gebhart/patrepeval huggingface dataset:
Three-dimensional photonic crystals created by single-step multi-directional plasma etching (2014)

We fabricate 3D photonic nanostructures by simultaneous multi-directional plasma etching. This simple and flexible method is enabled by controlling the ion-sheath in reactive-ion-etching equipment. We realize 3D photonic crystals on single-crystalline silicon wafers and show high reflectance (>95%) and low transmittance (<-15dB) at optical communication wavelengths, suggesting the formation of a complete photonic bandgap. Moreover, our method simply demonstrates Si-based 3D photonic crystals that show the photonic bandgap effect in a shorter wavelength range around 0.6 μm, where further fine structures are required.
The Reaction of Dimethyl N-cyanodithioiminocarbonate with Amino- and Oxo-azoles: A New General Synthesis of Methylsulfanylazoloazines (2001)

A novel and efficient method for the synthesis of a new variety of methylsulfanylazoloazines by the reaction of dimethyl N-cyanodithioiminocarbonate with diazoles containing amino and active methylene functions. The synthetic potential of the method is demonstrated.
Transferring the Concept of Multinuclearity to Ruthenium Complexes for Improvement of Anticancer Activity (2009)

Multinuclear platinum anticancer complexes are a proven option to overcome resistance of established anticancer compounds. Transferring this concept to ruthenium complexes led to the synthesis of dinuclear Ru(II)-arene compounds containing a bis(pyridinone)alkane ligand linker. A pronounced influence of the spacer length on the in vitro anticancer activity was found, which is correlated to the lipophilicity of the complexes. IC(50) values in the same dimension as for established platinum drugs were found in human tumor cell lines. No cross-resistance to oxoplatin, a cisplatin prodrug, was observed for the most active complex in three resistant cell lines; in fact, a 10-fold reversal of sensitivity in two of the oxoplatin-resistant lines was found. (Bio)analytical characterization of the representative examples showed that the ruthenium complexes hydrolyze rapidly, forming predominantly diaqua species that exhibit affinity toward transferrin and DNA, indicating that both proteins and nucleobases are potential targets.
Role of Ribosome and Translocon Complex during Folding of Influenza Hemagglutinin in the Endoplasmic Reticulum of Living Cells (2000)

Protein folding in the living cell begins cotranslationally. To analyze how it is influenced by the ribosome and by the translocon complex during translocation into the endoplasmic reticulum, we expressed a mutant influenza hemagglutinin (a type I membrane glycoprotein) with a C-terminal extension. Analysis of the nascent chains by two-dimensional SDS-PAGE showed that ribosome attachment as such had little effect on ectodomain folding or trimer assembly. However, as long as the chains were ribosome bound and inside the translocon complex, formation of disulfides was partially suppressed, trimerization was inhibited, and the protein protected against aggregation.
Computing with Metabolic Machines (2018)

If Turing were a first-year graduate student interested in computers, he would probably migrate into the field of computational biology. During his studies, he presented a work about a mathematical and computational model of the morphogenesis process, in which chemical substances react together. Moreover, a protein can be thought of as a computational element, i.e. a processing unit, able to transform an input into an output signal. Thus, in a biochemical pathway, an enzyme reads the amount of reactants (substrates) and converts them in products. In this work, we consider the biochemical pathway in unicellular organisms (e.g. bacteria) as a living computer, and we are able to program it in order to obtain desired outputs. The genome sequence is thought of as an executable code specified by a set of commands in a sort of ad-hoc low-level programming language. Each combination of genes is coded as a string of bits $y \in \left \{ 0 , 1 \right \}^L$, each of which represents a gene set. By turning off a gene set, we turn off the chemical reaction associated with it. Through an optimal executable code stored in the ``memory'' of bacteria, we are able to simultaneously maximise the concentration of two or more metabolites of interest. Finally, we use the Robustness Analysis and a new Sensitivity Analysis method to investigate both the fragility of the computation carried out by bacteria and the most important entities in the mathematical relations used to model them.
CONJUGATION AS PUBLIC KEY AGREEMENT PROTOCOL IN MOBILE CRYPTOGRAPHY (2010)

