gebhart/patrepeval huggingface dataset:
G-quadruplex induced stabilization by 2′-deoxy-2′-fluoro-d-arabinonucleic acids (2′F-ANA) (2007)

The impact of 2'-deoxy-2'-fluoroarabinonucleotide residues (2'F-araN) on different G-quadruplexes derived from a thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2), an anti-HIV phosphorothioate aptamer PS-d(T2G4T2) and a DNA telomeric sequence d(G4T4G4) via UV thermal melting (T(m)) and circular dichroism (CD) experiments has been investigated. Generally, replacement of deoxyguanosines that adopt the anti conformation (anti-guanines) with 2'F-araG can stabilize G-quartets and maintain the quadruplex conformation, while replacement of syn-guanines with 2'F-araG is not favored and results in a dramatic switch to an alternative quadruplex conformation. It was found that incorporation of 2'F-araG or T residues into a thrombin-binding DNA G-quadruplex stabilizes the complex (DeltaT(m) up to approximately +3 degrees C/2'F-araN modification); 2'F-araN units also increased the half-life in 10% fetal bovine serum (FBS) up to 48-fold. Two modified thrombin-binding aptamers (PG13 and PG14) show an approximately 4-fold increase in binding affinity to thrombin, as assessed via a nitrocellulose filter binding assay, both with increased thermal stability (approximately 1 degrees C/2'F-ANA modification increase in T(m)) and nuclease resistance (4-7-fold) as well. Therefore, the 2'-deoxy-2'-fluoro-d-arabinonucleic acid (2'F-ANA) modification is well suited to tune (and improve) the physicochemical and biological properties of naturally occurring DNA G-quartets.
Security design in distributed computing applications (1993)

The software developer designing a security architecture for a distributed application is often faced with practical constraints that further complicate an already difficult task. These include limited resources and conflicting requirements. The goal will often be to simply provide as much effective security as possible, targeted at the end-user security needs. To achieve this goal, the developer must be able to systematically determine where security problems exist, understand the impact of security mechanisms as they are designed, determine which problems have and have not been addressed, explore alternative designs, and build on the architecture in the future. Current approaches to secure system design do not meet these requirements. Although much is understood about many aspects of computer security, little attention has been given to the the issue of how to integrate this knowledge into a design process; of how to generate and maintain a security architecture in a systematic, pre...
The DEC: processing scientific data over the Internet (2002)

We present the Distributed Batch Controller (DBC), a system built to support batch processing of large scientific datasets. The DBC implements a federation of autonomous workstation pools, which may be widely distributed. Individual batch jobs are executed using idle workstations in these pools. Input data are staged to the pool before processing begins. We describe the architecture and implementation of the DBC, and present the results of experiments in which it is used to perform image compression.
<title>Optical Digital Data Storage Technologies With Semiconductor Laser Nead</title> (1983)

A laboratory model optical disk file memory for digital data storage is developed. User storage capacity is 2GBytes per disk and data transfer rate is 350KBytes/sec. Average seek time is 150msec. Several new technologies supporting the device are also described in detail.
Single camera based spectral domain polarization sensitive optical coherence tomography (2007)

We developed a new spectral domain polarization sensitive optical coherence tomography (SD PS-OCT) system that requires only a single spectrometer CCD camera. The spectra of the horizontal and vertical polarization channels are imaged adjacent to each other on a 2048 pixel line scan camera, using 1024 pixels for each channel. Advantages of the system are reduced costs and complexity, lower demands on timing and triggering circuitry, and higher robustness against camera misalignments. We discuss the additional postprocessing required to accommodate for spectral distortions, show calibration measurements in a test sample, and finally demonstrate the system for measuring human ocular tissue in vivo.
Guidelines for DIC in geotechnical engineering research (2016)

Digital image correlation (DIC), also known as particle image velocimetry (PIV), has become a well-established approach for the calculation of field displacements in geotechnical engineering. However, commercial and open-source DIC/PIV software is often used without full realisation of the implications of various parameters on accuracy and efficiency. In this paper, a critical evaluation of the various methods and components of DIC relevant to geotechnical applications is presented. In addition, new algorithms are presented to address some specific problems encountered when using DIC techniques in geotechnical research. Examples and comparisons are presented to support the proposed guidelines, and thus demonstrate the effectiveness of the newly developed techniques.
FR-901228 Fujisawa/National Cancer Institute. (2002)

