gebhart/patrepeval huggingface dataset:
High-throughput Screening of Carbohydrate-degrading Enzymes Using Novel Insoluble Chromogenic Substrate Assay Kits (2016)

Carbohydrates active enzymes (CAZymes) have multiple roles in vivo and are widely used for industrial processing in the biofuel, textile, detergent, paper and food industries. A deeper understanding of CAZymes is important from both fundamental biology and industrial standpoints. Vast numbers of CAZymes exist in nature (especially in microorganisms) and hundreds of thousands have been cataloged and described in the carbohydrate active enzyme database (CAZy). However, the rate of discovery of putative enzymes has outstripped our ability to biochemically characterize their activities. One reason for this is that advances in genome and transcriptome sequencing, together with associated bioinformatics tools allow for rapid identification of candidate CAZymes, but technology for determining an enzyme's biochemical characteristics has advanced more slowly. To address this technology gap, a novel high-throughput assay kit based on insoluble chromogenic substrates is described here. Two distinct substrate types were produced: Chromogenic Polymer Hydrogel (CPH) substrates (made from purified polysaccharides and proteins) and Insoluble Chromogenic Biomass (ICB) substrates (made from complex biomass materials). Both CPH and ICB substrates are provided in a 96-well high-throughput assay system. The CPH substrates can be made in four different colors, enabling them to be mixed together and thus increasing assay throughput. The protocol describes a 96-well plate assay and illustrates how this assay can be used for screening the activities of enzymes, enzyme cocktails, and broths.
Silicon carbide 2002 -- materials, processing and devices : symposium held December 2-4, 2002, Boston, Massachusetts, U.S.A. (2003)

Advances in silicon carbide materials, processing and device design have recently resulted in implementation of SiC-based electronic systems and offer great promise in high-voltage, high-temperature and high-frequency applications. This volume focuses on new developments in basic science of SiC materials as well as rapidly maturing device technologies. The challenges in this field include understanding and decreasing defect densities in bulk SiC crystals, controlling morphology and residual impurities in epilayers, optimization of implant activation and oxide-SiC interfaces, and developing novel device structures. This book brings together the crystal growers, physicists and device experts needed to continue the rapid pace of silicon-carbide-based technology. Topics include: epitaxial growth; characterization/defects; MOS technology; SiC processing and devices.
Counterpropagating Twin Photons by Parametric Fluorescence (2002)

An original geometry for parametric fluorescence is proposed and analyzed theoretically, in which counterpropagating twin photons are emitted in a thin waveguide. In this original down-conversion process, a dramatic decrease of the spectral signal bandwidth at degeneracy is expected, as compared to usual parametric fluorescence processes. The possibility of using the counterpropagating twin photons for quantum cryptography is emphasized. It is shown that the realization of a fibered semiconductor source of Einstein-Podolsky-Rosen photons is possible by this method.
Circular of the Bureau of Standards no. 427: (1940)

The production of synthetic rubber on a commercial scale in the United States and abroad has increased very greatly in recent years. The increasing use of synthetic rubber in this comitry has been due entirely to its superiority over the natural product for many applications. In some other countries it has been developed as a substitute for natural rubber as a measure of national economic self-sufficiency. Consequently, there has been a growing interest m the development of synthetic rubber in America. In response to frequent requests for information, this Circular has been prepared at the National Bureau of Standards to furnish a comprehensive summary and a complete bibliography of the literature regarding the different varieties of modern synthetic rubber.
Density, Viscosity, and Performances of Carbon Dioxide Capture in 16 Absorbents of Amine + Ionic Liquid + H2O, Ionic Liquid + H2O, and Amine + H2O Systems (2010)

