gebhart/patrepeval huggingface dataset:
Fast impedance spectroscopy: General aspects and performance study for single ion channel measurements (2000)

In the present work, we propose a novel technical approach in time domain impedance spectroscopy enabling both enhanced time and current resolution by an improved data analysis and hardware setup. We introduce nonstationary time-to-frequency conversion methods such as short-time Fourier transform and wavelet transform resulting in an improved time resolution. The combination of a time domain impedance spectrometer with a patch-clamp amplifier enables the resolution of gigaohm impedance at low perturbation signal amplitudes. A fast impedance spectroscopy (FIS) setup is presented which is optimized for biophysical application of single ion channel measurements in supported biomembranes. The applicability and performance of the technique is first evaluated by simulations. It is then verified by measurements on model circuits which exhibit the characteristic key properties of single ion channel measurements. Here, FIS improves the time resolution by about three orders of magnitude down to milliseconds. The general aspects derived in this work are also valid in other fields, where the spectral information of a perturbation applied on a system and its response is analyzed, e.g., mechanical impedance spectroscopy and microrheology.
Planar Format Holograms Having A Wide Viewing Angle And Illuminated By A Nearby Point Source (1989)

An important feature for an effective display hologram is a wide viewing angle so that the autostereoscopic aspects of holography are dramatically evident. A short conjugate distance between the light source and the hologram can simplify the problem of supplying optimum illumination for display holograms and provide higher illumination intensity. These two desirable features, wide viewing angle and nearby point source illumination, have been incorporated simultaneously in planar format white light-illuminated transmission holographic stereograms made from computer graphics. This talk will discuss design considerations related to these two issues. We have achieved conjugate distances of 15 cm for illumination with a tungsten light bulb and viewing angles >70°.
Computer-aided recognition of myopic tilted optic disc using deep learning algorithms in fundus photography (2020)

We developed an automated deep learning-based system to detect optic disc tilt. The model demonstrated excellent agreement with the previous clinical criteria, and the results are promising for developing future programs to adjust and identify the effect of optic disc tilt on ophthalmic measurements.
The Expression of a Barley HνNAS1 Nicotianamine Synthase Gene Promoter-gus Fusion Gene in Transgenic Tobacco is Induced by Fe-deficiency in Roots (2001)

Nicotianamine (NA) is a precursor for mugineic acid-family phytosiderophores, which are a critical component of the Fe aquisition process in graminaceous plants. In addition, nicotianamine synthase (NAS) is strongly induced in these plants by Fe deficiency. NA is essential for Fe metabolism also in dicots, but NAS is not induced by Fe deficiency. We introduced a barley HvNAS1 promoter-gus fusion gene into tobacco. GUS activity was induced in the roots of these plants by Fe deficiency, and was constitutively expressed at a low level in their leaves.
Determination of Time-Resolved Heat Transfer Coefficient and Adiabatic Effectiveness Waveforms With Unsteady Film Cooling (2012)

Traditional hot gas path film cooling characterization involves the use of wind tunnel models to measure the spatial adiabatic effectiveness (η) and heat transfer coefficient (h) distributions. Periodic unsteadiness in the flow, however, causes fluctuations in both η and h. In this paper we present a novel inverse heat transfer methodology that may be used to approximate the η(t) and h(t) waveforms. The technique is a modification of the traditional transient heat transfer technique that, with steady flow conditions only, allows the determination of η and h from a single experiment by measuring the surface temperature history as the material changes temperature after sudden immersion in the flow. However, unlike the traditional transient technique, this new algorithm contains no assumption of steadiness in the formulation of the governing differential equations for heat transfer into a semi-infinite slab. The technique was tested by devising arbitrary waveforms for η and h at a point on a film cooled surface and running a computational simulation of an actual experimental model experiencing those flow conditions. The surface temperature history was corrupted with random noise to simulate actual surface temperature measurements and then fed into an algorithm developed here that successfully and consistently approximated the η(t) and h(t) waveforms.
Dynamic Upscaling of Multiphase Flow in Porous Media via Adaptive Reconstruction of Fine Scale Variables (2009)

Abstract We propose an upscaling method that is based on dynamic simulation of a given model in which the accuracy of the upscaled model is continuously monitored via indirect error-measures. If the indirect error measures are bigger than a specified tolerance, the upscaled model is dynamically updated with approximate fine scale information that is reconstructed by a multi-scale finite volume method (Jenny et al., JCP 217: 627–641, 2006). Upscaling of multi-phase flow entails a detailed flow information in the underlying fine scale. We apply adaptive prolongation and restriction operators for flow and transport equations in constructing an approximate fine scale solution. This new method eliminates inaccuracy associated with the traditional upscaling method which relies on prescribed inaccurate boundary conditions in computing upscaled variables. The new upscaling algorithm is validated for two-phase, incompressible flow in two dimensional porous media with heterogeneous permeabilities. It is demonstrated that the dynamically upscaled model achieves high numerical efficiency than the fine-scale models and also provides an excellent agreement with the reference solution computed from fine-scale simulation.
A non-negative approach to semi-supervised separation of speech from noise with the use of temporal dynamics (2011)

