gebhart/patrepeval huggingface dataset:
Mechanically Tunable Hollow Silica Ultrathin Nanoshells for Ultrasound Contrast Agents (2015)

Perfluoropentane (PFP) gas filled biodegradable iron-doped silica nanoshells have been demonstrated as long-lived ultrasound contrast agents. Nanoshells are synthesized by a sol-gel process with tetramethyl orthosilicate (TMOS) and iron ethoxide. Substituting a fraction of the TMOS with R-substituted trialkoxysilanes produces ultrathin nanoshells with varying shell thicknesses and morphologies composed of fused nanoflakes. The ultrathin nanoshells had continuous ultrasound Doppler imaging lifetimes exceeding 3 hours, were twice as bright using contrast specific imaging, and had decreased pressure thresholds compared to control nanoshells synthesized with just TMOS. Transmission electron microscopy (TEM) showed that the R-group substituted trialkoxysilanes could reduce the mechanically critical nanoshell layer to 1.4 nm. These ultrathin nanoshells have the mechanical behavior of weakly linked nanoflakes but the chemical stability of silica. The synthesis can be adapted for general fabrication of three-dimensional nanostructures composed of nanoflakes, which have thicknesses from 1.4-3.8 nm and diameters from 2-23 nm.
Scalable Remote Rendering with Depth and Motion‐flow Augmented Streaming (2011)

Abstract In this paper, we focus on efficient compression and streaming of frames rendered from a dynamic 3D model. Remote rendering and on‐the‐fly streaming become increasingly attractive for interactive applications. Data is kept confidential and only images are sent to the client. Even if the client's hardware resources are modest, the user can interact with state‐of‐the‐art rendering applications executed on the server. Our solution focuses on augmented video information, e.g., by depth, which is key to increase robustness with respect to data loss, image reconstruction, and is an important feature for stereo vision and other client‐side applications. Two major challenges arise in such a setup. First, the server workload has to be controlled to support many clients, second the data transfer needs to be efficient. Consequently, our contributions are twofold. First, we reduce the server‐based computations by making use of sparse sampling and temporal consistency to avoid expensive pixel evaluations. Second, our data‐transfer solution takes limited bandwidths into account, is robust to information loss, and compression and decompression are efficient enough to support real‐time interaction. Our key insight is to tailor our method explicitly for rendered 3D content and shift some computations on client GPUs, to better balance the server/client workload. Our framework is progressive, scalable, and allows us to stream augmented high‐resolution (e.g., HD‐ready) frames with small bandwidth on standard hardware.
Tumor necrosis factor as effector molecule in monocyte mediated cytotoxicity. (1986)

A newly developed assay system which uses actinomycin D (Act D) pretreated Wehi 164 target cells allows for the measurement of human monocyte cytotoxicity in a 7-h 51Cr release assay. Using the monocyte specific monoclonal antibody M42 in a direct rosetting procedure we confirm herein that among human peripheral blood mononuclear cells cytotoxicity is restricted to monocytes. When applying stringent conditions that exclude exogenous lipopolysaccharide (LPS) we could demonstrate that as little as 0.1 ng of LPS per ml triggers this cytotoxicity. Further, a factor can be detected in supernatants of mononuclear cells which is also cytotoxic against Act D treated Wehi 164 cells. This cytotoxic factor can be triggered by LPS within 4 h, but at as low a LPS concentration as 0.001 ng/ml. Since one of the LPS triggered monocyte products is tumor necrosis factor (TNF), we tested the effect of recombinant TNF cloned from the U937 cell line and we could show potent lytic activity against Act D pretreated but not, or only minimally, against untreated Wehi 164 target cells. Recombinant TNF rapidly lysed the target with significant specific release occurring as early as after 3 h in the assay. By contrast, recombinant interleukin 1 gave no lysis while lymphotoxin derived from the RPMI 1788 cell line was effective. An affinity purified antiserum directed against TNF neutralized the lytic activity of recombinant TNF and also the cytotoxic factor produced by LPS triggered mononuclear cells, while the antiserum was ineffective against lymphotoxin. Further, the antiserum when added to the assay of effector cells and Act D treated Wehi 164 cells also completely ablated cytotoxic activity. Size fractionation of cytotoxic factor and recombinant TNF by high pressure liquid chromatography led to a superimposable peak of cytotoxicity in the molecular weight range of 9,500-17,000. Further, immunoblotting with the anti-TNF antibody revealed the same Mr 15,500-16,500 band for the recombinant TNF and LPS triggered cytotoxic factor. Taken together, our data demonstrate that the cytotoxic activity of human monocytes against Act D treated Wehi 164 is mediated entirely by a LPS triggered molecule that is very similar or identical to the human tumor necrosis factor. The assay system thus provides a powerful tool to analyze the biology of TNF in humans.
Capillary flow control using hydrophobic patterns (2007)

