gebhart/patrepeval huggingface dataset:
The UvsY protein of bacteriophage T4 modulates recombination-dependent DNA synthesis in vitro. (1990)

An in vitro system containing the T4 gene 43, 45, 44/62, 32, dda, and uvsX proteins catalyzes DNA synthesis that is dependent on the synapsis step of homologous genetic recombination. The rate of DNA synthesis in this system is highly dependent on the concentration of the uvsX recombinase (a recA-like protein). Here we report the effect of the T4 uvsY protein, a recombination accessory protein, on this reaction. Low concentrations of uvsY protein greatly stimulate DNA synthesis at low concentrations of uvsX protein, but these same concentrations inhibit DNA synthesis at high concentrations of uvsX protein. As a result, the addition of small amounts of uvsY protein lowers the minimum concentration of uvsX protein needed for the reaction 8-fold, and it lowers the uvsX protein concentration for maximum activity 4-fold. The uvsY protein can affect either the initiation or elongation phase of DNA synthesis, depending on the concentration of uvsX protein present. The implications of these results for the function of the uvsY protein in T4 DNA replication in vivo are discussed.
Frame-level temporal calibration of video sequences from unsynchronized cameras by using projective invariants (2006)

This paper describes a new method for temporally calibrating multiple cameras by image processing operations. Existing multi-camera algorithms assume that the input sequences are synchronized either by genlock or by time stamp information and a centralized server. Yet, hardware-based synchronization increases installation cost. Hence, using image information is necessary to align frames from the cameras whose clocks are not synchronized. Our method uses image processing to find the frame offset between sequences so that they can be aligned. We track foreground objects, extract a point of interest for each object as its current location, and find the corresponding location of the object in the other sequence by using projective invariants in P/sup 2/. Our algorithm recovers the frame offset by matching the tracks in different views, and finding the most reliable match out of the possible track pairs. This method does not require information about intrinsic or extrinsic camera parameters, and thanks to information obtained from multiple tracks, is robust to possible errors in background subtraction or location extraction. We present results on different sequences from the PETS2001 database, which show the robustness of the algorithm in recovering the frame offset.
Optimization with Sparsity-Inducing Penalties (2011)

Sparse estimation methods are aimed at using or obtaining parsimonious representations of data or models. They were first dedicated to linear variable selection but numerous extensions have now emerged such as structured sparsity or kernel selection. It turns out that many of the related estimation problems can be cast as convex optimization problems by regularizing the empirical risk with appropriate nonsmooth norms. Optimization with Sparsity-Inducing Penalties presents optimization tools and techniques dedicated to such sparsity-inducing penalties from a general perspective. It covers proximal methods, block-coordinate descent, reweighted ?2-penalized techniques, working-set and homotopy methods, as well as non-convex formulations and extensions, and provides an extensive set of experiments to compare various algorithms from a computational point of view. The presentation of Optimization with Sparsity-Inducing Penalties is essentially based on existing literature, but the process of constructing a general framework leads naturally to new results, connections and points of view. It is an ideal reference on the topic for anyone working in machine learning and related areas.
Suppression of natural xenophile antibodies with the novel immunomodulating drug leflunomide. (1992)

NATURAL xenophile antibodies (NXA) and induced xenophile antibodies (XA) are considered a major barrier to organ transplantation between phylogeneticaliy discordant species and are held to be responsible for hyperacute and acute rejection of xenogeneic organs.! The aims of this study were (1) to analyze the kinetics of NXA and XA in the xenogeneic model rat antihuman, which allows experimental manipulation, and (2) to manipulate NXA and XA production by the new immunomodulating drug leftunomide (LF). LF is thought to preferentially inhibit T-dependent B-Iymphocyte proliferation by antagonizing a T-helper cell-derived soluble, B-cell activating factor, possibly an interleukin.
Photoluminescence quenching of Alq3 by metal deposition: A surface analytical investigation (1998)

