gebhart/patrepeval huggingface dataset:
CRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 15 (2018)

Fascin is an actin binding and bundling protein that is not expressed in normal epithelial tissues but overexpressed in a variety of invasive epithelial tumors. It has a critical role in cancer cell metastasis by promoting cell migration and invasion. Here we report the crystal structures of fascin in complex with a series of novel and potent inhibitors. Structure-based elaboration of these compounds enabled the development of a series with nanomolar affinities for fascin, good physicochemical properties and the ability to inhibit fascin-mediated bundling of filamentous actin. These compounds provide promising starting points for fascin-targeted anti-metastatic therapies.
Time reversal in acoustics (1996)

Abstract Time-reversal invariance is a very powerful concept in classical and quantum mechanics. However, simple experimental evidence of this concept is difficult to obtain. In the field of acoustic waves, time-reversal experiments may be achieved much more simply by using time-reversal mirrors made of large ultrasonic piezoelectric transducer arrays. This paper describes the principles of time-reversal acoustics and shows the numerous applications of time-reversal mirrors in medical applications (imaging and therapy) as well as in non-destructive testing of solid media (detection of flaws). Experimental results illustrating these applications will be present.
Bipolar ESD Power Clamps (2015)

ESD power clamps for Bipolar technology, suitable for Silicon, Silicon Germanium, Silicon Germanium Carbon, Gallium Arsenide and Indium Phosphide technologies will be discussed. The bipolar classes of power clamps discussed include both forward-bias, and reverse-bias breakdown trigger networks as well as capacitively-triggered networks; these include diode string trigger networks, Zener-breakdown triggered power clamps, and BVCEO-breakdown triggered power clamps. Triple-well ESD power clamps will also be discussed.
Targeted inhibition of the gatekeeper mutant T315I of Bcr-Abl by an Aurora kinase inhibitor (2007)

3253 Imatinib, a tyrosine kinase inhibitor that blocks the catalytic activity of Bcr-Abl, is currently the first line therapeutic for patients with chronic myelogenous leukemia (CML) and Philadelphia (Ph) chromosome-positive acute lymphoblastic leukemia (ALL). However, many patients treated with imatinib develop resistance to therapy and the majority of relapses is due to point mutations in the kinase domain of Bcr-Abl. Second generation Bcr-Abl inhibitors, such as nilotinib and dasatinib, inhibit many of the imatinib-resistant mutations to various degrees, with the exception of the T315I mutation located in the gatekeeper position of the kinase domain. The clinical importance of T315I mutation, that accounts for ~20% of clinically observed mutations, is expected to increase in the future in CML and ALL patients since it will represent the major mechanism of resistance to first and/or second generation inhibitors. In our drug development process, we developed PHA-739358, a targeted Aurora kinase inhibitor that shows significant crossreactivity against the Abl kinase. We present here data demonstrating that this compound is capable of inhibiting the wild type Abl as well as the most clinically frequent imatinib-resistant Abl mutants, comprising the T315I mutant. Inhibition is observed both in vitro and in cell line models and it is due to the ability of the inhibitor to bind with high affinity to the Abl kinase domain. Interestingly, increased activity and affinity has been observed against the T315I mutant. The analysis of the crystallographic structure of the active, phosphorylated T315I mutant kinase domain complexed with PHA-739358 indicates that the compound accomodates into the ATP-binding pocket avoiding the hydrophobic pocket and without making any steric clash with the isoleucine side chain of the mutated gatekeeper. Furthermore, favourable hydrophobic interaction between the inhibitor and the isoleucine side chain would explain the higher activity of the compound against the T315I with respect to the wild type protein and the other mutants. Clinical trials using PHA-739358 to assess efficacy in CML and Ph-positive ALL patients who had resistance to imatinib, including patients bearing the T315I mutation, have been initiated. Since the number of patients with the T315I mutation is expected to increase in the future in patients treated with first and/or second generation inhibitors, PHA-739358 holds promise for treating this patient population.
Isoflavonoid Glycosides from the Rhizomes of Iris germanica. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
1.5 μm sub-picosecond pulse generation from an InGaAsP DFB diode laser synchronized with a mode-locked Ti:sapphire laser (2002)

