gebhart/patrepeval huggingface dataset:
Untargeted, spectral library‐free analysis of data‐independent acquisition proteomics data generated using Orbitrap mass spectrometers (2016)

We describe an improved version of the data-independent acquisition (DIA) computational analysis tool DIA-Umpire, and show that it enables highly sensitive, untargeted, and direct (spectral library-free) analysis of DIA data obtained using the Orbitrap family of mass spectrometers. DIA-Umpire v2 implements an improved feature detection algorithm with two additional filters based on the isotope pattern and fractional peptide mass analysis. The targeted re-extraction step of DIA-Umpire is updated with an improved scoring function and a more robust, semiparametric mixture modeling of the resulting scores for computing posterior probabilities of correct peptide identification in a targeted setting. Using two publicly available Q Exactive DIA datasets generated using HEK-293 cells and human liver microtissues, we demonstrate that DIA-Umpire can identify similar number of peptide ions, but with better identification reproducibility between replicates and samples, as with conventional data-dependent acquisition. We further demonstrate the utility of DIA-Umpire using a series of Orbitrap Fusion DIA experiments with HeLa cell lysates profiled using conventional data-dependent acquisition and using DIA with different isolation window widths.
Chronic 3-Nitropropionic Acid Treatment in Baboons Replicates the Cognitive and Motor Deficits of Huntington’s Disease (1996)

We showed recently that chronic administration of the mitochondrial inhibitor 3-nitropropionic acid (3NP) in primates produces various dyskinetic movements and dystonic postures associated with selective striatal lesions displaying many similarities with the pathological features of Huntington's disease (HD). In the present study, we examined whether such a toxic treatment could also induce frontal-type deficits similar to those observed in HD patients. Cognitive performances of 3NP-treated and control baboons were compared using the object retrieval detour task (ORDT), a test designed to assess the functional integrity of the frontostriatal pathway in human and nonhuman primates. During the same time, the motor function of each animal was assessed under spontaneous "no drug" conditions, and time-sampled neurological observations were used after apomorphine administration. A significant impairment in the ORDT was observed in the 3NP animals after 3-6 weeks of treatment, occurring in the absence of spontaneous abnormal movements by in the presence of apomorphine-inducible dyskinesias. Prolonged 3NP treatment resulted in the progressive appearance of spontaneous abnormal movements. Histological evaluation of these animals showed selective bilateral caudate-putamen lesions with sparing of the cerebral cortex, notably the prefrontal cortex. The present study demonstrates that chronic 3NP treatment replicates in primates the basic pathophysiological triad of HD, including spontaneous abnormal movements, progressive striatal degeneration, and a frontostriatal syndrome of cognitive impairment.
Detecting Linguistic Characteristics of Alzheimer’s Dementia by Interpreting Neural Models (2018)

Sweta Karlekar, Tong Niu, Mohit Bansal. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 2 (Short Papers). 2018.
Isotopic Variations in Meteoric Waters (1961)

The relationship between deuterium and oxygen-18 concentrations in natural meteoric waters from many parts of the world has been determined with a mass spectrometer. The isotopic enrichments, relative to ocean water, display a linear correlation over the entire range for waters which have not undergone excessive evaporation.
[Effects of murine bone marrow endothelial cell conditioned medium on the growth of yolk sac hematopoietic stem cells and progenitors]. (2002)

Murine bone marrow endothelial cell conditioned medium could support the growth and proliferation of yolk sac hematopoitic stem cells and progenitors, and this promoting effect was further enhanced by addition of FL and TPO.
Asymmetric Hubbard Model and Mott Metal-Insulator Transition (2004)

Starting from the standard Hubbard model, this paper obtained an asymmetric Hamiltonian for the half-filled strongly correlated system by ignoring the jumping of electrons with spin-σ between lattice sites when the motion of electrons with spin σ is considered. The mean field approximation is applied to get the quasi-particle spectrum of the Hamiltonian. The results at zero-temperature and finite temperature are analyzed,the possibility and critical temperature of Mott metal-insulator transition is also investigated.
Antifouling coatings for optoelectronic tweezers (2009)