We analyze a key agreement algorithm realization, not using Diffie-Hellman approach, but using matrix powers and conjugation. Introduced in a theoretical frame by Sakalauskas et. al. in 2007, it is here implemented in J2ME on mobile devices (Nokia N70 equipped with Symbian S60 operating system). We study its appli-ability and performances and compare them with Elliptic Curve and standard Diffie-Hellman Bouncy Castle implementation, freely available on the web.
Immunodominant T-cell epitopes of MOG reside in its transmembrane and cytoplasmic domains in EAE (2014)

Transmembrane and cytoplasmic domains of MOG contain immunodominant T-cell epitopes in EAE. A CNS autoantigen can also contain nonpathogenic stimulatory T-cell epitopes. Recognition that a myelin antigen contains multiple encephalitogenic and nonencephalitogenic determinants may have implications for therapeutic development in MS.
Walter Crane 1845 1915: Artist, Designer and Socialist (1990)

Walter Crane 1845–1915: Artist, Designer and Socialist Get access GREG SMITH and SARAH HYDE (eds). Lund Humphries , London , 1989 . 151 pp. illus. £10.50 paper. ISBN 0 85331 5531 . HAZEL CLARK HAZEL CLARK Ravensbourne College of Design and Communication Search for other works by this author on: Oxford Academic Google Scholar Journal of Design History, Volume 3, Issue 1, 1990, Page 79, https://doi.org/10.1093/jdh/3.1.79 Published: 01 March 1990
Saliva concentrations of some selected proteins and glycoprotein markers in man after supplementary intake of beta-carotene. (1988)

Vitamin A has profound effects on cell biology, morphology and function of excretory cells. In the present study we investigated the effect of supplementation with beta-carotene (provitamin A) on the secretion of salivary glycoproteins and some antibacterial components. Eighty-nine men, drawn from a larger double-blind pilot study among Finnish men of a high socio-economic standard, participated in this study which lasted for 60 days. The men were allocated either to beta-carotene supplementation of 20 mg a day or to placebo treatment. At the end of the study samples of stimulated whole and parotid saliva were collected and examined for total protein as well as hexosamine, sialic acid, thiocyanate and the activity of salivary peroxidase. The secretion rate of whole saliva was calculated and the activities of lysozyme, a bacteria aggregating glycoprotein (BAGP) and secretory IgA were measured in parotid saliva. Significantly higher levels of beta-carotene, but not retinol, were found in serum and whole saliva in the beta-carotene group compared to the placebo group. Retinol or beta-carotene could not be detected in parotid saliva. No difference was found either in saliva secretion rate or in the composition of whole or parotid saliva between the beta-carotene and the placebo group.
A planar-doped 2D-hole gas base AlGaAs/GaAs heterojunction bipolar transistor grown by molecular beam epitaxy (1988)

A novel type of AlGaAs/GaAs heterojunction bipolar transistor (HBT) which uses a two-dimensional (2-D) hole gas base formed by planar doping using molecular-beam epitaxy (MBE) has been demonstrated. The base consists of a submonolayer of Be atoms of sheet concentration 0.5-5*10/sup 13/ cm/sup -2/ which is deposited during growth interruption by MBE. The transistor structure exhibits DC current gains up to 700. The effective base transit time is negligible in these transistors and it is postulated that very high-speed nonequilibrium transport may occur in the collector region.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Multiplexed Volume Bragg Gratings in Narrowand Broad-band Spectral Systems: Analysis and Application (2015)

University of Minnesota Ph.D. dissertation. May 2015. Major: Electrical/Computer Engineering. Advisor: James Leger. 1 computer file (PDF); x, 115 pages.
A Control Theoretical Approach to Congestion Control in Packet Networks (2004)

In this paper, we introduce a control theoretical analysis of the closed-loop congestion control problem in packet networks. The control theoretical approach is used in a proportional rate controller, where packets are admitted into the network in accordance with network buffer occupancy. A Smith Predictor is used to deal with large propagation delays, common to high speed backbone networks. The analytical approach leads to accurate predictions regarding both transients as well as steady-state behavior of buffers and input rates. Moreover, it exposes tradeoffs regarding buffer dimensioning, packet loss, and throughput.
Switching effect in organic charge transfer complex crystals (1989)

