gebhart/patrepeval huggingface dataset:
The Nucleotide Sequence around the Capripoxvirus Thymidine Kinase Gene Reveals a Gene Shared Specifically with Leporipoxvirus (1989)

We have extended previous comparisons of genetic organization between poxvirus genera by sequencing a 2.5K genomic fragment from isolate KS-1 (Kenya sheep-1) of the genus capripoxvirus. The fragment is located in the central region of the capripoxvirus genome and contains three complete and two incomplete open reading frames (ORFs). One of the complete ORFs is a gene for thymidine kinase (TK). This gene, with one of the other two complete ORFs and both the incomplete ORFs, are homologous to four contiguous ORFs from the central region of vaccinia virus (VV) DNA. They also match four ORFs of fowlpox virus (FPV) DNA, three of which are contiguous and the fourth, the FPV TK gene, is located elsewhere on the FPV genome. The third complete ORF of the capripoxvirus DNA fragment is located between the TK gene and the capripoxvirus homologue of the ORF immediately downstream of the VV TK gene. We show that a homologue to this third ORF is absent from VV and FPV DNAs, but is present downstream of the TK gene on Shope fibroma virus DNA. The sequence immediately upstream of the capripoxvirus homologue of a VV late gene contains a motif which is required for VV late gene expression. The motif required for VV early gene transcription termination is present in eight positions in the capripoxvirus sequence, and five of these positions are consistent with the motif having an equivalent function in capripoxvirus to that in VV.
Atrial Natriuretic Factor-SV40 T Antigen Transgenes Produce Tumors and Cardiac Arrhythmias in Mice (1988)

Transgenic mice that carry fusions between the transcriptional regulatory sequences of atrial natriuretic factor (a hormone intimately involved in the regulation of blood pressure) and those encoding SV40 T antigen (an oncoprotein) were generated. Although both atria express the fusion gene, the pathological response to T antigen is asymmetrical. The right atrium undergoes a several hundredfold increase in mass while the left atrium remains relatively normal in size. Hyperplasia is accompanied by a progressive increase in both the frequency and severity of abnormalities in the atrial conduction system, which ultimately result in death.
Enhancer, Repressor, and Promoter Specificities Combine to Regulate the Rat α-Fetoprotein Gene (1991)

The upstream transcription control region of the rat α-fetoprotein (AFP) gene was analyzed using transient expression of CAT genes in HepG2 cells which express the gene; H4C3 cells which repress the AFP gene but express the albumin gene; and four nonexpressing cell lines. Deletion analysis based on the DNA sequence resolved three upstream enhancers corresponding to the mouse AFP enhancers, but showed additional weak effects from flanking sequences. Quantitative experiments demonstrated that the three enhancers were additive when acting through a single promoter and did not confirm the presence of a distal upstream repressor. All three enhancers stimulated the AFP, albumin, or thymidine kinase (tk) promoter in HepG2, but only the tk and albumin promoters in H4C3. Deletion of a proximal repressor region near the AFP promoter allowed expression in H4C3 cells with the AFP promoter. Thus, the liver-specific developmental repressor is near the AFP promoter, and H4C3 cells provide an in vitro system for analysis of this repressor in transfection assays. The repressor region also blocked expression of the SV40 enhancer through the AFP promoter in hepatic and nonhepatic cell lines, but when this enhancer was combined with an AFP promoter from which the repressor region was deleted, the combination showed expression in all six cell lines studied. AFP expression results from a combination of enhancer, promoter, and repressor activities, and the repressor is functional with a heterologous enhancer in a variety of cells.
A soluble blue-light-emitting polymer (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA soluble blue-light-emitting polymerZ. Yang, I. Sokolik, and F. E. KaraszCite this: Macromolecules 1993, 26, 5, 1188–1190Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/ma00057a047https://doi.org/10.1021/ma00057a047research-articleACS PublicationsRequest reuse permissionsArticle Views840Altmetric-Citations355LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Defective forebrain development in mice lacking gp330/megalin. (1996)

