gebhart/patrepeval huggingface dataset:
Abstract 763: Analytical validation of Ki67/CD8 duplex IHC assay using computational tissue analysis (cTATM) (2017)

Abstract Chromogenic multiplex immunohistochemistry (IHC) assays enable investigation of the spatial relationships between tumor and immune cells, which is thought to be important for understanding and predicting therapeutic response. Development and analytical validation of multiplex IHC assays enables the use of such assays to simultaneously investigate multiple biomarkers as predictors of clinical response. In this study, we analytically validated a chromogenic duplex IHC assay that quantifies Ki67 and CD8 in formalin-fixed, paraffin-embedded non-small cell lung cancer tissues. Five performance criteria were selected and evaluated based on Clinical Laboratory Standards Institute guidelines: reportable range, analytical sensitivity, analytical specificity, accuracy, and precision. Similar to analytical validation studies for monoplex IHC assays, this study utilized a reference method and multiple days of staining. The percentage of cells positive for Ki67 nuclear staining and/or CD8 membrane staining were quantified using our computational Tissue Analysis (cTATM) platform. Performance of the Ki67/CD8 chromogenic duplex IHC assay was considered acceptable for the five criteria evaluated. Once the performance of the assay was established, additional exploratory cTA-based endpoints were examined, including the quantification of each biomarker in the tumor compartment and the tumor microenvironment, and analysis of the spatial arrangement of immune cells relative to tumor cells. In conclusion, Flagship’s cTA platform allows for more consistent quantification of individual analytes on dual-stained tissue sections, enabling investigation of complex biological questions that cannot be achieved with traditional tissue-based manual endpoints. Citation Format: Staci J. Kearney, Joshua C. Black, Benjamin J. Landis, Sally Koegler, Brooke Hirsch, Roberto Gianani. Analytical validation of Ki67/CD8 duplex IHC assay using computational tissue analysis (cTATM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 763. doi:10.1158/1538-7445.AM2017-763
TRAC (2007)

Traffic congestion is a major cause of concern in many cities. A real-time information dissemination system announcing current traffic conditions to travelers is increasingly becoming a necessity in this context. The recent DSRC research initiative[1] envisions a deployment of DSRC access points (APs) along the road side to enable Vehicle to Roadside Communication (VRC) for this purpose. However, even if such an infrastructure is deployed on the roadside, it is not trivial to design a system that distributes on-demand traffic information. Existing solutions employ a centrialized design where the traffic information is stored at a central database and the vehicles then query the database for information of their interest. Such solutions are simply not scalable due to the huge volume of queries the central database would have to handle. Moreover, such a communication architecture does not take into account the fact that traffic related queries are location sensitive and that the sources for a particular query also tend to be localized .
<title>First application of second-generation steel-free deck slabs for bridge rehabilitation</title> (2004)

The arching action in concrete deck slabs for girder bridges is utilized fully in steel-free deck slabs. These concrete slabs, requiring no tensile reinforcement, are confined longitudinally by making them composite with the girders, and transversely by external steel straps connecting the top flanges of external girders. Between 1995 and 1999, five steel-free deck slabs without any tensile reinforcement were cast on Canadian bridges. All these slabs developed fairly wide full-depth cracks roughly midway between the girders. While extensive fatigue testing done in the past three years has confirmed that the presence of even wide cracks does not pose any danger to the safety of the structures, wide cracks are generally not acceptable to bridge engineers. The developers of the steel-free deck slabs have now conceded that these slabs should be reinforced with a crack-control mesh of nominal glass fibre reinforced polymer (GFRP) bars. Steel-free deck slabs with crack-control meshes are being referred as the second generation slabs. With the help of testing on full-scale models, it has been found that deck slabs with GFRP bars have the best fatigue resistance and those with steel bars the worst.
Etodolac, aspirin, and gastrointestinal microbleeding (1984)

