gebhart/patrepeval huggingface dataset:
4-Hydroxybenzoate-coenzyme A ligase from Rhodopseudomonas palustris: purification, gene sequence, and role in anaerobic degradation (1994)

Anaerobic metabolism of most aromatic acids is initiated by coenzyme A thioester formation. Rhodopseudomonas palustris grows well under anaerobic, phototrophic conditions with many aromatic acids, including benzoate and 4-hydroxybenzoate, as a carbon source. A coenzyme A ligase that reacts with 4-hydroxybenzoate was purified from 4-hydroxybenzoate-grown cells of R. palustris. This enzyme required MgATP, reduced coenzyme A, and 4-hydroxybenzoate, benzoate, or cyclohex-1,4-dienecarboxylate for optimal activity but also used phosphopantetheine, cyclohex-2,5-dienecarboxylate, and 4-fluorobenzoate at lower rates. The 4-hydroxybenzoate-coenzyme A ligase differed in molecular characteristics from a previously described benzoate-coenzyme A ligase from R. palustris, and the two ligases did not cross-react immunologically. The gene encoding the 4-hydroxybenzoate enzyme was cloned and sequenced. The deduced gene product showed about 20% amino acid identity with bacterial coenzyme A ligases involved in aerobic degradation of aromatic acids. An R. palustris mutant carrying a disrupted 4-hydroxybenzoate-coenzyme A ligase gene was unable to grow with 4-hydroxybenzoate under anaerobic conditions, indicating that the enzyme is essential for anaerobic degradation of this compound.
Single-shot measurement of the complete spatiotemporal field of an ultrashort laser pulse (2006)

We present a technique for measuring the full spatiotemporal electric field of a femtosecond pulse on a single shot. Using a simple apparatus, we generate multiple replicas of the pulse to be measured and record numerous spatially separated digital holograms at different frequencies using a spectrally-resolved reference pulse on a single-exposure digital hologram. We then numerically reconstruct the complete electric field, E(<i>x,y,r</i>), using a direct algorithm. The technique is demonstrated using pulses from a modelocked Ti:Sapphire oscillator.
Imprinting of the MEDEA Polycomb Gene in the Arabidopsis Endosperm (1999)

Tetsu Kinoshita, Ramin Yadegari, John J. Harada, Robert B. Goldberg, Robert L. Fischer, Imprinting of the MEDEA Polycomb Gene in the Arabidopsis Endosperm, The Plant Cell, Vol. 11, No. 10 (Oct., 1999), pp. 1945-1952
Tamoxifen inhibits angiogenesis in estrogen receptor-negative animal models. (2000)

Inhibition of tumor angiogenesis is a therapeutic strategy that can inhibit tumor growth and metastases. The aim of this study was to determine whether the estrogen receptor (ER) ligand drug tamoxifen has antiangiogenic effects. We used three different models of angiogenesis, including measurement of microvessel densities in murine tumors, ex vivo aortic ring assays, and corneal pocket assays. ER-negative fibrosarcoma tumors in tamoxifen-treated ovariectomized rats had significantly less vessel formation compared with untreated animals (median microvessel density, 53.6 versus 94.3 counts/per x 200 field; P = 0.002). Rat aortic rings treated with tamoxifen at several different concentrations demonstrated significantly less vascular sprouting than control rings (P = 0.0001). Corneal pocket assays performed in tamoxifen-treated rats compared with control and estrogen-treated rats demonstrated decreased vascular length (0.88 mm versus 1.26 mm versus 1.47 mm; P = 0.022) and vessel area (21% versus 34% versus 47%; P = 0.018). These three animal models all showed significant inhibition of angiogenesis by tamoxifen and suggest a possible contributory mechanism of ER-independent manipulation by tamoxifen in the treatment and prevention of breast cancer. These studies raise the question as to whether or not newer ER ligand drugs might possess even more potent antiangiogenic effects, which in turn could lead to the broadening of the clinical usefulness of these compounds in a number of diseases. More importantly, these studies suggest that the antiangiogenic effects of tamoxifen are due, in part, to ER-independent mechanisms.
CA 125 in Ovarian Cancer: Advances and Controversy (1998)

