gebhart/patrepeval huggingface dataset:
Double <i>EGFR</i> mutants containing rare <i>EGFR</i> mutant types show reduced <i>in vitro</i> response to gefitinib compared with common activating missense mutations (2009)

Epidermal growth factor receptor (EGFR) mutations are common in lung adenocarcinomas, especially from nonsmoking women of Asian descent. We have previously shown EGFR mutations occur in >70% of lung adenocarcinoma from nonsmokers in our population with a complex mutational profile, including 13% of EGFR double mutations. In this study, we investigated the in vitro gefitinib response of four EGFR double mutants identified in untreated patients, including Q787R+L858R, E709A+G719C, T790M+L858R, and H870R+L858R. The phosphorylation profiles of EGFR and downstream effectors AKT, STAT3/5, and ERK1/2 were compared by immunoblot analyses among the single and double mutants transfected into H358 cells. Results showed that mutants responded to in vitro gefitinib treatment with different sensitivities. The G719C and L858R single mutants showed the highest gefitinib sensitivity compared with the corresponding coexisting single mutants E709A, Q787R, H870R, and T790M. The double mutants E709A+G719C, Q787R+L858R, and H870R+L858R showed attenuated responses to gefitinib in the EGFR and downstream effector phosphorylation profiles compared with G719C or L858R alone. T790M+L858R showed strong resistance to gefitinib. Clinically, the patient whose tumor contained H870R+L858R showed tumor stabilization by 250 mg oral gefitinib daily but cerebral metastasis developed 6 months later. Correlation with the in vitro phosphorylation profile of H870R+L858R suggested that treatment failure was probably due to inadequate suppression of EGFR signaling by the drug level attainable in the cerebrospinal fluid at the given oral dosage. Overall, the findings suggested that rare types of EGFR substitution mutations could confer relative gefitinib resistance when combined with the common activating mutants.
Interferon-gamma inhibits the intrahepatocytic development of malaria parasites in vitro. (1987)

In this study, we examined the activity of recombinant interferon (IFN)-gamma against Plasmodium berghei exoerythrocytic forms (EEF) grown in vitro within the highly differentiated human hepatoma cell line HEPG2. We assayed the effect of IFN-gamma on parasite growth by DNA hybridization using a P. berghei specific DNA probe. The specific activity of IFN-gamma against EEF is very high, and depends upon the time of lymphokine addition. When IFN-gamma is added to HEPG2 cells containing intracellular EEF, 6 hr after sporozoite invasion, parasite DNA replication is inhibited by approximately 75% at 10(3) U/ml and 50% at 1 U/ml. This treatment can either abolish or greatly reduce the infectivity of EEF for mice. When added earlier, 3 hr after completion of sporozoite invasion, IFN-gamma inhibits parasite replication to an even greater degree. The highest levels of inhibition were obtained when IFN-gamma was added 6 hr prior to sporozoite invasion (100% inhibition at 10(2) U/ml, approximately 55% inhibition at 0.1 U/ml, and 17% inhibition at 0.001 U/ml). We found that HEPG2 cells express approximately 44,000 surface receptors for IFN-gamma. These data are consistent with the view that IFN-gamma exerts its antimalarial activity by binding to surface receptors on hepatocytes and inducing intracellular changes unfavorable for parasite development. Tryptophan starvation does not appear to be involved in this process. These findings also support the idea that IFN-gamma, released from immune T cells upon encountering sporozoite antigen, may be an important effector mechanism in sterile immunity to sporozoite challenge.
Cross-domain learning methods for high-level visual concept classification (2008)

Exploding amounts of multimedia data increasingly require automatic indexing and classification, e.g. training classifiers to produce high-level features, or semantic concepts, chosen to represent image content, like car, person, etc. When changing the applied domain (i.e. from news domain to consumer home videos), the classifiers trained in one domain often perform poorly in the other domain due to changes in feature distributions. Additionally, classifiers trained on the new domain alone may suffer from too few positive training samples. Appropriately adapting data/models from an old domain to help classify data in a new domain is an important issue. In this work, we develop a new cross-domain SVM (CDSVM) algorithm for adapting previously learned support vectors from one domain to help classification in another domain. Better precision is obtained with almost no additional computational cost. Also, we give a comprehensive summary and comparative study of the state-of-the-art SVM-based cross-domain learning methods. Evaluation over the latest large-scale TRECVID benchmark data set shows that our CDSVM method can improve mean average precision over 36 concepts by 7.5%. For further performance gain, we also propose an intuitive selection criterion to determine which cross-domain learning method to use for each concept.
Interaction of influenza virus hemagglutinin with target membrane lipids is a key step in virus-induced hemolysis and fusion at pH 5.2. (1981)

