gebhart/patrepeval huggingface dataset:
Caspases as Targets for Anti-Inflammatory and Anti-Apoptotic Drug Discovery (2000)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTCaspases as Targets for Anti-Inflammatory and Anti-Apoptotic Drug DiscoveryRobert V. Talanian, Kenneth D. Brady, and Vincent L. CrynsView Author Information BASF Bioresearch Corporation, 100 Research Drive, Worcester, Massachusetts 01605, and Endocrinology Division, Northwestern University Medical School, 303 East Chicago Avenue, Chicago, Illinois 60611 Cite this: J. Med. Chem. 2000, 43, 18, 3351–3371Publication Date (Web):August 19, 2000Publication History Received15 February 2000Published online19 August 2000Published inissue 1 September 2000https://pubs.acs.org/doi/10.1021/jm000060fhttps://doi.org/10.1021/jm000060freview-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1291Altmetric-Citations91LEARN 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:Apoptosis,Inhibition,Inhibitors,Monomers,Peptides and proteins Get e-Alerts
Bacterial membrane lipids in the action of antimicrobial agents (2010)

Many antimicrobial agents that target bacteria are cationic and can interact with the anionic lipid components that are exposed on the bacterial membrane. Bacteria vary widely in the nature of the major lipid components that are in the cell membrane. Those bacteria with both anionic as well as zwitterionic or neutral lipids can be induced to form domains in the presence of antimicrobial peptides possessing several cationic charges. This segregation of anionic and zwitterionic lipids into domains can result in the arrest of cell growth or in cell death. Such agents are generally more toxic to Gram-negative bacteria, than to Gram-positive ones. These findings emphasize the importance of the lipid composition of bacterial membranes in determining the susceptibility of the organism to the action of certain antimicrobial agents.
Regulation of Protein Kinase C by the Cytoskeletal Protein Calponin (2000)

Previous studies from this laboratory have shown that, upon agonist activation, calponin co-immunoprecipitates and co-localizes with protein kinase Cepsilon (PKCepsilon) in vascular smooth muscle cells. In the present study we demonstrate that calponin binds directly to the regulatory domain of PKC both in overlay assays and, under native conditions, by sedimentation with lipid vesicles. Calponin was found to bind to the C2 region of both PKCepsilon and PKCalpha with possible involvement of C1B. The C2 region of PKCepsilon binds to the calponin repeats with a requirement for the region between amino acids 160 and 182. We have also found that calponin can directly activate PKC autophosphorylation. By using anti-phosphoantibodies to residue Ser-660 of PKCbetaII, we found that calponin, in a lipid-independent manner, increased auto-phosphorylation of PKCalpha, -epsilon, and -betaII severalfold compared with control conditions. Similarly, calponin was found to increase the amount of (32)P-labeled phosphate incorporated into PKC from [gamma-(32)P]ATP. We also observed that calponin addition strongly increased the incorporation of radiolabeled phosphate into an exogenous PKC peptide substrate, suggesting an activation of enzyme activity. Thus, these results raise the possibility that calponin may function in smooth muscle to regulate PKC activity by facilitating the phosphorylation of PKC.
Circuit Conditions for Parametric Amplification (1958)

ABSTRACT It is shown that signals may be amplified in a circuit which consists exclusively of passive elements if a non-linear or a time-varying reactance is present. Emphasis is placed on describing the physical model which makes amplification possible and the circuit conditions which must be satisfied. The differences between parametric amplifiers and mixers or modulators are discussed.
Optimal number of features as a function of sample size for various classification rules (2004)

e-dougherty@ee.tamu.edu.
Stage at presentation and survival of white and black patients with prostate carcinoma (1993)

This study suggests that factors other than eligibility for medical care may be responsible for the higher proportion of black men with prostate carcinoma presenting with Stage D prostate carcinoma.
On the Security of a Bidirectional Proxy Re-Encryption Scheme from PKC 2010. (2010)

