gebhart/patrepeval huggingface dataset:
pH-Dependent Behavior of Surface-immobilized Artificial Leucine Zipper Proteins (2004)

The coiled-coil protein motif occurs in over 200 proteins and has generated interest for a range of applications requiring surface immobilization of the constituent peptides. This paper describes an investigation of the environment-responsive behavior of a monolayer of surface-immobilized artificial proteins, which are known to assemble to form coiled-coil structures in bulk solution. An extended version of the quartz crystal microbalance (QCM-D) and surface plasmon resonance (SPR) are independently employed to characterize the adsorption of the proteins to a gold surface. The data suggest that the molecules arrange in a closely packed layer orientated perpendicular to the surface. QCM-D measurements are also employed to measure pH-induced changes in the resonant frequency (f) and the energy dissipation factor (D) of a gold-coated quartz crystal functionalized with the formed monolayer. Exposure of the protein monolayer to a pH 4.5 solution results in a shift of 43 Hz in f and a shift of -0.7 x 10(-6) in D as compared to pH 7.4. In contrast, increasing the pH to 11.2, results in f and D shifts of -17 Hz and 0.6 x 10(-6), respectively. The magnitude of the observed shifts suggests that the proteins form a rigid layer at low pH that can be hydrated to a fluid layer as the pH is increased. These observations correlate with spectroscopic changes that indicate a reduction in the helical content of the protein in bulk solutions of high pH.
Pyrroles and related compounds. Part XVI. Synthesis of protoporphyrin-IX by the a- and b-oxobilane routes (1971)

2-Ethyl-2-devinylprotoporphyrin-IX dimethyl ester has been synthesised by the a-oxobilane route, the 4-vinyl group being introduced by a new method, viz. transformation of a β-acetoxyethyl side-chain present in one of the intermediate pyrroles. Protoporphyrin-IX dimethyl ester has also been prepared by both the a- and b-oxobilane routes, again with β-acetoxyethyl groups as precursors of the two vinyl groups in the porphyrin. The use of a pentachlorophenyl pyrromethane ester in the a-oxobilane synthesis and of a t-butyl pyrromethane ester in the b-oxobilane route enables these syntheses to be carried out in an entirely rational fashion without involving symmetrical intermediates, because the nuclear pentachlorophenyl ester can be selectivety cleaved by mild alkaline hydrolysis, and the nuclear t-butyl ester by trifluoroacetic acid in the presence of nuclear benzyl esters. The intermediate oxophlorin formed in the b-oxobilane route undergoes exchange with tritium at the meso-position opposite the oxo-group, and thus the oxo-function facilitates the synthesis of δ-meso-tritiated protoporphyrin-IX required for biosynthetic experiments in the chlorophyll field. Attempts to prepare the 2,4-divinyl-β-oxophlorin were frustrated by preferential formation of a cyclic ether from the 4-substituent and the β-oxygen atom.
Application of a six-port network to a near-field antenna measurement system (1985)

The configuration and calibration of a six-port network analyser for application in near-field antenna measurements is described. The suitability of the new measurement system is illustrated by experimental results.
Minocycline prevents dynorphin-induced neurotoxicity during neuropathic pain in rats (2014)

Despite many advances, our understanding of the involvement of prodynorphin systems in the development of neuropathic pain is not fully understood. Recent studies suggest an important role of neuro-glial interactions in the dynorphin effects associated with neuropathic pain conditions. Our studies show that minocycline reduced prodynorphin mRNA levels that were previously elevated in the spinal and/or dorsal root ganglia (DRG) following sciatic nerve injury. The repeated intrathecal administration of minocycline enhanced the analgesic effects of low-dose dynorphin (0.15 nmol) and U50,488H (25-100 nmol) and prevented the development of flaccid paralysis following high-dose dynorphin administration (15 nmol), suggesting a neuroprotective effect. Minocycline reverts the expression of IL-1β and IL-6 mRNA within the spinal cord and IL-1β mRNA in DRG, which was elevated following intrathecal administration of dynorphin (15 nmol). These results suggest an important role of these proinflammatory cytokines in the development of the neurotoxic effects of dynorphin. Similar to minocycline, a selective inhibitor of MMP-9 (MMP-9 levels are reduced by minocycline) exerts an analgesic effect in behavioral studies, and its administration prevents the occurrence of flaccid paralysis caused by high-dose dynorphin administration (15 nmol). In conclusion, our results underline the importance of neuro-glial interactions as evidenced by the involvement of IL-1β and IL-6 and the minocycline effect in dynorphin-induced toxicity, which suggests that drugs that alter the prodynorphin system could be used to better control neuropathic pain.
Coronary Artery Bypass in Asian Patients (1993)

