gebhart/patrepeval huggingface dataset:
The in vitro effects of cytokines on expansion and migration of megakaryocyte progenitors (2000)

Increasing the number of megakaryocyte progenitors in stem cell transplants by ex vivo expansion culture may be an approach to accelerate platelet recovery in patients undergoing high-dose chemotherapy. We evaluated the effect of three different cytokine combinations on expansion, with special emphasis on the type of colony formation and migration of megakaryocytic cells. The number of clonogenic megakaryocyte progenitors (colony-forming units-megakaryocyte; CFU-Mk) with high- (> 20 cells/colony) and low-proliferative capacity (5-20 cells/colony) and the number of megakaryocytic (CD61+) cells were significantly increased by including interleukin 3 (IL-3) or IL-3 + IL-6 + IL-11 + Flt3-ligand to cultures containing megakaryocyte growth and development factor (MGDF) plus stem cell factor (SCF). No difference in the maturation of megakaryocytes from all three cytokine combinations to platelets were observed, as demonstrated by electron microscopy. In chemotaxis experiments, the migration towards stromal cell-derived factor 1 (SDF-1) was shown to be reduced for CD61+ cells and megakaryocyte progenitors cultured in other cytokines besides MGDF + SCF. The reduced migration was related to a lower expression of CXCR4, the receptor for SDF-1, on megakaryocytes from the proliferating cultures. These in vitro results demonstrate that expansion in IL-3 and other cytokines besides MGDF + SCF significantly impair the capacity of megakaryocytic cells to migrate.
A Re-Evaluation of the Frequency of CD8+ T Cells Specific for EBV in Healthy Virus Carriers (1999)

EBV is a gammaherpesvirus that can establish both nonproductive (latent) and productive (lytic) infections within the cells of its host. Although T cell responses to EBV latent proteins have been well characterized, little is known about the importance of responses to lytic proteins in long term virus carriers. Here we have compared the frequencies of CD8+ T cells specific for EBV latent and lytic Ags in healthy virus carriers, using three techniques: limiting dilution analysis, enzyme-linked immunospot assay, and FACS staining with tetrameric MHC-peptide complexes. T cells specific for EBV lytic protein epitopes were readily detectable in all donors and were usually more abundant than those specific for latent epitopes. We infer that direct T cell control of viral replicative lesions is maintained in long term carriers of EBV and is an important component of the immune response to this virus. Estimates of CD8+ T cell frequencies varied considerably according to methodology; values obtained from MHC-peptide tetramer staining were, on the average, 4.4-fold higher than those obtained from enzyme-linked immunospot assays, which were, in turn, on the average, 5.3-fold higher than those obtained from limiting dilution analysis. Tetramer staining showed that as many as 5.5% circulating CD8+ T cells in a virus carrier were specific for a single EBV lytic protein epitope. Such values are much greater than previously imagined and illustrate how antigenic challenge from a persistent herpesvirus can influence the composition of the host's CD8+ T cell pool.
Expression of the Escherichia coli malPQ operon remains unaffected after drastic alteration of its promoter (1983)

The malPQ operon, one of the three operons of the maltose regulon, is positively controlled by the product of gene malT. The starting point for malPQ transcription was deduced from experiments which involved a hybridization of in vivo-synthesized malPQ mRNA with adequate DNA probes, followed either by a digestion of nonhybridized DNA (S1 nuclease mapping) or by an extension of the hybridized probe (reverse transcriptase mapping). In the wild-type strain, this starting point was 37 nucleotides upstream from the initiation codon for malP. This analysis was also performed on a double mutant which contained both a 13-base pair deletion and a 3-base pair insertion in the promoter region. This double mutant expressed the malPQ operon exactly as the wild-type strain did, in a maltose-inducible manner. In this strain, the starting point for malPQ transcription was shifted 11 nucleotides downstream from the wild-type location. An analysis of these results suggests that (i) the binding site for the malT product is located upstream from the region which is severely altered in the double mutant, i.e., upstream from position -31; and (ii) the 30-base pair sequence which precedes the transcription starting point contains very few positions which are essential for promoter activity.
DETECTION OF ESCHERICHIA COLI O157 IN RAW BEEF USING A CCD BASED LIGHT SCATTERING INSTRUMENT (2002)