Ovarian cancer continues to be a major health threat for women. The American Cancer Society estimates that in the United States in 1998, 25 400 new cases will be diagnosed and 14 500 women will die as a result of this disease (1). Most of these cancers are epithelial in origin, as germ cell tumors of the ovary represent only ∼5% of the total. Approximately 70% of epithelial ovarian cancers will occur in women who are over the age of 50 years, and more than one-half of the women will be diagnosed with advanced disease. Thus, these women will have a 5-year survival rate of <30%. Certainly, there is great need for improved diagnostic methods to permit detection of this disease at an early stage, as well as more effective treatments for adenocarcinoma of the ovary.

CA 125, the first serum tumor marker test for epithelial cancer of the ovary, was introduced by Bast et al. in 1983 (3). The murine monoclonal antibody (OC125) that is used to detect the CA 125 antigen was obtained after immunization with the OVCA 433 cell line (4). The original CA 125 test used the OC125 antibody as both the capture and indicator antibody in a radioimmunometric assay. More recently, the CA 125 II test has been developed, which uses the M 11 monoclonal antibody as the capture antibody for CA 125. A recent epitope-mapping workshop conducted by the International Society of Oncodevelopmental Biology and Medicine (ISOBM) has defined the binding characteristics of monoclonal antibodies reactive with CA 125 and has identified two major regions on the antigen, which are called OC125-like and M 11-like epitopes (5). The CA 125 antigen is actually a heterogeneous mixture of glycoproteins with a molecular weight range of 200-1000 kDa, but lower molecular weight species have also been …
Spectral-based color separation algorithm development for multiple-ink color reproduction (1999)

Conventional four-color printing systems are limited by an insufficient number of degrees of freedom for tuning the visible region of the spectrum; as a consequence, they are often limited to metameric color reproductions. That is, color matches defined for a single observer and illuminant (usually CIE illuminant D50 and the 1931 standard observer) are often unstable when viewed under other illuminants or by other observers. For critical color-matching applications, such as catalog sales and artwork reproductions, the results are usually disappointing due to typical uncontrolled lighting and viewing. Furthermore, the existing multiple-ink printing systems, which all focus on expanding color gamut, do not alleviate metamerism since their separation algorithms are trichromatic in nature. The advantage of an increased number of degrees of freedom is not exploited. A research and development program has been initiated at the Rochester Institute of Technology's Munsell Color Science Laboratory to develop a spectral-based color reproduction system Research has included multi-spectral acquisition systems and spectral-based printing. The current research is concerned with bridging these analysis and synthesis stages of color reproduction. The goal of the doctoral research was to minimize IV metamerism between originals and their corresponding reproductions, thus best approaching spectral matches. Accomplishing this goal required first estimating the spectral properties of the colorants used to create the original object or set of objects. After the possible colorants were statistically uncovered, they were correlated to an existing ink database for determining an optimal ink set. An algorithm was developed for predicting ink overprints, known as the Neugebauer secondary, tertiary, quaternary primaries, etc., which is the required information for color synthesis using a halftone printing process. Once all the required Neugebauer primaries were determined, a spectralbased printing model minimizing metamerism was derived to calculate the corresponding color separations for each selected ink. The various research components were tested computationally and experimentally. Finally, a DuPont Waterproof system was used as a representation of halftone printing process to output each color separation in order to test several computational subsystems. This completes the chain of a spectral-based output system. Five modules of this chain were developed and discussed in this dissertation.
Ka-Band FET Oscillator (Short Paper) (1985)

The design and performance of GaAs FET oscillators operating near 36 GHz are presented. The oscillators used readily available GaAs FET's and were built in a microstrip circuit configuration. An output power of about +8 dBm was obtained with two devices in a single oscillator.
MDM2 does not influence p53-mediated sensitivity to DNA-damaging drugs. (2002)

