gebhart/patrepeval huggingface dataset:
A Human Torque Teno Virus Encodes a MicroRNA That Inhibits Interferon Signaling (2013)

Torque teno viruses (TTVs) are a group of viruses with small, circular DNA genomes. Members of this family are thought to ubiquitously infect humans, although causal disease associations are currently lacking. At present, there is no understanding of how infection with this diverse group of viruses is so prevalent. Using a combined computational and synthetic approach, we predict and identify miRNA-coding regions in diverse human TTVs and provide evidence for TTV miRNA production in vivo. The TTV miRNAs are transcribed by RNA polymerase II, processed by Drosha and Dicer, and are active in RISC. A TTV mutant defective for miRNA production replicates as well as wild type virus genome; demonstrating that the TTV miRNA is dispensable for genome replication in a cell culture model. We demonstrate that a recombinant TTV genome is capable of expressing an exogenous miRNA, indicating the potential utility of TTV as a small RNA vector. Gene expression profiling of host cells identifies N-myc (and STAT) interactor (NMI) as a target of a TTV miRNA. NMI transcripts are directly regulated through a binding site in the 3'UTR. SiRNA knockdown of NMI contributes to a decreased response to interferon signaling. Consistent with this, we show that a TTV miRNA mediates a decreased response to IFN and increased cellular proliferation in the presence of IFN. Thus, we add Annelloviridae to the growing list of virus families that encode miRNAs, and suggest that miRNA-mediated immune evasion can contribute to the pervasiveness associated with some of these viruses.
[Computer-assisted technologies in dentistry]. (1990)

The introduction and production of the Cerec-System was the first time, when a method of computer-aided design and manufacturing (CAD/CAM) of dental restorations moves to the chairside. New technologies like optical impression, solid modelling of crown shapes by CAD-Programs or computer controlled milling were acquired from the field of industrial production. Nevertheless, the Cerec-Systems is indicated only in a limited range of clinical situations, and the production of a well fitting computer-designed full crown is not yet possible at this stage of development. It can only be guessed whether these advancements will be achieved in the near future.
Photonic Signal Processing on Electronic Scales: Electro-Optical Field-Effect Nanoplasmonic Modulator (2012)

We develop a highly efficient approach for the modulation of photonic signals at the nanoscale, combining an ultrasubwavelength plasmonic guiding scheme with a robust electroabsorption effect in degenerate semiconductors. We numerically demonstrate an active electro-optical field-effect nanoplasmonic modulator with a revolutionary size of just 25 × 30 × 100 nm(3), providing signal extinction ratios as high as 2 at switching voltages of only 1 V. The design is compatible with complementary metal-oxide-semiconductor (CMOS) technology and allows low-loss insertion in standard plasmonic and Si-photonic circuitry.
Edit wear and read wear (1992)

We describe two applications that illustrate the idea of computational wear in the domain of document processing. By graphically depicting the history of author and reader interactions with documents, these applications offer otherwise unavailable information to guide work. We discuss how their design accords with a theory of professional work and an informational physics perspective on interface design.
Work, power and energy (1996)

When an elastic string, natural length a, modulus of elasticity λ, is stretched by a distance x, the tension in the string is \( T = \lambda \frac{x}{a} \).
Synthesis and properties of carboxymethyl cellulose‐graft‐poly(acrylic acid‐co‐acrylamide) as a novel cellulose‐based superabsorbent (2006)

Abstract A new cellulose‐based superabsorbent polymer, carboxymethyl cellulose‐ graft ‐poly(acrylic acid‐ co ‐acrylamide), was prepared by the free‐radical grafting solution polymerization of acrylic acid (AA) and acrylamide (AM) monomers onto carboxymethyl cellulose (CMC) in the presence of N,N ′‐methylenebisacrylamide as a crosslinker with a redox couple of potassium persulfate and sodium metabisulfite as an initiator. The influences of reaction variables such as the initiator content, crosslinker content, bath temperature, molar ratio of AA to AM, and weight ratio of the monomers to CMC on the water absorbency of the carboxymethylcellulose‐ graft ‐poly(acrylic acid‐ co ‐acrylamide) copolymer were investigated. The copolymer's structures were characterized with Fourier transform infrared spectroscopy. The optimum reaction conditions were obtained as follows: the bath temperature was 50°C; the molar ratio of AA to AM was 3 : 1; the mass ratio of the monomers to CMC was 4 : 1; and the weight percentages of the crosslinker and initiator with respect to the monomers were 0.75 and 1%, respectively. The maximum water absorbency of the optimized product was 920 g/g for distilled water and 85 g/g for a 0.9 wt % aqueous NaCl solution. In addition, the superabsorbent possessed good water retention and salt resistance. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 103: 1382–1388, 2007
Molecular Mechanisms of IL-2 Gene Regulation Following Costimulation Through LFA-1 (2001)

