gebhart/patrepeval huggingface dataset:
Functional analysis of the p10 gene 5′ leader sequence of the<i>Autographa californica</i>nuclear polyhedrosis virus (1988)

Deletions were made in the 5' non-coding (leader) sequence of the Autographa californica nuclear polyhedrosis virus (AcNPV) p10 gene which progressively removed nucleotides upstream from the ATG translation initiation codon. The effect of these deletions on p10 gene expression was studied using a transient expression assay. Fragments containing the putative promoter and the entire or partly deleted 5' leader sequence of the p10 gene were inserted in front of the chloramphenicol acetyltransferase (CAT) gene in the pSVO-CAT construct. Transfection of AcNPV-infected Spodoptera frugiperda cells with these plasmids resulted in higher CAT expression with increasing representation of the 5' leader sequence. The lowest level of CAT expression was found with a construct containing only 10% of the 5' leader sequence, but this was enhanced on average by 50-fold if the entire 5' leader sequence was retained. The results indicate that the entire 5' leader sequence of the p10 gene is necessary for the high level of expression. The normal transcription initiation site was utilized in the transient expression of CAT. The data are discussed in relation to the strong promoter of the baculovirus polyhedrin gene.
3D modeling of environments contaminated with chemical, biological, radiological and nuclear (CBRN) agents (2008)

CBRN Crime Scene Modeler (C2SM) is a prototype 3D modeling system for first responders investigating environments contaminated with Chemical, Biological, Radiological and Nuclear agents. The prototype operates on board a small robotic platform or a hand-held device. The sensor suite includes stereo and high resolution cameras, a long wave infra red camera, chemical detector, and two gamma detectors (directional and non-directional). C2SM has been recently tested in field trials where it was teleoperated within an indoor environment with gamma radiation sources present. The system has successfully created multi-modal 3D models (geometry, colour, IR and gamma radiation), correctly identified location of radiation sources and provided high resolution images of these sources.
Loge: A Self-Organizing Disk Controller (1991)

Loge is a disk controller that organizes data based on the I/O stream, rather than on interpretations of file system structure. Unlike a conventional design, where data location is a static decision made when blocks are allocated, Loge places blocks dynamically, choosing an optimal location for each write at the time the data is written to the disk. Write performance on Loge is largely independent of the I/O stream, and in
Structure of the Amide I Band of Peptides Measured by Femtosecond Nonlinear-Infrared Spectroscopy (1998)

Femtosecond infrared (IR) pump probe and dynamic hole burning experiments were used to examine the ultrafast response of the modes in the 1600−1700 cm-1 region (the so-called amide I modes) of N-methylacetamide (NMA) and three small globular peptides, apamin, scyllatoxin, and bovine pancreatic trypsin inhibitor (BPTI). A value of 16 cm-1 was found for the anharmonicity of the amide I vibration. Vibrational relaxation of the amide I modes of all investigated peptides occurs in ca. 1.2 ps. An even faster value of 450 fs is obtained for NMA, a model for the peptide unit. The vibrational relaxation is dominated by intramolecular energy redistribution (IVR) and reflects an intrinsic property of the peptide group in any environment. Dynamic hole burning experiments with a narrow band pump pulse which selectively excites only a subset of the amide I eigenstates reveal that energy migration between different amide I states is slow compared with vibrational relaxation. Two-dimensional pump−probe (2D-IR) spectra that display the spectral response of the amide I band as a function of the frequency of the narrow band pump pulse show that the amide I states are nevertheless delocalized along the peptide backbone. A simple excitonic coupling model describes the nonlinear pump−probe spectrum, and it reproduces the experimental 2D-IR spectra. It is estimated that the accessible peptide excitons are delocalized over a length of ca. 8 Å.
THE FINE STRUCTURE OF ELASTIC FIBERS (1966)

