gebhart/patrepeval huggingface dataset:
Structural Basis of a Thiol-Disulfide Oxidoreductase in the Hedgehog-Forming Actinobacterium Corynebacterium matruchotii (2018)

The actinobacterium <i>Corynebacterium matruchotii</i> has been implicated in nucleation of oral microbial consortia leading to biofilm formation. Due to the lack of genetic tools, little is known about basic cellular processes, including protein secretion and folding, in this organism. We report here a survey of the <i>C. matruchotii</i> genome, which encodes a large number of exported proteins containing paired cysteine residues, and identified an oxidoreductase that is highly homologous to the <i>Corynebacterium diphtheriae</i> thiol-disulfide oxidoreductase MdbA (MdbA<sub>Cd</sub>). Crystallization studies uncovered that the 1.2-Å resolution structure of <i>C. matruchotii</i> MdbA (MdbA<sub>Cm</sub>) possesses two conserved features found in actinobacterial MdbA enzymes, a thioredoxin-like fold and an extended α-helical domain. By reconstituting the disulfide bond-forming machine <i>in vitro</i>, we demonstrated that MdbA<sub>Cm</sub> catalyzes disulfide bond formation within the actinobacterial pilin FimA. A new gene deletion method supported that <i>mdbA</i> is essential in <i>C. matruchotii</i> Remarkably, heterologous expression of MdbA<sub>Cm</sub> in the <i>C. diphtheriae</i> Δ<i>mdbA</i> mutant rescued its known defects in cell growth and morphology, toxin production, and pilus assembly, and this thiol-disulfide oxidoreductase activity required the catalytic motif CXXC. Altogether, the results suggest that MdbA<sub>Cm</sub> is a major thiol-disulfide oxidoreductase, which likely mediates posttranslocational protein folding in <i>C. matruchotii</i> by a mechanism that is conserved in <i>Actinobacteria</i><b>IMPORTANCE</b> The actinobacterium <i>Corynebacterium matruchotii</i> has been implicated in the development of oral biofilms or dental plaque; however, little is known about the basic cellular processes in this organism. We report here a high-resolution structure of a <i>C. matruchotii</i> oxidoreductase that is highly homologous to the <i>Corynebacterium diphtheriae</i> thiol-disulfide oxidoreductase MdbA. By biochemical analysis, we demonstrated that <i>C. matruchotii</i> MdbA catalyzes disulfide bond formation <i>in vitro</i> Furthermore, a new gene deletion method revealed that deletion of <i>mdbA</i> is lethal in <i>C. matruchotii</i> Remarkably, <i>C. matruchotii</i> MdbA can replace <i>C. diphtheriae</i> MdbA to maintain normal cell growth and morphology, toxin production, and pilus assembly. Overall, our studies support the hypothesis that <i>C. matruchotii</i> utilizes MdbA as a major oxidoreductase to catalyze oxidative protein folding.
Photoacoustic hygrometer for icing wind tunnel water content measurement: design, analysis, and intercomparison (2021)

Abstract. This work describes the latest design, calibration and application of a near-infrared laser diode-based photoacoustic (PA) hygrometer developed for total water content measurement in simulated atmospheric freezing precipitation and high ice water content conditions with relevance in fundamental icing research, aviation testing, and certification. The single-wavelength and single-pass PA absorption cell is calibrated for molar water vapor fractions with a two-pressure humidity generator integrated into the instrument. Laboratory calibration showed an estimated measurement accuracy better than 3.3 % in the water vapor mole fraction range of 510–12 360 ppm (5 % from 250–21 200 ppm) with a theoretical limit of detection (3σ) of 3.2 ppm. The hygrometer is examined in combination with a basic isokinetic evaporator probe (IKP) and sampling system designed for icing wind tunnel applications, for which a general description of total condensed water content (CWC) measurements and uncertainties are presented. Despite the current limitation of the IKP to a hydrometeor mass flux below 90 gm-2s-1, a CWC measurement accuracy better than 20 % is achieved by the instrument above a CWC of 0.14 g m−3 in cold air (−30 ∘C) with suitable background humidity measurement. Results of a comparison to the Cranfield University IKP instrument in freezing drizzle and rain show a CWC agreement of the two instruments within 20 %, which demonstrates the potential of PA hygrometers for water content measurement in atmospheric icing conditions.
NeRV: Neural Representations for Videos (2021)

