gebhart/patrepeval huggingface dataset:
Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target (2011)

This review presents detailed information about the structure of triplet repeat RNA and addresses the simple sequence repeats of normal and expanded lengths in the context of the physiological and pathogenic roles played in human cells. First, we discuss the occurrence and frequency of various trinucleotide repeats in transcripts and classify them according to the propensity to form RNA structures of different architectures and stabilities. We show that repeats capable of forming hairpin structures are overrepresented in exons, which implies that they may have important functions. We further describe long triplet repeat RNA as a pathogenic agent by presenting human neurological diseases caused by triplet repeat expansions in which mutant RNA gains a toxic function. Prominent examples of these diseases include myotonic dystrophy type 1 and fragile X-associated tremor ataxia syndrome, which are triggered by mutant CUG and CGG repeats, respectively. In addition, we discuss RNA-mediated pathogenesis in polyglutamine disorders such as Huntington's disease and spinocerebellar ataxia type 3, in which expanded CAG repeats may act as an auxiliary toxic agent. Finally, triplet repeat RNA is presented as a therapeutic target. We describe various concepts and approaches aimed at the selective inhibition of mutant transcript activity in experimental therapies developed for repeat-associated diseases.
Image compression via joint statistical characterization in the wavelet domain (1999)

We develop a probability model for natural images, based on empirical observation of their statistics in the wavelet transform domain. Pairs of wavelet coefficients, corresponding to basis functions at adjacent spatial locations, orientations, and scales, are found to be non-Gaussian in both their marginal and joint statistical properties. Specifically, their marginals are heavy-tailed, and although they are typically decorrelated, their magnitudes are highly correlated. We propose a Markov model that explains these dependencies using a linear predictor for magnitude coupled with both multiplicative and additive uncertainties, and show that it accounts for the statistics of a wide variety of images including photographic images, graphical images, and medical images. In order to directly demonstrate the power of the model, we construct an image coder called EPWIC (embedded predictive wavelet image coder), in which subband coefficients are encoded one bitplane at a time using a nonadaptive arithmetic encoder that utilizes conditional probabilities calculated from the model. Bitplanes are ordered using a greedy algorithm that considers the MSE reduction per encoded bit. The decoder uses the statistical model to predict coefficient values based on the bits it has received. Despite the simplicity of the model, the rate-distortion performance of the coder is roughly comparable to the best image coders in the literature.
Kinetic sequence discrimination of cationic bis-PNAs upon targeting of double-stranded DNA (1998)

Strand displacement binding kinetics of cationic pseudoisocytosine-containing linked homopyrimidine peptide nucleic acids (bis-PNAs) to fully matched and singly mismatched decapurine targets in double-stranded DNA (dsDNA) are reported. PNA-dsDNA complex formation was monitored by gel mobility shift assay and pseudo-first order kinetics of binding was obeyed in all cases studied. The kinetic specificity of PNA binding to dsDNA, defined as the ratio of the initial rates of binding to matched and mismatched targets, increases with increasing ionic strength, whereas the apparent rate constant for bis-PNA-dsDNA complex formation decreases exponentially. Surprisingly, at very low ionic strength two equally charged bis-PNAs which have the same sequence of nucleobases but different linkers and consequently different locations of three positive charges differ in their specificity of binding by one order of magnitude. Under appropriate experimental conditions the kinetic specificity for bis-PNA targeting of dsDNA is as high as 300. Thus multiply charged cationic bis-PNAs containing pseudoisocytosines (J bases) in the Hoogsteen strand combined with enhanced binding affinity also exhibit very high sequence specificity, thereby making such reagents extremely efficient for sequence-specific targeting of duplex DNA.
Studies on the Biosynthesis of the Hydroxylysine-linked Disaccharide Unit of Basement Membranes and Collagens (1971)

