gebhart/patrepeval huggingface dataset:
5΄-Vinylphosphonate improves tissue accumulation and efficacy of conjugated siRNAs in vivo (2017)

5΄-Vinylphosphonate modification of siRNAs protects them from phosphatases, and improves silencing activity. Here, we show that 5΄-vinylphosphonate confers novel properties to siRNAs. Specifically, 5΄-vinylphosphonate (i) increases siRNA accumulation in tissues, (ii) extends duration of silencing in multiple organs and (iii) protects siRNAs from 5΄-to-3΄ exonucleases. Delivery of conjugated siRNAs requires extensive chemical modifications to achieve stability in vivo. Because chemically modified siRNAs are poor substrates for phosphorylation by kinases, and 5΄-phosphate is required for loading into RNA-induced silencing complex, the synthetic addition of a 5΄-phosphate on a fully modified siRNA guide strand is expected to be beneficial. Here, we show that synthetic phosphorylation of fully modified cholesterol-conjugated siRNAs increases their potency and efficacy in vitro, but when delivered systemically to mice, the 5΄-phosphate is removed within 2 hours. The 5΄-phosphate mimic 5΄-(E)-vinylphosphonate stabilizes the 5΄ end of the guide strand by protecting it from phosphatases and 5΄-to-3΄ exonucleases. The improved stability increases guide strand accumulation and retention in tissues, which significantly enhances the efficacy of cholesterol-conjugated siRNAs and the duration of silencing in vivo. Moreover, we show that 5΄-(E)-vinylphosphonate stabilizes 5΄ phosphate, thereby enabling systemic delivery to and silencing in kidney and heart.
Bovine endothelial cells transformed in vitro by benzo(a)pyrene (1983)

A cloned strain of bovine vascular endothelial cells with a finite in vitro lifespan was treated with benzo(a)pyrene (BP) after approximately 75% of its lifespan was completed. Untreated cultures of this strain senesced upon serial subcultivation and contained large, nondividing cells. In three out of seven trials, BP treatment produced transformed lines with altered phenotypic characteristics. The transformed cells appeared in the cultures concomitant with the senescence of the parent cells. All transformed cell lines examined exhibited indefinite lifespans and altered karyotypes. Two of the lines retained most of the characteristics of normal endothelial cells, except that one became aneuploid and the other polyploid. Neither of these lines formed tumors when inoculated into nude mice. The remaining two lines retained mostly diploid karyotypes, but a high percentage of cells contained Robertsonian translocations. In one line cell volume was markedly reduced. In addition, these lines grew in multilayers, were anchorage independent, and proliferated in medium containing 0.5% serum. When 10(7) cells of these lines were injected into nude mice, tumors appeared within 1 week and were identified as malignant hemangioendotheliomas of bovine origin.
Binding of amyloid β‐peptide to mitochondrial hydroxyacyl‐CoA dehydrogenase (ERAB): regulation of an SDR enzyme activity with implications for apoptosis in Alzheimer's disease (1999)

The intracellular amyloid beta-peptide (A beta) binding protein, ERAB, a member of the short-chain dehydrogenase/reductase (SDR) family, is known to mediate apoptosis in different cell lines and to be a class II hydroxyacyl-CoA dehydrogenase. The A beta peptide inhibits the enzymatic reaction in a mixed type fashion with a Ki of 1.2 micromol/l and a KiES of 0.3 micromol/l, using 3-hydroxybutyryl-CoA. The peptide region necessary for inhibition comprises residues 12-24 of A beta1-40, covering the 16-20 fragment, which is the minimum sequence for the blockade of A beta polymerization, but that minimal fragment is not sufficient for more than marginal inhibition. The localization of ERAB to the endoplasmic reticulum and mitochondria suggests a complex interaction with components of the programmed cell death machinery. The interaction of A beta with ERAB further links oxidoreductase activity with both apoptosis and amyloid toxicity.
SOX9 Is Expressed in Normal Prostate Basal Cells and Regulates Androgen Receptor Expression in Prostate Cancer Cells (2007)

