gebhart/patrepeval huggingface dataset:
Optical workstation with concurrent, independent multiphoton imaging and experimental laser microbeam capabilities (2003)

Experimental laser microbeam techniques have become established tools for studying living specimens. A steerable, focused laser beam may be used for a variety of experimental manipulations such as laser microsurgery, optical trapping, localized photolysis of caged bioactive probes, and patterned photobleaching. Typically, purpose-designed experimental systems have been constructed for each of these applications. In order to assess the consequences of such experimental optical interventions, long-term, microscopic observation of the specimen is often required. Multiphoton excitation, because of its ability to obtain high-contrast images from deep within a specimen with minimal phototoxic effects, is a preferred technique for in vivo imaging. An optical workstation is described that combines the functionality of an experimental optical microbeam apparatus with a sensitive multiphoton imaging system designed for use with living specimens. Design considerations are discussed and examples of ongoing biological applications are presented. The integrated optical workstation concept offers advantages in terms of flexibility and versatility relative to systems implemented with separate imaging and experimental components.
Engineering Central Metabolic Pathways for High-Level Flavonoid Production in Escherichia coli (2007)

The identification of optimal genotypes that result in improved production of recombinant metabolites remains an engineering conundrum. In the present work, various strategies to reengineer central metabolism in Escherichia coli were explored for robust synthesis of flavanones, the common precursors of plant flavonoid secondary metabolites. Augmentation of the intracellular malonyl coenzyme A (malonyl-CoA) pool through the coordinated overexpression of four acetyl-CoA carboxylase (ACC) subunits from Photorhabdus luminescens (PlACC) under a constitutive promoter resulted in an increase in flavanone production up to 576%. Exploration of macromolecule complexes to optimize metabolic efficiency demonstrated that auxiliary expression of PlACC with biotin ligase from the same species (BirAPl) further elevated flavanone synthesis up to 1,166%. However, the coexpression of PlACC with Escherichia coli BirA (BirAEc) caused a marked decrease in flavanone production. Activity improvement was reconstituted with the coexpression of PlACC with a chimeric BirA consisting of the N terminus of BirAEc and the C terminus of BirAPl. In another approach, high levels of flavanone synthesis were achieved through the amplification of acetate assimilation pathways combined with the overexpression of ACC. Overall, the metabolic engineering of central metabolic pathways described in the present work increased the production of pinocembrin, naringenin, and eriodictyol in 36 h up to 1,379%, 183%, and 373%, respectively, over production with the strains expressing only the flavonoid pathway, which corresponded to 429 mg/liter, 119 mg/liter, and 52 mg/liter, respectively.
Seroma Prevention in a Rat Mastectomy Model (1996)

Seroma formation following mastectomy and axillary dissection remains a common and significant problem contributing to patient morbidity and health-care costs. Previous data have suggested that fibrin sealant (FS), a biological adhesive, is capable of controlling lymphatic leakage and assisting with skin graft adhesion. In this study, the use of an experimental, light-activated FS under development by CryoLife (CFS) was evaluated in a rat mastectomy model in order to reduce seroma formation. CFS is a premixed form of FS, containing an inactivator that is reversed in the presence of light, causing sealant to form. In this model, rats underwent mastectomy and extensive dissection of the axillary lymphovasculature. Next, 1 ml of saline or FS was applied to the operative site and the wound was closed. Three groups of animals were evaluated 5 days postoperatively by measuring the volume (in milliliters) of seroma able to be aspirated from the surgical site. The saline control group (N = 20) had a seroma volume (mean +/- standard deviation [SD]) of 4.2 +/- 2.9 ml, while a form of CFS containing human fibrinogen (80 to 100 mg per milliliter) and human thrombin (20 U per milliliter) (N = 20) had a significantly smaller seroma volume of 1.1 +/- 1.6 ml (p < 0.001 analysis of variance). University of Virginia (UVA) FS, containing human fibrinogen (20 mg per milliliter) and bovine thrombin (500 U per milliliter) (N = 20), had a seroma volume of 2.0 +/- 1.6 ml (p < 0.01, compared to control; p > 0.2, compared to CFS). Thus, this form of CFS significantly reduced seroma formation compared to saline control and also appeared to result in a smaller fluid accumulation than with UVA FS, although this trend was not statistically significant. These data suggest that the use of CFS may help to reduce seroma formation in humans.
Residual stress minimum in nanocrystalline diamond films (2006)

