gebhart/patrepeval huggingface dataset:
Rubber Elongation Factor (REF), a Major Allergen Component in Hevea brasiliensis Latex Has Amyloid Properties (2012)

REF (Hevb1) and SRPP (Hevb3) are two major components of Hevea brasiliensis latex, well known for their allergenic properties. They are obviously taking part in the biosynthesis of natural rubber, but their exact function is still unclear. They could be involved in defense/stress mechanisms after tapping or directly acting on the isoprenoid biosynthetic pathway. The structure of these two proteins is still not described. In this work, it was discovered that REF has amyloid properties, contrary to SRPP. We investigated their structure by CD, TEM, ATR-FTIR and WAXS and neatly showed the presence of β-sheet organized aggregates for REF, whereas SRPP mainly fold as a helical protein. Both proteins are highly hydrophobic but differ in their interaction with lipid monolayers used to mimic the monomembrane surrounding the rubber particles. Ellipsometry experiments showed that REF seems to penetrate deeply into the monolayer and SRPP only binds to the lipid surface. These results could therefore clarify the role of these two paralogous proteins in latex production, either in the coagulation of natural rubber or in stress-related responses. To our knowledge, this is the first report of an amyloid formed from a plant protein. This suggests also the presence of functional amyloid in the plant kingdom.
GATA-1 interacts with the myeloid PU.1 transcription factor and represses PU.1-dependent transcription (2000)

The GATA-1 transcription factor is capable of suppressing the myeloid gene expression program when ectopically expressed in myeloid cells. We examined the ability of GATA-1 to repress the expression and function of the PU.1 transcription factor, a central regulator of myeloid differentiation. We found that GATA-1 is capable of suppressing the myeloid phenotype without interfering with PU.1 gene expression, but instead was capable of inhibiting the activity of the PU.1 protein in a dose-dependent manner. This inhibition was independent of the ability of GATA-1 to bind DNA, suggesting that it is mediated by protein-protein interaction. We examined the ability of PU.1 to interact with GATA-1 and found a direct interaction between the PU.1 ETS domain and the C-terminal finger region of GATA-1. Replacing the PU.1 ETS domain with the GAL4 DNA-binding domain removed the ability of GATA-1 to inhibit PU.1 activity, indicating that the PU.1 DNA-binding domain, rather than the transactivation domain, is the target for GATA-1-mediated repression. We therefore propose that GATA-1 represses myeloid gene expression, at least in part, through its ability to directly interact with the PU.1 ETS domain and thereby interfere with PU.1 function. (Blood. 2000;95:2543-2551)
Mobile device fingerprinting considered harmful for risk-based authentication (2015)

In this paper, we present a critical assessment of the use of device fingerprinting for risk-based authentication in a state-of-practice identity and access management system. Risk-based authentication automatically elevates the level of authentication whenever a particular risk threshold is exceeded. Contemporary identity and access management systems frequently leverage browser-based device fingerprints to recognize trusted devices of a certain individual. We analyzed the variability and the predictability of mobile device fingerprints. Our research shows that particularly for mobile devices the fingerprints carry a lot of similarity, even across models and brands, making them less reliable for risk assessment and step-up authentication.
Polymerization of vinyl monomers containing boron. I. B‐trivinyl‐N‐triphenylborazine and B‐triallyl‐N‐triphenylborazine (1961)

Abstract Synthesis of B ‐trivinyl‐ N ‐triphenylborazine is reported. Polymerization of this compound and of B ‐triallyl‐ N ‐triphenylborazine is discussed. The vinyl derivative does not homopolymerize, but the allyl compound polymerizes with difficulty, yielding a gel. Both of these borazines copolymerize with styrene and with methyl methacylate. The vinyl compound is comparable to these reference monomers in reactivity toward their radicals. These results are explained by assuming that the steric effect of phenyl groups makes adjacent vinyl groups inaccessible to hindered reactants. This steric effect prevents an assessment of stabilization of vinyl radicals by resonance and polarity in the borazine ring.
HNRNPA1-mediated 3′ UTR length changes of HN1 contributes to cancer- and senescence-associated phenotypes (2019)

