gebhart/patrepeval huggingface dataset:
Elucidating Surface Ligand-Dependent Kinetic Enhancement of Proteolytic Activity at Surface-Modified Quantum Dots (2017)

Combining biomolecules such as enzymes with nanoparticles has much to offer for creating next generation synergistically functional bionanomaterials. However, almost nothing is known about how these two disparate components interact at this critical biomolecular-materials interface to give rise to improved activity and emergent properties. Here we examine how the nanoparticle surface can influence and increase localized enzyme activity using a designer experimental system consisting of trypsin proteolysis acting on peptide-substrates displayed around semiconductor quantum dots (QDs). To minimize the complexity of analyzing this system, only the chemical nature of the QD surface functionalizing ligands were modified. This was accomplished by synthesizing a series of QD ligands that were either positively or negatively charged, zwitterionic, neutral, and with differing lengths. The QDs were then assembled with different ratios of dye-labeled peptide substrates and exposed to trypsin giving rise to progress curves that were monitored by Förster resonance energy transfer (FRET). The resulting trypsin activity profiles were analyzed in the context of detailed molecular dynamics simulations of key interactions occurring at this interface. Overall, we find that a combination of factors can give rise to a localized activity that was 35-fold higher than comparable freely diffusing enzyme-substrate interactions. Contributing factors include the peptide substrate being prominently displayed extending from the QD surface and not sterically hindered by the longer surface ligands in conjunction with the presence of electrostatic and other productive attractive forces between the enzyme and the QD surface. An intimate understanding of such critical interactions at this interface can produce a set of guidelines that will allow the rational design of next generation high-activity bionanocomposites and theranostics.
Improved Wide Operating Temperature Range of LiNiCoAiO2-based Li-ion Cells with Methyl Propionate-based Electrolytes (2012)

Demonstration of wide operating temperature range Li-ion electrolytes Methyl propionate-based wide operating temperature range electrolytes were demonstrated to provide dramatic improvement of the low temperature capability of Quallion prototype Li-ion cells (MCMB-LiNiCoAlO2). Some formulations were observed to deliver over 60% of the room temperature capacity using a 5C rate at - 40oC !! Represents over a 4-fold improvement over the baseline electrolyte system. Demonstrated operational capability of a number of systems over a wide temperature range (-40 to +70 C) Demonstrated reasonably good long term cycle life performance at high temperature (i.e., at +40deg and +50 C) A number of formulations containing electrolytes additives (i.e., FEC, VC, LiBOB, and lithium oxalate) have been shown to have enhanced lithium kinetics at low temperature and promising high temperature resilience. Demonstrated good performance in larger capacity (12 Ah) Quallion Li-ion cells with methyl propionate-based electrolytes. Current efforts focused upon performing life studies and the impact upon low temperature capability.
All semiconductor laser Doppler anemometer at 155 μm (2008)

We report to our best knowledge the first all semiconductor Laser Doppler Anemometer (LIDAR) for wind speed determination. We will present the design and first experimental results on a focusing coherent cw laser Doppler anemometer for measuring atmospheric wind velocities in the 10 meters to 300 meters distance range. Especially, we will demonstrate that both the output power as well as the demanding coherence properties required from the laser source can be accomplished by an all semiconductor laser. Preliminary tests at a distance of 40 meters indicate a typical signal to noise ratio of 9 dB. This result is obtained at a clear day with an up-date rate of 12 Hz.
Highly electronegative metallic contacts to semiconductors using polymeric sulfur nitride (1976)

The Schottky barriers formed on n-ZnS and n-ZnSe by polymeric sulfur nitride have been compared to barriers formed by Au. Barrier energies as determined by photoresponse, current-voltage, and capacitance-voltage methods show that (SN)x is approximately 1.0 eV higher than Au on n-ZnS and 0.3–0.4 eV higher than Au on n-ZnSe. We believe that this is the first report of any metallic contact more electronegative than Au.
<i>V</i>-groove distributed feedback laser for 1.3–1.55 μm operation (1986)

