gebhart/patrepeval huggingface dataset:
Neural-network-based analysis of EEG data using the neuromorphic TrueNorth chip for brain-machine interfaces (2017)

Electroencephalography (EEG) is a noninvasive way to record brain activity by means of measuring electrical fields arising from neural activation. Being relatively inexpensive, safe, and readily available, EEG-based techniques have been studied as potential methods for controlling brain-machine interfaces. Previous attempts to analyze EEG signals have focused on well-characterized sensorimotor data features. However, the brain-machine interface field seems to have stagnated in improving motor decoding using this method. One way to overcome this hurdle is to use neural-network-based classification methods to analyze brain-activity data. In this paper, we describe the novel neural networks we created for analyzing existing EEG data. Although these neural networks were programmed, trained, and tested in a conventional central processing unit or graphics processing unit environment, their novelty lies in their full compatibility with IBM's recently introduced ultralow power, neuromorphic TrueNorth chip infrastructure, thus, constituting the analytical units in the next generation of neurobionic mobile devices. We report on the development of a new EEG signal classifier built on a spiking neural network that runs on the TrueNorth platform. Using a modified back-propagation training method that employs trinary weights, we demonstrate state-of-the-art classification accuracy.
Ultrathin Covalently Bound Organic Layers on Mica: Formation of Atomically Flat Biofunctionalizable Surfaces (2017)

Mica is the substrate of choice for microscopic visualization of a wide variety of intricate nanostructures. Unfortunately, the lack of a facile strategy for its modification has prevented the on-mica assembly of nanostructures. Herein, we disclose a convenient catechol-based linker that enables various surface-bound metal-free click reactions, and an easy modification of mica with DNA nanostructures and a horseradish peroxidase mimicking hemin/G-quadruplex DNAzyme.
Relay-Reconfigurable Intelligent Surface Cooperation for\n Energy-Efficient Multiuser Systems (2021)

Reconfigurable intelligent surfaces (RIS) have drawn considerable attention\nrecently due to their controllable scattering elements that are able to direct\nelectromagnetic waves into desirable directions. Although RISs share some\nsimilarities with relays, the two have fundamental differences impacting their\nperformance. To harness the benefits of both relaying and RISs, a multi-user\ncommunication system is proposed in this paper wherein a relay and an RIS\ncooperate to improve performance in terms of energy efficiency. To utilize the\nRIS efficiently, the discrete phase shifts of the RIS elements are optimized\nalong with the beamforming matrices at the transmitter and the relay, targeting\nthe minimization of the total transmit power subject to a quality-of-service\n(QoS) constraint. Then, two suboptimal efficient solutions are proposed for the\nresulting discrete and non-convex problem, one based on singular value\ndecomposition (SVD) and uplink-downlink duality and the other is based on SVD\ncombined with zero-forcing. Simulations show that the proposed solutions\noutperform a system with either a relay or an RIS only, especially when both\nare closer to the users than to the base-station.\n
Gold nanopyramidal plasmonic crystals for label-free biosensing (2010)

We developed a wafer-scale 3D plasmonic crystal consisting of gold nanopyramid arrays using a colloidal templating technique. These surface plasmons in the arrays allow us to obtain real-time, label-free and high sensitivity biomolecular binding measurements. In our research, we found the sensing capabilities improved while the detection limit of the alcohol dehydrogenase sensing was down to pM. The features of low cost fabrication and real-time, label-free, specific and quantitative measurement capabilities suggest promise for the gold nanopyramid arrays in both biological and chemically based analytical detection systems.
Streptomycin Induced Stress Response in Salmonella enterica Serovar Typhimurium Shows Distinct Colony Scatter Signature (2015)

