gebhart/patrepeval huggingface dataset:
Reviews in Computational Chemistry, Vol. 9 Edited by Kenny B. Lipkowitz and Donald B. Boyd (Indiana University-Purdue University at Indianapolis). Wiley/VCH:  New York. 1996. xxxiii + 282 pp. $120.00. ISBN 1-56081-930-8. (1998)

ADVERTISEMENT RETURN TO ISSUEPREVBook ReviewNEXTReviews in Computational Chemistry, Vol. 9 Edited by Kenny B. Lipkowitz and Donald B. Boyd (Indiana University-Purdue University at Indianapolis). Wiley/VCH: New York. 1996. xxxiii + 282 pp. $120.00. ISBN 1-56081-930-8.Vivian CodyView Author Information Hauptman-Woodward Medical Research InstituteCite this: J. Am. Chem. Soc. 1998, 120, 11, 2692Publication Date (Web):January 30, 1998Publication History Published online30 January 1998Published inissue 1 March 1998https://pubs.acs.org/doi/10.1021/ja975681lhttps://doi.org/10.1021/ja975681lbook-reviewACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views47Altmetric-Citations-LEARN 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 SUBJECTS:Chemical calculations,Computational chemistry,Free energy,Molecular mechanics,Oligosaccharides Get e-Alerts
Ultrafast sequencing of oligodeoxyribonucleo tides by FAB-mass spectrometry (1982)

A fully instrumental method is described for the bidirectional sequencing of oligodeoxyribonucleotides. The method makes use of the negative ion fragmentation patterns of fast atom bombardment mass spectrometry. It is less time consuming than any other sequencing procedure known to date. Since one sequencing run takes as little as one hour, this new method is anticipated to cut down considerably the time required for the controlled synthesis of oligodeoxyribonucleotides of (currently) up to ten nucleotide units in length.
The past decade: fibrinogen. (2005)

This paper reviews the advances in understanding of fibrinogen structure and function, its genetic and environmental determinants, role in the process of hemostasis, platelet aggregation, plasma viscosity and erythrocyte aggregation, cellular and matrix interactions, inflammation, wound healing, tumor development, atherogenesis and involvement in pathogenesis of diseases, that have been made over the past decade. Future studies will seek to define precise mechanisms of complex gene-environment interactions that influence fibrinogen levels and its complex role in the pathogenesis of fibrinogen-associated diseases.
Evidence of p53-Dependent Cross-Talk between Ribosome Biogenesis and the Cell Cycle: Effects of Nucleolar Protein Bop1 on G1/S Transition (2001)

Bop1 is a novel nucleolar protein involved in rRNA processing and ribosome assembly. We have previously shown that expression of Bop1Delta, an amino-terminally truncated Bop1 that acts as a dominant negative mutant in mouse cells, results in inhibition of 28S and 5.8S rRNA formation and deficiency of newly synthesized 60S ribosomal subunits (Z. Strezoska, D. G. Pestov, and L. F. Lau, Mol. Cell. Biol. 20:5516-5528, 2000). Perturbation of Bop1 activities by Bop1Delta also induces a powerful yet reversible cell cycle arrest in 3T3 fibroblasts. In the present study, we show that asynchronously growing cells are arrested by Bop1Delta in a highly concerted fashion in the G(1) phase. Kinase activities of the G(1)-specific Cdk2 and Cdk4 complexes were downregulated in cells expressing Bop1Delta, whereas levels of the Cdk inhibitors p21 and p27 were concomitantly increased. The cells also displayed lack of hyperphosphorylation of retinoblastoma protein (pRb) and decreased expression of cyclin A, indicating their inability to progress through the restriction point. Inactivation of functional p53 abrogated this Bop1Delta-induced cell cycle arrest but did not restore normal rRNA processing. These findings show that deficiencies in ribosome synthesis can be uncoupled from cell cycle arrest and reveal a new role for the p53 pathway as a mediator of the signaling link between ribosome biogenesis and the cell cycle. We propose that aberrant rRNA processing and/or ribosome biogenesis may cause "nucleolar stress," leading to cell cycle arrest in a p53-dependent manner.
Total synthesis of prostaglandins F1.alpha., E1, F2.alpha., and E2 (natural forms) from a common synthetic intermediate (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of prostaglandins F1.alpha., E1, F2.alpha., and E2 (natural forms) from a common synthetic intermediateElias J. Corey, Ryozi Noyori, and Thomas K. SchaafCite this: J. Am. Chem. Soc. 1970, 92, 8, 2586–2587Publication Date (Print):April 1, 1970Publication History Published online1 May 2002Published inissue 1 April 1970https://pubs.acs.org/doi/10.1021/ja00711a083https://doi.org/10.1021/ja00711a083research-articleACS PublicationsRequest reuse permissionsArticle Views1208Altmetric-Citations71LEARN 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
Location of the platelet binding site in zymogen coagulation factor IX (2001)

