gebhart/patrepeval huggingface dataset:
Factorial Sampling Plans for Preliminary Computational Experiments (1991)

A computational model is a representation of some physical or other system of interest, first expressed mathematically and then implemented in the form of a computer program; it may be viewed as a function of inputs that, when evaluated, produces outputs. Motivation for this article comes from computational models that are deterministic, complicated enough to make classical mathematical analysis impractical and that have a moderate-to-large number of inputs. The problem of designing computational experiments to determine which inputs have important effects on an output is considered. The proposed experimental plans are composed of individually randomized one-factor-at-a-time designs, and data analysis is based on the resulting random sample of observed elementary effects, those changes in an output due solely to changes in a particular input. Advantages of this approach include a lack of reliance on assumptions of relative sparsity of important inputs, monotonicity of outputs with respect to inputs, or adequacy of a low-order polynomial as an approximation to the computational model.
Profiling of gene expression changes caused by p53 gain-of-function mutant alleles in prostate cancer cells (2005)

While different p53GOF mutants result in overall distinct expression profiles, they share a common set of differentially-expressed genes that can be used to signify their presence and provide insight into mechanisms underlying androgen independence.
Norovirus P Particle, a Novel Platform for Vaccine Development and Antibody Production (2010)

The norovirus P particle is an octahedral nanoparticle formed by 24 copies of the protrusion (P) domain of the norovirus capsid protein. This P particle is easily produced in Escherichia coli, extremely stable, and highly immunogenic. There are three surface loops per P domain, making a total of 72 loops per particle, and these are potential sites for foreign antigen presentation for immune enhancement. To prove this concept, a small peptide (His tag, 7 amino acids [aa]) and a large antigen (rotavirus VP8, 159 aa) were inserted into one of the loops. Neither insertion affects P particle formation, while both antigens were presented well on the P particle surface. The immune-enhancement effect of the P particle was demonstrated by significantly increased antibody titers induced by the P particle-presented antigens compared to the titers induced by free antigens. In addition, the measured neutralization antibody titers and levels of protection against rotavirus shedding in mice immunized with the VP8 chimeric P particles were significantly higher than those of mice immunized with the free VP8 antigen. Sera from P particle-VP8 chimera-vaccinated animals also blocked norovirus virus-like particle (VLP) binding to the histo-blood group antigen (HBGA) receptors. From these data, the P particle appears to be an excellent vaccine platform for antigen presentation. The readily available three surface loops and the great capacity for foreign antigen insertion make this platform attractive for wide application in vaccine development and antibody production. The P particle-VP8 chimeras may serve as a dual vaccine against both rotavirus and norovirus.
Hair cell inspired mechanotransduction with a gel-supported, artificial lipid membrane (2011)

A gel-supported lipid bilayer formed at the base of an artificial hair is used as the transduction element in an artificial, membrane-based hair cell sensor inspired by the structure and function of mammalian hair cells. This paper describes the initial fabrication and characterization of a bioderived, soft-material alternative to previous artificial hair cells that used the transduction properties of synthetic materials for flow and touch sensing. Under an applied air flow, the artificial hair structure vibrates, triggering a picoamp-level electrical current across the lipid bilayer. Experimental analysis of this mechanoelectrical transduction process supports the hypothesis that the current is produced by a time-varying change in the capacitance of the membrane caused by the vibration of the hair. Specifically, frequency analysis of both the motion of the hair and the measured current show that both phenomena occur at similar frequencies (0.1–1.0 kHz), which suggests that changes in capacitance occur as a result of membrane bending during excitation. In this paper, the bilayer-based hair cell sensor is experimentally characterized to understand the effects of transmembrane potential, the applied air flow, and the dimensions of the hair.
ChemInform Abstract: Reaction of N‐Arylisoindoles with Maleimide Derivatives. (1988)