The tissue distribution in the rat of the glucosyl-and galactosyltransferases involved in the biosynthesis of the hydroxylysine-linked disaccharide (2-O-cY-D-glUCOpyranOSyl- n-galactose) and monosaccharide (galactose) units has been investigated.High levels of these enzymes have been found in tissues rich in collagen and basement membranes, including cartilage, uterus, skin, spleen, lung, kidney cortex, and thyroid.Low levels were present in liver, while brain and heart were almost devoid of these enzymes.The relative amounts of these two glycosyltransferases varied, with cartilage, skin, spleen, and lung having similar levels of the two enzymes, while in kidney, thyroid, and uterus there was more of the glucosyl-than the galactosyltransf erase.The two enzymes could be purified from cartilage by Bio-Gel A-1.5m filtration in a manner similar to that previously used for the kidney cortex.The activity of the two glycosyltransferases varied with age in a parallel manner, reaching a maximum at about 9 days after birth, and falling off thereafter to reach levels of about 10% of the maximum in the mature animals.A marked increase in the level of the glucosyltransferase of the uterus was observed in pregnancy, with a doubling of the specific activity and a 16-fold increase in the total activity.The enzyme decreased toward normal in the postpartum state.Measurement of the glucosyltransferase in the renal cortex of alloxan diabetic rats indicated a highly significant increase in activity over age-matched normals, and was believed to reflect an increased synthesis of basement membrane in the diabetic kidney.Differential centrifugation of kidney cortex homogenates in buffered sucrose indicated that both the glucosyl-and galactosyltransferase were present primarily in a rapidly sedimenting particle fraction (650 and 2000 x g), as well as in the high speed supernatant (100,000 x g).The amount
The effect of 5,6-dimethylxanthenone-4-acetic acid on tumour necrosis factor production by human immune cells. (1997)

5,6-dimethylxanthenone-4-acetic acid (5,6-MeXAA) is a potent anti-tumour agent which is undergoing early clinical evaluation. It was developed as an improved analogue of flavone acetic acid (FAA) which failed in clinical trial although it had impressive anti-tumour activity in mice. It has been postulated that one possible reason for the clinical failure of FAA was its inability to induce cytokines, especially tumour necrosis factor (TNF) in humans whereas this was seen as an important component of its mechanism of action in mice. Previous studies have demonstrated that 5,6-MeXAA induces mRNA for TNF in the human HL-60 cell line although the protein was not detected. This study has demonstrated mRNA for TNF alpha by RT-PCR in human and murine immune cells incubated with either 5,6-MeXAA, FAA or in culture medium alone. Using a bioassay technique 5,6-MeXAA and FAA were shown to induce TNF production in vitro by murine macrophages but TNF was not detected when human or murine peripheral blood mononuclear cells were stimulated with these agents. A small but significant production of TNF was seen in the HL-60 cell line after 5,6-MeXAA treatment suggesting 5,6-MeXAA can directly stimulate human cells to produce TNF albeit at low levels.
Interaction of polycationic antibiotics with Pseudomonas aeruginosa lipopolysaccharide and lipid A studied by using dansyl-polymyxin (1986)

A fluorescent derivative of polymyxin B (dansyl-polymyxin) was used to study the interaction of polycations with lipopolysaccharide (LPS) and lipid A from Pseudomonas aeruginosa. Dansyl-polymyxin became bound to LPS and lipid A sites, including Mg2+-binding sites, resulting in a 20-fold enhancement of fluorescence. A Hill plot of the binding data showed that the binding of dansyl-polymyxin to LPS was cooperative (n = 1.98) and of high affinity (S0.5 = 0.38 microM). The maximal binding capacity of LPS was approximately four molecules of dansyl-polymyxin per mol of LPS. The dansyl-polymyxin interaction with lipid A displayed similar kinetics (n = 2.26; S0.5 = 0.38 microM), and the maximal binding capacity was approximately 2 mol of dansyl-polymyxin per mol of lipid A. A variety of polycationic compounds, including gentamicin, streptomycin, and polymyxin B, as well as Mg2+, were able to displace dansyl-polymyxin bound to LPS or to lipid A. Marked differences both in terms of the degree of displacement and in terms of the amount of competing polycation required to displace a given amount of dansyl-polymyxin were observed. Addition of excess polymyxin B resulted in displacement of all of the dansyl-polymyxin, demonstrating that only polymyxin-binding sites were being probed. Our data demonstrate that polymyxin B binds to multiple sites on LPS, including sites which bind aminoglycoside antibiotics and other polycationic compounds.
Characterization of the Murine Antigenic Determinant, Designated L3T4a, Recognized by Monoclonal Antibody GK 1.5: Expression of L3T4a by Functional T Cell Clones Appears to Correlate Primarily with Class II MHC Antigen‐Reactivity (1983)