The assembly of the tenase complex on the surface of the platelet is an essential step in maintaining normal hemostasis as evidenced by the serious hemorrhagic diathesis associated with either factor IX (FIX) or factor VIII deficiencies. Understanding the regions and or residues of FIX crucial for proper binding to platelets has important clinical implications. The ability of FIX to bind activated platelets in the presence of 4 mmol/l CaCl2 was examined using electrophoretic light-scattering experiments. Wild-type FIX binds to activated platelets with dissociation constant Kd = 7.9 nmol/l. Activated FIX binds to activated platelets with Kd = 2 nmol/l. Activated factor VII does not bind activated platelets at physiological concentrations. The Gla domain of FIX is important for the binding of FIX to activated platelets since a chimera with a factor VII (FVII) template and FIX Gla [FVII(FIXGla)] has Kd = 9.6 nmol/l, and a chimera with a FVII template and FIX Gla, A and the first epidermal growth factor domain (EGF1) [FVII(FIXGla,A,EGF1)] has Kd = 9.7 nmol/l, but a chimera with a FIX template and a FVII Gla [FIX(FVIIGla)] does not bind activated platelets. Altering the fifth residue of FIX from a lysine to an alanine (Lys5<--Ala) abolishes the mutant from binding to collagen but does not affect FIX binding to the activated platelet (Kd = 9.8 nmol/l). Point mutations involved with residues 4 and 5 (Gly4<--Phe and Lys5<--no residue), residue 9 (Phe9<--Ala), residue 10 (Val10<--Lys) and residues 9-11 (Phe9<--Met, Val10<--Lys, Glu11<--Lys) do not bind to activated platelets.
Coaxial Group III−Nitride Nanowire Photovoltaics (2009)

Coaxial core/shell nanowires represent an important class of nanoscale building blocks with substantial potential for exploring new concepts and materials for solar energy conversion. Here, we report the first experimental realization of coaxial group III-nitride nanowire photovoltaic (PV) devices, n-GaN/i-In(x)Ga(1-x)N/p-GaN, where variation of indium mole fraction is used to control the active layer band gap and hence light absorption. Current-voltage data reveal clear diode characteristics with ideality factors from 3.9 to 5.6. Electroluminescence measurements demonstrate tunable emission from 556 to 371 nm and thus confirm band gap variations in the In(x)Ga(1-x)N active layer from 2.25 to 3.34 eV as In composition is varied. Simulated one-sun AM 1.5G illumination yielded open-circuit voltages (V(oc)) from 1.0 to 2.0 V and short-circuit current densities (J(sc)) from 0.39 to 0.059 mA/cm(2) as In composition is decreased from 0.27 to 0 and a maximum efficiency of approximately 0.19%. The n-GaN/i-In(x)Ga(1-x)N/p-GaN nanowire devices are highly robust and exhibit enhanced efficiencies for concentrated solar light illuminations as well as single nanowire J(sc) values as high as 390 mA/cm(2) under intense short-wavelength illumination. The ability to rationally tune the structure and composition of these core/shell III-nitride nanowires will make them a powerful platform for exploring nanoenabled PVs in the future.
Surface-induced dissociation in tandem quadrupole mass spectrometers: A comparison of three designs (1992)

