gebhart/patrepeval huggingface dataset:
An FPGA-specific approach to floating-point accumulation and sum-of-products (2008)

This article studies two common situations where the flexibility of FPGAs allows one to design application-specific floating-point operators which are more efficient and more accurate than those offered by processors and GPUs. First, for applications involving the addition of a large number of floating-point values, an ad-hoc accumulator is proposed. By tailoring its parameters to the numerical requirements of the application, it can be made arbitrarily accurate, at an area cost comparable to that of a standard floating-point adder, and at a higher frequency. The second example is the sum-of-product operation, which is the building block of matrix computations. A novel architecture is proposed that feeds the previous accumulator out of a floating-point multiplier whose rounding logic has been removed, again improving the area/accuracy tradeoff. These architectures are implemented within the FloPoCo generator, freely available under the LGPL.
Blockade of Protein Geranylgeranylation Inhibits Cdk2-Dependent p27<sup>Kip1</sup> Phosphorylation on Thr187 and Accumulates p27<sup>Kip1</sup> in the Nucleus: Implications for Breast Cancer Therapy (2009)

We describe the design of a potent and selective peptidomimetic inhibitor of geranylgeranyltransferase I (GGTI), GGTI-2418, and its methyl ester GGTI-2417, which increases the levels of the cyclin-dependent kinase (Cdk) inhibitor p27(Kip1) and induces breast tumor regression in vivo. Experiments with p27(Kip1) small interfering RNA in breast cancer cells and p27(Kip1) null murine embryonic fibroblasts demonstrate that the ability of GGTI-2417 to induce cell death requires p27(Kip1). GGTI-2417 inhibits the Cdk2-mediated phosphorylation of p27(Kip1) at Thr187 and accumulates p27(Kip1) in the nucleus. In nude mouse xenografts, GGTI-2418 suppresses the growth of human breast tumors. Furthermore, in ErbB2 transgenic mice, GGTI-2418 increases p27(Kip1) and induces significant regression of breast tumors. We conclude that GGTIs' antitumor activity is, at least in part, due to inhibiting Cdk2-dependent p27(Kip1) phosphorylation at Thr187 and accumulating nuclear p27(Kip1). Thus, GGTI treatment might improve the poor prognosis of breast cancer patients with low nuclear p27(Kip1) levels.
Distribution and metabolism of the natural anticarcinogen phenethyl isothiocyanate in A/J mice (1990)

The distribution and metabolism of phenethyl isothiocyanate (PEITC), a naturally occurring anticarcinogen, was investigated in A/J mice. Mice were administered 5 mumol of [14C]PEITC (2 microCi/mouse) by gavage and killed at 1, 2, 4, 8, 24, 48 or 72 h after dosing. Radioactivity present in the spleen, heart, liver, lung, kidney, brain, urine and feces was measured. Lung, the target tissue of PEITC inhibition of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) lung tumorigenesis, showed maximum radioactivity between 4 and 8 h after dosing, suggesting this time period would be optimal for maximal inhibition by PEITC in A/J mice. Approximately 50% of the total radioactivity was excreted within 24 h after dosing with nearly 80% of radioactivity found in urine and feces at 72 h. Two metabolites were isolated by reverse-phase HPLC from urine of mice treated with PEITC. The identities of these metabolites were determined by comparison with synthetic standards and by NMR and MS. The major metabolite was a cyclic mercaptopyruvic acid conjugate, whereas the minor metabolite was an N-acetylcysteine conjugate. Approximately 25% of the administered dose of PEITC was excreted as the cyclic mercaptopyruvic acid conjugate and 10% as the N-acetylcysteine conjugate. These results suggest that urinary metabolites of PEITC may provide potentially useful dosimeters for this natural anticarcinogen.
Writing handwritten messages on a small touchscreen (2013)

We present a method for composing handwritten messages on a small touchscreen device. A word is entered by drawing overlapped, screen sized letters on top of each other. The system does not require gestures or timeouts to delimit characters within a word - it automatically segments the overlapping strokes and renders the message in real-time as the user is writing. The auto-segmentation algorithm was designed for practicality; it is extremely simple, requires only public domain data for training, and runs very fast on low-power devices. Drawings may also be included with the text. Experimental data indicates the effectiveness of our system, even for novice users.
Monitoring X-ray contrast agent injections with Doppler ultrasound (2008)

