gebhart/patrepeval huggingface dataset:
Automated Quantitative Bone Analysis in<i>In Vivo</i>X-ray Micro-Computed Tomography (2017)

Measurement and analysis of bone morphometry in 3D micro-computed tomography volumes using automated image processing and analysis improve the accuracy, consistency, reproducibility, and speed of preclinical osteological research studies. Automating segmentation and separation of individual bones in 3D micro-computed tomography volumes of murine models presents significant challenges considering partial volume effects and joints with thin spacing, i.e., 50 to [Formula: see text]. In this paper, novel hybrid splitting filters are presented to overcome the challenge of automated bone separation. This is achieved by enhancing joint contrast using rotationally invariant second-derivative operators. These filters generate split components that seed marker-controlled watershed segmentation. In addition, these filters can be used to separate metaphysis and epiphysis in long bones, e.g., femur, and remove the metaphyseal growth plate from the detected bone mask in morphometric measurements. Moreover, for slice-by-slice stereological measurements of long bones, particularly curved bones, such as tibia, the accuracy of the analysis can be improved if the planar measurements are guided to follow the longitudinal direction of the bone. In this paper, an approach is presented for characterizing the bone medial axis using morphological thinning and centerline operations. Building upon the medial axis, a novel framework is presented to automatically guide stereological measurements of long bones and enhance measurement accuracy and consistency. These image processing and analysis approaches are combined in an automated streamlined software workflow and applied to a range of in vivo micro-computed tomography studies for validation.
<title>Broadband absorption spectroscopy by combining frequency-domain and steady-state techniques</title> (2001)

A technique for measuring broadband near-infrared absorption spectra of turbid media is presented using a combination of frequency-domain (FD) and steady-state (SS) reflectance methods. Most of the wavelength coverage is provided by a white-light SS measurement, while the FD data are acquired at a few selected wavelengths. Coefficients of absorption ((mu) <SUB>a</SUB>) and reduced scattering ((mu) <SUB>s</SUB>') derived from the FD data are used to intensity-calibrate the SS measurements and to estimate (mu) <SUB>s</SUB>' at all wavelengths in the spectral window of interest. After these steps are performed, (mu) <SUB>a</SUB> can be determined by comparing the SS reflectance values to the predictions of diffusion theory, wavelength by wavelength. We present an application of this method to breast tumor characterization. A case study of a fibroadenoma is shown, where different absorption spectra were found between the normal and the tumor sides.
Computational Design and Synthesis of Nitrogen-Substituted Carbon and Silicon Clathrates (2013)

A computational approach was utilized to design the framework and to identify potential guest atoms for stabilizing nitrogen-substituted carbon and silicon clathrates. Two new series of N-substituted carbon and silicon clathrates compounds were discovered as potential candidate materials. One of the hybrid C\bond N clathrates was successfully synthesized using an industrial arc-melting technique. The theoretical bulk moduli of these N-substituted carbon and silicon clathrates were computed and they are comparable to those of C3N4, Si3N4, and SiC. Some N-substituted carbon clathrates may be suitable for application as hard materials.
Accelerated Pavement Testing Using Fast Falling-Weight Deflectometer (2016)

A newly designed Falling Weight Deflectometer (FWD) has been developed that significantly speeds up the testing process and overall productivity of the device. The new device is currently being referred to as the Fast FWD or FFWD for short. The speed of the device, and the fact that it is capable of imparting full scale truck wheel loads to the pavement surface suggested that it might be a viable tool for conducting accelerated pavement testing experiments. Two pavement test sections were tested to failure with the FFWD. Preliminary tests show that the FFWD can be used as an intermediate tool, between the small scale laboratory tests (bending beam, shear, and triaxial tests) and full scale accelerated pavement tests.
Treatment of heterotopic ossification through remote ATP hydrolysis (2014)

