gebhart/patrepeval huggingface dataset:
Detecting Adversarial Examples in Learning-Enabled Cyber-Physical Systems using Variational Autoencoder for Regression (2020)

Learning-enabled components (LECs) are widely used in cyber-physical systems (CPS) since they can handle the uncertainty and variability of the environment and increase the level of autonomy. However, it has been shown that LECs such as deep neural networks (DNN) are not robust and adversarial examples can cause the model to make a false prediction. The paper considers the problem of efficiently detecting adversarial examples in LECs used for regression in CPS. The proposed approach is based on inductive conformal prediction and uses a regression model based on variational autoencoder. The architecture allows to take into consideration both the input and the neural network prediction for detecting adversarial, and more generally, out-of-distribution examples. We demonstrate the method using an advanced emergency braking system implemented in an open source simulator for self-driving cars where a DNN is used to estimate the distance to an obstacle. The simulation results show that the method can effectively detect adversarial examples with a short detection delay.
Spatial variation of the underwater soundscape over coral reefs in the Northwestern Hawaiian Islands (2014)

Coral reefs create a complex acoustic environment, dominated by sounds produced by benthic creatures such as crustaceans and echinoderms. While there is growing interest in the use of ambient underwater biological sound as a gauge of ecological state, extracting meaningful information from recordings is a challenging task. Single hydrophone (omnidirectional) recorders can provide summary time and frequency information, but as the spatial distribution of reef creatures is heterogeneous, the properties of reef sound arriving at the receiver vary with position and arrival angle. Consequently, the locations and acoustic characteristics of individual sound producers remain unknown. An L-shaped hydrophone array, providing direction-and-range sensing capability, can be used to reveal the spatial variability of reef sounds. Comparisons can then be made between sound sources and other spatially referenced information such as photographic data. During the summer of 2012, such an array was deployed near four different benthic ecosystems in the Northwestern Hawaiian Islands, ranging from high-latitude coral reefs to communities dominated by algal turf. Using conventional and adaptive acoustic focusing (equivalent to curved-wavefront beamforming), time-varying maps of sound production from benthic organisms were created. Comparisons with the distribution of nearby sea floor features, and the makeup of benthic communities, will be discussed.
Combined co-solvent and pressure effect on kinetics of a peptide hydrolysis: an activity-based approach (2019)

The application of co-solvents and high pressure has been reported to be an efficient means to tune the kinetics of enzyme-catalyzed reactions. Co-solvents and pressure can lead to increased reaction rates without sacrificing enzyme stability, while temperature and pH operation windows are generally very narrow. Quantitative prediction of co-solvent and pressure effects on enzymatic reactions has not been successfully addressed in the literature. Herein, we are introducing a thermodynamic approach that is based on molecular interactions in the form of activity coefficients of substrate and of enzyme in the multi-component solution. This allowed us to quantitatively predict the combined effect of co-solvent and pressure on the kinetic constants, i.e. the Michaelis constant K<sub>M</sub> and the catalytic constant k<sub>cat</sub>, of an α-CT-catalyzed peptide hydrolysis reaction. The reaction was studied in the presence of different types of co-solvents and at pressures up to 2 kbar, and quantitative predictions could be obtained for K<sub>M</sub>, k<sub>cat</sub>, and finally even primary Michaelis-Menten plots using activity coefficients provided by the thermodynamic model PC-SAFT.
Melatonin and cancer suppression: insights into its effects on DNA methylation (2022)

