gebhart/patrepeval huggingface dataset:
Phorbol ester inhibits 13‐cis‐retinoic acid‐induced hydrolysis of phosphatidylinositol 4,5‐bisphosphate in cultured murine keratinocytes: A possible negative feedback via protein kinase C‐activation (1991)

The incubation of double-labelled [( 14C]-glycerol and [3H]-myoinositol) keratinocytes with 13-cis retinoic acid induced the transient and simultaneous release of [3H]-inositol trisphosphate ([3H]-InsP3) and [14C]-diacylglycerol ([14C]-DAG) indicating that a possible mode of action of this retinoid on murine keratinocytes may be at least in part the early transient release of the two putative messengers (InsP3 and DAG) from phosphatidylinositol-4,5 bisphosphate (PtdIns4, 5P2). In contrast, the preincubation of the keratinocytes with 12-O-tetradecanoylphorbol-13-acetate (TPA) prior to incubation with 13-cis-RA suppressed the 13-cis-RA-induced release of [3H]-InsP3 and [14C]-DAG. The specificity of the TPA effect was established by the lack of effect of the biologically inactive 4 alpha-phorbol 12, 13-didecanoate. Furthermore, the incubation of the TPA-primed keratinocytes with 13-cis-RA caused a delayed and sustained accumulation of [14C]-DAG. An exploration of the source of this late release of [14C]-DAG revealed that this [14C]-DAG was released from non-inositol containing phospholipids, particularly, phosphatidylcholine. This latter DAG released in the TPA-primed cells correlated with the translocation of the cytoplasmic protein kinase C (PKC) activity to the membrane associated PKC activity. Taken together, these results suggest that alteration of PKC activity, presumably induced by DAG released from non-inositol phospholipids, may play a major role in the TPA-induced negative feedback inhibition of 13-cis RA-induced hydrolysis of keratinocyte PtdIns4, 5P2.
Molecular recognition of DNA by small molecules. Synthesis of bis(methidium)spermine, a DNA polyintercalating molecule (1978)

The molecular recognition of DNA by small molecules is an important macromolecular receptor-drug interaction in the field of chemotherapy. The formation of noncovalently bound nucleic acid-drug complexes produces profound pharmacological effects by interfering with biological processes in which nucleic acids participate. The fact that DNA is a defined macromolecular receptor allows a rational approach to drug design and permits a unique opportunity for studying site-specific drug-binding processes. The therapeutic importance and the possibility for a detailed chemical understanding of the mechanism of action of these DNA-drug complexes provide sufficient stimulus to develop a rational methodology for optimizing the thermodynamics, kinetics, sequence specificity, structural specificity, and chemical specificity of these binding ligands.
Attributes2Classname: A Discriminative Model for Attribute-Based Unsupervised Zero-Shot Learning (2017)

We propose a novel approach for unsupervised zero-shot learning (ZSL) of classes based on their names. Most existing unsupervised ZSL methods aim to learn a model for directly comparing image features and class names. However, this proves to be a difficult task due to dominance of non-visual semantics in underlying vector-space embeddings of class names. To address this issue, we discriminatively learn a word representation such that the similarities between class and combination of attribute names fall in line with the visual similarity. Contrary to the traditional zero-shot learning approaches that are built upon attribute presence, our approach bypasses the laborious attribute-class relation annotations for unseen classes. In addition, our proposed approach renders text-only training possible, hence, the training can be augmented without the need to collect additional image data. The experimental results show that our method yields state-of-the-art results for unsupervised ZSL in three benchmark datasets.
Postoperative Nomogram for Disease Recurrence After Radical Prostatectomy for Prostate Cancer (1999)

A postoperative nomogram has been developed that can be used to predict the 7-year probability of disease recurrence among men treated with radical prostatectomy.
Knowledge representation in fuzzy logic (1989)

The author presents a summary of the basic concepts and techniques underlying the application of fuzzy logic to knowledge representation. He then describes a number of examples relating to its use as a computational system for dealing with uncertainty and imprecision in the context of knowledge, meaning, and inference. It is noted that one of the basic aims of fuzzy logic is to provide a computational framework for knowledge representation and inference in an environment of uncertainty and imprecision. In such environments, fuzzy logic is effective when the solutions need not be precise and/or it is acceptable for a conclusion to have a dispositional rather than categorical validity. The importance of fuzzy logic derives from the fact that there are many real-world applications which fit these conditions, especially in the realm of knowledge-based systems for decision-making and control.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Local and systemic total antioxidant capacity in periodontitis and health (2004)

