gebhart/patrepeval huggingface dataset:
Raman Spectroscopy Provides a Powerful Diagnostic Tool for Accurate Determination of Albumin Glycation (2012)

We present the first demonstration of glycated albumin detection and quantification using Raman spectroscopy without the addition of reagents. Glycated albumin is an important marker for monitoring the long-term glycemic history of diabetics, especially as its concentrations, in contrast to glycated hemoglobin levels, are unaffected by changes in erythrocyte life times. Clinically, glycated albumin concentrations show a strong correlation with the development of serious diabetes complications including nephropathy and retinopathy. In this article, we propose and evaluate the efficacy of Raman spectroscopy for determination of this important analyte. By utilizing the pre-concentration obtained through drop-coating deposition, we show that glycation of albumin leads to subtle, but consistent, changes in vibrational features, which with the help of multivariate classification techniques can be used to discriminate glycated albumin from the unglycated variant with 100% accuracy. Moreover, we demonstrate that the calibration model developed on the glycated albumin spectral dataset shows high predictive power, even at substantially lower concentrations than those typically encountered in clinical practice. In fact, the limit of detection for glycated albumin measurements is calculated to be approximately four times lower than its minimum physiological concentration. Importantly, in relation to the existing detection methods for glycated albumin, the proposed method is also completely reagent-free, requires barely any sample preparation and has the potential for simultaneous determination of glycated hemoglobin levels as well. Given these key advantages, we believe that the proposed approach can provide a uniquely powerful tool for quantification of glycation status of proteins in biopharmaceutical development as well as for glycemic marker determination in routine clinical diagnostics in the future.
SU‐E‐J‐165: Ghost Marker Prediction, Detection and Elimination in Marker‐Based Optical Tracking Systems (2014)

Purpose: In optical tracking system (OTS), ghost marker (GM) limits users' flexibility in marker placement and can lead to incorrect patient setup or system execution failure. This work aims to model the phenomenon of GM and propose robust algorithms for GM prediction, detection and elimination. Methods: Two GMs occur when two markers and two sensors of the OTS are coplanar. However, when one marker gradually moves out of the plane and breaks the coplanar condition, both GMs briefly remain before they completely disappear. To explain this effect, we expanded line‐line intersection definition and the coplanar condition: two lines intersect when their distance is less than threshold Ω and involved points are said to be coplanar within Ω. We fixed one marker and moved the other through the plane with a 0.1 mm step length. Sensor positions were calculated using a back projection method when coplanar condition was strictly satisfied. Ω was determined as line‐line distance when ghost marker first appeared. The prediction algorithm checks whether any two given markers are coplanar with the two sensors within Ω; the detection algorithm checks whether any marker is near the intersection of lines connecting sensors and two other markers. A backtracking pattern matching algorithm matches markers to reference markers and eliminates unmatched ones as GMs. The algorithms were validated with two phantoms and 40 SBRT patients using 5~8 markers. Results: The prediction success rates were 97.7% and 89.6% and the detection success rates were 100% on the two phantoms (1544 ' 2045 samples). The matching success rates were 100% on both phantoms and patients. Conclusion: The proposed model precisely explains the phenomenon of GMs in marker‐based OTS. The proposed detection and matching algorithms guarantee complete elimination of GMs, thus avoiding errors in SBRT tracking and providing user maximum flexibility in marker placement.
Cannabidiol and (−)Δ <sup>9</sup> -tetrahydrocannabinol are neuroprotective antioxidants (1998)

