gebhart/patrepeval huggingface dataset:
Mechanical Properties of Polyelectrolyte Complex Films Based on Polyvinylamine and Carboxymethyl Cellulose (2006)

Homogeneous polyelectrolyte complex films were cast from mixtures of poly(vinylamine-co-vinylformamide) and carboxymethyl cellulose (CMC) in 50% formic acid aqueous solution with compositions varying between CMC blended with pure polyvinylamine (PVAm) and CMC blended with pure poly(N-vinylformamide) (PNVF). The tensile strength and tensile modulus of the complex films were measured as functions of polymer ratio, molecular weight, function group content, and water content. PVAm addition lowered the strength and modulus of dry CMC whereas PNVF did not; intermediate PVAm−PNVF copolymers gave intermediate results. Mechanical strength decreased with increasing molecular weight of CMC and carboxyl content, but was not affected by molecular weight of PVAm. The mechanical properties of all the films decreased with increasing water content. CMC:PVAm films were swollen gels in water, whereas CMC:PNVF films dissolved in water. Heating did not improve the mechanical strength, whereas cross-linking with 5% glutaraldehyde doubled the strength. It was proposed that hydrogen bonding was the predominant intermolecular force responsible for the strength of dry film blends whereas ionic bonds between CMC-carboxyl and PVAm-ammonium ions were responsible for the integrity of water swollen polyelectrolyte films.
Cis-acting Elements and DNA-Binding Proteins Involved in CO2-Responsive Transcriptional Activation of Cah1 Encoding a Periplasmic Carbonic Anhydrase in Chlamydomonas reinhardtii (2003)

Expression of Cah1, encoding a periplasmic carbonic anhydrase in Chlamydomonas reinhardtii Dangeard, is activated when cells are exposed to low-CO2 conditions (0.04% [v/v]) in light. By using an arylsulfatase reporter gene, a regulatory region essential for the transcriptional activation of Cah1 was delimited to a 63-bp fragment between -293 and -231 relative to the transcription start site. Linker-scan analysis of the 63-bp region identified two enhancer elements, EE-1 (AGATTTTCACCGGTTGGAAGGAGGT) and EE-2 (CGACTTACGAA). Gel mobility shift assays indicated that nuclear extracts purified from cells grown under low-CO2 conditions in light contained DNA-binding proteins specifically interacting with EE-1 and EE-2. Gel mobility shift assays using mutant oligonucleotide probes revealed that the protein binding to EE-1 preferentially recognized a 9-bp sequence stretch (AGATTTTCA) of EE-1, containing a conserved sequence motif named EEC, GANTTNC, which is also present in EE-2. The EE-1- and EE-2-binding proteins interacted with the EECs contained in both of the two enhancer elements in vitro. Four EECs in the 5'-upstream region from -651 to -231 of Cah1 played a central role in the transcriptional activation of Cah1 under low-CO2 conditions. These EEC-binding proteins were present even in cells grown under high-CO2 conditions (5% [v/v]) or in the dark when Cah1 is not activated. On the basis of these results, the relationship between the transcriptional regulation of Cah1 and protein-binding to the enhancer elements in the 5'-upstream region of Cah1 is discussed.
Kynurenine aminotransferase and glutamine transaminase K of Escherichia coli: identity with aspartate aminotransferase (2001)

The present study describes the isolation of a protein from Escherichia coli possessing kynurenine aminotransferase (KAT) activity and its identification as aspartate aminotransferase (AspAT). KAT catalyses the transamination of kynurenine and 3-hydroxykynurenine to kynurenic acid and xanthurenic acid respectively, and the enzyme activity can be easily detected in E. coli cells. Separation of the E. coli protein possessing KAT activity through various chromatographic steps led to the isolation of the enzyme. N-terminal sequencing of the purified protein determined its first 10 N-terminal amino acid residues, which were identical with those of the E. coli AspAT. Recombinant AspAT (R-AspAT), homologously expressed in an E. coli/pET22b expression system, was capable of catalysing the transamination of both l-kynurenine (Km = 3mM; Vmax = 7.9μmol·min−1·mg−1) and 3-hydroxy-dl-kynurenine (Km = 3.7mM; Vmax = 1.25μmol·min−1·mg−1) in the presence of pyruvate as an amino acceptor, and exhibited its maximum activity at temperatures between 50–60°C and at a pH of approx. 7.0. Like mammalian KATs, R-AspAT also displayed high glutamine transaminase K activity when l-phenylalanine was used as an amino donor (Km = 8mM; Vmax = 20.6μmol·min−1·mg−1). The exact match of the first ten N-terminal amino acid residues of the KAT-active protein with that of AspAT, in conjunction with the high KAT activity of R-AspAT, provides convincing evidence that the identity of the E. coli protein is AspAT.
Transferable self-welding silver nanowire network as high performance transparent flexible electrode (2013)

