gebhart/patrepeval huggingface dataset:
A Study of Membrane Activity in Rat Prostate Cancer Cells: An Evaluation of the FM1–43 Dye Technique (2000)

A study was initiated to test whether the FM1-43 dye technique could be applied to the study of endocytic membrane activity in two rodent prostate cancer (MAT-LyLu and AT-2) cell lines of markedly different metastatic ability. The lipophilic dye FM1-43, which has frequently been used to monitor endo/exocytic activity in excitable cells was employed. We found, as in excitable tissues, that both strongly metastatic (MAT-LyLu) and weakly metastatic (AT-2) cells in culture take up FM1-43 to give vesicular staining of a variable pattern, which appeared to differ between the two cell lines. However, unlike excitable tissues, neither cell line subsequently released the dye. Indeed, both cell lines retained the dye through several rounds of cell division suggesting that dye incorporated by cells does not enter the endo/exocytotic cycle. Uptake of dye was independent of temperature, Na+/K+ gradients, pH or metabolism. We suggest that passive accumulation of FM1-43 can occur in cancer cells and should not, automatically, be interpreted as evidence of endocytosis.
Pressure-driven spatiotemporal control of the laminar flow interface in a microfluidic network (2007)

We describe a system for dynamically adjusting the position of the laminar interface between two fluids flowing inside a microfluidic channel, with a time response of less than 0.1 s, through feedback control of the channel inlet pressure.
Test-station for flexible semi-automatic wafer-level silicon photonics testing (2016)

Silicon photonics technologies are a particularly attractive solution for developing low-cost optical interconnects with high performance. Imec is developing a silicon photonics technology platform. Developing this platform requires continuous process optimization and design verification, both of which are enabled by the flexible wafer-level test solution that is presented in this paper. The test station enables semi-automatic optical and electro-optical testing of passive and active silicon photonics components and circuits, including waveguides, fiber grating couplers, photodetectors, modulators, filters etc. The measured insertion loss of fiber grating couplers is repeatable to within 0.07dB (6σ), for photodetector responsivity the repeatability is around 0.02A/W (6σ). Calibration procedures have been designed to ensure the long-term reproducibility of measurement results. This is demonstrated with wafer-level measurement data for fiber grating couplers and photodetectors that were gathered over a five-month period. The reproducibility over this period is 0.8dB for the insertion loss and 0.09A/W for the responsivity measurement.
The Relationship between Vegetative Maturity and the First Stage of Cold Acclimation1 (1978)

Abstract Red-osier dogwood ( Cornus stolonifera Michx.) plants were grown outdoors in a lathhouse to study the relationship between vegetative maturity and the first stage of cold acclimation. Both microscopic observations and electrical impedance ratios used to measure damage of frozen stem sections verified the close association of the onset of the first stage of cold acclimation and vegetative maturity. The relationship of these processes to dormancy development is discussed.
A stochastic model for impact of LER on BEOL TDDB (2017)

TDDB lifetime projections at operating voltages for backend of line (BEOL) dielectrics have been based on accelerated testing at high fields and extrapolation to operating conditions based on electric field dependent dielectric wear-out models. A major complication in this approach is the impact of line-edge roughness (LER) which can lead to inaccuracies in lifetime projection due to creation of electrical field in-homogeneities in the test structure as well as non-uniform charge percolation effects. This paper shows a more robust approach of lifetime projection to operating voltages that uses as input experimentally measured LER statistical characteristics, an assumed field acceleration model and percolation model. The veracity of the assumed acceleration model is verified post priori by its ability to fit or describe the data set in entirety. The paper studies the impact of LER when the underlying acceleration model is Root-E (RE) as well as Power-Law (PL) and shows that the power-law model exhibits unique characteristics with respect to LER impact due to an absence of a characteristic field in power-law.
Junction Temperature Estimation Based on Updating RC Network for Different Liquid Cooling Conditions (2019)

