gebhart/patrepeval huggingface dataset:
Sparse inverse kernel Gaussian Process regression (2013)

Abstract Regression problems on massive data sets are ubiquitous in many application domains including the Internet, earth and space sciences, and finances. Gaussian Process regression (GPR) is a popular technique for modeling the input–output relations of a set of variables under the assumption that the weight vector has a Gaussian prior. However, it is challenging to apply GPR to large data sets since prediction based on the learned model requires inversion of an order n kernel matrix. Approximate solutions for sparse Gaussian Processes have been proposed for sparse problems. However, in almost all cases, these solution techniques are agnostic to the input domain and do not preserve the similarity structure in the data. As a result, although these solutions sometimes provide excellent accuracy, the models do not have interpretability. Such interpretable sparsity patterns are very important for many applications. We propose a new technique for sparse GPR that allows us to compute a parsimonious model while preserving the interpretability of the sparsity structure in the data. We discuss how the inverse kernel matrix used in Gaussian Process prediction gives valuable domain information and then adapt the inverse covariance estimation from Gaussian graphical models to estimate the Gaussian kernel. We solve the optimization problem using the alternating direction method of multipliers that is amenable to parallel computation. We compare the performance of this algorithm to different existing methods for sparse covariance regression in terms of both speed and accuracy. We demonstrate the performance of our method in terms of accuracy, scalability, and interpretability on two different satellite data sets from the climate domain. © 2013 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 6: 205–220, 2013
Correction: Corrigendum: A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization (2017)

This corrects the article DOI: 10.1038/ncomms10144.
Amino Acids and Peptides. XX. Preparation of .BETA.-Cyclododecyl Aspartate and Its Application to Synthesis of Fibronectin- and Laminin-Related Peptides. (1994)

beta-Cyclododecyl aspartate was prepared and its application to peptide synthesis was examined. Derivatives of beta-cyclododecyl aspartate are more likely to crystallize and should be useful for peptide synthesis. The cyclododecyl ester was much stable to bases than the benzyl ester and rather more stable than the cyclohexyl ester. It was removable by HF treatment and trifluoromethanesulfonic acid treatment. beta-Cyclododecyl aspartate was used for synthesis of laminin- and fibronectin-related peptides by solid phase and liquid phase methods.
Cyber–Physical Systems: Close Encounters Between Two Parallel Worlds [Point of View] (2010)

Technology, science, and engineering continue to redefine physical world capabilities. Take mobility of humans, for example. In the 20th century, transportation systems moved us to unimaginable distances, speeds on earth and made us set foot on the Moon. Star Trek popularized teleportation, a fictitious technology that instantly allows us to "go where no person has gone before." Before end of the century, Internet and wireless networking helped to create the parallel "cyber world," virtually "teleporting" us great distances to interact with remote objects, people, and places. In the new millennium, our restless society's need for such ground-breaking capabilities in time and space has never been greater. Cyber-physical system (CPS) is a promising new class of systems that deeply embed cyber capabilities in the physical world, either on humans, infrastructure or platforms, to transform interactions with the physical world. Advances in the cyber world such as communications, networking, sensing, computing, storage, and control, as well as in the physical world such as materials, hardware, and renewable "green" fuels, are all rapidly converging to realize this class of highly collaborative computational systems that are reliant on sensors and actuators to monitor and effect change.Tomorrow's CPS is expected to enrich cyber-physical interactions by intimately coupling assets and dynamics of the physical and engineered systems with the computing and communications of cyber systems, at grand scales and depths from nanosystems to geographically dispersed systems-of-systems. It must be able to adapt rapidly to anomalies in the environment and embrace the evolution of technologies while still providing critical assertions of performance and other constraints.
Scalable Fabrication of Porous Microchannel Nerve Guidance Scaffolds with Complex Geometries (2019)