gp330/megalin, a member of the low density lipoprotein (LDL) receptor gene family, is expressed on the apical surfaces of epithelial tissues, including the neuroepithelium, where it mediates the endocytic uptake of diverse macromolecules, such as cholesterol-carrying lipoproteins, proteases, and antiproteinases. Megalin knockout mice manifest abnormalities in epithelial tissues including lung and kidney that normally express the protein and they die perinatally from respiratory insufficiency. In brain, impaired proliferation of neuroepithelium produces a holoprosencephalic syndrome, characterized by lack of olfactory bulbs, forebrain fusion, and a common ventricular system. Similar syndromes in humans and animals are caused by insufficient supply of cholesterol during development. Because megalin can bind lipoproteins, we propose that the receptor is part of the maternal-fetal lipoprotein transport system and mediates the endocytic uptake of essential nutrients in the postgastrulation stage.
Quantitative Analysis of Small-Subunit rRNA Genes in Mixed Microbial Populations via 5′-Nuclease Assays (2000)

Few techniques are currently available for quantifying specific prokaryotic taxa in environmental samples. Quantification of specific genotypes has relied mainly on oligonucleotide hybridization to extracted rRNA or intact rRNA in whole cells. However, low abundance and cellular rRNA content limit the application of these techniques in aquatic environments. In this study, we applied a newly developed quantitative PCR assay (5'-nuclease assay, also known as TaqMan) to quantify specific small-subunit (SSU) rRNA genes (rDNAs) from uncultivated planktonic prokaryotes in Monterey Bay. Primer and probe combinations for quantification of SSU rDNAs at the domain and group levels were developed and tested for specificity and quantitative reliability. We examined the spatial and temporal variations of SSU rDNAs from Synechococcus plus Prochlorococcus and marine Archaea and compared the results of the quantitative PCR assays to those obtained by alternative methods. The 5'-nuclease assays reliably quantified rDNAs over at least 4 orders of magnitude and accurately measured the proportions of genes in artificial mixtures. The spatial and temporal distributions of planktonic microbial groups measured by the 5'-nuclease assays were similar to the distributions estimated by quantitative oligonucleotide probe hybridization, whole-cell hybridization assays, and flow cytometry.
Analysis of Structural Properties which Possibly Are Characteristic for the 3'-Terminal Sequence of the Genome RNA of Flaviviruses (1986)

Recently we have shown that an open reading frame comprising 10290 nucleotides is present on the infectious, single-stranded genome RNA of the West Nile flavivirus. We have now isolated cloned cDNA representing the 3'-terminal untranslated region of this molecule. The sequence of this region which comprises 571 nucleotides is given in this report. Recently, the nucleotide sequence of the genome RNA of the yellow fever flavivirus has been described. A comparative analysis of the 3'-terminal untranslated nucleotide sequences present in each genome suggests that in flaviviruses this region probably has the following properties. It has a heteropolymeric sequence at the 3' terminus. It contains one or more oligonucleotide sequences that are repeated. An extensive stem and loop structure can be folded from the nucleotide sequences present at the 3' terminus. The stem of this structure contains a conserved region introducing a defined mismatch into the stem. The loop of this structure probably contains short conserved oligonucleotide sequences in analogous positions. In both viruses the oligonucleotide CAUAUUGAC (AG)CC(UA) GGGA(UA) AGAC lies closely in front of the sequence which can be folded into the stem of the 3'-terminal stem and loop structure and the oligonucleotide CUAGAGGUUAGAGGAGACCC is strictly conserved between both viruses. The analyses indicate that the 3'-terminal untranslated region of the genome of flaviviruses probably has rather unique characteristics of primary and secondary structure. Possible implications of these findings are discussed.
Mass spectrometry imaging (MSI) of metals in mouse spinal cord by laser ablation ICP-MS (2012)