Optoelectronic tweezers enables parallel manipulation of individual single cells using optical addressing and optically induced dielectrophoretic force. This provides a useful platform for performing a variety of biological functions, such as cell manipulation, cell sorting, and cell electroporation. However, in order to obtain more reliable cellular manipulation, especially of adherent mammalian cells, antifouling coatings need to be used to avoid non-specific cell adherence. Two antifouling coatings are discussed here, which can reduce the amount of non-specific adherence by as much as a factor of 30.
Nanoparticle-doped large area PMMA plates with controlled optical diffusion (2013)

Large-area nanocomposite plates (35 cm × 35 cm × 1 cm) with tuned optical diffusion were successfully prepared. The poly(methyl-methacrylate) matrix is synthesized by bulk polymerization, and “doped” with some ppm of commercial TiO2 nanoparticles. These are surface modified with 1-octylphosphonic acid in order to stabilize them in the monomer, as shown by repeated Dynamic Light Scattering measurements over long times. TEM images show that the dispersed TiO2 nanoparticles are aggregated in irregular and porous clusters of about 100 nm in diameter. The size of these aggregates is also confirmed by UV-visible transmission measurements. TEM images of slices prepared from plates confirm that the nanoparticles do not further aggregate during bulk polymerization. Optical diffusion could be characterized in detail, thanks to the large size of the nanocomposites, by using a home-made optical set-up. This allowed the observation of a number of subtle optical effects related to multiple-scattering, and the direct observation of a ‘blue sky effect’ associated with the small size of the nanoparticles involved in diffusion.
Effect of pre-curing process on epoxy resin foaming using carbon dioxide as blowing agent (2016)

A thermosetting epoxy resin system consisting of diglycidylether of bisphenol A (DGEBA) and m-xylylenediamine (MXDA) was successfully foamed by carbon dioxide (CO 2 ) using two-step batch process. Isothermal curing kinetics of epoxy system was developed to help control the pre-curing degree of resin under different pre-curing conditions. Samples with different pre-curing degrees were prepared and then foamed via temperature-rising foaming process. It was found that the pre-curing degree was a crucial index for the foamability of epoxy resin. The effects of pre-curing conditions on curing reaction as well as further foaming results were investigated, and the results showed that the pre-curing degree from 37.7% to 46.3% was the proper foaming range for the chosen epoxy resin. With increasing pre-curing degrees from 37.7% to 51.6%, viscosity and elasticity of pre-cured resins increased, and correspondingly, average cell size of epoxy foams decreased from 329.8 µm to 60.8 µm while cell density increased from 1.4 × 10 5 cells/cm 3 to 8.6 × 10 5 cells/cm 3 . Furthermore, the foamed samples with the same pre-curing degree had similar cell morphology regardless of pre-curing conditions.
Use of a surface-acoustic-wave delay line to provide pseudocoherence in a clutter-reference pulse Doppler radar (1973)

A surface-acoustic-wave delay line has been used to provide a coherent reference signal in a small-pulse Doppler radar. Preliminary experiments using the device gave a 10–12 dB gain in Doppler signal when compared with a clutter reference system operating in a low-clutter environment. A simple theory is given which describes expected performance when using noncoherent detection.
Enhanced Clustering Analysis And Visualization Using Kohonen'S Self-Organizing Feature Map Networks (2008)

Cluster analysis is the name given to a diverse collection of techniques that can be used to classify objects (e.g. individuals, quadrats, species etc). While Kohonen's Self-Organizing Feature Map (SOFM) or Self-Organizing Map (SOM) networks have been successfully applied as a classification tool to various problem domains, including speech recognition, image data compression, image or character recognition, robot control and medical diagnosis, its potential as a robust substitute for clustering analysis remains relatively unresearched. SOM networks combine competitive learning with dimensionality reduction by smoothing the clusters with respect to an a priori grid and provide a powerful tool for data visualization. In this paper, SOM is used for creating a toroidal mapping of two-dimensional lattice to perform cluster analysis on results of a chemical analysis of wines produced in the same region in Italy but derived from three different cultivators, referred to as the “wine recognition data" located in the University of California-Irvine database. The results are encouraging and it is believed that SOM would make an appealing and powerful decision-support system tool for clustering tasks and for data visualization.
Enhanced Reliability of Photovoltaic Systems with Energy Storage and Controls (2008)

