gebhart/patrepeval huggingface dataset:
Real-Time Production Optimization of Offshore Oil and Gas Production Systems: A Technology Survey (2006)

Abstract The information flow used for optimization of an offshore oil production plant is described. The elements in this description include data acquisition, data storage, processing facility model updating, well model updating, reservoir model updating, production planning, reservoir planning, and strategic planning. Methods for well allocation, gas lift and gas/water injection optimization and updating of the models are reviewed in relationship with the information flow described. Challenges of real time optimization are discussed.
ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets (2018)

Supplementary data are available at Bioinformatics online.
A Method for Continuous Measurement of the Carbon Dioxide Tension on the Cerebral Cortex (1961)

Abstract S iesjö B. K. A method for continuous measurement of the carbon dioxide tension on the cerebral cortex. A method has been developed for direct, continuous measurement of the pCO 2 on the surface of the cerebral cortex, using a modification of the tissue pCO 2 electrode earlier described (H ertz S iesjö 1959). The modification was made for the purpose of increasing the stability and accuracy of the measurements. The drift of the electrode was thereby reduced to less than 1 mV in five hours and the accuracy was increased to about ± 1.5 per cent. A reduction of the concavity of the pH glass membrane limited the response time of the pCO 2 electrode to 25–30 sec following a twofold increase in pCO 2 . A description is given of the procedures for calibrating, suspending and thermostatting the electrode. The validity and reproducibility of the pCO 2 values obtained when the electrode was applied to the cortical surface were investigated in cat experiments during respiratory and circulatory steady states. It was found that within a relatively wide range the pCO 2 was independent of the pressure exerted by the electrode on the cortical surface. Provided that the tissue did not present any swelling and that the tissue surface was not damaged or allowed to dry, the pC 2 varied very little (coefficient of variation 1.5 per cent) when the electrode was repeatedly applied to the same or to different cortical areas. The influence of superficial cortical vessels was confined to the larger veins (diameter 0.5–1 mm), across which slightly higher (1–5 mm Hg) values were recorded. The findings are discussed in relation to the applicability of the method in studies of the acid‐base metabolism of the tissue.
MDC1 Regulates DNA-PK Autophosphorylation in Response to DNA Damage (2004)

DNA damage initiates signaling events through kinase cascades that result in cell cycle checkpoint control and DNA repair. However, it is not yet clear how the signaling pathways relay to DNA damage repair. Using the repeat region of checkpoint protein MDC1 (mediator of DNA damage checkpoint protein 1), we identified DNA-PKcs/Ku as MDC1-associated proteins. Here, we show that MDC1 directly interacts with the Ku/DNA-PKcs complex. Down-regulation of MDC1 resulted in defective phospho-DNA-PKcs foci formation and DNA-PKcs autophosphorylation, suggesting that MDC1 regulates autophosphorylation of DNA-PKcs following DNA damage. Furthermore, DNA-PK-dependent DNA damage repair is defective in cells depleted of MDC1. Taken together, these results suggest that the MDC1 repeat region is involved in protein-protein interaction with DNA-PKcs/Ku, and MDC1 regulates DNA damage repair by influencing DNA-PK autophosphorylation. Therefore, MDC1 acts not only as a mediator of DNA damage checkpoint but also as a mediator of DNA damage repair.
Safety of guselkumab in patients with moderate‐to‐severe psoriasis treated through 100 weeks: a pooled analysis from the randomized VOYAGE 1 and VOYAGE 2 studies (2018)

The safety profile for guselkumab remains favourable through 100 weeks of treatment in patients with moderate-to-severe psoriasis.
PROTAC Degradation of IRAK4 for the Treatment of Cancer (2019)

ADVERTISEMENT RETURN TO ISSUEPREVPatent HighlightNEXTPROTAC Degradation of IRAK4 for the Treatment of CancerRobert B. Kargbo*Robert B. KargboUsona Institute, 277 Granada Drive, San Luis Obispo, California 93401-7337, United States*E-mail: [email protected]More by Robert B. Kargbohttp://orcid.org/0000-0002-5539-6343Cite this: ACS Med. Chem. Lett. 2019, 10, 10, 1370–1371Publication Date (Web):September 30, 2019Publication History Received15 September 2019Published online30 September 2019Published inissue 10 October 2019https://pubs.acs.org/doi/10.1021/acsmedchemlett.9b00423https://doi.org/10.1021/acsmedchemlett.9b00423editorialACS PublicationsCopyright © 2019 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views4728Altmetric-Citations10LEARN 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 PDF (499 KB) Get e-AlertscloseSUBJECTS:Cancer therapy,Cell signaling,Degradation,Peptides and proteins,Receptors Get e-Alerts
Stabilization of Microsatellite Sequences by Variant Repeats in the Yeast Saccharomyces cerevisiae (1997)

We examined the effect of a single variant repeat on the stability of a 51-base pair (bp) microsatellite (poly GT). We found that the insertion stabilizes the microsatellite about fivefold in wild-type strains. The stabilizing effect of the variant base was also observed in strains with mutations in the DNA mismatch repair genes pms1, msh2 and msh3, indicating that this effect does not require a functional DNA mismatch repair system. Most of the microsatellite alterations in the pms1, msh2 and msh3 strains were additions or deletions of single GT repeats, but about half of the alterations in the wild-type and msh6 strains were large (> 8 bp) deletions or additions.
2-Pyrrolinodoxorubicin and its peptide-vectorized form bypass multidrug resistance (2004)

A well-known mechanism leading to the emergence of multidrug-resistant tumor cells is the overexpression of P-glycoprotein, which is capable of lowering intracellular drug concentrations. In the present study, we tested the capability of 2-pyrrolinodoxorubicin (p-DOX), a highly potent derivative of DOX, to bypass multidrug resistance. The accumulation, intracellular distribution and cytotoxicity of p-DOX were tested in two cell lines (K562 and A2780) and their DOX-resistant counterparts (K562/ADR and A2780/ADR). Cellular accumulation and cytotoxicity were dramatically lowered for DOX in resistant cell lines, in comparison with non-resistant cells. In contrast, cellular accumulation, intracellular distribution and cytotoxicity of p-DOX were independent of the nature of the cell lines. The p-DOX showed potent dose-dependent inhibition of cell growth against resistant cells as compared with DOX. After treatment of resistant cells with verapamil, the intracellular levels of DOX were markedly increased and consequent cytotoxicity improved. In contrast, treatment of resistant cells with verapamil did not cause any further enhancement of cell uptake or an increase in the cytotoxic effect of the derivative p-DOX, indicating that the compound bypasses the P-glycoprotein. Finally, we show that vectorization of p-DOX by a peptide vector (SynB3) which has been shown to enhance the brain uptake of DOX and to decrease its heart accumulation does not affect this property. These results indicate that p-DOX and its vectorized form are potent and effective in overcoming multidrug resistance.
Tafamidis for transthyretin familial amyloid polyneuropathy (2012)

This study provides Class II evidence that 20 mg tafamidis QD was associated with no difference in clinical progression in patients with TTR-FAP, as measured by the NIS-LL and the Norfolk QOL-DN score. Secondary outcomes demonstrated a significant delay in peripheral neurologic impairment with tafamidis, which was well tolerated over 18 months.
Tell Me Dave: Context-Sensitive Grounding of Natural Language to Manipulation Instructions (2014)

We consider performing a sequence of mobile manipulation tasks with instructions given in natural language (NL). Given a new environment, even a simple task such as of boiling water would be performed quite differently depending on the presence, location and state of the objects. We start by collecting a dataset of task descriptions in free-form natural language and the corresponding grounded task-logs of the tasks performed in an online robot simulator. We then build a library of verbenvironment-instructions that represents the possible instructions for each verb in that environment-these may or may not be valid for a different environment and task context.
MOLECULAR DETERMINANTS OF RHIZOSPHERE COLONIZATION BY PSEUDOMONAS (2001)