We propose a novel neural representation for videos (NeRV) which encodes videos in neural networks. Unlike conventional representations that treat videos as frame sequences, we represent videos as neural networks taking frame index as input. Given a frame index, NeRV outputs the corresponding RGB image. Video encoding in NeRV is simply fitting a neural network to video frames and decoding process is a simple feedforward operation. As an image-wise implicit representation, NeRV output the whole image and shows great efficiency compared to pixel-wise implicit representation, improving the encoding speed by 25x to 70x, the decoding speed by 38x to 132x, while achieving better video quality. With such a representation, we can treat videos as neural networks, simplifying several video-related tasks. For example, conventional video compression methods are restricted by a long and complex pipeline, specifically designed for the task. In contrast, with NeRV, we can use any neural network compression method as a proxy for video compression, and achieve comparable performance to traditional frame-based video compression approaches (H.264, HEVC \etc). Besides compression, we demonstrate the generalization of NeRV for video denoising. The source code and pre-trained model can be found at https://github.com/haochen-rye/NeRV.git.
Figure 2 from Dual repair modulation reverses Temozolomide resistance <i>in vitro</i> (2023)

Figure 2 from Dual repair modulation reverses Temozolomide resistance &lt;i&gt;in vitro&lt;/i&gt;
Genes harbouring susceptibility SNPs are differentially expressed in the breast cancer subtypes (2007)

Recently, genome-wide association studies of breast cancer revealed single nucleotide polymorphisms (SNPs) in five genes with novel association to susceptibility. While there is little doubt that the novel susceptibility markers produced from such highly powered studies are true, the mechanisms by which they cause the susceptibility remain undetermined. We have looked at the expression levels of the identified genes in tumours and found that they are highly significantly differentially expressed between the five established breast cancer subtypes. Also, a significant association between SNPs in these genes and their expression in tumours was seen as well as a significantly different frequency of the SNPs between the subtypes. This suggests that the observed genes are associated with different breast cancer subtypes, and may exert their effect through their expression in the tumours. Thus, future studies stratifying patients by their molecular subtypes may give much more power to classic case control studies, and genes of no or borderline significance may appear to be high-penetrant for certain subtypes and, therefore, be identifiable.
A NEW SPECIES OF THE LITHOBIID GENUS NAMPABIUS FROM TENNESSEE (1925)

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Topics in the application of the Zeeman effect. (1990)

The Zeeman effect which causes splitting of atomic lines has been applied in atomic absorption spectroscopy to correct for background absorption. In this study, two aspects of Zeeman background correction were investigated: (i) Fourier analysis of the response of the instruments using a.c. magnetic fields; (ii) application to discharge cells used as atomisers operated at atmospheric pressure.
Infrared multiphoton microscopy beyond 1 micron: system design and biomedical applications (2007)

Here we present the first results of a new multi photon excitation microscopy setup which extends the excitation wavelengths far beyond one micron. A synchronously pumped femtosecond-OPO (OPO PP-Automatic, APE) pumped by a femtosecond-Ti:Sapphire oscillator is used as the light source. Up to 500nm tuning can be achieved in the NIR (for instance 1100-1600nm) with fixed pump frequency and a single optics set. Automated tuning makes it an ideal tool for MPE-, SHG- and THG microscopy, which is demonstrated in combination with an optimized scanner / microscope / detection system. Together with the Ti:Sapphire pump laser (Coherent Chameleon) excitation wavelengths from 700 to 1600nm are achieved. A single-beam scanner (LaVision BioTec) was optimized for Ti:Sapphire and OPO wavelength ranges including dispersion compensation for maintaining the short pulses at the sample site as well as an overall transmission of 30-38% for the OPO range (measured up to 1400nm). Measurements on human dermis with excitation above 1 micron, compared to lower wavelengths, showed doubling of the penetration depths, strongly reduced photo damage, and by 30fold increased excitation efficiency and 10fold reduced photobleaching of red fluorescent dyes, including RFP and Cy5.5. 1100nm-excited SHG efficiency of collagen was 10 to 30fold stronger, compared to 880 nm, yet autofluorescence was decreased by up to 4 times resulting in a significantly improved signal-to-noise ratio for the detection of fluorescent dyes. The resolution is slightly reduced in comparison to Ti:Sapphire excitation, which corresponds well to the longer excitation wavelength used.
Boundary-interior principle for microbial navigation in geometric confinement (2020)