These findings suggest that the antioxidant capacity of GCF is both qualitatively and quantitatively distinct from that of saliva, plasma and serum. Whether changes in the GCF compartment in periodontitis reflect predisposition to or the results of ROS-mediated damage remains unclear. Reduced plasma total antioxidant defence could result from low-grade systemic inflammation induced by the host response to periodontal bacteria, or may be an innate feature of periodontitis patients.
Genomic organization of Borna disease virus. (1994)

Borna disease virus is a neurotropic negative-strand RNA virus that infects a wide range of vertebrate hosts, causing disturbances in movement and behavior. We have cloned and sequenced the 8910-nucleotide viral genome by using RNA from Borna disease virus particles. The viral genome has complementary 3' and 5' termini and contains antisense information for five open reading frames. Homology to Filoviridae, Paramyxoviridae, and Rhabdoviridae is found in both cistronic and extracistronic regions. Northern analysis indicates that the virus transcribes mono- and polycistronic RNAs and uses termination/polyadenylylation signals reminiscent of those observed in other negative-strand RNA viruses. Borna disease virus is likely to represent a previously unrecognized genus, bornaviruses, or family, Bornaviridae, within the order Mononegavirales.
Interaction of nucleosome core particles with distamycin and echinomycin: analysis of the effect of DNA sequences (1987)

Two fragments of Xenopus borealis DNA 135 and 189 base-pairs long were separately incorporated into nucleosome core particles by reconstitution with chicken erythrocyte histones, and incubated with echinomycin (a bis-intercalating antitumor antibiotic) or distamycin (a minor groove-binding, non-intercalating antibiotic). Controlled digestion of these defined sequence core particles using DNAase I revealed new cleavage products, indicative of a change in orientation of the DNA molecule on the surface of the nucleosome. This new rotational setting of DNA within the core particle induced by antibiotic binding appears to be practically independent of DNA sequence, although some differences were noted between the patterns of fragments observed in the various experiments, most likely reflecting the exact number and disposition of the antibiotic binding sites.
The Limitations of MALDI-TOF Mass Spectrometry in the Analysis of Wide Polydisperse Polymers (2000)

Average molecular weight determination of polymers with polydispersities greater than 1.2 is an ongoing challenge in the field of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Mass discrimination effects observed in the analysis of these polymers have been attributed to sample preparation, desorption/ionization, and instrumental factors. In an effort to separate these factors, we studied poly(methyl methacrylate) (PMMA) standards using two different ion detection systems installed on the same time-of-flight mass analyzer. Equimass blends of narrow PMMA standards were used to simulate a polymer with a wide polydispersity. MALDI-MS analysis was also performed on a PMMA standard with a polydispersity of 1.7. All samples were analyzed by size exclusion chromatography for comparison. Although sample preparation and ionization/desorption factors were found to influence the spectral appearance of the MMA distributions, we demonstrate that, under similar sample preparation and instrument conditions, different ion detection systems produce different results for synthetic polymer blends. The differences in the detector responses for the blends and wide polydisperse standard arise from several factors related to the ion detection system: (1) detection mechanisms, (2) saturation effects, and (3) signal-to-noise limitations.
Automated design of the surface positions of protein helices (1997)

Using a protein design algorithm that quantitatively considers side-chain interactions, the design of surface residues of alpha helices was examined. Three scoring functions were tested: a hydrogen-bond potential, a hydrogen-bond potential in conjunction with a penalty for uncompensated burial of polar hydrogens, and a hydrogen-bond potential in combination with helix propensity. The solvent exposed residues of a homodimeric coiled coil based on GCN4-p1 were designed by using the Dead-End Elimination Theorem to find the optimal amino acid sequence for each scoring function. The corresponding peptides were synthesized and characterized by circular dichroism spectroscopy and size exclusion chromatography. The designed peptides were dimeric and nearly 100% helical at 1 degree C, with melting temperatures from 69-72 degrees C, over 12 degrees C higher than GCN4-p1, whereas a random hydrophilic sequence at the surface positions produced a peptide that melted at 15 degrees C. Analysis of the designed sequences suggests that helix propensity is the key factor in sequence design for surface helical positions.
Competition between (+)-Catechin and (−)-Epicatechin in Acetaldehyde-Induced Polymerization of Flavanols (1999)

