gebhart/patrepeval huggingface dataset:
Four Classes of Salicylate-Induced Tobacco Genes (1998)

We have identified and characterized fragments of 15 salicylic acid (SA) early response genes. The kinetics of induction and response to cycloheximide (CHX) treatment allowed classification of genes into four groups. Classes I-III are characterized by immediate-early responses, showing increased accumulation of mRNA within 30 min of SA treatment. Moreover, CHX did not block induction of these genes, indicating that latent cellular factors mediate the SA response. Class IV genes were induced more slowly, but still within 2 to 3 h of SA treatment, and required protein synthesis for expression. Although identified in this study as SA-responsive genes, several could also be induced by other compounds. Two genes were characterized in more detail, including isolation of cDNA sequences and additional analysis of gene expression. Sequence analysis revealed that the class I gene, C18-1, is the previously identified ethylene response element binding protein 1 (EREBP1), an ethylene-induced transcription factor for basic pathogenesis-related (PR) genes, whereas the class III gene, G8-1, is a novel sequence. G8-1 was found to be strongly induced only by SA and its active analogs and was exquisitely sensitive to low SA concentrations. These and other genes were found to be activated at early times following tobacco mosaic virus infection of resistant tobacco genotypes.
The organ uptake of intravenously administered colloidal particles can be altered using a non‐ionic surfactant (Poloxamer 338) (1984)

Small polystyrene particles coated with a high Mr non-ionic surfactant (Poloxamer 338) are diverted from the reticuloendothelial system of the liver and spleen to other tissue sites. These results are discussed in terms of the adsorption of the Poloxamer to the particle surface and the implications for drug targeting.
The role of C-reactive protein in the resolution of bacterial infection (2001)

C-reactive protein is an acute phase protein in man and an important component of the innate immune system. C-reactive protein activates the classical pathway of complement, which is one of its main mechanisms in providing host defense. It has recently been recognized that C-reactive protein interacts with the cells of the immune system by binding to Fc gamma receptors. It may thus bridge the gap between innate and adaptive immunity and provide an early, effective antibacterial response. Furthermore, as it protects against the damaging inflammatory response to lipopolysaccharide and cytokines, it may prevent the lethal side-effects of bacterial products. The recent identification of the interaction of C-reactive protein with Fc gamma receptors will lead to an enhanced understanding of C-reactive protein and its role in both the innate and acquired immune systems.
Electrochemical sterilization of bacteria adsorbed on granular activated carbon (1992)

The electrochemical sterilization of bacteria adsorbed on granular activated carbon (GAC) was demonstrated. The survival ratio of bacteria on GAC was dependent upon the applied potential. The survival ratio of Escherichia coli, Staphylococcus aureus, Bacillus subtilis and Saccharomyces cerevisiae vs. saturated calomel electrode (SCE) was below 1% at 0.75, 0.8, 1.0 and 0.65 V, respectively. The electrochemical sterilization of tap water containing E. coli was carried out when 3.5 ml of the cell suspension (4.0 × 102 cells/ml was incubated with 2.0 g of GAC for 5 h at 0.7 V vs. SCE. The number of E. coli adsorbed on GAC and the cell concentration in the water decreased rapidly. E. coli on GAC were electrochemically killed and the cell numbers did not increase.
A mobile service platform using proxy technology: Research Articles (2006)

This paper proposes iMobile, a proxy-based platform for developing mobile services for various mobile devices and wireless access technologies. iMobile acts as a message gateway that allows mobile devices to relay messages to each other through various protocols on different access networks. It allows mobile devices to access internet services, corporate databases and to control various network devices. iMobile implements three key abstractions: dev-let, info-let and app-let. An info-let provides abstract view of information space. An app-let implements service or application logic by processing information from various info-lets. A dev-let receives and sends messages through any particular protocols for mobile devices. The let engine supports user and device profiles for personalization and transcoding, and invokes proper app-lets and info-lets to answer requests from a dev-let. The iMobile modular architecture allows developers to write device drivers, information access methods and application logic independently from each other. Copyright © 2005 John Wiley & Sons, Ltd.
Identification and Characterization of Mitochondrial Targeting Sequence of Human Apurinic/Apyrimidinic Endonuclease 1 (2010)

