gebhart/patrepeval huggingface dataset:
Electron Transfer Studies Between New Fad-Dependent Glucose Dehydrogenase and Different Osmium Polymers (Applications in Biosensors and Biofuel Cells) (2015)

A new extracellular flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase from Glomerella cingulata ( Gc GDH) was electrochemically studied as a recognition element in glucose biosensors. The redox enzyme was recombinantly produced in Pichia pastoris , homogeneously purified and its glucose oxidizing properties on spectrographic graphite electrodes were investigated. Six different Os-polymers, the redox potentials of which ranging in a broad potential window between +15 and +489 mV vs. NHE, were used to immobilize and “wire” Gc GDH to the spectrographic graphite electrode’s surface. The Gc GDH/Os-polymer modified electrodes were evaluated by chronoamperometry using flow injection analysis. The current response was investigated using a step-wisely increased applied potential. It was observed that the ratio of Gc GDH:Os-polymer and the overall loading of the enzyme electrode significantly affect the performance of the enzyme electrode for glucose oxidation. The best suited Os-polymer [Os(4,4¢-dimethyl-2,2¢-bipyridine) 2 (PVI)Cl] + had a potential of +309 mV vs. NHE and the optimum Gc GDH:Os-polymer ratio was 1:2 yielding a maximum current density of 493 µAcm -2 at a 30 mM glucose concentration. Key words: Glucose dehydrogenase, FAD, Os-polymers, glucose biosensor, chronoamperometry, oxygen reactivity.
The Effect of Respiration on the Contrast and Sharpness of Liver Lesions in MRI (1995)

This work demonstrates the effects of through-plane motion due to respiration on contrast and sharpness of liver lesions in MRI. The effects of slice coverage with and without such respiratory motion is also reported. This work is comprised of two parts: a theoretical prediction of liver-lesion contrast and blur with and without respiration and an experimental validation using gel phantoms of the predicted results. Both theory and experiment show a loss of contrast, increasing with amplitude of the peak-to-peak motion. The loss of contrast for a 5-mm lesion at normal respiration of 15 mm peak-to-peak superior-inferior motion is approximately 10% with a low order sorted respiratory ordered phase encoding acquisition and approximately 50% for an unsorted acquisition. Lesion blur is greatest for the low order sorted acquisition while the unsorted and high sort acquisitions maintain edge definition. Breath-hold imaging is potentially superior to nonbreath-hold imaging in liver lesion contrast and edge definition, but is more sensitive to inadequate slice coverage.
Inversion of surficial sediment thickness from under-ice acoustic transmission measurement (2021)

The under-ice acoustic transmission experiment of 2013, conducted under ice cover in the Fram Strait, was analyzed for bottom interactions for the purpose of developing a model of the seabed. Using the acoustic signals, as well as data from other sources, including cores, gravimetric, refraction, and seismic surveys, it was deduced that the seabed may be modeled as a thin surficial layer overlaid on a deeper sediment. The modeling was based on the Biot–Stoll model for acoustic propagation in porous sediments, aided by more recent developments that improve parameter estimation and depth dependence due to consolidation. At every stage, elastic and fluid approximations were explored to simplify the model and improve computational efficiency. It was found the surficial layer could be approximated as a fluid, but the deeper sediment required an elastic model. The full Biot–Stoll model, while instrumental in guiding the model construction, was not needed for the final computation. The model could be made to agree with the measurements by adjusting the surficial layer thickness.
Influenza B mutant viruses with truncated NS1 proteins grow efficiently in Vero cells and are immunogenic in mice (2009)