We investigated the streptomycin-induced stress response in Salmonella enterica serovars with a laser optical sensor, BARDOT (bacterial rapid detection using optical scattering technology). Initially, the top 20 S. enterica serovars were screened for their response to streptomycin at 100 μg/mL. All, but four S. enterica serovars were resistant to streptomycin. The MIC of streptomycin-sensitive serovars (Enteritidis, Muenchen, Mississippi, and Schwarzengrund) varied from 12.5 to 50 μg/mL, while streptomycin-resistant serovar (Typhimurium) from 125-250 μg/mL. Two streptomycin-sensitive serovars (Enteritidis and Mississippi) were grown on brain heart infusion (BHI) agar plates containing sub-inhibitory concentration of streptomycin (1.25-5 μg/mL) and a streptomycin-resistant serovar (Typhimurium) was grown on BHI containing 25-50 μg/mL of streptomycin and the colonies (1.2 ± 0.1 mm diameter) were scanned using BARDOT. Data show substantial qualitative and quantitative differences in the colony scatter patterns of Salmonella grown in the presence of streptomycin than the colonies grown in absence of antibiotic. Mass-spectrometry identified overexpression of chaperonin GroEL, which possibly contributed to the observed differences in the colony scatter patterns. Quantitative RT-PCR and immunoassay confirmed streptomycin-induced GroEL expression while, aminoglycoside adenylyltransferase (aadA), aminoglycoside efflux pump (aep), multidrug resistance subunit acrA, and ribosomal protein S12 (rpsL), involved in streptomycin resistance, were unaltered. The study highlights suitability of the BARDOT as a non-invasive, label-free tool for investigating stress response in Salmonella in conjunction with the molecular and immunoassay methods.
Comparison of Methods for Profiling O-Glycosylation (2009)

The Human Proteome Organisation Human Disease Glycomics/Proteome Initiative recently coordinated a multi-institutional study that evaluated methodologies that are widely used for defining the N-glycan content in glycoproteins. The study convincingly endorsed mass spectrometry as the technique of choice for glycomic profiling in the discovery phase of diagnostic research. The present study reports the extension of the Human Disease Glycomics/Proteome Initiative's activities to an assessment of the methodologies currently used for O-glycan analysis. Three samples of IgA1 isolated from the serum of patients with multiple myeloma were distributed to 15 laboratories worldwide for O-glycomics analysis. A variety of mass spectrometric and chromatographic procedures representative of current methodologies were used. Similar to the previous N-glycan study, the results convincingly confirmed the pre-eminent performance of MS for O-glycan profiling. Two general strategies were found to give the most reliable data, namely direct MS analysis of mixtures of permethylated reduced glycans in the positive ion mode and analysis of native reduced glycans in the negative ion mode using LC-MS approaches. In addition, mass spectrometric methodologies to analyze O-glycopeptides were also successful.
Structure–Activity Relationships of Cyclic Lactam Analogues of α-Melanocyte-Stimulating Hormone (α-MSH) Targeting the Human Melanocortin-3 Receptor (2007)

A variety of dicarboxylic acid linkers introduced between the alpha-amino group of Pro(6) and the -amino group of Lys(10) of the cyclic lactam alpha-melanocyte-stimulating hormone (alpha-MSH)-derived Pro(6)-D-Phe(7)/D-Nal(2')(7)-Arg(8)-Trp(9)-Lys(10)-NH2 pentapeptide template lead to nanomolar range and selective hMC3R agonists and antagonists. Replacement of the Pro(6) residue and the dicarboxylic acid linker with 2,3-pyrazine-dicarboxylic acid furnished a highly selective nanomolar range hMC3R partial agonist (analogue 12, c[CO-2,3-pyrazine-CO-D-Phe-Arg-Trp-Lys]-NH2, EC50 = 27 nM, 70% max cAMP) and an hMC3R antagonist (analogue 13, c[CO-2,3-pyrazine-CO-D-Nal(2')-Arg-Trp-Lys]-NH2, IC50 = 23 nM). Modeling experiments suggest that 2,3-pyrazinedicarboxylic acid stabilizes a beta-turn-like structure with the D-Phe/D-Nal(2') residues, which explains the high potency of the corresponding peptides. Placement of a Nle residue in position 6 produced a hMC3R/hMC5R antagonist (analogue 15, c[CO-(CH 2)2-CO-Nle-D-Nal(2')-Arg-Trp-Lys]-NH2, IC50 = 12 and 17 nM, respectively), similarly to the previously described cyclic gamma-melanocyte-stimulating hormone (gamma-MSH)-derived hMC3R/hMC5R antagonists. These newly developed melanotropins will serve as critical biochemical tools for elucidating the full spectrum of functions performed by the physiologically important melanocortin-3 receptor.
Differential diagnosis of mild cognitive impairment and Alzheimer's disease using structural MRI cortical thickness, hippocampal shape, hippocampal texture, and volumetry (2016)

