gebhart/patrepeval huggingface dataset:
Amplification and expression of the bcl-1 gene in human solid tumor cell lines. (1992)

The bcl-1 gene maps to chromosome 11q13 and has recently been shown to be a member of the cyclin gene family. Amplification of the chromosome region containing bcl-1 occurs frequently in breast cancer, squamous cell cancer, and other tumor types. We have hypothesized that amplification results in altered expression of the bcl-1 gene, contributing to carcinogenesis. In this work, we studied bcl-1 gene amplification and expression in a panel of human cell line. bcl-1 is expressed in all cell lines studied. The level of expression tends to be higher in amplified cell lines. We also screened these cell lines for int-2 and hst-1 expression, genes which are frequently coamplified with bcl-1. No int-2 expression was detected, and the two cell lines expressing hst-1 were unamplified. Our data provide support for the importance of bcl-1 in carcinogenesis.
Training an asymmetric signal perceptron through reinforcement in an artificial chemistry (2014)

State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be reprogrammed or trained once fabricated. The implementation of adaptive biochemical systems that would offer flexibility through programmability and autonomous adaptation faces major challenges because of the large number of required chemical species as well as the timing-sensitive feedback loops required for learning. In this paper, we begin addressing these challenges with a novel chemical perceptron that can solve all 14 linearly separable logic functions. The system performs asymmetric chemical arithmetic, learns through reinforcement and supports both Michaelis-Menten as well as mass-action kinetics. To enable cascading of the chemical perceptrons, we introduce thresholds that amplify the outputs. The simplicity of our model makes an actual wet implementation, in particular by DNA-strand displacement, possible.
Inverse Pre-deformation of Finite Element Mesh for Large Deformation Analysis (2005)

The process of finite element analysis that deals with large deformation often produces distorted elements in the later stages of the analysis. These distorted elements lead to analysis problems, such as inaccurate solutions, slow convergence, and premature termination of the analysis. This paper proposes a new mesh generation algorithm to mesh the input part for pure Lagrangian analysis, where our goal is to improve the shape quality of the elements along the analysis process to reduce the number of inverted elements at the later stage, and to decrease the possibility of premature termination of the analysis. One pre-analysis is required to collect geometric and stress information in the analysis. The proposed method then uses the deformed-shape boundary known from the pre-analysis, finds the optimal node locations, considers the stress information to control the mesh sizes, as well as control the mesh directionality, generates meshes on the deformed boundary, and finally, maps the elements back to the undeformed boundary using inverse bilinear mapping. The proposed method has been tested on two forging example problems. The results indicate that the method can improve the shape quality of the elements at the later stage of the analysis, and consequently extend the life of the analysis, thereby reducing the chance of premature analysis termination.
Gold Nanoparticle-Enhanced Secondary Ion Mass Spectrometry Imaging of Peptides on Self-Assembled Monolayers (2006)

We demonstrate the use of gold nanoparticles (AuNPs) to enhance the secondary ion emission of peptides in time-of-flight secondary ion mass spectrometry (TOF-SIMS). The signal intensity of peptides adsorbed onto AuNPs was significantly increased when compared to that of self-assembled monolayers (SAMs). This gold nanoparticle-enhanced SIMS, termed NE-SIMS, enabled the sensitive detection of subtle modifications of peptides, such as phosphorylation. From a quantitative analysis of the amounts of adsorbed peptides and AuNPs on SAMs using quartz crystal microbalance and surface plasmon resonance spectroscopy, the ratio of peptide molecule to AuNP on amine-SAMs was revealed to be 18-19:1. When considering the ratio of peptide to matrix (1:10(3)-10(6)) employed in a matrix-enhanced SIMS, the use of AuNPs gave rise to a significantly increased secondary ion emission of peptides. Peptides were adsorbed onto patterned AuNPs on SAMs using a microfluidic system, and well-contrasted molecular ion images were obtained. NE-SIMS is expected to be applied to a chip-based analysis of modification of biomolecules in a label-free manner.
Acid-Induced Degradation of Phosphorescent Dopants for OLEDs and Its Application to the Synthesis of Tris-heteroleptic Iridium(III) Bis-cyclometalated Complexes (2011)

