gebhart/patrepeval huggingface dataset:
Isolation and characterization of cellulose-degrading bacteria from the deep subsurface of the Homestake gold mine, Lead, South Dakota, USA (2009)

The present study investigated the cultivable mesophilic (37 degrees C) and thermophilic (60 degrees C) cellulose-degrading bacterial diversity in a weathered soil-like sample collected from the deep subsurface (1.5 km depth) of the Homestake gold mine in Lead, South Dakota, USA. Chemical characterization of the sample by X-ray fluorescence spectroscopy revealed a high amount of toxic heavy metals such as Cu, Cr, Pb, Ni, and Zn. Molecular community structures were determined by phylogenetic analysis of 16S rRNA gene sequences retrieved from enrichment cultures growing in presence of microcrystalline cellulose as the sole source of carbon. All phylotypes retrieved from enrichment cultures were affiliated to Firmicutes. Cellulose-degrading mesophilic and thermophilic pure cultures belonging to the genera Brevibacillus, Paenibacillus, Bacillus, and Geobacillus were isolated from enrichment cultures, and selected cultures were studied for enzyme activities. For a mesophilic isolate (DUSELG12), the optimum pH and temperature for carboxymethyl cellulase (CMCase) were 5.5 and 55 degrees C, while for a thermophilic isolate (DUSELR7) they were 5.0 and 75 degrees C, respectively. Furthermore, DUSELG12 retained about 40% CMCase activity after incubation at 60 degrees C for 8 h. Most remarkably, thermophilic isolate, DUSELR7 retained 26% CMCase activity at 60 degrees C up to a period of 300 h. Overall, the present work revealed the presence of different cellulose-degrading bacterial lineages in the unique deep subsurface environment of the mine. The results also have strong implications for biological conversion of cellulosic agricultural and forestry wastes to commodity chemicals including sugars.
Human T-lymphotropic Virus Type I Tax Activates I-κB Kinase by Inhibiting I-κB Kinase-associated Serine/Threonine Protein Phosphatase 2A (2003)

I-kappa B kinase (IKK) is a serine/threonine kinase that phosphorylates I-kappa B alpha and I-kappa B beta and targets them for polyubiquitination and proteasome-mediated degradation. IKK consists of two highly related catalytic subunits, alpha and beta, and a regulatory gamma subunit, which becomes activated after serine phosphorylation of the activation loops of the catalytic domains. The human T-lymphotropic retrovirus type-I trans-activator, Tax, has been shown to interact directly with IKK gamma and activates IKK via a mechanism not fully understood. Here we demonstrate that IKK binds serine/threonine protein phosphatase 2A (PP2A), and via a tripartite protein-protein interaction, Tax, IKK gamma, and PP2A form a stable ternary complex. In vitro, PP2A down-regulates active IKK prepared from Tax-producing MT4 cells. In the presence of Tax, however, the ability of PP2A to inactivate IKK is diminished. Despite their interaction with IKK gamma, PP2A-interaction-defective Tax mutants failed to activate NF-kappa B. Our data support the notion that IKK gamma-associated PP2A is responsible for the rapid deactivation of IKK, and inhibition of PP2A by Tax in the context of IKK x PP2A x Tax ternary complex leads to constitutive IKK and NF-kappa B activation.
Macrophage nitric oxide synthase gene: two upstream regions mediate induction by interferon gamma and lipopolysaccharide. (1993)

