gebhart/patrepeval huggingface dataset:
PRO-051, an antisense oligonucleotide for the potential treatment of Duchenne muscular dystrophy. (2010)

PRO-051 (GSK-2402968), being developed by GlaxoSmithKline plc, under license from Leiden University Medical Center and Prosensa Therapeutics BV, is a 2'-O-methyl phosphorothioate antisense oligonucleotide for the potential treatment of Duchenne muscular dystrophy (DMD). The PRO-051 oligonucleotide sequence induces skipping of exon 51 of the dystrophin gene by binding to a sequence within the dystrophin pre-mRNA and masking the exon inclusion signals that are used for splicing. Removal of exon 51 from an exon 45 to 50, 47 to 50, 48 to 50, 49 to 50, 50, 52 or 52 to 63 deleted transcript allows restoration of the open reading frame and synthesis of an internally truncated, semi-functional dystrophin protein. By targeting exon 51, approximately 13% of patients with DMD could be treated, the largest proportion of patients that could benefit from targeting a single dystrophin exon. A proof-of-concept clinical trial of PRO-051 in patients with DMD demonstrated that a single intramuscular administration of PRO-051 induced exon skipping within muscle fibers adjacent to the injection site, while biopsies revealed dystrophin expression in treated but not control muscle fibers. At the time of publication, a phase I/IIa trial to evaluate subcutaneous delivery of PRO-051 had been completed, although full results were yet to be published.
Rat carbamyl-phosphate synthetase I gene. Promoter sequence and tissue-specific transcriptional regulation in vitro. (1987)

The region flanking the 5'-end of the rat gene encoding the cytoplasmic precursor of carbamyl-phosphate synthetase I, a mitochondrial matrix enzyme, has been cloned and partially characterized. S1 nuclease and primer extension analyses position the starts of transcription 138-140 nucleotides upstream of the translation initiation codon. Exon 1 contains this untranslated sequence and extends downstream to include the coding region for the pre-enzyme signal peptide (38 amino acids) plus 4 amino acids from the amino terminus of the mature protein. The 5'-flanking sequence contains typical promoter elements, including putative TATA and CAAT motifs at -21 and -82 nucleotides, respectively. In addition, several copies of consensus sequences corresponding to the H4TF-1 recognition element, GATTTC, together with the enhancer-like octamer, ATTTGCAT, are also present. Carbamyl-phosphate synthetase I is a cell-type specific enzyme, being expressed only in hepatocytes and epithelial cells of the intestinal mucosa. It is also synthesized at relatively high levels in the hepatoma cell line, Hep G2. Employing pCPS2.1, a minigene containing the promoter and part of exon 1, we show that nuclear extracts from Hep G2 support accurate carbamyl-phosphate synthetase I gene transcription in vitro. No such activity was observed, however, in extracts from HeLa, a cell line which does not express carbamyl-phosphate synthetase I.
Real-time 3D model acquisition (2002)

The digitization of the 3D shape of real objects is a rapidly expanding field, with applications in entertainment, design, and archaeology. We propose a new 3D model acquisition system that permits the user to rotate an object by hand and see a continuously-updated model as the object is scanned. This tight feedback loop allows the user to find and fill holes in the model in real time, and determine when the object has been completely covered. Our system is based on a 60 Hz. structured-light rangefinder, a real-time variant of ICP (iterative closest points) for alignment, and point-based merging and rendering algorithms. We demonstrate the ability of our prototype to scan objects faster and with greater ease than conventional model acquisition pipelines.
Analysis of Deoxyribonucleotides with Principal Component and Partial Least-Squares Regression of UV Spectra after Fourier Preprocessing (1990)

