gebhart/patrepeval huggingface dataset:
Comprehensive Profiling of Glycosphingolipid Glycans Using a Novel Broad Specificity Endoglycoceramidase in a High-Throughput Workflow (2016)

The biological function of glycosphingolipids (GSLs) is largely determined by their glycan headgroup moiety. This has placed a renewed emphasis on detailed GSL headgroup structural analysis. Comprehensive profiling of GSL headgroups in biological samples requires the use of endoglycoceramidases with broad substrate specificity and a robust workflow that enables their high-throughput analysis. We present here the first high-throughput glyco-analytical platform for GSL headgroup profiling. The workflow features enzymatic release of GSL glycans with a novel broad-specificity endoglycoceramidase I (EGCase I) from Rhodococcus triatomea, selective glycan capture on hydrazide beads on a robotics platform, 2AB-fluorescent glycan labeling, and analysis by UPLC-HILIC-FLD. R. triatomea EGCase I displayed a wider specificity than known EGCases and was able to efficiently hydrolyze gangliosides, globosides, (n)Lc-type GSLs, and cerebrosides. Our workflow was validated on purified GSL standard lipids and was applied to the characterization of GSLs extracted from several mammalian cell lines and human serum. This study should facilitate the analytical workflow in functional glycomics studies and biomarker discovery.
A low–order unstructured–mesh approach for computational electromagnetics in the time domain (2004)

Maxwell's curl equations in the time domain are solved using an explicit linear finite-element approach implemented on unstructured tetrahedral meshes. For the simulation of scattering problems, a perfectly matched layer is added at the artificial far-field boundary, created by the truncation of the physical domain prior to the numerical solution. The complete solution procedure is parallelized. The computational challenges that are encountered when attempting simulations at higher frequencies suggest that the implementation of a hybrid algorithm could have certain advantages. The hybrid approach adopted uses a combination of the finite-element procedure and the well-known low operation count/low storage finite-difference time-domain method. Examples are included to demonstrate the numerical performance of the techniques that are described.
Therapeutic utility of palmitoylethanolamide in the treatment of neuropathic pain associated with various pathological conditions: a case series (2012)

Palmitoylethanolamide (PEA), an endogenous fatty acid amide, has been demonstrated to bind to a receptor in the cell nucleus - the peroxisome proliferator-activated receptor - and performs a great variety of biological functions related to chronic and neuropathic pain and inflammation, as has been demonstrated in clinical trials. These include peripheral neuropathies such as diabetic neuropathy, chemotherapy-induced peripheral neuropathy, carpal tunnel syndrome, sciatic pain, osteoarthritis, low-back pain, failed back surgery syndrome, dental pains, neuropathic pain in stroke and multiple sclerosis, chronic pelvic pain, postherpetic neuralgia, and vaginal pains. Probably due to the fact that PEA is an endogenous modulator as well as a compound in food, such as eggs and milk, no serious side effects have been reported, nor have drug-drug interactions. This article presents a case series describing the application and potential efficacy and safety of PEA in the treatment of various syndromes associated with chronic pain that is poorly responsive to standard therapies.
Recent developments in autoimmune liver diseases (1997)

Several diseases are regarded as autoimmune liver diseases. Apart from the cholestatic liver diseases, primary biliary cirrhosis, primary sclerosing cholangitis, these include autoimmune hepatitis, hepatitis as part of the autoimmune polyendocrine syndrome type 1 (APS-1) and particular overlap syndromes such as autoimmune cholangitis (also called antimitochondrial antibody negative primary biliary cirrhosis [PBC]), overlap syndrome chronic active hepatitis (CAH)/PBC and the overlap syndrome primary sclerosing hepatitis (PSC)/CAH. In addition, auto-antibodies may be observed during the course of chronic viral hepatitis, in particular chronic hepatitis C and D. Finally, a small number of drug-induced liver diseases is immune mediated. The following article will review our recent progress in the field of autoimmune hepatitis including APS-1 and autoimmunity in viral hepatitis and immune-mediated drug-induced liver disease.
Synthetic mRNAs for manipulating cellular phenotypes: an overview (2014)

