gebhart/patrepeval huggingface dataset:
Liver proteomics. Methods and protocols. (2012)

1. Cell Surface Capturing (CSC) Technologies for the Surfaceome Discovery of Hepatocytes Damaris Bausch-Fluck, Hofmann Andreas, and Bernd Wollscheid 2. An On-Target Desalting and Concentration Sample Preparation Protocol for MALDI-MS and MS/MS Analysus Xumin Zhang, Quanhui Wang, Xiaomin Lou, Haidan Sun, Peter Roepstorff, and Siqi Liu 3. Plasma Membrane Isolation using Immobilized Concanavalin A Magnetic Beads Yu-Chen Lee, Martina Srajer Gajdoski, Djuro Josic, and Sue-Hwa Lin 4. Analysis of the Cattle Liver Proteome by High-sensitive Liquid Chromatography Coupled with Mass Spectrometry method Anna Maria Timperio, Gian Maria D'Amici, Lello Zolla 5. Producing a One-Dimensional Proteomic Map for Human Liver Cytochromes P450 Natalia A. Petushkova and Andrey V. Lisitsa 6. Assessing Heterogeneity of Peroxisomes-Isolation of Two Subpopulations from Rat Liver Markus Islinger, Afsaneh Abdolzade-Bavil, Sven Liebler, Gerhardt Weber, Alfred Volkl 7. Purification and Proteomic Analysis of Liver Membrane Skeletons Jintang He, Yashu Liu, Qingsong Wang and Jianguo Ji 8. Liver Plasma Membranes: An Effective Method to Analyze Membrane Proteome Rui Cao and Songping Liang 9. Quantitative analysis of liver Golgi Proteome in the Cell Cycle Xuequn Chen, Philip C. Andrews and Yanzhuang Wang 10. Glycoproteins and Glycosylation: Apolipoprotein C3 Glycoforms by top-down MALDI-TOF Mass Spectrometry Yan Zhang, Alan R. Sinaiko, Gary L. Nelsestuen 11. Phosphoproteomic Analysis of Liver Homogenates Gokhan Demirkan, Arthur R. Salomon, and Philip A. Gruppuso 12. A Combination of Affinity Chromatography, 2D DIGE and Mass Spectrometry to Analyze the Phosphoproteome of Liver Progenitor Cells Enrique Santamaria, Virginia Sanchez-Quiles, Joaquin Fernandez-Irigoyen and Fernando J. Corrales 13. Identifying Acetylated Proteins in Mitosis Eva Rodriguez-Suarez, Jose M. Mato, and Felix Elortza 14. Comparative Proteome Analysis of a Human Liver Cell Line Stably Transfected with Hepatitis D Virus Full-length cDNA Celso Cunha and Ana V. Coelho 15. Identification of New Autoimmune Hepatitis-specific Autoantigens by using Protein Microarray Technology Lin Wu, and Guang Song 16. Proteomics Analysis of Human Non-alcoholic Fatty Liver Eva Rodriguez-Suarez, Jose M. Mato and Felix Elortza 17. Proteomic Methods for Biomarker Discovery in a Rat Model of Alcohol Steatosis Billy W. Newton, William K. Russell, David H. Russell, Shashi K. Ramaiah, and Arul Jayaraman 18. Targeted Mass Spectrometry-based Metabolomic Profiling through Multiple Reaction Monitoring of Liver and other Biological Matrices Angelo D'Alessandro, Federica Gevi,, Lello Zolla 19. Discovery of Lamin B1 and Vimentin as Circulating Biomarkers for Early Hepatocellular Carcinoma Kwong-Fai Won and John M. Luk 20. Combinatorial Peptide Ligand Libraries to Discover Liver Disease Biomarkers in Plasma Samples Gian Maria D'Amici, Anna Maria Timperio, Sara Rinalducci, Lello Zolla 21. Isolation of Urinary Exosomes from Animal Models to Unravel Non-invasive Disease Biomarkers Javier Conde-Vancells and Juan M. Falcon-Perez
Self‐Assembly of the Cephalopod Protein Reflectin (2016)

Films from the cephalopod protein reflectin demonstrate multifaceted functionality as infrared camouflage coatings, proton transport media, and substrates for growth of neural stem cells. A detailed study of the in vitro formation, structural characteristics, and stimulus response of such films is presented. The reported observations hold implications for the design and development of advanced cephalopod-inspired functional materials.
Experimental investigation of polarisation rotation insemiconductor optical amplifiers (2004)