Dually targeted mitochondrial proteins usually possess an unconventional mitochondrial targeting sequence (MTS), which makes them difficult to predict by current bioinformatics approaches. Human apurinic/apyrimidinic endonuclease (APE1) plays a central role in the cellular response to oxidative stress. It is a dually targeted protein preferentially residing in the nucleus with conditional distribution in the mitochondria. However, the mitochondrial translocation mechanism of APE1 is not well characterized because it harbors an unconventional MTS that is difficult to predict by bioinformatics analysis. Two experimental approaches were combined in this study to identify the MTS of APE1. First, the interactions between the peptides from APE1 and the three purified translocase receptors of the outer mitochondrial membrane (Tom) were evaluated using a peptide array screen. Consequently, the intracellular distribution of green fluorescent protein-tagged, truncated, or mutated APE1 proteins was traced by tag detection. The results demonstrated that the only MTS of APE1 is harbored within residues 289-318 in the C terminus, which is normally masked by the intact N-terminal structure. As a dually targeted mitochondrial protein, APE1 possesses a special distribution pattern of different subcellular targeting signals, the identification of which sheds light on future prediction of MTSs.
Pineal Melatonin Secretion Drives the Reproductive Response to Daylength in the Ewe* (1983)

This study was conducted to determine whether the pineal indoleamine melatonin mediates the effects of photoperiod on the capacity of estradiol to inhibit LH secretion in the ewe. Patterns of serum melatonin were characterized in pineal-intact ovariectomized ewes treated with sc Silastic estradiol implants and exposed to 90-day alternations between long and short photoperiods. High fluctuating levels of serum melatonin were found during the night, with the duration of elevated serum levels corresponding to the length of the dark period. Transfer from long to short photoperiods caused a rapid change in the duration of nightly melatonin secretion and reduced the negative feedback potency of estradiol upon LH secretion during the natural anestrous season. In pinealectomized ewes, the night-time rise of melatonin was absent, and transfer from long to short days failed to reverse the capacity of estradiol to inhibit LH secretion during anestrus. Nightly infusions of melatonin restored patterns of this indoleamine similar to those observed in pineal-intact ewes exposed to the 90-day alternation between long and short days. The melatonin infusions also restored the reproductive response to the inductive photoperiod: in every ewe, the negative feedback effects of estradiol upon LH secretion were diminished after transfer from long to short days. The amplitude and latency of this escape matched those of pineal-intact animals. We conclude that the pineal mediates the reproductive response of the ewe to inductive photoperiods through its daily rhythm of melatonin secretion.
Osmotic regulation of cytokine synthesis in vitro. (1995)

These studies were undertaken to investigate the therapeutic mechanism of saturated solutions of KI, used to treat infectious and inflammatory diseases. The addition of 12-50 mM KI to cultured human peripheral blood mononuclear cells resulted in 319-395 mosM final solute concentration and induced interleukin (IL)-8 synthesis. Maximal IL-8 production was seen when 40 mM salt was added (375 mosM) and was equal to IL-8 induced by endotoxin or IL-1 alpha. However, there was no induction of IL-1 alpha, IL-1 beta, or tumor necrosis factor to account for the synthesis of IL-8; the effect of KI was not due to contaminating endotoxins. Hyperosmolar NaCl also induced IL-8 and increased steady-state levels of IL-8 mRNA similar to those induced by IL-1 alpha. IL-8 gene expression was elevated for 96 hr in peripheral blood mononuclear cells incubated with hyperosmolar NaCl. In human THP-1 macrophagic cells, osmotic stimulation with KI, NaI, or NaCl also induced IL-8 production. IL-1 signal transduction includes the phosphorylation of the p38 mitogen-activated protein kinase that is observed following osmotic stress. Using specific blockade of this kinase, a dose-response inhibition of hyperosmolar NaCl-induced IL-8 synthesis was observed, similar to that in cells stimulated with IL-1. Thus, these studies suggest that IL-1 and osmotic shock utilize the same mitogen-activated protein kinase for signal transduction and IL-8 synthesis.
A HOTLink/networked PC data acquisition and image reconstruction system for a high-resolution whole-body PET with respiratory or ECG-gated performance (2003)

An ultrahigh-resolution positron emission tomography (PET) camera in whole-body scanning or gated imaging study needs super computer-processing power for creating a huge sinogram as well as doing image reconstruction. A fast HOTLink serial bus attached to networked cluster personal computers (PC) has been developed for this special purpose. In general, the coincidence data from a PET camera is unidirectional; therefore, an additional daisy-chain bus using high-speed HOTLink (400 Mb/s, Cypress Semiconductor, inc.) transmitters and receivers is designed to carry the coincidence data to the entire networked (LAN) computers (PCs), the data from HOTLink are interfaced to a PC through a fast PCI I/O board (80 Mbyte/s). The overall architecture for the image acquisition and reconstruction computing system for a whole-body PET scanning is a pipeline design. One PC will acquire sinogram data for one bed position, and after completion of data acquisition that PC will begin to reconstruct the image. Meanwhile, another PC in the network will start data acquisition for the next bed position. The image results from the previous PC will be sent to a master computer for final tabulation and storage through the standard network, and then it will be free for processing a new bed position.
Functional epigenetic approach identifies frequently methylated genes in Ewing sarcoma (2013)

