gebhart/patrepeval huggingface dataset:
Characterization and quantification of biological micropatterns using cluster SIMS (2010)

Micropatterning is used widely in biosensor development, tissue engineering and basic biology. Creation of biological micropatterns typically involves multiple sequential steps that may lead to cross-contamination and may contribute to sub-optimal performance of the surface. Therefore, there is a need to develop novel strategies for characterizing location-specific chemical composition of biological micropatterns. In this paper, C(60) (+) ToF-SIMS operating in the event-by-event bombardment-detection mode was used for spatially resolved chemical analysis of micropatterned indium tin oxide (ITO) surfaces. Fabrication of the micropatterns involved multiple steps including self-assembly of poly (ethylene glycol) (PEG)-silane, patterning of photoresist, treatment with oxygen plasma and adsorption of collagen (I). The ITO surfaces were analyzed with 26 keV C(60) (+)SIMS run in the event-by-event bombardment-detection mode at different steps of the modification process. We were able to evaluate the extent of cross-contamination between different steps and quantify coverage of the immobilized species. The methodology described here provides a novel means for characterizing the composition of biological micropatterns in a quantitative and spatially-resolved manner.
Magnetization reversal and magnetic anisotropy in patterned Co/Pd multilayer thin films (2008)

( Co / Pd ) N multilayers exhibit high vertical magnetic anisotropy and have been extensively explored as recording medium candidates for high density magnetic recording applications. In this work, (Co/Pd)N multilayers are deposited by magnetron sputtering and patterned into large periodic arrays of 200 nm islands to enable controlled domain wall injection for quantitative comparison of magnetic anisotropy energies. Magnetic properties are correlated with x-ray photoelectron spectroscopy data, an approach commonly used to probe the binding energies and valence band positions. Confirming theoretical predictions, it is demonstrated that the degree of d-shell hybridization at Co/Pd interfaces directly correlated with the magnitude of magnetic anisotropy.
31P chemical-shift tensors in barium diethyl phosphate and urea-phosphoric acid: model compounds for phospholipid head-group studies (1978)

The molecular orientations of the 31P chemical-shift tensors in the phosphodiester barium diethyl phosphate (BDEP) and in the nonesterified urea-H3PO4 (UPA) complex were determined from single-crystal studies. Although the tensors possess qualitatively similar orientations, there are differences between the two tensors of the order of 20 degrees. The principal values of the BDEP tensor are within 5% of those found in powder spectra of phospholipids, and, for this and other reasons, which are discussed in detail, we believe BDEP is a good model chemical-shift tensor for lipid phosphate. With the BDEP tensor alone, one can label certain head-group conformations as improbable, and, in conjunction with oriented bilayer spectra, one can determine the conformation of lipid head groups. In addition, we suggest a technique for orienting crystals based on the transformation properties of shift tensors, and we demonstrate this method by applying it to UPA. Finally, our results allow us to assess the effect of shift anisotropy relaxation on 31P liquid spectra at high fields.
Wavelet-based figure of merit for macro-uniformity (2013)

Wavelets are a powerful tool that can be applied to problems in image processing and analysis. They provide a multi-scale decomposition of an original image into average terms and detail terms that capture the characteristics of the image at different scales. In this project, we develop a figure of merit for macro-uniformity that is based on wavelets. We use the Haar basis to decompose the image of the scanned page into eleven levels. Starting from the lowest frequency level, we group the eleven levels into three non-overlapping separate frequency bands, each containing three levels. Each frequency band image consists of the superposition of the detail images within that band. We next compute 1-D horizontal and vertical projections for each frequency band image. For each frequency band image projection, we develop a structural approximation that summarizes the essential visual characteristics of that projection. For the coarsest band comprising levels 9,10,11, we use a generalized square-wave approximation. For the next coarsest band comprising levels 6,7,8, we use a piecewise linear spline approximation. For the finest bands comprising levels 3,4,5, we use a spectral decomposition. For each 1-D approximation signal, we define an appropriate set of scalar-valued features. These features are used to design two predictors one based on linear regression and the other based on the support vector machine, which are trained with data from our image quality ruler experiments with human subjects.
High-performance organic circuits based on precisely aligned single-crystal arrays (2018)

