gebhart/patrepeval huggingface dataset:
Statistical timing analysis using bounds and selective enumeration (2003)

The growing impact of within-die process variation has created the need for statistical timing analysis, where gate delays are modeled as random variables. Statistical timing analysis has traditionally suffered from exponential run time complexity with circuit size, due to arrival time dependencies created by reconverging paths in the circuit. In this paper, we propose a new approach to statistical timing analysis which uses statistical bounds and selective enumeration to refine these bounds. First, we provide a formal definition of the statistical delay of a circuit and derive a statistical timing analysis method from this definition. Since this method for finding the exact statistical delay has exponential run time complexity with circuit size, we also propose a new method for computing statistical bounds which has linear run time complexity. We prove the correctness of the proposed bounds. Since we provide both a lower and upper bound on the true statistical delay, we can determine the quality of the bounds. If the computed bounds are not sufficiently close to each other, we propose a heuristic to iteratively improve the bounds using selective enumeration of the sample space with additional run time. The proposed methods were implemented and tested on benchmark circuits. The results demonstrate that the proposed bounds have only a small error, which can be further reduced using selective enumeration with modest additional run time.
MRP3, BCRP, and P-Glycoprotein Activities are Prognostic Factors in Adult Acute Myeloid Leukemia (2005)

BCRP and MRP3 may also be involved in chemoresistance in AML, especially MRP3 in patients with M5 FAB. Additional modulation of BCRP or MRP3 to Pgp modulation may be necessary in some patients in order to improve the treatment outcome.
Naturally Occurring Clavines: Antagonism/Partial Agonism at 5-HT<sub>2A</sub>Receptors and Antagonism at α<sub>1</sub>-Adrenoceptors in Blood Vessels (1996)

The interaction of eight typical representatives of naturally occurring clavines (agroclavine, costaclavine, dihydrolysergol-l, elymoclavine, festuclavine, lysergene, lysergol, and pyroclavine) with 5-HT2A receptors and alpha 1-adrenoceptors was studied in rat tail artery and aorta, respectively. Clavines antagonized 5-HT-induced contractions with calculated pKB values (pKP values for partial agonists) of 4.84-7.81 and (R)-phenylephrine-induced contractions with calculated pKB values of 5.34-7.09. Specificity of clavines at 5-HT2A receptors relative to alpha 1-adrenoceptors was rather low. Low affinity for costaclavine at both 5-HT2A receptors (pKP = 4.84 +/- 0.06) and alpha 1-adrenoceptors (pKB = 5.34 +/- 0.05) indicates that the trans-junction of ring C and D of the ergoline pharmacophore is crucial for the binding of ergolines to these sites. Lysergol, lysergene, and costaclavine produced non-parallel displacements of the 5-HT concentration-response curve in the rat tail artery and caused small contractions by themselves. Lysergol contracted the rat tail artery with a pEC50 of 6.36 +/- 0.04 and an intrinsic activity of 0.18 +/- 0.03 with respect to 5-HT. Lysergol-induced contractile responses were surmountably antagonized by ketanserin (10 nM) with a pKB of 9.1 which is consistent with an interaction of lysergol with 5-HT2A receptors. The pKP for the lysergol-5-HT2A receptor complex calculated from concentration-response curves to lysergol was 6.88 +/- 0.07 and did not match the pKP of 7.66 +/- 0.02 calculated from antagonism by lysergol of the contractile response to 5-HT. This suggests that lysergol and 5-HT possibly bind in two slightly different orientations at the 5-HT2A receptor. It is concluded that partial agonism and pure antagonism at 5-HT2A receptors on the one side and antagonism at alpha 1-adrenoceptors on the other side may contribute to the noxious effects of naturally occurring clavines.
A scale-independent signal processing method for sequence analysis (1990)

In this paper, we present methods to detect and localize patterns in biologically related protein sequences (family). The patterns common to the sequences of the family are detected by using Fourier analysis. No previous scales (codes) are needed, they are actually produced as a result of the analysis procedure, together with the frequencies of the Fourier decompositions. Characteristic features of the family are thus expressed as (code-frequency) pairs. Various tools are proposed in order to localize the patterns, to compare the codes, and to evaluate the proximity of an arbitrary sequence to the investigated family. The general strategy is illustrated on a family composed of calcium-binding proteins.
Chameleon: a system for solving the data-translation problem (1989)

