gebhart/patrepeval huggingface dataset:
Using Surrogate Modeling in the Prediction of Fibrinogen Adsorption onto Polymer Surfaces (2004)

We present a Surrogate (semiempirical) Model for prediction of protein adsorption onto the surfaces of biodegradable polymers that have been designed for tissue engineering applications. The protein used in these studies, fibrinogen, is known to play a key role in blood clotting. Therefore, fibrinogen adsorption dictates the performance of implants exposed to blood. The Surrogate Model combines molecular modeling, machine learning and an Artificial Neural Network. This novel approach includes an accounting for experimental error using a Monte Carlo analysis. Briefly, measurements of human fibrinogen adsorption were obtained for 45 polymers. A total of 106 molecular descriptors were generated for each polymer. Of these, 102 descriptors were computed using the Molecular Operating Environment (MOE) software based upon the polymer chemical structures, two represented different monomer types, and two were measured experimentally. The Surrogate Model was developed in two stages. In the first stage, the three descriptors with the highest correlation to adsorption were determined by calculating the information gain of each descriptor. Here a Monte Carlo approach enabled a direct assessment of the effect of the experimental uncertainty on the results. The three highest-ranking descriptors, defined as those with the highest information gain for the sample set, were then selected as the input variables for the second stage, an Artificial Neural Network (ANN) to predict fibrinogen adsorption. The ANN was trained using one-half of the experimental data set (the training set) selected at random. The effect of experimental error on predictive capability was again explored using a Monte Carlo analysis. The accuracy of the ANN was assessed by comparison of the predicted values for fibrinogen adsorption with the experimental data for the remaining polymers (the validation set). The mean value of the Pearson correlation coefficient for the validation data sets was 0.54 +/- 0.12. The average root-mean-square (relative) error in prediction for the validation data sets is 38%. This is an order of magnitude less than the range of experimental values (i.e., 366%) and compares favorably with the average percent relative standard deviation of the experimental measurements (i.e., 17.9%). The effects of each of the user-defined parameters in the ANN were explored. None were observed to have a significant effect on the results. Thus, the Surrogate Model can be used to accurately and unambiguously identify polymers whose fibrinogen absorption is at the limits of the range (i.e., low or high) which is an essential requirement for assessing polymers for regenerative tissue applications.
Size Matters: Digital Social Networks and Language Change (2020)

Social networks play a role in language variation and change, and the social network theory has offered a powerful tool in modeling innovation diffusion. Networks are characterized by ties of varying strength which influence how novel information is accessed. It is widely held that weak-ties promote change, whereas strong ties lead to norm-enforcing communities that resist change. However, the model is primarily suited to investigate small ego networks, and its predictive power remains to be tested in large digital networks of mobile individuals. This article revisits the social network model in sociolinguistics and investigates network size as a crucial component in the theory. We specifically concentrate on whether the distinction between weak and strong ties levels in large networks over 100 nodes. The article presents two computational methods that can handle large and messy social media data and render them usable for analyzing networks, thus expanding the empirical and methodological basis from small-scale ethnographic observations. The first method aims to uncover broad quantitative patterns in data and utilizes a cohort-based approach to network size. The second is an algorithm-based approach that uses mutual interaction parameters on Twitter. Our results gained from both methods suggest that network size plays a role, and that the distinction between weak ties and slightly stronger ties levels out once the network size grows beyond roughly 120 nodes. This finding is closely similar to the findings in other fields of the study of social networks and calls for new research avenues in computational sociolinguistics.
High channel mobility 4H-SiC metal-oxide-semiconductor field-effect transistor with low temperature metal-organic chemical-vapor deposition grown Al2O3 gate insulator (2008)

Ultrahigh channel mobility is demonstrated for 4H-SiC metal-oxide-semiconductor field-effect transistors (MOSFETs) with Al2O3 gate insulators fabricated at low temperatures by metal-organic chemical-vapor deposition. Relatively high field effect channel mobility of 64cm2∕Vs is obtained when the Al2O3 gate insulator is deposited at 190°C. Furthermore, extremely high field effect mobility of 284cm2∕Vs was obtained for a MOSFET fabricated with an ultrathin thermally grown SiOx layer inserted between the Al2O3 and SiC.
HSP60 possesses a GTPase activity and mediates protein folding with HSP10 (2017)

Abstract The mammalian molecular chaperone, HSP60, plays an essential role in protein homeostasis through mediating protein folding and assembly. The structure and ATP-dependent function of HSP60 has been well established in recent studies. After ATP, GTP is the major cellular nucleotide. In this paper, we have investigated the role of GTP in the activity of HSP60. It was found that HSP60 has different properties with respect to allostery, complex formation and protein folding activity depending on the nucleoside triphosphate present. The presence of GTP slightly affected the ATPase activity of HSP60 during protein folding. These results provide clues as to the functional mechanism of the HSP60-HSP10 complex.
<em>In vivo</em> <sup>19</sup>F MRI for Cell Tracking (2013)