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has been developed as a powerful MS imaging (MSI) tool for the direct investigation of element distributions in biological tissues. Here, this technique was adapted for the analysis of native mouse spinal cord cryosections of 3.1 mm × 1.7 mm by implementing a new conventional ablation system (NWR-213) and improving the spatial resolution from 120 μm to 65 μm in routine mode. Element images of the spinal cord are provided for the first time and the metalloarchitecture was established using a multimodal atlas approach. Furthermore, the spatial distribution of Rb was mapped for the first time in biological tissue. Metal concentrations were quantified using matrix-matched laboratory standards and normalization of the respective ion intensities to the average (13)C ion intensity of standards and samples as a surrogate of slice thickness. The "butterfly" shape of the central spinal grey matter was visualized in positive contrast by the distributions of Fe, Mn, Cu and Zn and in negative contrast by C and P. Mg, Na, K, S and Rb showed a more homogenous distribution. The concentrations averaged throughout grey matter and white matter were 8 and 4 μg g(-1) of Fe, 3 and 2 μg g(-1) of Cu, 8 and 5 μg g(-1) of Zn, 0.4 and 0.2 μg g(-1) of Mn. The carbon concentration in white matter exceeded that of grey matter by a factor of 1.44. Zn and Cu at 9 and 4 μg g(-1), respectively, were particularly enriched in the laminae I and II, in line with the high synaptic and cellular density there. Surprisingly Zn but not Cu was enriched in the central channel. Rb occurred at 0.3 μg g(-1) with a distribution pattern congruent to that of K. The coefficients of variation were 6%, 5%, 8% and 10% for Fe, Cu, Zn and Mn, respectively, throughout three different animals measured on different days. These MSI analyses of healthy wild type spinal cords demonstrate the suitability of the established techniques for investigating diseased or transgenic states in future imaging studies.
Review on Triggered Liposomal Drug Delivery with a Focus on Ultrasound (2015)

Chemotherapy is widely used for cancer treatment; however, it causes unwanted side effects in patients. To avoid these adverse effects, nanocarriers have been developed, which can be loaded with the chemotherapeutic agents, directed to the cancer site and, once there, are exposed to stimuli that will trigger the drug release. Liposomes can be chemically modified to increase their circulation time, their stability, and their sensitivity to specific stimulus. Additionally, ligands can be conjugated to their surface, allowing for their specific binding to receptors overexpressed on the surface of cancer cells and the subsequent internalization via endocytosis. Using a triggering mechanism, including temperature, ultrasound, enzymes or a change in pH, the release of the drug is controlled and induced inside the cells, hence avoiding drug release in systemic circulation, which in turn reduces the undesired side effects of conventional chemotherapy. Ultrasound has been widely studied as a drug release trigger from liposomes, due to its well-known physics and previous uses in medicine. This review focuses on liposome-based drug delivery systems, using different trigger mechanisms, with a focus on ultrasound. The physical mechanisms of ultrasound release are also investigated and the results of in vitro and in vivo studies are summarized.
A compact dual‐port, dual‐frequency SSFIP/PIFA antenna with high decoupling (1999)

A new type of dual-port, dual-frequency SSFIP/PIFA antenna is described. Its main characteristics are a wide bandwidth at both frequencies, high isolation between ports, and simple construction, together with good radiation properties. As an example of application, a DECT+DCS 1800/WLAN antenna has been realized, and is described in detail with measured data. ©1999 John Wiley & Sons, Inc. Microwave Opt Technol Lett 22: 373–378, 1999
Human endothelial cell response to gram-negative lipopolysaccharide assessed with cDNA microarrays (2001)

To assess the feasibility of using cDNA microarrays to understand the response of endothelial cells to lipopolysaccharide (LPS) and to evaluate potentially beneficial agents in treatment of septic shock, human umbilical vein endothelial cells were exposed to Escherichia coli LPS for 1, 4, 7, 12, or 24 h. Total RNA was isolated and reverse-transcribed into (33)P-labeled cDNA probes that were hybridized to human GeneFilter microarrays containing approximately 4,000 genes. The mRNA levels of several genes known to respond to LPS changed after stimulation. In addition, a number of genes not previously implicated in the response of endothelial cells to LPS also appeared to be altered in expression. Nuclear factor-kappaB (NF-kappaB) was shown to play an important role in regulating genes identified from the microarray studies. Pretreatment of endothelial cells with a specific NF-kappaB translocation inhibitor eliminated most of the alterations in gene expression. Quantitative RT-PCR results independently confirmed the microarray results for monocyte chemotactic protein-1 and interleukin-8, and enzyme-linked immunosorbent assays demonstrated that augmented transcription was followed by translation and secretion.
Brazilian Tensile Strength Test of Orgainc-rich Shale (2015)

Abstract Tensile strength is a critical parameter for hydraulic fracturing, predicting crack initiation and propagation in reservoirs, especially in shale reservoirs with complex natural fractures and fissures. The tensile strength of conventional rocks, such as sandstone and limestone, has been well studied and documented. There are many studies of the tensile strength of laminated shale, which focus on scale effects, loading direction, and temperature effects; however, the studies on effects of mineralogy and the water content on tensile strength of organic-rich shales are very limited. The objectives of this paper are to: 1) Critically review the key parameters that affect the tensile strength of shale; and 2) Experimentally examine the effects of water content, mineralogy and lamination on tensile strength. To do so, a rigorous workflow is followed: 1) Each 1 in. long shale sample is cut into two sub-samples, A and B, of similar length; 2) X-ray computed tomography scan is performed to diagnose pre-existing cracks and defects inside the core plugs; 3) Nuclear magnetic resonance (NMR) is then used to measure the air dry samples’ water content; 5) Sample A is placed on a load frame to measure the tensile strength; 5) Sample B is vacuumed and then saturated; 6) NMR is used to measure the water content after saturation; 7) Tensile strength of the saturated sample B is measured; 8) Samples are crushed, and X-ray diffraction (XRD), scanning electron microsope (SEM) and pyrolysis methods are used to estimate the mineralogy and total organic content (TOC). A total of 70 Mancos and 48 Eagle Ford shale samples have been tested. The experiment results show that: 1) Bedding plane/lamination has a significant effect on Eagle Ford tensile strength, but no pronounced impact observed for the Mancos shale; 2) The imbibed water significantly reduces the tensile strength by 4.4% to 51.7% as water content increases from 4.45% to 11.7%; 3) Pre-existing detectable micro-fractures can significantly reduce the tensile strength by up to 66%; 4) Eagle Ford exhibits typical brittle hard rock failure configuration, with primary facture and secondary fracture being observed, while for the Mancos shale, only primary fractures are observed; 5) Acoustic velocity test results confirm that Eagle Ford is mechanically transversely isotropic, and Mancos is likely mechanically isotropic.
An Efficient Strategy To Isolate Full-Length cDNAs Based on an mRNA Cap Retention Procedure (CAPture) (1995)

The ability to generate cDNA libraries is one of the most fundamental procedures in contemporary molecular biology. One of the major drawbacks of current methods is that most cDNAs present in any given library are incomplete, rendering the characterization of genes an inefficient and time-consuming task. We have developed an affinity selection procedure using a fusion protein containing the murine cap-binding protein (eukaryotic initiation factor 4E), coupled to a solid support matrix, that allows for the purification of mRNAs via the 5' cap structure. When combined with a single-strand-specific RNase digestion step, specific retention of complete cDNA-RNA duplexes following first-strand synthesis is achieved. This method can be used to generate cDNA libraries in which polyadenylated and nonpolyadenylated mRNAs are equally represented and to enrich for full-length or 5'-end clones, thus facilitating cDNA cloning and promoter mapping.
Thrombospondin and Apoptosis: Molecular Mechanisms and Use for Design of Complementation Treatments (2008)