A comprehensive data translation system is described with the following characteristics: (1) it is derived from a formal model of the translation task; (2) it supports the building of translation tools; (3) it supports the use of translation tools; and (4) it is accessible to its targeted end users. A software architecture to achieve the translation capability is fully implemented. Translators have been generated using the architecture, both by the original software developers and by industrial associates who have installed the architecture at their own sites.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Nanomolar-Potency Small Molecule Inhibitor of Regulator of G-Protein Signaling Proteins (2011)

Regulators of G-protein signaling (RGS) proteins are potent negative modulators of signal transduction through G-protein-coupled receptors. They function by binding to activated (GTP-bound) Gα subunits and accelerating the rate of GTP hydrolysis. Modulation of RGS activity by small molecules is an attractive mechanism for fine-tuning GPCR signaling for therapeutic and research purposes. Here we describe the pharmacologic properties and mechanism of action of CCG-50014, the most potent small molecule RGS inhibitor to date. It has an IC(50) for RGS4 of 30 nM and is >20-fold selective for RGS4 over other RGS proteins. CCG-50014 binds covalently to the RGS, forming an adduct on two cysteine residues located in an allosteric regulatory site. It is not a general cysteine alkylator as it does not inhibit activity of the cysteine protease papain at concentrations >3000-fold higher than those required to inhibit RGS4 function. It is also >1000-fold more potent as an RGS4 inhibitor than are the cysteine alkylators N-ethylmaleimide and iodoacetamide. Analysis of the cysteine reactivity of the compound shows that compound binding to Cys(107) in RGS8 inhibits Gα binding in a manner that can be reversed by cleavage of the compound-RGS disulfide bond. If the compound reacts with Cys(160) in RGS8, the adduct induces RGS denaturation, and activity cannot be restored by removal of the compound. The high potency and good selectivity of CCG-50014 make it a useful tool for studying the functional roles of RGS4.
Robustness of IFDMA as Air Interface Candidate for Future High Rate Mobile Radio Systems (2005)

Abstract. The Interleaved Frequency Division Multiple Access (IFDMA) scheme is a candidate for next generation mobile radio systems. IFDMA is based on compression, repetition and subsequent user dependent frequency shift of a modulated signal. As in OFDMA, multiple access is enabled by the assignment of overlapping but mutually orthogonal subcarriers to each user. It provides various advantages such as low peak to average power ratio, orthogonality of the signals of different users even for transmission over a time dispersive channel and low complexity. However, IFDMA is sensitive to frequency offsets. In this paper, a derivation of IFDMA based on a generalised OFDMA signal model with specific precoding and specific subcarrier allocation is presented. Moreover, simulation results showing the robustness properties of IFDMA against frequency errors are given.
Mikrobiologische Assimilation von anorganischem Stickstoff in der Rhizosphäre (2001)

The objective of the investigation was to study the relationship between EUF (Electro Ultra Filtration) extractable N, EUF extractable carbon and interlayer NH4 + on net N mineralization and N uptake of ryegrass (Lolium multiflorum cv. ‘Aubade’) cultivated in Mitscherlich pots on 20 different arable soils. Grass of the first harvest (first cut) exclusively fed from nitrate and N uptake of the first cut was significantly correlated with the EUF extracted nitrate in the soil at seeding (r = 0,96***). In average from this nitrate about half was taken up by the grass and half was assimilated (immobilized) by soil microorganisms. This immobilized N was correlated with the organic C extracted by EUF at seeding (r = 0,50*). The grass of the second and third harvest exclusively drew N from the organic soil N pool and N uptake of grass was correlated with EUF Norg (r = 0,66**, second cut and r = 0,55*, third cut). Interlayer ammonium significantly decreased during the growth period, but this decrease was not correlated with the N uptake of the grass. The experiment shows that the N sources for grass differed during the experimental period with high nitrate concentrations at the beginning of the growth period causing N immobilization and later plants feeding from organic N. From the results it is concluded that the microbial assimilation (immobilization) of inorganic N depends on the presence of inorganic N, mainly nitrate, and on the supply of microbes with metabolizable organic carbon predominantly provided by plant roots. Therefore it is suggested that the nitrate immobilization mainly occurs in the rhizosphere.
Expression and Clinical Role of Protein of Regenerating Liver (PRL) Phosphatases in Ovarian Carcinoma (2011)