Availability of high quality synthetic mRNAs (syn-mRNAs) has enabled progress in their applications. Important structural features and quality requirements are discussed. Developments in the application of mRNA-mediated manipulation of cells are presented (i) mRNA-directed expression of antigens in dendritic cells for vaccination projects in oncogenesis, infectious disease and allergy prevention; (ii) reprogramming of human fibroblasts to induced pluripotent stem cells with their subsequent differentiation to the desired cell type; (iii) applications in gene therapy.
Shear strength and compressibility of tire chips for use as retaining wall backfill (1993)

Scrap tires that have been cut into chips are coarse grained, free draining, and have a low compacted density, thus offering significant advantages for use as lightweight fill and retaining wall backfill. The engineering properties needed to put tire chips into use are presented. The properties determined for tire chips, from three suppliers, are gradation, specific gravity, compacted density, shear strength, compressibility, and coefficient of lateral earth pressure at rest. The 76-mm (3-in.) maximum size and high compressibility of the tire chips necessitated design and fabrication of custom-made testing equipment. The tests showed that the tire chips are composed of uniformly graded, gravel-sized particles that absorb only a small amount of water. Their compacted density is 0.618 to 0.642 Mg/cu m (38.6 to 40.1 pcf), which is about one-third that of compacted soils. The shear strength was measured in a large-scale direct shear apparatus. The friction angle and cohesion intercept ranged from 19 to 25 degrees and 8 to 11 kPa (160 to 240 psf), respectively. The compressibility tests showed that tire chips are highly compressible on initial loading, but that the compressibility on subsequent unloading and reloading cycles is less. The horizontal stress was measured during these tests and showed that the coefficient of lateral earth pressure at rest varied from 0.26 for tire chips with a large amount of steel belt exposed at the cut edges to 0.47 for tire chips composed entirely of glass-belted tires.
Natural history of spinal and bulbar muscular atrophy (SBMA): a study of 223 Japanese patients (2006)

Spinal and bulbar muscular atrophy (SBMA) is an adult-onset motoneuron disease caused by a CAG-repeat expansion in the androgen receptor (AR) gene and for which no curative therapy exists. However, since recent research may provide opportunities for medical treatment, information concerning the natural history of SBMA would be beneficial in planning future clinical trials. We investigated the natural course of SBMA as assessed by nine activities of daily living (ADL) milestones in 223 Japanese SBMA patients (mean age at data collection = 55.2 years; range = 30-87 years) followed from 1 to 20 years. All the patients were diagnosed by genetic analysis. Hand tremor was an early event that was noticed at a median age of 33 years. Muscular weakness occurred predominantly in the lower limbs, and was noticed at a median age of 44 years, followed by the requirement of a handrail to ascend stairs at 49, dysarthria at 50, dysphagia at 54, use of a cane at 59 and a wheelchair at 61 years. Twenty-one of the patients developed pneumonia at a median age of 62 and 15 of them died at a median age of 65 years. The most common cause of death in these cases was pneumonia and respiratory failure. The ages at onset of each ADL milestone were strongly correlated with the length of CAG repeats in the AR gene. However CAG-repeat length did not correlate with the time intervals between each ADL milestone, suggesting that although the onset age of each ADL milestone depends on the CAG-repeat length in the AR gene, the rate of disease progression does not. The levels of serum testosterone, an important triggering factor for polyglutamine-mediated motoneuron degeneration, were maintained at relatively high levels even at advanced ages. These results provide beneficial information for future clinical therapeutic trials, although further detailed prospective studies are also needed.
Osteoarthritis: MR Imaging Findings in Different Stages of Disease and Correlation with Clinical Findings (2003)

Cartilage lesions, bone marrow edema pattern, and meniscal and ligamentous lesions were frequently demonstrated on MR images in patients with advanced osteoarthritis. Clinical findings showed no significant correlations with KL score and extent of findings at MR imaging.
A novel mammalian Smt3‐specific isopeptidase 1 (SMT3IP1) localized in the nucleolus at interphase (2000)

