gebhart/patrepeval huggingface dataset:
Dynamic MRI of plantar flexion: A comprehensive repeatability study of electrical stimulation-gated muscle contraction standardized on evoked force (2020)

Quantification of skeletal muscle contraction in Magnetic Resonance Imaging (MRI) is a non-invasive method for studying muscle motion and deformation. The aim of this study was to evaluate the repeatability of quantitative measures such as strain, based on single slice dynamic MRI synchronized with neuromuscular electrical stimulation (NMES) and standardized to a similar relative force level across various individuals. Unilateral electrical stimulation of the triceps surae muscles was applied in eight volunteers during single-slice, three-directional phase contrast MRI acquisition at a 3T MRI scanner. To assess repeatability, the same process was executed on two different days by standardizing the stimulation aiming at evoking a fixed percentage of their maximal voluntary force in the same position. Except from the force, the effect of using the current as reference was evaluated on day two as a secondary acquisition. Finally, the presence of fatigue induced by NMES was assessed (on day one) by examining the difference between consecutive measurements. Strain maps were derived from the acquired slice at every time point; distribution of strain in the muscle and peak strain over the muscle of interest were evaluated for repeatability. It was found that fatigue did not have an appreciable effect on the results. The stimulation settings based on evoked force produced more repeatable results with respect to using the current as the only reference, with an intraclass correlation coefficient between different days of 0.95 for the former versus 0.88 for the latter. In conclusion, for repeatable strain imaging it is advisable to record the force output of the evoked contraction and use that for the standardization of the NMES setup rather than the current.
Bicyclic Helical Peptides as Dual Inhibitors Selective for Bcl2A1 and Mcl-1 Proteins (2018)

A 26-residue peptide BimBH3 binds indiscriminately to multiple oncogenic Bcl2 proteins that regulate apoptosis of cancer cells. Specific inhibition of the BimBH3-Bcl2A1 protein-protein interaction was obtained in vitro and in cancer cells by shortening the peptide to 14 residues, inserting two cyclization constraints to stabilize a water-stable α-helix, and incorporating an N-terminal acrylamide electrophile for selective covalent bonding to Bcl2A1. Mass spectrometry of trypsin-digested bands on electrophoresis gels established covalent bonding of an electrophilic helix to just one of the three cysteines in Bcl2A1, the one (Cys55) at the BimBH3-Bcl2A1 protein-protein interaction interface. Optimizing the helix-inducing constraints and the sequence subsequently enabled electrophile removal without loss of inhibitor potency. The bicyclic helical peptides were potent, cell permeable, plasma-stable, dual inhibitors of Bcl2A1 and Mcl-1 with high selectivity over other Bcl2 proteins. One bicyclic peptide was shown to inhibit the interaction between a pro-apoptotic protein (Bim) and either endogenous Bcl2A1 or Mcl-1, to induce apoptosis of SKMel28 human melanoma cells, and to sensitize them for enhanced cell death by the anticancer drug etoposide. These approaches look promising for chemically silencing intracellular proteins.
Hyperspectral Imager for the Coastal Ocean (HICO): Overview, Operational Updates, and Coastal Ocean Applications (2014)

The Hyperspectral Imager for the Coastal Ocean (HICO) was built to measure in‐water properties of complex coastal regions. HICO enables synoptic coverage; 100‐meter spatial resolution for sampling the variability and spatial irregularity of coastal waters; and high spectral resolution to untangle the signals from chlorophyll, colored dissolved organic matter, suspended sediments and varying bottom types. HICO was built by the Naval Research Laboratory, installed on the International Space Station (ISS) in September 2009, and operated for ONR for the first three years. In 2013, NASA assumed sponsorship of operations in order to leverage HICO's ability to address their Earth monitoring mission. This has opened up access of HICO data to the broad research community. Over 8000 images are now available on NASA's Ocean Color Website (http://oceancolor.gsfc.nasa.gov/cgi/browse.pl?sen=hi). Oregon State University's HICO website (http://hico.coas.oregonstate.edu) remains the portal for researchers to request new collections and access their requested data. We will present updates on HICO's calibration and improvements in geolocation and show examples of the use of HICO data to address issues in the coastal ocean and Great Lakes.
Synthesis and Search for Design Principles of New Electron Accepting Polymers for All-Polymer Solar Cells (2014)

