gebhart/patrepeval huggingface dataset:
An Interaction between a MYC Protein and an EREBP Protein Is Involved in Transcriptional Regulation of the Rice Wx Gene (2003)

We previously demonstrated that a 31-bp nucleotide sequence located upstream of the rice Wx gene played an important role in its expression. We further showed that this cis-acting regulator interacts with nuclear proteins extracted from developing rice endosperm. We used the 31-bp sequence as bait in a yeast one-hybrid system to isolate several cDNA clones from a rice cDNA expression library. One of these cDNAs encodes a MYC protein, designated OsBP-5, which is 335 amino acids long and contains a putative basic helix-loop-helix-ZIP DNA-binding domain. This domain exhibits 50% amino acid sequence identity with the R/B proteins that regulate the expression of genes involved in anthocyanin biosynthesis in plants. The results of electrophoretic mobility shift assays (EMSAs) and Southwestern gel blots indicate that this protein binds specifically to the CAACGTG motif within the 31-bp sequence. However, by itself, the OsBP-5 protein is unable to trans-activate a lacZ reporter gene controlled by the 31-bp sequence when tested in a yeast expression system. Interestingly, OsBP-5 can trans-activate this reporter gene when another protein, OsEBP-89, a member of the EREBP family of transcription factors, is present. Furthermore, in vitro pull-down experiments show that a protein isolated from developing rice endosperm interacts with the OsBP-5 protein, and Western blots confirm that the interacting protein is OsEBP-89. The formation of a supershift band in EMSAs also indicates that two proteins interact with each other. Interference of OsBP-5 gene expression by double-stranded RNA reduces the amylose content in mature seed of transgenic rice plants but has no visible effect on their phenotype. These results suggest that the OsBP-5 and OsEBP-89 proteins act synergistically, perhaps as a heterodimer, to regulate the transcription of the rice Wx gene.
Mending the broken brain: neuroimmune interactions in neurogenesis (2010)

Neuroimmune networks and the brain endocannabinoid system contribute to the maintenance of neurogenesis. Cytokines and chemokines are important neuroinflammatory mediators that are involved in the pathological processes resulting from brain trauma, ischemia and chronic neurodegenerative diseases. However, they are also involved in brain repair and recovery. Compelling evidence obtained, in vivo and in vitro, establish a dynamic interplay between the endocannabinoid system, the immune system and neural stem/progenitor cells (NSC) in order to promote brain self-repair. Cross-talk between inflammatory mediators and NSC might have important consequences for neural development and brain repair. In addition, brain immune cells (microglia) support NSC renewal, migration and lineage specification. The proliferation and differentiation of multipotent NSC must be precisely controlled during the development of the CNS, as well as for adult brain repair. Although signalling through neuroimmune networks has been implicated in many aspects of neural development, how it affects NSC remains unclear. However, recent findings have clearly demonstrated that there is bi-directional cross-talk between NSC, and the neuroimmune network to control the signals involved in self-renewal and differentiation of NSC. Specifically, there is evidence emerging that neuroimmune interactions control the generation of new functional neurones from adult NSC. Here, we review the evidence that neuroimmune networks contribute to neurogenesis, focusing on the regulatory mechanisms that favour the immune system (immune cells and immune molecules) as a novel element in the coordination of the self-renewal, migration and differentiation of NSC in the CNS. In conjunction, these data suggest a novel mode of action for the immune system in neurogenesis that may be of therapeutic interest in the emerging field of brain repair.
SiON high-refractive-index waveguide and planar lightwave circuits (2003)

The rapidly growing optical communication market requires photonic components with ever-increasing functionality and complexity that can be fabricated reliably at low cost. Of the various approaches used to fabricate photonic components, those based on planar waveguides have achieved high performance and represent a promising path toward compact integration of optical functions. We present an overview of an approach used to produce an optical single-mode waveguide. Through its strong mode confinement, the approach makes it possible to integrate optical filter functions with higher functionality, as required for high-data-rate communication networks. The waveguide is based on the use of a silicon oxynitride (SiON) core and silicon oxide cladding layers, and can be fabricated using conventional chip fabrication techniques. Using the new approach, conventional passive optical components such as arrayed waveguide gratings for wavelength-division-multiplexed transmission systems can be fabricated in a more compact way than using standard silica-on-silicon waveguide methods. Moreover, the realization of more enhanced, adaptive optical functions such as finite-impulse-response as well as infinite-impulse-response filters is possible. Reconfiguration is achieved through the thermo-optic effect. A reconfigurable gain-flattening filter and an adaptive dispersion compensator are presented as examples.
Aflibercept (VEGF-TRAP): The Next Anti-VEGF Drug (2011)

