gebhart/patrepeval huggingface dataset:
Conotoxins: Targeted Peptide Ligands from Snail Venoms (1990)

Several hundred species of Conus snails produce a wide array of small (12-30 AA) and mostly tightly disulfide bonded peptide ligands with high affinity for a diverse set of receptor and ion channel types. These include nicotinic acetylcholine receptors, neuronal calcium channels, muscle sodium channels, vasopressin receptors, and N-methyl-D-aspartate (NMDA) receptors. Some general features of the structure, function, and evolution of biologically active peptides isolated from Conus venom are presented.
Total Synthesis of Ingenol (2004)

A total synthesis of the biologically important diterpene ingenol has been completed. Ring-closing olefin metathesis was used to construct the strained "inside-outside" tetracyclic skeleton, and a series of diastereoselective reactions were employed to complete the synthesis. Another naturally occurring ingenane, 20-deoxyingenol, has also been prepared.
Support vector machine active learning for image retrieval (2001)

Relevance feedback is often a critical component when designing image databases. With these databases it is difficult to specify queries directly and explicitly. Relevance feedback interactively determinines a user's desired output or query concept by asking the user whether certain proposed images are relevant or not. For a relevance feedback algorithm to be effective, it must grasp a user's query concept accurately and quickly, while also only asking the user to label a small number of images. We propose the use of a support vector machine active learning algorithm for conducting effective relevance feedback for image retrieval. The algorithm selects the most informative images to query a user and quickly learns a boundary that separates the images that satisfy the user's query concept from the rest of the dataset. Experimental results show that our algorithm achieves significantly higher search accuracy than traditional query refinement schemes after just three to four rounds of relevance feedback.
C-Type Starch from High-Amylose Rice Resistant Starch Granules Modified by Antisense RNA Inhibition of Starch Branching Enzyme (2010)

High-amylose starch is a source of resistant starch (RS) which has a great benefit on human health. A transgenic rice line (TRS) enriched amylose and RS had been developed by antisense RNA inhibition of starch branching enzymes. In this study, the native starch granules were isolated from TRS grains as well as the wild type, and their crystalline type was carefully investigated before and after acid hydrolysis. In high-amylose TRS rice, the C-type starch, which might result from the combination of both A-type and B-type starch, was observed and subsequently confirmed by multiple physical techniques, including X-ray powder diffraction, solid-state nuclear magnetic resonance, and Fourier transform infrared. Moreover, the change of starch crystalline structure from C- to B-type during acid hydrolysis was also observed in this RS-rich rice. These data could add to our understanding of not only the polymorph structure of cereal starch but also why high-amylose starch is more resistant to digestion.
Improving reverse time migration angle gathers by efficient wavefield separation (2017)

Angle-domain common-image gathers (ADCIGs) play an important role for migration quality control and velocity analysis. ADCIGs can be constructed by using optical flow to compute propagation directions of seismic waves, which originate and propagate from source and receiver locations. When upgoing and downgoing waves interfere with each other, the optical flow method can generate incorrect propagation angles and produce problematic ADCIGs. To overcome this problem, separating upgoing and downgoing waves is required. The challenge is that separating the wavefields often requires huge memory to store all the snapshots of the propagating 3D wavefields. We have developed a computationally efficient algorithm to separate the wavefields into upgoing and downgoing waves by storing only one additional snapshot of the wavefields at a single time step. Applying the optical flow method on the separated downgoing wavefield produces improved ADCIGs; the improvements are well-verified by tests on synthetic and field data sets.
Curcumin inhibits the mammalian target of rapamycin‐mediated signaling pathways in cancer cells (2006)

