gebhart/patrepeval huggingface dataset:
Specific cleavage of DNA molecules at RecA-mediated triple-strand structure (2004)

A novel procedure to cleave DNA molecules at any desired base sequence is presented. This procedure is based upon our finding that double-stranded DNA molecules at a site where RecA-mediated triple-stranded DNA structure with a complimentary deoxyoligonucleotide is located can be cleaved by a single-strand specific nuclease, such as nuclease S1 or BAL31, between the first base at the 5' termini of the deoxyoligonucleotides and the nearest base proximal to the 5' termini. Accordingly, the sequence as well as the number of the cleavage sites to be cleaved can be custom designed by selecting deoxyoligonucleotides with specific base sequences for triple-stranded DNA formation. The basic characteristics of the cleavage reaction and typical applications of the procedure are presented with actual results, including those which involve cleavage of complex genomic DNA at the very sites one desires.
Steroids and Spinal Cord Injury (1998)

The National Acute Spinal Cord Injury Study (NASCIS) 2 and 3 trials are often cited as evidence that high-dose methylprednisolone is an efficacious intervention in the management of acute spinal cord injury. Neither of these studies convincingly demonstrate the benefit of steroids. There are concerns about the statistical analysis, randomization, and clinical end points. Even if the putative gains are statistically valid, the clinical benefits are questionable. Furthermore, the benefits of this intervention may not warrant the possible risks. This paper comments on these two clinical trials.
Fresh bone marrow introduction into porous scaffolds using a simple low‐pressure loading method for effective osteogenesis in a rabbit model (2008)

Recent advances in tissue engineering techniques have allowed porous biomaterials to be combined with osteogenic cells for effective bone regeneration. We developed a simple low-pressure cell-loading method using only syringes and stopcocks, and examined the effect of this method on osteogenesis when applied to the combination of highly porous beta-tricalcium phosphate (beta-TCP) and fresh autologous bone marrow. Both block and granule beta-TCP scaffolds were used to prepare implants in three different ways: without bone marrow as a control, with bone marrow that was allowed to penetrate spontaneously under atmospheric pressure (AP group), and with bone marrow that was seeded under low pressure (ULP group). These implants were transplanted into rabbit intramuscular sites, and the samples were examined biologically and histologically. The penetration efficiency of the block implants after marrow introduction was significantly higher in the ULP group than in the AP group. In the transplanted block samples, alkaline phosphatase activity was significantly higher in the ULP group at 2 weeks after implantation, and significantly more newly formed bone was observed in the ULP group at both 5 and 10 weeks compared with the AP group. Similar results were observed even in the experiment using beta-TCP granules, which are smaller than the blocks and frequently used clinically. Because of its convenience and safety, this low-pressure method might be a novel, effective treatment to promote osteogenesis with bone marrow in clinical bone reconstruction surgeries.
Development of DSP-based control system for master-slave manipulation (2011)

A dual arm master-slave servo-manipulator system has been developed for use in a pyroprocess integrated demonstration facility at Korea Atomic Energy Research Institute. The slave manipulator with a reach of 1.6 m can handle a 25 kgf payload in any posture, where the gravity force of remote tools or handling equipment has a great impact on the position tracking error which produces the unnecessary force that operator does not have to feel. In this work, we developed a DSP-based remote control system and applied a time delay controller for accurate tracking control of the manipulator. Experimental results show that the time delay controller has good performance on the master-slave tracking task compared with the conventional PD controller.
Application of Acoustoelasticity to Evaluate Stress Relaxation in API 5L x70 Steel for Pipelines (2005)

