gebhart/patrepeval huggingface dataset:
Discovering structural correlations in α‐helices (1994)

We have developed a new representation for structural and functional motifs in protein sequences based on correlations between pairs of amino acids and applied it to alpha-helical and beta-sheet sequences. Existing probabilistic methods for representing and analyzing protein sequences have traditionally assumed conditional independence of evidence. In other words, amino acids are assumed to have no effect on each other. However, analyses of protein structures have repeatedly demonstrated the importance of interactions between amino acids in conferring both structure and function. Using Bayesian networks, we are able to model the relationships between amino acids at distinct positions in a protein sequence in addition to the amino acid distributions at each position. We have also developed an automated program for discovering sequence correlations using standard statistical tests and validation techniques. In this paper, we test this program on sequences from secondary structure motifs, namely alpha-helices and beta-sheets. In each case, the correlations our program discovers correspond well with known physical and chemical interactions between amino acids in structures. Furthermore, we show that, using different chemical alphabets for the amino acids, we discover structural relationships based on the same chemical principle used in constructing the alphabet. This new representation of 3-dimensional features in protein motifs, such as those arising from structural or functional constraints on the sequence, can be used to improve sequence analysis tools including pattern analysis and database search.
<title>Bearing monitoring</title> (2001)

At Ford Motor Company, thrust bearing in drill motors is often damaged by metal chips. Since the vibration frequency is several Hz only, it is very difficult to use accelerometers to pick up the vibration signals. Under the support of Ford and NASA, we propose to use a piezo film as a sensor to pick up the slow vibrations of the bearing. Then a neural net based fault detection algorithm is applied to differentiate normal bearing from bad bearing. The first step involves a Fast Fourier Transform which essentially extracts the significant frequency components in the sensor. Then Principal Component Analysis is used to further reduce the dimension of the frequency components by extracting the principal features inside the frequency components. The features can then be used to indicate the status of bearing. Experimental results are very encouraging.
A Facile General Route to α-Keto Esters and α-Diketones (1990)

A novel synthetic route to α-keto esters and α-diketones through ozonolytic fragmentation of α-substituted acetoacetic esters and α-substituted acetylacetones is described.
Anti-GQ1b ganglioside antibodies mediate complement-dependent destruction of the motor nerve terminal (2001)

Miller-Fisher syndrome is an autoimmune neuropathy characterized by ataxia, areflexia and ophthalmoplegia, and in the majority of cases the presence of high titres of anti-GQ1b ganglioside antibodies. In an ex vivo model, human and mouse anti-GQ1b antibodies have been shown previously to induce a complement-dependent alpha-latrotoxin-like effect on the murine motor endplate, i.e. they bring about massive quantal release of acetylcholine and eventually block neuromuscular transmission. Using immunofluorescence microscopy with image analysis, we show here that the late stages of this electrophysiological effect temporally coincide with the loss of heavy neurofilament (200 kDa) and type III beta-tubulin immunostaining and structural breakdown of the nerve terminal, as demonstrated by electron microscopy. Ultrastructurally, axon terminals were disorganized, depleted of vesicles, and subdivided by the infiltrating processes of capping Schwann cells. These findings provide clear pathological evidence to support a role for anti-ganglioside antibodies in mediating nerve terminal injury and further advance the view that this site may be of importance as a target in some human neuropathies.
Adaptive color conversion algorithm to achieve both high brightness and wide color gamut (2009)

We present a new color conversion algorithm for the new projector with the forth liquid crystal panel which controls the yellow light separately from RGB lights of the three-LCD system. This algorithm controls the volume of yellow light and corrects distorted color based on image analysis, and thus achieves high brightness and wide color gamut.
Synthesis of Bipyridine-Centered Diblock Copolymers (2003)

A series of bipyridine-centered diblock copolymers, bpy(A)(B), containing PMMA, PS, PCL, PLA, and PEG chains were synthesized via sequential, orthogonal strategies from unsymmetrical, difunctional bipyridine ligands. Specifically, the combination of atom transfer radical polymerization (ATRP) and ring-opening polymerization (ROP) generally produced bpy(PCL)(PMMA) (16) and bpy(PS)(PCL) (14) samples with anticipated molecular weights and low polydispersities (PDIs = 1.1−1.2). ROP or ATRP was also used in conjunction with a polymer coupling strategy to synthesize bpy(PEG)(R) diblocks with a bipyridine binding site at the block junction where R = PCL (12), PLA (13), or PMMA (21). Polymers with low PDIs were again generated in all cases (PDI ∼ 1.2−1.3). The particular design explored in this study could ultimately lead to block copolymeric metal complexes that form ordered assemblies with metal ions at microdomain interfaces.
Autonomous quadrotor flight using onboard RGB-D visual odometry (2014)

