gebhart/patrepeval huggingface dataset:
The Use of Nuclear Transfer to Produce Transgenic Pigs (2002)

Manipulation of the pig genome has the potential to improve pig production and offers powerful biomedical applications. Genetic manipulation of mammals has been possible for over two decades, but the technology available has proven both difficult and inefficient. The development of new techniques to enhance efficiency and overcome the complications of random insertion is of importance. Nuclear transfer combined with homologous recombination provides a possible solution: precise genetic modifications in the pig genome may be induced via homologous recombination, and viable offspring can be produced by nuclear transfer using cultured transfected cell lines. The technique is still ineffective, but it is believed to have immense potential. One area that would benefit from the technology is that of xenotransplantation: transgenic pigs are expected to be available as organ donors in the foreseeable future.
The quotient image: class-based re-rendering and recognition with varying illuminations (2001)

The paper addresses the problem of "class-based" image-based recognition and rendering with varying illumination. The rendering problem is defined as follows: Given a single input image of an object and a sample of images with varying illumination conditions of other objects of the same general class, re-render the input image to simulate new illumination conditions. The class-based recognition problem is similarly defined: Given a single image of an object in a database of images of other objects, some of them multiply sampled under varying illumination, identify (match) any novel image of that object under varying illumination with the single image of that object in the database. We focus on Lambertian surface classes and, in particular, the class of human faces. The key result in our approach is based on a definition of an illumination invariant signature image which enables an analytic generation of the image space with varying illumination. We show that a small database of objects-in our experiments as few as two objects-is sufficient for generating the image space with varying illumination of any new object of the class from a single input image of that object. In many cases, the recognition results outperform by far conventional methods and the re-rendering is of remarkable quality considering the size of the database of example images and the mild preprocess required for making the algorithm work.
Advances in clinical next-generation sequencing: target enrichment and sequencing technologies (2015)

The huge parallel sequencing capabilities of next generation sequencing technologies have made them the tools of choice to characterize genomic aberrations for research and diagnostic purposes. For clinical applications, screening the whole genome or exome is challenging owing to the large genomic area to be sequenced, associated costs, complexity of data, and lack of known clinical significance of all genes. Consequently, routine screening involves limited markers with established clinical relevance. This process, referred to as targeted genome sequencing, requires selective enrichment of the genomic areas comprising these markers via one of several primer or probe-based enrichment strategies, followed by sequencing of the enriched genomic areas. Here, the authors review current target enrichment approaches and next generation sequencing platforms, focusing on the underlying principles, capabilities, and limitations of each technology along with validation and implementation for clinical testing.
A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets (2008)

Well-defined relationships between oligonucleotide properties and hybridization signal intensities (HSI) can aid chip design, data normalization and true biological knowledge discovery. We clarify these relationships using the data from two microarray experiments containing over three million probes from 48 high-density chips. We find that melting temperature (T(m)) has the most significant effect on HSI while length for the long oligonucleotides studied has very little effect. Analysis of positional effect using a linear model provides evidence that the protruding ends of probes contribute more than tethered ends to HSI, which is further validated by specifically designed match fragment sliding and extension experiments. The impact of sequence similarity (SeqS) on HSI is not significant in comparison with other oligonucleotide properties. Using regression and regression tree analysis, we prioritize these oligonucleotide properties based on their effects on HSI. The implications of our discoveries for the design of unbiased oligonucleotides are discussed. We propose that isothermal probes designed by varying the length is a viable strategy to reduce sequence bias, though imposing selection constraints on other oligonucleotide properties is also essential.
Selective Enhancement of P-Type Calcium Currents by Isoproterenol in the Rat Amygdala (1998)