Investigations of blue phosphorescent organic light emitting diodes (OLEDs) based on [Ir(2-(2,4-difluorophenyl)pyridine)(2)(picolinate)] (FIrPic) have pointed to the cleavage of the picolinate as a possible reason for device instability. We reproduced the loss of picolinate and acetylacetonate ancillary ligands in solution by the addition of Brønsted or Lewis acids. When hydrochloric acid is added to a solution of a [Ir(C^N)(2)(X^O)] complex (C^N = 2-phenylpyridine (ppy) or 2-(2,4-difluorophenyl)pyridine (diFppy) and X^O = picolinate (pic) or acetylacetonate (acac)), the cleavage of the ancillary ligand results in the direct formation of the chloro-bridged iridium(III) dimer [{Ir(C^N)(2)(μ-Cl)}(2)]. When triflic acid or boron trifluoride are used, a source of chloride (here tetrabutylammonium chloride) is added to obtain the same chloro-bridged iridium(III) dimer. Then, we advantageously used this degradation reaction for the efficient synthesis of tris-heteroleptic cyclometalated iridium(III) complexes [Ir(C^N(1))(C^N(2))(L)], a family of cyclometalated complexes otherwise challenging to prepare. We used an iridium(I) complex, [{Ir(COD)(μ-Cl)}(2)], and a stoichiometric amount of two different C^N ligands (C^N(1) = ppy; C^N(2) = diFppy) as starting materials for the swift preparation of the chloro-bridged iridium(III) dimers. After reacting the mixture with acetylacetonate and subsequent purification, the tris-heteroleptic complex [Ir(ppy)(diFppy)(acac)] could be isolated with good yield from the crude containing as well the bis-heteroleptic complexes [Ir(ppy)(2)(acac)] and [Ir(diFppy)(2)(acac)]. Reaction of the tris-heteroleptic acac complex with hydrochloric acid gives pure heteroleptic chloro-bridged iridium dimer [{Ir(ppy)(diFppy)(μ-Cl)}(2)], which can be used as starting material for the preparation of a new tris-heteroleptic iridium(III) complex based on these two C^N ligands. Finally, we use DFT/LR-TDDFT to rationalize the impact of the two different C^N ligands on the observed photophysical and electrochemical properties.
Mapping short DNA sequencing reads and calling variants using mapping quality scores (2008)

New sequencing technologies promise a new era in the use of DNA sequence. However, some of these technologies produce very short reads, typically of a few tens of base pairs, and to use these reads effectively requires new algorithms and software. In particular, there is a major issue in efficiently aligning short reads to a reference genome and handling ambiguity or lack of accuracy in this alignment. Here we introduce the concept of mapping quality, a measure of the confidence that a read actually comes from the position it is aligned to by the mapping algorithm. We describe the software MAQ that can build assemblies by mapping shotgun short reads to a reference genome, using quality scores to derive genotype calls of the consensus sequence of a diploid genome, e.g., from a human sample. MAQ makes full use of mate-pair information and estimates the error probability of each read alignment. Error probabilities are also derived for the final genotype calls, using a Bayesian statistical model that incorporates the mapping qualities, error probabilities from the raw sequence quality scores, sampling of the two haplotypes, and an empirical model for correlated errors at a site. Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net.
(Diisopropoxymethylsilyl)methyl Grignard reagent: a new, practically useful nucleophilic hydroxymethylating agent (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT(Diisopropoxymethylsilyl)methyl Grignard reagent: a new, practically useful nucleophilic hydroxymethylating agentKohei Tamao, Neyoshi Ishida, and Makoto KumadaCite this: J. Org. Chem. 1983, 48, 12, 2120–2122Publication Date (Print):June 1, 1983Publication History Published online1 May 2002Published inissue 1 June 1983https://pubs.acs.org/doi/10.1021/jo00160a046https://doi.org/10.1021/jo00160a046research-articleACS PublicationsRequest reuse permissionsArticle Views2388Altmetric-Citations208LEARN 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
Evaluation of a rapid screening method for chemical contaminants of concern in four food-related matrices using QuEChERS extraction, UHPLC and high resolution mass spectrometry (2011)

