gebhart/patrepeval huggingface dataset:
P38-β/SAPK-inhibiting and apoptosis-inducing activities of (E)-4-chloro-2-((3-ethoxy-2-hydroxybenzylidene) amino)phenol (2020)

The present study has three purposes; first evaluating cytotoxicity of (E)-4-chloro-2-((3-ethoxy-2-hydroxybenzylidene)amino)phenol (ACES), second deciphering ACES-mediated cellular death mechanism, and third estimating ACES-mediated alterations in the expressions of mitogen-activated protein kinase (MAPK) pathway-related genes. Neutral red uptake assay, cell cycle analysis, mitochondrial membrane potential (MMP), reactive oxygen species (ROS) measurements, caspase 3/7 and 9 activations, and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) were implemented. IC<sub>50</sub> values of ACES-treated five cells were around 4-6 µg/mL. However, Caco-2 and Huh-7 cells were found to be twofold resistant and fivefold sensitive with IC<sub>50</sub> values of 11 µg/mL and 0.93 µg/mL, respectively. In this study, it was initially reported that ACES exhibits selective cytotoxicity to Huh-7 cells. In addition, ACES induced apoptosis by nuclear fragmentation, MMP disruption, and intracellular ROS elevation in MCF-7 cells. qRT-PCR experiment indicated the expressions of 30 genes including <i>ATF2</i>, <i>CREB1</i>, <i>MYC</i>, <i>NFATC4</i> (NFAT3), <i>CCNA1</i>, <i>CCNB1</i>, <i>CCND2</i>, <i>CDK2</i>, <i>CDKN1A</i> (p21CIP1), <i>CDKN1C</i> (p57KIP2), <i>CDKN2A</i> (p16INK4a), <i>CDKN2B</i> (p15INK4b), <i>DLK1</i>, <i>NRAS</i>, <i>CDC42</i>, <i>PAK1</i>, <i>MAP4K1</i> (HPK1), <i>MAP3K3</i> (MEKK3), <i>MAP2K3</i> (MEK3), <i>MAP2K6</i> (MEK6), <i>MOS</i>, <i>MAPK1</i> (ERK2), <i>MAPK8</i> (JNK1), <i>MAPK10</i> (JNK3), <i>MAPK11</i> (p38-β), <i>LAMTOR3</i> (MP1), <i>MAPK8IP2</i> (JIP-1), <i>PRDX6</i> (AOP2), <i>COL1A1</i>, and <i>HSPA5</i> (Grp78) were downregulated at least 1.5-fold. Moreover, ACES effectively inhibited expressions of genes that code for elements of p38-β/stress-activated protein kinase (SAPK) pathway. ACES has the potential to be used for the reversal of trastuzumab resistance in breast cancer patients by inhibiting p38/SAPK pathway in MCF-7 cells. Therefore, with the selective cytotoxic, apoptosis-inducing, and p38-β/SAPK-inhibiting activities, ACES can be utilized for developing a novel anticancer drug.
Killing Them with Kindness? In-Hive Medications May Inhibit Xenobiotic Efflux Transporters and Endanger Honey Bees (2011)

Many bee hives receive regular treatments of oxytetracycline and acaricides for prevention and treatment of disease and parasites. Our results suggest that seasonal co-application of these medicines to bee hives could increase the adverse effects of these and perhaps other pesticides. Our results also demonstrate the utility of a mechanism-based strategy. By identifying pesticides and apicultural medicines that are substrates and inhibitors of xenobiotic transporters we prioritize the testing of those chemical combinations most likely to result in adverse interactions.
Expanded Anticancer Therapeutic Window of Hexon-modified Oncolytic Adenovirus (2009)