New electron withdrawing monomers, thieno[2′,3′:5′,6′]pyrido[3,4-g]thieno[3,2-c]isoquinoline-5,11(4H,10H)-dione (TPTI) and fluorenedicyclopentathiophene dimalononitrile (CN), have been developed and used to form 12 alternating polymers having different monomer combinations: (a) weak donating monomer–strong accepting monomer, (b) weak accepting monomer–strong accepting monomer, (c) weak accepting monomer–weak accepting monomer, and (d) strong donating monomer–strong accepting monomer. It was found that lowest unoccupied molecular orbital (LUMO) energy levels of polymers are significantly determined by stronger electron accepting monomers and highest occupied molecular orbital (HOMO) energy levels by the weak electron accepting monomers. In addition, fluorescent quantum yields of the TPTI-based polymers in chloroform solution are significantly decreased as the LUMO energy levels of the TPTI series of polymers become deeper. The quantum yield was found to be closely related with the photovoltaic properties, which reflects the effect of internal polarization on the photovoltaic properties. Only the electron accepting polymers showing SCLC mobility higher than 10–4 cm2/(V s) exhibited photovoltaic performance in blend films with a donor polymer, and the PTB7:PNPDI (1:1.8 w/w) device exhibited the highest power conversion efficiency of 1.03% (Voc = 0.69 V, Jsc = −4.13 mA/cm2, FF = 0.36) under AM 1.5G condition, 100 W/cm2. We provide a large set of systematic structure–property relationships, which gives new perspectives for the design of electron accepting materials.
Biooxidation of Primary Alcohols to Aldehydes through Hydrogen Transfer Employing Janibacter terrae (2010)

Abstract Chemoselective oxidations still represent a challenge for chemists. Lyophilized cells of Janibacter terrae were employed for the chemoselective oxidation of primary alcohols to the corresponding aldehydes by hydrogen transfer with the use of acetaldehyde as the hydrogen acceptor. Secondary alcohol moieties were transformed at a much slower rate. The substrate spectrum encompasses substituted benzyl alcohols, whereby substrates with a substituent in the meta position were well tolerated, whereas only very small substituents were tolerated in the ortho position. Furthermore, n ‐alkanols and allylic alcohols were transformed with good conversions. The biocatalyst was compatible with DMSO as a water miscible organic solvent up to 30 % v/v.
Neural Unsigned Distance Fields for Implicit Function Learning (2020)

In this work we target a learnable output representation that allows continuous, high resolution outputs of arbitrary shape. Recent works represent 3D surfaces implicitly with a Neural Network, thereby breaking previous barriers in resolution, and ability to represent diverse topologies. However, neural implicit representations are limited to closed surfaces, which divide the space into inside and outside. Many real world objects such as walls of a scene scanned by a sensor, clothing, or a car with inner structures are not closed. This constitutes a significant barrier, in terms of data pre-processing (objects need to be artificially closed creating artifacts), and the ability to output open surfaces. In this work, we propose Neural Distance Fields (NDF), a neural network based model which predicts the unsigned distance field for arbitrary 3D shapes given sparse point clouds. NDF represent surfaces at high resolutions as prior implicit models, but do not require closed surface data, and significantly broaden the class of representable shapes in the output. NDF allow to extract the surface as very dense point clouds and as meshes. We also show that NDF allow for surface normal calculation and can be rendered using a slight modification of sphere tracing. We find NDF can be used for multi-target regression (multiple outputs for one input) with techniques that have been exclusively used for rendering in graphics. Experiments on ShapeNet show that NDF, while simple, is the state-of-the art, and allows to reconstruct shapes with inner structures, such as the chairs inside a bus. Notably, we show that NDF are not restricted to 3D shapes, and can approximate more general open surfaces such as curves, manifolds, and functions. Code is available for research at https://virtualhumans.mpi-inf.mpg.de/ndf/.
Particle Size and Support Effects in Electrocatalysis (2013)

