gebhart/patrepeval huggingface dataset:
Molecular structure effects on dry etching behavior of Si-containing resists in oxygen plasma (2010)

The authors have studied the influence of Si–O bonding in the polymer structure of Si-containing resists on O2 plasma etch behavior. Three polymers were synthesized with the same Si wt % (12.1%) and varying number of Si–O bonds (0, 1, or 2). The etch resistance during the plasma process was measured by monitoring the film thickness removed using real-time in situ ellipsometry. After plasma exposure, surface chemical changes and roughness were characterized by x-ray photoelectron spectroscopy and atomic force microscopy, respectively. For O2 plasma exposure without substrate bias, all polymers showed the formation of a ∼1 nm SiO2 layer at the surface that acted as a barrier to further oxygen etching. Adding Si–O bonds to the polymer structure at constant wt % Si greatly reduced the etch rate and Si loss during oxygen plasma etching relative to the case of no such bonds. Polymers with one Si–O bond in the polymer structure showed identical etch behavior to polymers with the same wt % Si and two Si–O bonds. However, increasing the number of Si–O bonds in the structure decreased the glass transition temperature of the polymer, leading to the formation of micron-sized wrinkles after plasma exposure. When a substrate bias was applied, the etch rate and the rate of Si loss increased due to sputtering of the SiO2 layer by energetic ions. For 90% N2/O2 discharges with substrate bias, a typical oxygen-based pattern transfer plasma condition, the etch rates of the polymers with the Si–O bond were lower and the SiO2 layer thickness formed was larger than that formed in pure O2 discharges with substrate bias. For all gas discharge conditions, polymers with pre-existing Si–O bonds showed less Si loss.
Patient dose from CT: a literature review. (2007)

More research is needed to develop and implement uniform dose tracking procedures and protocols for minimizing patient dose.
Particle Filtering for Large-Dimensional State Spaces With Multimodal Observation Likelihoods (2008)

We study efficient importance sampling techniques for particle filtering (PF) when either (a) the observation likelihood (OL) is frequently multimodal or heavy-tailed, or (b) the state space dimension is large or both. When the OL is multimodal, but the state transition pdf (STP) is narrow enough, the optimal importance density is usually unimodal. Under this assumption, many techniques have been proposed. But when the STP is broad, this assumption does not hold. We study how existing techniques can be generalized to situations where the optimal importance density is multimodal, but is unimodal conditioned on a part of the state vector. Sufficient conditions to test for the unimodality of this conditional posterior are derived. Our result is directly extendable to testing for unimodality of any posterior. The number of particles N to accurately track using a PF increases with state space dimension, thus making any regular PF impractical for large dimensional tracking problems. But in most such problems, most of the state change occurs in only a few dimensions, while the change in the rest of the dimensions is small. Using this property, we propose to replace importance sampling from a large part of the state space (whose conditional posterior is narrow enough) by just tracking the mode of the conditional posterior. This introduces some extra error, but it also greatly reduces the importance sampling dimension. The net effect is much smaller error for a given N, especially when the available N is small. An important class of large dimensional problems with multimodal OL is tracking spatially varying physical quantities such as temperature or pressure in a large area using a network of sensors which may be nonlinear and/or may have nonnegligible failure probabilities. Improved performance of our proposed algorithms over existing PFs is demonstrated for this problem.
High-performance liquid chromatography separation and intact mass analysis of detergent-solubilized integral membrane proteins (2010)

We have developed a method for intact mass analysis of detergent-solubilized and purified integral membrane proteins using liquid chromatography-mass spectrometry (LC-MS) with methanol as the organic mobile phase. Membrane proteins and detergents are separated chromatographically during the isocratic stage of the gradient profile from a 150-mm C3 reversed-phase column. The mass accuracy is comparable to standard methods employed for soluble proteins; the sensitivity is 10-fold lower, requiring 0.2-5 μg of protein. The method is also compatible with our standard LC-MS method used for intact mass analysis of soluble proteins and may therefore be applied on a multiuser instrument or in a high-throughput environment.
What do you do, titanium? Insight into the role of titanium oxide as a water oxidation promoter in hematite-based photoanodes (2015)