In this paper, we demonstrate high-performance organic logic circuits based on precisely controlled organic single-crystal arrays. Well-aligned microrod shaped 2,7-dioctyl[1]benzothieno[3,2-<i>b</i>][1]benzothiophene (C8-BTBT) single-crystal organic thin-film-transistors (OTFTs) were fabricated <i>via</i> solvent mediated molecular tailoring with a polymeric sacrificial layer, exhibiting saturation mobility of >2 cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup>. Using this approach, precise placement of organic crystal arrays in a controlled orientation was successfully achieved, enabling the fabrication of OTFT-based inverter circuits with a gain of 1.37 (V V<sup>-1</sup>). Furthermore, it was demonstrated that, by varying the number of single-crystal microrods, the device dimension and corresponding circuit performance can be modulated. A high-performance inverter operation with various interdigitating single-crystal microrod arrays can thus be achieved.
One‐Pot Sequential Photoredox Chemistry and Asymmetric Transfer Hydrogenation with a Single Catalyst (2018)

A sequential process is reported, in which different photoredox reactions are placed in sequence with asymmetric transfer hydrogenations of aryl ketones to provide a diverse set of chiral alcohols with enantioselectivities of up to 99 % ee . The method relies on a single chiral‐at‐metal catalyst which is added at the beginning of the two step sequence and only a final purification of the reaction product is required.
Thermo-Optical Arrays of Flexible Nanoscale Nanomembranes Freely Suspended over Microfabricated Cavities as IR Microimagers (2006)

We fabricated an array of microscopic cavities sealed with a freely suspended layer-by-layer nanomembrane. We observed that the convex−concave shape transition controlled by thermal expansion and contraction of air in the sealed microcavities facilitates a fast optical response to minute temperature variations and allows for direct visualization of the IR laser beam footprint in real time. Such sealed cavity arrays will pave the way toward a new generation of uncooled, miniature, ultrasensitive, thermal microimagers.
BIO17: Simulating Thrombus Formation In A Blood Oxygenator Considering Fibrin Formation, Platelet Activity, And Contact Activation (2022)

A numerical simulation of thrombus formation was performed in a blood oxygenator hollow fiber bundle microchannel. The numerical results were compared with in-vitro data. A model of factor XII contact activation, platelet activation, and fibrin formation was used to simulate thrombus formation. The simulating approach is based on the model of Wu et al.1, which solves the Navier-Stokes equations for flow dynamics and convection-diffusion-reaction equations for blood constituent concentrations. The geometry has a path length of 2 cm with fiber rods of 380 µm diameters and 40% packing density (see fig. 1A.) The simulation was conducted for an average fiber bundle velocity of 16 cm/min, which is similar to the velocity in commercial oxygenators. Blood constituent concentrations and properties were assumed to be those of healthy human participants. The model was implemented and solved in OpenFOAM. The numerical results after 10 min were compared to experimental studies that lasted 15 min. Despite the time course difference, interesting similarities were observed. After 10 min of simulation, clot formed preferentially downstream towards the narrowing outlet (see fig. 1B.) Minor platelet aggregation was observed, and the main constituent of the thrombus was fibrin (see fig. 1C and 1D.) Both observations are in line with the experimental results from Lai2 as it is shown figure 1E where the thrombus is shown in red downstream the oxygenator. The model captured the fibrin trail observed experimentally behind the fiber bundles (see Fig. 1C and F). Our results suggest that when simulating thrombosis in blood oxygenators, fibrin formation must be included, which could be explained by the large surface area to volume ratio and low velocities in the oxygenator. References 1.Lai, A. (2019). Carnegie Mellon University. 2.Wu, et al. (2017). Scientific Reports. Figure 1. A) Blood oxygenator geometry. B) Thrombus volume fraction field at middle plane. C) Fibrin concentration field behind fiber bundles. D) Middle plane fibrin concentration field. E) Experimental thrombus probability maps. F) Experimental thrombus composition. Red arrows indicate the flow direction.
Syphilitic balanitis of Follmann in a patient with a history of previous infection (2023)