A novel Smt3-specific isopeptidase, SMT3IP1, was cloned using a yeast two-hybrid screen with Smt3b as bait. The clone, named SMT3IP1 (Smt3-specific isopeptidase 1), which bound to Smt3b but not SUMO-1 in the two-hybrid system, was distantly related to budding yeast Saccharomyces cerevisiae Ulp1, human SENP1 or human SUSP1. The catalytic domains in the C-terminal region were very similar, but the N-terminal region was quite different to other enzymes. The cysteine, histidine and asparatic acid residues in the catalytic domains were conserved. SMT3IP1 expressed by the baculovirus-expression system had the ability to cleave SUMO-1 or Smt3b from SUMO-1/RanGAP1 or Smt3b/RanGAP1 conjugates, respectively, and the activity was a little stronger towards the Smt3b conjugate than towards the SUMO-1 conjugate. Furthermore, the enzyme bound more strongly to Smt3a and Smt3b than to SUMO-1 in vitro. The enzyme did not cleave Nedd8 from Nedd8/cullin-1. Nor did it cleave ubiquitin from ubiquitinated p53. SMT3IP1 was localized almost exclusively at the nucleolus during interphase. The N-terminal sequence was responsible for the nucleolar localization of this enzyme. Whether SMT3IP1 functions in the nucleolus or just stays there before it functions in the nucleus, as shown in the case of CDC14 phosphatase, remains to be elucidated.
Chemical composition of sandstones, excluding carbonate and volcanic sands (1963)

Chemistry of the oceans I. Geochemistry of the biosphere J. Chemistry of rock-forming minerals K. Volcanic emanations, by
Suppression of Leukotriene B4 Biosynthesis by Endogenous Adenosine in Ligand-activated Human Neutrophils (1997)

Adenosine (Ado) has been shown to suppress several functional responses of human polymorphonuclear leukocytes (PMNs). The current study investigated whether endogenous Ado regulates the biosynthesis of leukotriene (LT)B4 in ligand-stimulated PMNs. Measurements of Ado in PMN resuspended in Hanks' buffered salt solution (HBSS) or plasma showed a cell concentration- and time-dependent accumulation of the nucleoside. The removal of endogenous Ado with either Ado deaminase or the blockade of its action by the Ado A2a receptor antagonist, 8-(3-chlorostyryl) caffeine, markedly increased LTB4 biosynthesis upon ligand stimulation in HBSS. Similarly, LTB4 synthesis by ligand-stimulated PMNs in plasma (containing recombinant LTA4 hydrolase to allow the conversion of protein-bound LTA4) was strongly enhanced by addition of Ado deaminase. Addition of red blood cells to suspensions of PMNs in plasma mimicked the effect of adding Ado deaminase and LTA4 hydrolase in enhancing LTB4 biosynthesis upon ligand stimulation. This effect of red blood cells on LTB4 biosynthesis was blocked by dipyridamole, an inhibitor of Ado transport, or captopril, an inhibitor of LTA4 hydrolase. These results demonstrate that endogenous Ado efficiently downregulates ligand-stimulated LTB4 biosynthesis in PMN suspensions, pointing out a potentially important regulatory function of Ado in inflammatory exudates. These results also unveil a dual role for red blood cells in upregulating LTB4 biosynthesis, namely, the removal of endogenous Ado and the conversion of LTA4 released by activated PMNs.
The Synthesis and Cyclodehydration of 4-(3-Aryl-1,3-dioxopropyl)-5-phenyl-1<i>H</i>-1,2,3-triazoles. Novel Substituted Pyrrolo[1,2-<i>c</i>][1,2,3]triazoles (1994)

Abstract The polyfunctionalized title triazolyl 1,3-diketones have been prepared by the addition-cyclization reaction of sodium azide to 1,5-diaryl-4-pentyne-1,3-diones, in the first instance, in good yields. These intermediate triazoles can readily be cyclodehydrated to the corresponding 3,6-diaryl-4H-pyrrolo[1,2-c][1,2,3]triazol-4-one derivatives. This cyclodehydration furnishes a new method of synthesis of a new class of pyrrolo[1,2-c][1,2,3]triazoles. The structures of the above compounds were confirmed from their spectral characteristics.
Aligned SF/P(LLA‐CL)‐blended nanofibers encapsulating nerve growth factor for peripheral nerve regeneration (2013)