Abstract Diels‐Alder reaction of the isoindoles (III) with the maleimides (II) under kinetic control gives the endo‐adducts (I).
Relationships between the structure of taxol analogs and their antimitotic activity (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRelationships between the structure of taxol analogs and their antimitotic activityFrancoise Gueritte-Voegelein, Daniel Guenard, Francois Lavelle, Marie Therese Le Goff, Lydie Mangatal, and Pierre PotierCite this: J. Med. Chem. 1991, 34, 3, 992–998Publication Date (Print):March 1, 1991Publication History Published online1 May 2002Published inissue 1 March 1991https://pubs.acs.org/doi/10.1021/jm00107a017https://doi.org/10.1021/jm00107a017research-articleACS PublicationsRequest reuse permissionsArticle Views1453Altmetric-Citations436LEARN 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
Molecular analysis of the Corynebacterium glutamicum gdh gene encoding glutamate dehydrogenase (1992)

The Corynebacterium glutamicum gdh gene encoding NADP-dependent glutamate dehydrogenase (GDH) has been isolated by complementation of the Escherichia coli gdh mutant PA340. The gdh gene was subcloned into the E. coli/C. glutamicum shuttle vector pEK0 and introduced into C. glutamicum. Recombinant strains showed approximately eightfold higher specific GDH activity (15U mg protein-1) relative to the wild type (1.8U mg protein-1). Physiological studies with wild-type and recombinant C. glutamicum strains revealed no indication of significant regulation of gdh expression. The DNA sequence of 2082 bp, including the gdh gene, 5'-, and 3'-flanking regions, was determined. The structural gene consists of 1344 bp and codes for a polypeptide of 448 amino acid residues (Mr 49,152) showing up to 53.6% identity with reported amino acid sequences of glutamate dehydrogenases from other organisms. Northern blot hybridization revealed a 1.65kb mRNA transcript, indicating that the gdh gene of C. glutamicum is monocistronic. Transcription occurred from a G residue located 284 bp upstream of the AUG considered to be the translational initiation codon.
Ruthenium-catalysed carbenoid cyclopropanation reactions with diazo compounds (2004)

The transition-metal catalysed cyclopropanation of olefinic bonds using diazo compounds as a carbene source is among the best developed and most useful transformations available to the synthetic organic chemist. Nevertheless, the quest for new catalyst/ligand systems continues in order to further extend the scope of this method and to identify more economical catalytic systems. In this tutorial review, several different ruthenium complexes are presented which have recently emerged as suitable catalysts for carbenoid cyclopropanation. For the model reaction--cyclopropanation of styrene(s) with diazoacetates--and also for some intramolecular cyclopropanation reactions highly remarkable results in terms of catalyst efficiency, product yields, dia- and enantioselectivity have been reported.
Treatment of metastatic melanoma with an orally available inhibitor of the Ras-Raf-MAPK cascade. (2003)

The Ras-Raf-MAPK pathway is constitutively activated in the majority of melanomas because of a mutation in the BRAF gene. It has been hypothesized that activation of this pathway is crucial for the genesis and maintenance of melanoma and therefore represents an attractive clinical target for metastatic disease. We synthesized a previously characterized MAP kinase kinase inhibitor to test the effect that blocking the Ras-Raf-MAPK pathway would have on the establishment and maintenance of melanoma metastases. Oral administration of CI 1040 inhibited formation of pulmonary metastases and caused rapid regression of established pulmonary metastases in the mouse. Our findings indicate that Ras-Raf-MAPK activation provides crucial signals for the survival of melanoma cells at ectopic sites and that the pharmacological inhibition of this pathway is a promising target for melanoma therapy.
IRS-1 activates phosphatidylinositol 3'-kinase by associating with src homology 2 domains of p85. (1992)

