gebhart/patrepeval huggingface dataset:
PyXlinkViewer: a flexible tool for visualisation of protein chemical crosslinking data within the PyMOL molecular graphics system (2020)

Abstract Chemical crosslinking-mass spectrometry (XL-MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL-MS data yields inter-residue restraints that can be compared with high-resolution structural data. Distances greater than the crosslinker spacer-arm can reveal lowly-populated “excited” states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of structural data. Despite increasing uptake of XL-MS, there are few tools to enable rapid and facile mapping of XL-MS data onto high-resolution structures or structural models. PyXlinkViewer is a user-friendly plugin for PyMOL v2 that maps intra-protein, inter-protein and dead-end crosslinks onto protein structures/models and automates the calculation of inter-residue distances for the detected crosslinks. This enables rapid visualisation of XL-MS data, assessment of whether a set of detected crosslinks is congruent with structural data, and easy production of high-quality images for publication.
Synthesis and crystal structure of 1,1′-bis{[4-(pyridin-2-yl)-1,2,3-triazol-1-yl]methyl}ferrocene, and its complexation with CuI (2020)

The title compound, [Fe(C<sub>13</sub>H<sub>11</sub>N<sub>4</sub>)<sub>2</sub>], was synthesized starting from 1,1'-ferro-cene-di-carb-oxy-lic acid in a three-step reaction sequence. The di-carb-oxy-lic acid was reduced to 1,1'-ferrocenedi-methanol using LiAlH<sub>4</sub> and subsequently converted to 1,1'-bis-(azido-meth-yl)ferrocene in the presence of NaN<sub>3</sub>. The diazide was treated with 2-ethynyl-pyridine under 'click' conditions to give the title compound in 75% yield. The Fe<sup>II</sup> center lies on an inversion center in the crystal. The two pyridyl-triazole wings are oriented in an <i>anti</i> conformation and positioned <i>exo</i> from the Fe<sup>II</sup> center. In the solid state, the mol-ecules inter-act by C-H⋯N, C-H⋯π, and π-π inter-actions. The complexation of the ligand with [Cu(CH<sub>3</sub>CN)<sub>4</sub>](PF<sub>6</sub>) gives a tetra-nuclear dimeric complex.
ChemInform Abstract: The Total Synthesis of (+)‐Ionomycin. (1990)

Abstract The calcium complex (XVI) of the title polyether antibiotic is synthesized via aldol coupling of the fragments (VII) and (XIV).
&#x201C;Active flux&#x201D; orientation vector sensorless control of IPMSM (2008)

This paper presents a novel strategy for the vector control of IPMSM, without signal injection. The overall performance of the motion-sensorless control depends strongly on the accuracy of the rotor position and speed estimation. The proposed state observer is based on the concept of the ldquoactive fluxrdquo (or ldquotorque producing fluxrdquo), which ldquoturns all the salient-pole rotor ac machines into nonsalient-pole onesrdquo. As well as giving a detailed explanation of the concept, the paper demonstrates, through a wide range of experimental results, the effectiveness of the active flux observer under half full rated torque operating conditions in 2 rpm-1000 rpm speed range.
Emergency power supply using flywheel and doubly fed induction generator (2009)

An emergency power supply (EPS) using an induction generator with a fly-wheel energy storage is investigated. Two different exciting system for the wounded rotor winding have been investigated. The principles of the operation and experimental results are shown. The results of start-up and steady state condition indicate that the inverter rating of the doubly fed induction generator is reduced fairly.
Scientific Advances Made Possible by User Facilities (2006)

