gebhart/patrepeval huggingface dataset:
Antisense Oligodeoxynucleotide: Inhibitor of Splicing of mRNA of Human Immunodeficiency Virus (1992)

Antisense oligodeoxynucleotide (ODN), which are directed against the splice acceptor site of exon II of the regulatory gene tat of the human immunodeficiency virus type 1 (HIV-1), have been described. These 20-mer ODN's displayed moderate anti-HIV activity in vitro. Using the same antisense ODN (termed ODN-2), which was additionally modified and protected both at the 3'- and the 5'-terminus by two phosphorothioate internucleotide linkages, a strong anti-HIV activity (EC50: 2.7 micrograms/ml) could be measured in the HIV-1/CEM- and HIV-1/HeLa-T4+ cell system. The analogous ODNs which were protected only at one end were either inactive (up to 10 micrograms/ml) or displayed a low antiviral activity. Time kinetic studies revealed that the antisense ODN-2 reduced the release of HIV-1 already after an incubation time of 1 h. By applying S1 nuclease protection procedures, it could be established that the antisense ODN-2 inhibited splicing of high molecular weight transcript to the 2-kb tat mRNA in HIV-1-infected CEM cells. Transfection experiments with pU3R-III chloramphenicol acetyltransferase expression vector in HeLa-T4+ cells revealed that the antisense ODN-2 blocked the Tat protein-mediated transactivation process. In co-transfection experiments using pSV2tat72 or scrape loading studies with purified Tat, the transactivation was restored. These data indicate that the selected antisense ODN-2 displays its anti-HIV effect by blocking the splicing process leading to the functional 2-kb tat mRNA.
Codon usage tabulated from the international DNA sequence databases (1997)

The codon usage in individual protein genes has been calculated using the nucleotide sequence obtained from the GenBank Genetic Sequence Database. Sum of the codon use of each organism has been also calculated. The data files can be obtained from anonymous ftp sites of DDBJ, DISC and EBI. The list of codon usage of genes in organisms was made searchable by name of organism through a web site. The compilation has been synchronized with a major release of GenBank.
Phase-only matched filtering (1984)

From image processing work, we know that the phase information is significantly more important than amplitude information in preserving the features of a visual scene. Is the same true in the case of a matched filter? From previous work [

	 J. L.
	 Horner
	 
	, 
Appl. Opt.21, 
4511(
1982)], we know that a pure phase correlation filter can have an optical efficiency of 100% in an optical correlation system. We examine this relationship between phase and amplitude in the case of alphanumeric characters, with and without noise, using a computer simulation. We compare the phase-only and amplitude-only filters to the classical matched filter using the criteria of discrimination, correlation peak, and optical efficiency. Three-dimensional plots of the autocorrelation and cross-correlation functions are presented and discussed.
Ras and TGFβ cooperatively regulate epithelial cell plasticity and metastasis (2002)

Multistep carcinogenesis involves more than six discrete events also important in normal development and cell behavior. Of these, local invasion and metastasis cause most cancer deaths but are the least well understood molecularly. We employed a combined in vitro/in vivo carcinogenesis model, that is, polarized Ha-Ras-transformed mammary epithelial cells (EpRas), to dissect the role of Ras downstream signaling pathways in epithelial cell plasticity, tumorigenesis, and metastasis. Ha-Ras cooperates with transforming growth factor beta (TGFbeta) to cause epithelial mesenchymal transition (EMT) characterized by spindle-like cell morphology, loss of epithelial markers, and induction of mesenchymal markers. EMT requires continuous TGFbeta receptor (TGFbeta-R) and oncogenic Ras signaling and is stabilized by autocrine TGFbeta production. In contrast, fibroblast growth factors, hepatocyte growth factor/scatter factor, or TGFbeta alone induce scattering, a spindle-like cell phenotype fully reversible after factor withdrawal, which does not involve sustained marker changes. Using specific inhibitors and effector-specific Ras mutants, we show that a hyperactive Raf/mitogen-activated protein kinase (MAPK) is required for EMT, whereas activation of phosphatidylinositol 3-kinase (PI3K) causes scattering and protects from TGFbeta-induced apoptosis. Hyperactivation of the PI3K pathway or the Raf/MAPK pathway are sufficient for tumorigenesis, whereas EMT in vivo and metastasis required a hyperactive Raf/MAPK pathway. Thus, EMT seems to be a close in vitro correlate of metastasis, both requiring synergism between TGFbeta-R and Raf/MAPK signaling.
Grating coupling for intersubband emission (1997)

