gebhart/patrepeval huggingface dataset:
PREREQUISITES FOR AFFECTIVE SIGNAL PROCESSING (ASP) – PART II (2010)

Last year, in van den Broek et al. (2009a), a start was made with defining prerequisites for affective signal processing (ASP). Four prerequisites were identified: validation (e.g., mapping of constructs on signals), triangulation, a physiology-driven approach, and contributions of the signal processing community. In parallel with this paper, in van den Broek et al. (2010) another set of two prerequisites is presented: integration of biosignals and physical characteristic. This paper continues this quest and defines two additional prerequisites: identification of users and theoretical specification. In addition, the second part of a review on the classification of emotions through ASP is presented; the first part can be found in van den Broek et al. (2009a).
Purification of the catalyst of adenylate cyclase. (1986)

The catalytic moiety of hormone-sensitive adenylate cyclase has been purified from bovine brain. It is isolated largely without its guanine nucleotide-binding regulatory protein, Gs, by affinity chromatography on 7-O-hemisuccinyldeacetylforskolin-agarose. It appears to be a single polypeptide which migrates on sodium dodecyl sulfate-polyacrylamide gels with an apparent Mr of approximately 120,000. When subjected to electrophoresis on gradient (5-10%) sodium dodecyl sulfate-polyacrylamide gels, it displays a larger apparent Mr of 150,000. The adenylate cyclase activity of the preparation can be stimulated by the addition of Gs, forskolin, or calcium-calmodulin. The preparation has been reconstituted with purified beta-adrenergic receptors and Gs to form a hormone-stimulated adenylate cyclase system (May, D., Ross, E.M., Gilman, A.G., and Smigel, M.D. (1985) J. Biol. Chem. 260, 15829-15833). In contrast to its stimulation by Gs, inhibition by the alpha subunits of Gi and Go, G proteins known to be coupled to inhibitory receptors (Sternweis, P., and Florio, V. (1985) J. Biol. Chem. 260, 3477-3483), is not seen. Preparations of adenylate cyclase show varying degrees of inhibition by added G protein beta . gamma subunit. This inhibition can be explained as reflecting a variable, small (under 5%) contamination of the preparation by Gs alpha which would be deactivated by complexing with the added beta . gamma subunit.
The nucleoid-associated protein HUβ affects global gene expression in Porphyromonas gingivalis (2012)

HU is a non-sequence-specific DNA-binding protein and one of the most abundant nucleoid-associated proteins in the bacterial cell. Like Escherichia coli, the genome of Porphyromonas gingivalis is predicted to encode both the HUα (PG1258) and the HUβ (PG0121) subunit. We have previously reported that PG0121 encodes a non-specific DNA-binding protein and that PG0121 is co-transcribed with the K-antigen capsule synthesis operon. We also reported that deletion of PG0121 resulted in downregulation of capsule operon expression and produced a P. gingivalis strain that is phenotypically deficient in surface polysaccharide production. Here, we show through complementation experiments in an E. coli MG1655 hupAB double mutant strain that PG0121 encodes a functional HU homologue. Microarray and quantitative RT-PCR analysis were used to further investigate global transcriptional regulation by HUβ using comparative expression profiling of the PG0121 (HUβ) mutant strain to the parent strain, W83. Our analysis determined that expression of genes encoding proteins involved in a variety of biological functions, including iron acquisition, cell division and translation, as well as a number of predicted nucleoid associated proteins were altered in the PG0121 mutant. Phenotypic and quantitative real-time-PCR (qRT-PCR) analyses determined that under iron-limiting growth conditions, cell division and viability were defective in the PG0121 mutant. Collectively, our studies show that PG0121 does indeed encode a functional HU homologue, and HUβ has global regulatory functions in P. gingivalis; it affects not only production of capsular polysaccharides but also expression of genes involved in basic functions, such as cell wall synthesis, cell division and iron uptake.
Anaerobic citrate metabolism and its regulation in enterobacteria. (1997)

