gebhart/patrepeval huggingface dataset:
Seven Novel Variants of the Staphylococcal Chromosomal Cassette mec in Methicillin-Resistant Staphylococcus aureus Isolates from Ireland (2005)

Methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered in Irish hospitals between 1971 and 2002 were characterized using multilocus sequence typing (MLST) (n = 130) and SCCmec typing (n = 172). Where atypical SCCmec typing results were obtained, PCR amplification of entire SCCmec elements, analysis of amplimer mobility, and nucleotide sequencing were undertaken. MLST revealed that 129/130 isolates had the same genotypes as internationally spread MRSA clones, including ST239, ST247, ST250, ST5, ST22, ST36, and ST8. A novel genotype, ST496, was identified in one isolate. Half of the isolates (86/172) had SCCmec type I, IA, II, III, or IV. The remaining 86 isolates harbored novel SCCmec variants in three distinct genetic backgrounds: (i) 74/86 had genotype ST8 and either one of five novel SCCmec II (IIA, IIB, IIC, IID, and IIE) or one of two novel SCCmec IV (IVE and IVF) variants; (ii) 3/86 had genotype ST239 and a novel SCCmec III variant; (iii) 9/86 had a novel SCCmec I variant associated with ST250. SCCmec IVE and IVF were similar to SCCmec IVc and IVb, respectively, but differed in the region downstream of mecA. The five SCCmec II variants were similar to SCCmec IVb in the region upstream of the ccr complex but otherwise were similar to SCCmec II, except for the following regions: SCCmec IIA and IID had a novel mec complex, A.4 (Delta mecI-IS1182-Delta mecI-mecR1-mecA-IS431mec); SCCmec IIC and IIE had a novel mec complex, A.3 (IS1182-Delta mecI-mecR1-mecA-IS431mec); SCCmec IID and IIE lacked pUB110; SCCmec IIC and IIE lacked a region of DNA between Tn554 and the mec complex; and SCCmec IIB lacked Tn554. This study has demonstrated a hitherto-undescribed degree of diversity within SCCmec.
Lateral fluid percussion injury of the brain induces CCL20 inflammatory chemokine expression in rats (2011)

These results demonstrate that the systemic inflammatory reaction to TBI starts earlier than the local brain response and suggest that spleen- and/ or thymus-derived CCL20 might play a role in promoting neuronal injury and central nervous system inflammation in response to mild TBI.
Novel arrangement of immunoglobulin variable domains: x-ray crystallographic analysis of the .lambda.-chain dimer Bence-Jones protein Loc (1985)

We have characterized and crystallized a human lambda I light-chain dimer, Bence-Jones protein Loc, which has variable (V) region antigenic determinants characteristic for the lambda I subgroup and constant (C) region determinants of the C lambda I gene Mcg. The crystal structure was determined to 3-A resolution; the R factor is 0.27. The angle formed by the twofold axes of the V and C domains, the "elbow bend", is 97 degrees, the smallest found so far for an antibody fragment. The antigen-binding site formed by the two V domains of the Loc light chain differs significantly from those of other immunoglobulin molecules (light-chain dimers and Fab fragments) for which X-ray crystallographic data are available. Whereas, in other antibody fragments, the V domains are related by a local twofold axis, a local twofold screw axis with a translational component of 3.5 A relates the V domains in protein Loc. In contrast to the classic antigen binding "pocket" formed by V domain interactions in the previously characterized antibody structures, the V region associations in protein Loc result in a central protrusion in the binding site, with grooves on two sides of the protrusion. The structure of protein Loc indicates that immunoglobulins are physically capable of forming a more diverse spectrum of antigen-binding sites than has been heretofore apparent. Moreover, the unusual protruding nature of the binding site may be analogous to structures required for some anti-idiotypic antibodies. Further, the complementarity-determining residues form parts of two independent grooves.(ABSTRACT TRUNCATED AT 250 WORDS)
Slow intracellular trafficking of catalase nanoparticles targeted to ICAM-1 protects endothelial cells from oxidative stress (2003)

