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Sile Hu, Davide Ciliberti, Andres D Grosmark, Frédéric Michon, Daoyun Ji, Hector Penagos, György Buzsáki, Matthew A Wilson, Fabian Kloosterman, Zhe Chen
Uncovering spatial representations from large-scale ensemble spike activity in specific brain circuits provides valuable feedback in closed-loop experiments. We develop a graphics processing unit (GPU)-powered population-decoding system for ultrafast reconstruction of spatial positions from rodents' unsorted spatiotemporal spiking patterns, during run behavior or sleep. In comparison with an optimized quad-core central processing unit (CPU) implementation, our approach achieves an ∼20- to 50-fold increase in speed in eight tested rat hippocampal, cortical, and thalamic ensemble recordings, with real-time decoding speed (approximately fraction of a millisecond per spike) and scalability up to thousands of channels...
December 4, 2018: Cell Reports
Yi-Bo Yang, Jian Liang, Yu-Jiang Bi, Ying Chen, Terrence Draper, Keh-Fei Liu, Zhaofeng Liu
We report results on the proton mass decomposition and also on related quark and glue momentum fractions. The results are based on overlap valence fermions on four ensembles of N_{f}=2+1 domain wall fermion configurations with three lattice spacings and three volumes, and several pion masses including the physical pion mass. With fully nonperturbative renormalization (and universal normalization on both quark and gluon), we find that the quark energy and glue field energy contribute 32(4)(4)% and 36(5)(4)% respectively in the MS[over ¯] (modified minimal substraction) scheme at μ=2  GeV...
November 23, 2018: Physical Review Letters
Alik S Widge, Matthew Boggess, Alexander P Rockhill, Andrew Mullen, Shivani Sheopory, Roman Loonis, Daniel K Freeman, Earl K Miller
Oscillations of the brain's local field potential (LFP) may coordinate neural ensembles and brain networks. It has been difficult to causally test this model or to translate its implications into treatments, because there are few reliable ways to alter LFP oscillations. We developed a closed-loop analog circuit to enhance brain oscillations by feeding them back into cortex through phase-locked transcranial electrical stimulation. We tested the system in a rhesus macaque with chronically implanted electrode arrays, targeting 8-15 Hz (alpha) oscillations...
2018: PloS One
Panagiotis C Petris, Stefanos D Anogiannakis, Panagiotis-Nikolaos Tzounis, Doros N Theodorou
A complete thermodynamic analysis of mixtures consisting of molecules with complex chemical constitution can be rather demanding. Kirkwood-Buff theory of solutions allows the estimation of thermodynamic properties which cannot be directly extracted from atomistic simulations, such as the Gibbs energy of mixing (Δmix G). In this work we perform molecular dynamics simulations of n-hexane/ethanol binary mixtures in the liquid state under two temperature-pressure conditions and at various mole fractions. Based on the recently published methodology of Galata et al...
December 5, 2018: Journal of Physical Chemistry. B
Huaping Guo, Xiaoyu Diao, Hongbing Liu
Rotation Forest is an ensemble learning approach achieving better performance comparing to Bagging and Boosting through building accurate and diverse classifiers using rotated feature space. However, like other conventional classifiers, Rotation Forest does not work well on the imbalanced data which are characterized as having much less examples of one class (minority class) than the other (majority class), and the cost of misclassifying minority class examples is often much more expensive than the contrary cases...
2018: Computational Intelligence and Neuroscience
Anhui Wang, Zhichao Zhang, Guohui Li
The accuracy of molecular mechanics force fields is of vital importance in biomolecular simulations. However, the admittedly more accurate polarizable force fields were recently reported to be less able to reproduce the experimental properties comparing with additive force fields in some cases. Here, we perform long-time scaled molecular dynamics simulations to systematically evaluate the effect of explicit electronic polarization in polarizable force fields. The results show that the inclusion of electrostatic polarization effect in polarizable force fields can improve their accuracies in protein structure refinement and generate conformational ensembles more approximate to experiments for intrinsically disordered proteins...
December 5, 2018: Journal of Physical Chemistry Letters
Dmitry V Matyushov, Marshall D Newton
We present a thermodynamic analysis of the activation barrier for reactions which can be monitored through the difference in the energies of reactants and products defined as the reaction coordinate (electron and atom transfer, enzyme catalysis, etc). The free-energy surfaces along the reaction coordinate are separated into the enthalpy and entropy surfaces. For the Gaussian statistics of the reaction coordinate, the free-energy surfaces are parabolas, and the entropy surface is an inverted parabola. Its maximum coincides with the transition state for reactions with zero value of the reaction free energy...
