gebhart/patrepeval huggingface dataset:
Seismic velocities in transversely isotropic media, II (1980)

Abstract P-wave, SV-wave, and SH-wave velocities are computed for transversely isotropic solids formed from two isotropic solids. The combinations are shale-sandstone and shale-limestone solids of an earlier paper (Levin, 1979), but one velocity of the nonshale component is allowed to vary over the range of Poisson's ratios sigma = 0 to sigma = 0.45, i.e., from a rigid solid to a near-liquid.When the S-wave velocity of either the sandstone or limestone is varied, the ratio of horizontal P-wave velocity to vertical P-wave velocity goes through a maximum as sigma increases and subsequently falls to values less than unity as sigma approaches 0.5. The P-wave velocity that would be found with a short surface spread also goes through a maximum and, at sigma = 0.5, is less than the P-wave velocity of either isotropic component. SV-wave velocities found for data from a short spread are unreasonably large; SH-wave velocities decrease monotonically as sigma increases, but the ratio of horizontal SH-wave velocity to vertical SH-wave velocity goes through a minimum of unity.
PocketPicker: analysis of ligand binding-sites with shape descriptors (2007)

The pocket prediction routine of PocketPicker is a useful tool for identification of potential protein binding-pockets. It produces a convenient representation of binding-site shapes including an intuitive description of their accessibility. The shape-descriptor for automated classification of binding-site geometries can be used as an additional tool complementing elaborate manual inspections.
LPCVD silicon-rich silicon nitride films for applications in micromechanics, studied with statistical experimental design* (1996)

A systematic investigation of the influence of the process parameters temperature, pressure, total gas flow, and SiH2Cl2:NH3 gas flow ratio on the residual stress, the refractive index, and its nonuniformity across a wafer, the growth rate, the film thickness nonuniformity across a wafer, and the Si/N incorporation ratio of low pressure chemical vapor deposition SixNy films has been performed. As a tool for complete characterization of the property-deposition parameter relations, a full factorial experimental design was used to determine the dominant process parameters and their interactions. From this study it could be concluded that, in decreasing order of importance, the gas flow ratio of Si and N containing precursors, temperature, and pressure are the most relevant parameters determining the mechanical and optical properties of the films and the deposition rate and nonuniformity in film properties across a wafer. The established relations between properties and deposition parameters were fitted with physical–chemical models, including a film growth model based on a Freundlich adsorption isotherm. The optimal deposition conditions for films to be used in micromechanical devices will be discussed.
Transient subversion of CD40 ligand function diminishes immune responses to adenovirus vectors in mouse liver and lung tissues (1996)

First-generation adenovirus vectors will have limited application in gene therapy for chronic diseases because of destructive host immune responses. Important immune effectors include CD8+ T cells, which mediate target cell destruction and ablate transgene expression, and B cells, which produce neutralizing antibodies that block effective readministration of vector. Previous studies indicated that activation of CD4+ T cells by virus capsid proteins is necessary for full realization of effector function of CD8+ T cells and B cells. In this paper, we present a strategy for preventing CD4+ T-cell activation by an adenovirus vector delivered to mouse liver and lung tissues which is based on interfering with T-cell priming via CD40 ligand-CD40 interactions. Adenovirus transgene expression was stabilized in mice genetically deficient in CD40 ligand (CD40L), and neutralizing antibody to adenovirus did not develop, allowing efficient readministration of vector. A transient blockade of T-cell activation with an antibody to CD40L infused into the animal at the time of adenovirus vector-mediated gene transfer led to stabilization of transgene expression and diminished production of neutralizing antibody, allowing readministration of vector. In vitro T-cell assays suggested that a block in the primary activation of CD4+ T cells was responsible for the lack of B-cell- and cytotoxic-T-cell-dependent responses. This suggests a strategy for improving the potential of adenovirus vectors based on administration of an antibody to CD40L at the time of vector administration.
Charging Damage During Plasma Enhanced SiN/SiO Thin Film Deposition (2006)

