seizure types, severe developmental delay, movement disorders, and elevated risk of sudden unexpected death in epilepsy (SUDEP). The mechanisms by whichSCN8Avariants lead to epilepsy are poorly understood, although heterologous expression systems and mouse models have demonstrated altered sodium current (INa) properties. To investigate these mechanisms using a patient-specific model system, we generated induced pluripotent stem cells (iPSCs) from three patients with missense variants inSCN8A: p.R1872>L (P1); p.V1592>L (P2); and p.N1759>S (P3). Using small molecule differentiation into excitatory neurons, iPSC-derived neurons from all three patients displayed altered INa. P1 and P2 had elevated persistent INa, while P3 had increased resurgent INacompared to controls. Further analyses focused on one of the patients with increased persistent INa(P1) and the patient with increased resurgent INa(P3). Excitatory cortical neurons from both patients had prolonged action potential (AP) repolarization and shorter axon initial segment lengths compared to controls, the latter analyzed by immunostaining for ankyrin-G. Using doxycycline-inducible expression of the neuronal transcription factors Neurogenin 1 and 2 to synchronize differentiation of induced excitatory cortical-like neurons (iNeurons), we investigated network activity and response to pharmacotherapies. Both patient neurons and iNeurons displayed similar abnormalities in AP repolarization. Patient iNeurons showed increased burstiness that was sensitive to phenytoin, currently a standard treatment for EIEE patients, or riluzole, an FDA-approved drug used in amyotrophic lateral sclerosis and known to block persistent and resurgent INa, at pharmacologically relevant concentrations. Patch-clamp recordings showed that riluzole suppressed spontaneous firing and increased the AP firing threshold of patient-derived neurons to more depolarized potentials. Our results indicate that patient-specific neurons are useful for modeling EIEE13 and demonstrateSCN8Avariant-specific mechanisms. Moreover, these findings suggest that patient-specific iPSC neuronal disease modeling offers a useful platform for discovering precision epilepsy therapies.
Fast estimation of L1-regularized linear models in the mass-univariate setting
Authors: Mohr Holger , Ruge Hannes 
Published: January 2020

AbstractIn certain modeling approaches, activation analyses of task-based fMRI data can involve a relatively large number of predictors. For example, in the encoding model approach, complex stimuli are represented in a high-dimensional feature space, resulting in design matrices with many predictors. Similarly, single-trial models and finite impulse response models may also encompass a large number of predictors. In settings where only few of those predictors are expected to be informative, a sparse model fit can be obtained via L1-regularization. However, estimating L1-regularized models requires an iterative fitting procedure, which considerably increases computation time compared to estimating unregularized or L2-regularized models, and complicates the application of L1-regularization on whole-brain data and large sample sizes. Here we provide several functions for estimating L1-regularized models that are optimized for the mass-univariate analysis approach. The package includes a parallel implementation of the coordinate descent algorithm for CPU-only systems and two implementations of the alternating direction method of multipliers algorithm requiring a GPU device. While the core algorithms are implemented in C++/CUDA, data input/output and parameter settings can be conveniently handled via Matlab. The CPU-based implementation is highly memory-efficient and provides considerable speed-up compared to the standard implementation not optimized for the mass-univariate approach. Further acceleration can be achieved on systems equipped with a CUDA-enabled GPU. Using the fastest GPU-based implementation, computation time for whole-brain estimates can be reduced from 9 hours to 5 minutes in an exemplary data setting. Overall, the provided package facilitates the use of L1-regularization for fMRI activation analyses and enables an efficient employment of L1-regularization on whole-brain data and large sample sizes.
A bright and high-performance genetically encoded Ca2+indicator based on mNeonGreen fluorescent protein
Authors: Zarowny Landon , Aggarwal Abhi , M.S. Rutten Virginia , Kolb Ilya ,   The GENIE Project, Patel Ronak , Huang Hsin-Yi , Chang Yu-Fen , Phan Tiffany , Kanyo Richard , Ahrens Misha , Allison W. Ted , Podgorski Kaspar , Campbell Robert E. 
Published: January 2020

