gebhart/patrepeval huggingface dataset:
Clustering Effects on Discontinuous Gold Film NanoCells (2004)

Reproducible negative differential resistance (NDR)-like switching behavior is observed in NanoCells. This behavior is attributed to the formation of filaments and clusters between the discontinuous gold films. Control experiments are performed by self-assembly of insulating molecules between the gold islands and conducting molecules on these islands. Additional control experiments are performed by removing the filaments and clusters between islands using a piranha bath. The results are consistent with theoretical predictions and extend the domain of molecular electronics based in organic molecules to include nanosized clusters as active units. This facilitates a scenario where synthetically accessible organic molecules, with defined characteristics, can be adjusted by metallic nanoclusters as an in situ fine-tuning element, able to compensate for the lack of addressing in the nanosize regime.
Crown Gall Disease and Prospects for Genetic Manipulation of Plants (1982)

Agrobacterium tumefaciens incites crown gall tumors when bacterial DNA integrates into plant nuclear DNA. Plant cells can express these integrated bacterial genes. Following insertion of desired genes into bacterial DNA using recombinant DNA techniques, this system permits introduction of these new genes into plant DNA. We discuss the potential for genetic manipulation of plants using Agrobacterium tumefaciens and the related organism Agrobacterium rhizogenes.
Molecular basis for the explanation of the exponential growth of polyelectrolyte multilayers (2002)

The structure of poly(l-lysine) (PLL)/hyaluronan (HA) polyelectrolyte multilayers formed by electrostatic self-assembly is studied by using confocal laser scanning microscopy, quartz crystal microbalance, and optical waveguide lightmode spectroscopy. These films exhibit an exponential growth regime where the thickness increases exponentially with the number of deposited layers, leading to micrometer thick films. Previously such a growth regime was suggested to result from an "in" and "out" diffusion of the PLL chains through the film during buildup, but direct evidence was lacking. The use of dye-conjugated polyelectrolytes now allows a direct three-dimensional visualization of the film construction by introducing fluorescent polyelectrolytes at different steps during the film buildup. We find that, as postulated, PLL diffuses throughout the film down into the substrate after each new PLL injection and out of the film after each PLL rinsing and further after each HA injection. As PLL reaches the outer layer of the film it interacts with the incoming HA, forming the new HA/PLL layer. The thickness of this new layer is thus proportional to the amount of PLL that diffuses out of the film during the buildup step, which explains the exponential growth regime. HA layers are also visualized but no diffusion is observed, leading to a stratified film structure. We believe that such a diffusion-based buildup mechanism explains most of the exponential-like growth processes of polyelectrolyte multilayers reported in the literature.
Characterization of tyrosyl kinase activity in human serum. (1985)

Tyrosyl kinase activity was detected in 1.0 microliter or less of human serum with the substrates angiotensin II, polyamino acid polymer Glu-Tyr (4:1), anti-pp60src IgG, and endogenous serum proteins. Most (about 84%) of the tyrosyl kinase activity was in the 100,000 X g soluble fraction from serum and a similar level of activity was found in the soluble fraction from plasma. Expression of tyrosyl kinase activity in individual serum samples differed more than 15-fold. The different levels of tyrosyl kinase activity were not likely due to phosphatases, proteases, ATPases, or kinase inhibitors and activators in serum. The normal serum and plasma tyrosyl kinase activities were not stimulated by epidermal growth factor, platelet-derived growth factor, insulin, or growth factors from fetal calf serum. Investigations of samples from patients with malignant disorders indicated that those with malignant melanoma contained the highest levels of serum tyrosyl kinase activity.
Reduced Oxidative Stress Contributes to the Lipid Lowering Effects of Isoquercitrin in Free Fatty Acids Induced Hepatocytes (2014)