Artificial nerve guidance conduits (NGCs) containing bioactive neurotrophic factors and topographical structure to biomimic native tissues are essential for efficient regeneration of nerve gaps. In this study, aligned SF/P(LLA-CL) nanofibers encapsulating nerve growth factor (NGF), which was stabilized by SF in core, were fabricated via a coaxial electrospinning technique. The controlled release of NGF from the nanofibers was evaluated using enzyme-linked immune sorbent assay (ELISA) and PC12 cell-based bioassay over a 60-day time period. The results demonstrated that NGF presented a sustained release and remained biological activity over 60 days. Nerve guidance conduits (NGCs) were fabricated by reeling the aligned SF/P(LLA-CL) nanofibrous scaffolds encapsulating NGF and then used as a bridge implanted across a 15-mm defect in the sciatic nerve of rats to promote nerve regeneration. The outcome in terms of regenerated nerve at 12 weeks was evaluated by a combination of electrophysiological assessment, histochemistry, and electron microscopy. All results clarified that the NGF-encapsulated-aligned SF/P(LLA-CL) NGCs promoted peripheral nerve regeneration significantly better than the aligned SF/P(LLA-CL) NGCs, suggesting that the released NGF from nanofibers could effectively promote the regeneration of peripheral nerve.
Carboxybiotin translocation mechanisms suggested by diffraction studies of biotin and its vitamers. (1980)

Biotin is a coenzyme that fixes CO2 for transfer in a family of carboxylase, decarboxylase, and transcarboxylase enzymes. Their enzyme reactions involve two basic steps during which a carboxybiotinyl intermediate forms at one site and translocates to a second (distinct) site for CO2 transfer. Our diffraction studies of biotin and its vitamers suggest that translocation involves rotation about one, or at most two, bonds in biotin's valeryl chain. The rotations are energetically economical gauche in equilibrium trans rotations about the two valeryl bonds nearest the biotin bicyclic ring. They move a carbon atom of a CO2 moiety bound at N-1' approximately 7 A, a distance in accord with spectroscopic measurements of one of the biotin enzymes. From our studies we infer that sulfur in biotin imparts to the valeryl chain a conformational variability necessary for bond rotation and, hence, translocation between catalytic sites.
Vascular Incorporation of Endothelial Colony-Forming Cells Is Essential for Functional Recovery of Murine Ischemic Tissue Following Cell Therapy (2011)

Endothelial-specific suicide gene technology demonstrates distinct mechanisms for ECFCs and MSCs, with complete abolishment of ECFC-mediated effects, whereas MSC-mediated effects remained unaffected. These data strengthen the notion that a dual-cell-based therapy represents a promising approach for vascular regeneration of ischemic tissue.
Periodically pulsed wet annealing approach for low-temperature processable amorphous InGaZnO thin film transistors with high electrical performance and ultrathin thickness (2016)

In this paper, a simple and controllable "wet pulse annealing" technique for the fabrication of flexible amorphous InGaZnO thin film transistors (a-IGZO TFTs) processed at low temperature (150 °C) by using scalable vacuum deposition is proposed. This method entailed the quick injection of water vapor for 0.1 s and purge treatment in dry ambient in one cycle; the supply content of water vapor was simply controlled by the number of pulse repetitions. The electrical transport characteristics revealed a remarkable performance of the a-IGZO TFTs prepared at the maximum process temperature of 150 °C (field-effect mobility of 13.3 cm(2) V(-1) s(-1); Ion/Ioff ratio ≈ 10(8); reduced I-V hysteresis), comparable to that of a-IGZO TFTs annealed at 350 °C in dry ambient. Upon analysis of the angle-resolved x-ray photoelectron spectroscopy, the good performance was attributed to the effective suppression of the formation of hydroxide and oxygen-related defects. Finally, by using the wet pulse annealing process, we fabricated, on a plastic substrate, an ultrathin flexible a-IGZO TFT with good electrical and bending performances.
Functionalized Mesoporous Hybrid Thin Films as Selective Membranes (2006)

Mesoporous thin films containing organic functionalities behave like selective membranes. Titania mesoporous films with an accessible cubic mesostructure are deposited on a conductive electrode (see figure). Organic groups (phenyl, hexadecyl, glycerol) are added to the pore surface by post-grafting. The transport properties of electrochemical probes such as ferrocyanide or ferrocenedimethanol within the pore system depend on the grafted functionalities. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2006/c2215_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
IDENTIFICATION OF EXCITABLE MEDIA USING CELLULAR AUTOMATA MODELS (2007)

