gebhart/patrepeval huggingface dataset:
Processive replication is contingent on the exonuclease subunit of DNA polymerase III holoenzyme. (1990)

In this report we have taken the reconstitution approach to study which subunits of the heterotrimer core polymerase (alpha, epsilon, theta) participate in the highly processive replication of long DNA templates by DNA polymerase III holoenzyme (holoenzyme). Comparison of the core and the alpha epsilon complex (the DNA polymerase and 3'-5' exonuclease subunits, respectively) shows they are both rapid and highly processive polymerases when they are reconstituted into a holoenzyme with the gamma complex (gamma delta delta' chi psi) and beta accessory proteins of holoenzyme. Specifically, holoenzyme reconstituted using either core or alpha epsilon completely replicates a uniquely primed 5.4-kilobase (kb) single-stranded DNA within 12 s in one binding event. Hence the theta subunit of core is not required for the processivity or speed of the holoenzyme. In contrast, when only the alpha subunit is reconstituted into the holoenzyme it is unable to replicate the entire 5.4-kb circle in one binding event but still retains a fairly high processivity of 1-3 kb and when given sufficient time for multiple binding events it finally finishes the entire circle. Therefore, highly processive DNA synthesis by holoenzyme is contingent on the epsilon exonuclease subunit. In light of these results the significance of the polymerase and exonuclease activities residing in two separate polypeptides is discussed.
Characterization and cloning of STAT5 from IM-9 cells and its activation by growth hormone. (1996)

The interaction of GH with its receptor has been shown to lead to the phosphorylation of the signal transducer and activator of transcription (STAT) family of transcription factors. We demonstrate here that GH activates the tyrosine phosphorylation of STAT5 in the human IM-9 lymphocyte cell line. Western blotting indicates that GH also activates STAT5 in human embryonic kidney cells (293), which stably express the rabbit GH receptor. Although it has been shown previously that GH activates both STATs 1 and 3 in the 3T3-F442A mouse preadipocyte cell line, we demonstrate that GH also activates STAT5 in these cells. Using electrophoretic mobility shift assay, we examined the interaction of proteins with DNA elements containing consensus STAT-binding sequences. Proteins prepared from GH-treated 3T3-F442A cells bound to the c-sis inducible element of the human c-fos gene (m67 SIE), whereas proteins from GH-treated IM-9 cells did not. However, proteins from GH-treated IM-9 cells did interact with oligonucleotides containing either an interferon response element or the lactogenic hormone-responsive region. Treatment of IM-9 cells with interferon-gamma also induced protein interactions with these elements although the complexes were distinctly different than those seen with GH treatment. Using STAT-specific antibodies, we demonstrate that the GH-induced DNA-protein complex formed with the lactogenic hormone-responsive region contained STAT5, while the interferon-gamma-induced complex contained STAT1. These results implicate STAT5 as a downstream mediator of GH action in IM-9 cells. We report here the cloning of two forms of STAT5, STAT5A and STAT5B, from an IM-9 cDNA library. Northern blot analysis demonstrated multiple-forms of STAT5 mRNA in IM-9 cells.
Reverse Tunneling for Mobile IP (1998)

Mobile IP uses tunneling from the home agent to the mobile node's care-of address, but rarely in the reverse direction.Usually, a mobile node sends its packets through a router on the foreign network, and assumes that routing is independent of source address.When this assumption is not true, it is convenient to establish a topologically correct reverse tunnel from the care-of address to the home agent.This document proposes backwards-compatible extensions to Mobile IP in order to support topologically correct reverse tunnels.This document does not attempt to solve the problems posed by firewalls located between the home agent and the mobile node's care-of address.
Differential Affinities of Visual Arrestin, βArrestin1, and βArrestin2 for G Protein-coupled Receptors Delineate Two Major Classes of Receptors (2000)