A sensitive and easy‐to‐perform instrumentational method for the detection of Escherichia coli O157 in raw minced beef is described. The detection is based on a light scattering immunoassay and a charge‐coupled device (CCD) direct readout spectrometer measuring the scattered light spectral signals at an optimized angle of 20° to the axis of transmitted light. Using latex particles coated with antibodies for E. coli O157, the method sensitivity has significantly improved comparing with the visual immunoassay assessment method when detecting the presence of this bacterium in spiked beef samples. The method is capable of detecting E. coli O157 at the level of 10 3 cfu mL ‐1 after 6 h of incubation of the spiked samples. This study has demonstrated a faster technique (within 8 h) for the detection of E. coli O157 in raw beef and a possible new application for the CCD based light scattering instrument.
Mitochondrial Dysfunction Confers Resistance to Multiple Drugs inCaenorhabditis elegans (2010)

In a previous genetic screen for Caenorhabditis elegans mutants that survive in the presence of an antimitotic drug, hemiasterlin, we identified eight strong mutants. Two of these were found to be resistant to multiple toxins, and in one of these we identified a missense mutation in phb-2, which encodes the mitochondrial protein prohibitin 2. Here we identify two additional mutations that confer drug resistance, spg-7 and har-1, also in genes encoding mitochondrial proteins. Other mitochondrial mutants, isp-1, eat-3, and clk-1, were also found to be drug-resistant. Respiratory complex inhibitors, FCCP and oligomycin, and a producer of reactive oxygen species (ROS), paraquat, all rescued wild-type worms from hemiasterlin toxicity. Worms lacking mitochondrial superoxide dismutase (MnSOD) were modestly drug-resistant, and elimination of MnSOD in the phb-2, har-1, and spg-7 mutants enhanced resistance. The antioxidant N-acetyl-l-cysteine prevented mitochondrial inhibitors from rescuing wild-type worms from hemiasterlin and sensitized mutants to the toxin, suggesting that a mechanism sensitive to ROS is necessary to trigger drug resistance in C. elegans. Using genetics, we show that this drug resistance requires pkc-1, the C. elegans ortholog of human PKCepsilon.
Use of Real-Time Quantitative PCR to Compare DNA Isolation Methods (1998)

PCR-based diagnostics of genomic DNA and DNA from viruses, microorganisms, or tumor cells are rapidly becoming routine practice in the clinical laboratory. DNA isolation is usually the first step toward detection. Because of expanding numbers of DNA isolation methods, the choice between methods is becoming increasingly difficult. Especially when a low amount of target DNA is present, when only a limited amount of clinical sample is available, or when PCR inhibitors are expected to be present, isolation efficiency, repeatability, and removal of PCR inhibitors by the isolation method become critical factors, seriously affecting the final outcome of the experiment.

Recently, a real-time quantitative PCR system [ABI PrismTM 7700 Sequence Detection System, Perkin-Elmer Applied Biosystems (PE)] was developed. Quantification is automatically performed in the exponential phase of the PCR reaction, where there is a linear relationship between the log of input target DNA quantity and the number of PCR cycles to reach an arbitrary fluorescence threshold (1)(2).

The objective of this study was to evaluate this PCR system for standardization of DNA isolation methods. Therefore, we added a known amount of marker DNA copies, close to the detection limit of the PCR, to plasma, which we chose because of recent developments in diagnostic molecular oncology (3)(4). After isolating the DNA with four different methods, we used the PCR system to determine isolation efficiency and repeatability of each method.

