gebhart/patrepeval huggingface dataset:
Cultivation of proteorhodopsin containing bacteria from the North Sea (2008)

The light dependent proton pump proteorhodopsin must be an important source of energy for bacteria in the oligotrophic ocean, as judged by its abundance, diversity, and spectral tuning to specific wavelengths. Until now, proteorhodopsin genes have mostly been found in tropical oceans, and only very few strains carrying proteorhodopsin were successfully cultured, e.g. Pelagibacter ubique SAR11, HTCC2207, and MED134. The latter is the only one were light was actually shown to stimulate growth at low carbon concentrations. Here we determined the diversity of proteorhodopsin genes in the total bacterioplankton of the North Sea close to the island of Helgoland, and isolated and characterized two new strains carrying proteorhodopsin. Using specific primers, cloning and sequencing, a large diversity of proteorhodopsin genes was discovered in the DNA of a filtered North Sea water sample. Oligocarbophilic bacteria were isolated by dilution plating a water sample on media without any added carbon sources except for those naturally present. Plates were incubated at in situ temperature (16°C) in a natural day-night cycle for 4 weeks. Appr. 250 isolates obtained in such a way were screened for the presence of the proteorhodopsin gene by PCR, resulting in the discovery ot two such strains, PRO95 and PRO100. 16S rRNA sequence analysis showed that they belong into the Bacteroidetes phylum. The proteorhodopsin sequence was completed by primer walking and the effect of light was studied in oligocarbophilic media.
Dislocation of Lattice Points for Impedance Matching of a Photonic Bandgap Cavity Resonator (2019)

A photonic bandgap (PBG) cavity resonator encompassing a metamaterial with a sparsely populated array of metallic rods has been arrived at for potential application in future generations of particle accelerators. The star-shape array was evolved from a two-dimensional triangle lattice with certain lattice points vacant. Optimized for the TM <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01</sub> - like mode with the electric field concentrated at the center while the higher-order modes (HOMs) are constrained from the center, the cavity is excited by a standard rectangular waveguide. Input matching is accomplished by fine tuning in the positions of selected metal rods in the two outer layers. The cavity-waveguide assembly was fabricated with copper and cold tested for resonance characteristics. A return loss of over 20 dB at the designed resonance frequency of 11.41 GHz was measured. A bead pull experiment was performed to confirm the uniformity of the field along the axis of the cavity resonator.
SBS threshold of segmented fibers (2005)

We present a rigorous analysis of stimulated Brillouin scattering (SBS) in nonuniform fibers consisting of segments with non-overlapping Brillouin gain spectra (BGS). For a span of two segments we predict the optimum configuration with maximum SBS threshold. Theoretical results agree well with measured values.
Terahertz time-domain spectroscopy technique for characterizing Ytterbium-doped Yttrium Aluminum Garnet Crystals (2006)

Terahertz time-domain spectroscopy has been employed to measure the optical constants of ytterbium-doped yttrium aluminum garnet (YbxY1−x)3Al5O12 crystals for nominal x values of 0.0, 0.1, 0.2, 0.5, 0.8 and 1.0 for frequencies ranging from 0.2 to 1.8 THz.
Finite-difference time-domain simulation of plasmonic nanoparticles (2006)

Recently noble metal nanoparticles have attracted strong interest due to their potential as nano-scale waveguides and lumped elements in the optical frequency range. Engheta et. al., (2005) showed that a non-metal nanoparticle can serve as a capacitor whereas a metal nanoparticle can serve as an inductor. This idea is interesting for the design of optical metamaterials, if the proposed nanoparticles are employed to implement the inductive/capacitive blocks in 2-D/3-D negative-refractive-index transmission line (NRI-TL) based metamaterials. Due to the difficulty of adjusting to the inherent numerical intricacies of this problem, simulating plasmonic nanoparticles becomes a challenge for commercial packages. Full-wave analysis through the finite-difference time-domain (FDTD) can provide an alternative to them. In this paper, we present the FDTD analysis of a silver nano sphere and compare its field pattern to that of a dielectric nano sphere. These results are also validated against data obtained from quasi-static theory.
Involvement of tyrosine phosphorylation in endothelin‐1‐induced calcium‐sensitization in rat small mesenteric arteries (1997)

