gebhart/patrepeval huggingface dataset:
The RU5 (‘R’) region from human leukaemia viruses (HTLV‐1) contains an internal ribosome entry site (IRES)‐like sequence (1996)

RNA fragments containing the complete R region and the beginning of the U5 region ('R') from the human T cell leukaemia virus 1 (HTLV-1) stimulated the translation of the second cistrons in bicistronic mRNAs. The 5' untranslated region from SV40 early genes (SU) which was unable to stimulate translation of second cistrons amplified markedly the internal ribosome entry site (IRES) effect of the HTLV-1 'R' fragments. The 'R' regions from HTLV-1 have therefore properties similar to internal ribosome entry sites (IRES) originally found in picornavirus. The beginning of the U5 region from HTLV-1 contains a polypyrimidine sequence which is known to play an essential role in the IRES activity in picornavirus. The same experiments carried out using the 'R' region from bovine leukaemia virus (BLV) showed that this sequence has at most a weak IRES effect. One retroviruses, HTLV-1 and perhaps others contain therefore an IRES activity. Interestingly, the combined SU 'R' sequence worked efficiently with different cistrons, different promoters and in all tested cell lines, whereas the poliovirus IRES was active in CHO cells but not in the mouse mammary cell line HC11. The SU 'R' sequence may therefore preferably be used to generate active bicistronic mRNAs.
Anti-dsDNA antibodies cross-react with ribosomal P proteins expressed on the surface of glomerular mesangial cells to exert a cytostatic effect. (1995)

Affinity-purified human polyclonal anti-double-stranded DNA antibodies (anti-dsDNA) exerted a cytostatic effect towards human and rat glomerular mesangial cells (MC). In order to identify the cognate antigens for anti-dsDNA on the surface of MC, we used these autoantibodies to probe a human renal lambda gt11 cDNA expression library. Two cDNA clones encoding the cognate proteins for the autoantibodies were isolated. Sequencing analysis of the two cDNA showed that they had 98.6% homology with the gene of the P0 and 99.2% homology with the gene of the P1 human acidic ribosomal phosphoproteins (P protein). Two galactosidase fusion proteins (125,000 and 150,000 MW) derived from the two cDNA inserts expressed in lysogenic Escherichia coli Y1089 could react with the original screening antibodies in an immunoblotting analysis. After transformation and expression of the full-length P1 clone in prokaryotic cells, the purified P1 protein was able to react with anti-dsDNA. In a cross-inhibition experiment, the dsDNA binding activity of anti-dsDNA was inhibited by a synthetic polypeptide corresponding to the carboxyl-terminal 20 amino acids of P protein and purified P1 protein in a dose-dependent manner, but this was less potent than the inhibition caused by calf thymus dsDNA. By use of well-defined systemic lupus erythematosus (SLE) sera, we found only sera containing a high titre of anti-dsDNA activity (> 300 IU/ml) reacted with P1 of rat MC lysate. Furthermore, the 38,000 and 19,000 MW macromolecules were proved to be the cognate antigens for anti-dsDNA expression on the surface of the MC, by Western blot of the MC plasma membrane lysates. These results suggest that anti-dsDNA may cross-react with ribosomal P proteins expressed on the surface of the MC and exert cytostasis towards these cells.
Reversibility of neuropathology in Tay–Sachs-related diseases (2013)

The GM2 gangliosidoses are progressive neurodegenerative disorders due to defects in the lysosomal β-N-acetylhexosaminidase system. Accumulation of β-hexosaminidases A and B substrates is presumed to cause this fatal condition. An authentic mouse model of Sandhoff disease (SD) with pathological characteristics resembling those noted in infantile GM2 gangliosidosis has been described. We have shown that expression of β-hexosaminidase by intracranial delivery of recombinant adeno-associated viral vectors to young adult SD mice can prevent many features of the disease and extends lifespan. To investigate the nature of the neurological injury in GM2 gangliosidosis and the extent of its reversibility, we have examined the evolution of disease in the SD mouse; we have moreover explored the effects of gene transfer delivered at key times during the course of the illness. Here we report greatly increased survival only when the therapeutic genes are expressed either before the disease is apparent or during its early manifestations. However, irrespective of when treatment was administered, widespread and abundant expression of β-hexosaminidase with consequent clearance of glycoconjugates, α-synuclein and ubiquitinated proteins, and abrogation of inflammatory responses and neuronal loss was observed. We also show that defects in myelination occur in early life and cannot be easily resolved when treatment is given to the adult brain. These results indicate that there is a limited temporal opportunity in which function and survival can be improved-but regardless of resolution of the cardinal pathological features of GM2 gangliosidosis, a point is reached when functional deterioration and death cannot be prevented.
Study of Diet Recommendation System based on Fuzzy Logic and Ontology (2015)

