gebhart/patrepeval huggingface dataset:
Automated Work Zone Information System on Urban Freeway Rehabilitation: California Implementation (2006)

In October 2004, about 9 lane km of deteriorated truck lanes on Interstate 15 at Devore in Southern California was rebuilt during 18 days with extended one roadbed full-closures with the counterflow traffic system and 24-h construction operations. The project implemented the automated work zone information system (AWIS) to reduce peak hour delay during construction by changing road user's travel patterns and diverting traffic to detour routes. This paper describes the design, performance, and validation of AWIS with monitored traffic data before and during construction used. The AWIS was installed to provide road users with real-time travel information so that they could avoid traffic delays in the construction work zone (CWZ) corridor. Travel times through the CWZ were estimated from speed data and enhanced in two ways: (a) portable and permanent changeable message signs on site and (b) off-site (project website) implementation with travel time messages, traffic snapshots, and video streaming. AWIS travel time was estimated at 90% of actual travel times as measured by probe vehicles. The peak hour traffic demand through the CWZ was reduced by up to 18%, with significant volume increases to detour freeways. The AWIS operation contributed to a decrease in the maximum delay for weekday peak hours (from expected 90 min to measured 50 min on average during construction). The outcome of this study will help transportation agencies and practitioners efficiently design and operate AWIS for highway rehabilitation under high traffic volume.
Evaluation of niobium effects on the longitudinal piezoelectric coefficients of Pb(Zr, Ti)O3 thin films (2000)

Pb(Zr, Ti)O 3 (PZT) and Pb(Zr, Ti, Nb)O3 (PNZT) thin films have been deposited on platinized silicon substrates by sputtering followed by a postannealing treatment. The Nb concentration in the films varied between 1 and 7 at. % with increments of 1 at. %. The effects of Nb modification on the piezoelectric response, and particularly on the longitudinal piezoelectric coefficient d33, have been investigated. The introduction of Nb enhances the dielectric and piezoelectric properties of the PZT films. The best doping level ranges from 1 up to 2 at. %. The relative dielectric constant εr, reaches 1100, and the maximum value of d33 is equal to 115 pm/V for a 1 at. % Nb-doped PZT in comparison to 820 and 55 pm/V for an undoped PZT film. PNZT films are suitable for microsystem applications.
The Metabolic Fate of Purified Glucoraphanin in F344 Rats (2007)

Dietary broccoli is commonly eaten cooked, exposing individuals to intact glucoraphanin rather than to its hydrolysis product, the anticarcinogenic isothiocyanate sulforaphane, since cooking destroys the hydrolyzing enzyme myrosinase. There is little information on the absorption and metabolism of glucoraphanin, due partly to the lack of purified compound. In this study, glucoraphanin was purified from broccoli seed and 150 mumol/kg was administered to male F344 rats. Glucoraphanin (5% of an oral dose) was recovered intact in urine, showing that it is absorbed intact, and no glucoraphanin or metabolites were found in feces. Total urinary products accounted for 20 and 45% of oral and intraperitonneal doses, respectively, including sulforaphane N-acetyl cysteine conjugate (12.5 and 2%), free sulforaphane (0.65 and 0.77%), sulforaphane nitrile (2 and 1.4%), and erucin (0.1 and 0.1%), respectively. Both glucoraphanin and its reduced form glucoerucin were identified in bile following intravenous glucoraphanin administration. We conclude that orally administered glucoraphanin is absorbed intact, undergoes enterohepatic circulation, and is hydrolyzed in the gut in F344 rats.
Neural Architecture Search with Reinforcement Learning (2016)

Neural networks are powerful and flexible models that work well for many difficult learning tasks in image, speech and natural language understanding. Despite their success, neural networks are still hard to design. In this paper, we use a recurrent network to generate the model descriptions of neural networks and train this RNN with reinforcement learning to maximize the expected accuracy of the generated architectures on a validation set. On the CIFAR-10 dataset, our method, starting from scratch, can design a novel network architecture that rivals the best human-invented architecture in terms of test set accuracy. Our CIFAR-10 model achieves a test error rate of 3.65, which is 0.09 percent better and 1.05x faster than the previous state-of-the-art model that used a similar architectural scheme. On the Penn Treebank dataset, our model can compose a novel recurrent cell that outperforms the widely-used LSTM cell, and other state-of-the-art baselines. Our cell achieves a test set perplexity of 62.4 on the Penn Treebank, which is 3.6 perplexity better than the previous state-of-the-art model. The cell can also be transferred to the character language modeling task on PTB and achieves a state-of-the-art perplexity of 1.214.
An evaluation of dynamic adaptive streaming over HTTP in vehicular environments (2012)