We describe a V-groove distributed feedback laser operating at λ=1.5 μm. A second-order diffraction grating has been defined by electron beam writing and transferred using ion beam milling after the crystal growth was completed. A single longitudinal mode operation with a mode rejection ratio larger than 5000:1 has been obtained under modulation rate of 1 GHz. The techniques used in this work can be applied to other types of buried heterostructure lasers.
WS-EPM: web services for enterprise project management (2004)

This work presents a new service-oriented architecture for enterprise project management that integrates business process, human resources and project management within an enterprise or across the value chain network. In the proposed WS-EPM framework, the project resources include business processes, skilled people, physical resources, control policies, and so forth. The project resources used in WS-EPM are described by WSResource properties language. In addition, the coordination of project resources is guided by a set of operations modeled by business process execution language for Web services (BPEL4WS). At the end of this paper, we present an industry application scenario that leverages the proposed WS-EPM for achieving maximum ROI with limited resources.
Highly linear heterogeneous-integrated Mach-Zehnder interferometer modulators on Si (2016)

In this paper we demonstrate highly linear Mach-Zehnder interferometer modulators utilizing heterogeneous integration on a Si substrate (HS-MZM). A record high dynamic range was achieved for silicon devices, obtained using hybrid III-V/Si phase modulation sections and single drive push-pull operation, demonstrating a spurious free dynamic range (SFDR) of 112 dB∙Hz<sup>2/3</sup> at 10 GHz, comparable to commercial Lithium Niobate MZMs.
ChemInform Abstract: New Pyrimidine Derivatives Possessing ALK Inhibitory Activities. (2014)

Abstract A variety of new pyrimidine derivatives such as (V) and (X) are designed, synthesized and evaluated for their anaplastic lymphoma kinase (ALK) inhibitory activities.
Size-Dependent Phase Diagram of Nanoscale Alloy Drops Used in Vapor−Liquid−Solid Growth of Semiconductor Nanowires (2010)

We use in situ observations during high-temperature transmission electron microscopy to quantify the exchange of semiconductor material between Au-Ge vapor--liquid--solid seed drops and Ge nanowires (NWs). By performing simultaneous measurements under identical conditions on arrays with systematic variations in NW diameter, we establish the nanoscale size dependence of the temperature-dependent equilibrium composition of the Au-Ge binary alloy. We find a significantly enhanced Ge solubility for drops on thin NWs compared to thicker ones. The controlled modification of the surface of the NW by an ordered carbon shell leads to drastic changes in the solubility.
Mitigating transmit B 1 inhomogeneity in the liver at 7T using multi-spoke parallel transmit RF pulse design. (2014)

In this work, the use of multi-spoke slice-selective parallel transmit (pTX) RF pulse was explored to address B 1+ inhomogeneity in the largest transverse section of the liver at 7T. The impact of the number of spokes was specifically investigated, considering RF pulses consisting of 2, 3 and 4 spokes, as well as single-spoke RF pulses corresponding to static B 1 shimming. Healthy volunteers were imaged on a whole body MR scanner equipped with an eight-channel transmit system. A robust and fast transmit B 1 (B 1+) estimation method was employed to obtain the eight-channel B 1+ maps within a single breath hold. Gradient echo (GRE) images of the liver were acquired using the four different RF pulses and the results were compared. The use of static B 1 shimming (i.e., 1-spoke RF pulse) resulted in partial improvement but significant signal dropouts were still observed in the target region. By comparison, the use of multi-spoke pTX RF pulse design gave rise to much improved excitation homogeneity without signal dropouts. These results demonstrate the effectiveness of multi-spoke pTX RF pulse design in B 1+ homogenization for liver magnetic resonance imaging (MRI) at 7T. The current findings at 7T may have implications for body imaging applications in clinical settings at 3T where B 1+ inhomogeneities are also known for degrading image quality in the torso.
<i>(Invited) </i>Multimodal Enzymatic Sensing for Continuous Wound Monitoring (2018)