High performance transparent electrodes (TEs) with figures-of-merit as high as 471 were assembled using ultralong silver nanowires (Ag NWs). A room-temperature plasma was employed to enhance the conductivity of the Ag NW TEs by simultaneously removing the insulating PVP layer coating on the NWs and welding the junctions tightly. Furthermore, we developed a general way to fabricate TEs regardless of substrate limitations by transferring the as-fabricated Ag NW network onto various substrates directly, and the transmittance can remain as high as 91% with a sheet resistivity of 13 Ω/sq. The highly robust and stable flexible TEs will have broad applications in flexible optoelectronic and electronic devices.
Elements Within the -Lactoglobulin Gene Inhibit Expression of Human Serum Albumin cDNA and Minigenes in Transfected Cells but Rescue Their Expression in the Mammary Gland of Transgenic Mice (1996)

Two new beta-lactoglobulin (BLG)/human serum albumin (HSA) hybrid gene vectors were constructed and tested for expression in COS-7 cells and in transgenic mice. The HSA sequences were inserted between the second and sixth BLG exons. Transient transfection experiments with these vectors as well as a series of additional vectors with either the BLG 5'- or 3'- intragenic sequences revealed that sequences within BLG exon 1/intron 1/exon 2 abrogated BLG- directed HSA expression in vitro, regardless of the presence of HSA introns or the origin of the 3' polyadenylation signal. In contrast, the same BLG expression cassette enabled the efficient expression of HSA cDNA or minigene in the mammary gland of transgenic mice with subsequent secretion of the corresponding protein into the milk of 56 and 82%, respectively of the mouse strains at levels up to 0.3 mg/ml. Previous attempts to express HSA cDNA inserted into exon 1 of the BLG gene had failed [Shani,M., Barash,I., Nathan,M., Ricca,G., Searfoss,G.H., Dekel,I., Faerman,A., Givol,D. and Hurwitz,D.R. (1992) Transgenic Res. 1, 195- 208]. The new BLG expression cassette conferred more stringent tissue specific expression than previously described BLG/HSA constructs [Barash,I, Faerman,A., Ratovitsky,T, Puzis,R., Nathan,M., Hurwitz,D.R. and Shani, M. (1994) Transgenic Res. 3, 141-151]. However, it was not able to insulate the transgenes from the surrounding host DNA sequences and did not result in copy number dependent expression in transgenics. Together, the in vitro and in vivo results suggest both positive and negative regulatory elements within the BLG intragenic sequences evaluated. The new BLG construct represents an extremely valuable vector for the efficient expression of cDNAs in the mammary gland of transgenic animals.
Hypoxic induction of the human erythropoietin gene: cooperation between the promoter and enhancer, each of which contains steroid receptor response elements. (1992)

Transcription of the human erythropoietin (Epo) gene is stimulated by exposure to hypoxia and/or cobalt in whole animals and in Hep3B cells. We have systematically investigated the promoter and 3' enhancer elements necessary for this induction by transient transfection of Hep3B cells. We define a promoter region of 53 bp and an enhancer region of 43 bp that confer hypoxia and cobalt inducibility. Each element gives rise to a 6- to 10-fold induction alone. In combination they produce a 50-fold induction after stimulation, similar to the 50- to 100-fold induction of the endogenous Epo gene. Two areas of DNA sequence homology are present in these regions. We demonstrate specific DNA-protein interactions in the enhancer and the ability of the promoter element to compete with these interactions in electrophoretic mobility shift assays. DNase I footprinting and methylation interference data further refine the cis-acting element in the 43-bp enhancer to a short region containing a direct repeat of a steroid/thyroid hormone receptor response element half-site separated by a 2-bp gap. Two half-site consensus sequences are also present in the 53-bp promoter. Site-specific mutation of the half-site sequences in the enhancer destroys the functional activity of the enhancer.
The 19-Kilodalton Adenovirus E1B Transforming Protein Inhibits Programmed Cell Death and Prevents Cytolysis by Tumor Necrosis Factor α (1992)

