gebhart/patrepeval huggingface dataset:
Sum-networks from incidence structures: construction and capacity\n analysis (2016)

A sum-network is an instance of a network coding problem over a directed\nacyclic network in which each terminal node wants to compute the sum over a\nfinite field of the information observed at all the source nodes. Many\ncharacteristics of the well-studied multiple unicast network communication\nproblem also hold for sum-networks due to a known reduction between instances\nof these two problems. In this work, we describe an algorithm to construct\nfamilies of sum-network instances using incidence structures. The computation\ncapacity of several of these sum-network families is characterized. We\ndemonstrate that unlike the multiple unicast problem, the computation capacity\nof sum-networks depends on the characteristic of the finite field over which\nthe sum is computed. This dependence is very strong; we show examples of\nsum-networks that have a rate-1 solution over one characteristic but a rate\nclose to zero over a different characteristic. Additionally, a sum-network can\nhave an arbitrary different number of computation capacities for different\nalphabets. This is contrast to the multiple unicast problem where it is known\nthat the capacity is independent of the network coding alphabet.\n
Multiplexed Sandwich Immunoassays Using Electrochemiluminescence Imaging Resolved at the Single Bead Level (2009)

A new class of bead-based microarray that uses electrogenerated chemiluminescence (ECL) as a readout mechanism to detect multiple antigens simultaneously is presented. This platform demonstrates the possibility of performing highly multiplexed assays using ECL because all the individual sensing beads in the array are simultaneously imaged and individually resolved by ECL. Duplex and triplex assay results are demonstrated as well as a cross reactivity study.
Microstructural characteristics in friction stir welded aluminium alloys (2001)

(2001). Microstructural characteristics in friction stir welded aluminium alloys. Welding International: Vol. 15, No. 9, pp. 693-698.
Whole-cell biochips for bio-sensing: integration of live cells and inanimate surfaces (2010)

Recent advances in the convergence of the biological, chemical, physical, and engineering sciences have opened new avenues of research into the interfacing of diverse biological moieties with inanimate platforms. A main aspect of this field, the integration of live cells with micro-machined platforms for high throughput and bio-sensing applications, is the subject of the present review. These unique hybrid systems are configured in a manner that ensures positioning of the cells in designated patterns, and enables cellular viability maintenance, and monitoring of cellular functionality. Here we review both animate and inanimate surface properties and how they affect cellular attachment, describe relevant modifications of both types of surfaces, list technologies for platform engineering and for cell deposition in the desired configurations, and discuss the influence of various deposition and immobilization methods on the viability and performance of the immobilized cells.
Dependence of the coupling properties between a plasmonic antenna array and a sub-wavelength epsilon-near-zero film on structural and material parameters (2021)

The resonance properties of a plasmonic dipole antenna array depend on its geometry and the properties of its surrounding medium. The linear optical properties of an array of plasmonic dipole antennas can be modified with the inclusion of an epsilon-near-zero (ENZ) thin film. In this work, we numerically investigate the roles of the antenna dimensions, the ENZ film thickness and loss, and the separation between the antenna and the ENZ film in determining the linear optical response of the antenna–ENZ metasurface. The results show that for a sufficiently small separation, the linear optical properties of the antenna array are determined by the strong or ultrastrong coupling with the ENZ film and are only weakly dependent on the antenna geometry. We show that for metasurfaces with thick, lossy ENZ films, the lower polariton branch is not observable due to the high loss of ENZ films. Since the dependence of the upper polariton on antenna length is weak, this results in a single antenna-length-invariant resonance. However, in the presence of low-loss ENZ films, the lower polariton branch is also visible for antenna–ENZ metasurfaces with thicker ENZ films, indicating a strong coupling between the antenna array and the ENZ film. For a given antenna geometry, the coupling strength increases with increasing thickness of the ENZ film and can reach up to ∼50% of the zero-permittivity frequency of the ENZ film, indicating an ultrastrong coupling between the plasmonic antenna array and the ENZ film.
Abstract 4492: Blockade of angiopoietin-2 or Tie2 is equally effective at inhibiting tumor growth and reducing tumor vessel density in most human tumor xenograft models (2014)