Principal component (PCR) and partial least-squares (PLS) regression with Fourier preprocessing of ultraviolet spectra have been evaluated for the analysis of mixtures of the four major nucleotides of DNA. Results have been compared with those obtained without Fourier preprocessing and with those obtained with a straightforward P-matrix approach with optimum wavelength selection. Calibrations were developed and tested with the use of sixteen standard and fourteen unknown mixtures. The standards and nine of the unknowns followed the typical base equivalences found in DNA. For these nine unknowns, the best average percent error in the Fourier domain was 0.61%, as compared to 0.65% in the spectral domain. The remaining five unknowns, in which the nucleotide concentrations were independent of each other, provided a particularly difficult test of each method's ability to distinguish the components. For these unknowns, the best errors in the Fourier and spectral domains were 1.20 and 1.85%, respectively. For assessment of the effect of protein, the analysis was repeated with varying amounts of albumin up to 36% by weight added to the mixtures. All of the full spectral methods (PCR and PLS in the spectral and Fourier domains) were able to compensate for the spectral interference of the added protein and produced results as good as those without the protein. For nucleotide mixtures, ultraviolet spectroscopy represents a rapid, economical, sensitive, and nondestructive alternative to existing techniques.
Inhibition of tobramycin diffusion by binding to alginate (1988)

[3H]tobramycin bound to sodium alginate and to exopolysaccharide prepared from two mucoid strains of Pseudomonas aeruginosa. Binding to sodium alginate was similar to binding to exopolysaccharide, both in the dependence on tobramycin concentration and in the maximum binding observed at saturation. Incorporation of sodium alginate into agar plates reduced the zone sizes of growth inhibition caused by tobramycin. The reductions in zone sizes were quantitatively accounted for by the binding of tobramycin to sodium alginate during diffusion of the antibiotic away from the well in which it had been placed at the start of the experiment. However, the binding of tobramycin to the exopolysaccharide of P. aeruginosa, and the resulting inhibition of diffusion of the antibiotic, did not significantly increase the penetration time of a spherical microcolony with a radius of 125 micron, such as might be found in the respiratory tract of a patient with cystic fibrosis (from a 90% penetration time of 12 s in the absence of exopolysaccharide to one of 35 s with an exopolysaccharide concentration of 1.0% [wt/vol]).
Fast, simultaneous, and sensitive detection of staphylococci (2003)

The rapid DNA isolation method used in conjunction with the optimised PCR makes it possible to confirm the presence or absence of extremely small numbers of bacteria. Using real time PCR would shorten the procedure even further. This method might therefore contribute to more timely and specific interventions.
Glutathione peroxidase in amyotrophic lateral sclerosis: the effects of selenium supplementation. (1998)

The activity of glutathione peroxidase (GSH-Px) as well as the activities of other antioxidative enzymes: CuZn superoxide dismutase (CuZn SOD), catalase (CAT), glutathione reductase (GR) in erythrocytes, as well as the activity of plasma glutathione transferase (GST), and the plasma content of vitamins E and C were evaluated in 35 sporadic amyotrophic lateral sclerosis (sALS) patients. The results revealed significantly decreased activity of both GSH-Px and CuZn SOD in sALS patients compared with the control. These data showed that a disturbed oxidative/antioxidative balance in sALS patients exists not only in motoneurons but also in the blood. The effect of exogenously administered selenium (Se), antioxidants, amino acids, a Ca2+ channel blocker such as nimodipine, and their combination in Alsamin was evaluated by screening parameter levels after 9 weeks of treatment. Only the use of all components together enhanced the activity of GSH-Px and the amount of vitamin E in sALS patients. Judging by the results of clinical trials, this treatment slowed the course of the disease.
Joint rate control with look-ahead for multi-program video coding (2000)

In this paper, we present a new joint rate control algorithm for a multi-program video compression system using MPEG-2 compatible video encoders. The proposed joint rate control is based on both the feedback and look-ahead approaches. It dynamically distributes the channel bandwidth among the program encoders according to the relative complexities of the programs using picture and coding statistics. As opposed to previous works in this area, our algorithm does not restrict the encoders to operate with identical group of pictures (GOP) structures, i.e. the GOP boundaries need not be synchronized among the different encoders. The proposed algorithm allows adaptive distribution of the channel bandwidth among the programs, even at the start of encoding. Furthermore, it assures quick reaction to scene changes, where a feedback approach requires an unavoidable delay. Experimental results show that the proposed joint rate control with look-ahead results in improved picture quality in comparison with a pure feedback approach.
B-Cell Lymphoma of Ampulla of Vater (1995)

