gebhart/patrepeval huggingface dataset:
Properties of circular dumbbell RNA/DNA chimeric oligonucleotides containing antisense phosphodiester oligonucleotides (1999)

We have designed a new class of oligonucleotides, "dumbbell RNA/DNA chimeric phosphodiesters", containing two alkyl loop structures with RNA/DNA base pairs (sense (RNA) and antisense (DNA) in the double helical stem. The reaction of nicked (NDRDON) and circular (CDRDON) dumbbell RNA/DNA chimeric oligonucleotides with RNaseH gave the corresponding antisense phosphodiester oligonucleotide together with the sense RNA cleavage products. The liberated antisense phosphodiester oligodeoxynucleotide was bound to the target 35mer RNA, which gave 35mer RNA cleavage products by treatment with RNaseH. The circular dumbbell RNA/DNA chimeric oligonucleotide showed more nuclease resistance than the linear antisense phosphodiester oligodeoxynucleotide(anti-ODN) and the nicked dumbbell RNA/DNA chimeric oligonucleotide.
Video indexing based on mosaic representations (1998)

Video is a rich source of information. It provides visual information about scenes. This information is implicitly buried inside the raw video data, however, and is provided with the cost of very high temporal redundancy. While the standard sequential form of video storage is adequate for viewing in a movie mode, it fails to support rapid access to information of interest that is required in many of the emerging applications of video. This paper presents an approach for efficient access, use and manipulation of video data. The video data are first transformed from their sequential and redundant frame-based representation, in which the information about the scene is distributed over many frames, to an explicit and compact scene-based representation, to which each frame can be directly related. This compact reorganization of the video data supports nonlinear browsing and efficient indexing to provide rapid access directly to information of interest. This paper describes a new set of methods for indexing into the video sequence based on the scene-based representation. These indexing methods are based on geometric and dynamic information contained in the video. These methods complement the more traditional content-based indexing methods, which utilize image appearance information (namely, color and texture properties) but are considerably simpler to achieve and are highly computationally efficient.
A second-site revertant of a defective herpes simplex virus ICP4 protein with restored regulatory activities and impaired DNA-binding properties (1991)

A mutant of herpes simplex virus type 1, vi12, encodes a DNA-binding- and transactivation-deficient ICP4 polypeptide. Because of the mutation, the vi12 virus does not grow on Vero cells but must be propagated on cells that express complementing levels of wild-type ICP4 (E5 cells). A pseudorevertant of vi12, designated pri12, was isolated on the basis of the restored ability to replicate on Vero cells. In addition to the original i12 insertion mutation at amino acid 320, the ICP4 molecule expressed from pri12 possesses an alanine to valine substitution at amino acid 342 within the ICP4 gene. The infectivity of pri12 on Vero cells as measured by burst size is elevated by 5 orders of magnitude relative to that observed for vi12, reflecting the restored ability of the mutant ICP4 molecule possessing the alanine to valine substitution to activate transcription and thus support viral replication. Despite the restored regulatory activities of the pri12 ICP4 molecule, the ability of the pseudorevertant ICP4 molecule to form a high-affinity, specific interaction with the consensus binding site was still impaired relative to that of wild-type ICP4. This observation suggests that the in vitro-measured DNA-binding properties of ICP4 may not reflect the functional interactions occurring in vivo that mediate transcriptional activation.
Electrophysiological Maturation and Integration of Murine Fetal Cardiomyocytes After Transplantation (2007)

In the present study, we investigated the electrophysiological maturation and integration of immature cardiomyocytes after transplantation; maturation and integration are essential to achieve the cardiac regeneration. Murine fetal cardiomyocytes (FCMs) (d12.5-d15.5) expressing enhanced green fluorescent protein under the control of the alpha-actin promoter were injected into cryoinjured areas and adjacent myocardium of cryoinjured mouse ventricles. Viable short axis tissue slices (thickness, 150 microm) of the ventricles were prepared 5 to 6 days after transplantation. Glass microelectrodes were used for measurements of action potentials in transplanted FCMs and host cardiomyocytes within the slices. Stimulation at frequencies of up to 10 Hz was performed via a unipolar electrode placed in viable host tissue. Transplanted FCMs could be distinguished clearly from host tissue by their green fluorescence and their electrophysiological properties: maximal upstroke velocity (V(max)) was significantly lower and action potential duration at 50% repolarization (APD(50)) was significantly longer compared with values of adult cardiomyocytes. Transplanted FCMs surrounded by cryoinjured tissue showed spontaneous electrical and contractile activity, which was in no case synchronous with host tissue. V(max) and APD(50) of these nonintegrated cells matched values of cultivated dissociated FCMs. In contrast, 82% of transplanted FCMs surrounded by viable host tissue were electrically integrated; ie, electrical and contractile activity was synchronous with host tissue and these cells had more mature action potential parameters (significantly higher V(max) and shorter APD(50)) compared with nonintegrated FCMs. In conclusion, electrophysiological maturation and integration of transplanted FCMs depend on an embedment in viable host myocardium. FCMs surrounded by cryoinjured tissue maintain physiological but immature AP properties.
Genetically Encoded Initiator for Polymer Growth from Proteins (2010)

