gebhart/patrepeval huggingface dataset:
Molecular characterization of a protein-tyrosine-phosphatase enriched in striatum. (1991)

A cDNA clone encoding a neural-specific putative protein-tyrosine-phosphatase (protein-tyrosine-phosphate phosphohydrolase, EC 3.1.3.48) has been isolated from a rat striatal cDNA library. The deduced amino acid sequence predicts a protein of approximately 369 amino acids with a strong homology to other members of the family of protein-tyrosine-phosphatases. In vitro translation produces a protein with an apparent molecular mass of 46 kDa. A potential attachment mechanism to the cytoplasmic membrane is suggested by a myristoylation amino acid-consensus sequence at the N terminus of the protein. RNA analyses of various regions of rat brain reveal a 3-kilobase (kb) and a 4.4-kb mRNA. The 3-kb mRNA is highly enriched within the striatum relative to other brain areas and has been termed a "striatum enriched phosphatase" (STEP). In contrast, the 4.4-kb message is most abundant in the cerebral cortex and rare in the striatum. These two messages appear to be alternatively processed RNA transcripts of a single gene.
Formaldehyde Fixation Contributes to Detoxification for Growth of a Nonmethylotroph, Burkholderia cepacia TM1, on Vanillic Acid (2003)

During bacterial degradation of methoxylated lignin monomers, such as vanillin and vanillic acid, formaldehyde is released through the reaction catalyzed by vanillic acid demethylase. When Burkholderia cepacia TM1 was grown on vanillin or vanillic acid as the sole carbon source, the enzymes 3-hexulose-6-phosphate synthase (HPS) and 6-phospho-3-hexuloisomerase (PHI) were induced. These enzymes were also expressed during growth on Luria-Bertani medium containing formaldehyde. To understand the roles of these enzymes, the hps and phi genes from a methylotrophic bacterium, Methylomonas aminofaciens 77a, were introduced into B. cepacia TM1. The transformant strain constitutively expressed the genes for HPS and PHI, and these activities were two- or threefold higher than the activities in the wild strain. Incorporation of [14C]formaldehyde into the cell constituents was increased by overexpression of the genes. Furthermore, the degradation of vanillic acid and the growth yield were significantly improved at a high concentration of vanillic acid (60 mM) in the transformant strain. These results suggest that HPS and PHI play significant roles in the detoxification and assimilation of formaldehyde. This is the first report that enhancement of the HPS/PHI pathway could improve the degradation of vanillic acid in nonmethylotrophic bacteria.
Exon Array Profiling Detects EML4-ALK Fusion in Breast, Colorectal, and Non–Small Cell Lung Cancers (2009)

The echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) fusion gene has been identified as an oncogene in a subset of non-small cell lung cancers (NSCLC). We used profiling of cancer genomes on an exon array to develop a novel computational method for the global search of gene rearrangements. This approach led to the detection of EML4-ALK fusion in breast and colorectal carcinomas in addition to NSCLC. Screening of a large collection of patient tumor samples showed the presence of EML4-ALK fusion in 2.4% of breast (5 of 209), 2.4% of colorectal (2 of 83), and in 11.3% of NSCLC (12 of 106). Besides previously known EML4-ALK variants 1 (E13; A20) and 2 (E20; A20), a novel variant E21; A20 was found in colorectal carcinoma. The presence of an EML-ALK rearrangement was verified by identifying genomic fusion points in tumor samples representative of breast, colon, and NSCLC. EML4-ALK translocation was also confirmed by fluorescence in situ hybridization assay, which revealed its substantial heterogeneity in both primary tumors and tumor-derived cell lines. To elucidate the functional significance of EML4-ALK, we examined the growth of cell lines harboring the fusion following EML4 and ALK silencing by small interfering RNA. Significant growth inhibition was observed in some but not all cell lines, suggesting their variable dependence on ALK-mediated cell survival signaling. Collectively, these findings show the recurrence of EML4-ALK fusion in multiple solid tumors and further substantiate its role in tumorigenesis.
Towards Hydrogen Evolution Initiated by LED Light: 2‐(1H‐1,2,3‐Triazol‐4‐yl)pyridine‐Containing Polymers as Photocatalyst (2015)