Zhu, Liyin; Slee, Gregory R.; Domenico, Don R.; Mao, Chuanyan; Howard, John M. Author Information
Epithelial-Mesenchymal Transition in Pancreatic Cancer: A Review (2017)

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive solid malignancies and is characterized by its insensitivity to current therapy. The invasion and metastasis of solid tumors such as PDAC are complex processes involving many factors. Recent insights into the role of cancer stem cells (CSCs) and the epithelial-mesenchymal transition (EMT) in tumorigenesis have increased the knowledge base and highlighted new therapeutic targets of this disease. The process of EMT is regulated by a complex network of cytokines, transcription factors, growth factors, signaling pathways, and the tumor microenvironment, exhibiting CSC-like properties. The transition of solid cancer cells from an epithelial to a mesenchymal phenotype increases their migratory and invasive properties, thus promoting metastasis. In PDAC, the exact influence of EMT on the biological behaviors of cancer cells and its impact on clinical therapy remain controversial, but the therapeutic strategy of combining EMT inhibition with chemotherapy deserves attention. Alternatively, anti-inflammatory therapy that targets the interaction between inflammation and EMT is a valid strategy for treating the premalignant stage of tumor progression. In this review, we summarize the latest research on EMT and the potential relationship between EMT and PDAC.
Phosphorylation of Tau by Fyn: Implications for Alzheimer's Disease (2004)

The abnormal phosphorylation of tau protein on serines and threonines is a hallmark characteristic of the neurofibrillary tangles of Alzheimer's disease (AD). The discovery that tau could be phosphorylated on tyrosine and evidence that Abeta signal transduction involved tyrosine phosphorylation led us to question whether tyrosine phosphorylation of tau occurred during the neurodegenerative process. In this study we determined that human tau tyr18 was phosphorylated by the src family tyrosine kinase fyn. By developing both polyclonal and monoclonal probes specific for phospho-tyr18, we found that the phosphorylation of tau at tyr18 occurred at early developmental stages in mouse but was absent in the adult. Our phosphospecific probes also revealed that paired helical filament preparations exhibited phospho-tyr18 reactivity that was sensitive to phosphotyrosine-specific protein phosphatase treatment. Moreover, immunocytochemical studies indicated that tyrosine phosphorylated tau was present in the neurofibrillary tangles in AD brain. However, the staining pattern excluded neuropil threads and dystrophic neurites indicating that tyrosine phosphorylated tau was distributed in AD brain in a manner dissimilar from other abnormally phosphorylated tau. We also found evidence suggesting that differentially phosphorylated tau existed within degenerating neurons. Our data add new support for a role for fyn in the neurodegenerative process.
Design of useful peptide antigens. (1999)

Well-designed anti-peptide antibodies provide the specificity and control for everyday and cutting-edge applications. Pragmatic peptide antigen design principles can be used to help ensure production of successful antibodies. Issues of peptide chemistry, sequence selection, antigen preparation, antibody handling, and experimental needs must be taken into consideration in the planning stages.
Detection of NO2 down to ppb Levels Using Individual and Multiple In2O3 Nanowire Devices (2004)

We demonstrate detection of NO2 down to ppb levels using transistors based on both single and multiple In2O3 nanowires operating at room temperature. This represents orders-of-magnitude improvement over previously reported metal oxide film or nanowire/nanobelt sensors. A comparison between the single and multiple nanowire sensors reveals that the latter have numerous advantages in terms of great reliability, high sensitivity, and simplicity in fabrication. Furthermore, selective detection of NO2 can be readily achieved with multiple-nanowire sensors even with other common chemicals such as NH3, O2, CO, and H2 around.
Evaluation of plasma, erythrocytes, and brochoalveolar lavage fluid antioxidant defense system in sulfur mustard-injured patients (2010)

