gebhart/patrepeval huggingface dataset:
Optimized Weighted Performance Index for Objective Evaluation of Border-Detection Methods in Dermoscopy Images (2011)

Quantitative evaluation of the existing border-detection methods is commonly performed by using different metrics. This is inherently problematic due to the different characteristics of each metric. This paper presents a novel approach for objective evaluation of border-detection methods in dermoscopy images by introducing a comprehensive evaluation metric: optimized weighted performance index. The index is formed as a nonlinear weighted function of the six commonly used metrics of sensitivity, specificity, accuracy, precision, border error, and similarity. Constrained nonlinear multivariable optimization techniques are applied to determine the optimal set of weights that result in the maximum value of the index. This index is used as an effective measure of the value of a given border-detection method and, thus, provides a basis for comparison with other methods. To demonstrate the effectiveness of the proposed index, it is used to evaluate five recent border-detection methods applied on a set of 55 high-resolution dermoscopy images.
Integrated Dual‐Mode Chromatography to Enrich Extracellular Vesicles from Plasma (2020)

Purifying extracellular vesicles (EVs) from complex biological fluids is a critical step in analyzing EVs molecularly. Plasma lipoprotein particles (LPPs) are a significant confounding factor as they outnumber EVs >10<sup>4</sup> -fold. Given their overlap in size, LPPs cannot be completely removed using standard size-exclusion chromatography. Density-based separation of LPPs can be applied but is impractical for routine use in clinical research and practice. Here a new separation approach, known as dual-mode chromatography (DMC), capable of enriching plasma EVs, and depleting LPPs is reported. DMC conveniently integrates two orthogonal separation steps in a single column device: i) size exclusion to remove high-density lipoproteins (HDLs) that are smaller than EVs; and ii) cation exchange to clear positively charged ApoB100-containing LPPs, mostly (very) low-density lipoproteins (V)LDLs, from negatively charged EVs. The strategy enables DMC to deplete most LPPs (>97% of HDLs and >99% of (V)LDLs) from human plasma, while retaining EVs (>30% of input). Furthermore, the two-in-one operation is fast (15 min per sample) and equipment-free. With abundant LPPs removed, DMC-prepared samples facilitate EV identification in imaging analyses and improve the accuracy for EV protein analysis.
Replica molding using polymeric materials: A practical step toward nanomanufacturing (1997)

The reliable fabrication of nanostructures is polymer materials , i.e. structures with feature sizes below 100 nm, is an important goal if progress in the application of such materials in electronic, magnetic, and optical devices is to be maintained. Replica molding has been used extensively to produce micrometer sized features. Here, the technique is extended to the nanometer regime such as that shown in the figure. fig. magnified image
Making the connections: physical and electric interactions in biohybrid photosynthetic systems (2023)

Biohybrid photosynthesis systems, which combine biological and non-biological materials, have attracted recent interest in solar-to-chemical energy conversion. However, the solar efficiencies of such systems remain low, despite advances in both artificial photosynthesis and synthetic biology. Here we discuss the potential of conjugated organic materials as photosensitisers for biological hybrid systems compared to traditional inorganic semiconductors. Organic materials offer the ability to tune both photophysical properties and the specific physicochemical interactions between the photosensitiser and biological cells, thus improving stability and charge transfer. We highlight the state-of-the-art and opportunities for new approaches in designing new biohybrid systems. This perspective also summarises the current understanding of the underlying electron transport process and highlights the research areas that need to be pursued to underpin the development of hybrid photosynthesis systems.
[Human renal urate transpoter URAT1 mediates the transport of salicylate]. (2010)