Despite the importance of protein-polymer bioconjugates, there is no general method for producing homogeneous recombinant protein that contains polymer initiators at defined sites. To address this deficiency, we designed the amino acid 4-(2'-bromoisobutyramido)phenylalanine (1) as an initiator in atom-transfer radical polymerization (ATRP) that would provide a stable linkage between the protein and growing polymer. We synthesized 1 and evolved a Methanococcus jannaschii tyrosyl-tRNA synthetase/tRNA(CUA) pair to genetically encode this initiator in response to an amber codon. To demonstrate the utility of this initiator, we produced green fluorescent protein (GFP) with 1 site-specifically incorporated on its surface (GFP-1). Purified GFP-1 was then used as an initiator under standard ATRP conditions with a monomer, oligo(ethylene oxide) monomethyl ether methacrylate, efficiently producing a polymer-GFP bioconjugate where the polymer is connected at our selected site on GFP.
Identification of renal natriuretic peptide receptor subpopulations by use of the non‐peptide antagonist, HS‐142‐1 (1994)

1. The renal actions of natriuretic peptides are dictated by the distribution of guanylyl cyclase-linked (NPRA and NPRB) and non-guanylyl cyclase-linked (NPRC) receptors. Natriuretic peptide receptors have previously been distinguished on the basis of their differential affinity for peptide fragments and analogues; however, most of the available ligands are not fully selective. We have used the specific guanylyl cyclase-linked receptor antagonist, HS-142-1, to investigate the differential distribution of natriuretic peptide receptor subtypes in the human, bovine and rat kidney. 2. Specific, high affinity 3-([125I]-iodotyrosyl)-rat-ANP-(1-28)([125I]-rANP1-28) binding sites were identified in all three species, localized to glomeruli, inner medulla, intrarenal arteries and regions in the outer medulla corresponding to vasa recta bundles. Binding sites were also identified in the smooth muscle lining of the hilar region in the bovine and rat kidney. 3. In the rat, [125I]-rANP1-28 binding was inhibited by unlabelled peptide sequences with a rank order of potency (rANP1-28 > pCNP1-22 > C-ANP4-23). The glomeruli exhibited a heterogeneous population of binding sites, C-ANP4-23 and pCNP1-22 producing a significantly better fit to a two component inhibition curve compared to the single component curve for rANP1-28. 4. Competitive inhibition experiments with the receptor selective ligands, C-ANP4-23 and HS-142-1, suggested that, like the rat, human and bovine glomeruli possessed a heterogeneous population of binding sites, whilst those in the inner medulla and intrarenal arteries of all three species represented a homogeneous population. Rat glomeruli exhibited a high proportion (>80%) of the NPRc receptor subtype whereas in human and bovine glomeruli this receptor represented less than 20% of the total population, the majority of binding sites being HS-142-1-sensitive.5. C-ANP4-23 exhibited a significantly higher inhibitory potency for binding sites in rat glomeruli compared to those in human and bovine kidney whilst HS-142-1 was significantly more potent in the rat and bovine kidney compared to man. No evidence was found to suggest the presence of a renal NPRBreceptor subtype.6. The relative density, affinity and proportion of natriuretic receptor subtypes in the kidney exhibit significant species differences. HS-142-1 may be a valuable tool in further elucidating the localization and function of these receptors, but heterogeneity between species should be considered when selecting experimental models.
CHEMICAL MAKERS TRY BIOTECH PATHS (1998)

RETURN TO ISSUEPREVNewsNEXTCHEMICAL MAKERS TRY BIOTECH PATHSVitamins and a new DuPont polyester are paving the way for biocatalysis useMICHAEL MCCOYView Author Information C&EN Northeast News BureauCite this: Chem. Eng. News 1998, 76, 25, 13–19Publication Date (Print):June 22, 1998Publication History Published online12 November 2010Published inissue 22 June 1998https://pubs.acs.org/doi/10.1021/cen-v076n025.p013https://doi.org/10.1021/cen-v076n025.p013newsACS PublicationsCopyright © 1998 American Chemical SocietyArticle Views7Altmetric-Citations19LEARN 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 options SUBJECTS:Biotechnology,Fermentation Get e-Alerts
Simple reflection technique for measuring the electro-optic coefficient of poled polymers (1990)