The integrin LFA-1 serves as an accessory molecule in T cell activation. In addition to its well-known role as an adhesion molecule, LFA-1 can contribute to T cell activation and up-regulation of IL-2 gene expression. However, the specific mechanisms by which LFA-1 influences T cell activation have not been elucidated. Therefore, we examined the impact of LFA-1:ICAM-1 interactions on transcriptional and posttranscriptional IL-2 gene regulation, using a costimulation-negative cell line transfected with MHC class II alone, or in combination with ICAM-1 or B7-1. IL-2 transcription was assessed utilizing transgenic mice expressing an IL-2 promoter luciferase reporter construct crossed to DO11.10 TCR-transgenic mice, and IL-2 mRNA stability was evaluated by real-time RT-PCR. Comparison of naive and previously activated T cells demonstrates a dramatic increase in IL-2-luciferase transcription in activated T cells that can, in part, be attributed to downstream signaling events. Costimulation through LFA-1 enhances transcription of the transgenic reporter construct across a wide Ag dose range, but does not affect IL-2 mRNA stability. In contrast, CD28 costimulation is clearly mediated through up-regulation of IL-2 transcription and through enhancement of mRNA stability. These results indicate that the primary pathway whereby engagement of LFA-1 through its ligand ICAM-1 up-regulates IL-2 gene expression is through enhanced IL-2 transcription, in the absence of any effect on IL-2 mRNA stabilization.
Spherical nanoporous LiCoPO4/C composites as high performance cathode materials for rechargeable lithium-ion batteries (2011)

Spherical nanoporous LiCoPO4/C composite microparticles were synthesized from soluble precursors by spray pyrolysis. They consisted of ∼70 nm primary particles agglomerated into micron-sized spheres with an average pore size of 68 nm and a 3–5 nm thick conformal carbon coating comprising 2.4% carbon by weight. The material delivered a reversible capacity of 123 mAh g−1 at C/10 rate, and showed excellent cycling behavior and rate capability. The good electrochemical performance is due to the presence of three-dimensional networks for both electronic and ionic transport.
Scattered Data Approximation (2004)

Many practical applications require the reconstruction of a multivariate function from discrete, unstructured data. This book gives a self-contained, complete introduction into this subject. It concentrates on truly meshless methods such as radial basis functions, moving least squares, and partitions of unity. The book starts with an overview on typical applications of scattered data approximation, coming from surface reconstruction, fluid-structure interaction, and the numerical solution of partial differential equations. It then leads the reader from basic properties to the current state of research, addressing all important issues, such as existence, uniqueness, approximation properties, numerical stability, and efficient implementation. Each chapter ends with a section giving information on the historical background and hints for further reading. Complete proofs are included, making this perfectly suited for graduate courses on multivariate approximation and it can be used to support courses in computer-aided geometric design, and meshless methods for partial differential equations.
Thrombopoietin-Induced Stimulation of Megakaryocyte- Enriched Bone Marrow Cultures (1979)