When the motion of a motile cell is observed closely, it appears erratic, and yet the combination of nonequilibrium forces and surfaces can produce striking examples of collective organization in microbial systems. While our current understanding is based on bulk systems or idealized geometries, it is not clear at which length scale self-organization emerges. Here, using experiments, analytical and numerical calculations we study the motion of motile cells under controlled microfluidic conditions, and demonstrate that a robust topology of probability flux loops organizes active motion even at the level of a single cell exploring an isolated habitat. By accounting for the interplay of activity and interfacial forces, we find that the boundary's curvature determines the nonequilibrium probability fluxes of the motion, which can be controlled directly. We theoretically predict a universal relation between fluxes and global geometric properties that is directly confirmed by experiments. Our findings open the possibility to decipher the most probable trajectories of motile cells and may enable the design of active topological materials.
Tunable blue organic light emitting diode based on aluminum calixarene supramolecular complex (2004)

In this letter, the results of supramolecular organic light emitting diodes using a calix[4] arene complex thin film as emitter and electron transporting layer are presented. The devices were grown onto glass substrates coated with indium-tin-oxide layer and aluminum thick (150nm) cathode. By applying a dc voltage between the device electrodes in forward bias condition, a blue light emission in the active area of the device was observed. It was found that the electroluminescent emission peak can be tuned between 470 and 510nm changing the applied voltage bias from 4.3 to 5.4V. The observed tunable emission can be associated with an energy transfer from the calixarene compound.
Circulating procalcitonin and cleavage products in septicaemia compared with medullary thyroid carcinoma (2002)

ProCT and 10 and 8 kDa proCT fragments were recognised in the circulation of septic patients. They were different from the known proCT-processing products PAS-57, CT(1-32) and PDN-21 identified in the serum of normal subjects and of MTC patients. Distinct cleavage of proCT may contribute to the symptoms of septicaemia.
Exploration of Intercell Wireless Millimeter-Wave Communication in the Landscape of Intelligent Metasurfaces (2019)

Software-defined metasurfaces are electromagnetically ultra-thin, artificial components that can provide engineered and externally controllable functionalities. The control over these functionalities is enabled by the metasurface tunability, which is implemented by embedded electronic circuits that modify locally the surface resistance and reactance. Integrating controllers within the metasurface able them to intercommunicate and adaptively reconfigure, thus imparting a desired electromagnetic operation, opens the path towards the creation of an artificially intelligent (AI) fabric where each unit cell can have its own sensing, programmable computing, and actuation facilities. In this work we take a crucial step towards bringing the AI metasurface technology to emerging applications, in particular exploring the wireless mm-wave intercell communication capabilities in a software-defined HyperSurface designed for operation in the microwave regime. We examine three different wireless communication channels within the landscape of the reflective metasurface: Firstly, in the layer where the control electronics of the HyperSurface lie, secondly inside a dedicated layer enclosed between two metallic plates, and, thirdly, inside the metasurface itself. For each case we examine the physical implementation of the mm-wave transceiver nodes, we quantify communication channel metrics, and we identify complexity vs. performance trade-offs.
Bioactive Glasses (2021)

Bioactive phosphosilicate glasses release ions when in contact with physiological solutions and show surface reactions leading to the formation of a biomimetic apatite layer. This surface layer allows for protein adhesion, cell attachment and proliferation, and formation of a strong interfacial bond between bioactive glass and bone. In addition, the ability of bioactive glasses to degrade in vivo makes it possible for them to be replaced by new bone and, thus, to aid in the regeneration of bone tissue. These reactions are possible owing to the highly disrupted structure of bioactive glasses, containing large concentrations of modifier ions and nonbridging oxygens. Bioactive glasses have been used clinically since the mid-1980s, mainly to treat bone defects. However, their mineralizing properties have led to their use in oral care products for the treatment of sensitive teeth and the remineralization of enamel.
Virulence of aMycobacterium tuberculosisclinical isolate in mice is determined by failure to induce Th1 type immunity and is associated with induction of IFN-α/β (2001)