One of the significant hurdles toward safe and efficacious systemic treatment of cancer with oncolytic adenoviruses (Ads) is dose-limiting hepatotoxicity that prevents the increase of a therapeutic dose. In this study, we expanded the therapeutic window of oncolytic serotype 5 Ad (Ad5) by a genetic modification of hypervariable loop 5 (HVR5) in the capsid protein hexon that prevented infection of hepatocytes due to ablation of binding to blood factors. This oncolytic virus, Ad-GL-HB, had significantly reduced levels of hepatocyte transduction in immunocompetent and immunodeficient mice as compared to parental virus Ad-GL. The hepatocyte detargeting decreased liver damage and increased the maximum tolerated dose of Ad-GL-HB tenfold relative to that of Ad-GL. Intravenous (i.v.) injection of Ad-GL or Ad-GL-HB into tumor-bearing mice produced equally increased survival rates demonstrating that while Ad-GL-HB detargeted hepatocytes, it sustained tumor cell infection after systemic administration. The significantly improved safety of the virus allowed it to be used at increased doses for improved systemic antitumor efficacy. Our results suggest that hexon modifications provide valuable strategies for systemic oncolytic Ad therapy.
Highly Comparative Feature-Based Time-Series Classification (2014)

A highly comparative, feature-based approach to time series classification is introduced that uses an extensive database of algorithms to extract thousands of interpretable features from time series. These features are derived from across the scientific time-series analysis literature, and include summaries of time series in terms of their correlation structure, distribution, entropy, stationarity, scaling properties, and fits to a range of time-series models. After computing thousands of features for each time series in a training set, those that are most informative of the class structure are selected using greedy forward feature selection with a linear classifier. The resulting feature-based classifiers automatically learn the differences between classes using a reduced number of time-series properties, and circumvent the need to calculate distances between time series. Representing time series in this way results in orders of magnitude of dimensionality reduction, allowing the method to perform well on very large data sets containing long time series or time series of different lengths. For many of the data sets studied, classification performance exceeded that of conventional instance-based classifiers, including one nearest neighbor classifiers using euclidean distances and dynamic time warping and, most importantly, the features selected provide an understanding of the properties of the data set, insight that can guide further scientific investigation.
Dependence of Hearing Changes on the Dose of Intratympanically Applied Gentamicin: A Meta‐Analysis Using Mathematical Simulations of Clinical Drug Delivery Protocols (2008)

One-shot application protocols produce gentamicin doses in the cochlea that have minimal risk to hearing at the frequencies tested. Repeated or continuous application protocols result in higher doses that in some cases damage hearing. The high variability of hearing changes, even with low gentamicin doses, calls into question the rationale for using individual hearing changes to titrate the applied dose.
Enhanced Response of Blood Monocytes to In Vitro Lipopolysaccharide-Challenge in Patients With Recurrent Unstable Angina (2001)

Mononuclear cells of patients with recurrent phases of instability exhibit an enhanced production of IL-6 in response to low-dose of LPS, correlated with baseline CRP levels, 6 months after the last acute event. This persisting enhanced acute-phase responsiveness may help explain the association between CRP and acute coronary events.
Heparin-Associated Thrombocytopenia (1984)

Heparin-associated thrombocytopenia is a relatively common complication of heparin therapy occurring in approximately 5% of the patients who receive this drug. The incidence is higher with bovine heparin then with porcine heparin. Onset of heparin-associated thrombocytopenia usually occurs 6 to 12 days after initiation of treatment and by itself has a low morbidity. Heparin-associated thrombocytopenia plus arterial thrombosis can cause major complications including stroke, heart attack, and death. The incidence of heparin-associated thrombocytopenia plus arterial thrombosis is lower than that for heparin-associated thrombocytopenia alone. The diagnosis of heparin-associated thrombocytopenia remains one of exclusion, but testing for the presence of a heparin-dependent platelet-aggregating factor may prove to be useful. Analysis of the time of onset suggests a strategy for prevention. Oral anticoagulants could be started concomitantly with the heparin so that it could be discontinued in several days. This approach may prevent most episodes of heparin-associated thrombocytopenia.
Hybrid Solar Cells with Prescribed Nanoscale Morphologies Based on Hyperbranched Semiconductor Nanocrystals (2006)

