gebhart/patrepeval huggingface dataset:
Characteristics of amorphous and polycrystalline silicon films deposited at 120 °C by electron cyclotron resonance plasma-enhanced chemical vapor deposition (1998)

Amorphous and polycrystalline silicon (poly-Si) films, deposited by an electron cyclotron resonance plasma-enhanced chemical vapor deposition system at 120 °C, have been investigated. All films have been grown with either hydrogen or argon dilution. Using the films with the hydrogen dilution, the effect of rf (13.56 MHz) substrate bias has also been studied. Analysis with x-ray diffraction shows that films grown with Ar dilution and no rf bias do not show any crystallinity while the corresponding films deposited with H2 dilution and no rf bias contain a significant amount of the crystalline phase. With only a 3:1 H2 to silane ratio, highly crystallized films can be grown at 120 °C. In the presence of rf (13.56 MHz) substrate bias, there is a decrease of crystallinity in films. It has been found from cross-sectional transmission electron microscopy that films deposited without rf bias develop a very uniform columnar structure whereas films made with rf bias develop a closely packed, continuous but more amorphous structure. It is found that these changes caused by rf bias affect the photoluminescence intensity.
Differential Regulation of the Alpha/Beta Interferon-Stimulated Jak/Stat Pathway by the SH2 Domain-Containing Tyrosine Phosphatase SHPTP1 (1995)

Interferons (IFNs) induce early-response genes by stimulating Janus family (Jak) tyrosine kinases, leading to tyrosine phosphorylation of Stat transcription factors. Previous studies implicated protein-tyrosine phosphatase (PTP) activity in the control of IFN-regulated Jak/Stat signaling, but the specific PTPs responsible remained unidentified. We have found that SH2 domain-containing PTP1 (SHPTP1; also called PTP1C, HCP, or SHP) reversibly associates with the IFN-alpha receptor complex upon IFN addition. Compared with macrophages from normal littermate controls, macrophages from motheaten mice, which lack SHPTP1, show dramatically increased Jak1 and Stat1 alpha tyrosine phosphorylation, whereas Tyk2 and Stat2 activation is largely unaffected. These findings correlate with selectively increased complex formation on a gamma response element, but not an IFN-stimulated response element, in motheaten macrophages. Our results establish that SHPTP1 selectively regulates distinct components of Jak/Stat signal transduction pathways in vivo.
Inhibition of polycyclic aromatic hydrocarbon-induced neoplasia by naturally occurring indoles. (1978)

Indole-3-carbinol, 3,3'-diindolylmethane, and indole-3-acetonitrile, three indoles occurring in edible cruciferous vegetables, have been studied for their effects on 7,12-dimethylbenz(a)anthracene-induced mammary tumor formation in female Sprague-Dawley rats and on benzo(a)pyrene-induced neoplasia of the forestomach in female ICR/Ha mice. When given by p.o. intubation 20 hr prior to 7,12-dimethylbenz(a)anthracene administration, indole-3-carbinol and 3,3'-diindolylmethane had an inhibitory effect on mammary tumor formation, but indole-3-acetonitrile was inactive. Indole-3-carbinol when added to the diet for 8 days prior to challenge with 7,12-dimethylbenz(a)anthracene inhibited mammary tumor formation, whereas indole-3-acetonitrile did not. Dietary administration of all three indoles inhibited benzo(a)pyrene-induced neoplasia of the forestomach in ICR/Ha mice. The identification of dietary constituents that can inhibit chemical carcinogens ultimately may be of value in understanding the balance of factors that determines the neoplastic response to these cancer-producing agents in the environment.
Suppression of Bmp4 signaling by the zinc-finger repressors Osr1 and Osr2 is required for Wnt/β-catenin-mediated lung specification in Xenopus (2012)