A series of novel ionic liquids, 2-aminoethanol tetrafluoroborate ([MEA][BF4]), 2-[2-hydroxyethyl(methyl)amino] ethanol tetrafluoroborate ([MDEA][BF4]), 2-[2-hydroxyethyl(methyl)amino] ethanol chloride ([MDEA][Cl]), 2-[2-hydroxyethyl(methyl)amino] ethanol phosphate ([MDEA][PO4]), and 2-[2-hydroxyethyl(methyl)amino] ethanol sulfate ([MDEA][SO4]), were synthesized and characterized for carbon dioxide capture in this work. Densities and viscosities of ionic liquids (1-butyl-3-methylimidazolium tetrafluoroborate, [MEA][BF4], [MDEA][BF4], [MDEA][Cl], [MDEA][PO4], and [MDEA][SO4]), amines + ionic liquids + H2O, ionic liquids + H2O, and amines + H2O were measured at temperatures ranging from (303.15 to 343.15) K at different mass fractions. These 16 different absorbents were prepared by mixing two or three compounds of 2-aminoethanol (MEA), 2-[2-hydroxyethyl(methyl)amino] ethanol (MDEA), 2-[bis(2-hydroxyethyl)amino] ethanol (TEA), ionic liquids, and water. The carbon dioxide capture rate and carbon dioxide capture capacity in the 16 different absorbents were measured at 303.15 K and 1.50 MPa. The experimental results showed that the viscosities of these absorbents are less than 17.00 mPa·s at 303.15 K. Among these absorbents, the MDEA + [MDEA][Cl] + H2O + piperazine system shows the best performance on carbon dioxide capture.
Wine microbiology is driven by vineyard and winery anthropogenic factors (2016)

The effects of different anthropic activities (vineyard: phytosanitary protection; winery: pressing and sulfiting) on the fungal populations of grape berries were studied. The global diversity of fungal populations (moulds and yeasts) was performed by pyrosequencing. The anthropic activities studied modified fungal diversity. Thus, a decrease in biodiversity was measured for three successive vintages for the grapes of the plot cultivated with Organic protection compared to plots treated with Conventional and Ecophyto protections. The fungal populations were then considerably modified by the pressing-clarification step. The addition of sulfur dioxide also modified population dynamics and favoured the domination of the species Saccharomyces cerevisiae during fermentation. The non-targeted chemical analysis of musts and wines by FT-ICR-MS showed that the wines could be discriminated at the end of alcoholic fermentation as a function of adding SO<sub>2</sub> or not, but also and above all as a function of phytosanitary protection, regardless of whether these fermentations took place in the presence of SO<sub>2</sub> or not. Thus, the existence of signatures in wines of chemical diversity and microbiology linked to vineyard protection has been highlighted.
π–π stacked DNA G-wire nanostructures formed by a short G-rich oligonucleotide containing a 3′–3′ inversion of polarity site (2020)

Rod-shaped G-wire assemblies potentially useful to obtain new hybrid and conducting materials were obtained by annealing short G-rich oligonucleotides incorporating a 3′–3′ inversion of polarity site in the presence of potassium or ammonium ions.
Overview of the studies on authentication of gelatin using Fourier Transform Infrared spectroscopy coupled with chemometrics (2021)

Background and objective: In recent years, global market of halal products has been greatly developed. Sign of "Halal" on foods’ label refers to their appropriateness for Muslim and Jewish buyers, which are banned from consumption of non-halal products such as porcine derived gelatin. Pig derivatives are marketed frequently in the world because they are relatively cheap and available. Therefore, development of simple and fast methods for authentication of halal foods and raw materials has been required. At this review, we studied one of common authentication approaches for qualification of gelatin by Fourier transform infrared spectroscopy (FT-IR). Results and conclusion: Several analytical methods were conducted for evaluation of gelatin in foods. Among them, FT-IR was relatively interested because it is a simple, fast and reliable method and does not require complicated sample preparation. In some cases, it was superior to the molecular method of polymerase chain reactions (PCR) in detection of gelatin’s origin by least analytical uncertainties. Although, analysis of FT-IR results by modeling approaches such as chemometrics classification increases effectiveness of the developed method. In this review, we will show that FT-IR can be used routinely as alternative or complementary method to identify the source of gelatin with high precision.
Sputtered C-Axis Inclined Piezoelectric Films and Shear Wave Resonators (1983)