The promoter region of the mouse gene for macrophage-inducible nitric oxide synthase (mac-NOS; EC 1.14.13.39) has been characterized. A putative TATA box is 30 base pairs upstream of the transcription start site. Computer analysis reveals numerous potential binding sites for transcription factors, many of them associated with stimuli that induce mac-NOS expression. To localize functionally important portions of the regulatory region, we constructed deletion mutants of the mac-NOS 5' flanking region and placed them upstream of a luciferase reporter gene. The macrophage cell line RAW 264.7, when transfected with a minimal promoter construct, expresses little luciferase activity when stimulated by lipopolysaccharide (LPS), interferon gamma (IFN-gamma), or both. Maximal expression depends on two discrete regulatory regions upstream of the putative TATA box. Region I (position -48 to -209) increases luciferase activity approximately 75-fold over the minimal promoter construct. Region I contains LPS-related responsive elements, including a binding site for nuclear factor interleukin 6 (NF-IL6) and the kappa B binding site for NF-kappa B, suggesting that this region regulates LPS-induced expression of the mac-NOS gene. Region II (position -913 to -1029) alone does not increase luciferase expression, but together with region I it causes an additional 10-fold increase in expression. Together the two regions increase expression 750-fold over activity obtained from a minimal promoter construct. Region II contains motifs for binding IFN-related transcription factors and thus probably is responsible for IFN-mediated regulation of LPS-induced mac-NOS. Delineation of these two cooperative regions explains at the level of transcription how IFN-gamma and LPS act in concert to induce maximally the mac-NOS gene and, furthermore, how IFN-gamma augments the inflammatory response to LPS.
Novel in vitro gene transfer method for study of local modulators in vascular smooth muscle cells. (1993)

Although many in vitro gene transfer methods already exist, such as calcium phosphate precipitation, electroporation, or cationic liposomes, these methods cause significant cell injury and cell death. The study of the biology of endogenous autocrine-paracrine vasoactive systems such as the renin-angiotensin system in vascular cells is limited by the lack of a suitable gene transfer method with high efficiency of transfection and expression that will permit cell biology studies. Recently, the Sendai virus (hemagglutinating virus of Japan, HVJ)-liposome-mediated gene transfer method has been shown to be an efficient and nontoxic method of gene transfer. In this study, we characterized the efficiency and suitability of the HVJ method for vascular biology research. Using SV40 T-antigen complementary DNA (cDNA), we initially compared the efficiency of the HVJ method and lipofection for transfection of cultured vascular smooth muscle cells (VSMCs). We observed that after 35 minutes of incubation, the HVJ method exhibited a 10-fold higher efficiency of transfection than lipofection. We used this method to study vascular angiotensin converting enzyme (ACE) expression in cultured VSMCs and cultured rat carotid arteries in vitro. The HVJ method of transfection of human ACE cDNA into VSMCs and COS cells was significantly more efficient than lipofection. Using this method, we demonstrated that transfection of ACE cDNA resulted in increased DNA synthesis, which was inhibited by the specific angiotensin II receptor antagonist DuP 753 (10(-6) M).(ABSTRACT TRUNCATED AT 250 WORDS)
Entry of genital Chlamydia trachomatis into polarized human epithelial cells (1989)

To study the initial invasion process(es) of genital chlamydiae, a model system consisting of hormonally maintained primary cultures of human endometrial gland epithelial cells (HEGEC), grown in a polarized orientation on collagen-coated filters, was utilized. After Chlamydia trachomatis inoculation of the apical surface of polarized HEGEC, chlamydiae were readily visualized, by transmission electron microscopy, in coated pits and coated vesicles. This was true for HEGEC maintained in physiologic concentrations of estrogen (proliferative phase) and of estrogen plus progesterone (secretory phase), despite the finding that association of chlamydiae with secretory-phase HEGEC is significantly reduced (P = 0.025; A.S. Maslow, C.H. Davis, J. Choong, and P.B. Wyrick, Am. J. Obstet. Gynecol. 159:1006-1014, 1988). In contrast, chlamydiae were rarely observed in the clathrin-associated structures if the HEGEC were cultured on plastic surfaces. The same pattern of coated pit versus noncoated pit entry was reproducible in HeLa cells. The quantity of coated pits associated with isolated membrane sheets derived from HeLa cells, grown on poly-L-lysine-coated cover slips in medium containing the female hormones, was not significantly different as monitored by radiolabeling studies and by laser scanning microscopy. These data suggest that culture conditions which mimic in vivo cellular organization may enhance entry into coated pits for some obligate intracellular pathogens.
A Session Initiation Protocol (SIP) Event Package for Registrations (2004)

