gebhart/patrepeval huggingface dataset:
Systemic lupus erythematosus. Antibodies to DNA, DNA-binding proteins, and histones. (1994)

Pathogenic autoantibodies to DNA are frequently associated with autoantibodies to chromatin-associated proteins such as histones or the Ku (p70/p80) antigens. In view of the increasing evidence that autoantibody production is antigen-driven, and because DNA is packaged with proteins in the cell, we suggest that anti-DNA antibodies may arise in response to DNA-protein complexes rather than naked DNA. Recent studies of the specificities of autoantibodies directed against the components of nucleosomes and transcriptional complexes are consistent with this hypothesis. The possible clinical significance of immune recognition of various types of chromatin complexes in autoimmune disease is discussed.
Transgenic mouse models of spinal and bulbar muscular atrophy (SBMA) (2003)

Spinal and bulbar muscular atrophy (SBMA) is a late-onset motor neuron disease characterized by proximal muscle atrophy, weakness, contraction fasciculations, and bulbar involvement. Only males develop symptoms, while female carriers usually are asymptomatic. A specific treatment for SBMA has not been established. The molecular basis of SBMA is the expansion of a trinucleotide CAG repeat, which encodes the polyglutamine (polyQ) tract, in the first exon of the androgen receptor (AR) gene. The pathologic hallmark is nuclear inclusions (NIs) containing the mutant and truncated AR with expanded polyQ in the residual motor neurons in the brainstem and spinal cord as well as in some other visceral organs. Several transgenic (Tg) mouse models have been created for studying the pathogenesis of SBMA. The Tg mouse model carrying pure 239 CAGs under human AR promoter and another model carrying truncated AR with expanded CAGs show motor impairment and nuclear NIs in spinal motor neurons. Interestingly, Tg mice carrying full-length human AR with expanded polyQ demonstrate progressive motor impairment and neurogenic pathology as well as sexual difference of phenotypes. These models recapitulate the phenotypic expression observed in SBMA. The ligand-dependent nuclear localization of the mutant AR is found to be involved in the disease mechanism, and hormonal therapy is suggested to be a therapeutic approach applicable to SBMA.
Protective effect of L-propionylcarnitine on cyclosporine-induced nephrotoxicity. (1995)

Nephrotoxicity has represented the major limitation in the use of cyclosporine A (CyA). The structural abnormalities at the level of the proximal tubular cells are necrosis, vacuolisation and lipid droplets, as well as CyA-induced glomerular afferent arteriole constriction and granular juxtaglomerular cell hyperplasia. The mode of action of vasoconstriction is not well known, but there appears to be substantial impairment of endothelial cell function leading to enhanced release of vasoconstrictors such as endothelin and thromboxane. L-propionylcarnitine (PC), one of the most potent analogues of carnitine, is able to correct and to prevent alterations in endothelial membrane permeability and it has been identified in the kidney of various animal species. To investigate a possible reduction of CyA-induced nephrotoxocity, we examined the effects of a pretreatment with PC before administering several doses of CyA in an isolated and perfused rat kidney. The histological findings showed that the perfusion with PC reduces the vasoconstrictive effect of CyA on the glomerular capillaries and preserves the tubular epithelium. The ratio of the diameter between the glomerular capillary tuft and Bowman's capsule was higher, while at the tubular level the ratio internal-diameter/diameter evaluated at the level of the basal membrane was lower in PC + CyA perfused kidneys than in only CyA perfused ones. The final value of perfusion pressure was lower in PC + CyA perfused kidneys than in only CyA perfused ones, confirming the histological findings. The release induced by CyA of alanine aminopeptidase (AAP) and N-acetyl-glucosaminidase (NAG), markers of tubular damage, was significantly reduced by pretreatment with PC. These data suggest that the pretreatment with PC reduces the CyA-induced nephrotoxicity in an isolated and perfused rat kidney.
A phenomenology-based approach to the automated recognition of materials in HYDICE imagery (1998)