Coronary artery disease in Asians deserves far more attention than it has received in the literature to date. Most of the available reports focus on immigrants from the Indian subcontinent. These immigrants have a significantly higher risk of coronary artery disease than either their compatriots who do not emigrate or the indigenous population of their adopted countries. This finding cannot be explained on the basis of standard coronary risk factors. There is a general clinical impression that Asians of all nationalities have smaller coronary arteries and more diffuse coronary disease than other ethnic groups; therefore, they are less suitable candidates for conventional bypass grafting. This impression remains a source of controversy. Our experience at the Texas Heart Institute indicates that, after coronary bypass surgery, early and long-term results in Asians are as satisfactory as in other ethnic groups. However, much more research is needed to explain the many paradoxical aspects of coronary disease in Asian patients.
RAPD markers for genetic differentiation of species within <i>Polytrichum</i> (<i>Pofytrichaceae, Musci</i>): a preliminary survey (2000)

Summary Zouhair, R., Corradini, P., Defontaine A. & Hallet, J. N.: RAPD markers for genetic differentiation of species within Polytrichum ( Polytrichaceae, Musci ): a preliminary survey – Taxon 49: 217–229. 2000. – ISSN 0040‐0262. A combination of morphological data and RAPD markers were analysed using thirty colonies from Brittany (France) in six taxa of Polytrichum: P. commune, P. c. var. perigoniale, P. formosum, P. juniperinum, P. piliferum, and P. strictum. Ten primers selected for the RAPD study produced 166 polymorphic markers useful for cluster analysis. The Jaccard index of similarity was high within and among taxa and varied from 0.56 between P. commune and P. formosum to 0.89 between P. formosum and P. juniperinum. For the morphological study, shape of terminal cells of the green lamellae covering the upper surface of leaves allowed differentiation of taxa. In P. commune var. perigoniale these cells were narrower and less deeply notched than in P. commune. The diameter of leaves was scored for many individuals of the six taxa and revealed a sexual dimorphism for size. Female plants have a significantly larger leaf rosette diameter than male plants. Morphological results are largely consistent with RAPD data. However, the high level of genetic differences of P. c. var. perigoniale and P. strictum with other taxa demonstrates the potential of molecular and genetic data in phylogenetic analysis among closely related taxa. The cluster analysis divides the taxa into two groups: (1) P. commune, P. formosum and P. c. var. perigoniale; and (2) P. juniperinum, P. piliferum, and P. strictum. The results do not support splitting the genus into Polytrichum and Polytrichastrum nor the possibility of hybrid origin of P. c. var. perigoniale between P. commune and P. formosum.
Antibody dependent cellular cytotoxicity activity of a novel anti-PD-L1 antibody, avelumab (MSB0010718C), on human tumor cells. (2015)