December 4, 2018: Journal of Physical Chemistry. B
Yajie Zhang, Yanfen Wang, Haishan Niu
Maize, rice, wheat and soybean-the major staple food crops in China-have a crucial role in national food security and economic development. Predictions of changes in the requirements for irrigation water in food crop production under climate change may provide scientific support for the optimum allocation of water resources and measures to mitigate climate change. We conducted a spatial grid-based analysis using projections of future climate generated by a bias-correction and spatial disaggregation multi-model ensemble for three representative concentration pathway scenarios (RCP2...
November 26, 2018: Science of the Total Environment
Maartje M C Bastings, Thomas M Hermans, A J H Spiering, Erwin W L Kemps, Lorenzo Albertazzi, Eva E Kurisinkal, Patricia Y W Dankers
The most basic function of synthetic microenvironments for tissue engineering is to act as a physical substrate for cell attachment, migration, and proliferation, similar to the natural cell environment. Functionalization of supramolecular materials with guest compounds that display the same recognition moieties is a common strategy to introduce biofunctionality. However, besides a robust interaction with the material, a certain level of dynamics needs to be conserved for an adaptive interface toward the living environment...
December 4, 2018: Macromolecular Bioscience
Hossein Tavallali, Gohar Deilamy-Rad, Narges Mosallanejad
The paper proposes a method that exhibits operational simplicity for the indirect spectrophotometric determination of oxalate ion. We developed Reactive Blue 4 (RB4) as a sensor by complexation with copper ion as a simple, inexpensive yet selective colorimetric chemosensing ensemble for the recognition of oxalate over other available competitive analytes via indicator displacement assay (IDA) in both solution (aqueous medium) and solid state (paper-based experiment). The addition of oxalate to RB4-Cu2+ complex changed the colour from sky blue to dark blue due to the regeneration of RB4 by the chelation of oxalate as the competitive analyte with Cu2+ ...
September 2018: Food Technology and Biotechnology
John T Fasullo, R Steven Nerem
The satellite altimeter record has provided an unprecedented database for understanding sea-level rise and has recently reached a major milestone at 25 years in length. A challenge now exists in understanding its broader significance and its consequences for sea-level rise in the coming decades and beyond. A key question is whether the pattern of altimeter-era change is representative of longer-term trends driven by anthropogenic forcing. In this work, two multimember climate ensembles, the Community Earth System Model (CESM) and the Earth System Model Version 2M (ESM2M), are used to estimate patterns of forced change [also known as the forced response (FR)] and their magnitudes relative to internal variability...
December 3, 2018: Proceedings of the National Academy of Sciences of the United States of America
Marielle A Wälti, Joseph Steiner, Fanjie Meng, Hoi Sung Chung, John M Louis, Rodolfo Ghirlando, Vitali Tugarinov, Avindra Nath, G Marius Clore
The human chaperonin Hsp60 is thought to play a role in the progression of Alzheimer's disease by mitigating against intracellular β-amyloid stress. Here, we show that the bacterial homolog GroEL (51% sequence identity) reduces the neurotoxic effects of amyloid-β(1-42) (Aβ42) on human neural stem cell-derived neuronal cultures. To understand the mechanism of GroEL-mediated abrogation of neurotoxicity, we studied the interaction of Aβ42 with GroEL using a variety of biophysical techniques. Aβ42 binds to GroEL as a monomer with a lifetime of ∼1 ms, as determined from global analysis of multiple relaxation-based NMR experiments...
December 3, 2018: Proceedings of the National Academy of Sciences of the United States of America
John Elson, Steve Eckels
Quantifying the impact of clothing thermal and evaporation resistance is essential to providing representative boundary conditions for physiological modeling. In many models, sweat is assumed to drip off the skin surface to the environment and is not captured in clothing. In high metabolic rate and high temperature and humidity conditions the sweat produced by the body has the potential to saturate semipermeable clothing ensembles, changing the assumptions of the model. Workers, athletes and soldiers commonly wear encapsulating versions of such clothing to protect against environmental hazards...
