gebhart/patrepeval huggingface dataset:
A microtensiometer for the analysis of bioadhesive microspheres. (1996)

Bioadhesive polymer microspheres are potential vehicles for the delivery of bioactive agents to mucosal tissues. Bioadhesive delivery devices could improve drug absorption, enhance bioavailability, and increase patient compliance by minimizing dosing regimens. Identification of bioadhesive materials is the first phase in developing bioadhesive drug delivery systems. Additionally, quantification and analysis of the bioadhesive event are essential to successful development of a new generation of adhesive delivery systems. A unique, microbalance-based instrument was developed to analyze bioadhesive forces between polymer microspheres and mucosal tissue segments. A contact angle analyzer, with a custom-made physiologic tissue chamber, was linked to a computer via the serial port. Software was used to modify the microbalance operation to behave as a microtensiometer with a sensitivity of 0.1 microN. After mounting a microsphere and tissue segment in the balance and adjusting the experimental settings, the instrument performs a tensile experiment and automatically determines the following parameters: compressive deformation, peak compressive load, compressive work, yield point, deformation to yield, returned work, peak tensile load, deformation to peak tensile load, fracture strength, deformation to failure, and tensile work. Using this device the authors identified several bioadhesive materials ideally suited for orally-delivered, controlled-release systems. GI-transit studies in rats showed strong correlation between increased GI-residence time and strong bioadhesive interactions.
Ultrasound elastography for carpal tunnel pressure measurement: A cadaveric validation study (2017)

Carpal tunnel pressure is a key factor in the etiology of carpal tunnel syndrome. Numerous approaches have been conducted to measure carpal tunnel pressure. However, most techniques are invasive and take time and effort. We have developed an innovative approach to noninvasively assess the tunnel pressure by using the ultrasound surface wave elastography (USWE) technique. In a previous study it was shown that the shear wave speed in a tendon increased linearly with increasing tunnel pressure enclosed the tendon in a simple tendon model. This study aimed to examine the relationship between the carpal tunnel pressure and the shear wave speeds inside and outside the carpal tunnel in a human cadaveric model. The result showed that the shear wave speed inside the carpal tunnel increased linearly with created carpal tunnel pressure, while the shear wave speed outside the carpal tunnel remained constant. These findings suggest that noninvasive measurement of carpal tunnel pressure is possible by measuring the shear wave speed in the tendon. After fully establishing this technology and being applicable in clinic, it would be useful in the diagnosis of carpal tunnel syndrome. For that reason, further validation with this technique in both healthy controls and patients with carpal tunnel syndrome is required. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:477-483, 2018.
Complex Discrete Wavelet Transform Based Motion Estimation For Vision-Based Tracking Of Targets (2005)

Publication in the conference proceedings of EUSIPCO, Antalya, Turkey, 2005
Real-time processing for virtual circuits in ATM switching (2002)

We propose adding real-time hardware primitives to packet switches, ATM in particular, to provide efficient support for inward multicasting similar to some of today's switches that support real-time multicast in the switch hardware. To implement this, we propose extending the lookup table used for routing by adding additional opcode and operand fields (or pointers to those fields) into the routing table and by including ALU circuitry to process these fields and corresponding fields in the arriving cells. With the rapid capacity growth of today's RAM and the modest gate count required for ALUs, memory word widths can be extended with minimal additional chip count and the ALU can be a small addition in a header processing VLSI, thereby giving only a modest increase in complexity. The benefit of including real-time processing in the switch is that it is now possible to solve the ACK implosion problem associated with high-speed reliable multicasting transport protocols. By keeping the primitives as general as possible, other applications can benefit from these real-time primitives.
Compact focusing system for ion and electron beams (2002)