This report summarizes efforts to reconfigure loads during outages to allow individual customers the opportunity to enhance the reliability of their electric service through the management of their loads, photovoltaics, and energy storage devices.
Viscous Flow of a Liquid Over a Rotating Surface With Gas Drag (1963)

Differential equations are set up to describe the viscous flow of a liquid on a rotating surface with a shear stress exerted by a flowing gas stream along the surface and normal to the radial direction. Such a problem is met in the low-pressure stages of a steam turbine. The equations are solved first for a uniform flux of liquid onto the surface along a radial boundary R > R0, where R is the radial position and R0 is constant. It is then shown that absence of liquid flowing in along the radial boundary for R < R0 casts what is called a “flow shadow” and that two solutions of the equations are required, one for the “shadow flow” and one for the “main flow” region. The solutions are extended to the case where the shear stress exerted by the gas varies in a manner described by a simple power function of the distance along the surface, x, normal to the radial direction. All these solutions can be represented on a single graph showing streamlines and the shadow boundary. In conclusion, it is demonstrated that the two solutions for the main and shadow flows are special cases of a more general solution in which flow in along the radial boundary at x = 0 varies as 1−R0R1/32
Induction of Labour with Prostaglandins E <sub>1</sub> and E <sub>2</sub> (1970)

The use of intravenous infusions of prostaglandin E (E(1) or E(2)) for the induction of labour was studied in 25 patients at or near term. Labour was successfully induced in 23 patients. The pattern of uterine motility produced resembled that of normal labour. No hypertonus was recorded nor were there any undesirable side-effects.
ChemInform Abstract: Nanoalloys: From Theory to Applications of Alloy Clusters and Nanoparticles (2008)

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 of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Enhanced Catalytic Activity toward O<sub>2</sub> Reduction on Pt-Modified La<sub>1–<i>x</i></sub>Sr<sub><i>x</i></sub>Co<sub>1–<i>y</i></sub>Fe<sub><i>y</i></sub>O<sub>3−δ</sub> Cathode: A Combination Study of First-Principles Calculation and Experiment (2014)

Using the first-principles calculation and the electronic conductivity relaxation (ECR) experimental technique, we investigated the adsorption and dissociation behaviors of O2 on Pt-modified La0.625Sr0.375Co0.25Fe0.75O3−δ (LSCF) surface. Toward the O2 reduction, the calculation results show that the perfect LSCF (100) surface is catalytically less active than both the defective (100) surface and the perfect (110) surface. O2 molecule can weakly adsorb on the perfect LSCF (100) surface with a small adsorption energy of about −0.30 eV, but the dissociation energy barrier of the O2 molecule is about 1.33–1.43 eV. Doping of Pt cluster on the LSCF (100) surface can remarkably enhance its catalytic activity. The adsorption energies of O2 molecules become −1.16 and −1.89 eV for the interfacial Feint site and the Ptbri bridge site of Pt4-cluster, respectively. Meanwhile, the dissociation energy barriers are reduced to 0.37 and 0.53 eV, respectively. The migration energy barrier of the dissociated oxygen from the interfacial Pt to the LSCF surface is 0.66 eV, and it is 2.58 eV from the top site of the Pt cluster to the interfacial Pt site, suggesting that it is extremely difficult for oxygen to migrate over the Pt cluster. The Bader charge analysis results further indicate that the charges transferring from Pt cluster to LSCF surface promote the adsorption and dissociation of O2 molecules. Experimentally, a dramatic decrease of the surface oxygen exchange relaxation time was observed on Pt-modified LSCF cathode, with a chemical surface exchange coefficient increased from 6.05 × 10–5 cm/s of the bare LSCF cathode to 4.04 × 10–4 cm/s of the Pt-modified LSCF cathode, agreeing very well with our theoretical predictions.
Locating and Isolating DC Faults in Multi-Terminal DC Systems (2007)