The inflammatory cytokine, vascular endothelial growth factor (VEGF), plays a central role in human growth and development, and vascular maintenance. VEGF mediated angiogenesis is essential for tumor growth, as well as exudative age-related macular degeneration, proliferative diabetic retinopathy and retinopathy of prematurity, all of which are characterized by abnormal neovascularization. Ischemia and inflammation also lead to VEGF-mediated breakdown of the blood-retinal barrier, which causes vision diminishing macular edema. To combat these effects, anti-VEGF drugs (antibodies, aptamers, and tyrosine kinase inhibitors) have been developed for both systemic and local (intraocular) use. The next drug to receive regulatory approval will probably be aflibercept (VEGF-Trap), a fusion protein with high VEGF affinity attributed to binding sequences from the native receptors VEGFR1 and VEGFR2. Aflibercept monotherapy significantly reduces tumor growth and extends survival in several orthotropic animal models, and has both prevented and reduced the growth of experimental choroidal neovascularization. Ongoing phase III trials are evaluating the effectiveness of aflibercept combined with chemotherapy in patients with advanced carcinomas. The phase III VELOUR trial determined that patients receiving aflibercept with irinotecan/5-FU as second line chemotherapy for metastatic colorectal cancer experienced extended progression free survival and overall survival. Intravitreal aflibercept improved visual acuity in patients with exudative age-related macular degeneration and was non-inferior to standard therapy (ranibizumab). Ongoing phase III trials are investigating the use of aflibercept for retinal vein occlusions and diabetic macular edema. A regulatory approval application for use in exudative macular degeneration has been filed, with a decision expected by late 2011.
A CMOS image sensor with analog two-dimensional DCT-based compression circuits for one-chip cameras (1997)

This paper presents a CMOS image sensor with on-chip compression using an analog two-dimensional discrete cosine transform (2-D DCT) processor and a variable quantization level analog-to-digital converter (ADC). The analog 2-D DCT processor is essentially suitable for the on-sensor image compression, since the analog image sensor signal can be directly processed. The small and low-power nature of the analog design allows us to achieve low-power, low-cost, one-chip digital video cameras. The 8/spl times/8-point analog 2-D DCT processor is designed with fully differential switched-capacitor circuits to obtain sufficient precision for video compression purposes. An imager array has a dedicated eight-channel parallel readout scheme for direct encoding with the analog 2-D DCT processor. The variable level quantization after the 2-D DCT can be performed by the ADC at the same time. A prototype CMOS image sensor integrating these core circuits for compression is implemented based on triple-metal double-polysilicon 0.35-/spl mu/m CMOS technology. Image encoding using the implemented analog 2-D DCT processor to the image captured by the sensor is successfully performed. The maximum peak signal-to-noise ratio (PSNR) is 36.7 dB.
중국 사과의 생산과 수출현황 및 고찰 (2011)

China is the largest country which produce apple in the world. Apple industry plays a very important role in chinese agriculture section, especially for farmers` income. Recently chinese apple industry has been developing very quickly because of export. When the chinese apple goes to the world markets, it is also face up with some challenges. Apple industry is a labor intensive industry, so the labor inputs` proportion is very large. China has large labour force and the cost of production is relatively inexpensive. However, the technology, the quality and safety standards are not popularized, so there are difficulties for chinese apples market to enter into developed countries` market. This paper will first introduce about chinese apple industry`s current situation, focuses on the apple`s productivity and the changes of apple price. Secondly will introduce the current situation of apple`s export.
Oligomerization-induced Conformational Change in the C-terminal Region of Nel-like Molecule 1 (NELL1) Protein Is Necessary for the Efficient Mediation of Murine MC3T3-E1 Cell Adhesion and Spreading (2014)