The reactions of (+)-catechin and (-)-epicatechin in the presence of acetaldehyde were studied in model solution systems. When incubated separately with acetaldehyde and at pH values varying from 2.2 to 4. 0, reactions were faster with (-)-epicatechin than with (+)-catechin. In mixtures containing both (+)-catechin and (-)-epicatechin with acetaldehyde, new compounds besides the homogeneous bridged derivatives were detected. These compounds were concluded to be hetero-oligomers consisting of (+)-catechin and (-)-epicatechin linked with an ethyl bridge. In this case, the reaction of (-)-epicatechin was faster than that of (+)-catechin. This was also observed in solutions containing the two flavanols and the (+)-catechin-ethanol intermediate. Under these conditions, the homogeneous (+)-catechin bridged dimers and heterogeneous dimers were obtained by action of the intermediate on (+)-catechin and (-)-epicatechin, respectively. In addition, the homogeneous (-)-epicatechin ethyl-bridged dimers were also detected, showing that ethyl linkages underwent depolymerization and recombination reactions.
Effects of aging on changing arterial compliance and left ventricular load in a northern Chinese urban community. (1983)

Pulse wave velocity (PWV) was measured by means of transcutaneous Doppler techniques in the aorta, right arm, and right leg of 480 normal subjects of both sexes in urban Beijing, China (age range 3 to 89 years, mean age 41 +/- 20.8 SD); supine blood pressure was recorded in the brachial artery of each subject with standard sphygmomanometric procedures. Serum cholesterol was determined in a subgroup of 79 subjects (age 17 to 85 years, mean 47 +/- 26 SD). PWV (y in cm/sec) was found to vary with age (x, years) at each of the three locations according to the following regression equations: aorta, y = 9.2x + 615, r = .673 (p less than .001); right arm, y = 4.8x + 998, r = .453 (p less than .001); right leg, y = 5.6x + 791, r = .630 (p less than .001). Systolic, diastolic, mean, and pulse pressures were found to increase with age. PWV also increased with mean supine blood pressure but was not related to serum cholesterol (average 4.49 +/- 0.11 [SEM], mmol/l). Compared with that of Western populations, serum cholesterol tended to be lower at all age groups, systolic pressure higher at ages over 35 years, and PWV higher at all ages. Because change in PWV is directly related to change in arterial compliance, these results indicate that aging and not concomitant atherosclerosis (known to be rare in Asian populations) is the dominant factor associated with reduced arterial compliance and increased left ventricular load in these subjects.
The Catalytic Subunit of Phosphoinositide 3-Kinase: Requirements for Oncogenicity (2000)

The retroviral oncogene p3k (v-p3k) of avian sarcoma virus 16 (ASV16) codes for the catalytic subunit of phosphoinositide (PI) 3-kinase, p110alpha. The v-P3k protein is oncogenic in vivo and in vitro; its cellular counterpart, c-P3k, lacks oncogenicity. Fusion of viral Gag sequences to the amino terminus of c-P3k activates the transforming potential. Activation can also be achieved by the addition of a myristylation signal to the amino terminus or of a farnesylation signal to the carboxyl terminus of c-P3k. A mutated myristylation signal was equally effective; it also caused a strong increase in the kinase activity of P3k. Mutations that inactivate lipid kinase activity abolish oncogenicity. The transforming activity of P3k is correlated with the ability to induce activating phosphorylation in Akt. Point mutations and amino-terminal deletions recorded in v-P3k were shown to be irrelevant to the activation of oncogenic potential. Interactions of P3k with the regulatory subunit of PI 3-kinase, p85, or with Ras are not required for transformation. These results support the conclusion that the oncogenicity of P3k depends on constitutive lipid kinase activity. Akt is an important and probably essential downstream component of the oncogenic signal from P3k.
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method (2007)

Antigen presenting cells (APCs) sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II) molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC) and three mouse H2-IA alleles. The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR), we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. The SMM-align method was shown to outperform other state of the art MHC class II prediction methods. The method predicts quantitative peptide:MHC binding affinity values, making it ideally suited for rational epitope discovery. The method has been trained and evaluated on the, to our knowledge, largest benchmark data set publicly available and covers the nine HLA-DR supertypes suggested as well as three mouse H2-IA allele. Both the peptide benchmark data set, and SMM-align prediction method (NetMHCII) are made publicly available.
Tinnitus (2002)

