gebhart/patrepeval huggingface dataset:
The AGE‐receptor in the pathogenesis of diabetic complications (2001)

Native glucose-derived glycation derivatives (advanced glycation end products, AGE) in vascular, renal and neuronal tissues contribute to organ damage. Glycation derivatives include a number of chemically and cell-reactive substances, also termed glycoxidation products or glycotoxins (GT). Cell-associated AGE-specific receptors (AGE-Rs), AGE-R1-3, RAGE, as well as the scavenger receptors ScR-II and CD-36 that are present on vascular, renal, hemopoietic, and neuronal/glial cells, serve in the regulation of AGE uptake and removal. AGE-Rs also modulate cell activation, growth-related mediators, and cell proliferation, consequently influencing organ structure/function. This occurs via oxidant stress triggered via receptor-dependent or -independent pathways, and leads to signal activation pathways, resulting in pro-inflammatory responses. In susceptible individuals, the AGE-R expression/function may be subject to environmental or gene-related modulation, which in turn may influence tissue-specific gene functions. In this context, altered expression and activity of AGE-R components has recently been found in both mouse diabetes models and humans with diabetic complications. Although several gene polymorphisms are detected in most AGE-R components, no significant correlation to diabetic complications has as yet been found. Further investigation is underway to define whether primary or secondary genetic links of pathogenic significance exist in this system. Various AGE-binding peptides or soluble receptors have emerged as potential sequestering agents for toxic AGEs as potential therapies for diabetic complications.
Sub-micrometer Conducting Polyaniline Tubes Prepared from Polymer Fiber Templates (2004)

Polyaniline tubes have been prepared using sub-micrometer polymer fibers as templates. The core fibers were fabricated by a nonmechanical electrostatic process known as electrospinning. Conductive polyaniline (PANi) was coated on the surface of preformed polymer nanofibers through in situ deposition. The removal of the core from the resulting PANi coaxial fibers by pyrolysis leads to the formation of PANi tubular materials, which undergo reversible doping between the conducting and insulating phase with acid or base.
Nucleation-controlled polymerization of human monoclonal immunoglobulin G cryoglobulins. (1982)

The kinetics of the polymerization of human monoclonal cryoimmunoglobulins at low temperature was investigated in temperature jump experiments by monitoring the changes in turbidity resulting from the scattering of incident light by the polymers. Above a critical concentration between 2 and 3 mg/ml, depending on the ionic strength, the kinetics were characterized by a concentration-dependent lag phase and initial rate of self-assembly. Under equilibrium conditions which favored polymerization, the only stable intermediate detected by analytical ultracentrifugation was the dimer. Although purified monomers were unable to self-associate at 4 degrees C, addition of trace amounts of autologous dimers promoted polymerization. The apparent rate of polymerization was shown to be slow (k = 4.7 X 10(-4) M-1 s-1), and the process was governed by an equilibrium constant of 4.6 X 10(4) M-1. The initial rate of self-assembly was proportional to the product of the monomer concentration and the concentration of promoter (i.e. dimer). The rate of depolymerization was three orders of magnitude greater than the rate of polymerization and was proportional to the concentration of polymers present. These results suggest that the polymerization of monoclonal cryoimmunoglobulins is a nucleation-controlled process in which dimerization is the rate-limiting step. Kinetic studies on the polymerization of Fab and F(ab')2 fragments from cryoimmunoglobulins and a comparison of cryogel ultrastructure by electron microscopy suggested that the interaction site between monomers is located in the Fab region. Since the polymerization of monomers was only induced by autologous dimers and not dimers from other cryoimmunoglobulins, it was concluded that the hypervariable regions play a specific role in the condensation reaction. The fact that one cryoimmunoglobulin has a well defined antibody activity against streptolysin O argued against a low temperature-induced auto-anti-idiotype mechanism. Reduction of the interchain disulfide bonds of the Fab fragments abolished their ability to polymerize, probably by inducing a conformational change a considerable distance away in the variable domains of the molecules.
Hierarchical Aggregation for Information Visualization: Overview, Techniques, and Design Guidelines (2009)

