gebhart/patrepeval huggingface dataset:
Production of medakafish chimeras from a stable embryonic stem cell line (1998)

Embryonic stem (ES) cell lines provide a unique tool for introducing targeted or random genetic alterations through gene replacement, insertional mutagenesis, and gene addition because they offer the possibility for in vitro selection for the desired, but extremely rare, recombinant genotypes. So far only mouse blastocyst embryos are known to have the competence to give rise to such ES cell lines. We recently have established a stable cell line (Mes1) from blastulae of the medakafish (Oryzias latipes) that shows all characteristics of mouse ES cells in vitro. Here, we demonstrate that Mes1 cells also have the competence for chimera formation; 90% of host blastulae transplanted with Mes1 cells developed into chimeric fry. This high frequency was not compromised by cryostorage or DNA transfection of the donor cells. The Mes1 cells contributed to numerous organs derived from all three germ layers and differentiated into various types of functional cells, most readily observable in pigmented chimeras. These features suggest the possibility that Mes1 cells may be a fish equivalent of mouse ES cells and that medaka can be used as another system for the application of the ES cell technology.
Disulfide bridges of a cysteine-rich repeat of the LDL receptor ligand-binding domain (1995)

The low density lipoprotein (LDL) receptor is the prototype of a family of structurally related cell surface receptors that mediate the endocytosis of multiple ligands in mammalian cells. Its ligand-binding domain consists of seven cysteine-rich ligand-binding repeats, each approximately 40 amino acid residues long. Ligand-binding repeats occur in other members of the LDL receptor (LDLR) gene family and in a number of functionally unrelated proteins. As a first step toward an understanding of the structure and function of LB repeats, we have expressed the amino-terminal ligand-binding repeat (LB1) of the human LDLR as a recombinant peptide (rLB1) and have determined its disulfide-pairing scheme. Oxidative folding of rLB1 yielded a single isomer which contained three disulfide bonds. This isomer reacted with a conformation-specific monoclonal antibody (IgG-C7) made to LB1 in the native LDLR, suggesting that rLB1 was correctly folded. rLB1 was resistant to digestion with trypsin, chymotrypsin, and V8 protease, consistent with a tightly folded structure. Disulfide bond connections were established using two separate approaches. Digestion with the nonspecific proteolytic enzyme proteinase K yielded an 8 amino acid peptide with a single disulfide bond which connected Cys(IV) and Cys(VI). In the second approach, disulfide bonds were sequentially reduced with tris(2-carboxyethyl)phosphine and the resulting cysteine residues alkylated with iodoacetamide. An analysis of peptides which contained two cysteinylacetamide residues, derived from a single reduced disulfide bond, showed that Cys(I) and Cys(III) were disulfide-bonded and confirmed the presence of a disulfide bond between Cys(IV) and Cys(VI). We infer that the remaining disulfide bond bridges Cys(II) and Cys(V).(ABSTRACT TRUNCATED AT 250 WORDS)
MSOCKS: an architecture for transport layer mobility (2002)

Mobile nodes of the future will be equiped with multiple network interfaces to take advantage of overlay networks, yet no current mobility systems provide full support for the simultaneous use of multiple interfaces. The need for such support arises when multiple connectivity options are available with different cost, coverage, latency and bandwidth characteristics, and applications want their data to flow over the interface that best matches the characteristics of the data. We present an architecture called transport layer mobility that allows mobile nodes to not only change their point of attachment to the Internet, but also to control which network interfaces are used for the different kinds of data leaving from and arriving at the mobile node. We implement our transport layer mobility scheme using a split connection proxy architecture and a new technique called TCP splice that gives split connection proxy systems the same end to-end semantics as normal TCP connections.
Calibration-free absolute quantification of optical absorption coefficients using acoustic spectra in 3D photoacoustic microscopy of biological tissue (2010)

Optical absorption is closely associated with many physiological important parameters, such as the concentration and oxygen saturation of hemoglobin, and it can be used to quantify the concentrations of nonfluorescent molecules. We propose a method to use acoustic spectra of photoacoustic signals to quantify the absolute optical absorption. This method is self-calibrating and thus insensitive to variations in the optical fluence. Factors such as system bandwidth and acoustic attenuation can affect the quantification but can be canceled by dividing the acoustic spectra measured at two optical wavelengths. Using optical-resolution photoacoustic microscopy, we quantified the absolute optical absorption of black ink samples with various concentrations. We also quantified both the concentration and oxygen saturation of hemoglobin in a live mouse in absolute units.
A 20/30 GHz personal access satellite system design (2003)