3038 Background: The programmed death-1 receptor (PD-1) and its ligand (PD-L1) are key therapeutic targets in the reactivation of the immune response against multiple cancers. Avelumab (MSB0010718C) is a fully human anti-PD-L1 IgG1 antibody currently being investigated in clinical trials. In addition to disruption of immune suppressive signaling induced by the binding of PD-L1 on tumor cells with PD-1 on tumor infiltrating immune cells, avelumab was designed to mediate antibody dependent cellular cytotoxicity (ADCC). Other anti-PD-1/anti-PD-L1 monoclonal antibodies (mAbs) undergoing clinical evaluation are either of the IgG1 isotype and modified to remove ADCC activity or of the IgG4 isotype, which does not mediate ADCC. We present data from preclinical studies examining the ability of avelumab to induce ADCC and factors affecting tumor cell sensitivity to this mechanism. Methods: The ability of avelumab to induce lysis of human carcinoma cells was assessed using whole peripheral blood mononuclear cells (PBMCs) or purified natural killer (NK) cells as effectors. PD-L1 expression was reported as % positive tumor cells and mean fluorescence intensity (MFI) as determined by flow cytometry. Results: Using PBMCs as effectors, avelumab induced ADCC in 8/18 human carcinoma cell lines; tumor cell lysis positively correlated with the percentage of PD-L1 positive tumor cells and PD-L1 MFI. Lysis was increased when NK cells were used as effectors. Pretreating tumor cell lines with IFN-γ increased PD-L1 expression, but augmented lysis in only 4/10 cell lines. Preactivating NK cells with IL-12, however, increased lysis, suggesting a potential for synergy by combining avelumab with IL-12–based therapy. Little or no lysis was observed in NK-mediated ADCC assays vs whole PBMCs or dendritic cells isolated from PBMCs. A tumor cell line insensitive to lysis by CD8+T cells was lysed by ADCC using NK cells and avelumab. Conclusions: Avelumab induced lysis of many human tumor cell lines via ADCC. Further clinical trials are necessary to determine whether the additional mechanism of inducing tumor lysis by ADCC will result in enhanced clinical activity compared with similar agents without ADCC activity.
A New Chemical Approach to Human ABO Histo-Blood Group Type 2 Antigens (2013)

A new chemical approach to synthesizing human ABO histo-blood type 2 antigenic determinants was developed. N-Phthaloyl-protected lactosaminyl thioglycoside derived from lactulose via the Heyns rearrangement was employed to obtain a type 2 core disaccharide. Use of this scheme lowered the overall number of reaction steps. Stereoselective construction of the α-galactosaminide/galactoside found in A- and B-antigens, respectively, was achieved by using a unique di-tert-butylsilylene-directed α-glycosylation method. The proposed synthetic scheme provides an alternative to existing procedures for preparing ABO blood group antigens.
Design and implementation of a new sliding-mode observer for speed-sensorless control of induction machine (2002)

In this letter, a new sliding-mode-sensorless control algorithm is proposed for the field-oriented induction machine drive. In the proposed algorithm, the terms containing flux, speed, and rotor time constant, which are common in both current and flux equations, in the current model of the induction machine are estimated by a sliding function. The flux and speed estimation accuracy is guaranteed when the error between the actual current and observed current converges to zero. Hence, the fourth-order system is reduced to two second-order systems, and the speed estimation becomes very simple and robust to the parameter uncertainties. The new approach is verified by simulation and experimental results.
Peak Capacity Optimization of Peptide Separations in Reversed-Phase Gradient Elution Chromatography:  Fixed Column Format (2006)

The optimization of peak capacity in gradient elution RPLC is essential for the separation of multicomponent samples such as those encountered in proteomic research. In this work, we study the effect of gradient time (tG), flow rate (F), temperature (T), and final eluent strength (phi(final)) on the peak capacity of separations of peptides that are representative of the range in peptides found in a tryptic digest. We find that there are very strong interactions between the individual variables (e.g., flow rate and gradient time) which make the optimization quite complicated. On a given column, one should first set the gradient time to the longest tolerable and then set the temperature to the highest achievable with the instrument. Next, the flow rate should be optimized using a reasonable but arbitrary value of phi(final). Last, the final eluent strength should be adjusted so that the last solute elutes as close as possible to the gradient time. We also develop an easily implemented, highly efficient, and effective Monte Carlo search strategy to simultaneously optimize all the variables. We find that gradient steepness is an important parameter that influences peak capacity and an optimum range of gradient steepness exists in which the peak capacity is maximized.
Poisson–Boltzmann for oppositely charged bodies: an explicit derivation (2009)

The interaction between two parallel charged plates in ionic solution is a general starting point for studying colloidal complexes. An intuitive expression of the pressure exerted on the plates is usually proposed, which includes an electrostatic plus an osmotic contribution. We present here an explicit and self-consistent derivation of this formula in the only framework of the Poisson–Boltzmann (PB) theory. We also show that, depending on external constraints, the correct thermodynamic potential can differ from the usual PB free energy. For asymmetric, oppositely charged plates, the resulting expression predicts a non-trivial equilibrium position with the plates separated by a finite distance. The depth of this energy minimum is decisive for the stability of the complex. It is therefore crucial to obtain its explicit dependence on the charge densities of the plates and on the ion concentration. Analytic expressions for the position and depth of the energy minimum were derived in 1975 by Ohshima [Colloid Polym. Sci. 253, 150 (1975)] but, surprisingly, these important results seem to have been overlooked. We retrieve these expressions in a simpler formalism, more familiar to the physics community, and give a physical interpretation of the observed behavior.
Analysis of the Polycystins in Aortic Vascular Smooth Muscle Cells (2003)