The fine structure of developing elastic fibers in bovine ligamentum nuchae and rat flexor digital tendon was examined. Elastic fibers were found to contain two distinct morphologic components in sections stained with uranyl acetate and lead. These components are 100 A fibrils and a central, almost amorphous nonstaining area. During development, the first identifiable elastic fibers are composed of aggregates of fine fibrils approximately 100 A in diameter. With advancing age, somewhat amorphous regions appear surrounded by these fibrils. These regions increase in prominence until in mature elastic fibers they are the predominant structure surrounded by a mantle of 100 A fibrils. Specific staining characteristics for each of the two components of the elastic fiber as well as for the collagen fibrils in these tissues can be demonstrated after staining with lead, uranyl acetate, or phosphotungstic acid. The 100 A fibrils stain with both uranyl acetate and lead, whereas the central regions of the elastic fibers stain only with phosphotungstic acid. Collagen fibrils stain with uranyl acetate or phosphotungstic acid, but not with lead. These staining reactions imply either a chemical or an organizational difference in these structures. The significance and possible nature of the two morphologic components of the elastic fiber remain to be elucidated.
Predicting macroscopic transport properties using microscopic image data (2006)

We consider eight data sets obtained from synchrotron computed microtomographic experiments performed on natural and synthetic sandstones at the GSECARS 13‐BM beam line at the Advanced Photon Source. Four data sets were collected on glass bead packs sintered to differing bulk densities; each of these data sets contains just over 225 million voxels (661 × 661 × 517), with voxel resolution of 3.34 μm. The other four data sets were collected from a single sample of natural sandstone. For the natural sandstone, three data sets were collected from different subvolumes within the sample, with these three data sets identical in size and resolution to those acquired for the sintered glass bead packs. A fourth data set was collected for one of the same subvolumes but at twice the resolution; this data set contains just over 1.6 billion voxels (1327 × 1327 × 920), with voxel resolution of 1.67 μm. Following processing to extract binary descriptions of the two‐phase (solid and pore) structure, the image data are analyzed to calculate porosity and specific surface area. The binarized image data are applied directly in massively parallel numerical simulations of single‐phase fluid flow performed using the lattice Boltzmann method; development of novel boundary conditions to facilitate efficient handling of these very large data sets is also described. The permeabilities predicted from 1 to 3 mm 3 image volumes characterized at a length scale of ∼1.7–3.4 μm are compared to experimental measurements of intrinsic permeability performed at bench conditions on standard core‐sized samples (25.4 mm in diameter × 50.8 mm in length, or ∼26 cm 3 ). The macroscopic permeability computed from the image data agree remarkably well with the experimentally measured bulk permeability over several orders of magnitude range in permeability and equate to over 4 orders of magnitude scale‐up. The results provide insight on the representative volume and length scales necessary to characterize geometrically complex porous media and predict fluid transport properties at the macroscale.
T-Cell Subsets That Harbor Human Immunodeficiency Virus (HIV) In Vivo: Implications for HIV Pathogenesis (2004)

Identification of T-cell subsets that are infected in vivo is essential to understanding the pathogenesis of human immunodeficiency virus (HIV) disease; however, this goal has been beset with technical challenges. Here, we used polychromatic flow cytometry to sort multiple T-cell subsets to 99.8% purity, followed by quantitative PCR to quantify HIV gag DNA directly ex vivo. We show that resting memory CD4(+) T cells are the predominantly infected cells but that terminally differentiated memory CD4(+) T cells contain 10-fold fewer copies of HIV DNA. Memory CD8(+) T cells can also be infected upon upregulation of CD4; however, this is infrequent and HIV-specific CD8(+) T cells are not infected preferentially. Naïve CD4(+) T-cell infection is rare and principally confined to those peripheral T cells that have proliferated. Furthermore, the virus is essentially absent from naïve CD8(+) T cells, suggesting that the thymus is not a major source of HIV-infected T cells in the periphery. These data illuminate the underlying mechanisms that distort T-cell homeostasis in HIV infection.
Vaccinia virus infection induces a stress response that leads to association of Hsp70 with viral proteins (1992)