In PKC 2010, Matsuda, Nishimaki and Tanaka proposed a bidirectional proxy reencryption (PRE) scheme without bilinear maps, and claimed that their scheme is chosenciphertext secure in the standard model. However, by giving a concrete attack, in this paper we indicate that their PRE scheme fails to achieve the chosen-ciphertext security. The purpose of this paper is to clarify the fact that, it is still an open problem to come up with a chosen-ciphertext secure PRE scheme without bilinear maps in the standard model.
Cortical demyelination and diffuse white matter injury in multiple sclerosis (2005)

Focal demyelinated plaques in white matter, which are the hallmark of multiple sclerosis pathology, only partially explain the patient's clinical deficits. We thus analysed global brain pathology in multiple sclerosis, focusing on the normal-appearing white matter (NAWM) and the cortex. Autopsy tissue from 52 multiple sclerosis patients (acute, relapsing-remitting, primary and secondary progressive multiple sclerosis) and from 30 controls was analysed using quantitative morphological techniques. New and active focal inflammatory demyelinating lesions in the white matter were mainly present in patients with acute and relapsing multiple sclerosis, while diffuse injury of the NAWM and cortical demyelination were characteristic hallmarks of primary and secondary progressive multiple sclerosis. Cortical demyelination and injury of the NAWM, reflected by diffuse axonal injury with profound microglia activation, occurred on the background of a global inflammatory response in the whole brain and meninges. There was only a marginal correlation between focal lesion load in the white matter and diffuse white matter injury, or cortical pathology, respectively. Our data suggest that multiple sclerosis starts as a focal inflammatory disease of the CNS, which gives rise to circumscribed demyelinated plaques in the white matter. With chronicity, diffuse inflammation accumulates throughout the whole brain, and is associated with slowly progressive axonal injury in the NAWM and cortical demyelination.
Immunochemical characterization of factor VIII inhibitors. (1984)

Factor VIII inhibitors are antibodies, predominantly of the IgG class, that inactivate factor VIII procoagulant activity. They do not fix complement and cannot be detected by standard immunoprecipitin assays. Their immunochemical properties are unusual, for the alloantibodies have consistent light chain restriction (kappa) and most allo- and auto- anti-VIII:C are predominantly or exclusively IgG4. This property may be responsible for the lack of complement fixation and immunoprecipitation. Human anti-VIII:C react with several different VIII:C antigenic determinants, and recent studies have begun to characterize the major epitopes. In addition, anti-VIII:C idiotypes have been identified using both rabbit anti-idiotype serum and monoclonal antibodies. These reagents provide a new way to obtain more precise immunochemical characterization.
De Novo Peptide Sequencing via Tandem Mass Spectrometry (1999)

Peptide sequencing via tandem mass spectrometry (MS/MS) is one of the most powerful tools in proteomics for identifying proteins. Because complete genome sequences are accumulating rapidly, the recent trend in interpretation of MS/MS spectra has been database search. However, de novo MS/MS spectral interpretation remains an open problem typically involving manual interpretation by expert mass spectrometrists. We have developed a new algorithm, SHERENGA, for de novo interpretation that automatically learns fragment ion types and intensity thresholds from a collection of test spectra generated from any type of mass spectrometer. The test data are used to construct optimal path scoring in the graph representations of MS/MS spectra. A ranked list of high scoring paths corresponds to potential peptide sequences. SHERENGA is most useful for interpreting sequences of peptides resulting from unknown proteins and for validating the results of database search algorithms in fully automated, high-throughput peptide sequencing.
Nearly Monodisperse and Shape-Controlled CdSe Nanocrystals via Alternative Routes:  Nucleation and Growth (2002)

