gebhart/patrepeval huggingface dataset:
Identification of genes expressed in malignant cells that promote invasion. (2003)

To systematically identify genes related to invasion a three-dimensional multicellular matrix invasion assay was used to classify human tumor cell lines as stromal invasion positive or stromal invasion negative. Cells from two of the primary cell types of the stromal compartment [endothelial cells (HMVEC) and myofibroblasts (HDF)] were assayed for invasion into tumor cell clusters (breast carcinoma, ovarian carcinoma, prostate carcinoma, lung carcinoma, and melanoma). Four tumor cell lines (MDA-MB231, SKOV-3, A375, and MEL624) scored invasion positive, and four tumor cell lines (LNCaP, DU145, PC3, and A549) scored invasion negative. Serial analysis of gene expression (SAGE) libraries generated from the tumor cell lines were analyzed by GeneSpring Hierarchical clustering, t test, and chi(2) test. Clusters emerged that reflected the behavior in the cell culture assay. Of the 47 most highly differentially expressed genes, 30 were selected for confirmation by real-time PCR, and 9 had good correlation with normalized serial analysis of gene expression tag counts. The strongest correlations were for bone marrow stromal antigen 2, stathmin-like 3, tumor necrosis factor receptor superfamily member 5, and hepatocyte growth factor tyrosine kinase substrate. In situ hybridization of metastatic and nonmetastatic ovarian cancer demonstrated selective expression of bone marrow stromal antigen 2 and tumor necrosis factor receptor superfamily member 5 in the metastatic disease. This combination approach appears to be a powerful tool for identifying genes that may be useful as diagnostic markers and/or as therapeutic targets for invasive solid tumors.
Marine natural products (1987)

D. J. Faulkner, Nat. Prod. Rep., 1987, 4, 539 DOI: 10.1039/NP9870400539
New Insights Into the Viscosity of Polymer-Based In-Situ-Gelled Acids (2010)

Summary Diversion techniques must be employed to remove all the damage from the entire producing interval. Diversion in carbonates is more difficult than in sandstones because of the ability of acid to significantly increase the permeability in carbonates as the acid dissolves carbonate rocks. The apparent viscosity of the in-situ-gelled acid based on polymer plays a key role in diversion because it creates a viscosity differential in treated and untreated zones. An extensive literature survey and field data show that there is no agreement on the effectiveness of this acid system. Therefore, this study was conducted to better understand this acid system and determine factors that impact its viscosity buildup. Three commercially available in-situ acids were examined. The effect of salts and iron (III) [Fe(III)] contamination on the apparent viscosity of these acids was examined in detail. Several new findings were identified, including that polymer and other additives were separated out of the acid when these acids were prepared in high-salinity brines. Preparing the in-situ-gelled acid with saline waters decreased the viscosity of the acid in live and partially neutralized conditions. Concentrated hydrochloric acid (HCl) solutions produced high concentrations of calcium ion that reduced the viscosity of the in-situ-gelled acid system. Therefore, in-situ-gelled acids that are based on polymers should be used at low HCl concentrations (3 to 5 wt% HCl). Sodium (NaCl), calcium (CaCl2), or ferric chloride (FeCl3) reduced the apparent viscosity of live gelled acids. A brown precipitate was noted during the neutralization of acid systems that contained Fe (III), even in the presence of the recommended concentration of iron-control agents. Therefore, in-situ-gelled acids that are based on polymers should be prepared using low salinity waters and used at low HCl concentrations (3 to 5 wt% HCl).
Putative oncogenic role of the erythropoietin receptor in murine and human erythroleukemia cells (1994)

To determine whether the erythropoietin receptor (Epo-R) plays a role in the course of malignant erythropoietic disorders, this gene was studied in murine and human erythroleukemia cells. An altered Epo-R gene was found in a murine Friend erythroleukemia cell line, FCL1, due to a spleen focus-forming virus (SFFV) long terminal repeat insertion within the noncoding region of the first exon, leading to Epo-R mRNA overexpression. A similar mechanism of Epo-R activation has previously been described in the T3CL-2 Friend erythroleukemia cell line. An elevated number of Epo-binding sites has been observed in two human erythroleukemia cell lines, TF-1 and UT7. In UT7 cells, homogeneously staining region of the short arm of chromosome 19 [hsr (19)] was evidenced, which contained an amplification of the Epo-R gene. This Epo- R gene amplification was confirmed by the quantification of Southern blots in which the intensity of the Epo-R signal was compared in UT7 DNA and in DNA from normal cells. The Epo-R gene was present in UT7 at a mean number of seven to eight copies per cell. Interestingly, the Epo- R gene was rearranged; the breakpoint region was located near the 3′ end of the gene, 3 kb downstream from the end of the last exon. Taken together, these results suggest that, in both murine and human systems, genetic alterations of the Epo-R gene are not rare events and could be involved in the occurrence of the erythroleukemic process.
High-Efficiency p-Type Silicon Heterojunction Solar Cells (2006)

