gebhart/patrepeval huggingface dataset:
Type I Interferons (1998)

Type I interferons (IFNs) constitute a family of structurally related proteins that are all derived from the same ancestral gene and act on a common cell-surface receptor. Contrary to many other cytokines, the production of type I IFNs is not a specialized function, and all cells in the organism can produce them, usually as a result of induction by viruses, via the formation of double-stranded RNA. Type I IFNs are indeed responsible for the first line of defense during virus infection and act through the induction of a great number of proteins. Of these, at least thirty have been characterized, and there are probably many more. In addition to their direct antiviral effect, type I IFNs exert a wide variety of other activities, such as for example the induction of various cytokines and the stimulation of different effector cells of the immune system. Due to these pleiotropic effects, recombinant interferons are used in the clinic to treat a variety of diseases, among which cancer, viral hepatitis and multiple sclerosis.
Regulation of Phosphoinositide-Specific Phospholipase C (2001)

Eleven distinct isoforms of phosphoinositide-specific phospholipase C (PLC), which are grouped into four subfamilies (beta, gamma, delta, and epsilon), have been identified in mammals. These isozymes catalyze the hydrolysis of phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] to inositol 1,4,5-trisphosphate and diacylglycerol in response to the activation of more than 100 different cell surface receptors. All PLC isoforms contain X and Y domains, which form the catalytic core, as well as various combinations of regulatory domains that are common to many other signaling proteins. These regulatory domains serve to target PLC isozymes to the vicinity of their substrate or activators through protein-protein or protein-lipid interactions. These domains (with their binding partners in parentheses or brackets) include the pleckstrin homology (PH) domain [PtdIns(3)P, beta gamma subunits of G proteins] and the COOH-terminal region including the C2 domain (GTP-bound alpha subunit of Gq) of PLC-beta; the PH domain [PtdIns(3,4,5)P3] and Src homology 2 domain [tyrosine-phosphorylated proteins, PtdIns(3,4,5)P3] of PLC-gamma; the PH domain [PtdIns(4,5)P2] and C2 domain (Ca2+) of PLC-delta; and the Ras binding domain (GTP-bound Ras) of PLC-epsilon. The presence of distinct regulatory domains in PLC isoforms renders them susceptible to different modes of activation. Given that the partners that interact with these regulatory domains of PLC isozymes are generated or eliminated in specific regions of the cell in response to changes in receptor status, the activation and deactivation of each PLC isoform are likely highly regulated processes.
Cellular Mechanisms of Tissue Fibrosis. 1. Common and organ-specific mechanisms associated with tissue fibrosis (2012)

Fibrosis is a pathological scarring process that leads to destruction of organ architecture and impairment of organ function. Chronic loss of organ function in most organs, including bone marrow, heart, intestine, kidney, liver, lung, and skin, is associated with fibrosis, contributing to an estimated one third of natural deaths worldwide. Effective therapies to prevent or to even reverse existing fibrotic lesions are not yet available in any organ. There is hope that an understanding of common fibrosis pathways will lead to development of antifibrotic therapies that are effective in all of these tissues in the future. Here we review common and organ-specific pathways of tissue fibrosis.
Musculoskeletal involvement in systemic lupus erythematosus (2004)

Involvement of the musculoskeletal system is common if not universal in the clinical course of systemic lupus erythematosus (SLE). Joint involvement on the whole does not cause major erosive disease, however, recent developments in musculoskeletal imaging show clearly the presence of significant bony and soft tissue involvement. It might well explain the frequently observed discordance between the clinical signs and the articular symptoms assuming that fibromyalgia has been excluded. The clear demonstration of tendon involvement in SLE by MRI would merit considering tendonitis and tenosynovitis as candidates for inclusion in the diagnostic criteria.
In Vivo and In Vitro Activities of the gp130-Stimulating Designer Cytokine Hyper-IL-6 (1998)

IL-6 is a multifactorial cytokine mediating acute inflammatory responses in the liver. When IL-6 binds to a specific receptor (IL-6R), the IL-6/IL-6R complex associates with the signal transducer gp130, initiating intracellular signaling. A soluble form of the IL-6R (sIL-6R) renders target cells sensitive to IL-6 that do not express the IL-6R on their surfaces. A designer cytokine, termed Hyper-IL-6, consisting of IL-6 covalently linked to the sIL-6R was fully active on gp130-expressing cells at 100- to 1000-fold lower concentrations than unlinked IL-6 and IL-6R. Mice were injected i.p. with Hyper-IL-6 or IL-6. Upon injection of Hyper-IL-6 into mice, the acute phase response, as measured by haptoglobin mRNA expression in the liver, was markedly increased and lasted significantly longer compared with that in mice injected with a 10-fold higher dose of IL-6 alone. On human hepatoma cells, Hyper-IL-6 caused similar effects, indicating that the longer lasting response to the fusion protein could not only be explained by the longer plasma half-life of the fusion protein. Experiments using iodinated IL-6 and Hyper-IL-6 revealed that Hyper-IL-6 bound with high affinity to gp130 and was less efficiently internalized. This effect might explain the longer lasting activity of this protein on cells. The highly active IL-6/sIL-6R designer protein might be of significant clinical importance for the stimulation of cells that are more responsive to the IL-6/sIL-6R complex than to IL-6 alone. Such cells include hemopoietic progenitor cells and hepatocytes.
Mutual Information, Fisher Information, and Population Coding (1998)