Present wound care is primarily visual, entailing repeated clinical trips. A biosensing system offering direct longitudinal measures of healing can assist to bridge the time between occurrence of wounds and their management. Purine metabolites, xanthine and uric acid, are known to have high correlation with wound chronicity and healing. With increased apoptosis, concentrations of these analytes reportedly increase. In this study, their biochemical pathways in purine metabolism are explored to provide a method to monitor healing on a multimodal sensing platform. This work employs enzymes xanthine oxidase and uricase, for detection of uric acid and xanthine respectively. pH of wounds change with healing, from alkaline to acidic, shifting the potential of detection. Effects of pH have been investigated on the same platform enabling real-time calibration, attempting to provide improved assessment of tissue recovery. Nanomaterials of carbon (C) and gold (Au) have been utilized here, to improve the sensitivity of detection.
Spectral X-Ray CT Image Reconstruction with a Combination of Energy-Integrating and Photon-Counting Detectors (2016)

The purpose of this paper is to develop an algorithm for hybrid spectral computed tomography (CT) which combines energy-integrating and photon-counting detectors. While the energy-integrating scan is global, the photon-counting scan can have a local field of view (FOV). The algorithm synthesizes both spectral data and energy-integrating data. Low rank and sparsity prior is used for spectral CT reconstruction. An initial estimation is obtained from the projection data based on physical principles of x-ray interaction with the matter, which provides a more accurate Taylor expansion than previous work and can guarantee the convergence of the algorithm. Numerical simulation with clinical CT images are performed. The proposed algorithm produces very good spectral features outside the FOV when no K-edge material exists. Exterior reconstruction of K-edge material can be partially achieved.
Multi-scale image fusion for x-ray grating-based mammography (2012)

X-ray phase contrast imaging (PCI) can provide high sensitivity of weakly absorbing low-Z objects in medical and biological fields, especially in mammography. Grating-based differential phase contrast (DPC) method is the most potential PCI method for clinic applications because it can works well with conventional X-ray tube and it can retrieve attenuation, DPC and dark-field information of the samples in a single scanning. Three kinds of information have different details and contrast which represent different physical characteristics of X-rays with matters. Hence, image fusion can show the most desirable characteristics of each image.
Synthesis and Characterization of Pb(Zr, Ti)O-Pb(Nb, Zn)O Thin Film Cantilevers for Energy Harvesting Applications (2012)

A complete analysis of the morphology, crystallographic orientation, and resulting electrical properties of Pb(Zr 0.53 ,Ti 0.47 ) Pb(Nb 1/3 , Zn 2/3 )O 3 (PZT-PZN) thin films, as well as the electrical behavior when integrated in a cantilever for energy harvesting applications, is presented. The PZT-PZN films were deposited using sol-gel methods. We report that using 20% excess Pb, a nucleation layer of PbTiO 3 (PT), and a fast ramp rate provides large grains, as well as denser films. The PZT-PZN is deposited on a stack of TiO 2 /PECVD SiO 2 /Si 3 N 4 /thermal SiO 2 /Poly-Si/Si. This stack is designed to allow wet-etching the poly-Si layer to release the cantilever structures. It was also found that the introduction of the poly-Si layer results in larger grains in the PZT-PZN film. PZT-PZN films with a dielectric constant of 3200 and maximum polarization of 30 μ C/cm 2 were obtained. The fabricated cantilever devices produced ~ 300–400 mV peak-to-peak depending on the cantilever design. Experimental results are compared with simulations.
Murine pulmonary surfactant SP-A gene: cloning, sequence, and transcriptional activity (1992)