An experimental study of polarisation rotation in a semiconductor optical amplifier is
presented. Two techniques are used to investigate the gain and birefringence along the two
eigenmodes of the component waveguide, with and without injection. The first investigation is
based on the residual reflectivity of the facet mirrors. From the modulation depth of polarisation
resolved spectra, the gain and the refractive indices of these modes are determined. The second
investigation takes into account the variation of the eigenmode gain and refractive indices as a
function of injected power over the range 83.3 to 413 mW. The results of these two experiments are
compared, and it is determined that the refractive index and the single-pass gain along the
horizontal axis of the waveguide are higher than those along the vertical axis. Both gain and
refractive index differences increase as a function of injected power in the sample under test.
Furthermore, it is concluded that polarisation rotation in this component is heavily influenced by the
power dependence of the relative gain in the TE and TM modes and birefringence.
Faber approximation to the Mori-Zwazing equation (2017)

We develop a new effective approximation of the Mori-Zwanzig equation based on operator series expansions of the orthogonal dynamics propagator. In particular, we study the Faber series, which yields asymptotically optimal approximations converging at least $R$-superlinearly with the polynomial order for linear dynamical systems. We provide a through theoretical analysis of the new method and present numerical applications to random wave propagation and harmonic chains of oscillators interacting on the Bethe lattice and on graphs with arbitrary topology.
Carbohydrate‐active enzymes revealed in Coptotermes formosanus (Isoptera: Rhinotermitidae) transcriptome (2012)

Coptotermes formosanus is one of the most destructive wood-feeding termites. To understand the molecular mechanisms that regulate the development of the termite, a normalized C. formosanus cDNA library was constructed using mixed RNA isolated from workers, soldiers, nymphs and alates of both sexes. The sequencing of this library generated 131 636 expressed sequence tags (ESTs) and 25 939 assembled unigenes. The carbohydrate-active enzymes (CAZymes) revealed in this library were analysed in the present report. A total of 509 putative CAZymes were identified. Diverse cellulolytic enzymes were uncovered from both the host termite and from symbionts harboured by the termite, which were possibly the result of the high efficiency of cellulose utilization. CAZymes associated with trehalose biosynthetic and metabolic pathways were also identified, which are potential regulators of the physiological activities of trehalose, an important insect blood sugar. Representative CAZyme coding genes in glycoside hydrolase family 1 (GH1) were quantitatively analysed. The results showed that the five GH1 β-glucosidase genes were expressed differentially among different castes and one of them was female alate-specific. Overall, the normalized EST library provides a comprehensive genetic resource of C. formosanus and will serve a diverse range of research areas. The CAZymes represent one of the repositories of enzymes useful for physiological studies and applications in sugar-based biofuel production.
[Time-frequency analysis of ventricular fibrillation and the effects of amiodarone]. (2007)

This study is to quantify time-varying dominant frequencies in electrocardiogram (ECG) during the ventricular fibrillation (VF). Orthogonal ECG (sagittal, x; transverse, y; and longitudinal, z) and the transvenous two-leads defibrillation systems were set in 19 dogs. Time-frequency analysis was used to assess changes in the dominant frequency within ECG recorded in dogs during trials of 10-30 s of VF. In 4 additional dogs, the dominant frequencies were compared during 10 s of VF before and after administration of amiodarone. Results showed that in the 427 trials of 10 s VF and 335 trials of 30 s VF, average variation in the dominant frequency was considerable, between +/- 12%-18%. The frequencies orthogonal ECG during 10 s VF were distributed symmetrically above and below the mean frequency like a normal distribution. In the 79 trials with administration of amiodarone during 10 s VF in all three ECG, the mean frequencies decreased from 6.5 (x), 7.4 (y) and 7.0 Hz (z) to 6.1, 6.4 and 6.3 Hz (P < 0.01), respectively, and the variation in dominant frequencies decreased from 1.18, 1.38 and 1.19 to 0.98, 1.11 and 1.02 Hz (P < 0.05) respectively. The results confirmed that the frequencies of 10-30 s VF in ECG vary considerably and continuously, and amiodarone decreases this variation.
Synthesis of 21‐(3‐Methylbutyl)cholest‐5‐ene‐3β,3′,25‐triol and 21‐(2‐Methylpropoxy)cholest‐5‐ene‐2′,3β,25‐triol, the First “Double Side Chain” Cholesterol Analogues (1997)