Using a candidate gene approach we recently identified frequent methylation of the RASSF2 gene associated with poor overall survival in Ewing sarcoma (ES). To identify effective biomarkers in ES on a genome-wide scale, we used a functionally proven epigenetic approach, in which gene expression was induced in ES cell lines by treatment with a demethylating agent followed by hybridization onto high density gene expression microarrays. After following a strict selection criterion, 34 genes were selected for expression and methylation analysis in ES cell lines and primary ES. Eight genes (CTHRC1, DNAJA4, ECHDC2, NEFH, NPTX2, PHF11, RARRES2, TSGA14) showed methylation frequencies of>20% in ES tumors (range 24-71%), these genes were expressed in human bone marrow derived mesenchymal stem cells (hBMSC) and hypermethylation was associated with transcriptional silencing. Methylation of NPTX2 or PHF11 was associated with poorer prognosis in ES. In addition, six of the above genes also showed methylation frequency of>20% (range 36-50%) in osteosarcomas. Identification of these genes may provide insights into bone cancer tumorigenesis and development of epigenetic biomarkers for prognosis and detection of these rare tumor types.
Inducible overexpression of oat arginine decarboxylase in transgenic tobacco plants (1997)

To test the possible interaction of polyamines in plant growth responses, transgenic tobacco plants containing the Avena sativa L. (oat) arginine decarboxylase (ADC) gene under the control of a tetracycline-inducible promoter were generated. Inducible overexpression of oat ADC in transgenic tobacco led to an accumulation of ADC mRNA, increased ADC activity and changes in polyamine levels. Transgenic lines, induced during vegetative stage, displayed different degrees of an altered phenotype, the severity of which was correlated with putrescine content. These phenotypic changes were characterized by short internodes, thin stems and leaves, leaf chlorosis and necrosis, as well as reduced root growth. This is the first report to show altered phenotypes as a consequence of polyamine changes under tetracycline-induction in in vivo conditions. Interestingly, overexpression of oat ADC in tobacco resulted in similar detrimental effects to those observed by ADC activation induced by osmotic stress in the homologous oat leaf system. In the context of the role of specific polyamines in plant growth and development, the present results indicate that activation of the ADC pathway leading to high levels of endogenous putrescine (or its catabolytes) is toxic for the vegetative growth of the plant. In contrast, no visible phenotypic effects were observed in flowering plants following tetracycline induction. Further characterization of the different transgenic lines may shed light on the action of specific polyamines in different plant developmental processes.
Anti-TNF-α Agents in the Treatment of Immune-Mediated Inflammatory Diseases: Mechanisms of Action and Pitfalls (2010)

TNF-α is a potent inducer of the inflammatory response, a key regulator of innate immunity and plays an important role in the regulation of Th1 immune responses against intracellular bacteria and certain viral infections. However, dysregulated TNF can also contribute to numerous pathological situations. These include immune-mediated inflammatory diseases (IMIDs) including rheumatoid arthritis, Crohn's disease, psoriatic arthritis, ankylosing spondylitis, ulcerative colitis and severe chronic plaque psoriasis. Animal and human studies concerning the role of TNF-α in IMIDs have led to the development of a therapy based on TNF blockage. This article focuses first on the potential mechanisms by which the three currently licensed agents, adalimumab, etarnecept and infliximab, decrease the inflammatory activity of patients with different IMIDs. Second, it focuses on the risks, precautions and complications of the use of TNF-α inhibitors in these patients.
Hydrogel‐Perfluorocarbon Composite Scaffold Promotes Oxygen Transport to Immobilized Cells (2008)

Cell encapsulation provides cells a three-dimensional structure to mimic physiological conditions and improve cell signaling, proliferation, and tissue organization as compared to monolayer culture. Encapsulation devices often encounter poor mass transport, especially for oxygen, where critical dissolved levels must be met to ensure both cell survival and functionality. To enhance oxygen transport, we utilized perfluorocarbon (PFC) oxygen vectors, specifically perfluorooctyl bromide (PFOB) immobilized in an alginate matrix. Metabolic activity of HepG2 liver cells encapsulated in 1% alginate/10% PFOB composite system was 47-104% higher than alginate systems lacking PFOB. A cubic model was developed to understand the oxygen transport mechanism in the alginate/PFOB composite system. The theoretical flux enhancement in alginate systems containing 10% PFOB was 18% higher than in alginate-only systems. Oxygen uptake rates (OURs) of HepG2 cells were enhanced with 10% PFOB addition under both 20% and 5% O2 boundary conditions, by 8% and 15%, respectively. Model predictions were qualitatively and quantitatively verified with direct experimental OUR measurements using both a perfusion reactor and oxygen sensing plate, demonstrating a greater OUR enhancement under physiological O2 boundary conditions (i.e., 5% O2). Inclusion of PFCs in an encapsulation matrix is a useful strategy for overcoming oxygen limitations and ensuring cell viability and functionality both for large devices (>1 mm) and over extended time periods. Although our results specifically indicate positive enhancements in metabolic activity using the model HepG2 liver system encapsulated in alginate, PFCs could be useful for improving/stabilizing oxygen supply in a wide range of cell types and hydrogels.
The HaloTag™: A Novel Technology for Cell Imaging and Protein Analysis (2006)