We present a model for building, visualizing, and interacting with multiscale representations of information visualization techniques using hierarchical aggregation. The motivation for this work is to make visual representations more visually scalable and less cluttered. The model allows for augmenting existing techniques with multiscale functionality, as well as for designing new visualization and interaction techniques that conform to this new class of visual representations. We give some examples of how to use the model for standard information visualization techniques such as scatterplots, parallel coordinates, and node-link diagrams, and discuss existing techniques that are based on hierarchical aggregation. This yields a set of design guidelines for aggregated visualizations. We also present a basic vocabulary of interaction techniques suitable for navigating these multiscale visualizations.
Structure of Gramicidin A in a Lipid Bilayer Environment Determined Using Molecular Dynamics Simulations and Solid-State NMR Data (2003)

Two different high-resolution structures recently have been proposed for the membrane-spanning gramicidin A channel: one based on solid-state NMR experiments in oriented phospholipid bilayers (Ketchem, R. R.; Roux, B.; Cross, T. A. Structure 1997, 5, 1655-1669; Protein Data Bank, PDB:1MAG); and one based on two-dimensional NMR in detergent micelles (Townsley, L. E.; Tucker, W. A.; Sham, S.; Hinton, J. F. Biochemistry 2001, 40, 11676-11686; PDB:1JNO). Despite overall agreement, the two structures differ in peptide backbone pitch and the orientation of several side chains; in particular that of the Trp at position 9. Given the importance of the peptide backbone and Trp side chains for ion permeation, we undertook an investigation of the two structures using molecular dynamics simulation with an explicit lipid bilayer membrane, similar to the system used for the solid-state NMR experiments. Based on 0.1 micros of simulation, both backbone structures converge to a structure with 6.25 residues per turn, in agreement with X-ray scattering, and broad agreement with SS backbone NMR observables. The side chain of Trp 9 is mobile, more so than Trp 11, 13, and 15, and undergoes spontaneous transitions between the orientations in 1JNO and 1MAG. Based on empirical fitting to the NMR results, and umbrella sampling calculations, we conclude that Trp 9 spends 80% of the time in the 1JNO orientation and 20% in the 1MAG orientation. These results underscore the utility of molecular dynamics simulations in the analysis and interpretation of structural information from solid-state NMR.
Therapeutic Angiogenesis (1993)

We have proposed the term "therapeutic angiogenesis" to describe the induction or stimulation of neovascularization for the treatment or prevention of pathological clinical situations characterized by local hypovascularity. Evidence also shows that "clinically normal" healing and tissue regeneration can be improved or accelerated by therapeutic angiogenesis. Traditionally, therapeutic angiogenesis has been achieved by surgical methods, ie, the transposition of autologous tissues with uncompromised vasculature and high angiogenic potential such as omentum majus flaps and muscle flaps. Recent advances in the understanding of the biological process of neovascularization as well as the discovery and cloning of angiogenic cytokines may add a new clinical tool: therapeutic angiogenesis by pharmaceutical methods. Based on the results of animal studies and preliminary clinical trials, this review is aimed to give a state-of-the-art compilation of (1) those angiogenesis factors that appear promising in clinical application for therapeutic angiogenesis and (2) the surgical indication fields with near-term potential for therapeutic angiogenesis by use of angiogenic cytokines.
Circulating Angiogenesis Regulators in Cancer Patients (2001)

Although there are no known factors with established clinical utility, circulating angiogenesis regulators may be useful in several situations. They could be used to determine the risk of developing cancer, to screen for early detection, to distinguish benign from malignant disease, and to distinguish between different types of malignancies. In patients with established malignancies such factors might be used to determine prognosis, to predict the response to therapy, and to monitor the clinical course. Further investigations are warranted to assess the specific utility of each factor.
Inorganic and Organometallic Polymers (1988)

