gebhart/patrepeval huggingface dataset:
Shifted termination assay (STA) fragment analysis to detect BRAF V600 mutations in papillary thyroid carcinomas (2013)

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5684057089135749.
128x128 InGaAs detector array for 1.0-1.7 μm (1990)

A two-dimensional 128 x 128 detector array for the 1.0 - 1.7 micron spectral region has been demonstrated with indium gallium arsenide. The 30 micron square pixels had 60 micron spacing in both directions and were designed to be compatible with a 2D Reticon multiplexer. Dark currents below 100 pA, capacitance near 0.1 pF, and quantum efficiencies above 80 percent were measured. Probe maps of dark current and quantum efficiency are presented along with pixel dropout data and wafer yield which was as high as 99.89 percent (7 dropouts) in an area of 6528 pixels and 99.37 percent (103 dropouts) over an entire 128 x 128 pixel region.
Detection of MCT and MCTC types of human mast cells by immunohistochemistry using new monoclonal anti-tryptase and anti-chymase antibodies. (1989)

We developed an improved immunohistochemical technique for distinguishing human mast cells of the MCT (tryptase-positive, chymase-negative) and MCTC (tryptase-positive, chymase-positive) types utilizing a biotinylated murine anti-chymase monoclonal antibody (MAb), termed B7, and an alkaline phosphatase-conjugated murine anti-tryptase MAb, termed G3. The B7 MAb also was used to show the selective presence of chymase in mast cells. The distribution of MCT and MCTC cells in Carnoy's fluid-fixed tissue sections of human lung, skin, small intestine, and tonsils was analyzed by the new technique and the results compared to those obtained with the older method using a rabbit polyclonal antichymase antibody and a mouse anti-tryptase MAb in indirect immunoperoxidase and indirect immunoalkaline phosphatase protocols, respectively. In tissues known to contain predominantly mature mast cells, there were no quantitative differences between the two techniques, although the staining intensity achieved with the anti-chymase MAb was greater and without development of high background, compared to results achieved with the polyclonal antibody. MCT cells were the predominant type seen in the alveoli of the lung (93%) and in the small intestinal mucosa (81%). MCTC cells predominanted in the skin (99%) and in the small intestinal submucosa (77%) and, to a lesser degree, in tonsils (60%). However, in newborn foreskin tissue which contains predominantly immature forms of mast cells, 75% of all mast cells were stained uniformly and intensely with B7, whereas only 43% were stained with the polyclonal anti-chymase antibody. Therefore, the use of MAb provides for better standardization of reagents and more accurate assessment of the distribution of human MCT and MCTC cells in tissues than previously available methods.
Increased production of gliotoxin is related to the formation of biofilm by<i>Aspergillus fumigatus</i>: an immunological approach (2014)

Gliotoxin (GT) belongs to the epipolythiodioxopiperazine class of toxins secreted from certain fungi including Aspergillus fumigatus, which is the most prolific producer of this secondary metabolite. Recently, enhanced amounts of GT were found in in vitro biofilm-grown A. fumigatus mycelium. To further correlate the A. fumigatus biofilm growth phenotype with the enhanced secretion of GT, a polyclonal antibody (pAb) was produced by immunizing mice against GT. By an indirect immunofluorescent assay, pAb was then able to recognize specifically GT onto A. fumigatus Af293 biofilm formed on human pulmonary epithelial cells. Then, treating Af293 biofilms with a compound which reduces the GT disulfide bonds provoked shutdown of the GT-specific immunofluorescence (IF) signals along the hyphae. To explore the potential of GT for diagnostic use, pAb was shown to react with GT on hyphae into Aspergillus culture-positive respiratory tract specimens from patients with probable invasive aspergillosis (IA) and into tissue specimens from the lungs of patients with proven IA. As the presence of fungal hyphae in clinical specimens strongly indicates the in vivo A. fumigatus growth as a biofilm, anti-GT antibodies could be a specific and sensitive diagnostic tool for detecting A. fumigatus biofilm-associated clinical infections.
Characterization and comparison of four serine- and arginine-rich (SR) protein kinases (1997)