Contemporary influenza B virus strains were generated encoding C-terminally truncated NS1 proteins. Viable viruses containing the N-terminal 14, 38, 57 or 80 aa of the NS1 protein were rescued in Vero cells. The influenza B virus NS1-truncated mutants were impaired in their ability to counteract interferon (IFN) production, induce antiviral pro-inflammatory cytokines early after infection and show attenuated or restricted growth in IFN-competent hosts. In Vero cells, all of the mutant viruses replicated to high titres comparable to the wild-type influenza B virus. Mice that received a single, intranasal immunization of the NS1-truncated mutants elicited an antibody response and protection against wild-type virus challenge. Therefore, these NS1-truncated mutants should prove useful as potential candidates for live-attenuated influenza virus vaccines.
BNIP3L/Nix-induced mitochondrial fission, mitophagy, and impaired myocyte glucose uptake are abrogated by PRKA/PKA phosphorylation (2020)

Lipotoxicity is a form of cellular stress caused by the accumulation of lipids resulting in mitochondrial dysfunction and insulin resistance in muscle. Previously, we demonstrated that the mitophagy receptor BNIP3L/Nix is responsive to lipotoxicity and accumulates in response to a high-fat (HF) feeding. To provide a better understanding of this observation, we undertook gene expression array and shot-gun metabolomics studies in soleus muscle from rodents on an HF diet. Interestingly, we observed a modest reduction in several autophagy-related genes. Moreover, we observed alterations in the fatty acyl composition of cardiolipins and phosphatidic acids. Given the reported roles of these phospholipids and BNIP3L in mitochondrial dynamics, we investigated aberrant mitochondrial turnover as a mechanism of impaired myocyte insulin signaling. In a series of gain-of-function and loss-of-function experiments in rodent and human myotubes, we demonstrate that BNIP3L accumulation triggers mitochondrial depolarization, calcium-dependent activation of DNM1L/DRP1, and mitophagy. In addition, BNIP3L can inhibit insulin signaling through activation of MTOR-RPS6KB/p70S6 kinase inhibition of IRS1, which is contingent on phosphatidic acids and RHEB. Finally, we demonstrate that BNIP3L-induced mitophagy and impaired glucose uptake can be reversed by direct phosphorylation of BNIP3L by PRKA/PKA, leading to the translocation of BNIP3L from the mitochondria and sarcoplasmic reticulum to the cytosol. These findings provide insight into the role of BNIP3L, mitochondrial turnover, and impaired myocyte insulin signaling during an overfed state when overall autophagy-related gene expression is reduced. Furthermore, our data suggest a mechanism by which exercise or pharmacological activation of PRKA may overcome myocyte insulin resistance.<b>Abbreviations:</b> BCL2: B cell leukemia/lymphoma 2; BNIP3L/Nix: BCL2/adenovirus E1B interacting protein 3-like; DNM1L/DRP1: dynamin 1-like; FUNDC1: FUN14 domain containing 1; IRS1: insulin receptor substrate 1; MAP1LC3A/LC3: microtubule-associated protein 1 light chain 3 alpha; MFN1: mitofusin 1; MFN2: mitofusin 2; MTOR: mechanistic target of rapamycin kinase; OPA1: OPA1 mitochondrial dynamin like GTPase; PDE4i: phosphodiesterase 4 inhibitor; PLD1: phospholipase D1; PLD6: phospholipase D family member 6; PRKA/PKA: protein kinase, AMP-activated; PRKCD/PKCδ: protein kinase C, delta; PRKCQ/PKCθ: protein kinase C, theta; RHEB: Ras homolog enriched in brain; RPS6KB/p70S6K: ribosomal protein S6 kinase; SQSTM1/p62: sequestosome 1; YWHAB/14-3-3β: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta.
DynamicMC: An Open-source GUI Program Coupled with MCNP for Modeling Relative Dynamic Movement of Radioactive Source and ORNL Phantom in a 3-dimensional Radiation Field (2023)