The leading cause of death in autosomal dominant polycystic kidney disease (ADPKD) is cardiovascular. However, little is known about the pathogenesis of these manifestations. The present study was undertaken to characterize the ADPKD proteins, the polycystins, in vascular smooth muscle cells. It was demonstrated that the expression of polycystin-1 is developmentally regulated, whereas polycystin-2 has a more constant level of expression. A polycystin-1 subpopulation was immunoprecipitated by polycystin-2, indicating an in vivo interaction of these two proteins. Analysis with glycosidase and cell surface biotinylation indicates that some polycystin-1 products, but not polycystin-2, are located on the plasma membrane. Immunofluorescence showed that most of the polycystin-1 and polycystin-2 was cytoplasmic but that persistent polycystin-1 staining was located in proximity to the cell surface after a Triton-X extraction, whereas no clear surface localization of polycystin-2 was detected. Immuno-gold electron microscopy revealed that polycystin-1 was localized at the plasma membrane and sarcoplasmic reticulum, whereas polycystin-2 was mainly located in the sarcoplasmic reticulum. Both polycystins were found to be associated with dense plaques. These observations are consistent with an important role of the polycystins in the development, maintenance, and function of the myoelastic arterial organization and with the vascular phenotype associated with ADPKD.
Cover Image (2018)

The cover image, by John Hamilton et al., is based on the Research Article Roux-en-Y gastric bypass surgery normalizes dopamine D1, D2, and DAT levels, DOI: 10.1002/syn.22058
Damage tolerance of Symmetric Buffer Strip Laminates (1992)

The feasibility of using buffer strips for improving the notched strength and crack arrest capability with several combinations of main panel and buffer strip materials is investigated. The results show that a proper selection of main panel and buffer strip material ensures crack arrest and improved notch strength.
Random pattern testability of the open defect detection method using application of time-variable electric field (2003)

In this paper, random pattern testability of the open defect defection method is discussed. In the test method, time-variable electric field is applied from the outside of ICs so as to vary the voltage at floating nodes caused by a defect. To detect opens the excessive supply current caused by the applied electric field is measured. The test pattern requirements for detecting opens are shown. The fault coverage for open defects is calculated for benchmark circuits. The experimental results shows random pattern can be effectively utilized for the test method even if it cannot attain high fault coverage for stuck-at-faults.
Intelligent linguistic architectures : variations on themes by Ronald M. Kaplan (2006)

Ronald M. Kaplan has made foundational contributions to the development of computational linguistic research and linguistic theory, particularly within Lexical-Functional Grammar. Intelligent Linguistic Architectures, a tribute to Kaplan's cutting-edge work, collects computational and theoretical linguistics papers in his research areas. From machine translation to grammar engineering, from formal issues to semantic theory, this ambitious volume represents the newest developments in linguistic scholarship.
Approximate Nearest Subspace Search with Applications to Pattern Recognition (2007)

Linear and affine subspaces are commonly used to describe appearance of objects under different lighting, viewpoint, articulation, and identity. A natural problem arising from their use is - given a query image portion represented as a point in some high dimensional space - find a subspace near to the query. This paper presents an efficient solution to the approximate nearest subspace problem for both linear and affine subspaces. Our method is based on a simple reduction to the problem of nearest point search, and can thus employ tree based search or locality sensitive hashing to find a near subspace. Further speedup may be achieved by using random projections to lower the dimensionality of the problem. We provide theoretical proofs of correctness and error bounds of our construction and demonstrate its capabilities on synthetic and real data. Our experiments demonstrate that an approximate nearest subspace can be located significantly faster than the exact nearest subspace, while at the same time it can find better matches compared to a similar search on points, in the presence of variations due to viewpoint, lighting etc.
Transseptal Stent Treatment of Anastomotic Stricture after Repair of Partial Anomalous Pulmonary Venous Return (2003)

