gebhart/patrepeval huggingface dataset:
Resensitization of Akt Induced Docetaxel Resistance in Breast Cancer by ‘Iturin A’ a Lipopeptide Molecule from Marine Bacteria Bacillus megaterium (2017)

Development of the resistance is the major problem in cancer therapy. Docetaxel is a taxol alkaloid that is frequently used in metastatic breast cancer. However, resistance often limits the usefulness of this drug in many breast cancer patients. Manipulation of resistant cells to re-sensitize to the therapeutic effect of docetaxel is current strategy to overcome this problem. Here, we have introduced 'Iturin A' as a potent chemosensitizer in docetaxel resistant breast cancer cells. Combination of Iturin A and docetaxel treatment significantly hampered the proliferation of docetaxel resistant MDA-MB-231 and MDA-MB-468 breast cancer cells. Cell cycle analysis also showed massive amount of apoptotic population (Sub G0/G1) in combination therapy. A number of apoptotic and anti-apoptotic proteins were significantly altered in dual drug treated groups. Caspase 3 dependent cell death was observed in dual treatment. Molecular mechanism study showed that over-expression of Akt and its downstream signaling pathway was associated with docetaxel resistance. Iturin A significantly reduced Akt signaling pathway in resistant cells. This mechanistic action might be the reason behind the chemo-sensitization effect of Iturin A in docetaxel resistant breast cancer cells. In conclusion, Iturin A resensitized the resistant breast cancer cells to docetaxel therapy by inhibiting Akt activity.
Next-generation bis-locked nucleic acids with stacking linker and 2′-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes (2016)

Targeting and invading double-stranded DNA with synthetic oligonucleotides under physiological conditions remain a challenge. Bis-locked nucleic acids (bisLNAs) are clamp-forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson-Crick binding. To improve the bisLNA design, we investigated its mechanism of binding. Our results suggest that bisLNAs bind via Hoogsteen-arm first, followed by Watson-Crick arm invasion, initiated at the tail. Based on this proposed hybridization mechanism, we designed next-generation bisLNAs with a novel linker able to stack to adjacent nucleobases, a new strategy previously not applied for any type of clamp-constructs. Although the Hoogsteen-arm limits the invasion, upon incorporation of the stacking linker, bisLNA invasion is significantly more efficient than for non-clamp, or nucleotide-linker containing LNA-constructs. Further improvements were obtained by substituting LNA with 2'-glycylamino-LNA, contributing a positive charge. For regular bisLNAs a 14-nt tail significantly enhances invasion. However, when two stacking linkers were incorporated, tail-less bisLNAs were able to efficiently invade. Finally, successful targeting of plasmids inside bacteria clearly demonstrates that strand invasion can take place in a biologically relevant context.
High-Throughput In-Memory Computing for Binary Deep Neural Networks With Monolithically Integrated RRAM and 90-nm CMOS (2020)

Deep neural network (DNN) hardware designs have been bottlenecked by conventional memories, such as SRAM due to density, leakage, and parallel computing challenges. Resistive devices can address the density and volatility issues but have been limited by peripheral circuit integration. In this work, we present a resistive RAM (RRAM)-based in-memory computing (IMC) design, which is fabricated in 90-nm CMOS with monolithic integration of RRAM devices. We integrated a 128 × 64 RRAM array with CMOS peripheral circuits, including row/column decoders and flash analog-to-digital converters (ADCs), which collectively become a core component for scalable RRAM-based IMC for large DNNs. To maximize IMC parallelism, we assert all 128 wordlines of the RRAM array simultaneously, perform analog computing along the bitlines, and digitize the bitline voltages using ADCs. The resistance distribution of low-resistance states is tightened by an iterative write-verify scheme. Prototype chip measurements demonstrate high binary DNN accuracy of 98.5% for MNIST and 83.5% for CIFAR-10 data sets, with 24 TOPS/W and 158 GOPS. This represents 22.3× and 10.1× improvements in throughput and energy-delay product (EDP), respectively, compared with the state-of-the-art literature, which can enable intelligent functionalities for area-/energy-constrained edge computing devices.
Selective dehydrogenation/oxygenation of 3-methylindole by cytochrome p450 enzymes. (2001)

