gebhart/patrepeval huggingface dataset:
IDENTIFICATION OF THE TRYPSIN INHIBITOR OF EGG WHITE WITH OVOMUCOID (1947)

The trypsin inhibiting action of egg white, which has been known for over 40 years, has not been identified with any of the recognized components (1) of egg white.Suggestions made in this regard include the postulates (a) that difficultly digestible proteins of egg white displaced trypsin from the substrate (casein) (2), (b) that the antitrypsin is associated with the globulin fraction of egg white (3), and (c) that the inhibitor is probably a protein hydrolysis product but not a true protein (4).Balls and Swenson (4), who made the most complete study of the inhibitor, found that it was neither lipide nor carbohydrate (exclusively) and that it had about the same nitrogen content (slightly low), optical rotation, and sulfur content as are now recognized for ovomucoid.Meyer et al. ( 5) reported that a highly active antitrypsin sample sent them by Dr. Swenson showed the properties and composition of an egg mucoid.They stated that '(the inhibitory effect of egg white preparations on tryptic activity is probably due to a mucoid."However, the activity reported by Balls and Swenson for their best preparation indicated that the inhibitor represented less than 1 per cent of the egg white solids, which, of course, is less than one-tenth of the ovomucoid in egg white.Possible explanation of this result, which conflicts with the results reported in this paper, may lie in the use for assay purposes of enzyme precursors, which were activated by enterokinase, generally in the presence of inhibitor.The complication introduced by the use of precursors and enterokinase (a common practice at the time the work was done) is illustrated by the reports that the inhibitor was an antikinase (6), that it possibly acted by displacing enterokinase from its combination with the enzyme (4), and that the inhibitor was not an antikinase (7, 2).This report concerns a component of egg white that inhibits trypsin containing no enterokinase.Primary consideration is given to data indicating that antitryptic activity is a characteristic of "native" ovomucoid.The considerations include the distribution of the inhibitor in hen's eggs, preparation and fractional precipitation of the inhibitor, comparison of the
Functional Analysis of Cyclin-Dependent Kinase Inhibitors of Arabidopsis (2001)

Cyclin-dependent kinase inhibitors, such as the mammalian p27(Kip1) protein, regulate correct cell cycle progression and the integration of developmental signals with the core cell cycle machinery. These inhibitors have been described in plants, but their function remains unresolved. We have isolated seven genes from Arabidopsis that encode proteins with distant sequence homology with p27(Kip1), designated Kip-related proteins (KRPs). The KRPs were characterized by their domain organization and transcript profiles. With the exception of KRP5, all presented the same cyclin-dependent kinase binding specificity. When overproduced, KRP2 dramatically inhibited cell cycle progression in leaf primordia cells without affecting the temporal pattern of cell division and differentiation. Mature transgenic leaves were serrated and consisted of enlarged cells. Although the ploidy levels in young leaves were unaffected, endoreduplication was suppressed in older leaves. We conclude that KRP2 exerts a plant growth inhibitory activity by reducing cell proliferation in leaves, but, in contrast to its mammalian counterparts, it may not control the timing of cell cycle exit and differentiation.
The effects of head movement on dual-axis cervical accelerometry signals (2010)

These differences indicate that head motions induce additional non-dominant spectral components in dual-axis cervical recordings. The results presented here suggest that head motion ought to be considered in the development of medical devices based on dual-axis cervical accelerometery signals.
Purification and Characterization of a Membrane Bound Neutral pH Optimum Magnesium-dependent and Phosphatidylserine-stimulated Sphingomyelinase from Rat Brain (1998)

Sphingomyelin hydrolysis and ceramide generation catalyzed by sphingomyelinases (SMase) are key components of the signaling pathways in cytokine- and stress-induced cellular responses. In this study, we report the partial purification and characterization of the membrane bound, neutral pH optimal, and magnesium-dependent SMase (N-SMase) from rat brain. Proteins from Triton X-100 extract of brain membrane were purified sequentially with DEAE-Sephacel, heparin-Sepharose, ceramic hydroxyapatite, Mono Q, phenyl-Superose, and Superose 12 column chromatography. After eight purification steps, the specific activity of the enzyme increased by 3030-fold over the brain homogenate. The enzyme hydrolyzed sphingomyelin but not phosphatidylcholine and its activity was dependent upon magnesium with an optimal pH of 7.5 and a native pI of 5.2. Delipidation of the enzyme through chromatographic purification or by extraction with 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonic acid followed by gel filtration revealed that the enzyme became increasingly dependent on phosphatidylserine (PS). Up to 20-fold stimulation was observed with PS whereas other lipids examined were either ineffective or only mildly stimulatory. The Km of the enzyme for substrate sphingomyelin (3.4 mol %) was not affected by PS. The highly purified enzyme was inhibited by glutathione with a >95% inhibition observed with 3 mM glutathione and with a Hill number calculated at approximately 8. The significance of these results to the regulation of N-SMase is discussed.
Second messenger cascade specificity and pharmacological selectivity of the human P2Y1‐purinoceptor (1996)