In recent years, the search to develop large-area solar cells at low cost has led to research on photovoltaic (PV) systems based on nanocomposites containing conjugated polymers. These composite films can be synthesized and processed at lower costs and with greater versatility than the solid state inorganic semiconductors that comprise today's solar cells. However, the best nanocomposite solar cells are based on a complex architecture, consisting of a fine blend of interpenetrating and percolating donor and acceptor materials. Cell performance is strongly dependent on blend morphology, and solution-based fabrication techniques often result in uncontrolled and irreproducible blends, whose composite morphologies are difficult to characterize accurately. Here we incorporate three-dimensional hyperbranched colloidal semiconductor nanocrystals in solution-processed hybrid organic-inorganic solar cells, yielding reproducible and controlled nanoscale morphology.
ACEI/D but notAGT(-6)A/G polymorphism is a risk factor for mortality in ARDS (2006)

The intrapulmonary renin–angiotensin system via tissue concentration of angiotensin II or bradykinin may have multiple effects on pulmonary pathophysiology. Therefore, it was investigated whether the presence of the D allele of the angiotensin-converting enzyme ( ACE ) insertion/deletion (I/D) polymorphism or the A allele of angiotensinogen ( AGT ) promoter polymorphism (-6)A/G are independent risk factors for 30-day survival in acute respiratory distress syndrome (ARDS) patients. In a prospective study, adults (Germans of Caucasian ethnicity ) with ARDS (n = 84) were recruited from the current authors’ intensive care unit and genotyped for the ACE I/D and the AGT (-6)A/G polymorphisms, as were 200 healthy Caucasian controls. Mortality was increased in the ACE DD genotype compared with the I allele, and the ACE I/D polymorphism was an independent prognostic factor for 30-day survival. Patients with a homozygous DD genotype were at highest risk for death (hazard ratio 5.7; 95% confidence interval 1.7–19.2) compared with the II genotype. In contrast, the AGT (-6)A/G polymorphism was neither associated with an increased risk for development of ARDS nor with outcome. In patients with acute respiratory distress syndrome, the angiotensin-converting enzyme insertion/deletion polymorphism but not the angiotensinogen (-6)A/G promoter polymorphism is an independent risk factor with a pronounced effect on 30-day survival.
Stimulation of T cells via the TAP molecule, a member in a family of activating proteins encoded in the Ly-6 locus. (1987)

T-cell activating protein, TAP, is a Ly-6 encoded 12,000 dalton glycoprotein involved in the activation of murine T cells. TAP is distinct from other known surface activating structures, such as the T cell receptor/T3 complex and Thy-1. This study investigates the mechanism of activation via the TAP molecule. Soluble alpha TAP monoclonal antibody (MAb) is sufficient for T cell activation. This, however, requires cross-linking because F(ab) monovalent antibody is not stimulatory unless cross-linked by a second antibody. Immediately after cross-linking, there is a rapid influx of calcium, which is comparable with concanavalin A or T cell receptor triggered responses. Subsequently, interleukin 2 (IL 2) is produced, and IL 2 receptors (IL 2R) are expressed. TAP-stimulated T cell proliferation is driven by this autocrine pathway because it is inhibited by alpha IL 2R MAb. Thus TAP-mediated activation appears to share a common final pathway with other mitogenic stimuli. A nonactivating alpha TAP MAb was observed to stimulate T cells upon additional cross-linking. Given this observation, we asked whether other Ly-6 linked proteins might share similar activating potential. We show that at least three distinct Ly-6 linked molecules are capable of stimulating T hybrid clones and/or heterogeneous T lymphocytes. Thus it appears that the Ly-6 locus encodes a family of activating cell surface molecules.
Interactions between Organized, Surface-Confined Monolayers and Liquid-Phase Probe Molecules. 4. Synthesis and Characterization of Nanoporous Molecular Assemblies: Mechanism of Probe Penetration (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInteractions between Organized, Surface-Confined Monolayers and Liquid-Phase Probe Molecules. 4. Synthesis and Characterization of Nanoporous Molecular Assemblies: Mechanism of Probe PenetrationOrawon Chailapakul and Richard M CrooksCite this: Langmuir 1995, 11, 4, 1329–1340Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/la00004a046https://doi.org/10.1021/la00004a046research-articleACS PublicationsRequest reuse permissionsArticle Views408Altmetric-Citations145LEARN 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
Historical incidence of Perthida leafminer species (Lepidoptera) in southwest Western Australia based on herbarium specimens (1999)