We describe here the properties of mAb GK1.5, which recognizes a cell surface molecule designated L3T4; the determinant on L3T4 recognized by mAb GK1.5 is designated L3T4a. We present evidence here that: i) the expression of L3T4a by murine T cell clones correlates primarily with class II MHC antigen-reactivity; ii) mAb GK1.5 blocks all class II MHC antigen-specific functions (cytolysis, proliferation, release of lymphokines) by murine class II MHC antigen-reactive T cell clones, although there appears to be clonal heterogeneity in the degree to which these functions are blocked by mAb GK1.5; iii) mAb GK1.5 blocks class II MHC antigen-specific release of IL-2 from cloned T cell hybridomas by blocking class II MHC antigen-specific binding; and iv) L3T4 is very similar to the human Leu3/T4 antigen. The properties of mAb GK1.5 (complement fixation, reactivity with all mouse strains tested, profound blocking of all class II MHC antigen-specific functions by murine T cells, usefulness for FACS analyses, and usefulness for immuno-precipitation/SDS-PAGE analyses) make it suitable for investigating both the role of class II MHC antigen-reactive T cells in various immunological phenomena and the mechanistic basis, at the molecular level, of class II MHC antigen-reactivity by murine T cells.
The Cis-Trans Isomerization of Conjugated compounds (1955)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTThe Cis-Trans Isomerization of Conjugated compoundsGeorge M. WymanCite this: Chem. Rev. 1955, 55, 4, 625–657Publication Date (Print):August 1, 1955Publication History Published online1 May 2002Published inissue 1 August 1955https://pubs.acs.org/doi/10.1021/cr50004a001https://doi.org/10.1021/cr50004a001research-articleACS PublicationsRequest reuse permissionsArticle Views2135Altmetric-Citations128LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Environment matting and compositing (1999)

Article Environment matting and compositing Share on Authors: Douglas E. Zongker University of Washington University of WashingtonView Profile , Dawn M. Werner University of Washington University of WashingtonView Profile , Brian Curless University of Washington University of WashingtonView Profile , David H. Salesin University of Washington and Microsoft Research University of Washington and Microsoft ResearchView Profile Authors Info & Claims SIGGRAPH '99: Proceedings of the 26th annual conference on Computer graphics and interactive techniquesJuly 1999 Pages 205–214https://doi.org/10.1145/311535.311558Online:01 July 1999Publication History 151citation1,247DownloadsMetricsTotal Citations151Total Downloads1,247Last 12 Months45Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Development of a Novel Artificial Matrix with Cell Adhesion Peptides for Cell Culture and Artificial and Hybrid Organs (1989)

The authors present a novel artificial matrix with high cell adhesion and growth rate that was produced by chemical fixation of an RGD-containing peptide (Arg-Gly-Asp) on a polyvinyl alcohol (PVA) surface. The logical sequence behind the molecular design of an artificial matrix that mimics natural adhesive proteins, such as fibronectin, is based on the fact that an RGD tripeptidyl amino sequence is the minimal common adhesion site of adhesive proteins. Activation of surface hydroxyl groups by carbonyl diimidazole successfully incorporated GRGDSP (Gly-Arg-Gly-Asp-Ser-Pro) onto PVA films. The resultant film surface was found to be bioactive, molecularly recognizing the adhesive receptor of bovine endothelial cells. Thus, the artificial matrix mimics active adhesion sites and serves as a novel artificial matrix that may be useful for cell culture, tissue-compatible implants, and hybrid artificial organs.
Identification of a Metalloprotease-Chemokine Signaling System in the Ovarian Cancer Microenvironment: Implications for Antiangiogenic Therapy (2010)