Nanocrystalline diamond films have been deposited on silicon nitride substrates by hot filament chemical vapor deposition. Gas mixtures of CH4–H2–Ar were used with variation of the Ar∕H2 ratio in order to study the influence of the Ar content on the formation of nondiamond phases at the grain boundaries and thus in the film residual stress assessed by x-ray diffraction techniques. By varying this ratio it is possible to optimize conditions, decreasing the film’s residual stress to a minimum of 0.09GPa.
Jabber HTTP Polling (2009)

This document defines an XMPP protocol extension that enables access to a Jabber server from behind firewalls which do not allow outgoing sockets on port 5222, via HTTP requests.
Simulation of Hamiltonian light-beam propagation in nonlinear media (1998)

The simulation of nonlinear wave propagation in the ray regime, i.e., in the limit of geometrical optics, is discussed. The medium involved is nonlinear, which means that the field amplitudes affect the constitutive parameters (e.g., dielectric constant) involved in the propagation formalism. Conventionally, linear ray propagation is computed by the use of Hamilton’s ray equations whose terms are derived from the appropriate dispersion equation. The formalism used to solve such a set of equations is the Runge–Kutta algorithm in one of its variants. In the present case of nonlinear propagation, a proper dispersion equation must first be established from which the rays can be computed. Linear ray tracing with Hamilton’s ray theory allows for the computation of ray trajectories and wave fronts. The convergence or divergence of rays suggests heuristic methods for computing the variation of amplitudes. Here, terms appearing in the Hamiltonian ray equations involve field amplitudes, which themselves are determined by the convergence (or divergence) of the rays. This dictates the simultaneous computation of a beam comprising many rays, so it is necessary to modify the original Runge–Kutta scheme by building into it some iteration mechanism such that the process converges to the values that take into account the amplitude effect. This research attempts to modify the existing propagation formalism and apply the new algorithm to simple problems of nonlinear ray propagation. The results display self-focusing effects characteristic of nonlinear optics problems. The influence of weak losses on the beam propagation and its self focusing is also discussed. Some displayed results obtained by simulating the modified formalism seem to be physically plausible and are in excellent agreement with experimental results reported in the literature.
Midkine concentrations in fine‐needle aspiration of benign and malignant thyroid nodules (2014)

The findings indicate that, in FNA samples, the MDK/Tg ratio in PTC is greater than in benign thyroid nodules, raising the possibility that this approach might provide adjunctive diagnostic or prognostic information to complement existing approaches.
25-Hydroxycholesterol-3-sulfate attenuates inflammatory response via PPARγ signaling in human THP-1 macrophages (2012)

The nuclear receptor peroxisome proliferator-activated receptors (PPARs) are important in regulating lipid metabolism and inflammatory responses in macrophages. Activation of PPARγ represses key inflammatory response gene expressions. Recently, we identified a new cholesterol metabolite, 25-hydroxycholesterol-3-sulfate (25HC3S), as a potent regulatory molecule of lipid metabolism. In this paper, we report the effect of 25HC3S and its precursor 25-hydroxycholesterol (25HC) on PPARγ activity and on inflammatory responses. Addition of 25HC3S to human macrophages markedly increased nuclear PPARγ and cytosol IκB and decreased nuclear NF-κB protein levels. PPARγ response element reporter gene assays showed that 25HC3S significantly increased luciferase activities. PPARγ competitor assay showed that the K(i) for 25HC3S was ∼1 μM, similar to those of other known natural ligands. NF-κB-dependent promoter reporter gene assays showed that 25HC3S suppressed TNFα-induced luciferase activities only when cotransfected with pcDNAI-PPARγ plasmid. In addition, 25HC3S decreased LPS-induced expression and release of IL-1β. In the PPARγ-specific siRNA transfected macrophages or in the presence of PPARγ-specific antagonist, 25HC3S failed to increase IκB and to suppress TNFα and IL-1β expression. In contrast to 25HC3S, its precursor 25HC, a known liver X receptor ligand, decreased nuclear PPARγ and cytosol IκB and increased nuclear NF-κB protein levels. We conclude that 25HC3S acts in macrophages as a PPARγ ligand and suppresses inflammatory responses via the PPARγ/IκB/NF-κB signaling pathway.
RANK is the intrinsic hematopoietic cell surface receptor that controls osteoclastogenesis and regulation of bone mass and calcium metabolism (2000)

