gebhart/patrepeval huggingface dataset:
In Vitro and in Vivo Studies on the Radical-Scavenging Activity of Tea (1998)

The effects of tea (Camellia sinensis L.) of three types on excessive free radicals were examined utilizing spin trapping, 1,1-diphenyl-2-picrylhydrazyl radical, lipid peroxidation, and lactate dehydrogenase leakage from cultured cells. Green tea extract presented significant antiradical effects in these four assay systems, whereas oolong tea and black tea extracts showed a rather weak protective effect against free radicals. A more potent scavenger effect using cultured cells was found with a green tea tannin mixture. Similarly to the effects of the green tea tannin mixture, (−)-epigallocatechin 3-O-gallate, its main ingredient, had an inhibitory effect on oxidative stress-induced apoptosis. The activities of the antioxidation enzymes in rats after subtotal nephrectomy were increased, suggesting a protective action against oxidative stress. The increased levels of uremic toxins in the blood were also reduced in rats given (−)-epigallocatechin 3-O-gallate. These findings indicate that (−)-epigallocatechin 3-O-gallate helps to inhibit the progression of renal failure by scavenging radicals. Keywords: Tea; (−)-epigallocatechin 3-O-gallate; free radical; hydroxyl radical; apoptosis; DNA fragmentation; renal epithelial cell; nephrectomy
Ion exchange resins for the purification of monoclonal antibodies from animal cell culture. (1994)

We have compared various ion exchangers for monoclonal antibody (MAb) purification using different starting materials such as ascitic fluid and cell culture supernatant. Twelve cation and anion exchange resins were tested so far. Purification of MAbs with regard to the starting material is described. In well-defined conditions of adsorption (20 mM MES buffer, pH 6.50), one purification step based on cation-exchange chromatography is generally sufficient to achieve at least 90% purity of the MAb, even when produced by animal cell culture. Cation-exchange supports exhibit higher capacity for MAbs compared to anion exchangers. Among the cation exchangers tested, we have selected the cross-linked matrix S Sepharose FF for its large specificity and capacity for MAbs. Considering these key parameters and also the good mechanical resistance of the S Sepharose FF, we describe how, by varying the flow rate, sample concentration, and size of the column, the productivity may be improved in a monoclonal antibody purification process. Finally, a general 'gram scale' purification protocol of MAbs produced by animal cell cultures is proposed. This protocol, based on economical adsorption conditions and three steps of elution (100 mM, 200 mM and 1 M NaCl), allows the recovery of highly purified MAbs.
Unified Blind Method for Multi-Image Super-Resolution and Single/Multi-Image Blur Deconvolution (2013)

This paper presents, for the first time, a unified blind method for multi-image super-resolution (MISR or SR), single-image blur deconvolution (SIBD), and multi-image blur deconvolution (MIBD) of low-resolution (LR) images degraded by linear space-invariant (LSI) blur, aliasing, and additive white Gaussian noise (AWGN). The proposed approach is based on alternating minimization (AM) of a new cost function with respect to the unknown high-resolution (HR) image and blurs. The regularization term for the HR image is based upon the Huber-Markov random field (HMRF) model, which is a type of variational integral that exploits the piecewise smooth nature of the HR image. The blur estimation process is supported by an edge-emphasizing smoothing operation, which improves the quality of blur estimates by enhancing strong soft edges toward step edges, while filtering out weak structures. The parameters are updated gradually so that the number of salient edges used for blur estimation increases at each iteration. For better performance, the blur estimation is done in the filter domain rather than the pixel domain, i.e., using the gradients of the LR and HR images. The regularization term for the blur is Gaussian (L2 norm), which allows for fast noniterative optimization in the frequency domain. We accelerate the processing time of SR reconstruction by separating the upsampling and registration processes from the optimization procedure. Simulation results on both synthetic and real-life images (from a novel computational imager) confirm the robustness and effectiveness of the proposed method.
Composite CDMA—a statistical mechanics analysis (2009)