The present work introduces an open-source graphical user interface (GUI) computer program called DynamicMC. The present program has the ability to generate ORNL phantom input script for the Monte Carlo N-Particle (MCNP) package. The relative dynamic movement of the radiation source with respect to the ORNL phantom can be modeled, which essentially resembles the dynamic movement of source-to-target (i.e., human phantom) distance in a 3-dimensional radiation field. The present program makes the organ-based dosimetry of the human body much easier, as users are not required to write lengthy scripts or deal with any programming that many may find tedious, time consuming, and error prone. In this paper, we have demonstrated that the present program can successfully model simple and complex relative dynamic movements (i.e., those involving rotation of source and human phantom in a 3-dimensional field). The present program would be useful for organ-based dosimetry and could also be used as a tool for teaching nuclear radiation physics and its interaction with the human body.
RE: SECONDARY MALIGNANCIES IN DIFFERENT FORMS OF URINARY DIVERSION USING ISOLATED GUT (2005)

No AccessJournal of UrologyLetters to the Editor/Erratum1 May 2005RE: SECONDARY MALIGNANCIES IN DIFFERENT FORMS OF URINARY DIVERSION USING ISOLATED GUTis correction ofSECONDARY MALIGNANCIES IN DIFFERENT FORMS OF URINARY DIVERSION USING ISOLATED GUT John Lavelle, Patrick Shenot, Christopher Smith, and Michael B. Chancellor John LavelleJohn Lavelle More articles by this author , Patrick ShenotPatrick Shenot More articles by this author , Christopher SmithChristopher Smith More articles by this author , and Michael B. ChancellorMichael B. Chancellor More articles by this author View All Author Informationhttps://doi.org/10.1097/00005392-200505000-00158AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "RE: SECONDARY MALIGNANCIES IN DIFFERENT FORMS OF URINARY DIVERSION USING ISOLATED GUT." The Journal of Urology, 173(5), p. 1831 Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania© 2005 by American Urological Association, Inc.FiguresReferencesRelatedDetailsRelated articlesJournal of Urology9 Nov 2018SECONDARY MALIGNANCIES IN DIFFERENT FORMS OF URINARY DIVERSION USING ISOLATED GUT Volume 173Issue 5May 2005Page: 1831 Advertisement Copyright & Permissions© 2005 by American Urological Association, Inc.MetricsAuthor Information John Lavelle More articles by this author Patrick Shenot More articles by this author Christopher Smith More articles by this author Michael B. Chancellor More articles by this author Expand All Advertisement PDF downloadLoading ...
Efficient Cross-talk Reduction of Nanophotonic Circuits Enabled by Fabrication Friendly Periodic Silicon Strip Arrays (2017)

Reduction of the crosstalk between adjacent photonic components has been regarded as one of the most effective, yet most challenging approaches for increasing the packing density of photonic integrated circuits. Recently, extensive efforts have been devoted to this field, leading to a number of elaborate designs, such as waveguide supperlattice and nanophotonic cloaking, among others. Here we develop a simple and efficient crosstalk reduction approach for silicon-based nanophotonic circuits by introducing a periodic array of silicon strips between adjacent waveguides. Studies indicate that the coupling lengths can be extended by more than two orders of magnitude for a waveguide pair with an edge-to-edge distance of ~λ/3 at the telecommunication wavelength. Further investigations reveal that our method is effective for both strongly and weakly confined silicon photonic modes, and works well over a broad band of operational wavelengths. In addition, the crosstalk reduction technique is shown to be capable of improving the coupling lengths of other elements as well, such as vertical silicon slot waveguides. Our approach offers a promising platform for creating ultra-compact functional components that is fabrication friendly, thereby providing a feasible route toward the realization of photonic integrated circuits with ultra-high packing densities.
A 1.9Gb/s 358mW 16-to-256 State Reconfigurable Viterbi Accelerator in 9Onm CMOS (2007)

A 16-to-256 state coarse-grain reconfigurable Viterbi accelerator fabricated in 1.3V, 90nm dual-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> CMOS technology is described for 3.8GHz operation, with 1.9Gb/s data rate in 32-state mode. Radix-4 ripple-carry ACS circuits, reconfigurable path metric read/write control and tree-bitline traceback memory circuits with programmable ring-buffer decoders enable 358mW total power, measured at 1.3V, 50 °C, with performance scalable to 2.35Gb/s at 17V, 50 °C.
419 A CTS team approach to identifying thematic constructs related to kratom use during pregnancy and breastfeeding: A qualitative analysis of social media posts – ADDENDUM (2023)