Embryonic development of the respiratory system is regulated by a series of mesenchymal-epithelial interactions that are only partially understood. Mesenchymal FGF and Wnt2/Wnt2b signaling are implicated in specification of mammalian pulmonary progenitors from the ventral foregut endoderm, but their epistatic relationship and downstream targets are largely unknown. In addition, how wnt2 and wnt2b are regulated in the developing foregut mesenchyme is unknown. We show that the Odd-skipped-related (Osr) zinc-finger transcriptional repressors Osr1 and Osr2 are redundantly required for Xenopus lung specification in a molecular pathway linking foregut pattering by FGFs to Wnt-mediated lung specification and RA-regulated lung bud growth. FGF and RA signals are required for robust osr1 and osr2 expression in the foregut endoderm and surrounding lateral plate mesoderm (lpm) prior to respiratory specification. Depletion of both Osr1 and Osr2 (Osr1/Osr2) results in agenesis of the lungs, trachea and esophagus. The foregut lpm of Osr1/Osr2-depleted embryos fails to express wnt2, wnt2b and raldh2, and consequently Nkx2.1(+) progenitors are not specified. Our data suggest that Osr1/Osr2 normally repress bmp4 expression in the lpm, and that BMP signaling negatively regulates the wnt2b domain. These results significantly advance our understanding of early lung development and may impact strategies to differentiate respiratory tissue from stem cells.
Association of an ice-nucleating pseudomonad with cultures of the marine dinoflagellate, <I>Heterocapsa niei</I> (1985)

Etude en vue d'isoler, d'identifier et de caracteriser des bacteries inductrices de noyaux de congelation a partir de sources marines
Roles of 34 Virulence Genes in the Evolution of Hospital‐ and Community‐Associated Strains of Methicillin‐Resistant Staphylococcus aureus (2006)

The horizontal transfer of virulence genes, although infrequent, is epidemiologically associated with the emergence of new virulent strains of MRSA.
Design of an on–chip random number generator using metastability (2002)

This paper shows that the internal noise in a bistable exhibits a Gaussian distribution, and is close to the value expected from thermal agitation. We describe a random number generator based on this property that is capable of on chip integration, and is a primary source of high entropy data at 100MHz. The device is held close to metastability by a feedback loop, and is therefore relatively insensitive to circuit asymmetries and drift. Measurements of post-processed data from this source also show a relatively high bit rate and sequences of 223bits are shown to pass stringent tests for randomness.
NovelKCNQ1 mutations associated with recessive and dominant congenital long QT Syndromes: Evidence for variable hearing phenotype associated with R518X (2000)

Congenital long QT syndrome may be transmitted as either an autosomal dominant or recessive trait. Two families with the autosomal recessive Jervell and Lange-Nielsen syndrome (JLNS), and one family with the autosomal dominant Romano-Ward syndrome (RWS) were evaluated for mutations in KCNQ1. Two different novel frameshift mutations were discovered in one of the JLNS families (1188delC) and in the RWS family (504delG). A third allele (R518X) was observed in the second JLNS family. The R518X allele was previously associated with recessive long QT syndrome without deafness, but was present in a congenitally deaf proband in our study. These data extend the range of known KCNQ1 mutations associated with both recessive and dominant forms of congenital long QT syndrome, and demonstrate that the R518X allele may be associated with or without congenital deafness.
Low power signal processing architectures for network microsensors (1997)

Low power signal processing systems are required for distributed network microsensor technology. Network microsensors now provide a new monitoring and control capability for civil and military applications in transportation, manufacturing, biomedical technology, environmental management, and safety and security systems. Signal processing methods for event detection have been developed with low power, parallel architectures that optimize performance for unique sensor system requirements. Implementation of parallel datapatbs with shared arithmetic elements enables high throughput at low clock rate. This method has been used to implement a microsensor spectrum analyzer for a 200 sample/s measurement system. This 0.8p CMOS device operates with a 1M drain current at a 3V supply bias. ', ' I--1 / !
A delay insensitive regular expression recognizer (2018)

Abstract: "Several types of synchronous Regular Expression (RE) recognizers have been proposed by several authors. This paper describes a self-timed and delay-independent RE recognizer. The problem is non-trivial because of the [epsilon]-closure operation that is implicitly performed every cycle of the recognition process. The design is based on expression-tree recognizers, and has a self-timed cycle time O(h) where h is the high of the parse tree of the RE. Since it is an expression-tree recognizer it has a compact O(N) layout algorithm, where N is the size of the RE. The design also results in an synchronous RE recognizer with the shortest worst case cycle time O(h) reported for recognizers with area O(N).
Thieme Chemistry Journal Awardees - Where Are They Now? Approaches to Tagetitoxin and its Decarboxy Analogue from d-Glucose (2009)

