gebhart/patrepeval huggingface dataset:
Using electronic neutron generators in active interrogation to detect shielded fissionable material (2008)

Experiments have been performed at Idaho National Laboratory to study methodology and instrumentation for performing neutron active interrogation die-away analyses for the purpose of detecting shielded fissionable material. Here we report initial work using a portable DT electronic neutron generator with a He-3 fast neutron detector to detect shielded fissionable material including enriched uranium and reactor grade plutonium. Measurements have been taken of bare material as well as of material hidden within a large plywood cube. Results from this work have demonstrated the efficacy of the die-away neutron measurement technique for quickly detecting the presence of special nuclear material hidden within plywood shields by analyzing the time dependent neutron signals in-between neutron generator pulses. Using a DT electronic neutron generator operating at 300 Hz with a yield of approximately 0.36 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> neutrons per second, 2.2 kg of enriched uranium hidden within a 0.60 m x 0.60 m x 0.70 m volume of plywood was positively detected with a measurement signal 2-sigma above the passive background within 1 second. Similarly, for a 500 second measurement period a lower detection limit of approaching the gram level could be expected with the same simple set-up.
Transcriptome-wide association study reveals cholesterol metabolism gene Lpl is a key regulator of cognitive dysfunction (2022)

Cholesterol metabolism in the brain plays a crucial role in normal physiological function, and its aberrations are associated with cognitive dysfunction. The present study aimed to determine which cholesterol-related genes play a vital role in cognitive dysfunction and to dissect its underlying molecular mechanisms using a systems genetics approach in the BXD mice family. We first systematically analyzed the association of expression of 280 hippocampal genes related to cholesterol metabolism with cognition-related traits and identified lipoprotein lipase (Lpl) as a critical regulator. This was further confirmed by phenome-wide association studies that indicate Lpl associated with hippocampus volume residuals and anxiety-related traits. By performing expression quantitative trait locus mapping, we demonstrate that <i>Lpl</i> is strongly <i>cis-</i>regulated in the BXD hippocampus. We also identified ∼3,300 genes significantly (<i>p</i> < 0.05) correlated with the <i>Lpl</i> expression. Those genes are mainly involved in the regulation of neuron-related traits through the MAPK signaling pathway, axon guidance, synaptic vesicle cycle, and NF-kappa B signaling pathway. Furthermore, a protein-protein interaction network analysis identified several direct interactors of Lpl, including Rab3a, Akt1, Igf1, Crp, and Lrp1, which indicates that Lpl involves in the regulation of cognitive dysfunction through Rab3a-mediated synaptic vesicle cycle and Akt1/Igf1/Crp/Lrp1-mediated MAPK signaling pathway. Our findings demonstrate the importance of the Lpl, among the cholesterol-related genes, in regulating cognitive dysfunction and highlighting the potential signaling pathways, which may serve as novel therapeutic targets for the treatment of cognitive dysfunction.
Semi-Supervised Node Classification by Graph Convolutional Networks and\n Extracted Side Information (2020)

The nodes of a graph existing in a cluster are more likely to connect to each\nother than with other nodes in the graph. Then revealing some information about\nsome nodes, the structure of the graph (graph edges) provides this opportunity\nto know more information about other nodes. From this perspective, this paper\nrevisits the node classification task in a semi-supervised scenario by graph\nconvolutional networks (GCNs). The goal is to benefit from the flow of\ninformation that circulates around the revealed node labels. The contribution\nof this paper is twofold. First, this paper provides a method for extracting\nside information from a graph realization. Then a new GCN architecture is\npresented that combines the output of traditional GCN and the extracted side\ninformation. Another contribution of this paper is relevant to non-graph\nobservations (independent side information) that exists beside a graph\nrealization in many applications. Indeed, the extracted side information can be\nreplaced by a sequence of side information that is independent of the graph\nstructure. For both cases, the experiments on synthetic and real-world datasets\ndemonstrate that the proposed model achieves a higher prediction accuracy in\ncomparison to the existing state-of-the-art methods for the node classification\ntask.\n
Lithographic performance of recent DUV photoresists (1998)