We report a case of syphilitic balanitis of Follmann arising in a man with a history of prior infection with syphilis. Few cases have been described in the literature. In our case, a man with history of multiple unprotected sexual contacts presented with erosive balanitis and painless inguinal bilateral lymphadenopathy. All tests for sexually transmitted infections (STIs) performed were negative with the exception of serology for syphilis. We made the diagnosis of syphilitic balanitis of Follmann that was confirmed by prompt resolution after treatment.
A Six-DOF Force/Torque Sensor for Collaborative Robot and its Calibration Method (2017)

This study presents a new six-DOF force/torque sensor and its calibration method for a “collaborative robot or cobot”. This new calibration method applies the so-called “maximum likelihood estimation (MLE)”. MLE is used to determine and identify the parameters related to applied torques/forces and resulted deformations at varied locations of the sensor structure. Formulating the relations in a vector-matrix form, such parameters are captured as the coefficients in a matrix relating torques/forces to angular/linear deformations in different directions. In addition to applying MLE, finite element (FEM) modeling and analysis are conducted to generate realistic-like empirical data for the aforementioned calibration computation based on MLE. The matrix formed by these coefficients can then predict forces and torques with good accuracy via deformations detected by strain gauges. Seen in simulation results, the worst sum of error for three forces is less than 0.04%, while that for three torques is less than 0.00005%. Very small values of sum of error demonstrate a strong correlation of the model with the results obtained from MLE, indicating high precision in sensing forces and torques without decoupling matrix. The developed sensor is highly suitable for real-time sensing of multi-dimensional interactive forces/torques in industrial robots.
Adolescent substance abuse: Toward an integration of family systems and individual adaptation theories (1985)

Abstract Adolescent substance abuse is best understood as an adaptive behavior by an individual embedded within a rigid family organization. Substance abuse helps the individual deal with distress associated with family interactions. It becomes a means for raising estimates of self-appraisal and asserting some control over self and the environment. The family is involved in numerous ways in the substance abuse pattern. The fulcrum upon which adolescent substance abuse is poised is stasis in the developmental trajectories of individual and family, It becomes essential to family members to avoid the trauma of separation and individuation. The substance abuser does not become a unique and autonomous adult, but rather maintains a role within the family that has become imbued with special significance.
Integrated silicon carbide modulator for CMOS photonics (2021)

Abstract The electro-optic modulator encodes electrical signals onto an optical carrier, and is essential for the operation of global communication systems and data centers that society demands. An ideal modulator results from scalable semiconductor fabrication and is integrable with electronics. Accordingly, it is compatible with complementary metal-oxide-semiconductor (CMOS) fabrication processes. Moreover, modulators using the Pockels effect enables low loss, ultrafast, and wide-bandwidth data transmission. Although strained silicon-based modulators could satisfy these criteria, fundamental limitations such as two-photon absorption, poor thermal stability and a narrow transparency window hinder their performance. On the other hand, as a wide bandgap semiconductor material, silicon carbide is CMOS compatible and does not suffer from these limitations. Due to its combination of color centers, high breakdown voltage, and strong thermal conductivity, silicon carbide is a promising material for CMOS electronics and photonics with applications ranging from sensors to quantum and nonlinear photonics. Importantly, silicon carbide exhibits the Pockels effect, but a modulator has not been realized since the discovery of this effect more than three decades ago. Here we design, fabricate, and demonstrate the first Pockels modulator in silicon carbide. Specifically, we realize a waveguide-integrated, small form-factor, gigahertz-bandwidth modulator that can operate using CMOS-level drive voltages on a thin film of silicon carbide on insulator. Furthermore, the device features no signal degradation and stable operation at high optical intensities (913 kW/mm 2 ), allowing for high optical signal-to-noise ratios for long distance communications. Our work unites Pockels electro-optics with a CMOS platform to pave the way for foundry-compatible integrated photonics.
A new method of robotic rate control near singularities (2002)