The importance of the interfacial properties in organic light emitting devices (OLED) is well recognized. We will describe our recent efforts to understand interfaces in OLEDs using surface/interface analytical techniques in a well controlled ultrahigh vacuum environment. We observed severe photoluminescence quenching of organic thin films comprising of a model OLED material, namely tris-(8-hydroxyquinoline) aluminum (Alq3), upon deposition of a number of metals. Such quenching may severely affect the electroluminescence device efficiency. We have investigated the interfaces using x-ray photoemission spectroscopy and ultraviolet photoemission spectroscopy, and studied the intriguing process of the interface formation at an atomic/molecular level. We will show that microscopic surface and interface properties are intimately related to the device characteristics and performance.
Fabrication of Stable Metallic Patterns Embedded in Poly(dimethylsiloxane) and Model Applications in Non‐Planar Electronic and Lab‐on‐a‐Chip Device Patterning (2005)

Abstract This article describes the fabrication of durable metallic patterns that are embedded in poly(dimethylsiloxane) (PDMS) and demonstrates their use in several representative applications. The method involves the transfer and subsequent embedding of micrometer‐scale gold (and other thin‐film material) patterns into PDMS via adhesion chemistries mediated by silane coupling agents. We demonstrate the process as a suitable method for patterning stable functional metallization structures on PDMS, ones with limiting feature sizes less than 5 μm, and their subsequent utilization as structures suitable for use in applications ranging from soft‐lithographic patterning, non‐planar electronics, and microfluidic (lab‐on‐a‐chip, LOC) analytical systems. We demonstrate specifically that metal patterns embedded in both planar and spherically curved PDMS substrates can be used as compliant contact photomasks for conventional photolithographic processes. The non‐planar photomask fabricated with this technique has the same surface shape as the substrate, and thus facilitates the registration of structures in multilevel devices. This quality was specifically tested in a model demonstration in which an array of one hundred metal oxide semiconductor field‐effect transistor (MOSFET) devices was fabricated on a spherically curved Si single‐crystalline lens. The most significant opportunities for the processes reported here, however, appear to reside in applications in analytical chemistry that exploit devices fabricated using the methods of soft lithography. Toward this end, we demonstrate durably bonded metal patterns on PDMS that are appropriate for use in microfluidic, microanalytical, and microelectromechanical systems. We describe a multilayer metal‐electrode fabrication scheme (multilaminate metal–insulator–metal (MIM) structures that substantially enhance performance and stability) and use it to enable the construction of PDMS LOC devices using electrochemical detection. A polymer‐based microelectrochemical analytical system, one incorporating an electrode array for cyclic voltammetry and a microfluidic system for the electrophoretic separation of dopamine and catechol with amperometric detection, is demonstrated.
Anisotropic effective-medium modeling of the elastic properties of shales (1994)

Abstract Shales are complex porous materials, normally consisting of percolating and interpenetrating fluid and solid phases. The solid phase is generally comprised of several mineral components and forms an intricate and anisotropic microstructure. The shape, orientation, and connection of the two phases control the anisotropic elastic properties of the composite solid. We develop a theoretical framework that allows us to predict the effective elastic properties of shales. Its usefulness is demonstrated with numerical modeling and by comparison with established ultrasonic laboratory experiments. The theory is based on a combination of anisotropic formulations of the self-consistent (SCA) and differential effective-medium (DEM) ap proximations. This combination guarantees that both the fluid and solid phases percolate at all porosities. Our modeling of the elastic properties of shales proceeds in four steps. First, we consider the case of an aligned biconnected clay-fluid composite composed of ellipsoidal inclusions. Anisotropic elastic constants are estimated for a clay-fluid composite as a function of the fluid-filled porosity and the aspect ratio of the inclusions. Second, a new processing technique is developed to estimate the distribution of clay platelet orientations from digitized scanning electron microphotographs (SEM). Third, the derived clay platelet distribution is employed to estimate the effective elastic parameters of a solid comprising clay-fluid composites oriented at different angles. Finally, silt minerals are included in the calculations as isolated spherical inclusions.
Performance comparison of detection methods in magnetic recording (1990)