Abstract not Available.
New multiple access frame differential DS-UWB system (2005)

Non coherent differential systems for UWB transmission is a very attractive solution from a practical point of view. In this paper we propose a new multiple access frame differential direct sequence (DS) UWB system. We propose to use different number of frames for each user with the same bit period. Noise and multiaccess interference terms are significantly reduced. Receiver structure has a very low complexity. It's composed of a delay line, a multiplier, an integrator and a comparator to zero. In addition to that, acquisition time is periodic and integration window is fixed in the proposed scheme. Simulation results and theoretical expressions show a good performance in multiple access transmission
Direct Cytotoxicity of Polymorphonuclear Leukocyte Granule Proteins to Human Lung-derived Cells and Endothelial Cells (1990)

Neutrophils, in the course of defending the host against microbial invasion, release a potent arsenal of proteins that can potentially damage host tissues. Defensins are major peptides of human polymorphonuclear leukocyte (PMN) granules and are both broadly microbicidal and cytotoxic to several tumor cell lines. To determine whether these peptides could play a role in neutrophil-mediated lung injury, we examined the cytotoxicity of defensins and other PMN granule proteins in a chromium release assay with human lung-derived cell lines MRC-5 (lung fetal fibroblast), A549 (lung adenocarcinoma with features of alveolar epithelium), and primary cultures of human umbilical vein endothelial cells (HUVEC). Crude fractionation of an acid extract of human PMN granules yielded four fractions A-D. Only fraction D (containing mostly defensins) was significantly cytotoxic to all three target cells. In contrast, fraction A (containing myeloperoxidase and lactoferrin) and fraction C (containing lysozyme) had little effect, and fraction B (containing chiefly cathepsin G and elastase) was only injurious to endothelial cells. The cytotoxicity of whole PMN granule extracts on pulmonary epithelial and fibroblast targets could be completely accounted for by their defensin content. Fraction D- and defensin-mediated cytotoxicity was concentration dependent, required at least 10 to 12 h to become manifest, and was inhibited by serum. The role of these peptides in lung damage during acute and chronic inflammation deserves further study.
Batch fabricated sensors for magnetic force microscopy (1990)

In this letter we describe force sensors suitable for magnetic force microscopy (MFM) made by coating silicon microcantilevers with various thin magnetic films. These MFM force sensors can be batch fabricated and their magnetic properties tailored by choosing appropriate coatings. This is demonstrated by analyzing the MFM response for magnetization patterns written on a longitudinal recording test sample. Selectable components of the sample stray field can be measured by coating the tips with high coercivity films. Tips coated with low coercivity films such as Permalloy respond to the total stray field. Sample perturbations due to the tip stray field are small for thin-film tips, allowing the imaging of low coercivity samples such as Permalloy.
"Double-orifice" Technique To Repair Extensive Mitral Valve Excision Following Acute Endocarditis (1998)

Abstract The use of conservative surgical techniques to treat mitral valve regurgitation secondary to acute endocarditis is controversial. Reconstruction of the anterior leaflet may represent an additional challenge in such a setting. We report a case of mitral valve repair where extensive excision of the anterior leaflet and related chordae tendinea was necessary because of large vegetation secondary to acute endocarditis. The “double-orifice” technique was performed and allowed the salvage of the native valve. There was no recurrent infection at 6 months from surgery, with optimal hemodynamic results. (J Card Surg 7998; 73:24–26)
VJ REARRANGEMENTS OF THE TCRγ LOCUS IN PERIPHERAL T-CELL LYMPHOMAS: ANALYSIS BY POLYMERASE CHAIN REACTION AND DENATURING GRADIENT GEL ELECTROPHORESIS (1996)