The effects of etodolac, a new nonsteroidal anti-inflammatory drug, on gastrointestinal (GI) microbleeding were quantitatively assessed in two studies in healthy adult men. The first was a two-group, open-label, parallel comparison of etodolac, 600 mg/day, aspirin, 2600 mg/day, and placebo in 20 subjects; the second was a four-group, double-blind, parallel comparison of etodolac, 600, 800, and 1200 mg/day, aspirin, 2600 mg/day, and placebo in 41 subjects. Subjects in both studies received a single-blind placebo on days 1 through 7, either etodolac or aspirin on days 8 through 14, and a single-blind placebo on days 15 through 19. GI blood loss (milliliters per day) was estimated by the radiolabeled (51Cr) erythrocyte method and was based on daily radioactivity counts of stool specimens and regression-estimated daily blood radioactivity. Etodolac, 600 mg/day, induced no significant GI blood loss at any time during the experiments, nor was there significant blood loss after 800 and 1200 mg/day in experiment 2. Blood loss was noted after aspirin in both.
Cyclic tensile strain triggers a sequence of autocrine and paracrine signaling to regulate angiogenic sprouting in human vascular cells (2009)

Mechanical signals regulate blood vessel development in vivo, and have been demonstrated to regulate signal transduction of endothelial cell (EC) and smooth muscle cell (SMC) phenotype in vitro. However, it is unclear how the complex process of angiogenesis, which involves multiple cell types and growth factors that act in a spatiotemporally regulated manner, is triggered by a mechanical input. Here, we describe a mechanism for modulating vascular cells during sequential stages of an in vitro model of early angiogenesis by applying cyclic tensile strain. Cyclic strain of human umbilical vein (HUV)ECs up-regulated the secretion of angiopoietin (Ang)-2 and PDGF-betabeta, and enhanced endothelial migration and sprout formation, whereas effects were eliminated with shRNA knockdown of endogenous Ang-2. Applying strain to colonies of HUVEC, cocultured on the same micropatterned substrate with nonstrained human aortic (HA)SMCs, led to a directed migration of the HASMC toward migrating HUVECs, with diminished recruitment when PDGF receptors were neutralized. These results demonstrate that a singular mechanical cue (cyclic tensile strain) can trigger a cascade of autocrine and paracrine signaling events between ECs and SMCs critical to the angiogenic process.
Fusion Reactor Safety Research Program annual report, FY-79 (1980)

The objective of the program is the development, coordination, and execution of activities related to magnetic fusion devices and reactors that will: (a) identify and evaluate potential hazards, (b) assess and disclose potential environmental impacts, and (c) develop design standards and criteria that eliminate, mitigate, or reduce those hazards and impacts. The program will provide a sound basis for licensing fusion reactors. Included in this report are portions of four reports from two outside contractors, discussions of the several areas in which EG and G Idaho is conducting research activities, a discussion of proposed program plan development, mention of special tasks, a review of fusion technology program coordination by EG and G with other laboratories, and a brief view of proposed FY-80 activities.
Lower and upper bounds on the switching activity in scheduled data flow graphs (1999)

In this paper we present an approach to calculate lower and upper bounds for the switching activity in scheduled data flow graphs. The technique can be used to prune the design space in high level synthesis for low power before allocation and binding of functional units and registers. The low power allocation and binding problem is formulated. It is shown that this problem can be relaxed to the bipartite weighted matching problem which is solvable in O(n3) where n is the number of functional units or registers, respectively. The application of the technique on benchmarks shows the tightness of the bounds. Most of the investigated bounds were less than 1% off the minimum respectively maximum solutions.
A theoretical study of α‐substituted cyclopropyl and isopropyl radicals (1985)

Abstract The structures of α‐ X ‐cyclopropyl and α‐ X ‐isopropyl radicals ( X = H, CH 3 , NH 2 , OH, F, CN, and NC) are reported at the RHF 3‐21G level of theory. The isopropyl radicals are pyramidal with out‐of‐plane angles varying from 12° ( X = CN) to 39° ( X = NH 2 ), and barriers to inversion ranging from 0.4 kcal/mol ( X = H) to 4.0 kcal/mol ( X = NH 2 ). The cyclopropyl radicals have larger out‐of‐plane angles, from 39.9° ( X = CN) to 49.4° ( X = NH 2 ), and their barriers to inversion, which increase with the inclusion of polarization functions, vary from 5.5 kcal/mol ( X = H) to 16.7 kcal/mol ( X = F). In both types of radicals the amino group is the most stabilizing substituent, while the α‐fluoro has little effect. The β‐fluoro group is weakly destabilizing in the cyclopropyl radical. The strain energies of the cyclopropyl radicals (36–43 kcal/mol) are compared with those of similarly substituted anions, cations, and cyclopropanes.
Estimating Flow-Through Balance Momentum Tares with CFD (Invited) (2016)