A novel method of controlling robotic manipulators near singularities is introduced. In traditional rate control, a local first-order approximation of the robot kinematics is used, which may fail at a singularity. However, if the approximation is extended to the second order, it becomes possible to solve for the joint rates. The proposed method uses a multidimensional Newton-Raphson technique to solve the resulting set of coupled, quadratic equations. The method is presented in conjunction with a description of rate control in the complex domain, which allows for end-effector locations outside the manipulators workspace. Two examples employing quadratic rate control are presented for a 6R robot in a singular configuration, and one example applying the method to a closed trajectory is shown.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nine of 16 Stereoisomeric Polyhydroxylated Proline Amides Are Potent β-N-Acetylhexosaminidase Inhibitors (2014)

All 16 stereoisomeric N-methyl 5-(hydroxymethyl)-3,4-dihydroxyproline amides have been synthesized from lactones accessible from the enantiomers of glucuronolactone. Nine stereoisomers, including all eight with a (3R)-hydroxyl configuration, are low to submicromolar inhibitors of β-N-acetylhexosaminidases. A structural correlation between the proline amides is found with the ADMDP-acetamide analogues bearing an acetamidomethylpyrrolidine motif. The proline amides are generally more potent than their ADMDP-acetamide equivalents. β-N-Acetylhexosaminidase inhibition by an azetidine ADMDP-acetamide analogue is compared to an azetidine carboxylic acid amide. None of the amides are good α-N-acetylgalactosaminidase inhibitors.
Design and fabrication of a dual-element off-axis near-eye optical magnifier (2007)

The key contribution is the design, analysis, and fabrication of a dual-element off-axis magnifier to improve the state of the art in catadioptric magnifiers. The catadioptric magnifier is composed of a free-form mirror and a lens with a diffractive optical element. A monocular magnifier was prototyped, to our knowledge for the first time, with the specifications of an 8 mm exit pupil, 20 degrees diagonal full field of view, 15 mm eye clearance, 1.5 arcmin resolution, and operating in the photopic visual regime.
Boosting the Sensitivity of Ligand–Protein Screening by NMR of Long-Lived States (2012)

A new NMR method for the study of ligand-protein interactions exploits the unusual lifetimes of long-lived states (LLSs). The new method provides better contrast between bound and free ligands and requires a protein-ligand ratio ca. 25 times lower than for established T(1ρ) methods, thus saving on costly proteins. The new LLS method was applied to the screening of inhibitors of urokinase-type plasminogen activator (uPA), which is a prototypical target of cancer research. With only 10 μM protein, a dissociation constant (K(D)) of 180 ± 20 nM was determined for the strong ligand (inhibitor) UK-18, which can be compared with K(D) = 157 ± 39 nM determined by the established surface plasmon resonance method.
V1 and V2 Domains of HIV Envelope Contribute to CCR5 Antagonist Resistance (2019)