Nanotechnologies promise new means for drug delivery. ICAM-1 is a good target for vascular immunotargeting of nanoparticles to the perturbed endothelium, although endothelial cells do not internalize monomeric anti-ICAM-1 antibodies. However, coupling ICAM-1 antibodies to nanoparticles creates multivalent ligands that enter cells via an amiloride-sensitive endocytic pathway that does not require clathrin or caveolin. Fluorescence microscopy revealed that internalized anti-ICAM nanoparticles are retained in a stable form in early endosomes for an unusually long time (1-2 h) and subsequently were degraded following slow transport to lysosomes. Inhibition of lysosome acidification by chloroquine delayed degradation without affecting anti-ICAM trafficking. Also, the microtubule disrupting agent nocodazole delayed degradation by inhibiting anti-ICAM nanoparticle trafficking to lysosomes. Addition of catalase to create anti-ICAM nanoparticles with antioxidant activity did not affect the mechanisms of nanoparticle uptake or trafficking. Intracellular anti-ICAM/catalase nanoparticles were active, because endothelial cells were resistant to H2O2-induced oxidative injury for 1-2 h after nanoparticle uptake. Chloroquine and nocodazole increased the duration of antioxidant protection by decreasing the extent of anti-ICAM/catalase degradation. Therefore, the unique trafficking pathway followed by internalized anti-ICAM nanoparticles seems well suited for targeted delivery of therapeutic enzymes to endothelial cells and may provide a basis for treatment of acute vascular oxidative stress.
Developmental aspects of spinal cord and limb regeneration (1995)

The ability of birds and mammals to regenerate tissues is limited. By contrast, urodele amphibians can regenerate a variety of injured tissues such as intestine, cardiac muscle, lens and neural retina, as well as entire structures such as limbs, tail and lower jaw. This regenerative capacity is associated with the ability to form masses of mesenchyme cells (blastemas) that differentiate into the missing tissues or parts. Understanding the mechanisms that underlie blastema formation in urodeles will provide valuable tools with which to achieve the goal of stimulating regeneration in mammalian tissues that do not naturally regenerate. Here we discuss an example of tissue regeneration (spinal cord) and an example of epimorphic appendage regeneration (limb) in the axolotl Ambystoma mexicanum, emphasizing analysis of the processes that produce the regeneration blastema and of the tissue interactions and blastemal products that contribute to the regeneration-promoting environment.
Absence of Major Histocompatibility Complex Class I on Neural Stem Cells Does Not Permit Natural Killer Cell Killing and Prevents Recognition by Alloreactive Cytotoxic T Lymphocytes In Vitro (2004)

Potential applications of neural stem cells (NSCs) for transplantation requires understanding myosin heavy chain (MHC) expression and the ability of T cells and natural killer (NK) cells to recognize this progenitor population. Cells from the cortices of day-13 embryonic (E13) B6 (H-2(b)) mice were explanted and cultured to expand NSCs. Analysis of P2-P17-cultured cells using anti-MHC class I/II monoclonal antibodies (mAbs) showed marginal expression of both products. Although recombinant murine interferon-gamma (rmIFN gamma) exposure did not alter the multipotential capacity of these stem cells, titration of mrIFN gamma NSC cultures demonstrated that MHC molecules could be strongly upregulated after addition of 3 ng/ml rmIFN gamma for 60 hours. To assess the susceptibility of NSCs with low or absent versus high levels of MHC expression to lysis by cytotoxic T lymphocyte (CTL) and NK populations, untreated and rmIFN gamma-treated NSC target cells were examined. Untreated NSCs were not recognized by BALB/c (H-2(d)) allospecific anti-H-2(b) CTL, consistent with the mAb findings; however, upregulation of MHC products on both early and later passaged NSCs resulted in their efficient lysis by CTL. NK cells were prepared from syngeneic B6 or allogeneic BALB/c mice. Although NK cells effectively killed control YAC-1 target cells, these effectors did not kill MHC-deficient (or expressing) NSC targets. Thus, similar to hematopoietic, embryonic, and mesenchymal stem cell populations, unmanipulated NSCs are not readily killed by T and NK cells. These findings suggest that following transplant into syngeneic or allogeneic recipients, NSCs may exhibit diminished susceptibility to clearance by host T- and NK-cell populations.
Dengue Virus-Specific and Flavivirus Group Determinants Identified with Monoclonal Antibodies by Indirect Immunofluorescence (1982)

Monoclonal antibodies produced against the four dengue virus serotypes identified four categories of reactions by immunofluorescence: flavivirus group reactive, dengue complex specific, dengue subcomplex specific (DEN-1, DEN-3), and dengue serotype specific. This is the first time that monospecific antibodies have been available for all of these unique antigenic determinants. Hybridoma cell lines producing dengue type-specific antibodies have been deposited in the Hybridoma Cell Bank of the American Type Culture Collection (Rockville, MD) for general distribution.
A central role for inflammation in the pathogenesis of diabetic retinopathy (2004)

