gebhart/patrepeval huggingface dataset:
A New Genus of the Order Actinomycetales, Couchioplanes gen. nov., with Descriptions of Couchioplanes caeruleus (Horan and Brodsky 1986) comb. nov. and Couchioplanes caeruleus subsp. azureus subsp. nov. (1994)

During our taxonomic study of motile actinomycetes, soil isolate RA 335 was found to form a blue substrate mycelium and aerial mycelia with motile arthrospores and to have lysine as the cell wall diamino acid. Actinoplanes caeruleus IFO 13939T (T = type strain) and "Actinoplanes azureus" IFO 13993T are known to have the same characteristics. Therefore, the taxonomic position of these three strains was studied. Aerial mycelia of these strains fragmented during the growth cycle and produced motile spores arranged in chains within the mycelia. Sporangia were not observed. The strains contained menaquinone 9(H4), had guanine-plus-cytosine contents of 69.9 to 72.1 mol%, and had D-glutamic acid, D- and L-serine, glycine, L-alanine, and L-lysine as cell wall amino acids (type A3 alpha). The taxonomic characteristics of these strains differ from those of the previously described motile actinomycetes. On the basis of morphological, physiological, and chemotaxonomic data and the results of DNA-DNA hybridization and comparative 16S rRNA studies, we propose a new genus, Couchioplanes, for these organisms. The type species is Couchioplanes caeruleus comb. nov. (type strain, IFO 13939), which is divided into two subspecies, Couchioplanes caeruleus subsp. caeruleus subsp. nov. (type strain, IFO 13939) for A. caeruleus IFO 13939T and strain RA 335 and Couchioplanes caeruleus subsp. azureus (type strain, IFO 13993) for "A. azureus" IFO 13993T.
View Synthesis using Depth Map for 3D Video (2009)

Abstract — Three-dimensional (3D) video involves stereoscopic or multi-view images to provide depth experience through 3D display systems. Binocular cues are perceived by rendering proper viewpoint images obtained at slightly different view angles. Since the number of viewpoints of the multi-view video is limited, 3D display devices should generate arbitrary viewpoint images using available adjacent view images. In this paper, after we explain a view synthesis method briefly, we propose a new compensation algorithm for view synthesis errors around object boundaries. We describe a 3D warping technique exploiting the depth map for viewpoint shifting and a hole filling method using multi-view images. Then, we propose an algorithm to remove boundary noises that are generated due to mismatches of object edges in the color and depth images. The proposed method reduces annoying boundary noises near object edges by replacing erroneous textures with alternative textures from the other reference image. Using the proposed method, we can generate perceptually improved images for 3D video systems. I.
Cloning and Expression of a Rat Acetylcholinesterase Subunit: Generation of Multiple Molecular Forms and Complementarity with a Torpedo Collagenic Subunit (1993)

We obtained a cDNA clone encoding one type of catalytic subunit of acetylcholinesterase (AChE) from rat brain (T subunit). The coding sequence shows a high frequency of (G+C) at the third position of the codons (66%), as already noted for several AChEs, in contrast with mammalian butyrylcholinesterase. The predicted primary sequence of rat AChE presents only 11 amino acid differences, including one in the signal peptide, from that of the mouse T subunit. In particular, four alanines in the mouse sequence are replaced by serine or threonine. In northern blots, a rat AChE probe indicates the presence of major 3.2- and 2.4-kb mRNAs, expressed in the CNS as well as in some peripheral tissues, including muscle and spleen. In vivo, we found that the proportions of G1, G2, and G4 forms are highly variable in different brain areas. We did not observe any glycolipid-anchored G2 form, which would be derived from an H subunit. We expressed the cloned rat AChE in COS cells: The transfected cells produce principally an amphiphilic G1a form, together with amphiphilic G2a and G4a forms, and a nonamphiphilic G4na form. The amphiphilic G1a and G2a forms correspond to type II forms, which are predominant in muscle and brain of higher vertebrates. The cells also release G4na, G2a, and G1a in the culture medium. These experiments show that all the forms observed in the CNS in vivo may be obtained from the T subunit. By co-transfecting COS cells with the rat T subunit and the Torpedo collagenic subunit, we obtained chimeric collagen-tailed forms. This cross-species complementarity demonstrates that the interaction domains of the catalytic and structural subunits are highly conserved during evolution.
Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways (2013)