A strawman design for a personal access satellite system (PASS) to provide low-bit-rate voice and data services to users in the contiguous United States (CONUS) in the early 2000s using the 20/30 GHz band is presented. As currently envisaged, the PASS system links suppliers throughput CONUS with users in 142 fixed spot beams of 0.35 degrees beamwidth in one satellite hop; user-to-user communication requires two satellite hops. Through the use of time-division multiple access (TDMA) on the forward link and frequency-division multiple access (FDMA) on the return link, this system will support 2000 duplex voice channels at 4.8 kb/s with a satellite of moderate size and weight. For the user terminal, four antenna designs that trade-off compact size, cost, and electrical performance are described. Last, an experimentation plan taking advantage of planned Ka-band satellite capabilities is outlined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Survey of Text Summarization Extractive Techniques (2010)

Text Summarization is condensing the source text into a shorter version preserving its information content and overall meaning. It is very difficult for human beings to manually summarize large documents of text. Text Summarization methods can be classified into extractive and Abstractive summarization. An extractive summarization method consists of selecting important sentences, paragraphs etc. from the original document and concatenating them into shorter form. The importance of sentences is decided based on statistical and linguistic features of sentences. An Abstractive summarization method consists of understanding the original text and re-telling it in fewer words. It uses linguistic methods to examine and interpret the text and then to find the new concepts and expressions to best describe it by generating a new shorter text that conveys the most important information from the original text document. In this paper, a Survey of Text Summarization Extractive techniques has been presented.
The Multitasking Mast Cell: Positive and Negative Roles in the Progression of Autoimmunity (2007)

Among the potential outcomes of an aberrantly functioning immune system are allergic disease and autoimmunity. Although it has been assumed that the underlying mechanisms mediating these conditions are completely different, recent evidence shows that mast cells provide a common link. Mast cells reside in most tissues, are particularly prevalent at sites of Ag entry, and act as sentinel cells of the immune system. They express many inflammatory mediators that affect both innate and adaptive cellular function. They contribute to pathologic allergic inflammation but also serve an important protective role in bacterial and parasite infections. Given the proinflammatory nature of autoimmune responses, it is not surprising that studies using murine models of autoimmunity clearly implicate mast cells in the initiation and/or progression of autoimmune disease. In this review, we discuss the defined and hypothesized mechanisms of mast cell influence on autoimmune diseases, including their surprising and newly discovered role as anti-inflammatory cells.
Crystal structures of BaMgF4-xOx/2thin films (2001)

Abstract A chemical deposition method has been employed to synthesize BaMg4 thin films. Crystal structures of the grown thin films were found to be sensitive to thermal treatment conditions. Only the thin films heated at 550°C for 1 to 2 hours exhibited BaMgF4-type structure. Surface composition analysis indicated that anions in the thin films contained not only fluorine ions, but oxygen ions as well. The virtual composition of the thin films is thus BaMg4-xOx/2, instead of BaMgF4. The phase transformation and the crystal structures of BaMgF4-xOx/2 thin films at different synthesized temperatures were investigated. A new cubic structure of BaMgF4-xOx/2 was identified.
Phase Slips and Interfaces in D-Wave Superconductors (1999)

We consider a model (100) interface between two d-wave superconductors. By solving the Bogoliubov de Gennes equation on a tight binding lattice, we study the properties of the interface as a function of the interface barrier. We contrast the two scenarios: (i) an order parameter phase difference of $θ=0$ across the interface, and (ii) a phase slip of $θ=π$ across the interface. We find resonant sub-gap structure in the density of states only when there is a phase slip present. We show that the local s-wave and ``p-wave like'' order parameter components are strongly influenced by the barrier profile and by the phase slip. The temperature dependence of the local p-wave order parameter follows the underlying bulk $T_c$ for p-wave superconductivity implying that this could be measured by a suitable tunneling experiment. We also calculate the Josephson critical current as a function of the strength of the insulating barrier at the interface.
Matrix‐assisted laser desorption/ionization mass spectrometry of synthetic oligodeoxyribonucleotides (1992)