December 2018: Journal of Thermal Biology
Konrad Pieszko, Jarosław Hiczkiewicz, Paweł Budzianowski, Janusz Rzeźniczak, Jan Budzianowski, Jerzy Błaszczyński, Roman Słowiński, Paweł Burchardt
BACKGROUND: Increased systemic and local inflammation play a vital role in the pathophysiology of acute coronary syndrome. This study aimed to assess the usefulness of selected machine learning methods and hematological markers of inflammation in predicting short-term outcomes of acute coronary syndrome (ACS). METHODS: We analyzed the predictive importance of laboratory and clinical features in 6769 hospitalizations of patients with ACS. Two binary classifications were considered: significant coronary lesion (SCL) or lack of SCL, and in-hospital death or survival...
December 3, 2018: Journal of Translational Medicine
Hwejin Jung, Bumsoo Kim, Inyeop Lee, Junhyun Lee, Jaewoo Kang
BACKGROUND: Accurately detecting and examining lung nodules early is key in diagnosing lung cancers and thus one of the best ways to prevent lung cancer deaths. Radiologists spend countless hours detecting small spherical-shaped nodules in computed tomography (CT) images. In addition, even after detecting nodule candidates, a considerable amount of effort and time is required for them to determine whether they are real nodules. The aim of this paper is to introduce a high performance nodule classification method that uses three dimensional deep convolutional neural networks (DCNNs) and an ensemble method to distinguish nodules between non-nodules...
December 3, 2018: BMC Medical Imaging
Luhao Zhang, Maodong Li, Zhirong Liu
Intrinsically disordered proteins/regions (IDPs/IDRs) are prevalent in allosteric regulation. It was previously thought that intrinsic disorder is favorable for maximizing the allosteric coupling. Here, we propose a comprehensive ensemble model to compare the roles of both order-order transition and disorder-order transition in allosteric effect. It is revealed that the MWC pathway (order-order transition) has a higher probability than the EAM pathway (disorder-order transition) in allostery, suggesting a complicated role of IDPs/IDRs in regulatory proteins...
December 3, 2018: PLoS Computational Biology
(no author information available yet)
BACKGROUND: Although a preventable and treatable disease, tuberculosis causes more than a million deaths each year. As countries work towards achieving the Sustainable Development Goal (SDG) target to end the tuberculosis epidemic by 2030, robust assessments of the levels and trends of the burden of tuberculosis are crucial to inform policy and programme decision making. We assessed the levels and trends in the fatal and non-fatal burden of tuberculosis by drug resistance and HIV status for 195 countries and territories from 1990 to 2016...
December 2018: Lancet Infectious Diseases
(no author information available yet)
BACKGROUND: Acute meningitis has a high case-fatality rate and survivors can have severe lifelong disability. We aimed to provide a comprehensive assessment of the levels and trends of global meningitis burden that could help to guide introduction, continuation, and ongoing development of vaccines and treatment programmes. METHODS: The Global Burden of Diseases, Injuries, and Risk Factors (GBD) 2016 study estimated meningitis burden due to one of four types of cause: pneumococcal, meningococcal, Haemophilus influenzae type b, and a residual category of other causes...
December 2018: Lancet Neurology
Anna-Cathrine Neumann, David Bauer, Michael Hölscher, Christoph Haisch, Andreas Wieser
Tuberculosis is currently the single most deadly infectious disease in the world and a public health priority as defined by WHO. Although the disease is in general curable, treatment success is hampered by the necessity of a long and side effect prone treatment. Low treatment efficiency may be partly due to the special growth states mycobacteria enter to avoid being killed by antibiotics and to persist longer within the host. Such growth states have been recently defined as dormant or persistent. We produced dormant model-organism cultures using an acidification model and characterized those by a multi-layered approach using mass spectrometry (MALDI-TOF), microscopy (SEM, Raman), and microbiological techniques (CFU, OD600, ATP-levels)...
December 3, 2018: Analytical Chemistry
Julia Prei Szlig, Daniel Kage, Katrin Hoffmann, Todd J Martínez, Ute Resch-Genger, Martin Presselt
The fluorescence lifetime is a key property of fluorophores that can be utilized for microenvironment probing, analyte sensing, and multiplexing as well as barcoding applications. For the rational design of lifetime probes and barcodes, theoretical methods have been developed to enable the ab initio prediction of this parameter, which depends strongly on interactions with solvent molecules and other chemical species in the emitter´s immediate environment. In this work, we investigate how a conductor-like screening model (COSMO) can account for variations in fluorescence lifetimes that are caused by such fluorophore-solvent interactions...
December 3, 2018: Journal of Physical Chemistry. A
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