In the context of parameter estimation and model selection, it is only quite recently that a direct link between the Fisher information and information-theoretic quantities has been exhibited. We give an interpretation of this link within the standard framework of information theory. We show that in the context of population coding, the mutual information between the activity of a large array of neurons and a stimulus to which the neurons are tuned is naturally related to the Fisher information. In the light of this result, we consider the optimization of the tuning curves parameters in the case of neurons responding to a stimulus represented by an angular variable.
Principles of Toxicology (1997)

Principles of toxicology , Principles of toxicology , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
Antisense Inhibition of c-fes Proto-oncogene Blocks PMA-Induced Macrophage Differentiation in HL60 and in FDC-P1/MAC-11 Cells (1997)

To gain some insight into the role of c-fes in macrophage differentiation, we have analyzed the ability of HL60 leukemic promyelocytic cells and FDC-P1/MAC-11 murine myeloid precursor cells to differentiate in response to phorbol esters after inhibition of c-fes function. Fes inactivation has been obtained by using oligodeoxynucleotides (ODN) complementary to the 5' region of c-fes mRNA and to 5' splice junctions of c-fes primary transcript. After 5 days (d) in culture, in several separate experiments performed with different ODN preparations, a complete inhibition of c-fes expression was observed in HL60 and in FDC-P1/MAC-11 cells. No perturbation of cell growth was evident in our experimental conditions in both cell lines after c-fes inhibition. Furthermore, in HL60 cells lacking c-fes product, an almost complete downregulation of the alpha 4 beta 1 fibronectin receptor occurred. However, in both cell lines, the induction of macrophage differentiation by phorbol esters resulted in an almost complete maturation arrest as evaluated by morphological, cytochemical, immunological criteria, and by the cytofluorimetric cell cycle analysis. A loss of the adhesion capacity of both myeloid cell lines, when compared to terminally differentiated macrophages, was also observed. These results suggest that HL60 and FDC-P1/MAC-11 cells, when treated with phorbol 12-myristate 13-acetate, require c-fes protein expression to activate the genetic program underlying macrophage differentiation.
High Specificity in Protein Recognition by Hydrogen‐Bond‐Surrogate α‐Helices: Selective Inhibition of the p53/MDM2 Complex (2010)

Split kit: Synthetic helices target chosen protein–protein interactions with high specificity, as assessed by an in vitro split-protein reassembly assay. By using the p53/MDM2 complex as a model system, both the efficacy of the designed ligands and the suitability of the split-protein assay were determined. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
MIMIC: Finding Optima by Estimating Probability Densities (1996)

In many optimization problems, the structure of solutions reflects complex relationships between the different input parameters. For example, experience may tell us that certain parameters are closely related and should not be explored independently. Similarly, ex-perience may establish that a subset of parameters must take on particular values. Any search of the cost landscape should take advantage of these relationships. We present MIMIC, a framework in which we analyze the global structure of the optimization land-scape. A novel and efficient algorithm for the estimation of this structure is derived. We use knowledge of this structure to guide a randomized search through the solution space and, in turn, to re-fine our estimate ofthe structure. Our technique obtains significant speed gains over other randomized optimization procedures. 1
Hysterectomy vs. resectoscopic endometrial ablation for the control of abnormal uterine bleeding. A cost-comparative study. (1994)

This study compared the costs of endometrial ablation using the uterine resectoscope to those of hysterectomy in a group of patients treated for abnormal uterine bleeding who were enrolled in a national managed health care organization. The cost of endometrial ablation during the periprocedural period was significantly lower than that of hysterectomy, with much of the difference coming from the hospitalization required for the latter procedure. The postprocedural cost for ablation was higher than for hysterectomy owing to the need for second ablations or hysterectomy in 13 of the 85 ablation patients. Preprocedure costs were not different between ablation and hysterectomy. A reanalysis of the data, however, that excluded patients who required a second ablation or hysterectomy suggested that these additional procedures were responsible for the higher postprocedural costs in the ablation group. Resectoscopic endometrial ablation for the treatment of abnormal uterine bleeding resulted in lower periprocedure costs and lower overall treatment costs to the health plan in the groups studied as compared with hysterectomy. Greater familiarity with the technique of resectoscopic endometrial ablation, improved patient selection for the procedure and the use of appropriate pharmacotherapy for suppressing endometrial growth prior to ablation probably substantially improve the rate of success, reduce postprocedural costs and further enhance the cost advantage of this procedure.
Live-attenuated bacteria as a cancer vaccine vector (2013)