A reproducible current switching effect has been observed in various mixed-stack organic charge transfer crystals whose ionicities are close to the neutral-ionic phase boundary. This effect appears to be related to the intrinsic nonlinear conductivity, which has recently been reported in these crystals. This switching has a reasonably large delay time and our results indicate that it is a bulk property of the crystals. Discussion is given on the possible mechanism of this effect.
Modelling of the gas-phase phosphate group loss and rearrangement in phosphorylated peptides (2011)

The gas-phase dissociation of phosphorylated peptides was modelled using a combination of quantum mechanics and the Rice-Ramsperger-Kassel-Marcus theory. Potential energy surfaces and unimolecular reaction rates for several low-energy fragmentation and rearrangement pathways were estimated, and a general mechanism was proposed. The neutral loss of the phosphoric acid was mainly an outcome of the intramolecular nucleophilic substitution mechanism. The mechanism involves a nucleophilic attack of the phosphorylated amino acid N-terminal carbonyl oxygen on β-carbon, yielding a cyclic five-membered oxazoline product ion. Regardless of the proton mobility, the pathway was charge directed either by a mobile proton or by a positively charged side chain of some basic residue. Although the mechanistic aspects of the phosphate loss are not influenced by the proton mobility environment, it does affect ion abundances. Results suggest that under the mobile proton environment, the interplay between phosphoric acid neutral loss product ion and backbone cleavage fragments should occur. On the other hand, when proton mobility is limited, neutral loss product ion may predominate. The fragmentation dynamics of phosphoserine versus phosphothreonine containing peptides suggests that H(3)PO(4) neutral loss from phosphothreonine containing peptides is less abundant than that from their phosphoserine containing analogs. During the low-energy CID of phosphorylated peptides in the millisecond time range, typical for ion trap instruments, a phosphate group rearrangement may happen, resulting in an interchange between the phosphorylated and the hydroxylated residues. Unimolecular dissociation rate constants imply the low abundance of such scrambled product ions.
Detection of two tissue-specific DNA-binding proteins with affinity for sites in the mouse beta-globin intervening sequence 2. (1988)

To identify proteins from uninduced murine erythroleukemia nuclear extracts which specifically bind to sequences from the DNase I-hypersensitive region within the mouse beta-globin intervening sequence 2 (IVS2), a gel electrophoretic mobility shift assay was used. Two distinct sequence-specific binding proteins were detected. The specific binding sites for these factors were delineated by both DNase I protection footprinting and methylation interference. Factor B1 bound specifically to two homologous sites, B1-A and B1-B, approximately 100 base pairs apart within the IVS2 and on opposite strands. These two regions could interact with factor B1 independently. Factor B1 was limited to cells of hematopoietic lineages. Factor B2 bound to a site approximately 5 base pairs away from the B1-A site and was limited to cells of the erythroid lineage. The limited tissue distribution of these factors and the locations of their binding sites suggest that one or both of these factors may be involved in the formation of the tissue-specific DNase I-hypersensitive site in the IVS2 of the mouse beta-globin gene.
Regulation by corticosteroids of Th1 and Th2 cytokine production in human CD4+ effector T cells generated from CD45RO- and CD45RO+ subsets (1995)

Corticosteroids (CS) are widely used as immunosuppressive and anti-inflammatory agents, but their mechanism of action is not well understood. In this study we analyzed the effects of CS on the growth and differentiation of human CD4+45RO- "naive" and CD4+45RO+ "memory" T cells. To generate effector T cells secreting large amounts of Th1 and Th2 cytokines, FACS-sorted naive and memory subsets were primed and restimulated in vitro via the TCR in the presence of IL-2. CS added during priming reduced clonal expansion of both T cell populations, but the memory subset was 100-fold less sensitive. At lower concentrations, CS favored the development of effector T cells (from both subsets), which upon restimulation produced large amounts of the anti-inflammatory cytokine IL-10, but low amounts of IL-4, IL-5, or IFN-gamma. Interestingly, CS displayed different effects if it was added only during the restimulation of effector T cells. CS were unable to suppress clonal expansion of restimulated effector T cells. In effector T cells derived from the naive subset, CS induced production of IL-4 and IL-10, but blocked production of IL-5 and IFN-gamma. In effector T cells generated from the memory subset, CS blocked production of IL-4, IL-5, and IL-10, but inhibited production of IFN-gamma by only 50%, even if 100-fold higher concentrations of CS were applied. These results indicate that persistent TCR stimulation, e.g., in chronic infection, may reduce the sensitivity of T cells to the antiproliferative effects of CS. Furthermore, the potential of CS to increase or suppress IL-4 and IL-10 production depending on the stage of T cell activation may explain in part the beneficial effects of CS in the treatment of acute inflammation and chronic allergic/asthmatic diseases.
Performance of an Optimized Paper-Based Test for Rapid Visual Measurement of Alanine Aminotransferase (ALT) in Fingerstick and Venipuncture Samples (2015)