The adenovirus E1A and E1B proteins are required for transformation of primary rodent cells. When expressed in the absence of the 19,000-dalton (19K) E1B protein, however, the E1A proteins are acutely cytotoxic and induce host cell chromosomal DNA fragmentation and cytolysis, analogous to cells undergoing programmed cell death (apoptosis). E1A alone can efficiently initiate the formation of foci which subsequently undergo abortive transformation whereby stimulation of cell growth is counteracted by continual cell death. Cell lines with an immortalized growth potential eventually arise with low frequency. Coexpression of the E1B 19K protein with E1A is sufficient to overcome abortive transformation to produce high-frequency transformation. Like E1A, the tumoricidal cytokine tumor necrosis factor alpha (TNF-alpha) evokes a programmed cell death response in many tumor cell lines by inducing DNA fragmentation and cytolysis. Expression of the E1B 19K protein by viral infection, by transient expression, or in transformed cells completely and specifically blocks this TNF-alpha-induced DNA fragmentation and cell death. Cosegregation of 19K protein transforming activity with protection from TNF-alpha-mediated cytolysis demonstrates that both activities are likely the consequence of the same function of the protein. Therefore, we propose that by suppressing an intrinsic cell death mechanism activated by TNF-alpha or E1A, the E1B 19K protein enhances the transforming activity of E1A and enables adenovirus to evade TNF-alpha-dependent immune surveillance.
Tissue Transglutaminase Is an Integrin-Binding Adhesion Coreceptor for Fibronectin (2000)

The protein cross-linking enzyme tissue transglutaminase binds in vitro with high affinity to fibronectin via its 42-kD gelatin-binding domain. Here we report that cell surface transglutaminase mediates adhesion and spreading of cells on the 42-kD fibronectin fragment, which lacks integrin-binding motifs. Overexpression of tissue transglutaminase increases its amount on the cell surface, enhances adhesion and spreading on fibronectin and its 42-kD fragment, enlarges focal adhesions, and amplifies adhesion-dependent phosphorylation of focal adhesion kinase. These effects are specific for tissue transglutaminase and are not shared by its functional homologue, a catalytic subunit of factor XIII. Adhesive function of tissue transglutaminase does not require its cross-linking activity but depends on its stable noncovalent association with integrins. Transglutaminase interacts directly with multiple integrins of beta1 and beta3 subfamilies, but not with beta2 integrins. Complexes of transglutaminase with integrins are formed inside the cell during biosynthesis and accumulate on the surface and in focal adhesions. Together our results demonstrate that tissue transglutaminase mediates the interaction of integrins with fibronectin, thereby acting as an integrin-associated coreceptor to promote cell adhesion and spreading.
SITES OF ACTION OF MOJAVE TOXIN ISOLATED FROM THE VENOM OF THE MOJAVE RATTLESNAKE (1980)

Mojave toxin isolated from the venom of the Mojave rattlesnake ( Crotalus scutulatus scutulatus ) produced an irreversible blockade of the contractile response of the mouse hemidiaphragm to stimulation of the phrenic nerve in vitro , at concentrations of 0.16 to 20 μg/ml; the response to direct stimulation was not affected over a testing period of several hours. Mojave toxin (1 to 4 μg/g) was injected into the tail vein of mice and the intoxicated hemidiaphragm preparation was removed either for testing the contractile response or for intracellular recording. In fully intoxicated hemidiaphragms the contractile response to indirect stimulation was either small and transient or absent, whilst the response to direct stimulation was well maintained. Intracellular recording showed that resting membrane potentials of the muscle fibres were within the normal range. Endplates were difficult to locate but miniature endplate potentials (m.e.p.ps) were recorded at sites at which neurally evoked responses either could not be detected or did not exceed 2 mV which corresponds to transmitter release of a few quanta only. The mean frequency of m.e.p.ps at fully intoxicated endplates was not significantly different from controls but potassium depolarization produced only a small increase in m.e.p.p. frequency relative to the control response. A 50 Hz tetanus had no effect on m.e.p.p. frequency. When a sub‐lethal dose (3 μg) of Mojave toxin was injected into one hindlimb of mice and the tissues examined at 72 h, there was histological evidence of myonecrosis. The isolated perfused heart of the rat was exposed to recycled Mojave toxin (50 and 100 μg/ml) but showed no change in rate or force of ventricular contraction. Post‐mortem examination of intoxicated mice showed a frequent incidence of localized areas of interstitial and intra‐alveolar haemorrhage in the lungs. Other organs including skin and muscle were not affected. Mojave toxin showed antigenic similarities to crotoxin, the lethal neurotoxin in the venom of the South American rattlesnake, as determined by the ability of antiserum raised against crotoxin to neutralize Mojave toxin. With systemic Mojave intoxication of rapid onset, the cause of death was respiratory paralysis. However, the toxin acts at multiple sites at differing rates of action. With a slower rate of intoxication, impaired respiration may act synergistically with cardiovascular changes to produce circulatory failure. The desirability of using an antivenin with a high titre against Mojave toxin is indicated.
A sex recognition glycoprotein is encoded by the plus mating-type gene fus1 of Chlamydomonas reinhardtii. (1996)