Grating coupling for surface-emitting intersubband light-emitting diodes (LEDs) and lasers are analyzed with a numerical method. The grating efficiency is calculated as functions of the grating periodicity and filling factor, and the vertical confinement thickness. The coupling loss is related linearly with the grating efficiency, which should be maximized for LEDs to couple out the spontaneous emission, but kept low for lasers to reduce the lasing threshold.
The vitronectin receptor alpha v beta 3 binds fibronectin and acts in concert with alpha 5 beta 1 in promoting cellular attachment and spreading on fibronectin. (1990)

The vitronectin receptor (alpha v beta 3) is a member of the integrin superfamily of adhesive protein receptors that mediate a wide spectrum of adhesive cellular interactions, including attachment to vitronectin, von Willebrand factor, fibrinogen, and thrombospondin. We have studied the binding of fibronectin to the purified vitronectin receptor, and the role of this receptor in the attachment of cells to fibronectin. A solid-phase microtiter assay was developed to investigate the binding properties of the vitronectin receptor. Purified alpha v beta 3 bound fibronectin with high affinity in a saturable, divalent cation-dependent manner. Binding was inhibited by soluble vitronectin, by RGD-containing peptides, and by LM609, a monoclonal antibody against the vitronectin receptor known to inhibit the binding of adhesive proteins to alpha v beta 3. Immunoinhibition experiments showed that M21 human melanoma cells, which express the fibronectin receptor, alpha 5 beta 1, as well as alpha v beta 3, used both of these integrins to attach and spread on fibronectin. In support of this finding, M21-L cells, a variant cell line that specifically lacks alpha v beta 3 but expresses alpha v beta 1, attached and spread poorly on fibronectin. In addition, alpha v beta 3 from surface-labeled M21 cells was retained, and selectively eluted by RGDS from a fibronectin affinity column. These results indicate that alpha v beta 3 acts in concert with alpha 5 beta 1 in promoting fibronectin recognition by these cells. We conclude that fibronectin binds to the alpha v beta 3 vitronectin receptor specifically and with high affinity, and that this interaction is biologically relevant in supporting cell adhesion to matrix proteins.
Mutasynthesis of Rapamycin Analogues through the Manipulation of a Gene Governing Starter Unit Biosynthesis (2005)

The surprising discovery has been made that the gene product RapK is required for production of the starter unit in the rapamycin polyketide cluster. It is shown that a deletion mutant (Streptomyces hygroscopicus MG2–10) provides a clean background for the mutasynthesis of pre-rapamycin (the precursor to rapamycin, see structure) when fed with novel starter units. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z462784_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The therapeutic potential of CRF1 antagonists for anxiety (2004)

Preclinical studies suggest that the brain corticotropin-releasing factor (CRF) systems mediate anxiety-like behavioural and somatic responses through actions at the CRF1 receptor. CRF1 antagonists block the anxiogenic-like effects of CRF and stress in animal models. Cerebrospinal fluid levels of CRF are elevated in some anxiety disorders and normalise with effective treatment, further implicating CRF systems as a therapeutic target. Prototypical CRF1 antagonists are highly lipophilic, non-competitive antagonists of peptide ligands. Modification of the chemotype and the identification of novel pharmacophores are yielding more drug-like structures with increased hydrophilicity at physiological pHs. Newer compounds exhibit improved solubility, pharmacokinetic properties, potency and efficacy. Several clinical candidates have entered Phase I/II trials. However, unmet challenges await resolution during further discovery, clinical development and therapeutic application of CRF1 antagonists.
TSG-6 Protein, a Negative Regulator of Inflammatory Arthritis, Forms a Ternary Complex with Murine Mast Cell Tryptases and Heparin (2011)

