gebhart/patrepeval huggingface dataset:
[Expression Analysis and Epigenetics of MicroRNA let-7b in Acute Lymphoblastic Leukemia]. (2015)

In the patients with ALL, the expression of microRNA let-7b is regulated by methylation of CpG islands in the region of genomic promoter. The microRNA let-7b may act as a tumor suppressor, whose low expression is involved in ALL development, indicating the microRNA let-7b may become a new therapeutic target for ALL.
Microwave stepped-index luneberg lenses (1958)

Since materials with a continuous variation of index of refraction were unavailable for the construction of spherical Luneberg lenses, an investigation was made of stepped-index lenses in which the desired continuous variation of index with radius was approximated by a number of constant-index spherical shells. Experimental data on two-dimensional, <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TE_{10}</tex> mode, stepped-index Luneberg lenses indicated that 10 shells were sufficient for 18-inch diameter lenses for use at <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X</tex> band. Expanded polystyrene materials, developed with dielectric constants ranging from 1.1 to 2.0 in increments of 0.1, were used to construct 10-step, 18-inch diameter, spherical Luneberg lenses. Performance data for these lenses are given at wavelengths of 3.2, 1.8, and 0.8 centimeters.
Interaction of Calcitonin Gene-Related Peptide, Nitric Oxide and Histamine Release in Neurogenic Blood Flow and Afferent Activation in The Rat Cranial Dura Mater (2007)

Calcitonin gene-related peptide (CGRP), nitric oxide (NO) and histamine are implicated in primary headaches but their role in vascular and nociceptive events in the dura mater is not well described. In an in vitro preparation of the hemisected rat skull, CGRP and histamine release from the cranial dura was measured using enzyme-linked immunoassays. While the NO donator NONO(ate) (10(-4) M) was without effect, CGRP (10(-5) M) induced considerable histamine release from the rat cranial dura, which was blocked by the CGRP receptor antagonist CGRP(8-37) (10(-5) M). Conversely, histamine (10(-4) M) did not stimulate CGRP release. In vitro recordings from single rat meningeal afferents showed that only one of 12 mechanically identified units but several mechanically insensitive units responded to histamine (up to 10(-5) M). Increases in meningeal blood flow after histamine application (10(-4) M) to the rat cranial dura remained unchanged during CGRP receptor blockade with CGRP(8-37), inhibition of NO synthesis with L-NAME (20 mg/kg i.v.) and H(3) receptor blockade with thioperamide (10(-4) M). We conclude that histamine produces direct vasodilatation and activates a subset of largely non-mechanically sensitive, non-CGRP containing afferents in the rat meninges. Histamine is released from meningeal mast cells which are stimulated by CGRP. Similar mechanisms may be involved in the pathogenesis of headaches.
The application of biofilm science to the study and control of chronic bacterial infections (2003)

Unequivocal direct observations have established that the bacteria that cause device-related and other chronic infections grow in matrix-enclosed biofilms. The diagnostic and therapeutic strategies that have served us so well in the partial eradication of acute epidemic bacterial diseases have not yielded accurate data or favorable outcomes when applied to these biofilm diseases. We discuss the potential benefits of the application of the new methods and concepts developed by biofilm science and engineering to the clinical management of infectious diseases.
Kinetic Isotope Effect Studies of the Reaction Catalyzed by Uracil DNA Glycosylase:  Evidence for an Oxocarbenium Ion−Uracil Anion Intermediate (2000)

The DNA repair enzyme uracil DNA glycosylase catalyzes the first step in the uracil base excision repair pathway, the hydrolytic cleavage of the N-glycosidic bond of deoxyuridine in DNA. Here we report kinetic isotope effect (KIE) measurements that have allowed the determination of the transition-state structure for this important reaction. The small primary (13)C KIE (=1.010 +/- 0.009) and the large secondary alpha-deuterium KIE (=1.201 +/- 0.021) indicate that (i) the glycosidic bond is essentially completely broken in the transition state and (ii) there is significant sp(2) character at the anomeric carbon. Large secondary beta-deuterium KIEs were observed when [2'R-(2)H] = 1.102 +/- 0.011 and [2'S-(2)H] = 1.106 +/- 0.010. The nearly equal and large magnitudes of the two stereospecific beta-deuterium KIEs indicate strong hyperconjugation between the elongated glycosidic bond and both of the C2'-H2' bonds. Geometric interpretation of these beta-deuterium KIEs indicates that the furanose ring adopts a mild 3'-exo sugar pucker in the transition state, as would be expected for maximal stabilization of an oxocarbenium ion. Taken together, these results strongly indicate that the reaction proceeds through a dissociative transition state, with complete dissociation of the uracil anion followed by addition of water. To our knowledge, this is the first transition-state structure determined for enzymatic cleavage of the glycosidic linkage in a pyrimidine deoxyribonucleotide.
Quantization index modulation: a class of provably good methods for digital watermarking and information embedding (2001)