People are becoming very conscious about their health.
The PDZ-Ligand and Src-Homology Type 3 Domains of Epidemic Avian Influenza Virus NS1 Protein Modulate Human Src Kinase Activity during Viral Infection (2011)

The Non-structural 1 (NS1) protein of avian influenza (AI) viruses is important for pathogenicity. Here, we identify a previously unrecognized tandem PDZ-ligand (TPL) domain in the extreme carboxy terminus of NS1 proteins from a subset of globally circulating AI viruses. By using protein arrays we have identified several human PDZ-cellular ligands of this novel domain, one of which is the RIL protein, a known regulator of the cellular tyrosine kinase Src. We found that the AI NS1 proteins bind and stimulate human Src tyrosine kinase, through their carboxy terminal Src homology type 3-binding (SHB) domain. The physical interaction between NS1 and Src and the ability of AI viruses to modulate the phosphorylation status of Src during the infection, were found to be influenced by the TPL arrangement. These results indicate the potential for novel host-pathogen interactions mediated by the TPL and SHB domains of AI NS1 protein.
Minimizing the Instant and Accumulative Effects of Salt Permeability to Sustain Ultrahigh Osmotic Power Density (2013)

We have investigated the instant and accumulative effects of salt permeability on the sustainability of high power density in the pressure-retarded osmosis (PRO) process experimentally and theoretically. Thin-film composite (TFC) hollow-fiber membranes were prepared. A critical wall thickness was observed to ensure sufficient mechanical stability and hence a low salt permeability, B. The experimental results revealed that a lower B was essential to enhance the maximum power density from 15.3 W/m(2) to as high as 24.3 W/m(2) when 1 M NaCl and deionized water were feeds. Modeling work showed that a large B not only causes an instant drop in the initial water flux but also accelerates the flux decline at high hydraulic pressures, leading to reduced optimal operating pressure and maximal power density. However, the optimal operating pressure to harvest energy can be greater than one-half of the osmotic pressure gradient across the membrane if one can carefully design a PRO membrane with a large water permeability, small B value, and reasonably small structural parameter. It was also found that a high B accumulates salts in the feed, leads to the oversalinization of the feed, and largely lowers both the water flux and power density along the membrane module. Therefore, a low salt permeability is highly desirable to sustain high power density not only locally but also throughout the whole module.
Embryonic stem cells as a cellular model for neuroectodermal commitment and skin formation (2007)

Embryonic stem (ES) cells can be differentiated into many cell types in vitro, thus providing a potential unlimited supply of cells for cognitive in vitro studies and cell-based therapy. We recently reported the efficient derivation of ectodermal and epidermal cells from murine ES cells. These differentiated ES cells were able to form, in culture, a multilayered epidermis coupled with an underlying dermal compartment, similar to native skin. We clarified the function of BMP-4 in the binary neuroectodermal choice by stimulating sox-1(+) neural precursors to undergo specific apoptosis while inducing epidermal differentiation through DeltaNp63 gene activation. We further demonstrated that DeltaNp63 enhances ES-derived ectodermal cell proliferation and is necessary for epidermal commitment. This unique cellular model further provides a powerful tool for identifying the molecular mechanisms controlling normal skin development and for investigating p63-ectodermal dysplasia human congenital pathologies.
Plasma CVD-Grown <sup>10</sup>B-Enriched Boron Films for Si Neutron Detectors (1990)

