gebhart/patrepeval huggingface dataset:
Photoacoustic tomography with a limited-aperture planar sensor and a reverberant cavity (2007)

Biomedical photoacoustic tomography (PAT) is a soft-tissue imaging modality which combines the high spatial resolution of ultrasound (US) with the contrast and spectroscopic opportunities afforded by imaging optical absorption. Planar US arrays composed of piezoelectric or optical detector elements with small element sizes and fast acquisition times are readily available, making them an attractive option for imaging applications. An exact and efficient, FFT-based PAT reconstruction algorithm, that converts acoustic measurements recorded over a plane to a PAT image, is known. However, to capture sufficient data for an exact PAT reconstruction with a planar geometry requires an infinitely wide array. In practice it will be finite, resulting in a loss of resolution and introducing artefacts into the image. To overcome this limitation it is proposed that acoustic image sources, provided by enclosing the target in a reverberant cavity, are used to generate a periodically repeating sound field. Measurements of this periodic sound field can be used to reconstruct a PAT image exactly from measurements of reverberation made over a finite aperture. The existing FFT-based PAT reconstruction algorithm with only minor additional modifications can be used to generate the image in this case.
Atomic and Nuclear Physics (1987)

Experiment 8.01 Molecular size Equipment: Soap, chalk dust, wash bowl.
Genome-wide association analysis identifies genetic correlates of immune infiltrates in solid tumors (2017)

Therapeutic options for the treatment of an increasing variety of cancers have been expanded by the introduction of a new class of drugs, commonly referred to as checkpoint blocking agents, that target the host immune system to positively modulate anti-tumor immune response. Although efficacy of these agents has been linked to a pre-existing level of tumor immune infiltrate, it remains unclear why some patients exhibit deep and durable responses to these agents while others do not benefit. To examine the influence of tumor genetics on tumor immune state, we interrogated the relationship between somatic mutation and copy number alteration with infiltration levels of 7 immune cell types across 40 tumor cohorts in The Cancer Genome Atlas. Levels of cytotoxic T, regulatory T, total T, natural killer, and B cells, as well as monocytes and M2 macrophages, were estimated using a novel set of transcriptional signatures that were designed to resist interference from the cellular heterogeneity of tumors. Tumor mutational load and estimates of tumor purity were included in our association models to adjust for biases in multi-modal genomic data. Copy number alterations, mutations summarized at the gene level, and position-specific mutations were evaluated for association with tumor immune infiltration. We observed a strong relationship between copy number loss of a large region of chromosome 9p and decreased lymphocyte estimates in melanoma, pancreatic, and head/neck cancers. Mutations in the oncogenes PIK3CA, FGFR3, and RAS/RAF family members, as well as the tumor suppressor TP53, were linked to changes in immune infiltration, usually in restricted tumor types. Associations of specific WNT/beta-catenin pathway genetic changes with immune state were limited, but we noted a link between 9p loss and the expression of the WNT receptor FZD3, suggesting that there are interactions between 9p alteration and WNT pathways. Finally, two different cell death regulators, CASP8 and DIDO1, were often mutated in head/neck tumors that had higher lymphocyte infiltrates. In summary, our study supports the relevance of tumor genetics to questions of efficacy and resistance in checkpoint blockade therapies. It also highlights the need to assess genome-wide influences during exploration of any specific tumor pathway hypothesized to be relevant to therapeutic response. Some of the observed genetic links to immune state, like 9p loss, may influence response to cancer immune therapies. Others, like mutations in cell death pathways, may help guide combination therapeutic approaches.
Butyrolactone signalling circuits for synthetic biology (2015)

Signalling circuits based on quorum sensing mechanisms have been popular tools for synthetic biology. Recent advances in our understanding of the analogous systems regulating antibiotics production in soil bacteria suggest that these might provide useful complementary tools to increase the complexity of possible circuit designs. Here we discuss the diversity of these natural circuits, which use γ-butyrolactones (GBLs) as their main inter-cellular signal, highlighting the range of new building blocks they could provide, as well as a number of exciting recent applications of GBL-based circuits in heterologous systems. We conclude by presenting examples of the novel circuit complexity that could become accessible through the use of GBL-based designs.
PCEP Extensions for Stitching LSPs in Hierarchical Stateful PCE Model (2017)