Curcumin (diferuloylmethane), a polyphenol natural product of the plant Curcuma longa, is undergoing early clinical trials as a novel anticancer agent. However, the anticancer mechanism of curcumin remains to be elucidated. Here we show that curcumin inhibited growth of rhabdomyosarcoma cells (Rh1 and Rh30) (IC50 = 2-5 microM) and arrested cells in G1 phase of the cell cycle. Curcumin also induced apoptosis and inhibited the basal or type I insulin-like growth factor-induced motility of the cells. At physiological concentrations (2.5 microM), curcumin rapidly inhibited phosphorylation of the mammalian target of rapamycin (mTOR) and its downstream effector molecules, p70 S6 kinase 1 (S6K1) and eukaryotic initiation factor 4E (eIF4E) binding protein 1 (4E-BP1), in a panel of cell lines (Rh1, Rh30, DU145, MCF-7 and Hela). Curcumin also inhibited phosphorylation of Akt in the cells, but only at high concentrations (>40 microM). The data suggest that curcumin may execute its anticancer activity primarily by blocking mTOR-mediated signaling pathways in the tumor cells.
Enteropathogenic and enterohaemorrhagic Escherichia coli deliver a novel effector called Cif, which blocks cell cycle G2/M transition (2003)

Enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC) are closely related pathogens. Both use a type III secretion system (TTSS) encoded by the 'locus of enterocyte effacement' (LEE) to subvert and attach to epithelial cells through the injection of a repertoire of effector molecules. Here, we report the identification of a new TTSS translocated effector molecule called Cif, which blocks cell cycle G2/M transition and induces the formation of stress fibres through the recruitment of focal adhesions. Cif is not encoded by the LEE but by a lambdoid prophage present in EPEC and EHEC. A cif mutant causes localized effacement of microvilli and intimately attaches to the host cell surface, but is defective in the ability to block mitosis. When expressed in TTSS competent LEE-positive pathogens, Cif is injected into the infected epithelial cells. These cells arrested at the G2/M phase displayed accumulation of inactive phosphorylated Cdk1. In conclusion, Cif is a new member of a growing family of bacterial cyclomodulins that subvert the host eukaryotic cell cycle.
A Comparative Study of the Performance of IR Models on Duplicate Bug Detection (2012)

Open source projects incorporate bug triagers to help with the task of bug report assignment to developers. One of the tasks of a triager is to identify whether an incoming bug report is a duplicate of a pre-existing report. In order to detect duplicate bug reports, a triager either relies on his memory and experience or on the search capabilities of the bug repository. Both these approaches can be time consuming for the triager and may also lead to the misidentification of duplicates. In the literature, several approaches to automate duplicate bug report detection have been proposed. However, there has not been an exhaustive comparison of the performance of different IR models, especially with topic-based ones such as LSI and LDA. In this paper, we compare the performance of the traditional vector space model (using different weighting schemes) with that of topic based models, leveraging heuristics that incorporate exception stack frames, surface features, summary and long description from the free-form text in the bug report. We perform experiments on subsets of bug reports from Eclipse and Firefox and achieve a recall rate of 60% and 58% respectively. We find that word-based models, in particular a Log-Entropy based weighting scheme, outperform topic based ones such as LSI, LDA and Random Projections. Our findings also suggests that for the problem of duplicate bug detection, it is important to consider a project's domain and characteristics to devise a set of heuristics to achieve optimal results.
Metabolic derepression of alpha-amylase gene expression in suspension-cultured cells of rice. (1991)

We present evidence to show that the alpha-amylase gene family in rice is under two different modes of regulation: 1) hormonal regulation in germinating seeds, and 2) metabolic repression in cultured cells by available carbohydrate nutrients. Expression of alpha-amylase genes in deembryoed rice seeds is known to be induced by exogenous gibberellic acid. On the other hand, expression of alpha-amylase genes in suspension-cultured cells is induced by the deprivation of carbohydrate nutrient. A lag period of 2-4 h is required for the induction of alpha-amylase mRNA in sucrose-depleted medium. The induction of alpha-amylase expression is extraordinarily high and levels of alpha-amylase mRNA can be increased 8-20-folds after 24 h of sucrose starvation. The synthesis and secretion of alpha-amylase is also dependent upon the level of carbon source. The derepression or repression of alpha-amylase synthesis can be readily reversed by the deprivation or replenishment of sucrose in the medium, respectively. Glucose and fructose exert a repression on the alpha-amylase synthesis similar to that of sucrose. A hypothesis that explains the induction of alpha-amylase synthesis by carbohydrate starvation is proposed. Our data have suggested a hitherto undiscovered, potentially important control mechanism of carbohydrate metabolism in higher plants.
The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide (2004)