AbstractGenetically encodable calcium ion (Ca2+) indicators (GECIs) based on green fluorescent proteins (GFP) are powerful tools for imaging of cell signaling and neural activity in model organisms. Following almost two decades of steady improvements in theAequorea victoriaGFP (avGFP)-based GCaMP series of GECIs, the performance of the most recent generation (i.e., GCaMP7) may have reached its practical limit due to the inherent properties of GFP. In an effort to sustain the steady progression towards ever-improved GECIs, we undertook the development of a new GECI based on the bright monomeric GFP, mNeonGreen (mNG). The resulting indicator, mNG-GECO1, is 60% brighter than GCaMP6sin vitroand provides comparable performance as demonstrated by imaging Ca2+dynamics in cultured cells, primary neurons, andin vivoin larval zebrafish. These results suggest that mNG-GECO1 is a promising next-generation GECI that could inherit the mantle of GCaMP and allow the steady improvement of GECIs to continue for generations to come.
DCyFIR: a high-throughput CRISPR platform for multiplexed G protein-coupled receptor profiling and ligand discovery
Authors: Kapolka NJ , Taghon GJ , Rowe JB , Morgan WM , Enten JF , Isom DG 
Published: January 2020

AbstractMore than 800 G protein-coupled receptors (GPCRs) comprise the largest class of membrane receptors in humans. While there is ample biological understanding and many approved drugs for prototypic GPCRs, most GPCRs still lack well-defined biological ligands and drugs. Here, we report our efforts to tap the potential of understudied GPCRs by developing yeast-based technologies for high-throughput CRISPR engineering and GPCR ligand discovery. We refer to these technologies collectively as Dynamic Cyan induction by Functional Integrated Receptors: DCyFIR. A major advantage of DCyFIR is that GPCRs and other assay components are CRISPR-integrated directly into the yeast genome, making it possible to decode ligand specificity by profiling mixtures of GPCR-barcoded yeast strains in a single tube. To demonstrate the capabilities of DCyFIR, we engineered a yeast strain library of 30 human GPCRs and their 300 possible GPCR-Gα coupling combinations. Profiling of these 300 strains, using parallel (DCyFIRscreen) and multiplex (DCyFIRplex) DCyFIR modes, recapitulated known GPCR agonism with 100% accuracy, and identified unexpected interactions for the receptors ADRA2B, HCAR3, MTNR1A, S1PR1, and S1PR2. To demonstrate DCyFIR scalability, we profiled a library of 320 human metabolites and observed new GPCR-ligand interactions with amino acid, lipid, sugar, and steroid metabolites. Remarkably, many of these findings pertained to understudied “pharmacologically dark” receptors GPR4, GPR65, GPR68, and HCAR3. For example, we found that kynurenic acid activated HCAR3 with a nearly 20-fold lower EC50than GPR35, its known receptor. Taken together, these findings demonstrate the power of DCyFIR for identifying novel ligand interactions with prototypic and understudied GPCRs.Significance StatementG protein-coupled receptors (GPCRs) are the largest class of membrane receptors in humans. As such, GPCR signaling is central to human biology and medicine. While more than 30% of approved drugs target roughly 150 GPCRs, most receptors lack well-defined endogenous ligands and are currently not druggable. To address this challenge, we created a GPCR screening platform for ligand and drug discovery. This innovative technology enables the cost-effective profiling of ligands and drug compounds against mixtures of hundreds of GPCR-barcoded cell strains in a single experiment. Because a ligand or drug is tested against a collection of receptors all at once, our novel method accelerates the process of identifying potential GPCR ligands and drugs.
A hierarchical clustering and data fusion approach for disease subtype discovery
Authors: Pfeifer Bastian , Schimek Michael G. 
Published: January 2020