Titanium improves water oxidation yields over hematite photoanodes, tailoring its surface state density (kinetics) and hematite-pseudobrookite heterojunctions (energetics).
Recruitment and activation of Rac1 by the formation of E-cadherin-mediated cell-cell adhesion sites (2001)

Rac1, a member of the Rho family small GTPases, regulates E-cadherin-mediated cell-cell adhesion. However, it remains to be clarified how the localization and activation of Rac1 are regulated at sites of cell-cell contact. Here, using enhanced green fluorescence protein (EGFP)-tagged Rac1, we demonstrate that EGFP-Rac1 is colocalized with E-cadherin at sites of cell-cell contact and translocates to the cytosol during disruption of E-cadherin-mediated cell-cell adhesion by Ca(2+) chelation. Re-establishment of cell-cell adhesion by restoration of Ca(2)(+) caused EGFP-Rac1 to become relocalized, together with E-cadherin, at sites of cell-cell contact. Engagement of E-cadherin to the apical membrane by anti-E-cadherin antibody (ECCD-2) recruited EGFP-Rac1. We also investigated whether E-cadherin-mediated cell-cell adhesion induced Rac1 activation by measuring the amounts of GTP-bound Rac1 based on its specific binding to the Cdc42/Rac1 interactive binding region of p21-activated kinase. The formation of E-cadherin-mediated cell-cell adhesion induced Rac1 activation. This activation was inhibited by treatment of cells with a neutralizing antibody (DECMA-1) against E-cadherin, or with wortmannin, an inhibitor of phosphatidylinositol 3-kinase (PI 3-kinase). IQGAP1, an effector of Rac1, and EGFP-Rac1 behaved in a similar manner during the formation of E-cadherin-mediated cell-cell adhesion. Rac1 activation was also confirmed by measuring the amounts of coimmunoprecipitated Rac1 with IQGAP1 during the establishment of cell-cell adhesion. Taken together, these results suggest that Rac1 is recruited at sites of E-cadherin-mediated cell-cell adhesion and then activated, possibly through PI 3-kinase.
Simulation languages (1972)

Both novice and intermediate users of simulation analysis are confronted by a plethora of simulation languages, an 'alphabet soup' of acronyms. In our attempt to provide our readers with a Dictionary of Computer Simulation Languages we shall includes a series of articles on the different languages, with this first article devoted to PASS IV.
Alkaloids of <i>Cryptocarya phyllostemon</i> (1989)

The known alkaloids (-)-antofine (1), dehydroantofine (5),(-)-cryptowoline (6), (4- cryptowolidine (7), and (-)-cryptowolinol (8), were isolated from the New Caledonian lauraceous plant Cryptocarya phyllosternon, together with five new bases: two secophenanthro-indolizidines, (-)-phyllostemine (2) and (-)-phyllosteminine (3), one pyrrolidinylacetophenone, (-)-phyllostone (4), and two quaternary tetrahydrobenzylisoquinolines, (+)-phyllocryptine (9) and (+)-phyllocryptonine (10). Chemical and spectroscopic methods were used for identification and structural investigation. A synthesis of phyllocryptonine has permitted its stereostructure to be determined.
Advances in photonic MOEMS-MEMS device thinning and polishing (2010)

As devices continue to increase in density and complexity, ever more stringent specifications are placed on the wafer scale equipment manufacturers to produce higher quality and higher output. This results in greater investment and more resource being diverted into producing tools and processes which can meet the latest demanding criteria. Substrate materials employed in the fabrication process range from Silicon through InP and include GaAs, InSb and other optical networking or waveguide materials. With this diversity of substrate materials presented, controlling the geometries and surfaces grows progressively more challenging. This article highlights the key parameters which require close monitoring and control in order to produce highly precise wafers as part of the fabrication process. Several as cut and commercially available standard polished wafer materials were used in empirical trials to test tooling options in generating high levels of geometric control over the dimensions while producing high quality surface finishes. Specific attention was given to the measurement and control of: flatness; parallelism/TTV; surface roughness and final target thickness as common specifications required by the industry. By combining the process variables of: plate speed, download pressure, slurry flow rate and concentration, pad type and wafer travel path across the polish pad, the effect of altering these variables was recorded and analysed to realize the optimum process conditions for the materials under test. The results being then used to design improved methods and tooling for the thinning and polishing of photonic materials applied to MOEMS-MEMS device fabrication.
Facile Synthesis of Titanate Nanoflowers by a Hydrothermal Route (2008)