This paper describes the process used for estimating flow-through balance momentum tares. The interaction of jet engine exhausts on the BOEING/ERA Hybrid Wing Body (HWB) was simulated in the NFAC 40x80 wind tunnel at NASA Ames using a pair of turbine powered simulator (TPS) units. High-pressure air was passed through a flow-through balance and manifold before being delivered to the TPS units. The force and moment tares that result from the internal shear and pressure distribution were estimated using CFD. Validation of the CFD simulations for these complex internal flows is a challenge, given limited experimental data due to the complications of the internal geometry. Two CFD validation efforts are documented, and comparisons with experimental data from the final model installation are provided.
Tunable Dual-Band Microwave Devices based on a Combination of Left/Right-Handed Transmission Lines (2008)

Metamaterial transmission lines can be realized as a combination of transmission line sections with positive and negative dispersion. Such lines, which are also known as right- and left-handed transmission lines, exhibit different dispersion characteristics. Compared to homogeneous networks, the use of cascaded line sections gives additional degrees of freedom for improving the performance of microwave devices. For the design process, LC-equivalents of the right- and left-handed transmission line sections are used. This facilitates the consideration of tunable capacitors, e.g., varactor diodes, to provide frequency tuning of the devices. At the same time, the geometrical dimensions of the devices can be drastically reduced. This paper presents the results of simulation and experimental investigation of a miniature rat-race-ring and a dual-band filter free of spurious response, both manufactured as fully-integrated ceramic multilayer modules based on Low-Temperature Co-fired Ceramics. The design of tunable versions of these devices is also discussed.
Knowledge-based parameters for HMM speech recognition (2002)

This paper presents acoustic parameters (APs) that were motivated by phonetic feature theory and employed as a signal representation of speech in a hidden Markov model (HMM) recognition framework. Presently, the phonetic features considered are the manner features: sonorant, syllabic, nonsyllabic, noncontinuant and fricated. The objective of the parameters is to directly target the linguistic information in the signal and to reduce the speaker-dependent information that may yield large speech variability. To achieve these goals, the APs were defined in a relational manner across time or frequency. For evaluation, broad-class recognition experiments were conducted comparing the APs to cepstral-based parameters. The results of the experiments indicate that the APs are able to capture the phonetically relevant information in the speech signal and that, in comparison to the cepstral-based parameters, they are more able to reduce the interspeaker variability.
Low frequency gyro-synchrotron radio noise from the earth's outer radiation belt (1973)

The problem of detecting cyclotron and synchrotron noise from superthermal electrons is analyzed for the frequency range 30 kHz 300 kHz. Due to the earth's ionosphere, ground based observation of this noise is improbable. Therefore, the calculations are made for an observer in the interplanetary medium. In particular, the location is chosen in the geomagnetic equatorial plane at a geocentric distance of 32 earth radii. This position of the observer allows the theoretical results to be compared directly with data obtained from the radio astronomy experiment aboard the IMP-6 spacecraft.
A Versatile System for Ocular Topographic Sensing Based on Two Low Coherence Interferometers (1997)

Low coherence interferometry has emerged in the last decade as a powerful and high precision investigative tool for various applications and recently in medicine and particularly in ophthalmology [1-3].
Side Reactions Catalyzed by Ribulose-bisphosphate Carboxylase in the Presence and Absence of Small Subunits (1997)