Code Division Multiple Access (CDMA) in which the spreading code assignment to users contains a random element has recently become a cornerstone of CDMA research. The random element in the construction is particular attractive as it provides robustness and flexibility in utilising multi-access channels, whilst not making significant sacrifices in terms of transmission power. Random codes are generated from some ensemble, here we consider the possibility of combining two standard paradigms, sparsely and densely spread codes, in a single composite code ensemble. The composite code analysis includes a replica symmetric calculation of performance in the large system limit, and investigation of finite systems through a composite belief propagation algorithm. A variety of codes are examined with a focus on the high multi-access interference regime. In both the large size limit and finite systems we demonstrate scenarios in which the composite code has typical performance exceeding sparse and dense codes at equivalent signal to noise ratio.
Conjugated Polymer Sensors Built on π-Extended Borasiloxane Cages (2009)

An efficient 2 + 2 cyclocondensation with dihydroxysilane converted simple arylboronic acids to bifunctional borasiloxane cage molecules, which were subsequently electropolymerized to furnish air-stable thin films. The extended [p,pi]-conjugation that defines the rigid backbone of this new conjugated polymer (CP) motif gives rise to longer-wavelength UV-vis transitions upon oxidative doping, the spectral window and intensity of which can be modified by interaction with Lewis basic reagents. Notably, this boron-containing CP undergoes a rapid and reversible color change from green to orange upon exposure to volatile amine samples under ambient conditions. This direct naked-eye detection scheme can best be explained by invoking the reversible B-N dative bond formation that profoundly influences the p-pi* orbital overlap.
MATERIALS CONSIDERATIONS IN LIQUID METAL ION SOURCE DEVELOPMENT (1986)

Successful development of a liquid metal ion source depends upon the satisfactory confluence of several critical design considerations. At least nine desirable properties of the alloy and substrate exist which cannot be fully and simultaneously satisfied in a given contact system. A compromise must usually be made based upon the most important source characteristics. We review these properties, with emphasis on the material and thermodynamic behavior of liquid metal alloy surfaces.
Drug-Induced Cholestasis in the Perfused Rat Liver and Its Reversal by Tauroursodeoxycholate: An Ultrastructural Study (1992)

Chlorpromazine at a concentration of 250 microM and estradiol-17 beta-D-glucuronide at 17.5 microM on infusion led to a sharp reduction in bile flow by the in vitro perfused rat liver. This was accompanied by fragmentation and a loss of canalicular microvilli, dilatation of canaliculi, and thickening of pericanalicular ectoplasm. Less prominent were the smooth endoplasmic reticulum dilatation, lysosomal lamination, and the appearance of amorphous bile in hepatocyte cytoplasm. The bile flow and electron microscopy appearance were restored to normal by infusion of tauroursodeoxycholate in a concentration of 5 mumols/min for the estradiol-17 beta-D-glucuronide-induced cholestasis and 1.5 mumol/min for the chlorpromazine-induced cholestasis. Changes in ultrastructure paralleled changes in bile flow. These observations demonstrate the feasibility of electron microscopy studies on the perfused liver, and the rapidity with which cholestatic changes appear.
Strained germanium thin film membrane on silicon substrate for optoelectronics (2011)

This work presents a novel method to introduce a sustainable biaxial tensile strain larger than 1% in a thin Ge membrane using a stressor layer integrated on a Si substrate. Raman spectroscopy confirms 1.13% strain and photoluminescence shows a direct band gap reduction of 100meV with enhanced light emission efficiency. Simulation results predict that a combination of 1.1% strain and heavy n(+) doping reduces the required injected carrier density for population inversion by over a factor of 60. We also present the first highly strained Ge photodetector, showing an excellent responsivity well beyond 1.6um.
Regulation and roles of Cdc7 kinase under replication stress (2014)

