gebhart/patrepeval huggingface dataset:
Low-level p53 expression changes transactivation rules and reveals superactivating sequences (2012)

Transcriptional activation by the tumor suppressor p53 is considered to depend on cellular level, although there are few systems where this dependence on cellular level of p53 has been directly addressed. Previously, we reported that transactivation from p53 targets was sensitive to both p53 amount and DNA sequence, with some sequences being responsive to much lower p53 levels than others when examined in yeast model systems or human cells. Because p53 is normally present at low levels and perturbations might lead to small increases, we examined transactivation under limiting p53. Unlike the positive relationship between transactivation and binding affinity from target sequences at high cellular levels of human p53 in yeast, no such relationship was found at low levels. However, transactivation in the yeast system and the torsional flexibility of target sequences were highly correlated, revealing a unique structural relationship between transcriptional function and sequence. Surprisingly, a few sequences supported high transactivation at low p53 levels in yeast or when transfected into human cells. On the basis of kinetic and flexibility analyses the "supertransactivation" property was due to low binding off rates of flexible target sites. Interestingly, a supertransactivation response element can differentiate transcriptional capacities of many breast cancer-associated p53 mutants. Overall, these studies, which are relevant to other transcription factors, address the extent to which transactivation properties of p53 target sequences are determined by their intrinsic physical properties and reveal unique rules of engagement of target sequences at low p53 levels.
Using POS information for statistical machine translation into morphologically rich languages (2003)

When translating from languages with hardly any inflectional morphology like English into morphologically rich languages, the English word forms often do not contain enough information for producing the correct fullform in the target language. We investigate methods for improving the quality of such translations by making use of part-of-speech information and maximum entropy modeling. Results for translations from English into Spanish and Catalan are presented on the LC-STAR corpus which consists of spontaneously spoken dialogues in the domain of appointment scheduling and travel planning.
Low-Complexity Block Turbo Equalization for OFDM Systems in Time-Varying Channels (2007)

We propose a low-complexity block turbo equalizer for orthogonal frequency-division multiplexing (OFDM) systems in time-varying channels. The complexity of the proposed algorithm is linear in the number of subcarriers by exploiting the band structure of the frequency-domain channel matrix. The presented block turbo equalizer is based on a soft minimum mean squared error (MMSE) block linear equalizer (BLE).
The Relationship between Surface and Internal Sensitivity of Individual Grains (1968)

By use of sensitometric and processing techniques it is shown that for typical commercial emulsions the grains which do not form surface image readily are the more sensitive ones for internal-image formation. From residual grain size data it is shown that this relationship between surface and internal sensitivities exists within individual size classes. Arguments are presented in favour of the view that the reciprocal relationship between surface and internal sensitivity is due in part to inherent differences among grains. The observations emphasize that the surface/internal sensitivity ratio for grains of high surface sensitivity can exceed considerably the corresponding ratio for the emulsion layer as a whole for production of small or moderate densities.
Remote vibration sensing using a radio-frequency auto-oscillatory opto-electronic circuit with fibre-optical delay line (1995)

A new type of remote vibration sensor is proposed, based upon a RF self-excited optoelectronic system with a fibre-optical delay line. The key element of this system is a RF laser autogenerator with a multimode fibre-optical delay line composed of emitting and receiving fibres. The RF envelope superimposed on the light signal reflected from a vibrating surface depends on the modal composition of the signal in the fibre and thus carries information on the vibration frequencies and amplitudes in the ultrasonic region. Vibration amplitudes as small as 10 nm can be measured.
Culturing intestinal stem cells: applications for colorectal cancer research (2014)

Recent advance of sequencing technology has revealed genetic alterations in colorectal cancer (CRC). The biological function of recurrently mutated genes has been intensively investigated through mouse genetic models and CRC cell lines. Although these experimental models may not fully reflect biological traits of human intestinal epithelium, they provided insights into the understanding of intestinal stem cell self-renewal, leading to the development of novel human intestinal organoid culture system. Intestinal organoid culture enabled to expand normal or tumor epithelial cells in vitro retaining their stem cell self-renewal and multiple differentiation. Gene manipulation of these cultured cells may provide an attractive tool for investigating genetic events involved in colorectal carcinogenesis.
Transparent debugging of dynamically instrumented programs (2005)