Sexual fusion between plus and minus gametes of the unicellular green alga Chlamydomonas reinhardtii entails adhesion between plus-specific and minus-specific "fringe" proteins displayed on the plasma membrane of gametic mating structures. We report the identification of the gene (fus1) encoding the plus fringe glycoprotein, which resides in a unique domain of the mating-type plus (mt+) locus, and which was identified by transposon insertions in three fusion-defective mutant strains. Transformation with fus1+ restores fringe and fusion competence to these mutants and to the pseudo-plus mutant imp11 mt-, defective in minus differentiation. The fus1 gene is remarkable in lacking the codon bias found in all other nuclear genes of C. reinhardtii.
A new cancer genome anatomy project web resource for the community. (2001)

The National Cancer Institute's Cancer Genome Anatomy Project (CGAP) is developing publicly accessible information, technology, and material resources that provide a platform for the interface of cancer research and genomics. CGAP's efforts have focused toward (1) building and annotating catalogues of genes expressed during cancer development, (2) identifying polymorphisms in those genes, and (3) developing resources for the molecular characterization of cancer-related chromosomal aberrations. To date, CGAP has produced more than 1,000,000 expressed sequence tags, approximately 3,300,000 serial analysis of gene expression tags, and identified more than 10,000 human gene-based single-nucleotide polymorphisms. To enhance access to these datasets by the research community, a new Cancer Genome Project web site (http://cgap.nci.nih.gov/) is being introduced. The web site includes genomic data for humans and mice, including transcript sequence, gene expression patterns, single-nucleotide polymorphisms, clone resources, and cytogenetic information. Descriptions of the methods and reagents used in deriving the CGAP datasets are also provided. An extensive suite of informatics tools facilitates queries and analysis of the CGAP data by the community. One of the newest features of the CGAP web site is an electronic version of the Mitelman Database of Chromosome Aberrations in Cancer.
Implicit state enumeration of finite state machines using BDD's (2002)

The authors propose a novel method based on transition relations that only requires the ability to compute the BDD (binary decision diagram) for f/sub i/ and outperforms O. Coudert's (1990) algorithm for most examples. The method offers a simple notational framework to express the basic operations used in BDD-based state enumeration algorithms in a unified way and a set of techniques that can speed up range computation dramatically, including a variable ordering heuristic and a method based on transition relations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Transcutaneous electrical stimulation of the recurrent laryngeal nerve: A method of controlling vocal cord position (1986)

This study was designed to examine the feasibility of transcutaneous stimulation of the recurrent laryngeal nerve. Electrical activation of the recurrent laryngeal nerve was achieved by applying a blunt electrode to the intact neck skin at specific points along the tracheoesophageal groove in anesthetized adult dogs. The stimulus consisted of 10 mA cathodal pulses, each of 1 msec duration, delivered at a frequency of 10 Hz and increased by 10 Hz increments up to 100 Hz. Vocal cord excursion was directly related to the frequency of applied current. In all six dogs studies, stimulation at 30 Hz resulted in maximal ipsilateral vocal cord abduction, while stimulation at frequencies greater than 40 Hz resulted in ipsilateral vocal cord adduction up to or across the midline. Vocal cord movement was immediate and persisted for the duration of the stimulus train. Surrounding neck muscles were not visibly activated. We propose that the observed frequency-dependent movement of the vocal cords occurred because of the difference between the contraction times of the intrinsic abductor and adductor muscles of the larynx. Transcutaneous recurrent laryngeal nerve stimulation appears promising, both as a diagnostic aid in laryngoscopy and as a therapeutic tool in controlling the glottic aperture.
Amber InGaN-Based Light-Emitting Diodes Operable at High Ambient Temperatures (1998)