A compact ion and electron beam focusing column design has been developed in Plasma and Ion Source Technology Group at Lawrence Berkeley National Laboratory. The electrostatic ion beam-focusing column was simulated using 2D IGUN [R. Becker and W. B. Herrmansfeldt, Rev. Sci. Instrum. 63, 2756 (1992)] ion extraction and beam transport code. A new method has been developed to include finite ion temperature to the IGUN simulation (Reijonen et al., Proceedings of the LINAC Conference, 2000). The focused ion beam system includes an ion temperature collimator, which eliminates the large angle beam trajectories resulting in a small beam spot size. The small holes in the column electrodes are laser drilled, and are aligned by an optical comparator. Simulations show that focused beam spot size as small as 147 nm is achievable for a 40 keV argon beam. The compact electron beam focusing system consists of three elements: the plasma cathode, an electron temperature collimator (similar to the ion beam temperature collimator), and the focusing electrode elements. The total length of the system is less than 10 mm. The column design is performed using EGUN (W. B. Herrmansfeldt, Slac Report No. 331, 1988), electron beam computation code, and IGUN. Space charge effects as well as the electron temperature are incorporated in the computation. The simulations show that focused beam spot size of 60 nm can be achieved. Both columns use similar type rf-induction plasma generator. P+, BF2+, and O2+ ion species production by such source is also demonstrated.
Effect of Numerical Aperture on Light Injection from Sources at the Core/Cladding Interface of a Fiber Optic Fluorosensor (1993)

The fluorosensor discussed here is a fluorescent cladding optical fiber sensor. The sensitivity of such a sensor depends on the amount of light injected into the fiber core due to a fluorescent cladding. Conditions necessary for high injection, were experimentally determined for side excitation. Previous theoretical work has predicted that, for a side excited fiber, the refractive index difference between the core and cladding, n core − n clad , must be maximized to achieve high sensitivity. This prediction has used the exact field solution of an optical fiber and was qualitatively verified in the present work. This shows that standard optical fibers used for communication, which are weakly guiding, are not suitable for fluorosensor applications. Another result shows that the light injection increases with the fiber diameter.
Response to Comment on "Quantum State Transfer Between Matter and Light" (2005)

The comment by van Enk and Kimble ([ 1 ][1]) does not challenge the principal result of our study ([ 2 ][2])—that we achieved quantum state transfer from an atomic qubit to a photonic qubit. They also do not challenge our quantitative measurement of that transfer ([ 2 ][2]). We used the ratio of
Discriminative and Generative Classification Techniques Applied to Automated Neonatal Seizure Detection (2012)

A number of automated neonatal seizure detectors have been proposed in recent years. However, there exists a large variability in the morphology of seizure and background patterns, both across patients and over time. This has resulted in relatively poor performance from systems which have been tested over large datasets. Here, the benefits of employing a pattern recognition approach are discussed. Such a system may use numerous features paired with nonlinear classifiers. In particular, two types of nonlinear classifiers are contrasted for the task. Additionally, it is shown that the proposed architecture allows for efficient classifier combination which improves the performance of the algorithm. The resulting automated detector is shown to achieve field leading performance. A particular strength of the proposed algorithm is the performance of the algorithm when very low false detections are required, at 0.25 false detections per hour, the system is able to detect 75.4% of the seizure events.
Detection of nitrogen and phosphorus nutrient status in winter wheat using spectral radiance (1998)

Abstract Nitrogen (N) and phosphorus (P) are major limiting nutrient elements for crop production and continued interest lies in improving their use efficiency. Spectral radiance measurements were evaluated to identify optimum wavelengths for dual detection of N and P status in winter wheat (Triticum aestivum L.). A factorial treatment arrangement of N and P (0, 56, 112, and 168 kg N ha‐1 and 0, 14.5, and 29 kg P ha‐1) was used to further study N and P uptake and associated spectral properties at Perkins and Tipton, Oklahoma. A wide range of spectral radiance measurements (345–1, 145 nm) were obtained from each plot using a PSD 1000 Ocean Optics fiber optic spectrometer. At each reading date, 78 bands and 44 combination indices were generated to test for correlation with forage biomass and N and P uptake. Additional spectral radiance readings were collected using an integrated sensor which has photodiode detectors and interference filters for red and NIR. For this study, simple numerator/denominator indices were useful in predicting biomass, and N uptake and P uptake. Numerator wavelengths that ranged between 705 and 735 nm and denominator wavelengths between 505 and 545 nm provided reliable prediction of forage biomass, and N and P uptake over locations and Feekes growth stages 4 through 6. Using the photodiode sensor, NDVI [(NIR‐red)/(NIR+red)] and NR [(NIR/red)], were also good indices to predict biomass, and N and P uptake. However, no index was found to be good for detecting solely N and P concentration either using the spectrometer or photodiode sensor.
Self-Navigated Coronary Artery MR Angiography (2001)