In the emerging field of active and specific cancer immunotherapy, strategies using live-attenuated bacterial vectors have matured in terms of academic and industrial development. Different bacterial species can be genetically engineered to deliver antigen to APCs with strong adjuvant effects due to their microbial origin. Proteic or DNA-encoding antigen delivery routes and natural bacterial tropisms might differ among species, permitting different applications. After many academic efforts to resolve safety and efficacy issues, some firms have recently engaged clinical trials with live Listeria or Salmonella spp. We describe here the main technological advances that allowed bacteria to become one of the most promising vectors in cancer immunotherapy.
Superoxide dismutase: correlation with life-span and specific metabolic rate in primate species. (1980)

Much evidence now suggests that superoxide dismutase (superoxide:superoxide oxidoreductase, EC 1.15.1.1) may be a major intracellular protective enzyme against oxygen toxicity by catalyzing the removal of the superoxide radical. We examined the possible role this enzyme may have in determining the life-span of primate species. Superoxide dismutase specific activity levels were measured in cytoplasmic fractions of liver, brain, and heart of 2 rodent and 12 primate species. These species had maximum life-span potentials ranging from 3.5 to 95 years. Liver, brain, and heart had similar specific activity levels for a given species, but the levels for different species varied over 2-fold, with man having the highest level. No general correlation was found in the levels with life-span. However, the ratio of superoxide dismutase specific activity to specific metabolic rate of the tissue or of the whole adult organism was found to increase with increasing maximum lifespan potential for all the species. This correlation suggests that longer-lived species have a higher degree of protection against by-products of oxygen metabolism.
Photo-Induced Atomic Layer Deposition of Tantalum Oxide Thin Films from Ta(OC[sub 2]H[sub 5])[sub 5] and O[sub 2] (2003)

The growth of tantalum oxide thin films by photoinduced atomic layer deposition was investigated in the temperature range of 170-350°C using and as precursors. A self-limiting growth rate of 0.37 Å/cycle was achieved at the substrate temperature range of 190-285°C. All the films grown in this temperature range were amorphous and very smooth (<0.31 nm root-mean-square) as examined by X-ray diffractometer and atomic force microscopy. X-ray photoelectron spectroscopy analysis showed that the films grown at 260-350°C were almost stoichiometric. The refractive index (at 550 nm) and the optical bandgap were found to be ∼2.13 and ∼4.20 eV, while an average transmittance of ∼90% in the visible region was obtained. Electrical measurements performed on capacitors exhibited high dielectric constant (22-25) and a remarkably low leakage current density of at an applied field of 1 MV/cm, probably due to the presence of reactive oxygen atom species. The low leakage current was dominated by the Poole-Frenkel emission mechanism. © 2003 The Electrochemical Society. All rights reserved.
Thermal effects on acoustic streaming in standing waves (2003)

Acoustic streaming generated by standing waves in channels of arbitrary width is investigated analytically. In a previous paper by the authors [J. Acoust. Soc. Am. 113, 153-160 (2003)], a purely viscous fluid in a two-dimensional channel was considered. That analysis is extended here to a gas in which heat conduction and dependence of the viscosity on temperature are taken into account. Calculations are presented for typical working gases used in thermoacoustic engines at standard temperature and pressure. In channels that are very wide in comparison with the viscous penetration depth, which is the Rayleigh streaming regime, the influence of the two thermal effects is comparable but small. The same is true in very narrow channels, having widths on the order of the viscous penetration depth. In channels having intermediate widths, 10-20 times the viscous penetration depth, the effect of heat conduction can be substantial. The analysis is performed for cylindrical tubes as well as two-dimensional channels, and the results are found to be qualitatively the same.
HIF prolyl and asparaginyl hydroxylases in the biological response to intracellular O2 levels (2003)

Hypoxia-inducible factor (HIF) is a heterodimeric transcription factor that plays a crucial role in mediating cellular responses to oxygen. Oxygen availability influences multiple steps in HIF activation and recent studies have indicated that at least two steps in this process are governed by a novel mode of signal transduction involving enzymatic hydroxylation of specific amino acid residues in HIF-alpha subunits by a series of 2-oxoglutarate (2-OG)-dependent oxygenases. These enzymes are non-haem iron enzymes that use dioxygen in the hydroxylation reaction and therefore provide a direct link between the availability of molecular oxygen and regulation of HIF. Prolyl hydroxylation regulates proteolytic destruction of HIF-alpha by the von Hippel-Lindau ubiquitin ligase complex, whereas HIF-alpha asparaginyl hydroxylation regulates recruitment of transcriptional coactivators. The involvement of at least two distinct types of 2-OG-dependent oxygenase in oxygen-regulated transcription suggests that these enzymes may be well suited to a role in cellular oxygen sensing.
Energy backtransfer and infrared photoresponse in erbium-doped silicon p–n diodes (2000)