Salicylic acid derivatives are the most prescribed analgesic-antipyretic and anti-inflammatory agents. It is well known that salicylate has a paradoxical effect on renal urate excretion. At low doses (5 - 10 mg/dL serum), renal urate excretion is decreased, whereas at high doses (> 15 mg/dL serum), renal urate excretion is increased. Since the molecular identification of the renal apical urate/anion exchanger URAT1, it has been suggested that this protein is responsible for the paradoxical effect because of cis-inhibition of salicylate (1 mM) on urate uptake by URAT1-expressing oocytes. The purpose of this study was to examine whether or not URAT1 is responsible for the paradoxical effect of salicylate. In URAT1-stably expressing HEK293 (HEK293-URAT1) cells, salicylate inhibited [14C] urate uptake dose-dependently (IC50, 23.9 microM). URAT1 mediated the time-dependent uptake of [3H] salicylate in these cells. [3H] Salicylate uptake via URAT1 was inhibited by non-labelled urate and salicylate, and the uricosuric agent, benzbromarone. In the URAT1-expressing oocytes, we observed the time- and concentration-dependent transport of salicylate (Km : 25.3 microM). Moreover, non-labelled salicylate injected into the URATI-expressing oocytes stimulated [14C] urate uptake. These results suggest that the "paradoxical effect" of salicylate can be explained by two modes of salicylate interaction with URAT1 : (1) acting as an exchange substrate to facilitate urate reabsorption, and (2) acting as an inhibitor for urate reabsorption.
Ultrahigh-$Q$ Nanocavities in Two-Dimensional Photonic Crystal Slabs (2006)

In this paper, we discuss methods to suppress the radiation loss of ultrasmall cavities, of the size of the optical wavelength, in two-dimensional photonic crystal slabs. An important design concept to suppress radiation loss is introduced: The envelope of the cavity mode field should have no abrupt changes and should ideally follow a Gaussian function. Cubic wavelength order cavities, with experimental Q factors of 100 000 and nearly 1 000 000 are obtained by tailoring the envelope functions using air-hole shifts and multistep heterostructures, respectively. In addition, the experimental Q factors of the latest cavities are shown to be determined by the imperfections in the fabricated structures and not by the cavity design. The differences between the experimental and the theoretical Q factors are investigated in order to demonstrate how higher Q factors could be realized in the future
Fundamentals of Trapped Ion Mobility Spectrometry (2014)

Trapped ion mobility spectrometry (TIMS) is a relatively new gas-phase separation method that has been coupled to quadrupole orthogonal acceleration time-of-flight mass spectrometry. The TIMS analyzer is a segmented rf ion guide wherein ions are mobility-analyzed using an electric field that holds ions stationary against a moving gas, unlike conventional drift tube ion mobility spectrometry where the gas is stationary. Ions are initially trapped, and subsequently eluted from the TIMS analyzer over time according to their mobility (K). Though TIMS has achieved a high level of performance (R > 250) in a small device (<5 cm) using modest operating potentials (<300 V), a proper theory has yet to be produced. Here, we develop a quantitative theory for TIMS via mathematical derivation and simulations. A one-dimensional analytical model, used to predict the transit time and theoretical resolving power, is described. Theoretical trends are in agreement with experimental measurements performed as a function of K, pressure, and the axial electric field scan rate. The linear dependence of the transit time with 1/K provides a fundamental basis for determination of reduced mobility or collision cross section values by calibration. The quantitative description of TIMS provides an operational understanding of the analyzer, outlines the current performance capabilities, and provides insight into future avenues for improvement.
Observation of $\mathrm{t\overline{t}H}$ production (2018)

The observation of Higgs boson production in association with a top quark-antiquark pair is reported, based on a combined analysis of proton-proton collision data at center-of-mass energies of $\sqrt{s}=$ 7, 8, and 13 TeV, corresponding to integrated luminosities of up to 5.1, 19.7, and 35.9 fb$^{-1}$, respectively. The data were collected with the CMS detector at the CERN LHC. The results of statistically independent searches for Higgs bosons produced in conjunction with a top quark-antiquark pair and decaying to pairs of W bosons, Z bosons, photons, $\tau$ leptons, or bottom quark jets are combined to maximize sensitivity. An excess of events is observed, with a significance of 5.2 standard deviations, over the expectation from the background-only hypothesis. The corresponding expected significance from the standard model for a Higgs boson mass of 125.09 GeV is 4.2 standard deviations. The combined best fit signal strength normalized to the standard model prediction is 1.26${^{+0.31}_{-0.26}}$.
Ion trap mass analysis at high pressure: A theoretical view (2009)

