gebhart/patrepeval huggingface dataset:
YASS: Yet Another Spike Sorter (2017)

Abstract Spike sorting is a critical first step in extracting neural signals from large-scale electrophysiological data. This manuscript describes an efficient, reliable pipeline for spike sorting on dense multi-electrode arrays (MEAs), where neural signals appear across many electrodes and spike sorting currently represents a major computational bottleneck. We present several new techniques that make dense MEA spike sorting more robust and scalable. Our pipeline is based on an efficient multi-stage “triage-then-cluster-then-pursuit” approach that initially extracts only clean, high-quality waveforms from the electrophysiological time series by temporarily skipping noisy or “collided” events (representing two neurons firing synchronously). This is accomplished by developing a neural network detection method followed by efficient outlier triaging. The clean waveforms are then used to infer the set of neural spike waveform templates through nonparametric Bayesian clustering. Our clustering approach adapts a “coreset” approach for data reduction and uses efficient inference methods in a Dirichlet process mixture model framework to dramatically improve the scalability and reliability of the entire pipeline. The “triaged” waveforms are then finally recovered with matching-pursuit deconvolution techniques. The proposed methods improve on the state-of-the-art in terms of accuracy and stability on both real and biophysically-realistic simulated MEA data. Furthermore, the proposed pipeline is efficient, learning templates and clustering much faster than real-time for a ≃ 500-electrode dataset, using primarily a single CPU core.
Experimental Identification of the Second‐Order Non‐Hermitian Skin Effect with Physics‐Graph‐Informed Machine Learning (2022)

Topological phases of matter are conventionally characterized by the bulk-boundary correspondence in Hermitian systems. The topological invariant of the bulk in d dimensions corresponds to the number of (d - 1)-dimensional boundary states. By extension, higher-order topological insulators reveal a bulk-edge-corner correspondence, such that nth order topological phases feature (d - n)-dimensional boundary states. The advent of non-Hermitian topological systems sheds new light on the emergence of the non-Hermitian skin effect (NHSE) with an extensive number of boundary modes under open boundary conditions. Still, the higher-order NHSE remains largely unexplored, particularly in the experiment. An unsupervised approach-physics-graph-informed machine learning (PGIML)-to enhance the data mining ability of machine learning with limited domain knowledge is introduced. Through PGIML, the second-order NHSE in a 2D non-Hermitian topoelectrical circuit is experimentally demonstrated. The admittance spectra of the circuit exhibit an extensive number of corner skin modes and extreme sensitivity of the spectral flow to the boundary conditions. The violation of the conventional bulk-boundary correspondence in the second-order NHSE implies that modification of the topological band theory is inevitable in higher dimensional non-Hermitian systems.
Phosphorylation of lignin: characterization and investigation of the thermal decomposition (2017)

Lignin is an abundant polyphenol biopolymeric material chemically functionalisable to act as flame retardant in polymers.
Design and Demonstration of an Infrared Meanderline Phase Retarder (2007)

We compare design and measurements for a single-layer meanderline quarter-wave phase retarder, operating across the wavelength range from 8 to 12 micrometers (25 to 37.5 THz) in the infrared. The structure was fabricated using direct-write electron-beam lithography. With measured frequency-dependent material properties incorporated into a periodic-moment-method model, reasonable agreement is obtained for the spectral dependence of axial ratio and phase delay. As expected from theory, the single-layer meanderline design has relatively low throughput (23%), but with extension to multiple-layer designs, the meanderline approach offers significant potential benefits as compared to conventional birefringent crystalline waveplates in terms of spectral bandwidth, angular bandwidth, and cost. Simple changes in the lithographic geometry will allow designs to be developed for specific phase retardations over specified frequency ranges in the infrared, terahertz, or millimeter-wave bands, where custom-designed waveplates are not commercially available.
An SCR with Simple MIS Structure (1990)

A device to work as an SCR with a simple MIS p-n Structure is proposed and demonstrated. It employs two junction diodes, with a thin oxide layer grown prior to metallization. This device can act as a triac when a bi-directional ac voltage is applied, while acts as an SCR when a bias voltage is applied to the N-substrate.
Effects of Lidocaine and Articaine on Neuronal Survival and Recovery (2018)