Temperature-dependent measurements of the photoluminescence (PL) intensity, PL lifetime, and infrared photocurrent, were performed on an erbium-implanted silicon p–n junction in order to investigate the energy transfer processes between the silicon electronic system and the Er 4f energy levels. The device features excellent light trapping properties due to a textured front surface and a highly reflective rear surface. The PL intensity and PL lifetime measurements show weak temperature quenching of the erbium intra-4f transition at 1.535 μm for temperatures up to 150 K, attributed to Auger energy transfer to free carriers. For higher temperatures, much stronger quenching is observed, which is attributed to an energy backtransfer process, in which Er deexcites by generation of a bound exciton at an Er-related trap. Dissociation of this exciton leads to the generation of electron–hole pairs that can be collected as a photocurrent. In addition, nonradiative recombination takes place at the trap. It is shown for the first time that all temperature-dependent data for PL intensity, PL lifetime, and photocurrent can be described using a single model. By fitting all temperature-dependent data simultaneously, we are able to extract the numerical values of the parameters that determine the (temperature-dependent) energy transfer rates in erbium-doped silicon. While the external quantum efficiency of the photocurrent generation process is small (1.8×10−6) due to the small erbium absorption cross section and the low erbium concentration, the conversion of Er excitations into free e–h pairs occurs with an efficiency of 70% at room temperature.
Computer graphics animations of talking faces based on stochastic models (2002)

Animated computer graphics displays of the visible speech gestures of the human face have a number of potential applications. The paper describes a novel method for their creation by bringing together two statistically-based techniques, namely hidden Markov modelling and principal component analysis. The animations are derived from images of a real speaker's face and incorporate all the visible features of the primary articulators, including the lips, teeth and tongue, in a graphical display which does not use an artificial facial model. A pilot 'video speech synthesiser' of this kind has been implemented and tested on spoken digit strings.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Engineering multilevel overlay graphs for shortest-path queries (2008)

An overlay graph of a given graph G = ( V , E ) on a subset S ⊆ V is a graph with vertex set S and edges corresponding to shortest paths in G . In particular, we consider variations of the multilevel overlay graph used in Schulz et al. [2002] to speed up shortest-path computation. In this work, we follow up and present several vertex selection criteria, along with two general strategies of applying these criteria, to determine a subset S of a graph's vertices. The main contribution is a systematic experimental study where we investigate the impact of selection criteria and strategies on multilevel overlay graphs and the resulting speed-up achieved for shortest-path computation: Depending on selection strategy and graph type, a centrality index criterion, selection based on planar separators, and vertex degree turned out to perform best.
Cumulene photochemistry: photorearrangments of tetraphenyl and triphenyl C3 isomers (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCumulene photochemistry: photorearrangments of tetraphenyl and triphenyl C3 isomersMichael W. Klett and Richard P. JohnsonCite this: J. Am. Chem. Soc. 1985, 107, 13, 3963–3971Publication Date (Print):June 1, 1985Publication History Published online1 May 2002Published inissue 1 June 1985https://doi.org/10.1021/ja00299a036RIGHTS & PERMISSIONSArticle Views712Altmetric-Citations20LEARN 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 (1 MB) Get e-Alerts Get e-Alerts
Photogeneration and reactivity of acyl nitroso compounds (2011)

Acyl nitroso compounds have been generated by photolysis of several different classes of precursors including 9,10-dimethylanthracene adducts, nitrodiazo compounds, and 1,2,4-oxadiazole-4-oxides. Consideration of the nitronate-like resonance structure of nitrodiazo compounds led to an examination of the photochemistry of nitronates with α-leaving groups. Photolysis of such nitronates has been shown to generate an acyl nitroso species along with a carbene intermediate. Nanosecond time-resolved infrared (TRIR) spectroscopy has been used to detect photogenerated acyl nitroso compounds directly and to examine their reaction kinetics with amines and thiols. The mechanism of acyl nitroso aminolysis by primary amines involves general base catalysis, while the mechanism of aminolysis by secondary amines is strictly bimolecular. Thiols do not seem to be reactive with acyl nitroso compounds on the microsecond time scale, but thiolates are quite reactive. The reaction between benzoyl nitroside and an organic-soluble thiolate, tetrabutylammonium dodecanethiolate, proceeds via a proposed tetrahedral intermediate, which is observable by TRIR spectroscopy.