gebhart/patrepeval huggingface dataset:
Quantitative Assessment of Chromatin Immunoprecipitation Grade Antibodies Directed against Histone Modifications Reveals Patterns of Co-occurring Marks on Histone Protein Molecules (2012)

The defining step in most chromatin immunoprecipitation (ChIP) assays is the use of an antibody to enrich for a particular protein or histone modification state associated with segments of chromatin. The specificity of the antibody is critical to the interpretation of the experiment, yet this property is rarely reported. Here, we present a quantitative method using mass spectrometry to characterize the specificity of key histone H3 modification-targeting antibodies that have previously been used to characterize the "histone code." We further extend the use of these antibody reagents to the observation of long range correlations among disparate histone modifications. Using purified human histones representing the mixture of chromatin states present in living cells, we were able to quantify the degree of target enrichment and the specificity of several commonly used, commercially available ChIP grade antibodies. We found significant differences in enrichment efficiency among various reagents directed against four frequently studied chromatin marks: H3K4me2, H3K4me3, H3K9me3, and H3K27me3. For some antibodies, we also detected significant off target enrichment of alternate modifications at the same site (i.e., enrichment of H3K4me2 by an antibody directed against H3K4me3). Through cluster analysis, we were able to recognize patterns of co-enrichment of marks at different sites on the same histone protein. Surprisingly, these co-enrichments corresponded well to "canonical" chromatin states that are exemplary of activated and repressed regions of chromatin. Altogether, our findings suggest that 1) the results of ChIP experiments need to be evaluated with caution given the potential for cross-reactivity of the commonly used histone modification recognizing antibodies, 2) multiple marks with consistent biological interpretation exist on the same histone protein molecule, and 3) some components of the histone code may be transduced on single proteins in living cells.
Physiology and Morphology of Cells in the Ventral Nucleus of Trapezoid Body and Rostral Periolivary Regions of the Rat Superior Olivary Complex Studied in Slices (1996)

Intracellular recordings were obtained from cells in ventral and rostral zones of the rat superior olivary complex, using slice preparations. Cell morphology was studied by injecting the cells with biocytin. All cells exhibited regular discharge patterns to current injection through the recording microelectrode. In some cases, cells exhibited irregular discharge patterns at certain current strengths. It was postulated that such irregular discharge patterns might arise either from the behaviour of intrinsic membrane conductances or inhibitory inputs. Three distinct action potential shapes were identified and correlations with cell morphology suggest that these may correspond to three functional categories of neurones in these regions; efferents to the cochlea, efferents to cochlear nucleus and neurones involved in circuitry within the superior olivary complex. Many of the biocytin-filled cells exhibited axon collaterals forming local terminal arbors within the superior olivary complex. The major excitatory input from trapezoid fibres was shown to be glutamatergic and blockable by CNQX. Cells could also receive inhibitory input, although the precise origin and pharmacology of this input was not determined.
Effects of hydrophobic layers on evaporation from porous media (2008)

Early stages of evaporation from initially‐saturated porous media are marked by relatively high and constant evaporation rate (“stage 1”) supplied by capillary flow from the receding drying front to evaporating surface. At a characteristic front depth defined by pore size distribution, gravity exceeds capillary‐drive and interrupts liquid flow. Subsequently, evaporation falls to rates supported by vapor diffusion (“stage 2”). We investigated the role of thin hydrophobic layers on liquid phase continuity and on evaporative losses. Results confirm interruption of capillary flow by hydrophobic layers and overall reduction in evaporation mass loss. Persistence of capillary flow to the bottom of hydrophobic layer was evident by accumulation of dye tracer indicating formation of vaporization plane. Dye was not deposited on hydrophobic surfaces due to contact line configuration that promote evaporation away from pore walls. Evaporation flux across the hydrophobic layer was purely diffusive and proportional to diffusion length to the surface.
COMBINING TEXTURE SYNTHESIS AND DIFFUSION FOR IMAGE INPAINTING (2009)

Image inpainting or image completion consists in filling in the missing data of an image in a visually plausible way. Many works on this subject have been proposed these recent years. They can mainly be decomposed into two groups: geometric methods and texture synthesis methods. Texture synthesis methods work best with images containing only textures while geometric approaches are limited to smooth images containing strong edges. In this paper, we first present an extended state of the art. Then a new algorithm dedicated to both types of images is introduced. The basic idea is to decompose the original image into a structure and a texture image. Each of them is then filled in with some extensions of one of the best methods from the literature. A comparison with some existing methods on different natural images shows the strength of the proposed approach.
The compact torus (1981)