We have generated RANK (receptor activator of NF-κB) nullizygous mice to determine the molecular genetic interactions between osteoprotegerin, osteoprotegerin ligand, and RANK during bone resorption and remodeling processes. RANK −/− mice lack osteoclasts and have a profound defect in bone resorption and remodeling and in the development of the cartilaginous growth plates of endochondral bone. The osteopetrosis observed in these mice can be reversed by transplantation of bone marrow from rag1 −/− (recombinase activating gene 1) mice, indicating that RANK −/− mice have an intrinsic defect in osteoclast function. Calciotropic hormones and proresorptive cytokines that are known to induce bone resorption in mice and human were administered to RANK −/− mice without inducing hypercalcemia, although tumor necrosis factor α treatment leads to the rare appearance of osteoclast-like cells near the site of injection. Osteoclastogenesis can be initiated in RANK −/− mice by transfer of the RANK cDNA back into hematopoietic precursors, suggesting a means to critically evaluate RANK structural features required for bone resorption. Together these data indicate that RANK is the intrinsic cell surface determinant that mediates osteoprotegerin ligand effects on bone resorption and remodeling as well as the physiological and pathological effects of calciotropic hormones and proresorptive cytokines.
CD4+ T-Cell Help in the Tumor Milieu Is Required for Recruitment and Cytolytic Function of CD8+ T Lymphocytes (2010)

CD4 help for CD8(+) T lymphocytes prevents tolerance and promotes the survival of effector and memory CD8(+) T cells. Here, we describe additional helper functions that require CD4(+) T cells within the tumor environment. CD8(+) T-cell recruitment, proliferation, and effector function within the tumor were greatly enhanced by tumor-specific CD4(+) T cells. Recruitment of CD8(+) T cells was accelerated by IFN-γ-dependent production of chemokines. Production of interleukin-2 by tumor resident CD4(+) T cells enhanced CD8(+) T-cell proliferation and upregulated expression of granzyme B. These results highlight a novel role for tumor-specific CD4(+) T cells in promoting CD8(+) T-cell recruitment and cytolytic function, two previously unappreciated aspects of tumor-specific CD4 help.
The Polycomb Group Protein Complex of Drosophila melanogaster Has Different Compositions at Different Target Genes (1997)