We consider the problem of embedding one signal (e.g., a digital watermark), within another "host" signal to form a third, "composite" signal. The embedding is designed to achieve efficient tradeoffs among the three conflicting goals of maximizing the information-embedding rate, minimizing the distortion between the host signal and composite signal, and maximizing the robustness of the embedding. We introduce new classes of embedding methods, termed quantization index modulation (QIM) and distortion-compensated QIM (DC-QIM), and develop convenient realizations in the form of what we refer to as dither modulation. Using deterministic models to evaluate digital watermarking methods, we show that QIM is "provably good" against arbitrary bounded and fully informed attacks, which arise in several copyright applications, and in particular it achieves provably better rate distortion-robustness tradeoffs than currently popular spread-spectrum and low-bit(s) modulation methods. Furthermore, we show that for some important classes of probabilistic models, DC-QIM is optimal (capacity-achieving) and regular QIM is near-optimal. These include both additive white Gaussian noise (AWGN) channels, which may be good models for hybrid transmission applications such as digital audio broadcasting, and mean-square-error-constrained attack channels that model private-key watermarking applications.
Ultrafast Catalytic Alloy Nanomotors (2008)

Turbo nanomotors: A dramatic increase of the speed of fuel-driven nanowire motors is obtained using an Ag/Au alloy segment. These nanomotors offer speeds as high as 150 μm s−1 (75 body lengths per second), approaching those of the most efficient biomotors. The increase in the fuel decomposition rate associated with the electrochemical reactivity of Ag/Au alloys will enable the design of energy-efficient nanomotors.
Redox Hydrogel-Based Amperometric Bienzyme Electrodes for Fish Freshness Monitoring (2000)

This work presents the design and optimization of amperometric biosensors for the determination of biogenic amines (e.g., histamine, putrescine, cadaverine, tyramine, cystamine, agmatine, spermidine), commonly present in food products, and their application for monitoring of freshness in fish samples. The biosensors were used as the working electrodes of a three-electrode electrochemical cell of wall-jet type, operated at -50 mV vs Ag/AgCl, in a flow injection system. Two different bienzyme electrode designs were considered, one based on the two enzymes [a newly isolated and purified amine oxidase (AO) and horseradish peroxidase (HRP)] simply adsorbed onto graphite electrodes, and one when they were cross-linked to an Os-based redox polymer. The redox hydrogel-based biosensors showed better biosensors characteristics, i.e., sensitivity of 0.194 A M-1 cm-2 for putrescine and 0.073 A M-1 cm-2 for histamine, and detection limits (calculated as three times the signal-to-noise ratio) of 0.17 microM for putrescine and 0.33 microM for histamine. The optimized redox hydrogel-based biosensors were evaluated in terms of stability and selectivity, and were used for the determination of total amine content in fish samples kept for 10 days in different conditions.
An economic evaluation of the use of TNP on full-thickness wounds (2005)

This work was partly supported by the Plastic and Reconstructive Surgery Esser Foundation, and KCI Medical, Houten,The Netherlands. The authors have no conflicts of interest.
Antibodies to a conformational epitope on gp41 neutralize HIV-1 by destabilizing the Env spike (2015)