We investigated activation of beta-adrenergic receptor-adenylyl cyclase-cAMP cascade on the whole-cell voltage-dependent Ca2+ currents (ICa) in acutely isolated rat basolateral amygdala neurons. Application of beta-receptor agonist isoproterenol (Iso) caused a long-term enhancement of ICa. The effect of Iso was blocked by concurrent application of beta-receptor antagonist propranolol. However, delayed application of propranolol after the ICa enhancement did not affect Iso-induced potentiation, suggesting that the sustained effect was not caused by a slow washout of Iso. Nimodipine and omega-conotoxin-GVIA reduced the ICa by approximately 35 and approximately 29%, respectively, without reducing enhancement of ICa by Iso significantly. The modulation appeared to involve P-type current, because the enhancement was abolished after pretreatment with omega-agatoxin-IVA. Forskolin, an adenylyl cyclase activator, mimicked the action of Iso in enhancing ICa, and this effect was blocked by an inhibitor of cAMP cascade, indicating a cAMP-dependent mechanism. Iso also induced a long-term potentiation (LTP) of synaptic transmission, which could be prevented by P-type Ca2+ channel blockers. These results suggest that P-type Ca2+ channels were selectively upregulated in the basolateral amygdala neurons, and enhancement of P-type currents could contribute to presynaptic form of LTP.
Integrated on-chip Ba<inf>2</inf>Ti<inf>9</inf>O<inf>20</inf> dielectric resonator oscillator in GaAs technology (2009)

We report for the first time a 26 GHz K/Ka-band dielectric resonator oscillator (DRO) in 0.8 mum GaAs MESFET that had the Ba <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Ti <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">20</sub> dielectric resonator (DR) grown to the surface of the chip at a temperature of 150degC without destroying the devices of the IC. It was compared to a DRO that had a commercially available DR, Ba(Zn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/3</sub> Ta <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2/3</sub> )O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , epoxied to it. The Ba <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Ti <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">20</sub> DRO had a measured output power power of 5.68 dBm at 25.6 GHz and a phase noise of -114 dBc @ 1 MHz.
FGF21 treatment ameliorates alcoholic fatty liver through activation of AMPK-SIRT1 pathway (2014)

Fibroblast growth factor 21 (FGF21), a recently identified member of the FGF superfamily, is mainly secreted from the liver and adipose tissues and plays an important role in improving metabolic syndrome and homeostasis. The aim of this study is to evaluate the role of FGF21 in alcoholic fatty liver disease (AFLD) and to determine if it has a therapeutic effect on AFLD. In this paper, we tested the effect of FGF21 on alcohol-induced liver injury in a murine model of chronic ethanol gavage and alcohol-treated HepG2 cells. Male KM mice received single dose of 5 g/kg ethanol gavage every day for 6 weeks, which induced significant fatty liver and liver injury. The alcohol-induced fatty liver cell model was achieved by adding ethanol into the medium of HepG2 cell cultures at a final concentration of 75 mM for 9 days. Results showed that treatment with recombinant FGF21 ameliorated alcoholic fatty liver and liver injury both in a murine model of chronic ethanol gavage and alcohol-treated HepG2 cells. In addition, FGF21 treatment down-regulated the hepatic expression of fatty acid synthetic key enzyme, activated hepatic AMPK-SIRT1 pathway and significantly down-regulated hepatic oxidative stress protein. Taken together, FGF21 corrects multiple metabolic parameters of AFLD in vitro and in vivo by activation of the AMPK-SIRT1 pathway.
Standard for the transmission of IP datagrams over public data networks (1983)

This RFC specifies a standard adopted by CSNET, the VAN gateway, and
other organizations for the transmission of IP datagrams over the
X.25-based public data networks.
Histone Deacetylase 7 Silencing Alters Endothelial Cell Migration, a Key Step in Angiogenesis (2007)