Two- and three-component polymethacrylates, featuring a 2-(1-substituted-1H-1,2,3-triazol-4-yl)pyridine-based metal complex as photosensitizer, a viologen-type electron mediator, and a triethylene glycol methyl ether as solubilizing part are synthesized by statistical reversible addition-fragmentation chain transfer (RAFT) radical polymerization allowing the construction of well-defined copolymers. Thereby, heteroleptic ruthenium(II) and iridium(III) complexes serve as charged photosensitizers. In hydrogen evolution experiments, as proof-of-concept, triethylamine is utilized as a sacrificial donor and colloidal platinum as hydrogen evolving catalyst. The macromolecules bearing heteroleptic iridium(III) complexes of the general formula [Ir(ppy)2 (trzpy)]PF6 (ppy: 2-phenylpyridine; trzpy: 2-(1-substituted-1H-1,2,3-triazol-4-yl)pyridine) and [Ir(btac)2 (trzpy)]PF6 (btac: 3-(2-benzothiazolyl)-7-(diethylamino)coumarin) are photocatalytically active producing molecular hydrogen in water upon illumination at 470 nm. By changing the cyclometalating ligand from ppy to btac, the photocatalytic performance of the copolymer as reflected in the turnover number increases by two orders of magnitude.
Stimulus-Driven Brain Oscillations in the Alpha Range: Entrainment of Intrinsic Rhythms or Frequency-Following Response? (2014)

Human brain activity is rich in rhythms of various characteristic frequencies. The last few decades have seen an increase in their use as an explanatory means, with a vast literature describing manifold correlations between dynamics of brain rhythms and behavioral performance in perceptual and
Metallothionein expression in chloroplasts enhances mercury accumulation and phytoremediation capability (2011)

Genetic engineering to enhance mercury phytoremediation has been accomplished by expression of the merAB genes that protects the cell by converting Hg[II] into Hg[0] which volatilizes from the cell. A drawback of this approach is that toxic Hg is released back into the environment. A better phytoremediation strategy would be to accumulate mercury inside plants for subsequent retrieval. We report here the development of a transplastomic approach to express the mouse metallothionein gene (mt1) and accumulate mercury in high concentrations within plant cells. Real-time PCR analysis showed that up to 1284 copies of the mt1 gene were found per cell when compared with 1326 copies of the 16S rrn gene, thereby attaining homoplasmy. Past studies in chloroplast transformation used qualitative Southern blots to evaluate indirectly transgene copy number, whereas we used real-time PCR for the first time to establish homoplasmy and estimate transgene copy number and transcript levels. The mt1 transcript levels were very high with 183,000 copies per ng of RNA or 41% the abundance of the 16S rrn transcripts. The transplastomic lines were resistant up to 20 μm mercury and maintained high chlorophyll content and biomass. Although the transgenic plants accumulated high concentrations of mercury in all tissues, leaves accumulated up to 106 ng, indicating active phytoremediation and translocation of mercury. Such accumulation of mercury in plant tissues facilitates proper disposal or recycling. This study reports, for the first time, the use of metallothioneins in plants for mercury phytoremediation. Chloroplast genetic engineering approach is useful to express metal-scavenging proteins for phytoremediation.
Cytosolic Free-Calcium Concentrations in Normal Pancreatic Islet Cells: Effect of Secretagogues and Somatostatin (1987)

We have assessed the effect of somatostatin on glucose-, potassium-, forskolin-, and dibutyryl cAMP-induced changes in cytosolic free [Ca2+] in normal rat pancreatic islet cells with the new Ca2+ indicator fura 2. The cytosolic free [Ca2+] in islet cells incubated with nonstimulatory concentrations of glucose (30 mg/dl) ranged from 54 to 64 nM. In the presence of extracellular Ca2+ (1 mM), glucose (300 mg/dl) rapidly increased the cytosolic free [Ca2+] to a level of 90-110 nM. In the absence of extracellular Ca2+, glucose failed to increase the cytosolic free [Ca2+], which remained at a level of 55-60 nM. Somatostatin inhibited glucose-induced increases in cytosolic free [Ca2+] in a dose-dependent manner (maximal inhibition was 34%). Half-maximal inhibition was observed at 10(-9) M somatostatin, which correlated well with somatostatin binding to islet cells (Kd = 2.6 X 10(-10) M). Potassium (50 mM) rapidly increased the cytosolic free [Ca2+] to 110-120 nM, and its effect was not influenced by the presence of somatostatin. Forskolin (20 microM) and dibutyryl cAMP (1 mM) rapidly increased cytosolic free Ca2+ both in the presence and absence of extracellular Ca2+. More than 80% of the overall increase in cytosolic free-Ca2+ levels could be accounted for by the mobilization of intracellular Ca2+ stores. Somatostatin effectively blocked the forskolin effect (32% inhibition) but not the dibutyryl cAMP-induced effect. Somatostatin appears to inhibit secretagogue-induced increases in cytosolic free [Ca2+] by interfering with cAMP production and probably with Ca2+ transport across the cell membrane.
Retinoic acid-induced neural differentiation of embryonal carcinoma cells. (1983)