The novel sodium titanate nanoflowers were synthesized through a facile hydrothermal method. The as-grown nanoflowers were self-assembled by folded broad and thin nanosheets, which were formed by the assistance of ZnO nanostructure templates. The crystal structure was identified to be layered NaxH2−xTi2O5·H2O, and the formation process of the titanate nanoflowers was proposed as follows: ZnO flower-like nanorods in the alkali solution formed at the initial stage, and then the formed titanate nanosheets deposited on the surface of the frameworks of the ZnO nanorods, and finally the titanate nanoflowers were formed after the removal of ZnO framework.
Experimental analysis of above-IC inductor performance with different patterned ground shield configurations and dummy metals (2006)

This paper presents the characterization of various patterned ground shield configurations for single ended inductor layouts: center ground shield (CGS), simple ground shield (SGS) and perimeter ground shield (PGS). Experiments and simulations show that when the shields connect only to one side of single-ended above-IC inductor RF ground pad, an asymmetric Q-behavior is obtained. HFSS simulations indicate that a better performance may be obtained by a symmetrical connection of the shield to the RF ground. Furthermore, the influence of different metal shield widths and spacings, as well as the effect of dummy metal dimensions on the performance of inductors has been assessed
MalwareLab: Experimentation with Cybercrime Attack Tools. (2013)

Cybercrime attack tools (i.e. Exploit Kits) are reportedly\nresponsible for the majority of attacks affecting home\nusers. Exploit kits are traded in the black markets at\ndifferent prices and advertising different capabilities and\nfunctionalities. In this paper we present our experimental\napproach in testing 10 exploit kits leaked from the markets\nthat we deployed in an isolated environment, our\nMalwareLab. The purpose of this experiment is to test\nthese tools in terms of resiliency against changing software\nconfigurations in time. We present our experiment\ndesign and implementation, discuss challenges, lesson\nlearned and open problems, and present a preliminary\nanalysis of the results.
A theory of learning from different domains (2009)

Discriminative learning methods for classification perform well when training and test data are drawn from the same distribution. Often, however, we have plentiful labeled training data from a source domain but wish to learn a classifier which performs well on a target domain with a different distribution and little or no labeled training data. In this work we investigate two questions. First, under what conditions can a classifier trained from source data be expected to perform well on target data? Second, given a small amount of labeled target data, how should we combine it during training with the large amount of labeled source data to achieve the lowest target error at test time? We address the first question by bounding a classifier’s target error in terms of its source error and the divergence between the two domains. We give a classifier-induced divergence measure that can be estimated from finite, unlabeled samples from the domains. Under the assumption that there exists some hypothesis that performs well in both domains, we show that this quantity together with the empirical source error characterize the target error of a source-trained classifier. We answer the second question by bounding the target error of a model which minimizes a convex combination of the empirical source and target errors. Previous theoretical work has considered minimizing just the source error, just the target error, or weighting instances from the two domains equally. We show how to choose the optimal combination of source and target error as a function of the divergence, the sample sizes of both domains, and the complexity of the hypothesis class. The resulting bound generalizes the previously studied cases and is always at least as tight as a bound which considers minimizing only the target error or an equal weighting of source and target errors.
TLR3 agonists improve the immunostimulatory potential of cetuximab against EGFR<sup>+</sup>head and neck cancer cells (2013)