We present a semi-supervised source separation methodology to denoise speech by modeling speech as one source and noise as the other source. We model speech using the recently pro posed non-negative hidden Markov model, which uses multiple non-negative dictionaries and a Markov chain to jointly model spectral structure and temporal dynamics of speech. We perform separation of the speech and noise using the recently proposed non-negative factorial hidden Markov model. Although the speech model is learned from training data, the noise model is learned during the separation process and re quires no training data. We show that the proposed method achieves superior results to using non-negative spectrogram factorization, which ignores the non-stationarity and temporal dynamics of speech.
Target-less Scanner Color Calibration (1999)

The lack of a scanner calibration target representative of the image medium (substrate and colorants) often limits the accuracy of scanner color calibration. In this paper, a color calibration method is presented for photographic input media that does not require a calibration target. Using characteristic spectral measurements from the image(s) to be scanned, a model for the spectra on the medium is obtained through a principal component analysis. The spectral sensitivity of the scanner provides a model for its operation. By using a set-theoretic estimation method that combines the models for the scanner and the medium, the spectral reflectance of the input corresponding to a given set of scanner RGB values can be determined. This provides a spectral calibration for the scanner, which can readily be transformed into a color calibration under any suitable viewing illuminant. Results from simulations and actual calibrations demonstrate the value of the new method.
Functional evolution of the TICAM‐1 pathway for extrinsic RNA sensing (2008)

The type I interferon (IFN) is a host defense factor against microbial pathogens in vertebrates. In mammals, retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) in the cytoplasm are regarded as sensors for double-stranded RNA (dsRNA) and trigger IFN regulatory factor-3 (IRF-3) activation followed by type I IFN induction through the mitochondrial antiviral signaling (MAVS) adapter. This intrinsic pathway appears to link the main protective responses against RNA virus infection in mammals. On the other hand, human Toll-like receptor 3 (TLR3) is localized in the endosomal membrane or cell surface and signals the presence of extrinsic dsRNA. In response to RNA stimulation, TLR3 recruits the Toll-interleukin 1 receptor domain (TIR)-containing adapter molecule 1 (TICAM-1) adapter and induces IRF-3 activation followed by IFN-beta promoter activation. Human TLR3 is localized limitedly extent in myeloid dendritic cells, fibroblasts, and epithelial cells. The TICAM-1 and cytoplasmic MAVS pathways converge at the IRF-3-activating kinase in human cells. The reason for the involvement of this extrinsic mode of IFN-inducing pathways in the dsRNA response remains unknown. In fish, two TLRs, i.e. endoplasmic TLR3 and cell surface TLR22, participate in teleost IFN production without the activation of IRF-3. TLR22 is distinct from mammalian TLR3 in terms of cellular localization, ligand selection, and tissue distribution. TLR22 may be a functional substitute for human cell surface TLR3 and may serve as a surveillance molecule for detecting dsRNA virus infection and alerting the immune system for antiviral protection in fish. In this review, we discuss the fundamentals of the extrinsic dsRNA recognition system, which has evolved to induce cellular effectors to cope with dsRNA virus infection across different vertebrate species.
A Review of Basic to Clinical Studies of Irreversible Electroporation Therapy (2014)

The use of irreversible electroporation (IRE) for cancer treatment has increased sharply over the past decade. As a nonthermal therapy, IRE offers several potential benefits over other focal therapies, which include 1) short treatment delivery time, 2) reduced collateral thermal injury, and 3) the ability to treat tumors adjacent to major blood vessels. These advantages have stimulated widespread interest in basic through clinical studies of IRE. For instance, many in vitro and in vivo studies now identify treatment planning protocols (IRE threshold, pulse parameters, etc.), electrode delivery (electrode design, placement, intraoperative imaging methods, etc.), injury evaluation (methods and timing), and treatment efficacy in different cancer models. Therefore, this study reviews the in vitro, translational, and clinical studies of IRE cancer therapy based on major experimental studies particularly within the past decade. Further, this study provides organized data and facts to assist further research, optimization, and clinical applications of IRE.
Spectral shifts in metal-enhanced fluorescence (2014)