Cdc7 (cell division cycle 7) kinase together with its activation subunit ASK (also known as Dbf4) play pivotal roles in DNA replication and contribute also to other aspects of DNA metabolism such as DNA repair and recombination. While the biological significance of Cdc7 is widely appreciated, the molecular mechanisms through which Cdc7 kinase regulates these various DNA transactions remain largely obscure, including the role of Cdc7-ASK/Dbf4 under replication stress, a condition associated with diverse (patho)physiological scenarios. In this review, we first highlight the recent findings on a novel pathway that regulates the stability of the human Cdc7-ASK/Dbf4 complex under replication stress, its interplay with ATR-Chk1 signaling, and significance in the RAD18-dependent DNA damage bypass pathway. We also consider Cdc7 function in a broader context, considering both physiological conditions and pathologies associated with enhanced replication stress, particularly oncogenic transformation and tumorigenesis. Furthermore, we integrate the emerging evidence and propose a concept of Cdc7-ASK/Dbf4 contributing to genome integrity maintenance, through interplay with RAD18 that can serve as a molecular switch to dictate DNA repair pathway choice. Finally, we discuss the possibility of targeting Cdc7, particularly in the context of the Cdc7/RAD18-dependent translesion synthesis, as a potential innovative strategy for treatment of cancer.
The Role of IS-Flexibility for the Management of an E-Procurement System: A Case Study (2006)

A number of benefits of e-procurement systems have been identified by researchers and by practitioners.However, the selection of an appropriate solution from a large number of available solutions is still considered difficult in practice.Traditional cost-benefit and business strategy approaches fall short to provide guidelines regarding an appropriate, let alone optimal level of information system (IS) flexibility to support procurement processes, yet there is empirical evidence that insufficient as well as overly extensive IS flexibility can lead to sub-optimal results.In this paper, we present a case study of an e-procurement system at a Fortune 100 firm that confirms the importance of actively managing IS flexibility.We identify the expected time-frame of an e-procurement system as an important variable for the selection and the management of IS flexibility, in addition to business process characteristics that have been identified earlier as having an impact on flexibility requirements.
Analysis of Protein Prenylation In Vitro and In Vivo Using Functionalized Phosphoisoprenoids (2010)

Post-translational modifications (PTMs) expand the number of protein isoforms in eukaryotic proteome by orders of magnitude. Protein modification with isoprenoid lipids is a common PTM affecting hundreds of proteins controlling the transport of information and materials into, through, and out of the eukaryotic cell. In this modification, a soluble phosphoisoprenoid such as farnesyl (C15) or geranylgeranyl (C20) pyrophosphate moiety is recruited by one of three protein prenyltransferases to covalently modify a C-terminal cysteine(s) in a target protein. The three mammalian prenyltransferases are farnesyltransferase (FTase), geranylgeranyltransferase type I (GGTase I), and Rab geranylgeranyl transferase (also termed geranylgeranyltransferase type II - GGTase II). In this unit, synthetic isoprenoids conjugated to either a fluorophore or biotin group are used to assay the activity of protein prenyltransferases in vitro or to affinity tag prenylatable proteins in cell lysates. These protocols and their modifications can be used to study the mechanisms of protein prenylation, identify prenylation targets, and characterize inhibitors of protein prenyltransferases in vitro and in vivo.
Syntheses of Polycyclic Natural Products Employing the Intramolecular Double Michael Reaction (1993)