Diabetic retinopathy is a leading cause of adult vision loss and blindness. Much of the retinal damage that characterizes the disease results from retinal vascular leakage and nonperfusion. Diabetic retinal vascular leakage, capillary nonperfusion, and endothelial cell damage are temporary and spatially associated with retinal leukocyte stasis in early experimental diabetes. Retinal leukostasis increases within days of developing diabetes and correlates with the increased expression of retinal intercellular adhesion molecule-1 (ICAM-1) and CD18. Mice deficient in the genes encoding for the leukocyte adhesion molecules CD18 and ICAM-1 were studied in two models of diabetic retinopathy with respect to the long-term development of retinal vascular lesions. CD18-/- and ICAM-1-/- mice demonstrate significantly fewer adherent leukocytes in the retinal vasculature at 11 and 15 months after induction of diabetes with STZ. This condition is associated with fewer damaged endothelial cells and lesser vascular leakage. Galactosemia of up to 24 months causes pericyte and endothelial cell loss and formation of acellular capillaries. These changes are significantly reduced in CD18- and ICAM-1-deficient mice. Basement membrane thickening of the retinal vessels is increased in long-term galactosemic animals independent of the genetic strain. Here we show that chronic, low-grade subclinical inflammation is responsible for many of the signature vascular lesions of diabetic retinopathy. These data highlight the central and causal role of adherent leukocytes in the pathogenesis of diabetic retinopathy. They also underscore the potential utility of anti-inflammatory treatment in diabetic retinopathy.
Synthesis and characterization of a macromonomer crosslinker (2000)

A macromonomer crosslinker was synthesized by reacting an hydroxy-terminated ethylene–butylene diol copolymer with an excess of acrylic acid in toluene. 1H-, 13C-, and attached proton test (APT) NMR, Fourier transform IR, and gel permeation chromatography were used to characterize the macromonomer crosslinker. Its dilute solution behavior was also compared with the base diol. The addition of the ester moiety to the copolymer backbone did not involve any other side reactions, as evidenced by the similarities in the structures of the macromonomer crosslinker and the diol. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 77: 1362–1368, 2000
Engineered male sterility in plants. (1991)

We constructed two chimaeric ribonuclease genes that are specifically expressed in anthers of tobacco and rapeseed plants. The expression of these genes affects the production of functional and viable pollen yielding plants that are male sterile. This dominant gene for nuclear male sterility should facilitate the production of hybrid seed in various crops.
Identification of functionally related genes that stimulate early meiotic gene expression in yeast. (1993)

Meiosis and spore formation in the yeast Saccharomyces cerevisiae are associated with increased expression of sporulation-specific genes. One of these genes, IME2, encodes a putative protein kinase that is a positive regulator of other sporulation-specific genes. We have isolated mutations that cause reduced expression of an ime2-lacZ fusion gene. We found mutations in IME1, a known positive regultor of IME2, and MCK1, a known positive regulator of IME1. We also isolated recessive mutations in 12 other genes, which we designate RIM (Regulator of IME2) genes. Our analysis indicates that the defects in rim1, rim8, rim9 and rim13 mutants are a consequence of diminished IME1 expression and can be suppressed by expression of IME1 from the heterologous ACT1 promoter. These rim mutations also reduced expression of an ime1-HIS3 fusion, in which the HIS3 gene is expressed from the IME1 promoter, and caused reduced levels of IME1 RNA. Although the rim1, rim8, rim9 and rim13 mutant phenotypes are similar to those of mck1 mutants, we found that the defects in ime2-lacZ expression and sporulation of the mck1 rim double mutants were more severe than either single mutant. In contrast, the defects of the rim rim double mutants were similar to either single mutant. The rim1, rim8, rim9 and rim13 mutants also display slow growth at 17 degrees and share a smooth colony morphology that is not evident in mck1 mutants or isogenic wild-type strains. We suggest that RIM1, RIM8, RIM9 and RIM13 encode functionally related products that act in parallel to MCK1 to stimulate IME1 expression.
Variable and scalable security: protection of location information in mobile IP (2002)