The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120-gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. By using biochemical, biophysical and computational methods, we map the previously unknown trimer epitopes of two related antibodies, 3BC315 and 3BC176. A cryo-EM reconstruction of a soluble Env trimer bound to 3BC315 Fab at 9.3 Å resolution reveals that the antibody binds between two gp41 protomers, and neutralizes the virus by accelerating trimer decay. In contrast, bnAb 35O22 binding to a partially overlapping quaternary epitope at the gp120-gp41 interface does not induce decay. A conserved gp41-proximal glycan at N88 was also shown to play a role in the binding kinetics of 3BC176 and 3BC315. Finally, our data suggest that the dynamic structure of the Env trimer influences exposure of bnAb epitopes.
Human placenta protein-tyrosine-phosphatase: amino acid sequence and relationship to a family of receptor-like proteins. (1989)

The amino acid sequence of the cytosolic human placenta protein-tyrosine-phosphatase 1B (PTPase 1B; protein-tyrosine-phosphate phosphohydrolase, EC 3.1.3.48) has been determined. It consists of a single chain of 321 residues with an N-acetylated N-terminal methionine and an unusually proline-rich C-terminal region. The enzyme is structurally related to the two cytoplasmic domains of both the leukocyte common antigen CD45 and LAR, a CD45-like molecule with an external segment that resembles a neural cell adhesion molecule. A low molecular weight protein encoded by a cDNA clone from T cells also shows extensive sequence similarities. The present study defines homologous domains common to this diverse family of PTPases that includes both soluble and receptor-like transmembrane forms. The cysteinyl residues 121 and 215 of PTPase 1B are conserved among all members of the family and are candidates for involvement in catalysis since PTPase 1B is inactivated by thiol modifying reagents. Two segments rich in positively charged residues (residues 33-47 and 227-238) may provide sites of interaction with inhibitory anionic polymers such as heparin or poly(Glu/Tyr).
Proteolytic Cleavage and Phosphorylation of a Tumor-associated ErbB4 Isoform Promote Ligand-independent Survival and Cancer Cell Growth (2005)

The ErbB1 and ErbB2 receptors are oncogenes with therapeutic significance in human cancer, whereas the transforming potential of the related ErbB4 receptor has remained controversial. Here, we have addressed whether four alternatively spliced ErbB4 isoforms differ in regulating cellular responses relevant for tumor growth. We show that the two tumor necrosis factor-alpha converting enzyme (TACE)-cleavable ErbB4 isoforms (the juxtamembrane [JM]-a isoforms) were overexpressed in a subset of primary human breast cancers together with TACE. The overexpression of the JM-a cytoplasmic (CYT)-2 ErbB4 isoform promoted ErbB4 phosphorylation, survival of interleukin-3-dependent cells, and proliferation of breast cancer cells even in the absence of ligand stimulation, whereas activation of the other three ErbB4 isoforms required ligand stimulation. Ligand-independent cellular responses to ErbB4 JM-a CYT-2 overexpression were regulated by both tyrosine kinase activity and a two-step proteolytic generation of an intracellular receptor fragment involving first a TACE-like proteinase, followed by gamma-secretase activity. These data suggest a novel transforming mechanism for the ErbB4 receptor in human breast cancer that is 1) specific for a single receptor isoform and 2) depends on proteinase cleavage and kinase activity but not ligand activation of the receptor.
Abstract 2430: Gastric cancer cell lines with c-Met gene amplification are sensitive to growth inhibition by the bivalent c-Met antibody LA480 (2010)

Abstract Gastric cancer is common in Asia, and advanced disease is typically incurable. Development of effective treatments for gastric cancer is thus a high priority to address this highly unmet clinical need. c-Met gene amplification resulting in c-Met overexpression and pathway activation has been highly linked to tumor progression and metastasis. It has been reported that approximately 10-20% of gastric tumors have increased copy numbers of the MET gene. c-Met- amplified gastric cancer cell lines that are dependent on an activated c-Met pathway for cell growth have been reported to be highly sensitive to growth inhibition by small molecule inhibitors of c-Met. We report that LA480, a humanized monoclonal antibody specific for c-Met, can directly inhibit HGF-independent in vitro cell proliferation of three c-Met- amplified Asian gastric cell lines (MKN45, SNU-5, and NUGC-4), in a dose-dependent manner. After 48 hours of treatment with LA480, 60-70% percent inhibition of 3H-thymidine incorporation was observed. For one of these gastric lines (NUGC-4), sensitivity to LA480 increases with continuous passage of the culture. This increased sensitivity to LA480 over time appears to be associated with increased expression of cell surface c-Met and increased constitutive phospho-Met expression. In addition to inhibiting proliferation of c-Met- amplified Asian gastric lines, LA480 also directly inhibited proliferation of a c-Met- amplified gastric cell line (Hs 746T) from a Caucasian patient. These data suggest that targeting c-Met amplification with LA480 may be a promising treatment for gastric cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2430.
Herbicides and plants (1993)