SOX9 is a member of the SOX [Sry-related high-mobility group (HMG) box] family of HMG DNA-binding domain transcription factors and is required for the development and differentiation of multiple cell lineages. This report shows that basal epithelial cells express SOX9 in normal prostate, with no detectable expression in luminal epithelial cells. In contrast, SOX9 is expressed in primary prostate cancers in vivo, at a higher frequency in recurrent prostate cancer and in prostate cancer cell lines (LNCaP, CWR22, PC3, and DU145). SOX9 message and protein levels in prostate cancer cells were increased by treatment with glycogen synthase kinase 3beta inhibitor (SB415286), and SOX9 was reduced when beta-catenin was down-regulated by small interfering RNA (siRNA), indicating that SOX9 expression in prostate cancer is regulated by Wnt/beta-catenin signaling. SOX9 bound specifically to androgen receptor (AR) DNA-binding domain glutathione S-transferase fusion proteins, and this interaction was dependent on a short peptide immediately COOH-terminal to the DNA-binding domain (the C-terminal extension), which is required for interactions between steroid hormone receptors and the architectural HMG proteins. Exogenous SOX9 expressed at high nonphysiologic levels decreased AR expression and activity; however, at lower levels, SOX9 increased AR protein expression. Significantly, down-regulation of SOX9 by siRNA in prostate cancer cells reduced endogenous AR protein levels, and cell growth indicating that SOX9 contributes to AR regulation and decreased cellular proliferation. These results indicate that SOX9 in prostate basal cells supports the development and maintenance of the luminal epithelium and that a subset of prostate cancer cells may escape basal cell requirements through SOX9 expression.
Vascular Endothelial Growth Factor 165 Gene Transfer Augments Circulating Endothelial Progenitor Cells in Human Subjects (2000)

Preclinical studies in animal models and early results of clinical trials in patients suggest that intramuscular injection of naked plasmid DNA encoding vascular endothelial growth factor (VEGF) can promote neovascularization of ischemic tissues. Such neovascularization has been attributed exclusively to sprout formation of endothelial cells derived from preexisting vessels. We investigated the hypothesis that VEGF gene transfer may also augment the population of circulating endothelial progenitor cells (EPCs). In patients with critical limb ischemia receiving VEGF gene transfer, gene expression was documented by a transient increase in plasma levels of VEGF. A culture assay documented a significant increase in EPCs (219%, P<0.001), whereas patients who received an empty vector had no change in circulating EPCs, as was the case for volunteers who received saline injections (VEGF versus empty vector, P<0.001; VEGF versus saline, P<0.005). Fluorescence-activated cell sorter analysis disclosed an overall increase of up to 30-fold in endothelial lineage markers KDR (VEGF receptor-2), VE-cadherin, CD34, alpha(v)beta(3), and E-selectin after VEGF gene transfer. Constitutive overexpression of VEGF in patients with limb ischemia augments the population of circulating EPCs. These findings support the notion that neovascularization of human ischemic tissues after angiogenic growth factor therapy is not limited to angiogenesis but involves circulating endothelial precursors that may home to ischemic foci and differentiate in situ through a process of vasculogenesis.
Generalization of the Use of Random Copolymers To Control the Wetting Behavior of Block Copolymer Films (2008)

Random copolymer brushes of poly(styrene-r-methyl methacrylate) (PS-r-PMMA) have previously been used to control the wetting behavior of poly(styrene-b-methyl methacrylate) (PS-b-PMMA) block copolymer. Here we demonstrate that the use of random copolymer may be generalized to other block copolymer systems. A series of poly(styrene-r-2-vinylpyridine-r-hydroxyethyl methacrylate) (PS-r-P2VP-r-PHEMA) random copolymers was synthesized and evaluated as brush layers to control the orientation of domains in thin films of poly(styrene-b-2-vinylpyridine) (PS-b-P2VP) block copolymer. On nonpreferential brushes, thin films of PS-b-P2VP had a mixed orientation of domains consisting of a perpendicular orientation of lamellar domains near the copolymer−substrate interface and a parallel orientation of lamellar domains at free surface because of the lower surface energy of the PS block. The composition window of brushes that induce vertical orientation of domains near the substrate ranges from 47.8% styrene to 57.0% styrene, as determined by SEM and GISAXS measurements of films after removal of the parallel-oriented domains at surfaces (remaining film thickness ≈ 50 nm). When the PS-b-P2VP film was confined between two brushes having compositions within the above range, perpendicular-oriented lamellae that traversed the film thickness were obtained.
Polypeptides that inhibit human breast cancer cell division. (1979)