The objective of the compact torus approach is to provide toroidal magnetic-field configurations that are based primarily on plasma currents and can be freed from closely surrounding mechanical structures. Some familiar examples are the current-carrying plasma rings of reversed-field theta pinches and relativistic-electron ’’smoke ring’’ experiments. The spheromak concept adds an internal toroidal magnetic field component, in order to enhance MHD stability. In recent experiments, three different approaches have been used to generate spheromak plasmas: (1) the reversed-field theta pinch; (2) the coaxial plasma gun; (3) a new quasi-static method, based on the initial formation of a toroidal plasma sleeve around a mechanical ring that generates poloidal and toroidal fluxes, followed by field-line reconnection to form a detached spheromak plasma. The theoretical and experimental MHD stability results for the spheromak configuration are found to have common features.
Constrained control of Homogeneous Charge Compression Ignition (HCCI) engines (2010)

Homogeneous Charge Compression Ignition (HCCI) engines provide a possible solution for affordable, efficient and clean-burning power sources for either stationary power generator or advanced vehicles. In fact, HCCI engines integrate the advantages of both the spark ignition (SI) and compression ignition (CI) engines: (i) high fuel efficiency resulting from high compression ratio and rapid heat release and (ii) low NOx and low particulate matter (PM) emissions due to low cylinder peak temperature. Control of the HCCI engine, however, is difficult since its ignition cannot be directly actuated. The autoignition timing of HCCI combustion is determined by the cylinder charge conditions, rather than the spark timing or the fuel injection timing that are used to initiate combustion in SI and CI engines, respectively. Instead, controlled autoignition requires regulation of the charge properties, especially charge temperature, as demonstrated by many experimental results. Moreover, in order to realize the HCCI technology, several constraints in the system need to be considered. First, the combustion rate or cylinder pressure gradient should be constrained to avoid knocking. Since point-wise in time constraints in the combustion rate is needed constrained control will be necessary for the fuel and rebreathing lift commands. Second, the actuator constrains such as the limit range of the valve lift should also be explicitly take into account. For the purpose of model-based control development, we intend to first develop a HCCI engine model by extending a single cylinder HCCI engine model. The existence of a physics-based engine model, pointwise-in-time constraints and multiple actuators motivate the application of model-based optimization-control approaches such as Model Predictive Control (MPC). The model is used to predict the behavior of the system over a future horizon and an optimization-based methodology ensures optimal performance and satisfaction of constraints.
Relationship between Apparent Diffusion Coefficients at 3.0-T MR Imaging and Gleason Grade in Peripheral Zone Prostate Cancer (2011)

ADCs at 3.0 T showed an inverse relationship to Gleason grades in peripheral zone prostate cancer. A high discriminatory performance was achieved in the differentiation of low-, intermediate-, and high-grade cancer.
The separation of SEC curves of HDPE into flory distributions (1993)

Abstract A technique is reported here whereby molecular weight distribution curves from size exclusion chromatography (SEC) obtained on high‐density polyethylene (HDPE) can be deconvolved into a series of Flory‐distribution curves using a commercially available computer software system. Our analysis has shown that five to seven individual Flory distributions describe HDPE with better than a 99.9% degree of fit. We impute from this that upon taking proper precautions, we can consider these HDPE resins to be derived from at least this number of distinct catalyst sites and, furthermore, that modification of the sites will lead to a modification of the resultant resin. © 1993 John Wiley & Sons, Inc.
Well-width dependence of the excitonic lifetime in strained III-V quantum wells (1992)

The dependence of the excitonic lifetime on the well width in InGaAs/InP (unstrained), InGaAs/GaAs, and InGaAsP/InP strained quantum well heterostructures is investigated by time-resolved photoluminescence spectroscopy. We show that the main contribution to the lifetime variation comes from the change of the exciton binding energy. In the strained InGaAs/GaAs wells, the widest wells have a shorter lifetime than expected. We attribute this to the onset of plastic relaxation.
Privacy and emergency response in e-healthcare leveraging wireless body sensor networks (2010)

Electronic healthcare is becoming a vital part of our living environment and exhibits advantages over paper-based legacy systems. Privacy is the foremost concern of patients and the biggest impediment to e-healthcare deployment. In addressing privacy issues, conflicts from the functional requirements must be taken into account. One such requirement is efficient and effective response to medical emergencies. In this article, we provide detailed discussions on the privacy and security issues in e-healthcare systems and viable techniques for these issues. Furthermore, we demonstrate the design challenge in the fulfillment of conflicting goals through an exemplary scenario, where the wireless body sensor network is leveraged, and a sound solution is proposed to overcome the conflict.
HMG -CoA reductase: The active site lysine, the Sulfolobus solfataricus enzyme, and cloning of genes for two class II enzymes (1998)