Melatonin is an important naturally occurring hormone in mammals. Melatonin-mediated biological effects include the regulation of circadian rhythms, which is important for optimal human health. Also, melatonin has a broad range of immunoenhancing actions. Moreover, its oncostatic properties, especially regarding breast cancer, involve a variety cancer-inhibitory processes and are well documented. Due to their promising effects on the prognosis of cancer patients, anti-cancer drugs with epigenetic actions have attracted a significant amount of attention in recent years. Epigenetic modifications of cancers are categorized into three major processes including non-coding RNAs, histone modification, and DNA methylation. Hence, the modification of the latter epigenetic event is currently considered an effective strategy for treatment of cancer patients. Thereby, this report summarizes the available evidence that investigated melatonin-induced effects in altering the status of DNA methylation in different cancer cells and models, e.g., malignant glioma and breast carcinoma. Also, we discuss the role of artificial light at night (ALAN)-mediated inhibitory effects on melatonin secretion and subsequent impact on global DNA methylation of cancer cells.
Methods in Microarray Normalization (2008)

Scientists can use molecular profiling microarrays to compare healthy cells with their diseased counterparts and develop gene-specific treatments. Finding the best way to interpret original profiling data into accurate trends, however, continues to drive the development of normalization algorithms and software tools. Methods in Microarray Normaliza
Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers (2016)

Most genomic prediction studies fit only additive effects in models to estimate genomic breeding values (GEBV). However, if dominance genetic effects are an important source of variation for complex traits, accounting for them may improve the accuracy of GEBV. We investigated the effect of fitting dominance and additive effects on the accuracy of GEBV for eight egg production and quality traits in a purebred line of brown layers using pedigree or genomic information (42K single-nucleotide polymorphism (SNP) panel). Phenotypes were corrected for the effect of hatch date. Additive and dominance genetic variances were estimated using genomic-based [genomic best linear unbiased prediction (GBLUP)-REML and BayesC] and pedigree-based (PBLUP-REML) methods. Breeding values were predicted using a model that included both additive and dominance effects and a model that included only additive effects. The reference population consisted of approximately 1800 animals hatched between 2004 and 2009, while approximately 300 young animals hatched in 2010 were used for validation. Accuracy of prediction was computed as the correlation between phenotypes and estimated breeding values of the validation animals divided by the square root of the estimate of heritability in the whole population. The proportion of dominance variance to total phenotypic variance ranged from 0.03 to 0.22 with PBLUP-REML across traits, from 0 to 0.03 with GBLUP-REML and from 0.01 to 0.05 with BayesC. Accuracies of GEBV ranged from 0.28 to 0.60 across traits. Inclusion of dominance effects did not improve the accuracy of GEBV, and differences in their accuracies between genomic-based methods were small (0.01-0.05), with GBLUP-REML yielding higher prediction accuracies than BayesC for egg production, egg colour and yolk weight, while BayesC yielded higher accuracies than GBLUP-REML for the other traits. In conclusion, fitting dominance effects did not impact accuracy of genomic prediction of breeding values in this population.
cDNA cloning and characterisation of an α‐glucosidase gene from potato (Solanum tuberosum L.) (1998)

Using an Arabidopsis thaliana expressed sequence tag with sequence similarity to human lysosomal alpha-glucosidase as a probe, a potato cDNA was isolated. The cDNA encodes a polypeptide with an Mr value of 105,400 and the most significant matches of the deduced amino acid sequence are with members of family 31 of glucosyl transferase. The potato cDNA was expressed in a strain of Saccharomyces cerevisiae that is deficient in maltase activity and unable to grow using maltose as a carbon source (ABYSMAL81). Expression of the potato cDNA in the mutant yeast strain restores its ability to use maltose as a carbon source for growth. Additionally, alpha-glucosidase activity could be measured in extracts of the yeast cells following complementation. A range of maltodextrins were substrates for this activity. The steady-state expression level of the potato alpha-glucosidase gene was low in most tissues examined, the highest levels occurring in sprouting tubers and source leaves.
Precision design of novel poly(ionic liquid) (co)polymers by cobalt-mediated radical polymerization (CMRP) (2014)