Hydrogenated amorphous boron (a-B:H) films were deposited on Si crystal substrates using DC glow discharge in B 2 H 6 diluted to 1000 ppm in H 2 . We found that the rate of the deposition was about two times higher for 10 B-enriched B 2 H 6 than for natural B 2 H 6 . The deposition process was observed by optical emission spectroscopy of the DC glow. BH emission lines at 433.2 nm and 369.4 nm were strongly enhanced in the 10 B-enriched B 2 H 6 /H 2 compared with the natural B 2 H 6 /H 2 . This manifests an isotopic effect on the deposition rate of the a-B:H film. Concentrations of 10 B, 11 B and 1 H in the films were analyzed by SIMS. The hydrogen content of the films was found to be 3.9 × 10 23 atoms/cm 3 from the thermal hydrogen release measured by gas chromatography. The 10 B-enriched film was applied to construct a novel silicon neutron detector. It showed a satisfactory sensitivity for neutron detection.
Queueing disciplines for integrated fast packet networks (2003)

The authors focus on the problem of internodal link queueing in integrated fast packet networks. The queueing discipline used to multiplex packets onto an internodal link is an important element in the overall bandwidth management of an integrated fast packet network. The characteristics of and quality of service required by different traffic classes are reviewed and used as the basis for comparing alternative queueing disciplines. A hybrid weighted round-robin and head-of-line priority discipline are shown to provide appropriate allocation of the internodal link bandwidth among different traffic classes, while allowing decay differentiation within a traffic class.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Cloning and tissue-specific expression of cDNAs for the human and mouse homologues of rat pancreatitis-associated protein (PAP) (1993)

The nucleotide sequences of cDNAs encoding human and mouse homologous for rat pancreatitis-associated protein (PAP) (J. Iovanna et al. (1991) J. Biol. Chem. 266, 24664-24669) were determined. The expression level of PAP mRNA was very low in healthy pancreas, but an unexpectedly high level was found in normal small intestine.
Survey of Photonic and Plasmonic Interconnect Technologies for Intra-Datacenter and High-Performance Computing Communications (2018)

Large scale data centers (DC) and high performance computing (HPC) systems require more and more computing power at higher energy efficiency. They are already consuming megawatts of power, and a linear extrapolation of trends reveals that they may eventually lead to unrealistic power consumption scenarios in order to satisfy future requirements (e.g., Exascale computing). Conventional complementary metal oxide semiconductor (CMOS)-based electronic interconnects are not expected to keep up with the envisioned future board-to-board and chip-to-chip (within multi-chip-modules) interconnect requirements because of bandwidth-density and power-consumption limitations. However, low-power and high-speed optics-based interconnects are emerging as alternatives for DC and HPC communications; they offer unique opportunities for continued energy-efficiency and bandwidth-density improvements, although cost is a challenge at the shortest length scales. Plasmonics-based interconnects on the other hand, due to their extremely small size, offer another interesting solution for further scaling operational speed and energy efficiency. At the device-level, CMOS compatibility is also an important issue, since ultimately photonics or plasmonics will have to be co-integrated with electronics. In this paper, we survey the available literature and compare the aforementioned interconnect technologies, with respect to their suitability for high-speed and energy-efficient on-chip and offchip communications. This paper refers to relatively short links with potential applications in the following interconnect distance hierarchy: local group of racks, board to board, module to module, chip to chip, and on chip connections. We compare different interconnect device modules, including low-energy output devices (such as lasers, modulators, and LEDs), photodetectors, passive devices (i.e., waveguides and couplers) and electrical circuitry (such as laserdiode drivers, modulator drivers, transimpedance, and limiting amplifiers). We show that photonic technologies have the potential to meet the requirements for selected HPC and DC applications in a shorter term. We also present that plasmonic interconnect modules could offer ultra-compact active areas, leading to high integration bandwidth densities, and low device capacitances allowing for ultra-high bandwidth operation that would satisfy the application requirements further into the future.
Excimer laser light induced ablation and reactions at polymer surfaces as measured with a quartz-crystal microbalance (1988)