Researchers increasingly recognize that, as with standard supported heterogeneous catalysts, the activity and selectivity of supported metal electrocatalysts are influenced by particle size, particle structure, and catalyst support. Studies using model supported heterogeneous catalysts have provided information about these effects. Similarly, model electrochemical studies on supported metal electrocatalysts can provide insight into the factors determining catalytic activity. High-throughput methods for catalyst synthesis and screening can determine systematic trends in activity as a function of support and particle size with excellent statistical certainty. In this Account, we describe several such studies investigating methods for dispersing precious metals on both carbon and oxide supports, with particular emphasis on the prospects for the development of low-temperature fuel-cell electrocatalysts. One key finding is a decrease in catalytic activity with decreasing particle size independent of the support for both oxygen reduction and CO oxidation on supported gold and platinum. For these reactions, there appears to be an intrinsic particle size effect that results in a loss of activity at particle sizes below 2-3 nm. A titania support, however, also increases activity of gold particles in the electrooxidation of CO and in the reduction of oxygen, with an optimum at 3 nm particle size. This optimum may represent the superposition of competing effects: a titania-induced enhanced activity versus deactivation at small particle sizes. The titania support shows catalytic activity at potentials where carbon-supported and bulk-gold surfaces are normally oxidized and CO electrooxidation is poisoned. On the other hand, platinum on amorphous titania shows a different effect: the oxidation reduction reaction is strongly poisoned in the same particle size range. We correlated the influence of the titania support with titania-induced changes in the surface redox behavior of the platinum particles. For both supported gold and platinum particles in electrocatalysis, we observe parallels to the effects of particle size and support in the equivalent heterogeneous catalysts. Studies of model supported-metal electrocatalysts, performs efficiently using high throughput synthetic and screening methodologies, will lead to a better understanding of the mechanisms responsible for support and particle size effects in electrocatalysis, and will drive the development of more effective and robust catalysts in the future.
Black-Box Policy Search with Probabilistic Programs (2015)

In this work, we explore how probabilistic programs can be used to represent policies in sequential decision problems. In this formulation, a probabilistic program is a black-box stochastic simulator for both the problem domain and the agent. We relate classic policy gradient techniques to recently introduced black-box variational methods which generalize to probabilistic program inference. We present case studies in the Canadian traveler problem, Rock Sample, and a benchmark for optimal diagnosis inspired by Guess Who. Each study illustrates how programs can efficiently represent policies using moderate numbers of parameters.
Optimization and expansion of non-negative matrix factorization (2020)

We show through complexity analysis and experiments that our implementation converges faster than well-known methods. We also show that using NMF for tumour content deconvolution can achieve results similar to existing methods like ISOpure. Our proposed missing value imputation is more accurate than conventional methods like multiple imputation and comparable to missForest while achieving significantly better computational efficiency. Finally, we argue that the suggested rank tuning method based on missing value imputation is theoretically superior to existing methods. All algorithms are implemented in the R package NNLM, which is freely available on CRAN and Github.
Predicting Discharge Destination for Patients with Severe Motor Stroke: Important Functional Tasks (2000)

Many patients with severe stroke are capable of returning to the community after receiving rehabilitation services. The purpose of this study was to describe outcomes of patients with stroke in FIM-FRG STR1, a classification based on the Functional Independence Measure, and identify important functional tasks associated with discharge to home. FIM-FRG STR1 is one of nine subpopulations of stroke that have been identified based on motor/cognitive FIM subscale score and age. We reviewed the program evaluation data of 259 cases of stroke from 1993 to 1996. We performed a descriptive analysis of the data and a logistic regression analysis to determine which tasks measured by the FIM were associated with discharge destination, a key indicator of rehabilitation success. We found that three admission FIM variables (bladder management, toilet transfers, memory) and three discharge FIM variables (upper body dressing, bed/chair transfers, comprehension) were associated with discharge destination with up to 75% accuracy. The implications of these findings are discussed.
Comparison of threshold-based and watershed-based segmentation for the truncation compensation of PET/MR images (2012)