This paper presents a brain T1-weighted structural magnetic resonance imaging (MRI) biomarker that combines several individual MRI biomarkers (cortical thickness measurements, volumetric measurements, hippocampal shape, and hippocampal texture). The method was developed, trained, and evaluated using two publicly available reference datasets: a standardized dataset from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the imaging arm of the Australian Imaging Biomarkers and Lifestyle flagship study of ageing (AIBL). In addition, the method was evaluated by participation in the Computer-Aided Diagnosis of Dementia (CADDementia) challenge. Cross-validation using ADNI and AIBL data resulted in a multi-class classification accuracy of 62.7% for the discrimination of healthy normal controls (NC), subjects with mild cognitive impairment (MCI), and patients with Alzheimer's disease (AD). This performance generalized to the CADDementia challenge where the method, trained using the ADNI and AIBL data, achieved a classification accuracy 63.0%. The obtained classification accuracy resulted in a first place in the challenge, and the method was significantly better (McNemar's test) than the bottom 24 methods out of the total of 29 methods contributed by 15 different teams in the challenge. The method was further investigated with learning curve and feature selection experiments using ADNI and AIBL data. The learning curve experiments suggested that neither more training data nor a more complex classifier would have improved the obtained results. The feature selection experiment showed that both common and uncommon individual MRI biomarkers contributed to the performance; hippocampal volume, ventricular volume, hippocampal texture, and parietal lobe thickness were the most important. This study highlights the need for both subtle, localized measurements and global measurements in order to discriminate NC, MCI, and AD simultaneously based on a single structural MRI scan. It is likely that additional non-structural MRI features are needed to further improve the obtained performance, especially to improve the discrimination between NC and MCI.
Dielectric properties of Si3− ξ GeξN4 and Si3−ξCξN4: A density functional study (2013)

Using first principles calculations, we have studied the dielectric properties of crystalline α- and β-phase silicon germanium nitrides and silicon carbon nitrides, A3−ξBξN4 (A = Si, B = Ge or C, ξ=0,1,2,3). In silicon germanium nitrides, both the high-frequency and static dielectric constants increase monotonically with increasing germanium concentration, providing a straightforward way to tune the dielectric constant of these materials. In the case of silicon carbon nitrides, the high-frequency dielectric constant increases monotonically with increasing carbon concentration, but a more complex trend is observed for the static dielectric constant, which can be understood in terms of competition between changes in the unit-cell volume and the average oscillator strength. The computed static dielectric constants of C3N4, Si3N4, and Ge3N4 are 7.13, 7.69, and 9.74, respectively.
Low-level light therapy aids traumatic brain injury (2011)

Traumatic brain injury (TBI) caused by falls, motor vehicle accidents, and violence leads to skull fractures, intracranial hemorrhages, elevated intracranial pressure, and cerebral contusion. Severe and moderate TBI, accidental or inflicted, is a major health and socio-economic problem throughout theworld, especially in children and young adults. Despite promising preclinical data, most therapeutic trials for TBI performed in recent years have not demonstrated any significant improvement in outcomes.1 Because of this disappointing state of affairs, a plethora of experimental therapies that are not based on standard pharmaceutical agents have been investigated,2 including several physical treatments.3 Low-level laser therapy (LLLT), also known as photobiomodulation, is an emerging therapeutic approach in which cells or tissues are exposed to low-levels of red and near-IR light. Its experimental applications have broadened to include serious diseases such as heart attack,4 stroke,5 and spinal cord injury.6 LLLT may have beneficial effects in the acute treatment of TBI by increasing mitochondrial respiration, activating transcription factors, reducing key inflammatory mediators, inhibiting apoptosis (programmed cell death), stimulating angiogenesis, and increasing neurogenesis7 (see Figure 1). We studied the effect of an 810nm laser on several cellular processes in primary cortical neurons cultured from mouse embryonic brains. We found that at low fluences (0.3–3Jcm2/ mitochondrial respiration was stimulated, as shown by the increase in adenosine triphosphate (ATP), Ca2C; and mitochondrial membrane potential. This, in turn, generated low amounts of reactive oxygen species (ROS) and nitric oxide (NO) that activated signaling pathways and gene transcription without causing cytotoxicity (see Figure 2). At 10J/cm2; the stimulation of these parameters was reduced because instead of activating mitochondrial respiration, they damaged Figure 1. Possible mechanisms of transcranial low-level laser therapy (LLLT) for traumatic brain injury (TBI). Mitochondrial signaling causes increased neuronal survival; lowered edema, inflammation and excitotoxicity; and increased angiogenesis, neurotrophins, and neural progenitor cells. ROS: Reactive oxygen species. NO: Nitric oxide. NGF: Nerve growth factor. BDNF: Brain-derived neurotrophic factor. NT-3: Neurotrophin-3.
Intersubunit Bridge Formation Governs Agonist Efficacy at Nicotinic Acetylcholine α4β2 Receptors (2011)