Large-scale proteomic approaches have identified numerous mitochondrial acetylated proteins; however in most cases, their regulation by acetyltransferases and deacetylases remains unclear. Sirtuin 3 (SIRT3) is an NAD(+)-dependent mitochondrial protein deacetylase that has been shown to regulate a limited number of enzymes in key metabolic pathways. Here, we use a rigorous label-free quantitative MS approach (called MS1 Filtering) to analyze changes in lysine acetylation from mouse liver mitochondria in the absence of SIRT3. Among 483 proteins, a total of 2,187 unique sites of lysine acetylation were identified after affinity enrichment. MS1 Filtering revealed that lysine acetylation of 283 sites in 136 proteins was significantly increased in the absence of SIRT3 (at least twofold). A subset of these sites was independently validated using selected reaction monitoring MS. These data show that SIRT3 regulates acetylation on multiple proteins, often at multiple sites, across several metabolic pathways including fatty acid oxidation, ketogenesis, amino acid catabolism, and the urea and tricarboxylic acid cycles, as well as mitochondrial regulatory proteins. The widespread modification of key metabolic pathways greatly expands the number of known substrates and sites that are targeted by SIRT3 and establishes SIRT3 as a global regulator of mitochondrial protein acetylation with the capability of coordinating cellular responses to nutrient status and energy homeostasis.
Inhibition of Tumor Cell Growth by Murine Splenic Adherent Cells Stimulated with IFN-γ (1998)

We have previously reported that the growth of lymphocytes and tumor cells with lymphocyte lineage was strongly inhibited by a part of cloned macrophage hybridomas. This growth inhibition was accomplished by cell-to-cell contact and found to be attributed to lipid-like molecule(s) in a macrophage hybridoma cell membrane fraction. Instead of macrophage hybridomas, in the present study we utilized splenic adherent cells (SACs) that had been stimulated with IFN-γ to see whether they inhibited tumor cell growth or not. The results demonstrated that IFN-γ-stimulated but not unstimulated SACs showed a significant growth inhibition of BW-5147 tumor cells. This growth inhibition was not mainly mediated by prostaglandin E&lt;sub&gt;2&lt;/sub&gt; secreted from macrophages, since the inhibition was not reduced in the presence of indomethacin. Furthermore, as was reported previously in the case of macrophage hybridomas, the inhibitory activity resides in a lipid fraction of IFN-γ-stimulated SAC membrane.
Triplex forming oligonucleotide targeted to 3'UTR downregulates the expression of the bcl-2 proto-oncogene in HeLa cells (2001)

The bcl-2 proto-oncogene is overexpressed in a variety of human cancers and plays an important role in programmed cell death. Recent reports implied that the 3'-untranslated region (3'UTR) functions effectively in the regulation of gene expression. Here, we attempt to assay the ability of triplex forming oligonucleotides (TFOs) to inhibit expression of a target gene in vivo and to examine the potential of the 3'UTR of the bcl-2 proto-oncogene in the regulation of bcl-2 gene expression. To do this, we have developed a novel cellular system that involves transfection of a Doxycyclin inducible expression plasmid containing the bcl-2 ORF and the 3'UTR together with a TFO targeted to the 3'UTR of the bcl-2 proto-oncogene. Phosphorothioate-modified TFO targeted to the 3'UTR of the bcl-2 gene significantly downregulated the expression of the bcl-2 gene in HeLa cells as demonstrated by western blotting. Our results indicate that blocking the functions of the 3'UTR using the TFO can downregulate the expression of the targeted gene, and suggest that triplex strategy is a promising approach for oligonucleotide-based gene therapy. In addition, triplex-based sequence targeting may provide a useful tool for studying the regulation of gene expression.
Viral interleukin‐6 encoded by rhesus macaque rhadinovirus is associated with lymphoproliferative disorder (LPD) (2009)

Our data support the idea that vIL-6 may be critical to the development and progression of lymphoproliferative disorder in RRV/SIV-infected RM.
Kinetics and mechanism of acid‐catalyzed hydrolysis of the diazo functional group of diazophenylacetamide (2003)