In Drosophila the Polycomb group genes are required for the long-term maintenance of the repressed state of many developmental regulatory genes. Their gene products are thought to function in a common multimeric complex that associates with Polycomb group response elements (PREs) in target genes and regulates higher-order chromatin structure. We show that the chromodomain of Polycomb is necessary for protein-protein interactions within a Polycomb-Polyhomeotic complex. In addition, Posterior Sex Combs protein coimmunoprecipitates Polycomb and Polyhomeotic, indicating that they are members of a common multimeric protein complex. Immunoprecipitation experiments using in vivo cross-linked chromatin indicate that these three Polycomb group proteins are associated with identical regulatory elements of the selector gene engrailed in tissue culture cells. Polycomb, Polyhomeotic, and Posterior Sex Combs are, however, differentially distributed on regulatory sequences of the engrailed-related gene invected. This suggests that there may be multiple different Polycomb group protein complexes which function at different target sites. Furthermore, Polyhomeotic and Posterior Sex Combs are also associated with expressed genes. Polyhomeotic and Posterior Sex Combs may participate in a more general transcriptional mechanism that causes modulated gene repression, whereas the inclusion of Polycomb protein in the complex at PREs leads to stable silencing.
Synthesis of Nanocrystalline CuMS2 (M = In or Ga) through a Solvothermal Process (2000)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTSynthesis of Nanocrystalline CuMS2 (M = In or Ga) through a Solvothermal ProcessQingyi Lu, Junqing Hu, Kaibin Tang, Yitai Qian, Guien Zhou, and Xianming LiuView Author Information Structure Research Laboratory and Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China Cite this: Inorg. Chem. 2000, 39, 7, 1606–1607Publication Date (Web):March 17, 2000Publication History Received22 September 1999Published online17 March 2000Published inissue 1 April 2000https://pubs.acs.org/doi/10.1021/ic9911365https://doi.org/10.1021/ic9911365brief-reportACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1491Altmetric-Citations90LEARN 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 optionsGet e-Alertsclose SUBJECTS:Aromatic compounds,Copper sulfide,Hydrocarbons,Solvents,Transmission electron microscopy Get e-Alerts
A new cellulose-based microcarrier culturing system. (1980)

A search for new substrates to be used as microcarriers for culturing mammalian cells was carried out. Commercially available microgranular anion exchange DEAE-cellulose (DE-52 of Whatman) were investigated as microcarriers for anchorage-dependent-cells. Cells from CCL-1 mouse cell line were grown on the investigated microcarriers. Mouse interferon was successfully produced after induction with Sendai virus. Interferon yield per cell was similar to that obtained in monolayer culture.
Microxine, a New cdc2 Kinase Inhibitor from the Australian Marine Sponge Microxina Species (2001)

A new purine derivative microxine (1) was isolated from the Australian marine sponge Microxina sp. The compound was isolated via reversed-phase chromatography and its structure determined spectroscopically. Microxine was found to weakly inhibit cdc2 kinase activity with an IC(50) of 13 microM.
Constitutive/Hypoxic Degradation of HIF-α Proteins by the Proteasome Is Independent of von Hippel Lindau Protein Ubiquitylation and the Transactivation Activity of the Protein (2007)

The transcriptional activator complex HIF-1 plays a key role in the long term adaptation of cells and tissues to their hypoxic microenvironment by stimulating the expression of genes involved in angiogenesis and glycolysis. The expression of the HIF-1 complex is regulated by the levels of its HIF-alpha subunits that are degraded under normoxic conditions by the ubiquitin-proteasome system. Whereas this pathway of HIF-alpha protein degradation has been well characterized, little is known of their turnover during prolonged hypoxic conditions. Herein, we describe a pathway by which HIF-1alpha and HIF-2alpha proteins are constitutively degraded during hypoxia by the proteasome system, although without requirement of prior ubiquitylation. The constitutive/hypoxic degradation of HIF-alpha proteins is independent of the presence of VHL, binding to DNA, or the formation of a transcriptionally active HIF-1 complex. These results are further strengthened by the demonstration that HIF-alpha proteins are directly degraded in a reconstituted in vitro assay by the proteasome. Finally, we demonstrate that the persistent down-regulation of HIF-1alpha during prolonged hypoxia is mainly caused by a decreased production of the protein without change in its degradation rate. This constitutive, ubiquitin-independent proteasomal degradation pathway of HIF-alpha proteins has to be taken into account in understanding the biology as well as in the development of therapeutic interventions of highly hypoxic tumors.
Assessment of bronchial wall thickness and lumen diameter in human adults using multi‐detector computed tomography: comparison with theoretical models (2007)