Using Southern blotting for the diagnosis of clonality in peripheral T-cell lymphomas (PTCLs), analysis of the T-cell receptor (TCR) gamma gene rearrangement was shown to be more informative than that of the TCR beta gene rearrangement. In order to amplify every VJ gamma rearrangement, a polymerase chain reaction (PCR) procedure using newly designed GC-clamp primers has been developed. All primers can be mixed in a single multiplex PCR. PCR products are analysed by denaturing gradient gel electrophoresis (DGGE), providing tumour-specific imprints inasmuch as the procedure characterizes N sequence polymorphism at the VJ junctions. In a series of 30 PTCL cases, the PCR procedure demonstrated 27 cases to be clonally rearranged and failed in three cases. PCR was more accurate than Southern blotting, showing 47 rearranged gamma alleles, four of which were undetectable on the Southern blot. When lymphomas were studied at different sites and at relapse, the DGGE pattern remained unchanged. In PTCL, the proposed PCR is helpful for the diagnosis and staging of the disease and should improve the follow-up monitoring. The undetectability of clonal rearrangements in a few cases is discussed in the light of concepts of lymphomagenesis and T-cell differentiation.
Common Rail Injection System for Commercial Diesel Vehicles (1997)

&lt;div class="htmlview paragraph"&gt;Common Rail provides additional flexibility for the design and application of a diesel injection system.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Contrary to conventional injection systems pressure generation and injection are decoupled in the common rail system.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The injection pressure can be selected independent of engine speed and injected fuel quantity within certain limits.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The fuel combustion and the corresponding noise can be improved by increasing the fuel pressure up to 1400 bar and introducing pilot injection or multiple injection.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Furthermore the common rail system can replace conventional injection systems without requiring major engine modifications.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;BOSCH will provide this new injection system for the whole range of applications from light duty (30 kW per cylinder) to heavy duty vehicles (50 kW per cylinder).&lt;/div&gt;
DEQOR: a web-based tool for the design and quality control of siRNAs (2004)

RNA interference (RNAi) is a powerful tool for inhibiting the expression of a gene by mediating the degradation of the corresponding mRNA. The basis of this gene-specific inhibition is small, double-stranded RNAs (dsRNAs), also referred to as small interfering RNAs (siRNAs), that correspond in sequence to a part of the exon sequence of a silenced gene. The selection of siRNAs for a target gene is a crucial step in siRNA-mediated gene silencing. According to present knowledge, siRNAs must fulfill certain properties including sequence length, GC-content and nucleotide composition. Furthermore, the cross-silencing capability of dsRNAs for other genes must be evaluated. When designing siRNAs for chemical synthesis, most of these criteria are achievable by simple sequence analysis of target mRNAs, and the specificity can be evaluated by a single BLAST search against the transcriptome of the studied organism. A different method for raising siRNAs has, however, emerged which uses enzymatic digestion to hydrolyze long pieces of dsRNA into shorter molecules. These endoribonuclease-prepared siRNAs (esiRNAs or 'diced' RNAs) are less variable in their silencing capabilities and circumvent the laborious process of sequence selection for RNAi due to a broader range of products. Though powerful, this method might be more susceptible to cross-silencing genes other than the target itself. We have developed a web-based tool that facilitates the design and quality control of siRNAs for RNAi. The program, DEQOR, uses a scoring system based on state-of-the-art parameters for siRNA design to evaluate the inhibitory potency of siRNAs. DEQOR, therefore, can help to predict (i) regions in a gene that show high silencing capacity based on the base pair composition and (ii) siRNAs with high silencing potential for chemical synthesis. In addition, each siRNA arising from the input query is evaluated for possible cross-silencing activities by performing BLAST searches against the transcriptome or genome of a selected organism. DEQOR can therefore predict the probability that an mRNA fragment will cross-react with other genes in the cell and helps researchers to design experiments to test the specificity of esiRNAs or chemically designed siRNAs. DEQOR is freely available at http://cluster-1.mpi-cbg.de/Deqor/deqor.html.
Multimodal Strategies for Resuscitating Injured Cells (2006)