Tinnitus is a common but poorly understood disorder that has a strong association with aging. This review explains how to differentiate subjective from objective tinnitus. Although tinnitus is often associated with hearing loss, in many cases the origin may be central. Multiple treatment options may help in the management of this chronic condition.
Axin Pathway Activity Regulates in Vivo pY654-β-catenin Accumulation and Pulmonary Fibrosis (2011)

Epithelial to mesenchymal transition (EMT) and pulmonary fibrogenesis require epithelial integrin α3β1-mediated cross-talk between TGFβ1 and Wnt signaling pathways. One hallmark of this cross-talk is pY654-β-catenin accumulation, but whether pY654-β-catenin is a biomarker of fibrogenesis or functionally important is unknown. To clarify further the role of β-catenin in fibrosis, we explored pY654-β-catenin generation and function. α3β1 was required for TGFβ1-mediated activation of Src family kinases, and Src inhibition blocked both pY654 and EMT in primary alveolar epithelial cells (AECs). TGFβ1 stimulated β-catenin/Lef1-dependent promoter activity comparably in immortalized AECs stably expressing WT β-catenin as well as Y654E or Y654F β-catenin point mutants. But EMT was abrogated in the Tyr to Phe mutant. pY654-β-catenin was sensitive to the axin β-catenin turnover pathway as inhibition of tankyrase 1 led to high AEC axin levels, loss of pY654-β-catenin, and inhibition of EMT ex vivo. Mice given a tankyrase inhibitor (50 mg/kg orally) daily for 7 days beginning 10 days after intratracheal bleomycin had improved survival over controls. Treated mice developed raised axin levels in the lung that abrogated pY654-β-catenin and attenuated lung Snail1, Twist1, α-smooth muscle actin, and type I collagen accumulation. Total β-catenin levels were unaltered. These findings identify Src kinase(s) as a mediator of TGFβ1-induced pY654-β-catenin, provide evidence that pY654-β-catenin levels are a critical determinant of EMT and fibrogenesis, and suggest regulation of axin levels as a novel therapeutic approach to fibrotic disorders.
The cyclotides: novel macrocyclic peptides as scaffolds in drug design. (2002)

Cyclotides are a novel class of circular, disulfide-rich peptides (approximately 30 amino acids) that display a broad range of bioactivities and have exceptionally high stability. Their physical properties, which include resistance to thermal and enzymatic degradation, can be attributed to their unique cyclic backbone and knotted arrangement of disulfide bonds. The applicability of linear peptides as drugs is potentially limited by their susceptibility to proteolytic cleavage and poor bioavailability. Such limitations may be overcome by using the cyclotide framework as a scaffold onto which new activities may be engineered. The potential use of cyclotides for drug design is evaluated here, with reference to rapidly increasing knowledge of natural cyclotides and the emergence of new techniques in peptide engineering.
IL-23 receptor (IL-23R) gene protects against pediatric Crohnʼs disease (2007)

The protective IL-23R R381Q variant was particularly associated with CD in non-Jewish children. Thus, the initial whole genome association study based on ileal CD in adults has been extended to the pediatric population and beyond small bowel CD.
Definition of human rotavirus serotypes by plaque reduction assay (1982)

Twenty different human rotavirus reassortants were characterized serologically by a plaque reduction assay as belonging to one of three distinct serotypes. Fourteen were similar if not identical to our prototype Wa strain; two were like the prototype DS-1 strain, and four belonged to a third serotype for which a prototype has not yet been selected. Hyperimmune sera raised against the three serotypes were required to distinguish among them, since postinfection sera had lower titers and were more cross-reactive than hyperimmune sera. These results confirmed the ability of a qualitative cytopathic neutralization test to predict correctly the Wa or DS-1 serotype. A strain of rhesus rotavirus (MMU 18006) was identified as belonging to the newly defined third serotype. Finally, an attempt was made to correlate previously published serotype analysis by neutralization of fluorescent cell-forming units with the results determined by the plaque reduction neutralization assay.
Spectroscopic studies on exchange properties in through-ring cyclodextrin complexes of carbazole-viologen linked compounds: effects of spacer chain length (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSpectroscopic studies on exchange properties in through-ring cyclodextrin complexes of carbazole-viologen linked compounds: effects of spacer chain lengthHiroaki Yonemura, Motohiro Kasahara, Hide Saito, Hiroshi Nakamura, and Taku MatsuoCite this: J. Phys. Chem. 1992, 96, 14, 5765–5770Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/j100193a021https://doi.org/10.1021/j100193a021research-articleACS PublicationsRequest reuse permissionsArticle Views291Altmetric-Citations66LEARN 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 optionsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts