gebhart/patrepeval huggingface dataset:
c-Jun N-terminal Kinase Specifically Phosphorylates p66ShcA at Serine 36 in Response to Ultraviolet Irradiation (2001)

Mice lacking expression of the p66 isoform of the ShcA adaptor protein (p66(ShcA)) are less susceptible to oxidative stress and have an extended life span. Specifically, phosphorylation of p66(ShcA) at serine 36 is critical for the cell death response elicited by oxidative damage. We sought to identify the kinase(s) responsible for this phosphorylation. Utilizing the SH-SY5Y human neuroblastoma cell model, it is demonstrated that p66(ShcA) is phosphorylated on serine/threonine residues in response to UV irradiation. Both c-Jun N-terminal kinases (JNKs) and p38 mitogen-activated protein kinases are activated by UV irradiation, and we show that both are capable of phosphorylating serine 36 of p66(ShcA) in vitro. However, treatment of cells with a multiple lineage kinase inhibitor, CEP-1347, that blocks UV-induced JNK activation, but not p38, phosphatidylinositol 3-kinase, or MEK1 inhibitors, prevented p66(ShcA) phosphorylation in SH-SY5Y cells. Consistent with this finding, transfected activated JNK1, but not the kinase-dead JNK1, leads to phosphorylation of serine 36 of p66(ShcA) in Chinese hamster ovary cells. In conclusion, JNKs are the kinases that phosphorylate serine 36 of p66(ShcA) in response to UV irradiation in SH-SY5Y cells, and blocking p66(ShcA) phosphorylation by intervening in the JNK pathway may prevent cellular damage due to light-induced oxidative stress.
Tunneling lifetime of trapped condensates (2004)

Using the complex scaling transformation we calculate the tunneling lifetime of a condensate inside a magnetic/optical trap. We show that by varying the scattering length, the external potential acts like a 'selective membrane' which controls the direction of the flux of the cold atoms through the barriers and thereby controls the size of the stable condensate inside the trap.
Cover Picture: Werner Reutter: A Visionary Pioneer in Molecular Glycobiology (ChemBioChem 13/2017) (2017)

The cover picture shows the late Prof. Dr. Werner Reutter to whom this special issue of ChemBioChem is dedicated. Prof. Reutter was one of the most influential glycobiologists of his time and made numerous contributions to molecular and chemical biology as well as to medicinal research. Several of his major discoveries are highlighted on this cover image, for example his studies on d-galactosamine metabolism as well as the elucidation of key enzymatic steps in sialic acid biosynthesis including the epimerization of UDP-N-acetylglucosamine and the phosphorylation of N-acetylmannosamine by the bifunctional enzyme GNE. Finally, he contributed to the field of metabolic glycoengineering by showing that N-acylated mannosamines can be transformed to the corresponding sialic acids on cell surfaces and to the identification of carbohydrate-based inhibitors that block sialic acid biosynthesis. Cover image Jad Bou Reslan based on a photo kindly provided by Anja Reutter. More information can be found in the Editorial by C. P. R. Hackenberger et al. on page 1279 in Issue 13, 2017 (DOI: 10.1002/cbic.201700277).
Research on Fault Diagnosis Technology for Aviation Equipments Based on IETMs (2014)

In this paper on the basis of fault diagnosis for aviation equipments, an complex behavior of maintenance, IETMs are studied with respect to fault modules, data description and storage, fusion of fault trees and case-based reasoning, as well as integration with external diagnosis and other expert systems, etc., and solutions for fault diagnosis technology of IETMs are investigated to add new contents for fault diagnosis technology, so that IETMs are capable of providing further fault diagnosis strategies to maintenance personnel based on the traditional IETMs.
Drugging Hedgehog: signaling the pathway to translation (2013)

First discovered in Drosophila, the Hedgehog signaling pathway controls a wide range of developmental processes and is implicated in a variety of cancers. The success of a screen for chemical modulators of this pathway, published in 2002, opened a new chapter in the quest to translate the results of basic developmental biology research into therapeutic applications. Small molecule pathway agonists are now used to program stem cells, whilst antagonists are proving effective as anti-cancer therapies.
Target-tracking control design for a robotic fish with caudal fin (2013)