We have developed a new technique to measure the etch rate of polymer films under the ablative photodecomposition condition obtained by absorption of the far-UV radiation of the excimer laser. The technique is based on the use of a quartz-crystal microbalance interfaced with a microcomputer. It has high accuracy (17 ng/cm2). Etch rates of poly(ethylene terephthalate), polycarbonate, and polystyrene were measured as a function of the laser intensity, at 193 and 248 nm. The etch rate in the region of the ablation threshold intensity is obtained precisely. A slow ablation regime between the threshold and the linear regime is evidenced. For polycarbonate and polystyrene, a reaction of the irradiated surface with molecular oxygen accelerates the ablation process at low fluence of the 248 nm radiation. The degradation reaction of poly(ethylene therephthalate) is monitored as a function of fluence by selective dissolution in acetone. A sudden increase of the degraded depth is seen at the transition between the two ablation regimes. This is attributed to the melting of the surface.
Levels of Phenolic Acids and Tanshinones in<i>Salvia miltiorrhiza</i>Bge. cv.<i>sativa</i>and<i>Salvia bowleyanae</i>Dunn Roots During Growth (2011)

Abstract Phenolic acids and tanshinones are the bioactive compounds in Salvia miltiorrhiza Bge. and Salvia bowleyanae Dunn, in which anti-cancer action, cardioprotection, hepatoprotection, and other activities have been extensively studied. In this study, we monitored phenolic acid and tanshinone levels in the two Salvia species roots during 12 months (mos.) of field trial. The fresh root weights peaked at 8 mos. of growth for both S. miltiorrhiza Bge. cv. sativa (533.0 ± 98.22 g) and S. bowleyanae Dunn (277.0 ± 34.00 g). Salvianolic acid B was the most abundant phenolic acid in the two Salvia species, peaking at 4–12 and 5–12 mos. of growth for S. miltiorrhiza Bge. cv. sativa (35.82 ± 8.51 mg/g db) and S. bowleyanae Dunn (52.5 ± 5.81 mg/gdb), respectively. The total tanshinone (dihydrotanshinone, cryptotanshinone, tanshinone I, and tanshinone IIA) levels peaked at 6–8 mos. of growth for both S. miltiorrhiza Bge. cv. sativa (10.23 mg/g) and S. bowleyanae Dunn (3.70 mg/g), and then gradually decreased. Salvia miltiorrhiza Bge. cv. sativa had both greater phenolic acid and tanshinone production. In conclusion, an optimum cultivation time of 8 mos. has been established for the two Salvia species to obtain the greatest yields of phenolic acids and tanshinones.
Immune Response to Hepatitis B Virus Proteins: Relevance of the Murine Model (1991)

The experimental murine models offer unique opportunities to study the genetic, cellular, and molecular basis for variable immune responsiveness to HBV-encoded antigens. The mouse has provided a means of studying the immunogenicity of the pre-S regions of HBsAg and has elucidated the independent H-2-linked genes regulating antibody production to pre-S and S region determinants. The ability to circumvent genetic nonresponsiveness has implications for the design of future HBV vaccines. Mice also afforded the opportunity to examine the ability of HBcAg to activate B cells directly, and to prime Th cells capable of eliciting antibody to envelope proteins. These observations have potential clinical relevance, implications for vaccine design, and may explain the ability of HBcAg vaccination to protect against HBV infection. The murine system ha also facilitated the mapping of T-cell and B-cell recognition sites within HBV proteins, which at least conceptually enhances the prospects for development of a synthetic HBV vaccine. Antibody-binding sites appear to be similar in humans and mice; the extent to which their T-cell repertoires overlap is not known. However, the chemical and structural constraints imposed on T-cell antigenicity, and the fact that MHC-encoded class II molecules and the cellular mechanisms mediating T-cell recognition are conserved across species, make such overlaps appear likely. Furthermore, the ability to generate transgenic mice that express the various HBV proteins has yielded important insights into possible immunopathogenic mechanism and immunologic tolerance mechanisms that may predispose to chronic infection.
On/Off Switching of Magnetism and Electronic Wave Interference Patterns in Stacked Nanographite (2005)

Antiferromagnetism of stacked nanographite is investigated using the Hubbard-type model. We find that the open shell electronic structure can be an origin of the decreasing magnetic moment with decreasing inter-layer distance, as experiments of adsorption of molecules suggest. Next, possible charge-separated states are considered using the extended Hubbard model with nearest-neighbor repulsive interactions. The charge-polarized state could appear, when a static electric field is present in the graphene plane for example. Finally, superperiodic patterns with a long distance in a nanographene sheet observed by STM are discussed in terms of the interference of electronic wave functions with a static linear potential theoretically. In the analysis by the k • p model, the oscillation period decreases spatially in agreement with experiments.
Bovine Protein C Inhibitor Has a Unique Reactive Site and Can Transiently Inhibit Plasmin (2000)