MDM2 inhibits transactivation properties of the tumor suppressor protein p53 by binding to and facilitating proteasomal degradation of p53. Because MDM2 targets p53 for degradation, it was anticipated that cells that overexpress MDM2 would not contain functional wild-type p53 (wtp53). However, p53 and MDM2 in cells with damaged DNA can become phosphorylated, and their binding to each other can become inhibited. Thus, p53 remains functional and induces apoptosis of damaged cells. Here we report the results of experiments designed to investigate whether MDM2 amplification and overexpression can inhibit p53-mediated chemosensitivity to DNA-damaging drugs. Two cell lines in which MDM2 is amplified, NB-1691 and Rh18, were transduced with an adenoviral expression vector for p53 (Ad.p53). Although functional wtp53 was detected, no change in chemosensitivity was observed, suggesting that endogenous wtp53 may have been active in the MDM2-amplified cells. The adenoviral vector Ad.MDM2 was used to generate MDM2 expression in a rhabdomyosarcoma cell line, Rh30-CI.27, engineered to express inducible wtp53. When p53 expression was induced, cells became chemosensitive to actinomycin D in the presence or absence of MDM2 expression; this result suggests that MDM2 cannot inhibit p53-mediated chemosensitivity. There was no evidence of a reduced amount of MDM2-p53 binding after drug exposure, but the remaining unbound wtp53 may be functional and capable of potentiating cytotoxicity. In conclusion, MDM2 expression is important in inhibiting p53 function during tumor development but not during the DNA damage-mediated cytotoxic response.
Cu dual damascene for advanced metallisation (0.18 μm and beyond) (2003)

A review of specific steps performed during integration of Cu metallisation in a multilevel dual damascene architecture has been made. Several steps are identified as crucial processes for copper integration and a complete optimisation should include dual damascene architecture, barrier material and deposition process, copper deposition process and chemical mechanical polishing (CMP). All of these aspects are reviewed, illustrated with examples and discussed, including comparison of several dual damascene architectures, comparison of barrier material performance both for PVD and CVD processes, comparison of Cu ECD and Cu CVD approaches with a look at the complementary aspects of these methods. Copper contamination issues, a major concern for introduction of copper metallisation, are addressed in detail. On active devices, several barrier materials have been claimed as being efficient against copper diffusion. However, during process integration, contamination issues are faced before deposition of the barrier layers. Heavy contamination can occur either during Cu CMP or during dielectric etching and via opening on top of contacted copper lines. These residues concentrated at the dielectric surface would be effective sources for current leakage and shorts between interconnection lines. Several cleaning solutions to remove metal contamination are reviewed and their efficiencies compared.
Suspension of Bone Marrow–Derived Undifferentiated Mesenchymal Stromal Cells for Repair of Superficial Digital Flexor Tendon in Race Horses (2007)

It has been proven that mesenchymal stromal cells (MSCs) can differentiate into tenocytes. Attempts to repair tendon lesions have been performed, mainly using scaffold carriers in experimental settings. In this article, we describe the clinical use of undifferentiated MSCs in racehorses. Significant clinical recovery was achieved in 9 of 11 horses evaluated using ultrasound analysis and their ability to return to racing. Our results show that the suspension of a small number of undifferentiated MSCs may be sufficient to repair damaged tendons without the use of scaffold support. Ultrasound scanning showed that fibers were correctly oriented. By using undifferentiated cells, no ectopic bone deposition occurred. A sufficient number of cells was recovered for therapeutic purposes in all but 1 case. We suggest that the use of autologous MSCs is a safe therapeutic method for treating incompletely (i.e., not full-thickness) damaged tendons.
Characterization of the Liquid−Crystalline Phases in the Glycerol Monooleate/Diglycerol Monooleate/Water System (2000)

The ternary phase diagram of two nonionic polar lipids, glycerol monooleate (GMO) and diglycerol monooleate (DGMO), in water has been characterized through NMR, polarizing optical microscopy, SAXS, and rheological measurements. GMO in water forms a lamellar and two types of bicontinuous cubic phases. The diamond type exists in equilibrium with water. DGMO, with its bulky polar group, forms only lamellar structures that also coexist with water. In the ternary GMO/DGMO/water system, the regions of lamellar and cubic phases are significantly enlarged, and a swollen cubic phase of the gyroid type exists in equilibrium with water. Measurement of the viscoelastic properties revealed that the cubic phases are elastic, independent of the sample composition. The cubic phases become softer (the G‘ storage modulus decreases) with increasing water and DGMO content. A discontinuity is observed in the G‘ versus water content graph at the transition between the gyroid and the diamond cubic phases.
Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation (2009)

Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non-associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methylation status of over 25,000 CpG islands in the human genome. Experiments were performed to demonstrate low system noise in the methodology and that the array probes have a high signal to noise ratio. Methylation measurements between different cell lines were validated demonstrating the accuracy of measurement. We then identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter-associated islands in a set of breast and ovarian tumors. We demonstrate that this methodology accurately identifies methylation profiles in cancer and in principle it can differentiate any CpG methylation alterations and can be adapted to analyze other species.
Orígenes, ampliación y aplicaciones de la equivalencia de estímulos (2002)

El presente trabajo es una revision sobre las lineas actuales de investigacion dentro del fenomeno
de las clases de equivalencia, cuya principal caracteristica es la emergencia de relaciones de control de
estimulos sin entrenamiento directo. Se comienza con una descripcion de los estudios pioneros, las
propiedades definitorias del fenomeno y las razones relevantes para su estudio. Se continua con una
exploracion sobre los origenes de las relaciones no entrenadas, destacando la importancia de la
investigacion de laboratorio con no-humanos. Se concluye, por un lado, con la utilizacion del paradigma
de las clases de equivalencia en el estudio del razonamiento analogico; y por otro lado, con su uso
terapeutico en el tratamiento del autismo.
All-Dielectric Metamaterials: Path to Low Losses and High Spectral Selectivity (2013)

Ohmic losses severely limit the performance of metamaterials. High-index semiconductors offer an attractive alternative. We review several meta-surfaces based on silicon and silicon carbide enabling infrared applications such as polarization manipulation and thermal emission.
Postsynthetic N-methylation making a metal–organic framework responsive to alkylamines (2017)

The postsynthetically created electron-deficient 2,2'-bipyridinium moieties in a Zr-MOF provide charge-transfer interacting sites for recognizing and capturing alkylamines with excellent selectivity; meanwhile the MOF shows fast and reversible vapochromism and luminescence quenching in response to alkyamines.
Reversible Switching of DNA–Gold Nanoparticle Aggregation (2004)

Schaltbare Bildung von Materialien: Aktuator-Oligonucleotide, die mit den Linker-Oligomeren in den Partikelaggregaten hybridisieren, machen die Aggregation von DNA-modifizierten Goldnanopartikeln reversibel (siehe Schema). Dieser Ansatz ebnet den Weg zur Erzeugung programmierbarer funktioneller Materialien.
Interference Alignment on the Deterministic Channel and Application to Fully Connected Gaussian Interference Networks (2009)

An interference alignment example is constructed for the deterministic channel model of the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> -user interference channel. The deterministic channel example is then translated into the Gaussian setting, creating the first known example of a fully connected Gaussian <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> -user interference network with single antenna nodes, real, nonzero and constant channel coefficients, and no propagation delays where the degrees of freedom outerbound is achieved. An analogy is drawn between the propagation delay based interference alignment examples and the deterministic channel model which also allows similar constructions for the two-user <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X</i> channel as well.
Inhibition of lymphocyte endothelial adhesion and in vivo lymphocyte migration to cutaneous inflammation by TA-3, a new monoclonal antibody to rat LFA-1 (1992)

