gebhart/patrepeval huggingface dataset:
Electrodeposition of multilayered nanostructures for giant magnetoresistance and thermoelectric applications (2007)

The electrodeposition of novel materials such as multilayer nanotubes for giant magneto resistance (GMR) applications and bismuth telluride nanotubes for thermoelectric applications are presented in this dissertation. The motivation for the multilayer electrodeposition is the investigation of giant magnetoresistance (GMR), a change in the material resistance in an applied magnetic field as a consequence of antiferromagnetic coupling. The nanowire high aspect ratio geometry allows the measurement of GMR with the current applied perpendicular to the plane (CPP) of the multilayers, which has been theoretically identified as being larger than the GMR in the (CIP) configuration (current in plane of multilayers). The current perpendicular to the plane giant magneto-resistance (CPP)-(GMR) effect makes multilayered nanowires of huge interest as magnetic sensor materials. Electrodeposition is the most efficient method for fabricating magnetic nanowires. In addition to the cost-effectiveness, electrodeposition is one of the few methods that can overcome the geometrical restrictions of inserting metals into very deep nanometric recesses, making it the favored method for nanowire and nanotube fabrication. In this dissertation, the quaternary CoNiFeCu alloy system was investigated in order to electrodeposit multilayered nanowires/nanotubes for GMR effect. Electrodeposited multilayer CoNiFeCu/Cu nanowires and nanotubes were fabricated by pulsed applied electric potential and their giant magnetoresistance (GMR) behavior characterized. The effect of electrolyte concentration on the GMR was investigated. The FeSO4, CoSO4 and NiSO4 concentrations were varied to optimize the GMR and the saturation field of the multilayered nanowires. Nanolayer thicknesses were controlled and varied for commercially viable GMR results. Furthermore, the influence of electrolyte temperature on nanotube formation and the resulting GMR was explored. Micro fluidic magnetic nanoparticles sensors based on CoNiFeCu/Cu GMR nanowires were fabricated for the first time. The test results show that the sensors are highly sensitive to small nanoparticle concentrations. Employing the potentiostatic electrodeposition, nanotubes of bismuth-telluride (Bi2Te3) were obtained. The electrolyte concentration was varied and affected the nanotube formation and the resulting Seebeck coefficients.
Complex Effect of Adenovirus Early Region Proteins on Innate Immune System (2006)

Adenoviruses (Ads) cause acute and persistent infections. The genome of Ads has five early transcription units that are the first viral genes expressed during an active infection. The Early Region 1A (E1A) gene of the adenovirus genome is crucial for adenovirus transformation of the host cell. Ads E1A block some aspects of the innate immune system to enable viruses to invade the host cell. E1A suppresses nitric oxide (NO) production through transcriptional control of the inducible NO synthase (iNOS) gene. This inhibition of NO production may enable the virus to persist in human tissue because NO is an antiviral effector of the innate immune system. E1A also blocks secretory leukoprotease inhibitor (SLPI) and elafin/skin-derived antileukoproteinase (SKALP) secretion by alveolar epithelial cells. Recent scientific evidence suggests that SLPI and elafin/SKALP have broad-spectrum antibiotic activities that include bactericidal and antifungal properties. The inhibition of inflammation by Ad early region proteins is complex, as certain early region proteins can promote as well as inhibit inflammation depending on the genetic context of the virus. E1A DNA and protein are frequently detected in the lungs of chronic obstructive pulmonary disease (COPD) patients and it is associated with an increased inflammatory response. E1A enhances intercellular adhesion molecule-1 and interleukin-8 mRNA expression with lipopolysaccharide stimulation. Understanding the roles of the Ad gene products in the induction and inhibition of innate inflammatory functions will help us to clarify the pathogenesis of the chronic respiratory illness including COPD.
ClarIDHy: A phase 3, multicenter, randomized, double-blind study of AG-120 vs placebo in patients with an advanced cholangiocarcinoma with an IDH1 mutation. (2017)