In eukaryotes and archaea 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase catalyzes an early, rate-limiting reaction in isoprenoid biosynthesis that in humans is the target of drugs that reduce serum cholesterol levels. The only available crystal structure is that of the biodegradative enzyme from Pseudomonas mevalonii. This structure allowed the identification of an active site lysine, lysine 267. Mutation of lysine 267 to alanine, arginine, aspartate, histidine, or cysteine was accompanied by loss of detectable activity. Introduction of the non-naturally occurring amino acid aminoethylcysteine resulted in full recovery of activity. The future characterization of this modified enzyme will be important in the investigation of the role of lysine 267 in catalysis. In an attempt to identify in the enzyme from Syrian hamster the cognate residue of P. mevalonii lysine 267, lysines 690, 691, and 734 were mutated to alanine. While sequence alignments suggest lysine 734 as the active site lysine, the mutagenesis results did not allow the unequivocal assignment of the cognate residue. While the three mutant enzyme had detectable activity, all appeared impaired for catalysis with specific activities for enzymes K690A, K691A, and K734A of 0.2%, 1.6%, and 0.16% wild-type activity. Solution of a crystal structure of a biosynthetic HMG-CoA reductase would allow the identification of the active site lysine. The gene ( hmgA) for HMG-CoA reductase of the archaeon Sulfolobus solfataricus P2 was cloned and sequenced. S. solfataricus hmgA encodes a biosynthetic enzyme that was purified in 40% yield (specific activity 17.5 μU/mg at 50°C). The substrates are (S)-HMG-CoA (Km 17 μM) and NADPH (Km 23 μM). The enzyme was stable at 90°C and optimally active at pH 5.5 and 85°C. The thermostability of this enzyme makes it a good candidate for crystallization. Comparison of 50 sequences revealed two classes of HMG-CoA reductase. The catalytic domain of the human enzyme and the enzyme from P. mevalonii are proposed as canonical sequences for Class I and Class II HMG-CoA reductases, respectively. Only one Class II enzyme has previously been cloned, the biodegradative HMG-CoA reductase from P. mevalonii. Two new, apparently biosynthetic, Class II HMG-CoA reductase genes were cloned, from the eubacterium and Borrelia burgdorferi from the archaeon Archaeoglobus fulgidus.
Syntheses of core chain trisaccharides related to human blood group antigenic determinants (1982)

Trisaccharides related to the core chain of human blood group determinants were synthesized by way of the phthalimido-chloride method; namely, β-D-Galp-(1 → 3)-β-D-GlcNAcp-(1 → 6)-D-Galp (3), β-D-Galp-(1 → 3)-β-D-GlcNAcp-(1 → 3)-D-Galp (5), β-D-Galp-(1 → 4)-β-D-GlcNAcp-(1 → 6)-D-Galp (4), and β-D-Galp-(1 → 4)-β-D-GlcNAcp-(1 → 3)-D-Galp (6). The syntheses of the 8-methoxy-carbonyloctyl β-glycosides of these trisaccharides are also reported.
Reversible end-to-end assembly of gold nanorods using a disulfide-modified polypeptide (2008)

Directing the self-assembly of colloidal particles into nanostructures is of great interest in nanotechnology. Here, reversible end-to-end assembly of gold nanorods (GNR) is induced by pH-dependent changes in the secondary conformation of a disulfide-modified poly(L-glutamic acid) (SSPLGA). The disulfide anchoring group drives chemisorption of the polyacid onto the end of the gold nanorods in an ethanolic solution. A layer of poly(vinyl pyrrolidone) is adsorbed on the positively charged, surfactant-stabilized GNR to screen the surfactant bilayer charge and provide stability for dispersion of the GNR in ethanol. For comparison, irreversible end-to-end assembly using a bidentate ligand, namely 1,6-hexanedithiol, is also performed. Characterization of the modified GNR and its end-to-end linking behavior using SSPLGA and hexanedithiol is performed using dynamic light scattering (DLS), UV-vis absorption spectroscopy and transmission electron microscopy (TEM). Experimental results show that, in a colloidal solution of GNR-SSPLGA at a pH∼3.5, where the PLGA is in an α-helical conformation, the modified GNR self-assemble into one-dimensional nanostructures. The linking behavior can be reversed by increasing the pH (>8.5) to drive the conformation of the polypeptide to a random coil and this reversal with pH occurs rapidly within minutes. Cycling the pH multiple times between low and high pH values can be used to drive the formation of the nanostructures of the GNR and disperse them in solution.
Deep Dual Learning for Semantic Image Segmentation (2017)