Abstract Angiopoietin-1 (Ang1) and -2 (Ang2) regulate angiogenesis via the endothelial cell-specific receptor tyrosine kinase Tie2. Blocking Ang2 binding to Tie2 decreases vessel density and inhibits tumor growth in various human xenograft models. However, not all tumors respond to Ang2 blockade, which could be due to high Ang1 levels acting as another ligand for Tie2, to Ang2 activities independent of Tie2, or to a weak role for Ang-2/Tie2 signaling in these tumors. To elucidate if Ang1 plays an integral role in tumor angiogenesis and growth, we compared the effects of blocking Ang2 or Tie2 in various tumor xenografts with differing levels of Ang1 expression. We found that in six out of seven tumor models, antibodies that specifically bind Ang2 (REGN910, 10 mg/kg 2x/wk) or that bind Tie2 and block binding of both Ang1 and Ang2 (REGN1376, 10 mg/kg 2x/wk) were equally efficacious at inhibiting tumor growth and decreasing vessel density. In only one tumor model (Calu-6), blockade of Tie2 with REGN1376 was more effective than blockade of Ang2 (REGN910) at reducing tumor growth and decreasing tumor vessel density. Although Calu-6 tumors express high Ang1 levels, other tumors tested (Lox, LS174T) have comparable or higher Ang1 levels and respond similarly to Ang2 and Tie2 blockade, thus the levels of Ang1 do not account for the differential response of Calu-6 tumors. Taken together, our data suggest that Ang2 is the dominant ligand for Tie2 in the microenvironment of most tumors, and further, that the effects of Ang2 are mediated primarily via Tie2. These findings support the approach to specifically block the binding of Ang2 to Tie2 as an anti-angiogenic therapy. Citation Format: Alexander P. Adler, Christopher Daly, Asma A. Parveen, Thomas Nevins, Jing Shan, Jeanette Fairhurst, Tammy Huang, Joel Martin, Nicholas Papadopoulos, George D. Yancopoulos, Gavin Thurston, Gavin Thurston, Alexandra Eichten. Blockade of angiopoietin-2 or Tie2 is equally effective at inhibiting tumor growth and reducing tumor vessel density in most human tumor xenograft models. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4492. doi:10.1158/1538-7445.AM2014-4492
Role of Technology for the Management of AKI in Critically Ill Patients: From Adoptive Technology to Precision Continuous Renal Replacement Therapy (2016)

This paper reports on the continuous renal replacement therapy (CRRT) technology group recommendations and research proposals developed during the 17th Acute Dialysis Quality Initiative Meeting in Asiago, Italy. The group was tasked to address questions related to the impact of technology on acute kidney injury management. We discuss technological aspects of the decision to initiate CRRT and the components of the treatment prescription and delivery, the integration of information technology (IT) on overall patient management, the incorporation of CRRT into other 'non-renal' extracorporeal technologies such as ECMO and ECCO2R and the use of sorbents in sepsis and propose new areas for future research. Instead of reviewing current knowledge, the group focused on developing a renovated research agenda that reflects current and future technological advances, centered on innovations in new equipment, membranes and IT that will permit the integration of patient care and decision-making processes for years to come.
X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein (2019)

The bacterial flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase complex derived from Burkholderia cepacia (BcGDH) is a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. In this study, the X-ray structure of BcGDHγα, the catalytic subunit (α-subunit) of BcGDH complexed with a hitchhiker protein (γ-subunit), was determined. The most prominent feature of this enzyme is the presence of the 3Fe-4S cluster, which is located at the surface of the catalytic subunit and functions in intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The structure of the complex revealed that these two molecules are connected through disulfide bonds and hydrophobic interactions, and that the formation of disulfide bonds is required to stabilize the catalytic subunit. The structure of the complex revealed the putative position of the electron-transfer subunit. A comparison of the structures of BcGDHγα and membrane-bound fumarate reductases suggested that the whole BcGDH complex, which also includes the membrane-bound β-subunit containing three heme c moieties, may form a similar overall structure to fumarate reductases, thus accomplishing effective electron transfer.
Simultaneous Removal of Ammonia and Nitrate from Wastewater Using a Pulse Electrolysis Technique (2023)