Visual arrestin, betaarrestin1, and betaarrestin2 comprise a family of intracellular proteins that desensitize G protein-coupled receptors (GPCRs). In addition, betaarrestin1 and betaarrestin2 target desensitized receptors to clathrin-coated pits for endocytosis. Whether arrestins differ in their ability to interact with GPCRs in cells is not known. In this study, we visualize the interaction of arrestin family members with GPCRs in real time and in live cells using green fluorescent protein-tagged arrestins. In the absence of agonist, visual arrestin and betaarrestin1 were found in both the cytoplasm and nucleus of HEK-293 cells, whereas betaarrestin2 was found only in the cytoplasm. Analysis of agonist-mediated arrestin translocation to multiple GPCRs identified two major classes of receptors. Class A receptors (beta2 adrenergic receptor, mu opioid receptor, endothelin type A receptor, dopamine D1A receptor, and alpha1b adrenergic receptor) bound betaarrestin2 with higher affinity than betaarrestin1 and did not interact with visual arrestin. In contrast, class B receptors (angiotensin II type 1A receptor, neurotensin receptor 1, vasopressin V2 receptor, thyrotropin-releasing hormone receptor, and substance P receptor) bound both betaarrestin isoforms with similar high affinities and also interacted with visual arrestin. Switching the carboxyl-terminal tails of class A and class B receptors completely reversed the affinity of each receptor for the visual and non-visual arrestins. In addition, exchanging the betaarrestin1 and betaarrestin2 carboxyl termini reversed their extent of binding to class A receptors as well as their subcellular distribution. These results reveal for the first time marked differences in the ability of arrestin family members to bind GPCRs at the plasma membrane. Moreover, they show that visual arrestin can interact in cells with GPCRs other than rhodopsin. These findings suggest that GPCR signaling may be differentially regulated depending on the cellular complement of arrestin isoforms and the ability of arrestins to interact with other cellular proteins.
Pathological Study of Experimentally Induced Bovine Respiratory Syncytial Viral Infection in Lambs (1996)

An experimental model was designed to characterize lesions in the lung of lambs inoculated with bovine respiratory syncytial virus (BRSV). Twenty-five Merino lambs of both sexes, with a live weight of 17 +/- 3 kg, received an intratracheal inoculation of 20 ml saline solution containing 1.26 x 10(6) TCID50 BRSV (strain NMK-7) per ml. Lambs were slaughtered 1, 3, 7, 11 and 15 days postinoculation (DPI), and samples were taken for analysis using light-microscopic and immunohistochemical techniques. The results reflected the effect of the virus on airway epithelia. The presence of BRSV in ciliated bronchial and bronchiolar epithelial cells gave rise to cytopathological changes, including loss of cilia and cell necrosis; these changes might be expected to decrease the efficiency of mucociliary clearance, favouring the development of secondary bacterial bronchopneumonia. These results suggest a reduction in BRSV tropism for alveolar epithelia compared to bronchial and bronchiolar epithelia. Light-microscopic analysis revealed a narrowing of alveolar and airway lumina and a considerable interstitial inflammatory reaction.
Peroxidase Activity and Iodide Uptake in Hormone-Responsive and Hormone-Independent GR Mouse Mammary Tumors<xref ref-type="fn" rid="FN2">2</xref> (1979)

In his speech, Theodore Roosevelt attacks President Taft's "feeble intentions" and his unscrupulous tactics in his New Jersey campaign.
Apoptotic cell recognition receptors and scavenger receptors (2015)

Phosphatidylserine recognition receptors are a highly diverse set of receptors grouped by their ability to recognize the 'eat-me' signal phosphatidylserine on apoptotic cells. Most of the phosphatidylserine recognition receptors dampen inflammation by inducing the production of anti-inflammatory mediators during the phagocytosis of apoptotic corpses. However, many phosphatidylserine receptors are also capable of recognizing other ligands, with some receptors being categorized as scavenger receptors. It is now appreciated that these receptors can elicit different downstream events for particular ligands. Therefore, how phosphatidylserine recognition receptors mediate specific signals during recognition of apoptotic cells versus other ligands, and how this might help regulate the inflammatory state of a tissue is an important question that is not fully understood. Here, we revisit the work on signaling downstream of the phosphatidylserine recognition receptor BAI1, and evaluate how these and other signaling modules mediate signaling downstream from other receptors, including Stabilin-2, MerTK, and αvβ5. We also propose the concept that phosphatidylserine recognition receptors could be viewed as a subset of scavenger receptors that are capable of eliciting anti-inflammatory responses to apoptotic cells.
Ku70 acetylation mediates neuroblastoma cell death induced by histone deacetylase inhibitors (2005)

