gebhart/patrepeval huggingface dataset:
Role of Pseudomonas aeruginosa PhoP-PhoQ in resistance to antimicrobial cationic peptides and aminoglycosides (2000)

Resistance to the polycationic antibiotic polymyxin B and expression of the outer-membrane protein OprH in the opportunistic pathogen Pseudomonas aeruginosa both involve the PhoP-PhoQ two-component regulatory system. The genes for this system form an operon with oprH, oprH-phoP-phoQ, that responds to Mg(2+) starvation and PhoP levels. In this study, the Mg(2+)-regulated promoter for this operon was mapped upstream of oprH by primer-extension experiments. An oprH::xylE-Gm(R) mutant H855 was constructed and measurement of the catechol 2,3-dioxygenase activity expressed from this transcriptional fusion provided evidence for a second, weak promoter for phoP-phoQ. Wild-type P. aeruginosa PAO1 strain H103 was found to exhibit Mg(2+)-regulated resistance to the alpha-helical antimicrobial cationic peptide CP28 in addition to its previously characterized resistance to polymyxin B. Resistance to this peptide was unchanged in the OprH-null mutant H855 and a PhoP-null mutant H851. In contrast, PhoQ-null mutant H854 demonstrated constitutive CP28 resistance. Northern blot analysis revealed constitutive expression of phoP in this strain, implicating PhoP-PhoQ in the resistance of P. aeruginosa to cationic peptides. Furthermore, all three null-mutant strains demonstrated increased resistance to the aminoglycoside antibiotics streptomycin, kanamycin and amikacin. Two additional mutant strains, H895 and H896, were constructed that carried unmarked deletions in oprH and were found to exhibit aminoglycoside susceptibility equivalent to that of the wild-type. This result provided definitive evidence that OprH is not involved in P. aeruginosa aminoglycoside resistance and that the changes in resistance in strain H855 and a previously reported oprH mutant were due to polar effects on phoP-phoQ rather than loss of OprH expression. A role for PhoP-PhoQ in resistance to aminoglycosides is envisaged that is distinct from that in resistance to cationic peptides and polymyxin B.
A Low-Power Embedded SRAM for Wireless Applications (2007)

This paper introduces a novel ultra-low-power SRAM. A large power reduction is obtained by the use of four new techniques that allow for a wider and better trade-off between area, delay and active and passive energy consumption for low-power embedded SRAMs. The design targets wireless applications that require a moderate performance at an ultra-low-power consumption. The implemented design techniques consist of a more efficient memory databus, the exploitation of the dynamic read stability of SRAM cells, a new low-swing write technique and a distributed decoder. An 8-KB 5T SRAM was fabricated in a 0.18-mum technology. The measurement results confirm the feasibility and the usefulness of the proposed techniques. A reduction of active power consumption with a factor of 2 is reported as compared to the current state of the art. The results are generalized towards a 32-KB SRAM.
Broad 4-Hydroxyphenylpyruvate Dioxygenase Inhibitor Herbicide Tolerance in Soybean with an Optimized Enzyme and Expression Cassette (2014)

With an optimized expression cassette consisting of the soybean (Glycine max) native promoter modified for enhanced expression driving a chimeric gene coding for the soybean native amino-terminal 86 amino acids fused to an insensitive shuffled variant of maize (Zea mays) 4-hydroxyphenylpyruvate dioxygenase (HPPD), we achieved field tolerance in transgenic soybean plants to the HPPD-inhibiting herbicides mesotrione, isoxaflutole, and tembotrione. Directed evolution of maize HPPD was accomplished by progressively incorporating amino acids from naturally occurring diversity and novel substitutions identified by saturation mutagenesis, combined at random through shuffling. Localization of heterologously expressed HPPD mimicked that of the native enzyme, which was shown to be dually targeted to chloroplasts and the cytosol. Analysis of the native soybean HPPD gene revealed two transcription start sites, leading to transcripts encoding two HPPD polypeptides. The N-terminal region of the longer encoded peptide directs proteins to the chloroplast, while the short form remains in the cytosol. In contrast, maize HPPD was found almost exclusively in chloroplasts. Evolved HPPD enzymes showed insensitivity to five inhibitor herbicides. In 2013 field trials, transgenic soybean events made with optimized promoter and HPPD variant expression cassettes were tested with three herbicides and showed tolerance to four times the labeled rates of mesotrione and isoxaflutole and two times the labeled rates of tembotrione.
Supplementary Methods, Figure Legends, and References from Context-Dependent Role of Angiopoietin-1 Inhibition in the Suppression of Angiogenesis and Tumor Growth: Implications for AMG 386, an Angiopoietin-1/2–Neutralizing Peptibody (2023)