The failure of power converters and inverters due to thermal stress can threaten the safety and reliability of electrical vehicles (EVs). Junction temperature estimation for power devices is the key factor to maintain safe operation and to extend power device lifetime. This paper proposes a detailed transient Foster thermal model with updating RC parameters at 216 cooling conditions based on coolant flowrate (5L/min to 10.5L/min) and coolant temperature (5°C to 90°C) since the liquid coolant is the major heat dissipating path in the module. The vehicle controller can store and keep updating these 216 RC values based on the coolant temperature and coolant flowrate measurements to provide accurate online IGBT junction temperature estimation. Test data from supplier is used to validate the model at selected operating points.
Characterizing an entangled-photon source with classical detectors and measurements (2015)

Entangled-photon pairs are essential for many applications in quantum computation and communication, and quantum state tomography (QST) is the universal tool to characterize such entangled-photon sources. In QST, very low-power signals must be measured with single-photon detectors and coincidence logic. Here, we experimentally implement a new protocol, “stimulated-emission tomography” (SET), allowing us to obtain the information provided by QST when the photon pairs are generated by parametric fluorescence. This approach exploits a stimulated process that results in a signal several orders of magnitude larger than in QST. In particular, we characterize the polarization state of photons that would be generated in spontaneous parametric downconversion using SET. We find that SET accurately predicts the purity and concurrence of the spontaneously generated photons in agreement with the results of QST. We expect that SET will be extremely useful to characterize entanglement sources based on parametric fluorescence, providing a fast and efficient technique to potentially replace or supplement QST.
Reaction of phenol with singlet oxygen (2018)

Photo-degradation of organic pollutants plays an important role in their removal from the environment. This study provides an experimental and theoretical account of the reaction of singlet oxygen O2(1Δg) with the biodegradable-resistant species of phenol in an aqueous medium. The experiments combine customised LED-photoreactors, high-performance liquid chromatography (HPLC), and electron paramagnetic resonance (EPR) imaging, employing rose bengal as a sensitiser. Guided by density functional theory (DFT) calculations at the M062X level, we report the mechanism of the reaction and its kinetic model. Addition of O2(1Δg) to the phenol molecule branches into two competitive 1,4-cycloaddition and ortho ene-type routes, yielding 2,3-dioxabicyclo[2.2.2]octa-5,7-dien-1-ol (i.e., 1,4-endoperoxide 1-hydroxy-2,5-cyclohexadiene) and 2-hydroperoxycyclohexa-3,5-dien-1-one, respectively. Unimolecular rearrangements of the 1,4-endoperoxide proceed in a facile exothermic reaction to form the only experimentally detected product, para-benzoquinone. EPR revealed the nature of the oxidation intermediates and corroborated the appearance of O2(1Δg) as the only active radical participating in the photosensitised reaction. Additional experiments excluded the formation of hydroxyl (HO˙), hydroperoxyl (HO2˙), and phenoxy intermediates. We detected for the first time the para-semibenzoquinone anion (PSBQ), supporting the reaction pathway leading to the formation of para-benzoquinone. Our experiments and the water-solvation model result in the overall reaction rates of kr-solvation = 1.21 × 104 M-1 s-1 and kr = 1.14 × 104 M-1 s-1, respectively. These results have practical application to quantify the degradation of phenol in wastewater treatment.
Effect of Percutaneous Transluminal Angioplasty on the Stenosis of Autogenous Radiocephalic Arteriovenous Fistula for Hemodialysis (2016)

Purpose The purpose of this study was to evaluate the effectiveness of percutaneous transluminal angioplasty (PTA) on stenosis of autogenous radiocephalic arteriovenous fistula (RCF) for hemodialysis and to determine the factors influencing patency. Materials and Methods This retrospective study included 136 patients referred for PTA of RCF stenosis between March 2005 and July 2014. The technical success rate, complications, and patency rate were evaluated. The following factors were analyzed as they might influence patency: age, gender, site and duration of arteriovenous fistula, underlying disease, body mass index, hypercholesterolemia, smoking, peripheral artery or coronary artery occlusive disease, stenosis length/grade, cutting balloon, and balloon size. Results The initial technical success rate was 91.9% (125/136). Complications included vessel rupture (n = 2) and vessel dissection (n = 2). The patency rates at 6, 12, 24, and 48 months after PTA were 81.9, 67.1, 52.7, and 42.3%, respectively. The patency rate was higher in cases with longer (> 3 cm) stenosis (p = 0.04). Use of cutting balloon and larger size of balloon catheter made the patency longer, but this difference was not statistically significant (p = 0.637, 0.258). Conclusion PTA is a safe and effective way to manage stenosis in RCF. The length of stenosis was the only factor which affected the patency rate in this study.
Air side enhancement of heat transfer in an additively manufactured 1 kW heat exchanger for dry cooling applications (2017)