The local anesthetics lidocaine and articaine are among the most widely used drugs in the dentist's arsenal, relieving pain by blocking voltage-dependent Na<sup>+</sup> channels and thus preventing transmission of the pain signal. Given reports of infrequent but prolonged paresthesias with 4% articaine, we compared its neurotoxicity and functional impairment by screening cultured neural SH-SY5Y cells with formulations used in patients (2% lidocaine + 1:100,000 epinephrine or 4% articaine + 1:100,000 epinephrine) and with pure formulations of the drugs. Voltage-dependent sodium channels Na(v)1.2 and Na(v)1.7 were expressed in SH-SY5Y cells. To test the effects on viability, cells were exposed to drugs for 5 minutes, and after washing, cells were treated with the ratiometric Live/Dead assay. Articaine had no effect on the survival of SH-SY5Y cells, while lidocaine produced a significant reduction only when used as pure powder. To determine reversibility of blockage, wells were exposed to drugs for 5 minutes and returned for medium for 30 minutes, and the calcium elevation induced by depolarizing cells with a high-potassium solution was measured using the calcium indicator Fura-2. High potassium raised calcium in control SH-SY5Y cells and those treated with articaine, but lidocaine treatment significantly reduced the response. In conclusion, articaine does not damage neural cells more than lidocaine in this in vitro model. While this does not question the safety of lidocaine used clinically, it does suggest that articaine is no more neurotoxic, at least in the in vitro setting.
Copy Number and Expression Alterations of miRNAs in the Ovarian Cancer Cell Line OVCAR-3: Impact on Kallikrein 6 Protein Expression (2012)

The hsa-let-7 family member hsa-let-7a is a modulator of KLK6 protein expression that is independent of the KLK6 copy number status.
Mechanistic Study of Carbon Oxidation with NO2 and O2 in the Presence of a Ru/Na‐Y Catalyst (2009)

Abstract The oxidation of model soot by NO 2 and O 2 in the presence of a Ru/Na‐Y catalyst under conditions close to automotive exhaust gas after‐treatment systems is investigated. Isothermal oxidation experiments of a physical mixture of carbon black and catalyst were performed in a temperature range of 300–400 °C. A remarkable increase of the oxidation rate by NO 2 and O 2 in the presence of the Ru/Na‐Y catalyst was observed. An overall mechanism involving oxygen transfer from the Ru catalyst to the carbon surface leading to an increase of C(O) complexes is proposed. These C(O) complexes are destabilized in the presence of NO 2 increasing the carbon oxidation rate.
Dislocation‐Induced Structural and Luminescence Degradation in InAs Quantum Dot Emitters on Silicon (2023)

This study probes the extent to which dislocations reduce carrier lifetimes and alter growth morphology and luminescence in InAs quantum dots (QD) grown on silicon. These heterostructures are key ingredients to achieving a highly reliable monolithically integrated light source on silicon necessary for photonic‐integrated circuits. Around 20%–30% shorter carrier lifetimes are found at spatially resolved individual dislocations at room temperature using time‐resolved cathodoluminescence spectroscopy, highlighting the strong nonradiative impact of dislocations even against the three‐dimensional confinement of QDs. Beyond these direct effects of increased nonradiative recombination, it is found that misfit dislocations in the defect filter layers employed during III–V/Si growth alter the QD growth environment to induce a crosshatch‐like variation in QD emission color and intensity when the filter layer is positioned sufficiently close to the QD emitter layer. Sessile threading dislocations generate even more egregious hillock defects that also reduce emission intensities by altering layer thicknesses, as measured by transmission electron microscopy and atom probe tomography. This work presents a more complete picture of the impacts of dislocations relevant to the development of light sources for scalable silicon photonic integrated circuits.
Interactive iso-surface ray tracing of massive volumetric data sets (2007)

The visualization of iso-surfaces from gridded volume data is an important tool in many scientific applications. Today, it is possible to ray trace high-quality iso-surfaces at interactive frame rates even on commodity PCs. However, current algorithms fail if the data set exceeds a certain size either because they are not designed for outof- core data sets or the loading times are too high because there is too much overhead involved in the out-of-core (OOC) techniques. We propose a kD-tree based OOC data structure that allows to ray trace iso-surfaces of large volumetric data sets of many giga bytes at interactive frame rates on a single PC. A LOD technique is used to bridge loading times of data that is fetched asynchronously in the background. Using this framework we are able to ray trace iso-surfaces between 2 and 4 fps on a single dual-core Opteron PC at 640×480 resolution and an in-core memory footprint that is only a fraction of the entire data size.
TIPICO X: report of the 10th interactive infectious disease workshop on infectious diseases and vaccines (2020)