Various detection schemes suitable for magnetic recording are compared in terms of their effective signal-to-noise ratios. It is shown that at high densities the performance of conventional detectors such as a peak detector, a threshold detector with partial response equalization, a decision feedback equalizer, and a Viterbi algorithm detector tuned to a linearly truncated channel fall far below the optimum performance that can be achieved by the maximum-likelihood sequence detector (MLSD). It is shown that while implementing the full MLSD is clearly out of the question for high densities with severe intersymbol interference (ISI), there exists an efficient detection scheme which achieves an excellent compromise between hardware complexity and detection performance. This scheme, which is called the fixed-delay tree search with decision feedback, combines a fast and efficient tree-search algorithm with a decision feedback equalizer to cancel out a portion of ISI without noise enhancement. It is well suited for run-length-limited systems and attains performance close to that of MLSD while maintaining reasonable implementation cost and processing requirements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Performance of dynamic channel allocation in the DECT system (2002)

The authors present the results of computer simulations of an indoor wireless PABX system conforming to the Digital European Cordless Telecommunications (DECT) standard. Of particular interest is the evaluation of the dynamic channel allocation algorithm proposed by the DECT standard. It is shown that this system is capable of meeting the expected capacity requirements for high-density indoor applications as long as there are a sufficient number of base stations on each floor of the building. System performance has been measured in terms of setup blocking, handover blocking, lost calls, cleared traffic, and carrier-to-interference ratios.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Combination Therapy for Maximal Myocardial Infarct Size Reduction (2001)

The aim of this study was to test whether myocardial infarct size reduction would be optimized by combining three known effective therapies: cariporide, regional hypothermia, and ischemic preconditioning (CHIP). Before coronary artery occlusion (CAO), treated rabbits (CHIP, n = 7) received cariporide (0.3 mg/kg), ischemic preconditioning (7 minutes ischemia and 5 minutes reperfusion), then 20 minutes of mild regional hypothermia (34 degrees C). Control rabbits (n = 7) received saline and a 34-minute waiting period. All received 30 minutes of CAO and reperfusion. In another study, rabbits (n = 8 in each group) received 90 minutes of CAO. In the 30-minute protocol, the authors found that hearts in both groups were equally ischemic during CAO. Mean ischemic risk zones were similar in both groups; however, in CHIP hearts, infarct size was 4 +/- 1% of risk zone, a reduction of 91% compared with control rabbits (44 +/- 7% of the risk zone, P = 0.001). In the 90-minute protocol, risk zone size was similar in both groups, but infarct size in control hearts was 76 +/- 3% of the risk zone compared with 34 +/- 7% in CHIP treated hearts (P = 0.0003). In summary, the combined treatment provided extraordinary protection. Infarct comprised only 4% of the risk region after 30-minute ischemia-a far greater reduction than was previously observed in the same laboratory using any single intervention. After 90 minutes of ischemia, infarct was 55% lower in CHIP hearts, suggesting that this therapeutic approach dramatically reduces ischemia/reperfusion cell death, even during long occlusions.
Activating mutations in c-KIT and PDGFRα are exclusively found in gastrointestinal stromal tumors and not in other tumors overexpressing these imatinib mesylate target genes (2005)