Our cells and tissues are challenged constantly by exposure to extreme conditions that cause acute and chronic stress. Wounding at the cellular level is a common event, and results from cell exposure to supra-physiologic forces, or is the consequence of action by reactive chemical agents. An individual cellular wound results from either the alteration of protein or DNA structure, or the disruption of molecular assemblies, the most important of which is the cell's membranes. Tissue healing at the macroscopic level is a complex and coordinated process involving many different cell types while, in contrast, the wounds of individual cells heal primarily via biomolecular interactions. Like tissue wound healing, cellular wound healing involves the upregulation or acceleration of processes that are constitutively expressed in routine physiologic repair of cellular structures In addition, recent advances have been made in the identification of pharmaceutical strategies to aid the cellular repair response. Many of these strategies offer promise for augmenting the already present cellular repair mechanisms.
El uso de las etiquetas de identificación por radiofrecuencia en las empresas: ¿un nuevo riesgo para los derechos de los trabajadores? (2010)

Las etiquetas RED permiten controlar al trabajador durante la jornada y fuera de ella, almacenar datos personales, elaborar un �perfil productivo� a traves del seguimiento de las tareas, conocer los habitos personales y medicos de los trabajadores, etc.. De ahi la valoracion critica de los riesgos que comportan para los derechos fundamentales implicados: intimidad, proteccion de datos, libertad sindical, etc..
Dynamic three-dimensional reconstruction of ICUS images based on an ECG-gated pull-back device (2002)

Most systems used for three-dimensional (3-D) of two-dimensional intracoronary ultrasound (ICUS) images are based on an image acquisition with a pull-back device which withdraws the catheter with a constant speed, nor taking account of cardiac motion and coronary dynamics/pulsation. Cyclic changes of the vessel dimensions and the movement of the catheter inside the vessel result in artifacts and inaccuracies of quantitative measurements. This phenomenon limits accuracy and resolution when an attempt of 3-D reconstruction is performed, since images obtained in different phases of the cardiac cycle are compiled. To overcome these limitations the authors developed a custom-designed pull-back device driven by a stepping motor, which is controlled by a steering logic ensuring an ECG-gated image acquisition.
NON-RIGID SPECTRAL CORRESPONDENCE OF TRIANGLE MESHES (2007)

We present an algorithm for finding a meaningful vertex-to-vertex correspondence between two triangle meshes, which is designed to handle general non-rigid transformations. Our algorithm operates on embeddings of the two shapes in the spectral domain so as to normalize them with respect to uniform scaling and rigid-body transformation. Invari-ance to shape bending is achieved by relying on approximate geodesic point proximities on a mesh to capture its shape. To deal with moderate stretching, we first raise the issue of “eigenmode switching” and discuss heuristics to bring the eigenmodes to alignment. For additional non-rigid discrepancies in the spectral embeddings, we propose to use non-rigid alignment via thin-plate splines. This is combined with a refinement step based on geodesic proximities to improve dense correspondence. We show empirically that our algorithm outperforms previous spectral methods, as well as schemes that compute correspondence in the spatial domain via non-rigid iterative closest points or the use of local shape descriptors, e.g., 3D shape context. Finally, to speed up our algorithm, we examine the effect of using subsampling and Nyström method.
Pericardial tamponade in systemic sclerosis (scleroderma). (1979)

The frequency of pericardial disease in scleroderma found at necropsy in high. The clinical recognition of pericarditis with or without effusion is rare and tamponade with haemodynamic impairment is exceptional. Three patients with scleroderma presented with an acute syndrome of dyspnoea, chest pain, and cardiomegaly requiring pericardiocentesis for relief of pericardial tamponade. One patient died. The mechanism of the pericardial effusion remains unknown. The haemodynamic data recorded from one patient suggested that pericardial fibrosis in scleroderma may predispose to pericardial tamponade.
Direct calculation of electron density in density-functional theory: Implementation for benzene and a tetrapeptide (1991)

