gebhart/patrepeval huggingface dataset:
High-Field Quasiballistic Transport in Short Carbon Nanotubes (2004)

Single walled carbon nanotubes with Pd Ohmic contacts and lengths ranging from several microns down to 10 nm are investigated by electron transport experiments and theory. The mean-free path (MFP) for acoustic phonon scattering is estimated to be l(ap) approximately 300 nm, and that for optical phonon scattering is l(op) approximately 15 nm. Transport through very short (approximately 10 nm) nanotubes is free of significant acoustic and optical phonon scattering and thus ballistic and quasiballistic at the low- and high-bias voltage limits, respectively. High currents of up to 70 microA can flow through a short nanotube. Possible mechanisms for the eventual electrical breakdown of short nanotubes at high fields are discussed. The results presented here have important implications to high performance nanotube transistors and interconnects.
Efficient targeting of foreign genes into the tobacco plastid genome (1994)

The pPRV plasmids are vectors for targeted insertion of foreign genes into the tobacco plastid genome (ptDNA). The vectors are based on the pUC119 plasmid which replicates in E. coli but not in plastids. The spectinomycin resistance (aadA) gene and a multiple cloning site (MCS) are flanked by 1.8-kb and 1.2-kb ptDNA sequences. Biolistic delivery of vector DNA, followed by spectinomycin selection, yields plastid transformants at a reproducible frequency, approximately 1 transplastomic line per bombarded sample. The selected aadA gene and linked non-selectable genes cloned into the MCS are incorporated into the ptDNA by two homologous recombination events via the flanking ptDNA sequences. The transplastomes thus generated are stable, and are maternally transmitted to the seed progeny. The pPRV vector series targets insertions between the divergently transcribed trnV gene and the rps12/7 operon. The lack of readthrough transcription of appropriately oriented transgenes makes the vectors an ideal choice for the study of transgene promoter activity.
Oncogenic CARD11 Mutations in Human Diffuse Large B Cell Lymphoma (2008)

Diffuse large B cell lymphoma (DLBCL) is the most common form of non-Hodgkin's lymphoma. In the least curable (ABC) subtype of DLBCL, survival of the malignant cells is dependent on constitutive activation of the nuclear factor-kappaB (NF-kappaB) signaling pathway. In normal B cells, antigen receptor-induced NF-kappaB activation requires CARD11, a cytoplasmic scaffolding protein. To determine whether CARD11 contributes to tumorigenesis, we sequenced the CARD11 gene in human DLBCL tumors. We detected missense mutations in 7 of 73 ABC DLBCL biopsies (9.6%), all within exons encoding the coiled-coil domain. Experimental introduction of CARD11 coiled-coil domain mutants into lymphoma cell lines resulted in constitutive NF-kappaB activation and enhanced NF-kappaB activity upon antigen receptor stimulation. These results demonstrate that CARD11 is a bona fide oncogenein DLBCL, providing a genetic rationale for the development of pharmacological inhibitors of the CARD11 pathway for DLBCL therapy.
INORGANIC–ORGANIC HYBRID PHOTOREFRACTIVE MATERIALS BEARING THE BIFUNCTIONAL CHROMOPHORE (2005)

We prepared the photorefractive composite based on organic–inorganic hybrid materials containing charge-transporting molecules, second-order nonlinear optical chromophore, photosensitizer, and plasticizer either as a side chain unit or a guest molecule. New chromophore was synthesized to contain nonlinear optical chromophore and carbazole in one molecule. The functional chromophores were reacted to isocyanatotriethoxysilane to provide the functional precursor molecules. 2,4,7-Trinitrofluorenone (TNF) was added into the sol-gel materials to induce a charge-transfer complex. We also compared the gain coefficient of the photorefractive samples with the change of the concentration of the plasticizer, determined by two-beam coupling technique.
The Saccharomyces cerevisiae MSI4 gene encodes the yeast counterpart of component A of Rab geranylgeranyltransferase. (1994)