Ovarian cancer is a lethal gynecologic malignancy that may benefit from new therapies that block key paracrine pathways involved in tumor-stromal interactions and tumor vascularity. It was recently shown that matrix metalloprotease-1 (MMP1) activation of the G protein-coupled receptor protease-activated receptor-1 (PAR1) is an important stimulator of angiogenesis and metastasis in peritoneal mouse models of ovarian cancer. In the present study, we tested the hypothesis that MMP1-PAR1 promotes angiogenesis through its paracrine control of angiogenic chemokine receptors. We found that MMP1-PAR1 activation induces the secretion of several angiogenic factors from ovarian carcinoma cells, most prominently interleukin (IL)-8, growth-regulated oncogene-alpha (GRO-alpha), and monocyte chemoattractant protein-1. The secreted IL-8 and GRO-alpha acts on endothelial CXCR1/2 receptors in a paracrine manner to cause robust endothelial cell proliferation, tube formation, and migration. A cell-penetrating pepducin, X1/2pal-i3, which targets the conserved third intracellular loop of both CXCR1 and CXCR2 receptors, significantly inhibited endothelial cell proliferation, tube formation, angiogenesis, and ovarian tumor growth in mice. Matrigel plugs mixed with MMP1-stimulated, OVCAR-4-conditioned media showed a dramatic 33-fold increase in blood vessel formation in mice. The X1/2pal-i3 pepducin completely inhibited MMP1-dependent angiogenesis compared with a negative control pepducin or vehicle. Conversely, a vascular endothelial growth factor-directed antibody, Avastin, suppressed angiogenesis in mice but, as expected, was unable to inhibit IL-8 and GRO-alpha-dependent endothelial tube formation in vitro. These studies identify a critical MMP1-PAR1-CXCR1/2 paracrine pathway that might be therapeutically targeted for ovarian cancer treatment.
Structure and origin of the acute promyelocytic leukemia myl/RAR alpha cDNA and characterization of its retinoid-binding and transactivation properties. (1991)

Acute promyelocytic leukemia (APL) is characterized by the 15;17 chromosomal translocation. Cloning experiments have established that the chromosome 17 breakpoint maps to the RAR alpha and the 15 to the myl locus. The resulting chimeric gene is transcribed as a myl/RAR alpha fusion mRNA. By isolating both normal myl and APL myl/RAR alpha cDNAs, we showed that the myl/RAR alpha mRNA encodes for a putative fusion protein with a molecular weight of about 103 kDa, which is made up of 530 amino acids derived from the myl N-terminus and 402 amino acids originating from the RAR alpha C-terminus. The protein includes the RAR alpha DNA and retinoid-binding regions but lacks the A portion of the N-terminal region (A/B region) which is thought to contain one of the RAR alpha transactivation domains. The myl/RAR alpha protein acted as a retinoid-inducible transcription factor with both ligand-independent repressor and ligand-dependent activator functions in transactivation experiments of a retinoic acid-responsive gene. Myl/RAR alpha exerted this dual function three times more effectively than RAR alpha and had about 10-fold greater affinity for RA than RAR alpha. Comparison of myl/RAR alpha genomic and cDNA sequences from the same case demonstrated that both chromosome 15 and 17 breakpoints occurred within introns and the myl and RAR alpha sequences are spliced in the same polyadenylated RNA.
Building carbon nanotubes and their smart architectures (2002)

Carbon nanotubes have fascinating physical properties. In order to use these novel one-dimensional structures for applications (such as in electronic devices, mechanical reinforcements and nano-electromechanical systems) the structure of nanotubes needs to be tailored and various architectures have to be configured using nanotube building blocks. Firstly, in this paper we focus on the directed and self-assembly of nanotubes on planar substrates into hierarchical structures that include oriented arrays, and ordered bundles. These structures are achieved by patterning substrates with or without metal catalysts. Growth of nanotubes is typically achieved by chemical vapor deposition. Various strategies to build two- and three-dimensional architectures of nanotubes are described by this method. In addition to creating pristine nanotube arrays on planar substrates, the paper also covers some of our recent efforts in fabricating nanotube polymer hybrids. Recent efforts and challenges in manipulating nanotubes on surfaces and measuring transport properties are discussed. Results of noise measurements carried out on individual nanotubes; surface potential mapping and very high, long-term current carrying capacity (109–1010 A cm−2) are reported. In conclusion, a perspective is given on our recent efforts in creating controlled structures with nanotubes and measuring some of their properties.
Strand Exchange Protein 1 (Sep1) from Saccharomyces cerevisiae Does Not Promote Branch Migration in Vitro (1998)