Additive manufacturing is a fast-growing technique due to its ability to fabricate complex objects layer by layer from a preprogrammed digital model. Additive manufacturing can greatly enhance the heat exchanger manufacturing field, as it makes possible the fabrication of complex heat exchanger designs that are challenging to fabricate using conventional methods. In the present work, an air-to-water manifold-microchannel heat exchanger made of titanium alloy (Ti64) with size of 15 cm x 15 cm x 3.2 cm was fabricated using direct metal laser sintering (DMLS) additive manufacturing technique. The manifold-microchannel feeds the fluid flow into an array of parallel microchannels for better flow distribution as well as short flow travel length, thus yielding significantly enhanced heat transfer performance with low pressure drop penalty. Upon successful fabrication, the heat exchanger was experimentally tested, and the results were analyzed against conventional heat transfer surfaces. Based on the experimental results, for the case where the heat exchanger heat flow rate is 900 W, air-side Reynolds number is less than 100 and the temperature difference between the inlet air and water temperature is 27.5°C, heat transfer coefficient of 180 W/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> K and pressure drop of 100 Pa are observed. Compared to the conventional surfaces like wavy fin, louvered fin, and plain plate fins, up to 80%, 120%, and 190% improvement in air-side heat transfer coefficients were recorded, respectively, with an air-side pressure drop of less than 100 Pa. The results strongly suggest that additive manufacturing could be implemented for materials and complex designs that are otherwise difficult to fabricate with conventional technologies.
Toward More Sustainable Rechargeable Aqueous Batteries Using Plasma-Treated Cellulose-Based Li-Ion Electrodes (2020)

The use of water-soluble biobased binders (e.g., carboxymethylcellulose, CMC) in electrodes for aqueous Li-ion battery systems is typically impossible due to their inherent hydrophilicity that leads to a dissolution of the electrode and thus to a loss of mechanical cohesion and electronic percolation. To circumvent such limitations, a new composite electrode architecture made of water-soluble, biobased binders (CMC) protected by a thin membrane obtained in a nonthermal plasma at atmospheric pressure is reported. Using LiFePO4 as the environmental benign electrode material, it is shown that plasma-modified electrodes provide a stable reversible redox capacity for more than 85 days in a 1 mol/kg LiC2F6NO4S2 (LiTFSI) aqueous electrolyte. This novel architecture implies ecofriendly electrode manufacturing processes as well as substantial cost reduction of the whole battery system. This work represents the first step toward more sustainable aqueous Li-ion batteries.
Reconstructing weighted voting schemes from partial information about\n their power indices (2020)

A number of recent works [Goldberg 2006; O'Donnell and Servedio 2011; De,\nDiakonikolas, and Servedio 2017; De, Diakonikolas, Feldman, and Servedio 2014]\nhave considered the problem of approximately reconstructing an unknown weighted\nvoting scheme given information about various sorts of ``power indices'' that\ncharacterize the level of control that individual voters have over the final\noutcome. In the language of theoretical computer science, this is the problem\nof approximating an unknown linear threshold function (LTF) over $\\{-1, 1\\}^n$\ngiven some numerical measure (such as the function's $n$ ``Chow parameters,''\na.k.a. its degree-1 Fourier coefficients, or the vector of its $n$ Shapley\nindices) of how much each of the $n$ individual input variables affects the\noutcome of the function.\n In this paper we consider the problem of reconstructing an LTF given only\npartial information about its Chow parameters or Shapley indices; i.e. we are\ngiven only the Chow parameters or the Shapley indices corresponding to a subset\n$S \\subseteq [n]$ of the $n$ input variables. A natural goal in this partial\ninformation setting is to find an LTF whose Chow parameters or Shapley indices\ncorresponding to indices in $S$ accurately match the given Chow parameters or\nShapley indices of the unknown LTF. We refer to this as the Partial Inverse\nPower Index Problem.\n Our main results are a polynomial time algorithm for the\n($\\varepsilon$-approximate) Chow Parameters Partial Inverse Power Index Problem\nand a quasi-polynomial time algorithm for the ($\\varepsilon$-approximate)\nShapley Indices Partial Inverse Power Index Problem.\n
Transcatheter Tricuspid Valve-In-Ring and Aortic Valve-In-Valve Implantation (2017)