Oxidative stress interferes with hepatic lipid metabolism at various levels ranging from benign lipid storage to so-called second hit of inflammation activation. Isoquercitrin (IQ) is widely present flavonoid but its effects on hepatic lipid metabolism remain unknown. We used free fatty acids (FFA) induced lipid overload and oxidative stress model in two types of liver cells and measured cell viability, intracellular lipids, and reactive oxygen species (ROS) within hepatocytes. In addition, Intracellular triglycerides (TG), superoxide dismutase (SOD), and malondialdehyde (MDA) were examined. A novel in vitro model was used to evaluate correlation between lipid lowering and antioxidative activities. Furthermore, 34 major cytokines and corresponding ROS levels were analyzed in FFA/LPS induced coculture model between hepatocytes and Kupffer cells. At molecular level AMPK pathway was elucidated. We showed that IQ attenuated FFA induced lipid overload and ROS within hepatocytes. Further, IQ reversed FFA induced increase in intracellular TG SOD and MDA. It was shown that antioxidative activity of IQ correlates with its lipid lowering potentials. IQ reversed major proinflammatory cytokines and oxidative stress in FFA/LPS induced coculture model. Finally, AMPK pathway was found responsible for metabolic benefits at molecular level. IQ strikingly manifests antioxidative and related lipid lowering activities in hepatocytes.
Norhalichondrin A: an antitumor polyether macrolide from a marine sponge (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNorhalichondrin A: an antitumor polyether macrolide from a marine spongeDaisuke Uemura, Kanji Takahashi, Toshihiro Yamamoto, Chuji Katayama, Jiro Tanaka, Yasuaki Okumura, and Yoshimasa HirataCite this: J. Am. Chem. Soc. 1985, 107, 16, 4796–4798Publication Date (Print):August 1, 1985Publication History Published online1 May 2002Published inissue 1 August 1985https://pubs.acs.org/doi/10.1021/ja00302a042https://doi.org/10.1021/ja00302a042research-articleACS PublicationsRequest reuse permissionsArticle Views1544Altmetric-Citations243LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Self‐navigated spiral fMRI: Interleaved versus single‐shot (1998)

This study compares the measured activation volumes in motor cortex as well as the fluctuation noise and off-resonance characteristics for 1-, 2-, and 4-shot spiral gradient-recalled echo blood oxygen level dependent contrast functional magnetic resonance imaging (fMRI) acquisitions, under conditions of constant resolution and scan time and with two readout durations. Reconstructions were made with and without self-navigator correction. It was found that the navigator correction provided a 50% reduction in image fluctuation noise with 4-shot acquisitions, and that multishot acquisitions perform as well as single-shot techniques when self-navigation is employed. An analysis of blurring showed that off-resonance delta f causes blurring when delta f > 1/(2*Tad), where Tad is the readout duration. Off-resonance effects were readily corrected during reconstruction with retrospective linear shim, even with the longer readout duration needed for single-shot methods. With navigator and shim correction, single-shot and multishot spiral methods are highly effective for fMRI acquisitions.
A study on photosynthesis in leaves of haploid and doubled haploid pepper (2001)

Photosynthesis of haploid and doubled pepper derived from microspore (Capsicum annuum L.) was investigated. The net phososynthetic rate (Pn) of haploid plant was lower than that of doubled haploid in any photo flux density (PFD). Under lower light, the stomatal factor was the main cause of the Pn decrease in haploid plant leaves, whereas under normal light, the non-stomatal factors were the main causes. A remarkable photoinhibition of photosynthesis was observed in the haploid plant leaf under high light conditions. When plants were exposed to normal light, Pn, stomatal conductance (Gs), apparent quantum efficiencies (AQE) and carboxylation efficiences (CE) in haploid leaves were lower than those in doubled haploid, but the intercellular CO_(2) compensation point (#TAU#) and light compensation point of haploid plant leaves were higher than those of doubled haploid. These might be the important features of the differences between haploid and doubled haploid plant.
Serum Uric Acid Is a Strong Predictor of Stroke in Patients With Non–Insulin-Dependent Diabetes Mellitus (1998)

Our results indicate that hyperuricemia is a strong predictor of stroke events in middle-aged patients with NIDDM independently of other cardiovascular risk factors.
Potent antitumor activity of cabozantinib, a c‐MET and VEGFR2 inhibitor, in a colorectal cancer patient‐derived tumor explant model (2014)