Research Article| February 01, 2006 Scientific Advances Made Possible by User Facilities Gordon E. Brown, Jr.; Gordon E. Brown, Jr. 1Department of Geological & Environmental Sciences, Stanford University, Stanford, CA 94305-2115, USA E-mail: gordon@pangea.stanford.edu2Stanford Synchrotron Radiation Laboratory, 2575 Sand Hill Road, MS 69, SLAC, Menlo Park, CA 94025, USA Search for other works by this author on: GSW Google Scholar Georges Calas; Georges Calas 3Institut de Minéralogie et de Physique des Milieux Condensés, UMR CNRS 7590, Universités de Paris 6 et 7, IPGP, 140 rue de Lourmel, 75015 Paris, France E-mail: calas@lmcp.jussieu.fr Search for other works by this author on: GSW Google Scholar Russell J. Hemley Russell J. Hemley 4Geophysical Laboratory, Carnegie Institution of Washington, 5251 Broad Branch Rd NW, Washington, DC 20015, USA E-mail: r.hemley@gl.ciw.edu Search for other works by this author on: GSW Google Scholar Elements (2006) 2 (1): 23–30. https://doi.org/10.2113/gselements.2.1.23 Article history first online: 09 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation Gordon E. Brown, Georges Calas, Russell J. Hemley; Scientific Advances Made Possible by User Facilities. Elements 2006;; 2 (1): 23–30. doi: https://doi.org/10.2113/gselements.2.1.23 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyElements Search Advanced Search Abstract National scientific user facilities are becoming increasingly available to many different scientific communities in a number of countries. There is a growing use of these facilities by Earth and environmental scientists to study a broad range of materials and processes under realistic P-T and environmental conditions at unprecedented levels of energy and spatial resolution and elemental and isotopic sensitivity. The results of these studies are providing new insights into biogeochemical processes operating at Earth's surface as well as petrological, geochemical, and geophysical processes in Earth's interior. The availability of national user facilities is changing scientific approaches and is leading to multidisciplinary studies that were not possible a decade ago. You do not have access to this content, please speak to your institutional administrator if you feel you should have access.
Expression of GTPase-deficient G alpha 16 inhibits Swiss 3T3 cell growth (1994)

Expression of the GTPase-deficient G alpha 16 polypeptide G alpha 16Q212L, a member of the Gq family of heterotrimeric G proteins, constitutively activated phospholipase C beta activity in Swiss 3T3 cells. Expression of G alpha 16Q212L appears to persistently stimulte a low level of protein kinase C activity which also increases protein kinase A activity in Swiss 3T3 cells. Growth of G alpha 16Q212L expressing cells was significantly inhibited relative to wild-type Swiss 3T3 cells. Bombesin-stimulated DNA synthesis was completely inhibited in G alpha 16Q212L expressing clones, whereas the growth responses to platelet-derived growth factor (PDGF) and serum were inhibited 50-80% relative to wild-type cells. In addition to the inhibition of cell growth, G alpha 16Q212L expression significantly inhibited the stimulation of protein kinase C, Raf-1, MEK, mitogen-activated protein kinase, phospholipase A2 activity, and Ca2+ mobilization in response to PDGF. In contrast, PDGF receptor activation of phospholipase C gamma, phosphatidylinositol 3-kinase, and Ras GTP loading was similar in wild-type and G alpha 16Q212L expressing clones. PDGF regulation of membrane ruffling and actin fiber assembly, responses mediated in part by phosphatidylinositol 3-kinase, were unaffected in G alpha 16Q212L expressing clones. The growth inhibitory action of G alpha 16Q212L expression in Swiss 3T3 cells is downstream of the initial SH2 domain-encoded signal transduction proteins regulated in response to PDGF receptor autophosphorylation. The findings demonstrate that constitutively activated G alpha 16Q212L persistently activates phospholipase C activity and effectively inhibits a subset of cytoplasmic signal transduction pathways involved in growth factor tyrosine kinase receptor stimulation of cell growth. G16/Gq-regulated signal transduction can acutely stimulate specific response pathways involved in mitogenesis; but persistent activation of G16/Gq-regulated effectors, including phospholipase C beta, inhibit tyrosine kinase-initiated mitogenesis. One role for G16/Gq response systems may be to modulate growth factor receptor signaling.
Size effects in ultrathin epitaxial ferroelectric heterostructures (2004)

In this letter we report on the effect of thickness scaling in model PbZr0.2Ti0.8O3(PZT)∕SrRuO3 heterostructures. Although theoretical models for thickness scaling have been widely reported, direct quantitative experimental data for ultrathin perovskite (&amp;lt;10nm) films in the presence of real electrodes have still not been reported. In this letter we show a systematic quantitative experimental study of the thickness dependence of switched polarization in (001) epitaxial PZT films, 4to80nm thick. A preliminary model based on a modified Landau Ginzburg approach suggests that the nature of the electrostatics at the ferroelectric–electrode interface plays a significant role in the scaling of ferroelectric thin films.
Geiger-mode operation of back-illuminated GaN avalanche photodiodes (2007)