Commercially available photoresists from the major photoresist vendors are investigated using a PAS 5500/300 wafer stepper, a 31.1 mm diameter field size high throughput wafer stepper with variable NA capability up to 0.63. The critical dimension (CD) investigated is 0.25 micrometers and lower for dense and isolated lines and 0.25 micrometers for dense contact holes. The photoresist process performance is quantified by measuring exposure-defocus windows for a specific resolution using a CD SEM. Photoresists that are comparable with or better than APEX-E with RTC top coat, which is the current base line process for lines and spaces imaging performance, are Clariant AZ-DX1300 and Shin Etsu SEPR-4103PB50. Most recent photoresists have much improved delay performance when compared to APEX without top coat. Improvement, when an organic BARC is applied, depends on the actual photoresist characteristics. The optimal photoresist found for 0.25 micrometers contact holes is TOK DP015 C. This process operates at optimal conditions.
Performance modeling of virtualized custom logic computations (2014)

Virtualization of custom logic computations (i.e., by sharing a fixed function across distinct data streams), provides a means of reusing limited hardware resources. This is common practice in traditional processors where more than one user can share processor resources. In this paper, we virtualize a custom logic block using C-slow techniques to support fine-grain context-switching. We then develop and present an analytic model for several performance measures (throughput, latency, input queue occupancy) for both fine- and coarse-grained context switching. Next, we calibrate the analytic performance model with empirical measurements. We then validate the model via discrete-event simulation and use the model to predict the performance and develop optimal schedules for virtualized logic computations.
Loss of the TOR Kinase Tor2 Mimics Nitrogen Starvation and Activates the Sexual Development Pathway in Fission Yeast (2007)

Fission yeast has two TOR (target of rapamycin) kinases, namely Tor1 and Tor2. Tor1 is required for survival under stressed conditions, proper G(1) arrest, and sexual development. In contrast, Tor2 is essential for growth. To analyze the functions of Tor2, we constructed two temperature-sensitive tor2 mutants. Interestingly, at the restrictive temperature, these mutants mimicked nitrogen starvation by arresting the cell cycle in G(1) phase and initiating sexual development. Microarray analysis indicated that expression of nitrogen starvation-responsive genes was induced extensively when Tor2 function was suppressed, suggesting that Tor2 normally mediates a signal from the nitrogen source. As with mammalian and budding yeast TOR, we find that fission yeast TOR also forms multiprotein complexes analogous to TORC1 and TORC2. The raptor homologue, Mip1, likely forms a complex predominantly with Tor2, producing TORC1. The rictor/Avo3 homologue, Ste20, and the Avo1 homologue, Sin1, appear to form TORC2 mainly with Tor1 but may also bind Tor2. The Lst8 homologue, Wat1, binds to both Tor1 and Tor2. Our analysis shows, with respect to promotion of G(1) arrest and sexual development, that the loss of Tor1 (TORC2) and the loss of Tor2 (TORC1) exhibit opposite effects. This highlights an intriguing functional relationship among TOR kinase complexes in the fission yeast Schizosaccharomyces pombe.
Lead Optimization of 4-Acetylamino-2-(3,5-dimethylpyrazol-1-yl)-6-pyridylpyrimidines as A2AAdenosine Receptor Antagonists for the Treatment of Parkinson’s Disease (2008)

4-Acetylamino-2-(3,5-dimethylpyrazol-1-yl)-pyrimidines bearing substituted pyridyl groups as C-6 substituents were prepared as selective adenosine hA2A receptor antagonists for the treatment of Parkinson's disease. The 5-methoxy-3-pyridyl derivative 6g (hA2A Ki 2.3 nM, hA1 Ki 190 nM) was orally active at 3 mg/kg in a rat HIC model but exposure was poor in nonrodent species, presumably due to poor aqueous solubility. Follow-on compound 16a (hA2A Ki 0.83 nM, hA1 Ki 130 nM), bearing a 6-(morpholin-4-yl)-2-pyridyl substituent at C-6, had improved solubility and was orally efficacious (3 mg/kg, HIC) but showed time-dependent cytochrome P450 3A4 inhibition, possibly related to morpholine ring metabolism. Compound 16j (hA2A Ki 0.44 nM, hA1 Ki 80 nM), bearing a 6-(4-methoxypiperidin-1-yl)-2-pyridyl substituent at C-6, was sparingly soluble but had good oral exposure in rodent and nonrodent species, had no cytochrome P450 or human ether-a-go-go related gene channel issues, and was orally efficacious at 1 mg/kg in HIC and at 3 mg/kg for potentiation of l-dopa-induced contralateral rotations in 6-hydroxydopamine-lesioned rats.
AdReveal (2013)