This document defines a Session Initiation Protocol (SIP) event package for registrations. Through its REGISTER method, SIP allows a user agent to create, modify, and delete registrations. Registrations can also be altered by administrators in order to enforce policy. As a result, these registrations represent a piece of state in the network that can change dynamically. There are many cases where a user agent would like to be notified of changes in this state. This event package defines a mechanism by which those user agents can request and obtain such notifications.
TNP-470 (1999)

Proliferation of endothelial cells is critical to the formation of new blood vessels. These cells, which form the innermost layer of the vasculature, are normally in the G0 phase of the cell cycle. They are able to respond to several different growth factors, and this response can result in neovascularization or angiogenesis. Angiogenesis is a normal physiologic component of growth, reproduction, and wound healing. It is also a pathogenic and critical component of tumor growth and metastasis, and it is this aspect of angiogenesis that the development of TNP-470 addresses.
A budget-based algorithm for efficient subgraph matching on Huge Networks (2011)

As social network and RDF data grow dramatically in size to billions of edges, the ability to scalably answer queries posed over graph datasets becomes increasingly important. In this paper, we consider subgraph matching queries which are often posed to social networks and RDF databases - for such queries, we want to find all matching instances in a graph database. Past work on subgraph matching queries uses static cost models which can be very inaccurate due to long-tailed degree distributions commonly found in real world networks. We propose the BudgetMatch query answering algorithm. BudgetMatch costs and recosts query parts adaptively as it executes and learns more about the search space. We show that using this strategy, BudgetMatch can quickly answer complex subgraph queries on very large graph data. Specifically, on a real world social media data set consisting of 1.12 billion edges, we can answer complex subgraph queries in under one second and significantly outperform existing subgraph matching algorithms.
ROLE OF REVERSIBLE OXIDATION-REDUCTION OF ENZYME THIOLS-DISULFIDES IN METABOLIC REGULATION (1985)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
An orthopoxvirus-based vaccine reduces virus excretion after MERS-CoV infection in dromedary camels (2015)

Middle East respiratory syndrome coronavirus (MERS-CoV) infections have led to an ongoing outbreak in humans, which was fueled by multiple zoonotic MERS-CoV introductions from dromedary camels. In addition to the implementation of hygiene measures to limit further camel-to-human and human-to-human transmissions, vaccine-mediated reduction of MERS-CoV spread from the animal reservoir may be envisaged. Here we show that a modified vaccinia virus Ankara (MVA) vaccine expressing the MERS-CoV spike protein confers mucosal immunity in dromedary camels. Compared with results for control animals, we observed a significant reduction of excreted infectious virus and viral RNA transcripts in vaccinated animals upon MERS-CoV challenge. Protection correlated with the presence of serum neutralizing antibodies to MERS-CoV. Induction of MVA-specific antibodies that cross-neutralize camelpox virus would also provide protection against camelpox.
Dependence of antibody-mediated presentation of antigen on FcRn (2008)

The neonatal Fc receptor for IgG (FcRn) is a distant member of the MHC class I protein family. It binds IgG and albumin in a pH-dependent manner and protects these from catabolism by diverting them from a degradative fate in lysosomes. In addition, FcRn-mediated IgG transport across epithelial barriers is responsible for the transmission of IgG from mother to infant and can also enhance IgG-mediated antigen uptake across mucosal epithelia. We now show a previously undescribed role for FcRn in mediating the presentation of antigens by dendritic cells when antigens are present as a complex with antibody by uniquely directing multimeric immune complexes, but not monomeric IgG, to lysosomes.
Intermode dephasing in a superconducting stripline resonator (2010)

We study a superconducting stripline resonator (SSR) made of niobium, which is integrated with a superconducting interference device (SQUID). The large nonlinear inductance of the SQUID gives rise to a strong Kerr nonlinearity in the response of the SSR, which in turn results in strong coupling between different modes of the SSR. We experimentally demonstrate that such intermode coupling gives rise to dephasing of microwave photons. The dephasing rate depends periodically on the external magnetic flux applied to the SQUID, where the largest rate is obtained at half integer values (in units of the flux quantum). To account for our result we compare our findings with theory and find good agreement.
Metabolic Effects of 12-Month Percutaneous Dehydroepiandrosterone Replacement Therapy in Postmenopausal Women (1997)