The Environmental Protection Agency (EPA) considers ammonia and nitrate as large-scale threats to environmental quality and human health, causing impaired air quality, surface water eutrophication, and other serious health problems. This work examines the viability of using a pulse electrolysis technique to accomplish the simultaneous removal of ammonia and nitrate in an undivided flow cell using CuNi/PtIr supported on carbon electrocatalysts (CuNi/PtIr/C). Different series of PtIr/C and CuNi/C compositions were examined, and it was found that among all series of the synthesized catalysts, 60% Pt 9 Ir/C and 40% Cu 9 Ni/C had greater activity toward Ammonia Oxidation Reaction (AOR) and Nitrate Reduction Reaction (NRR), respectively. Throughout the pulsing potentials, the nitrogen contaminants were gradually removed with the overall reaction that generated harmless nitrogen and hydrogen gases. The average ammonia and nitrate removal rates were 5.17 ppm-ammonia and 0.074 ppm-nitrate/min, respectively. The selectivity of nitrate to ammonia was 82% with an average nitrate removal rate of 65%. The catalysts exhibited pronounced stability after 10 cycles of pulse electrolysis.
Photogenerated base in polymer curing and imaging: Design of reactive styrenic copolymers susceptible to a base‐catalyzed β‐elimination (1997)

A novel family of functionalized styrenic copolymers that are susceptible to a base-catalyzed β-elimination reaction is reported. The reactive copolymers, poly-{(2-phenyl-2-cyanoethoxycarbonyloxystyrene)-co-(4-hydroxystyrene)}, are prepared by chemical modification of poly(4-hydroxystyrene) using 2-phenyl-2-cyanoethyl chloroformate. A photoresist material consisting of the copolymer and bis[[(2-nitrobenzyl)-oxy] carbonyl]-4,4′-trimethylenedipiperidine used as an amine photogenerator affords positive tone images by UV irradiation. The effect of copolymer structure and composition on imaging, thermal stability, and the ease of β-elimination reaction is discussed. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 3543–3552 1997
Over What Length Scale Does an Inorganic Substrate Perturb the Structure of a Glassy Organic Semiconductor? (2020)

While the bulk structure of vapor-deposited glasses has been extensively studied, structure at buried interfaces has received little attention, despite being important for organic electronic applications. To learn about glass structure at buried interfaces, we study the structure of vapor-deposited glasses of the organic semiconductor DSA-Ph (1,4-di-[4-(<i>N</i>,<i>N</i>-diphenyl)amino]styrylbenzene) as a function of film thickness; the structure is probed with grazing incidence X-ray scattering. We deposit on silicon and gold substrates and span a film thickness range of 10-600 nm. Our experiments demonstrate that interfacial molecular packing in vapor-deposited glasses of DSA-Ph is more disordered compared to the bulk. At a deposition temperature near room temperature, we estimate ∼8 nm near the substrate can have modified molecular packing. Molecular dynamics simulations of a coarse-grained representation of DSA-Ph reveal a similar length scale. In both the simulations and the experiments, deposition temperature controls glass structure beyond this interfacial layer of a few nanometers.
Chemistry of Class 1 CRISPR-Cas effectors: Binding, editing, and regulation (2020)

Among the multiple antiviral defense mechanisms found in prokaryotes, CRISPR-Cas systems stand out as the only known RNA-programmed pathways for detecting and destroying bacteriophages and plasmids. Class 1 CRISPR-Cas systems, the most widespread and diverse of these adaptive immune systems, use an RNA-guided multiprotein complex to find foreign nucleic acids and trigger their destruction. In this review, we describe how these multisubunit complexes target and cleave DNA and RNA and how regulatory molecules control their activities. We also highlight similarities to and differences from Class 2 CRISPR-Cas systems, which use a single-protein effector, as well as other types of bacterial and eukaryotic immune systems. We summarize current applications of the Class 1 CRISPR-Cas systems for DNA/RNA modification, control of gene expression, and nucleic acid detection.
Leveraging multi-layer imager detector design to improve low-dose performance for megavoltage cone-beam computed tomography (2017)