The mass-selective manipulation of ions at elevated pressure, including mass analysis, ion isolation, or excitation, is of great interest for the development of mass spectrometry instrumentation, particularly for systems in which ion traps are employed as mass analyzers or storage devices. While experimental exploration of high-pressure mass analysis is limited by various difficulties, such as ion detection or electrical discharge at high-pressure, theoretical methods have been developed in this work to study ion/neutral collision effects within quadrupole ion traps and to explore their performance at pressures up to 1 Torr. Ion trapping, isolation, excitation, and resonance ejection were investigated over a wide pressure range. The theoretically calculated data were compared with available experimental data for pressures up to 50 mTorr, allowing the prediction of ion trap performance at pressures more than 10 times higher.
A bio-inspired analog silicon retina with Michaelis-Menten auto-adaptive pixels sensitive to small and large changes in light (2015)

In this paper, we present: (i) a novel analog silicon retina featuring auto-adaptive pixels that obey the Michaelis-Menten law, i.e. V=V(m) I(n)/I(n)+σ(n); (ii) a method of characterizing silicon retinas, which makes it possible to accurately assess the pixels' response to transient luminous changes in a ±3-decade range, as well as changes in the initial steady-state intensity in a 7-decade range. The novel pixel, called M(2)APix, which stands for Michaelis-Menten Auto-Adaptive Pixel, can auto-adapt in a 7-decade range and responds appropriately to step changes up to ±3 decades in size without causing any saturation of the Very Large Scale Integration (VLSI) transistors. Thanks to the intrinsic properties of the Michaelis-Menten equation, the pixel output always remains within a constant limited voltage range. The range of the Analog to Digital Converter (ADC) was therefore adjusted so as to obtain a Least Significant Bit (LSB) voltage of 2.35mV and an effective resolution of about 9 bits. The results presented here show that the M(2)APix produced a quasi-linear contrast response once it had adapted to the average luminosity. Differently to what occurs in its biological counterparts, neither the sensitivity to changes in light nor the contrast response of the M(2)APix depend on the mean luminosity (i.e. the ambient lighting conditions). Lastly, a full comparison between the M(2)APix and the Delbrück auto-adaptive pixel is provided.
Imputation of Human Mobility Data for Comprehensive Risk Models (2023)

Sensor-equipped wearable devices are becoming increasingly popular in the healthcare industry, with some equipped with GPS and Proximity sensors as well. Raw (GPS) trajectories obtained through human-centric systems like body worn senors, and enriched with semantic annotations generate huge actionable insights for downstream domain specific applications like epidemic risk modeling. However, trajectory data suffer from missing data problem owing to various technical as well as behavioral factors. Our paper shows that, for a semantic trajectory dataset and using coarse grain semantic location for both prediction and imputation purposes, a simple ensemble classifier-based model can outperform the existing deep models where trajectory imputation is almost real-time delay.
Insights of biomass recalcitrance in naturalPopulus trichocarpavariants for biomass conversion (2017)

The recalcitrance of natural<italic>Populus</italic>variants was elucidated.
Atomic force microscopy: a tool for surface science (1991)

The understanding and manipulation of surfaces have been greatly helped by a variety of atomic force microscopes.
C02-Angiographie: Blutflußmessung mit injizierten Gasblasen - Carbon Dioxide Angiography: Blood Flow Measurement with Injected Gas Bubbles (1992)

The use of CO2 gas as a contrast medium for visualizing blood vessels has been considerably facilitated by the development of a gas metering device for mechanical injection of CO2. The present paper describes the possibility of using CO2 not only for visualizing blood vessel morphology, but also for the diagnostic evaluation of the haemodynamics within the vessels. For this reason in vitro experiments with an artery simulation model were undertaken to examine the behaviour of injected gas bubbles. The information thus obtained was then translated to animal experiments.
Paper 29: The Contribution of Posteroinferior Capsule Tightness to Subacromial Impingement During Pitching Motion (2012)