Sputtered piezoelectric films are being studied for potential application to VHF through microwave frequency acoustic wave devices. This paper reports on the growth and characterization of C-axis inclined ZnO and AlN films for shear wave resonators. Orientation relationships for shear wave excitation were calculated for these films which suggest a nearly pure shear wave could be excited with films having C-axis orientation approximately 45/sup 0/ from the surface normal. At other angles, quasi-shear and quasi-longitudinal waves are excited. The well oriented ZnO or AlN films with C-axis inclined from the film normal were grown in a reactive dc planar magnetron sputtering system having an auxiliary anode structure. These films were evaluated by scanning electron microscopy (SEM) and BAW device measurements. The columnar structure of the C-axis crystallites, inclined from the Si substrate normal, was clearly visible in SEM. Films having C-axis inclination angles up to 45/sup 0/ and thicknesses up to 10 microns have been obtained. Composite resonators were fabricated by sputtering ZnO or AlN films onto the p/sup +/ Si membrane. Typically, these resonators exhibited Q s of about 5000 in 200 MHz to 500 MHz fundamental resonance range. Of particular interest is the temperature compensation of resonant frequency.more » Resonators having an absolute temperature coefficient of series resonant frequency of less than 1 ppM/C/sup 0/ around room temperature have been made for both ZnO/Si and AlN/Si composite structures. The temperature coefficient of the ZnO and AlN plate resonators was also measured to be -36.2 ppM/C/sup 0/ and -25 ppM/C/sup 0/ which suggested the temperature coefficient of the p/sup +/ Si membrane to be about +9 ppM/C/sup 0/ in the shear mode.« less
Interobserver reliability in the histopathologic diagnosis of oral pre‐malignant and malignant lesions (2004)

These data suggest that the presence of inflammation, lesion site, and biopsy technique modifies the reliability of oral lesion histologic diagnoses.
A mouse pancreatic organoid model to compare PD-L1 blocking antibodies (2022)

Immune checkpoint inhibitors (ICIs) have changed the therapeutic landscape for cancer patients, but diabetes, a rare, severe immune-related endocrinopathy, is linked to ICI therapy. It is unclear whether glycosylation of ICIs may play a role in the development of this adverse event and how the physiological effects of different ICIs on pancreatic cells should be evaluated. We used a mouse pancreatic organoid model to compare three PD-L1 blocking antibodies in the presence or absence of IFNγ using a metabolic bioanalyzer. Modulation of ICI glycosylation altered its metabolic effects on mouse pancreatic organoids, suggesting that this model could be used to monitor and compare ICIs and to study the mechanisms underlying the development of IC-mediated diabetes.
Regularized Training of Nearest Neighbor Language Models (2021)

Including memory banks in a natural language processing architecture increases model capacity by equipping it with additional data at inference time. In this paper, we build upon $k$NN-LM \citep{khandelwal20generalization}, which uses a pre-trained language model together with an exhaustive $k$NN search through the training data (memory bank) to achieve state-of-the-art results. We investigate whether we can improve the $k$NN-LM performance by instead training a LM with the knowledge that we will be using a $k$NN post-hoc. We achieved significant improvement using our method on language modeling tasks on \texttt{WIKI-2} and \texttt{WIKI-103}. The main phenomenon that we encounter is that adding a simple L2 regularization on the activations (not weights) of the model, a transformer, improves the post-hoc $k$NN classification performance. We explore some possible reasons for this improvement. In particular, we find that the added L2 regularization seems to improve the performance for high-frequency words without deteriorating the performance for low frequency ones.
Fabrication of high performance AlGaN/GaN FinFET by utilizing anisotropic wet etching in TMAH solution (2015)

AlGaN/GaN-based fin-shaped field-effect transistors (FinFETs) with very steep sidewall and various fin-widths (W <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">fin</sub> ) have been fabricated by utilizing electron-beam lithography and additional anisotropic sidewall wet etch in tetramethyl ammonium hydroxide (TMAH) solution. The device with W <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">fin</sub> of 180 nm exhibits normally-on performance with threshold voltage of -3.5 V and extremely broad transconductance (g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> ) characteristic ranging from -2 to ~ 3 V at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> = 5 V which is essential for high linearity device performance. This broad g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> characteristic is because the current from the side-wall MOS channel becomes comparable to that from the two-dimensional electron gas (2DEG) channel and hence significantly contributes to the total device current. On the other hand, devices with smaller W <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">fin</sub> = 50 and 100 nm exhibit normally-off performance with positive threshold voltage of 2.0 and 0.6 V, respectively, and less broad g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> characteristics because the current from the side-wall MOS channel dominates the total device current.
P01.05 Development of signal amplification for spatially-resolved, highly multiplexed biomarker analysis of human tumor tissues (2020)