A thickened bronchial wall is the morphological substratum of most diseases of the airway. Theoretical and clinical models of bronchial morphometry have so far focused on bronchial lumen diameter, and bronchial length and angles, mainly assessed from bronchial casts. However, these models do not provide information on bronchial wall thickness. This paper reports in vivo values of cross-sectional wall area, lumen area, wall thickness and lumen diameter in ten healthy subjects as assessed by multi-detector computed tomography. A validated dedicated software package was used to measure these morphometric parameters up to the 14th bronchial generation, with respect to Weibel's model of bronchial morphometry, and up to the 12th according to Boyden's classification. Measured lumen diameters and homothety ratios were compared with theoretical values obtained from previously published studies, and no difference was found when considering dichotomic division of the bronchial tree. Mean wall area, lumen area, wall thickness and lumen diameter were then provided according to bronchial generation order, and mean homothety ratios were computed for wall area, lumen area and wall thickness as well as equations giving the mean value of each parameter for a given bronchial generation with respect to its value in generation 0 (trachea). Multi-detector computed tomography measurements of bronchial morphometric parameters may help to improve our knowledge of bronchial anatomy in vivo, our understanding of the pathophysiology of bronchial diseases and the evaluation of pharmacological effects on the bronchial wall.
Single-mode, single-lobe operation of surface-emitting, second-order distributed feedback lasers (1999)

A thin p-cladding InGaAs/InGaP/GaAs laser structure (λ=0.977 μm) with a second-order Au/air grating (70% duty cycle) and asymmetrically coated (30%, 5% reflectivity) cleaved facets emits in a diffraction-limited (0.11°) single lobe in a direction virtually normal to the chip surface. The near-field pattern corresponds to (grating) phase shifts of 10° and 40° at the low- and high-reflectivity cleaved-mirror facets. An analysis of 30%/0% coated, 500-μm-long devices shows that single-lobe surface emission occurs for a wide variation in grating phase with respect to the high reflectivity mirror, ΔφHR: 10°–80°. For 99%/0% coated devices, single-lobe emission occurs with relatively uniform near-field intensity profile and external differential quantum efficiency ηd around 20% for ΔφHR values close to π/4 (i.e., in the 45°–65° range). Single-lobe emission normal to the chip surface (i.e., symmetric-mode lasing) can then be obtained from devices without cleaved mirrors by introducing a phase shift close to π/2 in the center of the second-order grating. For the structure used, a phase shift of 90°–130° in the center of 1-mm-long gratings is found to provide single-lobe surface emission with substantially uniform near-field profile, and ηd values as high as 22%. Increasing the grating-section length increases ηd (e.g., 35% for 1.5-mm-long gratings) at some price in near-field uniformity.
Reversal of the interferon-sensitive phenotype of a vaccinia virus lacking E3L by expression of the reovirus S4 gene (1995)

The vaccinia virus (VV) E3L gene, which encodes a potent inhibitor of the interferon (IFN)-induced, double-stranded RNA (dsRNA)-dependent protein kinase, PKR, is thought to be involved in the IFN-resistant phenotype of VV. The E3L gene products, p25 and p20, act as inhibitors of PKR, presumably by binding and sequestering activator dsRNA from the kinase. In this study we demonstrate that VV with the E3L gene specifically deleted (vP1080) was sensitive to the antiviral effects of IFN and debilitated in its ability to rescue vesicular stomatitis virus from the antiviral effects of IFN. Infection of L929 cells with E3L-minus virus led to rRNA degradation typical of activation of the 2'-5'-oligoadenylate synthetase/RNase L system, and extracts of infected cells lacked the PKR-inhibitory activity characteristic of wild-type VV. The reovirus S4 gene, which encodes a dsRNA-binding protein (sigma 3) that can also inhibit PKR activation by binding and sequestering activator dsRNA, was inserted into vP1080. The resultant virus (vP1112) was partially resistant to the antiviral effects of IFN in comparison with vP1080. Further studies demonstrated that transient expression of the reovirus sigma 3 protein rescued E3L-minus VV replication in HeLa cells. In these studies, rescue by sigma 3 mutants correlated with their ability to bind dsRNA. Finally, vP112 was also able to rescue the replication of the IFN-sensitive virus vesicular stomatitis virus in a manner similar to that of wild-type VV. Together, these results suggest that the reovirus S4 gene can replace the VV E3L gene with respect to interference with the IFN-induced antiviral activity.