Global inhibition of class I and II histone deacetylases (HDACs) impairs angiogenesis. Herein, we have undertaken the identification of the specific HDAC(s) with activity that is necessary for the development of blood vessels. Using small interfering RNAs, we observed that HDAC7 silencing in endothelial cells altered their morphology, their migration, and their capacity to form capillary tube-like structures in vitro but did not affect cell adhesion, proliferation, or apoptosis. Among several factors known to be involved in angiogenesis, platelet-derived growth factor-B (PDGF-B) and its receptor (PDGFR-beta) were the most upregulated genes following HDAC7 silencing. We demonstrated that their increased expression induced by HDAC7 silencing was partially responsible for the inhibition of endothelial cell migration. In addition, we have also shown that treatment of endothelial cells with phorbol 12-myristate 13-acetate resulted in the exportation of HDAC7 out of the nucleus through a protein kinase C/protein kinase D activation pathway and induced, similarly to HDAC7 silencing, an increase in PDGF-B expression, as well as a partial inhibition of endothelial cell migration. Collectively, these data identified HDAC7 as a key modulator of endothelial cell migration and hence angiogenesis, at least in part, by regulating PDGF-B/PDGFR-beta gene expression. Because angiogenesis is required for tumor progression, HDAC7 may represent a rational target for therapeutic intervention against cancer.
THE USE OF LEAD CITRATE AT HIGH pH AS AN ELECTRON-OPAQUE STAIN IN ELECTRON MICROSCOPY (1963)

Aqueous solutions of lead salts (1, 2) and saturated
eXtreme chirped pulse amplification-beyond the fundamental energy storage limit of semiconductor optical amplifiers (2006)

In this paper, we propose a novel method, called "eXtreme chirped pulse amplification (X-CPA)," to overcome the fundamental energy storage limit of a semiconductor optical amplifier. The method is studied numerically and experimentally. Based on the X-CPA concept, 1.4-kW record peak power is generated from an all-semiconductor X-CPA system. Prior to an extreme pulse compression stage, greater than microjoules output energies of 20 ns extremely stretched pulses are extracted from a flared semiconductor optical amplifier.
Determinants of Substrate Specificity in ω-Aminotransferases (2005)

Ornithine aminotransferase and 4-aminobutyrate aminotransferase are related pyridoxal phosphate-dependent enzymes having different substrate specificities. The atomic structures of these enzymes have shown (i) that active site differences are limited to the steric positions occupied by two tyrosine residues in ornithine aminotransferase and (ii) that, uniquely among related, structurally characterized aminotransferases, the conserved arginine that binds the alpha-carboxylate of alpha-amino acids interacts tightly with a glutamate residue. To determine the contribution of these residues to the specificities of the enzymes, we analyzed site-directed mutants of ornithine aminotransferase by rapid reaction kinetics, x-ray crystallography, and 13C NMR spectroscopy. Mutation of one tyrosine (Tyr-85) to isoleucine, as found in aminobutyrate aminotransferase, decreased the rate of the reaction of the enzyme with ornithine 1000-fold and increased that with 4-aminobutyrate 16-fold, indicating that Tyr-85 is a major determinant of specificity toward ornithine. Unexpectedly, the limiting rate of the second half of the reaction, conversion of ketoglutarate to glutamate, was greatly increased, although the kinetics of the reverse reaction were unaffected. A mutant in which the glutamate (Glu-235) that interacts with the conserved arginine was replaced by alanine retained its regiospecificity for the delta-amino group of ornithine, but the glutamate reaction was enhanced 650-fold, whereas only a 5-fold enhancement of the ketoglutarate reaction rate resulted. A model is proposed in which conversion of the enzyme to its pyridoxamine phosphate form disrupts the internal glutamate-arginine interaction, thus enabling ketoglutarate but not glutamate to be a good substrate.
Advanced Anode Materials for Li-Ion Batteries (1998)