A method combining QuEChERS extraction, ultra-high pressure liquid chromatography and full scan high resolution mass spectrometry was evaluated for its use in screening for chemical residues and contaminants in animal-related food matrices. The method was evaluated by analysis of multiple replicates of whole milk, muscle tissue, liver tissue and corn silage. Analytes tested included plant alkaloids, carbamate and organophosphate pesticides, and several types of veterinary drugs. A database containing the chemical formula for each analyte was used to calculate accurate mass-to-charge ratios for expected pseudo-molecular ions. This information, as well as retention times, was used to identify analytes. Of 118 compounds chosen for analysis, 86 were detectable in all fortified replicates of at least one matrix at levels ranging from 1.0 to 5000 ng/g. Variability of response, as measured in % relative standard deviation of peak areas over seven replicate fortified sample analyses, was found to differ among the classes of analytes, ranging from <10% to >100%. Retention times were stable and analytes were routinely detected at measured mass-to-charge ratios within 2 ppm of their theoretical mass-to-charge ratios. These results indicate that the combination of generic extraction and chromatographic procedures with full scan high resolution mass spectrometry can serve as a useful method for screening complex matrices.
Teslaphoresis of Carbon Nanotubes (2016)

This paper introduces Teslaphoresis, the directed motion and self-assembly of matter by a Tesla coil, and studies this electrokinetic phenomenon using single-walled carbon nanotubes (CNTs). Conventional directed self-assembly of matter using electric fields has been restricted to small scale structures, but with Teslaphoresis, we exceed this limitation by using the Tesla coil's antenna to create a gradient high-voltage force field that projects into free space. CNTs placed within the Teslaphoretic (TEP) field polarize and self-assemble into wires that span from the nanoscale to the macroscale, the longest thus far being 15 cm. We show that the TEP field not only directs the self-assembly of long nanotube wires at remote distances (>30 cm) but can also wirelessly power nanotube-based LED circuits. Furthermore, individualized CNTs self-organize to form long parallel arrays with high fidelity alignment to the TEP field. Thus, Teslaphoresis is effective for directed self-assembly from the bottom-up to the macroscale.
Controlled-release and local delivery of therapeutic antibodies (2004)

Human and humanised antibodies are now poised to become a major new class of protein-based therapeutic agents. A significant fraction of new drugs in clinical testing (approximately 20% in 2002) are antibody classes. Monoclonal antibodies (mAbs) with high affinities against newly discovered disease targets, both cellularly and extracellularly, are now clinically proven to elicit high bioactivities against numerous diseases, including tumours, infections, asthma, inflammation, arthritis and osteoporosis. Clinical humanised antibody delivery is typically intravenous, with large multiple doses (grams) required for systemic volumes of distribution. Due to the relatively high costs of both this drug type, and its common mode of administration, alternatives are sought where doses might be reduced and the bioavailability and efficacy enhanced. Local, controlled-release methods that deliver antibodies locally to site of disease, offer new possibilities with these potential advantages. However, protein drugs frequently exhibit formulation challenges when packaged in delivery vehicles, and as globular proteins, antibodies are no exception. Several examples of mAb controlled-release and local delivery strategies against several disease targets are reviewed. Importantly, several antibody delivery methods work in tandem with existing clinically-accepted therapeutics, sometimes exhibiting potentiating or synergistic effects in animal models with small molecule, systemically administered drugs.
Matrix‐assisted laser desorption mass spectrometry of oligodeoxythmidylic acids (1992)