Protein C inhibitor (PCI) regulates the anticoagulant protein C pathway by neutralizing activated protein C and thrombin-thrombomodulin complex in the human hemostatic system. In this study, we cloned a full-length bovine PCI cDNA encoding a putative 19-residue signal peptide and a 385-residue mature protein; this showed 70.6%, 70.6%, 57.5% and 59.6% amino acid sequence homology with the human, rhesus monkey, rat and mouse PCIs, respectively. Bovine PCI mRNA (2.1 kb in size) was expressed strongly in the liver, and moderately in the kidney and testis, but not in other tissues tested. Bovine PCI has a putative reactive site peptide bond, Lys-Ser, that is different from the reactive site sequence (Arg-Ser) of other species' PCI. We found that bovine PCI transiently inhibits bovine plasmin, but not human plasmin. Western blot analysis showed that the reactive site of bovine PCI is cleaved during the course of complex formation with bovine plasmin; degraded PCI is released from the complex gradually concomitant with the recovery of plasmin activity. These findings suggest that bovine PCI plays a role not only in the protein C pathway but also in the fibrinolytic activity of bovine hemostatic system.
Imaging the Clear Cell Renal Cell Carcinoma Proteome (2012)

Imaging mass spectrometry identified and mapped specific peptides that accurately distinguished malignant from normal renal tissue. This demonstrates its potential as a novel, high throughput approach to clear cell renal cell carcinoma biomarker discovery. Given the multiple pathways and known heterogeneity involved in tumors such as clear cell renal cell carcinoma, multiple peptide signatures that maintain their spatial relationships may outperform traditional protein biomarkers.
Functional Characterization of the Ocular Prostaglandin F2α (PGF2α) Receptor (1997)

Prostaglandin F2alpha (PGF2alpha) is a product of cyclooxygenase-catalyzed metabolism of arachidonic acid. Recently, PGF2alpha analogs have been hypothesized to reduce intraocular pressure via relaxation of the ciliary muscle. To investigate the molecular basis of PGF2alpha receptor (FP) activation in the eye, we cloned the FP from a human ciliary body (hcb) cDNA library. The open reading frame of the hcb-FP cDNA was identical to the uterine FP cDNA. The hcb-FP appeared to be predominantly membrane-localized, as visualized by an FP-specific peptide antibody, and coupled to inositol phosphate formation when stably expressed in HEK 293 cells. Interestingly, the hcb-FP could also be activated by the F2 isoprostane, 12-iso-PGF2alpha, in addition to its cognate ligand, PGF2alpha. 12-iso-PGF2alpha was less potent (EC50 = 5 microM) than PGF2alpha (EC50 = 10 nM) in generating inositol phosphates via the hcb-FP in HEK 293 cells. Both ligands also stimulated mitogenesis in NIH 3T3 cells. Although 12-iso-PGF2alpha caused a dose-dependent activation of the FP, it failed to activate the recombinant human prostacyclin receptor and caused only minimal activation of the thromboxane receptor isoforms stably expressed in HEK 293 cells. Four additional F2 isoprostanes, 8-iso-PGF2alpha, IPF2alpha-I, IPF2alpha-III, and 9beta,11beta-PGF2, caused trivial, or no, activation of the FP. Consistent with these observations, only PGF2alpha and 12-iso-PGF2alpha caused rapid homologous desensitization of FP and also exhibited cross-desensitization, with PGF2alpha resulting in a maximum of approximately 60% desensitization. The human FP may thus be activated specifically, by the free radical-catalyzed F2 isoprostane, 12-iso-PGF2alpha, in addition to the cyclooxygenase product, PGF2alpha. Incidental receptor activation by isoprostanes may complement the actions of PGF2alpha in clinical syndromes where oxidant stress and augmented prostaglandin biosynthesis coincide.
Optical technique for producing 0.1-μ periodic surface structures (1973)

Surface corrugations with a period of 1108 Å and a depth of [inverted lazy s] 500 Å have been fabricated in glass. These corrugations were first produced in a photoresist film on glass by the optical interference of two 3250-Å laser beams. The corrugation was transferred to the glass by ion beam etching.