A simple reflection technique for measuring the electro-optic coefficient of nonlinear optical polymeric films is described. The technique is based on the polarization rotation of a laser beam due to the electro-optic effect. It requires no waveguiding and can be used to measure polymeric films during, as well as after, the electrical poling process. The results are in excellent agreement with those obtained from the more conventional but much more time consuming waveguiding method.
The spot 14 protein inhibits growth and induces differentiation and cell death of human MCF-7 breast cancer cells (2005)

The S14 (spot 14) gene encodes a protein that is predominantly expressed in lipogenic tissues, such as the liver, white and brown adipose tissues and the lactating mammary glands. Accumulated evidence suggests that S14 could play an important role in the induction of lipogenic enzymes. In humans, the S14 locus resides in the chromosome region 11q13, which is frequently amplified in breast tumours, and as a result, it has been suggested that this protein could play a role in the metabolism and growth of these kinds of tumours. In the present study, we have examined the effects of S14 overexpression in MCF-7 human breast cancer cells. We found that S14 causes (i) an inhibition of cell proliferation and of anchorage-independent growth, (ii) a marked reduction in the number of viable cells and (iii) the induction of differentiation and cell death of these cells. The inhibition of cell growth was associated with a decrease in the expression of cyclin D1 and a reduction of cyclin D1 promoter activity. Increased expression of S14 also caused the accumulation of cytochrome c in the cytosol and loss of mitochondrial membrane potential. These findings suggest that S14 may function as an important modulator of tumorigenesis in human breast by decreasing cell growth and inducing cell death and differentiation.
Determination of Nucleic Acid Recognition Sequences by SELEX (2003)

Interactions of proteins with nucleic acids play important roles in biological phenomenon. Almost every stage in the regulation of gene expression involves the interaction of proteins with specific nucleic acids sequences. The identification of the nucleic acid recognition sequence of a given DNA-binding protein is therefore often the first step to be undertaken in the study of its biological function. Over the last 10 yr, the SELEX procedure (systematic evolution of ligands by exponential enrichment) has been used to identify high-affinity nucleic acids ligands for a large number of different proteins. The method was first described for the identification of the DNA and RNA target sequences of nucleic-acid-binding proteins (1,2) but has since been used for the selection of the nucleic acid sequence ligands for other kinds of molecules (3). SELEX uses the power of genetic selection while taking advantage of in vitro biochemistry. It is a rapid technique that is relatively easy to implement and can accelerate and simplify nucleic-acid/protein interaction studies.
Generation and Characterization of a Mutant of Influenza A Virus Selected with the Neuraminidase Inhibitor BCX-140 (1998)

Influenza neuraminidase (NA) plays an important role in viral replication, and characterization of viruses resistant to NA inhibitors will help elucidate the role of active-site residues. This information will assist in designing better inhibitors targeted to essential active-site residues that cannot generate drug-resistant mutations. In the present study we used the benzoic acid-based inhibitor BCX-140 to select and characterize resistant viruses. BCX-140 binds to the NA active site in an orientation that is opposite that of a sialic acid-based compound, 4-guanidino-2,4-dideoxy-2,3-dehydro-N-acetylneuraminic acid (GANA). Thus, the guanidino group of BCX-140 binds to Glu-276, whereas in GANA the guanidino group binds to Glu-119. We passaged influenza A/Singapore/1/57 (H2N2) in Madin-Darby canine kidney cells in the presence of BCX-140, and virus resistant to this inhibitor was selected after six passages. The NA of this mutant was still sensitive to inhibition by BCX-140. However, the mutant virus was resistant to BCX-140 in plaque and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays. Sequence analysis of hemagglutinin (HA) and NA genes revealed changes in both, although none were in the active site of the NA. Depending on the method of selection of the resistant virus, two types of changes associated with the sialic acid binding site were seen in the HA. One is a change in HA1 of Ala-133 to Thr, a residue close to the binding site, while the other change was Arg-132 of HA1 to Gln, which in HA1 of serotype H3 is a sialic acid contact (Asn-137). Binding studies revealed that both types of resistant viruses had reduced receptor binding affinity compared to that of the wild type. Thus, resistance to BCX-140 was generated by modifying the HA. NA active-site residue 276 may be essential for activity, and thus, it cannot be changed to generate resistance. However, drug-induced changes in the HA can result in a virus that is less dependent on NA activity for growth in cells and, hence, resistant to NA inhibitors.
Curved surface reconstruction using a simple structured light method (1996)