To address the pressing need to provide transparency into the online targeted advertising ecosystem, we present AdReveal, a practical measurement and analysis framework, that provides a first look at the prevalence of different ad targeting mechanisms. We design and implement a browser based tool that provides detailed measurements of online display ads, and develop analysis techniques to characterize the contextual, behavioral and re-marketing based targeting mechanisms used by advertisers. Our analysis is based on a large dataset consisting of measurements from 103K webpages and 139K display ads. Our results show that advertisers frequently target users based on their online interests; almost half of the ad categories employ behavioral targeting. Ads related to Insurance, Real Estate and Travel and Tourism make extensive use of behavioral targeting. Furthermore, up to 65% of ad categories received by users are behaviorally targeted. Finally, our analysis of re-marketing shows that it is adopted by a wide range of websites and the most commonly targeted re-marketing based ads are from the Travel and Tourism and Shopping categories.
Tachykinin Antagonists in Asthma and Inflammation (2020)

The term “tachykinin” was coined to describe the relatively fast development of the contractile action produced by these peptides in smooth muscles. In addition to vasodilatation and leakage of plasma proteins, the adhesion of granulocytes to endothelial cells and their subsequent migration into inflamed tissues is an integral and important component of neurogenic inflammation. In particular, the prominent inflammatory and proinflammatory actions exerted by tachykinins (TKs) in the airways and in other regions of the body provide the basis for speculating a role of TK receptor antagonists as a new class of drugs to be used for treatment of asthma and/or other inflammatory diseases. A complex question is whether stimulation of granulocyte infiltration into tissues by TKs is a direct effect on granulocytes or is produced indirectly; clearly, the results of studies implicating mast cells degranulation in granulocyte migration by substance P favor the second hypothesis.
Twist-bend heliconical chiral nematic liquid crystal phase of an achiral rigid bent-core mesogen (2014)

The chiral, heliconical (twist-bend) nematic ground state is reported in an achiral, rigid, bent-core mesogen (UD68). Similar to the nematic twist-bend (N(TB)) phase observed in bent molecular dimers, the N(TB) phase of UD68 forms macroscopic, smecticlike focal-conic textures and exhibits nanoscale, periodic modulation with no associated modulation of the electron density, i.e., without a detectable lamellar x-ray reflection peak. The N(TB) helical pitch is p(TB) ∼ 14 nm. When an electric field is applied normal to the helix axis, a weak electroclinic effect is observed, revealing 50-μm-scale left- and right-handed domains in a chiral conglomerate.
Hybrid electronic-photonic subwavelength cavities operating at terahertz frequencies (2013)

We report on the concept and realization of terahertz (THz) metallic/semiconductor cavities characterized by dimensions as small as ${\ensuremath{\lambda}}_{\mathrm{eff}}$/9 in all directions of space (or \ensuremath{\lambda}/30 with the vacuum wavelength). We experimentally prove that the capacitance and inductance of these devices are not interdependent, as in purely photonic cavities, but that they can be adjusted almost independently, as in an electronic circuit. This functionality proves that the dimensions of these hybrid electronic-photonic devices are intrinsically not limited by diffraction as in conventional photonic resonators. Using arguments from transmission line theory, we show that it is necessary to include at least one metallic loop in the cavity design to access this regime and we note, as a corollary, that some recent proposals to miniaturize THz resonators and devices beyond the diffraction limit do not meet this fundamental requirement. Our results shed a light on the ability to describe THz/metallic cavities in terms of circuit elements. Furthermore, upon insertion of electrical contacts, these extremely subwavelength resonators can potentially lead to advances in THz detectors and phased array antennas.
Experimental Investigation of the Effects of Fluid Properties and Geometry on Forced Convection in Finned Ducts With Flow Pulsation (2009)