Summary Herbicide activity depends upon the inherent ability of the active ingredient (AI) to interact with the target enzyme(s) and the efficiency of its delivery at the target site(s). In this paper consideration is given to the factors which influence effective target site delivery and activity of foliage and soil-applied compounds. In the case of foliage- applied herbicides, the efficiency of retention and cuticle penetration is influenced by the stage and habit of growth of the plant, leaf age and surface characteristics, the molecular and formulation features of the AI, and the environmental conditions before, during, or after spraying. These factors may influence the efficiency of uptake, translocation and metabolism of AI en route to the target sites. The action of soil-applied compounds is influenced by the physico-chemical properties of the AI, its adsorption/desorption on the clay-humus colloidal complex, and the absorption, transport and metabolism en route to the target sites. In particular the water solubility of the AI, its formulation and the climate conditions subsequent to spraying, may influence selectivity and environmental fate. Finally, the ability of plants to acquire herbicide tolerance is considered in relation to both crop and weed with particular reference to the mechanisms which can be used to induce tolerance in crop plants.
Preservation of humidity and heat of respiratory gases in spontaneously breathing, tracheostomized patients (1998)

In spontaneously breathing, tracheostomized intensive care unit patients, the Trach-Vent heat and moisture exchanger and the Aerodyne heated system achieved satisfactorily preservation of heat and humidity of inspired gases.
Introduction to random signals and applied kalman filtering: with MATLAB exercises and solutions (1997)

Probability and Random Variables: A Review. Mathematical Description of Random Signals. Response of Linear Systems to Random Inputs. Wiener Filtering. The Discrete Kalman Filter, State-Space Modeling, and Simulation. Prediction, Applications, and More Basics on Discrete Kalman Filtering. The Continuous Kalman Filter. Smoothing. Linearization and Additional Intermediate-Level Topics on Applied Kalman Filtering. More on Modeling: Integration of Noninertial Measurements Into INS. The Global Positioning System: A Case Study. Appendices. Index.
Dynamic binary translation and optimization (2001)

We describe a VLIW architecture designed specifically as a target for dynamic compilation of an existing instruction set architecture. This design approach offers the simplicity and high performance of statically scheduled architectures, achieves compatibility with an established architecture, and makes use of dynamic adaptation. Thus, the original architecture is implemented using dynamic compilation, a process we refer to as DAISY (Dynamically Architected Instruction Set from Yorktown). The dynamic compiler exploits runtime profile information to optimize translations so as to extract instruction level parallelism. This paper reports different design trade-offs in the DAISY system and their impact on final system performance. The results show high degrees of instruction parallelism with reasonable translation overhead and memory usage.
Identification of cDNA clones encoding different domains of the basement membrane heparan sulfate proteoglycan. (1988)

We have used antibodies to the basement membrane proteoglycan to screen lambda gt11 expression vector libraries and have isolated two cDNA clones, termed BPG 5 and BPG 7, which encode different portions of the core protein of the heparan sulfate basement membrane proteoglycan. These clones hybridize to a single mRNA species of approximately 12 kilobases. Amino acid sequences obtained on peptides derived from protease digests of the core protein were found in the deduced sequence, confirming the identity of these clones. BPG 5 spanned 1986 base pairs and has an open reading frame of 662 amino acids. The amino acid sequence deduced from BPG 5 contains two cysteine-rich domains and two internally homologous domains lacking cysteine. The cysteine-rich domains show homology to the cysteine-rich domains of the laminin chains. A globule-rod structure, similar to that of the short arms of the laminin chains, is proposed for this region of the proteoglycan. The other clone, BPG 7, is 2193 base pairs long and has an open reading frame of 731 amino acids. The deduced sequence contains eight internal repeats with 2 cysteine residues in each repeat. These repeats show homology to the neural-cell adhesion molecule N-CAM and the plasma alpha 1B-glycoprotein. Looping structures similar to these proteins and to other proteins of the immunoglobulin gene superfamily are proposed for this region of the proteoglycan. The sequence DSGEY was found four times in this domain and could be heparan sulfate attachment sites.
Heparinase production by anaerobic bacteria. (1987)