The nucleation and growth of colloidal CdSe nanocrystals with a variety of elongated shapes were explored in detail. The critical size nuclei for the system were magic sized nanoclusters, which possessed a sharp and dominated absorption peak at 349 nm. The formation of the unique magic sized nuclei in a broad monomer concentration range was not expected by the classic nucleation theory. We propose that this was a result of the extremely high chemical potential environment, that is, very high monomer concentrations in the solution, required for the growth of those elongated nanocrystals. The shape, size, and size/shape distributions of the resulting nanocrystals were all determined by two related factors, the magic sized nuclei and the concentration of the remaining monomers after the initial nucleation stage. Without any size sorting, nearly monodisperse CdSe quantum structures with different shapes were reproducibly synthesized by using the alternative cadmium precursors, cadmium-phosphonic acid complexes. A reasonably large excess of the cadmium precursor, which is less reactive than the Se precursor, was found beneficial for the system to reach the desired balance between nucleation and growth. The shape evolution and growth kinetics of these elongated nanocrystals were consistent with the diffusion-controlled model proposed previously. The branched nanocrystals had to grow at very high monomer concentrations because the multiple growth centers at the end of each branch must be fed with a very high diffusion flux to keep all branches in the 1D-growth mode. The rice-shaped nanocrystals were found as special products of the 3D-growth stage. The growth of the nanocrystals in the 1D-growth stage was proven to be not unidirectional after the length of the nanocrystals reached a certain threshold. Experimental results indicate that coordinating solvents and two ligands with distinguishable coordinating abilities are both not intrinsic requirements for the growth of elongated CdSe nanocrystals.
A colourless green fluorescent protein homologue from the non-fluorescent hydromedusa Aequorea coerulescens and its fluorescent mutants (2003)

We have cloned an unusual colourless green fluorescent protein (GFP)-like protein from Aequorea coerulescens (acGFPL). The A. coerulescens specimens displayed blue (not green) luminescence, and no fluorescence was detected in these medusae. Escherichia coli expressing wild-type acGFPL showed neither fluorescence nor visible coloration. Random mutagenesis generated green fluorescent mutants of acGFPL, with the strongest emitters found to contain an Glu(222)-->Gly (E222G) substitution, which removed the evolutionarily invariant Glu(222). Re-introduction of Glu(222) into the most fluorescent random mutant, named aceGFP, converted it into a colourless protein. This colourless aceGFP-G222E protein demonstrated a novel type of UV-induced photoconversion, from an immature non-fluorescent form into a green fluorescent form. Fluorescent aceGFP may be a useful biological tool, as it was able to be expressed in a number of mammalian cell lines. Furthermore, expression of a fusion protein of 'humanized' aceGFP and beta-actin produced a fluorescent pattern consistent with actin distribution in mammalian cells.
Functional and molecular expression of a voltage‐dependent K+ channel (Kv1.1) in interstitial cells of Cajal (2001)

1. Located within the gastrointestinal (GI) musculature are networks of cells known as interstitial cells of Cajal (ICC). ICC are associated with several functions including pacemaker activity that generates electrical slow waves and neurotransmission regulating GI motility. In this study we identified a voltage-dependent K(+) channel (Kv1.1) expressed in ICC and neurons but not in smooth muscle cells. 2. Transcriptional analyses demonstrated that Kv1.1 was expressed in whole tissue but not in isolated smooth muscle cells. Immunohistochemical co-localization of Kv1.1 with c-kit (a specific marker for ICC) and vimentin (a specific marker of neurons and ICC) indicated that Kv1.1-like immunoreactivity (Kv1.1-LI) was present in ICC and neurons of GI tissues of the dog, guinea-pig and mouse. Kv1.1-LI was not observed in smooth muscle cells of the circular and longitudinal muscle layers. 3. Kv1.1 was cloned from a canine colonic cDNA library and expressed in Xenopus oocytes. Pharmacological investigation of the electrophysiological properties of Kv1.1 demonstrated that the mamba snake toxin dendrotoxin-K (DTX-K) blocked the Kv1.1 outward current when expressed as a homotetrameric complex (EC(50) = 0.34 nM). Other Kv channels were insensitive to DTX-K. When Kv1.1 was expressed as a heterotetrameric complex with Kv1.5, block by DTX-K dominated, indicating that one or more subunits of Kv1.1 rendered the heterotetrameric channel sensitive to DTX-K. 4. In patch-clamp experiments on cultured murine fundus ICC, DTX-K blocked a component of the delayed rectifier outward current. The remaining, DTX-insensitive current (i.e. current in the presence of 10(-8) M DTX-K) was outwardly rectifying, rapidly activating, non-inactivating during 500 ms step depolarizations, and could be blocked by both tetraethylammonium (TEA) and 4-aminopyridine (4-AP). 5. In conclusion, Kv1.1 is expressed by ICC of several species. DTX-K is a specific blocker of Kv1.1 and heterotetrameric channels containing Kv1.1. This information is useful as a means of identifying ICC and in studies of the role of delayed rectifier K(+) currents in ICC functions.
Macrophage Colony Stimulating Factor Down-Regulates MCSF-Receptor Expression and Entry of Progenitors into the Osteoclast Lineage (1997)