To understand how virulent mycobacteria subvert host immunity and establish disease, we examined the differential response of mice to infection with various human outbreak Mycobacterium tuberculosis clinical isolates. One clinical isolate, HN878, was found to be hypervirulent, as demonstrated by unusually early death of infected immune-competent mice, compared with infection with other clinical isolates. The differential effect on survival required lymphocyte function because severe combined immunodeficiency (SCID) mice infected with HN878 or other clinical isolates all died at the same rate. The hypervirulence of HN878 was associated with failure to induce M. tuberculosis-specific proliferation and IFN-gamma production by spleen and lymph node cells from infected mice. In addition, 2- to 4-fold lower levels of tumor necrosis factor-alpha (TNF-alpha), IL-6, IL-12, and IFN-gamma mRNAs were observed in lungs of HN878-infected mice. IL-10, IL-4, and IL-5 mRNA levels were not significantly elevated in lungs of HN878 infected mice. In contrast, IFN-alpha mRNA levels were significantly higher in lungs of these mice. To further investigate the role of Type 1 IFNs, mice infected with HN878 were treated intranasally with purified IFN-alpha/beta. The treatment resulted in increased lung bacillary loads and even further reduced survival. These results suggest that the hypervirulence of HN878 may be due to failure of this strain to stimulate Th1 type immunity. In addition, the lack of development of Th1 immunity in response to HN878 appears to be associated with increased induction of Type 1 IFNs.
Manipulating the Nanoscale Optical Transmission with a\n Meta-Transmitarray (2013)

By applying the optical nanocircuit concepts to metasurfaces, we propose an\neffective route to locally control light transmission over a deeply\nsubwavelength scale. This concept realizes the optical equivalent of a\ntransmitarray, whose use is demonstrated for light bending and focusing with\nunprecedented efficiency over a subwavelength distance, with crucial benefits\nfor nano-optics applications. These findings may lead to large improvements in\nthe manipulation of optical transmission and processing of nanoscale optical\nsignals over conformal and Si-compatible substrates.\n
Transition from Waveguide to Two Microstrip Lines with Slot Radiators in the Millimeter-Wave Band (2011)

Many kinds of microstrip array antennas have been developed in the millimeter-wave band. In order to avoid feeding loss and the decrease of antenna gain by beam shift due to frequency changes, center-fed array antennas are advantageous. In this case, the element spacing around the feeding circuit of the transition from the waveguide to two microstrip lines is larger than one wavelength. Therefore, the sidelobe level grows significantly. In order to suppress the sidelobe level, we propose transitions with slot radiators. Moreover, any polarization angles can be achieved by changing the slot angle. A wide variety from 1.5% to 70% of slot radiator coupling powers can be achieved. To investigate the performance of the proposed transition, 10, 22 and 30-element center-fed microstrip comb-line antennas with the proposed transition were developed at 76.5GHz, and measured performance was evaluated in the millimeter-wave band.
Assessment of Aircraft Susceptibility/Vulnerability to Lightning and Development of Lightning-Protection Design Criteria (1982)

Possible approaches for assessing the susceptibility/vulnerability of aircraft to both the direct and indirect (induced) effects of lightning and for developing lightning-protection design criteria are examined. Particular emphasis is focused on methods that can be used to achieve a high level of confidence in aircraft safety and survival. Assessment factors and their uncertainties are qualitatively and quantitatively discussed. Lightning-protection design approaches involving both test and analysis as applied to the F-16 fighter aircraft and the NASA Space Shuttle are reviewed. A probabilistic or statistical approach is outlined (with examples) for predicting single and/or redundant equipment failure due to indirect lightning effects.
The promise and perils of exhaled breath condensates (2004)