Excitable media represent an important class of spatio-temporal systems which can be studied using cellular automata models. In the present study examples of excitable media behavior generated using simple cellular automata models are introduced. A mutual information algorithm is then derived to determine the neighborhood, the excitation threshold, and the number of excitation states. Based on this information two methods of identifying the rule which describes the excitable media pattern using a multimodel and a polynomial model are introduced. The results are illustrated using simulated examples and real data from a Belousov–Zhabotinskii experiment.
An imperceptible LSB image hiding on edge region using DES encryption (2017)

Sending image in a plain form has a high risk for the data being vulnerable to steal. Thus, due to reducing the risk, data security techniques should be implemented. Data security techniques can be done using Cryptography and Steganography. Based on the literature, the combination of cryptography and steganography can enhance results. Cryptography as one of science in information security, which used in the process of securing image. One of the cryptographic methods that have been used to secure the data is Data Encryption Standard (DES). This algorithm often implemented for the encryption process in an ATM machine and SIM card operator worldwide. Our proposed method firstly encrypts the image message using DES encryption. This process produces visible data, which is caused suspicion by others. In this paper, to conceal the encrypted image, we used steganography method. Our experiment chooses Least Significant Bit (LSB) based on canny edge detection. LSB algorithm was chosen because it is simple to be implemented and has good imperceptible value. Then, canny edge detection used to determines the coordinates of the object's edges of the cover image. We utilize the Canny coordinate result as the position to embed the image message because of the results more accurate and it can improve imperceptibility. Our experimental results were measured using Mean Square Error (MSE) and Peak Signal to Noise Ratio (PSNR). From the measurement, results obtained the best MSE value is 0.0038557 and PSNR are 72.2698 dB.
SplitStream (2003)

In tree-based multicast systems, a relatively small number of interior nodes carry the load of forwarding multicast messages. This works well when the interior nodes are highly-available, dedicated infrastructure routers but it poses a problem for application-level multicast in peer-to-peer systems. SplitStream addresses this problem by striping the content across a forest of interior-node-disjoint multicast trees that distributes the forwarding load among all participating peers. For example, it is possible to construct efficient SplitStream forests in which each peer contributes only as much forwarding bandwidth as it receives. Furthermore, with appropriate content encodings, SplitStream is highly robust to failures because a node failure causes the loss of a single stripe on average. We present the design and implementation of SplitStream and show experimental results obtained on an Internet testbed and via large-scale network simulation. The results show that SplitStream distributes the forwarding load among all peers and can accommodate peers with different bandwidth capacities while imposing low overhead for forest construction and maintenance.
Activation of a NO-cyclic GMP system by NO donors potentiates β-endorphin-induced antinociception in the mouse (1995)

Nitric oxide (NO) donors such as sodium nitroprusside (SNP, 0.01-1 micrograms) or 3-morpholino-sydnonimine (SIN-1, 0.1-10 micrograms) administered intracerebroventricularly (i.c.v) produced a dose-dependent potentiation of beta-endorphin-induced antinociception assessed by the tail-flick test in ICR mice. The same i.c.v. treatment with SNP or SIN-1 did not affect the antinociception induced by mu-, delta-, or kappa-opioid receptor agonists. The goal of the present study was to determine if the potentiation of the beta-endorphin-induced antinociception by NO donors is mediated by the activation of NO-cGMP system. Co-administration of hemoglobin (30-120 micrograms) or methylene blue (1.25-5 micrograms), but not N omega-nitro-L-arginine (1-5 micrograms) given i.c.v. dose-dependently attenuated the potentiating effects of SNP or SIN-1 on beta-endorphin-induced antinociception. However, the same i.c.v. treatments of mice with hemoglobin, methylene blue or N omega-nitro-L-arginine did not directly affect the i.c.v. administered beta-endorphin-induced antinociception. On the other hand, the treatment of mice with a combination of NO donor (SNP, 0.1 micrograms or SIN-1, 1 microgram) and zaprinast (a cGMP phosphodiesterase inhibitor, 1 microgram) further potentiated beta-endorphin-induced antinociception. These results indicate that the potentiating effect of SNP or SIN-1 on beta-endorphin-induced antinociception is mediated by the increased production of NO-cyclic GMP in the brain. However, the NO-cGMP system is not directly involved in the beta-endorphin-induced antinociception.