Abstract The 21‐(3‐hydroxy‐3‐methylbutyl)‐ and 21‐(2‐hydroxy‐2‐methylpropoxy)cholestane derivatives 3 and 5 , formally double chain hybrid (20 R )‐ and (20 S )‐cholesterol analogues, were synthesized. The C‐22 to C‐27 section of the 25‐hydroxycholestane side chain was established by stereoselective alkylation with 5‐bromo‐2‐methyl‐2‐(triethylsilyl)oxypentane of the pregnanoic ester 8 , derived from 3β‐acetoxyandrost‐5‐en‐17‐one ( 7 ). Reduction of the ester 9 to the 21‐alcohol 10 permitted elaboration of a second hydroxylated side chain, either via the tosylate 11 by alkynation/hydrogenation (yielding intermediate 13 ) or by alkylation of 10 with bromoacetate (yielding 14 ) followed by reaction with methyl magnesium bromide.
Comparative collector design in InGaAs and GaAsSb based InP DHBTs (2008)

In this paper we compare the base-collector transit time of GaAsSb- and InGaAs-based double heterojunction bipolar transistors (DHBT) at low and high collector current. Using a ldquotype IIrdquo base-collector heterostructure leads to a simpler design to increase the operating current range of the devices.
Correction to Gas Production from Methane Hydrate: A Laboratory Simulation of the Multistage Depressurization Test in Mallik, Northwest Territories, Canada (2017)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to Gas Production from Methane Hydrate: A Laboratory Simulation of the Multistage Depressurization Test in Mallik, Northwest Territories, CanadaKatja U. Heeschen*, Sven Abendroth, Mike Priegnitz, Erik Spangenberg, Jan Thaler, and Judith M. SchicksCite this: Energy Fuels 2017, 31, 2, 2106Publication Date (Web):January 30, 2017Publication History Published online30 January 2017Published inissue 16 February 2017https://doi.org/10.1021/acs.energyfuels.7b00051Copyright © 2017 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views446Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (689 KB) Get e-Alerts Get e-Alerts
Plans for utilizing the Cornell Electron Storage Ring as a test accelerator for ILC damping ring research and development (2007)

Beginning in April 2008, we propose to employ the Cornell electron storage ring (CESR) in a program of research and development for the international linear collider (ILC) Damping Rings (DR). This paper provides an update on the conceptual design issues for the CESR reconfiguration and details of the experimental program that will follow.
An Optimized Strategy for Small Files Storing and Accessing in HDFS (2017)

Nowadays, the most popular way of data storage is distributed storage and the most widespread cloud storage platform is HDFS. It successfully used by many notable companies since its excellent capability. Unfortunately, the original design of HDFS was to handle large files, when dealing with enormous quantity of small files, the situation is not very optimistic. To solve this problem, an optimized algorithm is introduced, it considers the size of small files when merging files into combine file, and generates map record for each small file. Meanwhile, we apply prefetching and caching mechanism to enhance the access efficiency. The experimental results show that the optimized strategy reduces the NameNode's memory and access time consumption, thus it can achieve better performance.
Laser optimisation for dispersion supported transmission systems (2005)

Ideal single-mode laser intrinsic parameters that optimise the performance of dispersion supported transmission (DST) systems are investigated. Laser parameter optimisation is performed to accomplish two goals: maximising the back-to-back sensitivity (BBS) and the total dispersion tolerance (TDT), with fixed laser bias and modulation currents, thus avoiding the usual DST laser current tailoring to the fibre length. Extensive numerical simulations reveal that significant improvement of DST system performance can be achieved by optimising simultaneous, independently and without restrictions, four laser intrinsic parameters; namely, linewidth enhancement factor (α), photon lifetime, gain parameter and gain compression factor (ɛ). The optimised laser shows good robustness of BBS and TDT to variations of those laser intrinsic parameters and a remarkable improvement in BBS and the TDT in comparison with the non-optimised DST system is achieved. It is shown that, to achieve the best DST performance at 20 Gbit/s using fixed laser currents, lasers with low α (α≃0.8) and high ɛ (ɛ≃10 × 10−23 m3) are required. The physical feasibility of the optimal laser intrinsic parameters is discussed from the standpoint of current laser technology. It is shown that a suboptimal set of laser intrinsic parameters consistent with strained multi-quantum well laser technology gives improved system performance.
Immunogenetic and microbial factors in acute anterior uveitis. (1997)

