gebhart/patrepeval huggingface dataset:
Microencapsulation of Bacteriophage Felix O1 into Chitosan-Alginate Microspheres for Oral Delivery (2008)

This paper reports the development of microencapsulated bacteriophage Felix O1 for oral delivery using a chitosan-alginate-CaCl(2) system. In vitro studies were used to determine the effects of simulated gastric fluid (SGF) and bile salts on the viability of free and encapsulated phage. Free phage Felix O1 was found to be extremely sensitive to acidic environments and was not detectable after a 5-min exposure to pHs below 3.7. In contrast, the number of microencapsulated phage decreased by 0.67 log units only, even at pH 2.4, for the same period of incubation. The viable count of microencapsulated phage decreased only 2.58 log units during a 1-h exposure to SGF with pepsin at pH 2.4. After 3 h of incubation in 1 and 2% bile solutions, the free phage count decreased by 1.29 and 1.67 log units, respectively, while the viability of encapsulated phage was fully maintained. Encapsulated phage was completely released from the microspheres upon exposure to simulated intestinal fluid (pH 6.8) within 6 h. The encapsulated phage in wet microspheres retained full viability when stored at 4 degrees C for the duration of the testing period (6 weeks). With the use of trehalose as a stabilizing agent, the microencapsulated phage in dried form had a 12.6% survival rate after storage for 6 weeks. The current encapsulation technique enables a large proportion of bacteriophage Felix O1 to remain bioactive in a simulated gastrointestinal tract environment, which indicates that these microspheres may facilitate delivery of therapeutic phage to the gut.
Melanoma Resembling Spindle and Epithelioid Cell Nevus (1979)

Three cases of malignant melanoma resembling spindle and epithelioid cell nevus histologically are presented. Lesions having histologic features of spindle and epithelioid cell nevus (Spitz nevus or juvenile melanoma) at or after puberty should be regarded with caution, particularly when they are heavily melanized. Such lesions are in a histologic "gray zone" and may be malignant. (<i>Arch Dermatol</i>115:1416-1420, 1979)
Circular Polymerase Extension Cloning (2013)

High-throughput genomics, proteomics, and the emerging field of synthetic biology demand ever more convenient, economical, and efficient technologies to assemble and clone genes, gene libraries, and synthetic pathways. Here, we describe an extremely simple, efficient, and cost-effective cloning method, circular polymerase extension cloning (CPEC), for complex, combinatorial, or multi-fragment assembly as well as routine cloning. This method uses a single polymerase to assemble and clone multiple inserts with any vector in a one-step reaction in vitro. No restriction digestion, ligation, or single-stranded homologous recombination is required.
Highly Conductive, Regioregular Alkoxy-Functionalized Polythiophenes:  A New Class of Stable, Low Band Gap Materials (2005)

Presented here is the synthesis and unique physical properties for a new class of highly processable regioregular poly(3-alkoxy-functionalized thiophenes). These polymers exhibit high electrical conductivities with very good stabilities (over 3 years) when doped with iodine vapor followed by exposure to ambient conditions.
A path-based timing-driven quadratic placement algorithm (2003)

This paper presents a path-based timing-driven quadratic placement algorithm. The delay of the path acts as the timing constraints. In the global optimization step, it tries to satisfy the timing constraints. In the partition step, it tries to decrease the cut number of critical paths. It has some special skills, such as decrease the delay on the longest path, pad assign, to decrease the delay further. Results show this algorithm can make the timing behavior improve more than 20%.
Inhibition of extracellular signal-regulated kinase (ERK) mediates cell cycle phase independent apoptosis in vinblastine-treated ML-1 cells. (2001)