MPEGs' Dynamic Adaptive Streaming over HTTP (MPEG-DASH) is an emerging standard designed for media delivery over the top of existing infrastructures and able to handle varying bandwidth conditions during a streaming session. This requirement is very important, specifically within mobile environments and, thus, DASH could potentially become a major driver for mobile multimedia streaming. Hence, this paper provides a detailed evaluation of our implementation of MPEG DASH compared to the most popular propriety systems, i.e., Microsoft Smooth Steaming, Adobe HTTP Dynamic Streaming, and Apple HTTP Live Streaming. In particular, these systems will be evaluated under restricted conditions which are due to vehicular mobility. In anticipation of the results, our prototype implementation of MPEG-DASH can very well compete with state-of-the-art solutions and, thus, can be regarded as a mature standard ready for industry adaption.
Chemical Approaches to Molecular Logic Elements for Addition and Subtraction (2007)

Molecular and supramolecular logic gates are candidates for computation at the nanoscale level. Nowadays all common logic operations can be mimicked with molecular devices based on chemical approaches. One step further towards molecular systems with increased logic capabilities is the addition or subtraction of binary digits. This Minireview describes recent developments to attain this goal, including bioinspired systems based on DNA and enzymes. Furthermore, chemical molecular logic gates are discussed and compared critically with regard to alternative concepts.
[Silicone oil tamponade as a risk factor of complications]. (2013)

Morphological study was performed in enucleated eyes with chronic uveitis and phthisis bulbi in patients after vitrectomy with silicone oil tamponade. Silicone oil as a foreign substance was showed to aggravate chronic inflammation that results in intraocular sclerotic processes.
Compact Error-Resilient Computational DNA Tiling Assemblies (2007)

The self-assembly process for bottom-up construction of nanostructures is of key importance to the emerging of the new scientific discipline of Nanoscience. For example, the self-assembly of DNA tile nanostructures into 2D and 3D lattices can be used to perform parallel universal computation and to manufacture patterned nanostructures from smaller unit components known as DNA tiles. However, self-assemblies at the molecular scale are prone to a quite high rate of error, and the key barrier to large-scale experimental implementation of DNA tiling is the high error rate in the self-assembly process. One major challenge to nanostructure self-assembly is to eliminate/limit these errors. The goals of this paper are to develop theoretical methods for compact error-resilient self-assembly, to analyze these by stochastic analysis and computer simulation (at a future date we also intend to demonstrate these error-resilient self-assembly methods by a series of laboratory experiments). Prior work by Winfree provided a innovative approach to decrease tiling self-assembly errors without decreasing the intrinsic error rate # of assembling a single tile, however, his technique resulted in a final structure that is four times the size of the original one. This paper describes various compact error-resilient tiling methods that do not increase the size of the tiling assembly. These methods apply to assembly of boolean arrays which perform input sensitive computations (among other computations). We first describe an error-resilient tiling using 2-way overlay redundancy such that a single pad mismatch between a tile and its immediate neighbor forces at least one further pad mismatch between a pair of adjacent tiles in the neighborhood of this tile. This drops the error rate from # to appr...
Trichloroethylene and chloroform degradation by a recombinant pseudomonad expressing soluble methane monooxygenase from Methylosinus trichosporium OB3b (1994)

Soluble methane monooxygenase (sMMO) from Methylosinus trichosporium OB3b can degrade many halogenated aliphatic compounds that are found in contaminated soil and groundwater. This enzyme oxidizes the most frequently detected pollutant, trichloroethylene (TCE), at least 50 times faster than other enzymes. However, slow growth of the strain, strong competition between TCE and methane for sMMO, and repression of the smmo locus by low concentrations of copper ions limit the use of this bacterium. To overcome these obstacles, the 5.5-kb smmo locus of M. trichosporium OB3b was cloned into a wide-host-range vector (to form pSMMO20), and this plasmid was electroporated into five Pseudomonas strains. The best TCE degradation results were obtained with Pseudomonas putida F1/pSMMO20. The plasmid was maintained stably, and all five of the sMMO proteins (alpha, beta, and gamma hydroxylase proteins, reductase, and component B) were observed clearly by both sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western immunoblotting. TCE degradation rates were quantified for P. putida F1/pSMMO20 with a gas chromatograph (Vmax = 5 nmol per min per mg of protein), and the recombinant strain mineralized 55% of the TCE (10 microM) as indicated by measuring chloride ion concentrations with a chloride ion-specific electrode. The maximum TCE degradation rate obtained with the recombinant strain was lower than that of M. trichosporium OB3b but greater than other TCE-degrading recombinants and most well-studied pseudomonads. In addition, this recombinant strain mineralizes chloroform (a specific substrate for sMMO), grows much faster than M. trichosporium OB3b, and degrades TCE without competitive inhibition from the growth substrate.
Zinc Induces Apoptosis That Can Be Suppressed by Lanthanum in C6 Rat Glioma Cells (2001)