While megavoltage cone-beam computed tomography (CBCT) using an electronic portal imaging device (EPID) provides many advantages over kilovoltage (kV) CBCT, clinical adoption is limited by its high doses. Multi-layer imager (MLI) EPIDs increase DQE(0) while maintaining high resolution. However, even well-designed, high-performance MLIs suffer from increased electronic noise from each readout, degrading low-dose image quality. To improve low-dose performance, shift-and-bin addition (ShiBA) imaging is proposed, leveraging the unique architecture of the MLI. ShiBA combines hardware readout-binning and super-resolution concepts, reducing electronic noise while maintaining native image sampling. The imaging performance of full-resolution (FR); standard, aligned binned (BIN); and ShiBA images in terms of noise power spectrum (NPS), electronic NPS, modulation transfer function (MTF), and the ideal observer signal-to-noise ratio (SNR)-the detectability index (d')-are compared. The FR 4-layer readout of the prototype MLI exhibits an electronic NPS magnitude 6-times higher than a state-of-the-art single layer (SLI) EPID. Although the MLI is built on the same readout platform as the SLI, with each layer exhibiting equivalent electronic noise, the multi-stage readout of the MLI results in electronic noise 50% higher than simple summation. Electronic noise is mitigated in both BIN and ShiBA imaging, reducing its total by ~12 times. ShiBA further reduces the NPS, effectively upsampling the image, resulting in a multiplication by a sinc<sup>2</sup> function. Normalized NPS show that neither ShiBA nor BIN otherwise affects image noise. The LSF shows that ShiBA removes the pixilation artifact of BIN images and mitigates the effect of detector shift, but does not quantifiably improve the MTF. ShiBA provides a pre-sampled representation of the images, mitigating phase dependence. Hardware binning strategies lower the quantum noise floor, with 2 × 2 implementation reducing the dose at which DQE(0) degrades by 10% from 0.01 MU to 0.004 MU, representing 20% improvement in d'.
A study of mixture formation processes in direct injection stratified charge gasoline engines by quantitative laser-induced fluorescence imaging and the infrared absorption method (2006)

Mixture formation processes were investigated of three types of direct injection stratified charge gasoline engine based on wall-guided, air-guided, and spray-guided concepts. Temporal and spatial variations of fuel concentration in the combustion chamber were measured by laser diagnostics such as quantitative laser-induced fluorescence (LIF) imaging and infrared absorption methods on a single-cylinder optical engine. It was found from the experiments that the direct injection gasoline engines based on both the wall-guided and air-guided concepts have long time intervals between the end of injection timing and ignition timing, and this demands early injection and ignition timings in the compression stroke, resulting in lower thermal efficiencies than those of the spray-guided concept. As for the spray-guided concept, fuel is ignited immediately after the end of injection, which enables near TDC (top dead centre) combustion, allowing lower fuel consumption than the other two. However, the condition for stable ignition and combustion achieved with the spray-guided concept is very narrow in terms of injection and ignition timings, so it is essential to widen the condition in order to make the concept a reality.
Monolayer Vanadium‐Doped Tungsten Disulfide: A Room‐Temperature Dilute Magnetic Semiconductor (2020)

Dilute magnetic semiconductors (DMS), achieved through substitutional doping of spin-polarized transition metals into semiconducting systems, enable experimental modulation of spin dynamics in ways that hold great promise for novel magneto-electric or magneto-optical devices, especially for two-dimensional (2D) systems such as transition metal dichalcogenides that accentuate interactions and activate valley degrees of freedom. Practical applications of 2D magnetism will likely require room-temperature operation, air stability, and (for magnetic semiconductors) the ability to achieve optimal doping levels without dopant aggregation. Here, room-temperature ferromagnetic order obtained in semiconducting vanadium-doped tungsten disulfide monolayers produced by a reliable single-step film sulfidation method across an exceptionally wide range of vanadium concentrations, up to 12 at% with minimal dopant aggregation, is described. These monolayers develop p-type transport as a function of vanadium incorporation and rapidly reach ambipolarity. Ferromagnetism peaks at an intermediate vanadium concentration of ~2 at% and decreases for higher concentrations, which is consistent with quenching due to orbital hybridization at closer vanadium-vanadium spacings, as supported by transmission electron microscopy, magnetometry, and first-principles calculations. Room-temperature 2D-DMS provide a new component to expand the functional scope of van der Waals heterostructures and bring semiconducting magnetic 2D heterostructures into the realm of practical application.
Heat Transfer and Film Cooling Effectiveness in a Linear Airfoil Cascade (1997)