SP-A is an abundant pulmonary surfactant-associated protein whose expression is controlled in a cell- and developmental-specific manner. To analyze regulation of SP-A gene expression, the murine SP-A gene was cloned and sequenced. The murine DBA/2J gene was approximately 4.6 kb in length comprised of six exons and five introns. Three mRNAs of 3.0, 1.7, and 0.9 kb were detected by Northern blot analysis of murine lung mRNA. Expression of the SP-A mRNAs was first detected at day 15 of gestation and increased dramatically before birth. A single SP-A gene was detected in the DBA/2J mouse genome. SP-A mRNA was detected in lung but not in the gastrointestinal tract, kidney, brain, liver, or heart and was detected by in situ hybridization in bronchial and alveolar cells of the murine lung. Primer extension analysis with a primer to exon three revealed two extension products differing by 9 bp in length, suggesting two closely juxtaposed transcription initiation sites. Chimeric gene(s) containing 1.8 kb of 5' SP-A sequences and the bacterial chloramphenicol acetyltransferase gene were expressed in pulmonary adenocarcinoma cells and in HeLa cells. Expression of the murine SP-A gene is partially controlled by non-cell-selective transcriptionally active sequences.
Speeding up Document Ranking with Rank-based Features (2015)

Learning to Rank (LtR) is an effective machine learning methodology for inducing high-quality document ranking functions. Given a query and a candidate set of documents, where query-document pairs are represented by feature vectors, a machine-learned function is used to reorder this set. In this paper we propose a new family of rank-based features, which extend the original feature vector associated with each query-document pair. Indeed, since they are derived as a function of the query-document pair and the full set of candidate documents to score, rank-based features provide additional information to better rank documents and return the most relevant ones. We report a comprehensive evaluation showing that rank-based features allow us to achieve the desired effectiveness with ranking models being up to 3.5 times smaller than models not using them, with a scoring time reduction up to 70%.
User-controllable learning of security and privacy policies (2008)

Studies have shown that users have great difficulty specifying their security and privacy policies in a variety of application domains. While machine learning techniques have successfully been used to refine models of user preferences, such as in recommender systems, they are generally configured as “black boxes ” that take control over the entire policy and severely restrict the ways in which the user can manipulate it. This article presents an alternative approach, referred to as user-controllable policy learning. It involves the incremental manipulation of policies in a context where system and user refine a common policy model. The user regularly provides feedback on decisions made based on the current policy. This feedback is used to identify (learn) incremental policy improvements which are presented as suggestions to the user. The user, in turn, can review these suggestions and decide which, if any, to accept. The incremental nature of the suggestions enhances usability, and because the user and the system manipulate a common policy representation, the user retains control and can still make policy modifications by hand. Results obtained using a neighborhood search implementation of this approach are presented in the context of data derived from the deployment of a friend finder application, where users can share their locations with others, subject to privacy policies they refine over time. We present results showing policy accuracy, which averages 60 % upon initial definition by our users, climbing as high as 90 % using our technique.
Maximum-likelihood co-channel interference cancellation with power control for cellular OFDM networks (2009)

In cellular Orthogonal Frequency Division Multiplexing (OFDM) networks, Co-Channel Interference (CCI) leads to severe degradation in the BER performance. To solve this problem, Maximum-Likelihood Estimation (MLE) CCI cancellation scheme has been proposed in the literature. MLE CCI cancellation scheme generates weighted replicas of the transmitted signals and selects replica with the smallest Euclidean distance from the received signal. When the received power of the desired and interference signals are nearly the same, the BER performance is degraded. In this paper, we propose an improved MLE CCI canceler with closed-loop Power Control (PC) scheme capable of detecting and combating against the equal received power situation at the Mobile Station (MS) receiver by using the newly introduced parameter Power Ratio (PR). At cell edge where Signal to Interferer Ratio (SIR) is considered to have average value between -5 and 10 dB, computer simulations show that the proposed closed-loop PC scheme has a gain of 7 dB at 28 km/h and about 2 dB at 120 km/h.
Unsupervised Detection of Web Trackers (2015)