Several species of enterobacteria are able to utilize citrate as carbon and energy source. Under oxic conditions in the presence of a functional tricarboxylic acid cycle, growth on this compound solely depends on an appropriate transport system. During anaerobiosis, when 2-oxoglutarate dehydrogenase is repressed, some species such as Klebsiella pneumoniae and Salmonella typhimurium, but not Escherichia coli, are capable of growth on citrate by a Na+-dependent pathway forming acetate, formate, and CO2 as products. During the last decade, several novel features associated with this type of fermentation have been discovered in K. pneumoniae. The biotin protein oxaloacetate decarboxylase, one of the key enzymes of the pathway besides citrate lyase, is a Na+ pump. Recently it has been shown that the proton required for the decarboxylation of carboxybiotin is taken up from the side to which Na+ ions are pumped, and a membrane-embedded aspartate residue that is probably involved both in Na+ and in H+ transport was identified. The Na+ gradient established by oxaloacetate decarboxylase drives citrate uptake via CitS, a homodimeric carrier protein with a simultaneous-type reaction mechanism, and NADH formation by reversed electron transfer involving formate dehydrogenase, quinone, and a Na+-dependent NADH:quinone oxidoreductase. All enzymes specifically required for citrate fermentation are induced under anoxic conditions in the presence of citrate and Na+ ions. The corresponding genes form a cluster on the chromosome and are organized as two divergently transcribed operons. Their co-ordinate expression is dependent on a two-component system consisting of the sensor kinase CitA and the response regulator CitB. The citAB genes are part of the cluster and are positively autoregulated. In addition to CitA/CitB, the cAMP receptor protein (Crp) is involved in the regulation of the citrate fermentation enzymes, subjecting them to catabolite repression.
Dorothy Russell Memorial Lecture The molecular pathology of Alzheimer's disease: are we any closer to understanding the neurodegenerative process? (1994)

Alzheimer's disease, the most common cause of dementia in the elderly, is rapidly becoming epidemic in the western world, with major social and economic ramifications. Thus enormous international scientific efforts are being made to increase our understanding of the pathogenesis of this disease, with the eventual goal of developing beneficial therapy. The two major neuropathological hallmarks of Alzheimer's disease (AD) are extracellular senile plaques, the principal component of which is the A beta amyloid peptide, and intraneuronal neurofibrillary tangles, which are composed of aggregated tau protein in the form of paired helical filaments (PHF). In the past decade, since the major proteinaceous components of these pathological markers have been identified, great strides have been made in elucidating the biochemical processes which may underlie their abnormal deposition and aggregation in Alzheimer's disease. Simultaneously, extensive population genetic analyses have identified mutations in the A beta amyloid precursor protein (APP) in a small number of pedigrees with familial Alzheimer's disease (FAD) whilst other FAD cases have been linked to an, as yet, unidentified marker on chromosome 14. Most recently, inheritance of the type 4 allele of apolipoprotein E has also been identified as a risk factor in sporadic AD. The challenge facing scientists now is to incorporate this wealth of exciting new biochemical and genetic data into a coherent model which can explain the long established neurochemical and histopathological lesions characteristic of AD.
Role of the Bp35 cell surface polypeptide in human B-cell activation. (1985)

A 35-kDa polypeptide, Bp35, expressed on the surface of all B cells, plays a role in B-cell activation. Monoclonal antibodies to Bp35 stimulate human tonsillar B cells to proliferate. The activation induced by anti-Bp35 is similar to anti-Ig-mediated in several ways: the activation does not require T cells but is augmented by T-cell-derived allogeneic factors; monovalent Fab fragments to Bp35 do not trigger proliferation but instead block activation by whole antibody, indicating that cross-linking is required; and induction by anti-Bp35, like the induction by anti-Ig, is inhibited by monoclonal anti-IgM via an Fc domain-dependent mechanism. However, several features of anti-Bp35-mediated proliferation are clearly different from activation by anti-Ig: anti-Bp35 monoclonal antibodies do not require attachment to beads to function, the proliferation induced by anti-Bp35 and anti-Ig is additive, and Fab fragments of anti-Bp35 augment proliferation induced by anti-Ig. Models for the possible function of the Bp35 polypeptide as either a "bridge" or a "second signal" with surface Ig in B-cell activation are discussed.
[A new strategy of gene therapy for hyperphenylalaninemia rats]. (2000)