Lymphocyte function-associated Ag-1 (LFA-1) or CD11a/CD18 mediates lymphocyte adhesion to cultured vascular endothelial cells (EC). Thus, LFA-1 likely plays a major role in lymphocyte migration out of the blood, but there is little information on this in vivo. Small peritoneal exudate lymphocytes (sPEL) and lymph node (LN) lymphoblasts adhere to cytokine-activated EC and preferentially migrate to cutaneous inflammatory sites. The role of LFA-1 in the adherence and in vivo migration of these T cells was determined. Because of a lack of anti-rat LFA-1, mAb were prepared to rat T cells. One mAb, TA-3, inhibited homotypic aggregation; T cell proliferation to Ag, alloantigens, and mitogens; stained all leukocytes; and immunoprecipitated 170- and 95-kDa polypeptides from lymphocytes and neutrophils. TA-3 binding to lymphocytes also required Ca2+, but not Mg2+. Thus, TA-3 appears to react with rat LFA-1. TA-3 inhibited spleen T cell adhesion to unstimulated EC by 30% and to IFN-gamma, TNF-alpha, IL-1 alpha, and LPS stimulated EC by 50 to 60% but inhibited sPEL EC adhesion by only 10%. TA-3 also strongly inhibited anti-CD3-stimulated LN T cell adherence. The migration of spleen T cells to delayed-type hypersensitivity and skin sites injected with LPS, poly I:C, IFN-gamma, IFN-alpha/beta, and TNF was inhibited by 72 to 88% by TA-3, and was decreased by 50% to peripheral LN. TA-3 caused less but still 50 to 60% inhibition of sPEL migration to inflamed skin. Lymphoblast migration to skin was inhibited 40 to 80% and to PLN by 30%. Migration of lymphocytes from all sources to mesenteric LN was inhibited by 32 to 60%. In conclusion, LFA-1 mediates much of the adherence of spleen T cells and lymphoblasts to EC in vitro, most of the migration of these cells to dermal inflammation and about 50% of the homing of LN and spleen T cells to peripheral and mesenteric LN. sPEL are less dependent on LFA-1 for adhesion to EC in vitro and for migration to inflamed skin and LN in vivo.
Performance evaluation of symmetric cryptography in embedded systems (2011)

We consider the problem of implementing security algorithms into embedded systems deployed in automation applications. Such systems are typically built on embedded microcontrollers with limited resources and as hardware changes may not be possible or convenient, the software based cryptography is a suitable solution. In this paper we present results of performance benchmarks of different software-implemented symmetric cryptography algorithms on 8 and 16-bit microcontroller platforms. The contribution of the work is in comparing performance of different algorithms, embedded microcontroller platforms, effects of optimizations and different implementations.
Organogelation and Hydrogelation of Low-Molecular-Weight Amphiphilic Dipeptides: pH Responsiveness in Phase-Selective Gelation and Dye Removal (2009)

The search for efficient low-molecular-weight gelators (LMWGs) with possible structure-activity correlation is on the rise. The present work reports a novel set of amphiphilic dipeptide-based carboxylic acids capable of efficiently gelating organic solvents. More interestingly, their sodium salts showed enhanced efficiency in organogelation with the additional ability to gelate water. Electrostatic interactions present in the aggregation of the sodium carboxylates of amphiphilic dipeptides seem to be important because some of the nongelator carboxylic acids turned out to be excellent gelators upon salt formation. The combinations and sequence of the amino acids in the dipeptide moiety were systematically altered to understand the collective importance of the nonpolar aliphatic/aromatic substitution in amino acids in the self-assembling behavior of amphiphiles. Almost a 20-fold enhancement in the gelation ability was observed on reversing the sequence of the amino acid residues, and in some cases, nongelators were transformed to efficient gelators. Spectroscopic and microscopic studies of these thermoreversible organo/hydrogels revealed that balanced participation of the noncovalent interactions including hydrogen bonding and van der Waals interactions are crucial for organo/hydrogelation. These dipeptides selectively gelate organic solvents from their mixtures with water, and the xerogels prepared from these organogels showed time-dependent adsorption of dyes such as crystal violet. The most remarkable feature of these gelators is the pH responsiveness, which was aptly utilized for the pH-dependent phase-selective gelation of either solvent in a biphasic mixture of oil and water. The dissimilar gelation ability of the acid and its salt originating from the pH responsiveness of the amphiphilic dipeptide was employed in the instant removal of large amounts of dyes for wastewater treatment.
Highly enantioselective three-component Povarov reaction catalyzed by SPINOL-phosphoric acids (2012)

Chiral SPINOL-phosphoric acids exhibited high activities and excellent diastereo- and enantioselectivities in the catalysis of the three-component Povarov reaction of benzyl N-vinylcarbamate, anilines and aldehydes with a catalyst loading of 5 mol%. The synthetic utility of this protocol was demonstrated by the asymmetric synthesis of enantioenriched benzo[e]indolizidine with excellent yield and excellent level of sterecontrol.