TPS4142 Background: Advanced cholangiocarcinoma (CC) is a life-threatening disease for which there are limited therapeutic options. Mutations in isocitrate dehydrogenase 1 (mIDH1) occur in up to 25% of intrahepatic CC cases. mIDH1 lead to epigenetic and genetic changes that promote oncogenesis via production of the oncometabolite, D-2-hydroxyglutarate (2-HG). AG-120 is a first-in-class oral inhibitor of the mIDH1 enzyme, and is being tested in a phase 1 study that enrolled 73 patients (pts) with mIDH1 CC who had received a median of 2 prior therapies (range 1–5). AG-120 has demonstrated a favorable safety profile and clinical activity in this study. Among the 72 efficacy evaluable pts (≥1 post-baseline response assessment or discontinued prematurely), 6% (n = 4) had a confirmed partial response and 56% (n = 40) had stable disease. Progression-free survival (PFS) rate at 6 months was 40% as of Dec 16, 2016. The 500 mg once daily (QD) dose of AG-120 was selected for the ongoing phase 3 study in mIDH1 CC described here. Methods: ClarIDHy is a global, phase 3, multicenter, double-blind study randomizing 186 pts with mIDH1 CC in a 2:1 ratio to AG-120 (500 mg QD) or matched placebo (NCT02989857). Key eligibility criteria: nonresectable or metastatic CC; documented mIDH1 based on central laboratory testing; ECOG 0–1; measurable disease (RECIST v1.1); documented disease progression following ≤2 prior systemic therapies in the advanced setting, including at least 1 gemcitabine- or 5-fluorouracil-containing regimen; and no prior mIDH inhibitor therapy. Crossover from the placebo arm to the AG-120 arm will be permitted. The primary endpoint is PFS as assessed by an independent review. Secondary endpoints include safety, tolerability, overall response rate, overall survival, pharmacokinetic and pharmacodynamic analyses on plasma, and quality of life as assessed by the EORTC QLQ-C30, EORTC QLQ-BIL21, and EQ-5D-5L instruments. An independent data monitoring committee will monitor the data throughout the study. The ClarIDHy study is currently activated at participating sites in the US and will be activated in centers throughout Europe and in South Korea. Clinical trial information: NCT02989857.
Deficit irrigation impact on lycopene, soluble solids, firmness and yield of diploid and triploid watermelon in three distinct environments (2004)

SummaryWater conservation practices are critical for production and quality of watermelon [Citrullus lanatus (Thunb.) Matsum & Nakai] in southern regions of the USA. The objective of this experiment was to determine the effects of deficit irrigation and environment on lycopene content, total soluble solids, firmness, and yield of diploid and triploid watermelon. Irrigation rates were 1.0 evapotranspiration (ET), 0.75 ET, and 0.5 ET, which were calculated based on climatic parameters applied to the Penman-Monteith equation. Diploid cultivars were ‘Summer Flavor 710’ and ‘Summer Flavor 800’, and triploid cultivars were ‘Summer Sweet 5244’ and ‘Super Seedless 7187’. To investigate if there was a consistent response in cultivars across diverse environments, three studies were conducted in remote Texas locations: Uvalde in the Wintergarden, Weslaco in the Rio Grande Valley, and Lubbock in the High Plains. To isolate the environmental effects due to weather and soil type, all experiments used similar cultural strategies (plant spacing, subsurface drip irrigation, black plastic mulch, and containerized transplants), except for transplanting and harvesting dates. Deficit irrigation reduced total marketable yield by 36% at Uvalde, 30% at Lubbock, and 15% in Weslaco, increasing the yield of small fruits (<5 kg). Location and irrigation rates had major influences on yield of diploid and triploid watermelon. Soluble solids content increased with deficit irrigation at 0.5 ET rate in triploids, but not in diploids. Flesh firmness also increased in triploids compared to diploids. Fruit lycopene content increased with maturity (7 and 22 d after ripening) at all irrigation rates and cultivars. This work across three diverse Texas locations confirms that deficit irrigation directly reduced yield, but does not reduce lycopene development and fruit quality of triploid watermelon.
Temporal resolution scalable video coding (2002)