3-Methylindole (3 MI) is a selective pulmonary toxicant, and cytochrome P450 (P450) bioactivation of 3 MI, through hydroxylation, epoxidation, or dehydrogenation pathways, is a prerequisite for toxicity. CYP2F1 and CYP2F3 exclusively catalyze the dehydrogenation of 3 MI to 3-methyleneindolenine, without detectable formation of the hydroxylation or epoxidation products. It was not known whether 3 MI is simply an excellent dehydrogenation substrate for all P450 enzymes, or whether certain cytochrome P450s responsible for 3 MI bioactivation have unique active sites that only catalyze the dehydrogenation of the molecule, while other P450s would catalyze only the oxygenation of 3 MI. Therefore, the kinetics of product formation by the CYP2F1 and CYP2F3 enzymes were compared with other cytochrome P450 enzymes. The enzymes tested were CYP1A1, CYP1A2, CYP1B1, and CYP2E1. The CYP1A1 and CYP1A2 enzymes produced all three 3 MI metabolites: the dehydrogenation product, 3-methyleneindolenine (V(max)/K(m) = 4 and 22, respectively); the hydroxylation product, indole-3-carbinol (V(max)/K(m) = 42 and 100, respectively); and the epoxidation product, 3-methyloxindole (V(max)/K(m) = 4 and 72, respectively). These CYP1A enzymes catalyzed oxygenation of 3 MI at much faster rates than dehydrogenation. CYP1B1 produced indole-3-carbinol (V(max)/K(m) = 85) and 3-methyloxindole (V(max)/K(m) = 7), and CYP2E1 only produced 3-methyloxindole (V(max)/K(m) = 98), but neither enzyme catalyzed the formation of the dehydrogenated product. Six additional P450 enzymes that were tested formed none of the dehydrogenation product. The ability of the various CYP1 family enzymes to catalyze the formation of all three major 3 MI metabolites, along with the specific oxygenation by CYP2E1, illustrates that dehydrogenation of 3 MI is not a substrate-directed process, but that the members of the CYP2F family possess unique active sites that specifically catalyze only the dehydrogenation mechanism.
Web services discovery based on schema matching (2007)

A web service is programmatically available application logic exposed over Internet. With the rapid development of e-commerce over Internet, web services have attracted much attention in recent years. Nowadays, enterprises are able to outsource their internal business processes as services and make them accessible via the Web. Then they can dynamically combine individual services to provide new value-added services. A main problem that remains is how to discover desired web services. In this paper, we propose a novel web services discovery strategy given a textual description of services. In particularly, we propose a new schema matching algorithm for supporting web-service operations matching. The matching algorithm catches not only structures, but also semantic information of schemas. We also propose a ranking strategy to satisfy a user’s top-k requirements. Experimental evaluation shows that our approach can achieve high precision and recall ratio.
Prolonged Expression of c-fos Suppresses Cell Cycle Entry of Dormant Hematopoietic Stem Cells (1999)

The proto-oncogene c-fos was transiently upregulated in primitive hematopoietic stem (Lin−Sca-1+) cells stimulated with stem cell factor, interleukin-3 (IL-3), and IL-6. To investigate a role of the c-fos in hematopoietic stem cells, we used bone marrow (BM) cells from transgenic mice carrying the c-fos gene under the control of the interferon-/β–inducible Mx-promoter (Mx–c-fos), and fetal liver cells from c-fos–deficient mice. Prolonged expression of the c-fos in Lin−Sca-1+ BM cells inhibited factor-dependent colony formation and hematopoiesis on a stromal cell layer by keeping them at G0/G1 phase of the cell cycle. These Lin−Sca-1+ BM cells on a stromal layer entered into the cell cycle whenever exogenous c-fos was downregulated. However, ectopic c-fos did not perturb colony formation by Lin−Sca-1+ BM cells after they entered the cell cycle. Furthermore, endogenous c-fos is not essential to cell cycle progression of hematopoietic stem cells because the factor-dependent and the stroma-dependent hematopoiesis by Lin−Sca-1+ fetal liver cells from c-fos–deficient mice was not impaired. These results suggest that the c-fos induced in primitive hematopoietic stem cells negatively controls cell cycle progression and maintains them in a dormant state.
Prognostic value of regulatory T cells and T helper 17 cells in high grade serous ovarian carcinoma (2022)