The large subunit core of ribulose-bisphosphate carboxylase from Synechococcus PCC 6301 expressed in Escherichia coli in the absence of its small subunits retains a trace of carboxylase activity (about 1% of the kcat of the holoenzyme) (Andrews, T. J (1988) J. Biol. Chem. 263, 12213-12219). During steady-state catalysis at substrate saturation, this residual activity diverted approximately 10% of the reaction flux to 1-deoxy-D-glycero-2,3-pentodiulose-5-phosphate as a result of beta elimination of inorganic phosphate from the first reaction intermediate, the 2,3-enediol form of ribulose bisphosphate. This indicates that the active site's ability to stabilize and/or retain this intermediate is compromised by the absence of small subunits. Epimerization and isomerization of the substrate resulting from misprotonation of the enediol intermediate were not significantly exacerbated by lack of small subunits. The residual carboxylating activity partitioned product between pyruvate and 3-phosphoglycerate in a ratio similar to that of the holoenzyme, indicating that stablization of the penultimate three-carbon aci-acid intermediate is not perturbed by lack of small subunits. The underlying instability of the five-carbon enediol intermediate was revealed, even with the holoenzyme, under conditions designed to lead to exhaustion of substrate CO2 (and O2). When carboxylation (and oxygenation) stalled upon exhaustion of gaseous substrate, both spinach and Synechococcus holoenzymes continued slowly to beta eliminate inorganic phosphate from and to misprotonate the enediol intermediate. With carboxylation and oxygenation blocked, the products of these side reactions of the enediol intermediate accumulated to readily detectable levels, illustrating the difficulties attendant upon ribulose-P2 carboxylase's use of this reactive species as a catalytic intermediate.
Design and performance evaluation of unbuffered self-routing networks for wideband packet switching (2002)

It is shown, through analysis and simulation, that the maximum throughput of an unbuffered self-routing network is greater for fixed packet lengths than for exponentially distributed packet lengths. This means that the maximum throughput of an unbuffered self-routing network will be different for different applications if they do not have the same packet length distribution.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Inhibition of the Translocation of Estrogen Receptor from the Cytoplasm into the Nucleus by Estrogen Receptor-Binding Factors1 (1982)

The molecular mechanism of the translocation of estrogen receptor (ER) from the cytoplasm into the nucleus was studied in an in vitro system taking into account the specific interactions of the basic constituents of the uterine ER-system which had been reported previously (Murayama, A. et al. (1980) J. Biochem. 88, 1457). It was found that ER is translocated from the cytoplasm into the nucleus in the form of vero-ER . estradiol (basic ER-unit bound with estradiol; sedimentation coefficient, 4.5S; Stokes radius, 44 A; Kd for estradiol, approximately 10(-10) M) dissociated from coexisting estrogen receptor-binding factors (ERBFs). ERBFs inhibited the translocation of vero-ER into nuclei through binding with it. The apparent equilibrium dissociation constants (Kd) of ERBFs for vero-ER were estimated by Scatchard analysis to be 2.6 X 10(-10) M ["5S" ER-forming factor ("5S" ER-FF)], 3.0 X 10(-9) M ("6S" ER-FF), and 2.5 X 10(-9) M ("8S" ER-FF), respectively. The inhibitory effects of ERBFs on the binding of vero-ER to the nucleus paralleled their association constants.
DNase I sensitivity of integrated simian virus 40 DNA. (1984)

We undertook an analysis of integrated simian virus 40 (SV40) DNA to learn whether the DNase I-sensitive region is retained in the integrated array of mouse transformants. Our results indicate that full-length integrated SV40 chromatin retains a DNase I-hypersensitive region at the same point as in nonintegrated SV40 chromatin. Thus, the lack of a DNase I-hypersensitive region is not likely to be the reason for nonpermissivity of SV40 in mouse cells. In addition, results reported here indicate that a deletion of about 200 base pairs of DNA in the region of the DNase I-hypersensitive site severely reduces the sensitivity of integrated SV40 chromatin. This result is similar to a previously reported result obtained with deletion mutants of SV40 analyzed in the lytic cycle. It is the first report of a DNA lesion affecting DNase I hypersensitivity of a mammalian chromosome.
Assessment of a low-cost protocol for an<i>ab initio</i>based prediction of the mixing enthalpy at elevated temperatures: The Fe-Mo system (2011)

