gebhart/patrepeval huggingface dataset:
Toward Verified Biological Models (2008)

The last several decades have witnessed a vast accumulation of biological data and data analysis. Many of these data sets represent only a small fraction of the system's behavior, making the visualization of full system behavior difficult. A more complete understanding of a biological system is gained when different types of data (and/or conclusions drawn from the data) are integrated into a larger-scale representation or model of the system. Ideally, this type of model is consistent with all available data about the system, and it is then used to generate additional hypotheses to be tested. Computer-based methods intended to formulate models that integrate various events and to test the consistency of these models with respect to the laboratory-based observations on which they are based are potentially very useful. In addition, in contrast to informal models, the consistency of such formal computer-based models with laboratory data can be tested rigorously by methods of formal verification. We combined two formal modeling approaches in computer science that were originally developed for non-biological system design. One is the inter-object approach using the language of live sequence charts (LSCs) with the Play-Engine tool, and the other is the intra-object approach using the language of statecharts and Rhapsody as the tool. Integration is carried out using InterPlay, a simulation engine coordinator. Using these tools, we constructed a combined model comprising three modules. One module represents the early lineage of the somatic gonad of C. elegans in LSCs, while a second more detailed module in statecharts represents an interaction between two cells within this lineage that determine their developmental outcome. Using the advantages of the tools, we created a third module representing a set of key experimental data using LSCs. We tested the combined statechart-LSC model by showing that the simulations were consistent with the set of experimental LSCs. This small-scale modular example demonstrates the potential for using similar approaches for verification by exhaustive testing of models by LSCs. It also shows the advantages of these approaches for modeling biology.
Porosity and Permeability Estimation by Gradient-Based History Matching Using Time-Lapse Seismic Data (2007)

Abstract A method based on the Gauss-Newton optimization technique for continuous model updating with respect to 4D seismic data is presented. The study uses a commercial finite difference black oil reservoir simulator and a standard rock physics model to predict seismic amplitudes as a function of porosity and permeabilities. The main objective of the study is to test the feasibility of using 4D seismic data as input to reservoir parameter estimation problems. The algorithm written for this study, which was initially developed for the estimation of saturation and pressure changes from time-lapse seismic data, consists of three parts: the reservoir simulator, the rock physics petro-elastic model, and the optimization algorithm. The time-lapse seismic data are used for observation purposes. In our example, a simulation model generated the seismic data, then the model was modified after this the algorithm was used to fit the data generated in the previous step. History matching of reservoir behavior is difficult because of the problem is not unique. More than one solution exists that matches the available data. Therefore, empirical knowledge about rock types from laboratory measurements are used to constraint the inversion process. The Gauss-Newton inversion reduces the misfit between observed and calculated time-lapse seismic amplitudes. With this method, it is possible to estimate porosity and permeability distributions from time-lapse data. Since these parameters are estimated for every single grid cell in the reservoir model, the number of model parameters is high, and therefore the problem will be underdetermined. Therefore, a good fit with the observation data is not necessary for a good estimation of the unknown reservoir properties. The methods for reducing the number of unknown parameters and the associated uncertainties is discussed.
Length-Dependent Conductance of Oligothiophenes (2014)

We have measured the single-molecule conductance of a family of oligothiophenes comprising 1-6 thiophene moieties terminated with methyl-sulfide linkers using the scanning tunneling microscope-based break-junction technique. We find an anomalous behavior: the peak of the conductance histogram distribution does not follow a clear exponential decay with increasing number of thiophene units in the chain. The electronic properties of the materials were characterized by optical spectroscopy and electrochemistry to gain an understanding of the factors affecting the conductance of these molecules. We postulate that different conformers in the junction are a contributing factor to the anomalous trend in the observed conductance as a function of molecule length.
The melanoma differentiation-associated gene mda-6, which encodes the cyclin-dependent kinase inhibitor p21, is differentially expressed during growth, differentiation and progression in human melanoma cells. (1995)