Heterotopic ossification (HO) is the pathologic development of ectopic bone in soft tissues because of a local or systemic inflammatory insult, such as burn injury or trauma. In HO, mesenchymal stem cells (MSCs) are inappropriately activated to undergo osteogenic differentiation. Through the correlation of in vitro assays and in vivo studies (dorsal scald burn with Achilles tenotomy), we have shown that burn injury enhances the osteogenic potential of MSCs and causes ectopic endochondral heterotopic bone formation and functional contractures through bone morphogenetic protein-mediated canonical SMAD signaling. We further demonstrated a prevention strategy for HO through adenosine triphosphate (ATP) hydrolysis at the burn site using apyrase. Burn site apyrase treatment decreased ATP, increased adenosine 3',5'-monophosphate, and decreased phosphorylation of SMAD1/5/8 in MSCs in vitro. This ATP hydrolysis also decreased HO formation and mitigated functional impairment in vivo. Similarly, selective inhibition of SMAD1/5/8 phosphorylation with LDN-193189 decreased HO formation and increased range of motion at the injury site in our burn model in vivo. Our results suggest that burn injury-exacerbated HO formation can be treated through therapeutics that target burn site ATP hydrolysis and modulation of SMAD1/5/8 phosphorylation.
A DWT-based perceptually lossless color image compression architecture (2002)

In this paper we propose a DWT-based perceptually lossless image compression algorithm and architecture. Many image-capturing devices acquire images in subsampled R-G-B format and have real-time constraints which prohibit conversion to other formats, generally preferred for image compression, such as Y-Cb-Cr. Therefore, we propose a compression algorithm which works performed directly on the subsampled R-G-B data. The scheme exploits the correlation between the color planes and the perceptual sensitivity of the human visual system in order to improve the compression ratio. Moreover it can be easily mapped into an integrated fast architecture yielding very high throughput.
ChemInform Abstract: New Small Molecule Inhibitors of Hepatitis C Virus. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Transgenic Expression of Pear PGIP in Tomato Limits Fungal Colonization (2000)

Transgenic tomato plants expressing the pear fruit polygalacturonase inhibitor protein (pPGIP) were used to demonstrate that this inhibitor of fungal pathogen endopolygalacturonases (endo-PGs) influences disease development. Transgenic expression of pPGIP resulted in abundant accumulation of the heterologous protein in all tissues and did not alter the expression of an endogenous tomato fruit PGIP (tPGIP). The pPGIP protein was detected, as expected, in the cell wall protein fraction in all transgenic tissues. Despite differential glycosylation in vegetative and fruit tissues, the expressed pPGIP was active in both tissues as an inhibitor of endo-PGs from Botrytis cinerea. The growth of B. cinerea on ripe tomato fruit expressing pPGIP was reduced, and tissue breakdown was diminished by as much as 15%, compared with nontransgenic fruit In transgenic leaves, the expression of pPGIP reduced lesions of macerated tissue approximately 25%, a reduction of symptoms of fungal growth similar to that observed with a B. cinerea strain in which a single endo-PG gene, Bcpg1, had been deleted (A. ten Have, W. Mulder, J. Visser, and J. A. L. van Kan, Mol. Plant-Microbe Interact. 11:1009-1016, 1998). Heterologous expression of pPGIP has demonstrated that PGIP inhibition of fungal PGs slows the expansion of disease lesions and the associated tissue maceration.
A spectral mixture process conditioned by Gibbs-based partitioning (2001)

An enhanced method of spectral mixture analysis is investigated for hyperspectral imagery of moderate-to-high scene complexity, where either a large set of fundamental materials may exist throughout, or where some of the fundamental members have spectra that are similar to each other. For a complex scene, the use of one large set of fundamental materials as the set of "endmembers" for performing spectral unmixing can cause unreliable estimates of material compositions at sites within the scene. In such cases, partitioning this large set of endmembers into a number of smaller sets is appropriate, where the smaller sets are associated with certain regions in a scene. Herein, a Gibbs-based algorithm is developed to partition hyperspectral imagery into regions of similarity. This partitioning algorithm provides an estimator of an underlying and unobserved process called a "partition process" that coexists with other underlying (and unobserved) processes, one of which is called a "spectral mixing process." The algorithm exploits the properties of a Markov random field (MRF) and the associated Gibbs equivalence theorem, using a suitably defined graph structure and a Gibbs distribution to model the partition process. Consequently, spatial consistency is imposed on the spectral content of sites in each partition. The enhanced spectral mixing process is then computed as a linear mixture model that is conditioned on the partition process. Experiments are performed using scenes of HYDICE imagery to validate the algorithm, where spectral mixture analysis is performed with and without conditioning on the partitioning process.
Optical fibre biosensors using enzymatic transducers to monitor glucose (2007)