API 5L x70 steel is used in long distance gas pipelines. The manufacturing procedure of tubes can introduce residual stresses into them. If these components are loaded with stress in service, the final value of the stress inside the part will be unknown. Knowing that the stresses can decrease with time without a stress relief process would allow designers to enhance the design codes. Although relaxation at low temperatures is not well known amongst current researchers, previous work performed in steel by Moffatt (1951) and Chance (2000) proved that residual stresses in welded joints can be reduced over time. This present work shows the application of an ultrasonic technique to verify stress relaxation in API 5L x70 plates. A special geometry was developed, so that each plate has uniaxial stress in the measurement region. Sixteen plates were tested, eight in the rolling direction and the remaining in the orthogonal direction. The plates were stress relieved using an initial heat treatment to set a stress free reference state. After that, they were welded to create the stress field in the area of investigation. A final step was to cut each one of the samples at specific intervals after the welding. After each step, the stress was measured with ultrasound in the uniaxial stress region. A record of the process was precisely established at the time of each step. The differences in the acoustoelastic constants with rolling direction and the variation of the Young's modulus were taken into account. The results showed clear effects of relaxation in those samples. The magnitude was much more pronounced than in UNS G10100 steel.
Aqueous extract ofPhyllanthus niruri(Euphorbiaceae) enhances the phenotypic and functional maturation of bone marrow-derived dendritic cells and their antigen-presentation function (2010)

Decoctions of Phyllanthus niruri (PN) (Fam. Euphorbiaceae) is promoted in traditional medicine of Africa, Asia, and South America as beneficial supplement for different infectious diseases, especially for viral hepatitis, tumor, and for immune compromised patients. This stimulated the interest in understanding the mechanisms by which the whole extract of the plant could stimulate the immune system. Dendritic cells (DCs) are professional antigen-presenting cells and provide a link between the innate and the adaptive immune responses. In the present study, the effects of lyophilized aqueous extract of PN on structural and functional maturation of murine bone marrow-derived DCs (BM-DCs) were investigated. Bone marrow cells were cultured in the presence of granulocyte macrophage-colony stimulating factor and interleukin-4 (IL-4) and the generated immature DCs were stimulated with PN (25, 50, and 100 microg/mL) or lipopolysaccharide (10 microg/mL) for 48 h. Results showed that treatment with PN increased the expression of major histocompatibility complex-II and the various makers for DCs maturation (CD40), activation (CD83), and costimulation (CD86) in a concentration-dependent manner. Consistent with the increase in phenotypic makers, functional maturation assay showed that treatment of BM-DCs with PN caused a decrease in fluorescein isothiocyanate-dextran pinocytosis and an increase in IL-12 in the supernatant. In a transgenic T-cell activation model, PN-treated BM-DCs presented Ova antigen to Ova-specific CD8(+) T cells from OT-1 mice more efficiently as demonstrated by increased T-cells proliferation and IL-2 production. Therefore, PN enhances the structural and functional maturation of BM-DCs and their antigen-presenting function. These effects are relevant in immunodeficient conditions, tumor control, and in infectious diseases.
Speciation and Solubility of Major Actinides Under the Deep Groundwater Conditions of Korea (2002)

The speciation and solubility of Am, Np, Pu and U have been analyzed by means of the geochemical code MUGREM, under the chemical conditions of domestic deep groundwater, in order to support the preliminary safety assessment for a Korean HLW disposal concept. Under the conditions of groundwaters studied, the stable solid phase is AmOHC (s) or Am(OH)(s), soddyite((U ) .2) or N (c), Np(OH)(am), and Pu(OH)(am) for Am, U, Np, and Pu, respectively. The dominating aqueous species are as follows: the complexes of Am(III), Am(OH) and Am(C ) , the complexes of U(VI), U (OH) and U (C ), the complexes of Np(IV), Np(OH)(aq) and Np(OH)C , and the complexes of Pu(IV), Pu(OH)(aq) and Pu(OH)C . The calculated solubilities exist between 1.9E-10 and 1.3E-9 mol/L for Am, between 5.6E-6 and 1.2E-4 mol/L for U, between 3.1E-9 and 1.3E-8 mol/L for Np, and between 6.6E-10 and 2.4E-10 mol/L for Pu, depending on groundwater conditions. The present solubilities of each actinide agree well with the results of other studies obtained under similar conditions.s.
PB1-F2 Expression by the 2009 Pandemic H1N1 Influenza Virus Has Minimal Impact on Virulence in Animal Models (2010)