1. We have studied the effect of endothelin-1 stimulation on protein tyrosine phosphorylation levels in intact small mesenteric arteries of the rat and investigated the effects of tyrosine kinase inhibition on the contractile response to this agonist. 2. Endothelin-1 stimulated a rapid (20 s), sustained (up to 20 min) and concentration-dependent (1-100 nM) increase in protein tyrosine phosphorylation levels which coincided temporally with the contractile response in intact and alpha-toxin permeabilized small artery preparations. Tyrosine phosphorylation was increased in four main clusters of proteins of apparent molecular mass 28-33, 56-61, 75-85 and 105-115 kDa. Endothelin-1-induced protein tyrosine phosphorylation was independent of extracellular calcium, antagonized by the tyrosine kinase inhibitor tyrphostin A23 but not by the inactive tyrphostin A1. 3. In intact small arteries tyrphostin A23 inhibited the force developed to endothelin-1 at all concentrations studied; at higher concentrations (10 and 100 nM) the profile of contraction was altered from a sustained to a transient response. Tyrphostin A1 inhibited the contractile response to endothelin-1 at all concentrations except 100 nM; the profile of the response was not altered. Neither tyrphostin affected the transient phasic contraction induced by endothelin-1 (100 nM) in the absence of extracellular calcium. 4. In rat alpha-toxin permeabilized mesenteric arteries endothelin-1 caused a concentration-dependent increase in force in the presence of 10 microM GTP and low (pCa 6.7) constant calcium, demonstrating increased sensitivity of the contractile apparatus to calcium. Tyrphostin A23 inhibited this response by approximately 50%, tyrphostin A1 did not affect endothelin-1-induced calcium sensitization of force. 5. We conclude that increased tyrosine phosphorylation is important in the contractile response induced by endothelin-1 in intact small mesenteric arteries. Furthermore our data implicate activation of this signalling pathway in the tonic phase of contraction possibly through modulation of the sensitivity of the contractile apparatus to calcium.
Application of integral reinforcement learning for optimal control of a high speed flux-switching permanent magnet machine (2016)

A novel control method using H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> tracking and integral reinforcement learning is applied to a flux-switching permanent magnet (FSPM) machine in a hostile environment. The proposed controller can maintain high performance in the presence of motor parameter uncertainties and load disturbances. The conventional design procedure for an H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</inf> controller is to solve the Hamilton-Jacobi-Isaacs (HJI) equation which requires full information of the system model. The novel control method, the integral reinforcement learning (IRL) makes use of neural networks to parametrically represent the control policy and the performance of system, and learns the solution of HJI equations online. Therefore, the FSPM machine can work optimally under parameter uncertainties due to different operating conditions. The simulation in Matlab/Simulink vividly illustrates the control performance for a 45kW, rotor speed 9000 rpm, 12/5 poles flux-switching permanent magnet machine.
CEO phase-locked 5.7-fs pulses through filamentation (2005)

Self-compression of a CEO phase-locked 43 fs, 0.84 mJ pulse during filamentation leads to a CFO-phase locked 5.7-fs, 0.38-mJ pulse with an excellent spatial mode. The obtained pulse bandwidth exceeds 600 THz theoretically 1.8-fs pulses.
Plant-Produced Mouse-Specific Zona Pellucida 3 Peptide Induces Immune Responses in Mice (2023)

Contraceptive vaccines are designed to stimulate autoimmune responses to molecules involved in the reproductive process. A mouse-specific peptide from zona pellucida 3 (mZP3) has been proposed as a target epitope. Here, we employed a plant expression system for the production of glycosylated mZP3 and evaluated the immunogenicity of plant-produced mZP3-based antigens in a female BALB/c mouse model. In the mZP3-1 antigen, mZP3 fused with a T-cell epitope of tetanus toxoid, a histidine tag, and a SEKDEL sequence. A fusion antigen (GFP-mZP3-1) and a polypeptide antigen containing three repeats of mZP3 (mZP3-3) were also examined. Glycosylation of mZP3 should be achieved by targeting proteins to the endoplasmic reticulum. <i>Agrobacterium</i>-mediated transient expression of antigens resulted in successful production of mZP3 in <i>Nicotiana benthamiana</i>. Compared with mZP3-1, GFP-mZP3-1 and mZP3-3 increased the production of the mZP3 peptide by more than 20 and 25 times, respectively. The glycosylation of the proteins was indicated by their size and their binding to a carbohydrate-binding protein. Both plant-produced GFP-mZP3-1 and mZP3-3 antigens were immunogenic in mice; however, mZP3-3 generated significantly higher levels of serum antibodies against mZP3. Induced antibodies recognized native zona pellucida of wild mouse, and specific binding of antibodies to the oocytes was observed in immunohistochemical studies. Therefore, these preliminary results indicated that the plants can be an efficient system for the production of immunogenic mZP3 peptide, which may affect the fertility of wild mice.
Energy Consumption Enhancement of Reverse-Biased Silicon-Based Mach–Zehnder Modulators Using Corrugated Slow Light Waveguides (2018)