The depsipeptide FR-901228 is a histone deacetylas inhibitor under development by Fujisawa and the National Cancer Institute as a potential treatment for neoplasm. By May 2002, phase II trials had commenced in the US [452248], [461017].
HIF-1alpha-mediated up-regulation of vascular endothelial growth factor, independent of basic fibroblast growth factor, is important in the switch to the angiogenic phenotype during early tumorigenesis. (2001)

The switch to the angiogenic phenotype represents a critical checkpoint during tumor progression. The acquisition of new capillary vessels provides newly vascularized tumor nodules with a distinct biological advantage over their avascular counterparts by conferring upon them the ability to expand and develop both locally and metastatically. To identify the molecules and mechanisms underlying this rate-limiting step in successful tumorigenesis, we have developed an in vivo tumor model that reproducibly recapitulates the angiogenic switch. Using this model, we have analyzed vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF), and hypoxia-inducible factor-1alpha (HIF-1alpha) expression and activity in both avascular and vascular growth phases of the tumor. A significantly higher level of VEGF protein was detected in avascular tumor nodules compared with vascular nodules. As avascular tumors became vascularized, VEGF levels decreased approximately 10-fold. In contrast, bFGF levels were not elevated in avascular nodules but rather were detected at levels approximately 2 times higher in vascular nodules compared with the avascular tumor nodules. Given that VEGF is transcriptionally regulated by HIF-1alpha, immunohistochemical studies of chondrosarcoma nodules were conducted and revealed that the nuclear translocation of HIF-1alpha was detected exclusively in avascular tumor nodules. This study implicates HIF-1alpha-mediated up-regulation of VEGF but not bFGF in the switch to the angiogenic phenotype during tumorigenesis.
.eta.5-Cyclohexadienyltricarbonylchromium(0) complexes from addition of carbon nucleophiles to .eta.6-benzenetricarbonylchromium(0). Formation, chemical and spectroscopic features, and x-ray diffraction analysis (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT.eta.5-Cyclohexadienyltricarbonylchromium(0) complexes from addition of carbon nucleophiles to .eta.6-benzenetricarbonylchromium(0). Formation, chemical and spectroscopic features, and x-ray diffraction analysisM. F. Semmelhack, H. T. Hall Jr., R. Farina, M. Yoshifuji, G. Clark, T. Bargar, K. Hirotsu, and J. ClardyCite this: J. Am. Chem. Soc. 1979, 101, 13, 3535–3544Publication Date (Print):June 1, 1979Publication History Published online1 May 2002Published inissue 1 June 1979https://pubs.acs.org/doi/10.1021/ja00507a019https://doi.org/10.1021/ja00507a019research-articleACS PublicationsRequest reuse permissionsArticle Views475Altmetric-Citations131LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Aglycosylated IgG variants expressed in bacteria that selectively bind FcγRI potentiate tumor cell killing by monocyte-dendritic cells (2009)

The N-linked glycan of immunoglobulin G (IgG) is indispensable for the interaction of the Fc domain with Fcgamma receptors on effector cells and the clearance of target cells via antibody dependent cell-mediated cytotoxicity (ADCC). Escherichia coli expressed, aglycosylated Fc domains bind effector FcgammaRs poorly and cannot elicit ADCC. Using a novel bacterial display/flow cytometric library screening system we isolated Fc variants that bind to FcgammaRI (CD64) with nanomolar affinity. Binding was critically dependent on amino acid substitutions (E382V, and to a lesser extent, M428I) distal to the putative FcgammaRI binding epitope within the CH3 domain. These mutations did not adversely affect its pH-dependent interaction with FcRn in vitro nor its serum persistence in vivo. Remarkably, the anti-Her2 IgG trastuzumab containing the E382V, M428I substitutions and expressed in E. coli exhibited highly selective binding to FcgammaRI but not to the other activating receptors (FcgammaRIIa, FcgammaRIIIa) nor to the inhibitory receptor, FcgammaRIIb. In contrast, the glycosylated version of trastuzumab (E382V, M428I) purified from HEK293T cells bound to all Fcgamma receptors in a manner similar to that of clinical grade trastuzumab. E. coli-purified trastuzumab (E382V, M428I), but not glycosylated trastuzumab (E382V, M428I) or clinical grade trastuzumab, was capable of potentiating the killing of Her2 overexpressing tumor cells with dendritic cells (DCs) as effectors. These results indicate that aglycosylated IgGs can be engineered to display unique FcgammaR selectivity profiles that, in turn, mediate ADCC via mechanisms that are not normally displayed by glycosylated monoclonal antibodies.
Self-assembly on copper surface by using imidazole derivative for corrosion protection (2018)