"Inorganic and organometallic" in the context of this Symposium is meant to describe macromolecules which usually contain inorganic elements in the chain and organic moieties as pendant groups. The subtitle delineates elements of primary focus: "Macromolecules Containing Silicon, Phosphorus and Other Inorganic Elements." The term "macromolecules" implies that the subject matter includes chain molecules that may be built up of repeat units, as well as more complex ring, branched, or crosslinked species (for example, see Organo-Oxo-Element Macromolecules Related to Sol-Gel Processes, and contributions by Murray (p. 408) or Seyferth (p. 143)).
Activation of stress response gene SIRT1 by BCR-ABL promotes leukemogenesis (2011)

The tyrosine kinase inhibitor imatinib is highly effective in the treatment of chronic myelogenous leukemia (CML), but primary and acquired resistance of CML cells to the drug offset its efficacy. Molecular mechanisms for resistance of CML to tyrosine kinase inhibitors are not fully understood. In the present study, we show that BCR-ABL activates the expression of the mammalian stress response gene SIRT1 in hematopoietic progenitor cells and that this involves STAT5 signaling. SIRT1 activation promotes CML cell survival and proliferation associated with deacetylation of multiple SIRT1 substrates, including FOXO1, p53, and Ku70. Imatinib-mediated inhibition of BCR-ABL kinase activity partially reduces SIRT1 expression and SIRT1 inhibition further sensitizes CML cells to imatinib-induced apoptosis. Knockout of SIRT1 suppresses BCR-ABL transformation of mouse BM cells and the development of a CML-like myeloproliferative disease, and treatment of mice with the SIRT1 inhibitor tenovin-6 deters disease progression. The combination of SIRT1 gene knockout and imatinib treatment further extends the survival of CML mice. Our results suggest that SIRT1 is a novel survival pathway activated by BCR-ABL expression in hematopoietic progenitor cells, which promotes oncogenic transformation and leukemogenesis. Our findings suggest further exploration of SIRT1 as a therapeutic target for CML treatment to overcome resistance.
Software Development for Rule-Based Spreadsheet Data Extraction and Transformation (2019)

The paper proposes a knowledge-based software platform to generate applications for spreadsheet data extraction and transformation. The platform includes a flexible table object model and a domain-specific language for expressing user-defined rules of table analysis and interpretation. They serve to represent knowledge of table layout and content features, as well as their interpretation, depended on transformation goals. The platform enables translating such user-defined rules to Java programs. The generated source code is serialized as a project prepared for building an executable application by using the Maven tool. The execution of the generated application transforms spreadsheet data from arbitrary form defined by the rules to the canonical one. The empirical results demonstrate the applicability of the software platform to develop applications for converting data from arbitrary spreadsheet tables originated from various domains to relational flat file databases.
Single‐Crystal Germanium Growth on Amorphous Silicon (2011)

Abstract Growing single‐crystal semiconductors directly on an amorphous substrate without epitaxy or wafer bonding has long been a significant fundamental challenge in materials science. Such technology is especially important for semiconductor devices that require cost‐effective, high‐throughput fabrication, including thin‐film solar cells and transistors on glass substrates as well as large‐scale active photonic circuits on Si using back‐end‐of‐line CMOS technology. This work demonstrates a CMOS‐compatible method of fabricating high‐quality germanium single crystals on amorphous silicon at low temperatures of &lt;450 °C. Grain orientation selection by geometric confinement of polycrystalline germanium films selectively grown on amorphous silicon by chemical vapor deposition is presented, where the confinement selects the fast‐growing grains for extended growth and eventually leads to single crystalline material. Germanium crystals grown using this method exhibit (110) texture and twin‐mediated growth. A model of confined growth is developed to predict the optimal confining channel dimensions for consistent, single‐crystal growth. Germanium films grown from one‐dimensional confinement exhibit a 200% grain size increase at 1 μm film thickness compared to unconfined films, while 2D confinement growth achieved single crystal Ge. The area of single crystalline Ge on amorphous layers is only limited by the growth time. Significant enhancement in room temperature photoluminescence and reduction in residual carrier density have been achieved using confined growth, demonstrating excellent optoelectronic properties. This growth method is readily extensible to any materials system capable of selective non‐epitaxial deposition, thus allowing for the fabrication of devices from high‐quality single crystal material when only an amorphous substrate is available.
Directing Transition from Innate to Acquired Immunity: Defining a Role for IL-6 (2005)