The present study analyzed the expression and clinical role of the protein of regenerating liver (PRL) phosphatase family in ovarian carcinoma. PRL1-3 mRNA expression was studied in 184 tumors (100 effusions, 57 primary carcinomas, 27 solid metastases) using RT-PCR. PRL-3 protein expression was analyzed in 157 tumors by Western blotting. PRL-1 mRNA levels were significantly higher in effusions compared to solid tumors (p < 0.001), and both PRL-1 and PRL-2 were overexpressed in pleural compared to peritoneal effusions (p = 0.001). PRL-3 protein expression was significantly higher in primary diagnosis pre-chemotherapy compared to post-chemotherapy disease recurrence effusions (p = 0.003). PRL-1 mRNA expression in effusions correlated with longer overall survival (p = 0.032), and higher levels of both PRL-1 and PRL-2 mRNA correlated with longer overall survival for patients with pre-chemotherapy effusions (p = 0.022 and p = 0.02, respectively). Analysis of the effect of laminin on PRL-3 expression in ovarian carcinoma cells in vitro showed dose-dependent PRL-3 expression in response to exogenous laminin, mediated by Phospholipase D. In contrast to previous studies associating PRL-3 with poor outcome, our data show that PRL-3 expression has no clinical role in ovarian carcinoma, whereas PRL-1 and PRL-2 expression is associated with longer survival, suggesting that PRL phosphatases may be markers of improved outcome in this cancer.
Broadband fiber-laser-pumped CW OPO for red, green, blue laser generation (2009)

We report a cw-RGB laser based on a broadband Yb-fiber-laser pumped OPO with intra- and extra-cavity wavelength converters. At 25-W pump power, the laser generated 5, 0.5, and 0.01-W at 633, 532, and 450-nm, respectively.
The Yng1p Plant Homeodomain Finger Is a Methyl-Histone Binding Module That Recognizes Lysine 4-Methylated Histone H3 (2006)

The ING (inhibitor of growth) protein family includes a group of homologous nuclear proteins that share a highly conserved plant homeodomain (PHD) finger domain at their carboxyl termini. Members of this family are found in multiprotein complexes that posttranslationally modify histones, suggesting that these proteins serve a general role in permitting various enzymatic activities to interact with nucleosomes. There are three members of the ING family in Saccharomyces cerevisiae: Yng1p, Yng2p, and Pho23p. Yng1p is a component of the NuA3 histone acetyltransferase complex and is required for the interaction of NuA3 with chromatin. To gain insight into the function of the ING proteins, we made use of a genetic strategy to identify genes required for the binding of Yng1p to histones. Using the toxicity of YNG1 overexpression as a tool, we showed that Yng1p interacts with the amino-terminal tail of histone H3 and that this interaction can be disrupted by loss of lysine 4 methylation within this tail. Additionally, we mapped the region of Yng1p required for overexpression of toxicity to the PHD finger, showed that this region capable of binding lysine 4-methylated histone H3 in vitro, and demonstrated that mutations of the PHD finger that abolish binding in vitro are no longer toxic in vivo. These results identify a novel function for the Yng1p PHD finger in promoting stabilization of the NuA3 complex at chromatin through recognition of histone H3 lysine 4 methylation.
An application of real-time IPC controller based ATM cell (2002)

A high performance IPC (Inter-Processor Communication) controller for the multiprocessors of an ATM switching system is proposed in this paper. This IPC controller accommodates the ATM cell assembly and reassembly functions and allows high-speed interprocessor data transfer via ATM switch. The IPC controller structure consists of the segmentation part and the reassembly part for processing AAL type 5. The IPC protocol is implemented sliding window method. The real message ratio and the LPC controller performance is computed according to user packet size. The real message ratio is increased as the user packet size increases because of header overhead. And the maximum real message ratio is about 0.8 in maximum user packet size 496 bytes. The throughput is optimal at packet size 80.
The development of a tunable, single-frequency ultraviolet laser source for UV Filtered Rayleigh Scattering (1994)