All known vertebrate chromatin insulators interact with the highly conserved, multivalent 11-zinc finger nuclear factor CTCF to demarcate expression domains by blocking enhancer or silencer signals in a position-dependent manner. Recent observations document that the properties of CTCF include reading and propagating the epigenetic state of the differentially methylated H19 imprinting control region. To assess whether these findings may reflect a universal role for CTCF targets, we identified more than 200 new CTCF target sites by generating DNA microarrays of clones derived from chromatin-immunopurified (ChIP) DNA followed by ChIP-on-chip hybridization analysis. Target sites include not only known loci involved in multiple cellular functions, such as metabolism, neurogenesis, growth, apoptosis, and signalling, but potentially also heterochromatic sequences. Using a novel insulator trapping assay, we also show that the majority of these targets manifest insulator functions with a continuous distribution of stringency. As these targets are generally DNA methylation-free as determined by antibodies against 5-methylcytidine and a methyl-binding protein (MBD2), a CTCF-based network correlates with genome-wide epigenetic states.
Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides (2015)

Thousands of long non-coding RNAs (lncRNAs) have been identified in mammalian cells. Some have important functions and their dysregulation can contribute to a variety of disease states. However, most lncRNAs have not been functionally characterized. Complicating their study, lncRNAs have widely varying subcellular distributions: some reside predominantly in the nucleus, the cytoplasm or in both compartments. One method to query function is to suppress expression and examine the resulting phenotype. Methods to suppress expression of mRNAs include antisense oligonucleotides (ASOs) and RNA interference (RNAi). Antisense and RNAi-based gene-knockdown methods vary in efficacy between different cellular compartments. It is not known if this affects their ability to suppress lncRNAs. To address whether localization of the lncRNA influences susceptibility to degradation by either ASOs or RNAi, nuclear lncRNAs (MALAT1 and NEAT1), cytoplasmic lncRNAs (DANCR and OIP5-AS1) and dual-localized lncRNAs (TUG1, CasC7 and HOTAIR) were compared for knockdown efficiency. We found that nuclear lncRNAs were more effectively suppressed using ASOs, cytoplasmic lncRNAs were more effectively suppressed using RNAi and dual-localized lncRNAs were suppressed using both methods. A mixed-modality approach combining ASOs and RNAi reagents improved knockdown efficacy, particularly for those lncRNAs that localize to both nuclear and cytoplasmic compartments.
21.2: Full‐Functional System Liquid Crystal Display Using CG‐Silicon Technology (2004)

Abstract We developed a system panel where a CPU, a graphic controller, memories, and an audio circuit are monolithically formed on a glass substrate forming an LCD, by using CG‐Silicon technology. The logic circuit comprises approximately 120,000 TFTs. This is the world first full‐functional system panel on which all the circuits required for system operations are mounted except large capacity memories.
Deregulation of TDP-43 in amyotrophic lateral sclerosis triggers nuclear factor κB–mediated pathogenic pathways (2011)

TDP-43 (TAR DNA-binding protein 43) inclusions are a hallmark of amyotrophic lateral sclerosis (ALS). In this study, we report that TDP-43 and nuclear factor κB (NF-κB) p65 messenger RNA and protein expression is higher in spinal cords in ALS patients than healthy individuals. TDP-43 interacts with and colocalizes with p65 in glial and neuronal cells from ALS patients and mice expressing wild-type and mutant TDP-43 transgenes but not in cells from healthy individuals or nontransgenic mice. TDP-43 acted as a co-activator of p65, and glial cells expressing higher amounts of TDP-43 produced more proinflammatory cytokines and neurotoxic mediators after stimulation with lipopolysaccharide or reactive oxygen species. TDP-43 overexpression in neurons also increased their vulnerability to toxic mediators. Treatment of TDP-43 mice with Withaferin A, an inhibitor of NF-κB activity, reduced denervation in the neuromuscular junction and ALS disease symptoms. We propose that TDP-43 deregulation contributes to ALS pathogenesis in part by enhancing NF-κB activation and that NF-κB may constitute a therapeutic target for the disease.
Nerve growth factor, mast cells and arthritis (1995)