Dynamic instrumentation systems, used for program analysis, bug isolation, software security and simulations, are becoming increasingly popular. There exists a need to debug dynamically instrumented programs while keeping the presence of dynamic instrumentation system hidden from debug users. Existing debuggers use debug information in program binaries that have been generated by a compiler at static compile time, to provide their debug support. Since dynamic instrumentation systems generate program code at run-time, existing debuggers are not able to provide the same kind of debug support. The most comprehensive existing debug techniques that satisfy this need, used by Tdb, require modification of existing debuggers. This paper provides an OS level approach that silently intercepts the communication between a debugger and the OS and uses a set of debug specifications to provide Tdb's transparent debugging. As a result, any existing debugger can be used to debug dynamically instrumented programs. The proposed techniques have been implemented on x86/Linux platform for the dynamic instrumentation system Pin.
[Conformational analysis of biologically active thyroliberin analogs by two-dimensional NMR spectroscopy]. (1992)

Preferable conformations of thyrotropin-releasing hormone (TRH, Glp-His-Pro-NH2) and its analogues Glp-Glu(R)-Pro-NH2 (R = NHCH(CH3)CH2Ar), Glp-Gln-Abu-NH2, Dho-Gln-Abu-NH2 in DMSO solution are determined using two-dimensional 1H NMR spectroscopy (delta-J-correlated, COSY and NOESY). Torsion angles psi i and chi i for every amino acid were calculated on the basis of the spin-spin coupling constants 3JNH-C alpha H and 3JC alpha H-C beta H values. The NOESY data were used for selecting the peptide conformations realized in solution. Distances between protons interacting by the dipole mechanism (d-contacts) were calculated using NOE values. These experiments allow one to estimate the torsion angles psi (between C alpha H-CO). TRH has an intramolecular H-bond between NH2-protons and His carbonyl with the torsion angles omega 3 = 180 degrees and psi 3 = 0 degrees. It is formation of this H-bond that apparently promotes the domination of the trans configuration of the His-Pro peptide bond. An intramolecular NH2-C alpha CO (Glp) H-bonding is revealed in other investigated compounds. It is known that a similar conformation of the TRH is realized in the course of its interaction with receptor.
Enterovirus Infection, CXC Chemokine Ligand 10 (CXCL10), and CXCR3 Circuit (2009)

These results strongly suggest the presence of a circuit for the destruction of beta-cells in fulminant type 1 diabetes. Enterovirus infection of the pancreas initiates coexpression of interferon-gamma and CXCL10 in beta-cells. CXCL10 secreted from beta-cells activates and attracts autoreactive T-cells and macrophages to the islets via CXCR3. These infiltrating autoreactive T-cells and macrophages release inflammatory cytokines including interferon-gamma in the islets, not only damaging beta-cells but also accelerating CXCL10 generation in residual beta-cells and thus further activating cell-mediated autoimmunity until all beta-cells have been destroyed.
Synthesis and characterization of poly(ϵ‐caprolactone)–poly(<scp>L</scp>‐lactide) diblock copolymers with an organic amino calcium catalyst (2006)

Abstract The quasiliving characteristics of the ring‐opening polymerization of ϵ‐caprolactone (CL) catalyzed by an organic amino calcium were demonstrated. Taking advantage of this feature, we synthesized a series of poly(ϵ‐caprolactone) (PCL)–poly( L ‐lactide) (PLA) diblock copolymers with the sequential addition of the monomers CL and L ‐lactide. The block structure was confirmed by 1 H‐NMR, 13 C‐NMR, and gel permeation chromatography analysis. The crystalline structure of the copolymers was investigated by differential scanning calorimetry and wide‐angle X‐ray diffraction analysis. When the molecular weight of the PLA block was high enough, phase separation took place in the block copolymer to form PCL and PLA domains, respectively. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102: 2654–2660, 2006
High-efficiency optical transfer of torque to a nematic liquid crystal droplet (2003)