NELL1 is a large oligomeric secretory glycoprotein that functions as an osteoinductive factor. NELL1 contains several conserved domains, has structural similarities to thrombospondin 1, and supports osteoblastic cell adhesion through integrins. To define the structural requirements for NELL1-mediated cell adhesion, we prepared a series of recombinant NELL1 proteins (intact, deleted, and cysteine-mutant) from a mammalian expression system and tested their activities. A deletion analysis demonstrated that the C-terminal cysteine-rich region of NELL1 is critical for the cell adhesion activity of NELL1. Reducing agent treatment decreased the cell adhesion activity of full-length NELL1 but not of its C-terminal fragments, suggesting that the intramolecular disulfide bonds within this region are not functionally necessary but that other disulfide linkages in the N-terminal region of NELL1 may be involved in cell adhesion activity. By replacing cysteine residues with serines around the coiled-coil domain of NELL1, which is responsible for oligomerization, we created a mutant NELL1 protein that was unable to form homo-oligomers, and this monomeric mutant showed substantially lower cell adhesion activity than intact NELL1. These results suggest that an oligomerization-induced conformational change in the C-terminal region of NELL1 is important for the efficient mediation of cell adhesion and spreading by NELL1.
SDS Surfactants on Carbon Nanotubes: Aggregate Morphology (2009)

Although carbon nanotubes have attracted enormous research interest, their practical application is still hindered, primarily, by the difficulty of separating them into samples monodispersed in diameter, chirality, and length. Recent advances show that ultracentrifugating carbon nanotube dispersions stabilized by surfactants is a promising route for achieving the desired separation. For further perfectioning this procedure it is necessary to know how surfactants adsorb on nanotubes of different diameters, which determines the nanotube−surfactant aggregate effective density and the nanotube−nanotube potential of mean force. Because only limited experimental data are available to elucidate these phenomena, we report here an extensive all-atom molecular dynamics study on the morphology of sodium dodecyl sulfate (SDS) surfactant aggregates adsorbed on (6,6), (12,12), and (20,20) single walled carbon nanotubes at room conditions. Our calculations reveal that the nanotube diameter is the primary factor that determines the morphology of the aggregates because of a competition between the entropic and energetic advantage encountered by the surfactants when they wrap one nanotube, and the enthalpic penalty faced during this process due to bending of the surfactant molecule. The data are in qualitative agreement with the neutron scattering results reported by Yurekli et al. [J. Am. Chem. Soc. 2004, 126, 9902], and for the first time provide an atomic-level description helpful in designing better separation, as well as stabilization techniques for aqueous carbon nanotube dispersions.
Sodium requirement for capacitation and membrane fusion during the guinea-pig sperm acrosome reaction (1984)

Guinea-pig spermatozoa, incubated in a minimal culture medium (MCM-PL) containing 150 mM-Na+ and no added K+, capacitate within 2 h and respond to added Ca2+ with maximal percentage of acrosome reactions. When spermatozoa, initially capacitated in Medium MCM-PL, were washed and resuspended in saline-based media, the motile spermatozoa showed acrosome reactions only in response to added Ca2+ at an extracellular pH greater than 7.4. In contrast, resuspension of capacitated spermatozoa into isotonic sucrose or choline-based media containing no added Na+ and K+ (pH 7.8) did not support acrosome reactions in response to the addition of Ca2+. Examination under the electron microscope showed that these spermatozoa responded to added Ca2+ with swelling or cavitation of the acrosomal matrix but fusion of the plasma membrane and acrosomal membrane did not occur. Treatment of spermatozoa with monensin, a monovalent cationic ionophore, induced rapid acrosome reactions in the presence of extracellular Ca2+ and Na+. In contrast, spermatozoa incubated for 3 h in a sucrose-based Na+-deficient medium or Medium MCM-PL containing 10 mM-KCl failed to give a significant percentage of acrosome reactions in response to the addition of Ca2+, but the addition of ouabain (0.1 mM) prevented the K+ inhibition. Amiloride, a sodium channel blocker in various other tissues, retarded the development of acrosome reactions of spermatozoa incubated in Medium MCM-PL. Based on these data, it appears that an increase in intracellular Na+ has a functional role in acquisition of guinea-pig sperm fertilizing ability.
Design, Synthesis and Activity of Ascorbic Acid Prodrugs of Nipecotic, Kynurenic and Diclophenamic Acids, Liable to Increase Neurotropic Activity (2001)

To improve the entry of certain drugs into brain, ascorbic acid (AA) conjugates of these drugs were synthesized and their capacity to interact with SVCT2 ascorbate transporters was explored. Kinetic studies clearly indicate that all of the conjugates were able to competitively inhibit ascorbate transport in human retinal pigment epithelial cells (HRPE). In vivo studies, in a mouse model system, demonstrate that conjugate 3 is better absorbed compared to the nonconjugated parent drug.
2,4-Diamino-5-benzylpyrimidines and analogs as antibacterial agents. 6. A one-step synthesis of new trimethoprim derivatives and activity analysis by molecular modeling (1983)