Histone deacetylase inhibitors (HDACIs) are therapeutic drugs that inhibit deacetylase activity, thereby increasing acetylation of many proteins, including histones. HDACIs have antineoplastic effects in preclinical and clinical trials and are being considered for cancers with unmet therapeutic need, including neuroblastoma (NB). Uncertainty of how HDACI-induced protein acetylation leads to cell death, however, makes it difficult to determine which tumors are likely to be responsive to these agents. Here, we show that NB cells are sensitive to HDACIs, and that the mechanism by which HDACIs induce apoptosis involves Bax. In these cells, Bax associates with cytoplasmic Ku70, a protein that typically increases chemotherapy resistance. Our data show that in NB cells Ku70 binds to Bax in an acetylation-sensitive manner. Upon HDACI treatment, acetylated Ku70 releases Bax, allowing it to translocate to mitochondria and trigger cytochrome c release, leading to caspase-dependent death. This study shows that Ku70 is an important Bax-binding protein, and that this interaction can be therapeutically regulated in NB cells. Whereas the Bax-binding ability of Ku70 allows it to block apoptosis in response to certain agents, it is also a molecular target for the action of HDACIs, and in this context, a mediator of NB cell death.
Nonpeptidic Propargylamines as Inhibitors of Lysine Specific Demethylase 1 (LSD1) with Cellular Activity (2013)

Lysine demethylases play an important role in epigenetic regulation and thus in the development of diseases like cancer or neurodegenerative disorders. As the lysine specific demethylase 1 (LSD1/KDM1) has been strongly connected to androgen and estrogen dependent gene expression, it serves as a promising target for the therapy of hormone dependent cancer. Here, we report on the discovery of new small molecule inhibitors of LSD1 containing a propargylamine warhead, starting out from lysine containing substrate analogues. On the basis of these substrate mimicking inhibitors, we were able to increase potency by a combination of similarity-based virtual screening and subsequent synthetic optimization resulting in more druglike LSD1 inhibitors that led to histone hypermethylation in breast cancer cells.
Sensitivity of K562 human chronic myelogenous leukemia blast cells transfected with a human multidrug resistance cDNA to cytotoxic drugs and differentiating agents. (1993)

The blast crisis of chronic myelogenous leukemia (CML) is refractory to most forms of cancer chemotherapy, but may be amenable to drugs that differentiate rather than kill leukemic cells. One mechanism implicated in resistance to cytodestructive drugs is overexpression of P-glycoprotein, the MDR1 gene product. While several classes of drugs sensitize multidrug-resistant (MDR) cells by interfering with the function of P-glycoprotein in vitro, few sensitizers have been effective in vivo. We have developed a preclinical model of MDR/CML uncomplicated by other mechanisms of drug resistance to evaluate the effects of MDR1 overexpression on cytodestructive and differentiation therapy and the ability of sensitizers to restore chemosensitivity in this disease. The CML-derived cell line K562 was transfected with a human MDR1 cDNA from the pHaMDR1/A expression vector and selected with vinblastine. Resistant K562 clones were 20-30-fold resistant to vinblastine, were cross-resistant to doxorubicin and etoposide, and remained sensitive to cytosine arabinoside, 6-thioguanine, hydroxyurea, and mechlorethamine. Resistance was associated with decreased cellular accumulation of cytotoxic drug and was reversed by cyclosporin A and trans-flupenthixol. The MDR phenotype did not adversely affect the ability of K562 cells to produce fetal hemoglobin in response to hemin, and was associated with increased responsiveness of cells to differentiate with cytosine arabinoside. Upon differentiation, the resistant clones increased MDR1 mRNA and P-glycoprotein. These studies suggest that the overexpression of the MDR1 gene in CML may not adversely affect the ability to undergo erythroid differentiation and that these resistant K562 cell lines are good models for studying drug resistance mediated by P-glycoprotein in CML.
An Adaptive Strategy for Hybrid Image Coding (1981)