This document extends the Path Communication Element Communication
Protocol (PCEP) to coordinate an end-to-end inter-domain tunnel setup
over a multi-domain networks in the context of Hierarchical Stateful
PCE environments. This document uses Stitching Label (SL) to stich
per-domain LSPs.
Association of a Toll‐like receptor 1 polymorphism with heightened Th1 inflammatory responses and antibiotic‐refractory Lyme arthritis (2012)

The TLR1-1805GG polymorphism in B burgdorferi RST1-infected patients was associated with stronger Th1-like inflammatory responses, an environment that may set the stage for antibiotic-refractory arthritis.
Ammonia detection by using quantum-cascade laser photoacoustic spectroscopy (2006)

A pulsed quantum-cascade distributed-feedback laser, temperature tunable from -41 degrees C to +31.6 degrees C, and a resonant differential photoacoustic detector are used to measure trace-gas concentrations to as low as 66 parts per 10(9) by volume (ppbv) ammonia at a low laser power of 2 mW. Good agreement between the experimental spectrum and the simulated HITRAN spectrum of NH3 is found in the spectral range between 1046 and 1052 cm(-1). A detection limit of 30 ppbv ammonia at a signal-to-noise ratio of 1 was obtained with the quantum-cascade laser (QCL) photoacoustic (PA) setup. Concentration changes of approximately 50 ppbv were detectable with this compact and versatile QCL-based PA detection system. The performance of the PA detector, characterized by the product of the incident laser power and the minimum detectable absorption coefficient, was 4.7 x 10-9 W cm(-1).
Effect of electric field pulses on the viability and on the membrane‐bound immunoglobulins of LPS‐activated murine B‐lymphocytes: Correlation with the cell cycle (1994)

The effects of microsecond electropulses (1-5 kV/cm) on the viability of murine B lymphocytes and on their binding of antibodies by surface immunoglobulin (Ig) were studied in relation to the cell cycle. Before electropulsing, cultures given 48 h mitogenic stimulation showed at least two cell subpopulations, which were distinguishable by their levels of surface-Ig expression as assessed with FITC-labelled antibodies against mouse Ig. The immunofluorescence intensity of cells in S and G2/M phases was higher than that of G0/G1 cells. After exposure of the mitogen-stimulated lymphocytes to three exponentially decaying (time constant tau = 5-40 microseconds) electric field pulses, dye exclusion assay showed that pulsing at 1 or 2 kV/cm (at 4 degrees C or 20 degrees C) did not cause permeabilization. Field strengths of 3, 4, or 5 kV/cm resulted in 20%, 45%, or 70% of dye-permeable cells, respectively, if the pulsed cells were transferred to phosphate-buffered saline on ice for 30 min. Incubation in full medium at 37 degrees C for 30 min ("resealing") significantly decreased the percentage of permeabilized cells. Electropulsed G0/G1 cells were not only more resistant to direct electric exposure (tolerated higher field strengths) than S + G2/M cells but also responded better to resealing. The surface Ig of lymphocytes pulsed at higher fields and low temperature (4 or 5 kV/cm, tau = 5 microseconds, three pulses, 4 degrees C) was less easily immunostained than in controls or in cells pulsed at 2 kV/cm or less. At 5 kV/cm those cells that were not permeabilized showed a greater reduction in immunostaining, especially if resealed.
Literature Review in Informal Learning with Technology Outside School (2007)