IRS-1 is an insulin receptor substrate that undergoes tyrosine phosphorylation and associates with the phosphatidylinositol (PtdIns) 3'-kinase immediately after insulin stimulation. Recombinant IRS-1 protein was tyrosine phosphorylated by the insulin receptor in vitro and associated with the PtdIns 3'-kinase from lysates of quiescent 3T3 fibroblasts. Bacterial fusion proteins containing the src homology 2 domains (SH2 domains) of the 85-kDa subunit (p85) of the PtdIns 3'-kinase bound quantitatively to tyrosine phosphorylated, but not unphosphorylated, IRS-1, and this association was blocked by phosphotyrosine-containing synthetic peptides. Moreover, the phosphorylated peptides and the SH2 domains each inhibited binding of PtdIns 3'-kinase to IRS-1. Phosphorylated IRS-1 activated PtdIns 3'-kinase in anti-p85 immunoprecipitates in vitro, and this activation was blocked by SH2 domain fusion proteins. These data suggest that the interaction between PtdIns 3'-kinase and IRS-1 is mediated by tyrosine phosphorylated motifs on IRS-1 and the SH2 domains of p85, and IRS-1 activates PtdIns 3'-kinase by binding to the SH2 domains of p85. Thus, IRS-1 likely serves to transmit the insulin signal by binding and regulating intracellular enzymes containing SH2 domains.
Identification and Disruption of Two Discrete Loci Encoding Hyaluronic Acid Capsule Biosynthesis Genes hasA , hasB , and hasC in Streptococcus uberis (2001)

The hyaluronic acid capsule of Streptococcus uberis has been implicated in conferring resistance to phagocytosis by bovine neutrophils. Construction of a bank of random insertion mutants of S. uberis (strain 0140J) was achieved using the pGh9::ISS1 mutagenesis system (22). Phenotypic screening of approximately 5,000 clones enabled the isolation of 11 acapsular mutants. Southern hybridization indicated that two mutants carried a lesion within a group of genes similar to those involved in the assembly of the hyaluronic acid capsule found in the group A Streptococcus (GAS) has operon. The DNA sequence flanking the points of insertion confirmed the presence of homologues of GAS hasA and hasB in S. uberis. The DNA sequence flanking the ISS1 insertion in another mutant identified a homologue of hasC in S. uberis. The GAS hasABC operon structure was not conserved in S. uberis, and two discrete loci comprising homologues of either hasAB or hasC were identified. Disruption of S. uberis hasA or hasC resulted in the complete cessation of hyaluronic acid capsule production. Correspondingly, these mutants were found to have lost their resistance to phagocytosis by bovine neutrophils. The bactericidal action of bovine neutrophils on S. uberis 0140J was shown unequivocally to depend upon the capsule status of the bacterium.
Coagulation factor Xa stimulates platelet-derived growth factor release and mitogenesis in cultured vascular smooth muscle cells of rat. (1996)

The mitogenic effect of activated coagulation factor X (factor Xa) was examined in cultured aortic smooth muscle cells (VSMC) from Wistar-Kyoto rats (WKY). Factor Xa stimulated DNA synthesis and cell growth in VSMC, not through the phospholipase C-protein kinase C pathway because increase of inositol monophosphate (IP) accumulation and intracellular Ca2+ concentration was not observed, but probably via the PDGF receptor tyrosine kinase pathway since the pathway's components, Ras, Raf-1, MAPK (both 42 and 44 kD), and the transcription factors, c-Fos and c-Jun, were activated. These appeared to be effected by the serine protease activity of factor Xa, since in the presence of serine protease inhibitors such as PMSF, leupeptin, benzamidine, TAP anticoagulant, and TLCK, the latter three being specific inhibitors of the factor Xa, active site, the effects were completely blocked. Anti-factor Xa mAb, 5224, which specifically negated the activity of factor Xa, also inhibited completely the mitogenic effect of factor Xa, but not that of thrombin. Addition of PDGF did not affect the effect of factor Xa, which, however, was inhibited by anti-PDGF-AB antibody. This observation and the activation of PDGF receptor tyrosine kinase pathway suggested that the factor Xa might exert its effect via PDGF-like function. Direct measurement confirmed that factor Xa stimulated the release of PDGF from VSMC. Factor Xa, therefore, exerts serine protease activity on VSMC, causing somehow the release of PDGF, that in turn acts on the PDGF receptor tyrosine kinase; the pathway is then turned on, leading eventually to DNA synthesis and cell proliferation.
Adsorption of Vitamin E on Mesoporous Carbon Molecular Sieves (2005)