The ability to specifically label proteins with a wide range of optical properties and functionalities can help reveal information about protein functions and dynamics in living cells. Here, we describe a technology for covalent tethering of organic probes directly to a specially designed reporting protein expressed in live cells. The reporting protein can be used in a manner similar to green fluorescent protein, except that the fluorophore might be interchanged among a variety of standard dyes. This allows living cells to be imaged at different wavelengths without requiring changes to the underlying genetic constructs, and the colors can be rapidly switched to allow temporal analysis of protein fate. The stability of the bond permits imaging of live cells during long time periods, imaging of fixed cells, and multiplexing with different cell/protein analysis techniques. The dyes can also be exchanged with other functional molecules, such as biotin to serve as an affinity handle, or even solid supports for direct covalent immobilization. The technology complements existing methods and provides new options for cell imaging and protein analysis.
Tissue elasticity properties as biomarkers for prostate cancer (2008)

In this paper we evaluate tissue elasticity as a longstanding but qualitative biomarker for prostate cancer and sonoelastography as an emerging imaging tool for providing qualitative and quantitative measurements of prostate tissue stiffness. A Kelvin-Voigt Fractional Derivative (KVFD) viscoelastic model was used to characterize mechanical stress relaxation data measured from human prostate tissue samples. Mechanical testing results revealed that the viscosity parameter for cancerous prostate tissue is greater than that derived from normal tissue by a factor of approximately 2.4. It was also determined that a significant difference exists between normal and cancerous prostate tissue stiffness (p < 0.01) yielding an average elastic contrast that increases from 2.1 at 0.1 Hz to 2.5 at 150 Hz. Qualitative sonoelastographic results show promise for cancer detection in prostate and may prove to be an effective adjunct imaging technique for biopsy guidance. Elasticity images obtained with quantitative sonoelastography agree with mechanical testing and histological results. Overall, results indicate tissue elasticity is a promising biomarker for prostate cancer.
Synthetic studies on quassinoids: total synthesis of (-)-chaparrinone, (-)-glaucarubolone, and (+)-glaucarubinone (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthetic studies on quassinoids: total synthesis of (-)-chaparrinone, (-)-glaucarubolone, and (+)-glaucarubinonePaul A. Grieco, Jon L. Collins, Eric D. Moher, Thomas J. Fleck, and Raymond S. GrossCite this: J. Am. Chem. Soc. 1993, 115, 14, 6078–6093Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/ja00067a025https://doi.org/10.1021/ja00067a025research-articleACS PublicationsRequest reuse permissionsArticle Views1909Altmetric-Citations91LEARN 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
Improved pitch prediction with fractional delays in CELP coding (2002)

A scheme is discussed for long-term prediction in CELP (code-excited linear predictive) coding using fractional delay prediction. This technique permits a more accurate representation of voiced speech and achieves an improvement of synthetic quality for female speakers. The higher complexity of this type of predictor relative to the classical one is its major disadvantage. Suboptimal schemes in which the search for the functional pitch delay is restricted to a neighborhood of an integer pitch estimate can be envisaged to decrease the computational load.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Learning Rule Ensembles for Ordinal Classification with Monotonicity Constraints (2009)

Ordinal classification problems with monotonicity constraints (also referred to as multicriteria classification problems) often appear in real-life applications, however, they are considered relatively less frequently in theoretical studies than regular classification problems. We introduce a rule induction algorithm based on the statistical learning approach that is tailored for this type of problems. The algorithm first monotonizes the dataset (excludes strongly inconsistent objects), using Stochastic Dominance-based Rough Set Approach, and then uses forward stagewise additive modeling framework for generating a monotone rule ensemble. Experimental results indicate that taking into account knowledge about order andmonotonicity constraints in the classifier can improve the prediction accuracy.
Efficiently support MapReduce-like computation models inside parallel DBMS (2009)

While parallel DBMSs do support large scale parallel query processing on partitioned data, the reach of more general applications relies on User Defined Functions (UDFs). However, the existent UDF technology is insufficient both conceptually and practically. A UDF is not a relation-in, relation-out operator, which restricts its ability to model complex applications defined on a set of tuples rather than on a single one, and to be composed with other relational operators in a query. Further, to interact with the query execution efficiently, a UDF must be coded with complex interactions with DBMS internal data structures and system calls which is often beyond the expertise of an analytics application developer.