We describe the isolation of MSI4 as a multicopy suppressor of ira1 (inhibitory regulator of Ras). We find it encodes a 66-kDa protein with three regions similar to component A of Rab geranylgeranyltransferase and Rab guanine nucleotide dissociation inhibitor. A gene disruption experiment showed that MSI4 is essential for cell growth. To investigate its functions further, we constructed a strain whose MSI4 is driven by the GAL1 promoter. This strain accumulated the endoplasmic reticulum precursor form of a vacuolar enzyme, carboxypeptidase Y, under the restrictive conditions. Moreover, we showed that the activity of geranylgeranyl-transferase for Ypt1p was very low in the mutant shifted to glucose medium. We propose that the MSI4 gene product is a yeast counterpart of component A of Rab geranylgeranyltransferase that is essential for Ypt1p to localize on membranes.
Electrical Contacting of Flavoenzymes and NAD(P)+-Dependent Enzymes by Reconstitution and Affinity Interactions on Phenylboronic Acid Monolayers Associated with Au-Electrodes (2002)

The preparation of integrated, electrically contacted, flavoenzyme and NAD(P)(+)-dependent enzyme-electrodes is described. The reconstitution of apo-glucose oxidase, apo-GOx, on a FAD cofactor linked to a pyrroloquinoline quinone (PQQ) phenylboronic acid monolayer yields an electrically contacted enzyme monolayer (surface coverage 2.1 x 10(-)(12) mol cm(-)(2)) exhibiting a turnover rate of 700 s(-)(1) (at 22 +/- 2 degrees C). The system is characterized by microgravimetric quartz-crystal microbalance analyses, Faradaic impedance spectroscopy, rotating disk electrode experiments, and cyclic voltammetry. The performance of the enzyme-electrode for glucose sensing is described. Similarly, the electrically contacted enzyme-electrodes of NAD(P)(+)-dependent enzymes malate dehydrogenase, MalD, and lactate dehydrogenase, LDH, are prepared by the cross-linking of affinity complexes generated between the enzymes and the NADP(+) and NAD(+) cofactors linked to a pyrroloquinoline quinone phenylboronic acid monolayer, respectively. The MalD enzyme-electrode (surface coverage 1.2 x 10(-)(12) mol cm(-)(2)) exhibits a turnover rate of 190 s(-)(1), whereas the LDH enzyme-electrode (surface coverage 7.0 x 10(-)(12) mol cm(-)(2)) reveals a turnover rate of 2.5 s(-)(1). Chronoamperometric experiments reveal that the NAD(+) cofactor is linked to the PQQ-phenylboronic acid by two different binding modes. The integration of the LDH with the two NAD(+) cofactor configurations yields enzyme assemblies differing by 1 order of magnitude in their bioelectrocatalytic activities.
Whole genome DNA copy number changes identified by high density oligonucleotide arrays (2004)

Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous microarray-based methods have been used to identify chromosomal gains and losses; however, they are unable to genotype alleles at the level of single nucleotide polymorphisms (SNPs). Here we describe a novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA), to identify genome-wide chromosomal gains and losses at high resolution. WGSA simultaneously genotypes over 10,000 SNPs by allele-specific hybridisation to perfect match (PM) and mismatch (MM) probes synthesised on a single array. The copy number algorithm jointly uses PM intensity and discrimination ratios between paired PM and MM intensity values to identify and estimate genetic copy number changes. Values from an experimental sample are compared with SNP-specific distributions derived from a reference set containing over 100 normal individuals to gain statistical power. Genomic regions with statistically significant copy number changes can be identified using both single point analysis and contiguous point analysis of SNP intensities. We identified multiple regions of amplification and deletion using a panel of human breast cancer cell lines. We verified these results using an independent method based on quantitative polymerase chain reaction and found that our approach is both sensitive and specific and can tolerate samples which contain a mixture of both tumour and normal DNA. In addition, by using known allele frequencies from the reference set, statistically significant genomic intervals can be identified containing contiguous stretches of homozygous markers, potentially allowing the detection of regions undergoing loss of heterozygosity (LOH) without the need for a matched normal control sample. The coupling of LOH analysis, via SNP genotyping, with copy number estimations using a single array provides additional insight into the structure of genomic alterations. With mean and median inter-SNP euchromatin distances of 244 kilobases (kb) and 119 kb, respectively, this method affords a resolution that is not easily achievable with non-oligonucleotide-based experimental approaches.
Nonpathogenic, Environmental Fungi Induce Activation and Degranulation of Human Eosinophils (2005)