Antiangiogenic therapy is commonly used for the treatment of colorectal cancer (CRC). Although patients derive some clinical benefit, treatment resistance inevitably occurs. The MET signaling pathway has been proposed to be a major contributor of resistance to antiangiogenic therapy. MET is upregulated in response to vascular endothelial growth factor pathway inhibition and plays an essential role in tumorigenesis and progression of tumors. In this study, we set out to determine the efficacy of cabozantinib in a preclinical CRC patient-derived tumor xenograft model. We demonstrate potent inhibitory effects on tumor growth in 80% of tumors treated. The greatest antitumor effects were observed in tumors that possess a mutation in the PIK3CA gene. The underlying antitumor mechanisms of cabozantinib consisted of inhibition of angiogenesis and Akt activation and significantly decreased expression of genes involved in the PI3K pathway. These findings support further evaluation of cabozantinib in patients with CRC. PIK3CA mutation as a predictive biomarker of sensitivity is intriguing and warrants further elucidation. A clinical trial of cabozantinib in refractory metastatic CRC is being activated.
Quantitative Analysis of Modified Proteins by LC−MS/MS of Peptides Labeled with Phenyl Isocyanate (2003)

Stable isotope tagging methods have enabled relative quantitation of proteins between samples in LC-MS/MS analyses. However, most such methods are not applicable to the differential quantitation of modified proteins because the isotope tagging reagents only react with certain peptides or because the reagents incorporate a mass increment that is too small to allow reliable quantitation on low resolution ion trap MS instruments. Here, we describe the use of d0- and d5-phenyl isocyanate (PIC) as N-terminal reactive tags for essentially all peptides in proteolytic digests. PIC reacts quantitatively with peptide N-terminal amines within minutes at neutral pH and the PIC-labeled peptides undergo informative MS/MS fragmentation. Ratios of d0- and d5-PIC-labeled derivatives of several model peptides were linear across a 10000-fold range of peptide concentration ratios, thus indicating a wide dynamic range for quantitation. Application of PIC labeling enabled relative quantitation of several styrene oxide adducts of human hemoglobin in LC-MS/MS analyses. PIC labeling offers a versatile means of quantifying changes in modified or variant protein forms in paired samples.
Evaluation of Intrathecal Routes of Administration for Adeno-Associated Viral Vectors in Large Animals (2017)

Delivery of adeno-associated viral (AAV) vectors into the cerebrospinal fluid (CSF) can achieve gene transfer to cells throughout the brain and spinal cord, potentially making many neurological diseases tractable gene therapy targets. Identifying the optimal route of CSF access for intrathecal AAV delivery will be a critical step in translating this approach to clinical practice. We previously demonstrated that vector injection into the cisterna magna is a safe and effective method for intrathecal AAV delivery in nonhuman primates; however, this procedure is not commonly used in clinical practice. More routine methods of administration into the CSF are now being explored, including intracerebroventricular (ICV) injection and injection through a lumbar puncture. In this study, we compared ICV and intracisternal (IC) AAV administration in dogs. We also evaluated vector administration via lumbar puncture in nonhuman primates, with some animals placed in the Trendelenburg position after injection, a maneuver that has been suggested to improve cranial distribution of vector. In the dog study, ICV and IC vector administration resulted in similarly efficient transduction throughout the brain and spinal cord. However, animals in the ICV cohort developed encephalitis associated with a T-cell response to the transgene product, a phenomenon that was not observed in the IC cohort. In the nonhuman primate study, transduction efficiency was not improved by placing animals in the Trendelenburg position after injection. These findings illustrate important limitations of commonly used methods for CSF access in the context of AAV delivery, and will be important for informing the selection of a route of administration for first-in-human studies.
Positive and negative factors regulate the transcription of the ETS2 gene via an oncogene-responsive-like unit within the ETS2 promoter region. (1991)