In this paper we propose a novel target-tracking control scheme for a carangiform robotic fish based on a faithful dynamic model that combines rigid-body dynamics with Lighthill's large-amplitude elongated-body theory. We first average the dynamic model under periodic tail-actuation, which results in an average model with tail-beat patterns (bias, frequency, and amplitude) as new control inputs that are nonlinearly coupled. By introducing two new state variables, the orientation angle error and the distance between the robotic fish body and the target location, we derived the dynamic equations for these variables, which are then used in backstepping-based controller design. A hybrid controller is proposed, where the switching is determined by whether the orientation error is above a threshold value. Using Lyapunov analysis, we show that the trajectory of the robotic fish will converge to the target point if the given condition is satisfied. Finally, the effectiveness of the proposed control strategy is demonstrated through simulation results.
Electronic states at aluminum nitride (0001)-1×1 surfaces (1999)

We investigate the electronic structure of aluminum nitride (0001)-1×1 surfaces via direct and inverse photoemission spectroscopy. Bulk and surface sensitive measurements on clean surfaces and surfaces exposed to oxygen or cesium demonstrate the existence of filled and empty surface states which extend more than 1 eV beyond the valence- and conduction-band edges. The filled states are tentatively associated with Al dangling or back bonds. The measurement of the top of the valence band upon removal of the filled states leads to a determination of an electron affinity equal to 1.9±0.2 eV. The empty surface states are presumed to play a role in the pinning of the Fermi level in the upper part of the gap and are consistent with the anticipated metallicity of the surface.
Intraoperative biliary tree imaging with cholyl-lysyl-fluorescein: an experimental study in the rabbit. (1996)

Iatrogenic bile duct injury during cholecystectomy is the most serious complication of this surgical procedure. Initial reports suggest that this complication is particularly troublesome during laparoscopic cholecystectomy. Proper identification of the biliary anatomy in the subhepatic region is the only way to avoid this catastrophe. The potential benefits of a simple, reliable method for intraoperative delineation of biliary anatomy are self-evident. In this experimental study on rabbits, we show how the simple i.v. injection of a fluorescent bile salt, cholyl-lysyl-fluorescein, enables the surgeon to visualize the entire biliary tree in anatomic detail.
Marine Ecosystem Analysis of Gouldsboro and Dyer Bays, Maine (2020)

In the early 1980s, the National Oceanic and Atmospheric Administration (NOAA) initiated an ecosystem analysis of Gouldsboro Bay in eastern Maine as part of a planned marine sanctuary. The original report to NOAA by Walter H. Adey was not published after the sanctuary concept for Maine was abandoned. Because significant human-related climatic and ecosystem changes are underway in the Gulf of Maine, that report provides valuable baseline data and is included as the Appendix to this volume. After qualitatively describing the geological, physical, chemical, and biogeographical features of Gouldsboro Bay and adjacent Dyer Bay, we quantitatively describe the principal bay ecological communities with data collected during the 1981–1983 ecosystem assessment as well as additional measurements taken within the past decade. We then undertake a comparison of the primary productivity of these bays with the Google Earth Pro polygon tool to determine component areas. Benthic taxa are the dominant primary producers in both bays: rockweeds (primarily Ascophyllum nodosum, with Fucus vesiculosus secondary) in the intertidal; Irish moss (Chondrus crispus, with Fucus distichus secondary) as a near monoculture in the lowest intertidal (infralittoral); kelps (primarily Saccharina latissima, Laminaria digitata, and Agarum clathratum) in the rocky subtidal; and the angiosperm Zostera marina (seagrass) in soft bottom substrate. The rocky intertidal, dominated by Ascophyllum with a specific productivity of 10.6 kg/m2/year, provides nearly one-third of all bay productivity. Because of the proportionally greater shore length relative to area of Dyer Bay, it has 45% greater productivity for its surface area than Gouldsboro Bay. Kelp has a specific productivity value of 7.2 kg/m2/year, and Zostera of 1.2 kg/m2/year. The kelps provide approximately 20% of Gouldsboro Bay’s primary productivity and 35% of that of Dyer Bay. Zostera provides roughly 20% of total primary productivity in Gouldsboro Bay and 12% in Dyer Bay. With a primary productivity of 1.73 kg/m2/year, salt marshes provide only 3.7% (Gouldsboro) and 2.6% (Dyer) of total primary productivity. With a primary productivity of 0.06 kg/m2/year, plankton account for 23.8% of Gouldsboro Bay and 16% of Dyer Bay primary productivity.
Understanding collateral evolution in Linux device drivers (2006)