SpA represent the commonest underlying rheumatic disorders associated with acute anterior uveitis. The majority of patients with acute anterior uveitis possess HLA-B27 regardless of whether there is underlying SpA. Patients with acute anterior uveitis show increased frequency of anti-Yersinia antibodies compared with controls. Many of these antibodies appear to be directed against antigenic determinants shared among gram negative bacteria and thus cannot constitute definitive evidence for a causal role specifically for Yersinia in acute anterior uveitis. Acute anterior uveitis represents an interplay of host susceptibility and microbial triggers, as is the case for the SpA in general.
<title>Highly coherent high-energy high-order harmonic generation</title> (2001)

We demonstrated the generation of highly-coherent high-order harmonics and their energy scaling in the soft x-ray region using 30-fs Ti:sapphire laser pulses. By adjusting the gas density and the pump laser focusing, an output energy as high as 0.5 (mu) J was achieved with good spatial beam quality having a beam divergence of 2 mrad at the 27th harmonic (30 nm).
Modeling safety and security interdependencies with BDMP (Boolean logic Driven Markov Processes) (2010)

Safety and security issues are increasingly converging on the same critical systems, leading to new situations in which these closely interdependent notions should now be considered together. Indeed, the related requirements, technical and organizational measures can have various interactions and side-effects ranging from mutual reinforcements to complete antagonisms. A better characterization of these interdependencies is needed to ensure a controlled level of risk for the systems concerned by such a convergence. This paper describes the state of the art on this open issue and presents a new approach based on BDMP (Boolean logic Driven Markov Processes), allowing graphical modeling and advanced characterization of safety and security interdependencies. A simple use-case is used through diverse modeling variants, illustrating the capabilities, the contributions but also the limits with respect to other works dealing with safety and security interdependencies. We believe the proposed approach constitutes an original and valuable tool which could find its place in the ongoing research aiming at tackling this open and challenging task.
The temporal and extrastriatal D2/D3 receptor binding profile of aripiprazole in patients with schizophrenia (2007)

Grunder, Gerhard; Vernaleken, Ingo Bernd; Boy, Christian; Bröcheler, Anno; Fellows, Christine; Janouschek, Hildegard; Hellmann, Sandra Ulrike; Hiemke, Christoph; Bartenstein, Peter; Wong, Dean F.; Rösch, Frank; Büll, Udalrich
Hybrid superaggregate morphology as a result of aggregation in a cluster-dense aerosol (2006)

From the digitized pictures of soot clusters formed after the explosion of a hydrocarbon gas mixed with oxygen, the cluster morphology was determined by two different methods: structure factor and perimeter analysis. We find a hybrid, superaggregate morphology characterized by a fractal dimension of D approximately equal to 1.8 between the monomer size, ca. 50 nm, and 1 microm and D approximately equal to 2.6 at larger length scales up to approximately 10 microm. The superaggregate morphology is a consequence of late-stage aggregation in a cluster-dense regime near a gel point.
Acetylcholine receptors and myasthenia (2000)

Much progress has been made in the 26 years since initial studies of the first purified acetylcholine receptors (AChRs) led to the discovery that an antibody-mediated autoimmune response to AChRs causes the muscular weakness and fatigability characteristic of myasthenia gravis (MG) and its animal model, experimental autoimmune myasthenia gravis (EAMG). Now, the structure of muscle AChRs is much better known. Monoclonal antibodies to muscle AChRs, developed as model autoantibodies for studies of EAMG, were used for initial purifications of neuronal AChRs, and now many homologous subunits of neuronal nicotinic AChRs have been cloned. There is a basic understanding of the pathological mechanisms by which autoantibodies to AChRs impair neuromuscular transmission. Immunodiagnostic assays for MG are used routinely. Nonspecific approaches to immunosuppressive therapy have been refined. However, fundamental mysteries remain regarding what initiates and sustains the autoimmune response to muscle AChRs and how to specifically suppress this autoimmune response using a practical therapy. Many rare congenital myasthenic syndromes have been elegantly shown to result from mutations in muscle AChRs. These studies have provided insights into AChR structure and function as well as into the pathological mechanisms of these diseases. Evidence has been found for autoimmune responses even to some central nervous system neurotransmitter receptors, but only one neuronal AChR has so far been implicated in an autoimmune disease. Thus far, only two neuronal AChR mutations have been found to be associated with a rare form of epilepsy, but many more neuronal AChR mutations will probably be found to be associated with disease in the years ahead.
Proteome response at the edge of protein aggregation (2015)