<b>Background</b> Transcatheter heart valve (THV) therapies have shown to be an alternative to surgical valve replacement, especially in high-risk patients requiring redo surgery. However, reports of transcatheter-based interventions in tricuspid valve position are scarce. <b>Case Description</b> Here, we report a case of successful concomitant transcatheter aortic valve-in-valve (ViV) and tricuspid valve-in-ring (ViR) procedures using a 23-mm CoreValve Evolut R THV (Medtronic, Inc., Minneapolis, Minnesota, United States) in aortic position and a 29-mm SAPIEN3 (Edwards Lifesciences, Inc., Irvine, California, United States) THV in tricuspid position. <b>Conclusion</b> This case demonstrates feasibility of concomitant transcatheter aortic ViV and tricuspid ViR procedures.
Error bounds from extra-precise iterative refinement (2006)

We present the design and testing of an algorithm for iterative refinement of the solution of linear equations where the residual is computed with extra precision. This algorithm was originally proposed in 1948 and analyzed in the 1960s as a means to compute very accurate solutions to all but the most ill-conditioned linear systems. However, two obstacles have until now prevented its adoption in standard subroutine libraries like LAPACK: (1) There was no standard way to access the higher precision arithmetic needed to compute residuals, and (2) it was unclear how to compute a reliable error bound for the computed solution. The completion of the new BLAS Technical Forum Standard has essentially removed the first obstacle. To overcome the second obstacle, we show how the application of iterative refinement can be used to compute an error bound in any norm at small cost and use this to compute both an error bound in the usual infinity norm, and a componentwise relative error bound.We report extensive test results on over 6.2 million matrices of dimensions 5, 10, 100, and 1000. As long as a normwise (componentwise) condition number computed by the algorithm is less than 1/ max{10, √n }ε w , the computed normwise (componentwise) error bound is at most 2 max{10, √n } · ε w , and indeed bounds the true error. Here, n is the matrix dimension and ε w = 2 -24 is the working precision. Residuals were computed in double precision (53 bits of precision). In other words, the algorithm always computed a tiny error at negligible extra cost for most linear systems. For worse conditioned problems (which we can detect using condition estimation), we obtained small correct error bounds in over 90% of cases.
Fluid model for window-based congestion control mechanism (2001)

We study the stability of two queueing delay-based congestion control algorithms, the (p, 1)-proportionally fair algorithm and the global optimization algorithm. We linearize the systems around the intended operating point and show that these algorithms are stable within a range of feedback delay. Based on these linearized systems we study the impact of various (cascade) compensators on the system. We show that the PID control improves the transient behavior of the system. We simulate both the linearized system and non-linear system and illustrate the validity of the analysis and improvement in the system behavior with compensators.
The impact of different human IgG capture molecules on the kinetics analysis of antibody-antigen interaction (2020)

Surface plasmon resonance (SPR) is a well-established method to characterize biomolecular interactions and is widely used in drug discovery and development. Here, we demonstrate that capture surfaces profoundly impact the binding kinetics parameters that are measured for antibody-antigen interactions. Six unique antibody-antigen interactions were characterized using eight different anti-human IgG capture surfaces. The antigen binding affinities for six different human monoclonal antibodies (hmAbs) captured using three different goat anti-human Fc (AHC) polyclonal antibody (pAb) surfaces were in reasonable agreement (3-7-fold weaker) with those measured by kinetic exclusion assay (KinExA). In contrast, up to 81, 32, 489, 2826, and 219-fold weaker antigen binding affinities were measured using mouse AHC mAb, Protein G, Protein A, Protein A/G, and Protein L surfaces, respectively. Protein A, Protein A/G and Protein G interacted with the Fab of hmAbs, possibly affecting antigen binding to hmAbs captured over these surfaces. Additional studies revealed that mouse AHC mAb binds hmAbs with a weak affinity (5.5-36.3 nM) and t<sub>½</sub> values of 1.4-3.3min, compared to the sub-nanomolar affinities of the goat AHC pAbs. These results emphasize the value of measuring binding kinetics of the capture molecule before immobilizing them onto the sensor surface to perform capture kinetics assays on label-free biosensors.
PGMax: Factor Graphs for Discrete Probabilistic Graphical Models and Loopy Belief Propagation in JAX (2022)