In order to recognize an object's spectral signature and to identify that object, it is necessary to define the object's signature in contrast to relevant background materials, whether the object encompasses whole pixels or is part of a mixed pixel. The authors have developed an object recognition technique that performs automated materials recognition with respect to a spectral database. As part of the recognition process, the technique also orders the spectral database according to how similar a spectrum is to a given pixel. The technique performs this ordering at each step of an iterative demixing process, giving a hierarchical partitioning of the data with respect to a given pixel spectrum. The authors are using an ATR tool to understand database structure. The ATR tool is useful for this because it partitions the database as part of the process. The method operates on the whole pixel, reducing the pixel to mixed components if needed. The method also uses statistically significant thresholds to decide what is in the pixel. The authors show the application of this tool to determining spectral signatures for 5 selected objects in a HYDICE image, based on the relevant spectral database. They use an ATR tool, that called the residual correlation method (RCM). The RCM is based on an iterative solution to a set of linear mixing equations. The RCM can be used to recognize subpixel or whole pixel targets using multispectral or hyperspectral imagery. The foundation for the RCM is the linear mixing model (LMM). The LMM models each spectrum in an image as a linear combination of a set of contributing subpixel components.
Analysis of theEscherichia coligenome. III. DNA sequence of the region from 87.2 to 89.2 minutes (1993)

The DNA sequence of 96.5 kilobases of the Escherichia coli K-12 genome has been determined, spanning the region between rrnA at 87.2 minutes and katG at 89.2 minutes on the genetic map. The sequence includes 84 open reading frames, of which 46 code for unidentified proteins. Six previously mapped but unsequenced genes have been identified in this span: mob, fdhD, rhaD, rhaA, rhaB, and kdgT. In addition, five new genes have been assigned: the heat shock genes hslU and hsIV, and the genes fdoG, fdoH, and fdol, which encode the three subunits of formate dehydrogenase-O. The arrangement of the genes relative to possible promoters and terminators suggests 57 potential transcription units. Other features include the precise location of the bacteriophage P2 attachment site attP211 , and eleven REP elements, including one containing 9 REP sequences-one of the largest such elements known. This segment brings the total length of contiguous finished sequence to 325 kilobases.
Cone photoreceptor topography in the retina of sexually mature Pacific salmonid fishes (1997)

We examined the retinal cone topography in sexually mature individuals from four species of Pacific salmonid fishes by using semithin plastic sections. We identified variations in cone density and cone arrangements and noted the presence of putative ultraviolet (UV) cones. Putative UV cones were found over an area extending dorsotemporally from the center of the retina. Because most of the putative UV cones are believed to disappear in early ontogeny, their presence over a large proportion (15-20%) of the surface area of the adult retina suggests that they may be reincorporated prior to or at sexual maturity, at least in rainbow trout. Cone density varied across the retina, with highest values at the peripheral margin. Relatively high densities were observed ventrotemporally (in all specimens) and, to a lesser extent, dorsonasally (7 of 11 specimens). The higher cone density in the ventrotemporal retina may represent a retinal specialization in the part of the visual field located above and in front of the animal. Lowest cone densities were found dorsocentrally and coincided approximately with the distribution of putative UV cones, raising the possibility that these cones may not be used in visual tasks requiring the higher visual acuity normally associated with higher cone densities. We also report a novel cone arrangement that consists of rows of double cones inserted between rows composed of single-double cone pairs alternating in position.
INTELLIGENT CAR : HISTORY AND THE FUTURE IN JAPAN AND TOYOTA (1998)

This paper begins with an overview of the history of vehicle information services in Japan. It then describes the online information service known as MONET (MObile NETwork) which offers features such as : real-time traffic information, a link to an in- vehicle navigation system, parking information, motorist aid, email capabilities, and news and weather reports.
Bone allografts (2007)

Bone allografts can be used in any kind of surgery involving bone from minor defects to major bone loss after tumour resection. This review describes the various types of bone grafts and the current knowledge on bone allografts, from procurement and preparation to implantation. The surgical conditions for optimising the incorporation of bone are outlined, and surgeon expectations from a bone allograft discussed.
Characterization of homogentisate prenyltransferases involved in plastoquinone‐9 and tocochromanol biosynthesis (2006)