Rhizosphere colonization is one of the first steps in the pathogenesis of soilborne microorganisms. It can also be crucial for the action of microbial inoculants used as biofertilizers, biopesticides, phytostimulators, and bioremediators. Pseudomonas, one of the best root colonizers, is therefore used as a model root colonizer. This review focuses on (a) the temporal-spatial description of root-colonizing bacteria as visualized by confocal laser scanning microscopal analysis of autofluorescent microorganisms, and (b) bacterial genes and traits involved in root colonization. The results show a strong parallel between traits used for the colonization of roots and of animal tissues, indicating the general importance of such a study. Finally, we identify several noteworthy areas for future research.
Unique forms of human and mouse nuclear receptor corepressor SMRT (1999)

Nuclear hormone receptors have been shown to repress transcription in the absence of ligand. This repression is mediated by a corepressor complex that contains the Sin3A protein and histone deacetylases (HDAC1 and 2). Studies by several groups demonstrate that this complex is recruited to nuclear receptors through the highly related corepressors SMRT (silencing mediator of retinoid acid and thyroid hormone receptor) and N-CoR (nuclear receptor corepressor). We describe here the cloning, characterization, and chromosomal mapping of forms of human and mouse SMRT that includes a 1,000-aa extension, which reveals striking homology to the amino terminus of N-CoR. Structure and function studies of wild-type and natural splicing variants suggest the presence of 3-4 amino terminal domains that repress in a cooperative as well as mechanistically distinct fashion.
High-Level Neuronal Expression of Aβ1–42in Wild-Type Human Amyloid Protein Precursor Transgenic Mice: Synaptotoxicity without Plaque Formation (2000)

Amyloid plaques are a neuropathological hallmark of Alzheimer's disease (AD), but their relationship to neurodegeneration and dementia remains controversial. In contrast, there is a good correlation in AD between cognitive decline and loss of synaptophysin-immunoreactive (SYN-IR) presynaptic terminals in specific brain regions. We used expression-matched transgenic mouse lines to compare the effects of different human amyloid protein precursors (hAPP) and their products on plaque formation and SYN-IR presynaptic terminals. Four distinct minigenes were generated encoding wild-type hAPP or hAPP carrying mutations that alter the production of amyloidogenic Abeta peptides. The platelet-derived growth factor beta chain promoter was used to express these constructs in neurons. hAPP mutations associated with familial AD (FAD) increased cerebral Abeta(1-42) levels, whereas an experimental mutation of the beta-secretase cleavage site (671(M-->I)) eliminated production of human Abeta. High levels of Abeta(1-42) resulted in age-dependent formation of amyloid plaques in FAD-mutant hAPP mice but not in expression-matched wild-type hAPP mice. Yet, significant decreases in the density of SYN-IR presynaptic terminals were found in both groups of mice. Across mice from different transgenic lines, the density of SYN-IR presynaptic terminals correlated inversely with Abeta levels but not with hAPP levels or plaque load. We conclude that Abeta is synaptotoxic even in the absence of plaques and that high levels of Abeta(1-42) are insufficient to induce plaque formation in mice expressing wild-type hAPP. Our results support the emerging view that plaque-independent Abeta toxicity plays an important role in the development of synaptic deficits in AD and related conditions.
Epidermal growth factor-dependent association of phosphatidylinositol 3-kinase with the erbB3 gene product. (1994)

The ErbB3 protein is a member of the ErbB subfamily of receptor protein tyrosine kinases. In the present study, the mechanism by which the ErbB3 protein is phosphorylated and the signal-transducing functions of this phosphorylated protein were investigated. When phosphorylated by the epidermal growth factor receptor in vitro, the ErbB3 protein strongly associated with the regulatory p85 subunit and the catalytic activity of phosphatidylinositol (PI) 3-kinase. The association of PI 3-kinase with ErbB3 in human breast cancer cells was found to be correlated with the constitutive phosphorylation of ErbB3 on tyrosine residues. In MDA-MB-468 breast cancer cells in which the ErbB3 protein is not constitutively phosphorylated, stimulation with epidermal growth factor led to the phosphorylation of ErbB3 on tyrosine residues and the formation of a functional signal transduction complex involving the ErbB3 protein and PI 3-kinase. These results suggest that the ErbB3 protein can be phosphorylated on tyrosine residues by a cross-phosphorylation mechanism and that the phosphorylated ErbB3 protein can couple other growth factor receptor protein tyrosine kinases to the PI 3-kinase pathway in a manner similar to the insulin receptor substrate 1 protein.
From arthritis to Alzheimer's disease: current concepts on the pathogenesis of amyloidosis (1987)