Chemotherapeutic agents induce alterations in intracellular signal transduction cascades that culminate in the initiation of the apoptotic program. Here, the relationship between the mitogen-activated protein kinase (MAPK) response and apoptosis in ML-1 cells treated with vinblastine and paclitaxel was investigated. We show that these compounds elicit different effects on MAPKs with vinblastine, but not paclitaxel, increasing both c-Jun-NH2-terminal kinase (JNK) and p38 activity. However, vinblastine and paclitaxel both induced apoptosis with similar kinetics, suggesting that increased JNK and p38 activity is not required for apoptosis that is induced by microtubule interfering agents. Strikingly, the abrogation of extracellular signal-regulated kinase (ERK)-signaling by the MAPK/ERK kinase (MEK)1/2 inhibitor PD098059 in combination with vinblastine robustly induced apoptosis in ML-1 cells at a rate much faster than treatment with vinblastine alone and occurred at all phases of the cell cycle. This apoptotic induction was attributed to JNK activation because: (a) non-JNK-activating concentrations of vinblastine failed to increase apoptosis in the presence of PD098059; (b) apoptosis induced by paclitaxel, which did not activate JNK, was not potentiated by PD098059; and (c) transduction of an inhibitor of JNK activity partially suppressed both JNK activity and apoptosis induced by vinblastine plus PD098059. Additionally, we found that the activation of JNK by vinblastine occurred upstream of effector caspase activation because treatment with a pan-specific caspase inhibitor (valine-alanine-aspartate-fluoromethylketone) resulted in complete abrogation of apoptosis with no effect on MAPK signaling. Taken together, these data suggest that inhibition of the MEK-->ERK signal transduction cascade alleviates cell cycle dependence for vinblastine-induced apoptosis by a mechanism that requires JNK activation.
Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants (2008)

Linking genomic signatures to gene coexpression analysis provides a unique method of relating an observed plant phenotype to changes in gene expression that underlie that phenotype. Such information is critical to current and future investigations in plant biology and, in particular, to evolutionary ecology, where a mechanistic understanding of adaptive physiological responses to abiotic stress can provide researchers with a tool of great predictive value in understanding species and population level adaptation to climate change.
Hormone-induced progesterone receptor phosphorylation consists of sequential DNA-independent and DNA-dependent stages: analysis with zinc finger mutants and the progesterone antagonist ZK98299. (1992)

Human progesterone receptors (hPRs) are phosphorylated at multiple serine residues, first in a basal step and then in a hormone-induced step. To determine whether hormone-induced phosphorylation precedes or follows the interaction of hPRs with DNA two strategies were used. (i) DNA binding was prevented or altered with site-specific mutants of the A form of hPR; (ii) DNA binding of wild-type hPR forms A and B was prevented with the progesterone antagonist ZK98299. Two hPRA mutants were constructed: DBDCys, which lacks a critical cysteine residue in the first zinc finger, and DBDsp, which is mutated at three discriminatory amino acids to change its DNA binding specificity from a progesterone response element to an estrogen response element. Receptors were transiently expressed in PR-negative cells and were intranuclear. DBDCys did not bind DNA in vitro and DBDsp bound only the estrogen response element. Transiently expressed hPRA and DBDsp showed the upward shift in electrophoretic mobility characteristic of hormone-induced phosphorylation; it was absent with DBDCys. Hormone-induced [32P] orthophosphate incorporation into transiently expressed DBDCys was reduced 60% compared to hPRA and DBDsp but was not eliminated. ZK98299 binds hPRs but prevents their interaction with DNA. Compared to R5020, the antagonist reduced phosphorylation of hPRB and hPRA in T47D breast cancer cells by 60% and totally prevented the mobility shift. We conclude that the hormone-induced phosphorylation of hPR includes DNA-independent and DNA-dependent stages and that only DNA-dependent sites contribute to the mobility shift.
Thrombopoietin from beginning to end (2014)

In the two decades since its cloning, thrombopoietin (TPO) has emerged not only as a critical haematopoietic cytokine, but also serves as a great example of bench-to-bedside research. Thrombopoietin, produced by the liver, is the primary regulator of megakaryocyte progenitor expansion and differentiation. Additionally, as TPO is vital for the maintenance of haematopoietic stem cells, it can truly be described as a pan-haematopoietic cytokine. Since recombinant TPO became available, the molecular mechanisms of TPO function have been the subject of extensive research. Via its receptor, c-Mpl (also termed MPL), TPO activates a wide array of downstream signalling pathways, promoting cellular survival and proliferation. Due to its central, non-redundant role in haematopoiesis, alterations of both the hormone and its receptor contribute to human disease; congenital and acquired states of thrombocytosis and thrombocytopenia and aplastic anaemia as a result from dysregulated TPO expression or functional alterations of c-Mpl. With TPO mimetics now in clinical use, the story of this haematopoietic cytokine represents a great success for biomedical research.
Possible peptide chain termination mutants in thymide kinase gene of a mammalian virus, herpes simplex virus. (1975)