It has been shown in vitro that Saccharomyces cerevisiae strand exchange protein 1 (Sep1) promotes the transfer of one strand of a linear duplex DNA to a homologous single-stranded DNA circle. Sep1 also has an exonuclease active on DNA and RNA. By using exonuclease III-treated linear duplex DNA with various lengths of single-stranded tail as well as Ca2+ to inhibit the exonuclease activity of Sep1, we show that the processivity of exonuclease activity of Sep1 is greater than previously reported. The results in this work also demonstrate that the joint molecule between the linear duplex and single-stranded circle observed from the Sep1-promoted strand transfer reaction is just the pairing between the long single-stranded tail of the linear duplex DNA (generated by the exonuclease activity of Sep1) and the single-stranded circular DNA. When a synthetic Holliday junction was used as substrate, branch migration facilitated by Sep1 could not be detected. Finally, using electron microscopy no alpha-structure, a joint molecule with displaced single-stranded DNA tail that indicates branch migration could be observed. The results imply that Sep1 cannot promote branch migration in vitro. Further investigation is needed to determine the role of Sep1 in recombination in vivo.
A compact and scalable free-space optical crossbar (1991)

The authors have introduced the design for a compact and scalable free-space optical crossbar. A 256 channel system switching from monomode fibres to multimode fibres which can operate at up to 1 Gbit/s per channel should be realisable using currently available technology. This scheme operates by the use of a diffractive fanout element to multiply image an array of Gaussian beamlets onto a reflective electrically addressed liquid crystal spatial light modulator. This scheme demonstrates an excellent application for computer generated fanout holograms. Experimental investigations have demonstrated that crosstalk between adjacent channels is greatly reduced by the use of Gaussian beamlets.
A/sup 2/DL-an Adaptive Automatic Display Layout system (2002)

With advances in computer technology, complex applications are being developed which involve multi-window operations. With the increasing number of windows on the desktop, effective viewing of all the necessary information for a task becomes difficult. A significant portion of the user's time is spent in opening/closing or moving/resizing the windows. Since these window interface housekeeping activities are not directly related to the user's task domain, time spent on window management causes an increase in the actual task completion time, resulting in reduced user throughput. We propose the A/sup 2/DL (Adaptive Automatic Display Layout) system, which performs window management functions to free the user's cognitive and temporal resources to work on task domain activities rather than managing the multi-window desktop. Our system aims to automate and adapt the layout of the windows according to the current user and his current task domain, thereby enhancing the overall human-computer system performance.
Efficient Generation and Cryopreservation of Cardiomyocytes Derived from Human Embryonic Stem Cells (2010)

These results demonstrate that cardiomyocytes of high quality can be efficiently generated and cryopreserved using hESCs maintained in serum-free medium, a step forward towards the application of these cells to human clinical use or drug discovery.
Endoxifen, a New Cornerstone of Breast Cancer Therapy: Demonstration of Safety, Tolerability, and Systemic Bioavailability in Healthy Human Subjects (2010)

Endoxifen is an active metabolite of tamoxifen, a drug used in the treatment of breast cancer. In order to be clinically effective, tamoxifen must be converted to endoxifen by cytochrome P450 2D6 (CYP2D6). A study involving single escalating oral doses was conducted in humans to evaluate the safety, tolerability, and pharmacokinetics (PK) of endoxifen. This is the first study demonstrating that single oral doses of endoxifen are safe and well tolerated and have sufficient bioavailability to reach systemically effective levels in human subjects. Furthermore, it was found that endoxifen is rapidly absorbed and systemically available and that it displays dose proportionality in peak drug concentrations in plasma (C(max)) and area under the concentration-time curve extrapolated from 0 to ∞ (AUC(0-∞)) over the dose range 0.5-4.0 mg.