The neuroprotective actions of cannabidiol and other cannabinoids were examined in rat cortical neuron cultures exposed to toxic levels of the excitatory neurotransmitter glutamate. Glutamate toxicity was reduced by both cannabidiol, a nonpsychoactive constituent of marijuana, and the psychotropic cannabinoid (-)Delta9-tetrahydrocannabinol (THC). Cannabinoids protected equally well against neurotoxicity mediated by N-methyl-D-aspartate receptors, 2-amino-3-(4-butyl-3-hydroxyisoxazol-5-yl)propionic acid receptors, or kainate receptors. N-methyl-D-aspartate receptor-induced toxicity has been shown to be calcium dependent; this study demonstrates that 2-amino-3-(4-butyl-3-hydroxyisoxazol-5-yl)propionic acid/kainate receptor-type neurotoxicity is also calcium-dependent, partly mediated by voltage sensitive calcium channels. The neuroprotection observed with cannabidiol and THC was unaffected by cannabinoid receptor antagonist, indicating it to be cannabinoid receptor independent. Previous studies have shown that glutamate toxicity may be prevented by antioxidants. Cannabidiol, THC and several synthetic cannabinoids all were demonstrated to be antioxidants by cyclic voltametry. Cannabidiol and THC also were shown to prevent hydroperoxide-induced oxidative damage as well as or better than other antioxidants in a chemical (Fenton reaction) system and neuronal cultures. Cannabidiol was more protective against glutamate neurotoxicity than either ascorbate or alpha-tocopherol, indicating it to be a potent antioxidant. These data also suggest that the naturally occurring, nonpsychotropic cannabinoid, cannabidiol, may be a potentially useful therapeutic agent for the treatment of oxidative neurological disorders such as cerebral ischemia.
Cysteine-Conjugated Metabolite of Ginger Component [6]-Shogaol Serves as a Carrier of [6]-Shogaol in Cancer Cells and in Mice (2013)

Shogaols, a series of major constituents in dried ginger (Zingiber officinale), show high anticancer potencies. Previously, we reported that a major metabolite resulting from the mercapturic acid pathway, 5-cysteinyl-[6]-shogaol (M2), showed comparable growth inhibitory effects toward cancer cells to [6]-shogaol (6S). Here, we probe the mechanism by which M2 exerts its bioactivity. We utilized a series of chemical stability tests in conjunction with bioassays to show that thiol-conjugates display chemopreventative potency by acting as carriers of active ginger component 6S. M2 chemical degradation to 6S was observed in an environment most resembling physiological conditions, with a pH of 7.4 at 37 °C. The metabolic profiles of M2 in cancer cells HCT-116 and H-1299 resembled those of 6S, indicating that its biotransformation route was initiated by deconjugation. Further, the presence of excess glutathione significantly delayed 6S and M2 metabolism and counteracted cell death induced by 6S and M2, suggesting that increasing available free thiols exogenously both promoted the formation of 5-glutathionyl-[6]-shogaol (M13) and inhibited the production of free 6S from M2 deconjugation, resulting in delayed 6S cell entry and bioactivity. Given the chemopreventative properties of M2 and our observations in vitro, we investigated its metabolism in mice. M2 and 6S showed similar metabolic profiles in mouse urine and fecal samples. Six new thiol-conjugated metabolites (M16-M21), together with previously reported ones, were identified by LC/MS. In particular, the increase of 5-N-acetylcystenyl-[6]-shogaol (M5) and its 3'-demethylated product (M16) abundance in mouse feces after treatment with M2 indicates that in addition to acting as a carrier of 6S, M2 is also directly acetylated to M5, which is further demethylated to M16 in vivo. In conclusion, the cysteine-conjugated metabolite of [6]-shogaol M2 exerts its bioactivity by acting as a carrier of 6S in both cancer cells and in mice.
High purity amphotericin B (2007)

Taken together, these data indicate that AmBHP may represent a refinement of currently marketed AmB formulations, offering equal, if not better, efficacy with less toxicity.
Cytosolic expression of the <i>Bacillus amyloliquefaciens SacB</i> protein inhibits tissue development in transgenic tobacco and potato (1997)