The construction and performance of a novel enzyme based optical sensor for in situ continuous monitoring of glucose in biotechnological production processes is presented. Sensitive optical coatings are formed from inorganic - organic hybrid polymers ( ORMOCERR (R) s(10)) combined with a flurophore ( ruthenium complex) and an enzyme, and applied to lenses, declad polymer optical fibre ( POF) and polymer clad silica fibre ( PCS). The enzyme, glucose oxidase, catalyzes oxidization of glucose to gluconic acid by depleting oxygen. Oxygen consumption is determined by measuring the fluorescence lifetime of metal organic ruthenium complexes which are quenched by oxygen. The coatings developed were designed to adhere to glass and polymer surfaces, to be compatible with enzymes and ruthenium complexes, and were demonstrated both as double- and single- layer structures. The sensor response to gaseous oxygen, dissolved oxygen and dissolved glucose was measured via fluorescence lifetime changes. A best detection limit of 0.5% ( vol) has been determined for gaseous O-2 with selected ORMOCERR (R) sensing layers. Glucose concentrations were measured to a detection limit of 0.1 mmol L-1 over a range up to 30 mmol L-1. The sensor was usable for 30 days in a bioreactor. The opto- electronic instrumentation and performance in laboratory bioreactors and in an industrial reactor are evaluated.
Polyisobutylene-based polyurethanes. IX. synthesis, characterization, and properties of polyisobutylene-based poly(urethane-ureas) (2016)

Polyisobutylene (PIB)-based polyurethanes (PUs) exhibit unparalleled hydrolytic-oxidative-biologic stability and are melt processible, however, their mechanical (strength) properties are modest mainly due to insufficient H bonds. We posited and demonstrate that the ultimate properties of PIB-PUs are enhanced, while their melt processibility is maintained, by the judicious introduction of urea linkages, i.e., strong bifurcated H bonds, in the chain. The incorporation of bifurcated H bonds in PIB-PUs was achieved by using the conventional butane diol chain extender (CE) in combination with controlled amounts of amino alcohol as co-chain extender (co-CE). Polyurethanes containing both urethane and urea linkages are polyurethane-ureas (PUU). Specifically, PIB-PUUs prepared with PIB-diol/MDI together with 80/20 mole % butane diol/amino butanol exhibited ∼30 MPa tensile strength, ∼550% elongation, ∼80 Shore A hardness, and ∼137 °C flow temperature. Other amino alcohols, i.e., amino ethanol, -propanol, and -hexanol, were less effective co-CEs. 1H-NMR and FT-IR spectroscopies indicate the presence of bifurcated H bonds in PIB-PUUs prepared with CE/co-CE combinations. Characterization by differential scanning calorimetry, thermogravimetric analysis, dynamic mechanical thermal analysis, and creep experiments also suggest bifurcated H bonds in PIB-PUU. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 2361–2369
Rapid Detection and Differentiation of Wild-Type and Three Attenuated Lapinized Vaccine Strains of <i>Classical Swine Fever Virus</i> by Reverse Transcription Polymerase Chain Reaction (2008)