Examination of more than 500 herbarium specimens of Eucalyptus marginata and E. rudis for the presence of two species of leafminers, Perthida spp., indicated that these native insect species were very rare in southwest Western Australia until first recorded in metropolitan Perth in 1878 and 1897, respectively, when west coast populations of both leafminer species evidently increased dramatically. The first record from the south coast dates from 1901 near Albany. Evidence of leafminer populations on E. marginata remote from coastal settlements was not recorded until 1917, near Cranbrook. The first record in jarrah forest was in 1967, some 10 years after outbreaks of the pest insect are known to have occurred in the forest. The Perthida leafminer species on E. rudis was first recorded from inland areas in 1904 and appears to have increased more rapidly in abundance than the species found on E. marginata . These early geographical and species differences in incidence are discussed in terms of changing disturbance patterns, which have not been simultaneous across southwest Western Australia.
Immunomodulatory Effects of Statins (2002)

Clinical trials with statins have demonstrated a marked reduction of cardiovascular mortality. However, it remains controversial whether these clinical benefits stem from powerful cholesterol-lowering effects of statins or whether they are due in part to their cholesterol-independent effects on vascular function, plaque growth, plaque rupture, or thrombosis. The identification of several mechanisms through which statins decrease the recruitment of monocytes and T cells into the arterial wall and inhibit T cell activation and proliferation in vitro have prompted speculations that immunomodulatory effects of statins may be beneficial in recipients of organ transplants. Hypercholesterolemia is frequent in these patients, and delayed-type hypersensitivity reactions in the arterial walls of the graft may be compounded by chronic inflammation associated with conventional atherogenesis. To assess the potential clinical relevance of immunomodulatory effects of statins, the role of the immune system in atherogenesis and the effects of statins in vitro in experimental models and in clinical trials will be reviewed. It is concluded that despite solid in vitro evidence, clinical evidence for an independent immunosuppressive effect of statins in organ transplant patients is presently insufficient; however, further investigation of their in vivo occurrence and clinical relevance is warranted.
An automated multiplex oligonucleotide synthesizer: development of high-throughput, low-cost DNA synthesis. (1995)

An automated oligonucleotide synthesizer has been developed that can simultaneously and rapidly synthesize up to 96 different oligonucleotides in a 96-well microtiter format using phosphoramidite synthesis chemistry. A modified 96-well plate is positioned under reagent valve banks, and appropriate reagents are delivered into individual wells containing the growing oligonucleotide chain, which is bound to a solid support. Each well has a filter bottom that enables the removal of spent reagents while retaining the solid support matrix. A seal design is employed to control synthesis environment and the entire instrument is automated via computer control. Synthesis cycle times for 96 couplings are < 11 min, allowing a plate of 96 20-mers to be synthesized in < 5 hr. Oligonucleotide synthesis quality is comparable to commercial machines, with average coupling efficiencies routinely > 98% across the entire 96-well plate. No significant well-to-well variations in synthesis quality have been observed in > 6000 oligonucleotides synthesized to date. The reduced reagent usage and increased capacity allow the overall synthesis cost to drop by at least a factor of 10. With the development of this instrument, it is now practical and cost-effective to synthesize thousands to tens of thousands of oligonucleotides.
Nonlinear mapping of massive data sets by fuzzy clustering and neural networks (2001)

Producing good low-dimensional representations of high-dimensional data is a common and important task in many data mining applications. Two methods that have been particularly useful in this regard are multidimensional scaling and nonlinear mapping. These methods attempt to visualize a set of objects described by means of a dissimilarity or distance matrix on a low-dimensional display plane in a way that preserves the proximities of the objects to whatever extent is possible. Unfortunately, most known algorithms are of quadratic order, and their use has been limited to relatively small data sets. We recently demonstrated that nonlinear maps derived from a small random sample of a large data set exhibit the same structure and characteristics as that of the entire collection, and that this structure can be easily extracted by a neural network, making possible the scaling of data set orders of magnitude larger than those accessible with conventional methodologies. Here, we present a variant of this algorithm based on local learning. The method employs a fuzzy clustering methodology to partition the data space into a set of Voronoi polyhedra, and uses a separate neural network to perform the nonlinear mapping within each cell. We find that this local approach offers a number of advantages, and produces maps that are virtually indistinguishable from those derived with conventional algorithms. These advantages are discussed using examples from the fields of combinatorial chemistry and optical character recognition. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 373–386, 2001
Statistical Pattern Recognition (2002)