In the conventional structured light approach to 3D object surface reconstruction, it is well known that finding the correspondences between the camera rays and light rays is a difficult problem. In this research we present a novel approach that does not directly use the ray correspondences to derive the surface points as the intersection of the corresponding camera rays and light rays. Instead, we use a virtual linear grid line originating at a grid junction on the object surface being considered. The length and the orientation of the virtual linear grid line in the 3D space are first calculated. Then the 3D positions of the grid junction can be determined. Detailed derivations and experimental results using the real object data are reported.
Trypsin Cleaves Exclusively C-terminal to Arginine and Lysine Residues (2004)

Almost all large-scale projects in mass spectrometry-based proteomics use trypsin to convert protein mixtures into more readily analyzable peptide populations. When searching peptide fragmentation spectra against sequence databases, potentially matching peptide sequences can be required to conform to tryptic specificity, namely, cleavage exclusively C-terminal to arginine or lysine. In many published reports, however, significant numbers of proteins are identified by non-tryptic peptides. Here we use the sub-parts per million mass accuracy of a new ion trap Fourier transform mass spectrometer to achieve more than a 100-fold increased confidence in peptide identification compared with typical ion trap experiments and show that trypsin cleaves solely C-terminal to arginine and lysine. We find that non-tryptic peptides occur only as the C-terminal peptides of proteins and as breakup products of fully tryptic peptides N-terminal to an internal proline. Simulating lower mass accuracy led to a large number of proteins erroneously identified with non-tryptic peptide hits. Our results indicate that such peptide hits in previous studies should be re-examined and that peptide identification should be based on strict trypsin specificity.
Tissue-Engineered Bone Repair of Sheep Cranial Defects with Autologous Bone Marrow Stromal Cells (2001)

Cranial bone defect remains a major challenge to craniofacial surgeons because of limited availability of autologous bone graft to repair the defects and the donor site defects secondary to tissue harvesting. In contrast, tissue-engineering technique can generate a large bone tissue using small amount of autologous cells and therefore avoid these problems. Bone Marrow Stromal Cells (MSCs) have the potential of multi-lineage (including osteogenic) differentiation. The objective of this study was to investigate the potential of using autologous MSCs to repair cranial bone defects by a tissue-engineering approach. Autologous MSCs were isolated from eight adult sheep respectively and were in vitro expanded and induced to become osteogenic cells. Bilateral full-thickness defects (20 mm in diameter) of parietal bones were created in animals and the bone defects were either repaired with the bone implants constituted with MSCs and calcium alginate at the experimental side (n = 8) or treated with calcium alginate only without MSCs (n = 4) or left unrepaired (n = 4) at the control side. New bone tissues were observed either grossly or histologically at the defects of experimental group as early as 6 weeks post-repairing, but not in control groups. The engineered bone tissue became more mature at 18 weeks post-repairing. Three-dimensional computerized tomography (CT) scan revealed an almost complete repair of the defect of experimental group at 18 weeks. This study may provide insight for future clinical repair of cranial defect.
The Cell Biology of Human Aging (1976)

Of all the conflicting views on the causes of biologic aging, there is little disagreement with the axiom that, after reaching sexual maturity, individual members of a species accumulate physiologic decrements that lead to an increase in their likelihood of dying. In fact, for man the actuarial data, first analyzed by the English actuary Gompertz in 1825, reveal that the force of mortality doubles every seven years beyond the age of 30 — that is, after maturity, the rate and probability of dying are exponential with increasing age. The decrements in a variety of human physiologic functions, although subject to . . .
Regulated phosphorylation and dephosphorylation of GAL4, a transcriptional activator. (1989)

In yeast, galactose triggers a rapid GAL4-dependent induction of galactose/melibiose regulon (GAL/MEL) gene transcription, and glucose represses this activation. We discovered that alterations in the physical state of the GAL4 protein correlate with activation and repression of the GAL/MEL genes. Using Western immunoblot assay, we observe two electrophoretic forms of GAL4 protein-GAL4I and GAL4II-in noninduced cells. In the absence of glucose, the addition of galactose to such cells results in the rapid appearance of a third and slower-migrating form, GAL4III, which differs from at least GAL4I by phosphorylation. GAL80-deletion cells that constitutively transcribe galactose-responsive genes due to the lack of the GAL80 protein, an antagonist of the GAL4 protein, exhibit GAL4III without galactose addition. Addition of glucose, which results in rapid repression of galactose gene transcription, triggers a rapid elimination of GAL4III and an increase in GAL4II. Cycloheximide experiments provide evidence that the galactose- and glucose-triggered GAL4 protein mobility shifts are due to post-translational modification. GAL4III is labeled with [32P]phosphate in vivo; in vivo 35S-labeled GAL4III could be converted by phosphatase treatment in vitro to GAL4I. We present a model proposing that phosphorylation state changes in the GAL4 protein are key to modulating its activity.