Introduction Breath-held MR coronary angiography is limited by the brief time window available for data collection, which hinders the simultaneous achievement of high signal-to-noise ratio (SNR), good spatial resolution, and broad coverage. Multiple breath-held data sets can be collected from the same location and averaged. However, this approach suffers from problems with variability of diaphragm position across multiple breath holds. Respiratory navigation (1) allows for longer data collection, but can have problems with reproducibility, particularly in patients with irregular breathing (2). We present here an alternative method for improving the SNR of breath-held coronary artery MR angiography without increasing the number of breath holds or the breath-holding time. A single breathheld ECG-gated multi-slice interleaved spiral data set is acquired, followed by repeated imaging of the same location during free breathing. Each spiral interleaf from the breath-held data set is used as a standard for comparison with corresponding interleaves from the free-breathing data. Accepted interleaves are incorporated into a multislice, multi-average data set with increasing SNR over time. Methods Major branches of the coronaries were first located, with use of realtime interactive and ECG-gated MRI. Oblique multi-slice coronaryartery data sets were then acquired using ECG-gated interleaved spiral MRI, with spectral-spatial pulses to suppress fat (16 interleaves of 4096 points, 125 kHz BW, 20-24 cm FOV, slice thickness 3-5 mm). To test the self-navigation concept, multi-slice breath-held spiral data sets were acquired in roughly 16 s, followed by 10 to 12 additional data sets obtained from the same location during freebreathing. For the breath hold, subjects were instructed to breathe out part way, and were monitored with use of a respiratory bellows in order to ensure that the reference breath-hold position fell within the range of normal respiration. All data were stored in raw format and sent to a workstation for processing and reconstruction. Each free-breathing interleaf was compared to the corresponding breath-held interleaf by one of two methods: 1) calculation of the sum of the square of the difference between each complex point in the two interleaves, or 2) cross correlation of a region of interest around the coronary artery in the reconstructed reference interleaf with each corresponding reconstructed free-breathing interleaf. For method 1) those interleaves showing the smallest value of the sum were judged to best match the reference interleaf. For method 2) those interleaves whose correlation showed the most centered peak were considered most closely matched. The number of desired averages was specified, and the most closely matched free-breathing data at each interleaf angle were averaged together. Then the 16 averaged interleaves were assembled and reconstructed into an averaged image. This procedure was performed for each slice in the multi-slice data set.
<title>Improving mass detection by adaptive and multiscale processing in digitized mammograms</title> (1999)

A new CAD mass detection system was developed using adaptive and multi-scale processing methods for improving detection sensitivity/specificity, and its robustness to the variation in mammograms. The major techniques developed in system design include: (1) image standardization by applying a series of preprocessing to remove extrinsic signal, extract breast area, and normalize the image intensity; (2) multi- mode processing by decomposing image features using directional wavelet transform and non-linear multi-scale representation using anisotropic diffusion; (3) adaptive processing in image segmentation using localized adaptive thresholding and adaptive clustering; and (4) combined `hard'-`soft' classification by using a modified fuzzy decision tree and committee decision-making method. Evaluations and comparisons were taken with a training dataset containing 30 normal and 47 abnormal mammograms with totally 70 masses, and an independent testing dataset consisting of 100 normal images, 39 images with 48 minimal cancers and 25 images with 25 benign masses. A high detection performance of sensitivity TP equals 93% with false positive rate FP equals 3.1 per image and a good generalizability with TP equals 80% and FP equals 2.0 per image are obtained.
Proposed Method and Device for Obtaining Piezoelectric Constants of Ceramic Cylindrical Shells. (1974)