Blood from five healthy donors was collected in 10-mL EDTA tubes. Plasma was pooled and stored at −80 °C. A 12.8-kb plasmid containing a cDNA sequence construct of the bcr-abl gene translocation was used as marker DNA. The plasmid was linearized with a restriction enzyme, cleaned using a QIAquick column (QIAGEN), and quantified using GeneQuant II RNA/DNA calculator (Pharmacia). A 10-fold serial dilution of the marker DNA …
Miniemulsion Droplets as Single Molecule Nanoreactors for Polymerase Chain Reaction (2005)

Polymerase chain reaction (PCR) was successfully carried out inside stable and narrowly distributed water-in-oil nanodroplets with a size of 100-300 nm in diameter. The droplets were obtained by the miniemulsion process. Each aqueous droplet serves as a single nanoreactor for the PCR. It was found that the size of the droplets highly depends on the sonication parameters (i.e., time and amplitude) and that these parameters have a great influence on the final concentration of the PCR product. The parameters were chosen that way that conditions for single molecule chemistry were obtained, since the 3D-space is compartimentalized in small nanoreactors in each of which the same reaction takes place in a highly parallel fashion on every single DNA molecule.
Cytotoxicity of human peripheral blood and colostral leukocytes against Shigella species (1984)

We examined the ability of human peripheral blood leukocytes to kill strains of Shigella sonnei and Shigella flexneri by using a modified bactericidal assay. Antibody-dependent cellular cytotoxicity (ADCC) was demonstrated in the presence of specific rabbit immune serum directed against S. sonnei. With peripheral blood leukocytes from adults, ADCC was found only in the mononuclear cell and purified lymphocyte populations. Monocyte-macrophages and polymorphonuclear leukocytes were unable to demonstrate ADCC. Lymphocyte ADCC, which was not affected by the addition of phenylbutazone (an inhibitor of phagocytosis), was mediated by a non-T, Fc receptor-positive, HNK-1- cell. ADCC (using antiserum directed against virulent S. sonnei) was demonstrated against virulent S. sonnei but not against virulent S. sonnei or virulent S. flexneri. In contrast to leukocytes from adults, both mononuclear and polymorphonuclear cells from neonatal cord blood and from a patient with chronic granulomatous disease mediated anti-Shigella ADCC. Breast milk leukocytes (BMLs) collected 1 to 3 days postpartum were used as effector cells against virulent S. sonnei. The entire BML population, BMLs which did not adhere to plastic and BMLs which passed through nylon wool columns mediated both natural killer cytotoxicity and ADCC. In paired experiments, natural killer cytotoxicity and ADCC were significantly lower (30 to 45% inhibition) but not ablated, when phenylbutazone was added to BMLs and nylon wool-purified BMLs (P less than 0.05). These experiments suggest that colostral leukocytes mediated both extracellular and intracellular bacteriolysis in the presence and absence of specific antiserum. These mechanisms may be active in vivo in protection against shigellosis.
Identification and characterization of key residues in Zika virus envelope protein for virus assembly and entry (2022)

Zika virus (ZIKV), a family member in the <i>Flavivirus</i> genus, has re-emerged as a global public health concern. The envelope (E) proteins of flaviviruses play a dual role in viral assembly and entry. To identify the key residues of E in virus entry, we generated a ZIKV <i>trans</i>-complemented particle (ZIKV<sub>TCP</sub>) system, in which a subgenomic reporter replicon was packaged by <i>trans</i>-complementation with expression of CprME. We performed mutagenesis studies of the loop regions that protrude from the surface of the virion in the E ectodomains (DI, DII, DIII). Most mutated ZIKV<sub>TCPs</sub> exhibited deficient egress. Mutations in DII and in the hinge region of DI and DIII affected prM expression. With a bioorthogonal system, photocrosslinking experiments identified crosslinked intracellular E trimers and demonstrated that egress-deficient mutants in DIII impaired E trimerization. Of these mutants, an E-trimerization-dead mutation D389A that nears the E-E interface between two neighbouring spikes in the immature virion completely abolished viral egress. Several mutations abolished ZIKV<sub>TCPs</sub>' entry, without severely affecting viral egress. Further virus binding experiments demonstrated a deficiency of the mutated ZIKV<sub>TCPs</sub> in virus attachment. Strikingly, synthesized peptide containing residues of two mutants (268-273aa in DII) could bind to host cells and significantly compete for viral attachment and interfere with viral infection, suggesting an important role of these resides in virus entry. Our findings uncovered the requirement for DIII mediated-E trimerization in viral egress, and discovered a key residue group in DII that participates in virus entry.
Distinct structural characteristics of discoidin I subfamily receptor tyrosine kinases and complementary expression in human cancer. (1995)