We have previously shown that the P19 line of embryonal carcinoma cells develops into neurons, astroglia, and fibroblasts after aggregation and exposure to retinoic acid. The neurons were initially identified by their morphology and by the presence of neurofilaments within their cytoplasm. We have more fully documented the neuronal nature of these cells by showing that their cell surfaces display tetanus toxin receptors, a neuronal cell marker, and that choline acetyl-transferase and acetyl cholinesterase activities appear coordinately in neuron-containing cultures. Several days before the appearance of neurons, there is a marked decrease in the amount of an embryonal carcinoma surface antigen, and at the same time there is a substantial decrease in the volumes of individual cells. Various retinoids were able to induce the development of neurons in cultures of aggregated P19 cells, but it did not appear that polyamine metabolism was involved in the effect. We have isolated a mutant clone which does not differentiate in the presence of any of the drugs which are normally effective in inducing differentiation of P19 cells. This mutant and others may help to elucidate the chain of events triggered by retinoic acid and other differentiation-inducing drugs.
Study of MMLV RT&lt;sup&gt;-&lt;/sup&gt; Binding with DNA using Surface Plasmon Resonance Biosensor (2005)

Surface plasmon resonance biosensor technique was used to study the binding of Moloney murine leukemia virus reverse transcriptase without RNase H domain (MMLV RT-) with DNA in the absence and in the presence of inhibitors. Different DNA substrates, including single-stranded DNA (ssDNA), DNA template-primer (T-P) duplex and gapped DNA, were immobilized on the biosensor chip surface using streptavidin-biotin, and MMLV RT(-)-DNA binding kinetics were analyzed by different models. MMLV RT-; could bind with ssDNA and the binding was involved in conformation change. MMLV RT-; binding DNA T-P duplex and gapped DNA could be analyzed using the simple 1:1 Langmuir model. The lack of RNase H domain reduced the affinity between MMLV RT-; and T-P duplex. The effects of RT inhibitors, including efavirenz, nevirapine and quercetin, on the interaction between MMLV RT-; and gapped DNA were analyzed according to recovered kinetics parameters. Efavirenz slightly interfered with the binding between RT and DNA and the affinity constant in the presence of the inhibitor (K(A) = 1.21 x 10(6) M(-1)) was lower than in the absence of the inhibitor (KA = 4.61 x 10(6) M(-1)). Nevirapine induced relatively tight binding between RT and DNA and the affinity constant in the presence of the inhibitor (K(A) = 1.47 x 10(7) M(-1)) was approximately three folds higher than without nevirapine, mainly due to rapid association and slow dissociation. Quercetin, a flavonoid originating from plant which has previously shown strong inhibition of the activity of RT, was found to have minimal effect on the RT-DNA binding.
Optimization of a source-side-injection FAMOS cell for flash EPROM applications (2002)

A 0.6- mu m FAMOS cell structure, which features a lightly doped source region to achieve enhanced source-side-injection for channel hot electron programming, is presented. The use of the source-side-injection mechanism for EPROM programming has been previously proposed, but this work is the first time that a source-side-injection cell with a lightly doped source region has been fabricated and evaluated. The impact of the source dopant concentration and the depth of this non-overlapped LDD (lightly doped drain) region on cell programming performance has been characterized and optimized. The optimized cells exhibit excellent programmability for drain voltage down to 3.3 V. Studies of reliability issues and write/erase endurance results indicate that this cell is a viable candidate for 5-V, or 3.3-V, high-density flash EPROM applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cell adhesion in cancer (2003)

Cell adhesion is a key physiological event tightly coupled to other major cellular processes coordinating morphogenesis and histogenesis. Cell-to-cell and cell-to-extracellular matrix adhesion regulates the social behavior of cells in developing embryos and in the adult. These two adhesion systems also play a critical role in pathogenesis. In vertebrates, more than 3% of genes are thought to encode adhesion molecules. The largest cell adhesion molecule superfamily is that related to N-CAM, the members of which characteristically contain immunoglobulin domains. Cadherins, which also possess Ig domains, constitute another important superfamily with different properties. Integrins are major receptors for many extracellular matrix components. This review describes the structure and function of these adhesion systems and their impact in cancer invasion and metastasis.
Role of Arginine in the Stabilization of Proteins against Aggregation (2005)