Unlike previous pandemic viruses, the 2009 H1N1 pandemic influenza virus does not code for the virulence factor PB1-F2. The genome of the 2009 H1N1 virus contains three stop codons preventing PB1-F2 expression; however, PB1-F2 production could occur following genetic mutation or reassortment. Thus, it is of great interest to understand the impact that expression of the PB1-F2 protein might have in the context of the 2009 pandemic influenza virus, A/California/04/2009 (Cal/09). We have addressed this question by generating two Cal/09 viruses with productive PB1-F2 open reading frames containing either an asparagine at position 66 of PB1-F2 (66N) or a serine at position 66 (66S): this N66S change has previously been shown to be associated with increased virulence in mice. We used these viruses to investigate the effect on virulence conferred by expression of the 66N or the 66S PB1-F2 protein in both in vitro and in vivo systems. Our results show enhanced replication of the 66S virus in A549 cells, while studies of BALB/c and DBA/2 mice and ferrets revealed no significant differences in symptoms of infection with wild-type Cal/09 versus the 66N or 66S virus variant. Also, coinfection of mice with Streptococcus pneumoniae and the different viruses (recombinant wild-type [rWT] Cal/09 and the 66N and 66S viruses) did not result in significant differences in mortality. Mice infected with either PB1-F2-expressing virus did demonstrate altered protein levels of proinflammatory cytokines; differences were observed to be greater in infection caused by the 66S virus. In summary, our study demonstrates that PB1-F2 expression by the Cal/09 virus modulates the immune response to infection while having a minimal effect on virus virulence in two mammalian models.
The glycosylceramides of the nematodeCaenorhabditis elegans contain an unusual, branched‐chain sphingoid base (1995)

Caenorhabditis elegans was cultured in semi-defined medium containing yeast extract, soy peptone, glucose, hemoglobin, Tween 80, and sitosterol. Monoglycosylceramides were chromatographically purified from nematode extracts. Their structures were elucidated with mass spectrometry, nuclear magnetic resonance spectroscopy, and analysis of methanolysis products of the parent cerebrosides. The glycosylceramides were unusual in that the only long-chain sphingoid base detected was an iso-branched compound with a C-4 double bond (i.e., 15-methyl-2-aminohexadec-4-en-1,3-diol). Glucose was the only sugar moiety detected. The fatty acids consisted of a series of primarily straight-chain, saturated, 2-hydroxylated C20-C26 acids; some iso-branched analogs also occurred. The sphingomyelins of C. elegans were also hydrolyzed, and the same iso-branched C17 compound was the only sphingoid base detected. This is the first structural analysis of a nematode glycosphingolipid and the first report of an organism in which the long-chain sphingoid bases are entirely iso-branched.
<title>Objective quality measure of halftone images based on optimal pixel assignment</title> (1996)

An optimal pixel assignment model for objective quality measure of halftone images has been developed. The model is based on the smallest units for tone reproduction and edge reproduction. The correlation of the reproduction error between an original gray-scale image and the units-based images has been adopted in the model. Theoretical analysis and experimental results have shown that the model is efficient for the evaluation of halftone image quality.
Structure from Motion with Objects (2016)

This paper shows for the first time that is possible to reconstruct the position of rigid objects and to jointly recover affine camera calibration solely from a set of object detections in a video sequence. In practice, this work can be considered as the extension of Tomasi and Kanade factorization method using objects. Instead of using points to form a rank constrained measurement matrix, we can form a matrix with similar rank properties using 2D object detection proposals. In detail, we first fit an ellipse onto the image plane at each bounding box as given by the object detector. The collection of all the ellipses in the dual space is used to create a measurement matrix that gives a specific rank constraint. This matrix can be factorised and metrically upgraded in order to provide the affine camera matrices and the 3D position of the objects as an ellipsoid. Moreover, we recover the full 3D quadric thus giving additional information about object occupancy and 3D pose. Finally, we also show that 2D points measurements can be seamlessly included in the framework to reduce the number of objects required. This last aspect unifies the classical point-based Tomasi and Kanade approach with objects in a unique framework. Experiments with synthetic and real data show the feasibility of our approach for the affine camera case.
Three-dimensional intracellular calcium gradients in single human burst-forming units-erythroid-derived erythroblasts induced by erythropoietin. (1990)