Abstract The acid‐catalyzed hydrolysis of diazophenylacetamide giving mandelamide as product was found to occur with a normal ( k H / k D &gt;1) hydronium ion isotope effect and to be subject to general acid rather than specific hydronium ion catalysis. This shows that the reaction occurs by rate‐determining hydron transfer from the catalyzing acid to the diazo carbon atom of the substrate, followed by rapid displacement of the diazo group by water. Comparison of the rate of this reaction with those of the same process for other diazophenylacetic acid functional derivatives, PhCN 2 COX, reveals that the reactivity of these substrates is controlled by the electron‐releasing resonance ability of the group X. Copyright © 2003 John Wiley &amp; Sons, Ltd.
Tracking with Multiple Sensors (2005)

The thesis deals with the dynamic combination of mobile and stationary location sensors for a unified treatment of such sensors from the areas of Augmented Reality and Ubiquitous Computing, enabling intuitive user interfaces in intelligent environments. A graph-based formalism and a distributed implementation concept allow the unified treatment of all relevant sensor networks. A simulation of the underlying algorithms shows the viability of both the formalism and the implementation concept. In addition, a software architecture allowing the dynamic integration of mobile applications and sensors is described. Special focus is put on how to transmit configuration data in peer-to-peer networks. As a proof of concept, a game-playing application, Ubiquitous SHEEP, is described, demonstrating all key features described in this thesis in practice.
Subepidermal Moisture Is Associated With Early Pressure Ulcer Damage in Nursing Home Residents With Dark Skin Tones (2009)

Subepidermal moisture was associated with future (1 week later) PU in persons with dark skin tones. Subepidermal moisture threshold values may assist in detecting early PU in persons with dark skin tones, allowing for earlier intervention to prevent PU. These findings should be further evaluated in persons with dark skin tones.
A Summary of Environmentally Friendly Turbine Design Concepts (1999)

The Advanced Hydropower Turbine System Program (AHTS) was created in 1994 by the U.S. Department of Energy, Electric Power Research Institute, and the Hydropower Research Foundation. The Program’s main goal is to develop “environmentally friendly” hydropower turbines. The Program’s first accomplishment was the development of conceptual designs of new environmentally friendly turbines. In order to do so, two contractors were competitively selected. The ARL/NREC team of engineers and biologists provided a conceptual design for a new turbine runner*. The new runner has the potential to generate hydroelectricity at close to 90% efficiency. The Voith team produced new fish-friendly design criteria for Kaplan and Francis turbines that can be incorporated in units during rehabilitation projects or in new hydroelectric facilities**. These include the use of advanced plant operation, minimum gap runners, placement of wicket gates behind stay vanes, among others. The Voith team will also provide design criteria on aerating Francis turbines to increase dissolved oxygen content. Detailed reviews of the available literature on fish mortality studies, causation of injuries to fish, and available biological design criteria that would assist in the design of fish-friendly turbines were performed. This review identified a need for more biological studies in order to develop performance criteria to assist turbine manufacturers in designing a more fish-friendly turbine.
Human Rights Environmentalism: Forging Common Ground (1995)

Since the early 1970s, the international community has widely acknowledged the nexus between human rights and environmental protection. References to this association and even to a human right to some minimal quality of environment, can be found in numerous international instruments. The Stockholm Declaration on the Human Environment, for example, proclaims that human beings have the "fundamental right to freedom, equality and adequate conditions of life, in an environment of a quality that permits a life of dignity and well-being." Similarly, the Additional Protocol to the American Convention on Human Rights states that "everyone shall have the right to live in a healthy environment." Despite this widespread acknowledgement of the relationship between human rights and environmental protection, the convergence of these two ideals has remained primarily as an academic issue. On the practical level, efforts to develop a comprehensive strategy for addressing common themes, by both human rights an1d environmental activists, have been overshadowed by the individual needs and goals of each community.
Research issues in outlier detection for data streams (2014)

In applications, such as sensor networks and power usage monitoring, data are in the form of streams, each of which is an infinite sequence of data points with explicit or implicit timestamps and has special characteristics, such as transiency, uncertainty, dynamic data distribution, multidimensionality, and dynamic relationship. These characteristics introduce new research issues that make outlier detection for stream data more challenging than that for regular (non-stream) data. This paper discusses those research issues for applications where data come from a single stream as well as multiple streams.
In Vivo Selection of Biocompatible Alginates for Islet Encapsulation and Subcutaneous Transplantation (2009)

