gebhart/patrepeval huggingface dataset:
Isobaric Peptide Termini Labeling Utilizing Site-Specific N-Terminal Succinylation (2011)

Recently, we introduced a novel approach for protein quantification based on isobaric peptide termini labeling (IPTL). In IPTL, both peptide termini are dervatized in two separate chemical reactions with complementary isotopically labeled reagents to generate isobaric peptide pairs. Here, we describe a novel procedure for the two chemical reactions to enable a cost-effective and rapid method. We established a selective N-terminal peptide modification reaction using succinic anhydride. Dimethylation was used as second chemical reaction to derivatize lysine residues. Both reactions can be performed within 15 min in one pot, and micropurification of the peptides between the two reactions was not necessary. For data analysis, we developed the force-find algorithm in IsobariQ which searches for corresponding peaks to build up peak pairs in tandem mass spectrometry (MS/MS) spectra where Mascot could not identify opposite sequences. Utilizing force-find, the number of quantified proteins was improved by more than 50% in comparison to the standard data analysis in IsobariQ. This was applied to compare the proteome of HeLa cells incubated with S-trityl-l-cysteine (STLC) to induce mitotic arrest and apoptosis. More than 50 proteins were found to be quantitatively changed, and most of them were previously reported in other proteome analyses of apoptotic cells. Furthermore, we showed that the two complementary isotopic labels coelute during liquid chromatography (LC) separation and that the linearity of relative IPTL quantification is not affected by a complex protein background. Combining the optimized reactions for IPTL with the open source data analysis software IsobariQ including force-find, we present a straightforward and rapid approach for quantitative proteomics.
Flow channeling in a single fracture as a two‐dimensional strongly heterogeneous permeable medium (1989)

The void space of a rock fracture is conceptualized as a two‐dimensional heterogeneous system with variable apertures as a function of position in the fracture plane. The apertures are generated using geostatistical methods. Fluid flow is simulated with constant head boundary conditions on two opposite sides of the two‐dimensional flow region, with closed boundaries on the remaining two sides. The results show that the majority of flow tends to coalesce into certain preferred flow paths (channels) which offer the least resistance. Tracer transport is then simulated using a particle tracking method. The apertures along the paths taken by the tracer particles are found to obey a distribution different from that of all the apertures in the fracture. They obey a distribution with a larger mean and a smaller standard deviation. The shift in the distribution parameters increases with increasing values of variance for the apertures in the two‐dimensional fracture. Provided that the correlation length is no greater than one fifth of the scale of measurement, the aperture density distributions of tracer particle paths remain similar for flow in two orthogonal directions, even with anisotropy ratio of spatial correlation up to 5. These results may be applicable in general to flow and transport through a two‐dimensional strongly heterogeneous porous medium with a broad permeability distribution, where the dispersion of the system may be related to the parameters of the permeability distribution along preferred flow channels.
Production of Hydrogen by Steam Reforming of Glycerin on Ruthenium Catalyst (2005)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationProduction of Hydrogen by Steam Reforming of Glycerin on Ruthenium CatalystToshihide Hirai, Na-oki Ikenaga, Takanori Miyake, and Toshimitsu SuzukiView Author Information Department of Chemical Engineering, Faculty of Engineering, Kansai University, Suita, Osaka, 564-8680 Japan Cite this: Energy Fuels 2005, 19, 4, 1761–1762Publication Date (Web):June 16, 2005Publication History Received26 April 2005Revised27 May 2005Published online16 June 2005Published inissue 1 July 2005https://pubs.acs.org/doi/10.1021/ef050121qhttps://doi.org/10.1021/ef050121qrapid-communicationACS PublicationsCopyright © 2005 American Chemical SocietyRequest reuse permissionsArticle Views3039Altmetric-Citations223LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Catalysts,Lipids,Ruthenium,Water Get e-Alerts
Cigarette smoking affects oxidative protein folding in endoplasmic reticulum by modifying protein disulfide isomerase (2012)