Eosinophils and their products are probably important in the pathophysiology of allergic diseases, such as bronchial asthma, and in host immunity to certain organisms. An association between environmental fungal exposure and asthma has been long recognized clinically. Although products of microorganisms (e.g., lipopolysaccharides) directly activate certain inflammatory cells (e.g., macrophages), the mechanism(s) that triggers eosinophil degranulation is unknown. In this study we investigated whether human eosinophils have an innate immune response to certain fungal organisms. We incubated human eosinophils with extracts from seven environmental airborne fungi (Alternaria alternata, Aspergillus versicolor, Bipolaris sorokiniana, Candida albicans, Cladosporium herbarum, Curvularia spicifera, and Penicillium notatum). Alternaria and Penicillium induced calcium-dependent exocytosis (e.g., eosinophil-derived neurotoxin release) in eosinophils from normal individuals. Alternaria also strongly induced other activation events in eosinophils, including increases in intracellular calcium concentration, cell surface expression of CD63 and CD11b, and production of IL-8. Other fungi did not induce eosinophil degranulation, and Alternaria did not induce neutrophil activation, suggesting specificity for fungal species and cell type. The Alternaria-induced eosinophil degranulation was pertussis toxin sensitive and desensitized by preincubating cells with G protein-coupled receptor agonists, platelet-activating factor, or FMLP. The eosinophil-stimulating activity in Alternaria extract was highly heat labile and had an M(r) of approximately 60 kDa. Thus, eosinophils, but not neutrophils, possess G protein-dependent cellular activation machinery that directly responds to an Alternaria protein product(s). This innate response by eosinophils to certain environmental fungi may be important in host defense and in the exacerbation of inflammation in asthma and allergic diseases.
Induction of the Differentiation of Lentoids from Primate Embryonic Stem Cells (2003)

The differentiation of primate ES cells into lentoids can be achieved by treatment with SIDA. ES cells can be used to facilitate a greater understanding of the mechanisms functioning in differentiation in vivo and in vitro.
Stimulation of cloned human T lymphocytes via the CD3 or CD28 molecules induces enhancement in vascular endothelial permeability to macromolecules with participation of type‐1 and type‐2 intercellular adhesion pathways (1990)

Perivascular accumulation of CD29+CD45R0+ memory T lymphocytes at sites of chronic inflammation such as rheumatoid synovium is commonly associated with the localized increase in the endothelial permeability. We have recently demonstrated that a direct interaction between activated CD29+CD45R0+ memory T lymphocytes and vascular endothelial cells (EC) results in the increased permeability of EC. In this report, we have investigated effects on antigen-specific T cell receptor (TcR) alpha/beta+ human T lymphocyte clones on the endothelial permeability to albumin. Our results show that CD29+CD45R0+ cloned human T lymphocytes augment endothelial permeability by a noncytolytic process requiring surface contact between T lymphocytes and EC. Both cytolytic and noncytolytic cloned T lymphocytes were capable of augmenting endothelial permeability and this process did not involve active lysis of EC. Stimulation of T lymphocytes via the CD3/TcR or CD28 molecules resulted in significant enhancement in the ability of T lymphocytes to influence endothelial permeability. Pretreatment of T lymphocytes with monoclonal antibodies directed at either CD11a/CD18 (LFA-1) or CD2 molecules or that of EC with monoclonal antibodies directed at either CD54 (ICAM-1) or CD58 (LFA-3) molecules significantly inhibited T lymphocyte-induced enhancement in endothelial permeability, thus indicating that activated T lymphocytes utilize both type-1 (CD11a/CD18CD54) and type-2 (CD2CD58) intercellular adhesion pathways to augment endothelial permeability and signals received via CD3 or CD28 molecules on T lymphocytes further enhance this process. Furthermore, proinflammatory cytokines interleukin 1 and tumor necrosis factor but not proinflammatory cytokines interleukin 1 and tumor necrosis factor but not interleukin 6 induced resistance in EC to T lymphocyte-mediated effects on their permeability. Collectively, these observations may provide insights into molecular mechanism(s) underlying pathophysiology of localized chronic inflammatory responses in general and more specifically selective accumulation of chronically activated memory T lymphocytes at sites of chronic inflammation.
A Long-Acting Prostacyclin Agonist with Thromboxane Inhibitory Activity for Pulmonary Hypertension (2005)