TSG-6 (TNF-α-stimulated gene/protein 6), a hyaluronan (HA)-binding protein, has been implicated in the negative regulation of inflammatory tissue destruction. However, little is known about the tissue/cell-specific expression of TSG-6 in inflammatory processes, due to the lack of appropriate reagents for the detection of this protein in vivo. Here, we report on the development of a highly sensitive detection system and its use in cartilage proteoglycan (aggrecan)-induced arthritis, an autoimmune murine model of rheumatoid arthritis. We found significant correlation between serum concentrations of TSG-6 and arthritis severity throughout the disease process, making TSG-6 a better biomarker of inflammation than any of the other arthritis-related cytokines measured in this study. TSG-6 was present in arthritic joint tissue extracts together with the heavy chains of inter-α-inhibitor (IαI). Whereas TSG-6 was broadly detectable in arthritic synovial tissue, the highest level of TSG-6 was co-localized with tryptases in the heparin-containing secretory granules of mast cells. In vitro, TSG-6 formed complexes with the tryptases murine mast cell protease-6 and -7 via either heparin or HA. In vivo TSG-6-tryptase association could also be detected in arthritic joint extracts by co-immunoprecipitation. TSG-6 has been reported to suppress inflammatory tissue destruction by enhancing the serine protease-inhibitory activity of IαI against plasmin. TSG-6 achieves this by transferring heavy chains from IαI to HA, thus liberating the active bikunin subunit of IαI. Because bikunin is also present in mast cell granules, we propose that TSG-6 can promote inhibition of tryptase activity via a mechanism similar to inhibition of plasmin.
Progenitor-Enriched Adipose Tissue Transplantation as Rescue for Breast Implant Complications (2009)

Breast enhancement with artificial implants is one of the most frequently performed cosmetic surgeries but is associated with various complications, such as capsular contracture, that lead to implant removal or replacement at a relatively high rate. For replacement, we used transplantation of progenitor-supplemented adipose tissue (cell-assisted lipotransfer; CAL) in 15 patients. The stromal vascular fraction containing adipose tissue progenitor cells obtained from liposuction aspirates was used to enrich for progenitor cells in the graft. Overall, clinical results were very satisfactory, and no major abnormalities were seen on magnetic resonance imaging or mammogram after 12 months. Postoperative atrophy of injected fat was minimal and did not change substantially after 2 months. Surviving fat volume at 12 months was 155 +/- 50 mL (Right; mean +/- SD) and 143 +/- 80 mL (Left) following lipoinjection from an initial mean of 264 mL. These preliminary results suggest that CAL is a suitable methodology for the replacement of breast implants.
The fibromyalgia impact questionnaire: development and validation. (1991)

An instrument has been developed to assess the current health status of women with the fibromyalgia syndrome. The Fibromyalgia Impact Questionnaire (FIQ) is a brief 10-item, self-administered instrument that measures physical functioning, work status, depression, anxiety, sleep, pain, stiffness, fatigue, and well being. We describe its development and validation. This initial assessment indicates that the FIQ has sufficient evidence of reliability and validity to warrant further testing in both research and clinical situations.
Antibiotic Inducibility of the MexXY Multidrug Efflux System of Pseudomonas aeruginosa : Involvement of the Antibiotic-Inducible PA5471 Gene Product (2006)

The MexXY components of the MexXY-OprM multidrug efflux system of Pseudomonas aeruginosa are encoded by a MexZ repressor-regulated operon that is inducible by antibiotics that target the ribosome. Mutant strains disrupted in a gene, PA5471, were shown to be compromised for drug-inducible mexXY expression and, therefore, MexXY-OprM-mediated antimicrobial resistance. The PA5471 gene was inducible by the same ribosome-targeting agents that induce mexXY expression. Moreover, vector-driven expression of cloned PA5471 was sufficient to promote mexXY expression and MexXY-mediated resistance in the absence of antibiotic exposure, consistent with PA5471 directly or indirectly activating mexXY expression following its own upregulation in response to antibiotics. The requirement for PA5471 for mexXY expression and antimicrobial resistance was, however, obviated in mutants lacking the MexZ repressor of mexXY expression, suggesting that PA5471 directly or indirectly modulates MexZ activity in effecting mexXY expression. While the recruitment of PA5471 and MexXY in response to ribosome disruption by antimicrobials is consistent with their genes playing a role in protecting cells from the adverse consequences of disrupting the translation process, reminiscent of trans-translation, these genes appear to operate independently in their contribution to resistance: mutants defective in trans-translation showed a much more modest (twofold) decrease in resistance to ribosome-targeting agents than those lacking PA5471 or MexXY, and this decrease was observed whether functional PA5471/MexXY was present or not.
Photocrosslinking of Gelatin Macromers to Synthesize Porous Hydrogels That Promote Valvular Interstitial Cell Function (2009)