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Separations with Fluorous Silica Gel and Related Materials (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
High-resolution MAS NMR analysis of PI3-SH3 amyloid fibrils: Backbone conformation and implications for protofilament assembly and structure (2010)

The SH3 domain of the PI3 kinase (PI3-SH3 or PI3K-SH3) readily aggregates into fibrils in vitro and has served as an important model system in the investigation of the molecular properties and mechanism of formation of amyloid fibrils. We describe the molecular conformation of PI3-SH3 in amyloid fibril form as revealed by magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy. The MAS NMR spectra of these fibrils display excellent resolution, with narrow &lt;sup&gt;13&lt;/sup&gt;C and &lt;sup&gt;15&lt;/sup&gt;N line widths, representing a high degree of structural order and the absence of extensive molecular motion for the majority of the polypeptide chain. We have identified the spin systems of 82 of the 86 residues in the protein and obtained sequential resonance assignments for 75 of them. Chemical shift analysis indicates that the protein subunits making up the fibril adopt a compact conformation consisting of four well-defined β-sheet regions and four random-coil elements with varying degrees of local dynamics or disorder. The backbone conformation of PI3-SH3 in fibril form differs significantly from that of the native state of the protein, both in secondary structure and in the location of dynamic or disordered segments. The site-specific MAS NMR analysis of PI3-SH3 fibrils we report here is compared with previously published mechanistic and structural data, resulting in a detailed interpretation of the factors that mediate fibril formation by PI3-SH3 and allowing us to propose a possible model of the core structure of the fibrils. Our results confirm the structural similarities between PI3-SH3 fibrils and amyloid assemblies directly related to degenerative and infectious diseases.
Data-Driven Multiscale Science for Tread Compounding (2022)

ABSTRACT Tread compounding has always been faced with the simultaneous optimization of multiple performance properties, most of which have tradeoffs between the properties. The search for overcoming these conflicting tradeoffs have led many companies in the tire industry to discover and develop material physics-based platforms. This report describes some of our efforts to quantify compound structures and properties at multiple scales, and their subsequent application in compound design. Integration of experiment and simulation has been found to be critical to highlighting the levers in data-driven multiscale compound tread design.
Supplementary Table S5 from Systematic Interrogation of 3q26 Identifies <i>TLOC1</i> and <i>SKIL</i> as Cancer Drivers (2023)

&lt;p&gt;Supplementary Table S5 - XLSX file 48K, Intersection of gene expression signatures that correlate with either high SKIL or low SMAD4 gene expression&lt;/p&gt;
Active control of sound fields in elastic cylinders (1987)

Much interest has recently arisen over the use of active noise and vibration control in various applications where weight considerations are important. The results of research directed towards applying active methods for reducing noise in the cabins of propeller aircraft will be reviewed. Two differing techniques of implementing the active control will be discussed. The first consists of placing active acoustic sources in the interior space in order to achieve cancellation. The second method relies on active control of the transmitted acoustical energy by vibrational force inputs applied directly to the cylinder wall. Both theoretical and experimental results using simplified models of aircraft fuselages will be presented and the mechanisms inherent in the control action will be outlined.
Smart-ML: A System for Machine Learning Model Exploration using Pipeline Graph (2020)

In this paper, we describe an overarching ML system with a simple programming interface that leverages existing AI and ML frameworks to make the task of model exploration easier. The proposed system introduces a new programming construct namely pipeline graph (a directed acyclic graph) consisting of multiple machine learning operations provided by different ML repositories. End user uses the pipeline graph as a common interface for modeling different ML tasks such as classification, regression, and timeseries prediction, while enabling efficient execution on different environments (Spark, Celery and Cloud). We further annotated the pipeline graph with a hyper-parameter grid and an option to try-out a wide range of optimization strategies (i.e., Random, Bayesian, Bandit, AutoLearn, etc). Given a large pre-defined pipeline graph along with its hyper-parameters, we provided a general-purpose, scalable and efficient pipeline-graph exploration technique to provide the automated solutions to a variety of ML tasks. We compare our automated approach to several state-of-the-art automated AI systems and find that we achieve performance comparable to the best results, while often producing simpler pipelines using off the shelf components. Our evaluation suite consists of experiments on 60+ classifications and regressions datasets.
Percutaneous Nephrolithotomy With Mazzariello-Caprini Forceps (1983)