Ferulic acid, sinapinic acid and 2,5-dihydroxybenzoic acid (DHBA) have been tested as matrix materials for matrix-assisted laser desorption of the pure oligonucleotide pd(T)12 and a mixture of oligonucleotides pd(T)12 through pd(T)18 using pulsed 337 nm radiation combined with reflecting time-of-flight mass spectrometry. The three matrix materials are compared with respect to obtainable mass resolution, degree of fragmentation, and adduct formation for these oligonucleotides. DHBA was found to produce the least fragmentation and adduct formation, as well as the highest mass resolution.
Phenotypic properties of cultured tumor cells: Integrin αIIbβ3 expression, tumor‐cell‐induced platelet aggregation, and tumor‐cell adhesion to endothelium as important parameters of experimental metastasis (1993)

The present study was undertaken to investigate the factors involved in determining the metastatic potential of cultured cells derived from solid tumors. We first investigated the effects of cell source and culture conditions on lung colony formation by i.v. injected B16a (B16 amelanotic melanoma) cells and inhibition of tumor colony formation by the thromboxane A2 synthase inhibitor, CGS14854. Prolonged culture resulted in a 10-fold decrease in the incidence of B16a lung colonies, whereas passage in vivo for 150 days did not affect lung colony formation by tumor cells isolated from enzymatic dispersates by centrifugal elutriation. Cultured B16a cells maintained at low density (LD) and harvested at low passage (LP) formed significantly more lung colonies than B16a cells harvested at high densities (HD) or high passage (HP). Over-confluent tumor cells produced even lower number of lung colonies. Lung colony formation by elutriated B16a cells (i.e., cells freshly isolated from tumor tissue) was consistently inhibited by CGS14854, whereas inhibition of lung colony formation by cultured B16a cells was dependent upon culture conditions. CGS14854 was ineffective or less effective against HD/HP B16a cells. The differences in lung colony formation between LD, HD and elutriated B16a cells were not due to differential cell-cycle distribution. Mechanistic studies indicated that LD/LP tumor cells induced aggregation of homologous platelets, whereas HD/HP B16a cells failed to induce significant platelet aggregation. Aggregation of homologous platelets correlated positively with lung-colonizing ability. Additionally, LD/LP cells demonstrated higher adhesion to endothelium than HD/HP B16a cells. Finally, LD/LP B16a cells expressed higher levels of alpha IIb beta 3 integrins than HD/HP tumor cells, as determined by flow cytometry and immunofluorescence.
Micropatterning tractional forces in living cells (2002)

Here we describe a method for quantifying traction in cells that are physically constrained within micron-sized adhesive islands of defined shape and size on the surface of flexible polyacrylamide gels that contain fluorescent microbeads (0.2-microm diameter). Smooth muscle cells were plated onto square (50 x 50 microm) or circular (25- or 50-microm diameter) adhesive islands that were created on the surface of the gels by applying a collagen coating through microengineered holes in an elastomeric membrane that was later removed. Adherent cells spread to take on the size and shape of the islands and cell tractions were quantitated by mapping displacement fields of the fluorescent microbeads within the gel. Cells on round islands did not exhibit any preferential direction of force application, but they exerted their strongest traction at sites where they formed protrusions. When cells were confined to squares, traction was highest in the corners both in the absence and presence of the contractile agonist, histamine, and cell protrusions were also observed in these regions. Quantitation of the mean traction exerted by cells cultured on the different islands revealed that cell tension increased as cell spreading was promoted. These results provide a mechanical basis for past studies that demonstrated a similar correlation between spreading and growth within various anchorage-dependent cells. This new approach for analyzing the spatial distribution of mechanical forces beneath individual cells that are experimentally constrained to defined sizes and shapes may provide additional insight into the biophysical basis of cell regulation.
Dynamic Shadow Mask Technique:  A Universal Tool for Nanoscience (2004)

A comprehensive instrument, designed for fabricating nanostructures by evaporation through a dynamic shadow mask in ultrahigh vacuum, is described. The versatility and performance of the instrument is demonstrated through a series of examples, allowing for applications that are impossible to achieve with traditional nanopatterning methods. Clean nanostructures or entire devices made of different materials and on various substrates can be fabricated. The technique is compatible with fundamental surface science and can be easily interfaced with other fabrication and characterization techniques.
Herpes Simplex Virus Glycoprotein Treatment of Recurrent Genital Herpes (1988)