Loss of internal rotation as well as excessive external rotation has been recognized in baseball pitchers. Tightness of the posteroinferior capsule including the posterior band of the inferior glenohumeral ligament is assumed to be the cause of this loss (Burkhart, 2003). Previously, the posterior capsule tightness was speculated to lead to subacromial impingement during shoulder flexion and horizontal adduction (Harryman, 1990). Although intra-articular (internal) impingement during the pitching motion is well accepted, the relationship between the posterior capsule tightness and subacromial (external) impingement is unclear.
A brief report on working smarter with Agile software development (2010)

Agile software development methods have proven to be a substantial catalyst for improvements in software quality, speed of delivery, and fitness for use, and are a driver behind the IBM Smarter Planet™ initiative, which involves intelligent approaches that address the needs of a world that is becoming increasingly interconnected and instrumented. Software vendors who use a traditional or waterfall approach (i.e., sequential software development process) for requirement analysis and development often find that they cannot react with sufficient speed to meet rapidly changing market demand. As a result, stakeholders must wait for the vendor to complete a lengthy development cycle, which, when complete, may miss the market window for the software or fail to adequately address other needs of these stakeholders. Agile development methods, as practiced across geographically diverse and broad development teams at IBM, directly address this issue. One purpose of this paper is simply to provide a brief high-level overview and record of the adoption of these practices and methods across a large company, i.e., the IBM Corporation.
An Interactive Recommendation System for 2nd Language Vocabulary Learning - Vocabulometer 2.0 (2019)

According to linguistics, one of the major challenges for language learners is to find materials adapted to their skill. By continuously analyzing the reading activity of the user, the proposed system estimates the user's vocabulary and recommends documents adapted to her/his skill. In this article we improve the Vocabulometer platform by taking into account the user's interest for some topics and the document complexity. We implemented a text classification method and complex word identification analysis that refine the recommendation process and guarantees a level of difficulty of recommended texts in accordance with the level of vocabulary of each user.
Experimentally validated multiphysics computational model of refracting shock wave lithotripter. (2011)

We will present a computational model of the focusing of an electromagnetically induced pressure pulse by an acoustic lens and subsequent shock wave formation. Linear elasticity equations for the lens are solved simultaneously with Euler hydrodynamic equations for water considered to be a compressible medium with a Tait equation of state. The adaptive mesh refinement model allows both three-dimensional and two-dimensional axisymmetric computations. A number of coupling approaches at the lens-water interface are investigated by comparison to experimental results: transfer only of pressure boundary condition, coupling of displacement velocities, and a buffer linear elasticity region in the water immediately adjacent to lens. The model is validated against single-medium measurements (water or lens material), and the complete experimental shock wave formation process. Initial results from a crack propagation model in stone simulants placed at the lithotripter focus will also be presented.
Scalable training of hierarchical topic models (2018)

Large-scale topic models serve as basic tools for feature extraction and dimensionality reduction in many practical applications. As a natural extension of flat topic models, hierarchical topic models (HTMs) are able to learn topics of different levels of abstraction, which lead to deeper understanding and better generalization than their flat counterparts. However, existing scalable systems for flat topic models cannot handle HTMs, due to their complicated data structures such as trees and concurrent dynamically growing matrices, as well as their susceptibility to local optima. In this paper, we study the hierarchical latent Dirichlet allocation (hLDA) model which is a powerful nonparametric Bayesian HTM. We propose an efficient partially collapsed Gibbs sampling algorithm for hLDA, as well as an initialization strategy to deal with local optima introduced by tree-structured models. We also identify new system challenges in building scalable systems for HTMs, and propose efficient data layout for vectorizing HTM as well as distributed data structures including dynamic matrices and trees. Empirical studies show that our system is 87 times more efficient than the previous open-source implementation for hLDA, and can scale to thousands of CPU cores. We demonstrate our scalability on a 131-million-document corpus with 28 billion tokens, which is 4--5 orders of magnitude larger than previously used corpus. Our distributed implementation can extract 1,722 topics from the corpus with 50 machines in just 7 hours.
Learning the Matching Function (2015)