A fifteen-step route has been developed from 1,6-anhydro-β-d-glucopyranose to a C-alkynyl glycoside precursor of decarboxytagetitoxin. Preparation of 1,6-anhydro-5-C-vinyl-β-d-gluco-pyranose, a potential precursor of tagetitoxin, is also described.
Obesity predisposes to Th17 bias (2009)

Obesity is associated with numerous inflammatory conditions including atherosclerosis, autoimmune disease and cancer. Although the precise mechanisms are unknown, obesity-associated rises in TNF-alpha, IL-6 and TGF-beta are believed to contribute. Here we demonstrate that obesity selectively promotes an expansion of the Th17 T-cell sublineage, a subset with prominent pro-inflammatory roles. T-cells from diet-induced obese mice expand Th17 cell pools and produce progressively more IL-17 than lean littermates in an IL-6-dependent process. The increased Th17 bias was associated with more pronounced autoimmune disease as confirmed in two disease models, EAE and trinitrobenzene sulfonic acid colitis. In both, diet-induced obese mice developed more severe early disease and histopathology with increased IL-17(+) T-cell pools in target tissues. The well-described association of obesity with inflammatory and autoimmune disease is mechanistically linked to a Th17 bias.
Isolation and transplantation of multipotential populations of epidermal growth factor–responsive, neural progenitor cells from the canine brain (1997)

Glial cell transplantation into myelin-deficient rodent models has resulted in myelination of axons and restoration of conduction velocity. The shaking (sh) pup canine myelin mutant is a useful model in which to test the ability to repair human myelin diseases, but as in humans, the canine donor supply for allografting is limited. A solution may be provided by self-renewing epidermal growth factor (EGF)-responsive multipotential neural progenitor cell populations (“neurospheres”). Nonadherent spherical clusters, similar in appearance to murine neurospheres, have been obtained from the brain of perinatal wildtype (wt) canine brain and expanded in vitro in the presence of EGF for at least 6 months. Most of the cells in these clusters express a nestin-related protein. Within 1–2 weeks after removal of EGF, cells from the clusters generate neurons, astrocytes, and both oligodendroglial progenitors and oligodendrocytes. Transplantation of lacZ-expressing wt neurospheres into the myelin-deficient (md) rat showed that a proportion of the cells differentiated into oligodendrocytes and produced myelin. In addition, cells from the neurosphere populations survived at least 6 weeks after grafting into a 14-day postnatal sh pup recipient and at least 2 weeks after grafting into an adult sh pup recipient. Thus, neurospheres provide a new source of allogeneic donor cells for transplantation studies in this mutant. J. Neurosci. Res. 50:862–871, 1997. © 1997 Wiley-Liss, Inc.
Characterization of EcR and RXR Homologues in the Ixodid Tick,Amblyomma americanum(L.) (1999)

Ecdysteroid hormones have been shown to regulate growth and development in insects, chelicerates and crustaceans. While they presumably mediate analogous functions in all arthropods, their action outside Insecta is poorly understood. Ecdysteroid receptors are heterodimeric proteins composed of two nuclear receptor superfamily members, the ecdysone receptor (EcR) and Ultraspiracle (USP), the invertebrate homologue of retinoid x receptors (RXRs). When paired, EcR/USP dimers function as ligand-activated transcription factors, binding to DNA response elements in target genes and activating transcription. A curious feature of the insect EcR and USP homologues isolated to date is the striking degree of heterogeneity in both EcR and USP proteins, relative to vertebrate nuclear receptor homologues. This feature has raised a number of questions regarding their evolution and functional equivalence. To examine the question of ecdysteroid action in ixodid ticks, we isolated chelicerate EcR and RXR homologues from the ixodid tick, Amblyomma americanum. Like insects, ticks possess a single EcR homologue that encodes multiple protein isoforms. However, ticks possess at least two RXR genes that encode proteins with greater overall similarity to vertebrate RXRs. While tick EcR and RXR proteins can partner to form functional ecdysteroid receptors, the DNA and ligand binding domains of tick EcR and RXR proteins are quite divergent, and suggest that there may be important functional differences in both DNA and ligand binding of tick ecdysteroid receptors.
Isolation of a Singh's Aedes albopictus Cell Clone Sensitive to Dengue and Chikungunya Viruses (1978)