Abstract : The active elements of many Navy sonar sources and hydrophones consist of one or more electrostrictive cylindrical shells. The performance of these transducers depends on the values of the piezoelectric coefficients (g sub 31, g sub 33, d sub 31, d sub 33). A method is presented for rapidly determining the piezoelectric constants (d sub 31, d sub 33, g sub 31, g sub 33) of an unprepared cylindrical shell polarized radially, axially, or circumferentially. Design considerations for a device which implements this method are discussed. (Modified author abstract)
Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns (2017)

DNA methylation patterns are greatly altered in prostate cancer tissue in comparison to benign-adjacent tissue. We have discovered patterns of DNA methylation marks that can distinguish prostate cancers with high specificity and sensitivity in multiple patient tissue cohorts, and we have identified transcription factors binding in these differentially methylated regions that may play important roles in prostate cancer development.
Infrared position sensitive detector (IRPSD) (2008)

We have developed a two-dimensional thermal infrared array sensor called the Infrared Position Sensitive Detector (IRPSD). The IRPSD has two thermometers for row and column in a pixel, and thermometers in a row or column are serially connected. The serial connection of thermometers produces the sum of signals from the pixels in each row and column. With this array architecture, the IRPSD can extract some specific information without digital image processing. The IRPSD is capable of performing position detection and number counting operations for hot (or cold) objects. Information on the position can be obtained from the row and column that has maximum outputs, and the number can be counted by adding all outputs in rows or columns. We adapt a thermopile made of a p-type polysilicon and aluminum as thermometers. We have developed two IRPSDs. One is a prototype device for verifying the concept, and the other is an improved device with higher responsivity. Evaluation of these devices has shown that the IRPSD has the potential to be applied to a wide variety of applications.
α-Helix Mimetics as Modulators of Aβ Self-Assembly (2017)

A key molecular species in Alzheimer's disease (AD) is the Aβ<sub>42</sub> alloform of Aβ peptide, which is dominant in the amyloid plaques deposited in the brains of AD patients. Recent studies have decisively demonstrated that the prefibrillar soluble oligomers are the neurotoxic culprits and are associated with the pathology of AD. Nascent Aβ<sub>42</sub> is predominantly disordered but samples α-helical conformations covering residues 15-24 and 29-35 in the presence of micelles and structure-inducing solvents. In this report, a focused library of oligopyridylamide based α-helical mimetics was designed to target the central α-helix subdomain of Aβ (Aβ<sub>13-26</sub>). A tripyridylamide, ADH-41, was identified as one of the most potent antagonists of Aβ fibrillation. Amyloid-assembly kinetics, transmission electron microscopy (TEM), and atomic force microscopy (AFM) show that ADH-41 wholly suppresses the aggregation of Aβ at a substoichiometric dose. Dot blot and ELISA assays demonstrate the inhibition of the putative neurotoxic Aβ oligomers. ADH-41 targets Aβ in a sequence and structure-specific manner, as it did not have any effect on the aggregation of islet amyloid polypeptide (IAPP), a peptide which shares sequence similarity with Aβ. Spectroscopic studies using NMR and CD confirm induction of α-helicity in Aβ mediated by ADH-41. Calorimetric and fluorescence titrations yielded binding affinity in the low micromolar range. ADH-41 was also effective at inhibiting the seed-catalyzed aggregation of Aβ probably by modulating the Aβ conformation into a fiber incompetent structure. Overall, we speculate that ADH-41 directs Aβ into off-pathway structures, and thereby alters various solution based functions of Aβ. Cell-based assays to assess the effect of ADH-41 on Aβ are underway and will be presented in due course.
Simple and effective generation of transgene-free induced pluripotent stem cells using an auto-erasable Sendai virus vector responding to microRNA-302 (2017)