For most of us, discussion about learning is inextricably related to formal education systems. However, any interest in the role of ICTs in children’s learning forces the recognition that many children are immersed in ICT-related activities in their homes and with their friends. This recognition requires us to acknowledge a wider ecology of education where schools,homes, playtime, the library and the museum all play their part. This review focuses specifically on children's informal learning with technologies outside school. This review, then, will begin by discussing the key theoretical approaches to learning that have emerged through studies of learning in alternative settings and with ICTs and then go on to map out the landscape of children and young people's access to and use of digital technologies outside school. The review will then draw out key characteristics of children's informal learning with digital technologies through case study examples before, in the final section, offering a synthesis of the theoretical and policy implications of such studies.
Green Synthesis of Silver Nanoparticles through Reduction with Solanum xanthocarpum L. Berry Extract: Characterization, Antimicrobial and Urease Inhibitory Activities against Helicobacter pylori (2012)

A green synthesis route for the production of silver nanoparticles using methanol extract from Solanum xanthocarpum berry (SXE) is reported in the present investigation. Silver nanoparticles (AgNps), having a surface plasmon resonance (SPR) band centered at 406 nm, were synthesized by reacting SXE (as capping as well as reducing agent) with AgNO(3) during a 25 min process at 45 °C. The synthesized AgNps were characterized using UV-Visible spectrophotometry, powdered X-ray diffraction, and transmission electron microscopy (TEM). The results showed that the time of reaction, temperature and volume ratio of SXE to AgNO(3) could accelerate the reduction rate of Ag(+) and affect the AgNps size and shape. The nanoparticles were found to be about 10 nm in size, mono-dispersed in nature, and spherical in shape. In vitro anti-Helicobacter pylori activity of synthesized AgNps was tested against 34 clinical isolates and two reference strains of Helicobacter pylori by the agar dilution method and compared with AgNO(3) and four standard drugs, namely amoxicillin (AMX), clarithromycin (CLA), metronidazole (MNZ) and tetracycline (TET), being used in anti-H. pylori therapy. Typical AgNps sample (S1) effectively inhibited the growth of H. pylori, indicating a stronger anti-H. pylori activity than that of AgNO(3) or MNZ, being almost equally potent to TET and less potent than AMX and CLA. AgNps under study were found to be equally efficient against the antibiotic-resistant and antibiotic-susceptible strains of H. pylori. Besides, in the H. pylori urease inhibitory assay, S1 also exhibited a significant inhibition. Lineweaver-Burk plots revealed that the mechanism of inhibition was noncompetitive.
Crack-free thick (∼5 µm) α-Ga<sub>2</sub>O<sub>3</sub> films on sapphire substrates with α-(Al,Ga)<sub>2</sub>O<sub>3</sub> buffer layers (2016)

Abstract To obtain crack-free thick α-Ga 2 O 3 films on sapphire substrates, effects and behaviors of buffer layers have been investigated. With the growth of an α-Ga 2 O 3 layer, there appeared an unintentionally formed layer in the sample, which was associated with stress accumulation and could be the seed for crack generation. We obtained a thick (∼5 µm) α-Ga 2 O 3 layer on a sapphire substrate with the insertion of α-(Al 0.12 Ga 0.88 ) 2 O 3 /α-(Al 0.02 Ga 0.98 ) 2 O 3 buffer layers, and for this sample, we did not observe the intermediate layer, suggesting that the buffer layers were effective for eliminating the stress accumulation at the α-Ga 2 O 3 /sapphire interface region.
Capacity and delay of hybrid wireless broadband access networks (2009)

An optical network is too costly to act as a broadband access network. On the other hand, a pure wireless ad hoc network with n nodes and total bandwidth of W bits per second cannot provide satisfactory broadband services since the pernode throughput diminishes as the number of users goes large. In this paper, we propose a hybrid wireless network, which is an integrated wireless and optical network, as the broadband access network. Specifically, we assume a hybrid wireless network consisting of n randomly distributed normal nodes, and m regularly placed base stations connected via an optical network. A source node transmits to its destination only with the help of normal nodes, i.e., in the ad hoc mode, if the destination can be reached within L (L /spl geq/ 1) hops from the source. Otherwise, the transmission will be carried out in the infrastructure mode, i.e., with the help of base stations. Two transmission modes share the same bandwidth of W bits/sec. We first study the throughput capacity of such a hybrid wireless network, and observe that the throughput capacity greatly depends on the maximum hop count L and the number of base stations m. We show that the throughput capacity of a hybrid wireless network can scale linearly with n only if m = Omega(n), and when we assign all the bandwidth to the infrastructure mode traffics. We then investigate the delay in hybrid wireless networks. We find that the average packet delay can be maintained as low as Theta(1) even when the per-node throughput capacity is Theta(W).
Suppression of reaginic antibodies with modified allergens. IV. Induction of suppressor T cells by conjugates of polyethylene glycol (PEG) and monomethoxy PEG with ovalbumin. (1981)