The α4β2 subtype of the nicotinic acetylcholine receptor has been pursued as a drug target for treatment of psychiatric and neurodegenerative disorders and smoking cessation aids for decades. Still, a thorough understanding of structure-function relationships of α4β2 agonists is lacking. Using binding experiments, electrophysiology and x-ray crystallography we have investigated a consecutive series of five prototypical pyridine-containing agonists derived from 1-(pyridin-3-yl)-1,4-diazepane. A correlation between binding affinities at α4β2 and the acetylcholine-binding protein from Lymnaea stagnalis (Ls-AChBP) confirms Ls-AChBP as structural surrogate for α4β2 receptors. Crystal structures of five agonists with efficacies at α4β2 from 21-76% were determined in complex with Ls-AChBP. No variation in closure of loop C is observed despite large efficacy variations. Instead, the efficacy of a compound appears tightly coupled to its ability to form a strong intersubunit bridge linking the primary and complementary binding interfaces. For the tested agonists, a specific halogen bond was observed to play a large role in establishing such strong intersubunit anchoring.
Experimental estimates of in-plane thermal conductivity in FePt-C granular thin film heat assisted magnetic recording media using a model layered system (2013)

Cross-plane thermal conductivity kth measurements of vertical stacks of FePt/C were used to estimate the in-plane thermal conductivity of Heat Assisted Magnetic Recording (HAMR) media that consist of columnar FePt grains segregated by thin C grain boundaries. FePt/C multilayers with varied repeat units and FePt layer thicknesses (chosen to represent HAMR media grain sizes) were measured using Frequency-Domain Thermoreflectance to determine kth in the direction normal to the layers. The data suggest that when FePt grains are less than 8 nm in diameter, the in-plane kth for HAMR media is below 1 W/m-K and the anisotropy of kth (cross-plane/in-plane) will exceed 10.
High power-conversion-efficiency operation of discrete Raman amplifiers using high Raman gain fiber and its bandwidth dependence (2004)

We investigate bandwidth dependence of power-conversion-efficiency for discrete Raman amplifiers using a high Raman gain fiber. The efficiency can be as high as 72% for a C+L-band booster amplifier, while 65% for a C-band amplifier.
A real-time driver monitoring system using a high sensitivity camera (2019)

Traffic accidents and mental stress are strongly correlated. Drivers under pressure are more easily to cause accidents. A system which could describe the mental state of a driver would be helpful to avoid such accidents. Multiple indices derived from analysis of heart rate variability (HRV) could be used in the estimation of mental state in humans; moreover, recent years, methods of non-contact heart rate estimation have been well studied and reached high accuracy. Based on both, we developed a real-time driver monitoring system which could not only estimate heart rate of the driver, but also indicate whether he is under pressure or not. This system delivers 2 outputs: heart rate(HR) and mental stress level (stress index). We utilized an 18-bit camera to grab frontal facial frames and independent component analysis (ICA) to extract haemoglobin signal from each frame. After temporal filtering and peak detection, R-R interval(RRI) will be obtained and HR measured. Mental stress estimation will start 30 seconds after we get the first RRI data, then a power spectrum analysis method will be applied to all of the HRV data within 30 seconds to generate powers of Low-Frequency and High-Frequency band data. The ratio of the powers in both bands, so called LF-HF ratio (LF/HF), will be delivered as a stress index to quantify the degree of mental stress. Finally, the validity of stress index is verified over arithmetic calculation and a number of driving-simulating scenarios.
Structural dependence of effective area and mode field diameter for holey fibers (2003)