Subcutaneous administration of a novel prostacyclin agonist (ONO-1301) markedly attenuated monocrotaline-induced pulmonary hypertension and improved survival in rats. The beneficial effects of ONO-1301 may occur through its long-lasting stimulation of cyclic adenosine 3', 5'-monophosphate and inhibition of thromboxane synthase.
The yeast RNA1 gene product necessary for RNA processing is located in the cytosol and apparently excluded from the nucleus. (1990)

The yeast RNA1 gene is required for RNA processing and nuclear transport of RNA. The rna1-1 mutation of this locus causes defects in pre-tRNA splicing, processing of the primary pre-rRNA transcript, production of mRNA and export of RNA from the nucleus to the cytosol. To understand how this gene product can pleiotropically affect these processes, we sought to determine the intracellular location of the RNA1 protein. As determined by indirect immunofluorescence localization and organelle fractionation, the RNA1 antigen is found exclusively or primarily in the cytoplasm. Only a tiny fraction of the endogenous protein could be localized to and functional in the nucleus. Furthermore, the RNA1 antigen does not localize differently under stress conditions. These findings suggest that the RNA1 protein is not directly involved in RNA processing but may modify nuclear proteins or otherwise transmit a signal from the cytosol to the nucleus or play a role in maintaining the integrity of the nucleus.
A Novel Mechanism for Wnt Activation of Canonical Signaling through the LRP6 Receptor (2003)

LDL receptor-related protein 6 (LRP6) is a Wnt coreceptor in the canonical signaling pathway, which plays essential roles in embryonic development. We demonstrate here that wild-type LRP6 forms an inactive dimer through interactions mediated by epidermal growth factor repeat regions within the extracellular domain. A truncated LRP6 comprising its transmembrane and cytoplasmic domains is expressed as a constitutively active monomer whose signaling ability is inhibited by forced dimerization. Conversely, Wnts are shown to activate canonical signaling through LRP6 by inducing an intracellular conformational switch which relieves allosteric inhibition imposed on the intracellular domains. Thus, Wnt canonical signaling through LRP6 establishes a novel mechanism for receptor activation which is opposite to the general paradigm of ligand-induced receptor oligomerization.
A high efficiency H2S gas sensor material: paper like Fe2O3/graphene nanosheets and structural alignment dependency of device efficiency (2014)

Preparation of paper like vertically arranged Fe<sub>2</sub>O<sub>3</sub>/graphene nanosheets and their application in H<sub>2</sub>S gas response with high efficiency.
The cardiovascular response at rest and during exercise in hypothyroid subjects to thyroxine substitution (1983)

Rapid and intense thyroxine substitution can lead to heart failure and myocardial infarction in hypothyroid patients. We have analyzed the normalization of the circulatory system in hypothyroid subjects on a gradual thyroxine substitution. Fourteen hypothyroid patients were studied repeatedly with an orthostatic test and a standardized symptom-limited exercise test during substitution. ST and T abnormalities were observed in 51 and 33%, respectively, before substitution. Many of these changes were normalized upon substitution at a dose level of 0.15 mg/d thyroxine. The pulse reaction to standing was enhanced early during substitution. The capacity to perform work, on the other hand, responded more slowly to thyroxine substitution, and was significantly increased only after six months of full substitution. This difference in the time course of recovery may be of clinical importance when substituting patients with hypothyroidism and ischemic heart disease.
Avicins, a family of triterpenoid saponins from Acacia victoriae (Bentham), suppress H- ras mutations and aneuploidy in a murine skin carcinogenesis model (2001)