A new route to 2,4-diamino-5-(4-hydroxybenzyl)pyrimidines has been developed that involves the condensation of 2,4-diamino-5-(hydroxymethyl)pyrimidine with phenols in acidic medium. The use of phenol and its 2,6-dialkyl derivatives produces 5-(4-hydroxybenzyl)pyrimidines exclusively. However, 2,6-dimethoxyphenol produces a mixture of 5-(3-hydroxy-2,4-dimethoxybenzyl)- and 5-(4-hydroxy-3,5-dimethoxybenzyl)pyrimidines. The phenolic condensation has been used to prepare a series of alkyl-substituted 5-(4-hydroxybenzyl)- and 5-(4-alkoxybenzyl)pyrimidines. The use of 1,2,3-trimethoxybenzene in place of a phenol produces 2,4-diamino-5-(2,3,4-trimethoxybenzyl)pyrimidine, a trimethoprim isomer with low antibacterial activity. The use of molecular models of several of the new ortho-substituted derivatives in the active site of dihydrofolate reductase has provided a rational explanation for their activities relative to trimethoprim.
Palmitoylated proteins in Ureaplasma urealyticum (1991)

After incubation of Ureaplasma urealyticum serotype 8 in the presence of 3H-labeled palmitic acid, about 25 acylated proteins were detected by electrophoresis and fluorography. Of these, at least six were shown to be antigenic by immunoprecipitation of solubilized palmitate-labeled cells with a homologous polyclonal serum. These six included the serotype 8-specific surface-expressed 96-kDa antigen. After phase partition of palmitate-labeled cells with Triton X-114, all but six acylated proteins partitioned entirely into the detergent phase. The others, including the 96-kDa antigen, partitioned preferentially into the detergent phase and were apparently amphipathic. These results are consistent with the acylated proteins being mainly membrane associated.
Effects of Fructus Ligustri Lucidi Extract on Bone Turnover and Calcium Balance in Ovariectomized Rats (2006)

The aim of this study was to evaluate the effect of Fructus Ligustri Lucidi (FLL), a kidney-tonifying Chinese herbal medicine, on the biochemical markers of bone turnover, calcium metabolism and balance in osteoporotic rat model developed by ovariectomy. Four weeks after surgical operation, animals were randomly assigned to one of the four treatments for 14 weeks: sham-operated control treated with vehicle (sham, n=8), ovariectomized group treated with vehicle (OVX, n=8), OVX group treated with 17beta-estradiol (E(2), n=10, 2 microg/kg/d) and OVX group treated with FLL extracts (FLL, n=10, 550 mg/kg/d). Serum osteocalcin and urinary deoxypyridinoline levels were upregulated in rats in response to OVX, suggesting that the bone turnover rate was accelerated in these animals. Treatment of OVX rats with FLL extract could prevent OVX-induced increase in bone turnover by suppression of both serum osteocalcin (p<0.05, vs. OVX) and urinary deoxypyridinoline (p<0.05, vs. OVX) levels. In addition, FLL extract could prevent OVX-induced loss of calcium in rats by increasing the intestinal calcium absorption rate (p<0.01, vs. OVX), suppressing urinary Ca excretion (p<0.05, vs. OVX) as well as increasing bone calcium content (p<0.05, vs. OVX). Our study is the first to report that FLL can modulate bone turnover and calcium balance in OVX rats and it might be a potential candidate for prevention and treatment of postmenopausal osteoporosis.
Induction of Apoptosis in Human Leukemia Cells by the CDK1 Inhibitor (2002)