reported that graphite electrodes are capable of reversible reactions involving the intercalation and de-intercalation of Li ions.It was during the late 1970's that Armand and Touzain (44) reviewed the application of intercalation compounds for battery electrode materials.They suggested that some graphite intercalation compounds may be good candidates as cathode materials (positive electrode) in high-energy-density batteries.Experimental cell were constructed, and electrochemical results were obtained in Li/1 M LiC104fLiX cells (LiX = C2sAuCl3, C10CuCh, C21TiF4, C11FeCl3, C29CrCh).In addition, they suggested that ionic intercalation compounds, such as alkali metal compounds that include K and Li, could be used as an anode material (negative electrode).In 1979, Pfluger et al. (45) demonstrated that highly oriented pyrolytic graphite (HOPG, Union Carbide) can be electrochemically intercalated with Li in a nonaqueous electrolyte containing a Li salt to form different compounds such as LiC6 and LiCt2 They observed that intercalation of Li in HOPG produced a color change from black to golden yellow by applying a voltage of 3-5 V. On reversing the polarity, the HOPG changed color from golden yellow to black.These experiments demonstrated the electrochromic effect based on Li intercalation of graphite.In the early 1980's, two U.S. Patents were issued to Basu (46,47) which described the use of Li-intercalated graphite (LiC6) for electrodes in molten salt (LiCl or LiCl-KCl) and nonaqueous (1,3-dioxolane) batteries.These patents were followed by other U.S. patents in the mid 1980's, and a large number of U.S. patents were issued in the 1990's.Of the many U.S. patents on carbon materials for Li-ion cells, the largest number is issued to Japanese companies.Following this trend has been the proliferation in the number of technical publications since about 1985 by Japanese researchers (included in Figure 1), about three times greater than the number of publications from U.S. researchers.This may help explain the dominance of Japanese companies in the commercialization ofLi-ion cells for the consumer market. STRUCTURE OF CARBON AND LITHIATED CARBONA detailed discussion on the physicochemical properties of carbons for electrochemical applications is presented by Kinoshita ( 48).Therefore, only a brief summary of the physicochemical properties of carbon is presented here.
Retroviral gene therapy with an immunoglobulin-antigen fusion construct protects from experimental autoimmune uveitis (2000)

Immunoglobulins can serve as tolerogenic carriers for antigens, and B cells can function as tolerogenic antigen-presenting cells. We used this principle to design a strategy for gene therapy of experimental autoimmune uveitis, a cell-mediated autoimmune disease model for human uveitis induced with the uveitogenic interphotoreceptor retinoid-binding protein (IRBP). A retroviral vector was constructed containing a major uveitogenic IRBP epitope in frame with mouse IgG1 heavy chain. This construct was used to transduce peripheral B cells, which were infused into syngeneic recipients. A single infusion of transduced cells, 10 days before uveitogenic challenge, protected mice from clinical disease induced with the epitope or with the native IRBP protein. Protected mice had reduced antigen-specific responses, but showed no evidence for a classic Th1/Th2 response shift or for generalized anergy. Protection was not transferable, arguing against a mechanism dependent on regulatory cells. Importantly, the treatment was protective when initiated 7 days after uveitogenic immunization or concurrently with adoptive transfer of primed uveitogenic T cells. We suggest that this form of gene therapy can induce epitope-specific protection not only in naive, but also in already primed recipients, thus providing a protocol for treatment of established autoimmunity.
[IFN-tau, a new interferon type I with antiretroviral activity]. (1999)

Type I interferon (IFN) such as IFN-alpha have demonstrated relative efficiency in HIV-infected patients with Kaposi's sarcoma. Nevertheless, their clinical uses have been restricted by several major side effects. IFN-tau is a non-cytotoxic type I IFN. In the present manuscript, we described its in vitro effects towards HIV replication and its mode of action. IFN-tau is a potent antiviral molecule that interferes with an early step of HIV biological cycle. Moreover, it induces IL-6 synthesis by macrophages, and this cytokine favorises its antiviral efficacy, probably by amplifying the induction of 2', 5'OAS and RNase L. Altogether, these results confirm the interest of IFN-tau as adjuvant therapy in HIV infection, and more particularly in HIV/HCV-infected patients.
In Vitro Assembly of Alphavirus Cores by Using Nucleocapsid Protein Expressed in Escherichia coli (1999)