Our results outline a positive prognostic effect for higher Tregs but not for Th17 in high grade serous tubo-ovarian carcinoma.
The New Naturalism of <i>Le Bestiaire d'Amour</i> (1988)

Preview this article: The New Naturalism of Le Bestiaire d'Amour, Page 1 of 1 < Previous page | Next page > /docserver/preview/fulltext/rein.1.04bee-1.gif
Chloroplast lipid synthesis and lipid trafficking through ER–plastid membrane contact sites (2012)

Plant chloroplasts contain an intricate photosynthetic membrane system, the thylakoids, and are surrounded by two envelope membranes at which thylakoid lipids are assembled. The glycoglycerolipids mono- and digalactosyldiacylglycerol, and sulfoquinovosyldiacylglycerol as well as phosphatidylglycerol, are present in thylakoid membranes, giving them a unique composition. Fatty acids are synthesized in the chloroplast and are either directly assembled into thylakoid lipids at the envelope membranes or exported to the ER (endoplasmic reticulum) for extraplastidic lipid assembly. A fraction of lipid precursors is reimported into the chloroplast for the synthesis of thylakoid lipids. Thus polar lipid assembly in plants requires tight co-ordination between the chloroplast and the ER and necessitates inter-organelle lipid trafficking. In the present paper, we discuss the current knowledge of the export of fatty acids from the chloroplast and the import of chloroplast lipid precursors assembled at the ER. Direct membrane contact sites between the ER and the chloroplast outer envelopes are discussed as possible conduits for lipid transfer.
Detecting Offensive Language in Tweets Using Deep Learning (2018)

This paper addresses the important problem of discerning hateful content in social media. We propose a detection scheme that is an ensemble of Recurrent Neural Network (RNN) classifiers, and it incorporates various features associated with user-related information, such as the users' tendency towards racism or sexism. These data are fed as input to the above classifiers along with the word frequency vectors derived from the textual content. Our approach has been evaluated on a publicly available corpus of 16k tweets, and the results demonstrate its effectiveness in comparison to existing state of the art solutions. More specifically, our scheme can successfully distinguish racism and sexism messages from normal text, and achieve higher classification quality than current state-of-the-art algorithms.
Polarization analysis of the eye movement correlogram (2004)

The eye movement correlogram is obtained by reverse correlation of eye velocity with the velocity of a randomly moving target. It resembles an impulse response, typically peaking at a latency between 100 and 200 milliseconds. The target can move randomly in two dimensions, and the analysis may be performed independently on the horizontal and vertical components. Striking differences are seen in the correlograms obtained in these two directions, which might arise in motor pathways, sensory pathways, or both. More detail can be gleaned about these differences from a “polarization” analysis. Instead of performing the analysis simply on the nominal horizontal and vertical axes, individual correlograms are computed for a densely sampled array of stimulus and measurement directions. The resulting set of signals is well-described by a linear superposition of two mechanisms having different time courses, and the geometric relation between the mechanisms can be estimated. We have used this method to probe how the visual system analyzes the motion of different types of stimuli by comparing the responses obtained while tracking a small spot to those obtained while tracking gratings and two-component plaids. The results for plaids cannot be simply described as the superposition of the responses to the component gratings, reflecting the fact that voluntary pursuit is controlled by the output of a high-level “pattern motion” stage. However, different responses are obtained for different plaids, reflecting biases in the computation of pattern motion. The Airspace Operations Systems (AOS) project of NASA's Airspace Systems program; R01-EY12986.
Atlas-based motion correction for on-line mr temperature mapping (2005)

Magnetic resonance (MR) temperature mapping can be used to monitor temperature changes in minimally invasive thermal therapies during the procedure. However, organs displacements due to physiological activity (heart and respiration) may induce important artifacts on apparent temperature maps. This paper presents a new method for motion quantification and correction in such MR images, in order to improve the precision of temperature estimation using the proton resonance frequency (PRF) shift. The PRF shift technique gives an estimate of the relative temperature variation, comparing contrast between dynamically acquired images and a reference data sets. The correction method described in this paper consists of two steps: a motion atlas is initially computed in a preparation phase; during the intervention, the appropriate reference image is chosen from the atlas, allowing correct computation of the temperature map despite tissue motion. This method can be applied to any type of image sequences and is not restricted to MR images.
A selection system for functional internal ribosome entry site (IRES) elements: Analysis of the requirement for a conserved GNRA tetraloop in the encephalomyocarditis virus IRES (1999)