Mutations in the viral gene coding for the thymidine kinase (ATP:thymidine 5'-phosphotransferase, EC 2.7.1.75) induced by herpes simplex virus have been obtained by selection of virus resistant to bromodeoxyuridine when grown in thymidine-kinase-deficient LMTK- mouse cells. Proteins labeled after infection of Vero (monkey) cells with herpes simplex virus were analyzed by gel electrophoresis and one protein of about 40,000 daltons was consistently altered in a number of thymidine-kinase-deficient mutants. Many viral mutants lacked this peptide and one class of these mutants induced the synthesis of new shorter peptides. Revertant virus could be selected which simultaneously regained the ability to induce thymidine kinase activity, regained the intact thymidine kinase peptide, and lost the ability to synthesize the shorter peptide fragment. These mutants comprise a class of animal virus mutants which have the properties expected of peptide chain termination mutants.
A system level implementation of Rijndael on a memory-slot based FPGA card (2003)

This paper describes system level issues encountered in a high performance implementation of a Rijndael encryption core on a memory-slot based reconfigurable computing platform called Pilchard. The Rijndael algorithm was adopted in 2000 by the US National Institute of Standards and Technology (NIST) as the Advanced Encryption Standard (AES). In the implementation of Rijndael, changing the number of unrolled rounds in the encryption core can affect the performance of the system. It is shown that for the design presented, the highest performance of 755 Mbit/sec was achieved by implementing a core with a single round. Although it is relatively easy to implement a high performance core on an FPGA, due to I/O bottlenecks, achieving high system level performance is more difficult. In order to optimize the performance of the host/FPGA interface, special instructions from the Intel Pentium III streaming SIMD extensions (SSE) along with write-combining memory operations were used. These features enabled the measured throughput of the AES core to reach 445 Mbit/sec which, although still slower than the AES core, was double that of an unoptimized interface.
Effect of Halogenation on Yellow Metal Corrosion: Inhibition by Triazoles (1994)

The adsorption isotherm and the corrosion rate profile for tolyltriazole (TT) and butylbenzotriazole (BBT) were presented as functions of immersion time in triazole solution. Formation of a triazole film on a yellow metal surface was shown to play a major role in corrosion inhibition. In the absence of triazole in bulk solution, halogenation was detrimental to TT and BBT surface films. The disruption mechanism was attributable to chemical decomposition of the adsorbed triazole by halogen. However, adding TT (&gt; 0.2 mg/L) to the halogen-based biocide solution improved stability of the protective TT film significantly. The improvement in stability was evident from the nearly unchanged surface coverage and lower corrosion rate. Based on this result, an enhanced TT-intermittent-feed method was developed. The metal surface was passivated initially with TT. Addition of halogen-based biocide was accompanied by a concurrent addition of TT (0.5 mg/L to 2 mg/L). Results demonstrated that the enhanced TT-intermittent-feed method performed better than the initial slug feeding of TT and BBT in inhibiting yellow metal corrosion.
Lateral prediction for noise attenuation by t-x and f-x techniques (1995)

Abstract Attenuating random noise with a prediction filter in the time-space domain generally produces results similar to those of predictions done in the frequency-space domain. However, in the presence of moderate- to high-amplitude noise, time-space or t-x prediction passes less random noise than does frequency-space, or f-x prediction. The f-x prediction may also produce false events in the presence of parallel events where t-x prediction does not. These advantages of t-x prediction are the result of its ability to control the length of the prediction filter in time. An f-x prediction produces an effective t-x domain filter that is as long in time as the input data. Gulunay's f-x domain prediction tends to bias the predictions toward the traces nearest the output trace, allowing somewhat more noise to be passed, but this bias may be overcome by modifying the system of equations used to calculate the filter. The 3-D extension to the 2-D t-x and f-x prediction techniques allows improved noise attenuation because more samples are used in the predictions, and the requirement that events be strictly linear is relaxed.
Removal of Pb<sup>2+</sup>, Cd<sup>2+</sup>, Fe<sup>3+</sup>, and Sr<sup>2+</sup>from Aqueous Solution by Selected Activated Carbons Derived from Date Pits (2008)