Abstract The one‐pot intramolecular double Michael reaction of compounds having two different α, β‐unsaturated carbonyl groups to form polycyclic compounds can be carried out by three different methods: in the first the substrate is treated with lithium hexamethyldisilazide, in the second with chlorotrimethylsilane, triethylamine, and zinc chloride at an elevated temperature, and in the third with tert ‐butyldimethylsilyl trifluoromethanesulfonate and triethylamine. The reaction proceeds with complete regioselectivity and high stereoselectivity following a stepwise mechanism. Spiro‐fused bicyclo[2.2.2]octane derivatives can be constructed with high stereoselectivity by the intromolecular double Michael reaction by using the first method. Enantiomerically pure atisine and the enantiomer of atisirene were synthesized stereoselectively by application of this methodology. The syntheses of steroids and angular triquinane‐type sesquiterpenoids were possible with the second method. Heterocyclic compounds with a bridgehead nitrogen atom were obtained by the reaction of α, β‐unsaturated amides following the second and third methods. The asymmetric synthesis of tylophorine with diastereofacial control was achieved by the intramolecular reaction according to the third method. The sulfur‐mediated intramolecular double Michael reaction utilizing the third method produced trans ‐hydroindane derivatives. Furthermore, the intramolecular Michael‐aldol reaction can be employed in synthesizing polycyclic systems with cyclobutane units by treatment with tert ‐butyldimethylsilyl trifluoromethanesulfonate in the presence of triethylamine. The intermolecular double Michael reaction and related reactions will also be described.
VeriCon (2014)

Software-defined networking (SDN) is a new paradigm for operating and managing computer networks. SDN enables logically-centralized control over network devices through a "controller" software that operates independently from the network hardware, and can be viewed as the network operating system. Network operators can run both inhouse and third-party SDN programs (often called applications) on top of the controller, e.g., to specify routing and access control policies. SDN opens up the possibility of applying formal methods to prove the correctness of computer networks. Indeed, recently much effort has been invested in applying finite state model checking to check that SDN programs behave correctly. However, in general, scaling these methods to large networks is challenging and, moreover, they cannot guarantee the absence of errors. We present VeriCon, the first system for verifying that an SDN program is correct on all admissible topologies and for all possible (infinite) sequences of network events. VeriCon either confirms the correctness of the controller program on all admissible network topologies or outputs a concrete counterexample. VeriCon uses first-order logic to specify admissible network topologies and desired network-wide invariants, and then implements classical Floyd-Hoare-Dijkstra deductive verification using Z3. Our preliminary experience indicates that VeriCon is able to rapidly verify correctness, or identify bugs, for a large repertoire of simple core SDN programs. VeriCon is compositional, in the sense that it verifies the correctness of execution of any single network event w.r.t. the specified invariant, and can thus scale to handle large programs. To relieve the burden of specifying inductive invariants from the programmer, VeriCon includes a separate procedure for inferring invariants, which is shown to be effective on simple controller programs. We view VeriCon as a first step en route to practical mechanisms for verifying network-wide invariants of SDN programs.
Homocarbonates as Substrates for the Enantioselective Enzymatic Protection of Amines (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTHomocarbonates as Substrates for the Enantioselective Enzymatic Protection of AminesBernard Orsat, Phil B. Alper, Wilna Moree, Ching-Pong Mak, and Chi-Huey WongView Author Information Department of Chemistry, The Scripps Research Institute, 10666 North Torrey Pines Road La Jolla, California 92037 Chemical Process Research and Development Sandoz Ltd., Basle, Switzerland Cite this: J. Am. Chem. Soc. 1996, 118, 3, 712–713Publication Date (Web):January 24, 1996Publication History Received28 September 1995Published online24 January 1996Published inissue 1 January 1996https://doi.org/10.1021/ja9533048Copyright © 1996 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views857Altmetric-Citations67LEARN 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 Read OnlinePDF (146 KB) Get e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Amines,Inorganic carbon compounds,Organic compounds,Peptides and proteins,Stereoselectivity Get e-Alerts
Atlas-based 3D-Shape Reconstruction from X-Ray Images (2006)