The amount of mobile and nomadic computing is expected to increase dramatically in the near future. Hand in hand with this ubiquitous mobile computing security and privacy problems show up, which have not been dealt with sufficiently up to now. The main problems are traffic analysis and the easy access to location information, for example in the popular Internet just by looking at the address headers of messages. The need for security and privacy supporting networks is discussed. We present the nondisclosure method (NDM) as a way to provide the user with variable and scalable security and privacy. We exemplarily demonstrate the applicability of NDM in an existing network by presenting an upward compatible protocol extension to the Internet protocol (IP), the secure IP in IP protocol. Its main design goal is the untraceability of network connections in mobile environments.
Therapeutic antibody engineering (2012)

Therapeutic antibody engineering , Therapeutic antibody engineering , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
Four Novel Three-Dimensional Triazole-Based Zinc(II) Metal−Organic Frameworks Controlled by the Spacers of Dicarboxylate Ligands:  Hydrothermal Synthesis, Crystal Structure, and Luminescence Properties (2007)

Four novel mixed-ligand metal−organic frameworks (MOFs), [Zn5(μ3-OH)2(BTA)2(tp)3]n (1), [Zn(BTA)(chdc)0.5]n (2), [Zn(BTA)(ap)0.5]n (3), and [Zn(BTA)(gt)0.5]n (4) (BTAH = benzotriazole, H2tp = terephthalic acid, H2chdc = 1,4-cyclohexanedicarboxylic acid, H2ap = adipic acid, and H2gt = glutaric acid), have been synthesized by the reaction of zinc(II) chloride and BTAH with four different aromatic/aliphatic binary acids under similar hydrothermal conditions. All these compounds are fully structurally characterized by elemental analysis, IR, single-crystal X-ray crystallography, and the bulk new materials were further identified by X-ray powder diffraction. Their compositional stability and photoluminescence properties were further investigated to establish the structure−properties relationships. Structural analysis reveals that 1 is a scarcely reported eight-connected three-dimensional (3-D) self-penetrating MOF with pentanuclear zinc clusters as secondary building units (SBUs); 2 is a 3-D infinite network with empty 34-membered hexanuclear zinc(II) metallamacrocycle channels; 3 and 4 are 3-D meso-racemic coordination polymers with a one-dimensional Zn-BTA helix chain motif, in which alternative right- and left-hand helical chains are linked together via ap for 3 and gt for 4. The much higher compositional stability up to 436 °C and strong solid-state luminescence emissions suggest that 1−4 are good candidates for light emission materials.
Spontaneously Arising Immortal Cell Line of Rat Retinal Pigmented Epithelial Cells (1993)

A continuous cell line of rat retinal pigment epithelium (RPE), named BPEI-1, has been established and characterized. Sheets of pure RPE cells, uncontaminated by choroidal or neural retinal cell types, were isolated from eyes of 7-day-old Long Evans rats and established in primary culture. The primary RPE cells became extensively spread and grew slowly for approximately 1 month, at which time a colony of small rapidly dividing cells spontaneously appeared. Following trypsinization, most of the typical primary RPE cells did not survive and were quickly outnumbered by the smaller cells, which gave rise to a cell line that was grown continuously for several hundred generations. When growing at the maximal rate in media containing 20% FBS (doubling time 18 h), the cells were fibroblastic and nearly devoid of pigment, but were capable of morphologic transition back to a pigmented, epithelioid form when cultured under low serum conditions. Evidence that these cells originated from RPE included specific immunolabeling with antibodies to cellular retinaldehyde binding protein and cytokeratin, negative GFAP immunoreactivity, and demonstration of avid phagocytosis of isolated rod outer segments by these cells. Partial characterization of choroidal cells eliminated the latter cells as possible contaminants which could have given rise to the cell line. The BPEI-1 cell line, and other rat RPE cell lines currently being developed from pigmented normal (LE, RCS rdy+p+) and retina] dystrophic (RCS p+) rats should facilitate biochemical and molecular biological approaches to study of RPE cell function in health and disease.
Hybrid JPEG Compression Using Color Based Segmentation (2015)

We cannot operate the whole image directly in some applications like image recognition or image compression because it is inefficient method. Therefore, before recognition or compression, many image segmentation algorithms were suggested to segment an image. Image segmentation operation is to rate or cluster an image into many regions depending on the feature of image. A hybrid image compression algorithm is suggested in this paper which segments the image into background and foreground parts and after that compresses the foreground image by using DCT technique. The foreground image is provided more importance than the background region. The color based segmentation method is used to segment image. The observed parameters are compression ratio (CR), mean square error (MSE), and peak signal to noise ratio (PSNR). The goal is to maximize the CR while preserving images' information. The foreground image has a good quality in this the proposed hybrid method.
Griffiths phase behaviour in a frustrated antiferromagnetic intermetallic compound (2015)