We have previously shown that the intracellular free Ca2+ increase induced by erythropoietin is likely related to differentiation rather than proliferation in human BFU-E-derived erythroblasts (1989. Blood. 73:1188-1194). Since cell differentiation involves transcription of specific regions of the genome, and since nuclear endonucleases responsible for single strand DNA breaks observed in cells undergoing differentiation are Ca2+ dependent, we investigated whether the erythropoietin-induced calcium signal is transmitted from cytosol to nucleus in this study. To elucidate subcellular Ca2+ gradients, the technique of optical sectioning microscopy was used. After determining the empirical three-dimensional point spread function of the video imaging system, contaminating light signals from optical planes above and below the focal plane of interest were removed by deconvolution using the nearest neighboring approach. Processed images did not reveal any discernible subcellular Ca2+ gradients in unstimulated erythroblasts. By contrast, with erythropoietin stimulation, there was a two- to threefold higher Ca2+ concentration in the nucleus compared to the surrounding cytoplasm. We suggest that the rise in nuclear Ca2+ may activate Ca2(+)-dependent endonucleases and initiate differentiation. The approach described here offers the opportunity to follow subcellular Ca2+ changes in response to a wide range of stimuli, allowing new insights into the role of regional Ca2+ changes in regulation of cell function.
Do personality traits predict the occurrence of Alzheimer's disease? (2000)

Our results support the assumption of specific premorbid characteristics in AD patients, ie increased neuroticism and rigidity. More research is needed to confirm the existence of typical premorbid personality traits in AD.
Higher diversity and abundance of denitrifying microorganisms in environments than considered previously (2015)

Denitrification is an important process in the global nitrogen cycle. The genes encoding NirK and NirS (nirK and nirS), which catalyze the reduction of nitrite to nitric oxide, have been used as marker genes to study the ecological behavior of denitrifiers in environments. However, conventional polymerase chain reaction (PCR) primers can only detect a limited range of the phylogenetically diverse nirK and nirS. Thus, we developed new PCR primers covering the diverse nirK and nirS. Clone library and qPCR analysis using the primers showed that nirK and nirS in terrestrial environments are more phylogenetically diverse and 2-6 times more abundant than those revealed with the conventional primers. RNA- and culture-based analyses using a cropland soil also suggested that microorganisms with previously unconsidered nirK or nirS are responsible for denitrification in the soil. PCR techniques still have a greater capacity for the deep analysis of target genes than PCR-independent methods including metagenome analysis, although efforts are needed to minimize the PCR biases. The methodology and the insights obtained here should allow us to achieve a more precise understanding of the ecological behavior of denitrifiers and facilitate more precise estimate of denitrification in environments.
Sex Differences in Constitutive Autophagy (2014)

Sex bias has been described nowadays in biomedical research on animal models, although sexual dimorphism has been confirmed widely under pathological and physiological conditions. The main objective of our work was to study the sex differences in constitutive autophagy in spinal cord and skeletal muscle tissue from wild type mice. To examine the influence of sex on autophagy, mRNA and proteins were extracted from male and female mice tissues. The expressions of microtubule-associated protein 1 light chain 3 (LC3) and sequestosome 1 (p62), markers to monitor autophagy, were analyzed at 40, 60, 90, and 120 days of age. We found significant sex differences in the expression of LC3 and p62 in both tissues at these ages. The results indicated that sex and tissue specific differences exist in constitutive autophagy. These data underlined the need to include both sexes in the experimental groups to minimize any sex bias.
Supramolecular Polymers Containing Terpyridine−Metal Complexes in the Side Chain (2007)

The synthesis of supramolecular polymers containing metal complexes in the side chain is described. Atom transfer radical polymerization (ATRP) was used to synthesize the macromolecular backbone, and the metal complex was attached via postpolymerization chemistry. Homopolymers containing [Ru(terpy)2]2+ in the side chain were prepared in which the complex contained either a long hydrophobic C16 alkyl group or only hydrogen at the 4‘-position. The homopolymers containing the long C16 alkyl groups showed lyotropic liquid crystalline (LC) behavior in chloroform solutions from room temperature to 60 °C and self-assembled in the bulk to form hexagonal arrays of cylinders. In addition, this alkyl side chain was observed to crystallize in the solid state. Homopolymers without the C16 alkyl group showed no lyotropic LC or any crystallization behavior. The material design emphasizes the relationship between the molecular structure and supramolecular organization of these polymers. It demonstrates that terpy complexes remain a versatile functionality for constructing supramolecular assemblies.
Fatigue damage prediction based on strain field estimates using a smoothed Kalman filter and sparse measurements (2018)