Nerve growth factor is a well-characterized neurotrophic protein required for the survival and differentiation of a variety of neuronal cell types both in the peripheral and central nervous systems. Recent studies indicate that nerve growth factor also plays a role in cells originating in the immune system, since it is synthesized by cells of immune system lineage and its level increases during inflammatory responses. Moreover, it has been shown that cytokines such as interleukin 1β and tumor necrosis factor-α are potent inducers of nerve growth factor secretion. These studies were recently confirmed and extended by demonstrating that cells normally present in inflammatory tissues, such as mast cells and lymphocytes, express nerve growth factor receptors and are receptive to the action of nerve growth factor. The aim of the present review is to outline the current understanding of mast cells and nerve growth factor in autoimmune diseases and particularly in arthritis. Biomedical Reviews 1995; 4: 7-14.
Risk of Cervical Cancer Associated with Extending the Interval between Cervical-Cancer Screenings (2003)

As compared with annual screening for three years, screening performed once three years after the last negative test in women 30 to 64 years of age who have had three or more consecutive negative Papanicolaou tests is associated with an average excess risk of cervical cancer of approximately 3 in 100,000.
Parthenolide reduces the frequency of ABCB5-positive cells and clonogenic capacity of melanoma cells from anchorage independent melanospheres (2013)

Growing evidence suggests that the cancer stem cell phenotype in melanoma is dynamically regulated. Therefore, effective therapies have to target simultaneously bulk tumor cells and melanoma stem-like cells. The aim of the present study was to investigate the effects of parthenolide on heterogeneous cancer cell populations from anchorage-independent melanospheres. Cells derived from nodular melanoma specimens were grown under serum-free sphere-forming conditions. The effects of parthenolide on cellular viability, immunophenotype and self-renewing capacity were assessed with cells from dissociated melanospheres. Its penetration capacity was evaluated with intact melanospheres. In melanoma cells that survived treatment with parthenolide, a different immunophenotype than that in untreated control was found. The frequency of cells expressing the ABCB5 transporter was markedly reduced. Most importantly, melanoma cells that survived parthenolide treatment lost their self-renewing capacity. Significantly lower influence of drug on cellular viability and frequency of ABCB5-positive cells was observed in intact melanospheres. The potential clinical significance of our findings is based on the ability of parthenolide to affect both bulk and melanoma stem-like cells with clonogenic capacity and high expression of the ABCB5 transporter. Its low penetration capacity, however, may limit its action to easily accessible melanoma cells, either circulating in the blood or those in the vicinity to blood vessels within the tumor. Because of limited penetration capacity of parthenolide, this drug should be further explored as a part of multimodal therapies rather than as a stand-alone therapeutic agent.
Inhibitors of protein kinase C. 1. 2,3-bisarylmaleimides (1992)

The design and synthesis of a series of novel inhibitors of protein kinase C (PKC) is described. These 2,3-bisarylmaleimides were derived from the structural lead provided by the indolocarbazoles, staurosporine and K252a. Optimum activity required the imide NH, both carbonyl groups, and the olefinic bond of the maleimide ring. 2,3-Bisindolylmaleimides were the most active, and the potency of these was improved by a chloro substituent at the 5-position of one indole ring (compound 28, IC50 0.11 microM). In a series of (phenylindolyl)maleimides, nitro compound 74 was most active (IC50 0.67 microM). Naphthalene 19 and benzothiophene 21 showed greater than 100-fold selectivity for inhibition of PKC over the closely related cAMP-dependent protein kinase (PKA).
Effective antiplatelet therapy does not prolong transgenic pig to baboon cardiac xenograft survival (2004)