Laboratory of Molecular Endocrinology and Clinical Endocrine Research Unit, CHUL Research Center and Laval University, Quebec, Canada. J Endocrinol 1996;150:S43-S50.
Application of DNQ-based microlithography to patterning bioactive molecules and cells (1996)

Photochemically induced surface functionality manipulation of Diazo-Naphto-Quinone/novolak polymeric films was used for controlling the specificity of the attachment and growth of neuronal cells and biologically active molecules (proteins and peptides) patterning. Different microlithographic techniques (standard positive tone, negative tone image reversal based on catalyzed decarboxylation, positive tone of image reversal resist, and surface imaging based on silylation), controlling the surface hydrophobicity and surface concentration of carboxylic groups, were assessed in the view of the suitability as microlithographic techniques for patterning biologically active molecules and cells. It was found that DNQ-based materials and techniques can be easily transferred in bio-microlithography, which is the building of laterally ordered architectures with biological structural elements.
[Tridentate N-N-N chelating systems as potential antitumor agents]. (1985)

Tridentate chelating agents, as potential antitumor agents, were prepared by condensing 2-quinolylhydrazines, 2-pyridylhydrazine and 2-benzothiazolylhydrazine with pyridine-2-aldehyde, 6-methylpyridine-2-aldehyde, 2-acetylpyridine and 2-benzoylpyridine. All compounds were tested against Lymphocytic leukemia P388. The active pyridine-2-aldehyde-4-methyl-2-quinolylhydrazone [1-(4'-methyl-2'-quinolyl)-3-(2'-pyridyl)-1,2-diaza-2-propene] (I d) was also tested against other experimental tumors and proved inactive.
Effect of srtA and srtB gene expression on the virulence of Staphylococcus aureus in animal models of infection (2004)

Results from this study substantiate the role of the srtA gene product in the establishment of infections and further studies are warranted to define and exploit this as a target for antimicrobial chemotherapy.
Evaluation of a lossless combiner in a LINC transmitter (2003)

Two combiners are compared for use in a LINC transmitter. Most LINC transmitters use matched hybrid combiners as they provide high isolation between input ports to provide undistorted signal combining. A tee combiner has also been explored for use in a LINC transmitter but was evaluated under the assumption of high input port isolation and perfectly matched amplifier outputs. This paper evaluates the use of a lossless tee combiner with input port coupling and unmatched amplifier outputs and their effects on the LINC transmitter's linearity and efficiency. It is shown that efficiency may be improved at the expense of overall transmitter distortion when a lossless tee combiner is used.
An Efficient Refolding Method for the Preparation of Recombinant Human Prethrombin-2 and Characterization of the Recombinant-Derived -Thrombin (2001)

Human recombinant prethrombin-2 was produced in Escherichia coli. The expressed prethrombin-2 formed intracellular inclusion bodies from which the protein was refolded by a simple one-step dilution process in buffer consisting of 50 mM Tris-HCl, containing 20 mM CaCl(2), 500 mM NaCl, 1 mM EDTA, 600 mM arginine, 1 mM cysteine, 0.1 mM cystine, 10% (v/v) glycerol, and 0.2% (w/v) Brij-58 at pH 8.5. After refolding, prethrombin-2 was purified by hirudin-based COOH-terminal peptide affinity chromatography, and then activated with Echis carinatus snake venom prothrombin activator (ecarin). The activated protein, alpha-thrombin, was then tested for several activities including activity toward chromogenic substrate, release of fibrinopeptide A from fibrinogen, activation of protein C, and thrombin-activatable fibrinolysis inhibitor, reactivity with antithrombin, clotting activity, and platelet aggregation. The kinetic data showed no differences in activity between our recombinant alpha-thrombin and plasma-derived alpha-thrombin. The yield of refolded recombinant human prethrombin-2 was about 4-7% of the starting amount of solubilized protein. In addition, the final yield of purified refolded protein was 0.5-1%, and about 1 mg of recombinant prethrombin-2 could be isolated from 1 liter of E. coli cell culture.
Disulfide vibrational spectra in the sulfur-sulfur and carbon-sulfur stretching region (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDisulfide vibrational spectra in the sulfur-sulfur and carbon-sulfur stretching regionErnest J. Bastian Jr. and R. Bruce MartinCite this: J. Phys. Chem. 1973, 77, 9, 1129–1133Publication Date (Print):April 1, 1973Publication History Published online1 May 2002Published inissue 1 April 1973https://pubs.acs.org/doi/10.1021/j100628a010https://doi.org/10.1021/j100628a010research-articleACS PublicationsRequest reuse permissionsArticle Views1581Altmetric-Citations64LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Nurr1, an orphan nuclear receptor, is a transcriptional activator of endogenous tyrosine hydroxylase in neural progenitor cells derived from the adult brain (1999)