Liquid cultures of bone marrow cells enriched for megakaryocytes were assayed for incorporation of 3H-thymidine (3H-TdR) into acid-precipitable cell digests to determine the effect of thrombopoietin on DNA synthesis. As previously described, thrombopoietin was prepared by ammonium sulfate fractionation of pooled plasma obtained from thrombocytopenic rabbits. A control fraction was prepared from normal rabbit plasma. The thrombopoietic activity of these fractions was determined in vivo with normal rabbits as assay animals and the rate of incorporation of 75Se-selenomethionine into newly formed platelets as an index of thrombopoietic activity of the infused material. Guinea pig megakaryocytes were purified using bovine serum albumin gradients. Bone marrow cultures containing 1.5-3.0x104 cells and 31%-71% megakaryocytes were incubated 18 h in modified Dulbecco’s MEM containing 10% of the concentrated plasma fractions from either thrombocytopenic or normal rabbits. In other control cultures, 0.9% NaCl was substituted for the plasma fractions. 3H-TdR incorporation was measured after cells were incubated for 3 h with 1 μCi/ml. The protein fraction containing thrombopoietin-stimulating activity caused a 25%-31% increase in 3H-TdR incorporation over that in cultures which were incubated with the similar fraction from normal plasma and a 29% increase over the activity in control cultures to which 0.9% NaCl had been added. These data suggest that thrombopoietin stimulates DNA synthesis in megakaryocytes and that this tecnique may be useful in assaying thrombopoietin in vitro.
Inhibitory mechanisms of H+‐ATPase inhibitor bafilomycin A1 and carbonic anhydrase II inhibitor acetazolamide on experimental bone resorption (1996)

The effects of the vacuolar-type H(+)-ATPase inhibitor bafilomycin A1 (baf.A1) and the carbonic anhydrase II inhibitor acetazolamide (AZ) on bone resorption and procathepsin L secretion of rat osteoclasts were investigated using the bone slice assay method, pit formation test. Baf.A1 completely suppressed osteoclastic bone resorption stimulated by parathyroid hormone (PTH), but did not affect procathepsin L secretion, while AZ suppressed both bone resorption and procathepsin L secretion. These findings suggest that bone resorption by procathepsin L secretion and its processing are regulated by proton production and proton secretion.
Searching heterogeneous and distributed maritime databases: A technology prototype (2006)

[Extract] Much of the data from archaeological investigations reside in heterogeneous databases in separate locations with different formats and dissimilar structures. In addition, data from individual excavations and other research are frequently placed in databases that are maintained and accessed solely by the group responsible for the project. Due to the differing file formats, lack of access via a cohesive network, and issues regarding ownership and use of data, researchers have found it difficult to query multiple databases in order to perform cross-site analysis. In the past, the archaeological community has attempted to solve this problem by requiring that data by integrated into a central database, such as the National Shipwreck Database.
OpenFlow for Wireless Mesh Networks (2011)

Several protocols for routing and forwarding in Wireless Mesh Networks (WMN) have been proposed, such as AODV, OLSR or B.A.T.M.A.N. However, providing support for e.g. flow-based routing where flows of one source take different paths through the network is hard to implement in a unified way using traditional routing protocols. OpenFlow is an emerging technology which makes network elements such as routers or switches programmable via a standardized interface. By using virtualization and flow-based routing, OpenFlow enables a rapid deployment of novel packet forwarding and routing algorithms, focusing on fixed networks. We propose an architecture that integrates OpenFlow with WMNs and provides such flow-based routing and forwarding capabilities. To demonstrate the feasibility of our OpenFlow based approach, we have implemented a simple solution to solve the problem of client mobility in a WMN which handles the fast migration of client addresses (e.g. IP addresses) between Mesh Access Points and the interaction with re-routing without the need for tunneling. Measurements from a real mesh testbed (KAUMesh) demonstrate the feasibility of our approach based on the evaluation of forwarding performance, control traffic and rule activation time.
Potential Therapeutic Benefit of C1-Esterase Inhibitor in Neuromyelitis Optica Evaluated In Vitro and in an Experimental Rat Model (2014)