During CT examinations, approximately 100 ml of X-ray contrast agent is regularly injected intravenously. In some rare cases, some or all the contrast agent may leak out of the vein and into the surrounding tissue, causing an extravasation. In other cases, equipment failure may prevent the contrast agent from being injected. This paper presents an ultrasound unit made for monitoring contrast agent injections during CT investigations. The unit uses a specially designed transducer attached to the arm of the patient, and a three-channel CW Doppler unit monitors the contrast agent injection continuously. The system has been tested on 198 patients in various CT centers. The preliminary results show that a correct injection is recognized by a strong increase in Doppler signal strength and velocity. Four cases of extravasations and equipment failure were detected as either delayed or missing increase in Doppler power.
A subjective evaluation on mixtures of crowdsourced audio recordings (2017)

Exploiting correlations in the audio, several works in the past have demonstrated the ability to automatically match and synchronize User Generated Recordings (UGRs) of the same event. Considering a small number of synchronized UGRs, we formulate in this paper simple linear audio mixing approaches to combine the available audio content. We use data from two different public events to perform a comparative listening test with the goal to assess the potential of such mixtures in improving the listening experience of the captured event, as opposed to when each UGR is consumed individually. The results of the listening tests indicate that, even with just a small number of overlapping UGRs, the outcome of the mixing process gains higher preference in comparison to original UGRs played back individually.
A new GPS-based method to estimate real driving emissions (2016)

So far, real driving emissions knowledge involves installing Portable Emissions Measurement Systems (PEMS). As a consequence, large scale campaigns of measurement are not feasible. This paper describes an innovative coupling of Information and Communication Technology (ICT) and physical modeling to turn the driver's smartphone into a virtual sensor of pollutant emissions of his/her vehicle. It consists of using the smartphone as a vehicle speed sensor and using cloud computing to make pollutant estimation. Large scale deployment of this approach provides i) decision-makers with precise information about pollutant emissions related to choices of standards or infrastructure ii) car drivers with their real footprint.
Scalable waveguide design for three-level operation in Neodymium doped fiber laser (2016)

We have constructed a double clad neodymium doped fiber laser operating on the three-level <sup>4</sup>F<sub>3/2</sub>→<sup>4</sup>I<sub>9/2</sub> transition. The laser has produced 11.5 W at 925 nm with 55% slope efficiency when pumped at 808 nm, comparable to the best previous results for a double-clad fiber configuration on this transition. Higher power pumping with both 808 nm and 880 nm sources resulted in an output of 27 W, albeit at lower slope efficiency. In both cases, output power was limited by available pump, indicating the potential for further power scaling. To suppress the stronger four-level <sup>4</sup>F<sub>3/2</sub>→<sup>4</sup>I<sub>11/2</sub> transition we developed a waveguide that provides spectral filtering distributed along the length of the fiber, based on an all-solid micro-structured optical fiber design, with resonant inclusions creating a leakage path to the cladding. The waveguide supports large mode areas and provides strong suppression at selectable wavelength bands, thus easing the restrictions on core and cladding sizes that limited power scaling of previous approaches.
Initial events at the bioactive glass surface in contact with protein‐containing solutions (2000)

Upon implantation, bioactive glass undergoes a series of reactions that leads to the formation of a calcium phosphate-rich layer. Most in vitro studies of the changes that occur on the surface of bioactive glass have employed the use of buffer solutions with compositions reflecting the ionic composition of interstitial fluid. Although these studies have documented the physical and chemical changes associated with bioactive glass immersed in aqueous media, they do not reveal the effect of serum proteins and cells that are present at the implantation site. In the present study, we document, using atomic force microscopy (AFM) and Rutherford backscattering spectrometry (RBS), significant differences in the reaction layer composition, thickness, morphology, and kinetics of formation arising from the presence of serum proteins. The data reveal that the uniform and rapid adsorption of serum proteins on the surface may serve to protect the surface from further direct interaction with the aqueous media, slowing down the transformation reactions. This finding is in agreement with previous studies that have shown that the presence of serum proteins significantly delays the formation of hydroxyapatite at the surface of bioactive glass. These data also support the hypothesis that initial reaction layers in vivo interact with cells in order to produce the tissue–bioactive glass interface typically observed on ex vivo specimens. © 2000 John Wiley & Sons, Inc. J Biomed Mater Res, 52, 825–830, 2000.
Two G-box-related sequences confer different expression patterns in transgenic tobacco. (1992)