Phosphorylated serine- and arginine-rich (SR) proteins are components of the spliceosomal complex, and have been implicated in the control of alternative splicing. Kinases that regulate the phosphorylation and possibly the intranuclear distribution of SR proteins may therefore contribute to changes in choice of splice site. We have cloned three mouse cDNAs with high sequence identity to the family of LAMMER kinases (i.e. kinases carrying the conserved signature EHLAMMERILG in the catalytic domain). A comparison of their amino acid sequences revealed two related subfamilies with high evolutionary conservation. We have compared the expression patterns of these proteins in mouse tissues and transformed cell lines with that of a previously cloned family member (mCLK1/STY), and detected various transcripts for each gene. This underlines previous findings of alternative splicing of mclk1/STY. Our results suggest that the proportions of products for each gene are regulated independently. We further demonstrate that all variants encode autophosphorylating proteins that can phosphorylate several biochemically purified SR proteins in vitro, leading to hyperphosphorylation of at least one SR protein in vivo. The observed tissue distributions and substrate specificities suggest that these kinases may all be constituents of a network of regulatory mechanisms that enable SR proteins to control RNA splicing.
Pyrrolnitrin analogues. XI--Synthesis and microbiological activity of new 1,4- and 1,5-diarylpyrroles. (1985)

The synthesis and microbiological activities of new 1,4- and 1,5-diarylpyrroles is reported. Antimicrobial data in comparison with fungal antibiotic pyrrolnitrin confirm an interesting antimicotic activity of 1,4-diarylpyrroles. On the contrary 1,5-diarylpyrroles show antibacterial activity and an unexpected antimicotic activity. The position of the 4-nitrophenyl group at C4 or C5 of the pyrrole ring influences antibacterial activity.
Vinblastine-induced Apoptosis Is Mediated by Discrete Alterations in Subcellular Location, Oligomeric Structure, and Activation Status of Specific Bcl-2 Family Members (2006)

To gain a broader insight into the role of Bcl-2 proteins in apoptosis induced after mitotic arrest, we investigated the subcellular location, oligomeric structure, and protein interactions of Bax, Bcl-2, and Bcl-xL in vinblastine-treated KB-3 cells. Vinblastine induced the translocation of Bax from the cytosol to the mitochondria, which was accompanied by conformational activation and oligomerization of Bax. Bcl-2 was located in the mitochondria, underwent multisite phosphorylation after vinblastine treatment, and was strictly monomeric under all conditions. In contrast, in control cells, Bcl-xL existed in both monomeric (30 kDa) and oligomeric (150 kDa) forms. Treatment with agents that induced Bcl-xL phosphorylation (microtubule inhibitors) caused loss of the 150-kDa form, but this species was unaffected by apoptotic stimuli that did not stimulate phosphorylation. Vinblastine also promoted Bax activation and Bax oligomerization in HCT116 colon cancer cells. Both wild-type and Bax-deficient HCT116 cells expressed the 150-kDa form of Bcl-xL, which was depleted similarly in both cell lines upon vinblastine treatment. Co-immunoprecipitation studies revealed that in untreated KB-3 cells inactive cytosolic Bax interacted with Bcl-xL, whereas in vinblastine-treated cells, activated mitochondrial Bax did not interact with Bcl-xL. Interaction of Bcl-2 with Bax was not observed under any condition. Overexpression of Bcl-xL inhibited vinblastine-induced Bax activation and Bax dimerization and in parallel inhibited apoptosis. The results indicate that vinblastine-induced apoptosis requires translocation, activation, and oligomerization of Bax and is associated with specific changes in the oligomeric properties of Bcl-xL, which occur independently of Bax.
Exceptional second-order nonlinear optical susceptibilities of quinoid systems (1981)

A new class of organic quinoid systems possessing intrinsically large, nonlinear second-order optical susceptibilities has been developed based on theoretical calculations and dc-induced second-harmonic generation measurements of the molecular second-order optical susceptibilities β. For one example, 2-(4-dicyanomethylenecyclohexa-2, 5-dienylidine)-imidazolidine (DCNQI), βx = −240±60×10−30 cm5/esu. The unusually large magnitude and sign originate from certain charge-correlated features in the quinoid ground and excited states.
Metal-Cation-Directed <i>de Novo</i> Assembly of a Functionalized Guest Molecule in the Nanospace of a Metal–Organic Framework (2014)