We tested the ability of avicins, a family of triterpenoid saponins obtained from Acacia victoriae (Bentham) (Leguminosae: Mimosoideae), to inhibit chemically induced mouse skin carcinogenesis. Varying doses of avicins were applied to shaved dorsal skin of SENCAR mice 15 min before application of 100 nmol of 7,12-dimethylbenz[a]anthracene (DMBA) twice a week for 4 weeks (complete carcinogenesis model). The dorsal skin of a second group of mice was treated with one dose of 10 nmol of DMBA. Avicins were then applied 15 min before repetitive doses of 2 microg of phorbol 12-tetradecanoate 13-acetate (TPA) twice a week for 8 weeks (initiation/promotion model). At 12 weeks, avicins produced a 70% decrease in the number of mice with papillomas and a greater than 90% reduction in the number of papillomas per mouse in both protocols. We also observed a 62% and 74% reduction by avicins in H-ras mutations at codon 61 in the DMBA and DMBA/TPA models, respectively, as well as a significant inhibition of the modified DNA base formation (8-OH-dG) in both protocols. Marked suppression of aneuploidy occurred with treatment at 16 weeks in the initiation/promotion experiment. These findings, when combined with the proapoptotic property of these compounds and their ability to inhibit hydrogen peroxide (H(2)O(2)) generation, nuclear factor-kappaB (NF-kappaB) activation, and inducible nitric oxide synthase (iNOS) induction reported elsewhere, suggest that avicins could prove exciting in reducing oxidative and nitrosative stress and thereby suppressing the development of human skin cancer and other epithelial malignancies.
Regulation of Translation in Eukaryotic Systems (1992)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
Vitamin D3 Inhibits Hedgehog Signaling and Proliferation in Murine Basal Cell Carcinomas (2011)

Constitutive Hedgehog (HH) signaling underlies several human tumors, including basal cell carcinoma (BCC). Recently, Bijlsma and colleagues reported a new biologic function for vitamin D3 in suppressing HH signaling in an in vitro model system. On the basis of that work, we have assessed effects of vitamin D3 on HH signaling and proliferation of murine BCCs in vitro and in vivo. We find that indeed in BCC cells, vitamin D3 blocks both proliferation and HH signaling as assessed by mRNA expression of the HH target gene Gli1. These effects of vitamin D3 on Gli1 expression and on BCC cell proliferation are comparable to the effects of cyclopamine, a known inhibitor of the HH pathway. These results are specific for vitamin D3, because the precursor 7-dehydrocholesterol and the downstream products 25-hydroxy vitamin D3 [25(OH)D] and 1,25-dihydroxy vitamin D3 [1,25(OH)(2)D] are considerably less effective in reducing either Gli1 mRNA or cellular proliferation. Moreover, these effects seem to be independent of the vitamin D receptor (VDR) because short hairpin RNA knockdown of VDR does not abrogate the anti-HH effects of D3 despite reducing expression of the VDR target gene 24-hydroxylase. Finally, topical vitamin D3 treatment of existing murine BCC tumors significantly decreases Gli1 and Ki67 staining. Thus, topical vitamin D3 acting via its HH inhibiting effect may hold promise as an effective anti-BCC agent.
Design of Liposomes for Enhanced Local Release of Drugs by Hyperthermia (1978)

Liposomes can be designed to release an entrapped drug preferentially at temperatures attainable by mild local hyperthermia. In a test system in vitro, protein synthesis by Escherichia coli is inhibited and killing of the cells is enhanced by heating neomycin-containing liposomes to their phase transition temperature to maximize drug release. In the presence of serum the ratio of release at 44 degrees C to that at 37 degrees C can be made greater than 100:1, suggesting possible applications in the treatment of tumors or local infection.
Label-Free Electrochemical Detection of Protein Based on a Ferrocene-Bearing Cationic Polythiophene and Aptamer (2006)

Two label-free electrochemical methods for the detection of human alpha-thrombin using a water-soluble, ferrocene-functionalized polythiophene transducer and a single-stranded oligonucleotide aptamer probe are described. The first approach is a direct method in which the recorded current decreases upon addition of the targeted protein. The second one requires more steps and the additional utilization of PNA probes and nuclease enzyme. This indirect method leads to an increase of the electrical signal as a function of the concentration of human alpha-thrombin with a detection limit of 75 fmol.
Antivirus Action of Acrolein, Glutaraldehyde and Oxidized Spermine (1971)

SUMMARY The inactivation of bacteriophages and myxoviruses by oxidized spermine, acrolein and glutaraldehyde has been studied. Oxidized spermine inactivated T5 and not T2 coliphages, while acrolein was more effective against T-even phages. Myxoviruses also differed in their sensitivity to the various aldehydes. This was determined by plaque counting or by assaying the haemagglutination activity after propagation in embryonated eggs. High-molecular (condensation?) products, which were formed when spermine was oxidized for several hours by small quantities of enzyme also inactivated viruses. These experiments stress the uniqueness of oxidized spermine as a virucidal agent, and do not support the hypothesis that its antivirus activity is due to the formation of acrolein as a spontaneous degradation product.