Medium sized (10-15 amino acids) polypeptides isolated from normal human urine inhibit the growth of five established cell lines of human mammary cancer. Cytostatic and cytotoxic effects are dose dependent and reversible at lower doses. Evidence suggests a block to cell division in S phase.
Automated region selection for analysis of dynamic cardiac SPECT data (1997)

Dynamic cardiac SPECT using Tc-99m labeled teboroxime can provide kinetic parameters (washin, washout) indicative of myocardial blood flow. A time-consuming and subjective step of the data analysis is drawing regions of interest to delineate blood pool and myocardial tissue regions. The time-activity curves of the regions are then used to estimate local kinetic parameters. In this work, the appropriate regions are found automatically, in a manner similar to that used for calculating maximum count circumferential profiles in conventional static cardiac studies. The drawbacks to applying standard static circumferential profile methods are the high noise level and high liver uptake common in dynamic teboroxime studies. Searching along each ray for maxima to locate the myocardium does not typically provide useful information. Here we propose an iterative scheme in which constraints are imposed on the radii searched along each ray. The constraints are based on the shape of the time-activity curves of the circumferential profile members and on an assumption that the short axis slices are approximately circular. The constraints eliminate outliers and help to reduce the effects of noise and liver activity. Kinetic parameter estimates from the automatically generated regions were comparable to estimates from manually selected regions in dynamic canine teboroxime studies.
Sub-μm, planarized, Nb-AlOx-Nb Josephson process for 125 mm wafers developed in partnership with Si technology (1991)

We have demonstrated a new planarized all-refractory technology for low Tc superconductivity (PARTS). With the exception of the Nb-AlOx-Nb trilayer preparation, the processing is done almost exclusively within an advanced Si technology fabrication facility. This approach has allowed us to leverage highly off of existing state-of-the-art lithography, metal etching, materials deposition, and planarization capabilities. Using chemical-mechanical polish as the planarization technique we have fabricated Josephson junctions ranging in size from 0.5–100 μm2. Junction quality is excellent with the figure of merit Vm typically exceeding 70 mV. PARTS has yielded fully functional integrated Josephson devices including magnetometers, gradiometers, and soliton oscillators.
A Single Mutation Converts a Novel Phosphotyrosine Binding Domain into a Dual-specificity Phosphatase (1995)

Dual-specificity protein-tyrosine phosphatases (dsPTPases) have been implicated in the inactivation of mitogen-activated protein kinases (MAPKs). We have identified a novel phosphoserine/threonine/tyrosine-binding protein (STYX) that is related in amino acid sequence to dsPTPases, except for the substitution of Gly for Cys in the conserved dsPTPase catalytic loop (HCXXGXXR(S/T)). cDNA subcloning and Northern blot analysis in mouse shows poly(A+) hybridization bands of 4.6, 2.4, 1.5, and 1.2 kilobases, with highest abundance in skeletal muscle, testis, and heart. Polymerase chain reaction amplification of reverse-transcribed poly(A+) RNA revealed an alternatively spliced form of STYX containing a unique carboxyl terminus. Bacterially expressed STYX is incapable of hydrolyzing Tyr(P)-containing substrates; however, mutation of Gly120 to Cys (G120C), which structurally mimics the active site of dsPTPases, confers phosphatase activity to this molecule. STYX-G120C mutant hydrolyzes p-nitrophenyl phosphate and dephosphorylates both Tyr(P) and Thr(P) residues of peptide sequences of MAPK homologues. The kinetic parameters of dephosphorylation are similar to human dsPTPase, Vaccinia H1-related, including inhibition by vanadate. We believe this is the first example of a naturally occurring "dominant negative" phosphotyrosine/serine/threonine-binding protein which is structurally related to dsPTPases.
Determinations of the DNA sequence of the mreB gene and of the gene products of the mre region that function in formation of the rod shape of Escherichia coli cells (1988)