Thrombospondin-1 is the first and most studied naturally occurring protein inhibitor of angiogenesis. Its characteristic multi-domain structure determines thrombospondin-1 divergent functions, which include but are not limited to the regulation of angiogenesis. Below we overview the structural determinants and receptors expressed on the endothelial and other cell types, that are at the root of thrombospondin-1 striking ability to block neovascularization. We specifically emphasize thrombospondin-1 direct apoptotic action on the remodeling vascular endothelium and summarize current knowledge of its pro-apoptotic signaling and transcriptional networks. Further, we provide comprehensive survey of the thrombospondin-based anti-angiogenic strategies with special focus on the combination treatments. We convincingly illustrate how precise knowledge of the pro-apoptotic events and intermediates elicited by thrombospondin in the vascular endothelial cells facilitates the design of the most effective treatment combinations, where the efficacy of thrombospondin-derived compounds is maximized by the partner drug(s) ("complementation" strategies) and provide examples of such fine-tuning of the thrombospondin-based anti-angiogenic treatments.
Hope on New AIDS Drugs, but Breast-Feeding Strategy Backfires (2007)

LOS ANGELES, CALIFORNIA--
 Two novel drugs show promise in hard-to-treat patients, but breast-feeding studies underscore the difficulty of applying advances in the real world. (Read more.)
The reality of trace binning in 3‐D marine surveying (1983)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1983The reality of trace binning in 3‐D marine surveyingAuthors: W. R. CottonJ. I. SandersW. R. CottonGeophysical Service Inc. and J. I. SandersGeophysical Service Inc.https://doi.org/10.1190/1.1893724 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1893724FiguresReferencesRelatedDetailsCited ByDetailed images of the shallow Alpine Fault Zone, New Zealand, determined from narrow-azimuth 3D seismic reflection dataA. E. Kaiser, H. Horstmeyer, A. G. Green, F. M. Campbell, R. M. Langridge, and A. F. McClymont11 January 2011 | GEOPHYSICS, Vol. 76, No. 1 SEG Technical Program Expanded Abstracts 1983ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1983 Pages: 646 publication data© 1983 Copyright © 1983 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 24 Mar 2005 CITATION INFORMATION W. R. Cotton and J. I. Sanders, (1983), "The reality of trace binning in 3‐D marine surveying," SEG Technical Program Expanded Abstracts : 565-568. https://doi.org/10.1190/1.1893724 Plain-Language Summary PDF DownloadLoading ...
Factors Affecting the Germination of Thick Suspensions of Bacillus subtilis Spores in L-Alanine Solution (1950)

SUMMARY: The rate of germination (defined as loss of heat-resistance accompanied by change in staining properties under specified conditions, with maintenance of viability) of thick suspensions of Bacillus subtilis spores in phosphate-buffered l-alanine solution increased with the time from harvesting. The maximum rate of germination was reached after about 20’ days storage in water at 20°. This effect could be retarded, but not reversed, by storage at low temperatures. The rate of germination may be temporarily accelerated by heat treatment. Germination was considerably retarded after treatment with mercuric chloride, and was completely inhibited by 8-hydroxyquinoline (oxine) and by 2:3-dimercaptopropanol (BAL) at 10 mm concentration. The latter effect was partially reversed by the addition of metals.
<title>Speckle contrast reduction in laser projection displays</title> (2002)

Speckle arises when coherent light scattered from a rough surface is detected by an intensity detector that has a finite aperture, such as an observer. In a laser projection display, the presence of speckle tends to mask the image information and therefore its reduction is highly desirable. Speckle contrast reduction is based on averaging a number of speckle configurations within the spatio-temporal resolution of the detector through diversification of the light parameters - angle, polarization, and wavelength. The maximum speckle contrast reduction for a given system will be derived, and two novel approaches to achieve the maximum reduction will be introduced. Application to the Grating Light Valve (GLV TM) laser projection system using the Hadamard diffuser has resulted in a suppression to 8% residual speckle contrast.