Neuromyelitis optica (NMO) is an autoimmune demyelinating disease of the central nervous system in which binding of anti-aquaporin-4 (AQP4) autoantibodies (NMO-IgG) to astrocytes causes complement-dependent cytotoxicity (CDC) and inflammation resulting in oligodendrocyte and neuronal injury. There is compelling evidence for a central role of complement in NMO pathogenesis. Here, we evaluated the potential of C1-esterase inhibitor (C1-inh) for complement-targeted therapy of NMO. C1-inh is an anti-inflammatory plasma protein with serine protease inhibition activity that has a broad range of biological activities on the contact (kallikrein), coagulation, fibrinolytic and complement systems. C1-inh is approved for therapy of hereditary angioedema (HAE) and has been studied in a small safety trial in acute NMO relapses (NCT 01759602). In vitro assays of NMO-IgG-dependent CDC showed C1-inh inhibition of human and rat complement, but with predicted minimal complement inhibition activity at a dose of 2000 units in humans. Inhibition of complement by C1-inh was potentiated by ∼10-fold by polysulfated macromolecules including heparin and dextran sulfate. In rats, intravenous C1-inh at a dose 30-fold greater than that approved to treat HAE inhibited serum complement activity by <5%, even when supplemented with heparin. Also, high-dose C1-inh did not reduce pathology in a rat model of NMO produced by intracerebral injection of NMO-IgG. Therefore, although C1r and C1s are targets of C1-inh, our in vitro data with human serum and in vivo data in rats suggest that the complement inhibition activity of C1-inh in serum is too low to confer clinical benefit in NMO.
IL-2 reverses established type 1 diabetes in NOD mice by a local effect on pancreatic regulatory T cells (2010)

Regulatory T cells (T reg cells) play a major role in controlling the pathogenic autoimmune process in type 1 diabetes (T1D). Interleukin 2 (IL-2), a cytokine which promotes T reg cell survival and function, may thus have therapeutic efficacy in T1D. We show that 5 d of low-dose IL-2 administration starting at the time of T1D onset can reverse established disease in NOD (nonobese diabetic) mice, with long-lasting effects. Low-dose IL-2 increases the number of T reg cells in the pancreas and induces expression of T reg cell-associated proteins including Foxp3, CD25, CTLA-4, ICOS (inducible T cell costimulator), and GITR (glucocorticoid-induced TNF receptor) in these cells. Treatment also suppresses interferon gamma production by pancreas-infiltrating T cells. Transcriptome analyses show that low-dose IL-2 exerts much greater influence on gene expression of T reg cells than effector T cells (T eff cells), suggesting that nonspecific activation of pathogenic T eff cells is less likely. We provide the first preclinical data showing that low-dose IL-2 can reverse established T1D, suggesting that this treatment merits evaluation in patients with T1D.
Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells (2013)

We examined the gene expression and DNA methylation of 49 human induced pluripotent stem cells (hiPSCs) and 10 human embryonic stem cells and found overlapped variations in gene expression and DNA methylation in the two types of human pluripotent stem cell lines. Comparisons of the in vitro neural differentiation of 40 hiPSCs and 10 human embryonic stem cells showed that seven hiPSC clones retained a significant number of undifferentiated cells even after neural differentiation culture and formed teratoma when transplanted into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression levels of several genes, including those expressed from long terminal repeats of specific human endogenous retroviruses. These data demonstrated a subset of hiPSC lines that have aberrant gene expression and defective potential in neural differentiation, which need to be identified and eliminated before applications in regenerative medicine.
Apoptosis mediated by the TNF-related cytokine and receptor families (1996)

T lymphocytes use several specialized mechanisms to induce apoptotic cell death. The tumor necrosis factor (TNF)-related family of membrane-anchored and secreted ligands represent a major mechanism regulating cell death and cell survival. These ligands also coordinate differentiation of tissue to defend against intracellular pathogens and regulate development of lymphoid tissue. Cellular responses are initiated by a corresponding family of specific receptors that includes two distinct TNFR (TNFR60 and TNFR80), Fas (CD95), CD40, p75NTF, and the recently identified lymphotoxin beta-receptor (LT beta R), among others. The MHC-encoded cytokines, TNF and LT alpha, form homomeric trimers, whereas LT beta assembles into heterotrimers with LT alpha, creating multimeric ligands with distinct receptor specificities. The signal transduction cascade is initiated by transmembrane aggregation (clustering) of receptor cytoplasmic domains induced by binding to their multivalent ligands. The TRAF family of Zn RING/finger proteins bind to TNFR80; CD40 and LT beta R are involved in induction NF kappa B and cell survival. TNFR60 and Fas interact with several distinct cytosolic proteins sharing the "death domain" homology region. TNF binding to TNFR60 activates a serine protein kinase activity and phosphoproteins are recruited to the receptor forming a multicomponent signaling complex. Thus, TNFRs use diverse sets of signaling molecules to initiate and regulate cell death and survival pathways.
Estimating positions and paths of moving objects (2002)