The DNA-protein interactions in the ETS2 promoter have been studied. Three distinct sequence motifs have been identified, each of which interacts with at least two distinctive protein complexes. The GC motif, possessing mirror symmetry, interacts with two ubiquitously identifiable complexes (S and S2); the PEA3 motif interacts with a ubiquitous (H1) and a tissue-specific (H3) complex; the H2 (an AP1-like) motif interacts also with a ubiquitous (H2a) and a tissue-specific (H2b) complex. Mutational analysis and correlation of the presence of defined complexes with the ETS2 mRNA levels indicate that the S, S2, H1, and H2b complexes have positive effects on ETS2 transcription, whereas the H3 and H2a have negative effects. The organization of the PEA3 with the AP1-like motif in the ETS2 promoter resembles the oncogene-responsive unit previously identified in the polyoma virus enhancer region. Our data suggest that cooperation between these two motifs is vital for ETS2 promoter function.
Adeno-associated virus 2-mediated gene transfer and functional expression of the human granulocyte-macrophage colony-stimulating factor. (1995)

It is becoming increasingly clear that the adeno-associated virus 2 (AAV)-based vector system may prove to be useful for high-efficiency gene transfer in human cells as well as for potential gene therapy in humans. A recombinant AAV vector containing the gene for a human hematopoietic growth factor, granulocyte-macrophage colony-stimulating factor (GM-CSF), was constructed and used to infect COS-1 cells, a monkey kidney cell line. COS-1 cells infected with the recombinant virus, but not mock-infected cells, expressed high levels of the human GM-CSF gene transcripts. Furthermore, in co-cultivation experiments with the recombinant virus-infected cells, but not in those with mock-infected cells, active proliferation of a GM-CSF-dependent human megakaryocytic leukemia cell line, M07e, could be obtained in the absence of exogenously added GM-CSF. The recombinant GM-CSF protein released into the supernatant was biologically active in progenitor cell assays carried out with primary human hematopoietic cells, and this activity was specifically abrogated by treatment of the supernatant with anti-GM-CSF antibodies. This recombinant virus may be potentially useful in the management and gene therapy of a variety of malignant disorders in the human hematopoietic system.
A New Subtype of Human T-Cell Leukemia Virus (HTLV-II) Associated with a T-Cell Variant of Hairy Cell Leukemia (1982)

Human T-cell leukemia virus (HTLV) is a human type-C RNA tumor virus (retrovirus) previously identified in and isolated from several patients with T-cell leukemias or lymphomas. The known virus isolates from the United States and Japan are closely related and are found in adults with an acute malignancy of mature T cells. A related retrovirus has been found in a patient (Mo) with a somewhat different disease (a T-cell variant of relatively benign hairy cell leukemia). Serum from Mo contains antibodies to the major internal core protein (p24) of HTLV. A T-cell line established from the spleen of Mo expresses HTLV antigens. However, HTLV from Mo is significantly different from all previous HTLV isolates in immunological cross-reactivity tests of p24. The usual prototype HTLV isolate is represented as HTLV-I, and the HTLV from Mo is represented as HTLV-II. Individual members of each subgroup may then be identified by subscript initials of the patient [for example, HTLV-I(CR), HTLV-I(MB), and HTLV-II(Mo)].
The tumor suppressor LKB1 kinase directly activates AMP-activated kinase and regulates apoptosis in response to energy stress (2004)

AMP-activated protein kinase (AMPK) is a highly conserved sensor of cellular energy status found in all eukaryotic cells. AMPK is activated by stimuli that increase the cellular AMP/ATP ratio. Essential to activation of AMPK is its phosphorylation at Thr-172 by an upstream kinase, AMPKK, whose identity in mammalian cells has remained elusive. Here we present biochemical and genetic evidence indicating that the LKB1 serine/threonine kinase, the gene inactivated in the Peutz-Jeghers familial cancer syndrome, is the dominant regulator of AMPK activation in several mammalian cell types. We show that LKB1 directly phosphorylates Thr-172 of AMPKalpha in vitro and activates its kinase activity. LKB1-deficient murine embryonic fibroblasts show nearly complete loss of Thr-172 phosphorylation and downstream AMPK signaling in response to a variety of stimuli that activate AMPK. Reintroduction of WT, but not kinase-dead, LKB1 into these cells restores AMPK activity. Furthermore, we show that LKB1 plays a biologically significant role in this pathway, because LKB1-deficient cells are hypersensitive to apoptosis induced by energy stress. On the basis of these results, we propose a model to explain the apparent paradox that LKB1 is a tumor suppressor, yet cells lacking LKB1 are resistant to cell transformation by conventional oncogenes and are sensitive to killing in response to agents that elevate AMP. The role of LKB1/AMPK in the survival of a subset of genetically defined tumor cells may provide opportunities for cancer therapeutics.
3D interpolation of irregular data with a POCS algorithm (2006)