We have analyzed the expression patterns conferred by two G-box-related motifs, a perfect palindromic sequence (PA, 5'-GCCACGTGGC-3') and motif I (Iwt, 5'-GTACGTGGCG-3'), in transgenic tobacco plants. A mutant version of motif I, Imu, was used as a negative control. PA is present in the promoters of several different genes, whereas Iwt is a conserved sequence found in abscisic acid-inducible promoters. Previously we have demonstrated that PA and Iwt, but not Imu, can bind to the tobacco transcription activator TAF-1 in vitro, with the PA sequence showing a 70-fold higher affinity as compared to Iwt. We found that tetramers of PA and Iwt, which differ by only 2 bp per 10-bp repeat, confer very different tissue-specific and expression patterns in transgenic tobacco plants. PA confers preferential expression in root tissues with a low level of activity in leaves, whereas Iwt directs developmentally regulated expression in seeds beginning 15 days after petals have fully expanded until seed maturation. Imu appears to be inactive because it gives the same expression pattern as the -90 cauliflower mosaic virus 35S promoter control. RNA gel blot analysis showed that the expression pattern of TAF-1 mRNA is similar to that directed by PA, suggesting that TAF-1 may be involved in the transcriptional regulation of PA.
Design of protein struts for self-assembling nanoconstructs (2002)

Bacteriophage T4 tail fibers have a quaternary structure of bent rigid rods, 3 x 160 nm in size. The four proteins which make up these organelles are able to self-assemble in an essentially irreversible manner. To use the self-assembly domains of these proteins as elements in construction of mesoscale structures, we must be able to rearrange these domains without affecting the self-assembly properties and add internal binding sites for other functional elements. Here we present results on several alterations of the P37 component of the T4 tail fiber that change its length and add novel protein sequences into the protein. One of these sequences is an antibody binding site that is used to inactivate phage carrying the modified gene.
Monoclonal antibody Y13-259 recognizes an epitope of the p21 ras molecule not directly involved in the GTP-binding activity of the protein. (1986)

The p21 products of ras proto-oncogenes are GTP-binding proteins with associated GTPase activity. Recent studies have indicated that ras p21 may be required for the initiation of normal cell DNA synthesis, since microinjection of a monoclonal antibody, Y13-259, blocks serum stimulation of DNA synthesis in quiescent cell cultures (L. S. Mulcahy, M.R. Smith, and D. W. Stacey, Nature [London] 313:241-243, 1985). We localized the structural domain within the p21 molecule recognized by the Y13-259 monoclonal antibody. By analysis of a series of bacterially expressed p21 deletion mutants, the monoclonal antibody was found to interact with a region between positions 70 and 89 in the p21 amino acid sequence. By comparison of the coding sequences of different p21 proteins recognized by this monoclonal antibody, a highly conserved amino acid region between positions 70 and 81 was found to be the most likely site for the epitope detected by the Y13-259 antibody. This monoclonal antibody was further shown not to interfere directly with in vitro biochemical functions of the molecule, including GTP binding, GTPase, and autokinase activities.
Porosity evaluation in aircraft composite parts using laser-ultrasound (2001)

In polymer-matrix composites, porosity must be evaluated and ultrasonic inspection is a proven technique to assess this parameter. To standardize reject criteria among different ultrasonic systems, ultrasonic systems must be quantitatively compared. Samples with different levels of porosity fabricated especially for a round robin were scanned using the laser-ultrasound facility built at Lockheed Martin Aerospace Fort Worth. The results obtained agree qualitatively and quantitatively with the results obtained on the same samples using conventional ultrasonic systems. Overall, the laser-ultrasound accuracy is equivalent to the average conventional system but with an inspection speed more than ten times faster.
Rapid-Cycling Populations of <i>Brassica</i> (1986)