In recent years, poly(ionic liquid)s (PIL)s were found to take an enabling role in important fields of polymer chemistry and material science. PILs combine the unique properties of ionic liquids with the flexibility and properties of macromolecular architectures giving rise to a new family of functional polymers that opens new area of applications such as polymer electrolytes in electrochemical devices, powerful dispersants and stabilizers, absorbing membranes, precursors for carbon materials, porous polymers, etc. In this communication, we will report on the implementation of organometallic-mediated radical polymerization (OMRP) technique for the precision synthesis of unprecedented PILS (co)polymers. We will discuss how an organocobalt complex can nicely control the growth of vinyl imidazolium chains and lead to PILS with predicted molar masses and low polydispersitiesunder mild experimental conditions. The huge potential of this system will be highlighted by describing the first one-pot synthesis of vinyl imidazolium-based block copolymers in heterogeneous conditions. This OMRP is unique for providing well-defined vinyl imidazolium based-copolymers that are not easily accessible by other controlled radical polymerization techniques, and opens therefore new rooms for advanced PILS applications.
Self-Assembly and Lyomesophases Formed by Long-Chain Alkoxymethyl-Nucleobase Derivatives (2000)

Amphiphilic complementary nucleobase derivatives, containing n-octadecyloxymethyl substituents at the N1 position of pyrimidine and N9 of purine, dissolved in chloroform form non-specific lyotropic mesophases, which were analyzed by optical polarizing microscopy. Molecular modeling studies visualize hypothetical horizontal and vertical nucleobase hydrogen-bonding and stacking arrangements, as well as aliphatic long-chain interstrand interaction.
The C-terminal Residues in the Alpha-interacting Domain (AID) Helix Anchor CaVβ Subunit Interaction and Modulation of CaV2.3 Channels (2004)

The alpha-interacting domain (AID) in the I-II linker of high voltage-activated (HVA) Ca(2+) channel alpha1 subunits binds with high affinity to Ca(V)beta auxiliary subunits. The recently solved crystal structures of the AID-Ca(V)beta complex in Ca(V)1.1/1.2 have revealed that this interaction occurs through a set of six mostly invariant residues Glu/Asp(6), Leu(7), Gly(9), Tyr(10), Trp(13), and Ile(14) (where the superscript refers to the position of the residue starting with the QQ signature doublet) distributed among three alpha-helical turns in the proximal section of the I-II linker. We show herein that alanine mutations of N-terminal AID residues Gln(1), Gln(2), Ile(3), Glu(4), Glu(6), Leu(7), and Gly(9) in Ca(V)2.3 did not abolish [(35)S]Ca(V)beta 1b or [(35)S]Ca(V)beta 3 subunit overlay binding to fusion proteins nor did they prevent the typical modulation of whole cell currents by Ca(V)beta 3. Mutations of the invariant Tyr(10) with either hydrophobic (Ala), aromatic (Phe), or positively charged (Arg, Lys) residues yielded Ca(V)beta 3-responsive whole cell currents, whereas mutations with negatively charged residues (Asp, Glu) disrupted Ca(V)beta 3 binding and modulation. In contrast, modulation and binding by Ca(V)beta 3 was significantly weakened in I14A (neutral and hydrophobic) and I14S (neutral and polar) mutants and eradicated in negatively charged I14D and I14E or positively charged I14R and I14K mutants. Ca(V)beta 3-induced modulation was only preserved with the conserved I14L mutation. Molecular replacement analyses carried out using a three-dimensional homology model of the AID helix from Ca(V)2.3 suggests that a high degree of hydrophobicity and a restrained binding pocket could account for the strict structural specificity of the interaction site found at position Ile(14). Altogether these results indicate that the C-terminal residues Trp(13) (1) and Ile(14) anchor Ca(V)beta subunit functional modulation of HVA Ca(2+) channels.
New polymerizing chemistries for through-silicon via etching (2012)