Statistical pattern recognition is a very active area of study and research, which has seen many advances in recent years. New and emerging applications - such as data mining, web searching, multimedia data retrieval, face recognition, and cursive handwriting recognition - require robust and efficient pattern recognition techniques. Statistical decision making and estimation are regarded as fundamental to the study of pattern recognition. Statistical Pattern Recognition, Second Edition has been fully updated with new methods, applications and references. It provides a comprehensive introduction to this vibrant area - with material drawn from engineering, statistics, computer science and the social sciences - and covers many application areas, such as database design, artificial neural networks, and decision support systems. * Provides a self-contained introduction to statistical pattern recognition. * Each technique described is illustrated by real examples. * Covers Bayesian methods, neural networks, support vector machines, and unsupervised classification. * Each section concludes with a description of the applications that have been addressed and with further developments of the theory. * Includes background material on dissimilarity, parameter estimation, data, linear algebra and probability. * Features a variety of exercises, from 'open-book' questions to more lengthy projects. The book is aimed primarily at senior undergraduate and graduate students studying statistical pattern recognition, pattern processing, neural networks, and data mining, in both statistics and engineering departments. It is also an excellent source of reference for technical professionals working in advanced information development environments. For further information on the techniques and applications discussed in this book please visit www.statistical-pattern-recognition.net
A Wound-Isolated Pseudomonas aeruginosa Grows a Biofilm In Vitro Within 10 Hours and Is Visualized by Light Microscopy (2003)

The rapidity of biofilm growth suggests that bacteria in wounds possess the capacity of producing this shield against antibiotics and immune effector cells early in the infection process. Therefore, efforts to prevent or slow the proliferation of bacteria and biofilms should occur soon after a wound is created. Additionally, this staining technique can be used to demonstrate the ability of agents to slow biofilm growth or to interrupt formed biofilm and may be useful in future studies of chronically infected wounds.
Analysis of Antibiotic Resistance Genes in Multidrug-Resistant Acinetobacter sp. Isolates from Military and Civilian Patients Treated at the Walter Reed Army Medical Center (2006)

Military medical facilities treating patients injured in Iraq and Afghanistan have identified a large number of multidrug-resistant (MDR) Acinetobacter baumannii isolates. In order to anticipate the impact of these pathogens on patient care, we analyzed the antibiotic resistance genes responsible for the MDR phenotype in Acinetobacter sp. isolates collected from patients at the Walter Reed Army Medical Center (WRAMC). Susceptibility testing, PCR amplification of the genetic determinants of resistance, and clonality were determined. Seventy-five unique patient isolates were included in this study: 53% were from bloodstream infections, 89% were resistant to at least three classes of antibiotics, and 15% were resistant to all nine antibiotics tested. Thirty-seven percent of the isolates were recovered from patients nosocomially infected or colonized at the WRAMC. Sixteen unique resistance genes or gene families and four mobile genetic elements were detected. In addition, this is the first report of bla(OXA-58)-like and bla(PER)-like genes in the U.S. MDR A. baumannii isolates with at least eight identified resistance determinants were recovered from 49 of the 75 patients. Molecular typing revealed multiple clones, with eight major clonal types being nosocomially acquired and with more than 60% of the isolates being related to three pan-European types. This report gives a "snapshot" of the complex genetic background responsible for antimicrobial resistance in Acinetobacter spp. from the WRAMC. Identifying genes associated with the MDR phenotype and defining patterns of transmission serve as a starting point for devising strategies to limit the clinical impact of these serious infections.