Previous studies have shown that Imatinib mesylate (Gleevec), a selective tyrosine kinase inhibitor of c-KIT and platelet-derived growth factor receptors (PDGFR), is highly effective in c-KIT/CD117-positive gastrointestinal stromal tumors (GIST), especially in those having activating mutations in c-kit exon 11. In addition, gain-of-function mutations in the juxtamembrane domain (exon 12) and the kinase activation loop (exon 18) of PDGFRalpha were found in GISTs. Importantly, the presence and type of these mutually exclusive c-KIT or PDGFRalpha mutations were found to be associated with the response to imatinib. Here, we examined the prevalence of c-kit exon 11 and PDGFRalpha exons 12 and 18 mutations in other tumor types known to express these tyrosine kinase receptors in order to explore which other cancer types may potentially benefit from imatinib treatment. We determined the mutational status of these commonly mutated exons by direct sequencing in 11 different tumor types (in total: 215 unrelated cases), including GIST, chordoma, and various distinct tumors of lung, brain and its coverings, and skin cancer. Of the 579 exons examined (211 c-kit exon 11, 192 PDGFRalpha exon 12, 142 PDGFRalpha exon18, 17 PDGFRbeta exon 12 and 17 PDGFRbeta exon 18), only 12 (all GIST) harbored mutations (10 c-kit exon 11 and 2 PDGFRalpha exon18). From these data we conclude that activating c-KIT and PDGFR mutations are sporadic in human cancers known to overexpress these tyrosine kinase receptor genes and suggest that, except in GIST, this overexpression is not correlated with activating mutations. The latter may imply that these wild-type c-KIT and PDGFR tumor types will probably not benefit from imatinib treatment.
Vibrational Promotion of Electron Transfer (2000)

By using laser methods to prepare specific quantum states of gas-phase nitric oxide molecules, we examined the role of vibrational motion in electron transfer to a molecule from a metal surface free from the complicating influence of solvation effects. The signature of the electron transfer process is a highly efficient multiquantum vibrational relaxation event, where the nitrogen oxide loses hundreds of kilojoules per mole of energy on a subpicosecond time scale. These results cannot be explained simply on the basis of Franck-Condon factors. The large-amplitude vibrational motion associated with molecules in high vibrational states strongly modulates the energetic driving force of the electron transfer reaction. These results show the importance of molecular vibration in promoting electron transfer reactions, a class of chemistry important to molecular electronics devices, solar energy conversion, and many biological processes.
Fabrication and Properties of Composites of Poly(ethylene oxide) and Functionalized Carbon Nanotubes (2002)

Chemically functionalized carbon nanotubes (see Figure) are shown to produce composites with improved uniformity and dispersion. At low nanotube loading, a significant enhancement of the mechanical properties can be obtained. Moreover, the polymer/nanotube composites show efficient load transfer between the fillers and the matrix.
A neuron-specific marker in the cerebral cortex (2011)

Objective To study the characteristics of a new neuron-specific marker in the cerebral cortex and its application method.Methods According to immunofluorescence principles,the neurons in the cerebral cortex cultured in vitro were stained by fluorescein isothiocyanate (FITC)-labeled Tet1; and FITC-Tet1 with NSE or GFAP was employed to determine whether the neurons can be marked and whether they can be distinguished from astrocytes; the conditions of application of FITC-Tet1 were quantified.The HEK and C6 cell lines were performed the above experiments as controls.Results The final concentration was the key factor,which indicated that when the FITC-Tet1 was about 30 μg/mL,the neuron marking ability was the best,and the astrocytes,HEK and C6 were not stained.Neither high (100μg/mL) or low (10μg/mL) levels of FITC-Tet1 were suitableforstainingneurons.Conclusion Tet1 can specifically combine with the neuron in the cerebral cortex,which may make it to be a new staining method or a targeting molecule to neurons in the central nervous system.

Key words: 
Cerebral cortex;  Neuron;  Biological marker;  Immunofluorescence
In vivo anticancer activity of vanillin semicarbazone (2012)

It can be concluded that VSC can therefore be considered as potent anticancer agent.
REMOVAL OF BUTTERFAT COD AND BOD5 IN INOCULATED SAND COLUMNS (1998)