We report on the determination of the difference in the refractive index between the ordinary and extraordinary rays in droplets of nematic liquid crystal E-44 at the wavelength of laser trapping, 1064 nm. This difference was calculated by measuring the ellipticity of laser tweezers for the moment at which rotation of the trapped droplet starts. The precision of this determination of the refractive index difference is approximately 5×10−3. Hydrophobic nematic liquid crystal E-44 formed 0.5–5-μm droplets when cast into D2O. The efficiency of the transfer of light torque to the liquid crystal droplets was determined to be 70% for the no-slip-boundary condition.
Classification of mammographic lesions into BI-RADS shape categories using the beamlet transform (2005)

We present a new algorithm and preliminary results for classifying lesions into BI-RADS shape categories: round, oval, lobulated, or irregular. By classifying masses into one of these categories, computer aided detection (CAD) systems will be able to provide additional information to radiologists. Thus, such a tool could potentially be used in conjunction with a CAD system to enable greater interaction and personalization. For this classification task, we have developed a new set of features using the Beamlet transform, which is a recently developed multi-scale image analysis transform. We trained a k-Nearest Neighbor classifier using images from the Digital Database for Digital Mammography (DDSM). The method was tested on a set of 25 images of each type and we obtained a classification accuracy of 78% for classifying masses as oval or round and an accuracy of 72% for classifying masses as lobulated or round.
A sulphonamido-indanone derivative CGP 28237 (ZK 34228), a novel non-steroidal anti-inflammatory agent without gastro-intestinal ulcerogenicity in rats. (1987)

CGP 28237 (5-methylsulphonylamino-6-phenoxy-1-indanone) belongs to a series of structurally novel indanones. The compound is a weak acid (pK = 6.98), but it does not contain a carboxylic group. CGP 28237 exhibits potent anti-inflammatory activity in developing and established adjuvant arthritis in rats (ED40 approximately 0.5 mg/kg p.o.) and good activity in carrageenin oedema (ED40 approximately 3 mg/kg p.o.). It inhibits yeast-induced fever in rats with ED50 values of 1, 2 and 10 mg/kg p.o. at 1, 3 and 5 hours after drug administration. The antinociceptive activity in mice (phenyl-p-benzoquinone writhing) and rats (acetic-acid writhing) is weak. CGP 28237 has been shown to be non-ulcerogenic in rats under acute and chronic test conditions: it does not cause mucosal lesions in the stomach at 2 X 400 mg/kg p.o., it does not enhance gastro-intestinal blood loss during 10 days' oral treatment with 400 mg/kg p.o., and it did not induce gastro-intestinal lesions in a 4-week toxicity study up to 1000 mg/kg p.o. Although CGP 28237 is not a cyclooxygenase inhibitor in bovine seminal vesicle microsomes, it inhibits prostaglandin synthesis in zymosan-stimulated murine macrophages (IC50 approximately 3 X 10(-6) mol/l) and protects rabbits against arachidonic acid-induced lung embolism with 10 mg/kg p.o. CGP 28237 may represent a novel anti-inflammatory drug with excellent gastro-intestinal tolerability.
Interfacial Tensions of Microbial Surfactants Determined by Real-Time Video Imaging of Pendant Drops (1992)

ABSTRACT This paper describes an instrument to measure the interfacial tension (IFT) of aqueous surfactant solutions and crude oil. The method involves injection of a drop of fluid (such as crude oil) into a second immiscible phase to determine the IFT between the two phases. The instrument is composed of an AT-class computer, optical cell, illumination, video camera and lens, video frame digitizer board, monitor, and software. The camera displays an image of the pendant drop on the monitor, which is then processed by the frame digitizer board and non-proprietary software to determine the IFT. Several binary and ternary phase systems were taken from the literature and used to measure the precision and accuracy of the instrument in determining IFTs. The instrument has been used to determine the IFTs for several bacterial supernatants and unfractionated acid precipitates of microbial cultures containing biosurfactants against medium to heavy crude oils. These experiments demonstrate that the use of automated video imaging of pendant drops is a simple and fast method to reliably determine interfacial tension between two immiscible liquid phases,- or between a gas and a liquid phase.
Detecting time series motifs under uniform scaling (2007)