Microbially induced carbonate precipitation (MICP) is a promising technique for remediating heavy metal-contaminated soils. However, the effectiveness of MICP in immobilizing Cd in alkaline calcareous soils, especially when applied in agricultural soils, remains unclear. Biochar and magnesium oxide are two environmentally friendly passivating materials, and there are few reports on the combined application of MICP with passivating materials for remediating heavy metal-contaminated soils. Additionally, the number of treatments with MICP cement and the concentration of calcium chloride during the MICP process can both affect the effectiveness of heavy metal immobilization by MICP. Therefore, we conducted MICP and MICP-biochar-magnesium oxide treatments on agricultural soils collected from Baiyin, Gansu Province (pH = 8.62), and analyzed the effects of the number of treatments with cement and the concentration of calcium chloride on the immobilization of Cd by MICP and combined treatments. The results showed that early-stage MICP could immobilize exchangeable cadmium and increase the residual cadmium content, especially with high-concentration calcium chloride MICP treatment. However, in the later stage, soil nitrification and exchange processes led to the dissolution of carbonate-bound cadmium and cadmium activation. The fixing effect of MICP influence whether the MICP-MgO-biochar is superior to the MgO-biochar. Four treatments with cement were more effective than single treatment in MICP-biochar-magnesium oxide treatment, and the MICP-biochar-magnesium oxide treatment with four treatments was the most effective, with passivation rates of 40.7% and 46.6% for exchangeable cadmium and bioavailable cadmium, respectively. However, attention should be paid to the increase in soil salinity. The main mechanism of MICP-magnesium oxide-biochar treatment in immobilizing cadmium was the formation of Cd(OH)<sub>2</sub>, followed by the formation of cadmium carbonate.
State management in Apache Flink® (2017)

Stream processors are emerging in industry as an apparatus that drives analytical but also mission critical services handling the core of persistent application logic. Thus, apart from scalability and low-latency, a rising system need is first-class support for application state together with strong consistency guarantees, and adaptivity to cluster reconfigurations, software patches and partial failures. Although prior systems research has addressed some of these specific problems, the practical challenge lies on how such guarantees can be materialized in a transparent, non-intrusive manner that relieves the user from unnecessary constraints. Such needs served as the main design principles of state management in Apache Flink, an open source, scalable stream processor. We present Flink's core pipelined, in-flight mechanism which guarantees the creation of lightweight, consistent, distributed snapshots of application state, progressively, without impacting continuous execution. Consistent snapshots cover all needs for system reconfiguration, fault tolerance and version management through coarse grained rollback recovery. Application state is declared explicitly to the system, allowing efficient partitioning and transparent commits to persistent storage. We further present Flink's backend implementations and mechanisms for high availability, external state queries and output commit. Finally, we demonstrate how these mechanisms behave in practice with metrics and large-deployment insights exhibiting the low performance trade-offs of our approach and the general benefits of exploiting asynchrony in continuous, yet sustainable system deployments.
Electron and hole transport in a wide bandgap organic phosphine oxide for blue electrophosphorescence (2008)

We report blue phosphorescent organic light-emitting devices (OLEDs) using an ambipolar host, N-(4-diphenylphosphoryl phenyl) carbazole (MPO12), doped with iridium (III) bis[(4,6-difluorophenyl)-pyridinato-N,C2′]picolinate (FIrpic). The external quantum efficiency and operating voltage is 9.1(±0.1)% and 4.8V, respectively, measured at a brightness of 800cd∕m2 with no outcoupling enhancement. By varying the layer structure of the OLEDs, we show that MPO12 is capable of transporting both electrons and holes, in contrast to previous demonstrations using diphosphine oxides, which only transported electrons. The improved hole transport results in improved device efficiency.
Explosive Blast Neurotrauma (2009)

Explosive blast traumatic brain injury (TBI) is one of the more serious wounds suffered by United States service members injured in the current conflicts in Iraq and Afghanistan. Some military medical treatments for blast TBI that have been introduced successfully in the war theater include decompressive craniectomy, cerebral angiography, transcranial Doppler, hypertonic resuscitation fluids, among others. Stateside neurosurgery, neuro-critical care, and rehabilitation for these patients have similarly progressed. With experience, military physicians have been able to clinically describe blast TBI across the entire severity spectrum. One important clinical finding is that a significant number of severe blast TBI victims develop pseudoaneurysms and vasospasm, which can lead to delayed decompensation. Another is that mild blast TBI shares clinical features with post-traumatic stress disorder (PTSD). Observations suggest that the mechanism by which explosive blast injures the central nervous system may be more complex than initially assumed. Rigorous study at the basic science and clinical levels, including detailed biomechanical analysis, is needed to improve understanding of this disease. A comprehensive epidemiological study is also warranted to determine the prevalence of this disease and the factors that contribute most to the risk of developing it. Sadly, this military-specific disease has significant potential to become a civilian one as well.
IL-12 Treatment of Endogenously Arising Murine Brain Tumors (2000)