AbstractRecent advances in multi-omics clustering methods enable a more fine-tuned separation of cancer patients into clinical relevant clusters. These advancements have the potential to provide a deeper understanding of cancer progression and may facilitate the treatment of cancer patients. Here, we present a simple hierarchical clustering and data fusion approach, namedHC-fused, for the detection of disease subtypes. Unlike other methods, the proposed approach naturally reports on the individual contribution of each single-omic to the data fusion process. We perform multi-view simulations withdisjointanddisjunctcluster elements across the views to highlight fundamentally different data integration behaviour of variousstate-of-the-artmethods.HC-fusedcombines the strengths of some recently published methods and shows superior performance on real world cancer data from the TCGA (The Cancer Genome Atlas) database. An R implementation of our method is available on GitHub (pievos101/HC-fused).
neuPrint: Analysis Tools for EM Connectomics
Authors: Clements Jody , Dolafi Tom , Umayam Lowell , Neubarth Nicole L. , Berg Stuart , Scheffer Louis K. , Plaza Stephen M. 
Published: January 2020

AbstractDue to technological advances in electron microscopy (EM) and deep learning, it is now practical to reconstruct a connectome, a description of neurons and the connections between them, for significant volumes of neural tissue. The limited scope of past reconstructions meant they were primarily used by domain experts, and performance was not a serious problem. But the new reconstructions, of common laboratory creatures such as the fruit flyDrosophila melanogaster, upend these assumptions. These natural neural networks now contain tens of thousands of neurons and tens of millions of connections between them, with yet larger reconstructions pending, and are of interest to a large community of non-specialists. This requires new tools that are easy to use and efficiently handle large data. We introduceneuPrintto address these data analysis challenges. neuPrint is a database and analysis ecosystem that organizes connectome data in a manner conducive to biological discovery. In particular, we propose a data model that allows users to access the connectome at different levels of abstraction primarily through a graph database, neo4j, and its powerfully expressive query languageCypher. neuPrint is compatible with modern connectome reconstruction workflows, providing tools for assessing reconstruction quality, and offering both batch and incremental updates to match modern connectome reconstruction flows. Finally, we introduce a web interface and programmer API that targets a diverse user skill set. We demonstrate the effectiveness and efficiency of neuPrint through example database queries.
Encoding of 3D Head Orienting Movements in Primary Visual Cortex
Authors: Guitchounts Grigori , Masis Javier , Wolff Steffen BE , Cox David 
Published: January 2020

AbstractAnimals actively sample from the sensory world by generating complex patterns of movement that evolve in three dimensions. At least some of these movements have been shown to influence neural codes in sensory areas. For example, in primary visual cortex (V1), locomotion-related neural activity influences sensory gain, encodes running speed, and predicts the direction of visual flow. As most experiments exploring movement-related modulation of V1 have been performed in head-fixed animals, it remains unclear whether or how the naturalistic movements used to interact with sensory stimuli– like head orienting–influence visual processing. Here we show that 3D head orienting movements modulate V1 neuronal activity in a direction-specific manner that also depends on the presence or absence of light. We identify two largely independent populations of movement-direction-tuned neurons that support this modulation, one of which is direction-tuned in the dark and the other in the light. Finally, we demonstrate that V1 gains access to a motor efference copy related to orientation from secondary motor cortex, which has been shown to control head orienting movements. These results suggest a mechanism through which sensory signals generated by purposeful movement can be distinguished from those arising in the outside world, and reveal a pervasive role of 3D movement in shaping sensory cortical dynamics.
Dynamical determinants of different spine movements and gait speeds in rotary and transverse gallops
Authors: Kamimura Tomoya , Aoi Shinya , Higurashi Yasuo , Wada Naomi , Tsuchiya Kazuo , Matsuno Fumitoshi 
Published: January 2020

AbstractQuadruped gallop is categorized into two types: rotary and transverse. While the rotary gallop involves two types of flight with different spine movements, the transverse gallop involves only one type of flight. The rotary gallop can achieve faster locomotion than the transverse gallop. To clarify these mechanisms from a dynamic viewpoint, we developed a simple model and derived periodic solutions by focusing on cheetahs and horses. The solutions gave a criterion to determine the flight type: while the ground reaction force does not change the direction of the spine movement for the rotary gallop, it changes for the transverse gallop, which was verified with the help of animal data. Furthermore, the criterion provided the mechanism by which the rotary gallop achieves higher-speed than the transverse gallop based on the flight duration. These findings improve our understanding of the mechanisms underlying different gaits that animals use.
Why most transporter mutations that cause antibiotic resistance are to efflux pumps rather than to import transporters
Authors: Mendes Pedro , Girardi Enrico , Superti-Furga Giulio , Kell Douglas B. 
Published: January 2020