TIPICO is an expert meeting and workshop that aims to provide the most recent evidence in the field of infectious diseases and vaccination. The 10th Interactive Infectious Disease TIPICO workshop took place in Santiago de Compostela, Spain, on November 21–22, 2019. Cutting-edge advances in vaccination against respiratory syncytial virus, Streptococcus pneumoniae, rotavirus, human papillomavirus, Neisseria meningitidis, influenza virus, and Salmonella Typhi were discussed. Furthermore, heterologous vaccine effects were updated, including the use of Bacillus Calmette-Guérin (BCG) vaccine as potential treatment for type 1 diabetes. Finally, the workshop also included presentations and discussion on emergent virus and zoonoses, vaccine resilience, building and sustaining confidence in vaccination, approaches to vaccine decision-making, pros and cons of compulsory vaccination, the latest advances in decoding infectious diseases by RNA gene signatures, and the application of big data approaches.
In-cylinder pressure sensor–based NOx model for real-time application in diesel engines (2017)

A real-time implementable, zero-dimensional model for predicting engine-out emissions of nitrogen oxides using in-cylinder pressure measurements is developed. The model is an extension of existing works in open literature that align well with the objectives of real-time implementation. The proposed model uses a simplified Zeldovich NO x mechanism that uses combustion-related parameters derived from simplified thermodynamic and combustion sub-models. The performance of the model is discussed for both a heavy-duty and a light-duty diesel engines. The model behavior is evaluated under input uncertainty so as to provide realistic performance bounds.
An investigation into bimetallic catalysts for base free oxidation of cellobiose and glucose (2017)

Abstract BACKGROUND The selective conversion of cellulose to gluconic acid under mild conditions is challenging as it has abundant intra‐and inter‐molecular hydrogen bonds that protect the β‐1,4‐glycosidic bonds and make it intrinsically recalcitrant to depolymerize. RESULTS Au‐Pd/ TiO 2 and Au‐Pt/ TiO 2 catalysts prepared by sol immobilization method without pre‐treatment are active and selective for the oxidation of glucose and cellobiose to gluconic acid under base‐free conditions. Important preparation parameters are the pre‐treatment of the catalyst and the metal ratio. CONCLUSION The optimized catalyst provided a good yield of gluconic acid from cellobiose and has opened up a new catalyst system for cellobiose conversion in terms of a heterogeneous catalyst. © 2017 Society of Chemical Industry
Symposium on Cortisol Secretion Abnormalities Honoring Dr. George P. Chrousos (2007)

Key words Cushing syndrome - cortisol resistance - hypothalamic-pituitary-adrenal axis - congenital adrenal hyperplasia - adrenal tumors - depression - corticotrophin-releasing hormone (CRH)
Magnetism and Chemical Structure of Spinel-Spinel Interfaces (2007)

We investigate the magnetic properties of the isostructural spinel-spinel interface of NiMn2O4(NMO)-Fe3O4. Although the magnetic transition temperature of the NMO film is preserved, both bulk and interface sensitive measurements demonstrate that the interface exhibits strong interfacial magnetic coupling up to room temperature. While NMO thin films have a ferrimagnetic transition temperature of 60K, both NiFe2O4 and MnFe2O4 are ferrimagnetic at room temperature. Our experimental results suggest that these magnetic properties arise from a thin interdiffused region of (Fe,Mn,Ni)3O4 at the interface leading to Mn and Ni magnetic properties similar to MnFe2O4 and NiFe2O4.
15-Copper(ii)-containing 36-tungsto-4-silicates(iv) [Cu15O2(OH)10X(A-α-SiW9O34)4]25−(X = Cl, Br): synthesis, structure, magnetic properties, and electrocatalytic CO2reduction (2018)