We report a 2 nm red shift in the fluorescence spectra observed for Rhodamine 800 dissolved in glycerol on copper substrates as compared to glass reference samples, suggesting a wavelength dependence of metal enhanced fluorescence. The full width half maximum of the blue-red spectra is about 1 nm narrower as compared to the reference sample. We speculate that the observation correlates with a specific interaction mechanism between the Rhodamine 800 transition dipole, the enhanced electric field, and subsequent plasmon coupling, an observation not yet reported.
Efficient fixed-point approximations of the 8x8 inverse discrete cosine transform (2007)

This paper describes fixed-point design methodologies and several resulting implementations of the Inverse Discrete Cosine Transform (IDCT) contributed by the authors to MPEG's work on defining the new 8x8 fixed point IDCT standard - ISO/IEC 23002-2. The algorithm currently specified in the Final Committee Draft (FCD) of this standard is also described herein.
Abstract 11921: Risk Stratification for Ventricular Arrhythmia in Patients With Repaired Tetralogy of Fallot (TOF) via Image-Based Computational Simulations: A Pilot Study (2016)

Introduction: Patients with repaired TOF have increased arrhythmia risk due to myocardial fibrosis, scar and right ventricular dilation. Current risk stratification lacks consistent predictive value and clinical practicality. We surmised that personalized models developed from cardiac late gadolinium enhancement MRI (LGE-MRI) could correctly assess risk of arrhythmia in patients with repaired TOF using our previously-validated Virtual Arrhythmia Risk Prediction (VARP) protocol. Methods: As a proof-of-concept retrospective study, we developed personalized 3D computational models of TOF hearts from LGE-MRI scans. Three patients with clinically disparate arrhythmia status were included: patient 1 (P1) had clinical episodes of sustained ventricular tachycardia (VT) and inducibility in electrophysiologic study (EPS); patient 2 (P2) had negative EPS despite documented runs of non-sustained VT; patient 3 (P3) had no clinical evidence of VT. Then, for each heart, we applied our VARP protocol to generate a computational model, including personalized representations of scar and fibrosis. We then assessed the inducibility of reentrant arrhythmia from 26 pacing sites. Results: For all three cases, VARP outcomes correlated with clinical observations. In the P1 model sustained VT was induced with rapid ventricular pacing, while only non-sustained VT was induced in the P2 model (Fig 1). No arrhythmia was induced in the P3 model. Reentrant wavefronts in P1 and P2 occurred near the right ventricular outflow tract (RVOT) or ventricular septal defect patch, common sites of reentry observed in EPS in patients with TOF (Fig 1). Conclusion: Application of the VARP approach in repaired TOF patients is feasible and has the potential to correctly identify patients with a high risk of developing arrhythmia. With additional validation this non-invasive technique could serve as an effective tool for longitudinal risk assessment and help guide clinical decision making.
A patient-specific reduced-order model for coronary circulation (2012)

We introduce a patient-specific model for coronary circulation, by combining anatomical, hemodynamic and functional information from medical images and other clinical observations. The main components of the coupled model are: a lumped heart model, a reduced-order model for hemodynamics in the arterial vessel tree (both healthy and stenosed), and a physiological model for the microvascular bed. The anatomy of the vessel tree is extracted from Coronary Computed Tomography Angiography (CTA) images, followed by an estimation of the impedance of the distal microvascular network. For the blood flow simulations, three states are modeled: rest, drug-induced hyperemia and intense exercise. The results show an excellent agreement with the literature and provide a model for virtual assessment of the flow and underlying functional measures in healthy and stenosed coronary arteries.
Effects of Thickness on Corneal Biomechanical Properties Using Optical Coherence Elastography (2018)

Corneal thickness and stiffness are correlated positively. A higher relaxation rate implied stiffer material properties after isotonic CXL treatment. Hypertonic CXL treatment results in a stiffness decrease that offsets the stiffness increase with CXL treatment.
FISH-RiboSyn: A Rapid Approach for Determining the Specific Growth Rate of a Distinct Microbial Population in a Mixed Culture (2007)

Determining the specific growth rate of a distinct microbial population in a mixed culture or environmental sample has long been an elusive parameter which is integral to describing the function of microbes in their environment. FISH-RiboSyn, is an in situ method that utilizes fluorescence in situ hybridization (FISH) with specific primers that target the interior region of both pre16S rRNA and mature 16S rRNA. FISH-RiboSyn provides an expedient method for determining the specific growth rate of a distinct microbial population in a mixed culture sample. Preliminary results demonstrate the linear increasing nature of fluorescence intensity as a function of chloramphenicol exposure time in pure cultures of Acinetobacter calcoaceticus.
Algorithms for Intravenous Insulin Delivery (2008)