Islet encapsulation requires several properties including (1) biocompatibility, (2) immunoprotection, and (3) oxygen diffusion for islet survival and diabetes correction. New chemical alginates were tested in vivo and compared with traditional high-mannuronate and -guluronate alginates. New alginates with coupled peptide sequence (sterile lyophilized high mannuronate [SLM]-RGD3% and sterile lyophilized high guluronate [SLG]-RGD3%), to improve encapsulated cell adherence in the matrix, and alginates with a very low viscosity (VLDM7% and VLDG7%), to reduce implant size by loading a higher number of islets per volume of polymer, were implanted subcutaneously in 70 Wistar rats for comparison with alginates of high viscosity and high content of mannuronic (SLM3%) or guluronic acids (SLG3%). Permeability of alginates to 36-, 75-, and 150-kDa lectins coupled to fluorescein isothiocynate was quantified before implantation and at 2, 4, and 12 weeks after implantation. Biocompatibility (fibrosis, graft stability, immunologic infiltration by CD3/CD68 cells, and neovascularization) was assessed at each explantation time. Permeability to small molecules was found for all alginates. Impermeability to 150-kDa molecules, such as IgG, was observed only for SLM3% before implantation and was maintained up to 12 weeks after implantation. SLM3% and SLG3% demonstrated better graft stability with lower CD3/CD68 recruitment and fibrosis than the other alginates. SLM3% induced a significantly higher angiogenesis and maintained oxygen pressure at approximately 40 mm Hg for up to 4 weeks after implantation as measured by in vivo electronic paramagnetic resonance oximetry. SLM-encapsulated pig islets implanted subcutaneously in rats demonstrated no inflammatory/immunologic reactions and islets functioned for up to 60 days without immunosuppression. A traditional alginate made of high mannuronic content (SLM3%) is an adapted material to immunoprotect islets in subcutaneous tissue. No improvement was found with lower viscosity and use of GRGDSP-peptide sequence.
Immunotherapy of BALB/c mice bearing Ehrlich ascites tumor with vitamin D-binding protein-derived macrophage activating factor. (1997)

Vitamin D3-binding protein (DBP; human DBP is known as Gc protein) is the precursor of macrophage activating factor (MAF). Treatment of mouse DBP with immobilized beta-galactosidase or treatment of human Gc protein with immobilized beta-galactosidase and sialidase generated a remarkably potent MAF, termed DBPMAF or GcMAF, respectively. The domain of Gc protein responsible for macrophage activation was cloned and enzymatically converted to the cloned MAF, designated CdMAF. In Ehrlich ascites tumor-bearing mice, tumor-specific serum alpha-N-acetylgalactosaminidase (NaGalase) activity increased linearly with time as the transplanted tumor cells grew in the peritoneal cavity. Therapeutic effects of DBPMAF, GcMAF, and CdMAF on mice bearing Ehrlich ascites tumor were assessed by survival time, the total tumor cell count in the peritoneal cavity, and serum NaGalase activity. Mice that received a single administration of DBPMAF or GcMAF (100 pg/mouse) on the same day after transplantation of tumor (1 x 10(5) cells) showed a mean survival time of 35 +/- 4 days, whereas tumor-bearing controls had a mean survival time of 16 +/- 2 days. When mice received the second DBPMAF or GcMAF administration at day 4, they survived more than 50 days. Mice that received two DBPMAF administrations, at days 4 and 8 after transplantation of 1 x 10(5) tumor cells, survived up to 32 +/- 4 days. At day 4 posttransplantation, the total tumor cell count in the peritoneal cavity was approximately 5 x 10(5) cells. Mice that received two DBPMAF administrations, at days 0 and 4 after transplantation of 5 x 10(5) tumor cells, also survived up to 32 +/- 4 days, while control mice that received the 5 x 10(5) ascites tumor cells only survived for 14 +/- 2 days. Four DBPMAF, GcMAF, or CdMAF administrations to mice transplanted with 5 x 10(5) Ehrlich ascites tumor cells with 4-day intervals showed an extended survival of at least 90 days and an insignificantly low serum NaGalase level between days 30 and 90.
Degradation of the Side Chain of (−)‐Sclareol: A Very Short Synthesis of nor‐Ambreinolide and Ambrox (2004)

Abstract The synthesis of nor‐Ambreinolide (8) from (‐)‐sclareol (1) was carried out by treatment with KMnO4‐Ac2O and further alkaline hydrolysis. 8 was directly transformed into (‐)‐ambrox (11) by reduction with metal borohydride in the presence of Lewis acids.
Nucleotide sugar transporters of the Golgi apparatus (2000)