Scalable video coding is important in a number of applications where video needs to be decoded and displayed at a variety of spatial and temporal resolution scales or when resilience to errors is necessary. In this paper, we investigate a temporal-domain approach for resolution scalable video coding. This approach was originally proposed to and since then has been included in the Moving Picture Experts Group (MPEG-2) standard. Temporal scalability, although not limited to, is particularly useful for applications such as, HDTV as well as for high quality telecommunication applications that may require high frame rate (e.g., 60 Hz) progressive video. Furthermore, it allows flexibility in use of progressive or interlaced video formats for coding even though the source video may be progressive with high frame rate. Our technique builds on the motion-compensated DCT framework of nonscalable (single layer) MPEG-2 video coding and adds motion compensated inter-layer coding. In our simulations we focus on the 2- layer temporally scalable coding and compare the performance of using progressive video format for both layers to that when interlaced video format is used for both layers; all interim video formats used are derived from original high temporal resolution progressive video. In each case we compare the performance of two inter-layer prediction configurations and evaluate their prediction efficiency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Low-power VLSI decoder architectures for LDPC codes (2002)

Iterative decoding of low-density parity check codes (LDPC) using the message-passing algorithm have proved to be extraordinarily effective compared to conventional maximum-likelihood decoding. However, the lack of any structural regularity in these essentially random codes is a major challenge for building a practical low-power LDPC decoder. In this paper, we jointly design the code and the decoder to induce the structural regularity needed for a reduced complexity parallel decoder architecture. This interconnect-driven code design approach eliminates the need for a complex interconnection network while still retaining the algorithmic performance promised by random codes. Moreover, we propose a new approach for computing reliability metrics based on the BCJR algorithm that reduces the message switching activity in the decoder compared to existing approaches. Simulations show that the proposed approach results in power savings of up to 85.64% over conventional implementations.
Photo Luminescent Properties of Polymer Derived Ceramics at Near Stoichiometric SiO 2 ‐xSiC‐y(H) Compositions (2014)

This chapter contains sections titled: Introduction Experimental Procedure Results and Discussion Summury Acknowledgements
PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination (2011)

An implementation of the PICS-Ord algorithm is available from http://scit.us/projects/ngila/wiki/PICS-Ord. It requires both the statistical software, R http://www.r-project.org and the alignment software Ngila http://scit.us/projects/ngila.
Synthesis of Palladium Nanoparticles Using a Continuous Flow Polymeric Micro Reactor (2004)

A continuous flow polymeric micro reactor, fabricated using a negative photo resist SU-8 on a 10 x 10 cm PEEK (polyetheretherketone) substrate by standard UV lithography, was utilized to synthesize palladium nanoparticles. The nanoparticles were characterized by Transmission Electron Microscopy, Selected Area Electron Diffraction and X-ray Diffraction. The Pd nanoparticles synthesized in the micro reactor were found to have a narrower size distribution when compared with those obtained by the conventional batch process.
Immunoassay using probe-labelling immunogold nanoparticles with silver staining enhancement via surface-enhanced Raman scattering (2004)

This paper reports a novel immunoassay based on surface-enhanced Raman scattering (SERS) and immunogold labelling with silver staining enhancement. Immunoreactions between immunogold colloids modified by a Raman-active probe molecule (e.g., 4-mercaptobenzoic acid) and antigens, which were captured by antibody-assembled chips such as silicon or quartz, were detected via SERS signals of Raman-active probe molecule. All the self-assembled steps were subjected to the measurements of ultraviolet-visible (UV-vis) spectra to monitor the formation of a sandwich structure onto a substrate. The immunoassay was performed by a sandwich structure consisting of three layers. The first layer was composed of immobilized antibody molecules of mouse polyclonal antibody against Hepatitis B virus surface antigen (PAb) on a silicon or quartz substrate. The second layer was the complementary Hepatitis B virus surface antigen (Antigen) molecules captured by PAb on the substrate. The third layer was composed of the probe-labelling immunogold nanoparticles, which were modified by mouse monoclonal antibody against Hepatitis B virus surface antigen (MAb) and 4-mercaptobenzoic acid (MBA) as the Raman-active probe on the surface of gold colloids. After silver staining enhancement, the antigen is identified by a SERS spectrum of MBA. A working curve of the intensity of a SERS signal at 1585 cm(-1) due to the [small nu](8a) aromatic ring vibration of MBA versus the concentration of analyte (Antigen) was obtained and the non-optimized detection limit for the Hepatitis B virus surface antigen was found to be as low as 0.5 [micro sign]g mL(-1).
Ultrasensitive laser measurements without tears (1997)