Picornavirus internal ribosome entry site (IRES) elements direct cap-independent internal initiation of protein synthesis within mammalian cells. These RNA elements (about 450 nt) contain extensive secondary structure including a hairpin loop with a conserved GNRA motif. Such loops are important in RNA-RNA and RNA-protein interactions. Plasmids that express dicistronic mRNAs of the structure GUS/IRES/HOOK have been constructed. The HOOK sequence encodes a cell-surface-targeted protein (sFv); the translation of this open reading frame within mammalian cells from these dicistronic mRNAs requires a functional IRES element. Cells that express the sFv can be selected from nonexpressing cells. A pool of up to 256 mutant encephalomyocarditis virus IRES elements was generated by converting the wild-type hairpin loop sequence (GCGA) to NNNN. Following transfection of this pool of mutants into COS-7 cells, plasmids were recovered from selected sFv-expressing cells. These DNAs were amplified in Escherichia coli and transfected again into COS-7 cells for further cycles to enrich for plasmids encoding functional IRES elements. The sequence of individual selected IRES elements was determined. All functional IRES elements had a tetraloop with a 3' terminal A residue. Optimal IRES activity, assayed in vitro and within cells, was obtained from plasmids encoding an IRES with the hairpin loop sequence fitting a RNRA consensus. In contrast, IRES elements containing YCYA tetraloops were severely defective.
Volumetric <i>B</i><sub>1</sub><sup>+</sup> Mapping of the Brain at 7T using DREAM (2013)

DREAM enables safe, very fast, and robust volumetric B1 (+) mapping of the brain at ultrahigh fields.
Multi-Oriented Scene Text Detection via Corner Localization and Region Segmentation (2018)

Previous deep learning based state-of-the-art scene text detection methods can be roughly classified into two categories. The first category treats scene text as a type of general objects and follows general object detection paradigm to localize scene text by regressing the text box locations, but troubled by the arbitrary-orientation and large aspect ratios of scene text. The second one segments text regions directly, but mostly needs complex post processing. In this paper, we present a method that combines the ideas of the two types of methods while avoiding their shortcomings. We propose to detect scene text by localizing corner points of text bounding boxes and segmenting text regions in relative positions. In inference stage, candidate boxes are generated by sampling and grouping corner points, which are further scored by segmentation maps and suppressed by NMS. Compared with previous methods, our method can handle long oriented text naturally and doesn't need complex post processing. The experiments on ICDAR2013, ICDAR2015, MSRA-TD500, MLT and COCO-Text demonstrate that the proposed algorithm achieves better or comparable results in both accuracy and efficiency. Based on VGG16, it achieves an F-measure of 84.3% on ICDAR2015 and 81.5% on MSRA-TD500.
Synthesis and complexation characteristics of phenanthroline and bipyridine diols (2004)

Neocuproine (2,9-dimethyl-1,10-phenanthroline) 1 was converted to achiral and chiral tetradentate phenanthroline diols 3a-c by addition to benzophenone, adamantanone and camphor, respectively. Analogously 6,6'-dimethyl-2,2'-bipyridine 2 was converted to diol 7a on baseinduced addition to benzophenone. Reactions with benzophenone and adamantanone proceeded smoothly although small amounts of mono adducts were also formed. Functionalization of 1 with (R)-camphor failed under the standard conditions. However, conversion of the lithio derivative 5 to the cerium chloride derivative 6 and subsequent reaction with (R)-camphor led to the phenanthroline diol 3c. Complexes of the diols 3 and 7 with zinc and copper were prepared. Xray analysis of the zinc complex 20 of diol 7a revealed a five coordinate zinc ion that is firmly embedded in the ligand. X-ray analysis of the Cu(acac) 2 complex 21 of diol 7a unexpectedly revealed this to be an acetate bridged di-copper species. This copper complex forms on recrystallization from ethyl acetate. The initial acac-complex apparently hydrolyses the ethyl acetate to provide the bridging acetate found in the di-copper complex 21. From 4,7-dichloro-2,9-dimethyl-1,10-phenanthroline 13 a "doubly armed" derivative 18 was prepared by substitution with two tetraethylene glycol "arms" followed by suitable derivatisation. A bridged derivative 19 was prepared by ring closure with an amine of the ditosylated tetraethylene glycol derivative. Attempts to prepare copper complexes of 18 and 19 were inconclusive.
Cloudberry: An HTML5 Cloud Phone Platform for Mobile Devices (2012)