We studied the impact of vaccinia virus infection on stress protein gene expression in human cells and investigated the possibility that eukaryotic heat shock proteins interact with viral components during assembly. Infection of human monocyte-macrophages by vaccinia virus caused a dramatic decrease in levels of cellular mRNAs such as those encoding actin and tubulin. In contrast, infection did not cause a significant reduction in the levels of Hsp90 and Hsp60 mRNAs and led to substantially increased levels of Hsp70 mRNAs. The accumulation of these stress protein mRNAs was due both to increases in their transcription rate and to their stability relative to other cellular mRNAs. The relative levels of the heat shock proteins and the other cellular proteins reflected the relative levels of their mRNAs. These results indicate that stress protein gene expression is relatively refractory to the generally deleterious effects of vaccinia virus infection on host cell gene expression. The continued expression of some of these stress proteins may be beneficial to the virus; the observations that the levels of Hsp70 are greatest at the peak of viral gene expression and that a large fraction of cellular Hsp70 is associated with vaccinia virus proteins suggest that Hsp70 is involved in vaccinia virus assembly.
A Novel Tetraester Construct That Reduces Cationic Lipid-Associated Cytotoxicity. Implications for the Onset of Cytotoxicity (1998)

The preparation of cationic amphiphiles that induce minor cytotoxic response during polynucleotide delivery into mammalian cells has been limited by the conventional use of ester, amide, or carbamate linkages to tether either the polar or the hydrophobic domains. The deleterious effects of ammonium-based lipidic salts on cellular processes have been well-established. The present report is the first example of a linchpin tetraester construct that utilizes ester linkages to tether both the polar and hydrophobic domains. Dimyristoyl and dioleoyl analogues were prepared from pentaerythritol, N,N-dimethylglycine, and their corresponding fatty acyl groups via successive diesterifications followed by amine quaternization. The resultant cationic tetraesters were examined in transfection (luciferase) and cell proliferation (MTS) assays using NIH 3T3 and 16HBE14o- cells. The tetraesters exhibited transfection activity comparable to the well-studied lipids DOTAP and DC-cholesterol (DC-chol) in both cell lines. The tetraester construct afforded no cytotoxicity in NIH3T3 cells and provided a significant lowering of cytotoxicity relative to DC-chol in the 16HBE14o- cells. The expression of green fluorescent protein (GFP) in both cell lines also was examined using the lipid panel. Comparison of fluorescent and corresponding phase-contrast images confirmed the chemical cytotoxicity results and revealed that the cytotoxic response was not dependent on transgene expression. Phase-contrast micrographs of cells treated with the cationic lipid panel in the absence of GFP plasmid showed identical morphology to the GFP-transfected cells, suggesting that the onset of a lipid-mediated cytotoxic response might occur at a stage prior to endosomal encapsulation.
The potential of genetically-engineered pigs in providing an alternative source of organs and cells for transplantation (2013)

There is a critical shortage of organs, cells, and corneas from deceased human donors worldwide. There are also shortages of human blood for transfusion. A potential solution to all of these problems is the transplantation of organs, cells, and corneas from a readily available animal species, such as the pig, and the transfusion of red blood cells from pigs into humans. However, to achieve these ends, major immunologic and other barriers have to be overcome. Considerable progress has been made in this respect by the genetic modification of pigs to protect their tissues from the primate immune response and to correct several molecular incompatibilities that exist between pig and primate. These have included knockout of genes responsible for the expression of major antigenic targets for primate natural anti-pig antibodies, insertion of human complement- and coagulation-regulatory transgenes, and knockdown of swine leukocyte antigens that stimulate the primate's adaptive immune response. As a result of these manipulations, the administration of novel immunosuppressive agents, and other innovations, pig hearts have now functioned in baboons for 6-8 months, pig islets have maintained normoglycemia in diabetic monkeys for > 1 year, and pig corneas have maintained transparency for several months. Clinical trials of pig islet transplantation are already in progress. Future developments will involve further genetic manipulations of the organ-source pig, with most of the genes that are likely to be beneficial already identified.
CONTROL OF M-CURRENT (1997)