Date pits (DP) are a huge solid waste in Egypt and are of little or no economic value and in fact present a disposal problem. The quantity of DP has been estimated at a million tons per year. DP have been used for the preparation of physically and chemically activated carbons. The raw materials were physically activated with steam or chemically by impregnation with 10% ferric chloride or calcium acetate. The present study deals with the factors affecting the uptake of (Pb2+, Cd2+, Fe3+, and Sr2+) as pollutants from aqueous solution using activated carbon developed from locally available material DP, by a one‐step steam pyrolysis in a batch mode. The effect of various factors—carbon type, carbon dosage, pH, initial concentration, and temperature on the adsorption capacity were quantitatively determined. The two equilibrium models, the Langmuir and Freundlich equations, were discussed. In this work, analyses and batch adsorption experiments have been carried out to characterize and understand the adsorption mechanism by modeling the adsorption kinetics. Concurrently removal of these cations from the aqueous medium were found to be affected by the presence of some anions, NO3 −, CO3 −2, SO4 −2 and masking agents, oxalic acid, and EDTA in solution.
X‐Ray Characterization of Melanins—II (1994)

Structural modeling of amorphous eumelanin has been carried out by comparing calculated data, S(q) and RDF(r), in reciprocal and real space, respectively, for limited random network models with the experimental X‐ray scattering data of tyrosine melanin (Cheng et al., 1994). A basic picture of the atomic arrangements in amorphous eumelanin, which accounts for the short and intermediate range order, has been formulated. This reveals domains of a fundamental “particle” dimension of R ∼ 15 Å, consisting of a paracrystalline array of disordered planar networks polymerized by 4‐8 DHI monomers with a graphite‐like stacking spacing of ∼ 3.45 Å, 4‐5 layers thick.
SLM/CCDD structures for high speed numerical computing and signal processing (1991)

The authors extend previous work concerning the development of novel spatial light modulators (SLMs)/charge-coupled devices detectors (CCDDs) based on optoelectronic architectures for performing high-speed numerical computing and signal processing. These architectures exploit the broadcast nature of light to achieve parallelism, thereby increasing throughput and reducing computing time. Architectures for performing basic vector and matrix multiplications are introduced. Various signal processing applications based on a simple SLM/CCDD-based device and its derivatives are also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Controlling logical inference in multilevel database systems (2003)

The potential for logical inference of high-level information based on lower-level visible data presents a threat to multilevel security. The author proposes a framework for studying these inference control problems, describes a representation for relevant semantics of the application, develops criteria for safety and security of a system to prevent these problems, and describes the functionality of the proposed classification tool in terms of a scenario for its use.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<i>Z</i>-Selective Intramolecular Horner−Wadsworth−Emmons Reaction for the Synthesis of Macrocyclic Lactones (2010)

When the substrates (ArO)(2)P(O)CH(2)CO(2)---CHO (Ar = Ph, o-t-BuPh) were added to a THF solution containing 3 equiv of NaH at 0 degrees C or NaI-DBU at rt over 1-10 h, the intramolecular Horner-Wadsworth-Emmons reaction proceeded efficiently to give the 12-18-membered-ring lactones in 69-93% yields with 89-100% Z selectivity. On the other hand, (EtO)(2)P(O)CH(2)CO(2)---CHO gave the 13-18-membered-ring lactones in 52-82% yields with 89-99% E selectivity using LiCl-DBU in MeCN or THF.
Effect of Clamping Load on the Performance of Proton Exchange Membrane Fuel Cell Stack and Its Optimization Design: A Review of Modeling and Experimental Research (2013)