Several applications require support for representing and analyzing moving objects. Such applications include wildlife tracking, emergency dispatch, vehicle navigation, fleet management, storm tracking, and military applications to name a few. Enhanced data collection technologies such as high resolution satellite imagery, videogrammetry and GPS in combination with wireless communications are rapidly increasing the feasibility of obtaining information on moving objects and fueling new research and development. In these applications there is a need to efficiently answer questions about moving objects such as where they are at a specific time, where they have been in the past, where they will be in the future, and their relationships to static or other moving objects. Complete knowledge of object movements is not possible but movements can be predicted with some degree of reliability. Positions and paths of moving objects can be estimated from a set of observations. This paper reports on an approach that uses movement profiles, and movement histories in addition to observations to more reliably estimate positions and paths of moving objects.
Plant Pathogenesis-Related Proteins Induced by Virus Infection (1990)

The hypersensitive response triggered by an incompatible plant-pathogen interaction is accompanied by numerous metabolic changes (for reviews see 5, 8, 20, 37, 1 19). One general effect is the induction of enzymes that are involved in the synthesis of ethylene, a plant hormone able to induce many stress responses. The induction of enzymes from the phenylpropanoid path­ way, oxidative enzymes, and hydroxyproline-rich glycoproteins (HRGP; ex­ tensin) is partially related to cell wall modifications that lead to the formation of a physical barrier to further spread of the pathogen from the site of infection. Peroxidases are involved in the polymerization of alcohol de­ rivatives of aromatic compounds such as coumaric, ferulic, and sinapic acid into lignin and suberin and the cross-linking of these polyphenols to extensin molecules from the cell wall matrix. In addition to inducing a defense aimed at localizing the pathogen, various antimicrobial compounds are synthesized. These compounds include phytoalexins synthesized along branches of the phenylpropanoid pathway leading to furano-coumarins or isoflavonoids,
cDNA Cloning of a Trichoderma reesei Cellulase and Demonstration of Endoglucanase Activity by Expression in Yeast (1997)

A Trichoderma reesei cDNA encoding a previously unknown protein with a C-terminal cellulose-binding domain was obtained by complementation screening of a T. reesei cDNA library in a sec1 yeast mutant impaired in protein secretion. The T. reesei protein shows amino acid similarity over its entire length to the Agaricus bisporus cellulose-induced protein CEL1 whose function is not known. These two proteins form a new glycosyl hydrolase family, number 61. Expression of the T. reesei cDNA in yeast showed that it encoded a protein with endoglucanase activity and thus the protein was named EGIV and the corresponding gene egl4. Polyclonal antibodies were prepared against EGIV produced in Escherichia coli and detected a 56-kDa protein in the T. reesei culture supernatant. Northern hybridisation revealed that T. reesei egl4 is regulated in the same manner as other cellulase genes of this fungus.
CULTURAL ANDGENETICAPPROACHES TOMANAGINGMYCOTOXINS INMAIZE (2003)

Infection of maize kernels by toxigenic fungi remains a challenging problem despite decades of research progress. Cultural practices, including crop rotation, tillage, planting date, and management of irrigation and fertilization, have limited effects on infection and subsequent mycotoxin accumulation. Current infrastructure and grain storage practices in developed countries can prevent postharvest development of mycotoxins, but this aspect remains a threat in developing countries, especially in tropical areas. Because most mycotoxin problems develop in the field, strategies are needed to prevent infection of growing plants by toxigenic fungi. Developing genetic resistance to Aspergillus flavus, Gibberella zeae, and Fusarium spp. (particularly F. verticillioides) in maize is a high priority. Sources of resistance to each of these pathogens have been identified and have been incorporated into public and private breeding programs. However, few, if any, commercial cultivars have adequate levels of resistance. Efforts to control infection or mycotoxin development through conventional breeding and genetic engineering are reviewed. The role of transgenic insect control in the prevention of mycotoxins in maize is discussed.