In vivo (19)F MRI allows quantitative cell tracking without the use of ionizing radiation. It is a noninvasive technique that can be applied to humans. Here, we describe a general protocol for cell labeling, imaging, and image processing. The technique is applicable to various cell types and animal models, although here we focus on a typical mouse model for tracking murine immune cells. The most important issues for cell labeling are described, as these are relevant to all models. Similarly, key imaging parameters are listed, although the details will vary depending on the MRI system and the individual setup. Finally, we include an image processing protocol for quantification. Variations for this, and other parts of the protocol, are assessed in the Discussion section. Based on the detailed procedure described here, the user will need to adapt the protocol for each specific cell type, cell label, animal model, and imaging setup. Note that the protocol can also be adapted for human use, as long as clinical restrictions are met.
GBNSC: The GigaBit Network Switch Controller (2003)

The GigaBit Network Switch Controller (GBNSC) is a process which controls the Washington University Gigabit Switch (WUGS) using in-band ATM control cells. The GBNSC is being developed by the Applied Research Laboratory (ARL) of Washington University in St. Louis. This document describes the design and implementation of the GBNSC and is intended for use by those interested in the functionality of the switch controller as well as developers who may be called on to update or maintain it. Version Notes: Version 1.0: All Ken Cox Version 1.1: John’s additions. More NCMO details.
Supplementary Methods from Global Evaluation of Eph Receptors and Ephrins in Lung Adenocarcinomas Identifies EphA4 as an Inhibitor of Cell Migration and Invasion (2023)

&lt;p&gt;PDF file, 102K, Supplementary Material and Methods for gene expression analysis are provided.&lt;/p&gt;
Overlayer-support interactions associated with the formation of a chemically modified interface: the nickel ferrocyanide derivatized nickel electrode (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOverlayer-support interactions associated with the formation of a chemically modified interface: the nickel ferrocyanide derivatized nickel electrodeLinda J. Amos, Michael H. Schmidt, Sujit Sinha, and Andrew B. BocarslyCite this: Langmuir 1986, 2, 5, 559–561Publication Date (Print):September 1, 1986Publication History Published online1 May 2002Published inissue 1 September 1986https://pubs.acs.org/doi/10.1021/la00071a005https://doi.org/10.1021/la00071a005research-articleACS PublicationsRequest reuse permissionsArticle Views105Altmetric-Citations17LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Exploring Seasonality in Mobile Cultural Heritage (2017)

We present results of an investigation into the role of seasonality in mobile cultural heritage applications. 45 participants in 26 groups used one of two applications when visiting the Finnish recreational island of Seurasaari. Each provided summer and winter content, but varied in how this was presented. We uncovered how users consider seasonality in content, seasonal preferences, as well as how different media becomes more or less interesting if shown in or out of season. We present design considerations for future researchers to consider seasonality in cultural heritage applications.
Uncertainty Quantification in CNN-Based Surface Prediction Using Shape Priors (2018)

Surface reconstruction is a vital tool in a wide range of areas of medical image analysis and clinical research. Despite the fact that many methods have proposed solutions to the reconstruction problem, most, due to their deterministic nature, do not directly address the issue of quantifying uncertainty associated with their predictions. We remedy this by proposing a novel probabilistic deep learning approach capable of simultaneous surface reconstruction and associated uncertainty prediction. The method incorporates prior shape information in the form of a principal component analysis (PCA) model. Experiments using the UK Biobank data show that our probabilistic approach outperforms an analogous deterministic PCA-based method in the task of 2D organ delineation and quantifies uncertainty by formulating distributions over predicted surface vertex positions.
Generation of Double-Labeled Reporter Cell Lines for Studying Co-Dynamics of Endogenous Proteins in Individual Human Cells (2010)