Deep neural networks have advanced many computer vision tasks, because of their compelling capacities to learn from large amount of labeled data. However, their performances are not fully exploited in semantic image segmentation as the scale of training set is limited, where per-pixel labelmaps are expensive to obtain. To reduce labeling efforts, a natural solution is to collect additional images from Internet that are associated with image-level tags. Unlike existing works that treated labelmaps and tags as independent supervisions, we present a novel learning setting, namely dual image segmentation (DIS), which consists of two complementary learning problems that are jointly solved. One predicts labelmaps and tags from images, and the other reconstructs the images using the predicted labelmaps. DIS has three appealing properties. 1) Given an image with tags only, its labelmap can be inferred by leveraging the images and tags as constraints. The estimated labelmaps that capture accurate object classes and boundaries are used as ground truths in training to boost performance. 2) DIS is able to clean tags that have noises. 3) DIS significantly reduces the number of per-pixel annotations in training, while still achieves state-of-the-art performance. Extensive experiments demonstrate the effectiveness of DIS, which outperforms an existing best-performing baseline by 12.6% on Pascal VOC 2012 test set, without any post-processing such as CRF/MRF smoothing.
Dynamic control of the permanent magnet-assisted reluctance synchronous machine (2007)

A digital signal processor-based control system for the permanent magnet-assisted reluctance synchronous machine, with the emphasis on dynamic performance, is proposed. A classical design approach is used to design the current and speed controllers for the machine. The stator current of the machine is controlled in such a way that the current angle in the dq synchronous reference frame is constant. The load–torque is estimated using a state space observer and compensation current based on the estimated load is used to improve the dynamic performance of the drive. The control system design is machine specific as it relies on data from finite-element analysis. Simulated and measured results on a 110-kW power level show that the resulting control system is stable and robust with good dynamic performance.
Alkyl Fluorosilicates (1946)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkyl FluorosilicatesDonald F. Peppard, Weldon G. Brown, and Warren C. JohnsonCite this: J. Am. Chem. Soc. 1946, 68, 1, 76–77Publication Date (Print):January 1, 1946Publication History Published online1 May 2002Published inissue 1 January 1946https://pubs.acs.org/doi/10.1021/ja01205a024https://doi.org/10.1021/ja01205a024research-articleACS PublicationsRequest reuse permissionsArticle Views143Altmetric-Citations9LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A New Data-Reduction Algorithm for Real-Time ECG Analysis (1982)

Typically the ECG is sampled at a rate of 200 samples/s or more, producing a large amount of data that are difficult to store, analyze, and transmit. Data-reduction algorithms that operate in real time reduce he amount of data without losing the clinical information content. They must also leave sufficient computation time available for ECG analysis. We describe here a new algorithm called CORTES that is suited for such real-time applications. This algorithm combines the best features of two other techniques called TP and AZTEC. We present the results of a study to find optimal experimental values for the controlling variables in CORTES. We compare the computations of root-mean-square reconstruction errors for a diversity of encoded ECG signals.
Rapid and Long-Term Immunity Elicited by DNA-Encoded Antibody Prophylaxis and DNA Vaccination Against Chikungunya Virus (2016)

A DNA-based dMAb strategy induced rapid protection against an emerging viral infection. This method can be combined with DNA vaccination as a novel strategy to provide both short- and long-term protection against this emerging infectious disease. These studies have implications for pathogen treatment and control strategies.
Laser Scanning – Evolution of the Discipline (2009)

This chapter contains sections titled: A Brief History of Laser Development for Topographic Surveying The Theodolite and the EDM Review of Previous Developments Terrestrial Laser Scanning Case Studies Reflecting Evolution and Availability of Laser Surveying Technology Summary This Book - Laser Scanning for the Environmental Sciences References
A urease-negative mutant of Helicobacter pylori constructed by allelic exchange mutagenesis lacks the ability to colonize the nude mouse stomach (1994)

The urease of Helicobacter pylori has been proposed to be one of its pathogenic factors. A kanamycin resistance determinant was inserted in a cloned urease gene, and transformation-mediated allelic exchange mutagenesis was carried out to introduce the disrupted gene into the corresponding wild-type chromosomal region of a clinical isolate of H. pylori, CPY3401. The resulting mutant, HPT73, had the null activity of urease. Nude mouse stomachs were challenged with these two isogenic strains to examine the role of urease in pathogenesis. Gastritis was found in the CPY3401-challenged stomachs, from which bacteria indistinguishable from CPY3401 were recovered. There was no gastritis in the HPT73-challenged stomachs, and we could not recover H. pylori from them. These results indicated that H. pylori urease is essential for colonizing the nude mouse stomach.