Microchannel scaffolds accelerate nerve repair by guiding growing neuronal processes across injury sites. Although geometry, materials chemistry, stiffness, and porosity have been shown to influence nerve growth within nerve guidance scaffolds, independent tuning of these properties in a high-throughput manner remains a challenge. Here, fiber drawing is combined with salt leaching to produce microchannels with tunable cross sections and porosity. This technique is applicable to an array of biochemically inert polymers, and it delivers hundreds of meters of porous microchannel fibers. Employing these fibers as filaments during 3D printing enables the production of microchannel scaffolds with geometries matching those of biological nerves, including branched topographies. Applied to sensory neurons, fiber-based porous microchannels enhance growth as compared to non-porous channels with matching materials and geometries. The combinatorial scaffold fabrication approach may advance the studies of neural regeneration and accelerate the development of nerve repair devices.
Synthetic Human Monoclonal Antibodies toward Staphylococcal Enterotoxin B (SEB) Protective against Toxic Shock Syndrome (2012)

Staphylococcal enterotoxin B (SEB) is a potent toxin that can cause toxic shock syndrome and act as a lethal and incapacitating agent when used as a bioweapon. There are currently no vaccines or immunotherapeutics available against this toxin. Using phage display technology, human antigen-binding fragments (Fabs) were selected against SEB, and proteins were produced in Escherichia coli cells and characterized for their binding affinity and their toxin neutralizing activity in vitro and in vivo. Highly protective Fabs were converted into full-length IgGs and produced in mammalian cells. Additionally, the production of anti-SEB antibodies was explored in the Nicotiana benthamiana plant expression system. Affinity maturation was performed to produce optimized lead anti-SEB antibody candidates with subnanomolar affinities. IgGs produced in N. benthamiana showed characteristics comparable with those of counterparts produced in mammalian cells. IgGs were tested for their therapeutic efficacy in the mouse toxic shock model using different challenge doses of SEB and a treatment with 200 μg of IgGs 1 h after SEB challenge. The lead candidates displayed full protection from lethal challenge over a wide range of SEB challenge doses. Furthermore, mice that were treated with anti-SEB IgG had significantly lower IFNγ and IL-2 levels in serum compared with mock-treated mice. In summary, these anti-SEB monoclonal antibodies represent excellent therapeutic candidates for further preclinical and clinical development.
Chelation-Assisted Substrate-Controlled Asymmetric Lithiation-Allylboration of Chiral Carbamate 1,2,4-Butanetriol Acetonide (2015)

The lithiation of 2-(2,2-dimethyl-1,3-dioxolan-4-yl)ethyl diisopropylcarbamate (1) is achieved freely by sec-butyllithium in diethylether with high lk-diastereoselectivity: the bicyclic chelate complexes 3a and 3b are reacted with electrophiles to form optically active precursors 4a and 4b with >95% diastereoselectivity. In addition, tertiary diamines can undergo an external complexation in contest with the internal oxygen ligand, leading to improved stereoselectivities. The further reactions of lithiated carbamates with trans alkenyl-9-BBN derivatives after 1,2 metallate rearrangements, gave the key intermediate α-substituted allylic boranes 7. Subsequent allylboration of aldehydes gave (Z)-anti-homoallylic alcohols 8 in good yield and excellent d.r.
Biomarkers Predictp53Gene Therapy Efficacy in Recurrent Squamous Cell Carcinoma of the Head and Neck (2009)