This note presents a simple method to control the speed of the autonomous capillary flow using an array of hydrophobic patterns. The microfluidic system in this note was composed of two planar parallel plates that were separated by spacers. The bottom plate had a hydrophilic microchannel which was surrounded by hydrophobic tracks. The top surface was relatively hydrophobic compared to the bottom plate. These hydrophobic tracks and the hydrophobic patterns in the middle of the microchannels were patterned using PDMS stamps by contact printing. By controlling the ratio of hydrophobic area to the whole channel width and the distance between two plates, it was possible to control the capillary flow speed at specific positions. Using this method, it is expected to achieve a sufficient incubation time for biological reactions in microfluidic devices using the capillary flow.
Rigid Amphiphiles for Membrane Protein Manipulation (2000)

The two nonhomologous membrane proteins bacteriorhodopsin and bovine rhodopsin can be extracted from their native membranes by the rigid tripod amphiphile 1. Both proteins are maintained in a stable, soluble form, which is a prerequisite for crystallization. This new class of amphiphiles can be easily modified and could prove to be very useful for membrane protein manipulation.
INDUCTION OF IMMUNITY AND TOLERANCE IN VITRO BY HAPTEN PROTEIN CONJUGATES (1972)

Of many dinitrophenylated (DNP) protein conjugates tested, only DNP conjugated to polymerized flagellin (DNP-POL) (or the structurally related bacterial flagella) elicited a primary anti-DNP response in vitro. Other DNP proteins, such as DNP-monomeric flagellin (DNP-MON), were capable of inducing secondary responses in vitro. The capacity of DNP-POL to immunize spleen cell suspensions devoid of thymus-derived cells was the reason for the greater immunogenicity of DNP-POL, since even large numbers of flagellin-reactive activated thymus cells did not increase the anti-DNP response of normal spleen cells immunized with DNP-POL, whereas the thymus-dependent response to DNP-MON was markedly increased. The capacity of various batches of DNP-POL to immunize normal spleen cells in vitro varied markedly, depending on the number of DNP groups conjugated. DNP-POL with few DNP groups conjugated was immunogenic, but even at very high concentrations did not induce tolerance. In contrast, highly conjugated DNP-POL did not immunize, but readily induced tolerance. DNP-POL with intermediate degrees of conjugation were, like unconjugated polymeric flagellin, capable of inducing both immunity and tolerance. Since DNP-POL immunizes bone marrow-derived lymphocytes (B cells) directly the reduced response was not due to a masking of carrier determinants, necessary for cell collaboration. By using mixed DNP-5-(dimethylamino)-1-naphthalyl (dansyl)-POL conjugates, it was found that the inhibitory effect of a high degree of hapten conjugated was hapten specific. Depolymerization of DNP-POL to DNP-MON, which does not induce primary anti-DNP responses, was excluded by centrifugation analysis and electron microscopy. The relationship of the degree of hapten conjugation on DNP-POL to the capacity to induce tolerance and immunity in B cells has clarified the mechanism of immunological triggering of these cells. A model of the mechanism of "signal" discrimination between immunity and tolerance in B cells, based on these findings, is proposed.
Vacuum microelectronic devices (1994)

In this review/tutorial paper, we cover the history, physics, and current status of vacuum microelectronic devices. First we overview the performance requirements of vacuum microelectronic devices necessary for them to replace, or fill voids left by, solid state devices. Next we discuss the physical characteristics of micro-field-emission sources important to device applications. These characteristics include fundamental features, such as current-voltage data and noise, in addition to engineering considerations, such as life expectancy and procedures for tube assembly. We conclude with a review of a wide variety of demonstrated and proposed devices based on vacuum microelectronic principles, including electron guns, microwave tubes, and flat-panel displays.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Compartmentalized Phosphodiesterase-2 Activity Blunts β-Adrenergic Cardiac Inotropy via an NO/cGMP-Dependent Pathway (2005)