AbstractGenotypic microbial resistance to antibiotics with intracellular targets commonly arises from mutations that increase the activities of transporters (pumps) that cause the efflux of intracellular antibiotics.A prioriit is not obvious why this is so much more common than are mutations that simply inhibit the activity of uptake transporters for the antibiotics. We analyse quantitatively a mathematical model consisting of one generic equilibrative transporter and one generic concentrative uptake transporter (representing any number of each), together with one generic efflux transporter. The initial conditions are designed to give an internal concentration of the antibiotic that is three times the minimum inhibitory concentration (MIC). The effect of varying the activity of each transporter type 100-fold is dramatically asymmetric, in that lowering the activities of individual uptake transporters has comparatively little effect on internal concentrations of the antibiotic. By contrast, increasing the activity of the efflux transporter lowers the internal antibiotic concentration to levels far below the MIC. Essentially, these phenomena occur because inhibiting individual influx transporters allows others to ‘take up the slack’, whereas increasing the activity of the generic efflux transporter cannot easily be compensated. The findings imply strongly that inhibiting efflux transporters is a much better approach for fighting antimicrobial resistance than is stimulating import transporters. This has obvious implications for the development of strategies to combat the development of microbial resistance to antibiotics and possibly also cancer therapeutics in human.
PE5-PPE4-EspG3trimer structure from mycobacterial ESX-3 secretion system gives insight into cognate substrate recognition by ESX systems
Authors: Williamson Zachary A. , Chaton Catherine T. , Ciocca William A. , Korotkova Natalia , Korotkov Konstantin V. 
Published: January 2020

ABSTRACTMycobacterium tuberculosis(Mtb) has evolved numerous type VII secretion (ESX) systems to secrete multiple factors important for both growth and virulence across their cell envelope. Three such systems; ESX-1, ESX-3, and ESX-5; have been shown to each secrete a unique set of substrates. A large class of these substrates secreted by these three systems are the PE and PPE families of proteins. Proper secretion of the PE-PPE proteins requires the presence of EspG, with each system encoding its own unique copy. There is no cross-talk between any of the ESX systems and how each EspG is recognizing its subset of PE-PPE proteins is currently unknown. The only current structural characterization of PE-PPE-EspG trimers is from the ESX-5 system. Here we present the crystal structure of the PE5mt-PPE4mt-EspG3mmtrimer, from the ESX-3 system. Our trimer reveals that EspG3mminteracts exclusively with PPE4mtin a similar manner to EspG5, shielding the hydrophobic tip of PPE4mtfrom solvent. The C-terminal helical domain of EspG3mmis dynamic, alternating between an ‘open’ and ‘closed’ form, and this movement is likely functionally relevant in the unloading of PE-PPE heterodimers at the secretion machinery. In contrast to the previously solved ESX-5 trimers, the PE-PPE heterodimer of our ESX-3 trimer is interacting with it’s chaperone at a drastically different angle, and presents different faces of the PPE protein to the chaperone. We conclude that the PPE-EspG interface from each ESX system has a unique shape complementarity that allows each EspG to discriminate amongst non-cognate PE-PPE pairs.
A Whole-Brain Regression Method to Identify Individual and Group Variations in Functional Connectivity
Authors: Zhao Yi , Caffo Brian S. , Wang Bingkai , Li Chiang-shan R. , Luo Xi 
Published: January 2020