A cDNA of Chlamydomonas reinhardtii encoding a plastidial homogentisate prenyltransferase was identified. Functional expression studies in Escherichia coli revealed that the enzyme possessed properties similar to the prenyltransferase of Arabidopsis thaliana encoded by At3g11950 but different from the phytyltransferases of A. thaliana and Synechocystis. Unlike the phytyltransferases, the C. reinhardtii and the respective A. thaliana enzyme showed highest activities with solanesyl diphosphate, but were hardly active with phytyl diphosphate. Hence, these data provide evidence that the latter represent homogentisate solanesyltransferases involved in plastoquinone-9 biosynthesis. Overexpression of At3g11950 in A. thaliana, however, suggests that the solanesyltransferase can affect tocopherol biosynthesis as well.
The Deubiquitinating Enzyme USP10 Regulates the Post-endocytic Sorting of Cystic Fibrosis Transmembrane Conductance Regulator in Airway Epithelial Cells (2009)

The cystic fibrosis transmembrane conductance regulator (CFTR), a member of the ABC transporter superfamily, is a cyclic AMP-regulated chloride channel and a regulator of other ion channels and transporters. In epithelial cells CFTR is rapidly endocytosed from the apical plasma membrane and efficiently recycles back to the plasma membrane. Because ubiquitination targets endocytosed CFTR for degradation in the lysosome, deubiquitinating enzymes (DUBs) are likely to facilitate CFTR recycling. Accordingly, the aim of this study was to identify DUBs that regulate the post-endocytic sorting of CFTR. Using an activity-based chemical screen to identify active DUBs in human airway epithelial cells, we demonstrated that Ubiquitin Specific Protease-10 (USP10) is located in early endosomes and regulates the deubiquitination of CFTR and its trafficking in the post-endocytic compartment. small interference RNA-mediated knockdown of USP10 increased the amount of ubiquitinated CFTR and its degradation in lysosomes, and reduced both apical membrane CFTR and CFTR-mediated chloride secretion. Moreover, a dominant negative USP10 (USP10-C424A) increased the amount of ubiquitinated CFTR and its degradation, whereas overexpression of wt-USP10 decreased the amount of ubiquitinated CFTR and increased the abundance of CFTR. These studies demonstrate a novel function for USP10 in facilitating the deubiquitination of CFTR in early endosomes and thereby enhancing the endocytic recycling of CFTR.
History of Organometallic Polymers (1981)

Abstract In the last 20 years a wide variety of new types of polymers has been prepared containing metals as an integral part of the polymer backbone. This paper summarizes deveopments in the following major areas: vinylic polymers, including vinyl metal-locene derivatives and vinylic tin monomers; condensation polymers; polyorganophosphazenes; coordination polymers; mixed valence polymers with electrical conductivity such as (SN)x, polyacetylene and polyphenylene; stacked polymers such as platinum blue, polyphthalocyanines, and TTF-TCNQ. The methods of synthesis and potential applications of these materials in areas such as catalysis, elastomers with low and high temperature stability, metallic conductors, semiconductors, bacteriacides, fungicides, and cancer chemotherapeutic agents are discussed.
Cytoplasmic RNA Polymerase in Escherichia coli (2001)

To obtain an estimate for the concentration of free functional RNA polymerase in the bacterial cytoplasm, the content of RNA polymerase beta and beta' subunits in DNA-free minicells from the minicell-producing Escherichia coli strain chi925 was determined. In bacteria grown in Luria-Bertani medium at 2.5 doublings/h, 1.0% of the total protein was RNA polymerase. The concentration of cytoplasmic RNA polymerase beta and beta' subunits in minicells produced by this strain corresponded to about 17% (or 2.5 microM) of the value found in whole cells. Literature data suggest that a similar portion of cytoplasmic RNA polymerase subunits is in RNA polymerase assembly intermediates and imply that free functional RNA polymerase can form a small percentage of the total functional enzyme in the cell. On infection with bacteriophage T7, 20% of the minicells produced progeny phage, whereas infection in 80% of the cells was abortive. RNA polymerase subunits in lysozyme-freeze-thaw lysates of minicells were associated with minicell envelopes and were without detectable activity in an in vitro transcription assay. Together, these results suggest that most functional RNA polymerase is associated with the DNA and that little if any segregates into DNA-free minicells.
Caspases as therapeutic targets in Alzheimer's disease: is it time to "cut" to the chase? (2009)