PURPOSE: Most recurrent squamous cell carcinomas of the head and neck have a dysfunctional p53 tumor suppressor pathway contributing to treatment resistance. We hypothesized that tumor p53 biomarkers may predict the efficacy of normal p53 delivered by gene therapy in these patients. EXPERIMENTAL DESIGN: Tumor p53 biomarkers were evaluated in 116 patients, including 29 treated with methotrexate in a phase III randomized controlled trial. Profiles favorable for p53 gene therapy efficacy were hypothesized to have either normal p53 gene sequences or low-level p53 protein expression, whereas unfavorable p53 inhibitor profiles were predicted to have high-level expression of mutated p53 that can inhibit normal p53 protein function. RESULTS: A statistically significant increase in tumor responses was observed for patients with favorable p53 efficacy profiles compared with those with unfavorable p53 inhibitor profiles [phase I/II trials: favorable (34 of 46, 74%) versus unfavorable (1 of 5, 20%), P = 0.0290; phase III trial: favorable (17 of 24, 71%) versus unfavorable (2 of 11, 18%), P = 0.0088]. In the phase III trial, there was statistically significant increased time to progression (TTP) and survival following p53 gene therapy in patients with favorable p53 profiles compared with unfavorable p53 inhibitor profiles (median TTP, 2.7 months versus 1.4 months, P = 0.0121; median survival, 7.2 months versus 2.7 months, P < 0.0001). In contrast, the biomarker profiles predictive of p53 gene therapy efficacy did not predict methotrexate response, TTP, or survival outcomes. CONCLUSIONS: These results indicate that tumor p53 biomarker profiles may predict p53 gene therapy efficacy in recurrent squamous cell carcinoma of the head and neck. (Clin Cancer Res 2009;15(24):7719-25).
Real-Time Signal Processing for Multiantenna Systems: Algorithms, Optimization, and Implementation on an Experimental Test-Bed (2006)

A recently realized concept of a reconfigurable hardware test-bed suitable for real-time mobile communication with multiple antennas is presented in this paper. We discuss the reasons and prerequisites for real-time capable MIMO transmission systems which may allow channel adaptive transmission to increase link stability and data throughput. We describe a concept of an efficient implementation of MIMO signal processing using FPGAs and DSPs. We focus on some basic linear and nonlinear MIMO detection and precoding algorithms and their optimization for a DSP target, and a few principal steps for computational performance enhancement are outlined. An experimental verification of several real-time MIMO transmission schemes at high data rates in a typical office scenario is presented and results on the achieved BER and throughput performance are given. The different transmission schemes used either channel state information at both sides of the link or at one side only (transmitter or receiver). Spectral efficiencies of more than 20 bits/s/Hz and a throughput of more than 150 Mbps were shown with a single-carrier transmission. The experimental results clearly show the feasibility of real-time high data rate MIMO techniques with state-of-the-art hardware and that more sophisticated baseband signal processing will be an essential part of future communication systems. A discussion on implementation challenges towards future wireless communication systems supporting higher data rates (1 Gbps and beyond) or high mobility concludes the paper.
Transvenous Lead Extraction during Cardiac Implantable Device Upgrade: Results from the Multicenter Swiss Lead Extraction Registry (2023)

TLE during device upgrade is effective and does not attribute a disproportionate risk to the upgrade procedure.
Bicyclic Imidazoles for Modular Synthesis of Chiral Imidazolium Salts (2010)

The preparation of new chiral bicyclic imidazoles 5 and their transformation into imidazolium salts 6 and 7 are reported. The utility of the salts as precursors for chiral N-heterocyclic carbenes was demonstrated by the synthesis of C-N-C pincer Ni-complex 13h, the structure of which was characterized by single-crystal X-ray analysis.
Geometric confinement influences cellular mechanical properties II -- intracellular variances in polarized cells. (2007)

During migration, asymmetrically polarized cells achieve motion by coordinating the protrusion and retraction of their leading and trailing edges, respectively. Although it is well known that local changes in the dynamics of actin cytoskeleton remodeling drive these processes, neither the cytoskeletal rheological properties of these migrating cells are well quantified nor is it understand how these rheological properties are regulated by underlying molecular processes. In this report, we have used soft lithography to create morphologically polarized cells in order to examine rheological differences between the front and rear zone of an NIH 3T3 cell posed for migration. In addition, we trapped superparamagnetic beads with optical tweezers and precisely placed them at specific locations on the immobilized cells. The beads were then allowed to endocytose overnight before magnetic tweezers experiments were performed to measure the local rheological properties of the leading and trailing edges. Our results indicate that the leading edge has an approximately 1.9 times higher shear modulus than the trailing edge and that this increase in shear modulus correlates with a greater density of filamentous actin, as measured by phalloidin-staining observed through quantitative 3D microscopy.
Effect of fixation angle and graft tension in double‐bundle anterior cruciate ligament reconstruction on knee biomechanics (2015)