Three different devices that-can be used for surface-induced dissociation (SID) m tandem quadrupole instruments are compared here. The designs were compared by examining the fragmentation of several compounds including benzene, W(CO)6, and (CH3)4N(+). These studies show that SID can be readily implemented on a variety of tandem quadrupoIe instruments and that the spectra obtained with the in-line and 90° instruments are similar. Evidence is presented that confirms that high average internal energies and narrow distributions of internal energy are available by this technique. Efficiencies for fragmentation of odd-electron ions are on the order of those previously reported by others. The overall SID efficiency for even-electron ions is higher than that for odd-electron ions of similar structure.
Metformin in Type 1 Diabetes (2003)

ur objective was to evaluate the diagnostic proficiency of the World Health Organization (WHO) and the National Cholesterol Education Program (NCEP)-III definitions (1,2) for the metabolic syndrome in a Mexican nationwide, population-based survey. Details of the sampling procedures have been previously described (3). The population was composed of 2,158 men and women aged 20 -69 years sampled after a 9-to 12-h fasting period. For the WHO criteria, insulin resistance was diagnosed if a nondiabetic case had fasting insulin concentrations 126 pmol/l (21 U/ml) (75th percentile in Mexican adults). The ageadjusted prevalence was 13.61% for the WHO criteria (n 268) and 26.6% for the NCEP-III definition (n 574). After excluding patients with diabetes, the prevalence was 9.2 and 21.4%, respectively. The agreement between the definitions was assessed in 1,969 subjects; 189 cases were eliminated due to the lack of a urine sample.
Private Ordering of Public Markets: The Rating Agency Paradox (2002)

Although merely private entities, rating agencies have a profound economic impact on global finance. At the same time, these entities have engaged in potential abuses, such as threatening to assign unrequested ratings in order to force companies to use their services. Nonetheless, rating agencies are largely unregulated in the United States and abroad. I examine whether rating agencies should be regulated and, if so, whether it is feasible for individual nations to regulate multinational entities of this type.
Alterations in the cyclic AMP signal transduction pathway regulating ribonucleotide reductase gene expression in malignant H‐ras transformed cell lines (1994)

Ribonucleotide reductase is a highly regulated activity responsible for reducing ribonucleotides to deoxyribonucleotides, which are required for DNA synthesis and DNA repair. We have tested the hypothesis that malignant cell populations contain alterations in signal pathways important in controlling the expression of the two genes that code for ribonucleotide reductase, R1 and R2. A series of radiation and H-ras transformed mouse 10T1/2 cell lines with increasing malignant potential were exposed to stimulators of cAMP synthesis (forskolin and cholera toxin), an inhibitor of cAMP degradation (3-isobutyl-1-methylxanthine) and a biologically stable analogue of cAMP (8-bromo-cAMP). Dramatic elevations in the expression of the R1 and R2 genes at the message and protein levels were observed in malignant metastatic populations, which were not detected in the normal parental cell line or in cells capable of benign tumor formation. These changes in ribonucleotide reductase gene expression occurred without any detectable modifications in the rates of DNA synthesis, showing that they were regulated by a novel mechanism independent of the S phase of the cell cycle. Furthermore, studies with forskolin (a stimulator of the protein kinase A signal pathway) and the tumor promoter 12-0-tetradecanoylphorbol-13-acetate (a stimulator of the protein kinase C signal pathway), alone or in combination, indicated that their effects on R1 and R2 gene expression in a highly malignant cell line were greater than when they were tested individually, suggesting that the two pathways modulating R1 and R2 gene expression can cooperate to regulate ribonucleotide reduction, and interestingly this can occur in a synergistic fashion. Also, a direct relationship between H-ras expression and ribonucleotide reductase gene expression was observed; analysis of forskolin mediated elevations in R1 and R2 message levels closely correlated with the levels of H-ras expression in the various cell lines. In total, these studies demonstrate that ribonucleotide reductase expression is controlled by a complex process, and malignant ras transformed cells contain alterations in the regulation of signal transduction pathways that lead to novel modifications in ribonucleotide reductase gene expression. This signal mechanism, which is aberrantly regulated in malignant cells, may be related to regulatory pathways involved in determining ribonucleotide reductase expression in a S phase independent manner during periods of DNA repair.
Identification of TIFA as an Adapter Protein That Links Tumor Necrosis Factor Receptor-associated Factor 6 (TRAF6) to Interleukin-1 (IL-1) Receptor-associated Kinase-1 (IRAK-1) in IL-1 Receptor Signaling (2003)