The data suggest that oxidative damage might have an important role for patients exposed to SM. SM may induce an oxidative stress response by depleting the antioxidant defense systems and increasing lipid peroxidation in lung cells.
Constrained component deployment in wide-area networks using AI planning techniques (2004)

Wide-area network applications are increasingly being built using component-based models, which enable integration of diverse functionality in modules distributed across the network. In such models, dynamic component selection and deployment enables an application to flexibly adapt to changing client and network characteristics, achieve load-balancing, and satisfy QoS requirements. Unfortunately, the problem of finding a valid component deployment is hard because one needs to decide on the set of components while satisfying various constraints resulting from application semantic requirements, network resource limitations, and interactions between the two. In this paper, we propose a general model for the component placement problem and present an algorithm for it, which is based on AI planning algorithms. We validate the effectiveness of our algorithm by demonstrating its scalability with respect to network size and number of components in the context of deployments generated for two example applications - a security-sensitive mail service, and a Webcast service - in a variety of network environments.
The Boolean Vector Machine [BVM] (1983)

We describe the architecture of a class of machines intended to solve computationally intensive problems much faster than can today's machines, at no increase in cost. We have investigated the programming of the BVM for several interesting algorithms on a BVM of 2 k bit positions per register. More theoretical study of implementations of such highly parallel algorithms is motivated.
Performance estimation of multistreamed, superscalar processors (1994)

Multistreamed processors can significantly improve processor throughput by allowing interleaved execution of instructions from multiple instruction streams. We present an analytical modeling technique to evaluate the effect of dynamically interleaving additional instruction streams within superscalar architectures. Using this technique, estimates of the instructions executed per cycle (IPC) for a processor architecture are quickly calculated given simple descriptions of the workload and hardware characteristics. To validate this technique, estimates of the SPEC89 benchmark suite obtained from the model are compared to results from a hardware simulator. Our results show that the technique produces accurate estimates with an average deviation of /spl sim/4% from the simulation results. Finally, we demonstrate that as the number of functional units increases, multistreaming is an effective technique to exploit these additional resources.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In vitro spontaneous osteoclastogenesis of human peripheral blood mononuclear cells is not crucially dependent on T lymphocytes (2009)

Abstract Objective In vitro spontaneous osteoclastogenesis from peripheral blood mononuclear cells (PBMCs) is increased in diseases with excessive bone loss. The purpose of this study was to reassess the role of T lymphocytes in this process. Methods Fresh or cryopreserved PBMCs obtained from healthy subjects and from patients with rheumatoid arthritis, psoriatic arthritis, and non‐psoriatic spondylarthritis were cultured at high density and stained for tartrate‐resistant acid phosphatase (TRAP). Resorption of mineralized matrix was assessed by a dentin disc assay. CD14+ monocytes and CD3+ T cells were selected using magnetically labeled antibodies. Results Numerous multinucleated, TRAP+, dentin‐resorbing osteoclasts developed spontaneously from fresh PBMCs from healthy individuals. This process was abrogated by T cell depletion and was restored by exogenous macrophage colony‐stimulating factor (M‐CSF) and RANKL, indicating the important role of T cells in spontaneous osteoclastogenesis in vitro. Using physiologic freezing and thawing as a model for the activation of PBMCs, spontaneous osteoclastogenesis was significantly increased in cryopreserved versus fresh cells. Under these conditions, spontaneous osteoclastogenesis was not dependent on T lymphocytes, since it was not influenced by T cell depletion and persisted in purified CD14+ cell cultures supplemented with M‐CSF and RANKL. In contrast to studies with fresh PBMCs, spontaneous osteoclastogenesis under these conditions did not appear to be clearly different between healthy subjects and patients with arthritis. Conclusion Spontaneous osteoclastogenesis in vitro is dependent on T lymphocytes or on the direct activation of monocytic cells, depending on the test conditions. This variability warrants better validation of the relevance of this functional test for in vivo osteoclastogenesis.
An update of N-acetylcysteine treatment for acute acetaminophen toxicity in children (2005)