The paper ALT test is highly accurate for serum testing, matching the reference method against which it was optimized better than the reference methods matched each other. A systematic difference exists between ALT values in fingerstick and paired serum samples, and can be addressed by application of a correction factor to fingerstick values. Remote reading of this device is feasible.
The ketogenic diet increases mitochondrial uncoupling protein levels and activity (2004)

Fatty acids are known to enhance mitochondrial uncoupling protein (UCP) activity. We asked whether a high-fat ketogenic diet (KD) increases UCP levels and activity in hippocampi of juvenile mice. Maximum mitochondrial respiration rates were significantly (p < 0.001) higher in KD- versus standard diet (SD)-treated animals, indicating increased UCP-mediated proton conductance that can reduce reactive oxygen species (ROS) production. Western blots showed significant (p < 0.05) or borderline significant increases in UCP2, UCP4, and UCP5 protein levels, and increased immunoreactivity to these three UCP isoforms was most prominently seen in the dentate gyrus of KD-fed mice. Finally, we found that oligomycin-induced ROS production was significantly (p < 0.05) lower in KD-fed mice than in SD controls. Collectively, our data suggest that a KD may exert neuroprotective effects by diminishing ROS production through activation of mitochondrial UCPs.
Modelling gene expression time-series with radial basis function neural networks (2005)

Gene expression time-series are discrete, noisy, short and usually unevenly sampled. Most of the existing methods used to compare expression profiles, operate directly on the time points. While modelling, the profiles can lead to more generalised, smooth characterisation of gene expressions. In this paper, a radial basis function neural network is employed to model gene expression time-series. The orthogonal least square method, used for selection of centres, is further combined with a width optimisation scheme. The experiments on a number of expression datasets have shown the advantages of the approach in terms of generalisation and approximation. The results on known datasets have indeed coincided with biological interpretations.
A pure hardware k-SAT solver architecture for FPGA based on generic tree-search (2017)

SAT (Boolean SATisfiability Problem) is a well studied type of NP-complete problem. Most SAT solvers rely on software implemented tree-search based algorithms. These algorithms, basically sequential or weakly parallel, are most often ineffective when dealing with large scale instances of SAT due to the large search space to be explored in order to find one solution. Despite several improvements and heuristics being proposed for this kind of approach, the fact remains that in real problems, the computational cost continues to be prohibitive. To improve SAT solvers performance, a new trend has emerged in the late years, introducing hardware acceleration. The proposed architectures are in general hybrid, combining software and hardware parts dedicated respectively to the decisional and hard-computional parts of the algorithm. Still, most the hybrid approaches remain constrained by their limited data-access bandwith capacity. In this paper, we propose a new approach, entirely based on hardware and not depending on the SAT-instance to be solved (treated as data). It is fully configurable at synthesis in regard to the level of parallel computation and parallel buffering, as to the size of the SAT instance that can be processed (maximal number of variables and maximal clause length, the total number of clauses being unlimited). One of the main goals is to allow a more effective use of the hardware computational power by reducing the dependence to data contained in low bandwith data storage (such as RAM).
N348I in the Connection Domain of HIV-1 Reverse Transcriptase Confers Zidovudine and Nevirapine Resistance (2007)