Mounting evidence suggests the involvement of caspases in the disease process associated with Alzheimer's disease (AD). The activation of caspases may be responsible for the neurodegeneration associated with AD and several recent studies have suggested that caspases may also play a role in promoting pathogenic mechanisms underlying this disease. Thus, caspase activation and cleavage of the amyloid precursor protein (APP) and tau may facilitate both the production of beta-amyloid (Abeta) as well as the formation of neurofibrillary tangles (NFTs). Because the activation of caspases in AD may be a proximal event that is not just associated with neurodegeneration, caspases are potential therapeutic targets for the treatment of this disorder. In this review, studies documenting the role of caspases in the AD brain will be discussed. In this context, a discussion of the therapeutic value of targeting caspase inhibition in the treatment of AD will be evaluated including drug targets, delivery and selectivity.
Color2Gray (2005)

Visually important image features often disappear when color images are converted to grayscale. The algorithm introduced here reduces such losses by attempting to preserve the salient features of the color image. The Color2Gray algorithm is a 3-step process: 1) convert RGB inputs to a perceptually uniform CIE L*a*b* color space, 2) use chrominance and luminance differences to create grayscale target differences between nearby image pixels, and 3) solve an optimization problem designed to selectively modulate the grayscale representation as a function of the chroma variation of the source image. The Color2Gray results offer viewers salient information missing from previous grayscale image creation methods.
Expression and function of Toll-like receptors 2 and 4 in human keratinocytes (2003)

Keratinocytes have the ability to kill pathogenic fungi and bacteria by producing antimicrobial substances. Recent studies suggest that microbial components use signaling molecules of the human Toll-like receptor (TLR) family to transduce signals in various cells. Here we provide evidence that keratinocytes express both TLR2 and TLR4 at the mRNA and protein levels, and show that TLR2 and TLR4 are present in the normal human epidermis in vivo and that their expression is regulated by microbial components. The expression of myeloid differentiation protein gene (MyD88), which is involved in the signaling pathway of many TLR, was also demonstrated in keratinocytes. LPS + IFN-gamma increased the expression of TLR2 and TLR4 50- and 5-fold respectively. Treatment of keratinocytes with Candida albicans, mannan, Mycobacterium tuberculosis or LPS with IFN-gamma resulted in the activation and nuclear translocation of NF-kappaB. Inhibition of NF-kappaB blocked the Candida-killing activity of keratinocytes, suggesting that the antimicrobial effect of keratinocytes requires NF-kappaB activation. LPS + IFN-gamma, C. albicans (4 Candida/KC), peptidoglycan (1 micro g/ml) or M. tuberculosis extract significantly increased IL-8 gene expression after 3 h of treatment (P < 0.05). The increases over the 0-h level were 15-, 8-, 10.8- and 7-fold, respectively. The microbial compound-induced increase in IL-8 gene expression could be inhibited by anti-TLR2 and anti-TLR4 neutralizing antibodies, suggesting that TLRs are involved in the pathogen-induced expression of this pro-inflammatory cytokine. Our findings stress the importance of the role of keratinocytes as a component of innate immunity.
Membrane-Associated Heparan Sulfate Proteoglycan Is a Receptor for Adeno-Associated Virus Type 2 Virions (1998)

The human parvovirus adeno-associated virus (AAV) infects a broad range of cell types, including human, nonhuman primate, canine, murine, and avian. Although little is known about the initial events of virus infection, AAV is currently being developed as a vector for human gene therapy. Using defined mutant CHO cell lines and standard biochemical assays, we demonstrate that heparan sulfate proteoglycans mediate both AAV attachment to and infection of target cells. Competition experiments using heparin, a soluble receptor analog, demonstrated dose-dependent inhibition of AAV attachment and infection. Enzymatic removal of heparan but not chondroitin sulfate moieties from the cell surface greatly reduced AAV attachment and infectivity. Finally, mutant cell lines that do not produce heparan sulfate proteoglycans were significantly impaired for both AAV binding and infection. This is the first report that proteoglycan has a role in cellular attachment of a parvovirus. Together, these results demonstrate that membrane-associated heparan sulfate proteoglycan serves as the viral receptor for AAV type 2, and provide an explanation for the broad host range of AAV. Identification of heparan sulfate proteoglycan as a viral receptor should facilitate development of new reagents for virus purification and provide critical information on the use of AAV as a gene therapy vector.
Development of novel DNA vaccine for VEGF in murine cancer model (2013)