A warm (315°C) wind tunnel test facility equipped with a linear cascade of film cooled vane airfoils was used in the simultaneous determination of the local gas side heat transfer coefficients and the adiabatic film cooling effectiveness. The test rig can be operated in either a steady-state or a transient mode. The steady-state operation provides adiabatic film cooling effectiveness values while the transient mode generates data for the determination of the local heat transfer coefficients from the temperature–time variations and of the film effectiveness from the steady wall temperatures within the same aerothermal environment. The linear cascade consists of five airfoils. The 14 percent cascade inlet free-stream turbulence intensity is generated by a perforated plate, positioned upstream of the airfoil leading edge. For the first transient tests, five cylinders having roughly the same blockage as the initial 20 percent axial chord of the airfoils were used. The cylinder stagnation point heat transfer coefficients compare well with values calculated from correlations. Static pressure distributions measured over an instrumented airfoil agree with inviscid predictions. Heat transfer coefficients and adiabatic film cooling effectiveness results were obtained with a smooth airfoil having three separate film injection locations, two along the suction side, and the third one covering the leading edge showerhead region. Near the film injection locations, the heat transfer coefficients increase with the blowing film. At the termination of the film cooled airfoil tests, the film holes were plugged and heat transfer tests were conducted with non-film cooled airfoils. These results agree with boundary layer code predictions.
Telecare for Patients With Type 1 Diabetes and Inadequate Glycemic Control (2004)

Telecare is associated with small effects on glycemic control in patients with type 1 diabetes on intensive insulin therapy but with inadequate glycemic control.
In situ detection of activated Bru Ig signaling complex by phosphol monoclonal antibodies (2016)

Bruton's tyrosine kinase (Btk) is a critical transducer of signals originating from the B cell antigen receptor (BCR). Dosage, sequential phosphorylation, and protein interactions are interdependent mechanisms influ- encing Btk function. Phosphopeptide-specific mAbs recogniz- ing two distinct phosphotyrosine modifications were used to quantify Btk activation by immunofluorescent techniques during B cell stimulation. In a population of cultured B cells stimulated by BCR crosslinking and analyzed by flow cytom- etry, transient phosphorylation of the regulatory Btk tyrosine residues (551Y and 223Y) was detected. The kinetics of phosphorylation of the residues were temporally distinct. Tyrosine 551, a transactivating substrate site for Src-family kinases, was maximally phosphorylated within -30 seconds of stimulation as monitored by flow cytometry. Tyrosine 223, an autophosphorylation site within the SH3 domain, was maxi- mally phosphorylated at =5 minutes. Btk returned to a low tyrosine phosphorylation level within 30 minutes, despite persistent elevation of global tyrosine phosphorylation. Co- localization of activated Btk molecules with the crosslinked BCR signaling complex was observed to coincide with the period of maximal Btk tyrosine phosphorylation when stim- ulated B cells were analyzed with confocal microscopy. The results of these in situ temporal and spatial analyses imply that Btk signaling occurs in the region of the Ig receptor signaling complex, suggesting a similar location for downstream targets
Atomic-detail simulation studies of tilted smectics (1994)

We describe preliminary results of realistic (atomic-detail) simulation studies of tilted smectic liquid crystals. Results obtained for a one-layer freely suspended thin film of DOBAMBC in the smectic C* phase are described in detail. Our studies show unambiguously that electrostatic interactions are not required to produce tilted smectic phases, and suggest that molecular tilt in DOBAMBC is driven by the anisotropic molecular shape. We also find evidence for tilt-induced bond orientational order in our simulations.