We present the development of a flexible, high power, narrow line width, tunable ultraviolet source for diagnostic application. By frequency tripling the output of a pulsed titanium-sapphire laser, we achieve broadly tunable (227-360 nm) ultraviolet light with high quality spatial and spectral resolution. We also present the characterization of a mercury vapor cell which provides a narrow band, sharp edge absorption filter at 253.7 nm. These two components form the basis for the extension of the Filtered Rayleigh Scattering technique into the ultraviolet. The UV-FRS system is comprised of four pieces: a single frequency, cw tunable Ti:Sapphire seeding source; a high-powered pulsed Ti:Sapphire oscillator; a third harmonic generator system; and an atomic mercury vapor filter. In this paper we discuss the development and characterization of each of these elements.
Enhanced Tumor-Specific Disulfiram Chemotherapy by <i>In Situ</i> Cu<sup>2+</sup> Chelation-Initiated Nontoxicity-to-Toxicity Transition (2019)

The antitumor activity of disulfiram (DSF), a traditional US Food and Drug Administration-approved drug for the treatment of "alcohol-dependence", is Cu<sup>2+</sup>-dependent, but the intrinsic anfractuous biodistribution of copper in the human body and copper toxicity induced by exogenous copper supply have severely hindered its <i>in vivo</i> application. Herein, we report an <i>in situ</i> Cu<sup>2+</sup> chelation-enhanced DSF-based cancer chemotherapy technique, using a tumor-specific "nontoxicity-to-toxicity" transition strategy based on hollow mesoporous silica nanoparticles as the functional carrier. Cu<sup>2+</sup>-doped, DSF-loaded hollow mesoporous silica nanoparticles were constructed for the rapid release of Cu<sup>2+</sup> ions induced by the mild acidic conditions of the tumor microenvironment. This resulted in the rapid biodegradation of the nanoparticles and accelerated DSF release once the particles were endocytosed into tumor cells. The resulting <i>in situ</i> chelation reaction between the coreleased Cu<sup>2+</sup> ions and DSF generated toxic CuET products and concurrently, Fenton-like reactions between the generated Cu<sup>+</sup> ions and the high levels of H<sub>2</sub>O<sub>2</sub> resulted in the production of reactive oxygen species (ROS) in the acidic tumor microenvironment. Both <i>in vitro</i> cellular assays and <i>in vivo</i> tumor-xenograft experiments demonstrated the efficient Cu-enhanced and tumor-specific chemotherapeutic efficacy of DSF, with cocontributions from highly toxic CuET complexes and ROS generated within tumors. This work provides a conceptual advancement of nanoparticle-enabled "nontoxicity-to-toxicity" transformation in tumors, to achieving high chemotherapeutic efficacy and biosafety.
Monocyte Migration Driven by Galectin-3 Occurs through Distinct Mechanisms Involving Selective Interactions with the Extracellular Matrix (2013)

Monocyte migration into tissues, an important event in inflammation, requires an intricate interplay between determinants on cell surfaces and extracellular matrix (ECM). Galectin-3 is able to modulate cell-ECM interactions and is an important mediator of inflammation. In this study, we sought to investigate whether interactions established between galectin-3 and ECM glycoproteins are involved in monocyte migration, given that the mechanisms by which monocytes move across the endothelium and through the extravascular tissue are poorly understood. Using the in vitro transwell system, we demonstrated that monocyte migration was potentiated in the presence of galectin-3 plus laminin or fibronectin, but not vitronectin, and was dependent on the carbohydrate recognition domain of the lectin. Only galectin-3-fibronectin combinations potentiated the migration of monocyte-derived macrophages. In binding assays, galectin-3 did not bind to fibronectin, whereas both the full-length and the truncated forms of the lectin, which retains carbohydrate binding ability, were able to bind to laminin. Our results show that monocytes migrate through distinct mechanisms and selective interactions with the extracellular matrix driven by galectin-3. We suggest that the lectin may bridge monocytes to laminin and may also activate these cells, resulting in the positive regulation of other adhesion molecules and cell adhesion to fibronectin.
Differentiation of Salmonella enterica based on PCR detection of selected somatic and flagellar antigens (2010)