We report the first successful demonstration of 1.5 /spl mu/m sub-picosecond pulse generation from a gain-switched InGaAsP distributed feedback laser diode synchronized with a mode locked Ti:sapphire laser. Note that the wavelength of 1.5 /spl mu/m is indispensable in the fiber optic telecommunication system while a mode-locked Ti:sapphire laser can generate sub-picosecond optical pulses at much shorter wavelength. Such a dual wavelength feature is very attractive and would provide new tools for the pump-and-probe characterization methods, including the electro-optic sampling, of high speed optoelectronic devices.
Linearization-based cross-layer design for throughput maximization in OFDMA wireless ad-hoc networks (2015)

In this paper, we consider joint routing, scheduling, and resource allocation to maximize the throughput of OFDMA based wireless ad-hoc networks subject to MAC layer and network layer constraints. Comparing with previous work (e.g., Rashtchi et al., ICC 2012) that assumes each subchannel to be orthogonally accessed by all network links through time sharing, we schedule the orthogonal multiple access (e.g., CDMA) among the outgoing links of each node to each subchannel and treat the interferences caused by other nodes as noise. We propose an iterative heuristic approach to decompose the original problem into subproblems, each of which can be solved approximately through linearization. Simulations demonstrate that, particularly in large networks, our proposed cross-layer design significantly outperforms the previously proposed “orthogonal-only” access.
Music self-similarity modeling using augmented nonnegative matrix factorization of block and stripe patterns (2013)

Self-similarity matrices have been widely used to analyze the sectional form of music signals, e.g. enabling the detection of parts such as verse and chorus in popular music. Two main types of structures often appear in self-similarity matrices: rectangular blocks of high similarity and diagonal stripes off the main diagonal that represent recurrent sequences. In this paper, we introduce a novel method to model both the block and stripe-like structures in self-similarity matrices and to pull them apart from each other. The model is an extension of the nonnegative matrix factorization, for which we present multiplicative update rules based on the generalized Kullback-Leibler divergence. The modeling power of the proposed method is illustrated with examples, and we demonstrate its application to the detection of sectional boundaries in music.
Glycolytic depolymerization of PET waste in a microwave reactor (2010)

Abstract Recycling of waste PET bottles was examined using glycolytic depolymerization with diethylene glycol, under microwave irradiation. The objective was to investigate if depolymerization using microwave energy could provide the same product distribution, while carried out in milder experimental conditions and/or shorter reaction times, resulting, thus besides to polymer recycling, in substantial energy saving. The reaction was carried out in a sealed microwave reactor in which the pressure and temperature were controlled. Experiments under constant temperature or microwave power were carried out at several time intervals. The main glycolysis product was analyzed and identified by FTIR measurements. The average molecular weight of the PET residues was found to decrease with the percentage of PET degradation. In the experiments carried out under constant microwave power, complete depolymerization was observed at irradiation powers greater than 150 W for 2 min, or 100 W for 5 min. In the constant temperature experiments, it was clear that at temperatures below 150°C no degradation occurs, whereas complete depolymerization takes place at temperatures greater than or equal to 180°C for 5 min. These results when compared to the conventional heating, where more than 4 h are needed for complete with PET degradation, confirm the importance of the microwave power technique and the substantial energy saving achieved. Finally, from a simple kinetic model the activation energy of the reaction was evaluated. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
Entropy in the molecular recognition of membrane protein-lipid interactions (2021)