Macrophage colony-stimulating factor (MCSF), although necessary for entry of precursors into the early preosteoclast pathway, inhibits osteoclastogenesis at high doses. To clarify the relationship between MCSF and osteoclast formation, we investigated the effect of exogenous MCSF in murine bone marrow culture. Precursor proliferation and the expression of MCSF-receptor were examined after 4 days of culture in the presence or absence of accessory stromal cells. In both mixed marrow and destromalized cell cultures, exogenous MCSF dose-dependently decreased 125I-MCSF binding (by 65 +/- 5.0% at 3500 and 87 +/- 16.7% at-7000 U/ml, respectively) while enhancing mononuclear cell proliferation after 3 days of exposure (by 2.8- and 6.3-fold, respectively). These effects were maintained 24 h after removal of exogenous MCSF and, as such, likely represented an MCSF-induced change in MCSF receptor-bearing cells. Exposure to exogenous MCSF (3500 U/ml) days 2-4 dose-dependently inhibited tartrate resistant acid phosphatase positive multinuclear cell (TRAP+ MNC) formation counted at the end of day 7, by 64.3 +/- 4.1%. This inhibition of TRAP+ MNC formation was preceded by a 92 +/- 9% decrease in the expression of carbonic anhydrase II mRNA measurable at 4 days. These results indicate that MCSF promotes proliferation of a population of cells expressing lower cognate receptor sites. Changes in MCSF-receptor expression appear to modulate the final lineage selection of the pluripotent monoblastic progenitor.
Masitinib for the treatment of systemic and cutaneous mastocytosis with handicap: A phase 2a study (2010)

Treatment options for patients suffering from indolent forms of mastocytosis remain inadequate with the hyperactivation of mast cells responsible for many of the disease's systemic manifestations. Masitinib is a potent and highly selective oral tyrosine kinase inhibitor. A combined inhibition of c-Kit and Lyn make it particularly efficient in controlling the activity of mast cells and therefore, of potential therapeutic benefit in mastocytosis. Masitinib was administered to 25 patients diagnosed as having systemic or cutaneous mastocytosis with related handicap (i.e., disabilities associated with flushes, depression, pruritus and quality-of-life) at the initial dose levels of 3 or 6 mg/kg/day over 12 weeks. In accordance with the AFIRMM study, response was based upon change of clinical symptoms associated with patient handicap at week 12 relative to baseline, regardless of disease subtype. Improvement was observed in all primary endpoints at week 12 including a reduction of flushes, Hamilton rating, and pruritus as compared with baseline by 64% (P = 0.0005), 43% (P = 0.0049), and 36% (P = 0.0077), respectively. An overall clinical response was observed in 14/25 patients (56%; [95%CI = 37%-75%]), with sustainable improvement observed throughout an extension phase (>60 weeks). Common adverse events were edema (44%), nausea (44%), muscle spasms (28%), and rash (28%), the majority of which were of mild or moderate severity with a significant decline in frequency observed after 12 weeks of treatment. One patient experienced a serious adverse event of reversible agranulocytosis. Masitinib is a promising treatment for indolent forms of mastocytosis with handicap and indicates acceptable tolerability for long-term treatment regimens.
Interleukin 18 together with interleukin 12 inhibits IgE production by induction of interferon-γ production from activated B cells (1997)