serogroups C2 (n = 35, 28.7%), B (n = 33, 27.1%), D9 (n = 29, 22.9%), E (n = 21, 17.2%), C1 (n = 2, 64%) and A (n = 2, 1.64%). Eight of the Salmonella strains from serogroup D were positive for Vi antigen. Two multiplex PCRs were optimized for detection of H1 antigens (Ha, Hb, Hd, r, z10, z6, g and m) and H2 antigens (1.5, 1.2, 1.6 and enx). Overall, the multiplex PCRs of O, H and Vi antigens results correctly serotyped 94 of 122 strains (77%). The most frequent serovars encountered were Salmonella weltevrerden, Salmonella enteritidis, Salmonella typhimurium, Salmonella hadar and Salmonella typhi. Application of DNA based technique for serogrouping and serotyping of the selected Salmonella enterica was found to be robust, quick, specific and reliable for the specific antigenic targets and is useful in the study area which lack complete serotyping facilities.
Influence of Cell Type, Initial Concentration, and Medium on the Inactivation Efficiency of Low-Temperature Plasma (2011)

It is now well known that low-temperature plasmas can inactivate bacteria effectively. At low doses, these plasmas can also help in the proliferation of healthy fibroblasts and detach damaged cells without causing necrosis. The combination of these characteristics leads to the possibility of using plasmas in biomedical applications such as wound healing. Although only limited understanding is available as to the mechanisms whereby plasmas interact with cells (prokaryotic or eukaryotic), it is now well established that the effects of plasmas on biological cells depend on the cell type, the cell concentration, and the medium supporting them. In this paper, we present clear visual evidence of these dependencies in the case of bacteria. Through simple imaging, we show that the size and shape of the inactivation zone depend on the type of bacteria, their initial concentrations, and the medium supporting the cells.
Multitemporal remote sensing of landscape dynamics and pattern change: describing natural and anthropogenic trends (2008)

Science and reporting information needs for monitoring dynamics in land cover over time have prompted research, and made operational, a wide variety of change detection methods utilizing multiple dates of remotely sensed data. Change detection procedures based upon spectral values are common; however, landscape pattern analysis approaches which utilize spatial information inherent within imagery present opportunities for the generation of unique and ecologically important information. While the use of two images may provide the means to identify change, the use of more than two images for long-term monitoring affords the ability to identify a greater range of processes of landscape change, including rates and dynamics. The main objective of this review is to investigate and summarize the methods and applications of land cover spatial pattern analysis using three or more image dates. The potential and the limitations of landscape pattern indices are identified and discussed to inform application recommendations. The second objective of this review is to make recommendations, including appropriate landscape pattern indices, for the application of landscape pattern analysis of a long time series of remotely sensed data to a case study involving the mountain pine beetle in British Columbia, Canada. The review concludes with recommendations for future research.
Microorganisms Resistant to Free-Living Amoebae (2004)

Free-living amoebae feed on bacteria, fungi, and algae. However, some microorganisms have evolved to become resistant to these protists. These amoeba-resistant microorganisms include established pathogens, such as Cryptococcus neoformans, Legionella spp., Chlamydophila pneumoniae, Mycobacterium avium, Listeria monocytogenes, Pseudomonas aeruginosa, and Francisella tularensis, and emerging pathogens, such as Bosea spp., Simkania negevensis, Parachlamydia acanthamoebae, and Legionella-like amoebal pathogens. Some of these amoeba-resistant bacteria (ARB) are lytic for their amoebal host, while others are considered endosymbionts, since a stable host-parasite ratio is maintained. Free-living amoebae represent an important reservoir of ARB and may, while encysted, protect the internalized bacteria from chlorine and other biocides. Free-living amoebae may act as a Trojan horse, bringing hidden ARB within the human "Troy," and may produce vesicles filled with ARB, increasing their transmission potential. Free-living amoebae may also play a role in the selection of virulence traits and in adaptation to survival in macrophages. Thus, intra-amoebal growth was found to enhance virulence, and similar mechanisms seem to be implicated in the survival of ARB in response to both amoebae and macrophages. Moreover, free-living amoebae represent a useful tool for the culture of some intracellular bacteria and new bacterial species that might be potential emerging pathogens.