The development of novel three-dimensional cell culture platforms for the culture of aortic valvular interstitial cells (VICs) has been fraught with many challenges. Although the most tunable, purely synthetic systems have not been successful at promoting cell survivability or function. On the other hand, entirely natural materials lack mechanical integrity. Here we explore a novel hybrid system consisting of gelatin macromers synthetically modified with methacrylate functionalities allowing for photoencapsulation of cells. Scanning electron microscopy observations show a microporous structure induced during polymerization within the hydrogel. This porous structure was tunable with polymerization rate and did not appear to have interconnected pores. Treatment with collagenase caused bulk erosion indicating enzymatic degradation controls the matrix remodeling. VICs, an important cell line for heart valve tissue engineering, were photoencapsulated and examined for cell-directed migration and differentiation. VICs were able to achieve their native morphology within 2 weeks of culture. The addition of the pro-fibrotic growth factor, transforming growth factor-beta1, accelerated this process and also was capable of inducing enhanced alpha-smooth muscle actin and collagen-1 expression, indicating a differentiation from quiescent fibroblasts to active myofibroblasts as demonstrated by quantitative real-time polymerase chain reaction and immunohistochemistry. Although these studies were limited to VICs, this novel hydrogel system may also be useful for studying other fibroblastic cell types.
Tuberculosis of Breast (1993)

Tuberculosis of the breast is an extremity rare disease in western countries and about 0.5% among entire breast in Korea and most of which involved persons between 20 to 40 years of age in female but it rarely developed in male, elderly patient and prepubertal woman. It may be primary-confined to the breast or secondary to tuberculosis elsewhere because of it's diagnostic difficult. Tuberculosis of breast, is confused to actinomycosis infection, abscess and carclnom.So, it is only diagnosed by histopathologic finding or inoculation in experimental animal. I expirienced 3 cases of tuberculosis of the breast in 23 years which were treated with antibiotics, antituberculosis medication and combined with surgical excision.
Sequence-specific recognition and cleavage of duplex DNA via triple-helix formation by oligonucleotides covalently linked to a phenanthroline-copper chelate. (1989)

Homopyrimidine oligodeoxynucleotides recognize the major groove of the DNA double helix at homopurine.homopyrimidine sequences by forming local triple helices. Phenanthroline was covalently attached to the 5' end of an 11-mer homopyrimidine oligonucleotide of sequence d(TTTCCTCCTCT). Simian virus 40 DNA, which contains a single target site for this oligonucleotide, was used as a substrate for the phenanthroline-oligonucleotide conjugate. In the presence of copper ions and a reducing agent, a single specific double-strand cleavage site was observed at 20 degrees C by agarose gel electrophoresis. The efficiency of double-strand cleavage was greater than 70% at 20 degrees C and pH 7.4. Secondary cleavage sites were observed when binding of the oligonucleotide to mismatched sequences was allowed to take place at low temperature. The exact location of the cleavage sites was determined by polyacrylamide gel electrophoresis of denatured fragments by using both simian virus 40 DNA and a synthetic DNA fragment containing the target sequence. The asymmetric distribution of the cleavage sites on the two strands revealed that the cleavage reaction took place in the minor groove even though the phenanthroline linker was located in the major groove. Linkers of different lengths were used to tether phenanthroline to the oligonucleotide and their relative efficacies of DNA cleavage were compared. Based on these comparative studies and on model building, it is proposed that the phenanthroline ring carried by the oligonucleotide intercalates from the major groove and that copper chelation locks the complex in place from within the minor groove where the cleavage reaction occurs.
2015 초등통합교과교육과정 개정을 위한 일 고찰 (2015)