The molecular mechanism of hemolysis and fusion by influenza virus in acidic media was studied. First, the effect of trypsin treatment on the activity of fibroblast-grown influenza virus was studied. The results showed that the split form of viral hemagglutinin, HA1 and HA2, but not the precursor, is responsible for the activity. Second, the interaction of egg-grown influenza virus, which contains the split hemagglutinin, with lipid liposomes was studied by spin labeling and electron microscopy. Phospholipid transfer from the viral envelope to the lipid bilayer membrane occurred within 30 s at pH 4.5-5.4. The transfer is largely independent of the lipid composition and the crystalline vs. liquid/crystalline state of the membrane. Virus-induced lysis of liposomes also took place rapidly in the same pH range. Envelope fusion with liposomes occurred at pH 5.2 but not at pH 7.0. These characteristic interactions were similar to those between influenza virus and erythrocytes reported previously. On the other hand, hemagglutinating virus of Japan did not interact with liposomes at neutral pH. These results suggest that protonation of the NH2-terminal segment of the HA2 form causes interaction of the segment with the lipid core of the target cell membrane, leading to hemolysis and fusion.
Polyphosphate and Orthophosphate Content of <i>Nitrosomonas europaea</i> as a Function of Growth (1970)

After inoculation of a stationary-phase culture of Nitrosomonas europaea into fresh growth solution, the cell-associated orthophosphate increased rapidly to 800 mumoles/g (wet weight), whereas the acid-insoluble long-chain polyphosphate content decreased rapidly to 22 mumoles/g. As growth proceeded, the orthophosphate content decreased rapidly to a level of 15 mumoles/g and the long-chain polyphosphate content gradually increased to 60 to 90 mumoles/g. When the pH of a culture of Nitrosomonas decreased during growth below approximately 7.4, the rate of nitrite and polyphosphate synthesis increased and the ratio of change in protein to change in nitrite decreased. When the pH of the culture was maintained above 7.6 throughout growth, polyphosphate accumulation, an increased rate of nitrite and polyphosphate synthesis, and a decreased ratio of change in protein to change in nitrite were not observed. Cells of Nitrosomonas apparently accumulated polyphosphate when adenosine triphosphate generated during the oxidation of ammonia to nitrite was not efficiently used to promote an increase in cell mass. The rapid hydrolysis of polyphosphate after the transfer of stationary-phase cells into fresh growth solution was found to be triggered primarily by the higher pH of the fresh growth solution. The efflux of orthophosphate during culture growth was not associated with a decrease in the pH of the growth solution. Data on the chemical composition of Nitrosomonas are presented.
Superconducting YBa2Cu3O7−<i>x</i> thin films on alkaline earth fluorides (1989)

Alkaline earth fluorides have low dielectric constants and large band gaps. In addition, they are chemically compatible with and several can be grown epitaxially on silicon and compound semiconductors. We have deposited YBa2Cu3O7−x thin films (200–500 nm thick) directly on (001) SrF2, (001) BaF2, (001) MgF2, and unoriented CaF2 single crystals by laser deposition. The substrate temperature was about 720 °C and the vacuum chamber was at 350 mTorr of oxygen. For this work, no additional annealing outside the deposition chamber was done after deposition. The deposited YBa2Cu3O7−x films were superconducting and exhibited transition temperatures Tc (R=0) of 83, 73, and 74 K on MgF2, SrF2, and BaF2, respectively. Structural studies by x-ray diffraction showed that YBa2Cu3O7−x films on MgF2, SrF2, and BaF2 were polycrystalline and exhibited some (00L) textures. Deposition on CaF2 substrates resulted in yellowish, insulating films with Ca- and Ba-rich interfacial reaction products.
Nuclear export of proteins in plants: AtXPO1 is the export receptor for leucine‐rich nuclear export signals in Arabidopsis thaliana (1999)

Transport across the nuclear envelope is mediated by transport receptors from the Importin beta family. We identified Exportin 1 from Arabidopsis (AtXPO1/AtCRM1) as the nuclear export receptor for proteins carrying leucine-rich nuclear export signals (NESs). AtXPO1 shares 42-50% identity with its functional homologues from humans and yeasts. We functionally characterised AtXPO1 by its interaction with NESs of animal and plant proteins, which is inhibited by the cytotoxin leptomycin B (LMB), and also by its interaction with the small GTPase Ran1 in the yeast two-hybrid system. Furthermore, we demonstrated the existence of a nuclear export pathway for proteins in plants. For the characterisation of nuclear export activities, we established an in vivo assay based on the localisation equilibrium of a GFP reporter protein fused to both a nuclear localisation signal (NLS) and an NES motif. Using this in vivo assay we demonstrated that the NES of the heterologous protein Rev is also functional in plants and that its export is inhibited by LMB. In addition, we identified a leucine-rich NES in the Arabidopsis protein AtRanBP1a. The NES, which is located at the carboxy terminus of the protein, is disrupted by mutating three long chain hydrophobic amino acid residues to alanine (L176A, L179A, V181A). In BY-2 protoplasts the NES of AtRanBP1a is functionally indistinguishable from the Rev NES. Our results demonstrate that the machinery for the nuclear export of proteins is functionally conserved in plants.
Mutators for transforming nonlinear resistor into memristor (2011)