The endoplasmic reticulum (ER) stress response (ERSR) and associated protein aggregation, is under investigation for its role in human diseases, including chronic obstructive pulmonary disease (COPD) where cigarette smoking (CS) is a risk factor for disease development. Our hypothesis states that CS-associated oxidative stress interferes with oxidative protein folding in the ER and elicits ERSR. We investigated ERSR induction following acute CS exposure and delineated mechanisms of CS-induced ERSR. Lung lysates from mice exposed or not to one cigarette were tested for activation of the ERSR. Up to 4-fold increase in phosphorylation of eIF2α and nuclear form of ATF6 was detected in CS-exposed animals. CS affected the formation of disulfide bonds through excessive posttranslational oxidation of protein disulfide isomerase (PDI). Increased amounts of complexes between PDI and its client proteins persisted in CS-exposed samples. BiP was not a constituent of these complexes, demonstrating the specificity of the early effects of CS exposure on ER. Disturbances in protein folding were accompanied by changes in the organization of ER network and ER exit sites. Our results provide evidence that ERSR is induced early in response to CS exposure and identifies the first known ER-resident target of CS PDI, demonstrating that CS affects oxidative protein folding.
Thermodynamic effects of active-site ligands on the reversible, partial unfolding of dodecameric glutamine synthetase from Escherichia coli: calorimetric studies (1992)

Dodecameric glutamine synthetase (GS) from Escherichia coli undergoes reversible, thermally induced partial unfolding without subunit dissociation. A single endotherm for Mn.GS (+/- active-site ligands) in the presence of 1 mM free Mn2+ and 100 mM KCl at pH 7 is observed by differential scanning calorimetry (DSC). Previous deconvolutions of DSC data for Mn.GS showed only two two-state transitions (with similar tm values; 51.6 +/- 2 degrees C), and indicated that cooperative interactions link partial unfolding reactions of all subunits within the Mn.enzyme dodecamer [Ginsburg, A., & Zolkiewski, M. (1991) Biochemistry 30, 9421]. A net uptake of 8.0 equiv of H+ by Mn.GS occurs during partial unfolding, as determined in the present DSC experiments conducted with four buffers having different heats of protonation at 50 degrees C. These data gave a value of 176 +/- 12 kcal (mol of dodecamer)-1 for delta Hcal corrected for buffer protonation. L-Glutamine and L-Met-(SR)-sulfoximine stabilize the Mn.GS dodecamer through the free energies of ligand binding, and these were shown to be partially and totally released, respectively, from the 12 active sites at high temperature. Ligand effects on Tm values from DSC were similar to those from spectral measurements of Trp and Tyr exposures in two subunit domains. Effects of varying [ADP] on DSC profiles of Mn.GS were complex; Tm is increased by low [ADP] and decreased by > 100 microM free ADP. This is due to the exposure of an additional low-affinity ADP binding site per GS subunit at high temperature with log K1' = 4.3 and log K2' = 3.6 at 60 degrees C relative to log K' = 5.5 for ADP binding at 30 degrees C, as determined by isothermal calorimetric and fluorescence titrations. Moreover, delta Hcal at > 27% saturation with ADP (corrected for ADP binding/dissociation) is approximately 80-100 kcal/mol more than in the absence of ligands. Changes in domain interactions could result from ADP bridging subunit contacts in the dodecamer. Each of the active-site ligands investigated here produces different effects on DSC profiles without uncoupling the extremely cooperative, partial unfolding reactions in the Mn.GS dodecamer.
A preliminary investigation of 3D preconditioned conjugate gradient reconstruction for cone-beam CT (2012)