The Cloudberry project has built a novel HTML5-based cloud phone—a mobile device in which all the device's user functionality is downloaded and cached dynamically from the Web, including all the applications and even the entire top-level user interface. One of the most central benefits of a cloud phone is that nearly any of its customer-facing features can be changed on millions of devices all over the world almost instantly. This will shorten application and service deployment and update life cycles significantly. From the user's perspective, the key benefit is multiple device ownership: the ability to access the same applications and data effortlessly from different devices without tedious installation, data copying, or synchronization hassles.
Implementing Sorting Networks with Spiking Neural P Systems (2008)

Spiking neural P systems simulate the behavior of neurons sending signals through axons. Recently, some applications concerning Boolean circuits and sorting algorithms have been proposed. In this paper, we study the ability of such systems to simulate a well known parallel sorting model, sorting networks. First, we construct spiking neural P systems which act as comparators of two values, and then show how to assemble these building blocks according to the topology of a sorting network of N values. In the second part of the paper, we formalize a framework to transform any sorting network into a network composed of comparators which sort n values, 2 < n < N, having the same behaviour as the original sorting network, but using fewer neurons and synapses than the direct simulation. A comparison between the two models proposed here and the sorting model of Ionescu and Sburlan is also given.
Pectin Methylesterification Impacts the Relationship Between Photosynthesis and Plant Growth in Arabidopsis thaliana (2016)

Photosynthesis occurs in mesophyll cells of specialized organs such as leaves. The rigid cell wall encapsulating photosynthetic cells controls the expansion and distribution of cells within photosynthetic tissues. The relationship between photosynthesis and plant growth is affected by leaf area. However, the underlying genetic mechanisms affecting carbon partitioning to different aspects of leaf growth are not known. To fill this gap, we analyzed Arabidopsis plants with altered levels of pectin methylesterification, which is known to modulate cell wall plasticity and plant growth. Pectin methylesterification levels were varied through manipulation of cotton Golgi-related (CGR) 2 or 3 genes encoding two functionally redundant pectin methyltransferases. Increased levels of methylesterification in a line over-expressing CGR2 (CGR2OX) resulted in highly expanded leaves with enhanced intercellular air spaces; reduced methylesterification in a mutant lacking both CGR-genes 2 and 3 (cgr2/3) resulted in thin but dense leaf mesophyll that limited CO2 diffusion to chloroplasts. Leaf, root, and plant dry weight were enhanced in CGR2OX but decreased in cgr2/3. Differences in growth between wild type and the CGR-mutants can be explained by carbon partitioning but not by variations in area-based photosynthesis. Therefore, photosynthesis drives growth through alterations in carbon partitioning to new leaf area growth and leaf mass per unit leaf area; however, CGR-mediated pectin methylesterification acts as a primary factor in this relationship through modulation of the expansion and positioning of the cells in leaves, which in turn drive carbon partitioning by generating dynamic carbon demands in leaf area growth and leaf mass per unit leaf area.
Energy and Reserve Co-optimization of a Combined Cycle Plant Using Mixed Integer Linear Programming (2014)

The growth in the importance of interruptible sources of energy is increasing the concerns of many electricity market regulators with respect to the reliability and stability of electricity supply. Decisions such as that to increase the number of reserve markets, their reserve requirements, or the role of reserve prices in the final electricity price have meant that generation plants are currently often operating with strategies to obtain not only large energy market quotes but also reserve ones. In this paper, a mixed integer linear programming (MILP) model is proposed to obtain the energy and reserve dispatch of a real combined cycle plant (CCP) to optimize its use on a weekly or annual basis. The dispatch is optimal in the sense that it maximizes the joint energy and reserve profits, including an estimation of the energy and reserve prices. The detailed technical and economic characteristics of the plant have been considered, such as start-ups, shut-downs, minimum hours for steam generation, supplementary firing, or natural gas contracts. The cases studies validate the main features of the mathematical model and analyze the computational efficiency in a realistic simulation.