The production of the alphavirus virion is a multistep event requiring the assembly of the nucleocapsid core in the cytoplasm and the maturation of the glycoproteins in the endoplasmic reticulum and the Golgi apparatus. These components associate during the budding process to produce the mature virion. The nucleocapsid proteins of Sindbis virus and Ross River virus have been produced in a T7-based Escherichia coli expression system and purified. In the presence of single-stranded but not double-stranded nucleic acid, the proteins oligomerize in vitro into core-like particles which resemble the native viral nucleocapsid cores. Despite their similarities, Sindbis virus and Ross River virus capsid proteins do not form mixed core-like particles. Truncated forms of the Sindbis capsid protein were used to establish amino acid requirements for assembly. A capsid protein starting at residue 19 [CP(19-264)] was fully competent for in vitro assembly, whereas proteins with further N-terminal truncations could not support assembly. However, a capsid protein starting at residue 32 or 81 was able to incorporate into particles in the presence of CP(19-264) or could inhibit assembly if its molar ratio relative to CP(19-264) was greater than 1:1. This system provides a basis for the molecular dissection of alphavirus core assembly.
FlowNet: Learning Optical Flow with Convolutional Networks (2015)

Convolutional neural networks (CNNs) have recently been very successful in a variety of computer vision tasks, especially on those linked to recognition. Optical flow estimation has not been among the tasks CNNs succeeded at. In this paper we construct CNNs which are capable of solving the optical flow estimation problem as a supervised learning task. We propose and compare two architectures: a generic architecture and another one including a layer that correlates feature vectors at different image locations. Since existing ground truth data sets are not sufficiently large to train a CNN, we generate a large synthetic Flying Chairs dataset. We show that networks trained on this unrealistic data still generalize very well to existing datasets such as Sintel and KITTI, achieving competitive accuracy at frame rates of 5 to 10 fps.
Fabrication of Poly(ethylene glycol) Hydrogel Microstructures Using Photolithography (2001)

The fabrication of hydrogel microstructures based upon poly(ethylene glycol) diacrylates, dimethacrylates, and tetraacrylates patterned photolithographically on silicon or glass substrates is described. A silicon/silicon dioxide surface was treated with 3-(trichlorosilyl)propyl methacrylate to form a self-assembled monolayer (SAM) with pendant acrylate groups. The SAM presence on the surface was verified using ellipsometry and time-of-flight secondary ion mass spectrometry. A solution containing an acrylated or methacrylated poly(ethylene glycol) derivative and a photoinitiator (2,2-dimethoxy-2-phenylacetophenone) was spin-coated onto the treated substrate, exposed to 365 nm ultraviolet light through a photomask, and developed with either toluene, water, or supercritical CO2. As a result of this process, three-dimensional, cross-linked PEG hydrogel microstructures were immobilized on the surface. Diameters of cylindrical array members were varied from 600 to 7 micrometers by the use of different photomasks, while height varied from 3 to 12 micrometers, depending on the molecular weight of the PEG macromer. In the case of 7 micrometers diameter elements, as many as 400 elements were reproducibly generated in a 1 mm2 square pattern. The resultant hydrogel patterns were hydrated for as long as 3 weeks without delamination from the substrate. In addition, micropatterning of different molecular weights of PEG was demonstrated. Arrays of hydrogel disks containing an immobilized protein conjugated to a pH sensitive fluorophore were also prepared. The pH sensitivity of the gel-immobilized dye was similar to that in an aqueous buffer, and no leaching of the dye-labeled protein from the hydrogel microstructure was observed over a 1 week period. Changes in fluorescence were also observed for immobilized fluorophore labeled acetylcholine esterase upon the addition of acetyl acholine.
Laser-diode-stimulated emission depletion microscopy (2003)

We report subdiffraction resolution in far-field fluorescence microscopy through laser-diode-stimulated emission depletion of molecular markers. The diode-generated focal intensities lead to a resolution improvement by ∼45% in both lateral directions. Excitation and stimulated emission are performed with electronically synchronized diode pulses of 50–70 ps and 300–400 ps duration, respectively. The subdiffraction resolution is utilized to resolve neighboring individual molecules.