An experimental study was conducted on the effects of flow pulsation on the convective heat transfer coefficients in a flat channel with series of regular spaced fins. Glycerol-water mixtures with dynamic viscosities in the range of 0.001–0.01 kg/ms were used as working fluids. The device contains fins fixed to the insulated wall opposite to the flat and smooth heat transfer surface to avoid any heat transfer enhancement by conduction of the fins. Pulsation amplitude xo=0.37 mm and pulsation frequencies f in the range of 10 Hz&lt;f&lt;47 Hz were applied, and a steady-flow Reynolds number in the laminar range of 10&lt;Re&lt;1100 was studied. The heat transfer coefficient was found to increase with increasing Prandtl number Pr at a constant oscillation Reynolds number Reosc. The effect of the dh/L ratio was found to be insignificant for the system with series of fins and flow pulsation due to proper fluid mixing in contrast to a steady finned flow. A decrease in heat transfer intensification was obtained at very low and high flow rates. The heat transfer was concluded to be dynamically controlled by the oscillation.
Nanoporous tin(IV) sulfides: Thermochemical properties (1995)

The porosity, the integrity of the framework and any envisaged applications of sulfide‐based nanoporous layered materials produced using organic templates, depend upon the stability of the materials with respect to the thermally induced template removal process. Here, the thermochemical properties of two such materials are examined using a variety of techniques and conclusions drawn concerning the thermal stability range and the reconstructio processes which take place.
Dynamic Control of Speed and Trajectories of Active Droplets in a Nematic Environment by Electric Field and Focused Laser Beam (2021)

One objective of active matter science is to unveil principles by which chaotic microscale dynamics could be transformed into useful work. A nematic liquid crystal environment offers a number of possibilities, one of which is a directional motion of an active droplet filled with an aqueous dispersion of swimming bacteria. In this work, using the responsiveness of the nematic to the electric field and light, we demonstrate how to control the direction and speed of active droplets. The dielectric response of nematic to the electric field causes two effects: 1) reorientation of the overall director, and 2) changing the symmetry of the director configuration around the droplet. The first effect redirects the propulsion direction while the second one changes the speed. A laser beam pointed to the vicinity of the droplet can trigger the desired director symmetry around the droplet, by switching between dipolar and quadrupolar configurations, thus affecting the motility and polarity of propulsion. The dynamic tuning of the direction and speed of active droplets represents a step forward in the development of controllable microswimmers.
Coherent-Image Reconstruction Using Convolutional Neural Networks (2019)

We describe a technique for incorporating convolutional-neural-network models into a comprehensive approach for coherent-image reconstruction in the presence of noise and phase errors using the consensus equilibrium framework.
Radio channel sounding using a circular horn antenna array in the horizontal plane in the 2.3 GHz band (2012)

This paper presents results from an outdoor radio propagation experiment at 2.35 GHz using a channel sounder and a spherical horn antenna array. The propagation test was performed in Aalborg city in Denmark. Comparing the ray-tracing results and the results obtained with the proposed method on the measured data shows a good match in both the spatial and time domains.
AT13148, an orally bioavailable AKT kinase inhibitor with potent anti-tumor activity in both in vitro and in vivo models exhibiting AKT pathway deregulation. (2007)

AT13148, an orally bioavailable AKT kinase inhibitor with potent anti-tumor activity in both in vitro and in vivo models exhibiting AKT pathway deregulation
Chemiresistive Carbon Nanotube Sensors for N-Nitrosodialkylamines (2019)