Model-based iterative reconstruction (MBIR) methods based on maximum a posteriori (MAP) estimation have been recently introduced to multi-slice CT scanners. The model-based approach has shown promising image quality improvement with reduced radiation dose compared to conventional FBP methods, but the associated high computation cost limits its widespread use in clinical environments. Among the various choices of numerical algorithms to optimize the MAP cost function, simultaneous update methods such as the conjugate gradient (CG) method have a relatively high level of parallelism to take full advantage of a new generation of many-core computing hardware. With proper preconditioning techniques, fast convergence speeds of CG algorithms have been demonstrated in 3D emission and 2D transmission reconstruction. However, 3D transmission reconstruction using preconditioned conjugate gradient (PCG) has not been reported. Additional challenges in applying PCG in 3D CT reconstruction include the large size of clinical CT data, shift-variant and incomplete sampling, and complex regularization schemes to meet the diagnostic standard of image quality. In this paper, we present a ramp-filter based PCG algorithm for 3D CT MBIR. Convergence speeds of algorithms with and without using the preconditioner are compared.
A fatty acid desaturase modulates the activation of defense signaling pathways in plants (2001)

Salicylic acid (SA) plays an important role in activating various plant defense responses, including expression of the pathogenesis-related (PR) genes and systemic acquired resistance. A critical positive regulator of the SA signaling pathway in Arabidopsis is encoded by the NPR1 gene. However, there is growing evidence that NPR1-independent pathways can also activate PR expression and disease resistance. To elucidate the components associated with NPR1-independent defense signaling, we isolated a suppressor of the npr1-5 allele, designated ssi2. The recessive ssi2 mutation confers constitutive PR gene expression, spontaneous lesion formation, and enhanced resistance to Peronospora parasitica. In contrast, a subset of defense responses regulated by the jasmonic acid (JA) signaling pathway, including expression of the defensin gene PDF1.2 and resistance to Botrytis cinerea, is impaired in ssi2 plants. With the use of a map-based approach, the SSI2 gene was cloned and shown to encode a stearoyl-ACP desaturase (S-ACP DES). S-ACP DES is an archetypical member of a family of soluble fatty acid (FA) desaturases; these enzymes play an important role in regulating the overall level of desaturated FAs in the cell. The activity of mutant S-ACP DES enzyme was reduced 10-fold, resulting in elevation of the 18:0 FA content in ssi2 plants. Because reduced S-ACP DES activity leads to the induction of certain defense responses and the inhibition of others, we propose that a FA-derived signal modulates crosstalk between different defense signaling pathways.
Review of the Prerogative to Withdraw Passports in South Africa (1988)

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Synthesis and Conformational Study of Water‐Soluble, Rigid, Rodlike Oligopiperidines (2005)

An oligomeric backbone of piperidine rings can be synthesized by solution or solid-phase synthesis. These oligomers adopt well-defined, rodlike structures with all the piperidine residues in chair conformations (see picture) both in solution (D2O, CD3OD) and the solid state. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z502991_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
AND EGF RECEPTOR BLOCKADE (1996)

Simultaneous treatment ofxenografts of human A431 vulvar squamous carcinoma cells and MDA-468 breast adenoma cells with anti-EGF receptor monoclonal antibody (MAb) plus maximal tolerated doses of cisplatinum (cis-DDP) results in eradication of well-established tumors that are resistant to either therapy when administered alone. Hypotheses that could explain this synergistic antitumor activity are presented. We suggest that activation of dual checkpoints by the combination therapy results in cell death.
Adaptive Large Margin Training for Multilabel Classification (2011)

Multilabel classification is a central problem in many areas of data analysis, including text and multimedia categorization, where individual data objects need to be assigned multiple labels. A key challenge in these tasks is to learn a classifier that can properly exploit label correlations without requiring exponential enumeration of label subsets during training or testing. We investigate novel loss functions for multilabel training within a large margin framework---identifying a simple alternative that yields improved generalization while still allowing efficient training. We furthermore show how covariances between the label models can be learned simultaneously with the classification model itself, in a jointly convex formulation, without compromising scalability. The resulting combination yields state of the art accuracy in multilabel webpage classification.
Robust Face Landmark Estimation under Occlusion (2013)

Human faces captured in real-world conditions present large variations in shape and occlusions due to differences in pose, expression, use of accessories such as sunglasses and hats and interactions with objects (e.g. food). Current face landmark estimation approaches struggle under such conditions since they fail to provide a principled way of handling outliers. We propose a novel method, called Robust Cascaded Pose Regression (RCPR) which reduces exposure to outliers by detecting occlusions explicitly and using robust shape-indexed features. We show that RCPR improves on previous landmark estimation methods on three popular face datasets (LFPW, LFW and HELEN). We further explore RCPR's performance by introducing a novel face dataset focused on occlusion, composed of 1,007 faces presenting a wide range of occlusion patterns. RCPR reduces failure cases by half on all four datasets, at the same time as it detects face occlusions with a 80/40% precision/recall.
REVIEWS (1954)