Understanding the molecular driving forces that underlie membrane protein-lipid interactions requires the characterization of their binding thermodynamics. Here, we employ native mass spectrometry in conjunction with a variable temperature apparatus to determine the thermodynamics of individual lipid binding events to the human G-protein-gated inward rectifier potassium channel, Kir3.2. We find that Kir3.2 displays distinct thermodynamic strategies to engage phosphatidylinositol (PI) and phosphorylated forms thereof. The addition of a 4’- phosphate to PI with 18:1-18:1 (DO) tails results in an increase in favorable entropy along with an enthalpic penalty. The binding of PI with two or more phosphates is more complex where lipids bind to Kir3.2 with the cytoplasmic domain in either a docked or extended configuration. Remarkably, the interaction of 4,5-bisphosphate DOPI (DOPI(4,5)P2) with Kir3.2 is solely driven by a large, favorable change in entropy. Installment of a third 3’-phosphate to DOPI(4,5)P2 results in an alternative thermodynamic strategy for the first binding event whereas each successive binding event shows strong enthalpy-entropy compensation. PI(4,5)P2 with 18:0-20:4 tails results in an inversion of thermodynamic parameters where the change in enthalpy now dominates. Collectively, the data show that entropy can indeed play important roles in regulating membrane protein-lipid interactions.
Fluidic Sensors based on Photonic Crystal Fiber Gratings: An Emerging Technology for Realizing Ultra-Low ThermoResponsive Sensing Platforms (2007)

We propose the use of photonic crystal fiber gratings (PCFGs) as fluidic sensors. The thermo-optical sensitivity response of PCFG-based sensors is found to be superior in comparison to conventional fiber Bragg gratings.
MR566A and MR566B, New Melanin Synthesis Inhibitors Produced by Trichoderma harzianum. II. Physico-chemical Properties and Structural Elucidation. (1997)

New melanin synthesis inhibitors (MR566A and B) and six related known isocyanocyclopentenes were isolated from the fermentation broth of Trichoderma harzianum, and their structures were elucidated by spectroscopic methods. The structures of novel isocyanides, MR566A (1) and B (2), were elucidated as 1-(3-chloro-1,2-dihydroxy-4-isocyano-4-cyclopenten-1-yl)etha nol, 1-(1,2,3-trihydroxy-3-isocyano-4-cyclopenten-1-yl)ethanol, respectively. The structure of novel oxazole, MR93B (9), was elucidated as 4-[(1Z)-3-hydroxy-2-hydroxymethyl-1-propen-1-yl]oxazole.
Application of MAPS to the Salinas-Monterey Urban Study (1979)

The MAPS (Methodology for Areawide Planning Studies) computer program, developed at the U. S. Army Engineer Waterways Experiment Station (WES), was used to evaluate the engineering aspects of alternative water supply plans for the Salinas-Monterey Urban Study conducted by the U. S. Army Engineer District, San Francisco. Using MAPS, the WES study team identified feasible water supply plans, developed staging for required facilities, and calculated capital and operation and maintenance costs for these facilities. The two countries in the study area, Santa Cruz and Monterey, were faced with different water supply problems, which were addressed using slightly different techniques, presented in the following paragraphs. In Santa Cruz County (except for the lower Pajaro area), water supply problems consisted chiefly of providing municipal water from an integrated system of surface and groundwater sources. MAPS simulations were used to identify potential diversions and reservoir sites to meet future needs. Source development was staged through the year 2020. In Monterey County, irrigation represents the principal use of water, which is derived almost solely from wells. The U. S. Geological Survey developed a finite element groundwater model to identify the effect of different water use rates on the groundwater resources. From this study, six measures for storing and transporting water were identified.
Addressing Mismatch Between the Peripheral and Local Nusselt Number for Non-Axisymmetric Flow Conditions: Redefining the Mean Temperature (2019)

For non-axisymmetric conditions, the traditional fluid mean (bulk) temperature at a tube cross section, subjected to constant heat flux, can be higher than the temperature of a point on the wall. This results in a mismatch between the direction of applied heat flux and the temperature difference resulting in (misleading) negative peripheral heat transfer coefficient and Nusselt number (Nu). The resulting cross-sectional Nu (average of peripheral Nu values) differs from that calculated from average surface temperature and mean temperature. To address this gap in the literature, a detailed procedure is investigated based on a radial mean temperature of individual lines calculated from the lowest temperature spot in the cross-section to wall points, physically satisfying the mechanism of actual heat transfer from hot to cold spots. Each radial line’s mean temperature is used to calculate a peripheral Nu. These peripheral and average Nu are always positive and matches with the cross-sectional Nu that is calculated using the traditional method – single average cross-sectional temperature. This method is verified for different duct geometries including circular, square, and rectangular. The method also succeeds in the estimation of the peripheral and cross-sectional Nu values for eccentric annular ducts that are inherently non-axisymmetric and have negative Nu values according to the published literature.
Ribozyme–Spherical Nucleic Acids (2015)