Vicriviroc (VCV) is a CCR5 antagonist that blocks the viral entry of CCR5-tropic (R5) virions by binding to and inducing a conformational change in the chemokine receptor. Clinical resistance to CCR5 antagonists occurs in two phases, competitive and noncompetitive stages. In this study, we analyzed two subjects, from a phase 2b VCV clinical trial, whose quasispecies contained R5 and dual-mixed virions at the earliest recorded time of virological failure (VF). Genotypic analysis of R5-tropic patient-derived envelope genes revealed significant changes in the V1/V2 coding domain and convergence toward a more homogenous sequence under VCV therapy. Additionally, a small population of baseline clones sharing similar V1/V2 and V3 domains with the predominant VF isolate was observed. These clones were denoted preresistant based on their genotype. Preresistant clones and chimeric clones containing V1/V2 regions isolated during VF displayed high 50% inhibitory concentration (IC<sub>50</sub>) values relative to those at baseline, consistent with early competitive resistance. Genotypic analysis of the dual-tropic clones also showed significant changes in the V1/V2 region, different from the resistant R5-tropic viruses. Our findings suggest that the V1/V2 domain plays a key role in the initial step of development of drug resistance.<b>IMPORTANCE</b> It is believed that each CCR5 antagonist-resistant isolate will develop its own unique set of mutations, making it difficult to identify a signature mutation that can effectively predict CCR5 antagonist resistance. This may explain why we do not observe shared mutations among clinical studies. The present study examined the earliest events in the development of drug resistance with viral quasispecies that continued the use of CCR5 for entry. Genotypic and phenotypic assays demonstrated a distinct role of the variable domain V1/V2 in competitive resistance to CCR5 antagonist therapy. Thus, future studies analyzing the development of clinical resistance should focus on the relationship between the V1/V2 and V3 domains.
Laser-induced (endo)vascular photothermal effects studied by combined brightfield and fluorescence microscopy in hamster dorsal skin fold venules (2007)

The putative features of the (endo)vascular photothermal response, characterized by laser-induced thermal denaturation of blood and vessel wall constituents, have been elucidated individually, but not simultaneously in dynamic, isolated in vivo systems. A hamster dorsal skin fold model in combination with brightfield/fluorescence intravital microscopy was used to examine the effect of laser pulse duration and blood flow velocity on the size of the thermal coagulum, its attachment behavior, and laser-mediated vasomotion. The size of the coagulum and the extent of vasoconstriction and latent vasodilation were proportional to the laser pulse duration, but pulse duration had no effect on coagulum attachment/dislodgement. Blood flow velocity exhibited no significant effect on the studied parameters. The (endo)vascular photothermal response is governed predominantly by laser energy deposition and to a marginal extent by blood flow velocity.
Improving Scalability of Personalized Recommendation Systems for Enterprise Knowledge Workers (2015)

Enterprise knowledge workers have been overwhelmed by the growing rate of incoming data in recent years. In this paper, we present a recommendation system with the goal of helping knowledge workers in discovering useful new content. In particular, our system builds personalized user models based on file activities on enterprise network file servers. Our models use novel features that are derived from file metadata and user collaboration. Through extensive evaluation on real-world enterprise data, we demonstrate the effectiveness of our system with high precision and recall values. Unfortunately, our experiments reveal that per-user models are unable to handle heavy workloads. To address this limitation, we propose a novel optimization technique, active feature-based model selection, that predicts the user models that should be applied on each test file. Such a technique can reduce the classification time per file by as much as 23 times without sacrificing accuracy. We also show how this technique can be extended to improve the scalability exponentially at marginal cost of prediction accuracy, e.g., we can gain 169 times faster performance on an average across all shares by sacrificing 4% of F-score.
Analyse par XPS d’empilements high-k metal gate et corrélation des décalages d’énergie de liaison à la présence de charge (2018)

International audience
ChemInform Abstract: Rendering Schrock‐Type Molybdenum Alkylidene Complexes Air Stable: User‐Friendly Precatalysts for Alkene Metathesis. (2011)

Abstract The decomplexation of phenanthroline or bipyridine ligands from several molybdenum alkylidene complexes using ZnCl 2 as activation agent releases tetracoordinate molybdenum complexes, which catalyze high‐yielding metathesis reactions under mild conditions (the activation is carried out at temperatures of 60 to 100°C, the metathesis reaction in the most cases at 25°C).