SUMMARY Fructans are linear or branched polymers containing a single sucrose and repeating fructose residues. An early model for fructan biosynthesis in higher plants suggested that partial synthesis of the polymer occurred in the cell cytosol. The current model suggests that synthesis requires the interaction of two separate fructosyltransferases located in the vacuole. Tobacco lines containing a chemically induced promoter, directing expression of the Bacillus amyloliquefaciens SacB gene in the present study, provided an opportunity to regulate and target fructan synthesis to the cytosol of transgenic plants. Induced expression of the gene led to rapid destruction of leaf tissue. Amino acid substitution at a highly conserved site (Arg 331 ) in the SacB gene reduced the fructosyltransferase efficiency without reducing the invertase activity of the enzyme. Expression of the mutant gene in transgenic tobacco also resulted in leaf damage. However, the appearance of necrotic tissue was greatly delayed. The results suggest that the phenotype is due to accumulation of fructan in the cytosol. Fructan metabolism in the cytosol of potato tubers was also detrimental to development. Tuber size and starch synthesis was significantly reduced in lines containing the untargeted gene. Transgenic tobacco and potato containing the SacB gene offer an opportunity to study the metabolism of fructan and the effect of accumulation on plant cell development.
Adapting human motions to humanoid robots through time warping based on a general motion feasibility index (2015)

Having human-like motions will make humanoid robots more predictable and safer for the people around them. An effective way to realize this would be to use human motions as reference. Due to different kinematic and dynamic properties between humans and humanoid robots, however, a human motion could be physically infeasible for a robot and cause the robot to fall over. Therefore, it is necessary to modify and adapt an infeasible human motion to the robot. This paper presents a method for adapting human motions to humanoid robots based on a technique called time warping, which modifies the time line of a reference motion to speed up or slow down the motion. By doing this, the velocity and acceleration profiles of the motion are changed and it is possible to turn an infeasible motion into a feasible one. The optimal time warping is obtained through a generalized motion feasibility index that quantifies the feasibility of a motion considering the friction and center-of-pressure constraints. Thanks to the generality of the index, the proposed motion adaptation method can be applied to motions on arbitrary terrains or number of links in contact with the environment. Through dynamics simulation, we demonstrate that the method facilitates the reproduction of human motions on a humanoid robot.
Template-Stripped Asymmetric Metallic Pyramids for Tunable Plasmonic Nanofocusing (2013)

We demonstrate a novel scheme for plasmonic nanofocusing with internally illuminated asymmetric metallic pyramidal tips using linearly polarized light. A wafer-scale array of sharp metallic pyramids is fabricated via template stripping with films of different thicknesses on opposing pyramid facets. This structural asymmetry is achieved through a one-step angled metal deposition that does not require any additional lithography processing and when internally illuminated enables the generation of plasmons using a Kretschmann-like coupling method on only one side of the pyramids. Plasmons traveling toward the tip on one side will converge at the apex, forming a nanoscale "hotspot." The asymmetry is necessary for these focusing effects since symmetric pyramids display destructive plasmon interference at the tip. Computer simulations confirm that internal illumination with linearly polarized light at normal incidence on these asymmetric pyramids will focus optical energy into nanoscale volumes. Far-field optical experiments demonstrate large field enhancements as well as angle-dependent spectral tuning of the reradiated light. Because of the low background light levels, wafer-scale fabrication, and a straightforward excitation scheme, these asymmetric pyramidal tips will find applications in near-field optical microscopy and array-based optical trapping.
Efficient Model Re-Estimation In Voice Conversion (2008)

Publication in the conference proceedings of EUSIPCO, Lausanne, Switzerland, 2008
N-best based supervised and unsupervised adaptation for native and non-native speakers in cars (1999)

A new set of techniques exploiting N-best hypotheses in supervised and unsupervised adaptation are presented. These techniques combine statistics extracted from the N-best hypotheses with a weight derived from a likelihood ratio confidence measure. In the case of supervised adaptation the knowledge of the correct string is used to perform N-best based corrective adaptation. Experiments run for continuous letter recognition recorded in a car environment show that weighting N-best sequences by a likelihood ratio confidence measure provides only marginal improvement as compared to 1-best unsupervised adaptation and N-best unsupervised adaptation with equal weighting. However, an N-best based supervised corrective adaptation method weighting correct letters positively and incorrect letters negatively, resulted in a 13% decrease of the error rate as compared with supervised adaptation. The largest improvement was obtained for non-native speakers.
Multiple-scattering aerosol lidar inversion method (1993)