Rapid-cycling populations of six economically important species in the genus Brassica have unusual potential for resolving many problems in plant biology and for use in education. Rapid-cycling brassicas can produce up to ten generations of seed per year and serve as models for research in genetics, host-parasite relations, molecular biology, cell biology, plant biochemistry, population biology, and plant breeding. Brassicas are a highly diverse group of crop plants that have great economic value as vegetables and as sources of condiment mustard, edible and industrial oil, animal fodder, and green manure. These plants can also be used in the classroom as convenient, rapidly responding, living plant materials for "hands on" learning at all levels of our educational system.
Firefly detection with half buffers (2018)

Fireflies, or noise spikes, are overly-bright pixels out of place compared to neighboring pixels, which are a common artifact in Monte Carlo ray traced images. They arise from low-probability events, and would be resolved in the limit as more samples are taken. However, these statistical anomalies are often so far out of the expected range that the time for them to converge, even barring numerical instabilities, is prohibitive. Aside from the general problem of fireflies marring a rendered image, their difference in color and variance values can cause problems for denoising solutions. For example, the distance calculation for non-local means filtering [Buades et al. 2005] presented in Rousselle et al. [2012] is not robust under extreme differences in variance.
Single-mode surface-plasmon laser (2000)

Surface-plasmon modes confined at the interface between a metal and a semiconductor are exploited in place of conventional dielectric waveguides for the realization of a λ∼17 μm semiconductor laser. The device is based on the quantum cascade concept and outperforms with its 38 mW of peak output power and 240 K of maximum operating temperature any previous semiconductor laser of comparable wavelength. Pure single-wavelength emission with a tuning rate of ∼1 nm/K is achieved using Bragg reflection from a two-metal grating that modulates the skin depth of the surface plasmons.
A Simply way to Generate Pancreatic Beta Cell Formation In Vivo through Ã¢Â€ÂœCellular Networking, Integration and ProcessingÃ¢Â€Â (2016)

Impaired insulin secretion is a characteristic feature of both type 1 and type 2 diabetes mellitus, and a variety of approaches have been employed to generate beta cells in vivo and in vitro [1-3]. Herein, we describe a completely novel approach to form beta cells in vivo in an adult wild type rodent model of diabetes [4]. Our method integrates multiple process of cellular physiology to regulate organ function and results in the long-term normalization of insulin secretion and glycemia and is not associated with pancreatic injury. We labeled our approach “Cellular Networking, Integration and Processing (CNIP)” to distinguish it from the term “system biology” which is used broadly to refer collectively to different levels of cellular, organ and animal physiology. The fundamental principle underlying CNIP is to simultaneously target and integrate three key levels of cellular physiology/metabolism/ molecular biology that have been implicate in beta cell formation. This is in contrast to the non-integrated model, which targets only nuclear reprogramming.
Mullerian-Inhibiting Substance Regulates Androgen Synthesis at the Transcriptional Level1 (1999)

Müllerian-inhibiting substance (MIS) is a hormone produced by Sertoli cells of the fetal testes that causes regression of the Müllerian ducts, the precursors to female reproductive tract structures that are present in the bipotential urogenital ridge. MIS is also produced in the adult gonads of both males and females, albeit at much lower levels than those measured during the fetal and perinatal periods. Adult transgenic mice chronically overexpressing MIS exhibit severe gonadal abnormalities and, in males, dramatically reduced levels of testosterone, which might lead to the incomplete virilization observed in some of the males. To understand the roles played by MIS in the adult gonad, we performed Northern analyses to show that the MIS type II receptor is expressed in purified Leydig cells and in two rodent Leydig cell lines, R2C and MA-10. Addition of purified recombinant human MIS to cultures of both R2C and MA-10 cells reduced steroid production. With MA-10 cells, the reduction of testosterone secretion into the medium was reduced to 1/10th of that in the control culture, which provided us with a means to study the molecular mechanisms underlying MIS-mediated suppression of testosterone synthesis. Northern analysis revealed that after stimulation with cAMP, the expression of messenger RNA for P450c17 hydroxylaselyase, the enzyme that catalyzes the conversion of progesterone to androstenedione, was reduced to background levels in the presence of MIS. Addition of cycloheximide, a protein synthesis inhibitor, did not prevent the effect of MIS, indicating a direct effect of MIS signal transduction on the expression of P450c17. Analysis of the transcriptional activity of Cyp17, the gene for murine P450c17, with Cyp17 promoter/luciferase reporter constructs shows that MIS regulates the transcription of Cyp17 in a concentration- and time-dependent manner. From our results, we conclude that MIS might play a physiological role in maintaining testosterone homeostasis. These findings will allow us in the future to use the transcriptional regulation of Cyp17 as a model to uncover the signal transduction pathways of MIS and the molecular mechanisms of its suppression of androgen synthesis.
Measuring Methanol Concentrations in a Vapor-Fed Direct Methanol Fuel Cell Using Laser Absorption Spectroscopy (2010)