Several easily implemented devices for doing ultrasensitive optical measurements with noisy lasers are presented. They are all-electronic noise cancellation circuits that largely eliminate excess laser intensity noise as a source of measurement error and are widely applicable. Shot-noise-limited optical measurements can now easily be made at baseband with noisy lasers. These circuits are especially useful in situations where strong intermodulation effects exist, such as current-tuned diode laser spectroscopy. These inexpensive devices (parts cost approximately $10) can be optimized for particular applications such as wideband or differential measurements. Although they cannot eliminate phase noise effects, they can reduce amplitude noise by 55-70 dB or more, even in unattended operation, and usually achieve the shot-noise limit. With 1-Hz signal-to-noise ratios of 150-160 dB, they allow performance equal or superior to a complex heterodyne system in many cases, while using much simpler dual-beam or homodyne approaches. Although these devices are related to earlier differential and ratiometric techniques, their noise cancellation performance is much better. They work well at modulation frequencies from dc to several megahertz and should be extensible to approximately 100 MHz. The circuits work by subtracting photocurrents directly, with feedback applied outside the signal path to continuously adjust the subtraction for perfect balance; thus the excess noise and spurious modulation ideally cancel at all frequencies, leaving only the shot noise. The noise cancellation bandwidth is independent of the feedback bandwidth; it depends only on the speeds of the photodiodes and of the bipolar junction transistors used. Two noise-canceled outputs are available; one is a high-pass filtered voltage proportional to the signal photocurrent and the other is a low-pass filtered voltage related to the log ratio of the signal and comparison photocurrents. For reasonable current densities, the noise floors of the outputs depend only on the shot noise of the signal beam. Four variations on the basic circuit are presented: low noise floor, high cancellation, differential high power, and ratio-only. Emphasis is placed on the detailed operation and design considerations, especially performance extension by compensation of the nonideal character of system components. Experience has shown that some applications advice is required by most users, so that is provided as well.
Rapid Microglial Response Around Amyloid Pathology after Systemic Anti-Aβ Antibody Administration in PDAPP Mice (2008)

Aggregation of amyloid-beta (Abeta) peptide in the brain in the form of neuritic plaques and cerebral amyloid angiopathy (CAA) is a key feature of Alzheimer's disease (AD). Microglial cells surround aggregated Abeta and are believed to play a role in AD pathogenesis. A therapy for AD that has entered clinical trials is the administration of anti-Abeta antibodies. One mechanism by which certain anti-Abeta antibodies have been proposed to exert their effects is via antibody-mediated microglial activation. Whether, when, or to what extent microglial activation occurs after systemic administration of anti-Abeta antibodies has not been fully assessed. We administered an anti-Abeta antibody (m3D6) that binds aggregated Abeta to PDAPP mice, an AD mouse model that was bred to contain fluorescent microglia. Three days after systemic administration of m3D6, there was a marked increase in both the number of microglial cells and processes per cell visualized in vivo by multiphoton microscopy. These changes required the Fc domain of m3D6 and were not observed with an antibody specific to soluble Abeta. These findings demonstrate that some effects of antibodies that recognize aggregated Abeta are rapid, involve microglia, and provide insight into the mechanism of action of a specific passive immunotherapy for AD.
Analysis of Inflammatory Cytokines in the Tears of Dry Eye Patients (2009)

Tears from dry eye patients contain significantly increased concentrations of cytokines that show correlation to severity of the disease. The upregulation of their respective genes in the conjunctiva suggests that the concentration increase is not the result of evaporative effects, but of overproduction. These findings suggest that cytokines may play an important role in dry eye disease and topical cytokine modulators may be explored as a therapeutic approach to dry eye disease.
A new runlength limited code for binary asymmetric channels (1992)

In write-once optical data storage, one is faced with an asymmetry between marks and non-marks due to the practical lower limit of the mark size. This is due to the fact that with increasing information density, the lengths of the non-marks diminish, but the marks cannot be made arbitrarily small. Van Uijen er al provided experimental evidence that coding techniques adapted to such an asymmetric channel would successfully combat the effect of intersymbol interference. Asymmetrical runlength-limited sequences can be characterised by four parameters (α, β, γ, δ) in the NRZ format, where (α and β are the minimum runlength of 0's, and 1's, respectively, and γ and δ are the maximum runlength of 0's and 1's, respectively.
The broad sweep of integrated microsystems (1998)