Zinc ions have both essential and toxic effects on mammalian cells. Here we report the ability of zinc to act as an inducer of apoptosis in C6 rat glioma cells. Incubation with 150 to 300 microM ZnCl2 caused cell death that was characterized as apoptotic by internucleosomal DNA fragmentation, formation of apoptotic bodies, nuclear fragmentation and breakdown of the mitochondrial membrane potential. On the other hand, zinc deprivation by the membrane permeable chelator TPEN [N,N,N',N',-tetrakis (2-pyridyl-methyl)-ethylenediamine] also induced programmed death in this cell line, indicating the existence of intracellular zinc levels below and above which apoptosis is induced. Zinc-induced apoptosis in C6 cells was independent of major signaling pathways (protein kinase C, mitogen activated protein kinase and guanylate cyclase) and protein synthesis, but was increased by facilitating zinc uptake with the ionophore pyrithione. Lanthanum(III)chloride was also able to increase the net zinc uptake, but nevertheless apoptotic features and zinc toxicity were reduced. Remarkably, lanthanum suppressed the zinc-induced breakdown of the mitochondrial membrane potential. We conclude that in C6 cells lanthanum acts in two different ways, as a promoter of net zinc uptake and as a suppressor of zinc-induced apoptosis.
Capacity Bounds and Power Allocation for Wireless Relay Channels (2005)

We consider three-node wireless relay channels in a Rayleigh-fading environment. Assuming transmitter channel state information (CSI), we study upper bounds and lower bounds on the outage capacity and the ergodic capacity. Our studies take into account practical constraints on the transmission/reception duplexing at the relay node and on the synchronization between the source node and the relay node. We also explore power allocation. Compared to the direct transmission and traditional multihop protocols, our results reveal that optimum relay channel signaling can significantly outperform multihop protocols, and that power allocation has a significant impact on the performance.
TGF‐β1 inhibits DNA synthesis and phosphorylation of the retinoblastoma gene product in a rat liver epithelial cell line (1992)

In the rat liver epithelial cell line, WB, the ability of TGF-beta 1 to inhibit DNA synthesis was shown to correlate with its ability to inhibit phosphorylation of the protein product of the retinoblastoma susceptibility gene, pRb. When WB cells were serum-starved, then refed with serum-containing medium, a peak of DNA synthesis occurred at about 18 h. Autoradiographs showed that 43.6% of cell nuclei could be labeled with 3H-thymidine at this time. When TGF-beta 1 was added simultaneously with serum, it blocked DNA synthesis and reduced the number of labeled nucleii to 6.3%. Cells treated with serum alone for 18 h also showed a pronounced increase in the highly phosphorylated form of pRb, as shown by mobility shifts in immunoblots, and in active phosphorylation of pRb, as shown by 32P incorporation. Simultaneous addition of TGF-beta 1 with serum abolished both 32P incorporation into pRb and its mobility shift on immunoblots. The effect of TGF-beta 1 on DNA synthesis measured at 18 h was sharply reduced if the cells were incubated with serum for 8 h (and thus allowed to enter S) before the addition of TGF-beta 1. If TGF-beta 1 was added after 8 h of serum treatment, its ability to inhibit pRb phosphorylation at 18 h was unchanged. If TGF-beta 1 was added after 13 h of serum treatment, its effects on pRb phosphorylation were reduced. Thus, as the cell population moved into S, the ability of TGF-beta 1 to inhibit both pRb phosphorylation and DNA synthesis was lost. In higher passages of WB cells the dose-response for inhibition of DNA synthesis by TGF-beta 1 was shifted to the right. Inhibition of pRb phosphorylation by TGF-beta 1 was also lost in higher passage WB cells. Thus, the passage-dependent loss of sensitivity to inhibition of DNA synthesis accompanied the loss of sensitivity to inhibition of pRb phosphorylation. Since the phosphorylation of pRb is believed to be required for the progression of cells from G1 to S, inhibition of pRb phosphorylation may be either a cause or a consequence of the G1 arrest of WB cells by TGF-beta 1.
A B72.3 Second-Generation-Monoclonal Antibody (CC49) Defines the Mucin-Carried Carbohydrate Epitope Galβ(1—3) [NeuAcα(2—6)]GalNAc (1989)