When individual proton exchange membrane fuel cells (PEMFCs) are assembled together to form a stack and provide energy for practical applications, an appropriate clamping load is usually required to render the stack high efficiency, high reliability, and excellent durability. From both modeling and experimental aspects, this article first highlights the effect of clamping load on the electron transfer, mass (water and reactant gases) transfer, and heat transfer in a PEMFC stack and then puts the attentions on the optimization design of clamping load with emphases on the optimal clamping load and the homogenous distribution of clamping load. This summary may deepen our understanding of the assembly of a PEMFC stack and provide referential information for the designer and manufacturer.
Design and testing of a new protection relay for variable speed DFI motor generators (2014)

This paper describes the design and testing of a new and innovative protection relay for protecting large variable speed Double Fed Induction (DFI) machines for pumped storage plants. The testing encompasses testing of the new protection with Non-Conventional Instrument Transformers (NCITs), Rogowski CTs and resistive voltage dividers, on a small DFI machine at EPFL as well as RTDS testing of the new protection on a large DFI machine, covering a range of stator and rotor fault conditions. For these machines low frequency currents are supplied to the rotor by means of VSC (Voltage Source Converter) power electronic converters from the AC system. ALSTOM is developing new protection to provide variable speed motor generators with a fully independent protection system that guarantees the plant's safety in all conditions. Currently, the market offers no protection relay to provide protection for extremely low frequency currents and voltages in variable speed rotors. The new protection relay will measure and monitor these signals, taking into account the start, stop and operation in both pump and generator modes. Cutting-edge “Digital Substation” technology, which incorporates NCITs with IEC 61850-9-2 LE process bus communications to the protection relays, is used to measure the low-frequency current and voltage signals. The main difficulties with the relay development are: (1) the dynamic variation of frequency; (2) the extremely low frequency; (3) the effect of the converter modulating the rotor voltage (PWM). New technology solutions have been developed, tested and implemented in a new relay to meet the challenging requirements to protect variable speed machines. ALSTOM offers a unique and complete protection package covering the entire variable speed machine (both stator and rotor) incorporating the latest NCIT and IEC 61850 technology.
Cross-layer throughput analysis for optical code labeled GMPLS networks (2005)

The use of optical CDMA as a labeling mechanism in generalized multi-protocol label switching (GMPLS) optical networks significantly increases the traffic isolation capabilities. These networks, referred to as optical code labeled GMPLS (OC-GMPLS), have higher resource utilization due to the finer flow granularity introduced into the network. In this paper we present a cross-layer mathematical model for the throughput of OC-GMPLS networks, which provides a quantitative measure for the performance of optical networks throughput taking into consideration the effect of the physical layer. The proposed mathematical model incorporates the physical layer effects on the network layer performance by expressing the throughput as a function of the physical layer bit error rate, as well as the network traffic parameters such as the number of users and the packet length. Using the developed analytical model we were able to demonstrate the significant enhancement in the network performance due to the use of OC-GMPLS. We also used our analytical model to derive several optimum network operating points, which are of great importance to network designers and researchers.
Raman Spectral Estimation via Fast Orthogonal Search (1997)

A Fourier transform (FT) spectrometer measures the autocorrelation (interferogram) of radiation emitted from a source and estimates the optical power spectral density through application of the discrete Fourier transform (DFT) to the recorded interferogram. Although a widely used method, FT spectrometry suffers because its frequency resolution is limited to the sampling rate divided by the number of time-series data points. A large number of points are therefore required to resolve an optical spectrum properly. In this paper, it is shown that a noise-resistant technique known as fast orthogonal search (FOS) can be used to achieve accurate optical spectrum estimation. Further, it is shown that frequency accuracy comparable to the DFT applied to the full interferogram can be obtained with FOS even if the original interferogram is contaminated with noise and then reduced by a factor of up to 10 by irregularly spaced sampling. The FOS application presented here is for the estimation of Raman spectra from interferograms acquired with an FT Raman spectrometer.
A Petri-net representation of the qualitative behaviour of a dynamical continuous-time system (1994)

In this paper an approach is presented how a qualitative model of a dynamical continuous-variable system can be set up. The method is based on Petri nets which have been successfully used so far to describe discrete-event systems. Places will be used to represent qualitative states whereas transitions model the qualitative state transitions of the system. The influence of input variables is reflected by labeling the transitions with input conditions. >