A VSC-MTDC (multi-terminal dc) system consists of voltage-source converters (VSCs) connected to a dc network at their dc terminals. The MTDC is most vulnerable to a dc fault which paralyses all the VSCs until the dc fault is cleared. As dc circuit breakers are expensive, this paper proposes a solution based on extinguishing the dc fault current by opening all the ac-circuit breakers (ac-CBs) which the VSCs are already equipped with on the ac-sides. However, it is necessary to identify which dc line is the faulted line (in case it is a permanent fault) so that it can be isolated by fast dc switches (which are much more economical than the dc circuit breakers), prior to restoring the MTDC system by re-closing all the ac-CBs. This paper presents the handshaking method, which locates and isolates the faulted dc line and restores the MTDC without telecommunication.
Molecular Scale Behavior in Alternative Propellant-Based Inhaler Formulations (2006)

Traditional pressurized metered dose inhaler (pMDI) formulations contain a drug either in solution or in suspension in a compressed propellant (1). Excipients commonly found in pMDIs include surfactants, which are used for valve lubrication and/or as stabilizers, and cosolvents that serve as aids in the solubilization of amphiphiles (2,3). Several alternative propellant-based inhaler formulations have been recently proposed (4). To a large extent, these novel formulations came as a response to difficulties encountered in transitioning from chlorofluorocarbon (CFC) to hydrofluoroalkane (HFA) propellants, as dictated by the Montreal Protocol. These alternatives to solution and (micronized) dispersion-based pMDIs also provide unique opportunities for the local and systemic delivery of biomolecules to and through the lungs (5). Such advances may give propellant-based inhaler formulations the necessary edge to compete with recent developments in dry powder inhaler (DPI) technology (6).
Automated mass spectrometry imaging with a matrix-assisted laser desorption ionization time-of-flight instrument (1999)

The automated use of a matrix-assisted laser desorption ionization (MALDI) mass spectrometer (MS) is described for image analysis of samples through implementation of new software for instrument control, data acquisition, and data analysis. The software permits automated acquisition of MS MALDI spectra to form an ordered data array and contains display features to provide images at one or more mass-to-charge ratio values. The technique can be used to scan tissue samples, blotted samples, gels, or other sample surfaces where the image analysis of that sample is required. The program achieves a time of typically 1 s per image point, permitting an analysis made up of large numbers of points with high spatial resolution up to 850 dpi. The features of the software are demonstrated in this paper with samples of printed images, where visible images can be compared to those obtained by mass spectrometry. Quantitative aspects are introduced by analyzing a series of sample spots containing different amounts of several proteins.
Wheat dwarf virus vectors replicate and express foreign genes in cells of monocotyledonous plants. (1991)

Wheat dwarf virus (WDV) is a geminivirus that infects monocotyledonous plants. To exploit the potential of WDV as a replicative gene vector, we developed a transient replication and expression system based on the transfection of protoplasts derived from Triticum monococcum suspension culture cells. Cloned genomic copies of various WDV isolates as well as mutants constructed in vitro were introduced into the protoplasts and assayed for their ability to replicate. As a result, regions of the WDV genome necessary or dispensable for the viral DNA replication could be defined. In addition, the gene encoding the viral capsid protein was replaced by three different bacterial marker genes, neomycin phosphotransferase, chloramphenicol acetyltransferase, and beta-galactosidase. The beta-galactosidase gene doubled the size of the WDV genome. The replication of the recombinant WDV genomes and the expression of these genes were monitored in suspension culture cells of T. monococcum. The potential of replicative expression vectors based on the WDV genome is discussed.
Synthesis, Characterization, and Biological Activity of Polyanion-cis-diammineplatinum(II) Complexes as Antitumor Agents (1992)