beta-Adrenergic signaling via cAMP generation and PKA activation mediates the positive inotropic effect of catecholamines on heart cells. Given the large diversity of protein kinase A targets within cardiac cells, a precisely regulated and confined activity of such signaling pathway is essential for specificity of response. Phosphodiesterases (PDEs) are the only route for degrading cAMP and are thus poised to regulate intracellular cAMP gradients. Their spatial confinement to discrete compartments and functional coupling to individual receptors provides an efficient way to control local [cAMP]i in a stimulus-specific manner. By performing real-time imaging of cyclic nucleotides in living ventriculocytes we identify a prominent role of PDE2 in selectively shaping the cAMP response to catecholamines via a pathway involving beta3-adrenergic receptors, NO generation and cGMP production. In cardiac myocytes, PDE2, being tightly coupled to the pool of adenylyl cyclases activated by beta-adrenergic receptor stimulation, coordinates cGMP and cAMP signaling in a novel feedback control loop of the beta-adrenergic pathway. In this, activation of beta3-adrenergic receptors counteracts cAMP generation obtained via stimulation of beta1/beta2-adrenoceptors. Our study illustrates the key role of compartmentalized PDE2 in the control of catecholamine-generated cAMP and furthers our understanding of localized cAMP signaling.
Using tool abstraction to compose systems (1992)

The tool abstraction paradigm, which supports the evolution of large-scale software systems by easing design changes in the system functions, is discussed. Systems that support tool abstraction are structured as a pool of abstract data structures shared by a collection of cooperating 'toolies', where each toolie provides a piece of the overall system function. When one toolie updates the shared data, other toolies must be notified: otherwise, cooperating-but-independent toolies may not execute, and the overall system function may be compromised. The KWIC (key word in context) index production system is used to illustrate the idea of tool abstraction. The relationship of tool abstraction to other concepts is examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An ordered table of primitive polynomials over GF(2) of degrees 2 through 19 for use with linear maximal sequence generators (1972)

The report contains a brief discussion of the practical aspects of generating binary linear maximal sequences. Included is a table of all primitive polynomials over GF(2) of degrees 2 through 19, not including reverses. These polynomials are ordered by the number of nonzero coefficients as well as by degree. This table is felt to complement other available tables. (Author)
Tetrahydropyridoazepines and tetrahydropyridoazepinones from the corresponding dihydroquinolones (1978)

Abstract The p ‐toluenesulfonate of 7,8‐dihydro‐5(6 H )quinoloneoxime( 3 ) was subjected of a Beckmann rearràngement. The resulting 2,3,4,5‐tetrahydro‐1 H ‐pyrido[3,2‐ b ]azepin‐2‐one ( 4 ) was reduced with lithium aluminum hydride affording 2,3,4,5‐tetrahydro‐1 H ‐pyrido[3,2‐ b ] azepine ( 5 ). 5,6‐l)ihydro‐8(7 H )quinolone ( 7 ), obtained by oxidation of 5,6,7,8‐tetrahydro‐8‐quinolinol ( 6 ), was converted into the p ‐toluenesulfonate of 5,6‐dihydro‐8(7 H )quinolone oxitne ( 9 ). Similarly the latter compound could be rearranged into 2,3,4,5‐letrahydro‐1 H ‐pyrido [2,3‐ b ] azepin‐2‐one ( 10 ) which on reduction produced 2,3,4,5‐tetrahydro‐1 H ‐pyrido [2,3‐ b ] azepine ( 11 ).
A Shared Binding Site for NAD+ and Coenzyme A in an Acetaldehyde Dehydrogenase Involved in Bacterial Degradation of Aromatic Compounds (2008)

The meta-cleavage pathway for catechol is a central pathway for the bacterial dissimilation of a wide variety of aromatic compounds, including phenols, methylphenols, naphthalenes, and biphenyls. The last enzyme of the pathway is a bifunctional aldolase/dehydrogenase that converts 4-hydroxy-2-ketovalerate to pyruvate and acetyl-CoA via acetaldehyde. The structure of the NAD (+)/CoASH-dependent aldehyde dehydrogenase subunit is similar to that of glyceraldehyde-3-phosphate dehydrogenase, with a Rossmann fold-based NAD (+) binding site observed in the NAD (+)-enzyme complex [Manjasetty, B. A., et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 6992-6997]. However, the location of the CoASH binding site was not determined. In this study, hydrogen-deuterium exchange experiments, coupled with peptic digest and mass spectrometry, were used to examine cofactor binding. The pattern of hydrogen-deuterium exchange in the presence of CoASH was almost identical to that observed with NAD (+), consistent with the two cofactors sharing a binding site. This is further supported by the observations that either CoASH or NAD (+) is able to elute the enzyme from an NAD (+) affinity column and that preincubation of the enzyme with NAD (+) protects against inactivation by CoASH. Consistent with these data, models of the CoASH complex generated using AUTODOCK showed that the docked conformation of CoASH can fully occupy the cavity containing the enzyme active site, superimposing with the NAD (+) cofactor observed in the X-ray crystal structure. Although CoASH binding Rossmann folds have been described previously, this is the first reported example of a Rossmann fold that can alternately bind CoASH or NAD (+) cofactors required for enzymatic catalysis.
Wettability of porous surfaces (1944)