Journal Article REVIEWS Get access The Fibres of Faith. By A. NORMAN ROLAND. Pp. 236. Independent Press. 10s. 6d. C. E. RAVEN C. E. RAVEN Search for other works by this author on: Oxford Academic Google Scholar The Journal of Theological Studies, Volume V, Issue 1, April 1954, Pages 144-b–145, https://doi.org/10.1093/jts/V.1.144-b Published: 01 April 1954
Transmission of images through highly nonlinear media by gradient-index lenses formed by incoherent solitons (2001)

We experimentally demonstrate image transmission through a noninstantaneous self-focusing medium. A partially spatially incoherent soliton is used to form a multimode waveguide in a photorefractive crystal, and the modes of that waveguide are used to transmit an incoherent image through this nonlinear medium.
Heterologous Production of Antimicrobial Peptides in <i>Propionibacterium freudenreichii</i> (2005)

Heterologous bacteriocin production in Propionibacterium freudenreichii is described. We developed an efficient system for DNA shuttling between Escherichia coli and P. freudenreichii using vector pAMT1. It is based on the P. freudenreichii rolling-circle replicating plasmid pLME108 and carries the cml(A)/cmx(A) chloramphenicol resistance marker. Introduction of the propionicin T1 structural gene (pctA) into pAMT1 under the control of the constitutive promoter (P4) yielded bacteriocin in amounts equal to those of the wild-type producer Propionibacterium thoenii 419. The P. freudenreichii clone showed propionicin T1 activity in coculture, killing 90% of sensitive bacteria within 48 h. The pamA gene from P. thoenii 419 encoding the protease-activated antimicrobial peptide (PAMP) was cloned and expressed in P. freudenreichii, resulting in secretion of the pro-PAMP protein. Like in the wild type, PAMP activation was dependent on externally added protease. Secretion of the antimicrobial peptide was obtained from a clone in which the pamA signal peptide and PAMP were fused in frame. The promoter region of pamA was identified by fusion of putative promoter fragments to the coding sequence of the pctA gene. The P4 and Ppamp promoters directed constitutive gene expression, and activity of both promoters was enhanced by elements upstream of the promoter core region.
La acción de tutela en Colombia (2000)

Pseudomyogenic hemangioendothelioma is an extremely rare soft tissue tumor, also named as epithelioid sarcoma-like hemangioendothelioma, which occurs more frequently in young adult males. It was originally recognized as a variant of epitheloid sarcoma, however it is now concluded as a distinctive, rarely metastasizing endothelial neoplasm. We present a case of pseudomyogenic hemangioendothelioma in the lower limb in a 49-year-old female who has a long course of disease and suffered from twice local recurrences and lymph node affection of the tumor. The mass was subcutaneous and the margins were ill-defined. Morphologically, the tumor cells show diversity, composed of large spindle cells and round cells, both with abundant eocinophilic cytoplasm, mimicking rhybdomyoplasts and epitheloid cells respectively. The tumor cells show diffuse strong expression of Factor VIII, Fli-1, INI-1, vimentin, MDM2, and CDK4, local expression of CD31, AE1/AE3, EMA and P63, and no expression of CD34, S-100, actin-sm, desmin, MyoD1, and HMB45. Based on these information, this case is diagnosed as pseudomyogenic hemangioendothelioma after ruling out the main differential diagnosises including epithelioid sarcoma, malignant peripheral nerve sheath tumor and rhabdomyosarcoma. From this case we suggest that pseudomyogenic hemangioendothelioma may be confused with a variety of soft tissue neoplasm histologically. The clinical feature of the case of a long course of disease with twice local recurrences and final lymph node involvement 10 years after excision of the primary tumor indicates a relative indolent behavior of this tumor.
Membrane Modification by Negatively Charged Stearyl-Polyoxyethylene Derivatives for Thermosensitive Liposomes: Reduced Liposomal Aggregation and Avoidance of Reticuloendothelial System Uptake (1994)