The energy efficiency of silicon modulators can be enhanced by increasing the doping level. As an alternative solution, slow light modulators based on corrugated waveguides can also be used for improving the energy efficiency. Using numerical and analytical tools, we show that for the same level of energy consumption reduction, the loss coefficient and the loss-modulation efficiency for the slow-light modulators are smaller than those for the modulators with an increased doping level. It is shown that the slow light structures with medium slow down factors (specifically slowdown factors of less than 6) can be reasonable candidates for enhancing the modulator's energy efficiency. For example, an energy consumption of less than 100 fJ/bit can be achieved at a slow-down factor of 6, using a doping level of 5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">17</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> for acceptors and 1 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">18</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> for donors.
Comparative Toxicity of Lunar, Martian Dust Simulants, and Urban Dust in Human Skin Fibroblast Cells (2015)

ABSTRACT The National Aeronautics and Space Administration (NASA) has plans to further their manned space exploration to Mars and possibly beyond. The potential toxicity of lunar and Martian dusts to astronauts is a big concern. Primary routes of exposure for astronauts are dermal contact, ocular contact, and inhalation. In this study, we focused on dermal contact exposure using human skin cells to investigate the cytotoxic and genotoxic effects of two fractions of lunar dust simulant (JSC-1A-vf, JSC-1A-f) and a Mars dust simulant (Mars-1A), and compared them to urban dust (urban particulate matter), as urban dust toxicity is better understood and thus, provides a good comparison. Our data show the three simulants and urban dust are cytotoxic to human skin cells. The JSC-1A-vf lunar dust simulant is more cytotoxic than the JSC-1A-f and urban dust. Urban dust cytotoxicity is similar to Mars dust simulant after 120 h exposure. All three dust simulants and urban dust show similar low genotoxicity effects. Our data suggest extraterrestrial dust can damage skin cells and may have the potential to be harmful to humans.
Analysis of the human serological response to Chlamydia trachomatis 60-kDa proteins by two-dimensional electrophoresis and immunoblotting (1991)

Earlier analyses of sera from humans and animals with chlamydial infections demonstrated a strong immune response to proteins of approximately 60 kDa. We have used two-dimensional (2D) electrophoresis followed by immunoblotting to more accurately define patient responses to the chlamydial 60-kDa cysteine-rich envelope protein (OMP2) and to the 57-kDa stress protein (SP) implicated in immunopathological damage. OMP2 and SP were separated on 2D gels by their distinct isoelectric points and identified by fluorography of [35S]-labelled proteins and cross-reaction with anti-mycobacterial antiserum, respectively. The majority of patients sera showed a strong reaction both to OMP2 and the SP (18/20 and 17/20 sera, respectively). Fewer sera (9/20 and 10/20 sera, respectively) reacted with two other polypeptides also present in the 60-kDa range by this analysis.
Circadian rhythm in the Ca2+‐inhibitable adenylyl cyclase activity of the rat striatum (1996)

In the present study, we demonstrate that the Ca(2+)-inhibitable adenylyl cyclase (AC) activity in the striatum exhibits a daily oscillation with a peak occurring around 10:00 h. A circadian fluctuation of the AC activity evoked by an A2a adenosine-selective agonist was also observed. Intrastriatal injection of an A2a-selective adenosine agonist or antagonist during the interval in which the Ca(2+)-inhibitable AC activity was at its peak resulted in a more significant alteration of locomotor activity than those observed at a later interval. The marked circadian variation in the Ca(2+)-inhibitable AC activity in the striatum appears to cause a circadian fluctuation in the action of at least one neuromodulator.
Genetic associations with severe COVID-19 (2021)