In this work, a new strategy is developed to encapsulate a metal-functionalized guest molecule into a metal–organic framework (MOF) via metal-cation-directed de novo assembly from the component fragments of the guest molecule. This strategy, as illustrated in proof-of-principle studies on the de novo assembly of metal(II) phthalocyanine molecules into bio-MOF-1, can circumvent some drawbacks of existing approaches for encapsulating guest molecules into MOFs, such as inaccessibility for larger guest molecules due to limitations of the MOF window size and disruption of the MOF framework structure by functionalized guest molecules. Overall, this work provides a general yet versatile approach for encapsulating a broader range of metal-functionalized guest molecules into MOFs for various applications.
Reusing existing object-oriented code as web services in a SOA (2013)

This paper describes the reuse of existing classes and methods in an existing object-oriented system as web services in a service-oriented architecture. The approach presented here identifies the interfaces and public methods which can be invoked from outside and generates a WSDL interface to access them. It is a bottom-up approach to creating web services which allows business processes to reuse existing functionality. The tool SoftReuse described in this paper not only generates interfaces to existing public methods in Java and C# code, but also generates a visual documentation of those interfaces and test scripts for testing them. The test scripts use assertions to generate service requests as well as to validate the service responses. The goal is to build the reused services into new S-BPM business processes. This is an extension of the work already made with procedural languages and presented at a previous MESOCA Workshop.
Privacy-Preserving Deep Learning Based on Multiparty Secure Computation: A Survey (2021)

Deep learning (DL) has demonstrated superior success in various of applications, such as image classification, speech recognition, and anomalous detection. The unprecedented performance gain of DL largely depends on tremendous training data, high-performance computation resources, and well-designed model structures. However, privacy concerns raise from such necessities. First, as the training data are usually distributed among multiple parties, directly exposing and collecting such large amount of data could violate the laws especially for private information, such as personal identities, medical records, and financial profiles. Second, locally deploying advantageous computation resources is costly for individual party having partial data. Third, direct release of well-trained model parameters threatens the information about training data or the intellectual property of model owners. Therefore, individual party prefers outsourcing computation (data) in a secure way to powerful cloud servers such as Microsoft Azure, and how to enable the cloud servers to perform DL algorithms without revealing data owners’ private information and model owners’ valuable parameters is emerging as an urgent task, which is termed as privacy-preserving (outsourcing) DL. In this article, we review the state-of-the-art researches in privacy-preserving DL based on multiparty secure computation with data encryption and summarize these techniques in both training phase and inference phase. Specifically, we categorize the techniques with respect to the linear and nonlinear computations, which are the two basic building blocks in DL. Following a comprehensive overview of each research scheme, we present primary technical hurdles needed to be addressed and discuss several promising directions for future research.
Heat Shock Gene Expression Is Controlled Primarily at the Translational Level in Carrot Cells and Somatic Embryos. (1992)

We have determined that the synthesis of heat shock proteins is regulated ultimately at the translational level in heat-shocked carrot callus cells and somatic embryos. Polysome analysis revealed that heat-shocked callus cells do not translate most heat shock transcripts, which they abundantly synthesize and accumulate. By contrast, heat-shocked globular embryos accumulate low levels of heat shock mRNA but selectively translate more of the heat shock mRNA molecules compared to callus cells and embryos of later stages. The overall result of these different translational control schemes is that undifferentiated callus cells and globular embryos synthesize comparable levels of heat shock proteins even though they have large differences in heat shock transcript levels.
SP 800-38B. Recommendation for Block Cipher Modes of Operation: the CMAC Mode for Authentication (2005)

This Recommendation specifies a message authentication code (MAC) algorithm based on a symmetric key block cipher. This block cipher-based MAC algorithm, called CMAC, may be used to provide assurance of the authenticity and, hence, the integrity of binary data.
Analysis of Phase Separation in High Performance PbTe–PbS Thermoelectric Materials (2012)