The exhaled breath condensate (EBC) approach provides a convenient and noninvasive approach for sampling the pulmonary epithelial lining fluid (ELF). Increased EBC concentrations of more than a dozen inflammatory markers and hydrogen ions have been reported in lung diseases associated with inflammation. However, the usefulness of EBC is compromised by uncertainties concerning the sources of the EBC droplets and by the extreme and variable dilution of ELF droplets with condensed water vapor ( approximately 20,000-fold). Reported increases in EBC concentrations may reflect proportionate increases in the total volume rather than the concentration of ELF droplets in the collected samples. Conclusions regarding ELF concentrations can only be made if this dilution is estimated with a dilutional indicator (e.g., conductivity of lyophilized EBC). In normal EBC samples, pH is effectively set by oral contamination with NH(3), and EBC pH cannot provide reliable information regarding ELF pH in normal subjects. Acidification of EBC observed in asthma and other conditions may reflect acidification of ELF, decreases in NH(3) added to the EBC, and/or the presence of gastric droplets in the EBC.
Accuracy analysis of a Hartmann-Shack wavefront sensor operated with a faint object (1994)

A detailed analysis of the characteristics, regularities, and relationships of the centroiding errors of image spots caused by discrete and limited sampling, photon noise, and readout noise of the detector in a Hartmann-Shack wavefront sensor, wherein an image intensified charge-coupled device used as a photon detector is presented. The theoretical analysis and experimental results herein prove useful for optimum design and application of the sensor.
Ion optics arithmetic and its implications for the positive ion CTR program (1980)

This paper discusses ion extraction optics formulations in which presheath ionization is shown to have a negligible effect on ion optics at optimum perveance; otherwise, the examples shown establish an ionization gradient instability. Infinite slot optics as a function of perveance and potential partitioning is delineated for the TFTR tetrode from 2-D considerations; finite slot optics at optimum perveance is delineated from 3-D considerations. Finally, further 2-D considerations yield an end slot design.
Components of visual prior entry (2010)

Purpose: The prior entry hypothesis suggests that attention accelerates visual processing, reducing the latency to perception for attended stimuli. Historical evidence for the hypothesis has been mixed, and the purpose of this study is to compare the contributions of attention, response bias, and sensory facilitation to the observed apparent prior entry effects. Methods: In separate sessions, observers judged the apparent simultaneity (SJ) or temporal order (TOJ) of the onsets of two peripheral targets, to one of which attention was oriented with either exogenous, endogenous, gaze-directed, isoluminant exogenous or multiple exogenous cues. The cue lead times (CLT) and the presentation intervals (SOA) between the targets were systematically varied. Results: The points of subjective simultaneity (PSS), the SOA at which the observers were maximally uncertain about the order of the targets, shifted significantly for the TOJ as a function of CLT for all cue types in a manner expected from the temporal dynamics of attention, however, decision models that included response biases could completely account for these shifts. The SOAs at which the SJ was maximum were not significantly different from zero for the endogenous and gaze-directed cues and were smaller than the TOJ shifts in the PSS for the exogenous cues. For multiple exogenous cues, the shift in the SJ maximum decreased with the number of cues, from about 20 ms with one cue to an asymptote of about 10 ms for six or more cues. Conclusions: Prior entry may only occur for attentional cues that cause transient activity at the target location, and the effects of these cues are composed of roughly equal attentional and non-attentional components. The results from TOJ experiments are difficult to interpret due to the contribution of response biases, but the SJ can function as a reliable test of prior entry. Prior entry is not a general property of attention but rather more likely a bottom-up sensory phenomenon.
Synthesis of 3-nitrobenzo[a]pyrene bay-region trans-7,8-diol anti-9,10-epoxide and the corresponding N2-deoxyguanosine adduct (1993)

3-Nitrobenzo[a]pyrene (3-nitro-BaP) is a potent mutagenic environmental contaminant, and its biological activities have been intensively studied. It is significant to prepare its reactive metabolites and the corresponding modified DNA adducts for biological studies. The synthesis of its oxidized proximate metabolite trans-7,8-dihydro-3-nitrobenzo[a]pyrene (3-nitro-BaP-trans-7,8-dihydrodiol, 1), its oxidized ultimate metabolite trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydro-3- nitrobenzo[a]pyrene (3-nitro-BaP-DE, 2), and the corresponding DNA adduct 10-(deoxyguanosin-N2-yl)-7,8,9-trihydroxy-7,8,9,10-tetrahydro-3- nitrobenzo[a]pyrene is described.