A method of analogue emulation of the memristor with its prescribed charge (q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</sub> ) - flux (φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</sub> ) constitutive relation is presented. The memristor is emulated via a resistor with nonlinear current (i <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</sub> ) - voltage (v <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</sub> ) relationship, and a mutator. The purpose of the mutator is to provide a similarity transformation of the current-voltage characteristic of the resistor into the constitutive relation of the memristor according to the equations q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</sub> =k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> i <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</sub> , φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</sub> =k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> v <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</sub> , or φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</sub> =k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> i <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</sub> , q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</sub> =k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> v <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</sub> , where k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> , k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> are real numbers fulfilling the condition k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> >;0. It is shown that there are eight versions of these mutators. One of them is selected for experimental verification.
Distributed geo-rectification of satellite images using Grid computing (2004)

Grid computing seeks to aggregate computing resources within an enterprise and leverage on resources not owned for compute-intensive applications. Geo-rectification is a process for correcting spatial location and orientation of a satellite image. This paper focuses on the parallelization of the compute-intensive satellite image geo-rectification problem on a cluster Grid. We discuss our approach to data and task partitioning, visualization technique and the archival of data. The computational tasks include wrapping satellite positional data to compensate the Earth curvature, and consist of several steps such as image re-sampling, resolution conversion and image matching. Experimental results obtained using commodity PC are discussed.
Definition of Metabolic Syndrome (2006)

To the Editor:

Ninomiya et al reported that metabolic syndrome is a significant risk factor for cardiovascular disease in the Japanese middle-aged population (the Hisayama Study).1 They discussed that metabolic syndrome was not predictive for cardiovascular disease among diabetic women in the Japanese Diabetes Complications Study (JDCS),2 though it was consistently predictive of cardiovascular disease not only in both men and women but also in subjects with diabetes in the Hisayama Study, and speculated that this discrepancy …
Flexible active‐matrix OLED displays: Challenges and progress (2007)

Abstract— Organic light‐emitting‐device (OLED) devices are very promising candidates for flexible‐display applications because of their organic thin‐film configuration and excellent optical and video performance. Recent progress of flexible‐OLED technologies for high‐performance full‐color active‐matrix OLED (AMOLED) displays will be presented and future challenges will be discussed. Specific focus is placed on technology components, including high‐efficiency phosphorescent OLED technology, substrates and backplanes for flexible displays, transparent compound cathode technology, conformal packaging, and the flexibility testing of these devices. Finally, the latest prototype in collaboration with LG. Phillips LCD, a flexible 4‐in. QVGA full‐color AMOLED built on amorphous‐silicon backplane, will be described.
High-speed characteristics at high input optical power of GaInAsP electroabsorption modulators (1988)

High-speed characteristics at high input optical power levels of GaInAsP double heterostructure electroabsorption modulators are investigated. It is shown that the bandwidth degradation due to high input optical power is strongly dependent on the absorption coefficient. A design to maintain highspeed characteristics under milliwatt range output power operation, and experimental results including a 100km single-mode fibre pulse transmission experiment, are demonstrated.
Construction of Incoherent Unit Norm Tight Frames With Application to Compressed Sensing (2014)

Despite the important properties of unit norm tight frames (UNTFs) and equiangular tight frames (ETFs), their construction has been proven extremely difficult. The few known techniques produce only a small number of such frames while imposing certain restrictions on frame dimensions. Motivated by the application of incoherent tight frames in compressed sensing (CS), we propose a methodology to construct incoherent UNTFs. When frame redundancy is not very high, the achieved maximal column correlation becomes close to the lowest possible bound. The proposed methodology may construct frames of any dimensions. The obtained frames are employed in CS to produce optimized projection matrices. Experimental results show that the proposed optimization technique improves CS signal recovery, increasing the reconstruction accuracy. Considering that the UNTFs and ETFs are important in sparse representations, channel coding, and communications, we expect that the proposed construction will be useful in other applications, besides the CS.
Absence of a Pharmacokinetic Interaction between Losartan and Hydrochlorothiazide (1995)