AbstractResting-state functional connectivity is an important and widely used measure of individual and group differences. These differences are typically attributed to various demographic and/or clinical factors. Yet, extant statistical methods are limited to linking covariates with variations in functional connectivity across subjects, especially at the voxel-wise level of the whole brain. This paper introduces a generalized linear model method that regresses whole-brain functional connectivity on covariates. Our approach builds on two methodological components. We first employ whole-brain group ICA to reduce the dimensionality of functional connectivity matrices, and then search for matrix variations associated with covariates using covariate assisted principal regression, a recently introduced covariance matrix regression method. We demonstrate the efficacy of this approach using a resting-state fMRI dataset of a medium-sized cohort of subjects obtained from the Human Connectome Project. The results show that the approach enjoys improved statistical power in detecting interaction effects of sex and alcohol on whole-brain functional connectivity, and in identifying the brain areas contributing significantly to the covariate-related differences in functional connectivity.
Oxygen supply limits the heat tolerance of locusts during the first instar only
Authors: Youngblood Jacob P. , VandenBrooks John M. , Babarinde Oluwatosin , Donnay Megan E. , Elliott Deanna B. , Fredette-Roman Jacob , Angilletta Michael J. 
Published: January 2020

AbstractExtreme heat directly limits an organism’s survival and reproduction, but scientists cannot agree on what causes organisms to lose function or die during heating. According to the theory of oxygen- and capacity-limitation of thermal tolerance, heat stress occurs when a warming organism’s demand for oxygen exceeds its supply, triggering a widespread drop in ATP concentration. This model predicts that an organism’s heat tolerance should decrease under hypoxia, yet most terrestrial organisms tolerate the same amount of warming across a wide range of oxygen concentrations. This point is especially true for adult insects, who deliver oxygen through highly efficient respiratory systems. However, oxygen limitation at high temperatures may be more common during immature life stages, which have less developed respiratory systems. To test this hypothesis, we measured the effects of heat and hypoxia on the survival of locusts (Schistocerca cancellata) throughout development. We demonstrate that the heat tolerance of locusts depends on oxygen supply during the first instar but not during later instars. This finding provides further support for the idea that oxygen limitation of thermal tolerance depends on respiratory performance, especially during immature life stages.
Opposing forms of adaptation in mouse visual cortex are controlled by distinct inhibitory microcircuits and gated by locomotion
Authors: Heintz Tristan G. , Hinojosa Antonio J. , Lagnado Leon 
Published: January 2020

SummaryCortical processing of sensory signals adjusts to changes in both the external world and the internal state of the animal. We investigated the neural circuitry by which these processes interact in the primary visual cortex of mice. An increase in contrast caused as many pyramidal cells (PCs) to sensitize as depress, reflecting the dynamics of adaptation in different types of interneuron (PV, SST and VIP). Optogenetic manipulations demonstrate that the net effect within PCs reflects the balance of PV inputs, driving depression, and a subset of SST interneurons, driving sensitization. Locomotor behaviour increased the gain of PC responses by disinhibition through both the VIP->SST and SST->PV pathways, thereby maintaining the balance between opposing forms of plasticity. These experiments reveal how inhibitory microcircuits interact to purpose different subsets of PCs for the signalling of increases or decreases in contrast while also allowing for behavioural control of gain across the population.
Threshold illumination for non-invasive imaging of cells and tissues
Authors: Emon M A Bashar , Knoll Samantha , Doha Umnia , Baietto Danielle , Ladehoff Lauren , Sivaguru Mayandi , Saif M Taher A 
Published: January 2020

AbstractFluorescent microscopy employs monochromatic light which can affect the cells being observed. We reported earlier that fibroblasts relax their contractile force in response to green light of typical intensity. Here we show that such effects are independent of extracellular matrix and type of cell. In addition, we establish a threshold light that invokes minimal effect on cells. We cultured fibroblasts on soft 2D elastic hydrogels embedded with fluorescent beads to trace substrate deformation. The beads move towards cell center when cells contract, but they move away when cells relax. We use relaxation/contraction ratio, λr, as a measure of cell response to light. The cells were exposed to green (wavelength, λ = 545-580 nm) and red (λ = 635-650 nm) light with a range of intensities. We find red light with intensity less than ~ 57 W/m2 results in λr = 1, i.e., cells maintain force homeostasis. Higher intensities and smaller wavelengths result in widespread force-relaxation in cells with λr > 1. We suggest the use of λ > 650 nm light with low intensity (I ≤ 57 W/m2) for time-lapse imaging of cells and tissues in order to avoid light-induced artifacts in experimental observations.