Adult rat-derived hippocampal progenitor cells express many of the molecules implicated in midbrain dopaminergic determination, including FGF receptors 1, 2 and 3, the sonic hedgehog receptor components Smo and Ptc, and the region-specific transcription factors Ptx3 and Nurr1. Here we use undifferentiated progenitors to probe the events leading to the dopaminergic phenotype and find that the influences of Nurr1 can be temporally and mechanistically uncoupled from the patterning influences of sonic hedgehog and FGF-8 or the more generic process of neuronal differentiation itself. In gain-of-function experiments, Nurr1 is able to activate transcription of the tyrosine hydroxylase gene by binding a response element within a region of the tyrosine hydroxylase promoter necessary for midbrain-specific expression. This activation is mediated through a retinoid X receptor independent mechanism and occurs in all precursors, regardless of differentiation status. Overexpression of Nurr1 does not affect proliferation or stimulate neuronal differentiation and has no influence on the expression of other dopaminergic markers. This uncoupling of tyrosine hydroxylase expression from other dopaminergic markers suggests that the midbrain dopaminergic identity is dictated by a combination of pan-dopaminergic (e.g., Shh/FGF-8) and region-specific (Nurr1) mechanisms.
Predominance of mononuclear cells expressing the chemokine receptor CCR5 in synovial effusions of patients with different forms of arthritis (1999)

The predominance of CCR5-positive mononuclear cells in the synovial effusions of patients with arthritis suggests an important role for CCR5 in the process of joint inflammation, and identifies CCR5 as a possible new target for therapeutic intervention.
Melatonin enhancement of splenocyte proliferation is attenuated by luzindole, a melatonin receptor antagonist (2001)

In addition to marked seasonal changes in reproductive, metabolic, and other physiological functions, many vertebrate species undergo seasonal changes in immune function. Despite growing evidence that photoperiod mediates seasonal changes in immune function, little is known regarding the neuroendocrine mechanisms underlying these changes. Increased immunity in short days is hypothesized to be due to the increase in the duration of nightly melatonin secretion, and recent studies indicate that melatonin acts directly on immune cells to enhance immune parameters. The present study examined the contribution of melatonin receptors in mediating the enhancement of splenocyte proliferation in response to the T cell mitogen Concanavalin A in mice. The administration of luzindole, a high-affinity melatonin receptor antagonist, either in vitro or in vivo significantly attenuated the ability of in vitro melatonin to enhance splenic lymphocyte proliferation during the day or night. In the absence of melatonin or luzindole, splenocyte proliferation was intrinsically higher during the night than during the day. In the absence of melatonin administration, luzindole reduced the ability of spleen cells to proliferate during the night, when endogenous melatonin concentrations are naturally high. This effect was not observed during the day, when melatonin concentrations are low. Taken together, these results suggest that melatonin enhancement of splenocyte proliferation is mediated directly by melatonin receptors on splenocytes and that there is diurnal variation in splenocyte proliferation in mice that is also mediated by splenic melatonin receptors.