To support the use of a combination of losartan, a highly specific and selective AT1 angiotensin II receptor antagonist, and hydrochlorothiazide for treatment of hypertension, a pharmacokinetic drug interaction study was conducted. In this open-label, randomized, three-period, crossover study, patients with mild to moderate hypertension received a 12.5-mg tablet of hydrochlorothiazide, a 50-mg losartan tablet, or a combination tablet of 12.5 mg of hydrochlorothiazide and 50 mg of losartan for 7 days. Twelve patients (age range, 35-55 years; mean age, 44 years) were allocated to treatment. Drug interactions were evaluated by comparing the 24-hour area under the concentration-time curve (AUC24) for losartan and its active metabolite, E-3174, when losartan (50 mg) was given alone or in combination with 12.5 mg hydrochlorothiazide. The urinary recovery over the 24-hour period of hydrochlorothiazide was compared for hydrochlorothiazide (12.5 mg) given alone or in combination with 50 mg losartan. A clinically significant interaction was defined as a treatment difference of more than 35%. There was no evidence of a clinically significant effect of hydrochlorothiazide on the pharmacokinetics of losartan or E-3174, as the geometric mean AUC24 ratio (90% confidence interval [CI]) was 1.02 (0.95, 1.09) for losartan and 1.02 (0.96, 1.09) for E-3174. Based on urinary recovery over a 24-hour period of hydrochlorothiazide, losartan did not affect the pharmacokinetics of hydrochlorothiazide, as the geometric mean ratio of urinary hydrochlorothiazide recovery (90% CI) was 0.898 (0.79, 1.20). There was a minor (17%) decrease in the AUC24 of hydrochlorothiazide after administration of the combination tablet. Coadministration of hydrochlorothiazide and losartan was well tolerated.
Synthesis of Zirconia-Based Solid Electrolyte Powders by the Coprecipitation Technique (1998)

The coprecipitation technique has been used in order to obtain zirconia-magnesia and zirconia-ceria powders with suitable purity and sinterability, respectively. To accomplish those requests, some processing variables have been systematic studied and optimized. Similar solid solutions have been prepared by the powder mixing technique for comparison purposes. Inductively coupled plasma, thermal neutron activation, nitrogen adsorption/desorption, thermal analyses and scanning electron microscopy techniques have been used for powder characterization. Cylindrical pellets were prepared by uniaxial and cold isostatic pressing. The characterization of the sintered pellets have been carried out by impedance spectroscopy, scanning electron microscopy and X-ray diffraction techniques. Zirconia-magnesia ceramics with a high degree of purity have been obtained, in agreement with impedance spectroscopy results that show no grain boundary blocking effects. For the zirconia-ceria system, sintered pellets with 98% of the theoretical density, and 0.5 μm average grain size have been obtained without using any comminution or special drying processes.
The Complexity of Some Problems on Subsequences and Supersequences (1978)

The complexity of finding the Longest Common Subsequence (LCS) and the Shortest Common Supersequence (SCS) of an arbRrary number of sequences IS considered We show that the yes/no version of the LCS problem is NP-complete for sequences over an alphabet of size 2, and that the yes/no SCS problem is NPcomplete for sequences over an alphabet of size 5 KEY WORDS AND PHRASES computational complexity, NP-completeness, longest common subsequence, shortest common supersequence CR CATEGORIES 5 23, 5 39
ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition (2015)

An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.
Performance Evaluation of Cyclic Pressure Pulsing in a Depleted, Naturally Fractured Reservoir with Stripper-Well Production (2011)

Abstract We present a parametric study on the operational parameters of cyclic pressure pulsing with N2 and CO2. We aim to develop a better understanding of how operational parameters affect the process performance in a shallow, naturally fractured, and depleted reservoir of the Big Andy Field in eastern Kentucky. The study includes analyses of various design parameters such as the injection rate, lengths of injection and soaking periods, cycle rate limits, and number of cycles. Incremental oil production, peak oil rate, and net present value (NPV) are considered as the performance criteria. Analyses have been performed using a single-well, dual-porosity, compositional reservoir model.
Test Power Reductions Through Computationally Efficient, Decoupled Scan Chain Modifications (2005)

SOC test time minimization hinges on the attainment of core test parallelism; yet test power constraints hamper this parallelism as excessive power dissipation may damage the SOC being tested. We propose a test power reduction methodology for SOC cores through scan chain modification. By inserting logic gates between scan cells, a given set of test vectors & captured responses is transformed into a new set of inserted stimuli & observed responses that yield fewer scan chain transitions. In identifying the best possible scan chain modification, we pursue a decoupled strategy wherein test data are decomposed into blocks, which are optimized for power in a mutually independent manner. The decoupled handling of test data blocks not only ensures significantly high levels of overall power reduction but it furthermore delivers computational efficiency at the same time. The proposed methodology is applicable to both fully, and partially specified test data; test data analysis in the latter case is performed on the basis of stimuli-directed controllability measures which we introduce. To explore the tradeoff between the test power reduction attained by the proposed methodology & the computational cost, we carry out an analysis that establishes the relationship between block granularity & the number of scan chain modifications. Such an analysis enables the utilization of the proposed methodology in a computationally efficient manner, while delivering solutions that comply with the stringent area & layout constraints in SOC as well.