A recently developed approach for the direct calculation of electron density is implemented for polyatomic molecules: benzene and a tetrapeptide with four glycine residues. The method uses the density as the basic variable, divides a system into subsystems, and determines the density for each subsystem. It is found that the method is capable of describing the electronic structure with accuracy comparable to the Kohn-Sham method. This substantiates the hope for ab initio calculations of large systems beyond the reach of conventional methods.
Qdot Nanobarcodes for Multiplexed Gene Expression Analysis (2006)

We report a quantum dot (Qdot) nanobarcode-based microbead random array platform for accurate and reproducible gene expression profiling in a high-throughput and multiplexed format. Four different sizes of Qdots, with emissions at 525, 545, 565, and 585 nm are mixed with a polymer and coated onto the 8-mum-diameter magnetic microbeads to generate a nanobarcoded bead termed as QBeads. Twelve intensity levels for each of the four colors were used. Gene-specific oligonucleotide probes are conjugated to the surface of each spectrally nanobarcoded bead to create a multiplexed panel, and biotinylated cRNAs are generated from sample total RNA and hybridized to the gene probes on the microbeads. A fifth streptavidin Qdot (655 nm or infrared Qdot) binds to biotin on the cRNA, acting as a quantification reporter. Target identity was decoded based on spectral profile and intensity ratios of the four coding Qdots (525, 545, 565, and 585 nm). The intensity of the 655 nm Qdot reflects the level of biotinylated cRNA captured on the beads and provides the quantification for the corresponding target gene. The system shows a sensitivity of < or =10(4) target molecules detectable with T7 amplification, a level that is better than the 10(5) number achievable with a high-density microarray system, and approaching the 10(3)-10(4) level usually observed for quantitative PCR (qPCR). The QBead nanobarcode system has a dynamic range of 3.5 logs, better than the 2-3 logs observed on various microarray platforms. The hybridization reaction is performed in liquid phase and completed in 1-2 hours, at least 1 order of magnitude faster than microarray-based hybridizations. Detectable fold change is lower than 1.4-fold, showing high precision even at close to single copy per cell level. Reproducibility for this proof-of-concept study approaches that of Affymetrix GeneChip microarray, with an R(2) value between two repeats at 0.984, and interwell CV around 5%. In addition, it provides increased flexibility, convenience, and cost-effectiveness in comparison to conventional gene expression profiling methods.
Chronic graft dysfunction in renal transplant patients1 (2002)

We conclude that PAI-1, whose secretion is determined in large part by metabolic and inflammatory factors, may be implicated in the rate of decline in renal function after transplantation.
The human urokinase-plasminogen activator gene and its promoter (1985)

The urokinase type of plasminogen activator (uPA) is subject to regulation by hormones, phorbol esters and oncogenic transformation. This enzyme has been suggested to play a key role in processes involving cell migration and tissue remodeling, and to be essential for tumor metastasis. In order to study these processes, we have isolated the human uPA gene, and have determined its entire nucleotide sequence. The gene is organized in 11 exons and is 6.4 kb long. The 5' end of uPA mRNA has been determined by both S1 mapping and primer extension experiments. A fragment of 800 bp containing the entire 5' flanking region shows promoter activity when introduced upstream of a bacterial chloramphenicol acetyltransferase gene and introduced into human cells. The hexanucleotide sequence GGCGGG, previously found at similar regions in several viral and eukaryotic promoters and shown to be essential for promoter activity (McKnight et al. (1984) Cell, 37, 253-262), is repeated three times between the CAAT and the TATA boxes.
Empirical investigation of closed-loop control of extensible continuum manipulators (2014)

This paper details closed-loop control experiments that were conducted on an extensible continuum manipulator, the OctArm. The performance of three controllers are shown here. The controllers can be classified into two categories: Closed-loop configuration-space control and closed-loop task-space teleoperation. Two controllers were tested in the configuration-space control experiments: a proportional-derivative (PD) controller and a nonlinear sliding-mode controller. The third controller is also shown in which the redundant extensible continuum manipulator tip tracks the motion of a kinematically-dissimilar non-redundant rigid-link master system. The results of these experiments confirm the ability of the control strategies to effectively control continuum robot hardware.