Time series motifs are approximately repeated patterns foundwithin the data. Such motifs have utility for many data mining algorithms, including rule-discovery,novelty-detection, summarization and clustering. Since the formalization of the problem and the introduction of efficient linear time algorithms, motif discovery has been successfully applied tomany domains, including medicine, motion capture, robotics and meteorology.In this work we show that most previous applications of time series motifs have been severely limited by the definition's brittleness to even slight changes of uniform scaling, the speed at which the patterns develop. We introduce a new algorithm that allows discovery of time series motifs with invariance to uniform scaling, and show that it produces objectively superior results in several important domains. Apart from being more general than all other motifdiscovery algorithms, a further contribution of our work isthat it is simpler than previous approaches, in particular we have drastically reduced the number of parameters that need to be specified.
Conservation of Ornamental Stone by<i>Myxococcus xanthus-</i>Induced Carbonate Biomineralization (2003)

Increasing environmental pollution in urban areas has been endangering the survival of carbonate stones in monuments and statuary for many decades. Numerous conservation treatments have been applied for the protection and consolidation of these works of art. Most of them, however, either release dangerous gases during curing or show very little efficacy. Bacterially induced carbonate mineralization has been proposed as a novel and environmentally friendly strategy for the conservation of deteriorated ornamental stone. However, the method appeared to display insufficient consolidation and plugging of pores. Here we report that Myxococcus xanthus-induced calcium carbonate precipitation efficiently protects and consolidates porous ornamental limestone. The newly formed carbonate cements calcite grains by depositing on the walls of the pores without plugging them. Sonication tests demonstrate that these new carbonate crystals are strongly attached to the substratum, mostly due to epitaxial growth on preexisting calcite grains. The new crystals are more stress resistant than the calcite grains of the original stone because they are organic-inorganic composites. Variations in the phosphate concentrations of the culture medium lead to changes in local pH and bacterial productivity. These affect the structure of the new cement and the type of precipitated CaCO(3) polymorph (vaterite or calcite). The manipulation of culture medium composition creates new ways of controlling bacterial biomineralization that in the future could be applied to the conservation of ornamental stone.
Exotic Plant Management in California Annual Grasslands (2007)

Abstract This chapter discusses the annual grassland systems occupying the coastal ranges, central valley, and Sierra Nevada foothills, describing the common non-native invasive species in California Valley and foothill grasslands, including their growth form, classification, and ecological and economic impacts. It also describes several techniques for invasive plant management in California grasslands.
Fast and processor efficient parallel matrix multiplication algorithms on a linear array with a reconfigurable pipelined bus system (1998)

We present efficient parallel matrix multiplication algorithms for linear arrays with reconfigurable pipelined bus systems (LARPBS). Such systems are able to support a large volume of parallel communication of various patterns in constant time. An LARPBS can also be reconfigured into many independent subsystems and, thus, is able to support parallel implementations of divide-and-conquer computations like Strassen's algorithm. The main contributions of the paper are as follows. We develop five matrix multiplication algorithms with varying degrees of parallelism on the LARPBS computing model; namely, MM/sub 1/, MM/sub 2/, MM/sub 3/, and compound algorithms C/sub 1/(/spl epsiv/)and C/sub 2/(/spl delta/). Algorithm C/sub 1/(/spl epsiv/) has adjustable time complexity in sublinear level. Algorithm C/sub 2/(/spl delta/) implies that it is feasible to achieve sublogarithmic time using /spl sigma/(N/sup 3/) processors for matrix multiplication on a realistic system. Algorithms MM/sub 3/, C/sub 1/(/spl epsiv/), and C/sub 2/(/spl delta/) all have o(/spl Nscr//sup 3/) cost and, hence, are very processor efficient. Algorithms MM/sub 1/, MM/sub 3/, and C/sub 1/(/spl epsiv/) are general-purpose matrix multiplication algorithms, where the array elements are in any ring. Algorithms MM/sub 2/ and C/sub 2/(/spl delta/) are applicable to array elements that are integers of bounded magnitude, or floating-point values of bounded precision and magnitude, or Boolean values. Extension of algorithms MM/sub 2/ and C/sub 2/(/spl delta/) to unbounded integers and reals are also discussed.
Design study of future 3-D PET systems (2002)