1. The coding sequence of the P2Y1-purinoceptor was cloned from a human genomic library. 2. The open reading frame encodes a protein of 373 amino acids that is 83% identical to the previously cloned chick and turkey P2Y1-purinoceptor and is > or = 95% homologous to the recently cloned rat, mouse, and bovine P2Y1-purinoceptors. 3. The human P2Y1-purinoceptor was stably expressed in 1321N1 human astrocytoma cells using a retroviral vector. Although the P2Y1-purinoceptor agonist, 2MeSATP, had no effect on inositol phosphate accumulation in cells infected with the P2Y1-purinoceptor virus. No effect of 2MeSATP on cyclic AMP accumulation was observed in P2Y1-receptor-expressing 1321N1 cells. 4. The pharmacological selectively of 18 purinoceptor agonists was established for the expressed human P2Y1-purinoceptor. 2MeSATp was more potent than ATP but less potent than 2MeSADP. ADP also was more potent than ATP. A similar maximal effect was observed with most agonists tested. However, alpha, beta-MeATP had no effect and 3'-NH2-3'-deoxyATP and A2P4 were partial agonists. The order of potency of agonists for activation of the turkey P2Y1-purinoceptor, also stably expressed in 1321N1 cells, was identical to that observed for the human P2Y1-purinoceptor. 5. C6 glioma cells express a P2Y-purinoceptor that inhibits adenylyl cyclase but does not activate phospholipase C. Expression of the human P2Y1-purinoceptor in C6 cells conferred 2MeSATP-stimulated inositol lipid hydrolysis to these cells. The phospholipase C-activating human P2Y1-purinoceptor could be delineated from the endogenous P2Y-purinoceptor of C6 glioma cells by use of the P2-purinoceptor antagonist, PPADS, which blocks the P2Y1-purinoceptor but does not block the endogenous P2Y-purinoceptor of C6 cells. P2-purinoceptor agonists also exhibited differential selectivities for activation of these two P2Y-purinoceptors.
Supercompilers for parallel and vector computers (1990)

Table of Contents * Supercomputer and Supercompilers * Supercomputer Architectures * Scalar Analysis * Data Dependence * Standard Transformations * Vectorization * Parallelization * Supercompilers and their Environments * Appendices
The Mechanism of the Acid- and Base-catalyzed Equilibration of Siloxanes (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Mechanism of the Acid- and Base-catalyzed Equilibration of SiloxanesSimon W. Kantor, Willard T. Grubb, and Robert C. OsthoffCite this: J. Am. Chem. Soc. 1954, 76, 20, 5190–5197Publication Date (Print):October 1, 1954Publication History Published online1 May 2002Published inissue 1 October 1954https://pubs.acs.org/doi/10.1021/ja01649a076https://doi.org/10.1021/ja01649a076research-articleACS PublicationsRequest reuse permissionsArticle Views1761Altmetric-Citations145LEARN 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
Cuttings transport in inclined and horizontal wellbore (2010)

Efficient cuttings transport and hole cleaning is very important for obtaining an effective drilling operation. In inclined and horizontal drilling, hole cleaning issues is a common and complex problem. This thesis explores the impact of various drilling parameters, and how they affect the required flow velocity and flow rate required for effective cuttings transport.\nThe main objectives of the thesis are outlined as follows:\n- To make a sufficient review of previous studies;\n- Explain the fundamentals of the cuttings transport parameters and definitions;\n- To introduce and explain in great details the empirical model focusing on the models of Larsen and Rubiandini;\n- To make an introduction to the mechanistic modeling approach focusing on demonstrating the complexity of these models;\n- To apply Larsen‟s and Rubiandini‟s models in order to compare and identify similarities and differences between the models;\n- To present some field experience from offshore;\n- To draw conclusions about what we can learn from earlier studies and research.\nThe thesis employs two models developed by an empirical approach, namely Larsen‟s model and Rubiandini‟s model. Two simulation scenarios have been considered. First, we have compared the models using the cases defined by Larsen from his experimental work. Then, an example well has been considered which mimics more operational conditions. Moreover, the thesis presents the mechanistic two-layer model developed by Kamp and Rivero, and demonstrates how the model has to be reformulated mathematically before a numerical method can be used for solving the model.\nThe analysis of the two empirical models showed that both models show the same trend for required cuttings transport flow velocity and flow rate when drilling parameters, such as mud weight, ROP, mud rheology and drill-pipe diameter varied. For the horizontal case, we observe that Larsen predicts flow rate that are not far from the flow rates typical seen in operations, however it slightly over predicts required cuttings transport velocity. Rubiandini‟s model seems to predict high flow rate required for cuttings transport. However, for the vertical case, the predicted rate seems to coincide with flow rates typical in operations. The main advantage of Rubiandini‟s model is that in his work, he considered RPM as a variable that could affect the cuttings transport.\nThe results also indicate that Larsen‟s model and Rubiandini‟s model show the opposite effect on required cuttings transport velocity when the cuttings size is a variable parameter. In the Larsen‟s model, smaller cuttings required higher flow velocity to be transported, while in the Rubiandini‟s model, the opposite is observed, namely larger cuttings need a higher flow velocity for transport in the wellbore.\nIn the conclusion, several recommendations on how to achieve better cuttings transport and hole cleaning are listed.
Cell Adhesion in Cancer (2012)