The amino acid arginine is frequently used as a solution additive to stabilize proteins against aggregation, especially in the process of protein refolding. Despite arginine's prevalence, the mechanism by which it stabilizes proteins is not presently understood. We propose that arginine deters aggregation by slowing protein-protein association reactions, with only a small concomitant effect on protein folding. The associated rate effect was observed experimentally in association of globular proteins (insulin and a monoclonal anti-insulin) and in refolding of carbonic anhydrase. We suggest that this effect arises because arginine is preferentially excluded from protein-protein encounter complexes but not from dissociated protein molecules. Such an effect is predicted by our gap effect theory [Baynes and Trout (2004) Biophys. J. 87, 1631] for "neutral crowder" additives such as arginine which are significantly larger than water but have only a small effect on the free energies of isolated protein molecules. The effect of arginine on refolding of carbonic anhydrase was also shown to be consistent with this hypothesis.
Nuclear Factor-κB — A Pivotal Transcription Factor in Chronic Inflammatory Diseases (1997)

In chronic inflammatory diseases, such as asthma, rheumatoid arthritis, inflammatory bowel disease, and psoriasis, several cytokines recruit activated immune and inflammatory cells to the site of lesions, thereby amplifying and perpetuating the inflammatory state.1 These activated cells produce many other mediators of inflammation.What causes these diseases is still a mystery, but the disease process results from an interplay of genetic and environmental factors. Genes, such as those for atopy in asthma and for HLA antigens in rheumatoid arthritis and inflammatory bowel disease, may determine a patient's susceptibility to the disease and the disease's severity, but environmental factors, often unknown, . . .
GEOMETRIC SURFACE MODIFICATION OF NOZZLES FOR COMPLETE TRANSFER OF LIQUID DROPS (2004)

We report a new and unique way of promoting the complete transfer of discrete liquid drops from a nozzle to printing surfaces when the transfer (i.e., printing) is made by the wettability differences between two surfaces as used in soft printing devices reported previously. Hypothesizing that the complete transfer of droplets can be promoted by reducing the surface energy at the nozzle surface, we propose a new nozzle design with serrated circumference. By geometrically limiting the liquid-solid contact area on the nozzle surface, the effective energy holding droplets back can be reduced. Tests of droplet transfers (~1 l in volume) from hydrophobic nozzles (~500 m in diameter) to hydrophilic printing surfaces (e.g., glass surfaces) confirm that the residual droplets can be eliminated and perfect transfer can be accomplished when the nozzles are made serrated.
The mechanism of adenosine to inosine conversion by the double-stranded RNA unwinding/modifying activity: a high-performance liquid chromatography-mass spectrometry analysis (1991)

We have used directly combined high-performance liquid chromatography-mass spectrometry (LC/MS) to examine the mechanism of the reaction catalyzed by the double-stranded RNA unwinding/modifying activity [Bass & Weintraub (1988) Cell 55, 1089-1098]. A double-stranded RNA substrate in which all adenosines were uniformly labeled with 13C was synthesized. An LC/MS analysis of the nucleoside products from the modified, labeled substrate confirmed that adenosine is modified to inosine during the unwinding/modifying reaction. Most importantly, we found that no carbons are exchanged during the reaction. By including H2(18)O in the reaction, we showed that water serves efficiently as the oxygen donor in vitro. These results are consistent with a hydrolytic deamination mechanism and rule out a base replacement mechanism. Although the double-stranded RNA unwinding/modifying activity appears to utilize a catalytic mechanism similar to that of adenosine deaminase, coformycin, a transition-state analogue, will not inhibit the unwinding/modifying activity.
Cross-talk between regulators of myeloid development: C/EBPα binds and activates the promoter of the PU.1 gene (2003)

