gebhart/patrepeval huggingface dataset:
Development of a diffraction imaging flow cytometer (2009)

Diffraction images record angle-resolved distribution of scattered light from a particle excited by coherent light and can correlate highly with the 3D morphology of a particle. We present a jet-in-fluid design of flow chamber for acquisition of clear diffraction images in a laminar flow. Diffraction images of polystyrene spheres of different diameters were acquired and found to correlate highly with the calculated ones based on the Mie theory. Fast Fourier transform analysis indicated that the measured images can be used to extract sphere diameter values. These results demonstrate the significant potentials of high-throughput diffraction imaging flow cytometry for extracting 3D morphological features of cells.
Path-length stabilized low-coherent reflection-type quantitative phase microscope for nanometer-resolution profiling of plasma membrane (2015)

We developed a portable and user-friendly prototype of low-coherent reflection-type quantitative phase microscope (QPM). Our setup is based on the full-field Linnik type phase-shifting interference microscope and is optimized for surface profiling of living cell’s membrane. Unlike commonly available transmission-type quantitative phase microscopes which reveal the optical thickness, our reflection-type setup can obtain the geometrical thickness (real shape) of the sample, decoupled with the refractive index. The coherence length of our imaging light source (halogen lamp) was approximately 1 micrometer so that we can selectively obtain the interference of the light reflected from the cell membranes whose reflectivity in culture medium is only on the order of 0.1%. Moreover our setup has a feedback controlled path-length stabilization circuit so that users can implement accurate phase shifting interferometry with one nanometer of reproducibility. The stabilization circuit allows installing our setup even in noisy environments such as biology labs without an optical bench. In this paper, we will also show our studies of recent biomedical applications, including imaging of cell plasma membrane and phase-resolved 3D tomography of living cells.
Context-dependent anticodon recognition by class I lysyl-tRNA synthetases (2000)

Lysyl-tRNA synthesis is catalyzed by two unrelated families of aminoacyl-tRNA synthetases. In most bacteria and all eukarya, the known lysyl-tRNA synthetases (LysRSs) are subclass IIb-type aminoacyl-tRNA synthetases, whereas many archaea and a scattering of bacteria contain an unrelated class I-type LysRS. Examination of the recognition of partially modified tRNA(Lys) anticodon variants by a bacterial (from Borrelia burgdorferi) and an archaeal (from Methanococcus maripaludis) class I lysyl-tRNA synthetase revealed differences in the pattern of anticodon recognition between the two enzymes. U35 and U36 were both important for recognition by the B. burgdorferi enzyme, whereas only U36 played a role in recognition by M. maripaludis LysRS. Examination of the phylogenetic distribution of class I LysRSs suggested a correlation between recognition of U35 and U36 and the presence of asparaginyl-tRNA synthetase (AsnRS), which also recognizes U35 and U36 in the anticodon of tRNA(Asn). However, the class II LysRS of Helicobacter pylori, an organism that lacks AsnRS, also recognizes both U35 and U36, indicating that the presence of AsnRS has solely influenced the phylogenetic distribution of class I LysRSs. These data suggest that competition between unrelated aminoacyl-tRNA synthetases for overlapping anticodon sequences is a determinant of the phylogenetic distribution of extant synthetase families. Such patterns of competition also provide a basis for the two separate horizontal gene transfer events hypothesized in the evolution of the class I lysyl-tRNA synthetases.
Microbial Rhodopsins: Diversity, Mechanisms, and Optogenetic Applications (2017)

Microbial rhodopsins are a family of photoactive retinylidene proteins widespread throughout the microbial world. They are notable for their diversity of function, using variations of a shared seven-transmembrane helix design and similar photochemical reactions to carry out distinctly different light-driven energy and sensory transduction processes. Their study has contributed to our understanding of how evolution modifies protein scaffolds to create new protein chemistry, and their use as tools to control membrane potential with light is fundamental to optogenetics for research and clinical applications. We review the currently known functions and present more in-depth assessment of three functionally and structurally distinct types discovered over the past two years: (a) anion channelrhodopsins (ACRs) from cryptophyte algae, which enable efficient optogenetic neural suppression; (b) cryptophyte cation channelrhodopsins (CCRs), structurally distinct from the green algae CCRs used extensively for neural activation and from cryptophyte ACRs; and
Miniaturized wireless power transfer systems using 3-D strongly coupled magnetic resonance (2017)