Cellular senescence has been regarded as a mechanism of tumor suppression. Studying the regulation of gene expression at various levels in cell senescence will shed light on cancer therapy. Alternative polyadenylation (APA) regulates gene expression by altering 3' untranslated regions (3' UTR) and plays important roles in diverse biological processes. However, whether APA of a specific gene functions in both cancer and senescence remains unclear. Here, we discovered that 3' UTR of <i>HN1</i> (or <i>JPT1</i>) showed shortening in cancers and lengthening in senescence, correlated well with its high expression in cancer cells and low expression in senescent cells, respectively. <i>HN1</i> transcripts with longer 3' UTR were less stable and produced less protein. Down-regulation of <i>HN1</i> induced senescence-associated phenotypes in both normal and cancer cells. Patients with higher <i>HN1</i> expression had lower survival rates in various carcinomas. Interestingly, down-regulating the splicing factor HNRNPA1 induced 3' UTR lengthening of <i>HN1</i> and senescence-associated phenotypes, which could be partially reversed by overexpressing <i>HN1</i>. Together, we revealed for the first time that HNRNPA1-mediated APA of <i>HN1</i> contributed to cancer- and senescence-related phenotypes. Given senescence is a cancer prevention mechanism, our discovery indicates the HNRNPA1-<i>HN1</i> axis as a potential target for cancer treatment.
Borrelia burgdorferi mutant lacking Osp: biological and immunological characterization (1995)

All Borrelia burgdorferi sensu lato isolates characterized to date have one or a combination of several major outer surface proteins (Osps). Mutants of B. burgdorferi lacking Osps were selected with polyclonal or monoclonal antibodies at a frequency of 10(-6) to 10(-5). One mutant that lacked OspA, -B, -C, and -D was further characterized. It was distinguished from the OspA+B+ cells by its (i) autoaggregation and slower growth rate, (ii) decreased plating efficiency on solid medium, (iii) serum and complement sensitivity, and (iv) diminished capacity to adhere to human umbilical vein endothelial cells. The Osp-less mutant was unable to evoke a detectable immune response after intradermal live cell immunization even though mutant survived in mouse skin for the same duration as wild-type cells. Polyclonal mouse serum raised against Osp-less cells inhibited growth of the mutant but not of wild-type cells, an indication that other antigens are present on the surface of the Osp-less mutant. Two types of monoclonal antibodies (MAbs) with growth-inhibiting properties for mutant cells were identified. The first type bound to a 13-kDa surface protein of B. burgdorferi sensu stricto and of B. afzelii. The MIC of the Fab fragment of one MAb of this type was 0.2 micrograms/ml. The second type of MAb to the Osp-less mutant did not bind to B. burgdorferi components by Western blotting (immunoblotting) but did not bind to unfixed, viable cells in immunofluorescence and growth inhibition assays. These studies revealed possible functions Osp proteins in borrelias, specifically serum resistance, and indicated that in the absence of Osp proteins, other antigens are expressed or become accessible at the cell surface.
Markets and Operations 2007 Q2 (2007)

This article reviews developments in global financial markets since the 2009 Q2 Quarterly Bulletin up to end-August 2009. The article also reviews the Bank’s official operations.
Amino Acids and Peptides; 59.1Synthesis of Biologically Active Cyclopeptides; 9.2Synthesis of 16 Isomers of Dolastatin 3;3I. Synthesis of the 2-(1-aminoalkyl)-thiazole-4-carboxylic Acids (1987)

The synthesis of the optically active Dolastatin 3 building block 2-(1-amino-3-cyanopropyl)-thiazole-4-carboxylic acid is described as a prerequisite for the total synthesis of dolastatin isomers.
Thrombin‐induced platelet endostatin release is blocked by a proteinase activated receptor‐4 (PAR4) antagonist (2001)