In a modern operating system (OS), device drivers can make up over 70% of the source code. Driver code is also heavily dependent on the rest of the OS, for functions and data structures defined in the kernel and driver support libraries. These properties pose a significant problem for OS evolution, as any changes in the interfaces exported by the kernel and driver support libraries can trigger a large number of adjustments in dependent drivers. These adjustments, which we refer to as collateral evolutions , may be complex, entailing substantial code reorganizations. As to our knowledge there exist no tools to help in this process, collateral evolution is thus time consuming and error prone.In this paper, we present a qualitative and quantitative assessment of collateral evolution in Linux device driver code. We provide a taxonomy of evolutions and collateral evolutions, and use an automated patch-analysis tool that we have developed to measure the number of evolutions and collateral evolutions that affect device drivers between Linux versions 2.2 and 2.6. In particular, we find that from one version of Linux to the next, collateral evolutions can account for up to 35% of the lines modified in such code.
Advances in the Mass Spectrometry of Membrane Proteins: From Individual Proteins to Intact Complexes (2011)

Rapid advances in structural genomics and in large-scale proteomic projects have yielded vast amounts of data on soluble proteins and their complexes. Despite these advances, progress in studying membrane proteins using mass spectrometry (MS) has been slow. This is due in part to the inherent solubility and dynamic properties of these proteins, but also to their low abundance and the absence of polar side chains in amino acid residues. Considerable progress in overcoming these challenges is, however, now being made for all levels of structural characterization. This progress includes MS studies of the primary structure of membrane proteins, wherein sophisticated enrichment and trapping procedures are allowing multiple posttranslational modifications to be defined through to the secondary structure level in which proteins and peptides have been probed using hydrogen exchange, covalent, or radiolytic labeling methods. Exciting possibilities now exist to go beyond primary and secondary structure to reveal the tertiary and quaternary interactions of soluble and membrane subunits within intact assemblies of more than 700 kDa.
Individually grown cobalt nanowires as magnetic force microscopy probes (2018)

AC electric fields were utilized in the growth of individual high-aspect ratio cobalt nanowires from simple salt solutions using the Directed Electrochemical Nanowire Assembly method. Nanowire diameters were tuned from the submicron scale to 40 nm by adjusting the AC voltage frequency and the growth solution concentration. The structural properties of the nanowires, including shape and crystallinity, were identified using electron microscopy. Hysteresis loops obtained along different directions of an individual nanowire using vibrating sample magnetometry showed that the magnetocrystalline anisotropy energy has the same order of magnitude as the shape anisotropy energy. Additionally, the saturation magnetization of an individual cobalt nanowire was estimated to be close to the bulk single crystal value. A small cobalt nanowire segment was grown from a conductive atomic force microscope cantilever tip that was utilized in magnetic force microscopy (MFM) imaging. The fabricated MFM tip provided moderate quality magnetic images of an iron-cobalt thin-film sample.
Autonomous Electric Race Car Design (2017)

Autonomous driving and electric vehicles are nowadays very active research and development areas. In this paper we present the conversion of a standard Kyburz eRod into an autonomous vehicle that can be operated in challenging environments such as Swiss mountain passes. The overall hardware and software architectures are described in detail with a special emphasis on the sensor requirements for autonomous vehicles operating in partially structured environments. Furthermore, the design process itself and the finalized system architecture are presented. The work shows state of the art results in localization and controls for self-driving high-performance electric vehicles. Test results of the overall system are presented, which show the importance of generalizable state estimation algorithms to handle a plethora of conditions.
Novel Dual-FCL Connection for Adding Distributed Generation to a Power Distribution Utility (2010)