The multiple-scattering contributions to lidar aerosol backscatter returns are measured by simultaneous detection at four concentric fields of view. A solution method is proposed to calculate, from the ratios of the lidar returns at the different fields of view, the range-resolved scattering coefficient. The method also provides the effective size of the aerosol particles responsible for the forward peak of the scattering phase function. Solutions from measurements performed in fog and clouds with a 1.054 μm lidar system are presented.
Hydrolyzable Polyureas Bearing Hindered Urea Bonds (2014)

Hydrolyzable polymers are widely used materials that have found numerous applications in biomedical, agricultural, plastic, and packaging industrials. They usually contain ester and other hydrolyzable bonds, such as anhydride, acetal, ketal, or imine, in their backbone structures. Here, we report the first design of hydrolyzable polyureas bearing dynamic hindered urea bonds (HUBs) that can reversibly dissociate to bulky amines and isocyanates, the latter of which can be further hydrolyzed by water, driving the equilibrium to facilitate the degradation of polyureas. Polyureas bearing 1-tert-butyl-1-ethylurea bonds that show high dynamicity (high bond dissociation rate), in the form of either linear polymers or cross-linked gels, can be completely degraded by water under mild conditions. Given the simplicity and low cost for the production of polyureas by simply mixing multifunctional bulky amines and isocyanates, the versatility of the structures, and the tunability of the degradation profiles of HUB-bearing polyureas, these materials are potentially of very broad applications.
A/D Conversion Using Asynchronous Delta-Sigma Modulation and Time-to-Digital Conversion (2010)

An analog-to-digital conversion (ADC) scheme based on asynchronous ΔΣ modulation and time-to-digital conversion is presented. An asynchronous ΔΣ modulator translates the analog input to an asynchronous duty-cycle modulated signal. Next, the edge locations are digitally measured using a time-to-digital converter (TDC). This information is then digitally processed into a conventional digital signal. The performance of this novel ADC scheme is theoretically analyzed and verified with simulations. With the proposed digital demodulation algorithm, 11-bit resolution can be obtained with an overcycling ratio (OCR) of only four, which is suitable for high bandwidth applications such as very high bit-rate digital subscriber line (VDSL). When a higher OCR can be tolerated, a gated ring-oscillator (GRO) TDC with an inherent first-order noise shaping property is suggested in combination with a digital continuous-time moving-average (CTMA) filter. This allows for resolutions in excess of 13 bits, which is suitable for ADSL2+. The proposed technique shifts the complexity toward the digital domain, leading to more compact ADC and reduced power consumption, and is, therefore, particularly suited for ADC in ultralow-voltage nanometer technologies that are used for high-speed data communication applications.
A Novel Adaptive Shading Correction Algorithm for Camera Systems (2016)

Lens Vignetting is a common distortion in imaging systems where the intensity of the image decreases gradually away from the image center. Incorrect compensation of this luminance degradation often results in a more disturbing artifact called color shading, where the resulting image is left with shades of different colors. This paper presents a novel adaptive technique to compensate for lens Vignetting, while preserving color saturation and eliminating the need for per-unit calibration. As a consequence, the performance of automatic white balance algorithms have also been improved. The proposed algorithm is lightweight and realizable on FPGA architecture for real time Vignetting correction. The experimental results indicate a significant improvement in the quality of the corrected images. It is expected that the proposed algorithm will be implemented on mobile Image Signal Processors (ISPs) in the near future.
Classification of malignant melanoma and benign skin lesions: implementation of automatic ABCD rule (2016)

The ABCD (asymmetry, border irregularity, colour and dermoscopic structure) rule of dermoscopy is a scoring method used by dermatologists to quantify dermoscopy findings and effectively separate melanoma from benign lesions. Automatic detection of the ABCD features and separation of benign lesions from melanoma could enable earlier detection of melanoma. In this study, automatic ABCD scoring of dermoscopy lesions is implemented. Pre‐processing enables automatic detection of hair using Gabor filters and lesion boundaries using geodesic active contours. Algorithms are implemented to extract the characteristics of ABCD attributes. Methods used here combine existing methods with novel methods to detect colour asymmetry and dermoscopic structures. To classify lesions as melanoma or benign nevus, the total dermoscopy score is calculated. The experimental results, using 200 dermoscopic images, where 80 are malignant melanomas and 120 benign lesions, show that the algorithm achieves 91.25% sensitivity of 91.25 and 95.83% specificity. This is comparable to the 92.8% sensitivity and 90.3% specificity reported for human implementation of the ABCD rule. The experimental results show that the extracted features can be used to build a promising classifier for melanoma detection.
Practical Synthesis of Enantiomerically Pure β<sup>2</sup>-Amino Acids via Proline-Catalyzed Diastereoselective Aminomethylation of Aldehydes (2007)