A simple one-step reverse transcription polymerase chain reaction (RT-PCR) method was developed based on T-rich insertions in the viral genome for simultaneous detection and differentiation of wild type and vaccine strains of Classical swine fever virus (CSFV). The CSFV-specific primers were designed to contain the sequences of the T-rich insertion sites that exist uniquely in the 3' nontranslated regions (3' NTR) of the genome of lapinized CSFV vaccine strains. By using a one-step RT-PCR or a nested PCR followed by an agarose gel electrophoresis or a multicapillary electrophoresis, the wild-type and lapinized vaccine strains of CSFV in clinical samples could be detected and accurately distinguished. These assays can be applied to at least 3 attenuated lapinized vaccine strains, lapinized Philippines Coronel (LPC), hog cholera lapinized virus (HCLV), and Chinese strain (C strain). The detection limit of the wild-type virus was 6.3 TCID(50) (50% tissue culture infective dose)/ml for RT-PCR and 0.63 TCID(50)/ml for nested PCR. In previous studies, notable T-rich insertions of 12-13 nucleotides (nt) were found in the 3' NTR of the genome of lapinized vaccine strains of CSFV. However, this study discovered that 2 T-rich insertions, 42 and 36 nt in length, are present in the viral genome of lapinized vaccine strains LPC/PRK (primary rabbit kidney) and LPC/TS (Tam-Sui), respectively. These T-rich insertions of 12, 36, and 42 nt length increases the size of PCR fragments, which are favorable genetic markers for rapid detection of and differentiation between wild-type and different lapinized vaccine strains of CSFV.
Dynamic element matching for highly linear digital-to-analog conversion (1999)

This paper presents a performance analysis of a dynamic element matching technique for low harmonic distortion digital-to-analog converters (DACs). The technique employs simple binary switches controlled by pseudo-random bit sequences to make appropriate selections in a bank of unit DAC-elements whose outputs are summed to form the output of the composite DAC. Harmonic distortion resulting from static mismatches of the unit DAC-elements is eliminated at the expense of an increased DAC noise floor. The analysis provides an expression for the power of the white DAC noise in terms of certain time-average means of the input and the static mismatch errors, and IC fabrication yield estimation data of the noise power are presented for selected DAC bit resolutions. Furthermore, a comparison with other reported DEM techniques for low harmonic distortion DACs shows that the technique considered here is of least hardware complexity.
Hypothesis test for the detection of moving targets in automotive radar (2017)

In this paper, we present a hypothesis test for the classification of moving targets in the sight of an automotive radar sensor. For this purpose, a statistical model of the relative velocity between a stationary target and the radar sensor has been developed. With respect to the statistical properties a confidence interval is calculated and targets with relative velocity lying outside this interval are classified as moving targets. Compared to existing algorithms our approach is able to give robust classification independent of the number of observed moving targets and is characterized by an instantaneous classification, a simple parameterization of the model and an automatic calculation of the discriminating threshold.
Ion-Selective Nano-optodes Incorporating Quantum Dots (2007)

Ion-selective quantum dots (ISQDs) have been produced that are capable of measuring physiologically relevant ions (such as Na+, K+, Cl-, etc.). ISQDs consist of quantum dots, an ion-selective polymer matrix, and a biocompatible coating. ISQDs work by selective ion extraction by the polymer matrix which leads to a change in the absorbance intensity of an embedded dye. This attenuates the intensity of the quantum dot by directly absorbing its fluorescence emission. As an example of this technology, a sodium-selective ISQD measures sodium over the range of 1 mM to 1 M with 200-fold selectivity over potassium and a resolution of 80 μM at 10 mM.
Enhanced brightness and efficiency in organic electroluminescent devices using SiO2 buffer layers (1999)

Organic electroluminescent devices using SiO2 as a hole-injecting buffer have been fabricated. With the presence of the buffer, the luminance of the device reaches 1820 cd/m2 at the current density of 20 mA/cm2, which corresponds to an efficiency of 9.1 cd/A. The enhancements in brightness and efficiency are attributed to an improved balance of hole and electron injections due to blocking of the injected holes by the buffer layer and a more homogeneous adhesion of the hole transporting layer to the anode.
Hierarchical Filtered Motion for Action Recognition in Crowded Videos (2011)