Endostatin is a potent endogenous inhibitor of angiogenesis that was recently shown to be stored in platelets and released in response to thrombin, but not ADP. In the present study, we have tested the hypothesis that thrombin-induced endostatin release from rat platelets is mediated via proteinase-activated receptor-4 (PAR4). Immunoprecipitation and Western blotting confirmed that endostatin is contained within rat platelets. Aggregation and release of endostatin could be elicited by thrombin (0.5 - 1.0 U ml(-1)) or by specific PAR4 agonist (AYPGKF-NH(2); AY-NH(2); 15 - 50 microM). Significant release of endostatin could be induced by a dose of thrombin below that necessary for induction of aggregation. An adenosine diphosphate (ADP) scavenger, apyrase, inhibited the platelet aggregation induced by thrombin, but not the release of endostatin. In contrast, a selective PAR4 antagonist (trans-cinnamoyl-YPGKF-NH(2); tcY-NH(2)) prevented endostatin release and aggregation induced by thrombin or by AY-NH(2). We conclude that thrombin-induced endostatin release from rat platelets is PAR4-mediated via an ADP-independent mechanism that can occur independently of platelet aggregation.
Solid-State Stabilization of α-Chymotrypsin and Catalase with Carbohydrates (2006)

We report a systematic investigation of the effects of five carbohydrates (fructose, sucrose, trehalose, maltotriose, and dextran), freeze-drying, and subsequent heat treatment (up to 8 days at 80 °C) on the structure and enzymatic activity of α-chymotrypsin and catalase. Importantly, we investigate high carbohydrate-to-protein mass ratio conditions (20:1 by mass) so as to minimize protein−protein interactions (e.g., protein aggregation). The activity of α-chymotrypsin is almost quantitatively recovered (greater than 80% of the initial activity) after lyophilization with or without added carbohydrates, and its conformation in the dried solid state as well as in an aqueous solution (after rehydration of lyophilized samples) is unchanged by the presence of carbohydrates. In contrast, catalase lyophilized without carbohydrates loses almost half of its activity upon reconstitution and shows significant structural changes in the dried state. The loss of activity and the lyophilization-induced structural alteration for catalase are appreciably reduced by addition of the lower molecular weight carbohydrates (fructose, sucrose, and trehalose). For protein preservation at elevated temperatures, the addition of carbohydrates at high carbohydrate-to-protein ratios (20:1 by mass) creates a glassy matrix dilute with respect to the protein, effectively minimizing intermolecular protein−protein interactions that could lead to protein aggregation in the solid state. It is also shown that the Maillard reaction between carbohydrates and proteins, which causes a significant loss of enzymatic activity, is successfully suppressed in glassy systems with less than 1% (w/w) water content. More significantly, a quantitative comparison is established for the first time between activity loss and the extent to which the Maillard reaction proceeds for dry glassy systems (as measured spectroscopically). Trehalose was found to be the most effective protector against prolonged heating: approximately 90% of α-chymotrypsin activity and 30% catalase activity are recovered upon reconstitution following 8 days at 80 °C in a trehalose matrix.
Glatiramer acetate in the treatment of multiple sclerosis (2007)

Glatiramer acetate is an immunomodulating drug used in the treatment of multiple sclerosis. It consists of a copolymer of amino acid residues in the same stoichiometric proportions as in myelin basic protein. Its mechanism of action is not entirely known and is probably multifaceted, with deletion of some immune cell populations and stimulation of others in these patients. Some mechanisms involve neuroprotectant effects. There is ample evidence of its efficacy in relapsing-remitting disease, using both clinical and imaging measures of disease activity, and in this paper we review the clinical and basic studies of this drug. Finally we discuss how some of its neuroprotectant effects may be useful in neurodegeneration such as is seen in more advanced cases of multiple sclerosis and other diseases such as amyotrophic lateral sclerosis and Parkinson's disease.
Practical synthesis of 5-phospho-D-ribosyl .alpha.-1-pyrophosphate (PRPP): enzymatic routes from ribose 5-phosphate or ribose (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPractical synthesis of 5-phospho-D-ribosyl .alpha.-1-pyrophosphate (PRPP): enzymatic routes from ribose 5-phosphate or riboseAkiva Gross, Obsidiana Abril, Jerome M. Lewis, Shimona Geresh, and George M. WhitesidesCite this: J. Am. Chem. Soc. 1983, 105, 25, 7428–7435Publication Date (Print):November 1, 1983Publication History Published online1 May 2002Published inissue 1 November 1983https://doi.org/10.1021/ja00363a037RIGHTS & PERMISSIONSArticle Views988Altmetric-Citations59LEARN 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 (1 MB) Get e-Alerts Get e-Alerts
The determination of the elastic field of an ellipsoidal inclusion, and related problems (1957)