CCAAT/enhancer-binding protein (C/EBP)alpha and PU.1 are required for myelopoiesis. Examination of the murine PU.1 promoter revealed several potential C/EBP-binding sites. Gel-shift assay demonstrated that C/EBPalpha expressed in 293T cells bound the site centered at -68 most potently. C/EBPalpha from 32D cl3 myeloid cell nuclear extracts also bound this site strongly, and endogenous C/EBPbeta did so to a lesser extent, whereas these C/EBP isoforms bound the neutrophil elastase promoter with equal affinity. The -68 site in the murine PU.1 promoter is conserved in the human PU.1 promoter. Mutation of the -68 C/EBP-binding site in a -85/+152 promoter segment linked to the luciferase cDNA reduced promoter activity fourfold in 293T cells in the presence of cotransfected C/EBPalpha and twofold in 32D cl3 myeloid cells. Induction of endogenous PU.1 RNA by C/EBPalpha-estradiol receptor (ER) in the presence of cycloheximide is obviated by mutation of the C/EBPalpha DNA-binding domain, and chromosomal immunoprecipitation demonstrated specific interaction of C/EBPalpha and C/EBPalpha-ER with the PU.1 promoter. Finally, PU.1 RNA is reduced several-fold in immortalized C/EBPalpha (-/-) compared with (+/-) cells. Together, these findings indicate that C/EBPalpha binds and activates the endogenous PU.1 gene in myeloid cells. Induction of PU.1 by C/EBPalpha may account for increased levels of PU.1 in myeloid as compared with B lymphoid cells and in this way, may contribute to the specification of myeloid progenitors.
Multiphoton Ionization Enhancement Using Two Phase-Coherent Laser Pulses (1995)

Modulations in the multiphoton ionization yield in Na are observed as a function of the relative delay between two identical 150 fsec laser pulses. The first pulse populates a coherent superposition state composed of ground and excited levels. The ionization yield during the second pulse depends on its phase relative to that of the nonstationary superposition state. Ionization enhancements of more than an order of magnitude can be achieved by exploiting coherences in the atom-laser system.
The dynamics of the T-cell antitumor response: chemokine-secreting dendritic cells can prime tumor-reactive T cells extranodally. (2001)

Direct administration of dendritic cells (DCs) genetically modified to express secondary lymphoid tissue chemokine (SLC) into growing B16 melanoma could result in a substantial, sustained influx of T cells within the mass with only a transient increase in T-cell numbers in the draining lymph node (DLN). DCs were retained at the tumor site with only a very small percentage trafficking to the DLN. The T cells infiltrating the tumor mass expressed the activation marker CD25 within 24 h and developed IFN-gamma-secreting function within 7 days as tumor growth was inhibited. Similar results were obtained in lymphotoxin alpha-/- mice, which lacked peripheral lymph nodes. Our data demonstrate that effective T-cell priming can occur extranodally and result in measurable antitumor effects in vivo.
Vaccination with filamentous bacteriophages targeting DEC‐205 induces DC maturation and potent anti‐tumor T‐cell responses in the absence of adjuvants (2011)

The efficacy of a new vaccine-delivery vector, based on the filamentous bacteriophage fd displaying a single-chain antibody fragment known to bind the mouse DC surface molecule DEC-205, is reported. We demonstrate both in vitro and in vivo an enhanced receptor-mediated uptake of phage particles expressing the anti-DEC-205 fragment by DCs. We also report that DCs targeted by fd virions in the absence of other stimuli produce IFN-α and IL-6, and acquire a mature phenotype. Moreover, DC-targeting with fd particles double-displaying the anti-DEC-205 fragment on the pIII protein and the OVA(257-264) antigenic determinant on the pVIII protein induced potent inhibition of the growth of the B16-OVA tumor in vivo. This protection was much stronger than other immunization strategies and similar to that induced by adoptively transferred DCs. Since targeting DEC-205 in the absence of DC activation/maturation agents has previously been described to result in tolerance, the ability of fd bacteriophages to induce a strong tumor-specific immune response by targeting DCs through DEC-205 is unexpected, and further validates the potential employment of this safe, versatile and inexpensive delivery system for vaccine formulation.
Modular design of the Enterococcus hirae muramidase-2 and Streptococcus faecalis autolysin (1992)

The mature forms of the extracellular muramidase-2 of Enterococcus hirae and Streptococcus faecalis autolysin have very similar primary structures. Each consists of an active-site-containing N-terminal domain fused to a multiple-repeat C-terminal domain. Polypeptide segments occurring at equivalent places in these two bacterial wall lytic enzymes have homologues in two phage lysozymes and in three functionally unrelated proteins, illustrating the principle that protein molecules frequently are constructed from modules that are linked in a single polypeptide chain.