Action recognition with cluttered and moving background is a challenging problem. One main difficulty lies in the fact that the motion field in an action region is contaminated by the background motions. We propose a hierarchical filtered motion (HFM) method to recognize actions in crowded videos by the use of motion history image (MHI) as basic representations of motion because of its robustness and efficiency. First, we detect interest points as the two-dimensional Harris corners with recent motion, e.g., locations with high intensities in the MHI. Then, a global spatial motion smoothing filter is applied to the gradients of the MHI to eliminate isolated unreliable or noisy motions. At each interest point, a local motion field filter is applied to the smoothed gradients of the MHI by computing structure proximity between any pixel in the local region and the interest point. Thus, the motion at a pixel is enhanced or weakened based on its structure proximity with the interest point. To validate its effectiveness, we characterize the spatial and temporal features by histograms of oriented gradient in the intensity image and the MHI, respectively, and use a Gaussian-mixture-model-based classifier for action recognition. The performance of the proposed approach achieves the state-of-the-art results on the KTH dataset that has clean background. More importantly, we perform cross-dataset action classification and detection experiments, where the KTH dataset is used for training, while the microsoft research (MSR) action dataset II that consists of crowded videos with people moving in the background is used for testing. Our experiments show that the proposed HFM method significantly outperforms existing techniques.
Endoprotease-Mediated Intracellular Protein Delivery Using Nanocapsules (2011)

Proteins possess distinct intracellular roles allowing them to have vast therapeutic applications. However, due to poor cellular permeability and fragility of most proteins, intracellular delivery of native, active proteins is challenging. We describe a biomimetic protein delivery vehicle which is degradable upon the digestion by furin, a ubiquitous intracellular protease, to release encapsulated cargos. Proteins were encapsulated in a nanosized matrix prepared with monomers and a bisacrylated peptide cross-linker which can be specifically recognized and cleaved by furin. Release of encapsulated protein was confirmed in a cell-free system upon proteolytic degradation of nanocapsules. In vitro cell culture studies demonstrated successful intracellular delivery of both nuclear and cytosolic proteins and confirmed the importance of furin-degradable construction for native protein release. This endoprotease-mediated intracellular delivery system may be extended to effectively deliver various biological therapeutics.
Characterisation of the late blight resistance in potato differential MaR9 reveals a qualitative resistance gene, R9a, residing in a cluster of Tm-2 2 homologs on chromosome IX (2015)

The durable late blight resistance in potato plant Ma R9 is genetically characterized. A novel R -gene is mapped. The monogenic nature and map positions of R9 are negated and rectified. Late blight of potato (Solanum tuberosum), caused by Phytophthora infestans, can effectively be managed by genetic resistance. The MaR9 differential plant provides durable resistance to a broad spectrum of late blight strains. This resistance is brought about by at least seven genes derived from S. demissum including R1, Rpi-abpt1, R3a, R3b, R4, R8 and, so far uncharacterized resistance gene(s). Here we set out to genetically characterize this additional resistance in MaR9. Three BC1 populations derived from MaR9 were identified that segregated for IPO-C resistance but that lacked R8. One BC1 population showed a continuous scale of resistance phenotypes, suggesting that multiple quantitative resistance genes were segregating. In two other BC1 populations resistance and susceptibility were segregating in a 1:1 ratio, suggesting a single qualitative resistance gene (R9a). A chromosome IX PCR marker, 184-81, fully co-segregated with R9a. The map position of R9a on the distal end of the lower arm of chromosome IX was confirmed using PCR markers GP101 and Stm1021. Successively, cluster-directed profiling (CDP) was carried out, revealing six closely linked markers. CDP(Sw)58, CDP(Sw)59 and CDP(Sw5)10 flanked the R9a gene at the distal end (5.8 cM) and, as expected, were highly homologous to Sw-5. CDP(Tm2)2 flanked R9a on the proximal side (2.9 cM). CDP(Tm2)6 and CDP(Tm2)7 fully co-segregated with resistance and had high homology to Tm-2 (2) , showing that R9a resides in a cluster of NBS-LRR genes with homology to Tm-2 (2) . Besides R9a, additional resistance of quantitative nature is found in MaR9, which remains to be genetically characterized.
Simulation of Dynamically Rolling Tire (2000)

Abstract The dynamically rolling tire is simulated by using an explicit finite element method. In this simulation, the complicated pattern shape and internal construction of the tire are modeled exactly since both these factors are very important for the performance properties of the tire. A very long calculation time is necessary for refined tire models, but, for practical tire development, the calculation time of this simulation is acceptable because of major advances in hardware, FEM software, and modeling techniques. The authors describe the model used in the simulation and report on the results of several properties under various rolling conditions of the tire evaluated by this method. The correlation between the simulation and the experiment appears good. Therefore, this simulation technique can be assumed very useful for actual tire development.