Recently introduced combined PET/MR scanners need to handle the specific problem that a limited MR field of view sometimes truncates arm or body contours, which prevents an accurate calculation of PET attenuation correction maps. Such maps of attenuation coefficients over body structures are required for a quantitatively correct PET image reconstruction. This paper addresses this problem by presenting a method that segments a preliminary reconstruction type of PET images, time of flight non-attenuation corrected (ToF-NAC) images, and outlining a processing pipeline that compensates the arm or body truncation with this segmentation. The impact of this truncation compensation is demonstrated together with a comparison of two segmentation methods, simple gray value threshold segmentation and a watershed algorithm on a gradient image. Our results indicate that with truncation compensation a clinically tolerable quantitative SUV error is robustly achievable.
Role of miRNAs in the hypoxic regulation of human embryonic stem cells (2016)

Searchable abstracts of presentations at key conferences on reproductive biology and medicine ISSN 2052-1472 (online)
Numerical methods for the topology optimization of structures that exhibit snap‐through (2002)

Abstract The inclusion of non‐linear elastic analyses into the topology optimization problem is necessary to capture the finite deformation response, e.g. the geometric non‐linear response of compliant mechanisms. In previous work, the non‐linear response is computed by standard non‐linear elastic finite element analysis. Here, we incorporate a load–displacement constraint method to traverse non‐linear equilibrium paths with limit points to design structures that exhibit snap‐through behaviour. To accomplish this, we modify the basic arc length algorithm and embed this analysis into the topology optimization problem. Copyright © 2002 John Wiley &amp; Sons, Ltd.
Viscous energy dissipation in laterally oscillating planar microstructures: a theoretical and experimental study (2002)

The authors investigate energy loss in an incompressible, viscous fluid layer that provides skin-friction damping for a laterally oscillating planar microstructure. The physical model for the viscous dissipation is based on Stokes-type fluid motion. In the theoretical analysis, the damping property of a fluid layer is characterized in terms of viscous energy dissipation, resulting in damping formulas for practical Q estimation. In the experimental study, surface-micromachined polysilicon resonators have been fabricated and tested under an electrostatic excitation in atmosphere. The estimated Q compares well with the Q measured for the test structures, as well as with the experimental Q reported by previous investigators. It is concluded that the Stokes-type damping model presents a more general damping treatment with better Q estimation, although discrepancies of 10 to 20% still remain between the estimated and measured Q. Possible sources of these discrepancies are discussed. The results of the study are applicable to damping design for microsensors and microactuators.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair (2018)

Fidelity of DNA replication is maintained using polymerase proofreading and the mismatch repair pathway. Tumors with loss of function of either mechanism have elevated mutation rates with characteristic mutational signatures. Here we report that tumors with concurrent loss of both polymerase proofreading and mismatch repair function have mutational patterns that are not a simple sum of the signatures of the individual alterations, but correspond to distinct, previously unexplained signatures: COSMIC database signatures 14 and 20. We then demonstrate that in all five cases in which the chronological order of events could be determined, polymerase epsilon proofreading alterations precede the defect in mismatch repair. Overall, we illustrate that multiple distinct mutational signatures can result from different combinations of a smaller number of mutational processes (of either damage or repair), which can influence the interpretation and discovery of mutational signatures.
A High-Throughput Mechanical Activator for Cartilage Engineering Enables Rapid Screening of in vitro Response of Tissue Models to Physiological and Supra-Physiological Loads (2021)