The combination of recombinant human fibroblast interferon (IFN-beta) and the antileukemic compound mezerein (MEZ) induces terminal differentiation with an irreversible loss of proliferative capacity in human melanoma cells. Using subtraction hybridization, cDNAs were identified that display enhanced expression in terminally differentiated and growth arrested human melanoma cells (Jiang and Fisher, 1993; Jiang et al., 1994a). A specific melanoma differentiation-associated (mda) cDNA, mda-6, is described whose expression inversely correlates with melanoma progression and growth. mda-6 is identical to WAF1/CIP1/SDI1 that encodes the M(r) 21,000 protein (p21) that is an inhibitor of cyclin-dependent kinases. Actively growing normal melanocyte, SV40-immortalized human melanocyte and dysplastic nevus cell lines synthesize elevated levels of mda-6 mRNA; whereas, actively proliferating radial and early vertical growth phase primary melanomas as well as metastatic human melanoma cells produce reduced levels of mda-6 mRNA. Treatment of primary and metastatic human melanoma cells with IFN-beta + MEZ results in growth inhibition and an increase in mda-6 expression. mda-6 expression also increases when human melanoma cells are grown to high saturation densities or when grown in serum-free medium. Using anti-p53 and anti-p21 antibodies, an inverse correlation is found between p53 and p21 protein levels during growth arrest and differentiation. Induction of growth arrest and terminal differentiation in H0-1 human melanoma cells by IFN-beta + MEZ results in a temporal decrease in wild-type p53 protein levels with a corresponding increase in p21 levels. In the Matrigel-assisted melanoma progression model, mda-6 expression decreases in early vertical growth phase primary human melanoma cells selected for autonomous or enhanced tumor formation in nude mice. In metastatic human melanoma cells displaying a loss of metastatic potential resulting from introduction of a normal human chromosome 6, mda-6 mRNA levels increase. Taken together, these studies indicate that mda-6 (p21) may function as a negative regulator of melanoma growth, progression and metastasis.
EPIC: Efficient prediction of IC manufacturing hotspots with a unified meta-classification formulation (2012)

In this paper we present EPIC, an efficient and effective predictor for IC manufacturing hotspots in deep sub-wavelength lithography. EPIC proposes a unified framework to combine different hotspot detection methods together, such as machine learning and pattern matching, using mathematical programming/optimization. EPIC algorithm has been tested on a number of industry benchmarks under advanced manufacturing conditions. It demonstrates so far the best capability in selectively combining the desirable features of various hotspot detection methods (3.5–8.2% accuracy improvement) as well as significant suppression of the detection noise (e.g., 80% false-alarm reduction). These characteristics make EPIC very suitable for conducting high performance physical verification and guiding efficient manufacturability friendly physical design.
[Myostatin blockade therapy for muscular atrophy]. (2011)

Myostatin, a member of the muscle-specific transforming growth factor (TGF)-β family, negatively regulates skeletal muscle growth. It inhibits muscle stem cell proliferation and differentiation and attenuates adult muscle fiber protein accretion, resulting in decreased skeletal muscle mass. As such, it has been considered a therapeutic target of muscular dystrophy. Notably, administration of a blocking antibody against myostatin ameliorated the pathophysiology of dystrophin-deficient mdx mice. Although a clinical trial of anti-myostatin antibody MYO-029 failed to achieve a significant outcome in patients with muscular dystrophies, various distinct approaches have been taken to establish anti-myostatin therapy, including myostatin decoy receptor ACE-031, small-molecule inhibitors against the myostatin receptor, and myostatin short intertering RNA with collagen-derived carrier particles. The clinical application of anti-myostatin therapeutics in treatment of patients with muscular dystrophy needs further evaluation for safety and specification of the target disease types among the various muscular dystrophies. In addition, myostatin inhibition could be effective for muscle-wasting conditions other than muscular dystrophy- for instance, steroid-induced myopathy, mitochondrial myopathy, or sarcopenia in elderly patients. Moreover, considerable evidence shows that myostatin regulates energy metabolism and that its inhibition can significantly attenuate the progression of obesity and diabetes. It may also be applicable for the prevention of metabolic syndrome. Thus, safe and potent anti-myostatin therapy will have a wide variety of applications in modern medicine.
Radiation-driven cannonball targets for high-convergence implosions (1993)

In the last few years, systematic studies on radiation hydrodynamics in the X-ray confining cavity and a fuel capsule have attained remarkable progress. This makes it possible to analyze quantitatively the energy transfer processes from laser to the fusion capsule and find uniform irradiation conditions of the fusion capsule driven by thermal X rays. As a result, reproducible and stable implosions were achieved. Throughout implosion experiments with the Gekko XII blue laser system (351 nm, kJ, 0.8 ns), good agreement of implosion has been obtained between the experiment and numerical simulations, assuming perfectly spherical symmetry, up to a radial convergence ratio of 15. Described are particularly the issues of (1) energy transfer processes from laser to a fuel capsule and conditions for uniform irradiation, (2) properties of the X-ray propagation through aluminum heated by X-ray radiation, and (3) dependence of the convergence ratio of Ri/Rf (where Ri and Rf are the initial and final radii) of the capsule on the initial fill pressure of D–T gas and its influence on the core parameters and fusion products to evaluate implosion sphericity.
The effect of chemical residues on the physical and electrical properties of chemical vapor deposited graphene transferred to SiO2 (2011)