Glycosylation, sulfation and phosphorylation of proteins, proteoglycans and lipids occur in the lumen of the Golgi apparatus. The nucleotide substrates of these reactions must be first transported from the cytosol into the Golgi lumen by specific transporters. The topology and structure of these hydrophobic, multi-transmembrane-spanning proteins are beginning to be understood.
Effect of porosity and pore size on microstructures and mechanical properties of poly‐ε‐caprolactone‐ hydroxyapatite composites (2008)

The influence of variant pore-size and porosity on the microstructure and the mechanical properties of poly-epsilon-caprolactone (PCL) and hydroxyapatite (HA) composite were examined for an optimal scaffold in bone tissue engineering. Three various amounts of sodium chloride (NaCl, as porogens) with two distinct particle size ranges (212-355 mum and 355-600 mum) were blended into PCL and HA mixture, followed by a leaching technique to generate PCL-HA scaffolds with various pores and porosity. The porosities of the scaffolds were correlated with the porogen size and concentration. The morphological properties of the resulting scaffolds were assessed by micro-computerized tomography (muCT), scanning electron microscopy (SEM), and energy dispersive X-ray analysis (EDX). Extensive PCL-HA pore interconnections with thinner pore walls were present in scaffolds with higher concentration (4:1 w/w) and larger particulate of porogen used in the fabrication process. Embedding of HA particles in the scaffold resulted in rough surfaces on the composites. Instron actuator testing indicated that the tensile strengths and Young's moduli of scaffolds were influenced by both the porosities and pore sizes of the scaffold. It was apparent that increasing the concentration of porogen compromised the mechanical properties; and a larger porogen particle size led to increased tensile strength but a reduction in Young's modulus. Overall, the data indicated that modification of the concentration and particle size of porogen altered the porous features and mechanical strength of HA-PCL scaffolds. This provided means to manipulate the properties of biocompatible cell-supporting scaffolds for use as bone graft substitutes.
Management of Chronic Discogenic Low Back Pain With a Thermal Intradiscal Catheter (2000)

A statistically significant improvement in functional outcome was obtained in patients with chronic discogenic low back pain treated thermally by the SpineCath.
Optimal Scheduling of Multicluster Tools With Constant Robot Moving Times, Part II: Tree-Like Topology Configurations (2010)

In this paper, we analyze optimal scheduling of a tree-like multicluster tool with single-blade robots and constant robot moving times. We present a recursive minimal cycle time algorithm to reveal a multi-unit resource cycle for multicluster tools under a given robot schedule. For a serial-cluster tool, we provide a closed-form formulation for the minimal cycle time. The formulation explicitly provides the interaction relationship among clusters. We further present decomposition conditions under which the optimal scheduling of multicluster becomes much easier and straightforward. Optimality conditions for the widely used robot pull schedule are also provided. An example from industry production is used to illustrate the analytical results. The decomposition and optimality conditions for the robot pull schedule are also illustrated by Monte Carlo simulation for the industrial example.
Antigen-receptor cross-linking and lipopolysaccharide trigger distinct phosphoinositide 3-kinase-dependent pathways to NF-κB activation in primary B cells (2001)

The NF-kappaB/Rel transcription factors play an important role in the expression of genes involved in B cell development, differentiation and function. Nuclear NF-kappaB is induced in B cells by engagement of either the BCR or CD40 or by stimulation with lipopolysaccharide (LPS). Despite the importance of NF-kappaB to B cell function, little is known about the signaling pathways leading to NF-kappaB activation. In this report we address the role of phosphoinositide 3'-kinase (PI 3-kinase) in BCR- and LPS-induced NF-kappaB activation using populations of primary murine resting B cells. Using the specific pharmacological inhibitors of PI 3-kinase, Wortmannin and LY294002, we demonstrate that PI 3-kinase activity is vital for BCR-induced NF-kappaB DNA-binding activity. Furthermore, we show that this is achieved via protein kinase C-dependent degradation of IkappaBalpha. Similar analyses reveal that PI 3-kinase is also critical in triggering NF-kappaB DNA-binding activity and IkappaBalpha degradation following LPS stimulation. Interestingly, a PKC inhibitor which blocked the BCR-induced IkappaBalpha degradation had no effect on the degradation of IkappaBalpha after LPS stimulation. Taken together, our results indicate the involvement of PI 3-kinase in at least two distinct signaling pathways leading to activation of NF-kappaB in B cells.