This review aims to classify algorithms for intravenous insulin infusion according to design. Essential input data include the current blood glucose (BG(current)), the previous blood glucose (BG(previous)), the test time of BG(current) (test time(current)), the test time of BG(previous) (test time(previous)), and the previous insulin infusion rate (IR(previous)). Output data consist of the next insulin infusion rate (IR(next)) and next test time. The classification differentiates between "IR" and "MR" algorithm types, both defined as a rule for assigning an insulin infusion rate (IR), having a glycemic target. Both types are capable of assigning the IR for the next iteration of the algorithm (IR(next)) as an increasing function of BG(current), IR(previous), and rate-of-change of BG with respect to time, each treated as an independent variable. Algorithms of the IR type directly seek to define IR(next) as an incremental adjustment to IR(previous). At test time(current), under an IR algorithm the differences in values of IR(next) that might be assigned depending upon the value of BG(current) are not necessarily continuously dependent upon, proportionate to, or commensurate with either the IR(previous) or the rate-of-change of BG. Algorithms of the MR type create a family of IR functions of BG differing according to maintenance rate (MR), each being an iso-MR curve. The change of IR(next) with respect to BG(current) is a strictly increasing function of MR. At test time(current), algorithms of the MR type use IR(previous) and the rate-of-change of BG to define the MR, multiplier, or column assignment, which will be used for patient assignment to the right iso-MR curve and as precedent for IR(next). Bolus insulin therapy is especially effective when used in proportion to carbohydrate load to cover anticipated incremental transitory enteral or parenteral carbohydrate exposure. Specific distinguishing algorithm design features and choice of parameters may be important to establish freedom from hypoglycemia, eliminate the need for administration of concentrated dextrose during euglycemia, control variability within the treatment course of individual patients, achieve adaptability to differing blood glucose targets, and minimize variability of glycemic control between treatment courses of different patients or patient populations. Areas for future work include the reduction of nursing burden, the development of a theory that will account for lag time of interstitial monitoring and pharmacodynamic delay of insulin action, and management strategies for the narrow euglycemic range. It is hoped that hypoglycemia and variability of control will become negligible problems, and that fear of hypoglycemia no longer will deflect investigators and caregivers from providing optimal glycemic management.
Auditory brainstem response testing in acoustic neuroma diagnosis (2002)

In the past year, there was a lack of published papers on using auditory brainstem responses for acoustic tumor diagnosis. This lack is probably caused by the large number of published studies demonstrating that standard auditory brainstem response measures frequently fail to detect small (≤ 1 cm) acoustic tumors. This article reviews (1) the current opinion that auditory brainstem responses cannot be used to diagnose or screen for small tumors, (2) the use of MRI for screening despite some drawbacks, (3) a hypothesis for the inadequacy of standard auditory brainstem response measures, and (4) a new measure, the stacked auditory brainstem response, that may provide the needed sensitivity for small tumor screening. It is conclusive that standard auditory brainstem response measures are inadequate for small tumor detection, but it is premature to conclude that other new auditory brainstem response measures, such as the stacked auditory brainstem response, cannot be used to screen effectively and play an important role in acoustic tumor diagnosis.
A new approach to acoustic filtering with lined ducts (1975)

We consider a lined duct which is divided into two parallel branches by means of a rigid partition. The phase speed of the fundamental mode in each branch depends on the liner configuration and can differ markedly from the free-space phase speed. If the liners in the two branches are not the same, the corresponding phase speeds will be different and a relative phase lag between the waves in the two branches results. This, in turn, leads to interference between these wave components (and their reflections), both at the exit and the entrance of the parallel branch pair. We have demonstrated both analytically and experimentally that this interference can be exploited for the purpose of obtaining a low-frequency attenuation which is substantially larger than the attenuation of the unpartitioned duct. [This work was supported in part by the U.S. Navy (Office of Naval Research) under Contract N00014-67-A-0204-0019 and in part by the U.S. Department of Transportation under Grant Agreement DOT-OS-3011.]
Thermal and Electrical Properties of Nanocomposites Based on Self‐Assembled Pristine Graphene (2016)

Thermodynamically‐driven exfoliation and self‐assembly of pristine graphene sheets is shown to provide thermally and electrically functional polymer composites. The spreading of graphene sheets at a high energy liquid/liquid interface is driven by lowering the overall energy of the system, and provides for the formation of water‐in‐oil emulsions stabilized by overlapping graphene sheets. Polymerization of the oil phase, followed by removal of the dispersed water phase, produces inexpensive and porous composite foams. Contact between the graphene‐stabilized water droplets provides a pathway for electrical and thermal transport through the composite. Unlike other graphene foams, the graphite used to synthesize these composites is natural flake material, with no oxidation, reduction, sonication, high temperature thermal treatment, addition of surfactants, or high shear mixing required. The result is an inexpensive, low‐density material that exhibits Joule heating and displays increasing electrical conductivity with decreasing thermal conductivity.