The 15-copper(ii)-containing 36-tungsto-4-silicates [Cu15O2(OH)10X(A-α-SiW9O34)4]25- (X = Cl, 1; Br, 2) have been prepared in 70% yield by reaction of the trilacunary 9-tungstosilicate precursor [A-α-SiW9O34]10- with Cu2+ ions in aqueous pH 8 medium. Both polyanions 1 and 2 were isolated as hydrated mixed potassium/sodium salts and characterized in the solid state by FT-IR, TGA, single-crystal XRD, and elemental analysis. DC magnetic susceptibility measurements from 1.8-300 K established the ground state to be paramagnetic with a magnetic moment corresponding to 15 uncoupled Cu2+ (S = 1/2) ions. EPR measurements and simulations were consistent with this analysis. Electrochemical studies were performed for polyanions 1 and 2 dissolved in solution to elucidate the electroactivity of both copper and tungstate sites. Using 2 as a representative example, the electrocatalytic activity towards CO2 reduction upon deposition on a glassy carbon electrode surface, while retaining selectivity relative to hydrogen evolution, was demonstrated.
A Wavelet Approach for the Estimation of Left Ventricular Early Filling\n Wave Propagation Velocity from Color-M-Mode Echocardiograms (2019)

Objective: This work evaluates a new approach for calculating the\nleft-ventricular (LV) early filling propagation velocity (VP) from color M-Mode\n(CMM) echocardiograms using wavelet analysis. Unlike current approaches, the\nmethod requires no assumptions, user inputs, or heuristic conventions.\nBackground: Current methods for measuring VP using CMM echocardiography do not\naccount for the spatiotemporal variation of the filling wave propagation\nvelocity. They are instead confined by empirical assumptions and user inputs\nthat significantly hinder the accuracy of VP, subsequently limiting its\nclinical utility. Methods: We evaluated three methods for measuring LV early\nfilling VP: conventional VP, the strength of propagation (VS), and VP\ndetermined from the most energetically important wave (Peak-VW), using 125\npatients (Group A) with normal filling (n=50), impaired relaxation (n=25),\npseudonormal filling (n=25) and restrictive filling (n=25), and in 69 patients\n(Group B) with normal (n=32), dilated (n=15), and hypertrophic ventricles\n(n=22). Results: Peak-VW most accurately distinguished normal left ventricles\nfrom diseased ones. Specifically, for Group A which spanned the stages of\ndiastolic function, using receiver operator characteristics (ROC) and measuring\ntheir corresponding area under the curve (AUC), the AUC for Peak-VW was 0.92,\nversus 0.62 for conventional VP, 0.63 for VS and 0.58 for intraventricular\npressure difference (IVPD). These correspond to a 50-70% improvement in\nclassification ability. Similar improvements were found using Group B.\nConclusion: A new determination of the LV early filling using wavelet analysis,\nPeak-VW, may provide a more accurate evaluation of diastolic function than the\nstandard method of determining Vp and enable better diagnostic classification\nof patients suffering with diastolic dysfunction.\n
A Metabolic Biofuel Cell: Conversion of Human Leukocyte Metabolic Activity to Electrical Currents (2011)

An investigation of the electrochemical activity of human white blood cells (WBC) for biofuel cell (BFC) applications is described. WBCs isolated from whole human blood were suspended in PBS and introduced into the anode compartment of a proton exchange membrane (PEM) fuel cell. The cathode compartment contained a 50 mM potassium ferricyanide solution. Average current densities between 0.9 and 1.6 μA cm-2 and open circuit potentials (Voc) between 83 and 102 mV were obtained, which were both higher than control values. Cyclic voltammetry was used to investigate the electrochemical activity of the activated WBCs in an attempt to elucidate the mechanism of electron transfer between the cells and electrode. Voltammograms were obtained for the WBCs, including peripheral blood mononuclear cells (PBMCs - a lymphocyte-monocyte mixture isolated on a Ficoll gradient), a B lymphoblastoid cell line (BLCL), and two leukemia cell lines, namely K562 and Jurkat. An oxidation peak at about 363 mV vs. SCE for the PMA (phorbol ester) activated primary cells, with a notable absence of a reduction peak was observed. Oxidation peaks were not observed for the BLCL, K562 or Jurkat cell lines. HPLC confirmed the release of serotonin (5-HT) from the PMA activated primary cells. It is believed that serotonin, among other biochemical species released by the activated cells, contributes to the observed BFC currents.
A Privacy-preserving Outsourcing Scheme for Zero-knowledge Proof Generation (2022)

We propose a privacy-preserving scheme to outsource zero-knowledge proof generation to a party that we call a worker. Our scheme can be applied to zk-SNARKs with a trusted setup, zero-knowledge proofs deployed in many applications. Compared to known privacy-preserving outsourcing schemes, our scheme is more practical in the sense that the computational and memory load on the worker is almost the same as that on the prover in cases where the provers generate proofs on their own.
Preparation of Negamycin Ointments. II (1986)