Abstract Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry has been used to mass analyze a variety of synthetic oligodeoxyribonucleotides ranging in size from 6 to 30 nucleotides. Molecular ions were observed almost exclusively, with little or no fragmentation and generally minor contributions from multiply charged species. Mixtures of poly d(T) 12–30 with low picomole amounts of each component gave well resolved peaks. These results are encouraging for the concept of DNA sequence analysis by mass spectrometry.
Reversal of ageing- and injury-induced vision loss by Tet-dependent epigenetic reprogramming (2019)

Ageing is a degenerative process leading to tissue dysfunction and death. A proposed cause of ageing is the accumulation of epigenetic noise, which disrupts youthful gene expression patterns that are required for cells to function optimally and recover from damage 1–3 . Changes to DNA methylation patterns over time form the basis of an ‘ageing clock’ 4, 5 , but whether old individuals retain information to reset the clock and, if so, whether this would improve tissue function is not known. Of all the tissues in the body, the central nervous system (CNS) is one of the first to lose regenerative capacity 6, 7 . Using the eye as a model tissue, we show that expression of Oct4, Sox2, and Klf4 genes (OSK) in mice resets youthful gene expression patterns and the DNA methylation age of retinal ganglion cells, promotes axon regeneration after optic nerve crush injury, and restores vision in a mouse model of glaucoma and in normal old mice. This process, which we call re co v ery of information v ia e pigenetic r eprogramming or REVIVER, requires the DNA demethylases Tet1 and Tet2, indicating that DNA methylation patterns don’t just indicate age, they participate in ageing. Thus, old tissues retain a faithful record of youthful epigenetic information that can be accessed for functional age reversal.
Association of IGF-I and IGF-II with myofiber regeneration in vivo (1999)

This study examined expression of insulinlike growth factor (IGF) in the myofibers and nonmyofibrillar structures of murine soleus muscle following contraction-induced damage. Identifying the cellular sources of this myogenic growth factor could improve muscle rehabilitation strategies. Immunohistochemical analysis of muscle sections indicated that the number of myofibers expressing both IGF-I and IGF-II increased significantly at 4, 7, and 10 days following injury, compared with control. Muscle spindles and vascular tissue expressed only IGF-II, and staining intensity did not change following injury. The number of fibers expressing developmental myosin heavy chain increased significantly at 7 and 10 days postinjury, and these usually coexpressed IGF. No IGF-specific staining of interstitial/inflammatory cells was observed. Therefore, expression of IGF after mechanically induced fiber damage occurs exclusively within regenerating fibers without supplemental delivery of IGF to the tissue by inflammatory cells or changes in constitutive expression of IGF-II in vascular tissue.
Design consideration and performance of a new MOS imaging device (1985)

The design considerations and performance of a new MOS imaging device with novel random noise suppression (RANS) circuits are described. This device consists of 492 × 388 photodiodes, a vertical shift register, and a horizontal BCD register integrated in p-wells. The RANS circuits accelerate the charge-transfer speed from vertical signal lines to a horizontal BCD register with 98-percent efficiency. They also decrease the effective signal line capacitance, so noise due to the transfer MOS switches is suppressed to obtain a high signal-to-noise ratio of 46 dB at a standard scene illumination of 180 lx (F1.4) with no image lag and blooming. Sweep out operation for the smear charge accumulated in the vertical signal lines realizes a sufficient signal-to-smear ratio of 69 dB at 1/10 vertical scene illumination.
Integrin linked kinase as a candidate downstream effector in proteinuria (2001)

ABSTRACT The kidney glomerulus is responsible for the generation of a protein‐free ultrafiltrate. After injury, it shows a characteristic, uniform response leading to progressive renal failure. Recent studies of hereditary proteinuric diseases have revealed mutations in molecules involved in podocyte cell‐cell and cell‐matrix interaction. Associated cellular signaling events activated in proteinuria have not been analyzed so far. To identify proteinuria‐induced molecules, we used mRNA differential display in glomeruli from children with congenital nephrotic syndrome of the Finnish type. An increase in integrin linked kinase (ILK) mRNA, a β 1 ‐integrin coupled serine threonine kinase, was identified. Observations suggest a role for ILK in glomerular failure. An up‐regulation of glomerular and Single‐podocyte ILK mRNA was found in two murine models of proteinuria. In cultured podocytes, integrin attachment to matrix inhibited ILK activity and podocyte damage with puromycin activated ILK. Stable overexpression of ILK in murine podocytes caused reduced matrix adhesion and led to considerable phenotype alteration compared with expression of a kinase‐defective ILK, paralleling aspects of in vivo podocyte damage. These results are consistent with ILK as a relevant player in the orchestration of podocyte matrix interaction and a candidate downstream regulator of podocyte permselectivity in glomerular diseases.
Novel cap analogs for in vitro synthesis of mRNAs with high translational efficiency (2004)