Abstract It is supposed that a region within an isotropic elastic solid undergoes a spontaneous change of form which, if the surrounding material were absent, would be some prescribed homogeneous deformation. Because of the presence of the surrounding material stresses will be present both inside and outside the region. The resulting elastic field may be found very simply with the help of a sequence of imaginary cutting, straining and welding operations. In particular, if the region is an ellipsoid the strain inside it is uniform and may be expressed in terms of tabu­lated elliptic integrals. In this case a further problem may be solved. An ellipsoidal region in an infinite medium has elastic constants different from those of the rest of the material; how does the presence of this inhomogeneity disturb an applied stress-field uniform at large distances? It is shown that to answer several questions of physical or engineering interest it is necessary to know only the relatively simple elastic field inside the ellipsoid.
VideoBERT: A Joint Model for Video and Language Representation Learning (2019)

Self-supervised learning has become increasingly important to leverage the abundance of unlabeled data available on platforms like YouTube. Whereas most existing approaches learn low-level representations, we propose a joint visual-linguistic model to learn high-level features without any explicit supervision. In particular, inspired by its recent success in language modeling, we build upon the BERT model to learn bidirectional joint distributions over sequences of visual and linguistic tokens, derived from vector quantization of video data and off-the-shelf speech recognition outputs, respectively. We use VideoBERT in numerous tasks, including action classification and video captioning. We show that it can be applied directly to open-vocabulary classification, and confirm that large amounts of training data and cross-modal information are critical to performance. Furthermore, we outperform the state-of-the-art on video captioning, and quantitative results verify that the model learns high-level semantic features.
Computer vision for microscopy diagnosis of malaria (2009)

This paper reviews computer vision and image analysis studies aiming at automated diagnosis or screening of malaria infection in microscope images of thin blood film smears. Existing works interpret the diagnosis problem differently or propose partial solutions to the problem. A critique of these works is furnished. In addition, a general pattern recognition framework to perform diagnosis, which includes image acquisition, pre-processing, segmentation, and pattern classification components, is described. The open problems are addressed and a perspective of the future work for realization of automated microscopy diagnosis of malaria is provided.
Total Capture: A 3D Deformation Model for Tracking Faces, Hands, and Bodies (2018)

The following topics are dealt with: learning (artificial intelligence); feature extraction; image classification; neural nets; image representation; object detection; image segmentation; convolution; feedforward neural nets; video signal processing.
Co-Delivery of siRNA and An Anticancer Drug for Treatment of Multidrug-Resistant Cancer (2008)

We demonstrate NDS-enhanced efficiency of chemotherapy to a level that cannot be achieved by applying its components separately.
Identification of Sensor Cysteines in Human Keap1 Modified by the Cancer Chemopreventive Agent Sulforaphane (2005)