Abstract Identification of host genetic factors that predispose individuals to severe COVID-19 is important, not only for understanding the disease and guiding the development of treatments, but also for risk prediction when combined to form a polygenic risk score (PRS). Using population controls, Pairo-Castineira et al. identified 12 SNPs (a panel of 8 SNPs and a panel of 6 SNPs, with two SNPs in both panels) associated with severe COVID-19. Using controls with asymptomatic or mild COVID-19, we were able to replicate the association with severe COVID-19 for only three of their SNPs and found marginal evidence for an association for one other. When combined as an 8-SNP PRS and a 6-SNP PRS, we found no evidence of association with severe COVID-19. The difference in our results and the results of Pairo-Castineira et al. might be the choice of controls: population controls vs controls with asymptomatic or mild COVID-19.
Butyrolactones and Diketopiperazines from Marine Microbes: Inhibition Effects on Dengue Virus Type 2 Replication (2016)

Two new compounds, 4<i>S</i>,10<i>R</i>-dihydroxy-11-methyl-dodec-2-en-1,4-olide (<b>1</b>) (butyrolactone-type) and cyclo-(4-<i>trans</i>-6-dihydroxy-proline-D-leucine) (<b>2</b>) (diketopiperazine-type), as well as one known 4<i>S</i>,10-dihydroxy-10-methyl-dodec-2-en-1,4-olide (<b>3</b>) and three known diketopiperazines, cyclo-(L-proline-L-leucine) (<b>4</b>), cyclo-(4-<i>trans</i>-hydroxy-L-proline-L-leucine) (<b>5</b>), and cyclo-(4-<i>trans</i>-hydroxy-L-proline-L-phenylalanine) (<b>6</b>), were isolated from the ethyl acetate extracts of <i>Streptomyces gougerotii</i> GT and <i>Microbulbifer variabilis</i> C-03. Compounds <b>3, 4, 5</b>, and <b>6</b> exhibited a significant reduction effect on dengue virus type 2 replication with EC<sub>50</sub> values of 21.2, 16.5, 12.3, and 11.2 µM, respectively.
Plague in Madagascar — A Tragic Opportunity for Improving Public Health (2017)

tional efficiencies and increased patient loyalty. Viewing in-person physician visits as a last resort sounds radical, but it just represents a deepened commitment to patient-centered care.
The Secondary Alkaline Zinc Electrode (1991)

Zinc is the most commonly used battery electrode, and zinc primary batteries have found numerous applications. The zinc electrode is electrochemically reversible in alkaline electrolytes, and there is a strong incentive to develop a practical secondary battery based on this metal. However, secondary batteries that use zinc electrodes typically exhibit short lifetimes, because of problems with zinc material redistribution and undesirable zinc morphologies that form during recharge. There has been a worldwide effort to develop a long‐lived secondary alkaline zinc electrode, and marked improvements in cell lifetimes have resulted. This article reviews these efforts, paying particular attention to research and development during the period 1975–1990.
Origin of the open circuit voltage in conjugated polymer-fullerene photovoltaic cells (2004)

We fabricated polymer-fullerene photovoltaic (PV) devices using various conjugated polymers, poly[2-methoxy-5-(2’-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV), poly{2-[4-(3,7-dimethyloctyloxy)-phenoxy]-1,4-phenylenevinyl-ene} (<i>p</i>-DMOP-PPV), and their copolymer system, <i>p</i>-DMOP-co-MEH-PPV. By comparing PV characteristics of such devices with a systematic change of the energy levels (ionization potential I<i>p</i> and electron affinity E<sub>a</sub>), we investigated the origin of open circuit voltage (V<sub>oc</sub>) of the devices. Our results indicate that the magnitude of V<sub>oc</sub> is governed by the difference between E<sub>a</sub> of the fullerene and I<sub>p</sub> of the polymer, which is not consistent with previous consideration of the work function difference between electrodes as in conventional metal-insulator-metal type devices.
Serial scheduling algorithm of LDPC decoding for multimedia transmission (2012)