We demonstrate how a limited number of ab initio calculations in combination with a simple Debye model can predict a concentration- and temperature-dependent mixing enthalpy for a binary system. Fe-Mo is taken as a test case, and our predictions are compared with phase diagram information and a recently measured heat of solution for Mo in Fe. Crystallographic and magnetic information is calculated for the $\ensuremath{\lambda}$ and $\ensuremath{\mu}$ intermetallic phases in the Fe-Mo phase diagram as well. The present methodology can be useful for making a quick survey of mixing enthalpies in a large set of binary systems, in particular in the dilute concentration ranges where tabulated data are often lacking and where calphad-style modeling is less reliable.
Effect of bone conditioning on primary stability of FRIALIT‐2<sup>®</sup> implants (2007)

The study shows that bone condensing yields an improved histologic implant-bone contact only in spongy bone, which was paralleled by radiographic-densitometric findings.
New Adaptive Calibration Method for Time Interleaved Analog to Digital Converters (2007)

International audience
Computational Insight Concerning Catalytic Decision Points of the Transition Metal Catalyzed [2 + 2 + 1] Cyclocarbonylation Reaction of Allenes (2006)

Rhodium and molybdenum catalyzed allenic [2 + 2 + 1] cycloaddition reactions give 4-alkylidene and α-alkylidene cylopentenones, respectively. The selective reaction of one double bond of the allene over another is controlled by the transition metal and not the substrate structure. Calculations were performed to explain this unique control element using the B3LYP functional as implemented in Gaussian 03. The 6-31G(d) basis set was applied to all elements except rhodium, which is described with the LANL2 effective core potential and the LANL2DZ basis set. The product-determining step for both reaction pathways is oxidative addition of the metal to the alkynyl allene to form the corresponding metallocycles B and B'. The transition state calculations strongly suggest that geometry constraints imposed by the metal in the transition state are the key controlling factor of the double bond selectivity. The transition state structure of rhodium-catalyzed oxidative addition has a distorted square planar geometry that affords a lower transition state energy when coordinated to the distal double bond of the allene. In turn, the distorted trigonal bipyramidal geometry of molybdenum in the transition state structure imposes conformational constraints upon binding to the distal double on the allene and thus leads to the energetically preferred complexation and reaction with the proximal double bond.
Force-Torque Input Enhances Medical VR Applications (2003)

Force-torque measuring input devices can significantly enhance the performance of classical simulation environments that are, for example, based on pure passive phantoms. Such devices allow not only the determination of force/torque amplitude and direction but also the contact point, where a torque-free force is applied to the phantom. The force/torque information can be displayed visually or acoustically, drive a realistic graphical animation environment or it can be saved and compared with a haptic library comprising the force/torque history of any medical specialist.
Quantum mechanics (2015)

The behavior of classical macroscopic particles – from baseballs to planets – is governed by Newtonian mechanics as we have described in the first chapters of this book. The behavior of very small particles, on the other hand, is governed by an entirely different collection of equations and rules that go under the name of “quantum mechanics” and these particles are referred to as quantum particles. These rules have analogies to classical mechanics, but are fundamentally different and somewhat mysterious as we discussed in Chapter 8. The fundamental principles of quantum mechanics cannot be proven to be correct. They were developed based on the results of experimental observation, by analogy with classical mechanics, and through the consideration of logical implications of the formalisms used. There is no way to derive the fundamental elements of quantum mechanics, any more than one could predict from first principles that Newtonian forces should add as vectors. On the other hand, quantum mechanics is among the most rigorously tested theories in science, and the predictions of quantum mechanics have, so far, always been in agreement with experiment. In this chapter, we will present quantum mechanics as a series of postulates and examine their implications in application to simple one-dimensional systems. In the next chapter we will examine quantum effects in real systems including atoms, molecules, crystals, and artificially engineered nano-structures.
Interseasonal heat storage in silica-alumina based composites (2013)

International @ ENERGIE+AJH:SBE:AAU