Ribozymes are highly structured RNA sequences that can be tailored to recognize and cleave specific stretches of mRNA. Their current therapeutic efficacy remains low due to their large size and structural instability compared to shorter therapeutically relevant RNA such as small interfering RNA (siRNA) and microRNA (miRNA). Herein, a synthetic strategy that makes use of the spherical nucleic acid (SNA) architecture to stabilize ribozymes and transfect them into live cells is reported. The properties of this novel ribozyme-SNA are characterized in the context of the targeted knockdown of O(6)-methylguanine-DNA methyltransferase (MGMT), a DNA repair protein involved in chemotherapeutic resistance of solid tumors, foremost glioblastoma multiforme (GBM). Data showing the direct cleavage of full-length MGMT mRNA, knockdown of MGMT protein, and increased sensitization of GBM cells to therapy-mediated apoptosis, independent of transfection agents, provide compelling evidence for the promising properties of this new chemical architecture.
Transient analysis of NCLMS and ZNCLMS algorithms (2016)

This work presents a transient analysis of the recently proposed Noise Constrained Least Mean Square (NCLMS) and the Zero Noise Constrained LMS (ZN CLMS) algorithms. The analysis reported here is based upon the concept of the fundamental energy conservation relation and therefore on an easy manipulation of the analysis. Moreover, new stability bounds are derived to guarantee the mean-square-error convergence of the two algorithms. Furthermore, as a by-product of this analysis, the steady-state mean-square-deviation (MSD) is also derived for the first time for these two algorithms. Finally, simulation results corroborate the theoretical findings.
The structure of an epidermal growth factor-receptor kinase inhibitor, erbstatin. (1986)

The discovery, isolation and biological studies of erbstatin (1) have been reported in the preceding paper in this journal1). In this communication, spectral studies of 1 and the result of crystal structure determination by X-ray diffraction methods are reported. 1H NMR spectroscopy of 1 in acetone-d6 at
Pseudomonas aeruginosa Dps (PA0962) Functions in H2O2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity (2023)

We report the structural, biochemical, and functional characterization of the product of gene PA0962 from <i>Pseudomonas aeruginosa</i> PAO1. The protein, termed Pa Dps, adopts the Dps subunit fold and oligomerizes into a nearly spherical 12-mer quaternary structure at pH 6.0 or in the presence of divalent cations at neutral pH and above. The 12-Mer Pa Dps contains two di-iron centers at the interface of each subunit dimer, coordinated by conserved His, Glu, and Asp residues. In vitro, the di-iron centers catalyze the oxidation of Fe<sup>2+</sup> utilizing H<sub>2</sub>O<sub>2</sub> (not O<sub>2</sub>) as an oxidant, suggesting Pa Dps functions to aid <i>P. aeruginosa</i> to survive H<sub>2</sub>O<sub>2</sub>-mediated oxidative stress. In agreement, a <i>P. aeruginosa</i> Δ<i>dps</i> mutant is significantly more susceptible to H<sub>2</sub>O<sub>2</sub> than the parent strain. The Pa Dps structure harbors a novel network of Tyr residues at the interface of each subunit dimer between the two di-iron centers, which captures radicals generated during Fe<sup>2+</sup> oxidation at the ferroxidase centers and forms di-tyrosine linkages, thus effectively trapping the radicals within the Dps shell. Surprisingly, incubating Pa Dps and DNA revealed unprecedented DNA cleaving activity that is independent of H<sub>2</sub>O<sub>2</sub> or O<sub>2</sub> but requires divalent cations and 12-mer Pa Dps.
Delayed Enhancement MR Imaging: Utility in Myocardial Assessment (2006)