In order to avoid reticuloendothelial system (RES) uptake and prolong systemic circulation of cisplatin (CDDP)-encapsulating thermosensitive liposomes, stearylpolyoxyethylene (POE) derivatives [SnC, stearyl-O-(CH2CH2O)n-CH2COONa] were incorporated as membrane modifiers into lipid bilayers composed of dipalmitoylphosphatidylcholine (DPPC) and distearoylphosphatidylcholine (DSPC). The incorporation of S2C, S5C, S10C or S15C [lipid/SnC = 10/2 (w/w)] greatly reduced liposomal aggregation without impairing liposomal stability. After being intravenously administered to rats, the liposomes remained longer in the systemic circulation and showed lower RES levels than the control liposomes. When incorporated into liposomes [DPPC/DSPC = 7/3 (w/w)], S10C provided the greatest increase in systemic circulation time and the RES-avoiding activity among the modifiers tested. The systemic elimination rate (the ratio of the percent of the dose systemically eliminated to the AUC of the liposome level) for this type of liposome was 0.24/hr, about one fourth the rate for the control liposomes, and the RES uptake rate (the ratio of the percent of the dose taken up by the RES to the AUC) was 0.04/hr, one seventh the rate for the control liposomes. The RES uptake rate for S10C 7/3-liposomes was similar to the rate reported for GM1 liposomes, although the systemic elimination rate was double that for the GM1 liposomes. The obtained RES avoidance activity can be attributed to decreased liposomal aggregation and increased surface hydrophilicity. This type of thermosensitive liposome should be more useful in hyperthermia-mediated targeted tumor drug delivery systems than the thermosensitive liposomes without the modifiers to avoid RES uptake.
The complex permeability of a high purity yttrium iron garnet (YIG) sputtered thin film (1993)

In previous articles various ion implantations were used to explore the magnetic characteristics of high purity single crystal Y3Fe5O12 (YIG) on GGG. The work presented here is an investigation of the rf characteristics of a high purity YIG film that is not a single crystal and is laid down as a thin film on a flexible substrate. The measured properties are quite different from the sintered form. The film has relatively low losses in the very high and ultrahigh frequencies.
High Resolution Gamma-Ray Telescopes And Medical Imagers Using Scintillating Fibers And Position Sensitive Photomultipliers (1989)

Recently developed high photon yielding fibers that are coupled to position sensitive photomultipliers provide good angular precision and good energy resolution in detecting gamma-rays. The UTD/UCLA High Resolution Gamma Ray Telescope consists of a scintillating plastic fiber Compton or Pair-Production Converter, a time projection gas chamber and scintillating fiber calorimeter. The calorimeter is designed to cover 7c-ray energies from 1 MeV to &gt; 20 GeV. The space-based telescope will be used for detecting i-rays from point-like astrophysical sources and diffused cosmic 1-rays. We present here the description of the telescope, and some preliminary results from a prototype Compton converter.
Correlation of the Protein Structure and Gelling Properties in Dried Egg White Products (2001)

The relationship between protein structure and aggregation, as well as heat-induced gelling properties, of seven dried egg white (DEW) products was investigated. Strong correlations were found between average molecular weight and hydrophobicity plus surface SH groups of DEW-soluble protein aggregate (SPA). This suggests that hydrophobic interactions and disulfide bond formation between protein molecules were involved in the aggregation. The average molecular weight of DEW products with alkaline pHs was relatively higher than those with neutral pHs and the same degree of protein unfolding, probably because of more disulfide bond formation between protein molecules. In addition, strong correlations were found between hydrophobicity, surface SH groups plus average molecular weight of DEW-SPA, and physical properties of the gels from DEW products. These data indicated that controlling the aggregation of DEW proteins in the dry state is crucial to controlling the gelling properties of DEW.