Supplementary Methods, Figure Legends, and References from Context-Dependent Role of Angiopoietin-1 Inhibition in the Suppression of Angiogenesis and Tumor Growth: Implications for AMG 386, an Angiopoietin-1/2–Neutralizing Peptibody
Nano and micro materials in a Pb-free world (2011)

This paper examines the use of nano and micro materials in the area of “Pb-free” technology. A variety of Pb-free materials for advanced organic packaging have been developed. These include capacitors as embedded passives, highly conducting nano-micro media for Z-interconnects, lead free assembly paste, and Z-interconnects suitable for Pb-free assembly. The electrical properties of capacitors fabricated from BaTiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> -epoxy nanocomposites showed a stable capacitance over a temperature range from 20°C to 120°C. Low resistivity paste, with volume resistivity in the range of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> ohm-cm to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> ohm-cm depending on composition, particle size, and loading can be used as conductive joints for high frequency and high density interconnect applications. A variety of metals including Cu, Ag, LMP (low melting point) and LMP-coated Cu fillers have been used to make lead free electrically conducting adhesive technology as an alternative to solders. The mechanical strength of the various Pb-free conducting pastes was characterized by the measurement of tensile strength. Most of the conducting pastes exhibited no fail even up to 1500 PSI. Reliability of the Pb-free structures was ascertained by IR-reflow, thermal cycling, PCT (Pressure Cooker Test) and solder shock. All capacitors experienced less than 5% change after 3X, Pb-free IR reflow and 1000 cycles of thermal cycling (ATC, DTC). Altogether, this is a new direction in the development of Pb-free Packages and more specifically in the development of substrates with Z-interconnects suitable for Pb-free assembly.
Tyrosine kinase activity may be necessary but is not sufficient for c-erbB1-mediated tissue-specific tumorigenicity (1994)

Expression of mutant avian c-erbB1 genes results in tissue-specific transformation in chickens. Site-directed mutagenesis was used to generate kinase-defective mutants of several tissue-specific v-erbB transforming mutants by replacement of the ATP-binding lysine residue in the kinase domain with an arginine residue. These kinase-defective v-erbB mutants were analyzed for their in vitro and in vivo transforming potentials. Specifically, kinase-defective mutants of erythroleukemogenic, hemangioma-inducing, and sarcomagenic v-erbB genes were assessed for their oncogenic potential. In vitro transformation potential was assessed by soft-agar colony formation in primary cultures of chick embryo fibroblasts (CEF). In vivo transformation potential was determined by infection of 1-day-old line 0 chicks with concentrated recombinant retrovirus and then monitoring of birds for tumor formation. These transformation assays demonstrate that kinase activity is absolutely essential for transformation by tissue-specific transforming mutants of the avian c-erbB1 gene. Since all of the tissue-specific v-erbB mutants characterized to date exhibit tyrosine kinase activity in vitro but do not transform all tissues in which they are expressed, we conclude that v-erbB-associated tyrosine kinase activity may be necessary but is not sufficient to induce tumor formation.
Insulation integrity of particle-contaminated GIS with dielectric coated electrodes (2002)

Electrical insulation performance of compressed gas insulated switchgear (GIS) and gas insulated transmission line (GITL) systems is adversely affected by metallic particle contaminants. Dielectric coatings help to improve the insulation performance in several ways. In this paper, dynamics of wire particle in a coaxial gas insulated transmission line (GITL) system with coated electrodes under AC voltage is studied using a computational algorithm. The possibility of the SF/sub 6/ gas insulation breakdown due to the presence of metallic contaminants was computed at different applied voltages and gas pressures. Results of laboratory experiments are presented.
Developments in Centrifugal Compressor Surge Control—A Technology Assessment (1994)