A number of recent studies have indicated that T cells can be stimulated to attack transplanted brain tumors in rodent models. As IL-12 has been shown to activate cytotoxic T cell responses, we tested the idea that it might stimulate a T cell response against endogenous brain tumors that arise in SV40 large T Ag transgenic mice (SV11). SV11 mice develop tumors of the choroid plexus, a specialization of the ependymal lining of the brain ventricles. They are a particularly relevant model of human disease, because they are immunocompetent but immunologically tolerant of the tumors. SV11 mice were treated with recombinant murine IL-12 for 10 days. Tumors grew more slowly than in control treated mice, and in some cases were reduced in size, as assessed by magnetic resonance imaging before and after treatment. At the end of treatment, tumors, but not brain parenchyma, exhibited extensive infiltration of activated CD8(+) and CD4(+) T cells. Tumors also showed a reduction in vascular density. Mice treated with IL-12 lived significantly longer than control mice. Tumors that progressed were nearly devoid of T cells, indicating that the T cell response was not sustained. In addition, some mice that had a substantial tumor burden at the beginning of treatment displayed evidence of immunosuppression, which might be related to TGF-ss2 detected in tumors. We conclude that IL-12 treatment can initiate an anti-tumor response even against endogenously arising brain tumors, but factors that will allow a sustained and more effective anti-tumor response need to be determined.
Relative stabilities of triple helices composed of combinations of DNA, RNA and 2'-O-methyl-RNA backbones: chimeric circular oligonucleotides as probes (1995)

Described is a systematic study of the effects of varied backbone structure on the stabilities of pyr.pur.pyr triple helices. The effects were measured using six circular 34 base oligonucleotides containing DNA (D), RNA (R) and/or 2'-O-methyl-RNA (M) residues designed to bind a complementary single-stranded purine target strand by triple helix formation. Eighteen different backbone combinations were studied at pH 5.5 and 7.0 by optical melting experiments and the results compared with the stabilities of the corresponding Watson-Crick duplexes. When the target purine strand is DNA, all circles form pH-dependent triple helical complexes which are considerably stronger than the duplexes alone. When RNA is the target, five of the nine complexes studied are of the pH-dependent triplex type and the other four complexes are not significantly stronger than the corresponding duplexes. The results are useful in the design of the highest affinity ligands for single- and double-stranded DNAs and RNAs and also point out novel ways to engender DNA- or RNA-selective binding.
Benchmarking Amazon EC2 for hig-performance scientific computing (2008)

How effective are commercial cloud computers for high-performance scientific computing compared to currently avaible alternatives? I aim to answer a specific instance of this question by examining the performance of Amazon EC2 for high-performance scientific applications. I used macro and micro benchmarks to study the performance of a cluster composed of EC2 high-CPU compute nodes and compared this against the performance of a cluster composed of equivalent processors avaible to the open scientific research community. My results show a significant performance gap in the examined clusters that system builders, computational scientist, and commercial cloud computing vendors need to be aware of .
Amino Acids. II. Synthesis of Cyclic Guanidino Acids1 (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAmino Acids. II. Synthesis of Cyclic Guanidino Acids1A. F. McKay and W. G. HattonCite this: J. Am. Chem. Soc. 1956, 78, 8, 1618–1620Publication Date (Print):April 1, 1956Publication History Published online1 May 2002Published inissue 1 April 1956https://pubs.acs.org/doi/10.1021/ja01589a032https://doi.org/10.1021/ja01589a032research-articleACS PublicationsRequest reuse permissionsArticle Views397Altmetric-Citations37LEARN 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
Immunogenicity and Efficacy inAotusMonkeys of Four RecombinantPlasmodium falciparumVaccines in Multiple Adjuvant Formulations Based on the 19-Kilodalton C Terminus of Merozoite Surface Protein 1 (2000)

The immunogenicity and protective efficacy of four versions of recombinant C-terminal 19-kDa epidermal growth factor-like region of the major surface protein 1 (rMSP1(19)) of Plasmodium falciparum was studied in Aotus monkeys. Vaccination with each of the four rMSP1(19) constructs elicited high levels of antibodies to MSP1(19) but only one construct, the 19-kDa fragment expressed as a secreted fusion protein from Saccharomyces cerevisiae (yP30P2MSP1(19)), induced a high degree of protective immunity in Aotus nancymai against lethal P. falciparum challenge. Protective formulation required Freund's adjuvant; vaccination with yP30P2MSP1(19) in six other adjuvants that are suitable for human use induced lower levels of antibody response and no protection. These results emphasize the need to continue the search for an adjuvant that is comparable to Freund's adjuvant in potency and is safe for use in humans.
High-Temperature Spectral Emittance of Oxides of Erbium, Samarium, Neodymium and Ytterbium (1972)