M-current is a non-inactivating potassium current found in many neuronal cell types. In each cell type, it is dominant in controlling membrane excitability by being the only sustained current in the range of action potential initiation. It can be modulated by a large array of receptor types, and the modulation can occur either by suppression or enhancement. Modulation of M-current has dramatic effects on neuronal excitability. This review discusses the numerous second messenger pathways that converge on regulation of this current: in particular, two forms of regulation of the M-current, receptor-mediated modulation and the control of macroscopic current amplitude by intracellular calcium. Both types of regulation are discussed with reference to the modulation of single-channel gating properties.
Applying Classical Ethical Theories to Ethical Decision Making in Public Relations (1994)

Public relations professionals and educators have different views about the real-world relevance of theories to public relations practice. This article links ethical theories to the management of the product recall of the Perrier Group of America. To enable public relations practitioners, as strategic communication managers, to respond effectively to potentially unethical organizational actions, this article also proposes a nonsituational theory-based approach to ethics in public relations. Finally, this article argues that an eclectic approach to problem solving be adopted because no single theory in itself is sufficient to guide the complex decision-making process that precedes the public conduct of the strategic communication manager.
Synthetic cooperation in engineered yeast populations (2007)

Cooperative interactions are key to diverse biological phenomena ranging from multicellularity to mutualism. Such diversity makes the ability to create and control cooperation desirable for potential applications in areas as varied as agriculture, pollutant treatment, and medicine. Here we show that persistent cooperation can be engineered by introducing a small set of genetic modifications into previously noninteracting cell populations. Specifically, we report the construction of a synthetic obligatory cooperative system, termed CoSMO (cooperation that is synthetic and mutually obligatory), which consists of a pair of nonmating yeast strains, each supplying an essential metabolite to the other strain. The behavior of the two strains in isolation, however, revealed unintended constraints that restrict cooperation, such as asymmetry in starvation tolerance and delays in nutrient release until near cell death. However, the joint system is shown mathematically and experimentally to be viable over a wide range of initial conditions, with oscillating population ratio settling to a value predicted by nutrient supply and consumption. Unexpectedly, even in the absence of explicitly engineered mechanisms to stabilize cooperation, the cooperative system can consistently develop increased ability to survive reductions in population density. Extending synthetic biology from the design of genetic circuits to the engineering of ecological interactions, CoSMO provides a quantitative system for linking processes at the cellular level to the collective behavior at the system level, as well as a genetically tractable system for studying the evolution of cooperation.
Galectin-1-Specific Inhibitors as a New Class of Compounds To Treat HIV-1 Infection (2011)

Despite significant improvements, antiretroviral therapies against HIV-1 are plagued by a high frequency of therapeutic failures that have been associated with acquisition of drug resistance. We recently reported that HIV-1 exploits a host glycan binding protein, galectin-1, to increase its attachment to host cells, thereby increasing its overall infectivity in susceptible cells. This finding suggests that host molecules such as galectin-1 could reduce the expected efficiency of HIV-1 drugs targeting early steps of the replicative cycle, such as attachment and entry processes. Thus, new classes of drugs that would interfere with galectin-1/HIV-1 interactions could benefit the current antiretroviral therapy. To further explore this possibility, experiments were conducted to discover leading compounds showing specific inhibition of galectin-1 activity in a cellular model of HIV-1 infection. Three lactoside compounds were found to modestly inhibit the interaction of galectin-1 with primary human CD4(+) T cells. Interestingly, these same inhibitors reduced the galectin-1-mediated increase in HIV-1 attachment to target cells in a much more efficient manner. More important, the tested lactoside derivatives also significantly decreased the galectin-1-dependent enhancement of HIV-1 infection. These observations deserve further attention when considering that the development of new drugs to prevent and treat HIV-1 infection remains a priority.
IC261 induces cell cycle arrest and apoptosis of human cancer cells via CK1δ/ɛ and Wnt/β-catenin independent inhibition of mitotic spindle formation (2011)