Abstract Phase immiscibility in PbTe–based thermoelectric materials is an effective means of top‐down synthesis of nanostructured composites exhibiting low lattice thermal conductivities. PbTe 1‐ x S x thermoelectric materials can be synthesized as metastable solid solution alloys through rapid quenching. Subsequent post‐annealing induces phase separation at the nanometer scale, producing nanostructures that increase phonon scattering and reduce lattice thermal conductivity. However, there has yet to be any study investigating in detail the local chemical structure of both the solid solution and nanostructured variants of this material system. Herein, quenched and annealed (i.e., solid solution and phase‐separated) samples of PbTe–PbS are analyzed by in situ high‐resolution synchrotron powder X‐ray diffraction, solid‐state 125 Te nuclear magnetic resonance (NMR), and infrared (IR) spectroscopy analysis. For high concentrations of PbS in PbTe, e.g., x >16%, NMR and IR analyses reveal that rapidly quenched samples exhibit incipient phase separation that is not detected by state‐of‐the‐art synchrotron X‐ray diffraction, providing an example of a PbTe thermoelectric “alloy” that is in fact phase inhomogeneous. Thermally‐induced PbS phase separation in PbTe–PbS occurs close to 200 °C for all compositions studied, and the solubility of the PbS phase in PbTe at elevated temperatures >500 °C is reported. The findings of this study suggest that there may be a large number of thermoelectric alloy systems that are phase inhomogeneous or nanostructured despite adherence to Vegard's Law of alloys, highlighting the importance of careful chemical characterization to differentiate between thermoelectric alloys and composites.
Interference measurements of non-Abelian e/4 & Abelian e/2 quasiparticle braiding (2019)

The quantum Hall states at filling factors ν=5/2 and 7/2 are expected to have Abelian charge-e/2 quasiparticles and non-Abelian charge-e/4 quasiparticles. The non-Abelian statistics of the latter is predicted to display a striking interferometric signature, the even-odd effect. By measuring resistance oscillations as a function of the magnetic field in Fabry-Pérot interferometers using new high-purity heterostructures, we for the first time report experimental evidence for the non-Abelian nature of excitations at ν=7/2. At both ν=5/2 and 7/2, we also examine, for the first time, the fermion parity, a topological quantum number of an even number of non-Abelian quasiparticles. The phase of observed e/4 oscillations is reproducible and stable over long times (hours) near both filling factors, indicating stability of the fermion parity. At both fractions, when phase fluctuations are observed, they are predominantly π phase flips, consistent with either fermion parity change or change in the number of the enclosed e/4 quasiparticles. We also examine lower-frequency oscillations attributable to Abelian interference processes in both states. Taken together, these results constitute new evidence for the non-Abelian nature of e/4 quasiparticles; the observed lifetime of their combined fermion parity further strengthens the case for their utility for topological quantum computation.
Coumarin Derivatives-Part II : Synthesis and Screening of Some New Schiff Base Analogues of Formyl-7-Methoxycoumarin (1979)

Research <em>& </em>Development Department, Indian Drugs & Pharmaceuticals Limited, Hyderabad-500 037 <em>Manuscript received 3 May 1978, accepted 30 August 2978</em> A series of new Schiff base analogues derived from 4-formyl-7-methoxycoumar in has been<br> synthesised and screened for their \(in\) \(vitro\) antibacterial, antimycobacterial, antifungal,<br> anti-amoebic and \(in\) \(vivo\)anthelmintic properties.
A perceptive remote-control 3D TV interface (2007)