Polyanion-cis-diammineplatinum(II) complexes were synthesized by the reaction of cis-[Pt(NH 3 ) 2 (OH 2 ) 2 ](NO 3 ) 2 with the polyanions containing vic- dicarboxylate ions along the polymer chain. The eleven polyanions used for this synthesis were the hydrolysis products of polymers obtained by radical alternating copolymerizations of maleic anhydride with dihydropyran deriva tives. For example, poly[(tetrahydropyran-5,6-diyl)(1,2-dicarboxyethylene)] de rivatives were synthesized, which contained substituents, such as hydroxy, methoxy, ethoxy, acetoxy, methoxycarbonyl and acetoxymethyl groups, on the 2, 3 and 4-positions of the tetrahydropyran ring. The complex formation of cis diammineplatinum(II) with vic-dicarboxylate groups was confirmed by the absorption at 1350 cm -1 for γ s (CO) coordinated with Pt(II). By changing the mole ratios of the reactants, the platinum content in the polyanion complexes can be controlled and every 5-15 repeating units of the polymers were found to contain one cis-diammineplatinum(II). The biological activity of the poly anion-Pt complexes as measured in vitro against A-549 nonsmall cell lung, SK-OV-3 ovarian, HCT-15 colon, XF-498 CNS and L1210 leukemia. After select ing active complexes, the increased life spans were measured against L1210 and found to be 244, 143 and 178% for the complexes (8), (13) and (16), respec tively.
MQTT Quality of Service versus Energy Consumption (2019)

IoT today invented for creating, editing and sharing information and data. Some sources predict the number of tens and hundreds billion connected devices for the year 2020-2025. One of the most popular standard machine-to-machine application layer protocols to interconnect the things and applications to the Internet of Things is Message Queuing Telemetry Transport protocol. Quality of service (QoS) deal with network performance elements like latency, error rate and uptime. MQTT provides three levels of QoS. Usage time of IoT devices is constrained by its most critical resource - battery. This paper deals with the estimation of energy consumption in transferring data using lightweight MQTT protocol over it different QoS levels. For experiments, we implemented client-server architecture and employ MQTT publish/subscribe protocol to transfer data between nodes.
Highly enhanced fluorescence of fluorophores inside a metallic nanocavity (2011)

Here we report the observation of significantly enhanced fluorescence from molecules placed inside a silver nanocavity, as compared to those without the silver coating.
Assessment of off-state negative gate voltage requirements for IGBTs (1998)

This paper addresses the need for off-state negative gate bias with insulated gate bipolar transistor (IGBT) devices that experience a dv/dt when in the off state. Factors considered include off-state gate bias voltage, gate impedance, reapplied dv/dt, and temperature. Theoretical calculation and experimental results for a high-voltage high-current IGBT supports the assessment of these factors.
The L/sub 2/-polynomial spline pyramid (1993)

The authors are concerned with the derivation of general methods for the L/sub 2/ approximation of signals by polynomial splines. The main result is that the expansion coefficients of the approximation are obtained by linear filtering and sampling. The authors apply those results to construct a L/sub 2/ polynomial spline pyramid that is a parametric multiresolution representation of a signal. This hierarchical data structure is generated by repeated application of a REDUCE function (prefilter and down-sampler). A complementary EXPAND function (up-sampler and post-filter) allows a finer resolution mapping of any coarser level of the pyramid. Four equivalent representations of this pyramid are considered, and the corresponding REDUCE and EXPAND filters are determined explicitly for polynomial splines of any order n (odd). Some image processing examples are presented. It is demonstrated that the performance of the Laplacian pyramid can be improved significantly by using a modified EXPAND function associated with the dual representation of a cubic spline pyramid.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Reactive Compatibilization of Polycarbonate and Poly(methyl methacrylate) in the Presence of a Novel Transesterification Catalyst SnCl<sub>2</sub>·2H<sub>2</sub>O (2011)

We compare the effectiveness of various known organometallic transesterification catalysts with a novel SnCl(2)·2H(2)O transesterification catalyst in the formation of homogeneous PC/PMMA blends with single T(g). It is shown that SnCl(2)·2H(2)O works more efficiently than the other organometallic transesterification catalysts. Even 0.1% (wt/wt) of SnCl(2)·2H(2)O is enough to establish an interaction between PC and PMMA phases, leading to the formation of a homogeneous PC/PMMA blend with single T(g) and single degradation temperature. FTIR, (1)H NMR, and XRD studies provide evidence of the formation of PC-g-PMMA graft copolymer, which acts as a compatibilizer between the PC and PMMA phases. A significant improvement in the optical transparency of the PC/10PMMA blend prepared using SnCl(2)·2H(2)O catalyst as compared with PC/10PMMA without any catalyst is observed. There is also a change in the morphology from granular in uncompatibilized blends to lamellar in the compatibilized blends.