Gas-phase absorption spectroscopy using a He–Ne laser enables the concentration of methanol vapor in a vapor-fed direct methanol fuel cell (DMFC) to be measured in real-time and in situ once high noise levels of the laser are corrected. The changes that methanol vapor concentrations bring to cell performance can be measured under various galvanostatic and potentiostatic conditions and analyzed with regard to methanol crossover and methanol transport capability. The absorption coefficient of +methanol vapor, , is nearly constant under the DMFC operating conditions at a wavelength of .
Properties of a Highly Punified Human Plasma Factor IX:c Therapeutic Concentrate Prepared by Conventional Chromatography (1989)

Abstract. We have characterized a highly purified (HP) factor IX concentrate intended for therapy of hemophilia B. The product has been prepared from pooled human plasma using a large‐scale procedure combining three conventional chromatographic steps based on DEAE ion exchange and affinity on immobilized heparin. The specific activity of the product was 119±10 IU factor IX:c/mg protein (n = 15), corresponding to a purification factor of about 9,000. The concentrate was free of the vitamin K‐dependent clotting factors II, VII and X and of proteins C and S. Most of the contaminants found in factor IX complex concentrate (PCC) were absent in this new product. High‐molecular‐weight kininogen, factors VIII, XI, XII or prekallikrein were not detected. There were no activated factors, such as factors IXa, and Xa, no thrombin and no phospholipids. Only two contaminants could be detected: C4 and inter‐alpha‐trypsin inhibitor (about 0.8 and 1.2mg/1,000 IU factor IX:c, respectively). The purity of the product, as compared to PCC, was confirmed by sodium dodecylsulfate polyacrylamide gel electrophoresis, cellulose acetate electrophoresis, Grabar‐Williams immunoelectrophoresis, and bidimensional immunoelectrophoresis. Thrombogenicity tests in rabbits revealed that the HP factor IX tested had a lower thrombogenic power than the PCC tested. The concentrate has been subjected to a 0.3% tri(n‐butyl) phosphate‐1% Tween 80 treatment for 6 h at 25°C during its production to reduce or eliminate the risk of transmission of plasma‐borne lipid‐enveloped viruses. These conditions inactivated more than 3.8 log 10 of vesicular stomatitis virus and more than 4.3 log 10 of sindbis virus within 1 and 2 h of treatment, respectively. These data demonstrate that a highly purified therapeutic clotting factor IX concentrate can be prepared from human plasma by conventional chromatographic methods.
Perceptual Validation Experiments for Evaluating the Quality of Wavelet-Synthesized Sounds (2002)

This paper describes three psychoacoustic experiments that evaluated the perceptual quality of sounds generated from a new wavelet-based synthesis technique. The synthesis technique provides a method for modeling and synthesizing perceptually compelling sound. The experiments define a methodology for evaluating the effectiveness of any synthesized sound. An identification task and a context-based rating task evaluated the perceptual quality of individual sounds. These experiments confirmed that the wavelet technique synthesizes a wide variety of compelling sounds from a small model set. The third experiment obtained sound similarity ratings. Psychological scaling methods were applied to the similarity ratings to generate both spatial and network models of the perceptual relations among the synthesized sounds. These analysis techniques helped to refine and extend the sound models. Overall, the studies provided a framework to validate synthesized sounds for a variety of applications including virtual reality and data sonification systems.