The matching function for the problem of stereo reconstruction or optical flow has been traditionally designed as a function of the distance between the features describing matched pixels. This approach works under assumption, that the appearance of pixels in two stereo cameras or in two consecutive video frames does not change dramatically. However, this might not be the case, if we try to match pixels over a large interval of time. In this paper we propose a method, which learns the matching function, that automatically finds the space of allowed changes in visual appearance, such as due to the motion blur, chromatic distortions, different colour calibration or seasonal changes. Furthermore, it automatically learns the importance of matching scores of contextual features at different relative locations and scales. Proposed classifier gives reliable estimations of pixel disparities already without any form of regularization. We evaluated our method on two standard problems - stereo matching on KITTI outdoor dataset, optical flow on Sintel data set, and on newly introduced TimeLapse change detection dataset. Our algorithm obtained very promising results comparable to the state-of-the-art.
Analysing Multi-Point Multi-Frequency Machine Vibrations using Optical Sampling (2018)

Vibration analysis is a key troubleshooting methodology for assessing the health of factory machinery. We propose an unobtrusive framework for at-a-distance visual estimation of such (possibly high frequency) vibrations, using a low fps (frames-per-second) camera that may, for example, be mounted on a worker's smart-glass. Our key innovation is to use an external stroboscopic light source (that, for example, may be provided by an assistive robot), to illuminate the machine with multiple mutually-prime strobing frequencies, and use the resulting aliased signals to efficiently estimate the different vibration frequencies via an enhanced version of the Chinese Remainder Theorem. Experimental results show that our technique estimates multiple such frequencies faster, and compares favourably to an equipment-mounted accelerometer alternative, with frequency estimation errors below 0.5% for vibrations occurring up to 500 Hz.
Pyrolyzed Carbon Fabrication Seminar. (2013)

Abstract not provided.
High-power, single-beam plasma wave tube (1994)

Short-pulse, ultra-broadband sources of RF radiation are needed for a variety of new applications. To meet this demand, we have developed and optimized a single-beam Plasma Wave Tube (PWT), The PWT is a unique microwave/millimeter-wave source which utilizes the interaction between beamexcited electron plasma waves to generate kilowatt-power (/spl sim/10 kW) radiation at microwave to millimeter-wave frequencies with a beam-to-radiation conversion efficiency of /spl ges/0.4%. In a single-beam PWT, an electron beam (/spl les/40 kV, /spl ges/200 A, 5-to-20-/spl mu/s pulse width) is injected into a gas-filled (e,g., hydrogen) cylindrical waveguide. The beam first ionizes the gas to generate a plasma, and then nonlinearly interacts with the plasma to generate radiation from 6-to-60 GHz. Slew rates of up to 7 GHz//spl mu/s have been measured during a single beam pulse. The radiation has a wide instantaneous bandwidth, typically 10 GHz or wider. Electron-beam transport through the waveguide is accomplished with no externally applied magnetic fields because the beam space charge is cancelled by the background plasma.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Letting go of O-glycans (2019)

The generation of free <i>N</i>-glycans, or unconjugated oligosaccharides derived from <i>N</i>-linked glycoproteins, is well understood, but whether a similar fate awaits <i>O</i>-linked glycoprotein carbohydrates was unknown. Hirayama <i>et al.</i> now reveal, by using only mannose as an energy source, the generation of free <i>O</i>-glycans in <i>Saccharomyces cerevisiae</i>, in the lumen of a secretory compartment, possibly the vacuole. These findings uncover the presence of a possible regulated degradation pathway for <i>O</i>-mannosylated glycoproteins.
A design strategy of exciton blocking materials using simulations and the analysis of device properties (2023)

A hole transporting type exciton blocking layer (hEBL) is one of the important device architecture components in phosphorescence organic light emitting diodes (PhOLEDs).