본 연구는 2015 바른 생활과 교육과정, 슬기로운 생활과 교육과정, 즐거운 생활과 교육과정을 개정하고 있는 현재 시점에서 초등통합교과교육과정의 역사에서 진일보하는 개정이 되기 위해서 무엇을 고려해야 하는지를 모색해 보고자 하였다. 이를 위해서 지난 5번의 국가수준의 통합교과 교육과정 어떤 모습으로 발전하고 성장해 왔는지를 살펴보았다. 그리고 이를 기초로 2015 개정 초등통합교과 교육과정 개발을 위해서 고려해 볼 점을 주로 2009 개정으로 인한 변화를 보완 정교화 하는 방향에서 다음과 같이 제안하였다. 첫째, 대주제의 역할과 기능에 대한 탐색이 필요하다. 둘째, 바ㆍ슬ㆍ즐 교과의 내용 및 필수학습 요소 구축이 필요하다.
Emulating Majorana fermions and their braiding by Ising spin chains (2017)

We analyze the control of Majorana zero-energy states by mapping the fermionic system onto a chain of Ising spins. Although the topological protection is lost for the Ising system, the mapping provides additional insight into the nature of the quantum states. By controlling the local magnetic field, one can separate the Ising chain into ferromagnetic and paramagnetic phases, corresponding to topological and nontopological sections of the fermionic system. In this paper we propose (topologically nonprotected) protocols performing the braiding operation, and in fact also more general rotations. We first consider a $T$-junction geometry, but we also propose a protocol for a purely one-dimensional (1D) system. Both setups rely on an extra spin-$\frac{1}{2}$ coupler. By including the extra spin in the $T$-junction geometry, we overcome limitations due to the 1D character of the Jordan--Wigner transformation. In the 1D geometry the coupler, which controls one of the Ising links, should be manipulated once the ferromagnetic (topological) section of the chain is moved far away. We also propose experimental implementations of our scheme. One is based on a chain of flux qubits which allows for all needed control fields. We also describe how to translate our scheme for the 1D setup to a chain of superconducting wires hosting each a pair of Majorana edge states.
Parenteral iron therapy options (2004)

Parenteral iron therapy is occasionally necessary for patients intolerant or unresponsive to oral iron therapy, for receiving recombinant erythropoietin therapy, or for use in treating functional iron deficiency. There are now three parenteral iron products available: iron dextran, ferric gluconate, and iron sucrose. We summarize the advantages and disadvantages of each product, including risk of anaphylaxis and hypersensitivity, dosage regimens, and costs. The increased availability of multiple parenteral iron preparations should decrease the need to use red cell transfusions in patients with iron-deficiency anemia.
Dioxygen Activation at Mononuclear Nonheme Iron Active Sites:  Enzymes, Models, and Intermediates (2004)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDioxygen Activation at Mononuclear Nonheme Iron Active Sites: Enzymes, Models, and IntermediatesMiquel Costas, Mark P. Mehn, Michael P. Jensen, and Lawrence QueView Author Information Departament de Quimica, Universitat de Girona, 17071, Girona, Spain, and Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455 Cite this: Chem. Rev. 2004, 104, 2, 939–986Publication Date (Web):January 28, 2004Publication History Received15 August 2003Published online28 January 2004Published inissue 1 February 2004https://pubs.acs.org/doi/10.1021/cr020628nhttps://doi.org/10.1021/cr020628nresearch-articleACS PublicationsCopyright © 2004 American Chemical SocietyRequest reuse permissionsArticle Views20000Altmetric-Citations2225LEARN 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 SUBJECTS:Hydrocarbons,Iron,Ligands,Metals,Peptides and proteins Get e-Alerts
Natural History of Progression After PSA Elevation Following Radical Prostatectomy (1999)

Several clinical parameters help predict the outcomes of men with PSA elevation after radical prostatectomy. These data may be useful in the design of clinical trials, the identification of men for enrollment into experimental protocols, and counseling men regarding the timing of administration of adjuvant therapies.