Mucus glycoproteins from bovine seminal plasma were demonstrated to express the MAbs CC49- and B72.3-defined epitopes on TAG 72 antigen. Inhibition studies with reductively cleaved mucin O-glycans from bovine seminal plasma and submaxillary glands revealed that CC49 binds specifically to a core-type sialyl-oligosaccharide alditol (fraction 2c), which could be defined with regard to its primary structure by FAB- and EI-mass spectrometry combined with methylation analysis: (formula; see text) Structurally related alditols NeuAc alpha(2-6)-GalNAc-ol, Gal beta(1-3)GalNAc-ol, NeuAc alpha(2-3)-Gal beta(1-3) [NeuAc alpha(2-6)] GalNAc-ol, GlcNAc beta(1-3) [NeuAc alpha(2-6)] GalNAc-ol or NeuAc alpha(2-3) Gal beta(1-3)GalNAc-ol were not inhibitory.
Platelet APP, ADAM 10 and BACE alterations in the early stages of Alzheimer disease (2004)

Amyloid precursor protein (APP), ADAM 10, and beta-site-APP cleaving enzyme (BACE) alterations were evaluated in platelets of 31 patients with Alzheimer disease (AD) and 15 age-matched controls. A significant modification of these proteins and enzymes involved in the amyloid cascade was detected from the earliest clinically detectable disease stage. This observation suggests that AD is associated with an early metabolic derangement toward amyloidogenic pathways and supports the potential value of APP and secretase measurements for early diagnosis of AD.
The Role of Tandem Acyl Carrier Protein Domains in Polyunsaturated Fatty Acid Biosynthesis (2008)

Acyl carrier protein (ACP) plays an essential role in fatty acid and polyketide biosynthesis, and most of the fatty acid synthases (FASs) and polyketide synthases (PKSs) known to date are characterized with a single ACP for each cycle of chain elongation. Polyunsaturated fatty acid (PUFA) biosynthesis is catalyzed by the PUFA synthase, and all PUFA synthases known to date contain tandem ACPs (ranging from 5 to 9). Using the Pfa PUFA synthase from Shewanella japonica as a model system, we report here that these tandem ACPs are functionally equivalent regardless of their physical location within the PUFA synthase subunit, but the total number of ACPs controls the overall PUFA titer. These findings set the stage to interrogate other domains and subunits of PUFA synthase for their roles in controlling the final PUFA products and could potentially be exploited to improve PUFA production.
Identification of Mycobacterium leprae antigens from a cosmid library: characterization of a 15-kilodalton antigen that is recognized by both the humoral and cellular immune systems in leprosy patients (1991)

Screening of the Mycobacterium leprae cosmid library with pooled sera from lepromatous leprosy (LL) patients by a colony immunoblot technique resulted in the identification of about 100 colonies that produced immunologically reactive proteins. Twenty-four of these clones were purified, analyzed, and found to comprise two groups according to the reactivity of the recombinant proteins with LL sera and to the DNA restriction patterns of the recombinant plasmids and cosmids. Proteins specified by clones from group I reacted strongly with LL patients' sera on a Western blot (immunoblot), demonstrating a 15-kDa protein band designated A15. The A15 antigen also reacted with pooled sera from patients with tuberculoid leprosy from the United States and Brazil. Clones from group II did not show any reactive protein band on a Western blot, when reacted with patients' sera. DNAs from cosmids of group II all contain a 10-kb PstI fragment that hybridized to the unique repetitive M. leprae DNA. Sequence analysis of a 1.2-kb fragment containing the entire coding sequence of A15 revealed three open reading frames (ORFs), only one of which (ORF II) contains sufficient genetic information to encode for A15. Part of the A15 gene was found to exist also in a group of lambda gt11:M. leprae clones previously isolated in our laboratory by immunological screening with LL patients' sera. One of the lambda gt11 clones (L8) expresses a beta-galactosidase fusion protein with 89 amino acids from the C terminus of A15. An important result was that the fusion protein was clearly recognized by T cells from leprosy patients. Interestingly, Mycobacterium tuberculosis-stimulated T cells from M. leprae nonresponder (LL as well as borderline tuberculoid) patients were able to respond to the isolated recombinant M. leprae antigen, indicating that nonresponsiveness to M. leprae antigens can be reversible. The sequence of the M. leprae DNA fused to the beta-galactosidase gene of lambda gt11 clone L8 was identical to that of a lambda gt11:M. leprae clone isolated recently that expresses an immunologically reactive fusion protein (S. Laal, Y. D. Sharma, H. K. Prasad, A. Murtaza, S. Singh, S. Tangri, R. Misra, and I. Nath, Proc. Natl. Acad. Sci. USA 88:1054-1058, 1991). Besides the complete sequence of the A15 gene, sequencing data of two flanking ORFs are presented. Downstream from ORF II (A15), ORF III has a high degree of similarity to the genes for tomato ATP-dependent proteases that are members of a larger class of highly conserved proteases ubiquitous among prokaryotes and eukaryotes.(ABSTRACT TRUNCATED AT 400 WORDS)
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data (2012)