AbstractWe have examined the effects of the CDK1 inhibitor CGP74514A on cell cycle- and apoptosis-related events in human leukemia cells. An 18-hr exposure to 5 mM CGP74514A induced mitochondrial damage (i.e., loss of Dym) and apoptosis in multiple human leukemia cell lines (e.g., U937, HL-60, KG-1, CCRF-CEM, Raji, and THP; range 30-95%). In U937 cells, CGP74514A- induced apoptosis (5 mM) became apparent within 4 hr and approached 100% by 24 hr. The pan- caspase inhibitor Boc-fmk and the caspase-8 inhibitor IETD-fmk opposed CGP74514A-induced caspase-9 activation and PARP degradation, but not cytochrome c or Smac/DIABLO release. CGP74514A-mediated apoptosis was substantially blocked by ectopic expression of full-length Bcl- 2, a loop-deleted mutant Bcl-2, and Bcl-xL. CGP74514A treatment (5 mM; 18 hr) resulted in increased p21CIP1 expression, p27KIP1 degradation, diminished E2F1 expression, and dephosphorylation of p34cdc2. It also induced early (i.e., within 2 hr) inhibition of CDK1 activity and dephosphorylation of pRb, followed by pRb degradation, but did not block pRb phosphorylation at CDK2- and CDK4- specific sites. These findings indicate that the selective CDK1 inhibitor, CGP74514A, induces complex changes in cell cycle-related proteins in human leukemia cells accompanied by extensive mitochondrial damage, caspase activation, and apoptosis.Key Words:Leukemia, CDK1 Inhibitor, Apoptosis, CGP74514A
Characterization of ibrutinib‐sensitive and ‐resistant mantle lymphoma cells (2014)

Ibrutinib inhibits Bruton tyrosine kinase (BTK), a key component of early B-cell receptor (BCR) signalling pathways. A multicentre phase 2 trial of ibrutinib in patients with relapsed/refractory mantle cell lymphoma (MCL) demonstrated a remarkable response rate. However, approximately one-third of patients have primary resistance to the drug while other patients appear to lose response and develop secondary resistance. Understanding the molecular mechanisms underlying ibrutinib sensitivity is of paramount importance. In this study, we investigated cell lines and primary MCL cells that display differential sensitivity to ibrutinib. We found that the primary cells display a higher BTK activity than normal B cells and MCL cells show differential sensitivity to BTK inhibition. Genetic knockdown of BTK inhibits the growth, survival and proliferation of ibrutinib-sensitive but not resistant MCL cell lines, suggesting that ibrutinib acts through BTK to produce its anti-tumour activities. Interestingly, inhibition of ERK1/2 and AKT, but not BTK phosphorylation per se, correlates well with cellular response to BTK inhibition in cell lines as well as in primary tumours. Our study suggests that, to prevent primary resistance or to overcome secondary resistance to BTK inhibition, a combinatory strategy that targets multiple components or multiple pathways may represent the most effective approach.
Detailed mapping of the antigenicity of the surface unit glycoprotein of equine infectious anemia virus by using synthetic peptide strategies (1992)

We describe here a detailed analysis of the antigenic determinants of the surface unit glycoprotein (gp90) of equine infectious anemia virus (EIAV), using a comprehensive panel of synthetic peptides in enzyme-linked immunosorbent assays with immune serum from naturally and experimentally infected horses and with a panel of gp90-specific neutralizing and nonneutralizing monoclonal antibodies. The results of these studies identify immunoreactive segments throughout the conserved and variable domains of gp90 but localize immunodominant (100% reactivity) determinants to the amino and carboxyl termini of the glycoprotein molecule. Analysis of peptide reactivities with longitudinal serum samples taken from experimentally infected ponies revealed that antibody responses to conserved B-cell determinants appeared earlier and at higher titers than do antibodies specific for determinants contained in the variable domain of gp90. These observations suggest an evolution of antibody responses in EIAV-infected ponies that may correspond to the establishment of immunological control of virus replication and disease routinely observed in EIAV infections. In addition, the mapping of monoclonal antibody epitopes to peptides of 9 to 12 amino acids demonstrated that all of the neutralizing epitopes are located in the variable domain of gp90. The arrangement of neutralizing epitopes and critical structural considerations suggest that EIAV gp90 contains a principal neutralizing domain similar to the V3 loop of human immunodeficiency virus type 1. These antigenic analyses provide an important foundation for further analyzing the protective immune response generated during persistent EIAV infections and also provide potential peptide substrates for diagnostic assays and for vaccine strategies.
Guidebook to protein toxins and their use in cell biology (1998)

1: Membrane permeabilizing toxins. 2: Toxins affecting signal transduction. 3: Toxins affecting protein synthesis. 4: Cytoskeleton-affecting toxins. 5: Toxins affecting the immune and inflammatory response. 6: Toxins affecting membrane traffic. 7: Sodium channel-targeted toxins. 8: Potassium channel-targeted toxins. 9: Calcium channel-targeted toxins. 10: Acetylcholine receptor targeted toxins. 11: Ryanodine receptor toxins. 12: Presynaptic toxins. 13: Glutamate receptor-targeted toxins