The AM-45°/30N and PL-15°/10N fixation most closely matched intact knee kinematics; however, stabilizing the knee during anterior tibial translation may risk an imbalance of the AM and the PL bundle loading. The results indicate that ACL bundle forces may not be restored even if the clinical assessment shows good results with the Lachman test and pivot-shift test. This may alter the loading on other structures of the knee.
Supramolecular Hemoprotein Assembly with a Periodic Structure Showing Heme–Heme Exciton Coupling (2018)

A supramolecular assembly of units of cytochrome b<sub>562</sub> with externally attached heme having intermolecular linkages formed via the heme-heme pocket interaction was investigated in an effort to construct a well-defined structure. The engineered site for surface attachment of heme at Cys80 in an N80C mutant of cytochrome b<sub>562</sub> provides the primary basis for the formation of the periodic assembly structure, which is characterized herein by circular dichroism (CD) spectroscopy and high-speed atomic force microscopy (AFM). This assembly represents the first example of the observation of a split-type Cotton effect by heme-heme exciton coupling in an artificial hemoprotein assembly system. Molecular dynamics simulations validated by simulated CD spectra, AFM images, and mutation experiments reveal that the assembly has a periodic helical structure with 3 nm pitches, suggesting the formation of the assembled structure is driven not only by the heme-heme pocket interaction but also by additional secondary hydrogen bonding and/or electrostatic interactions at the protein interfaces of the assembly.
Expression of Collagenase IV (Basement Membrane Collagenase) Activity in Murine Tumor Cell Hybrids That Differ in Metastatic Potential<xref ref-type="fn" rid="FN2">2</xref> (1985)

Expression of a basement membrane collagen-degrading metalloprotease activity (collagenase IV) was studied in a series of murine cell hybrids derived from fusions between highly metastatic cells (B16-F10RR) or moderately metastatic cells (UV-2237RR) and tumorigenic cells (K-1735 clone 16) or normal cells [peritoneal macrophages (PEC) or C3H mouse embryo fibroblasts (C3H-F)]. The collagenase IV activity of the parent cells and the hybrids was assayed in vitro and compared to the metastatic propensity of the same cells evaluated in both syngeneic (C57BL/6 X C3H/HeN)F1 mice and BALB/c nude mice. The level of collagenase IV activity secreted by the parent lines correlated with their metastatic capacity. The highly metastatic B16-F10RR line secreted the highest enzyme activity, whereas the tumorigenic but nonmetastatic K-1735 clone 16 and the normal parents PEC and C3H-F secreted the lowest enzyme activity. The enzyme activity was completely inhibited with EDTA. The hybrid derived from fusion of cells from two metastatic cell lines as well as hybrids derived from a metastatic and a nonmetastatic tumor cell line expressed higher levels of collagenase IV activity than either parent, and this expression was associated with a high ability to produce metastases in both nude and syngeneic mice. Fusion of metastatic cells with normal cells produced hybrid cells that exhibited suppression of both collagenase IV activity and metastatic capacity. Collagenase IV activity and metastatic propensity can, therefore, be altered by somatic cell hybridization; in the series of hybrids examined in these experiments the expression of type IV collagen-degrading metalloprotease activity and the metastatic ability were closely correlated, which suggests that collagenase IV activity and other properties required for metastasis are genetically linked.
Advantages and Limitations of Automated Storm Sewer Design (2002)

With many different levels of storm sewer models available, ranging from those based on solving the full St. Venant equations to simple spreadsheets, it's important for the engineer to select a design model with the right level of sophistication for the project at hand. This paper discusses the differences between the available types of models. For design purposes in small systems, automated design based on peak flow, whether generated from a steady state model or the peaks from a dynamic model, can greatly simplify the effort involved in pipe sizing. The paper presents the features of an automated design procedure and gives an example problem.
A Novel Class of Strain Measures for Digital Image Correlation (2015)