We developed DNA vaccine for vascular endothelial growth factor (VEGF), which may provide the therapeutic option instead of anti-VEGF antibody, bevacizumab. Plasmid containing VEGF mini-gene was constructed in the insertion of B-cell epitope of Hepatitis B core protein [HBc-VEGF], which was an epitope carrier. High titer of anti-VEGF antibody was observed in BALB/c mice which were intramuscularly immunized with HBc-VEGF by electropolator. In mice inoculated with colon 26 cells, tumor volume and microvessel density was decreased in HBc-VEGF with a significant prolonged survival. Co-treatment of purified IgG from immunized mice with HBc-VEGF showed in vitro neutralizing activity for VEGF-induced ERK phosphorylation and tube formation in cultured endothelial cells. Furthermore, intravitreally injection of this purified IgG reduced the neovessel formation in the mouse oxygen-induced retinopathy and laser-induced choroidal neovascularization models. These results first provided that DNA vaccine against VEGF possessed the anti-angiogenic effect, leading to prolonged survival in mouse cancer model.
Glucocorticoids and Insulin Promote the Differentiation of Human Adipocyte Precursor Cells into Fat Cells (1987)

To study the in vitro differentiation of human adipocyte precursor cells and its regulation by hormones, primary cultures of stromal vascular cells of human adipose tissue were established. A 30- to 70-fold increase in the number of developing fat cells was achieved by the addition of cortisol or related corticosteroids in the presence of insulin. Either of the two hormones alone was ineffective. The stimulatory action of cortisol was dose dependent and occurred at physiological concentrations. The results suggest that glucocorticoids may play a role in the development of human hyperplastic obesity by stimulating the formation of adipocytes from precursor cells.
Fluorescence Logic‐Signal‐Based Multiplex Detection of Nucleases with the Assembly of a Cationic Conjugated Polymer and Branched DNA (2009)

An energy-transfer cascade is generated from a cationic conjugated polymer (PFP) and negatively charged, Y-shaped DNA labeled with three dyes at its termini (fluorescein (Fl), Tex Red, and Cy5). Multistep fluorescence resonance energy transfer regulates the fluorescence intensities of PFP and the dyes. Different types of logic gates can be operated by observing the emission wavelengths of different dyes with multiplex nucleases as inputs.
The chemokine SDF1/CXCL12 and its receptor CXCR4 regulate mouse germ cell migration and survival (2003)

In mouse embryos, germ cells arise during gastrulation and migrate to the early gonad. First, they emerge from the primitive streak into the region of the endoderm that forms the hindgut. Later in development, a second phase of migration takes place in which they migrate out of the gut to the genital ridges. There, they co-assemble with somatic cells to form the gonad. In vitro studies in the mouse, and genetic studies in other organisms, suggest that at least part of this process is in response to secreted signals from other tissues. Recent genetic evidence in zebrafish has shown that the interaction between stromal cell-derived factor 1 (SDF1) and its G-protein-coupled receptor CXCR4, already known to control many types of normal and pathological cell migrations, is also required for the normal migration of primordial germ cells. We show that in the mouse, germ cell migration and survival requires the SDF1/CXCR4 interaction. First, migrating germ cells express CXCR4, whilst the body wall mesenchyme and genital ridges express the ligand SDF1. Second, the addition of exogenous SDF1 to living embryo cultures causes aberrant germ cell migration from the gut. Third, germ cells in embryos carrying targeted mutations in CXCR4 do not colonize the gonad normally. However, at earlier stages in the hindgut, germ cells are unaffected in CXCR4(-/-) embryos. Germ cell counts at different stages suggest that SDF1/CXCR4 interaction also mediates germ cell survival. These results show that the SDF1/CXCR4 interaction is specifically required for the colonization of the gonads by primordial germ cells, but not for earlier stages in germ cell migration. This demonstrates a high degree of evolutionary conservation of part of the mechanism, but also an area of evolutionary divergence.