The engineering L. L. expressing PAL activity can reduce the blood phe level of the hyperphenylalaninemia rats. This may be a potential way for PKU gene therapeutics.
Using Hydrogen Bonding to Control Carbamate C−N Rotamer Equilibria (1998)

In chloroform solution, the syn/anti rotamer ratios for N-(2-pyridyl)carbamates, 3, and N-phenylcarbamates, 4, are close to 0.05. Addition of the double hydrogen bonding acetic acid moderately stabilizes the syn rotamer of 4, but has no measurable effect on the syn/anti ratio for 3. Conversely, the hydrogen bond donor-acceptor-donor triad in 2,6-bis(octylamido)pyridine, 1, strongly stabilizes the syn rotamer of 3, but has no effect on the syn/anti ratio for 4. The K(a) for syn-3:1 is 10(3)-10(4) times higher than the K(a) for anti-3:1. This implies that the alkoxy oxygen in anti-3 is a much poorer hydrogen bond acceptor than the carbonyl oxygen in syn-3, most likely because of a combination of steric and electrostatic factors.
Synthesis of Oligonucleotides and Oligonucleotide Analogues (1989)

The aim of this review is to outline modern methods for synthesizing natural oligodeoxynucleotides and certain analogues that may be inhibitors of gene expression. As a consequence, several DNA chemical synthesis methodologies such as the phosphate diester and phosphate triester approaches, which are now primarily only of historical interest, will not be discussed, even though they contributed significantly towards solving many important biological problems (Khorana et al., 1966, 1972; Caruthers, 1980; Itakura et al., 1984). Instead the more recent methodologies, which involve phosphorus(III) chemistry, will be emphasized (the phosphite triester and H-phosphonate approaches). There are two reasons. First, these chemistries are compatible with polymer-supported DNA synthesis procedures — a method that is uniquely suited to automation. Second, since phosphorus(III) intermediates can be oxidized to a large number of analogues, these approaches offer a versatility for modifying DNA that is not available with the earlier-developed methodologies. There are, however, certain analogues having potential as inhibitors of gene expression that are currently prepared using phosphorus(V) chemistry. The synthesis of these analogues will also be outlined.
Role of Glycogen Synthase Kinase-3 in the Phosphatidylinositol 3-Kinase/Akt Cell Survival Pathway (1998)

Growth factor-dependent survival of a variety of mammalian cells is dependent on the activation of phosphatidylinositol (PI) 3-kinase and its downstream effector, the protein kinase Akt. Glycogen synthase kinase-3 (GSK-3) has been previously identified as a physiological target of Akt, which is inhibited by phosphorylation, so we have investigated the role of GSK-3 in cell survival. Overexpression of catalytically active GSK-3 induced apoptosis of both Rat-1 and PC12 cells, whereas dominant-negative GSK-3 prevented apoptosis following inhibition of PI 3-kinase. GSK-3 thus plays a critical role in regulation of apoptosis and represents a key downstream target of the PI 3-kinase/Akt survival signaling pathway.
Magnetically Aligned Membrane Model Systems with Positive Order Parameter:  Switching the Sign of Szz with Paramagnetic Ions (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTMagnetically Aligned Membrane Model Systems with Positive Order Parameter: Switching the Sign of Szz with Paramagnetic IonsR. Scott Prosser, Sheri A. Hunt, John A. DiNatale, and Regitze R. VoldView Author Information Department of Chemistry and Biochemistry University of California, San Diego La Jolla, California 92093-0359Cite this: J. Am. Chem. Soc. 1996, 118, 1, 269–270Publication Date (Web):January 10, 1996Publication History Received26 October 1995Published online10 January 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja953598xhttps://doi.org/10.1021/ja953598xrapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views767Altmetric-Citations177LEARN 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:Hydrogen isotopes,Ions,Lipids,Magnetic properties,Vesicles Get e-Alerts
Diagnosis and biomarkers of predementia in Alzheimer's disease (2010)