In this paper, a novel method using 3-D Strongly Coupled Magnetic Resonance (SCMR) is proposed in order to miniaturize Wireless Power Transfer (WPT) systems. This method successfully tuned the operating frequency to lower frequencies with excellent efficiencies, thereby reducing the size of SCMR systems. Also, 3-D SCMR systems based on two and three layered spiral resonators in opposite directions shift the working frequency to lower frequency efficiently, from 210 MHz to 162 MHz and 127 MHz, respectively.
1,2,3-Triazolylidene ruthenium(<scp>ii</scp>)-cyclometalated complexes and olefin selective hydrogenation catalysis (2014)

Silver(i) 1,2,3-triazol-5-ylidenes [(RCH(2)C(2)N(2)(NMe)Ph)(2)Ag][AgCl(2)] (R = Ph 3a, C(6)H(2)iPr(3) 3b, C(6)H(2)Me(3) 3c) and [(PhCH(2)C(2)N(2)(NMe)R)(2)Ag][AgCl(2)] (R = C(6)H(4)Me 3d, C(6)H(4)CF(3) 3e) were synthesized and subsequently treated with RuHCl(PPh(3))(3) and RuHCl(H(2))(PCy(3))(2). The reaction 3a of with RuHCl(PPh(3))(3) gave RuHCl(PPh(3))(2)(PhCH(2)C(2)N(2)(NMe)Ph) (4a1) as the minor product and the cyclometalated complex RuCl(PPh(3))(2)(PhCH(2)C(2)N(2)(NMe)C(6)H(4)) (4a2) as the major product. However, similar reaction with 3b selectively formed the cyclometalated complex RuCl(PPh(3))(2)((C(6)H(2)iPr(3))CH(2)C(2)N(2)(NMe)C(6)H(4)) (4b2). Similarly the silver(i) triazolylidenes 3a and 3b were reacted with RuHCl(H(2))(PCy(3))(2); gave RuHCl(PCy(3))(2)(PhCH(2)C(2)N(2)(NMe)Ph) (5a2), RuCl(PCy(3))(2)(PhCH(2)C(2)N(2)(NMe)C(6)H(4)) (5a2) and RuCl(PCy(3))(2)((C(6)H(2)iPr(3))CH(2)C(2)N(2)(NMe)C(6)H(4)) (5b2), respectively. Species 3c, 3d and 3e resulted in the cyclometalated complexes (5c2, 5d2 and 5e2) as the major products as well as the ruthenium-hydride complexes (5c1, 5d1 and 5e1) as the minor products. The cyclometalated species are derived from the ruthenium-hydride complexes via C(sp(2))-H activation. These Ru-complexes were shown to act as hydrogenation catalyst precursors for olefinic substrates including those containing a variety of functional groups.
5G Retro-Directive Quasi-Optical Lens Beamforming MIMO (2019)

This paper presents a beamspace MIMO dictated by the proposed quasi-optical lens with transceiver MMICs distributed on the focal plane in close proximity within the point spread of the lens, followed by a switching matrix module arbitrarily connecting p baseband units and n sets of transceivers. Ray-tracing diagrams explain the retro-directive channel propagation characteristics of the proposed quasi-optical beamforming MIMO, demonstrating that the returned signals from a remote terminal under interrogation will reach the nearby receiver in the focal plane, which points to a promising solution to green communications at more than one order of magnitude improvement in energy consumption for a particular case study.
A Triphonic Sound System for Television Broadcasting (1983)

A new three-channel audio matrix for use in multichannel sound television broadcasting is described. The proposed transmissions can be received by either a triphonic, biphonic, or monophonic receiver. The system utilizes two conventional stereophonic channels, plus a third channel which drives a center loudspeaker and which is used to subtract the center signal components from the left and right channels in a three-channel receiver. This eliminates the necessity for listeners to be positioned precisely halfway between the loudspeakers for optimum hearing conditions.
Relaxin Expression From Tumor-Targeting Adenoviruses and Its Intratumoral Spread, Apoptosis Induction, and Efficacy (2006)