Toll-like receptor 3 (TLR3) agonists have been extensively used as adjuvants for anticancer vaccines. However, their immunostimulatory effects and precise mechanisms of action in the presence of antineoplastic monoclonal antibodies (mAbs) have not yet been evaluated. We investigated the effect of TLR3 agonists on cetuximab-mediated antibody-dependent cellular cytotoxicity (ADCC) against head and neck cancer (HNC) cells, as well as on dendritic cell (DC) maturation and cross-priming of epidermal growth factor receptor (EGFR)-specific CD8<sup>+</sup> T cells. The cytotoxic activity of peripheral blood mononuclear cells (PBMCs) or isolated natural killer (NK) cells expressing polymorphic variants (at codon 158) of the Fcγ receptor IIIa (FcγIIIa) was determined in <sup>51</sup>Cr release assays upon incubation with the TLR3 agonist poly-ICLC. NK cell stimulation was measured based on activation and degranulation markers, while DC maturation in the presence of poly-ICLC was assessed using flow cytometry. The DC-mediated cross priming of EGFR-specific CD8<sup>+</sup> T cells was monitored upon in vitro stimulation with tetramer-based flow cytometry. TLR3-stimulated, unfractionated PBMCs from HNC patients mediated robust cetuximab-dependent ADCC, which was abrogated by NK-cell depletion. The cytolytic activity of TLR3-stimulated NK cells differed among cells expressing different polymorphic variants of FcγRIIIa, and NK cells exposed to both poly-ICLC and cetuximab expressed higher levels of CD107a and granzyme B than their counterparts exposed to either stimulus alone. Poly-ICLC plus cetuximab also induced a robust upregulation of CD80, CD83 and CD86 on the surface of DCs, a process that was partially NK-cell dependent. Furthermore, DCs matured in these conditions exhibited improved cross-priming abilities, resulting in higher numbers of EGFR-specific CD8<sup>+</sup> T cells. These findings suggest that TLR3 agonists may provide a convenient means to improve the efficacy of mAb-based anticancer regimens.
Medical management of brain metastases from lung cancer (Review) (2009)

Brain metastases are a frequent complication in patients with lung cancer and a significant cause of morbidity and mortality. The prognosis of these patients is poor. Medical therapies for brain metastases are neither well-studied nor established. This review analyzes the impact of medical treatment on survival by reviewing recent articles of the management of brain metastases from lung cancer patients. Chemotherapy for brain metastases from lung cancer is effective for both small cell and non-small cell lung cancer. Since brain metastases are part of systemic progression, chemotherapy should always be considered for the therapeutic management of brain metastases. Available data and response rates in lung cancer patients indicated that medical treatment for the management of brain metastases should be part of a multimodality treatment.
<i>rhomboid</i> and <i>Star</i> interact synergistically to promote EGFR/MAPK signaling during <i>Drosophila</i> wing vein development (1999)

Genes of the ventrolateral group in Drosophila are dedicated to developmental regulation of Egfr signaling in multiple processes including wing vein development. Among these genes, Egfr encodes the Drosophila EGF-Receptor, spitz (spi) and vein (vn) encode EGF-related ligands, and rhomboid (rho) and Star (S) encode membrane proteins. In this study, we show that rho-mediated hyperactivation of the EGFR/MAPK pathway is required for vein formation throughout late larval and early pupal development. Consistent with this observation, rho activity is necessary and sufficient to activate MAPK in vein primordium during late larval and early pupal stages. Epistasis studies using a dominant negative version of Egfr and a ligand-independent activated form of Egfr suggest that rho acts upstream of the receptor. We show that rho and S function in a common aspect of vein development since loss-of-function clones of rho or S result in nearly identical non-autonomous loss-of-vein phenotypes. Furthermore, mis-expression of rho and S in wild-type and mutant backgrounds reveals that these genes function in a synergistic and co-dependent manner. In contrast, spi does not play an essential role in the wing. These data indicate that rho and S act in concert, but independently of spi, to promote vein development through the EGFR/MAPK signaling pathway.
Chemical Evaluation of Betula Species in Japan. II. Constituents of Betula platyphylla var. japonica. (1996)