Use of magnetic resonance (MR) imaging for diagnosis of cardiac diseases and treatment monitoring is expanding. Delayed myocardial enhancement MR imaging is performed after administration of paramagnetic contrast agents and is used for a growing number of clinical applications. This technique was developed primarily for characterization of myocardial scarring after myocardial infarction. On delayed enhancement MR images, scarring or fibrosis appears as an area of high signal intensity that is typically subendocardial or transmural in a coronary artery distribution. However, delayed myocardial enhancement is not specific for myocardial infarction and can occur in a variety of other disorders, such as inflammatory or infectious diseases of the myocardium, cardiomyopathy, cardiac neoplasms, and congenital or genetic cardiac conditions, as well as after cardiac interventions. In nonischemic myocardial disease, the delayed enhancement usually does not occur in a coronary artery distribution and is often midwall rather than subendocardial or transmural. Therefore, the patient's clinical history is critical in the evaluation of delayed myocardial enhancement MR images.
Semantic Web Service Composition Based on a Closed World Assumption (2006)

Automation of Web service composition i.e., the process of forming new value added Web services is one of the most promising challenges in Web service research area. Such an automation does not involve only a richer semantic for Web service description but also reasoning processes about those descriptions. Semantics is supposed to be one of the key elements for the automation of Web service composition. Indeed semantic Web services enable a rich machine-understandable descriptions of their capabilities and processes in order to ease automation of processes such as discovery, selection and composition. In this paper one studies the functional level description of Web services and its impact on Web service composition hence the presentation of a formal model CLM (causal link matrix). The model supports a semantic context in order to find a correct, complete and consistent plan as an AI planning-based composition. The innovative and formal model follows a forward chaining-oriented composition. Moreover two methods of optimization (i.e., local-oriented and a global-oriented) of Web service composition are introduced to discover the best plan according to a semantic criterion i.e., the causal link between Web services
A 50MHz 1.5M Transistor ASIC For Biosequence Analysis (1991)

Identification and characterization of biological sequences are fundamental tasks of modern molecular biology. A major problem is to find biologically-significant methods for efficiently searching the large and rapidly-expanding DNA and protein sequence databases. One goal of the national Human Genome Initiative is to determine and analyze approximately 3 billion elements of human DNA sequence in the next 10 to 15 years. The BioSCAN chip implements the basic function central to several widely-used sequence analysis algorithms.1 A one-dimensional systolic array of 2,196 processing elements per chip covers over 90% of the area of this 1.5-milliontransistor ASIC.2
Radical Mediated C–H Functionalization of 3,6-Dichloropyridazine: Efficient Access to Novel Tetrahydropyridopyridazines (2015)

A radical mediated C-H functionalization of 3,6-dichloropyridazine using primary alcohols, t-BuOOH, and TiCl3 to access alkoxy pyridazines is described. This transformation is conducted open to air and on gram scale. A subsequent cyclization step can then be employed to efficiently access diversely substituted tetrahydropyridopyridazines with multiple functional handles.
A novel current dependent lithium ion capacitor model: Analysis and experimental driving cycle test validation (2017)

Nowadays, energy storage systems are playing an important role in several electrical applications. The modeling of these devices is very important, in particular, for electric vehicles, in order to understand and predict their behavior under different working conditions. Recently, the lithium-ion based solutions, and, in particular, lithium-ion capacitors (LiCs), are gaining a predominant position, as they display both high power and high energy densities. In the literature, different past works have modelled the LiCs using the electro-chemical impedance spectroscopy, a frequency domain technique. These models are able to represent the dynamic behavior of the LiC in a wide range of frequencies, currents and temperatures. On the other hand, they use a high number of parameters to be estimated, resulting quite complex to manage them. In the present paper, a novel current dependent LiC model, with only four unknown parameters characterized using a simple time domain technique, is presented.