Tumor necrosis factor receptor-associated factor 6 (TRAF6) transduces signals from members of the Toll/interleukin-1 (IL-1) receptor family by interacting with IL-1 receptor-associated kinase-1 (IRAK-1) after IRAK-1 is released from the receptor-MyD88 complex upon IL-1 stimulation. However, the molecular mechanisms underlying regulation of the IRAK-1/TRAF6 interaction are largely unknown. We have identified TIFA, a TRAF-interacting protein with a forkhead-associated (FHA) domain. The FHA domain is a motif known to bind directly to phosphothreonine and phosphoserine. In transient transfection assays, TIFA activates NFkappaBeta and c-Jun amino-terminal kinase. However, TIFA carrying a mutation that abolishes TRAF6 binding or mutations in the FHA domain that are known to abolish FHA domain binding to phosphopeptide fails to activate NFkappaBeta and c-Jun amino-terminal kinase. TIFA, when overexpressed, binds both TRAF6 and IRAK-1 and significantly enhances the IRAK-1/TRAF6 interaction. Furthermore, analysis of endogenous proteins indicates that TIFA associates with TRAF6 constitutively, whereas it associates with IRAK-1 in an IL-1 stimulation-dependent manner in vivo. Thus, TIFA is likely to mediate IRAK-1/TRAF6 interaction upon IL-1 stimulation.
Quantifiable Interactivity of Malicious URLs and the Social Media Ecosystem (2020)

Online social network (OSN) users are increasingly interacting with each other via articles, comments, and responses. When access control mechanisms are weak or absent, OSNs are perceived by attackers as rich environments for influencing public opinions via fake news posts or influencing commercial transactions via practices such as phishing. This has led to a body of research looking at potential ways to predict OSN user behavior using social science concepts such as conformity and the bandwagon effect. In this paper, we address the question of how social recommendation systems affect the occurrence of malicious URLs on Facebook, based on the assumption that there are no differences among recommendation systems in terms of delivering either legitimate or harmful information to users. Next, we use temporal features to build a prediction framework with &gt;75% accuracy to predict increases in certain user group behaviors. Our effort involves the demarcation of URL classes, from malicious URLs viewed as causing significant damage to annoying spam messages and advertisements. We offer this analysis to better understand OSN user sensors reactions to various categories of malicious URLs in order to mitigate their effects.
Converting Semi-structured Clinical Medical Records into Information and Knowledge (2005)

Clinical medical records contain a wealth of information, largely in free-textual form. Thus, means to extract structured information from free-text records becomes an important research endeavor. In this paper, we propose and implement an information extraction system that extracts three types of information - numeric values, medical terms and categorical value - from semi-structured patient records. Three approaches are proposed to solve the problems posed by each of the three types of values, respectively, and very good performance (precision and recall) is achieved. A novel link-grammar based approach was invented to associate feature and number in a sentence, and extremely high accuracy was achieved. A simple but efficient approach, using POS-based pattern and domain ontology, was adopted to extract medical terms of interest. Finally, an NLPbased feature extraction method coupled with an ID3 based decision tree is used to classify and extract categorical cases. This preliminary approach to categorical fields has, so far, proven to be quite effective.
Isolation of a genomic clone for bovine pancreatic trypsin inhibitor by using a unique-sequence synthetic DNA probe. (1983)