The chemopreventive agent sulforaphane is an isothiocyanate derived from cruciferous vegetables. Sulforaphane exerts cancer chemopreventive effects by inducing antioxidant/electrophile response element (ARE)-regulated phase 2 enzyme and antioxidant genes through activation of the transcription factor nuclear factor-E2-related factor 2 (Nrf2), which is regulated by the thiol-rich sensor protein Kelch-like ECH-associated protein 1 (Keap1). Sulforaphane is an electrophile that can react with protein thiols to form thionoacyl adducts. We hypothesized that, like other electrophilic Nrf2 activators, sulforaphane activates this system through specific modifications of the Keap1 protein. However, thionoacyl adducts are labile to hydrolysis and transacylation reactions, which complicate the identification of the sulforaphane adduct sites on Keap1. In this study, we characterized the stability of sulforaphane thionoacyl adducts and developed a liquid chromatography-tandem mass spectrometry method to map labile sulforaphane adduct sites formed on Keap1 in vitro. Sulforaphane displays a distinctly different pattern of Keap1 modification than previously studied ARE inducers that modify Keap1 by alkylation. Sulforaphane modified Keap1 most readily in the Kelch domain, rather than in the central linker domain, which is targeted by previously characterized ARE inducers. Also, in contrast to previously studied ARE inducers and as reported recently [Zhang, et al. (2005) J. Biol. Chem. 280, 30091-30099], sulforaphane treatment in vivo does not lead to the accumulation of ubiquitinated Keap1. Our observations suggest a novel mechanism for Nrf2 stabilization by sulforaphane-Keap1 thionoacyl adduct formation.
Crystalline lens radii of curvature from Purkinje and Scheimpflug imaging (2006)

We present a comparison between measurements of the radius of the anterior and posterior lens surface, which was performed using corrected Scheimpflug imaging and Purkinje imaging in the same group of participants (46 for the anterior lens, and 34 for the posterior lens). Comparisons were also made as a function of accommodation (0 to 7 D) in a subset of 11 eyes. Data were captured and processed using laboratory prototypes and custom processing algorithms [for optical and geometrical distortion correction in the Scheimpflug system and using either equivalent mirror (EM) or merit function (MF) methods for Purkinje]. We found statistically significant differences in 4 of 46 eyes for the anterior lens radius, and 10 of 34 eyes for the posterior radius (using the MF and individual biometric data to process the Purkinje images). For the anterior lens, the agreement increases using individual biometry as opposed to biometric data from a model eye. For the posterior lens, the agreement increases using the MF as opposed to the EM method. For the changes during accommodation, no significant difference between the two techniques was found. In conclusion, the results of the cross-validation using the Scheimpflug and Purkinje imaging technique show that both techniques provide comparable lens radii and similar changes with accommodation. Purkinje tends to overestimate posterior lens radius, whereas pupil size limits the acquisition of posterior lens data with the Scheimpflug camera. Computer simulations using the Scheimpflug data as input show that the consistent slight overestimation of the posterior lens radius using Purkinje imaging can be partly attributed to the asphericity of the lens surface.
A Hybrid solid-state storage architecture for the performance, energy consumption, and lifetime improvement (2010)

In recent years, many systems have employed NAND flash memory as storage devices because of its advantages of higher performance (compared to the traditional hard disk drive), high-density, random-access, increasing capacity, and falling cost. On the other hand, the performance of NAND flash memory is limited by its “erase-before-write” requirement. Log-based structures have been used to alleviate this problem by writing updated data to the clean space. Prior log-based methods, however, cannot avoid excessive erase operations when there are frequent updates, which quickly consume free pages, especially when some data are updated repeatedly. In this paper, we propose a hybrid architecture for the NAND flash memory storage, of which the log region is implemented using phase change random access memory (PRAM). Compared to traditional log-based architectures, it has the following advantages: (1) the PRAM log region allows in-place updating so that it significantly improves the usage efficiency of log pages by eliminating out-of-date log records; (2) it greatly reduces the traffic of reading from the NAND flash memory storage since the size of logs loaded for the read operation is decreased; (3) the energy consumption of the storage system is reduced as the overhead of writing and reading log data is decreased with the PRAM log region; (4) the lifetime of NAND flash memory is increased because the number of erase operations are reduced. To facilitate the PRAM log region, we propose several management policies. The simulation results show that our proposed methods can substantially improve the performance, energy consumption, and lifetime of the NAND flash memory storage <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> .