The effects of residues introduced during the transfer of chemical vapor deposited graphene from a Cu substrate to an insulating (SiO2) substrate on the physical and electrical of the transferred graphene are studied. X-ray photoelectron spectroscopy and atomic force microscopy show that this residue can be substantially reduced by annealing in vacuum. The impact of the removal of poly(methyl methacrylate) residue on the electrical properties of graphene field effect devices is demonstrated, including a nearly 2 × increase in average mobility from 1400 to 2700 cm2/Vs. The electrical results are compared with graphene doping measurements by Raman spectroscopy.
Nucleoside, Nucleotide, and Non-Nucleoside Inhibitors of Hepatitis C Virus NS5B RNA-Dependent RNA-Polymerase (2011)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTADDITION / CORRECTIONThis article has been corrected. View the notice.Nucleoside, Nucleotide, and Non-Nucleoside Inhibitors of Hepatitis C Virus NS5B RNA-Dependent RNA-PolymeraseMichael J. Sofia*, Wonsuk Chang, Phillip A. Furman, Ralph T. Mosley, and Bruce S. RossView Author Information Pharmasset, Inc., 303A College Road East, Princeton, New Jersey 08540, United States*Phone: 609-613-4123. Fax: 609-613-4150. E-mail: [email protected] or [email protected]Cite this: J. Med. Chem. 2012, 55, 6, 2481–2531Publication Date (Web):December 16, 2011Publication History Received13 October 2011Published online23 January 2012Published inissue 22 March 2012https://doi.org/10.1021/jm201384jCopyright © 2011 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views6817Altmetric-Citations219LEARN 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 Read OnlinePDF (4 MB) Get e-AlertsSUBJECTS:Genetics,Inhibitors,Nucleic acids,Peptides and proteins,Pharmaceuticals Get e-Alerts
Determination of the helix and β form of proteins in aqueous solution by circular dichroism (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of the helix and β form of proteins in aqueous solution by circular dichroismYee-Hsiung Chen, Jen Tsi Yang, and Kue Hung ChauCite this: Biochemistry 1974, 13, 16, 3350–3359Publication Date (Print):July 1, 1974Publication History Published online1 May 2002Published inissue 1 July 1974https://pubs.acs.org/doi/10.1021/bi00713a027https://doi.org/10.1021/bi00713a027research-articleACS PublicationsRequest reuse permissionsArticle Views4795Altmetric-Citations1650LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Electro-optical characteristics and switching behavior of the in-plane switching mode (1995)

Electro-optical characteristics related to the threshold behavior of liquid crystals when using the in-plane switching (IPS) mode were investigated with interdigital electrodes. In order to analyze the switching behavior of liquid crystals, an equation, which expresses the threshold transition, was derived using the continuum elastic theory. It was made clear that it was the electric field and not the voltage that drives the liquid crystals in the IPS mode. Significantly, an inversely proportional relationship between the threshold voltage and the gap between the substrates was found to hold. Furthermore, the electro-optical characteristics were recognized to change with the variation of the gap between the substrates. This behavior is due to the independence of electric field on liquid crystal layer normal.
Induction of Tumor-Specific CD4+ and CD8+ T-Cell Immunity in Cervical Cancer Patients by a Human Papillomavirus Type 16 E6 and E7 Long Peptides Vaccine (2008)

The HPV16 E6 and E7 synthetic long peptides vaccine is highly immunogenic, in that it increases the number and activity of HPV16-specific CD4(+) and CD8(+) T cells to a broad array of epitopes in all patients. The expansion of CD4(+) and CD8(+) tumor-specific T cells, both considered to be important in the antitumor response, indicates the immunotherapeutic potential of this vaccine. Notably, part of the vaccine-induced T cells display a CD4(+)CD25(+)Foxp3(+) phenotype that is frequently associated with regulatory T-cell function, suggesting that strategies to disarm this subset of T cells should be considered as components of immunotherapeutic modalities against HPV-induced cancers.
A soluble protein related to the HER-2 proto-oncogene product is released from human breast carcinoma cells. (1991)