Mazzariello-Caprini forceps were used percutaneously to remove a stone that was impacted distal to the ureteropelvic junction in a patient who had undergone several previous open pyelolithotomies. These forceps open by a rotational rather than a scissoring movement so the shaft size does not increase and they are well suited for operation through a narrow nephrostomy tract. The original design has been modified to allow passage over an angiographic guide wire, thereby placing the forceps precisely at the site of the stone. Also, with the angiographic guide wire to direct them the forceps can be used in a freshly established nephrostomy tract as well as in a mature tract. In our experience the Mazzariello-Caprini forceps have been most useful for nonoperative manipulation of renal and upper ureteral calculi.
Absolute Configurations of Naturally Occurring Quinones: Ventilagone (I) and Dunnione (II). (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
An Evaluation of Density Functional Theory and ab Initio Predictions for Bridge-Bonded Aluminum Compounds (1998)

Ab initio and density functional methods have been employed to study bridge bonding of aluminum compounds. Results for geometry optimizations and vibrational frequency calculations are found to be consistent with the recent literature. Heats of formation for the aluminum compounds dimethylaluminum hydride and trimethylaluminum are poorly described with density functional theory (DFT) methods including the hybrid DFT method. G2 calculations are closer to experimental values with estimated errors of −1.0 to −2.0 kcal/mol per Al−CH3 bond and −1.9 to −4.1 kcal/mol per Al−H bond. The major finding is that DFT methods poorly represent bridge bonding in aluminum compounds. While ab initio methods (represented by the MP2 method) reproduce experimental values within 2−3 kcal/mol, DFT methods, including the hybrid method, show errors of 5−12 kcal/mol. The DFT methods consistently under-bind the dimers of aluminum compounds with respect to two monomers. Exploration of the hybrid DFT functional shows that a better match between experiment and theory is provided by reducing the contribution of the Becke exchange correction. The binding energies are also found to be sensitive to the choice of correlation functional and the inclusion of “exact exchange”. Results for associated units larger than dimers indicate it may be difficult to successfully describe all bridge-bonded aluminum compounds with existing DFT methods.
Transmission Improvement in Fiber Radio Links using Semiconductor Laser (2008)

This investigation experimentally demonstrates the performance improvement in fiber- radio links by using a semiconductor laser. This technique improves receiver sensitivity over 4.5 dB by increasing the optical modulation depth.
ChemInform Abstract: Conjugate Addition of Diethylzinc to Enones Catalyzed by Homogeneous and Supported Chiral Ni‐Complexes. Cooperative Effect of the Support on Enantioselectivity. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Investment of attention as an analytic approach to cognitive dimensions. (1999)

Green’s Cognitive Dimensions of Notations framework has attracted sustained attention from researchers investigating programming (Yang et el., 1998; Roast & Siddiqi, 1996; Williams and Buehler, 1998) and other design activities in which the design notation is an essential element of the design process or product (Tweedie, 1995; Buckingham Shum and Hammond, 1994). More recently, the Cognitive Dimensions (CDs) have been applied in investigating the usability of other types of software notations, user interfaces, and “information artefacts” (Green and Blackwell, 1998; Britton and Jones, 1998). The increasing generality of CDs is both encouraging and challenging. It is encouraging in that it affirms the value of psychology of programming as a discipline that provides novel theoretical contributions to more general problems in cognitive ergonomics. It is challenging in that it draws our attention to issues that were less important in earlier formulations of CDs, but are required of general approaches to cognitive ergonomics.