In view of the growing prevalence of Alzheimer's disease (AD) worldwide, there is an urgent need for the development of better diagnostic tools and more effective therapeutic interventions. At the earliest stages of AD, no significant cognitive or functional impairment is detected by conventional clinical methods. However, new technologies based on structural and functional neuroimaging, and on the biochemical analysis of cerebrospinal fluid (CSF) may reveal correlates of intracerebral pathology in individuals with mild, predementia symptoms. These putative correlates are commonly referred to as AD-related biomarkers. The relevance of the early diagnosis of AD relies on the hypothesis that pharmacological interventions with disease-modifying compounds are likely to produce clinically relevant benefits if started early enough in the continuum towards dementia. Here we review the clinical characteristics of the prodromal and transitional states from normal cognitive ageing to dementia in AD. We further address recent developments in biomarker research to support the early diagnosis and prediction of dementia, and point out the challenges and perspectives for the translation of research data into clinical practice.
Distilling structure in Taverna scientific workflows: a refactoring approach (2014)

We have designed and implemented an approach to improving workflow structure by way of rewriting preserving workflow semantics. Future work includes considering our refactoring approach during the phase of workflow design and proposing guidelines for designing distilled workflows.
Function of simian virus 40 gene A in transforming infection (1975)

In productive infection by simian virus 40, the A gene is known to regulate the initiation of viral DNA replication and to control the synthesis of late viral RNA. The function of the A gene in transforming infection was investigated by the infection of a variety of cell species with six independently isolated temperature-sensitive mutants belonging to the A complementation group. The A mutants failed to initiate the stable transformation of cells during continuous infection at the restrictive temperature. After the establishment of transformation at the permissive temperature and a subsequent shift to the restrictive temperature to block the A function, however, two distinct virus-cell interactions were identified. In one case, the increased colony-forming capacity of transformed cells remained stable after the temperature shift. In the other case, the temperature shift decreased the capacity of transformed cells to form colonies to the level of untransformed control cells. The outcome of the virus-cell interaction depended both on the nature of the A mutation in a given cell species and on the species of the cell transformed by a given mutant. These findings suggest that the transformation process may require two distinct events, each related to A gene expression.
The way of synthesis: evolution of design and methods for natural products (2008)

Foreword. Preface. Part 1: Introduction. Part 2: Strategy and Tactics. Part 3: Comparative Design: Classics in Terpene Synthesis. Part 4: Comparative Design: Classics in Alkaloid Synthesis. Part 5: Miscellaneous Compounds. Part 6: Outlook. Part 7: Acknowledgments. Part 8: Appendix. Subject Index. Author Index. Index of personal recollection.
Hydrocarbonylation of prop-2-en-1-ol to butane-1,4-diol and 2-methylpropan-1-ol catalysed by rhodium triethylphosphine complexes (1996)

The hydrocarbonylation of prop-2-ene-1-ol catalysed by [Rh2(O2CMe)4]–PEt3, which gives [RhH(CO)(PEt3)2] as the active species, has been found to produce predominantly butane-1,4-diol and 2-methylpropan-1-ol with small amounts of 2-methylpropane-1,3-diol and propan-1-ol. Neither 2-enal nor 2-methylprop-2-en-1-ol are intermediates in the production of 2-methylpropan-1-ol. By carrying out the reaction under a variety of reaction conditions and by using deuterium-labelling studies it was possible to formulate a mechanism for the production of 2-methylpropan-1-ol which involves formation of the vinyl alcohol, 2-methylprop-1-en-1-ol, as the primary product followed by tautomerism and hydrogenation, provided that at least two PEt3 groups are co-ordinated to the rhodium. A dehydration is proposed to occur during the catalytic cycle from a cationic hydroxycarbene intermediate. Using propenyl ethers as substrates similar products are obtained presumably via loss of alcohol rather than dehydration. If less than two PEt3 groups are co-ordinated to rhodium the major branched-chain product from prop-2-en-1-ol is 2-methylpropane-1,3-diol. This is interpreted as indicating that protonation of the acyl intermediate and dehydration of the hydroxycarbene do not occur because of the lower electron density on the acyl O atom.
Progress in the Discovery of Biosynthetic Anticancer Drugs (1996)