In many cases x-ray images are the only basis for surgery planning. Nevertheless it is desirable to draw conclusions about the 3D-anatomy of the patient from such data. This work presents a method to reconstruct 3D shapes from few digital x-ray images on the basis of 3D-statistical shape models. At the core of this method lies an algorithm which optimizes a similarity measure assessing the difference between projections of the shape model and the x-ray images. Based on theoretical and experimental observations we propose to measure the distance between the silhouettes of the object in the projections. The method is tested on 23 synthetically generated x-rays from CT data sets of the the geometrically as well as topologically complex shape of the pelvic bone.
Pericyte MyD88 and IRAK4 control inflammatory and fibrotic responses to tissue injury (2016)

Fibrotic disease is associated with matrix deposition that results in the loss of organ function. Pericytes, the precursors of myofibroblasts, are a source of pathological matrix collagens and may be promising targets for treating fibrogenesis. Here, we have shown that pericytes activate a TLR2/4- and MyD88-dependent proinflammatory program in response to tissue injury. Similarly to classic immune cells, pericytes activate the NLRP3 inflammasome, leading to IL-1β and IL-18 secretion. Released IL-1β signals through pericyte MyD88 to amplify this response. Unexpectedly, we found that MyD88 and its downstream effector kinase IRAK4 intrinsically control pericyte migration and conversion to myofibroblasts. Specific ablation of MyD88 in pericytes or pharmacological inhibition of MyD88 signaling by an IRAK4 inhibitor in vivo protected against kidney injury by profoundly attenuating tissue injury, activation, and differentiation of myofibroblasts. Our data show that in pericytes, MyD88 and IRAK4 are key regulators of 2 major injury responses: inflammatory and fibrogenic. Moreover, these findings suggest that disruption of this MyD88-dependent pathway in pericytes might be a potential therapeutic approach to inhibit fibrogenesis and promote regeneration.
Bayesian Non-Parametric Hidden Markov Models with Applications in Genomics (2010)

We consider the development of Bayesian Nonparametric methods for product partition models such as Hidden Markov Models and change point models. Our approach uses a Mixture of Dirichlet Process (MDP) model for the unknown sampling distribution (likelihood) for the observations arising in each state and a computationally efficient data augmentation scheme to aid inference. The method uses novel MCMC methodology which combines recent retrospective sampling methods with the use of slice sampler variables. The methodology is computationally efficient, both in terms of MCMC mixing properties, and robustness to the length of the time series being investigated. Moreover, the method is easy to implement requiring little or no user-interaction. We apply our methodology to the analysis of genomic copy number variation.
Geochemical signatures of meltwater in mollusc shells from Antarctic coastal areas during the Holocene (1994)

P(論文)
<i>Pseudozyma aphidis</i>Induces Salicylic-Acid-Independent Resistance to<i>Clavibacter michiganensis</i>in Tomato Plants (2014)

The ability of plant pathogens to rapidly develop resistance to commonly used pesticides challenges efforts to maximize crop production. Fungal biocontrol agents have become an important alternative to chemical fungicides as a result of environmental concerns regarding conventional pesticides, including resistance issues. The complex mode of action of biocontrol agents reduces the likelihood that pathogens will develop resistance to them. We recently isolated a unique, biologically active isolate of the epiphytic fungus Pseudozyma aphidis. We show that the extracellular metabolites secreted by our P. aphidis isolate can inhibit Xanthomonas campestris pv. vesicatoria, X. campestris pv. campestris, Pseudomonas syringae pv. tomato, Erwinia amylovora, Clavibacter michiganensis, and Agrobacterium tumefaciens in vitro. Moreover, application of Pseudozyma aphidis spores on tomato plants in the greenhouse significantly reduced (by 60%) the incidence of bacterial wilt and canker disease caused by C. michiganensis subsp. michiganensis on those plants as well as disease severity by 35%. Furthermore, infected plants treated with P. aphidis were 25% taller than control infected plants. We found that P. aphidis activates PR1a-and other pathogenesis-related genes in tomato plants-and can trigger an induced-resistance response against C. michiganensis that proceeds in a salicylic-acid-independent manner, as shown using NahG-transgenic tomato plants.