The constituents of Betula platyphylla var. japonica were identified as follows : Fresh leaves : 12-O-acetyl-3-O-malonylbetulafolienetriol, 12-O-acetyl-3-O-malonylbetulafolienetriol oxide I (=papyriferic acid), 12-O-acetyl-betulafolienediolone, hydroxyhopanone, caryophyllene oxide, kaempferol 3-O-(4-O-acetyl)-α-L-rhamnopyran-oside, quercetin 3-O-(4-O-acetyl)-α-L-rhamnopyranoside. Outer bark : betulin, lupeol, betulinic acid, betulone, betulin 3-O-caffeate, oleanolic acid, oleanolic acid 3-O-acetate. Inner bark : (-)-catechin, (-)-catechin 7-O-β-D-xylopyranoside, rhododendrin (=betuloside), aceroside VII, aceroside VIII, 1, 7-bis[4-hydroxyphenyl]-3-hepten-5-one, 2-hydroxy-1, 7-bis[4-hydroxyphenyl]-3-hepten-5-one, acerogenin E, (3R)-3, 5'-dihydroxy-4'-methoxy-3', 4"-oxo-1, 7-diphenyl-1-heptene, 7α-hydroxy-β-sitosterol, 7β-hydroxy-β-sitosterol. Root bark : dammarenediol II 3-O-p-coumarate, dammarenediol II 3-O-caffeate, ocotillol II 3-O-caffeate, stigmast-4-ene-3-one. Spikes : caryo-phyllene oxide, (-)-rhododendrol (=betuligenol), 12-O-acetylbetulafolienetriol. The compounds with an asterisk are new.
Effects of Recombinant Human Tissue Inhibitor of Metalloproteinases‐2 (rh‐TIMP‐2) on Migration of Epidermal Keratinocytes <i>In vitro</i> and Wound Healing <i>In vivo</i> (2003)

Tissue inhibitors of metalloproteinases (TIMP), common inhibitors of matrix proteinases, have cell-promoting activity. We studied the effects of recombinant human tissue inhibitor of metalloproteinases-2 (rh-TIMP-2) on the migration of normal human epidermal keratinocytes (NHEK). An in vitro migration assay revealed that rh-TIMP-2 enhanced random migration (up to 170%, p<0.05) in a dose-dependent manner. When we applied rh-TIMP-2 solution (20 microg/20 microl/wound) daily to full-thickness wounds made with an 8-mm punch on the backs of healthy (n=8), aged (n=9), and diabetic (n=15) rodents, we observed faster wound closure (p<0.05) than in vehicle-treated controls. Accelerated wound closure was dose-dependent (0-20 microg/wound) in diabetic mice (n=6), and the optimal concentration was 10-20 microg of rh-TIMP-2/wound. Histological examinations performed on days 0, 5, 10, 15, and 20 in diabetic mice revealed faster migration of epidermal keratinocytes from wound edges. These results suggest that rh-TIMP-2 plays an important role in wound healing.
Diversity methods in phase monopulse tracking-a new approach (1991)

A novel approach relating target glint (difference between the phase-front gradient of the scattered field and the true target direction vector) to the analytic properties of the overall field is used to suggest a method by which the error in conventional (single frequency) phase monopulse trackers can be reduced. The approximate relationship between glint and amplitude is briefly developed, and an improved glint reduction scheme appropriate for single frequency data is described. The effectiveness in reducing direction angle error is demonstrated with simulated data. It is shown how techniques devised for multiple frequency data sets can be applied to multiple aspect data sets.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Male reproductive toxicology: comparison of the human to animal models. (1988)

The human male is of relatively low fertility and thus may be at greater risk from reproductive toxicants than are males of the common laboratory animal model species. Lack of knowledge of the physiological differences that contribute to interspecies variation between man and animals can prevent the effective application of animal data to the assessment of human reproductive risk. Evaluation of spermatogenesis from testicular histology, while uncommon, can provide valuable information about human reproductive risk. The measurement of sperm count or concentration has long been the most feasible approach for human semen evaluation, but may be an insensitive indicator of reproductive function because of high sample-to-sample variability. Interspecies extrapolation factors can be calculated by comparing the reduction in sperm count in humans and test species after exposure to drugs or chemicals. These factors can provide a realistic assessment of relative risk, provided that the sperm are counted at the appropriate time after exposure. However, the degree to which extrapolation factors derived for one agent, and only from sperm counts, can be generalized is not known. Monitoring of sperm motility and morphology parameters is also a common means of evaluating human semen quality, but these techniques are also hampered by the relatively high interindividual and intersample variability. Computer-assisted and morphometric approaches show promise of decreasing the subjective nature of these evaluations and increasing their value in risk assessment procedures. Improvements in predicting human reproductive risk can be expected to come from increased knowledge about reproductive mechanisms in man and animals, together with the utilization of objective measures of cellular indicators of male reproductive function.