Twenty clones were isolated from cultured Aedes albopictus (Singh) cells in the presence of anti-Chikungunya (CHIK) virus serum. Each clone was tested for its yields of Dengue (DEN) viruses, types 1, 2, 3 and 4, and also CHIK virus. Clone C6 showed the highest yield of each virus tested. Forty-three clones obtained by recloning C6 in the presence of anti-DEN sera showed almost the same virus yields as C6. One of the clones, C6/36, showed mild to extensive cytopathic effects several days after virus infection, in contrast to the original uncloned (SAAR) cells. Fluorescent antibody staining revealed that the amount of virus antigen accumulated in the cytoplasm was almost the same in every cell in the case of clone C6/36, while it was highly heterogeneous for uncloned SAAR cells. Growth curves of the viruses indicated that clone C6/36 gave a significantly higher yield for each virus than uncloned SAAR cells up to 7 days after infection. Virus sensitivity of the C6/36 clone did not change by growing the cells with the medium used for uncloned SAAR cells, nor did the virus sensitivity of uncloned cells increase in medium used for clone C6/36. However, the C6/36 clone became resistant to CHIK virus, but not to DEN or Sindbis viruses, after incubation with the medium used for another A. albopictus cell line (SAAK). The transfer of the specific resistance to CHIK may be mediated by some latent virus related to CHIK.
Human MicroRNA Targets (2004)

MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. The specific function of most mammalian miRNAs is unknown. We have predicted target sites on the 3' untranslated regions of human gene transcripts for all currently known 218 mammalian miRNAs to facilitate focused experiments. We report about 2,000 human genes with miRNA target sites conserved in mammals and about 250 human genes conserved as targets between mammals and fish. The prediction algorithm optimizes sequence complementarity using position-specific rules and relies on strict requirements of interspecies conservation. Experimental support for the validity of the method comes from known targets and from strong enrichment of predicted targets in mRNAs associated with the fragile X mental retardation protein in mammals. This is consistent with the hypothesis that miRNAs act as sequence-specific adaptors in the interaction of ribonuclear particles with translationally regulated messages. Overrepresented groups of targets include mRNAs coding for transcription factors, components of the miRNA machinery, and other proteins involved in translational regulation, as well as components of the ubiquitin machinery, representing novel feedback loops in gene regulation. Detailed information about target genes, target processes, and open-source software for target prediction (miRanda) is available at http://www.microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes.
Engineering disulfide bonds of the novel human β‐defensins hBD‐27 and hBD‐28: Differences in disulfide formation and biological activity among human β‐defensins (2004)

Human beta-defensins comprise a large number of peptides that play a functional role in the innate and adaptive immune system. Recently, clusters of new beta-defensin genes with predominant expression in testicular tissue have been discovered on different chromosomes by bioinformatics. beta-Defensins share a common pattern of three disulfides that are essential for their biological effects. Here we report for the first time the chemical synthesis of the new fully disulfide-bonded beta-defensins hBD-27 and hBD-28, and compare the results with synthetic procedures to obtain the known hBD-2 and hBD-3. While hBD-27 was readily converted into a product with the desired disulfide pattern by oxidative folding, hBD-28 required a selective protective group strategy to introduce the three disulfide bonds. The established synthetic processes were applied to the synthesis of hBD-2, which, like hBD-27, was accessible by oxidative folding, whereas hBD-3 required a selective strategy comparable to hBD-28. Experimental work demonstrated that trityl, acetamidomethyl, and t-butyl are superior to other protection strategies. However, the suitable pairwise arrangement of the protective groups can be different, as shown here for hBD-3 and hBD-28. Determination of the minimum inhibitory concentration against different bacteria revealed that hBD-27, in contrast to other beta-defensins tested, has virtually no antimicrobial activity. Compared to the other peptides tested, hBD-27 showed almost no cytotoxic activity, measured by hemoglobin release of erythrocytes. This might be due to the low positive net charge, which is significantly higher for hBD-2, hBD-3, and hBD-28.
Bivalent Inhibitor of the N-end Rule Pathway (1999)