Amyloid is a generic term referring to a group of diverse but specific extracellular protein deposits which all have common morphologic properties, staining characteristics, and x-ray diffraction and infrared spectra. This review considers the new classification of amyloids, based on the underlying peptides forming the protein fibril, and their diversity. The pathogenesis of inflammation-associated amyloid and its relationship to high density lipoprotein metabolism is examined in detail. The lessons learned from models of inflammation-associated amyloid are extended to the other amyloids (e.g., Alzheimer's disease), and potential reasons for the common structural properties of all amyloids are explored.
<title>Reversible image compression via multiresolution representation and predictive coding</title> (1993)

In this paper a new image transformation suited for reversible (lossless) image compression is presented. It uses a simple pyramid multiresolution scheme which is enhanced via predictive coding. The new transformation is similar to the subband decomposition, but it uses only integer operations. The number of bits required to represent the transformed image is kept small through careful scaling and truncations. The lossless coding compression rates are smaller than those obtained with predictive coding of equivalent complexity. It is also shown that the new transform can be effectively used, with the same coding algorithm, for both lossless and lossy compression. When used for lossy compression, its rate-distortion function is comparable to other efficient lossy compression methods.
Pcr-Based Diagnostics in Infectious Disease (1994)

Establishment of the PCR Laboratory PCR for Pathogenic Organisms for Specific Organ Systems PCR Protocols for the Testing of Specific Organisms.
Longitudinal MRI Study of Hippocampal Volume in Trauma Survivors With PTSD (2001)

Smaller hippocampal volume is not a necessary risk factor for developing PTSD and does not occur within 6 months of expressing the disorder. This brain abnormality might occur in individuals with chronic or complicated PTSD.
Inhibition of mitochondrial complex II affects dopamine metabolism and decreases its uptake into striatal synaptosomes. (2006)

The mitochondrial toxin, 3-nitropropionic acid (3-NP), is a specific inhibitor of succinate dehydrogenase, complex II in the mitochondrial respiratory chain. The aim of our study was to determine the relationship between inhibition of mitochondrial complex II and dopamine (DA) metabolism and its transport into rat striatal synaptosomes after exposure to 3-NP. The study was carried out using spectrophotometric, radiochemical and HPLC methods. Our data showed that inhibition of succinate dehydrogenase by intraperitoneal (i.p.) injection of 3-NP (cumulated dose 100 mg/kg in 4 days) significantly affected DA metabolism, leading to the accumulation of its metabolites, 3,4-dihydroxylphenylacetic acid (DOPAC) and homovanillic acid (HVA) in the rat striatum. These experimental conditions had no effect on free radical dependent lipid peroxidation in the brain. In vitro experiments revealed that DA and DOPAC significantly decrease lipid peroxidation in the brain homogenate. Moreover, 3-NP significantly inhibited [3H]DA uptake into striatal synaptosomes by specific dopamine transporter (DAT). The scavengers of superoxide radical (O2-) Tempol and Trolox had no effect on DAT function, but the nitric oxide synthase (NOS) inhibitor N w-nitro-L-arginine (100 microM) prevented 3-NP-evoked DAT down-regulation. In summary, our results indicate that inhibition of mitochondrial complex II by 3-NP enhances DA degradation and decreases its uptake into synaptosomes. It is suggested that NO and energy failure are responsible for alteration of the dopaminergic system in the striatum.
Electrochemical Fabrication of Amperometric Microenzyme Sensor (1989)