This study investigates a new fluorocarbon (FC) as an environmentally friendly gas chemistry for sidewall passivation during time-multiplexed plasma etch processes for through-silicon vias (TSVs). The effect of plasma processing conditions on TSV etch rate, etch selectivity, and sidewall roughness was examined. In addition, blanket fluorocarbon films were deposited, etched, and characterized with x-ray photoelectron spectroscopy (XPS) to study the effect of film chemistry on polymer growth and etch rates. XPS analysis of films deposited by low fluorine/carbon (F/C) ratio gases showed similarly low F/C ratios in the deposited films. This low F/C ratio also corresponded to an increased film deposition rate and etch resistance. Compared to octafluorocyclobutane (C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sub> ) processes, recipes with this FC had slightly lower etch rates while selectivity was slightly increased. Sidewall roughness of TSVs was the same between the two gases, and trench profiles were generally vertical.
A Family of Special Purpose Microprogrammable Digital Signal Processor IC's in an LPC Vocoder System (1983)

This paper discusses a family of digital signal processor integrated circuits designed to be the fundamental buitding blocks of an LPC vocoder, specifically LPC analysis, AMDF pitch extraction, and LPC synthesis. The IC's are custom designs intended to minimize silicon real estate for extremely high performance, novel DSP architectures, and high computational demand algorithms. Each IC shares a common architecture, that of a single internal data bus connecting input and output FIFO's, multiple arithmetic logic units, registers, and a microcode control bus. Each application is microprogrammed in register transfer language providing considerable flexibility. The CMOS design of each IC allows it to implement the high performance digital signal processing algorithms with minimal power consumption. The LPC synthesis IC allows various common filter topologies and residual excitation. The AMDF IC extracts the commonly used features for pitch and voicing. The LPC analyzer IC is microprogrammed to implement a flow form PARCOR LPC analysis. Algorithm architecture tradeoffs between computational load and memory are discussed.
Le musée Saint-Jean : un musée d'archéologie ? (1992)

International audience
Applications of Temperature‐Responsive Polymers Grafted onto Solid Core Nanoparticles (2018)

This chapter provides insights into the applications of different temperature-responsive polymers (TRPs) grafted to solid core inorganic nanoparticles and how their thermoresponsive nature can provide solutions to many of the problems associated with other nanoparticles. It describes the most common forms of TRPs reported in the literature, Poly(N-isopropylacrylamide) and poloxamers, as well as some more unusual TRPs, and considers how their use and function can be varied depending on the particle core. Silica nanoparticles decorated with TRPs have applications beyond the pharmaceutical industry. Metallic nanoparticles are formed from transition elements; however other types are available such as magnesium and calcium. Magnetic nanoparticles have several potential applications in drug delivery and biomaterials science, including cancer treatment. By combining the unique magnetic properties of these particles, with TRPs, it is possible to produce diverse multifunctional systems for drug delivery applications.
Molecular characterization of the family of the N-methyl-D-aspartate receptor subunits. (1993)

cDNA clones for four different N-methyl-D-aspartate (NMDA) receptor subunits (NMDAR2A-NMDAR2D) were isolated through polymerase chain reactions followed by molecular screening of a rat brain cDNA library. These subunits are only about 15% identical with the key subunit of the NMDA receptor (NMDAR1) but are highly homologous (approximately 50% homology) with one another. They also commonly possess large hydrophilic domains at both amino- and carboxyl-terminal sides of the four putative transmembrane segments. NMDAR2A and NMDAR2C expressed individually in Xenopus oocytes showed no electrophysiological response to agonists. However, these subunits in combined expression with NMDAR1 markedly potentiated the NMDAR1 activity and produced functional variability in the affinity of agonists, the effectiveness of antagonists, and the sensitivity to Mg2+ blockade. Thus, NMDAR1 is essential for the function of the NMDA receptor, and multiple NMDAR2 subunits potentiate and differentiate the function of the NMDA receptor by forming different heteromeric configurations with NMDAR1. Northern blotting and in situ hybridization analyses revealed that the expressions of individual mRNAs for the NMDAR2 subunits overlap in some brain regions but are also specialized in many other regions. This investigation demonstrates the anatomical and functional differences of the NMDAR2 subunits, which provide the molecular basis for the functional diversity of the NMDA receptor.
High-κ Dielectric Scaling for Nano-CMOS Technology (2017)