ADVERTISEMENT RETURN TO ISSUEPREVInvited ReviewNEXTProgress in the Discovery of Biosynthetic Anticancer Drugs 1George R. PettitView Author Information Cancer Research Institute and Department of Chemistry, Arizona State University, Tempe, Arizona 85287-2404 Cite this: J. Nat. Prod. 1996, 59, 8, 812–821Publication Date (Web):August 22, 1996Publication History Received6 May 1996Published online22 August 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/np9604386https://doi.org/10.1021/np9604386review-articleACS PublicationsCopyright © 1996 American Chemical Society and American Society of PharmacognosyRequest reuse permissionsArticle Views1478Altmetric-Citations121LEARN 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:Antineoplastic agents,Cancer,Cells,Chemical structure,Pharmaceuticals Get e-Alerts
Transcriptional Control Signals of a Eukaryotic Protein-Coding Gene (1982)

Transcriptional control signals of a model eukaryotic protein-coding gene have been identified by a new procedure of in vitro mutagenesis. This method allows small clusters of nucleotide residues to be substituted in a site-directed manner without causing the addition or deletion of other sequences. Transcription assays of a systematic series of these clustered point mutants have led to the identification of three distinct control signals located within the 105-nucleotide residues immediately upstream from the point where transcription begins.
Rational design and synthesis of a novel class of active site-targeted HIV protease inhibitors containing a hydroxymethylcarbonyl isostere. Use of phenylnorstatine or allophenylnorstatine as a transition-state mimic. (1991)

A novel class of HIV-1 protease inhibitors containing a hydroxymethylcarbonyl (HMC) isostere were designed from the substrate transition state and synthesized. Phenylnorstatine [Pns; (2R,3S)-3-amino-2-hydroxy-4-phenylbutyric acid] and the 2S diastereomer, (2S,3S)-3-amino-2-hydroxy-4-phenylbutyric acid, named allophenylnorstatine (Apns) were effective transition-state mimics, and incorporation of Pns-Pro or Apns-Pro at the P1-P1' site gave potent and specific HIV-1 protease inhibitors. In the inhibitory assays, the chemically synthesized [Ala67,95] HIV-1 protease was used.
Act1, an NF-κB-activating protein (2000)

Use of an NF-kappaB-dependent selectable marker facilitated the isolation of a cell line containing a cDNA encoding Act1, an NF-kappaB activator. Act1 associates with and activates IkappaB kinase (IKK), leading to the liberation of NF-kappaB from its complex with IkappaB. Many signaling pathways that liberate NF-kappaB also activate activating transcription factor (ATF) and activator protein 1 (AP-1) through Jun kinase (JNK). Act1 also activates JNK, suggesting that it might be part of a multifunctional complex involved in the activation of both NF-kappaB and JNK. Act1 fails to activate NF-kappaB in an IL-1-unresponsive mutant cell line in which all known signaling components are present, suggesting that it interacts with an unknown component in IL-1 signaling.
Saccharide-Dependent Induction of Chiral Helicity in Achiral Synthetic Hydrogen-Bonding Oligomers (2004)

Conformational transitions of biopolymers are well-known to be affected by noncovalent interactions with small molecules. We found that synthetic polymers, poly- and oligo(meta-ethynylpyridine)s, are guided to helical structures by uncharged hydrogen-bonding interactions with saccharides enclosed in the inner sphere of the polymers. Circular dichroism (CD) studies revealed that chirality of saccharide was transferred to the helical sense of the polymers. Among the n-octyl pyranosides of naturally important hexoses, beta-glucoside induced CDs most effectively. Size-regulated 18-mer and longer oligomers also showed the induced CDs similar to those for the polymers. Furthermore, native monosaccharides were extracted into less polar organic solvent with the help of the polymers, inducing similar CD signals.