3D TV is a turning point in the history of television. Here, technologies from computer graphics, computer vision, multimedia, telecommunications, broadcasting, and other related fields merge to expand the sensations provided by watching conventional 2D TV.1 As a result, there has been much research on multi-view image processing and 3D display.2, 3 However, most of the previous studies have focused on acquiring and displaying images while optimizing their ‘naturalness’, simplicity of computation, and real-time operation. Free-viewpoint TV (FTV)4 takes this idea forward. Free-viewpoint systems allow a viewer to look at a scene from the perspective that they want rather than what a director chooses to provide.1 In order to generate a scene according to the user’s requirements, a position in 3D space has to be defined as the view point. To achieve this, we suggest an intelligent approach that automatically generates reference viewpoints based on a theory of human visual attention.Many studies of visual attention and eye movements have shown that humans generally only attend to a few areas in an image rather than scanning the whole, and visual attention models provide a general approach to controlling the activities of active vision systems.5 These models of selective visual attention have been suggested on the basis of evidence in psychology, psychophysics, physiology, etc., and can also be exploited for our purposes. Figure 1 shows an examples of how our artificial human visual attention system can be used to obtain a basis position to generate a scene that corresponds to a user’s viewpoint. The system also simultaneously computes the intensity of salience of an object in a given region. In fact, several objects or regions can be detected in terms of their their individual saliencies, which can in turn be used to describe them. The system computes early visual features from a set of pre-attentive feature maps in a massively parallel way. Activity from all feature maps is combined Figure 1. Schematic diagram showing the proposed system based on a bottom-up approach to attention.
Plasmonic Approach to Enhanced Fluorescence for Applications in Biotechnology and the Life Sciences (2012)

One of the most rapidly growing areas of physics and nanotechnology is concerned with plasmonic effects on the nanometer scale; these have applications in sensing and imaging technologies. Nanoplasmonic colloids such as Ag and Au have been attracting active interest, and there has been a recent explosion in the use of these metallic nanostructures to modify the spectral properties of fluorophores favorably and to enhance the fluorescence emission intensity. In this feature article, we summarize our work over a range of nanoplasmonics-assisted biological applications such as flow cytometry, immunoassays, cell imaging and bioassays where we use custom-designed plasmonic nanostructures (Ag and Au) to enhance fluorescence signatures. This fluorophore-metal effect offers unique advantages in providing improved photostability and enhanced fluorescence signals. We discuss the plasmonic enhancement of lanthanide fluorophores whose long and microsecond lifetimes offer the advantage of background-free fluorescence detection, but low photon cycling rates lead to poor brightness. We also show that plasmonic colloids are capable of enhancing the emission of fluorescent nanoparticles, including upconverting nanocrystals and lanthanide nanocomposites.
Reactive Ion Etching as Cleaning Method Post Chemical Mechanical Polishing for Phase Change Memory Device (2008)

In order to improve nano-scale phase change memory performance, a super-clean interface should be obtained after chemical mechanical polishing (CMP) of Ge2Sb2Te5 phase change films. We use reactive ion etching (RIE) as the cleaning method. The cleaning effect is analysed by scanning electron microscopy and an energy dispersive spectrometer. The results show that particle residue on the surface has been removed. Meanwhile, Ge2Sb2Te5 material stoichiometric content ratios are unchanged. After the top electrode is deposited, current-voltage characteristics test demonstrates that the set threshold voltage is reduced from 13 V to 2.7V and the threshold current from 0.1mA to 0.025mA. Furthermore, we analyse the RIE cleaning principle and compare it with the ultrasonic method.
A novel method for the measurement of the von Neumann spike in detonating high explosives (2016)

We present detonation wave profiles measured in T2 (97 wt. % TATB) and TX1 (52 wt. % TATB and 45 wt. % HMX) high explosives. The experiments consisted in initiating a detonation wave in a 15 mm diameter cylinder of explosive using an explosive wire detonator and an explosive booster. Free surface velocity wave profiles were measured at the explosive/air interface using a Photon Doppler Velocimetry system. We demonstrate that a comparison of these free surface wave profiles with those measured at explosive/window interfaces in similar conditions allows to bracket the von Neumann spike in a narrow range. For T2, our measurements show that the spike pressure lies between 35.9 and 40.1 GPa, whereas for TX1, it lies between 42.3 and 47.0 GPa. The numerical simulations performed in support to these measurements show that they can be used to calibrate reactive burn models and also to check the accuracy of the detonation products equation of state at low pressure.