During cancer progression, cells lose their original tissue contacts, move through the extracellular matrix (ECM), enter into the lymphatic and/or blood system, extravasate, and ultimately form new tumors. Therefore, tumor cells inevitably experience alterations in cell-cell and cell-ECM adhesion and the transformation activities of tumor cells are highly influenced by cell adhesion via adhesion receptors such as cadherins, integrins, cell surface proteoglycans, and tetraspanins. These adhesion receptors, together with extracellular ligands in the tumor microenvironment, couple the extracellular environment to intracellular signals, thereby enhancing cancer cell migration, invasion, proliferation, and survival. Therefore, knowledge of the role of cell adhesion in cancer is key to understanding the development of cancer, and such knowledge could potentially form the basis for effective approaches to cancer treatment. Therefore, in this issue, we have invited several authors to address such issues.

The special issue will be composed of three parts. A set of four papers discuss regulatory mechanisms in the light of interesting issues that have arisen recently, such as the role of cell-ECM interactions in genetic mutations in tumors, as well as the important roles of lipid rafts, turnover of focal adhesions, and anoikis resistance in cancer cell adhesion and migration. All of these characteristics have been shown to be important in cancer cell adhesion, and recent findings provide potential mechanisms of tumor cell interactions and metastatic activities.

Another set of five papers of this special issue address the molecular level regulatory role of cell adhesion molecules such as integrins and the immunoglobulin super family and adhesion-related regulatory molecules such as plakoglobin, HIC-5, and prostaglandins. All of these molecules have received considerable attention in cell adhesion research and have distinct role(s) in different aspects of cancer progression, but all are important regulators of human carcinogenesis through their capacity to regulate cancer cell adhesion. However, because their roles in cancer cell adhesion and metastasis are still under investigation, this special issue addresses their functional significance, particularly in the context of cancer cell adhesion.

A set of two papers address the possibility of suppressing tumors by regulating cell adhesion status using ECM-derived functional peptides or a physiological regulator such as heparin. Research in this area will improve the understanding of cancer progression and may provide the basis for a new strategy for treating cancer.


Eok-Soo Oh

Motoharu Seiki

Martin Gotte

Jun Chung
Distribution and metabolism of mucopolysaccharides and glycoproteins in neuronal perikarya, astrocytes, and oligodendroglia (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDistribution and metabolism of mucopolysaccharides and glycoproteins in neuronal perikarya, astrocytes, and oligodendrogliaRichard U. Margolis and Renee K. MargolisCite this: Biochemistry 1974, 13, 14, 2849–2852Publication Date (Print):July 1, 1974Publication History Published online1 May 2002Published inissue 1 July 1974https://pubs.acs.org/doi/10.1021/bi00711a011https://doi.org/10.1021/bi00711a011research-articleACS PublicationsRequest reuse permissionsArticle Views60Altmetric-Citations70LEARN 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
An architecture for broadband virtual networks under customer control (2002)

Emerging ATM-based virtual private network (VPN) services offer customers a flexible way to interconnect customer premises networks (CPNs) via high-speed links. Compared with traditional leased lines, these services allow for rapid provisioning of VPN bandwidth through cooperative control between customer and provider. Customers can dynamically renegotiate the VPN bandwidth according to their current needs, paying only for the resources they actually use. In order to meet the various requirements and demands of different classes of VPN customers, a VPN provider must provide customers with the flexibility to choose their own control schemes and objectives. The focus of this paper is on enhancing the customer's capability of controlling a VPN. First, we propose a new scheme for a broadband VPN service, which is based on the virtual path group (VPG) concept. In our scheme, the customer performs VP control operations without interacting with the VPN provider, thus enabling the following merits: (1) the customer can share bandwidth among VPs that traverse the same physical network link in the provider's domain, thus using the VPN bandwidth more efficiently; (2) customers can perform VP control operations according to their own requirements and control objectives. Second, we outline an architecture for a customer-operated control system, which utilizes a VPG-based VPN service. The system is structured into three layers of control, which execute on different time scales. The functionalities of these layers are call processing, VP control, and VPN control, respectively. Finally, we evaluate the effectiveness of the control system, with respect to VP control.
Expression of a dominant negative form of cpSRP54 inhibits chloroplast biogenesis in Arabidopsis (1998)