The authors report the Geiger-mode operation of back-illuminated GaN avalanche photodiodes. The devices were fabricated on transparent AlN templates specifically for back illumination in order to enhance hole-initiated multiplication. The spectral response in Geiger-mode operation was analyzed under low photon fluxes. Single photon detection capabilities were demonstrated in devices with areas ranging from 225to14063μm2. Single photon detection efficiency of 20% and dark count rate &amp;lt;10kHz were achieved in the smallest devices.
ChemInform Abstract: 3,4‐Dihydro‐2H‐pyrrole‐2‐carbonitriles: Useful Intermediates in the Synthesis of Fused Pyrroles and 2,2′‐Bipyrroles. (2016)

Abstract Diarylated cyanopyrrolines are subjected to the reaction with α‐bromo‐ω‐chloroalkanes and dichloroalkene (XI) under different conditions.
Metabolomic Data Processing, Analysis, and Interpretation Using MetaboAnalyst (2011)

MetaboAnalyst is a comprehensive, Web-based tool designed for processing, analyzing, and interpreting metabolomic data. It handles most of the common metabolomic data types including compound concentration lists, spectral bin lists, peak lists, and raw MS spectra. In addition to providing a variety of data processing and normalization procedures, MetaboAnalyst supports a number of data-analysis tasks using a range of univariate, multivariate, and machine-learning methods. MetaboAnalyst also offers two newly developed approaches-Metabolite Set Enrichment Analysis (MSEA) and Metabolic Pathway Analysis (MetPA)-for metabolomic data interpretation. MSEA helps detect biologically meaningful metabolite sets that have been enriched in human metabolomic studies, while MetPA allows users to identify any metabolic pathways that have been perturbed. MetaboAnalyst enables facile interactive exploration and visualization of nearly all of its results. At the end of each session, it produces a detailed analysis report with graphical, tabular, and textual output that summarizes each analytical method used and each result generated.
Fractionation of Oligomers from Pretreated Olive Tree Pruning and its Enzymatic Hydrolysis (2012)

Olive tree pruning is a suitable raw material for ethanol production, and also an interesting biomass to obtain high value-added products such as oligosaccharides and antioxidants. It can have a positive effect on both the integral use of this agricultural residue and the improvement of ethanol yields. The aim of this study is to characterize and enzymatically hydrolyze the liquid fraction released during the steam explosion pretreatment of olive tree pruning. Steam-exploded olive tree pruning biomass was pretreated under 190 ºC for 25 minutes in a 2 L reactor. The prehydrolysate obtained from the hydrothermal treatment was purified in a HiLoad 16/60 Superdex 30 prep grade column. The three fractions collected were analyzed by high liquid size exclusion chromatography. Fraction F1 shows a molecular weight distribution of oligomers up to 20000 Da, F2 from 400 to 6000 Da and F3 contained low molecular weight compounds, monosaccharides and compounds with molecular weight up to 600 Da. The enzymatic hydrolysis of each of the fractions has been carried out with specific enzymes to depolymerize larger oligomers (glucoamylase, xylanase, cellulase) and thus to produce its selective hydrolysis. The highest proportion of oligosaccharides is in the first fraction with 43.4 % followed by fraction 2 with 33.6 %. The rest consists of monosaccharides and sugars with low degree of polymerization. The addition of enzymes to fractions F1 and F2 produces the oligomers hydrolysis to glucose, xylose, xylobiose, xylotriose and DP4.
Survey of mechanical assistance of the circulation and the present status of left-heart bypass. (1966)

The various types of mechanical circulatory assistance which recently have been developed are described. The techniques which appear to be most promising for clinical application are: veno-arterial bypass with oxygenation, synchronous arterial assistance, and closed-chest left-heart bypass.The effects of a left ventricular bypass on central hemodynamics and the oxygen requirements of the left ventricle are described. A bypass of 90% of the left ventricular output brings about a 30% reduction in the left ventricular myocardial oxygen requirement. Left atrial pressure is reduced. The central aortic mean pressure, the pulmonary artery pressure, and the right atrial pressure are not changed.
Retinoic Acid Attenuates β-Amyloid Deposition and Rescues Memory Deficits in an Alzheimer's Disease Transgenic Mouse Model (2008)