Proline-catalyzed diastereoselective aminomethylation of aldehydes using a chiral iminium ion, generated from a readily prepared precursor, provides alpha-substituted-beta-amino aldehydes with 85:15 to 90:10 dr. The alpha-substituted-beta-amino aldehydes can be reduced to beta-substituted-gamma-amino alcohols, the major diastereomer of which can be isolated via crystallization or column chromatography. The amino alcohols are efficiently transformed to protected beta2-amino acids, which are valuable building blocks for beta-peptides, natural products, and other interesting molecules. Because conditions for the aminomethylation and subsequent reactions are mild, beta2-amino acid derivatives with protected functional groups in the side chain, such as beta2-homoglutamic acid, beta2-homotyrosine, and beta2-homolysine, can be prepared in this way. The synthetic route is short, and purifications are simple; therefore, this method enables the preparation of protected beta2-amino acids in useful quantities.
A Cell-Free Protein Synthesis System from Insect Cells (2009)

The newly developed Transdirect in vitro translation system for mRNA templates utilizes an extract from cultured Spodoptera frugiperda 21 (Sf21) insect cells. An expression vector, pTD1, which includes a 5'-untranslated region (UTR) sequence from a baculovirus polyhedrin gene as a translational enhancer, designed to obtain maximum performance from the insect cell-free protein synthesis system. The combination of insect cell extract and the expression vector results in protein productivity of about 50 μg/mL of the translation reaction mixture. This is the highest protein productivity yet recorded among commercialized cell-free protein synthesis systems based on animal extracts.
Electromechanical behavior of [001]-textured Pb(Mg1/3Nb2/3)O3-PbTiO3 ceramics (2012)

[001]-textured Pb(Mg1/3Nb2/3)O3-PbTiO3 (PMN-PT) ceramics were synthesized by using templated grain growth method. Significantly high [001] texture degree corresponding to 0.98 Lotgering factor was achieved at 1 vol. % BaTiO3 template. Electromechanical properties for [001]-textured PMN-PT ceramics with 1 vol. % BaTiO3 were found to be d33 = 1000 pC/N, d31 = 371 pC/N, ɛr = 2591, and tanδ = ∼0.6%. Elastoelectric composite based modeling results showed that higher volume fraction of template reduces the overall dielectric constant and thus has adverse effect on the piezoelectric response. Clamping effect was modeled by deriving the changes in free energy as a function of applied electric field and microstructural boundary condition.
InAlGaAs Staircase Avalanche Photodiodes (1994)

Metal-organic vapor phase epitaxy (MOVPE)-grown InAlGaAs staircase avalanche photodiodes (APDs) with sawtooth graded-gap multiplication regions are demonstrated for the first time. Extremely high multiplication factors M of over 100, low dark currents of 550 nA at M =20, and high-gain-bandwidth products exceeding 100 GHz were confirmed in 10×200- Å sawtooth multilayer APDs.
Challenges in clockgating for a low power ASIC methodology (1999)

Gating the clock is an important technique used in low power design to disable unused modules of a circuit, Gating can save power by both preventing unnecessary activity in the logic modules as well as by eliminating power dissipation in the clock distribution network.There is an inherent pitfall though in implementing gating groups for hierarchical gated clock distribution because the groups are typically developed at the logic level with no information of the physical layout of the clocktree. Depending on the distribution of underlying sinks, maintaining gating groups can cause a wiring overhead that is potentially greater than the savings due to reduced switching. We look at modtjications of zero- skew tree algorithms to consider both the physical and logical aspects of hierarchical gating. The algorithms are applied to data taken from a low power ASK design. The best gated clocktree is created using both physical and logical information.