In hybrid coding technique, the sampled data are divided into blocks of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N \times M</tex> samples. Next, each block is transformed to generate a one-dimensional transform of each line in the block. The transform coefficients are then processed by a block of DPCM encoders which uncorrelate the data in the second dimension and qnantize the uncorrelated samples using appropriate quantizers. In this study an adaptive hybrid coding technique is proposed based on using a single quantizer (A/D converter) to quantize the transform coefficients and using a variable-rate algorithm for coding the quantized coefficients. The accuracy of the A/D converter (number of bits per sample) determines the fidelity of the system. The buffercontrol algorithm controls the accuracy of the A/D converter for each block resulting in a fixed-rate encoder system. Experimental results have shown a stable buffer condition and reconstructed images with a higher fidelity than nonadaptive hybrid systems.
Configuration of the 5′-Methyl Group Modulates the Biophysical and Biological Properties of Locked Nucleic Acid (LNA) Oligonucleotides (2010)

As part of a program aimed at exploring the structure- activity relationships of 2',4'-bridged nucleic acid (BNA) containing antisense oligonucleotides (ASOs), we report the synthesis and biophysical and biological properties of R- and S-5'-Me LNA modified oligonucleotides. We show that introduction of a methyl group in the (S) configuration at the 5'-position is compatible with the high affinity recognition of complementary nucleic acids observed with LNA. In contrast, introduction of a methyl group in the (R) configuration reversed the stabilization effect of LNA. NMR studies indicated that the R-5'-Me group changes the orientation around torsion angle γ from the +sc to the ap range at the nucleoside level, and this may in part be responsible for the poor hybridization behavior exhibited by this modification. In animal experiments, S-5'-Me-LNA modified gapmer antisense olignucleotides showed slightly reduced potency relative to the sequence matched LNA ASOs while improving the therapeutic profile.
An Architecture Framework for Transparent Instruction Set Customization in Embedded Processors (2005)

Instruction set customization is an effective way to improve processor performance. Critical portions of applicationdata-flow graphs are collapsed for accelerated execution on specialized hardware. Collapsing dataflow subgraphs will compress the latency along critical paths and reduces the number of intermediate results stored in the register file. While custom instructions can be effective, the time and cost of designing a new processor for each application is immense. To overcome this roadblock, this paper proposes a flexible architectural framework to transparently integrate custom instructions into a general-purpose processor. Hardware accelerators are added to the processor to execute the collapsed subgraphs. A simple microarchitectural interface is provided to support a plug-and-play model for integrating a wide range of accelerators into a pre-designed and verified processor core. The accelerators are exploited using an approach of static identification and dynamic realization. The compiler is responsible for identifying profitable subgraphs, while the hardware handles discovery, mapping, and execution of compatible subgraphs. This paper presents the design of a plug-and-play transparent accelerator system and evaluates the cost/performance implications of the design.
VisBio: A Computational Tool for Visualization of Multidimensional Biological Image Data (2004)

New laser scanning microscopy techniques enable biologists to acquire larger, more complex image datasets. Emerging imaging modalities such as multispectral, harmonic, and fluorescence lifetime can generate data with six or more dimensions; however, existing software is not well suited to the visualization or analysis of such data. To address these concerns, we have developed VisBio, an application and toolkit for visualization and analysis of multidimensional, biological image data of any dimensionality.
Antigenic and phenotypic variations of Haemophilus influenzae type b lipopolysaccharide and their relationship to virulence (1986)