Interleukin 18 (IL-18), originally called interferon (IFN)-gamma-inducing factor, is a recently cloned cytokine of approximately 18 kDa synthesized by Kupffer cells and activated macrophages. The major activity associated with this molecule is the induction of IFN-gamma production from anti-CD3-activated T helper 1 cells in the presence of IL-12. B cells produce IgG1 and IgE when stimulated with anti-CD40 and IL-4. Here we show that a combination of IL-12 and IL-18 induces anti-CD40-activated B cells to produce IFN-gamma, which inhibits IL-4-dependent IgE and IgG1 production and enhances IgG2a production without inhibiting the B cell proliferative response. We also show that 24.3% of B cells became positive for cytoplasmic IFN-gamma after being stimulated with IL-12 and IL-18. Furthermore, we show that, like splenic T cells stimulated with anti-CD3, IL-12, and IL-18, B cells produced high level of IFN-gamma in response to anti-CD40, IL-12, and IL-18. Injection of a mixture of IL-12 and IL-18 into mice inoculated with Nippostrongylus brasiliensis or injected with anti-IgD induced IFN-gamma-producing cells that inhibit IgE production in them. Furthermore, B cells obtained from normal mice could develop into IFN-gamma-producing cells in IFN-gamma(-/-) host mice in response to in vivo treatment with IL-12 and IL-18. These results indicate that IFN-gamma from activated B cells differentially regulates IgG1/IgE and IgG2a responses in vitro and in vivo, indicating that B cells act as regulatory cells in the immune response. Present results suggested that injection of IL-12 and IL-18 could present a unique approach for the treatment of allergic disorders.
SCAN: Learning Abstract Hierarchical Compositional Visual Concepts (2017)

The natural world is infinitely diverse, yet this diversity arises from a relatively small set of coherent properties and rules, such as the laws of physics or chemistry. We conjecture that biological intelligent systems are able to survive within their diverse environments by discovering the regularities that arise from these rules primarily through unsupervised experiences, and representing this knowledge as abstract concepts. Such representations possess useful properties of compositionality and hierarchical organisation, which allow intelligent agents to recombine a finite set of conceptual building blocks into an exponentially large set of useful new concepts. This paper describes SCAN (Symbol-Concept Association Network), a new framework for learning such concepts in the visual domain. We first use the previously published beta-VAE (Higgins et al., 2017a) architecture to learn a disentangled representation of the latent structure of the visual world, before training SCAN to extract abstract concepts grounded in such disentangled visual primitives through fast symbol association. Our approach requires very few pairings between symbols and images and makes no assumptions about the choice of symbol representations. Once trained, SCAN is capable of multimodal bi-directional inference, generating a diverse set of image samples from symbolic descriptions and vice versa. It also allows for traversal and manipulation of the implicit hierarchy of compositional visual concepts through symbolic instructions and learnt logical recombination operations. Such manipulations enable SCAN to invent and learn novel visual concepts through recombination of the few learnt concepts.
Neuroendocrine secretory protein 7B2: structure, expression and functions (2001)

7B2 is an acidic protein residing in the secretory granules of neuroendocrine cells. Its sequence has been elucidated in many phyla and species. It shows high similarity among mammals. A Pro-Pro-Asn-Pro-Cys-Pro polyproline motif is its most conserved feature, being carried by both vertebrate and invertebrate sequences. It is biosynthesized as a precursor protein that is cleaved into an N-terminal fragment and a C-terminal peptide. In neuroendocrine cells, 7B2 functions as a specific chaperone for the proprotein convertase (PC) 2. Through the sequence around its Pro-Pro-Asn-Pro-Cys-Pro motif, it binds to an inactive proPC2 and facilitates its transport from the endoplasmic reticulum to later compartments of the secretory pathway where the zymogen is proteolytically matured and activated. Its C-terminal peptide can inhibit PC2 in vitro and may contribute to keep the enzyme transiently inactive in vivo. The PC2–7B2 model defines a new neuroendocrine paradigm whereby proteolytic activation of prohormones and proneuropeptides in the secretory pathway is spatially and temporally regulated by the dynamics of interactions between converting enzymes and their binding proteins. Interestingly, unlike PC2-null mice, which are viable, 7B2-null mutants die early in life from Cushing's disease due to corticotropin (‘ACTH’) hypersecretion by the neurointermediate lobe, suggesting a possible involvement of 7B2 in secretory granule formation and in secretion regulation. The mechanism of this regulation is yet to be elucidated. 7B2has been shown to be a good marker of several neuroendocrine cell dysfunctions in humans. The possibility that anomalies in its structure and expression could be aetiological causes of some of these dysfunctions warrants investigation.