Enzyme electrodes were microfabricated by electrochemical incorporation of enzyme molecules into the continuously electrochemically developing micropores of platinum black particles. Two electrochemical processes, electrochemical adsorption of enzyme molecules and reductive deposition of metallic microparticles from its complexal form, were simultaneously carried out by using a microelectrode of diameter ranging from 10 to 200 μm. An amperometric glucose sensor, consisting of a glucose oxidase‐incorporated microelectrode, demonstrated high performance characteristics including high sensitivity and fast response.
The Evaluation of Thyroid Functions, Thyroid Antibodies, and Thyroid Volumes in Children with Epilepsy during Short‐Term Administration of Oxcarbazepine and Valproate (2006)

In this prospective study, it is documented that children under short-term OXC or VPA therapy showed altered thyroid functions similar to the changes observed after long-term treatment. Although, the clinical significance of these results need to be evaluated with future studies, this observation of altered thyroid functions points out that thyroid functions may need to be monitored closely in children receiving antiepileptic treatment, even in the short-time interval.
Epidemiology of sepsis: An update (2001)

Many studies have documented many aspects of the epidemiology of sepsis. However, the composite picture they provide, although rich in many aspects, remains incomplete and emphasizes the heterogeneity of the condition. Unfortunately, few population-based prospective cohort studies exist that allow us to accurately delineate the risk factors for sepsis, its course, and its outcome. To place new information, such as the role of genetic predisposition, in the correct context, it is essential that such studies be conducted.
The matrix metalloproteinase inhibitor BB-1101 prevents experimental autoimmune uveoretinitis (EAU) (1999)

EAU is characterized by breakdown of the blood-retinal barrier and extravasation of leucocytes into retinal tissue leading to destruction of photoreceptor cells. Matrix metalloproteinases (MMP) have been implicated in trafficking of cells into tissues, but their role in inflammatory eye disease is unclear. A synthetic MMP inhibitor, BB-1101, was administered subcutaneously, from either day 0 or day 7, to Lewis rats challenged with bovine S-antigen to induce EAU. When given up to day 14, BB-1101 reduced the incidence of disease and delayed the day of onset of clinical disease. When administered from day 7 until day 21, EAU was completely abrogated. A quantitative polymerase chain reaction (PCR) assay showed an increase of both matrilysin (MMP-7), neutrophil collagenase (MMP-8) and macrophage metalloproteinase (MMP-12) in retinas from EAU animals compared with naive controls. These enzymes are produced by activated leucocytes and act on components of the basement membrane. These results therefore implicate these MMP as integral to the development of pathology in EAU.
Mechanisms Mediating the Synergistic Anticancer Effects of Combined γ-Tocotrienol and Celecoxib Treatment (2011)

AIM: To characterize the intracellular signaling mechanisms mediating the synergistic anticancer effects of combined γ-tocotrienol and celecoxib treatment in neoplastic +SA mouse mammary epithelial cells in vitro. METHODS: +SA mammary tumor cells in different treatment groups were maintained in serum-free defined media containing 10ng/ml EGF as a mitogen and exposed to various doses of γ-tocotrienol and celecoxib alone or in combination. After a 96 hr culture period, cells were collected and whole cell lysates were subjected to Western blot analysis to determine treatment effects on intracellular signaling proteins associated with EGF-dependent mitogenesis and survival, and prostaglandin synthesis and responsiveness. RESULTS: Treatment with high doses of γ-tocotrienol or celecoxib alone inhibited Akt activation and downstream signaling and NFκB activation. Similar treatment with γ-tocotrienol also decreased concentration and activation of ErbB2-4 receptors, whereas celecoxib only inhibited ErbB2-4 receptor activation. In contrast, combined treatment with subeffective doses of γ-tocotrienol and celecoxib resulted in a large decrease ErbB2-4 receptor levels and activation, a decrease in PGE(2) levels, and a corresponding increase in prostaglandin EP2 and EP4 receptor levels. Combined treatment also induced an increase in the prostaglandin catabolizing enzyme, PGDH. CONCLUSION: The synergistic anticancer effects of combined low dose γ-tocotrienol and celecoxib treatment in +SA mammary tumor cells are mediated by COX-2-dependent mechanisms associated with a suppression in PGE(2) levels, as well as, COX-2-independent mechanisms associated with a reduction in ErbB2-4 receptor levels, activation, and subsequent reduction in downstream Akt and NFκB mitogenic signaling.