A novel dual-connection of fault current limiters is described for use when connecting new distributed generation plants to the electric grid. The operation and control scheme of this connection are described and analysed. The proximate arrangement of the two current limiters has the advantage that they can share one cryogenic system. The dual connection limits fault currents sufficiently to avoid disturbing the original protection relay schemes of the utilities, and also improves synchronism between the new generator and the grid. These benefits are proven by simulations of a 36 MW, 4.16 kV gas turbine generator connected to an infinite grid. This dual-FCL connection reduces fault current contributions of the DG by 97% (from 41 to 1 kA), and maintains the circuit breakers within their duty limits when a three-phase fault occurs at a bus connected to the DG. Otherwise, when a three-phase fault occurs in the infinite system, this connection limits the fault current contribution of the DG from 4.8 to 0.4 kA, and frequency oscillations of the DG from 0.14 to 0.01 Hz. The power continuity in the local network is improved, as the voltage sag at the bus connected to the DG is reduced by 96% (from 851 to 32 V) during and after serious short-circuit faults.
Binding of the γ-subunit of retinal rod-outer-segment phosphodiesterase with both transducin and the catalytic subunits of phosphodiesterase (1990)

The gamma-subunit of retinal rod-outer-segment phosphodiesterase (PDE-gamma) is a multifunctional protein which interacts directly with both of the catalytic subunits of PDE (PDE alpha/beta) and the alpha-subunit of the retinal G (guanine-nucleotide-binding)-protein transducin alpha (T alpha). We have previously reported that the PDE gamma binds to T alpha at residue nos. 24-45 [Morrison. Rider & Takemoto (1987) FEBS Lett. 222, 266-270]. In vitro this results in inhibition of T alpha GTP/GDP exchange [Morrison, Cunnick, Oppert & Takemoto (1989) J. Biol. Chem. 264, 11671-11681]. We now report that the inhibitory region of PDE gamma for PDE alpha/beta occurs at PDE gamma residues 54-87. This binding results in inhibition of either trypsin-solubilized or membrane-bound PDE alpha/beta. PDE gamma which has been treated with carboxypeptidase Y, removing the C-terminus, does not inhibit PDE alpha/beta, but does inhibit T alpha GTP/GDP exchange. Inhibition by PDE gamma can be removed by T alpha-guanosine 5'-[gamma-thio]triphosphate (GTP[S]) addition to membranes. This results in a displacement of PDE gamma, but not in removal of this subunit from the membrane [Whalen, Bitensky & Takemoto (1990) Biochem. J. 265, 655-658]. These results suggest that low levels of T alpha-GTP[S] can result in displacement of PDE gamma from the membrane in vitro as a GTP[S]-T alpha-PDE gamma complex. Further activation by high levels of T alpha-GTP[S] occurs by displacement of PDE gamma from its inhibitory site on PDE alpha/beta, but not in removal from the membrane.
Advanced Taxi Map Display Design for Low-Visibility Operations (1996)

Conducting gate to gate operations during reduced visibility conditions is a major impediment to scheduled and unscheduled flight operations in the National Airspace System (NAS). Takeoff and landing minima are predicated on aircraft equipage and airport visibility (e.g., at some major airports, operations are terminated when visibility is below 700 ft runway visual range (RVR). Although some aircraft can land with zero-zero visibility, there are no ground or flight deck systems that allow them to taxi under low visibility conditions. A map display system designed to support low visibility taxi was evaluated by 12 B-747 flight crews in NASA's Crew Vehicle System Research Facility (CVSRF). Three taxi-map conditions were compared: paper map only, basic moving map, and advanced moving map. Crews landed and taxied along 24 different taxi routes under three visibility conditions: unlimited visibility, 700 ft RVR, and 300 ft RVR. Taxi time, errors and workload were collected for each taxi operation. Video tape recordings captured crew interactions and head-up and head-down times. Taxi times and errors were significantly better for crews with electronic maps than for crews with a paper map. Although crews with the advanced map experienced significantly more head-down time, the head down interval was significantly less than with the paper map and crew workload was significantly less. During the post-flight design review, pilots identified improvements in procedures and formatting that might enhance performance. They developed a procedure for safely switching from the NAV display to the map; and in general their comments were very favorable.
Simultaneous deep generative modeling and clustering of single cell genomic data (2020)