Extracellular matrix degradation by relaxin expressed by adenoviruses increased viral distribution and tumor penetration, inhibited tumor growth and metastasis, and increased survival of mice.
Thermally Induced Failure of Polymer Dielectrics (2010)

Halogen precursor polymers to poly[(2,3-diphenyl-p-phenylene)vinylene] (DP-PPV) are examined for use as advanced capacitor dielectrics. The polymer is demonstrated to function as a good dielectric until it reaches a set temperature determined by the stability of the leaving groups. Conjugation of the polymer backbone at high temperature effectively disables the capacitor, providing a ‘built-in’ safety mechanism for electronic devices. Conducting Polymers.
The Absence and Application of Stable Carbon Isotopic Fractionation during the Reductive Dechlorination of Polychlorinated Biphenyls (2001)

A bacterial enrichment culture (specific to doubly flanked chlorine removal) reductively dechlorinated 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-CB) to 2,3,5-trichlorobiphenyl (2,3,5-CB) in aqueous media. Approximately 90% conversion to 2,3,5-CB occurred after 90 days, with no other products formed. The delta13C values of 2,3,4,5-CB and 2,3,5-CB were relatively constant over the course of the reaction, indicating a very small or no isotope effect. In addition, compound-specific delta13C analysis performed for every congener in three different lots of Aroclor 1268 showed an intrinsic isotopic trend of decreasing 13C abundance with increasing chlorine content, similar to observations in other commercial mixtures of polychlorinated biphenyls (PCBs). The results of this laboratory study suggest that microbial reductive dechlorination of PCBs in contaminated sediments will create congeners with more depleted delta13C values than native PCBs of similar chlorination. Such information may provide additional evidence for the occurrence of this process and aid in further understanding the biogeochemistry of these compounds.
Hafnium dioxide etch-stop layer for phase-shifting masks (1993)

Phase-shift masks were prepared using sputter deposited films for the phase-shift layer and etch stop layer on fused quartz silica substrates. It has been found that the combination of SiO2 for the phase-shift layer and HfO2 for the etch-stop layer offers a unique combination of properties advantageous for the preparation of phase-shift masks. The optical transmission properties of HfO2 layers with or without a SiO2 phase-shifting layer on quartz substrates are presented.
Murine interleukin 5 receptor isolated by immunoaffinity chromatography: comparison of determined N-terminal sequence and deduced primary sequence from cDNA and implication of a role of the intracytoplasmic domain (1991)

The murine interleukin 5 receptor (IL-5R) was identified by utilizing an immobilized IL-5 and an immobilized monoclonal antibody against the murein IL-5R (designated H7 mAb). The H7 mAb immunoaffinity-purified materials from the extract of cell-surface radioiodinated T88-M cells (an IL-5-dependent early B cell line) using 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) were reacted with an immobilized IL-5 matrix. SDS-PAGE of the adsorbed fraction revealed a single band at approximately 60 kDa. The binding of the 60 kDa protein to the immobilized IL-5 matrix was inhibited by the excess IL-5. The CHAPS-extract depleted of the 60 kDa protein by the absorption with H7 mAb did not contain any IL-5 binding proteins. Immunoaffinity procedure provided a final 7400-fold purification, based on an estimation of the content of the 60 kDa protein (approximate purity: 20%) from the silver-stained pattern of SDS-PAGE. Actin was copurified with the 60 kDa protein at an approximate ratio of 1:1, suggesting that the intracytoplasmic domain of the IL-5R may interact with actin. Furthermore, soluble IL-5R (molecular mass: 50 kDa) was purified by the H7 mAb-immunoaffinity chromatography. The purified soluble IL-5R was capable of inhibiting the binding of IL-5 to T88-M cells. Preparative SDS-PAGE followed by electroblotting onto a membrane permitted the determination of the N-terminal sequence of the IL-5R. The determined N-terminal sequence of the IL-5R and the deduced primary sequence from recently isolated cDNA were compared.
<title>Results of attacks on a claimed robust digital image watermark</title> (1998)