We investigated the possibility that herpes simplex virus (HSV) glycoproteins might provide potential immunotherapy for recurrent HSV disease by using the guinea pig model of genital HSV infection. In two experiments, after recovery from initial genital herpes, 58 animals were randomized either to receive a glycoprotein vaccine or to serve as controls. Both a mixture of HSV-2 glycoproteins derived from infected tissue cultures and a mixture of HSV-1 glycoproteins B and D, prepared by genetic engineering in mammalian cells, reduced the frequency (P less than .05) and severity (P less than .05) of subsequent herpetic recurrences. We conclude that recurrences of established herpesvirus disease may be altered by administering immunogenic viral proteins; thus, HSV glycoproteins may be useful as immunotherapeutic agents for controlling recurrent HSV infection in humans.
Safety Evaluation of LB20304, a New Quinolone Antibiotic (1995)

General pharmacology of LB20304, a quinolone antibiotic, were examined in terms of general behaviour, cardiovascular, and central nervous system. LB20304 at oral dose of 2,000 mg/kg did not induce significant behavioural changes in mice. In contrast with ciprofloxacin, LB20304 at dose of 20 mg/kg, iv. did not show any observable effects on the blood pressure in rats. Displacement of [H]muscimol binding to the rat brain synaptic membranes was measured. LB20304 was shown to be about five times less potent than ciprofloxacin in specific GABA receptor binding. Drug interaction between LB20304 and 4-biphenyl acetic acid, an active metabolite of fenbufen, was assessed in mice by measuring convulsion and/or subsequent death. A single oral pretreatment with 4-BPA at 400 mg/kg increased the incidence of convulsion and death after oral administration of ciprofloxacin at the doses of 25, 50, and 100 from zero of five to three of five, two of five, and four of five, respectively, whereas LB20304 alone or combination with 4-BPA caused neither convulsions nor death at the doses of 12.5, 25, 50, and 100 mg/kg, respectively. Quinolones-induced epileptogenic activities were assessed by a direct intracerebral injection of test articles. The CD values (nmole) are as follows; 169.47, 35.36, 105.29, and 88.67 for LB20304, ciprofloxacin, of loxacin, and lomefloxacin, respectively. From these data, LB 20304 at therapeutic doses seems to be much more safe than any other quinolones tested.d.
Molecular Vibration Spectra by Inelastic Electron Tunneling (1968)

An experimental and theoretical study has been carried out on the process of inelastic tunneling between metal films. The experimental results show that this process gives rise to the observation of vibrational spectra for molecules contained in the junction region. The phenomena have been studied for a number of molecular species and at temperatures ranging from 1 to 300\ifmmode^\circ\else\textdegree\fi{}K. The principal effect of temperature is to broaden the observed spectral lines which can be accounted for quantitatively by considering the thermal smearing of the electron distribution in metals. Two detailed interaction mechanisms are discussed which can give rise to infrared dipole or Raman selection rules. None of the experiments carried out thus far can distinguish between these two processes, because of the low symmetry of the molecules used. In addition to the vibrational spectra, it appears that it should be possible to observe electronic transitions as well.
Toll‐like receptor signalling on Tregs: to suppress or not to suppress? (2008)

To balance self-tolerance and immunity against pathogens or tumours, the immune system depends on both activation mechanisms and down-regulatory mechanisms. Immunologists have long been focusing on activation mechanisms, and a major breakthrough was the identification of the Toll-like receptor (TLR) family of proteins. TLRs recognize conserved molecular patterns present on pathogens, including bacteria, viruses, fungi and protozoa. Pathogen recognition via TLRs activates the innate as well as the adaptive immune response. The discovery of a suppressive T-cell subset that constitutively expresses the interleukin (IL)-2 receptor alpha-chain (CD25) has boosted efforts to investigate the negative regulation of immune responses. It is now well appreciated that these regulatory T cells (Tregs) play a pivotal role in controlling immune function. Interestingly, recent studies revealed that TLR2 signalling affects Treg expansion and function. This review will focus on the presence and influence of different TLRs on T lymphocytes, including Tregs, and their role in cancer.