Synthetic analogs of the N7-methylated guanosine triphosphate cap at the 5' end of eukaryotic mRNAs and snRNAs have played an important role in understanding their splicing, intracellular transport, translation, and turnover. We report here a new series of N7-benzylated dinucleoside tetraphosphate analogs, b7Gp4G, b7m(3'-O)Gp4G, and b7m2Gp4G, that extend our knowledge of the role of the cap in translation. We used these novel analogs, along with 10 previously synthesized analogs, to explore five parameters: binding affinity to eIF4E, inhibition of cap-dependent translation in a rabbit reticulocyte lysate system, efficiency of incorporation into RNAs during in vitro transcription (% capping), orientation of the analog in the synthetic mRNA (% correct orientation), and in vitro translational efficiency of mRNAs capped with the analog. The 13 cap analogs differed in modifications of the first (distal) and second (proximal) guanine moieties, the first and second ribose moieties, and the number of phosphate residues. Among these were analogs of the naturally occurring cap m3(2,2,7)Gp3G. These compounds varied by 61-fold in affinity for eIF4E, 146-fold in inhibition of cap-dependent translation, 1.4-fold in % capping, and 5.6-fold in % correct orientation. The most stimulatory analog enhanced translation 44-fold compared with uncapped RNA. mRNAs capped with b7m2Gp4G, m7Gp3m7G, b7m(3'-OGp4G, and m7Gp4m7G were translated 2.5-, 2.6-, 2.8-, and 3.1-fold more efficiently than mRNAs capped with m7Gp3G, respectively. Relative translational efficiencies could generally be explained in terms of cap affinity for eIF4E, % capping, and % correct orientation. The measurement of all five parameters provides insight into factors that contribute to translational efficiency.
Apoptosis and Necrosis in the Liver: A Tale of Two Deaths? (2006)

Death of hepatocytes and other hepatic cell types is a characteristic feature of liver diseases as diverse as cholestasis, viral hepatitis, ischemia/reperfusion, liver preservation for transplantation and drug/toxicant-induced injury. Cell death typically follows one of two patterns: oncotic necrosis and apoptosis. Necrosis is typically the consequence of acute metabolic perturbation with ATP depletion as occurs in ischemia/reperfusion and acute drug-induced hepatotoxicity. Apoptosis, in contrast, represents the execution of an ATP-dependent death program often initiated by death ligand/death receptor interactions, such as Fas ligand with Fas, which leads to a caspase activation cascade. A common event leading to both apoptosis and necrosis is mitochondrial permeabilization and dysfunction, although the mechanistic basis of mitochondrial injury may vary in different settings. Prevention of these modes of cell death is an important target of therapy, but controversies still exist regarding which mode of cell death predominates in various forms of liver disease and injury. Resolution of these controversies may come with the recognition that apoptosis and necrosis frequently represent alternate outcomes of the same cellular pathways to cell death, especially for cell death mediated by mitochondrial permeabilization. An understanding of processes leading to liver cell death will be important for development of effective interventions to prevent hepatocellular death leading to liver failure and to promote cancer and stellate cell death in malignancy and fibrotic disease.
CHANGES IN CONCENTRATION OF PROSTAGLANDIN F AND STEROIDS IN HUMAN CORPORA LUTEA IN RELATION TO GROWTH OF THE CORPUS LUTEUM AND LUTEOLYSIS (1976)