Administration of multiple injections of conjugates of ovalbumin (OA) and polyethylene glycol (PEG) or its monomethoxy derivative (mPEG) into mice which had been sensitized with 2,4-dinitrophenylated OA (DNP3-OA) abrogated both the anti-OA and anti-DNP IgE responses, in spite of additional injections of the sensitizing dose of DNP3-OA in the presence of A1(OH)3. Treatment of mice with OA-PEG in A1(OH)3 stimulated preferentially helper T cells, whereas injection of mice with OA-PEG in the absence of adjuvant elicited predominantly suppressor T cells. The unresponsive state of mice which had been treated 21 days earlier with OA-PEG could not be broken by the transfer of normal spleen cells and an additional sensitizing dose of DNP3-OA. Transfer of spleen cells from tolerized animals to normal mice dampened the capacity of the latter to mount both anti-DNP and anti-OA IgE responses; however, the suppressive effect of these cells was eliminated by treatment of the normal recipients with cyclophosphamide, which is a procedure known to inactive suppressor T cells, and hence it may be concluded that this effect was not due to the carryover of the tolerogen with the transferred cells. All these results provide strong support for the conclusion that the suppressor cells induced by the treatment of mice with OA-PEG and OA-mPEG conjugates belonged to a T cell subpopulation, and that the B cells of these mice were devoid of suppressive activity.
Overcoming Cu/CVD low-k integration challenges in a high performance interconnect technology (2002)

In this paper we describe how several challenges have been overcome in the integration of a high performance, manufacturable, Cu/CVD low-k (Coral) 0.13 /spl mu/m interconnect technology. Specifically, we discuss solving issues with 193 nm lithography for M1 using different hardmask schemes, and the challenges of 248 nm trench resist poisoning due to N-H evolution from open vias in a full via first dual damascene scheme. Optimization of the dual damascene dielectric stack and Cu CMP with regard to reliability concerns are also elucidated. Yield and reliability data are provided that demonstrate the manufacturability of the integration solutions that are discussed.
Chemoselective Reduction of Phosphine Oxides by 1,3‐Diphenyl‐Disiloxane (2017)

Reduction of phosphine oxides to the corresponding phosphines represents the most straightforward method to prepare these valuable reagents. However, existing methods to reduce phosphine oxides suffer from inadequate chemoselectivity due to the strength of the P=O bond and/or poor atom economy. Herein, we report the discovery of the most powerful chemoselective reductant for this transformation to date, 1,3-diphenyl-disiloxane (DPDS). Additive-free DPDS selectively reduces both secondary and tertiary phosphine oxides with retention of configuration even in the presence of aldehyde, nitro, ester, α,β-unsaturated carbonyls, azocarboxylates, and cyano functional groups. Arrhenius analysis indicates that the activation barrier for reduction by DPDS is significantly lower than any previously calculated silane reduction system. Inclusion of a catalytic Brønsted acid further reduced the activation barrier and led to the first silane-mediated reduction of acyclic phosphine oxides at room temperature.
Introduction to Transcription (2010)

Knowledge of transcription has moved forward at a furious pace over recent years, and an understanding of the processes involved in gene regulation and expression has become an essential element in biochemistry, genome biology, molecular biology and molecular genetics. In this timely book, the authors present an accessible, yet comprehensive, cover
Array Tomography: Rodent Brain Fixation and Embedding (2010)

Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. This protocol describes the fixation and processing required to prepare tissues for immunofluorescence array tomography.
Modeling value speculation: an optimal edge selection problem (2003)

Techniques for value speculation have been proposed for dynamically scheduled and statically scheduled machines to increase instruction-level parallelism (ILP) by breaking flow (true) dependences and allowing value-dependent operations to be executed speculatively. The effectiveness of value speculation depends upon the ability to select and break dependences to shorten overall execution time, while encountering penalties for value misprediction. To understand and improve the techniques for value speculation, we model value speculation as an optimal edge selection problem. The optimal edge selection problem involves finding a minimal set of edges (dependences) to break in a data dependence graph that achieves maximal benefits from value speculation, while taking the penalties for value misprediction into account. Based on three properties observed from the optimal edge selection problem, an efficient optimal edge selection algorithm is designed. From the experimental results of running the optimal edge selection algorithm for the 20 most heavily executed paths selected from each SPECint95 benchmark, several insights are shown. The average critical path reduction is 9.61 percent on an average and 25.57 percent at its maximum. Surprisingly, 66 percent of the edges selected by the optimal algorithm have value prediction accuracies over 99 percent. Moreover, most of the selected edges cross the middle of the data dependence graph. The selected producer operations thereby tend to reside in the upper portion of the data dependence graph, while the selected consumer operations appear toward the lower portion.
Chemical agents for reducing solubility of silica in 1N sodium hydroxide (1992)

A short experimental research project examined the effectiveness of several chemical agents for the control of alkali aggregate damage in concrete. The experimental program was conducted in three stages. The first stage was aimed at rapid evaluation of a number of chemical agents for their effectiveness in preventing dissolution of reactive silica in strong alkaline solutions. Promising chemical agents from Stage 1 were selected for use as admixtures and aggregate pre-treatments for the control of ASR in fresh concrete, and as penetrants for the control of ASR in hardened concrete. The results of the first stage are reported herein. Three chemicals - aluminum sulfate, zinc sulfate, and pyrogallol, were identified to be effective retardants of silica dissolution in a high alkali solution (1N sodium hydroxide). It was found that the concentration of chemical needed to reduce the solubility of silica by comparable proportions was higher for opal than for less reactive Spratts aggregate.
Discovery of micafungin (FK463): A novel antifungal drug derived from a natural product lead (2007)

Abstract FR901379, which is a novel, water-soluble, echinocandin-like lipopeptide, was isolated from a microbial culture broth. It showed potent in vivo antifungal activity against Candida albicans and inhibits the synthesis of 1,3-β-glucan. However, this compound had hemolytic activity and was also less active against Aspergillus fumigatus . To overcome these shortcomings, we synthesized FR131535 bearing an octyloxybenzoyl acyl side chain instead of a fatty acid. FR131535 retained the original activity displayed by FR901379, acquired potent anti- Aspergillus activity, and its hemolytic activity was significantly reduced. Further extensive chemical modification of FR901379 has led to the discovery of micafungin (FK463), which is effective against Candida and Aspergillus spp. Micafungin has been marketed in Japan and the United States as a candin-class parenteral antifungal agent for life-threatening mycoses.
Nanoscale InP islands embedded in InGaP (1995)

We have prepared small InP islands which are embedded in In0.485Ga0.515P grown on a (100) GaAs substrate by solid-source molecular beam epitaxy. The InP islands form due to the 3.7% lattice mismatch between In0.485Ga0.515P and InP. Atomic force microscopy measurements show that the island size is typically ∼50 nm in diameter and ∼5 nm in height for nominally two monolayers of InP deposited on In0.485Ga0.515P. The energy of the photoluminescence (PL) peak shifts from 1.85 to 1.53 eV as the nominal InP thickness increases from 2 to 10 monolayers. A minimum PL linewidth of 21.6 meV and the maximum intensity of the PL originating from the InP islands is observed for 7.3 monolayers InP.