The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. Ubr1p, the recognition (E3) component of the Saccharomyces cerevisiae N-end rule pathway, contains at least two substrate-binding sites. The type 1 site is specific for N-terminal basic residues Arg, Lys, and His. The type 2 site is specific for N-terminal bulky hydrophobic residues Phe, Leu, Trp, Tyr, and Ile. Previous work has shown that dipeptides bearing either type 1 or type 2 N-terminal residues act as weak but specific inhibitors of the N-end rule pathway. We took advantage of the two-site architecture of Ubr1p to explore the feasibility of bivalent N-end rule inhibitors, whose expected higher efficacy would result from higher affinity of the cooperative (bivalent) binding to Ubr1p. The inhibitor comprised mixed tetramers of beta-galactosidase that bore both N-terminal Arg (type 1 residue) and N-terminal Leu (type 2 residue) but that were resistant to proteolysis in vivo. Expression of these constructs in S. cerevisiae inhibited the N-end rule pathway much more strongly than the expression of otherwise identical beta-galactosidase tetramers whose N-terminal residues were exclusively Arg or exclusively Leu. In addition to demonstrating spatial proximity between the type 1 and type 2 substrate-binding sites of Ubr1p, these results provide a route to high affinity inhibitors of the N-end rule pathway.
Evaluation of the antibody-dependent cytotoxic capabilities of individual human monocytes. Role of FcgammaRI and FcgammaRII and the effects of cytokines at the single cell level. (1990)

In this report we present evidence that not all human peripheral blood monocytes mediate antibody-dependent cellular cytotoxicity (ADCC), and that this function may be determined on an individual cell by both the type and level of expression of FcR, and by the state of cellular activation and/or differentiation. Although the diverse range of effector and regulatory functions performed by human monocytes suggests the possibility of distinct subsets, it is not clear whether observed functional heterogeneity reflects the presence of true monocyte subpopulations, or whether this diversity represents a continuum of maturational states present in the peripheral circulation. In an attempt to address this question, we investigated the ability of human monocytes to carry out ADCC at the single cell level, with emphasis on the role of the three FcR for IgG (Fc gamma RI, Fc gamma RII, and Fc gamma RIII) in mediating cytotoxicity. Using a modified plaque assay, 58.3% +/- 4.9 of freshly isolated monocytes mediated ADCC, as evidenced by the formation of lytic plaques in monolayers of ox erythrocyte (oxE) target cells. Significant increases in the number of plaque-forming cells were observed after positive selection by flow microfluorimetry for those monocytes expressing high levels of Fc gamma RI and Rc gamma RII, but not Fc gamma RIII. Bispecific antibodies composed of Fab fragments of anti-oxE antibody covalently coupled to Fab fragments of anti-Fc gamma R antibodies were used to independently evaluate the ability of Fc gamma RI, Fc gamma RII, and Fc gamma RIII to mediate single cell cytotoxicity. Significant increases in the number of plaque-forming cells were observed in the presence of anti-Fc gamma RI x anti-oxE and anti-Fc gamma RII x anti-oxE bispecific antibodies, confirming the efficiency of Fc gamma RI and Fc gamma RII as cytotoxic trigger molecules on human monocytes. Incubation of monocytes with purified rIFN-gamma and granulocyte macrophage-CSF, but not IL-2, IL-3, IL-4, IL-6, or TNF-alpha, also resulted in significant increases in the number of monocytes mediating cytotoxicity, suggesting that cytotoxic ability at the single cell level may be influenced by factors which effect monocyte activation and differentiation, respectively. Overall, these studies demonstrate that freshly isolated human monocytes are heterogeneous in their ability to mediate ADCC, and suggest that this functional diversity arises not from discrete subpopulations of cells, but from a continuum of maturational/activational states present within the peripheral circulation.