Abstract Seismic surveys generally have irregular areas where data cannot be acquired. These data should often be interpolated. A projection onto convex sets (POCS) algorithm using Fourier transforms allows interpolation of irregularly populated grids of seismic data with a simple iterative method that produces high-quality results. The original 2D image restoration method, the Gerchberg-Saxton algorithm, is extended easily to higher dimensions, and the 3D version of the process used here produces much better interpolations than typical 2D methods. The only parameter that makes a substantial difference in the results is the number of iterations used, and this number can be overestimated without degrading the quality of the results. This simplicity is a significant advantage because it relieves the user of extensive parameter testing. Although the cost of the algorithm is several times the cost of typical 2D methods, the method is easily parallelized and still completely practical.
Modelling and Solving QoS Composition Problem Using Fuzzy DisCSP (2006)

Web service compositions have attracted considerable efforts in the context of supporting enterprise application integrations. For a composite service, in addition to its functional requirements, QoS requirements are important and deserve a special attention. The central question to a QoS composition problem is how to compose a service from different subcomponent services so that its overall QoS can satisfy certain requirements. In this paper, we propose an agent-based method using fuzzy distributed constraint satisfaction problem (fuzzy DisCSP) techniques to solve this problem. We show that by using the composition structures, local constraints can be constructed and used with DisCSP. We also present an a new algorithm called the fuzzy constraint satisfaction algorithm for distributed environment (FADE) to solve the problem and discuss our experiment in building a prototypical system to prove the feasibility of our approach
大学的营利属性与营利行为：比较与借鉴 — 美国营利性高等教育的特征 (2005)

过去，教育与营利似乎是一对相斥的概念：教育属于公立机构，通过政府财政预算获得经费，而营利活动则属于企业行为。在新的经济和社会环境下，这种格局开始发生变化，一方面部分大学组织的性质发生了变化，营利性机构渐渐涉足过去公立机构的职能范围；另一方面公立大学不再完全依靠政府拔款，开始向学生收取学费，并且从事一些营利性的活动。《民办教育促进法》在制定过程中，也无法绕开教育与营利性这对矛盾。为了解决《教育法》对教育机构属性的规定与现实情况之间的矛盾，《民办教育促进法》对于教育机构的营利问题进行了模糊处理，“合理回报”就是妥协的结果。目前人们在“教育产业化”认识问题上依然存在着较大的分歧。在国外虽然没有“教育产业化”这样的提法，但遇到的问题却是相同或相似的，因此高等教育市场化、商品化、私有化等是学术界十分关心的问题。特别是营利性高等教育机构的出现和迅速发展，更引起人们的高度关注。为此，本刊特别组织了这次笔谈，邀请国内外研究者分别从各个角度发表自己的看法。
Efficiently evolving programs through the search for novelty (2010)

A significant challenge in genetic programming is premature convergence to local optima, which often prevents evolution from solving problems. This paper introduces to genetic programming a method that originated in neuroevolution (i.e. the evolution of artificial neural networks) that circumvents the problem of deceptive local optima. The main idea is to search only for behavioral novelty instead of for higher fitness values. Although such novelty search abandons following the gradient of the fitness function, if such gradients are deceptive they may actually occlude paths through the search space towards the objective. Because there are only so many ways to behave, the search for behavioral novelty is often computationally feasible and differs significantly from random search. Counterintuitively, in both a deceptive maze navigation task and the artificial ant benchmark task, genetic programming with novelty search, which ignores the objective, outperforms traditional genetic programming that directly searches for optimal behavior. Additionally, novelty search evolves smaller program trees in every variation of the test domains. Novelty search thus appears less susceptible to bloat, another significant problem in genetic programming. The conclusion is that novelty search is a viable new tool for efficiently solving some deceptive problems in genetic programming.