<h3>Background</h3> Characterizing the complexities of the tumor microenvironment is fundamental to understanding cancer. Spatial relationships between infiltrating immune cells and the existing cellular matrix are now recognized as key determinants of tumor heterogeneity. Nevertheless, most available technologies for studying cells within the context of their tissue microenvironment, like traditional immunofluorescence (IF) and immunohistochemistry (IHC), are limited—allowing the visualization of only a few markers at a time. <h3>Materials and Methods</h3> CO-Detection by indEXing (CODEX<sup>®</sup>) technology has overcome this limitation through a DNA-based labeling strategy, involving the sequential addition and removal of dye-labeled oligonucleotide reporters to antibodies equipped with complementary oligonucleotide tags. In this manner, it is possible to visualize tens of antibodies in the same tissue, in situ and at cellular resolution. Additionally, CODEX<sup>®</sup> interfaces with existing inverted microscopes and provides a cost-effective, fully automated platform for ultra-high plex immunofluorescence imaging. We have expanded the CODEX<sup>®</sup> platform to include Tyramide Signal Amplification of weak fluorescent signals, i.e. from low-expression biomarkers. This approach was tested with key biomarkers used in routine analyses of the tumor microenvironment, including PD-L1, PD-1 and FOXP3. <h3>Results</h3> We demonstrate &gt;50X amplification of PD-L1, PD-1 and FOXP3 signals when compared to control tissues. Moreover, we successfully included our amplification step in the CODEX<sup>®</sup> labeling/imaging workflow, so that it was possible to analyze amplified PD-L1, PD-1 and FOXP3 signals concurrently with a panel of 20+ additional antibodies. Analysis of our data also generated unique biological insights, including increased PD-L1 expression in T<sub>reg</sub> cells and other tumor and stromal regions. <h3>Conclusions</h3> Our findings demonstrate the feasibility of amplifying weak biomarker signals in the CODEX® workflow. Furthermore, our experiments were conducted on human formalin fixed paraffin embedded tumor tissues, thereby demonstrating the applicability of CODEX® analyses for clinical and translational research agendas. <h3>Disclosure Information</h3> <b>O. Braubach:</b> A. Employment (full or part-time); Significant; Akoya Biosciences. <b>S. Mistry:</b> A. Employment (full or part-time); Significant; Akoya Biosciences. <b>G. Dakshinamoorthy:</b> A. Employment (full or part-time); Significant; Akoya Biosciences. <b>J. Yuan:</b> A. Employment (full or part-time); Significant; Akoya Biosciences. <b>P. Noordam:</b> A. Employment (full or part-time); Significant; Akoya Biosciences. <b>J. Kim:</b> A. Employment (full or part-time); Significant; Akoya Biosciences. <b>W. Lee:</b> A. Employment (full or part-time); Significant; Akoya Biosciences. <b>J. Kennedy-Darling:</b> A. Employment (full or part-time); Significant; Akoya Biosciences.
Ethical Decision-Making, Religious Beliefs and Software Piracy (2003)

Software piracy has become one of the major social and business problems in our society as the information technology era came to the fore. IT companies and software developers lost huge sums of money due to software piracy. Most people would not link software piracy, commercial morality and religious beliefs together. However, management researchers propose that the moral tendency of an individual may affect the respective person's ethical decision-making towards copyright infringements, specifically software piracy. Thus, this paper attempts to identify the cause and effect relationship between morality and ethical decision-making. This research examines the relationship between an individual's religious beliefs and ethical decision-making with regard to software piracy in a scenario-based vignette. The structural equation model (SEM) is used to identify this cause and effect relationship. The research findings suggest that an individual's religious beliefs are pertinent to the ethical decision-making process with specific reference to software piracy.
Comparision of Raman efficiencies in optical fibers (1994)