The production of heparinase by a wide range of anaerobic bacteria isolated from clinical specimens was investigated. None of the 29 strains of Bacteroides fragilis produced heparinase. Of 62 other Bacteroides tested, only two of four strains of B ovatus, two of three strains of B thetaiotaomicron, and two of four strains of B uniformis were heparinase producers. None of the 48 strains of fusobacteria or seven strains of Veillonella produced heparinase. The anaerobic cocci (19 peptococci and seven peptostreptococci) were also negative for heparinase production as were 46 Clostridium spp tested. It was concluded that heparinase production by anaerobic bacteria was unlikely to play a part in the regional thrombophlebitis that sometimes occurs in anaerobic infections.
Adaptive Servo-Ventilation for Central Sleep Apnea in Systolic Heart Failure (2015)

Adaptive servo-ventilation had no significant effect on the primary end point in patients who had heart failure with reduced ejection fraction and predominantly central sleep apnea, but all-cause and cardiovascular mortality were both increased with this therapy. (Funded by ResMed and others; SERVE-HF ClinicalTrials.gov number, NCT00733343.).
Characterization of syngeneic antiidiotypic monoclonal antibodies to murine anti-human high molecular weight melanoma-associated antigen monoclonal antibodies. (1989)

Hybridization with murine myeloma cells P3-X63-Ag8.653 of splenocytes from BALB/c mice immunized with syngeneic anti-human high molecular weight melanoma-associated Ag (HMW-MAA) mAb 149.53, 225.28, 763.74, and TP41.2 has resulted in the formation of antiidiotypic antibody-secreting hybridomas with a frequency ranging between 1.2% and 5.2%. No marked difference was detected in the frequency of antibody secreting hybridomas in the fusions generated from mice immunized with the four anti-HMW-MAA mAb, suggesting that the idiotopes expressed by each of them display similar immunogenicity in a syngeneic combination. The number of antiidiotypic mAb that did not inhibit the binding of immunizing mAb to melanoma cells was higher than that of those that died, suggesting that idiotopes not associated with the Ag-combining site are more immunogenic than those that are. The idiotopes recognized by mAb were not detected on a large panel of anti-HLA Class I mAb, anti-HLA Class II mAb, and anti-human melanoma-associated Ag mAb. The latter included also mAb that cross-inhibit the immunizing anti-HMW-MAA mAb. The idiotopes recognized by mAb were not detected on the isolated H and L chain of the immunizing anti-HMW-MAA mAb. Cross-blocking experiments with a selected number of antiidiotypic mAb identified three distinct idiotopes on mAb 149.53, 225.28, and TP41.2 and two on mAb 763.74. Three, 5, 2, and 5 antiidiotypic mAb to idiotopes within the Ag-combining site of mAb 149.53, 225.28, 763.74, and TP41.2, respectively, were tested for their ability to induce anti-HMW-MAA antibodies. Serological and immunochemical assays detected anti-HMW-MAA antibodies only in sera from BALB/c mice immunized with mAb MK2-23. Therefore, mAb MK2-23 can be classified as beta, while the remaining 14 can be classified as gamma.
Video frame rate up conversion using region based motion compensation (2004)

Video frame rate conversion is often recognized as video temporal interpolation. In this paper, a region-based approach to automated video frame rate conversion is presented. The region extraction is performed by spatially dividing the reference video frames. Since this step involves image segmentation, the resulting regions are under or over segmented. Consistent frame to frame region extraction is key to region based motion compensation. We propose a novel inter- and intra-frame region merging technique to compensate for inconsistent frame segmentation problem. The video frame rate is then up converted using the motion compensation and region interpolation between every pair of matching regions. The deformation parameters of the match region pair are estimated based on a non-linear estimation model. Heuristic techniques are used to eliminate overlapped and uncovered areas in the generated frames. Experimental results are presented to evaluate its strength over the popular block matching algorithm (BMA).