The purpose of this work was to investigate the feasibility of biodegradation of butterfat using an aerobic sandcolumnsystem. The columns were inoculated with lipolytic microorganisms to colonize the sand with an active biofilm.Butterfat was fed daily to the columns in artificial wastewaters that were supplemented with a surfactant or a detergent.Columns exhibited physical infiltration, trapping butterfat in the sand and resulted in an apparent high degree of COD andBOD5 removal from the effluent. The average BOD5 removal was 50% for the sand columns receiving butterfat anddetergent formulation, 36% for the columns receiving butterfat and surfactant formulation, and 57% for the columnsreceiving butterfat only. Biodegradation of trapped butterfat in the absence of a surfactant or detergent formulation was slowand incomplete. Sand columns receiving artificial wastewater containing butterfat supplemented with detergent showedsuperior performance in terms of COD and BOD5 removal efficiencies measured for effluent samples. The highest CODremoval of 14% from the entire system was achieved by feeding with butterfat and detergent formulation. Accumulation ofbiomass on the sand grains was monitored by measurement of ATP. Supplemental detergent formulation increased biomassaccumulation in the sand columns, suggesting improved contact between the microorganisms and the butterfat substrate.
The specific architecture of the anterior stroma accounts for maintenance of corneal curvature (2001)

The rigidity of the most anterior part of the corneal stroma in extreme hydration states points to an important role in maintenance of corneal curvature. Since a large part of this rigid anterior part of the stroma is either removed (PRK) or intersected (LASIK), it is possible that in the long run patients who underwent refractive surgery may be confronted with optical problems.
Applications of division by convergence (1964)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering, 1964.
Mechanism of Local Anesthetic Drug Action on Voltage-Gated Sodium Channels (2005)

Local anesthetic drugs interfere with excitation and conduction by action potentials in the nervous system and in the heart by blockade of the voltage-gated Na channel. Drug affinity varies with gating state of the channel. The drugs show low affinity at slow excitation rates, but high affinity when the channels are opened and inactivated during action potentials at high frequency, as they are during pain or during a cardiac arrhythmia. The drugs are thought to access their binding site in the inner pore by passage through the membrane and entry through the inner pore vestibule. There have been three major developments in the last decade that greatly increase our understanding of their mechanism of action. Firstly, amino acid residues critical to drug binding have been located by mutagenesis, and it is possible to develop a molecular model of the drug binding site. Secondly, a path for drug access directly from the outside has been characterized in the cardiac isoform of the channel. Thirdly, the hypothesis that high affinity binding stabilizes the fast inactivated conformation of the channel has been challenged. Rather, the drug may stabilize a slow inactivated state and immobilize the voltage sensor in domain III in its activated outward position. The combination of mutational study of the cloned Na channels and patch clamp offers the opportunity to understand the detailed molecular mechanism of drug action and to resolve drug structure-function.
The specificities of yeast methionine aminopeptidase and acetylation of amino-terminal methionine in vivo. Processing of altered iso-1-cytochromes c created by oligonucleotide transformation. (1990)

The specificities of methionine aminopeptidase and amino-terminal acetylation in the yeast Saccharomyces cerevisiae were investigated in vivo by sequencing a series of altered iso-1-cytochrome c. Twenty iso-1-cytochromes c, each having a different penultimate residue in the sequence Met-Xaa-Phe-Leu-, were created by transforming yeast directly with synthetic oligonucleotides. The degree of methionine cleavage and amino-terminal acetylation was estimated from the levels of pertinent peptides separated by high performance liquid chromatography. The results confirmed our earlier hypothesis (Sherman, F., Stewart, J. W., and Tsunasawa, S. (1985) BioEssays 3, 27-31) that methionine is completely removed from penultimate residues having radii of gyration of 1.29 A or less (glycine, alanine, serine, cysteine, threonine, proline, and valine). However, only partial cleavage occurred in the sequences Met-Thr-Pro-Leu- and Met-Val-Pro-Leu-, demonstrating that proline at the third position inhibits methionine cleavage when the penultimate residue has an intermediate radius of gyration. Acetylation of the retained amino-terminal methionine occurred completely with the Ac-Met-Glu-Phe-Leu- and Ac-Met-Asp-Phe-Leu- sequences and partially with the Ac-Met-Asn-Phe-Leu-sequence. Although the consensus for acetylation of the retained amino-terminal methionine is not completely known, these results and the results of published sequences indicated that Ac-Met-Glu- and Ac-Met-Asp- (methionine followed by an acidic residue) is sufficient for amino-terminal acetylation in eukaryotes but not in prokaryotes.