This paper presents the self-assembly of 1-(3-aminopropyl) imidazole (API) monolayer on the copper surface to study the inhibition effect of the API against copper corrosion in 3% NaCl solution. The optimum concentration and assembling time for the assembly of API on copper were ascertained using electrochemical impedance spectroscopy (EIS). It was found that the API self-assembled monolayer (SAM) was formed with the concentration of 1.0 mM of API at 24 h assembling time and the maximum inhibition efficiency that could be achieved was 93.10%. The API SAM on copper was characterized by Fourier transform infrared spectroscopy (FT-IR), energy dispersive X-ray analysis (EDX), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM) and water contact angle measurement (WCA). The presence of N and C signals in the XPS and EDX, show that the API molecules successfully anchor on the copper surface which demonstrates formation of API SAM on the copper surface. Corrosion protection capability of the copper modified with API was evaluated by the electrochemical polarization study (EPS) and scanning electron microscopy (SEM). The results of electrochemical and SEM analysis revealed that the API modified copper showed better corrosion protection in 3% NaCl solution.
Enhancement of monoclonal antibody uptake in human colon tumor xenografts following irradiation. (1990)

Indium-111-labeled AUA1 tumor-associated monoclonal antibody raised against an antigen of colon adenocarcinoma was used to evaluate the effect of ionizing radiation on antibody uptake by the LoVo adenocarcinoma cell line grown as a xenograft in nude mice. Tumors were exposed to single doses of external X-irradiation of between 400 and 1600 cGy followed, 24 h later, by administration of specific or nonspecific antibody. Animals were sacrificed 3 days after antibody administration. At doses higher than 400 cGy, tumor uptake with both specific and nonspecific antibody was significantly increased. No difference in changes in tumor volume was observed between the groups receiving irradiation and the controls. Specific antibody uptake by tumors was always significantly higher than nonspecific having an approximate 4-fold binding advantage. Vascular permeability and the vascular volume of irradiated and control tumors was measured 24 and 72 h after irradiation, using iodine-125-labeled nonspecific antibody and labelling of the red blood cells in vivo with 99mTcO4. At doses higher than 400 cGy, vascular permeability in the tumor 24 h after irradiation was significantly increased (P less than 0.05), while the vascular volume decreased (P less than 0.001) compared to control values. However at 72 h after irradiation there was no difference between treated and control groups. The results obtained in this study suggest a potential value of external irradiation to increase monoclonal antibody uptake by tumors governed mainly by the increased vascular permeability of the tumor vasculature soon after the irradiation exposure.
Contributions of the structural proteins of severe acute respiratory syndrome coronavirus to protective immunity (2004)

We investigated the contributions of the structural proteins of severe acute respiratory syndrome (SARS) coronavirus (CoV) to protective immunity by expressing them individually and in combinations from a recombinant parainfluenza virus (PIV) type 3 vector called BHPIV3. This vector provided direct immunization of the respiratory tract, the major site of SARS transmission, replication, and disease. The BHPIV3/SARS recombinants were evaluated for immunogenicity and protective efficacy in hamsters, which support a high level of pulmonary SARS-CoV replication. A single intranasal administration of BHPIV3 expressing the SARS-CoV spike protein (S) induced a high titer of SARS-CoV-neutralizing serum antibodies, only 2-fold less than that induced by SARS-CoV infection. The expression of S with the two other putative virion envelope proteins, the matrix M and small envelope E proteins, did not augment the neutralizing antibody response. In absence of S, expression of M and E or the nucleocapsid protein N did not induce a detectable serum SARS-CoV-neutralizing antibody response. Immunization with BHPIV3 expressing S provided complete protection against SARS-CoV challenge in the lower respiratory tract and partial protection in the upper respiratory tract. This was augmented slightly by coexpression with M and E. Expression of M, E, or N in the absence of S did not confer detectable protection. These results identify S among the structural proteins as the only significant SARS-CoV neutralization antigen and protective antigen and show that a single mucosal immunization is highly protective in an experimental animal that supports efficient replication of SARS-CoV.
Synergistic enhancement of type I and III collagen production in cultured fibroblasts by transforming growth factor‐β and ascorbate (1989)