The 6.5-kilobase mre region at 71 min in the Escherichia coli chromosome map, where genes involved in formation of a rod-shaped cell form a gene cluster, was analyzed by in vivo protein synthesis in a maxicell system and by base sequencing of DNA. An open reading frame that may code for a protein with an Mr of about 37,000 on sodium dodecyl sulfate-polyacrylamide gels was found and was correlated with the mreB gene. N-terminal amino acid sequencing of the hybrid mreB-lacZ protein confirmed the production by mreB of a protein of 347 amino acid residues with a molecular weight of 36,958. The amino acid sequence of this protein deduced from the DNA sequence showed close similarity with that of a protein of the ftsA gene which is involved in cell division of E. coli. Three other contiguous genes that formed three proteins with Mrs of about 40,000, 22,000, and 51,000, respectively, were detected downstream of the mreB gene by in vivo protein synthesis. The mreB protein and some of these three proteins may function together in determination of cell shape.
Classification of Inflammatory Bowel Disease (1989)

Infection, ischaemia, physical damage, or specific immunologic sensitivity should be excluded as far as possible before a diagnosis of non-specific inflammatory bowel disease is made. Non-specific inflammations can be subdivided on the basis of macroscopic and microscopic anatomical criteria. Macroscopic structural abnormalities can be recognized by clinical examination, endoscopy, radiology, and inspection of an operation specimen. These complementary methods of data collection combine with microscopic examinations of tissue to separate disorders that differ in prognosis and possible response to treatment. Anatomic classifications do not necessarily imply differences in aetiology and may change with advances in knowledge.
A duplicate image detection scheme using hash functions for database retrieval (2010)

This paper presents a new duplicate image detection scheme that employs hash functions to cope with the problem resulting from the large image database containing the fingerprints extracted from the images. Moreover, it utilizes the extracted features of the host image to generate a fingerprint, which is then classified in the database systematically. When the authentication of suspect images is needed, the scheme only compares the matches from the same image to decrease the comparison time. The scheme uses the feature vector from the fingerprints to build a hash pool structures, and utilizes the phase angle calculated from the feature vector to query the probably duplicate images in the image database. The experimental results show that the presented scheme performs well according to the recall and precision rates, hence demonstrating the effectiveness of the presented scheme.
Requirement for Invariant Chain in B Cell Maturation and Function (1996)

Previously the role of invariant chain (Ii) had been described only as a chaperone that facilitates folding and transport of major histocompatability complex class II molecules; here it is shown that Ii is required for B cell development. B cells from mice lacking Ii were found to have a low response to T-independent type II antigen and could not proliferate after the mice were injected with antigen. Study of cell surface markers revealed a developmental arrest that prevented immature virgin B cells from becoming mature B cells in the periphery. This block was independent of major histocompatability complex class II expression and was an intrinsic feature of B cells that correlated with the amount of Ii. Thus, Ii participates by an unknown mechanism in B cell maturation.
Gene Transfer and Expression in Plants (2004)

Until recently, agriculture and plant breeding relied solely on the accumulated experience of generations of farmers and breeders that is, on sexual transfer of genes between plant species. However, recent developments in plant molecular biology and genomics now give us access to knowledge and understanding of plant genomes and the possibility of modifying them. This chapter presents an updated overview of the two most powerful technologies for transferring genetic material (DNA) into plants: Agrobacterium-mediated transformation and microparticle bombardment (biolistics). Some of the topics that are discussed in detail are the main variables controlling the transformation efficiency that can be achieved using each one of these approaches; the advantages and limitations of each methodology; transient versus stable transformation approaches; the potential of some in planta transformation systems; alternatives to developing transgenic plants without selection markers; the availability of diverse genetic tools generated as part of the genome sequencing of different plant species; transgene expression, gene silencing, and their association with regulatory elements; and prospects and ways to possibly overcome some transgene expression difficulties, in particular the use of matrix-attachment regions (MARs).
Characterization and Neural Differentiation of Fetal Lung Mesenchymal Stem Cells (2005)

Mesenchymal stem cells (MSCs) have been successfully isolated from a broad range of adult, fetal, and other nonembryonic tissues. Fetal lung has been identified as a rich source of MSCs. However, the biological characteristics and differentiation potential of fetal lung MSCs remain to be explored. In this study, we established a series of methods for isolation and expansion of fetal lung MSCs. These MSCs could withstand more than 40 passages without obvious decline in proliferation ability, significant changes in morphology, and expression of cell markers. Flow cytometric analysis showed that fetal lung MSCs expressed CD13, CD29, CD44, CD90, CD105, CD166, and HLA-ABC, but not CD14, CD31, CD34, CD38, CD41a, CD42b, CD45, CD49d, CD61, CD106, CD133, and HLA-DR. Cell cycle analysis revealed that when the MSCs reached their log phase of growth, more than 90% of the cells were in G0/G1 phase while the proportion of cells in S phase and G2/M phase were about 5.56% and 2.08% cells, respectively. These MSCs could differentiate into neural cells in addition to their mesenchymal differentiation potential. Our data suggest that the fetal lung MSC population is an alternative source of stem cells for cell-based therapy of neurological defects or mesenchymal-originating diseases.
Long-term Endoscopic Remission of Crohn Disease after Autologous Stem Cell Transplantation for Acute Myeloid Leukaemia (2002)