Acetaminophen can lead to irreversible liver damage and even death in acute overdose. Outcome is related to the swiftness in which the antidote (N-acetylcysteine) is provided. In the United States, there are now available both the oral and intravenous forms of N-acetylcysteine, and pros and cons exist for each. With brisk and adequate treatment using either route, recovery can be complete, and liver function can be restored.
Nephron-Specific Disruption of Polycystin-1 Induces Cyclooxygenase-2–Mediated Blood Pressure Reduction Independent of Cystogenesis (2020)

These studies suggest that nephron polycystin-1 deficiency does not itself contribute to ADPKD hypertension and that it may, in fact, exert a relative salt-wasting effect. The work seems to comprise the first <i>in vivo</i> studies to describe a potential physiologic role for nephron polycystin-1 in the absence of cysts, tubule dilation, or enhanced cell proliferation.
Composition and Enzymatic Activity of the Extracellular Matrix Secreted by Germlings ofBotrytis cinerea (1999)

Germlings of Botrytis cinerea, an important fungal pathogen of plants, produce an extracellular matrix (ECM), or ensheathing film, that serves, in part, in their attachment (R. P. Doss, et al., Appl. Environ. Microbiol. 61:260-265, 1995). The composition of this film has been ascertained by using samples obtained by growing germlings on a glass surface, removing the fungal mycelium by vigorous washing, and collecting the tightly attached film by scraping the substratum with a razor blade. Slightly over half of the dry weight of the ECM was found to be carbohydrates (about 20%), proteins (about 28%), and lipids (about 6%). Hydrolysis of the carbohydrate portion of the ECM revealed that glucose was the most prominent monosaccharide present, comprising about 60% of the total monosaccharides. Also present were mannose (about 35%) and myo-inositol (about 5%). The proteinaceous fraction of the ECM was made up of a number of polypeptides separable by polyacrylamide gel electrophoresis. The lipid fraction of the ECM, analyzed by thin-layer chromatography, was made up of several simple lipid components, including free fatty acid, mono- and triacylglycerol, wax ester, fatty alcohol, and several unidentified components. No complex lipids were detected. Isolated ECM exhibited polygalacturonase and laccase activity and was able to catalyze the hydrolysis of p-nitrophenyl butyrate, a model substrate for assessing cutinase activity. Cellulase, pectin lyase, and pectin methyl esterase activities were noted with both heated and unheated ECM preparations. Proteinase activity was not detected.
Cellobiose Dehydrogenase – A Flavocytochrome from Wood-Degrading, Phytopathogenic and Saprotropic Fungi (2006)

Cellobiose dehydrogenase, the only currently known extracellular flavocytochrome, is formed not only by a number of wood-degrading but also by various phytopathogenic fungi. This inducible enzyme participates in early events of lignocellulose degradation, as investigated in several basidiomycete fungi at the transcriptional and translational level. However, its role in the ascomycete fungi is not yet obvious. Comprehensive sequence analysis of CDH-encoding genes and their translational products reveals significant sequence similarities along the entire sequences and also a common domain architecture. All known cellobiose dehydrogenases fall into two related subgroups. Class-I members are represented by sequences from basidiomycetes whereas class-II comprises longer, more complex sequences from ascomycete fungi. Cellobiose dehydrogenase is typically a monomeric protein consisting of two domains joined by a protease-sensitive linker region. Each larger (dehydrogenase) domain is flavin-associated while the smaller (cytochrome) domains are haem-binding. The latter shorter domains are unique sequence motifs for all currently known flavocytochromes. Each cytochrome domain of CDH can bind a single haem b as prosthetic group. The larger dehydrogenase domain belongs to the glucose-methanol-choline (GMC) oxidoreductase superfamily - a widespread flavoprotein evolutionary line. The larger domains can be further divided into a flavin-binding subdomain and a substrate-binding subdomain. In addition, the class-II (but not class-I) proteins can possess a short cellulose-binding module of type 1 at their C-termini. All the cellobiose dehydrogenases oxidise cellobiose, cellodextrins, and lactose to the corresponding lactones using a wide spectrum of different electron acceptors. Their flexible specificity serves as a base for the development of possible biotechnological applications.