In this paper we investigate the Raman efficiency of different fibers. Our results are important for the design and optimization of repeaterless systems using remotely pumped Er-doped fiber amplifiers.1,2 In these systems the Er-doped fiber amplifier is placed at a certain distance from the output end of the system and is remotely pumped by a 1.48-μm diode laser located at the output end. As the high-power pump laser propagates through the transmission fiber, it will provide Raman gain to the counterpropagating signal and, at the same time, will add noise to it. Indeed, Raman gains of 5.5 dB were reported in previous experiments using remotely pumped fiber amplifiers.1 The amount of gain that the signal will experience, as well as the amount of noise generated, will depend on the pump and signal wavelengths, the pump power, and the characteristics of the fiber used.
GW quasiparticle energy study of ternary tetradymite Bi2Te2Se and Bi2Te2S thin films (2015)

In this work, we have evaluated the quasiparticle energies of ternary tetradymite Bi2Te2Se and Bi2Te2S using first-principles calculation within the G0W0 methods. We have also performed a broad convergence tests in order to investigate the quasiparticle corrections to the structural parameters and to the semi core d electrons in both of the compounds. For each case, we have calculated the many-body corrections within a one-shot GW method of the compounds. Our results have shown that for Bi2Te2Se the GW corrections increase the band gap to almost 10%, and for specific atomic positions, the band structure shows a close value to the experimental one. For Bi2Te2S, despite increase in the band gap due to the GW corrections, possibility of bulk resistivity that can be significant for photovoltaic applications was observed.
Highly skewed T-cell receptor V-beta chain repertoire in the bone marrow is associated with response to immunosuppressive drug therapy in children with very severe aplastic anemia (2011)

One of the major obstacles of immunosuppressive therapy (IST) in children with severe aplastic anemia (SAA) comes from the often months-long unpredictability of bone-marrow (BM) recovery. In this prospective study in children with newly diagnosed very severe AA (n=10), who were enrolled in the therapy study SAA-BFM 94, we found a dramatically reduced diversity of both CD4+ and CD8+ BM cells, as scored by comprehensive V-beta chain T-cell receptor (TCR) analysis. Strongly skewed TCR V-beta pattern was highly predictive for good or at least partial treatment response (n=6, CD8+ complexity scoring median 35.5, range 24-73). In contrast, IST in patients with rather moderate reduction of TCR V-beta diversity (n=4, CD8+ complexity scoring median 109.5, range 82-124) always failed (P=0.0095). If confirmed in a larger series of patients, TCR V-beta repertoire in BM may help to assign children with SAA up-front either to IST or to allogeneic stem-cell transplantation.
Interoperability of Single-Mode and Multimode Data Links for Data Center and Optical Backplane Applications (2013)

We show that a multimode fiber can support both single-mode “Si-Photonics” and multimode VCSEL technologies. This allows designers of data centers and optical backplanes to install one fiber infrastructure that is compatible with both technologies.
Beware the Boojum: Caveats and Strengths of Avian Radar (2013)

Radar provides a useful and powerful tool to wildlife biologists and ornithologists. However, radar also has the potential for errors on a scale not previously possible. In this paper, we focus on the strengths and limitations of avian surveillance radars that use marine radar front-ends integrated with digital radar processors to provide 360° of coverage. Modern digital radar processors automatically extract target information, including such various target attributes as location, speed, heading, intensity, and radar cross-section (size) as functions of time. Such data can be stored indefinitely, providing a rich resource for ornithologists and wildlife managers. Interpreting these attributes in view of the sensor’s characteristics from which they are generated is the key to correctly deriving and exploiting application-specific information about birds and bats. We also discuss (1) weather radars and air-traffic control surveillance radars that could be used to monitor birds on larger, coarser spatial scales; (2) other nonsurveillance radar configurations, such as vertically scanning radars used for vertical profiling of birds along a particular corridor; and (3) Doppler, single-target tracking radars used for extracting radial velocity and wing-beat frequency information from individual birds for species identification purposes.