Haemophilus influenzae type b (Hib) strains NO100 and COL10 were found to produce bacteremia in infant rats at a much lower frequency than other Hib strains previously tested. These relatively avirulent strains were the only Hib strains among 200 clinical isolates examined to date which failed to react with two Hib lipopolysaccharide (LPS)-specific monoclonal antibodies (MAbs). LPS analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that strains NO100 and COL10 possessed LPS which migrated faster than the LPS of Hib strains that reacted with one of the two or with both of these MAbs. These observations suggested that the relative lack of virulence of strains NO100 and COL10 might be related to their unusual LPS phenotype. To determine whether alteration of LPS structure would affect the virulence of these strains, we identified and isolated isogenic LPS antigenic variants of strains NO100 and COL10 using the LPS-specific MAbs 4C4 and 5G8 in a colony blot radioimmunoassay. Antigenic variation of LPS was found to occur spontaneously in these two strains at a relatively high frequency in terms of both acquisition and loss of MAb reactivity (ca. 0.2 to 16.7%). LPS antigenic variants of strains NO100 and COL10 reactive with both MAbs 4C4 and 5G8 (4C4+ 5G8+) were more virulent in the infant rat model than their respective 4C4- 5G8- parental strains (P less than 0.01). An antigenic variant of COL10 reactive with only MAb 4C4 (4C4+ 5G8-) was also significantly more virulent than its 4C4- 5G8- parent. These LPS antigenic variants with increased virulence synthesized altered LPS molecules which possessed apparent molecular weights higher than those of the LPS of the parental strains. Increased resistance of strain NO100 to the bactericidal activity of normal infant rat serum was associated with changes in LPS structure, while strain COL10 and its LPS variants were all uniformly resistant to serum bactericidal activity. Our results demonstrate that (i) spontaneous antigenic and phenotypic variation of LPS occurs at a relatively high frequency in some strains of Hib; (ii) the higher-molecular-weight type of LPS is associated with the full expression of Hib virulence; (iii) LPS phenotype may not correlate with Hib serum resistance; and (iv) serum resistance of Hib is not an accurate indicator of virulence.
Noise in Structured-Light Stereo Depth Cameras: Modeling and its Applications (2015)

Depth maps obtained from commercially available structured-light stereo based depth cameras, such as the Kinect, are easy to use but are affected by significant amounts of noise. This paper is devoted to a study of the intrinsic noise characteristics of such depth maps, i.e. the standard deviation of noise in estimated depth varies quadratically with the distance of the object from the depth camera. We validate this theoretical model against empirical observations and demonstrate the utility of this noise model in three popular applications: depth map denoising, volumetric scan merging for 3D modeling, and identification of 3D planes in depth maps.
Effects of Long-Term Corn Consumption on Brain Serotonin and the Response to Electric Shock (1975)

Rats fed tryptophan-poor corn diets have reduced levels of brain serotonin and show increased responsiveness to electric shock. This diet-induced hyperalgesia can be reversed by feeding the animals diets with adequate amounts of tryptophan, or by systemic injections of the amino acid.
PEASE: predicting B-cell epitopes utilizing antibody sequence (2014)

yanay@ofranlab.org.
A Simple Method for the Production of a Two-Dimensional, Ordered Array of Small Latex Particles (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Simple Method for the Production of a Two-Dimensional, Ordered Array of Small Latex ParticlesR. Micheletto, H. Fukuda, and M. OhtsuCite this: Langmuir 1995, 11, 9, 3333–3336Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/la00009a012https://doi.org/10.1021/la00009a012research-articleACS PublicationsRequest reuse permissionsArticle Views3746Altmetric-Citations340LEARN 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
Comparison of toxicity of smoke from traditional and harm-reduction cigarettes using mouse embryonic stem cells as a novel model for preimplantation development (2008)

mESC provide a valuable model for toxicological studies on the preimplantation stage of development and were used to show that MS and SS smoke from traditional and harm-reduction cigarettes are detrimental to embryonic cells prior to implantation.
Diagnostic pitfalls in children with sleep disorders: two cases with hypersomnia (2008)

Sleep medicine needs to be given larger role in both training curriculum and post-graduate education for paediatricians.