PGMax is an open-source Python package for (a) easily specifying discrete Probabilistic Graphical Models (PGMs) as factor graphs; and (b) automatically running efficient and scalable loopy belief propagation (LBP) in JAX. PGMax supports general factor graphs with tractable factors, and leverages modern accelerators like GPUs for inference. Compared with existing alternatives, PGMax obtains higher-quality inference results with up to three orders-of-magnitude inference time speedups. PGMax additionally interacts seamlessly with the rapidly growing JAX ecosystem, opening up new research possibilities. Our source code, examples and documentation are available at https://github.com/deepmind/PGMax.
Optimization of a batch reactor to produce the elastomeric copolyester prepolymer copoly(ethylene‐polyoxyethylene terephthalate)(CEPT) (2001)

Abstract A mathematical algorithm that optimizes the reactor to produce the elastomeric copolyester copoly(ethylene‐polyoxyethylene terephthalate), CEPT, is shown in this work. The optimization was carried out this way: First, an initial isothermal guess of temperature profile is made and the differential equtions system, which describes the CEPT production process, is solved, Second, the reaction time is fixed and the objective function is calculated. Third, the adjoint variable equations system is solved and the Hamiltonian's function is calculated. Fourth, a new temperature profile is found by using the control vector iteraction procedure. Finally, steps one to three are repeated until the objective function reaches a minimum value. The results of the optimization establish that the copolytransesterification reactor should be operated initially to high temperature (about 285°C), which should be reduced quickly to near 250°C to purposely diminish the production of by‐products.
Ultra-high speed quantification of cell strain during cell-microbubble interactions (2022)

Interactions between oscillating microbubbles and cells are of fundamental importance in understanding cell behaviour, including mechanotransduction, during therapeutic microbubble treatment. However, it is challenging to quantify cell deformation due to the short time domains at which microbubble-induced deformations occur. Developments in both ultra-high speed imaging and image processing may allow for quantification of cell strain at high temporal and spatial resolutions. Here, we tested the hypothesis that ultra-high speed imaging and digital image correlation could be used to measure and quantify microbubble-induced cell deformation. A hypervision HPV-X camera and a custom-designed, compact acoustic cell-culture device were used together to image interactions between DSPC-microbubbles and MG-63 cells at up to 5 × 106 fps, under ultrasound exposure at 1 MHz. Dynamic cell deformation was measured using digital image correlation with MatchID software. Microbubbles associated with MG63 cells in the acoustic device. Microbubble oscillation resulted in a peak deformation of 350 nm and strain of 5% on the cell during the bubble expansion phase, isolated locally to the point of interaction. These data show that cell deformation can be quantified dynamically during bubble-cell interactions, suggesting that mechanical properties, and potentially corresponding therapeutic effects, can be quantified at high-frequency strain rates.
Shared B cell memory to coronaviruses and other pathogens varies in human age groups and tissues (2020)

Abstract Vaccination and infection promote the formation, tissue distribution, and clonal evolution of B cells encoding humoral immune memory. We evaluated convergent antigen-specific antibody genes of similar sequences shared between individuals in pediatric and adult blood, and deceased organ donor tissues. B cell memory varied for different pathogens. Polysaccharide antigen-specific clones were not exclusive to the spleen. Adults’ convergent clones often express mutated IgM or IgD in blood and are class-switched in lymphoid tissues; in contrast, children have abundant class-switched convergent clones in blood. Consistent with serological reports, pre-pandemic children had class-switched convergent clones to SARS-CoV-2, enriched in cross-reactive clones for seasonal coronaviruses, while adults showed few such clones in blood or lymphoid tissues. These results extend age-related and anatomical mapping of human humoral pathogen-specific immunity. One Sentence Summary Children have elevated frequencies of pathogen-specific class-switched memory B cells, including SARS-CoV-2-binding clones.