Department of Obstetrics and Gynaecology, University of Sydney, NS. W. 2006, Australia (Received 13 July 1976) Prostaglandin F2α(PGF2α) secreted from the uterus exerts a luteolytic effect on the corpus luteum in a number of species of non-pregnant mammals (see review of Labhsetwar, 1974). This luteolytic mechanism has not been demonstrated in non-pregnant women (Lyneham, Korda, Shutt, Smith & Shearman, 1975). Nor were Leader, Bygdeman, Cekan, Diczfalusy, Guerrero, Martin & Wiqvist (1975) able to demonstrate an accelerative effect of intra-uterine 15 (S) 15-methyl PGF2α or an inhibitory effect of oral indomethacin on post-abortion luteolysis in women in early pregnancy. The presence of PGF2α receptors however, in human corpora lutea (Powell, Hammarström, Samuelsson & Sjöberg, 1974) suggested the possibility of a local production of PGF2α within the ovary being responsible for luteolysis in women, and Korda, Shutt, Smith, Shearman & Lyneham (1975) were able to obtain a transient luteolysis when 0·5–1·0 mg
Selection of an active single chain Fv antibody from a protein linker library prepared by enzymatic inverse PCR. (1993)

Enzymatic inverse PCR mutagenesis was developed as a simple and reliable method for the construction of large libraries of site-directed mutants. Enzymatic inverse PCR library mutagenesis uses a single PCR fragment and is restriction-site independent. The usefulness of the technique was demonstrated by the design of a single chain linker for an antibody Fv fragment without computer modeling. The Fv fragment of an antibody specific for a metal chelate was expressed in active form in the periplasm of E. coli. The light and the heavy chains of the Fv are expressed as a bicistronic mRNA. Enzymatic inverse PCR mutagenesis was used to construct a library of 3 x 10(5) Fv mutants, in which the C-terminus of the light chain was connected to the N-terminus of the heavy chain by a 15-amino acid peptide linker of variable composition. After plating, active mutant colonies were identified by screening colony filter lifts with a radiolabeled hapten, N'-(2-hydroxyethyl)-p-thioureidobenzyl EDTA. About 0.2% of the mutants were positive, and a selected sFv clone was shown to have the same affinity as the Fv (9 x 10(9)) and was similar to the whole antibody (11 x 10(9)). This example compares favorably with both of the other approaches to constructing sFv's; namely, molecularly modeled linkers as well as universal linkers, which have often yielded significantly lower affinities than whole antibodies or Fabs. The enzymatic inverse PCR library mutagenesis approach is simple and reliable and can be used to obtain linkers for the great majority of antibodies for which no structural data are available. More generally, it can be used to modify DNA coding for any structural protein or regulatory element.
Chronic Pulmonary Artery Pressure Elevation Is Insufficient to Explain Right Heart Failure (2009)

These data brought into question the commonly held concept that RV failure associated with pulmonary hypertension is due strictly to the increased RV afterload.
Structure−Activity Relationships of the p38α MAP Kinase Inhibitor 1-(5-tert-Butyl-2-p-tolyl-2H-pyrazol-3-yl)-3-[4-(2-morpholin-4-yl-ethoxy)naph- thalen-1-yl]urea (BIRB 796) (2003)

We report on the structure-activity relationships (SAR) of 1-(5-tert-butyl-2-p-tolyl-2H-pyrazol-3-yl)-3-[4-(2-morpholin-4-yl-ethoxy)naphthalen-1-yl]urea (BIRB 796), an inhibitor of p38alpha MAP kinase which has advanced into human clinical trials for the treatment of autoimmune diseases. Thermal denaturation was used to establish molecular binding affinities for this class of p38alpha inhibitors. The tert-butyl group remains a critical binding element by occupying a lipophilic domain in the kinase which is exposed upon rearrangement of the activation loop. An aromatic ring attached to N-2 of the pyrazole nucleus provides important pi-CH(2) interactions with the kinase. The role of groups attached through an ethoxy group to the 4-position of the naphthalene and directed into the ATP-binding domain is elucidated. Pharmacophores with good hydrogen bonding potential, such as morpholine, pyridine, and imidazole, shift the melting temperature of p38alpha by 16-17 degrees C translating into K(d) values of 50-100 pM. Finally, we describe several compounds that potently inhibit TNF-alpha production when dosed orally in mice.
Power Outage—It Came From Outer Space (1998)

This article draws a correlation between solar flares and power surges and outages. It lists the US Space Environment Center (SEC) internet web site as a source of solar activity information to give early warning of solar events significant enough to cause electrical disturbances.