Casein kinase 1 delta and epsilon (CK1δ/ɛ) are key regulators of diverse cellular growth and survival processes including Wnt signaling, DNA repair and circadian rhythms. Recent studies suggest that they have an important role in oncogenesis. RNA interference screens identified CK1ɛ as a pro-survival factor in cancer cells in vitro and the CK1δ/ɛ-specific inhibitor IC261 is remarkably effective at selective, synthetic lethal killing of cancer cells. The recent development of the nanomolar CK1δ/ɛ-selective inhibitor, PF670462 (PF670) and the CK1ɛ-selective inhibitor PF4800567 (PF480) offers an opportunity to further test the role of CK1δ/ɛ in cancer. Unexpectedly, and unlike IC261, PF670 and PF480 were unable to induce cancer cell death. PF670 is a potent inhibitor of CK1δ/ɛ in cells; nanomolar concentrations are sufficient to inhibit CK1δ/ɛ activity as measured by repression of intramolecular autophosphorylation, phosphorylation of disheveled2 proteins and Wnt/β-catenin signaling. Likewise, small interfering RNA knockdown of CK1δ and CK1ɛ reduced Wnt/β-catenin signaling without affecting cell viability, further suggesting that CK1δ/ɛ inhibition may not be relevant to the IC261-induced cell death. Thus, while PF670 is a potent inhibitor of Wnt signaling, it only modestly inhibits cell proliferation. In contrast, while sub-micromolar concentrations of IC261 neither inhibited CK1δ/ɛ kinase activity nor blocked Wnt/β-catenin signaling in cancer cells, it caused a rapid induction of prometaphase arrest and subsequent apoptosis in multiple cancer cell lines. In a stepwise transformation model, IC261-induced killing required both overactive Ras and inactive p53. IC261 binds to tubulin with an affinity similar to colchicine and is a potent inhibitor of microtubule polymerization. This activity accounts for many of the diverse biological effects of IC261 and, most importantly, for its selective cancer cell killing.
The Family Video Archive (2003)

We present the Family Video Archive as a tool to give consumers the ability to annotate and browse large collections of informal family movies. The informal nature of home movies makes it difficult to use fully-automated techniques for scene detection and annotation. Our system explores the symbiosis between automated and manual techniques for annotation. We also explore the use of a zooming interaction paradigm for browsing and filtering large collections of video scenes.
Quantitation of <scp>DNA</scp> and <scp>RNA</scp> with Absorption and Fluorescence Spectroscopy (2011)

Quantitation of nucleic acids is a fundamental tool in molecular biology that requires accuracy, reliability, and the use of increasingly smaller sample volumes. This unit describes the traditional absorbance measurement at 260 nm and three more sensitive fluorescence techniques employing Hoechst 33258, ethidium bromide, and PicoGreen. The range of the assays covers 25 pg/ml to 50 µg/ml. Absorbance at 260 nm has an effective range from 1 to 50 µg/ml; Hoechst 33258 from 0.01 to 15 µg/ml; ethidium bromide from 0.1 to 10 µg/ml; and PicoGreen from 25 to 1000 pg/ml.
Cells treated with TAP-2 antisense oligonucleotides are potent antigen-presenting cells in vitro and in vivo (1996)

Treatment of RMA and EL4 cells or freshly isolated splenocytes with antisense (AS) oligonucleotides directed against the TAP-2 gene recreates the phenotype seen in cells that are genetically deficient in TAP function. Cells incubated with AS oligonucleotides exhibit reduced MHC class I expression on the cell surface, which can be increased by incubating the oligonucleotide-treated cells at 28 degrees C or by adding MHC haplotype-matched peptides to the culture medium. RMA cells or splenocytes treated with AS oligonucleotides and incubated with peptide were highly effective in generating primary CTL responses in vitro. The bulk of the AS oligonucleotide-responsive and CTL-inducing cells resided in the adherent fraction of splenocytes. Moreover, TAP-2 AS oligonucleotide-treated adherent splenocytes pulsed with OVA peptide elicited potent OVA-specific CTL responses in vivo and provided effective protection from challenge with tumor cells expressing the corresponding Ag. AS oligonucleotide technology provides a simple approach to develop broadly applicable methods for generating potent APC to study TAP function in normal cells and to identify other gene products involved in MHC class I presentation.
ChemInform Abstract: A Convenient Synthesis of Bisindolylmaleimides. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.