Placing either a visible or invisible mark on a document to help establish its ownership is not a new or revolutionary concept. For hundreds of years, owners of important documents or works of art have imprinted identifying marks onto them, not only to help establish their ownership, but also to discourage those who might wish to misappropriate the work. Today, invisible watermarking of digital images is attempted for those same purposes. To be useful, an ownership watermark must robustly survive and be detectable after any manipulation that does not damage a digital image beyond usability. In the extreme, the watermark must survive the printing and rescanning of the image. Additionally, the probability of detecting a watermark in an image that does not have one must be vanishingly small. An embodiment of invisible watermarking claiming to have these properties has been presented previously by the author. This paper reports the results of typical image manipulations and deliberate attacks on robust invisible watermarks of the type reported. Image manipulations include lossy JPEG compression, small angle rotation, linear and nonlinear resizing, cropping, and sharpening. Attacks include the superposition of uncorrelated noise fields, overmarking, and RSS alterations.
Quanitifying the Value of a Future Well Test with Reservior and Measurement Uncertainty (2009)

We present a consistent and functional methodology for conducting value-of-information (VoI) analysis on proposed well tests in the<br>presence of multiple critical uncertainties associated with the reservoir and the measurement/interpretation. Such uncertainties can<br>impact asset economics acutely when they influence recoverable hydrocarbons. A key feature of this analysis is that the value of the<br>measurement is determined before the measurement is made. Our demonstration uses an example of a marginal offshore asset where<br>severe compartmentalization is possible. In this example, the VoI is a critical deciding factor because it is not obvious a priori that this<br>value will justify the cost of the test in this marginal asset.
New Solids-Free Drill-in Fluid for Low Permeability Reservoirs (2001)

Abstract The most widely used drill-in and completion fluids for seepage loss control in payzone are water-based mud containing polymeric additives and sized calcium carbonate or sized salt. These inorganic bridging solids are very effective in sealing the pore throats of the porous matrix and preventing formation damage but owing to their brittleness they will grind down during circulation and handling. This particle degradation makes it difficult to maintain the correct particle size distribution during drilling operations and can cause a deep penetration of the finest solids into the formation. A novel, solids-free drill-in fluid system containing a biopolymer as viscosifier and a highly crosslinked starch and microfibrous cellulose as fluid loss control agents has been developed for drilling and completing low permeability formations. This fluid composition provides the qualities of both good drilling mud and a non-damaging completion fluid. This paper presents the laboratory results obtained from coreflooding tests carried out on this solids-free drill-in fluid in limestone cores with permeability lower than 100 mD. The synergistic interaction of the biopolymer with a highly crosslinked starch and a microfibrous cellulose material promotes the quick formation of a very thin (ca. 50-60 µm) and impermeable filter cake which prevents polymer and drilled solids invasion into the core. The results show that the filter cake can be completely removed by backflooding and the permeability can be completely recovered. The non-damaging effect of this drill-in fluid was also observed when its density was increased to 1.48 g/cm3 by potassium formate brine. Good filtration and rheological properties were also maintained when simulated drilled solids, e.g. reactive and non-reactive clays were added. Core plug invasion and thickness and the morphological structure of the filter cake, investigated by means of Scanning Electron Microscopy, is also discussed.
Transfer Printing of Sub-5 μm Graphene Electrodes for Flexible Microsupercapacitors (2018)

Printed graphene microsupercapacitors (MSCs) are attractive for scalable and low-cost on-chip energy storage for distributed electronic devices. Although electronic devices have experienced significant scaling to smaller formats, the corresponding miniaturization of energy storage components has been limited, with a typical resolution of ∼30 μm for printed graphene patterns to date. Transfer printing is demonstrated here for patterning graphene electrodes with fine line and spacing resolution less than 5 μm. The resulting devices exhibit an exceptionally small footprint (∼0.0067 mm<sup>2</sup>), which provides, to the best of our knowledge, the smallest printed graphene MSCs. Despite this, the devices retain excellent performance with a high areal capacitance of ∼6.63 mF/cm<sup>2</sup> along with excellent electrochemical stability and mechanical flexibility, resulting from an efficient nonplanar electrode structure and an optimized two-step photoannealing method. As a result, this miniaturization strategy facilitates the on-chip integration of printed graphene MSCs to power emerging electronic devices.
The Internet of Things (2020)