There are a number of surge control schemes in current use for centrifugal compressors employed in natural gas transmission systems. Basically, these schemes consist of a set of detection devices that either anticipate surge or detect it at its inception, and a set of control devices that act to prevent surge from occurring. A patent search was conducted in an attempt to assess the level and direction of technology development over the last 20 years and to define the focus for future R&amp;D activities. In addition, the paper presents the current state of technology in three areas: surge control, surge detection, and surge suppression. Patent data obtained from on-line databases showed that most of the emphasis has been on surge control rather than on detection and control and that the current trend in surge control will likely continue toward incremental improvement of a basic or conventional surge control strategy. Various surge suppression techniques can be grouped in two categories: (i) those that are focused on better compressor interior design, and (ii) others that attempt to suppress surge by external and operational means.
Bowtie Plasmonic Aperture for Single Quantum Emitter Absorption Measurement (2014)

Bowtie apertures with gap sizes of less than 30nm are fabricated successfully by lift-off process. Numerical modeling shows that they have mode area as small as 0.011(λ/n)2, which is two orders smaller than a conventional tightly focused laser spot.
Structure-activity relationships of analogs of pentamidine against Plasmodium falciparum and Leishmania mexicana amazonensis (1990)

The antiprotozoal compound 1,5-di(4-amidinophenoxy)pentane (pentamidine) and 36 of its analogs were screened for in vitro activity against Leishmania mexicana amazonensis clone 669 C4S (MHOM/BR/73/M2269) and Plasmodium falciparum clones W2 (Indochina III/CDC) and D6 (Sierra Leone I/CDC). Pentamidine and each of the analogs tested exhibited activity in vitro against L. m. amazonensis and P. falciparum. The pentamidine analogs were more effective against the P. falciparum clones than against L. m. amazonensis. P. falciparum was extremely susceptible to these compounds, with 50% inhibitory concentrations as low as 0.03 microM. While none of the analogs exhibited marked improvement in antileishmanial activity compared with pentamidine, 12 of the pentamidine analogs showed activity approximately equal to or greater than that of the parent compound. From the promising activity exhibited by the pentamidine analogs in this in vitro study and their potential for reduced toxicity relative to the parent drug, pentamidine-related compounds hold promise as new agents for the treatment of protozoal infections.
An introduction to micro-ecology patches (2010)

Bacterial systems offer excellent tests of how well the general theoretical predictions of ecology dynamics do or do not in fact conform to reality. We believe that the basic rules that govern the cohabitation of competing species for limited resources are the same from bacteria to man, we just don't know the rules, and that fundamental studies of the games bacteria play will give fundamental insight into the vastly more complex systems we hope to attack later. In this tutorial review we discuss how simplified micro-ecologies constructed using tools of micro and nanofabrication techniques offer some idea of how physical principles and analysis can address the issue of complex ecology dynamics.
Quantifying the Environmental Sensitivity of SSTDR Signals for Monitoring PV Strings (2021)

Current spread spectrum time-domain reflectometry (SSTDR) fault detection methods in photovoltaics compare measurements with a fault-free baselin.Yet, environmental factors, such as illuminance, temperature, and humidity, affect these signals and can negatively affect our ability to detect and locate faults. This article explains and quantifies the effects of environmental factors on SSTDR measurements. We demonstrate that illuminance, temperature, and humidity each significantly affect reflections from photovoltaic panels, which require the use of up to 240 baselines to prevent environmental variation from obscuring faults. We present a method to determine the number of required baselines in any given climate and motivate future work in baseline prediction.
Effective Degradation of Cellulose by Microwave Irradiation in Alkaline Solution (2021)

Abstract The utilization of lignocellulosic biomass is effective to produce chemicals and fuels, which are of importance for the establishment of a sustainable society. The conversion of cellulose, which is the main component of the lignocellulosic biomass, into significant chemicals that can be further converted to different chemicals or fuels in the subsequent step, under gentle conditions is a promising route. Organic acids such as acetic acid, glycolic acid and formic acid are significant chemicals are examples of such products. A novel method to producing important platform chemicals from Micro-crystalline cellulose was developed. Micro-crystalline cellulose was degraded as a result of an oxidation with potassium chlorate by microwave radiation, in a one-pot procedure, efficient reaction conditions such as short reaction time and full conversion of the cellulose were identified. The reaction products have been analyzed by 1 H, 13 C NMR, XPS, TGA and XRD.
Ni@Fe2O3 heterodimers: controlled synthesis and magnetically recyclable catalytic application for dehalogenation reactions (2012)