When browsing, users are consistently tracked by parties whose business builds on the value of collected data. The privacy implications are serious. Consumers and corporates do worry about the information they unknowingly expose to the outside world, and they claim for mechanisms to curb this leakage. Existing countermeasures to web tracking either base on hostname blacklists whose origin is impossible to know and must be continuously updated. This paper presents a novel, unsupervised methodology that leverages application-level traffic logs to automatically detect services running some tracking activity, thus enabling the generation of curated blacklists. The methodology builds on an algorithm that pinpoints pieces of information containing user identifiers exposed in URL queries in HTTP(S) transactions. We validate our algorithm over an artificial dataset obtained by visiting the top 200 most popular websites in the Alexa rank. Results are excellent. Our algorithm identifies 34 new third- party trackers not present in available blacklists. By analyzing the output of our algorithm, some privacy-related interactions emerge. For instance, we observe scenarios clearly hinting to Cookie Matching practice, for which information about users' activity gets shared across several different third-parties.
Development of a monoclonal antibody-based immunoassay for cyclic DNA adducts resulting from exposure to crotonaldehyde. (1987)

In order to develop an immunoassay for DNA modifications resulting from exposure to crotonaldehyde, monoclonal antibodies specific for the 8R,6R- and 8S,6S-stereoisomers of 3-(2-deoxy-beta-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8-hydroxy-6 - methylpyrimido[1,2-a]purine-10(3H)one were produced. These cyclic 1,N2-propanodeoxyguanosines are formed in DNA exposed to crotonaldehyde in vitro. Three of the four antibodies were most specific for one stereoisomer while the fourth was most specific for the other stereoisomer. Fifty % inhibition of binding in an enzyme-linked immunoabsorbent assay using two of these antibodies and capable of detecting 0.5 mumol of 1,N2-propanodeoxyguanosine per mol of deoxyguanosine was developed. The method was validated by comparison to results obtained with fluorescence assay.
iDedup: latency-aware, inline data deduplication for primary storage (2012)

Deduplication technologies are increasingly being deployed to reduce cost and increase space-efficiency in corporate data centers. However, prior research has not applied deduplication techniques inline to the request path for latency sensitive, primary workloads. This is primarily due to the extra latency these techniques introduce. Inherently, deduplicating data on disk causes fragmentation that increases seeks for subsequent sequential reads of the same data, thus, increasing latency. In addition, deduplicating data requires extra disk IOs to access on-disk deduplication metadata. In this paper, we propose an inline deduplication solution, iDedup, for primary workloads, while minimizing extra IOs and seeks.Our algorithm is based on two key insights from real-world workloads: i) spatial locality exists in duplicated primary data; and ii) temporal locality exists in the access patterns of duplicated data. Using the first insight, we selectively deduplicate only sequences of disk blocks. This reduces fragmentation and amortizes the seeks caused by deduplication. The second insight allows us to replace the expensive, on-disk, deduplication metadata with a smaller, in-memory cache. These techniques enable us to tradeoff capacity savings for performance, as demonstrated in our evaluation with real-world workloads. Our evaluation shows that iDedup achieves 60-70% of the maximum deduplication with less than a 5% CPU overhead and a 2-4% latency impact.
Design of New Two-Photon Absorbing Fluorophores (1998)

In very recent work we have developed design strategies which allow us to independently control the strength, position, fluorescence quantum yield and intersystem crossing rates for two-photon absorbing dyes. The position and strength of the band of the two-photon absorption peak in conjugated molecules can be controlled by varying the conjugation length (specifically by varying the double bonds or phenylene-vinylenc groups in the molecules) and also by appropriate substitution of the molecule with electron donating and electron withdrawing groups. In particular, we have developed several new two-photon fluorophores, as shown in Table 1 below, that have strong two- photon absorptivities and two-photon absorption wavelengths that are ideally suited for imaging of tissue using a Ti:sapphire laser operating between 700 and 950 nm. Compound 1 below is representative of conventional agent (bis-MSB) whereas compounds 2 - 4 are represenative of the new agents that we have developed.
Using LED sources to selectively heat blood for enhanced mid-IR imaging of vascular structures (2014)

We present experimental results that demonstrate the ability of mid-IR imaging to map blood vessels 0.75cm deep in muscle tissue. Selective heating of the blood with LED sources provides the contrast in these mid-IR images.