Articular cartilage is crucially influenced by loading during development, health, and disease. However, our knowledge of the mechanical conditions that promote engineered cartilage maturation or tissue repair is still incomplete. Current in vitro models that allow precise control of the local mechanical environment have been dramatically limited by very low throughput, usually just a few specimens per experiment. To overcome this constraint, we have developed a new device for the high throughput compressive loading of tissue constructs: the High Throughput Mechanical Activator for Cartilage Engineering (HiT-MACE), which allows the mechanoactivation of 6 times more samples than current technologies. With HiT-MACE we were able to apply cyclic loads in the physiological (e.g., equivalent to walking and normal daily activity) and supra-physiological range (e.g., injurious impacts or extensive overloading) to up to 24 samples in one single run. In this report, we compared the early response of cartilage to physiological and supra-physiological mechanical loading to the response to IL-1β exposure, a common but rudimentary in vitro model of cartilage osteoarthritis. Physiological loading rapidly upregulated gene expression of anabolic markers along the TGF-β1 pathway. Notably, TGF-β1 or serum was not included in the medium. Supra-physiological loading caused a mild catabolic response while IL-1β exposure drove a rapid anabolic shift. This aligns well with recent findings suggesting that overloading is a more realistic and biomimetic model of cartilage degeneration. Taken together, these findings showed that the application of HiT-MACE allowed the use of larger number of samples to generate higher volume of data to effectively explore cartilage mechanobiology, which will enable the design of more effective repair and rehabilitation strategies for degenerative cartilage pathologies.
Secrecy Performance of Finite-Sized Cooperative Single Carrier Systems With Unreliable Backhaul Connections (2016)

In this paper, the secrecy performance of finite-sized cooperative cyclic prefixed single carrier systems with multiple eavesdroppers and unreliable wireless backhaul connections across multiple transmitters is investigated. For nonidentical frequency-selective fading channels between the relay and destination nodes, secrecy performance metrics including the secrecy outage probability, ergodic secrecy rate, and probability of nonzero achievable secrecy rate are derived. Furthermore, the existence of performance limits on the secrecy outage probability and probability of non-zero achievable secrecy rate are verified for various backhaul scenarios. These limits are found to be exclusively determined by the backhaul reliability. For imperfect backhaul connections, it is found that the diversity gain promised by cooperative cyclic prefixed single-carrier systems cannot be achieved in the conventional asymptotic high signal-to-noise ratio region. Link-level simulations are conducted to verify the derived impact of backhaul reliability on the secrecy performance.
Baseline Fibulin3 Concentrations Are Associated with Incidence of Clinical Knee OA after 30 Months in Overweight and Obese Women (2015)

peer reviewed
The Escherichia coli Translation-Associated Heat Shock Protein YbeY Is Involved in rRNA Transcription Antitermination (2013)

A new group of translation-associated heat shock genes has been recently identified. One of these novel genes is ybeY which is highly conserved in bacteria. In Escherichia coli the YbeY protein is important for efficient translation at all temperatures and is essential at high temperatures. Deletion mutants of ybeY are defective in protein translation, due to impaired 30 S ribosomal subunits. Here we provide evidence which tie YbeY to the transcription antitermination process. Thus, in ybeY deletion mutants transcription is significantly inhibited when the "nut like" sequences required for transcriptional antitermination are present, while if these sequences are removed transcription is not affected by the mutation.
Frequency-Selective Mesh-to-Mesh Resampling for Color Upsampling of Point Clouds (2021)

With the increased use of virtual and augmented reality applications, the importance of point cloud data rises. High-quality capturing of point clouds is still expensive and thus, the need for point cloud super-resolution or point cloud upsampling techniques emerges. In this paper, we propose an interpolation scheme for color upsampling of three-dimensional color point clouds. As a point cloud represents an object’s surface in three-dimensional space, we first conduct a local transform of the surface into a two-dimensional plane. Secondly, we propose to apply a novel Frequency-Selective Mesh-to-Mesh Resampling (FSMMR) technique for the interpolation of the points in 2D. FSMMR generates a model of weighted superpositions of basis functions on scattered points. This model is then evaluated for the final points in order to increase the resolution of the original point cloud. Evaluation shows that our approach outperforms common interpolation schemes. Visual comparisons of the jaguar point cloud underlines the quality of our upsampling results. The high performance of FSMMR holds for various sampling densities of the input point cloud.