Recent studies have revealed that disruption of vitamin A signaling observed in Alzheimer's disease (AD) leads to beta-amyloid (Abeta) accumulation and memory deficits in rodents. The aim of the present study was to evaluate the therapeutic effect of all-trans retinoic acid (ATRA), an active metabolite of vitamin A, on the neuropathology and deficits of spatial learning and memory in amyloid precursor protein (APP) and presenilin 1 (PS1) double-transgenic mice, a well established AD mouse model. Here we report a robust decrease in brain Abeta deposition and tau phosphorylation in the blinded study of APP/PS1 transgenic mice treated intraperitoneally for 8 weeks with ATRA (20 mg/kg, three times weekly, initiated when the mice were 5 months old). This was accompanied by a significant decrease in the APP phosphorylation and processing. The activity of cyclin-dependent kinase 5, a major kinase involved in both APP and tau phosphorylation, was markedly downregulated by ATRA treatment. The ATRA-treated APP/PS1 mice showed decreased activation of microglia and astrocytes, attenuated neuronal degeneration, and improved spatial learning and memory compared with the vehicle-treated APP/PS1 mice. These results support ATRA as an effective therapeutic agent for the prevention and treatment of AD.
Optical characterization of the self-limiting effect in flow-rate modulation epitaxy of V-shaped GaAs quantum wire (1999)

Photoluminescence is used to characterize the self-limiting effect observed during flow-rate modulation epitaxy (FME) of GaAs quantum wires (QWRs) on V-grooved substrate. Our study found that not only the central thickness but also the overall cross-sectional wire shape is maintained to an atomic level in the self-limited growth regions. This result suggests that the self-limited FME technique is a very promising method for an atomically controlled fabrication of high-quality QWRs.
Innovative passive yaw damper to increase the stability and curve-taking performance of high-speed railway vehicles (2022)

Yaw dampers are implemented on high-speed trains to reduce their tendency towards unstable movement (hunting) while running at high-speed. Although they have a positive influence on the vehicle’s stability, these devices impose a steering resistance action on the bogies while negotiating tight curves at low speed, and so standard passive devices must be designed taking conflicting objective functions into account. This paper presents an innovative yaw damper able to overcome this trade-off by introducing a passive solution able to modify this component’s working behaviour during different vehicle operating conditions. To quantify the efficacy of this solution, numerical models of innovative and standard dampers were developed and validated by means of experimental tests. Then, they were co-simulated with a multibody model of a real test case vehicle running under different operating conditions.
A Mineral Seed Coating for Control of Seedling Diseases of Alfalfa Suitable for Organic Production Systems (2014)

Most alfalfa seed is treated with the fungicide mefenoxam (Apron XL) for control of soilborne seedling diseases caused by Phytophthora medicaginis and Pythium spp. However, Apron XL is not active against Aphanomyces euteiches, the causal agent of Aphanomyces root rot (ARR), an important component of the alfalfa seedling root rot complex. Moreover, Apron XL-treated seed cannot be used in organic production systems. A seed coating using aluminosilicate (natural zeolite) at a rate of 0.33 g of zeolite per gram of alfalfa seed was tested as an alfalfa seed treatment. Inoculated growth chamber trials were conducted to determine the percentage of seedlings protected from Phytophthora root rot (PRR) and ARR. The mineral seed coating resulted in significantly greater control of PRR, with a mean of 89% healthy seedlings (disease score of 1 or 2 on a 1-to-5 scale) compared with the Apron XL treatment, with a mean of 38% healthy seedlings, or the control treatment, with 15% healthy seedlings. The mineral seed coating also resulted in significantly greater protection against ARR, with 67% healthy seedlings compared with 3 and 2% healthy seedlings with the Apron XL and control treatments, respectively. The coated seed were used for in vitro assays with Pythium ultimum and P. paroecandrum to test for protection from seed rot and damping off. The mineral seed coating resulted in a significantly greater percentage of healthy seedlings compared with the Apron XL and control treatments. In growth chamber assays with naturally infested field soils with a range of disease pressure, the mineral seed coating resulted in a similar or greater percentage of healthy plants than the Apron XL treatment. The mineral coating had no effect on in vitro growth of Sinorhizobium meliloti, and nodule numbers were similar on roots from mineral-coated and untreated seed. These experiments indicate that the zeolite seed coating is a promising means of controlling seedling diseases in alfalfa production systems.
Having concomitant asthma phenotypes is common and independently relates to poor lung function in NHANES 2007–2012 (2018)