Proteins adopt defined structures and are crucial to most cellular functions. Their misfolding and aggregation is associated with numerous degenerative human disorders such as type II diabetes, Huntington's or Alzheimer's diseases. Here, we aim to understand why cells promote the formation of protein foci. Comparison of two amyloid-β-peptide variants, mostly insoluble but differently recruited by the cell (inclusion body versus diffused), reveals small differences in cell fitness and proteome response. We suggest that the levels of oxidative stress act as a sensor to trigger protein recruitment into foci. Our data support a common cytoplasmic response being able to discern and react to the specific properties of polypeptides.
3D T2-weighted imaging to shorten multiparametric prostate MRI protocols (2017)

• 3D shows equivalent image quality and lesion delineation compared to 2D T2w. • 3D T2w and 2D T2w image acquisition demonstrated comparable diagnostic performance. • Using a single 3D T2w acquisition may shorten the protocol by 40%. • Combined with short DCE, multiparametric protocols of 10 min are feasible.
Effect of Cigarette Smoke on Autoimmunity in Murine and Human Systemic Lupus Erythematosus (2005)

Several studies have found that smoking cigarettes is a risk factor for systemic lupus erythematosus (SLE). To examine this issue in a mouse model, we subjected pre-autoimmune MRL-lpr/lpr mice for 4 weeks to cigarette smoke to provide standardized smoke effluents equivalent to moderate or to heavy smoking habits for people. The spontaneous production of IgG anti-chromatin but not IgM anti-chromatin, anti-denatured DNA, or rheumatoid factor antibodies was lower in mice exposed to 250 mg/m3 particulates from mainstream smoke, and this suppression of autoimmunity was sustained for 8 weeks (p < 0.02). In contrast to control mice anti-chromatin activity in smoke-exposed mice began to increase in 16-week-old mice, reaching levels at 6 months that were two- to three-fold higher than controls for IgG (p < 0.03) and 10-fold higher for IgM (p < 0.001). There was no significant effect on total IgG or IgM. In newly diagnosed SLE patients, smoking was negatively correlated with IgG anti-DNA antibodies (p < 0.03). However, of nine patients who discontinued smoking prior to diagnosis, eight had elevated IgG anti-DNA compared to 29/79 never smokers and 9/31 smokers (p < 0.01 compared to former smokers). Inhaled cigarette smoke appears to have a long-lasting immunosuppressive effect on T-cell-dependent autoimmune responses, although autoantibodies increase to supra-elevated levels after the suppressive effect has abated.
DeepCx: A transition-based approach for shallow semantic parsing with complex constructional triggers (2018)

This paper introduces the SURFACE CON-STRUCTION LABELING (SCL) task, which expands the coverage of Shallow Semantic Parsing (SSP) to include frames triggered by complex constructions. We present DeepCx, a neural, transition-based system for SCL. As a test case for the approach, we apply DeepCx to the task of tagging causal language in English, which relies on a wider variety of constructions than are typically addressed in SSP. We report substantial improvements over previous tagging efforts on a causal language dataset. We also propose ways DeepCx could be extended to still more difficult constructions and to other semantic domains once appropriate datasets become available.
Graduate Training in the Preparation and Presentation of Research Reports (1957)

Graduate Training in the Preparation and Presentation of Research Reports Get access P. W. Wilson P. W. Wilson Department of Bacteriology, University of Wisconsin Search for other works by this author on: Oxford Academic Google Scholar AIBS Bulletin, Volume 7, Issue 5, November 1957, Pages 22–24, https://doi.org/10.2307/1292442 Published: 01 November 1957