Amplified expression of p185HER-2, the protein product of the HER-2/neu proto-oncogene, appears to be involved in carcinogenesis of human mammary epithelial cells. Our data suggest that an extracellular 130 Kda glycoprotein released from breast carcinoma cells may be related to the ectodomain of p185HER-2: (1) Both cellular p185HER-2 and extracellular p130, when reduced and alkylated, reacted with antipeptide antibody against the N-terminus of the HER-2 protein [alpha N(HER-21)] and reactivity was blocked by cognate peptide; (2) Neither p130 nor other extracellular proteins reacted with antiserum against the C-terminus of p185HER-2 [alpha C(HER-2)]; (3) Partial proteolysis of p185HER-2 generated an immunoreactive fragment of 130 kDa that was similar to extracellular p130; (4) Both p130 and p185HER-2 contained carbohydrate that bound to Con-A Sepharose; (5) The amount of p130 released from breast cells corresponded to the levels of expression of cellular p185HER-2. Release of the ectodomain of p185HER-2 from breast carcinoma cells may be involved in their malignant growth and may be a useful marker for assessing the expression of p185HER-2 in human tumors.
π-Conjugated molecules with fused rings for organic field-effect transistors: design, synthesis and applications (2009)

Pi-conjugated molecular materials with fused rings are the focus of considerable interest in the emerging area of organic electronics, since the combination of excellent charge carrier mobility and high stability may lead to their practical applications. This tutorial review discusses the synthesis, properties and applications of pi-conjugated organic semiconducting materials, especially those with fused rings. The achievements to date, the remaining problems and challenges, and the key research that needs to be done in the near future are all discussed.
Synthesis and photoexcited-state dynamics of aromatic group-bridged carotenoid-porphyrin dyads and carotenoid-porphyrin-pyromellitimide triads (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and photoexcited-state dynamics of aromatic group-bridged carotenoid-porphyrin dyads and carotenoid-porphyrin-pyromellitimide triadsAtsuhiro Osuka, Hiroko Yamada, Kazuhiro Maruyama, Noboru Mataga, Tsuyoshi Asahi, Masaya Ohkouchi, Tadashi Okada, Iwao Yamazaki, and Yoshinobu NishimuraCite this: J. Am. Chem. Soc. 1993, 115, 21, 9439–9452Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ja00074a009https://doi.org/10.1021/ja00074a009research-articleACS PublicationsRequest reuse permissionsArticle Views499Altmetric-Citations56LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Enantioselective binding of chiral 1,14-dimethyl[5]helicene–spermine ligands with B- and Z-DNA (2013)

Duplex DNA adopts a right-handed B-DNA conformation under physiological conditions. Z-DNA, meanwhile, has a left-handed helical structure and is in equilibrium with right-handed B-DNA. We recently reported that the bisnaphthyl maleimide-spermine conjugate (1) induced a B- to Z-DNA transition with high efficiency at low salt concentrations. It was also found that the bisnaphthyl ligand (1) spontaneously transformed into the corresponding [5]helicene derivative (2). Because [5]helicene 2 can potentially be chiral and because the chiral discrimination of B- and Z-DNA is also of interest, we became interested in whether enatiomerically pure [5]helicene-spermine conjugates might discriminate the chirality of B- or Z-DNA. In this study, we have demonstrated an efficient synthesis of chiral DNA-binding ligands by the conjugation of a [5]helicene unit with a spermine unit. These chiral helicene ligands exhibited recognition of B- and Z-DNA, with (P)-3 displaying preference for B-DNA and (M)-3 for Z-DNA. The characteristic features of the helicene-spermine ligands developed in this study include two points: the cationic spermine portion produces electrostatic interactions along the phosphate backbone of the minor groove, and the helicene forms complexes in an end-stacking mode. Such binding modes, together with the thermodynamic parameters, account for the mode of chiral recognition of (P)- and (M)-3 for B- and Z-DNA.
ETA-receptor antagonist prevents and reverses chronic hypoxia-induced pulmonary hypertension in rat (1995)

The selective endothelin-A (ETA)-receptor antagonist BQ-123 has been shown to prevent chronic hypoxia-induced pulmonary hypertension in the rat. Therefore in the current study we utilized BQ-123 to test the hypothesis that blockade of the ETA receptor can reverse as well as prevent the increase in mean pulmonary artery pressure, right ventricle-to-left ventricle plus septum ratio, and percent wall thickness in small (50-100 microns) pulmonary arteries observed in male Sprague-Dawley rats exposed to normobaric hypoxia (10% O2, 2 wk). Infusion of BQ-123 (0.4 mg.0.5 microliter-1.h-1 for 2 wk in 10% O2) begun after 2 wk of hypoxia significantly reversed the established pulmonary hypertension and prevented further progression of right ventricular hypertrophy during the third and fourth week of hypoxia. BQ-123 infusion instituted before exposure to hypoxia completely prevented the hypoxia-induced pulmonary hypertension, right ventricular hypertrophy, and pulmonary vascular remodeling. These findings suggest that, in the lung, hypoxia induced an increase synthesis of endothelin-1, which acts locally on ETA receptors to cause pulmonary hypertension, right heart hypertrophy, and pulmonary vascular remodeling, while ETA-receptor blockade can both prevent and reverse these processes.