Current detector technology based on BGO block-detectors is capable of achieving an intrinsic resolution of 3-4 mm. In order to fully utilize this high resolution, 3-D acquisition techniques are necessary resulting in an improved sensitivity of 6-7, compared to 2D technology. However, dead time problems start to get severe at administered doses 3-5 times lower than previously met in 2-D. In this work, the trade-off between the sensitivity increase given in 3-D at different system geometries and the noise increase due to system count rate limitations and random coincidences is studied, Based on Monte Carlo simulations, the amount of true, scatter and random coincidences have been estimated within a wide range of geometries. With a simple dead time model for the data collection system we have investigated if an optimized geometry can be found for brain function studies. The optimization is, as expected, not unique but is strongly dependent on the administered amount of activity as well as the choice of the dead time parameters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Machinery and processing: An overview of engine filtration (2008)

Many of the advances in automotive and heavy duty engine design in the past century have played out in filter element and media design. Filtration has helped to improve engine performance as we know it today. Here, David von Loesecke and Bob Murphey of Hollingsworth & Vose explore this rapidly changing industry by looking at the background of engine filtration and delving into where the industry is now.
TE and TM coupling coefficients for index-gain multigrating waveguides (1992)

The coupling coefficients of dielectric optical waveguides with more than one grating and with a periodic perturbation of the loss and gain are calculated for TE and TM modes. Analytical expressions for the coupling coefficient are given for the case of an asymmetric trapezoidal-like grating profile. Results obtained using various approximations of the unperturbed waveguide are presented and compared.
Kirchenrechtliche Lehrbücher in der Tschechoslowakei und in Jugoslawien (1930)

Article Kirchenrechtliche Lehrbücher in der Tschechoslowakei und in Jugoslawien was published on August 1, 1930 in the journal Zeitschrift der Savigny-Stiftung für Rechtsgeschichte: Kanonistische Abteilung (volume 19, issue 1).
Functionalized Fullerenes in Self-Assembled Monolayers (2011)

Anisotropy of intermolecular and molecule-substrate interactions holds the key to controlling the arrangement of fullerenes into 2D self-assembled monolayers (SAMs). The chemical reactivity of fullerenes allows functionalization of the carbon cages with sulfur-containing groups, thiols and thioethers, which facilitates the reliable adsorption of these molecules on gold substrates. A series of structurally related molecules, eight of which are new fullerene compounds, allows systematic investigation of the structural and functional parameters defining the geometry of fullerene SAMs. Scanning tunnelling microscopy (STM) measurements reveal that the chemical nature of the anchoring group appears to be crucial for the long-range order in fullerenes: the assembly of thiol-functionalized fullerenes is governed by strong molecule-surface interactions, which prohibit formation of ordered molecular arrays, while thioether-functionalized fullerenes, which have a weaker interaction with the surface than the thiols, form a variety of ordered 2D molecular arrays owing to noncovalent intermolecular interactions. A linear row of fullerene molecules is a recurring structural feature of the ordered SAMs, but the relative alignment and the spacing between the fullerene rows is strongly dependent on the size and shape of the spacer group linking the fullerene cage and the anchoring group. Careful control of the chemical functionality on the carbon cages enables positioning of fullerenes into at least four different packing arrangements, none of which have been observed before. Our new strategy for the controlled arrangement of fullerenes on surfaces at the molecular level will advance the development of practical applications for these nanomaterials.