The adsorption of vitamin E onto mesoporous carbons CMK-1 and CMK-3 from vitamin E solutions with different concentrations in nonpolar (n-heptane) and polar (n-butanol) solvent has been studied for the first time, and the results are compared to a conventional microporous carbon adsorbent, activated carbon. The amount of vitamin E adsorption on the different adsorbents depends on the solvent as well as the mesopore volume and the surface area of the adsorbent. It has been found that n-heptane is preferred to achieve a maximum amount of vitamin E adsorption. Among the carbon materials studied, CMK-3 shows the highest vitamin E adsorption due to the large specific mesopore volume of this adsorbent. CMK-3 was characterized after vitamin E adsorption to confirm the structure of the adsorbent and prove that the adsorption takes place in the channels of the mesoporous carbon adsorbent. XRD and nitrogen adsorption data recorded after vitamin E adsorption confirm the tight packing of the vitamin E molecules inside the mesopores of CMK-3.
Behavioral and Histological Characterization of Unilateral Cervical Spinal Cord Contusion Injury in Rats (2006)

Most experimental studies of spinal cord injury (SCI) in rats damage the thoracic cord, with the consequent functional loss being due to interruption of long tracts connecting the caudal spinal cord to the rostral nervous system. Less work has been done evaluating injury to the cervical cord, even though it is the most common level of human SCI. In addition to the long tracts, the cervical spinal cord contains the sensory and motor neurons responsible for upper extremity function. The purpose of this study was to further develop a rat model of cervical spinal cord contusion injury using a modified NYU/MASCIS weight drop device. Mild (6.25 mm) and moderate (12.5 mm) C5 unilateral injuries were produced. Behavioral recovery was examined using a grooming test, a paw preference test, a walkway test (The Catwalk), and a horizontal ladder test. Histological outcome measures included sparing at the lesion epicenter, sparing throughout the extent of the lesion, quantification of myelin loss rostral and caudal to the lesion, and motor neuron counts. Compared to controls, animals receiving SCI exhibited injury severity-specific deficits in forelimb, locomotor, and hindlimb function persisting for 6-weeks post-SCI. Histological analysis revealed ipsilateral containment of the injury, and differentiation between groups on all measures except motor neuron counts. This model has many advantages: (1) minimal animal care requirements post-SCI, (2) within subject controls, (3) functional loss involves primarily the ipsilateral forelimb, and (4) it is a behavioral and histological model for both gray and white matter damage caused by contusive SCI.
Stat3 Orchestrates Tumor Development and Progression: The Achilles Heel of Head and Neck Cancers? (2010)

Despite recent advancements in treatment modalities, the overall survival and quality of life of patients with head and neck squamous cell carcinoma (HNSCC) have not improved significantly over the past decade. With the increasing emergency of new biological agents, the development of novel treatment schemes based on cancer cell biology may be promising for this group of patients. We previously introduced the "oncogene addiction" concept as a rationale for molecular targeting in cancer therapy and prevention. In this context, an increasing number of preclinical studies have demonstrated that the Signal Transducers and Activators of transcription 3 (Stat3) transcription factor plays critical roles in the development and progression of a variety of tumors including HNSCC, by regulating cell proliferation, cell cycle progression, apoptosis, angiogenesis, immune evasion, Epithelial-Mesenchymal Transition (EMT) and through effects in cancer stem cells. The purpose of this review is to summarize current experimental and clinical evidence that suggest that HNSCC might be addicted to Stat3 and describe the molecular mechanisms that may explain this phenomenon. In addition, we discuss whether this addiction is an exploitable target for developing approaches for the treatment and prevention of HNSCC.
Simulation on Occupant Evacuation at a Public Site Based on SMARTFIRE and Building EXODUS (2017)