A prevalent overlap of commonly reported asthma phenotypes was observed among asthma patients from the general population, with implications for objective asthma outcomes. A broader approach may be required to better characterize asthma patients and prevent poor asthma outcomes.
Automated Submicrometer Defect Detection During VLSI Circuit Production (1987)

Statistical monitoring and control procedures are essential components of VLSI manufacturing operations. Inspection of defects, measurement of critical dimensions and measurement of registration overlay are the traditional methods of monitoring and controlling a photolithography process. This paper will focus on one function of a fully automated inspection system being developed by OSI; the automated detection of defects on multilayer patterned wafers with textured thin films. A system architecture is described consisting of integrated mechanical, electrical, optical and software components that have been tailored to the inspection of semiconductor device micropatterns. A brief review of vision algorithms is presented along with a comparison of the template matching approach and a new method introduced by OSI. The discussion includes the effects of normal process variations and texture of device patterns on defect detection and false defect rates. Finally, the paper will describe the methods in which the data is analyzed and presented to production personnel to establish a rapid means of monitoring and controlling the photolithography process.
Retinoic acid-dependent eye morphogenesis is orchestrated by neural crest cells (2005)

Using genetic approaches in the mouse, we show that the primary target tissue of retinoic acid (RA) action during eye morphogenesis is not the retina nor the corneal ectoderm, which both express RA-synthesizing retinaldehyde dehydrogenases (RALDH1 and RALDH3), but the neural crest cell-derived periocular mesenchyme (POM), which is devoid of RALDH. In POM, the effects of the paracrine RA signal are mediated by the nuclear RA receptors heterodimers RXRalpha/RARbeta and RXRalpha/RARgamma. These heterodimers appear to control: (1) the remodeling of the POM through activation of Eya2-related apoptosis; (2) the expression of Foxc1 and Pitx2, which play crucial roles in anterior eye segment development; and (3) the growth of the ventral retina. We additionally show that RALDH1 and RALDH3 are the only enzymes that are required for RA synthesis in the eye region from E10.5 to E13.5, and that patterning of the dorsoventral axis of the retina does not require RA.
Composition and Immunochemical Properties of the Cell Surface Proteins of Vibrio cholerae (1986)

The composition and immunochemical properties of cell surface proteins of Vibrio cholerae belonging to both the biotypes (classical and El Tor) and the serotypes (Ogawa and Inaba) were investigated. Proteins were isolated by extraction with EDTA/NaCl. When the extract was further treated with sodium deoxycholate, a product significantly enriched with the major protein was obtained. The surface localization of these proteins was confirmed by immunoelectron microscopy using protein A-colloidal gold particles as probes. Antisera to these proteins possessed complement-mediated bactericidal activities towards V. cholerae strains belonging to both the biotypes and the serotypes, and upon crossed immunoelectrophoresis produced several immunoprecipitation reactions towards whole-cell sonicates belonging to all types of V. cholerae. These proteins were immunogenic in the rabbit intestine, as antibodies of two classes (IgG and IgA) were detected in the intestinal fluids. The intestinal immune response was greatly enhanced when cell surface proteins were administered with liposomes. These results suggest that cell surface proteins represent common antigens of V. cholerae and can be explored as vaccine candidates against cholera.
MutationFinder: a high-performance system for extracting point mutation mentions from text (2007)

http://bionlp.sourceforge.net.
AID: An Energy Efficient Decoding Scheme for LDPC Codes in Wireless Body Area Sensor Networks (2013)

One of the major challenges in Wireless Body Area Networks (WBANs) is to prolong the lifetime of network. Tra- ditional research work focuses on minimizing transmit power; however, in the case of short range communication the consumption power in decoding is significantly larger than transmit power. This paper investigates the minimization of total power consumption by reducing the decoding power consumption. For achieving a desired Bit Error Rate (BER), we introduce some fundamental results on the basis of iterative message-passing algorithms for Low Density Parity Check Code (LDPC). To reduce energy dissipation in decoder, LDPC based coded communications between sensors are considered. Moreover, we evaluate the performance of LDPC at different code rates and introduce Adaptive Itera- tive Decoding (AID) by exploiting threshold on the number of iterations for a certain BER (10−4). In iterative LDPC decoding, the total energy consumption of network is reduced by 20 - 25%.