A. B. D. Cassie and S. Baxter, Trans. Faraday Soc., 1944, 40, 546 DOI: 10.1039/TF9444000546
Characterization of KCNQ5/Q3 potassium channels expressed in mammalian cells (2001)

Heteromeric KCNQ5/Q3 channels were stably expressed in Chinese Hamster ovary cells and characterized using the whole cell voltage-clamp technique. KCNQ5/Q3 channels were activated by the novel anticonvulsant, retigabine (EC(50) 1.4 microM) by a mechanism that involved drug-induced, leftward shifts in the voltage-dependence of channel activation (-31.8 mV by 30 microM retigabine). KCNQ5/Q3 channels were inhibited by linopirdine (IC(50) 7.7 microM) and barium (IC(50) 0.46 mM), at concentrations similar to those required to inhibit native M-currents. These findings identify KCNQ5/Q3 channels as a molecular target for retigabine and raise the possibility that activation of KCNQ5/Q3 channels may be responsible for some of the anti-convulsant activity of this agent. Furthermore, the sensitivity of KCNQ5/Q3 channels to linopirdine supports the possibility that potassium channels comprised of KCNQ5 and KCNQ3 may make a contribution to native M-currents.
Identification of residues in the insulin molecule important for binding to insulin-degrading enzyme (1990)

Insulin-degrading enzyme (IDE) hydrolyzes insulin at a limited number of sites. Although the positions of these cleavages are known, the residues of insulin important in its binding to IDE have not been defined. To this end, we have studied the binding of a variety of insulin analogues to the protease in a solid-phase binding assay using immunoimmobilized IDE. Since IDE binds insulin with 600-fold greater affinity than it does insulin-like growth factor I (25 nM and approximately 16,000 nM, respectively), the first set of analogues studied were hybrid molecules of insulin and IGF I. IGF I mutants [insB1-17,17-70]IGF I, [Tyr55,Gln56]IGF I, and [Phe23,Phe24,Tyr25]IGF I have been synthesized and share the property of having insulin-like amino acids at positions corresponding to primary sites of cleavage of insulin by IDE. Whereas the first two exhibit affinities for IDE similar to that of wild type IGF I, the [Phe23,Phe24,Tyr25]IGF I analogue has a 32-fold greater affinity for the immobilized enzyme. Replacement of Phe-23 by Ser eliminates this increase. Removal of the eight amino acid D-chain region of IGF I (which has been predicted to interfere with binding to the 23-25 region) results in a 25-fold increase in affinity for IDE, confirming the importance of residues 23-25 in the high-affinity recognition of IDE. A similar role for the corresponding (B24-26) residues of insulin is supported by the use of site-directed mutant and semisynthetic insulin analogues. Insulin mutants [B25-Asp]insulin and [B25-His]insulin display 16- and 20-fold decreases in IDE affinity versus wild-type insulin.(ABSTRACT TRUNCATED AT 250 WORDS)
Floating search methods for feature selection with nonmonotonic criterion functions (2002)

In this paper the recently developed "floating search" algorithms are presented and modified to a more compact form facilitating their direct comparison with the well known (l,r) search. The properties of the floating search methods are investigated, especially with respect to their tolerance to nonmonotonic criteria. Their computational efficiency is demonstrated by results on real data of high dimensionality.
Fundamentals of process control theory (1981)

From the Publisher:
ISA's all-time best-selling book is now updated and expanded, offering a way for you to teach yourself the complexities of process control theory. Fundamentals of Process Control Theory has been praised for its clear, stylish presentation of the principles of process automation and its excellent overview of advanced control techniques. 
More than just a reference book, it's a complete course on the subject, with exercises and answers to work through. Both theoretical and practical, this guide allows readers to teach themselves the fundamental scientific principles that govern process control, particularly feedback control. Its 17 self-study units provide a solid foundation in theory, as well as a discussion of recent technologies such as computer-integrated manufacturing, statistical process control, and expert systems. New chapters focus on the conceptual framework for an application, offering a practical understanding of the theory, along with specific illustrations on how concepts are implemented.
Multistep, sequential control of the trafficking and function of the multiple sulfatase deficiency gene product, SUMF1 by PDI, ERGIC-53 and ERp44 (2008)