Understanding the dynamic relationship between components of a system or pathway at the individual cell level is a current challenge. To address this, we developed an approach that allows simultaneous tracking of several endogenous proteins of choice within individual living human cells. The approach is based on fluorescent tagging of proteins at their native locus by directed gene targeting. A fluorescent tag-encoding DNA is introduced as a new exon into the intronic region of the gene of interest, resulting in expression of a full-length fluorescently tagged protein. We used this approach to establish human cell lines simultaneously expressing two components of a major antioxidant defense system, thioredoxin 1 (Trx) and thioredoxin reductase 1 (TrxR1), labeled with CFP and YFP, respectively. We find that the distributions of both proteins between nuclear and cytoplasmic compartments were highly variable between cells. However, the two proteins did not vary independently of each other: protein levels of Trx and TrxR1 in both the whole cell and the nucleus were substantially correlated. We further find that in response to a stress-inducing drug (CPT), both Trx and TrxR1 accumulated in the nuclei in a manner that was highly temporally correlated. This accumulation considerably reduced cell-to-cell variability in nuclear content of both proteins, suggesting a uniform response of the thioredoxin system to stress. These results indicate that Trx and TrxR1 act in concert in response to stress in regard to both time course and variability. Thus, our approach provides an efficient tool for studying dynamic relationship between components of systems of interest at a single-cell level.
On Base Station Antenna Beamwidth for Sectorized WCDMA Systems (2006)

The radiation pattern of a base station antenna in WCDMA networks is an important system design parameter since it has a strong influence on the interference distribution in the network. In this paper we study the problem of finding the azimuth beamwidth which optimizes system performance. We find the optimal beamwidth under a wide range of operating conditions for networks with 3 or 6 sectors per site. In particular, we investigate how the optimal beamwidth is affected by network irregularities and various environmental and system design parameters. The optimization problem is shown to be robust in the sense that a fairly large interval of beamwidths gives near-optimal performance.
Thermal Degradation of HfSiON Dielectrics Caused by TiN Gate Electrodes and Its Impact on Electrical Properties (2005)

We studied thermal reactions in TiN/HfSiON gate stacks and discussed their impact on electrical properties. Physical analysis revealed that reactions at the metal/high-k interface form a polycrystalline TiO2 layer at 700 °C. The interface between the TiN electrode and the ultrathin TiO2 interlayer remained smooth and the formation of this high-permittivity metal oxide layer did not cause any electrical degradation in terms of equivalent oxide thickness (EOT) versus gate leakage (Ig) characteristics. However, interface roughness and electrical degradation, such as increases in electrical thickness and interface-trap density, were present after annealing at 900 °C. At 1100 °C, we observed marked increases in EOT and Ig, which respectively indicated oxide (SiO2) growth at the bottom interface and dielectric degradation both of the interface TiO2 and HfSiON layers.
Improvement of sludge electrodewatering by anode flushing (2015)

An improvement of the sludge electrodewatering process is proposed: anode flushing by filtrate recirculation. According to this technique, the mixture of filtrates obtained at cathode and anode sides is used for continuous flushing of the anode chamber of the filter press during electrodewatering. Anode flushing aims to eliminate essential problems of electrodewatering: ohmic heating, rise of electric energy consumption, electrode corrosion, and filtrate contamination. This is attained by better control of the filtrate pH, the filter cake temperature, and the dryness at the anode side, where the physicochemical conditions are most aggressive. The efficiency of the proposed technique is evaluated at lab scale on drilling sludge electrodewatering with and without anode flushing. In experiments without anode flushing, increasing electric current density caused strong increase of anode temperature, desiccation of the filter cake at the anode side, rise of voltage, and significant alkaline contamination of filtrate. The application of anode flushing allowed controlling the electric field strength and temperature. Thus, the dewatering of the sludge has been extended at high electric field without damaging the filter equipment by drastic heating. Furthermore, it reduced filtrate contamination by neutralization of the electrolysis products.
Pilot-data power allocation for OFDM systems with amplify and forward relays (2014)

A three node amplify and forward (AF) relay system over a frequency-selective channel employing OFDM modulation is considered and the pilot-data power allocation that maximizes a lower bound on system capacity is obtained. The source transmits pilot tones, which are multiplexed with data tones, so that the destination can estimate the overall equivalent channel and perform data detection. Assuming no channel state information (CSI) at the transmitter and as in a practical system, allowing for imperfect channel estimation, a closed-form solution for the pilot-data power allocation is obtained at high SNR regime. An expression for the pilot-data power allocation is obtained for low SNR regime which can be solved numerically for the general case of arbitrary power delay profiles. For the special case of uniform power delay profile of the equivalent channel, a closed form solution is provided. Simulations are used to verify the derived results and show performance comparisons of capacity bound and symbol error rate.
Long Pulse Ion Diode For Planar Electrohydrodynamic Instability Studies (1991)

The electrohydrodynamic (EHD) ion source is one of the sources of singly-ionized lithium (Li <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> ) being investigated on Sandia National Laboratories' Particle Beam Fusion Accelerator II (PBFA-II). This ion source utilizes the fact that a planar layer of molten lithium is predicted to become EHD unstable in a strong electric field (10 MV /cm) and form cusp arrays from which ions may be field-evaporated. The EHD source is attractive because of its simplicity and its compatibility with repetitively pulsed operation. An experiment was proposed suggesting that the EHD instability be studied in a simple planar geometry so that growth rates and observations of cusp formation be compared with theoretical calculations. We describe such an experiment and the operation of the magnetically insulated diode in the absence of an ion source.
Guest Editorial Ophthalmic Image Analysis and Informatics (2020)