Transforming growth factor-beta (TGF-beta) is a prototype of a family of polypeptides that regulates cellular growth and phenotypic differentiation [(1986) Science 233, 532-534; (1987) Cell 49, 437-438]. TGF-beta injection induces angiogenesis and fibrosis locally [(1986) Proc. Natl. Acad. Sci. USA 83, 4167-4171; (1987) Science 237, 1333-1336] and stimulates the synthesis of extracellular matrix proteins, fibronectin, collagens, and proteoglycans in vitro in many cell types [(1986) J. Biol. Chem. 261, 4337-4345; (1987) Biochem J. 247, 597-604]. Ascorbate is also known to induce collagen synthesis and to promote wound healing [(1988) J. Invest. Dermatol. 90, 420-424; (1986) Coll. Rel. Res. 6, 455-466]. We report that in cultured human skin fibroblasts, ascorbate and TGF-beta synergistically enhance the biosynthesis of type I and III collagens and their steady-state mRNAs. TGF-beta alone has no enhancing effect on type III collagen synthesis. The cooperation between ascorbate and TGF-beta may be of significance in wound healing and in disorders of fibrosis.
컴퓨터교육 : 정보교사의 교수내용지식(PCK)에 대한 연구 (2015)

빠르게 변화하는 정보 과목의 교육과정은 교사의 변화를 필요로 한다. 특히 새로운 교육 내용을 학습자에게 가르칠 수 있는 능력인 교수내용지식은 교사의 핵심적인 능력으로서 교사교육의 중심 내용이 되어야 한다. 본 연구에서는 정보교과의 교수내용지식을 어떠한 형태로 정의하고 연구하는지에 대한 기초적인 내용을 탐구하였다.
Altered eicosanoid levels in human colon cancer. (1993)

Eicosanoids may participate in colon carcinogenesis, as evidenced from work in animal tumor models showing prevention of colon cancer by inhibitors of their synthesis and epidemiologic studies demonstrating reduced risk of colon cancer in long-term users of aspirin and other nonsteroidal antiinflammatory drugs (NSAIDs). The levels of prostaglandin E2 (PGE2), PGF2 alpha, PGI2, thromboxane A2 (TXA2), and leukotriene B4 (LTB4), which represent the cyclooxygenase and 5-lipoxygenase pathways, were determined in 21 pairs of surgically excised human colon cancer and histologically normal mucosa samples 5 to 10 cm away from the tumor. The levels of PGE2 were elevated in colon cancer samples as compared with histologically normal mucosa samples distant from the cancer (p < 0.01), whereas levels of prostacyclin (PGI2) were decreased (p < 0.05). The differences in the levels of PGF2 alpha, TXA2, and LTB4 between normal and malignant tissue were not statistically significant. No statistically significant association was found between the level of each of the eicosanoids assayed and Dukes' stage of colon cancer. These findings, confirming and extending earlier work from tumors and cell culture, suggest that the protective effect of aspirin and other NSAIDs in the development of human colon cancer may be mediated, at least in part, through their inhibition of arachidonic acid metabolism by cyclooxygenase.
Internet X.509 Public Key Infrastructure Time-Stamp Protocol (TSP) (2001)

This document describes the format of a request sent to a Time Stamping Authority (TSA) and of the response that is returned. It also establishes several security-relevant requirements for TSA operation, with regards to processing requests to generate responses.
p62cdc23 of Saccharomyces cerevisiae: a nuclear tetratricopeptide repeat protein with two mutable domains. (1993)