In this paper, the software of SMARTFIRE is applied to simulation a fire process at a long-distance passenger transport station. The results of SMARTFIRE can be used as environment condition of occupant evacuation. The software of Building EXODUS is applied to simulation the evacuation process with and without fire. Evacuation times with different number of occupants are calculated. If the density of occupants is relatively small, pedestrian flow during evacuation can take on a dilute state because of the large quantity of exits on public site. And evacuation time changes a little with the increase of the number of occupants in low range of density. If the density of occupants is comparatively big, the phenomena of queuing up at the exits and assembling at the bottlenecks will take place, resulting in an obviously long evacuation time; The influences of the use ratios of exit are analyzed, and balancing the use ratio of each exit can obviously improve the efficiency of evacuation; The influences of the fire simulated by SMARTFIRE are also analyzed. In addition to the factors of low visibility and low walking speed, the change of evacuation routes and the imbalance of the use ratio of each exit are also very important factors of fire.
Trichloroethylene: Parkinsonism and complex 1 mitochondrial neurotoxicity (2007)

Trichloroethylene, used extensively in industry and the military and a common environmental contaminant, joins other mitochondrial neurotoxins, MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) and some pesticides, as a risk factor for parkinsonism.
Multifunctional CPP Polymer System for Tumor-Targeted pDNA and siRNA Delivery (2010)

Cell-penetrating peptides (CPPs) are a very interesting class of molecules to be introduced in gene and siRNA vectors. They can be used to overcome one of the biggest hurdles in gene and siRNA delivery in vitro and in vivo, the transfer across cell membranes. This chapter describes protocols for the synthesis and biological evaluation of a polylysine-based polymer. In this carrier system, melittin is used as CPP with a high activity to disrupt membranes. pH-Labile masking is applied to render the lytic activity specific for intracellular acidic endolysosomal organelles.
Effect of high-aspect-ratio microstructures on cell growth and attachment (2002)

Smooth muscle cells were cultured on a variety of high-aspect-ratio PMMA, PDMS, and SU-8 microstructures. Three basic microstructures were used in these experiments: columns, holes, and curved surfaces (microlenses). Typical PMMA features were over 500 /spl mu/m in height, while the SU-8 and PDMS structures averaged 150 /spl mu/m in height. The smooth muscle cells showed a clear preference for smooth surfaces as compared to the areas containing microstructures, though smooth muscle cells showed the ability to grow on all structures and to attach on the steep sidewalls associated with the microstructures. Smooth muscle cell alignment was not directly improved by the structures, though evidence indicates that smaller structures may be able to do so. Gap dimensions between columns were also shown to be critical with regard to cell spreading and movement.
Phase-shifting and logical moiré (1991)

Logical moiré uses the logical operators (and, or, xor) to generate moiré fringes from two 1-bit binary gratings within the computer. Phase shifting of these moiré fringes is easily achieved by translating the computer-generated reference gratings in steps of one picture element (pixel). We analyze the phase-shift expressions based on three, four, and five shifted patterns by using logical moiré patterns. Both simulated and real moiré demonstrations are shown.
Silicon Nitride Thin Films Young's Modulus Determination by an Optical Non Destructive Method (1997)

The purpose of our study is to determine the Young's modulus of silicon nitride ( Si 3 N 4 ) thin films. With respect to the experimental material, we use commercially available atomic force microscopy (AFM) microcantilevers. The novelty lies in the procedure used to compare and therefore to validate the experimental results. First, the fundamental mode of Si 3 N 4 thin film microcantilevers is detected by means of the optical beam deflection (OBD) method. The resulting resonant frequency is subsequently introduced into the mechanical theoretical model to extract the value of the Young's modulus. A numerical modal analysis is performed to validate the experimental results using the same approach as that of the experiment. Finally, the Young's modulus obtained in this study is compared with those of other studies. The outcome shows that we have obtained a reliable protocol for Young's modulus estimation.