Appropriate control of leukocyte recruitment and activation is a fundamental requirement for competent host defense and resolving inflammation. A pivotal event that defines the successful outcome of any inflammatory event is the transition from innate to acquired immunity. In IL-6 deficiency, this process appears defective, and a series of in vivo studies have documented important roles for IL-6 in both the resolution of innate immunity and the development of acquired immune responses. Within this review, particular attention will be given to the regulatory properties of the soluble IL-6 receptor and how its activity may affect chronic disease progression.
Blood Vessel Enhancement and Segmentation Using Wavelet Transform (2009)

Retinal vessel segmentation is an essential step for the diagnoses of various eye diseases. An automated tool for blood vessel segmentation is useful to eye specialists for purpose of patient screening and clinical study. Vascular pattern is normally not visible in retinal images. In this paper, we present a method forenhancing, locating and segmenting blood vessels in images of retina. We present a method that uses 2-D Gabor wavelet and sharpening filter to enhance and sharpen the vascular pattern respectively. This technique locates and segments the blood vessels using edge detection algorithm and morphological operations. This technique is tested on publicly available STARE database of manually labeled images which has been established to facilitate comparative studies on segmentation of blood vessels in retinal images. The validation of our retinal image vessel segmentation technique is supported by experimental results.
[Commemorative lecture of receiving Imamura Memorial Prize. II. Mode of action of oligonucleotide fraction extracted from Mycobacterium bovis BCG]. (1994)

A fraction extracted from Mycobacterium bovis BCG was found to exhibit strong antitumor activity. This fraction, which was designated MY-1, caused some animal tumors to regress and/or prevent metastasis very effectively. MY-1 after digestion with DNase had almost completely reduced activity, while MY-1 digested with RNase did not. MY-1 also augmented natural killer (NK) cell activity of mouse spleen cells in vitro, and produced factors which showed anti-viral activity and rendered macrophages cytotoxic towards tumor cells. The function of the factor to activate macrophages was destroyed by treatment with anti-interferon (IFN)-gamma antibody, while the anti-viral activity was destroyed by treatment with anti-INF alpha/beta antibody. The oligonucleotides contained in MY-1 distributed in a broad range of molecular size, and peaked at 45 nucleotides. We synthesized 13 kinds of 45-mer nucleotides with sequence present in the known cDNA encoding various BCG proteins. Six out of these oligonucleotides, which contained one or more hexameric palindromic structures, showed strong antitumor activity, while the other without palindrome did not. These active oligonucleotides possessed the capability to induce IFN and to augment NK cell activity of mouse spleen cells by coincubation in vitro. When a portion of the sequence of the inactive oligonucleotides was substituted with either palindromic sequence of GACGTC, AGCGCT or AACGTT, the oligonucleotide acquired the ability to augment NK activity. In contrast, the oligonucleotides substituted with another palindromic sequence such as ACCGGT was without effect. Furthermore, exchange of two neighboring mononucleotides within, but not outside, the active palindromic sequence destroyed the ability of the oligonucleotide to augment NK activity.(ABSTRACT TRUNCATED AT 250 WORDS)
Molecular cloning of a human macrophage lectin specific for galactose. (1990)