The chloroplast homolog of the 54 kDa subunit of signal recognition particle is required for the in vitro targeting of chlorophyll a/b binding proteins (LHCP) to the thylakoid membrane. To explore the function of cpSRP54 in vivo, plants that are mutated in cpSRP54 function were generated. Dominant negative forms of cpSRP54 altered in single amino acids within the conserved guanine nucleotide binding domain were expressed in Arabidopsis. Transformed plants contained less than 30% of the wild-type level of cpSRP54 protein. As a consequence of the reduced cpSRP54 protein content, the first emerging leaves were yellow and contained immature chloroplasts. Although the chlorophyll (chl) content of the leaves was reduced by 75%, the chl a/b ratio was unaffected, indicating a role of cpSRP54 in the biogenesis of proteins besides LHCP. Many chloroplast proteins were less abundant in the first emerging leaves, including non-pigmented proteins, thylakoid proteins known to be targeted by alternative pathways, and soluble proteins. These observations indicate that the cpSRP54 mutation also has a pleiotropic effect on chloroplast biogenesis. Whereas the level of cpSRP54 remained low as the plants aged, leaves emerging subsequently had a wild-type appearance, suggesting that the adult plants compensated for the reduction in cpSRP54 protein.
Neuro-fuzzy decision trees for content popularity model and multi-genre movie recommendation system over social network (2009)

In this paper, we propose a framework of multi-genre movie recommender system based on neuro-fuzzy decision tree (NFDT) methodology. The system is capable of recommending list of movies in descending order of preference in response to user queries and profiles. The system also takes care of attempt to vote stuffing using novel application of fuzzy c-means clustering algorithm. Typical user query and profiles consists of content ratings for multiple genres like action, comedy, drama, music and many others. The distinctive point of the proposed approach is to handle recommender system generation as a supervised pattern classification problem, where in user reviews for multiple genres are conditions and overall star ratings are decisions. The entire recommender system is represented in the form of NFDT. Rules represented by NFDT also acts as a tool for understanding the combinations of contents driving popularity (and unpopularity) over certain social network. We have also proposed a modified inference mechanism based on matching and ordering of firing strength of each fuzzy decision tree path in response to user queries. The computational experiments have been presented on a sample real-world movie review database to judge the efficiency of the proposed recommender system.
Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants (2012)

Assessing the impact of variants of unknown significance (VUS) on splicing is a key issue in molecular diagnosis. This impact can be predicted by in silico tools, but proper evaluation and user guidelines are lacking. To fill this gap, we embarked upon the largest BRCA1 and BRCA2 splice study to date by testing 272 VUSs (327 analyses) within the BRCA splice network of Unicancer. All these VUSs were analyzed by using six tools (splice site prediction by neural network, splice site finder (SSF), MaxEntScan (MES), ESE finder, relative enhancer and silencer classification by unanimous enrichment, and human splicing finder) and the predictions obtained were compared with transcript analysis results. Combining MES and SSF gave 96% sensitivity and 83% specificity for VUSs occurring in the vicinity of consensus splice sites, that is, the surrounding 11 and 14 bases for the 5' and 3' sites, respectively. This study was also an opportunity to define guidelines for transcript analysis along with a tentative classification of splice variants. The guidelines drawn from this large series should be useful for the whole community, particularly in the context of growing sequencing capacities that require robust pipelines for variant interpretation.
Interaction of bumetanide derivatives with hepatocellular bile acid uptake (1993)

The loop diuretic bumetanide is an organic monocarboxylic organic anion assumed to be transported into hepatocytes by a transport system for bile acids. The structural requirements of 22 bumetanide analogues were analyzed for an interaction with bile acid uptake into isolated rat hepatocytes. Whereas bumetanide inhibited the hepatocellular uptake of [14C]cholate to the same degree as its own uptake, derivatization altered affinity and specificity and yielded compounds that selectively inhibited either cholate or taurocholate uptake or uptake of both. No correlation was found between the diuretic potency of bumetanide derivatives, reflecting the affinity to the Na(+)-K(+)-Cl- cotransporter, and their affinity to hepatic bile salt transport. Computer-aided model building combined with the calculation of potential energy maps showed a strictly amphipathic charge separation in bumetanide analogues as in bile acids. Ranking bumetanide compounds by their mean inhibitory concentration values, inhibition constants, and their type of competition, we conclude that at least three binding domains in the proteins are essential for recognition by bile acid transporters, namely two hydrophobic and an anionic side, and that for the anionic binding region a carbonyl atom in the ligands as an electron donor group is sufficient for ligand interaction.