This chapter discusses various concerns regarding the process, material, and device characteristics of the-state-of-the-art subnanometer high-k gate dielectrics. It highlights some potential options for future high-k processes. The scaling of gate dielectric physical thickness has been the major strategy for maintaining continuous downsizing and performance improvement of metal oxide semiconductor (MOS) devices for several decades. This scaling had once reached its technological limit at around 1 nm before the introduction of high-k gate dielectric materials. The chapter highlights various fundamental issues in the introduction of high-k materials, technological issues of thin film preparation, and electrical characteristics of advanced complementary metal–oxide–semiconductor (CMOS) devices based on state-of-the-art metal gate/high-k stacks. To further lower the equivalent oxide thickness (EOT) of gate dielectric films to around half nanometer, which is likely to be used in the technology node with the gate length of 6 nm, even higher-k-value materials and better interface layer control are indispensable.
Examining the Patient-Reported Outcomes Measurement Information System versus the Scoliosis Research Society–22r in adult spinal deformity (2019)

The authors found strong correlations between the SRS-22r Pain and Activity domains with corresponding PROMIS-PI and -PF scores. Pain measurements showed similar and strong ES and aSRM while the function measurements showed similar, moderate ES and aSRM at 2-year follow-up. These data support further exploration of the use of PROMIS-computer adaptive test instruments in ASD.
Characterization of pentocin TV35b, a bacteriocin-like peptide isolated from Lactobacillus pentosus with a fungistatic effect on Candida albicans (1999)

Lactobacillus pentosus TV35b, isolated from the posterior fornix secretions of the vagina of a prenatal patient, produced a bacteriocin-like peptide (pentocin TV35b), which is inhibitory to Clostridium sporogenes, Cl. tyrobutyricum, Lact. curvatus, Lact. fermentum, Lact. sake, Listeria innocua, Propionibacterium acidipropionici, Propionibacterium sp. and Candida albicans. The mechanism of activity of pentocin TV35b is bactericidal, as shown by a decrease in the viable cell numbers of Lact. sake from approximately 4 x 108 to less than 10 cfu ml - 1 over a period of 4 h. Pentocin TV35b added to the growth medium of C. albicans stimulated the formation of pseudohyphae during the first 36 h, followed by a slight repression in cell growth. Production of pentocin TV35b was at its maximum towards the end of the logarithmic growth phase of strain TV35b. The peptide was purified by ammonium sulphate precipitation, followed by SP-Sepharose cation exchange chromatography. The molecular size of pentocin TV35b was estimated to be between 2.35 and 3.4 kDa, according to tricine-SDS PAGE. However, results obtained by electrospray ionization mass spectroscopy indicated that the peptide is 3930.2 Da in size. Amino acid analysis performed by using the Pico-Tag(R) method and a Nova-Pak C18 HPLC column indicated that pentocin TV35b consists of 33 amino acids with a total mass of 3929.63 Da. Pentocin TV35b is inactivated when treated with papain and Proteinase K, but remains active after incubation at pH 1-10 for 2 h at 25 degrees C, and when heat-treated for 30 min at 100 degrees C.
Preparation of Porosity–Graded SOFC Anode Substrates (2006)

Abstract Porosity graded anode substrates for solid oxide fuel cells are considered to optimise the gas transport through the substrate by maintaining a high electrochemical activity for fuel oxidation at the anode/solid electrolyte interface. In this work, the fabrication of porosity graded anode substrates, made from nickel oxide and yttria‐modified zirconia and produced by dry uni‐axial pressing, are described. Using carbon as pore formers and adjusting the particle size distribution in the ceramic NiO‐YSZ masses, samples with gradually changing porosity are built up. The sintering behaviour of the individual layers is analysed and partly adjusted so the multi‐layer support can be co‐fired together with the YSZ electrolyte layer. In the oxidized state, four‐layer, porosity graded anode supported half‐cells with a dense YSZ electrolyte are demonstrated.