Mammary carcinoma kinase 10 (MCK-10) and colon carcinoma kinase 2 (CCK-2) constitute a subclass of receptor tyrosine kinases characterized by a discoidin I motif in the extracellular domain and a large cytoplasmic juxtamembrane (JM) region. While the ectodomain structure suggests a common role in cell aggregation, the JM domains of MCK-10 and CCK-2 are structurally most divergent and display features that suggest an involvement in signal generation and definition. MCK-10 occurs in at least three isoforms, which contain alternatively spliced consensus sequences for internalization and SH3 domain interaction. The presence of the 37 amino acid insert affects receptor autophosphorylation and changes ectodomain glycosylation. Proteolytic cleavage within the extracellular domain of MCK-10 generates a membrane-anchored kinase domain and releases a soluble ectodomain fragment including the discoidin I homology domain. CCK-2 and MCK-10 expression was found in connective and epithelial tissues, respectively, which in cancers of epithelial origin results in mutually exclusive expression in stroma and tumor cells, indicating a possible involvement of this class of RTKs in tumor invasion.
P1 Aspartate-Based Peptide .alpha.-((2,6-Dichlorobenzoyl)oxy)methyl Ketones as Potent Time-Dependent Inhibitors of Interleukin-1.beta.-Converting Enzyme (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTP1 Aspartate-Based Peptide .alpha.-((2,6-Dichlorobenzoyl)oxy)methyl Ketones as Potent Time-Dependent Inhibitors of Interleukin-1.beta.-Converting EnzymeRoland E. Dolle, Denton Hoyer, C. V. C. Prasad, Stanley J. Schmidt, Carla T. Helaszek, Robert E. Miller, and Mark A. AtorCite this: J. Med. Chem. 1994, 37, 5, 563–564Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/jm00031a003https://doi.org/10.1021/jm00031a003research-articleACS PublicationsRequest reuse permissionsArticle Views437Altmetric-Citations125LEARN 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
Mediation of Neuronal Apoptosis by Enhancement of Outward Potassium Current (1997)

Apoptosis of mouse neocortical neurons induced by serum deprivation or by staurosporine was associated with an early enhancement of delayed rectifier (IK) current and loss of total intracellular K+. This IK augmentation was not seen in neurons undergoing excitotoxic necrosis or in older neurons resistant to staurosporine-induced apoptosis. Attenuating outward K+ current with tetraethylammonium or elevated extracellular K+, but not blockers of Ca2+, Cl-, or other K+ channels, reduced apoptosis, even if associated increases in intracellular Ca2+ concentration were prevented. Furthermore, exposure to the K+ ionophore valinomycin or the K+-channel opener cromakalim induced apoptosis. Enhanced K+ efflux may mediate certain forms of neuronal apoptosis.
Regulation of the Murine αB-Crystallin/Small Heat Shock Protein Gene in Cardiac Muscle (1995)