Recent advances in single-cell technologies, including single-cell ATAC-seq (scATAC-seq), have enabled large-scale profiling of the chromatin accessibility landscape at the single cell level. However, the characteristics of scATAC-seq data, including high sparsity and high dimensionality, have greatly complicated the computational analysis. Here, we proposed scDEC, a computational tool for single cell ATAC-seq analysis with deep generative neural networks. scDEC is built on a pair of generative adversarial networks (GANs), and is capable of learning the latent representation and inferring the cell labels, simultaneously. In a series of experiments, scDEC demonstrates superior performance over other tools in scATAC-seq analysis across multiple datasets and experimental settings. In the downstream applications, we demonstrated that the generative power of scDEC helps to infer the trajectory and intermediate state of cells during differentiation and the latent features learned by scDEC can potentially reveal both biological cell types and within-cell-type variations.
Simplified Characterization of Building Thermal Response Rates (2015)

Building thermal response rates refer to those dynamic conditions when a building interior is not held in steady-state by the operation of its HVAC systems. A method is proposed and preliminary results demonstrated for using data available from the typical large-building Building Automation System (BAS) to automatically characterize temperature response rates at the zone level. The work described employs a data-based "black-box" inverse-model approach. It is proposed that such empirically derived response rates could then inform building control algorithms for optimization associated with building commissioning and on- going control over the operations phase of the building's life-cycle. The paper reports on work being conducted collaboratively by teams of engineers and computer scientists at New York Institute of Technology and the City College of New York.
The Mechanism of Cleavage Under Basic Conditions of Succinyl-Anchored Oligonucleotides (1998)

Abstract Studies with a model compound provide direct evidence that cleavage of succinyl-anchored oligonucleotides takes place by intramolecular nucleophilic attack of the conjugate base of the succinamide at the ester carbonyl group. An N-substituted succinimide is exclusively formed with piperidine, DBU and TBAF, but when ammonia is used-this general mechanism seems to coexist with ammonolysis of the succinate ester. Cleavage with TBAF is extremely fast.
Runway obstacle detection by controlled spatiotemporal image flow disparity (1996)

This paper proposes a method for detecting obstacles on a runway by controlling their expected disparities. By approximating the runway by a planar surface, the initial model flow field (MFF) corresponding to an obstacle-free runway is described by the data from on-board sensors (OBS). The error variance of the initial MFF is computed and used to estimate the MFF. Obstacles are detected by comparing the expected residual flow disparities with the residual flow field (RFF) estimated after warping (or stabilizing) an image using the MFF. Expected temporal and spatial disparities are obtained from the use of the OBS. This allows us to control the residual disparities by increasing the temporal baseline and/or by utilizing the spatial baseline if distant objects cannot be detected for a given temporal baseline. Experimental results for two real flight image sequences are presented.
Kinetics of esterification of lauric acid with fatty alcohols by lipase: effect of fatty alcohol (2002)

Abstract Lauric acid has been esterified with some C 1 –C 18 aliphatic alcohols by a commercial lipase, Lipolase 100 L, using isooctane as a solvent. When lauric acid and fatty alcohols were taken in the mole ratio 1:1, first order kinetics were observed for all the alcohols studied. The highest reaction rate was observed for n ‐butyl alcohol. Lauric acid was esterified with stearyl alcohol, in varying acid to alcohol mole ratios to explain the first order kinetics of the reaction. A kinetic model for the lipase‐catalysed esterification in a biphasic organic–aqueous system has been proposed. Based on the interfacial substrate concentration, an analytical rate equation for initial rate of the reaction was derived and confirmed with the experimental data. © 2002 Society of Chemical Industry
Evidence for Pseudogap Evolutions in High-Tc Iron Oxypnictides (2008)

We have performed a temperature-dependent angle-integrated laser photoemission study of iron oxypnictide superconductors LaFeAsO:F and LaFePO:F exhibiting critical transition temperatures (Tc's) of 26 K and 5 K, respectively. We find that high-Tc LaFeAsO:F exhibits a temperature-dependent pseudogap-like feature extending over ~0.1 eV about the Fermi level at 250 K, whereas such a feature is absent in low-Tc LaFePO:F. We also find ~20-meV pseudogap-like features and signatures of superconducting gaps both in LaFeAsO:F and LaFePO:F. We discuss the possible origins of the unusual pseudogap-like features through comparison with the high-Tc cuprates.