The murine Mac-2 protein is a galactose- and IgE-binding lectin secreted by inflammatory macrophages. We describe here the cloning and characterization of a cDNA representing the human homolog of Mac-2 (hMac-2). The amino acid sequence derived from the hMac-2 cDNA indicates that the protein is evolutionarily highly conserved, with 85% of its amino acid residues being similar to those in the murine homolog. This conservation is especially marked in the carboxyl-terminal lectin domain. The amino-terminal half of the protein is less conserved but still contains the repetitive proline-glycine-rich motif seen in the mouse protein. hMac-2 synthesized in vitro is recognized by the M3/38 monoclonal antibody to Mac-2 and binds to the desialylated glycoprotein asialofetuin and to laminin, a major component of basement membranes. These findings are discussed in the context of the potential functions of hMac-2.
Spatial engagement: The navigation of a novice teaching principal in a small rural community (2006)

This article proceeds from the contention that rural spaces presentparticular challenges for teaching principals of small schools. Thesechallenges are compounded for the novice principal in the first fewmonths of appointment (and perhaps even more so for females) whenit can often appear that “extraordinary spaces are emerging in ordinaryplaces” (Buchanan, 1997). We employ narrative accounts written inthe voice of a novice teaching principal to chronicle ways in which the(female) incumbent deals with and makes sense of the spatialinfluences on her work. We also examine how the incumbent’sconstruction of her professional identity is affected by her experiencesin the first few months of performing the role. The work concludeswith a discussion of the implications for the preparation anddevelopment of teaching principals who might encounter suchchallenging spaces.
Superconductor Digital Receiver Components (2005)

We have developed and experimentally demonstrated several new RSFQ circuits, designed as components for digital receivers that are being developed by HYPRES. The first circuit is a digital phase generator, which produces a periodic digital signal with a controllable phase shift. This signal is obtained by decimation of an external high frequency signal by a factor of 1024, and provides a controllable phase shift with digital precision of /spl pi//512. The second circuit, a precise digital static frequency divider, is capable of dividing of an input signal frequency by any integer value between 1 and 1024. The third circuit is a digital quadrature mixer performing digital downconversion of bit-stream data. This report presents results of experimental evaluation of these circuits at speeds in excess of 30 GHz.
Validation of Reference Genes for Gene Expression Studies in Virus-Infected Nicotiana benthamiana Using Quantitative Real-Time PCR (2012)

Nicotiana benthamiana is the most widely-used experimental host in plant virology. The recent release of the draft genome sequence for N. benthamiana consolidates its role as a model for plant-pathogen interactions. Quantitative real-time PCR (qPCR) is commonly employed for quantitative gene expression analysis. For valid qPCR analysis, accurate normalisation of gene expression against an appropriate internal control is required. Yet there has been little systematic investigation of reference gene stability in N. benthamiana under conditions of viral infections. In this study, the expression profiles of 16 commonly used housekeeping genes (GAPDH, 18S, EF1α, SAMD, L23, UK, PP2A, APR, UBI3, SAND, ACT, TUB, GBP, F-BOX, PPR and TIP41) were determined in N. benthamiana and those with acceptable expression levels were further selected for transcript stability analysis by qPCR of complementary DNA prepared from N. benthamiana leaf tissue infected with one of five RNA plant viruses (Tobacco necrosis virus A, Beet black scorch virus, Beet necrotic yellow vein virus, Barley stripe mosaic virus and Potato virus X). Gene stability was analysed in parallel by three commonly-used dedicated algorithms: geNorm, NormFinder and BestKeeper. Statistical analysis revealed that the PP2A, F-BOX and L23 genes were the most stable overall, and that the combination of these three genes was sufficient for accurate normalisation. In addition, the suitability of PP2A, F-BOX and L23 as reference genes was illustrated by expression-level analysis of AGO2 and RdR6 in virus-infected N. benthamiana leaves. This is the first study to systematically examine and evaluate the stability of different reference genes in N. benthamiana. Our results not only provide researchers studying these viruses a shortlist of potential housekeeping genes to use as normalisers for qPCR experiments, but should also guide the selection of appropriate reference genes for gene expression studies of N. benthamiana under other biotic and abiotic stress conditions.