The Internet can be configured to provide communications to a large number of Internet-of-Things (IoT) devices. Devices can be designed to address the need for network layers, from central servers, through gateways, down to edge devices, to grow unhindered, to discover and make accessible connected resources, and to support the ability to hide and compartmentalize connected resources. Network protocols can be part of the fabric supporting human accessible services that operate regardless of location, time, or space. Innovations can include service delivery and associated infrastructure, such as hardware and software. Services may be provided in accordance with specified Quality of Service (QoS) terms. The use of IoT devices and networks can be included in a heterogeneous network of connectivity including wired and wireless technologies.
Nonparametric Obstruction Detection for UWB Localization (2009)

Ultra-wide bandwidth (UWB) transmission is a promising technology for indoor localization due to its fine delay resolution and obstacle-penetration capabilities. However, the presence of walls and other obstacles introduces a positive bias in distance estimates, severely degrading localization accuracy. We have performed an extensive indoor measurement campaign with FCC-compliant UWB radios to quantify the effect of non-line-of-sight (NLOS) propagation. Based on this campaign, we extract key features that allow us to distinguish between NLOS and LOS conditions. We then propose a nonparametric approach based on support vector machines for NLOS identification, and compare it with existing parametric (i.e., model-based) approaches. Finally, we evaluate the impact on localization through Monte Carlo simulation. Our results show that it is possible to improve positioning accuracy relying solely on the received UWB signal.
Multiple lysophosphatidic acid acyltransferases in <i>Neisseria meningitidis</i> (1999)

Lysophosphatidic acid (LPA) and phosphatidic acid (PA) are critical phospholipid intermediates in the biosynthesis of cell membranes. In Escherichia coli, LPA acyltransferase (1-acyl-sn-glycerol-3-phosphate acyltransferase; EC 2.3.1.51) catalyses the transfer of an acyl chain from either acyl-coenzyme A or acyl-acyl carrier protein onto LPA to produce PA. While E. coli possesses one essential LPA acyltransferase (PlsC), Neisseria meningitidis possesses at least two LPA acyltransferases. This study describes the identification and characterization of nlaB (neisserial LPA acyltransferase B), the second LPA acyltransferase identified in N. meningitidis. The gene was located downstream of the Tn916 insertion in N. meningitidis mutant 469 and differed in nucleotide and predicted amino acid sequence from the previously characterized neisserial LPA acyltransferase homologue nlaA. NlaB has specific LPA acyltransferase activity, as demonstrated by complementation of an E. coli plsC(Ts) mutant in trans, by decreased levels of LPA acyltransferase activity in nlaB mutants and by lack of complementation of E. coli plsB26,X50, a mutant defective in the first acyltransferase step in phospholipid biosynthesis. Meningococcal nlaA mutants accumulated LPA and demonstrated alterations in membrane phospholipid composition, yet retained LPA acyltransferase activity. In contrast, meningococcal nlaB mutants exhibited decreased LPA acyltransferase activity, but did not accumulate LPA or display any other observable membrane changes. We propose that N. meningitidis possesses at least two LPA acyltransferases to provide for the production of a greater diversity of membrane phospholipids.
Construction of Transgenic Drosophila by Using the Site-Specific Integrase From Phage φC31 (2004)

Abstract The φC31 integrase functions efficiently in vitro and in Escherichia coli, yeast, and mammalian cells, mediating unidirectional site-specific recombination between its attB and attP recognition sites. Here we show that this site-specific integration system also functions efficiently in Drosophila melanogaster in cultured cells and in embryos. Intramolecular recombination in S2 cells on transfected plasmid DNA carrying the attB and attP recognition sites occurred at a frequency of 47%. In addition, several endogenous pseudo attP sites were identified in the fly genome that were recognized by the integrase and used as substrates for integration in S2 cells. Two lines of Drosophila were created by integrating an attP site into the genome with a P element. φC31 integrase injected into embryos as mRNA functioned to promote integration of an attB-containing plasmid into the attP site, resulting in up to 55% of fertile adults producing transgenic offspring. A total of 100% of these progeny carried a precise integration event at the genomic attP site. These experiments demonstrate the potential for precise genetic engineering of the Drosophila genome with the φC31 integrase system and will likely benefit research in Drosophila and other insects.