Transgene-free induced pluripotent stem cells (iPSCs) are valuable for both basic research and potential clinical applications. We previously reported that a replication-defective and persistent Sendai virus (SeVdp) vector harboring four reprogramming factors (SeVdp-iPS) can efficiently induce generation of transgene-free iPSCs. This vector can express all four factors stably and simultaneously without chromosomal integration and can be eliminated completely from reprogrammed cells by suppressing vector-derived RNA-dependent RNA polymerase. Here, we describe an improved SeVdp-iPS vector (SeVdp(KOSM)302L) that is automatically erased in response to microRNA-302 (miR-302), uniquely expressed in pluripotent stem cells (PSCs). Gene expression and genome replication of the SeVdp-302L vector, which contains miRNA-302a target sequences at the 3' untranslated region of L mRNA, are strongly suppressed in PSCs. Consequently, SeVdp(KOSM)302L induces expression of reprogramming factors in somatic cells, while it is automatically erased from cells successfully reprogrammed to express miR-302. As this vector can reprogram somatic cells into transgene-free iPSCs without the aid of exogenous short interfering RNA (siRNA), the results we present here demonstrate that this vector may become an invaluable tool for the generation of human iPSCs for future clinical applications.
Impurity Doping into SiC Semiconductor by Means of lon Implantation. (2000)

Research and development of ion implantation technique for SiC semiconductor have been performed. Hot-implantation of P ions into 6H-SiC raises the electron concentration in P-implanted n-type layers, showing that the hot-implantation enhances the electrical activation of P donors. The hole concentration in Al ion implanted 6H-SiC is found to increase due to co-implantation of C ions. This fact demonstrates that the electrical properties of Al-implanted p-type layers are improved by the C co-implantation. Using the ion implantation methods, SiC-based metal-oxide-semiconductor field-effect-transistors (MOSFETs) have been successfully fabricated. These results indicate that hot- and C co-implantations are quite useful for the fabrication of SiC devices.
Antibody-Free Quantification of Serum Chromogranin A by Targeted Mass Spectrometry (2021)

Abstract Background Chromogranin A (CgA) is a 48 kDa protein that serves as a diagnostically sensitive, but nonspecific, serum biomarker for neuroendocrine tumors. Immunoassays for CgA are not standardized and have a narrow dynamic range, which requires dilution of concentrated specimens. We developed and validated an antibody-free, liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based method for CgA without these limitations. Methods CgA was extracted from serum using a mixed-mode anion exchange solid-phase extraction plate, digested with trypsin, and analyzed by LC–MS/MS using well-characterized CgA calibration standards. After validation, the mass spectrometry method was compared with the CISBIO immunoassay using 200 serum specimens previously submitted for CgA analysis. Specimens with discordant results were reanalyzed by high-resolution mass spectrometry- (HRMS) -based methods to assess the contribution of truncated and post-translationally modified forms of CgA. Results The assay had a linear range of 50 to 50 000 ng/mL, recoveries between 89% and 115%, and intra- and interassay imprecision &lt;10%. LC–MS/MS assay results showed a Pearson’s correlation of r = 0.953 with the CISBIO immunoassay, with CgA values being a mean 2- to 4-fold higher. Concordance for CgA between the 2 assays was 80.9% (95% CI 72.8%–89.2%), showing substantial agreement. Truncation and posttranslational modification, including 2 phosphorylation sites that had not been previously observed or predicted to our knowledge, did not appear to contribute directly to discordance between the 2 assays. Conclusion Quantification of CgA by LC–MS/MS provides an analytically sensitive and reproducible alternative to commercially available immunoassays.
Standardized measurement of coronary inflammation using cardiovascular computed tomography: integration in clinical care as a prognostic medical device (2021)

Mapping of perivascular FAI on CCTA enables the non-invasive detection of coronary artery inflammation by quantifying spatial changes in perivascular fat composition. We now report the performance of a new medical device, CaRi-Heart®, which allows standardized measurement of coronary inflammation by calculating the FAI-Score of each coronary artery. The CaRi-Heart® device provides a reliable prediction of the patient's absolute risk for a fatal cardiac event by incorporating traditional cardiovascular risk factors along with comprehensive CCTA coronary plaque and perivascular adipose tissue phenotyping. This integration advances the prognostic utility of CCTA for individual patients and paves the way for its use as a dual diagnostic and prognostic tool among patients referred for CCTA.