The rare coexistence of a Griffiths phase (GP) and a geometrically frustrated antiferromagnetism in the non-stoichiometric intermetallic compound GdFe0.17Sn2 (the paramagnetic Weiss temperature θp ~ -59 K) is reported in this work. The compound forms in the Cmcm space group with large structural anisotropy (b/c ~ 4). Interestingly, all the atoms in the unit cell possess the same point group symmetry (Wycoff position 4c), which is rather rare. The frustration parameter, f = |θp|/TN has been established as 3.6, with the Néel temperature TN and Griffiths temperature TG being 16.5 and 32 K, respectively. The TG has been determined from the heat capacity measurement and also from the magnetocaloric effect (MCE). It is also shown that substantial difference in GP region may exist between zero field and field cooled measurements - a fact hitherto not emphasized so far.
IL-12 Deficiency in MRL- Fas lpr Mice Delays Nephritis and Intrarenal IFN-γ Expression, and Diminishes Systemic Pathology (2003)

Autoimmune disease in MRL-Fas(lpr) mice is characterized by fatal nephritis, systemic pathology, and autoantibodies, mimicking human lupus. We previously reported that 1) intrarenal IL-12 elicits nephritis by fostering the accumulation of intrarenal IFN-gamma-secreting T cells, and 2) MRL-Fas(lpr) mice deficient in the IFN-gamma receptor were spared from nephritis. Therefore, we hypothesized that eliminating IL-12 in MRL-Fas(lpr) mice reduces IFN-gamma-secreting cells and thereby prevents systemic pathology. For this purpose, we constructed an IL-12p40-deficient MRL-Fas(lpr)(IL-12(-/-)) strain. We determined that glomerular and interstitial, but not perivascular, renal pathology were decreased in IL-12(-/-) mice vs the wild-type (WT) strain (5 mo of age). Similarly, systemic pathology (lung, lacrimal and salivary glands, skin, and lymphadenopathy) was diminished. The intrarenal accumulation of T cells (CD4(+), CD8(+), CD4(-)CD8(-)B220(+)) and macrophages was dramatically reduced in IL-12(-/-) MRL-Fas(lpr) kidneys. We determined that there were fewer IFN-gamma transcripts (>70%) in the IL-12(-/-) protected kidneys compared with the WT kidneys. Similarly, cells propagated from IL-12(-/-) MRL-Fas(lpr) kidneys generated substantially less IFN-gamma when stimulated with IL-12 and IL-18 compared with those from WT kidneys, and we detected fewer CD8 and B220 T cells producing IFN-gamma in these IL-12(-/-) MRL-Fas(lpr) kidneys. Of note, survival was modestly extended in the IL-12(-/-) MRL-Fas(lpr) mice. While lung and lacrimal and salivary gland pathology remained reduced in moribund IL-12(-/-) MRL-Fas(lpr) mice, renal pathology and IFN-gamma expression were equivalent to those in the WT strain. Thus, we suggest that IL-12 is a therapeutic target for multiple tissues in lupus; however blocking IL-12 alone is not sufficient to confer enduring protection from lupus nephritis.
A FRET-Based Assay Platform for Ultra-High Density Drug Screening of Protein Kinases and Phosphatases (2002)

Protein phosphorylation is one of the major regulatory mechanisms involved in signal-induced cellular events, including cell proliferation, apoptosis, and metabolism. Because many facets of biology are regulated by protein phosphorylation, aberrant kinase and/or phosphatase activity forms the basis for many different types of pathology. The disease relevance of protein kinases and phosphatases has led many pharmaceutical and biotechnology companies to expend significant resources in lead discovery programs for these two target classes. The existence of >500 kinases and phosphatases encoded by the human genome necessitates development of methodologies for the rapid screening for novel and specific compound inhibitors. We describe here a fluorescence-based, molecular assay platform that is compatible with robotic, ultra-high throughput screening systems and can be applied to virtually all tyrosine and serine/threonine protein kinases and phosphatases. The assay has a coupled-enzyme format, utilizing the differential protease sensitivity of phosphorylated versus nonphosphorylated peptide substrates. In addition to screening individual kinases, the assay can be formatted such that kinase pathways are re-created in vitro to identify compounds that specifically interact with inactive kinases. Miniaturization of this assay format to the 1-microl scale allows for the rapid and accurate compound screening of a host of kinase and phosphatase targets, thereby facilitating the hunt for new leads for these target classes.