Purpose: To report the endovascular treatment of a stenosis of the pulmonary venous anastomosis following surgical treatment for partial anomalous pulmonary venous return. Case Report: A 60-year-old man presented with recurrent pleural effusions after correction of a partial anomalous left pulmonary venous return. Magnetic resonance imaging demonstrated focal stenosis at the anastomosis of the anomalous pulmonary vein to the left atrial appendage. Using a transseptal approach, the pulmonary vein stenosis was accessed and successfully stented. The patient's symptoms improved, and follow-up imaging demonstrated a patent stent without residual pressure gradient. Conclusions: Endovascular repair of a stenosis at the anastomosis of an anomalous pulmonary vein is possible and should be considered as a treatment option for this lesion.
Tb<sub>4</sub>FeGe<sub>8</sub> Grown in Liquid Gallium: trans‐cis Chains from the Distortion of a Planar Ge Square Net. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
ACETABULAR SHELL DEFORMATION AS A FUNCTION OF STIFFNESS AND BONE STRENGTH (2016)

INTRODUCTION Deformation of modular acetabular press-fit shells is of much interest for surgeons and manufacturers. Initial fixation is achieved through press-fit between shell and acetabulum with the shell mechanically deforming upon insertion. Shell deformation may disrupt the assembly process of modular systems and may adversely affect integrity and durability of the components and tribology of the bearing. The aim of the study was to show shell deformation as a function of bone and shell stiffness. METHODS The stiffness of the generic shells was determined using a uniaxial/ two point loading frame by applying different loads, and the change in dimension was measured by a coordinate measurement machine (CMM). Cadaver lab deformation measurements were done before and after insertion for 32 shells with 2 wall thicknesses and 11 shell sizes using the ATOS Triple Scan III (ATOS) optical system previously validated as a suitable measurement system to perform those measurements. Multiple deformation measurements per cadaver were performed by using both hip sides and stepwise increasing the reamed acetabulum by at least 1 mm, depending on sufficient residual bone stock. The under-reaming was varied between 0mm and 1mm, respectively. From the deformations, the resulting forces on the shells and bone stiffness were calculated assuming force equilibrium as well as linear-elastic material behaviour in each point at the rim of the shell. RESULTS Radial stiffness for shells with 3 mm wall thickness ranged between 6257 N/mm and 2920 N/mm, with 4 mm wall thickness it ranged between 14341 N/mm and 6875 N/mm. The radial shell deformation ranged between 3 µm and 187 µm. The resulting maximum radial forces acting on the shells ranged between 26 N and 916 N. From these values, bone stiffness [N/mm] at the point of the maximum deformation has been calculated. Adding the bone stiffness and the shell stiffness using the equation for serial springs, one obtains a positive correlation between total stiffness and maximum deformation. DISCUSSION The measured deformation values are within the same order of magnitude previously published [Lin 2006, Squire 2006]. The large variations of resulting maximum forces exhibit the need to further investigate shell deformation using commercial shell systems. The calculated bone stiffness at the point of the maximum deformation seems to be a valid predictor for expected shell deformation, but this also needs more data. A future goal is to determine expected shell deformation from bone data as a design rational.
Vehicle/arm coordination and multiple mobile manipulator decentralized cooperation (2002)

Mobile manipulation capabilities are key to many new applications of robotics in space, underwater construction, and service environments. This article discusses the ongoing effort at Stanford University for the development of multiple mobile manipulation systems and presents the basic models and methodologies for their analysis and control. This work builds on four methodologies we have previously developed for fixed-base manipulation: the operational space formulation for task-oriented robot motion and force control; the dextrous dynamic coordination of macro/mini structures for increased mechanical bandwidth of robot systems; the augmented object model for the manipulation of objects in a robot system with multiple arms; and the virtual linkage model for the characterization and control of internal forces in a multi-arm system. We present the extension of these methodologies to mobile manipulation systems and propose a new decentralized control structure for cooperative tasks. The article also discusses experimental results obtained with two holonomic mobile manipulation platforms we have designed and constructed at Stanford University.