Abstract We propose a novel class strain measures for use with digital image correlation (DIC). Whereas the traditional notion of compatibility (strain as the derivative of the displacement field) is problematic when the displacement field varies substantially because of either measurement noise or material irregularity, the proposed measure remains robust, well defined and invariant under rigid body motion. Moreover, when the displacement field is smooth, the classical and proposed strain measures are approximations of each other. We demonstrate, via several numerical examples, the potential of this new strain measure for problems with steep gradients. We also show how the non‐local strain provides an intrinsic mechanism for filtering high‐frequency content from the strain profile and so has a high signal to noise ratio. This is a convenient feature considering image noise and its impact on strain calculations.
All-optical label swapping networks and technologies (2000)

All-optical label swapping is a promising approach to ultra-high packet-rate routing and forwarding directly in the optical layer. In this paper, we review results of the DARPA Next Generation Internet program in all-optical label swapping at University of California at Santa Barbara (UCSB). We describe the overall network approach to encapsulate packets with optical labels and process forwarding and routing functions independent of packer bit rate and format. Various approaches to label coding using serial and subcarrier multiplexing addressing and the associated techniques for label erasure and rewriting, packet regeneration and packet-rate wavelength conversion are reviewed. These functions have been implemented using both fiber and semiconductor-based technologies and the ongoing effort at UCSB to integrate these functions is reported. We described experimental results for various components and label swapping functions and demonstration of 40 Gb/s optical label swapping. The advantages and disadvantages of using the various coding techniques and implementation technologies are discussed.
A compact fluorescence and polarization near-field scanning optical microscope (1998)

We present a transmission, fluorescence, and polarization near-field scanning optical microscope with shear-force feedback control that is small in size and simple to operate. This microscope features an ultrafine mechanical tip/sample approach with continuous manual submicron control over a range of several millimeters. The piezo-driven 12 μm x-y scan range is complimented by a 4 mm coarse mechanical translation range in each direction. The construction materials used in the mechanical feedback loop have been carefully chosen for thermal compatibility in order to reduce differential expansion and contraction between the tip and sample. A unique pressure-fit sample mount allows for quick and reliable sample exchange. Shear-force feedback light is delivered to the scan head via an optical fiber so that a remote laser of any type may be used as a source. This dither light is collimated and refocused onto the tip, delivering a consistently small spot which is collected by a high numerical aperture objective. This new scan head incorporates an optical system which will permit the linearization of scan piezo response similar to a scheme used successfully with atomic force microscopy. This is designed to both overcome the piezo’s inherent hysteresis and to eliminate drift during long duration spatial scans or spectroscopic measurements at a single location. The scan head design offers added flexibility due to the use of optical fibers to deliver the dither and scan linearization light, and functions in any orientation for use in conjunction with upright or inverted optical microscopes.
Modeling of divergent field experiments on layered polymer film (2014)

This paper describes a rapid and robust axisymmetric hybrid algorithm to simulate divergent field experiments on layered polymer film. The hybrid algorithm uses a source distribution technique based on an axisymmetric boundary integral equation method (BIEM) to solve the Poisson equation and a 4 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> order Runge-Kutta (RK4) method with an upwind scheme for time integration. Iterative stability is assured by satisfying the Courant-Friedrichs-Levy (CFL) stability criterion. The model computes dynamic temporal and spatial charge distributions assuming bipolar charge injection using Schottky emission and/or Fowler-Nordheim tunneling and field-dependent mobility while allowing for charge recombination and bulk and interfacial trapping/de-trapping. This model may be used to identify failure mechanisms such as charge packets, gaseous voids, and electroluminescence. Charge packets cause substantial increase of electric stress and could accelerate the breakdown of polymeric capacitors. Conditions for the creation of charge packets are identified and numerically demonstrated for a combination of impulsive step excitation, high charge injection, and discontinuous interface. Enhanced anisotropic interface conduction is shown to reduce charge accumulation, thus reducing E field contrast.