A favourable course of Crohn disease has been observed after allogeneic bone marrow transplantation. and there is now mounting evidence that autologous stem cell may be an effective treatment for severe autoimmune diseases. Here, we present the first long-term endoscopic follow-up of a patient with Crohn disease undergoing autologous stem cell transplantation for haematological disease. A 54-year-old woman developed Crohn disease and was submitted to ileocaecal resection. Four months after surgery, the patient contracted acute myeloid leukaemia. She was initially treated with chemotherapy, and subsequently underwent autologous stem cell transplantation. Following transplantation, the patient has remained in clinical remission regarding both diseases, without anti-inflammatory medication. She has undergone ileo-colonoscopy with normal findings at 1, 2, 3 and 5 years after transplantation. This case suggests that autologous stem cell transplantation can change not only the clinical course, but also the natural history of intestinal inflammation in Crohn disease. This has pathophysiological as well as therapeutic implications.
Acceleration of Amyloid Fibril Formation by Specific Binding of Aβ-(1–40) Peptide to Ganglioside-containing Membrane Vesicles (1997)

The interaction of Alzheimer's Abeta peptide and its fluorescent analogue with membrane vesicles was studied by spectrofluorometry, Congo Red binding, and electron microscopy. The peptide binds selectively to the membranes containing gangliosides with a binding affinity ranging from 10(-6) to 10(-7) M depending on the type of ganglioside sugar moiety. This interaction appears to be ganglioside-specific as under our experimental conditions (neutral pH, physiologically relevant ionic strength), no Abeta binding was observed to ganglioside-free membranes containing zwitterionic or acidic phospholipids. Importantly, the addition of ganglioside-containing vesicles to the peptide solution dramatically accelerates the rate of fibril formation as compared with that of the peptide alone. The present results strongly suggest that the membrane-bound form of the peptide may act as a specific "template" (seed) that catalyzes the fibrillogenesis process in vivo.
Soluble CTLA-4 can suppress autoantibody production and elicit long term unresponsiveness in a novel transgenic model. (1994)

Activation of Ag-specific T cells often requires costimulatory signals in addition to the primary signal mediated through the TCR. The CD28-B7 interaction provides one important costimulatory signal. Previous studies have shown that a soluble CD28 homologue, CTLA4lg, binds B7 with high affinity and can inhibit CD28-B7-mediated costimulation in vitro and in vivo. In this study we examined the ability of soluble human CTLA4lg to inhibit autoantibody production in vivo. For this purpose we used a novel transgenic (Tg) model of autoantibody production. Hepatitis B eAg-expressing Tg mice can be induced to produce autoantibody to the circulating autoantigen (HBeAg) by the injection of a T cell recognition site that fails to elicit T cell tolerance in these mice. Autoimmunity in this model is quantitative because serum autoantibody and autoantigen concentration are inversely correlated and easily measurable by ELISA. In this system a single regimen of CTLA4lg treatment significantly suppressed primary autoantibody production and variably led to long term unresponsiveness. Furthermore, in vivo treatment with CTLA4lg inhibited both T cell activation and T cell-B cell interactions.
Plasma-assisted InP-to-Si low temperature wafer bonding (2002)

The applicability of wafer bonding as a tool to integrate the dissimilar material system InP-to-Si is presented and discussed with recent examples of InP-based optoelectronic devices on Si. From there, the lowering of annealing temperature in wafer bonding by plasma-assisted bonding is the essence of this review paper. Lower annealing temperatures would further launch wafer bonding as a competitive technology and enable a wider use of it. Oxygen plasma treatment has been proven to be very feasible in achieving a strong bonding already at low temperatures. It was also seen that in our experimental setups the results depended on what plasma parameters that were used, since different plasma parameters create different surface conditions.