<i>N</i>-Nitrosamines are environmental genotoxicants that are widely encountered in air, water, and food. Contamination of indoor and outdoor air with <i>N</i>-nitrosamines has been reported on many occasions. Conventional detection of airborne <i>N</i>-nitrosamines requires sophisticated instrumentation, field sampling, and laboratory analysis. Herein, we report ultrasensitive carbon nanotube based chemiresistive sensors utilizing a cobalt(III) tetraphenylporphyrin selector element for the detection of <i>N</i>-nitrosamines. Concentrations as low as 1 ppb <i>N</i>-nitrosodimethylamine, <i>N</i>-nitrosodiethylamine, and <i>N</i>-nitrosodibutylamine were detected. We also demonstrate the integration of these sensors with a field deployable sensing node wherein the sensor response can be read online remotely.
Figure S1 from A Threshold of Systemic MAGE-A Gene Expression Predicting Survival in Resected Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Patient flow diagram&lt;/p&gt;
Estimation of ordinal pattern probabilities in fractional Brownian motion (2008)

For equidistant discretizations of fractional Brownian motion (fBm), the probabilities of ordinal patterns of order d=2 are monotonically related to the Hurst parameter H. By plugging the sample relative frequency of those patterns indicating changes between up and down into the monotonic relation to H, one obtains the Zero Crossing (ZC) estimator of the Hurst parameter which has found considerable attention in mathematical and applied research. In this paper, we generally discuss the estimation of ordinal pattern probabilities in fBm. As it turns out, according to the sufficiency principle, for ordinal patterns of order d=2 any reasonable estimator is an affine functional of the sample relative frequency of changes. We establish strong consistency of the estimators and show them to be asymptotically normal for H&lt;3/4. Further, we derive confidence intervals for the Hurst parameter. Simulation studies show that the ZC estimator has larger variance but less bias than the HEAF estimator of the Hurst parameter.
Fast high-efficiency integrated waveguide photodetectors using novel hybrid vertical/butt coupling geometry (1992)

We report a novel coupling geometry for integrated waveguide photodetectors−a hybrid vertical coupling/butt coupling scheme that allows the integration of fast, efficient, photodetectors with conventional double heterostructure waveguides. It can be employed to yield a planar, or pseudo-planar, surface that supports further levels of integration. The approach is demonstrated with a 25-μm-long p-i-n detector integrated with an InP/InGaAsP/InP waveguide, which displays a high (∼90%) efficiency and large (∼15 GHz) bandwidth. This is the fastest high-efficiency integrated waveguide photodetector reported to date.
Carboxymethylcellulose hydrogels support cns-derived tumor cell chemotactic migration (2015)

The local microenvironment plays an important role in maintaining the dynamics of the extracellular matrix (ECM) and the cell-ECM relationship. ECM is a complex network of molecules with distinct mechanical and biochemical characteristics. When the mechanisms that are in place to maintain ECM homeostasis are deregulated, most likely, this is the onset of cancer. The ECM becomes highly disorganized and the cell-matrix relationship changes, thus promoting alternations in cell mechanisms and metastasis. Medulloblastoma (MB) is one of the most common, malignant pediatric brain tumors in the United States. In order to gain a better understanding between the cell-ECM relationship and cell migratory responses in tumors we investigate 7 different types of ECM proteins via a MB-derived cell line: Poly-D-Lysine (PDL), Matrigel, Laminin, Collagen-1, Fibronectin, a 10% blend of Laminin-Collagen1, a 20% blend of Laminin-Collagen 1 and a new cellulose derived hydrogel, carboxymethylcellulose (CMC). Over time, the average changes in cell morphology, in 2D and 3D, are quantified. Data reveals CMC allows for a cell-ECM relationship typically believed to present in tumors, with cell exhibiting amoeboidal morphology that is believed to indicate the ready-ness of a cell to migrate within a given environment. Further investigation into the CMC hydrogels reveal a polysaccharide that allows for chemotactic study of MB-derived Daoy cells enabling minimal haptotactic migration conducive in the mechanistic study of the cells’ chemotactic behavior. Understanding the cell-ECM relationship provides insight into their interactions and the information obtained can be utilized in studying the natural migratory patterns of cells. CMC allows for such a behavior to be studied along with testing the motility of Daoy cells because the hydrogel provides minimal integrin interaction between the cells and the ECM. This study provides insights into understanding the mechanisms behind tumor-associated migratory patterns via chemokines. The data reflects a new possibility of tackling central nervous system (CNS) diseases by utilizing a platform of natural hydrogels to generate therapies inhibiting metastasis.