Normal spectral emittance data are reported for solid specimens of the oxides of erbium, samarium, neodymium, and ytterbium. The spectral emittance has been characterized over the spectral range of 0.5–5.0 µ and at sample temperatures from 1540 up to 1870 K.
Construction of a pH-Driven Supramolecular Nanovalve (2006)

[Structure: see text] The versatility of supramolecular chemistry has been exploited in constructing nanovalves based on mesoporous silica MCM-41 and the mutual recognition between secondary dialkylammonium ions and dibenzo[24]crown-8 (DB24C8). Naphthalene-containing dialkylammonium threads were tethered to the MCM-41, followed by loading with coumarin 460 and capping with DB24C8. Controlled release of coumarin 460 from the pores of MCM-41 was demonstrated using different bases. The rate of release of coumarin 460 from the nanovalves depends on the size of the base.
Genome Editing with Engineered Nucleases in Plants (2014)

Numerous examples of successful 'genome editing' now exist. Genome editing uses engineered nucleases as powerful tools to target specific DNA sequences to edit genes precisely in the genomes of both model and crop plants, as well as a variety of other organisms. The DNA-binding domains of zinc finger (ZF) proteins were the first to be used as genome editing tools, in the form of designed ZF nucleases (ZFNs). More recently, transcription activator-like effector nucleases (TALENs), as well as the clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) system, which utilizes RNA-DNA interactions, have proved useful. A key step in genome editing is the generation of a double-stranded DNA break that is specific to the target gene. This is achieved by custom-designed endonucleases, which enable site-directed mutagenesis via a non-homologous end-joining (NHEJ) repair pathway and/or gene targeting via homologous recombination (HR) to occur efficiently at specific sites in the genome. This review provides an overview of recent advances in genome editing technologies in plants, and discusses how these can provide insights into current plant molecular biology research and molecular breeding technology.
A Review on the Medicinal Importance of Pyridine Derivatives (2015)

Pyridine and its derivatives are the important chemical compounds with tremendous applications in the various fields. In this review we have summarized the medicinal and non-medicinal uses of number of pyridine derivatives. Pyridine derivatives have been reported for variety of biological activities and numbers of the compounds are in clinical uses. Pyridine derivatives also have increasing importance for modern medicinal applications.
Comparing support vector machines with Gaussian kernels to radial basis function classifiers (1997)

The support vector (SV) machine is a novel type of learning machine, based on statistical learning theory, which contains polynomial classifiers, neural networks, and radial basis function (RBF) networks as special cases. In the RBF case, the SV algorithm automatically determines centers, weights, and threshold that minimize an upper bound on the expected test error. The present study is devoted to an experimental comparison of these machines with a classical approach, where the centers are determined by X-means clustering, and the weights are computed using error backpropagation. We consider three machines, namely, a classical RBF machine, an SV machine with Gaussian kernel, and a hybrid system with the centers determined by the SV method and the weights trained by error backpropagation. Our results show that on the United States postal service database of handwritten digits, the SV machine achieves the highest recognition accuracy, followed by the hybrid system. The SV approach is thus not only theoretically well-founded but also superior in a practical application.
Methicillin-resistant Staphylococcus aureus and animals: zoonosis or humanosis? (2008)

Methicillin-resistant Staphylococcus aureus (MRSA) is increasing worldwide. Occasionally, animals are colonized or infected incidentally with human strains. Recently, however, new strains of MRSA emerging from within the animal kingdom, particularly in pigs, are causing human infection. MRSA has been reported in species as diverse as companion animals, horses and pigs, through to chinchillas, bats and parrots. In contrast, whereas strains of community-associated MRSA, the majority of which carry genes encoding Panton-Valentine leucocidin, are spreading rapidly in human populations, only sporadic cases have been reported in animals to date. Although MRSA has been found in some meat products, the implications for human infection through consumption are unclear. This review examines the epidemiology of MRSA in animals and human attendants/owners, the diagnosis and management of MRSA colonization, infection and infection control strategies in animals.
An amulet for trustworthy wearable mHealth (2012)

Mobile technology has significant potential to help revolutionize personal wellness and the delivery of healthcare. Mobile phones, wearable sensors, and home-based tele-medicine devices can help caregivers and individuals themselves better monitor and manage their health. While the potential benefits of this "mHealth" technology include better health, more effective healthcare, and reduced cost, this technology also poses significant security and privacy challenges. In this paper we propose Amulet, an mHealth architecture that provides strong security and privacy guarantees while remaining easy to use, and outline the research and engineering challenges required to realize the Amulet vision.