Ni@Fe(2)O(3) heterodimer nanoparticles (NPs) were synthesized by thermal decomposition of organometallic reactants. After functionalization, these Ni@Fe(2)O(3) heterodimers became water soluble. The pristine heterodimeric NPs were characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD), Mössbauer spectroscopy and magnetic susceptibility measurements. A special advantage of the heterodimers lies in the fact that nanodomains of different composition can be used as catalysts for the removal of environmentally hazardous halogenated pollutants.
Amphiphilic polyenic push–pull chromophores for nonlinear optical applications (2000)

Amphiphilic cationic polyenic push–pull chromophores which offer interesting supramolecular possibilities for second harmonic generation have been synthesised and their optical non-linearities studied for the first time by electric field induced second harmonic (EFISH) generation in solution.
Efficient Catalytic Enantioselective Synthesis of Unsaturated Amines:  Preparation of Small- and Medium-Ring Cyclic Amines through Mo-Catalyzed Asymmetric Ring-Closing Metathesis in the Absence of Solvent (2002)

The first catalytic asymmetric ring-closing metathesis method for the synthesis of N-containing heterocycles is reported; this is accomplished through Mo-catalyzed kinetic resolution or desymmetrization of unsaturated amines. Importantly, this catalytic asymmetric method delivers medium-ring unsaturated amines (including eight-membered rings) in high yield, with exceptional enantioselectivity and without the need for solvents. These enantioselective reactions can be effected by catalysts prepared in situ from commercially available reagents.
AttentionCode: Ultra-Reliable Feedback Codes for Short-Packet Communications (2022)

Ultra-reliable short-packet communication is a major challenge in future wireless networks with critical applications. To achieve ultra-reliable communications beyond 99.999%, this paper envisions a new interaction-based communication paradigm that exploits feedback from the receiver. We present AttentionCode, a new class of feedback codes leveraging deep learning (DL) technologies. The underpinnings of AttentionCode are three architectural innovations: AttentionNet, input restructuring, and adaptation to fading channels, accompanied by several training methods, including large-batch training, distributed learning, look-ahead optimizer, training-test signal-to-noise ratio (SNR) mismatch, and curriculum learning. The training methods can potentially be generalized to other wireless communication applications with machine learning. Numerical experiments verify that AttentionCode establishes a new state of the art among all DL-based feedback codes in both additive white Gaussian noise (AWGN) channels and fading channels. In AWGN channels with noiseless feedback, for example, AttentionCode achieves a block error rate (BLER) of $10^{-7}$ when the forward channel SNR is 0 dB for a block size of 50 bits, demonstrating the potential of AttentionCode to provide ultra-reliable short-packet communications.
Pes1 mutagenesis, experimental approach of knock-down-knock-in assay and conditional expression of Pes1 mutants (2011)

<b>Copyright information:</b>Taken from "The BRCT domain of mammalian Pes1 is crucial for nucleolar localization and rRNA processing"Nucleic Acids Research 2006;35(3):789-800.Published online 22 Dec 2006PMCID:PMC1807956.© 2006 The Author(s) () Panel of Pes1 deletion mutants harbouring a C-terminal HA-tag, as described previously. M9 and M10 are novel deletion mutants. NLS: classical nuclear localization signal; bip. NLS: bipartite NLS; Pescadillo_N: N-terminal region of Pes1 (Pfam-database: PF06732); BRCT: BRCT-domain; acidic regions: two glutamic acid rich regions; ΨKXE: consensus SUMOylation site; HA: hemagglutinin-tag. () Experimental approach of knock-down-knock-in assay. () Western blot analysis of knock-down-knock-in assay as described in (B). Expression of recombinant wt or mutant Pes1 proteins was analysed with the anti-HA antibody (3F10). Knock-down of endogenous Pes1 by siRNA was verified probing with the anti-Pes1 antibody (8E9). All mutants besides M5, M10 and M7 were also detected with the anti-Pes1 antibody. Equal loading was controlled by immunodetection of α-tubulin. Size-dependent discrimination of HA-tagged wt and endogenous Pes1 protein using the anti-Pes1 antibody is shown in the enlarged panel at the bottom.
Is This Your Final Answer? (2016)