To improve stability and antimicrobial activity of negamycin (NGM) in ointment preparation, chemical stability and in vitro release of NGM incorporated in ointment cking water phase and the combination effect of NGM and other antibiotics were investigated. In vitro release of NGM from fatty alcohol and propylene glycol base was greater than that from plastibase 50W and hydrophilic poloid. The release rate of NGM was further improved by modifying ingredients and compositions of FAPG base. The combinations of NGM and other antibiotics significantly improved antimicrobial activity against gram-positive bacterium, particularly the combination of NGM and tetracycline. The present data suggest the utility of FAPG base and the efficacy of the combination of NGM and tetracycline in the preparation of NGM ointment.
Reduced parts three-phase series-parallel UPS system with active filter capabilities (2004)

In this paper, a new three-phase series-parallel line-interactive uninterruptible power supply (UPS) topology is presented. The new topology has less number of power electronic devices as well as control functions. Most of the power is supplied directly from the AC line to the load. Therefore, the overall efficiency is higher than that of on-line UPS. Different operating modes of the system and series and parallel converters are investigated as well. Simulation and experimental results are presented, which show the viability of the proposed topology.
Advances in broad bandwidth light sources for ultrahigh resolution optical coherence tomography (2004)

Novel ultra-broad bandwidth light sources enabling unprecedented sub-2 microm axial resolution over the 400 nm-1700 nm wavelength range have been developed and evaluated with respect to their feasibility for clinical ultrahigh resolution optical coherence tomography (UHR OCT) applications. The state-of-the-art light sources described here include a compact Kerr lens mode locked Ti:sapphire laser (lambdaC = 785 nm, delta lambda = 260 nm, P(out) = 50 mW) and different nonlinear fibre-based light sources with spectral bandwidths (at full width at half maximum) up to 350 nm at lambdaC = 1130 nm and 470 nm at lambdaC = 1375 nm. In vitro UHR OCT imaging is demonstrated at multiple wavelengths in human cancer cells, animal ganglion cells as well as in neuropathologic and ophthalmic biopsies in order to compare and optimize UHR OCT image contrast, resolution and penetration depth.
P-glycoprotein expression in ovarian tumour biopsies taken before or after cytotoxic chemotherapy (1992)

SummarySummaryThe multi-drug resistance gene, MDRI, encodes a plasma membrane glycoprotein which is found in high levels in multi-drug resistant tumour cells and has been associated with resistance to a wide variety of structurally unrelated agents in vitro. P-glycoprotein expression was evaluated in frozen sections from 57 patients with epithelial ovarian cancer by the indirect immuno-peroxidase technique using the monoclonal antibody MRK 16. Normal ovaries (n = 15) and peritoneal (n = 37) biopsies taken with the tumour or normal ovarian tissue were also examined. P-glycoprotein expression was observed in 5 our of 36 patients (13 per cent) who had received no previous chemotherapy and in 4 out of 21 patients (19 per cent) who had undergone chemotherapy. No expression was observed in the normal ovary. One positively staining inclusion cyst was seen in the peritoneal biopsy material.Four of those who had had no chemotherapy and four of those who had. and who expressed the protein were considered clinically resistant to chemotherapy; 16 of the 21 patients who were biopsied following chemotherapy were in fact clinically resistant to chemotherapy. Therefore, although drug resistance is a major problem in the treatment of ovarian carcinoma, the low numbers of ovarian tumours expressing P-glycoprotein observed in this work indicates that P-glycoprotein probably does not play a major role in the development of resistance in the majority of ovarian tumours.
Theoretical and experimental characterization of a stationary low coherence interferometer for optical coherence tomography (2003)

A stationary low coherence interferometer for optical coherence tomography (linear OCT, LOCT) based on Young’s two-pinhole experiment is characterized theoretically. All OCT sensors either work in the time (TDOCT) or Fourier domain (FDOCT). In contrast to these setups, the interferometer described in this paper employs no moving parts in the reference arm and no spectrometers for depth profiling. Depth profiling is achieved by detecting the interference signal on a linear CCD-array. Different positions of the interference signal on the CCD-array correspond to different depths inside the sample. The interference signal of the setup and the sensitivity in the case of shot noise limited detection are derived theoretically and compared to sensors in the time domain. In-vitro images of porcine cornea demonstrate the clinical potential of the setup.