CDC23 is required in Saccharomyces cerevisiae for cell cycle progression through the G2/M transition. The CDC23 gene product contains tandem, imperfect repeats, termed tetratricopeptide repeats, (TPR) units common to a protein family that includes several other nuclear division CDC genes. In this report we have used mutagenesis to probe the functional significance of the TPR units within CDC23. Analysis of truncated derivatives indicates that the TPR block of CDC23 is necessary for the function or stability of the polypeptide. In-frame deletion of a single TPR unit within the repeat block proved sufficient to inactivate CDC23 in vivo, though this allele could rescue the temperature-sensitive defect of a cdc23 point mutant by intragenic complementation. By both in vitro and in vivo mutagenesis techniques, 17 thermolabile cdc23 alleles were produced and examined. Fourteen alleles contained single amino acid changes that were found to cluster within two distinct mutable domains, one of which encompasses the most canonical TPR unit found in CDC23. In addition, we have characterized CDC23 as a 62-kDa protein (p62cdc23) that is localized to the yeast nucleus. Our mutagenesis results suggest that TPR blocks form an essential domain within members of the TPR family.
Dri, Dietary Reference Intakes for Water, Potassium, Sodium, Chloride, and Sulfate (2005)

Dietary Reference Intakes for Water, Potassium, Sodium, Chloride, and Sulfate The Dietary Reference Intakes (DRIs) are quantitative estimates of nutrient intakes to be used for planning and assessing diets for healthy people. This new report, the sixth in a series of reports presenting dietary reference values for the intakes of nutrients by Americans and Canadians, establishes nutrient recommendations on water, potassium, and salt for health maintenance and the reduction of chronic disease risk. Dietary Reference Intakes for Water, Potassium, Sodium, Chloride, and Sulfate discusses in detail the role of water, potassium, salt, chloride, and sulfate in human physiology and health. The major findings in this book include the establishment of Adequate Intakes for total water (drinking water, beverages, and food), potassium, sodium, and chloride and the establishment of Tolerable Upper Intake levels for sodium and chloride. The book makes research recommendations for information needed to advance the understanding of human requirements for water and electrolytes, as well as adverse effects associated with the intake of excessive amounts of water, sodium, chloride, potassium, and sulfate. This book will be an invaluable reference for nutritionists, nutrition researchers, and food manufacturers.
Expression of Genes Coding for GerA and GerK Spore Germination Receptors Is Dependent on the Protein Phosphatase PrpE (2006)

The ability of Bacillus subtilis to form spores is a strategy for survival under unfavorable environmental conditions. It is equally crucial to break spore dormancy and return to vegetative growth at the appropriate time. Here we present data showing that the PrpE phosphatase is involved in the control of expression of genes coding for GerA receptors, which are necessary for L-alanine-induced spore germination. Moreover, PrpE is also involved in aspartic acid, glucose, fructose, and potassium (AGFK)-induced spore germination by controlling expression of genes coding for GerK receptors. In the absence of PrpE, the production of spores was essentially normal. However, L-alanine-induced spore germination and, to a lesser extent, the AGFK-induced pathway were abolished. In contrast, the germination pathway dependent on Ca2+-dipicolinate or dodecylamine remained intact. A protein phosphatase PrpE-green fluorescent protein fusion was localized to the prespore and to the dormant spore, consistent with a role in controlling expression of genes coding for GerA receptors. We propose that PrpE is an important element in a signal transduction pathway in Bacillus subtilis that controls the expression of genes coding for germination receptors.
Highly sensitive biosensing based on interference from light scattering in capillary tubes (2006)

Human IgG interactions with surface bound protein A are monitored label-free using microinterferometric backscatter detection. An electromagnetic wave-based model is developed and used to quantitatively describe the change in interference pattern as a consequence of the molecular interaction with the affinity layer on the fused silica capillary. Within the framework of the model it is of paramount importance to establish a valid stop criterion for the infinite summations involved in the fringe pattern computations. The high sensitivity towards surface changes, ease of changing the surface chemistry to other specific interacting layers, and simplicity of the optical sensor make this technique a powerful tool in biosensing.