Sulfatase modifying factor 1 (SUMF1) encodes for the formylglicine generating enzyme, which activates sulfatases by modifying a key cysteine residue within their catalytic domains. SUMF1 is mutated in patients affected by multiple sulfatase deficiency, a rare recessive disorder in which all sulfatase activities are impaired. Despite the absence of canonical retention/retrieval signals, SUMF1 is largely retained in the endoplasmic reticulum (ER), where it exerts its enzymatic activity on nascent sulfatases. Part of SUMF1 is secreted and paracrinally taken up by distant cells. Here we show that SUMF1 interacts with protein disulfide isomerase (PDI) and ERp44, two thioredoxin family members residing in the early secretory pathway, and with ERGIC-53, a lectin that shuttles between the ER and the Golgi. Functional assays reveal that these interactions are crucial for controlling SUMF1 traffic and function. PDI couples SUMF1 retention and activation in the ER. ERGIC-53 and ERp44 act downstream, favoring SUMF1 export from and retrieval to the ER, respectively. Silencing ERGIC-53 causes proteasomal degradation of SUMF1, while down-regulating ERp44 promotes its secretion. When over-expressed, each of three interactors favors intracellular accumulation. Our results reveal a multistep control of SUMF1 trafficking, with sequential interactions dynamically determining ER localization, activity and secretion.
Vacuüm als constructief bindmiddel (2010)

‘Ongebonden’ granulaat kan nagenoeg elke geometrische vorm beschrijven. Dit biedt perspectief voor de maakbaarheid van ‘vrije vormen’ in de huidige architectuur. Door dit granulaat in een flexibele, luchtdichte omhulling te brengen en het pakket vacuüm te zuigen ontstaat een constructieve binding (of beter gezegd voorspanning), waardoor krachten door het granulaat kunnen worden overgedragen.
Characterization of mutant forms of recombinant human properdin lacking single thrombospondin type I repeats. Identification of modules important for function (1995)

Properdin is a serum glycoprotein that up-regulates the alternative pathway of complement by stabilizing the C3b-Bb complex. It also binds sulfated glycoconjugates, such as sulfatide, in vitro. Properdin is composed of cyclic dimers, trimers, and tetramers of a 53-kDa monomeric subunit. The monomer contains an N-terminal region of no known homology and six thrombospondin type 1 repeats (TSRs) of approximately 60 amino acids. To identify the regions of properdin important for function, we have expressed human properdin, and mutant forms each lacking a single TSR, in Chinese hamster ovary cells. In addition, limited tryptic digestion yielded "nicked" properdin by the cleavage of one peptide bond in TSR5. The structural and functional properties of these altered forms of properdin were investigated. Properdin "nicked" in TSR5 is unable to bind C3b but retains its overall structure and its ability to bind sulfatide. The removal of TSR5 prevents C3b and sulfatide binding. Properdin lacking TSR4 is unable to stabilize the C3b-Bb complex but is able to bind C3b and sulfatide, and shows the presence of monomers and dimers in an electron microscope. Properdin without TSR3 is able to stabilize the C3b-Bb complex, to bind C3b and sulfatide, and forms dimers, trimers, and tetramers. Properdin lacking TSR6 is unable to form oligomers. The N-linked carbohydrate of properdin is not required for oligomerization or stabilization of the C3b-Bb complex. The results implicate TSR5 in both C3b and sulfatide binding, and suggest that TSR4 may also be involved in stabilization of the C3b-Bb complex.
In vitrocellular processes sprouting in cortex microexplants of adult rat brains induced by low power laser irradiation (1998)

The effect of He-Ne low power laser irradiation on the growth of cellular processes of microexplants of the brain cortex of adult rats in tissue culture was studied. Two 8-min doses of direct laser irradiation, 3.6 J/cm2 each given on two successive days, caused a significant amount of sprouting of cellular processes outgrowth in microexplants compared to small amounts produced by nonirradiated controls. This preliminary observation suggests that low power laser irradiation applied to the area of an experimentally injured nerve may induce neurite processes sprouting, thereby improving nerve tissue recovery.