The murine alpha B-crystallin/small heat shock protein gene is expressed at high levels in the lens and at lower levels in the heart, skeletal muscle, and numerous other tissues. Previously we have found a skeletal-muscle-preferred enhancer at positions -427 to -259 of the alpha B-crystallin gene containing at least four cis-acting regulatory elements (alpha BE-1, alpha BE-2, alpha BE-3, and MRF, which has an E box). Here we show that in transgenic mice, the alpha B-crystallin enhancer directs the chloramphenicol acetyltransferase reporter gene driven by the alpha B-crystallin promoter specifically to myocardiocytes of the heart. The alpha B-crystallin enhancer was active in conjugation with the herpes simplex virus thymidine kinase promoter/human growth hormone reporter gene in transfected rat myocardiocytes. DNase I footprinting and site-specific mutagenesis experiments showed that alpha BE-1, alpha BE-2, alpha BE-3, MRF, and a novel, heart-specific element called alpha BE-4 are required for alpha B-crystallin enhancer activity in transfected myocardiocytes. By contrast, alpha BE-4 is not utilized for enhancer activity in transfected lens or skeletal muscle cell lines. Alpha BE-4 contains an overlapping heat shock sequence and a reverse CArG box [5'-GG(A/T)6CC-3']. Electrophoretic mobility shift assays with an antibody to serum response factor and a CArG-box-competing sequence from the c-fos promoter indicated that a cardiac-specific protein with DNA-binding and antigenic similarities to serum response factor binds to alpha BE-4 via the reverse CArG box; electrophoretic mobility shift assays and antibody experiments with anti-USF antiserum and heart nuclear extract also raised the possibility that the MRF E box utilizes USF or an antigenically related protein. We conclude that the activity of the alpha B-crystallin enhancer in the heart utilizes a reverse CArG box and an E-box-dependent pathway.
Spectroscopic Evidence for Inner-Sphere Coordination of Metal Ions to the Active Site of a Hammerhead Ribozyme (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSpectroscopic Evidence for Inner-Sphere Coordination of Metal Ions to the Active Site of a Hammerhead RibozymeLynette A. Cunningham, Jing Li, and Yi LuView Author Information Department of Chemistry, University of Illinois Urbana, Illinois 61801 Cite this: J. Am. Chem. Soc. 1998, 120, 18, 4518–4519Publication Date (Web):April 28, 1998Publication History Received16 September 1997Published online28 April 1998Published inissue 1 May 1998https://pubs.acs.org/doi/10.1021/ja973251phttps://doi.org/10.1021/ja973251prapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views266Altmetric-Citations35LEARN 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 SUBJECTS:Absorption,Crystal cleavage,Ions,Metals,Oxygen Get e-Alerts
Correlation management and search for the Internet of Things (2016)

The Internet of Things (IoT) is a compelling paradigm, which aims to enable everyday physical things embedded with electronics, software, sensors, and network connectivity to collect and exchange data on the Internet. It is anticipated that by 2020, billions of things get connected to the Internet. Creating future IoT search engines is a key step towards unlocking answering the above question. Future search engines can potentially in revolutionise various applications in different domains. Existing approaches for searching the IoT use simple techniques to obtain a list of things for a query. The state of the art needs to be improved in different aspects. For instance, it is often disregarded that in the context of IoT, we have two types of users including machines and human users. In addition, many have complained about the absence of the real-world IoT data. Unsurprisingly, a common question that arises regularly nowadays is “Does the IoT already exist?”. So far, little has been known about the real-world situation on IoT, its attributes, the presentation of data and user interests. Moreover, existing approaches also disregard the attribute based correlations between things in the real-world. In this dissertation, we review the state of the art in IoT search domain and propose a novel framework to collect and analyse IoT data. Our system is also able to resolve IoT queries based on the knowledge that is acquired from the IoT data sources. Furthermore, we introduce a novel technique to extract the correlations between things. Our framework is capable of using the correlations to improve the quality of search results for both types of users. We investigate the scalability and the effectiveness of our approach using large scale and real-world datasets. Moreover, we investigate two case studies in transport systems in our research. The first case study, challenges the complex problem of taxi ridesharing in the context of smart cities. The second case study, involves a real-time prediction method for flight delays based on the IoT sourced data.