A rigorous full-vector finite element method is effectively applied to evaluating the effective area Aeff and the mode field diameter (MFD) of holey fibers (HFs) with finite cross sections. The effective modal spot size (a half of MFD), weff, is defined with the help of the second moment of the optical intensity distribution. The influence of hole diameter, hole pitch, operating wavelength, and number of rings of air holes on Aeff and weff is investigated in detail. As a result, it is shown that Aeff and weff are almost independent of the number of hole rings and that the relation Aeff = piweff 2, which is frequently utilized in the conventional optical fibers, does not always hold, especially in smaller air-filling fraction and/or longer wavelength regions. In addition, we find that for HFs with large air holes operating at longer wavelengths, the mode profiles of the two linearly polarized fundamental modes are significantly different from each other, even though they are degenerate. Using the values of Aeff and weff obtained here, the beam divergence and the nonlinear phase shift are calculated and are compared with the earlier experimental results.
Multi-Color Enhanced Fluorescence Imaging of a Breast Cancer Cell with A Hole-Arrayed Plasmonic Chip (2020)

Breast cancer cells of MDA-MB-231 express various types of membrane proteins in the cell membrane. In this study, two types of membrane proteins in MDA-MB-231 cells were observed using a plasmonic chip with an epifluorescence microscope. The targeted membrane proteins were epithelial cell adhesion molecules (EpCAMs) and epidermal growth factor receptor (EGFR), and Alexa<sup>®</sup>488-EGFR antibody and allophycocyanin (APC)-labeled EpCAM antibody were applied to the fluorescent detection. The plasmonic chip used in this study is composed of a two-dimensional hole-array structure, which is expected to enhance the fluorescence at different resonance wavelengths due to two kinds of grating pitches in a square side and a diagonal direction. As a result of multi-color imaging, the enhancement factor of Alexa<sup>®</sup>488-EGFR and APC-EpCAM was 13 ± 2 and 12 ± 2 times greater on the plasmonic chip, respectively. The excited wavelength or emission wavelength of each fluorescent agent is due to consistency with plasmon resonance wavelength in the hole-arrayed chip. The multi-color fluorescence images of breast cancer cells were improved by the hole-arrayed plasmonic chip.
Elaboration of Monodisperse Spherical Hollow Particles with Ordered Mesoporous Silica Shells via Dual Latex/Surfactant Templating: Radial Orientation of Mesopore Channels (2008)

Monodisperse spherical hollow nanoparticles of mesoporous silica featuring mesopores with a radial orientation in the silica shell were synthesized via a dual-templating method. Specifically designed polystyrene latexes with anionic or cationic surface charges acted as the core templates, while cetyltrimethylammonium bromide served as a co-template to structure the mesopore formation during tetraethoxysilane hydrolysis/condensation. The particles were well-separated and presented homogeneous mesoporous silica shells. Average particle diameters were less than 200 nm, and the particles displayed high values of specific surface area and pore volume. The shell thickness and the hollow core diameter could be tuned independently while the radial pore structure was preserved. A detailed analysis of the nitrogen adsorption-desorption isotherms proved that the central cavity was completely isolated from the external medium, that is, only accessible through the radial mesopores of the shell. Consequently, our particles gather the advantages of a well-defined structure, straight penetrating channels across the silica shell, and a high accessible porous volume of the central core. These properties make them far better candidates than simple mesoporous particles for any storage and/or controlled release applications.
Joint profiling of chromatin accessibility and gene expression in thousands of single cells (2018)

Although we can increasingly measure transcription, chromatin, methylation, and other aspects of molecular biology at single-cell resolution, most assays survey only one aspect of cellular biology. Here we describe sci-CAR, a combinatorial indexing-based coassay that jointly profiles chromatin accessibility and mRNA (CAR) in each of thousands of single cells. As a proof of concept, we apply sci-CAR to 4825 cells, including a time series of dexamethasone treatment, as well as to 11,296 cells from the adult mouse kidney. With the resulting data, we compare the pseudotemporal dynamics of chromatin accessibility and gene expression, reconstruct the chromatin accessibility profiles of cell types defined by RNA profiles, and link cis-regulatory sites to their target genes on the basis of the covariance of chromatin accessibility and transcription across large numbers of single cells.