In this paper, we consider a layered decoding algorithm for a performance improvement of LDPC. The proposed algorithm is based on a serial scheduling algorithm for the layered decoding of LDPC in which we consider check node degree, variable node degree, and the edge connection between the each node. Simulation results show that the proposed method improves about 0.2dB SNR gain compared with random schedule in a layered decoding. Especially when the maximum number of iteration and the code rate are low, the performance gain gets larger. This is desirable to the system which requires low per consumption and low latency such as WPAN system.
Dynamics of Hydrophobic Hydration of Benzene (1996)

The dynamics of hydrophobic hydration of benzene was examined by NMR for both the solute and the solvent water. The rotational dynamics of water in the benzene hydration shell was observed to be slower than that in the bulk. This idea, in addition to the data on solitary waters in organic solvents, shows that the rotational dynamics of a water correlates positively with the hydrogen-bond strength of the water with the surrounding environment. The temperature dependence of the rotational motion of the solute benzene was examined to probe the cage structure of water around the benzene. It reveals the competition between the exclusion volume effect of the solute and the attractive and directional effects of solvent structure. The similarity and difference between the rotational and translational mobilities of hydrophobic benzene are also discussed.
Patterning of Hydrophilic and Hydrophobic Gold and Magnetite Nanoparticles by Dip Pen Nanolithography (Small 18/2023) (2023)

Dip Pen Nanolithography In article number 2208069, Bart Jan Ravoo and co-workers report the surface patterning of nanoparticles using dip pen nanolithography. Metal and metal oxide nanoparticles functionalized with various organic ligands can be patterned in nanosized clusters. Depending on the polarity of the ligand shell, water or toluene is used as ink solvent. No modification of atomic force microscope (AFM) tip or substrate surface is required.
A low-power design method using multiple supply voltages (1997)

We present a low-power design method that utilizes the multiple supply voltages. The proposed method reduces the power consumption of random logic circuits by 47% on the average, with up to 15% area overhead, by the combination of Clustered Voltage Scaling (CVS) and by Row optimized Power Supply (RRPS) scheme. By the CVS scheme, the optimal netlist, that uses the minimized number of the level converters and the maximized number of the low Vdd gates under the timing constraints, is generated. To avoid the wiring resource consumption and the increase of the interconnect delay caused by the layout constraints of the multiple-supply-voltage design, a new power bus wiring scheme called RRPS is proposed. The proposed method is applied to a media processor chip Mpact/sup TM/ and achieved the above mentioned results. In this paper, the emphasis is put on the interrelation between the generation of the two-supply-voltage netlist with the CVS scheme and the layout technology, such as the power supply scheme and the placement of the multiple-supply-voltage gates. The clocking scheme for the multiple supply voltages is also discussed.
Interference Cancellation using a Single Snapshot (2006)

In this paper, we show that a single snapshot using a uniform linear array can be applied to interferences cancellation problems in spatial array signal processing. In this context, the antenna weight vector is calculated using a projection matrix constructed from a single snapshot instead of using the eigen-decomposition of the sample covariance matrix. The benefits of this method are two-fold; it reduces the computational cost required by the eigen-decomposition and the number of snapshots. We demonstrate the effectiveness of the proposed method through simulations of different scenarios including coherent and uncorrelated interferences
An optimal linear controller design for an underactuated unicycle (2011)

In this work, we develop a unicycle that consists of a wheel and a pendulum. The control objective is for unicycle to track a given trajectory while keep the pendulum at the balanced position. In the unicycle, the only actuator is a motor mounted on the chassis, which generates torque to drive wheel. Hence the unicycle is an underactuated mechanism, and the control problem is challenging. The dynamic model of the unicycle is derived first and linearized around an equilibrium. Next, a LQR controller with full state feedback is designed based on the linearized model. Due to existence of parametric uncertainties and model mismatch such as the ignorance of actuator dynamics in the practical unicycle, LQR is unable to achieve desired control performance. Iterative learning tuning (ILT) method is introduced to adjust LQR so as to improve the control response iteratively. In this work, we propose an ILT law to tune the state weighting matrix in LQR objective function. The ILT law is derived by minimizing a scalar cost function with respect to the weighting matrix. Through simulation and experiment results, the effectiveness of the proposed LQR and ILT approach is validated.