The papers in this special son focus on This special issue invited contributions reporting on methodological breakthroughs in artificial intelligence in ophthalmology, and systems and insights that make use of large-scale datasets linking across multiple imaging modalities, image phenotyping, and imaging omics. These papers presented in this special issue introduce the latest advances in the field of ophthalmic image analysis and informatics, which enable and drive the research, development, and application of key technologies into ocular healthcare.
Synthesis of Exciton Luminescent ZnO Nanocrystals Using Continuous Supercritical Microfluidics (2011)

ZnO-Nanokristalle hoher Qualität und mit rein UV-emittierenden Eigenschaften wurden in einem neuen Mikrofluidikverfahren hergestellt, das überkritische Fluide verwendet und Keimbildungs-/Wachstums- und Funktionalisierungsschritt trennt (siehe Bild). Diese ZnO-Nanokristalle (NCs) zeigen Excitonen-Lumineszenz ohne die klassische Fehlstellen-Lumineszenz. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Cry1F Resistance in Fall Armyworm Spodoptera frugiperda: Single Gene versus Pyramided Bt Maize (2014)

Evolution of insect resistance to transgenic crops containing Bacillus thuringiensis (Bt) genes is a serious threat to the sustainability of this technology. However, field resistance related to the reduced efficacy of Bt maize has not been documented in any lepidopteran pest in the mainland U.S. after 18 years of intensive Bt maize planting. Here we report compelling evidence of field resistance in the fall armyworm, Spodoptera frugiperda (J.E. Smith), to Cry1F maize (TC 3507) in the southeastern region of the U.S. An F2 screen showed a surprisingly high (0.293) Cry1F resistance allele frequency in a population collected in 2011 from non-Bt maize in south Florida. Field populations from non-Bt maize in 2012-2013 exhibited 18.8-fold to >85.4-fold resistance to purified Cry1F protein and those collected from unexpectedly damaged Bt maize plants at several locations in Florida and North Carolina had >85.4-fold resistance. In addition, reduced efficacy and control failure of Cry1F maize against natural populations of S. frugiperda were documented in field trials using Cry1F-based and pyramided Bt maize products in south Florida. The Cry1F-resistant S. frugiperda also showed a low level of cross-resistance to Cry1A.105 and related maize products, but not to Cry2Ab2 or Vip3A. The occurrence of Cry1F resistance in the U.S. mainland populations of S. frugiperda likely represents migration of insects from Puerto Rico, indicating the great challenges faced in achieving effective resistance management for long-distance migratory pests like S. frugiperda.
In situ Fabrication of a Dense/Porous Bi‐layered Ceramic Composite using Freeze Casting of a Ceramic–Camphene Slurry (2005)

Dense/porous bi‐layered ceramic composites were fabricated in situ by freeze casting a ceramic/camphene slurry with a low solid content (φ=20 vol%). The warm slurry was prepared at 55°C by ball milling and cast into a mold at 25°C, where the top surface of the cast body was exposed to air to allow for the controlled evaporation of molten camphene. This simple method produced a high solid content with negligible camphene (φ&gt;50 vol%) on the top layer, while maintaining a low solid loading with solidified camphene (φ∼20 vol%) in the inner region. The sintered sample showed a dense 125‐μm‐thick ceramic layer on a highly porous layer with a thickness of ∼1.7 mm and three‐dimensionally interconnected pore channels that were representative of entangled dendritic growth of the solidified camphene.
Geometrically uniform frames (2003)

We introduce a new class of finite-dimensional frames with strong symmetry properties, called geometrically uniform (GU) frames, that are defined over a finite Abelian group of unitary matrices and are generated by a single generating vector. The notion of GU frames is then extended to compound GU (CGU) frames which are generated by a finite Abelian group of unitary matrices using multiple generating vectors. The dual frame vectors and canonical tight frame vectors associated with GU frames are shown to be GU and, therefore, also generated by a single generating vector, which can be computed very efficiently using a Fourier transform (FT) defined over the generating group of the frame. Similarly, the dual frame vectors and canonical tight frame vectors associated with CGU frames are shown to be CGU. The impact of removing single or multiple elements from a GU frame is considered. A systematic method for constructing optimal GU frames from a given set of frame vectors that are not GU is also developed. Finally, the Euclidean distance properties of GU frames are discussed and conditions are derived on the Abelian group of unitary matrices to yield GU frames with strictly positive distance spectrum irrespective of the generating vector.