Unique-sequence synthetic DNA probes, based on the known amino acid sequence of bovine pancreatic trypsin inhibitor, were constructed from oligodeoxynucleotides. In genomic Southern blot experiments, these probes were shown to hybridize specifically to discrete restriction fragments. A synthetic probe also was used to isolate a cloned BPTI gene from a bovine genomic library. DNA sequence analysis of this clone indicated that the BPTI coding region was neither preceded by a start codon nor immediately followed by a termination codon. This suggests that the mature form of BPTI may be produced through proteolytic processing from a larger polypeptide precursor.
Membrane-type 5 matrix metalloproteinase is expressed in differentiated neurons and regulates axonal growth. (2001)

Expression of membrane-type (MT) 5 matrix metalloproteinase (MMP) in the mouse brain was examined. MT5-MMP was expressed in the cerebrum in embryos, but it declined after birth. In contrast, expression in the cerebellum started to increase postnatally and continued thereafter. The cells expressing MT5-MMP were postmitotic neurons that showed gelatinolytic activities. Specific expression of MT5-MMP was observed in the neurons but not in the glial cells when embryonal mouse carcinoma P19 cells were differentiated in vitro by retinoic acid treatment. Neurons isolated from dorsal root ganglia also expressed MT5-MMP, and it was localized at the edge of growth cone. Proteoglycans inhibit neurite extension and regulate synaptogenesis. The inhibitory effect of the proteoglycans on neurite extension of dorsal root ganglia neurons was effectively eliminated by recombinant MT5-MMP. Thus, MT5-MMP expressed in neurons may play a role in axonal growth that contributes to the regulation of neural network formation.
Selective cyanylation of sulfhydryl groups. II. Synthesis of 2-nitro-5-thiocyanatobenzoic acid (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelective cyanylation of sulfhydryl groups. II. Synthesis of 2-nitro-5-thiocyanatobenzoic acidAbraham Patchornik and Y. DeganiCite this: J. Org. Chem. 1971, 36, 18, 2727–2728Publication Date (Print):September 1, 1971Publication History Published online1 May 2002Published inissue 1 September 1971https://doi.org/10.1021/jo00817a039RIGHTS & PERMISSIONSArticle Views314Altmetric-Citations103LEARN 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 (334 KB) Get e-Alerts Get e-Alerts
Learning Local Image Descriptors with Deep Siamese and Triplet Convolutional Networks by Minimizing Global Loss Functions (2016)

Recent innovations in training deep convolutional neural network (ConvNet) models have motivated the design of new methods to automatically learn local image descriptors. The latest deep ConvNets proposed for this task consist of a siamese network that is trained by penalising misclassification of pairs of local image patches. Current results from machine learning show that replacing this siamese by a triplet network can improve the classification accuracy in several problems, but this has yet to be demonstrated for local image descriptor learning. Moreover, current siamese and triplet networks have been trained with stochastic gradient descent that computes the gradient from individual pairs or triplets of local image patches, which can make them prone to overfitting. In this paper, we first propose the use of triplet networks for the problem of local image descriptor learning. Furthermore, we also propose the use of a global loss that minimises the overall classification error in the training set, which can improve the generalisation capability of the model. Using the UBC benchmark dataset for comparing local image descriptors, we show that the triplet network produces a more accurate embedding than the siamese network in terms of the UBC dataset errors. Moreover, we also demonstrate that a combination of the triplet and global losses produces the best embedding in the field, using this triplet network. Finally, we also show that the use of the central-surround siamese network trained with the global loss produces the best result of the field on the UBC dataset.