High-efficiency amber InGaN single-quantum-well (SQW) structure light-emitting diodes (LEDs) with a luminous efficiency of 10 l m/W were developed. At a current of 20 mA, the external quantum efficiency, the output power and the emission wavelength of the amber InGaN SQW structure LEDs were 3.3%, 1.4 mW and 594 nm, respectively. The output power of InGaN LEDs was about twice as high as that of AlInGaP LEDs. There was a large difference in the temperature dependence of the output power between InGaN and AlInGaP LEDs. When the ambient temperature was increased from room temperature to 80°C, the output power of AlInGaP LEDs decreased dramatically. On the other hand, the output power of the InGaN LEDs remained almost constant.
Quantitative analysis of albumin uptake and transport in the rat microvessel endothelial monolayer (2003)

We determined the concentration dependence of albumin binding, uptake, and transport in confluent monolayers of cultured rat lung microvascular endothelial cells (RLMVEC). Transport of (125)I-albumin in RLMVEC monolayers occurred at a rate of 7.2 fmol. min(-1). 10(6) cells(-1). Albumin transport was inhibited by cell surface depletion of the 60-kDa albumin-binding glycoprotein gp60 and by disruption of caveolae using methyl-beta-cyclodextrin. By contrast, gp60 activation (by means of gp60 cross-linking using primary and secondary antibodies) increased (125)I-albumin uptake 2.3-fold. At 37 degrees C, (125)I-albumin uptake had a half time of 10 min and was competitively inhibited by unlabeled albumin (IC(50) = 1 microM). Using a two-site model, we estimated by Scatchard analysis the affinity (K(D)) and maximal capacity (B(max)) of albumin uptake to be 0.87 microM (K(D1)) and 0.47 pmol/10(6) cells (B(max1)) and 93.3 microM (K(D2)) and 20.2 pmol/10(6) cells (B(max2)). At 4 degrees C, we also observed two populations of specific binding sites, with high (K(D1) = 13.5 nM, 1% of the total) and low (K(D2) = 1.6 microM) affinity. On the basis of these data, we propose a model in which the two binding affinities represent the clustered and unclustered gp60 forms. The model predicts that fluid phase albumin in caveolae accounts for the bulk of albumin internalized and transported in the endothelial monolayer.
Identification of Selective Inhibitors of NAD+-dependent Deacetylases Using Phenotypic Screens in Yeast (2003)

Sir2 and Hst1 are NAD+-dependent deacetylases involved in transcriptional repression in yeast. The two enzymes are highly homologous yet have different sensitivity to the small-molecule inhibitor splitomicin (compound 1) (Bedalov, A., Gatbonton, T., Irvine, W. P., Gottschling, D. E., and Simon, J. A. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 15113-15118). We have now defined a critical amino acid residue within a small helical module of Hst1 that confers relative resistance to splitomicin. Parallel cell-based screens of 100 splitomicin analogues led to the identification of compounds that exhibit a higher degree of selectivity toward Sir2 or Hst1. A series of compounds based on a splitomicin derivative, dehydrosplitomicin (compound 2), effectively phenocopied a yeast strain that lacked Hst1 deacetylase while having no effect on the silencing activities of Sir2. In addition, we identified a compound with improved selectivity for Sir2. Selectivity was affirmed using whole-genome DNA microarray analysis. This study underscores the power of phenotypic screens in the development and characterization of selective inhibitors of enzyme functions.
Silicon epitaxial growth by rapid thermal processing chemical vapor deposition (1989)

High quality thin silicon epitaxial films have been grown on heavily doped p+ substrates using rapid thermal processing chemical vapor deposition with superior thickness and dopant profile control. The epitaxial growth kinetics have been studied by examining the dependence of growth rate on the deposition temperature, the volume percentage of SiH2Cl2, and the total gas flow rate. Submicron epitaxial layers with hyperabrupt dopant transition (&amp;lt;200 Å/decade) and excellent crystalline perfection with low defect density have been obtained.
A Monovalent Chimpanzee Adenovirus Ebola Vaccine Boosted with MVA (2015)

The ChAd3 vaccine boosted with MVA elicited B-cell and T-cell immune responses to ZEBOV that were superior to those induced by the ChAd3 vaccine alone. (Funded by the Wellcome Trust and others; ClinicalTrials.gov number, NCT02240875.).