Supplementary data are available at Bioinformatics online.
The Mouse <i>(Mus musculus)</i> Immunoglobulin Kappa Variable (IGKV) Genes and Joining (IGKJ) Segments (1998)

The 'Mouse (Mus musculus) Immunoglobulin Kappa Variable (IGKV) Genes and Joining (IGKJ) Segments', third report of the 'IMGT Locus on Focus' section, comprises four tables entitled: (1) 'Mouse (Mus musculus) germline IGKV gene table'; (2) 'Correspondence between Mouse (Mus musculus) IMGT IGKV subgroups and previous designations'; (3) 'Mouse (Mus musculus) germline IGKJ table', and (4) 'Mouse (Mus musculus) IGKJ allele table'. These tables are available at the IMGT Marie-Paule page from IMGT, the international ImMunoGeneTics database (http://imgt.cnusc.fr:8104) created by Marie-Paule Lefranc, CNRS, Université Montpellier II, Montpellier, France.
Glycaemic responses and hypocholesterolaemic effects of high-amylose barley diets on broiler chicks (1998)

The glucose and lipid responses of barley diets were investigated with chicks based on either flour or red dog (RD) from each of three barley cultivars, Glacier, covered high-amylose Glacier (HAG) and hull-less high-amylose Glacier (HHAG), with two maize control diets. Mean time interval blood glucose levels were higher (P<0·05) for chicks fed uncooked barley flour or RD, compared with controls. Total and LDL plasma cholesterol were lower (P<0·05) for chicks fed the HAG and HHAG flour and all barley RD diets. HDL cholesterol values for chicks fed Glacier and HHAG flour and HHAG RD diets were higher than controls. The LDL/HDL cholesterol ratios for chicks fed HAG and HHAG flour and all barley RD diets were lower (P<0·05) than controls. Lower body weights were observed in all chickens fed barley diets. The results suggest that the soluble fibre, mainly β-glucan and starch structures, in barley may be responsible for the hypocholesterolaemic effect. © 1998 SCI.
A Unique Autophosphorylation Site on Tie2/Tek Mediates Dok-R Phosphotyrosine Binding Domain Binding and Function (2003)

Tie2/Tek is an endothelial cell receptor tyrosine kinase that induces signal transduction pathways involved in cell migration upon angiopoietin-1 (Ang1) stimulation. To address the importance of the various tyrosine residues of Tie2 in signal transduction, we generated a series of Tie2 mutants and examined their signaling properties. Using this approach in conjunction with a phosphorylation state-specific antibody, we identified tyrosine residue 1106 on Tie2 as an Ang1-dependent autophosphorylation site that mediates binding and phosphorylation of the downstream-of-kinase-related (Dok-R) docking protein. This tyrosine residue is contained within a unique interaction motif for the phosphotyrosine binding domain of Dok-R, and the pleckstrin homology domain of Dok-R further contributes to Tie2 binding in a phosphatidylinositol 3'-kinase-dependent manner. Introduction of a Tie2 mutant lacking tyrosine residue 1106 into endothelial cells interferes with Dok-R phosphorylation in response to Ang1. Furthermore, this mutant is unable to restore the migration potential of endothelial cells derived from mice lacking Tie2. Together, these findings demonstrate that tyrosine residue 1106 on Tie2 is critical for coupling downstream cell migration signal transduction pathways with Ang1 stimulation in endothelial cells.