Micromachining mechanical, chemical, and optical components onto the same wafers as electronic circuits produces powerful systems that can understand and influence their environments.
Myosin light chain kinase transference induces myosin light chain activation and endothelial hyperpermeability (2000)

The actomyosin complex is the major cytoskeletal component that controls cell contraction. In this study, we investigated the effects of actomyosin interaction on endothelial barrier function and gap formation. Activated myosin light chain kinase (MLCK) protein was transferred into coronary venular endothelial cell (CVEC) monolayers. Uptake of the activated protein resulted in a significant shift in myosin light chain (MLC) from an unphosphorylated to a diphosphorylated form. In addition, MLCK induced a hyperpermeability response of the monolayer as measured by albumin transendothelial flux. Microscopic examination of MLCK-treated CVECs revealed widespread gap formation in the monolayer, loss of peripheral beta-catenin, and increases in actin stress fibers. Inhibition of all of the above responses by a specific MLCK inhibitor suggests they are the direct result of exogenously added MLCK. These data suggest that activation of MLCK in CVECs causes phosphorylation of MLC and contraction of CVECs, resulting in gap formation and concomitant increases in permeability. This study uses a novel technique to measure the effects of an activated kinase on both its substrate and cellular morphology and function through direct transference into endothelial cells.
Electrospun Nanofibers of Blends of Conjugated Polymers:  Morphology, Optical Properties, and Field-Effect Transistors (2005)

Electrospun nanofibers of two series of binary blends of poly[2-methoxy-5-(2-ethylhexoxy)-1,4-phenylenevinylene] (MEH−PPV) with regioregular poly(3-hexylthiophene) (PHT) and with poly(9,9-dioctylfluorene) (PFO) were prepared, and their morphology and optical and electrical properties were characterized. Morphological and photophysical studies showed that the phase-separated domains in MEH−PPV/PHT nanofibers (30−50 nm) are much smaller as compared to blend thin films (100−150 nm), and efficient energy transfer was observed in these blend nanofibers. The MEH−PPV/PFO blend nanofibers had cocontinuous or core−shell structures, and significant energy transfer was absent in these blend nanofibers as compared to bulk thin films. Field-effect transistors based on MEH−PPV/PHT blend nanofibers showed exponential dependence of hole mobility on blend composition. The hole mobility decreased from 1 × 10-4 cm2/(V s) in 20 wt % MEH−PPV blend nanofibers to 5 × 10-6 cm2/(V s) at 70 wt %. If corrected for the reduced channel area of the transistors, the effective hole mobility varies from 5 × 10-5 to 1 × 10-3 cm2/(V s) and is similar to that of spin-coated blend thin films. Our results demonstrate that electrospun nanofibers of binary blends of conjugated polymers have tunable, composition-dependent, optical, and electronic properties that can be exploited in field-effect transistors.
Efficient Multiview Maintenance under Insertion in Huge Social Networks (2014)

Applications to monitor various aspects of social networks are becoming increasingly popular. For instance, marketers want to look for semantic patterns relating to the content of tweets and Facebook posts relating to their products. Law enforcement agencies want to track behaviors involving potential criminals on the Internet by looking for certain patterns of behavior. Music companies want to track patterns of spread of illegal music. These applications allow multiple users to specify patterns of interest and monitor them in real time as new data gets added to the Web or to a social network. In this article we develop the concept of social network view servers in which all of these types of applications can be simultaneously monitored. The patterns of interest are expressed as views over an underlying graph or social network database. We show that a given set of views can be compiled in multiple possible ways to take advantage of common substructures and define the concept of an optimal merge . Though finding an optimal merge is shown to be NP-hard, we develop the AddView to find very good merges quickly. We develop a very fast MultiView algorithm that scalably and efficiently maintains multiple subgraph views when insertions are made to the social network database. We show that our algorithm is correct, study its complexity, and experimentally demonstrate that our algorithm can scalably handle updates to hundreds of views on 6 real-world social network databases with up to 540M edges.