Inhibition of platelet aggregation by a combination of aspirin and clopidogrel did not have a significant impact on the length of xenograft survival or on the development of microvascular thrombosis in this pig-to-primate model.
APPLYING AGENT TECHNOLOGY (1995)

Click to increase image sizeClick to decrease image size Additional informationNotes on contributorsNICHOLAS R. JENNINGSAddress correspondence to Nicholas R. Jennings. Department of Electronic Engineering, Queen Mary and Westfield College. Mile End Road, London El 4NS. United Kingdom. E-mail: N.R.Jennings@qmw.ac.uk.
Pulse Radiolysis Studies on the Fragmentation of Arylmethyl Quaternary Nitrogen Mustards by One-Electron Reduction in Aqueous Solution (1997)

The radical species formed on the reaction of eaq- with a series of aryl compounds, all containing a N,N-bis(2-chloroethyl)-N-methylammoniomethyl substituent, have been studied in neutral aqueous solutions by pulse radiolysis using optical absorption spectrophotometry. The benzene, 1, and 4-methylsulfonylbenzene, 2, derivatives fragmented immediately to yield different amounts of benzyl radicals, but the 2-nitrobenzene, 3, and 4-nitrobenzene, 4, derivatives were reduced to long-lived radical anions which decayed by bimolecular processes. These nitrobenzene derivatives differed from the corresponding benzyl halides in that they did not fragment to benzyl radicals. Similarly, no evidence was found for the formation of a benzyl-type radical from the radical anion of the 8-nitronaphthalene derivative, 5. However, benzyl-type radicals were produced upon intramolecular electron transfer from the initially formed radical anions of the 4-nitro-5-imidazole, 6, and the 5-nitro-2-pyrrole, 7, derivatives at rate constants of (8.0 ± 1.0) × 103 and (1.0 ± 0.1) × 104 s-1, respectively. The latter heterocyclic analogues provide an approach for release of cytotoxic tertiary amines via enzymatic or radiolytic reduction in hypoxic regions of tumors.
Porous Polypropylene Membranes with Different Carboxyl Polymer Brush Layers for Reversible Protein Binding via Surface-Initiated Graft Copolymerization (2005)

Photoinitiated surface-selective graft copolymerization onto polypropylene (PP) microfiltration membranes was performed using two different methods for coating the photoinitiator, benzophenone (BP), on the membrane surface. An already established adsorption method and a novel method based on preswelling of the PP in heptane, subsequent solvent exchange, and thus entrapping of the BP in the surface layer of the PP had been evaluated. With acrylic acid (AA) as the monomer, functional polymer brush structures on the entire membrane pore surface were obtained. Further variations of the grafted layer had been achieved by copolymerization of AA with acryl amide (AAm) and methylene bisacrylamide (MBAA). Characterization had been done mainly by detailed measurements of membrane permeability including pH dependency as well as the reversible binding of a protein (lysozyme, Lys) under membrane chromatography conditions. Compared with BP adsorption, the BP entrapping method yielded a less dense grafted layer with longer PAA chains at the same degree of functionalization (DG). This was due to somewhat lower immobilized BP amounts, but also less side reactions via nonselective photoinitiated cross-linking by dissolved BP. Unexpected properties of the PAA-co-AAm brush layers were their even larger swelling/deswelling as a function of a pH change (above and below the pKa of PAA) as compared with the PAA brushes. Both PAA-co-AAm and cross-linked PAA-co-MBAA layers showed Lys binding capacitiesmore than 10 times higher than monolayer adsorption onto the unmodified PP membrane surfaceand quantitative recoveries similar to PAA of the same DG; and the highest efficiencies of protein binding (Lys amount relative to amount graft copolymer) were achieved with the membranes prepared by the entrapping method. In general, the more controlled BP entrapping method had distinct advantages in terms of the control of grafted layer structure leading to an improved membrane adsorber performance.