This study provides the first in vivo evidence that treatment with RT inhibitors can select a mutation (i.e., N348I) outside the polymerase domain of the HIV-1 RT that confers dual-class resistance. Its emergence, which can happen early during therapy, may significantly impact on a patient's response to antiretroviral therapies containing zidovudine and nevirapine. This study also provides compelling evidence for investigating the role of other mutations in the connection and RNase H domains in virological failure.
On terrain acquisition by a point robot amidst polyhedral obstacles (1988)

The authors consider the problem of terrain model acquisition by a roving point placed in an unknown terrain populated by stationary polyhedral obstacles in two/three dimensions. The motivation for this problem is that after the terrain model is completely acquired, navigation from a source point to a destination point can be achieved along the collision-free paths. This can be done without the usage of sensors by applying the existing techniques for the find-path problem. In the paper, the point robot autonomous machine (PRAM) is used as a simplified abstract model for real-life roving robots. An algorithm is presented that enables PRAM to autonomously acquire the model of an unexplored obstacle terrain composed of an unknown number of polyhedral obstacles in two/three dimensions. In this method, PRAM undertakes a systematic exploration of the obstacle terrain with its sensor that detects all the edges and vertices visible from the present location, and builds the complete obstacle terrain model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Structural and optical properties of ZnO films on Si substrates using a γ-Al<sub>2</sub>O<sub>3</sub>buffer layer (2006)

High quality ZnO films have been successfully grown on a Si (100) substrate by metal organic chemical vapour deposition with a γ-Al2O3 buffer. The crystal structure, surface morphology and optical properties of the ZnO films were characterized by x-ray diffraction, Raman spectroscopy, atomic force microscopy and photoluminescence (PL) spectroscopy. The properties of the films with the Al2O3 buffer were improved in comparison with those of as-grown ZnO films. It is shown that the ZnO films with the γ-Al2O3 buffer grown on Si (100) substrates have a highly-preferential c-axis (0002) orientation, a narrow (0002) peak, smooth surface morphology and better PL spectral properties. This demonstrates that the use of γ-Al2O3/Si as a ZnO substrate is beneficial for reducing the residual stress for further growth of ZnO films, compared with the growth on bulk Si substrates.
Modelling, evaluation, and adaptive control of an instrumentation system (2002)

We present results from modeling and evaluating the JEWEL instrumentation system (IS), which is being used for runtime data collection from a distributed, real-time application. Our modeling and evaluation effort addresses two objectives: (1) providing early feedback to the system developers regarding the JEWEL IS configuration options for this application; and (2) evaluation of the design alternatives for an adaptive controller to control the overhead and intrusion of the JEWEL IS to a real-time video conferencing application. For JEWEL IS design, we compare two data collection and forwarding policies (collect-and-forward and batch-and-forward). For the design of the adaptive controller, we compare two adaptation policies (static and dynamic adaptation) and two policies to schedule the implementation of the control decisions (distributed and centralized scheduling). Results reported in this paper indicate that the batch-and-forward policy for IS design static adaptation policy with distributed scheduling for the adaptive controller design meet the domain-specific requirements.
Automated multidimensional image analysis reveals a role for Abl in embryonic wound repair (2014)

The embryonic epidermis displays a remarkable ability to repair wounds rapidly. Embryonic wound repair is driven by the evolutionary conserved redistribution of cytoskeletal and junctional proteins around the wound. Drosophila has emerged as a model to screen for factors implicated in wound closure. However, genetic screens have been limited by the use of manual analysis methods. We introduce MEDUSA, a novel image-analysis tool for the automated quantification of multicellular and molecular dynamics from time-lapse confocal microscopy data. We validate MEDUSA by quantifying wound closure in Drosophila embryos, and we show that the results of our automated analysis are comparable to analysis by manual delineation and tracking of the wounds, while significantly reducing the processing time. We demonstrate that MEDUSA can also be applied to the investigation of cellular behaviors in three and four dimensions. Using MEDUSA, we find that the conserved nonreceptor tyrosine kinase Abelson (Abl) contributes to rapid embryonic wound closure. We demonstrate that Abl plays a role in the organization of filamentous actin and the redistribution of the junctional protein β-catenin at the wound margin during embryonic wound repair. Finally, we discuss different models for the role of Abl in the regulation of actin architecture and adhesion dynamics at the wound margin.