Answers on mobile search result pages have become a common way to attempt to satisfy users without them needing to click on search results. Many different types of answers exist, such as weather, flight and currency answers. Understanding the effect that these different answer types have on mobile user behavior and how they contribute to satisfaction is important for search engine evaluation. We study these two aspects by analyzing the logs of a commercial search engine and through a user study. Our results show that user click, abandonment and engagement behavior differs depending on the answer types present on a page. Furthermore, we find that satisfaction rates differ in the presence of different answer types with simple answer types, such as time zone answers, leading to more satisfaction than more complex answers, such as news answers. Our findings have implications for the study and application of user satisfaction for search systems.
AssemblyNet: A large ensemble of CNNs for 3D whole brain MRI segmentation (2020)

Whole brain segmentation of fine-grained structures using deep learning (DL) is a very challenging task since the number of anatomical labels is very high compared to the number of available training images. To address this problem, previous DL methods proposed to use a single convolution neural network (CNN) or few independent CNNs. In this paper, we present a novel ensemble method based on a large number of CNNs processing different overlapping brain areas. Inspired by parliamentary decision-making systems, we propose a framework called AssemblyNet, made of two "assemblies" of U-Nets. Such a parliamentary system is capable of dealing with complex decisions, unseen problem and reaching a relevant consensus. AssemblyNet introduces sharing of knowledge among neighboring U-Nets, an "amendment" procedure made by the second assembly at higher-resolution to refine the decision taken by the first one, and a final decision obtained by majority voting. During our validation, AssemblyNet showed competitive performance compared to state-of-the-art methods such as U-Net, Joint label fusion and SLANT. Moreover, we investigated the scan-rescan consistency and the robustness to disease effects of our method. These experiences demonstrated the reliability of AssemblyNet. Finally, we showed the interest of using semi-supervised learning to improve the performance of our method.
Bayesian classification, anomaly detection, and survival analysis using network inputs with application to the microbiome (2020)

While the study of a single network is well-established, technological advances now allow for the collection of multiple networks with relative ease. Increasingly, anywhere from several to thousands of networks can be created from brain imaging, gene co-expression data, or microbiome measurements. And these networks, in turn, are being looked to as potentially powerful features to be used in modeling. However, with networks being non-Euclidean in nature, how best to incorporate them into standard modeling tasks is not obvious. In this paper, we propose a Bayesian modeling framework that provides a unified approach to binary classification, anomaly detection, and survival analysis with network inputs. We encode the networks in the kernel of a Gaussian process prior via their pairwise differences and we discuss several choices of provably positive definite kernel that can be plugged into our models. Although our methods are widely applicable, we are motivated here in particular by microbiome research (where network analysis is emerging as the standard approach for capturing the interconnectedness of microbial taxa across both time and space) and its potential for reducing preterm delivery and improving personalization of prenatal care.
Hybrid Lumped-Element and Finite Element Model for Novel Synthetic Jet Actuator Shapes (2023)

A modeling approach was developed that combines lumped-element and finite element methods for analysis of synthetic jet actuator (SJA) geometries that deviate significantly from an ideal Helmholtz resonator. The diaphragm was modeled using the finite element method (FEM) coupled to lumped-element equations that govern the fluid flow. The loss coefficient [Formula: see text] was estimated based on the geometry of the cavity and orifice. A pressure acoustic FEM model of the cavity and orifice was used to determine a characteristic resonance frequency to use in place of the Helmholtz resonance frequency that appeared in the lumped element equations. The results were validated using experimental data for SJAs with geometries that deviate significantly from the Helmholtz resonator idealization. The combination of replacing the Helmholtz frequency with a more accurate characteristic frequency and using a computed value for the loss coefficient was shown to provide more accurate performance predictions for low-profile SJA designs.