In this work, we address the problem of fatigue damage prediction in a truck component excited by road induced vibrations. The damage is computed from strains estimated from sparse measurements of ...
Photoacoustic-derived biomarkers of nanobubble-mediated cancer treatment response (2021)

Gas-filled nanobubbles (NBs) have been used for contrast enhanced ultrasound (US) molecular imaging similar to their microbubble (MB) counterparts. In this work we explore the use of NBs as cancer therapeutic vehicles to enhance radiation therapy and examine the role of photoacoustic (PA) imaging for quantifying the tissue response. Experiments were conducted in 58 mice bearing prostate cancer tumors. The treatment groups consisted of untreated controls (n=14), 8Gy radiation (n=14), US+MB (n=8), US+NB (n=5), US+MB+8Gy (n=12) and US+NB+8Gy (n=5). PA imaging was conducted using the VevoLAZR 21 MHz probe at pre-treatment, 2h and 24h post-treatment. To examine the changes in the tumor microenvironment post-treatment, we measured the tumor oxygen saturation (sO2), total hemoglobin (HbT) and the spectral slope (SS) as a surrogate measurement of vessel size. Histology measures of tumor vascularity/vessel size (CD31) and cellular death (TUNEL) allowed us to interpret the PA biomarker changes. The PA biomarkers revealed the following changes for the US+NB+8Gy group: (a) a 20% decrease in tumor sO2, (b) a 30% increase in tHb and (c) 20% decrease SS. These results suggest that NBs induce vessel damage from US-induced cavitation. Histology elucidates these findings: CD31 staining measuring vascularity decreases by 80% at 24h–this causes the drop in sO2 and increase in HbT; the size of vessels decreases by 10%–this is captured by the SS change. This work shows that PA imaging biomarkers can quantify these vascular changes which in turn enhance the radiation-induced cell death (up to 40%, as measured by TUNEL staining).
Respiratory Motion Compensation in PET/MR: Evaluation of an Integrated Approach (2016)

642 Objectives Respiratory motion leads to blurred structures in PET images of the abdomen and thorax, and hence hampers the detection and quantification of lesions. An MR-based motion-correction framework for PET images was evaluated quantitatively. Methods On an integrated PET/MR (Siemens Biograph mMR) 5 minutes of PET as well as radial MR data (T1-weighted, stack-of-stars 3D, spoiled GRE, golden-angle sampling, Resolution: 1.56x1.56x4.5mm3) were acquired simultaneously. A respiratory signal was extracted from the k-space of the MR data (“self-gating”) and used to sort MR acquisitions and PET listmode events into 5 respiratory bins (1). A high-resolution motion model was calculated from the reconstructed MR-bins using non-rigid registration. The PET images were reconstructed by means of a prototypical motion-correction software (Siemens Molecular Imaging, Knoxville), which uses gated sinograms and the motion model to iteratively calculate a motion-compensated PET image (2). The lesions were analyzed conventionally with regard to their shape (rising and falling lesion edge) as well as their tracer activity concentration. In addition, image sharpness was evaluated using a frequency-threshold metric, which detects the occurrence of high spatial frequencies and resembles a more realistic assessment of improved object appearance. Results F-18 FDG (n = 8) and Ga-68 DOTANOC (n = 7) PET/MR data of 15 patients (55 ± 18 y) were reconstructed by means of the motion-correction framework as well as using conventional averaging. The motion compensation increased the image sharpness by 49.8%. In 19 evaluated lesions motion compensation led to a median increase in SUVpeak by 10.4±7.6% (mean ± SD). The slope of the cranio-caudal lesion edges increased by 34.9±53.3% and 39.5±42.1%. The attached figure depicts sagittal slices of uncompensated and motion-compensated reconstructions, as well as cranio-caudal intensity profiles through the depicted lesion. Conclusions MR-based motion correction in PET images using all available data leads to significantly sharper PET structures without compromising SNR.