In this paper we present a navigation system for Micro Aerial Vehicles (MAV) based on information provided by a visual odometry algorithm processing data from an RGB-D camera. The visual odometry algorithm uses an uncertainty analysis of the depth information to align newly observed features against a global sparse model of previously detected 3D features. The visual odometry provides updates at roughly 30 Hz that is fused at 1 KHz with the inertial sensor data through a Kalman Filter. The high-rate pose estimation is used as feedback for the controller, enabling autonomous flight. We developed a 4DOF path planner and implemented a real-time 3D SLAM where all the system runs on-board. The experimental results and live video demonstrates the autonomous flight and 3D SLAM capabilities of the quadrotor with our system.
High-fidelity controlled-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msup><mml:mi>σ</mml:mi><mml:mi>Z</mml:mi></mml:msup></mml:math>gate for resonator-based superconducting quantum computers (2013)

A possible building block for a scalable quantum computer has recently been demonstrated [Mariantoni et al., Science 334, 61 (2011)]. This architecture consists of superconducting qubits capacitively coupled both to individual memory resonators as well as a common bus. In this work we study a natural primitive entangling gate for this and related resonator-based architectures, which consists of a controlled-${\ensuremath{\sigma}}^{z}$ (cz) operation between a qubit and the bus. The cz gate is implemented with the aid of the noncomputational qubit $|2\ensuremath{\rangle}$ state [Strauch et al., Phys. Rev. Lett. 91, 167005 (2003)]. Assuming phase or transmon qubits with 300 MHz anharmonicity, we show that by using only low frequency qubit-bias control it is possible to implement the qubit-bus cz gate with 99.9$%$ (99.99$%$) fidelity in about $17\phantom{\rule{0.16em}{0ex}}\mathrm{ns}$ ($23\phantom{\rule{0.16em}{0ex}}\mathrm{ns}$) with a realistic two-parameter pulse profile, plus two auxiliary $z$ rotations. The fidelity measure we refer to here is a state-averaged intrinsic process fidelity, which does not include any effects of noise or decoherence. These results apply to a multiqubit device that includes strongly coupled memory resonators. We investigate the performance of the qubit-bus cz gate as a function of qubit anharmonicity, identify the dominant intrinsic error mechanism and derive an associated fidelity estimator, quantify the pulse shape sensitivity and precision requirements, simulate qubit-qubit cz gates that are mediated by the bus resonator, and also attempt a global optimization of system parameters including resonator frequencies and couplings. Our results are relevant for a wide range of superconducting hardware designs that incorporate resonators and suggest that it should be possible to demonstrate a $99.9%$ cz gate with existing transmon qubits, which would constitute an important step towards the development of an error-corrected superconducting quantum computer.
Hydration and Plasticity Following Long-term Use of a Moisturizer: A Single-blind Study (2002)

Skin hydration is thought to have an influence on skin plasticity, and moisturizers have therefore gained widespread use. However, the effects of long-term moisturizer use on the mechanical properties and the long-term correlation between plasticity and hydration of human skin in vivo remain unknown. Nineteen healthy volunteers applied a moisturizer to the volar surface of their forearms for 3 weeks, once daily on one arm and twice daily on the other. The skin capacitance, distensibility, hysteresis and elasticity were measured in both treated areas and in an untreated regional control area. Measurements were carried out at baseline, at one-week intervals during the trial and one week after the termination. Data were assessed in a single-blind fashion. No change was found in any of the mechanical parameters in the moisturizer-treated skin compared to the control. The capacitance of skin was found to increase independently of dose. One week after termination of the treatment, the skin capacitance remained increased. No dose-response effect was seen, however. Long-term use of moisturizers increases skin capacitance significantly, but does not change the mechanical properties. In vivo skin hydration is a poor predictor of skin mechanics.
Synthesis, absolute configuration, and molecular modeling study of etoxadrol, a potent phencyclidine-like agonist (1988)

Etoxadrol (2a), one of the eight possible optical isomers of 2-ethyl-2-phenyl-4-(2-piperidyl)-1,3-dioxolane, was synthesized from (S,S)-1-(2-piperidyl)-1,2-ethanediol, which was obtained from cleavage of dexoxadrol (1a, (S,S)-2,2-diphenyl-4-(2-piperidyl)-1,3-dioxolane). The absolute configuration of etoxadrol hydrochloride, a phencyclidine-like compound biologically, was determined to be 2S, 4S, and 6S at its three chiral centers by single-crystal X-ray analysis. Epietoxadrol (2b), epimeric with etoxadrol at the C-2 center, was also obtained from the synthesis. This much less potent enantiomer has the 2R,4S,6S configuration. The affinity of etoxadrol to the phencyclidine binding site was found to be comparable to that of phencyclidine itself and was 35 times more potent than its epimer, epietoxadrol. Three diastereomeric mixtures were prepared that had low affinity for the phencyclidine site. In studies of the discriminative stimulus properties of these compounds, it was found that only etoxadrol substituted for the phencyclidine stimulus. With use of computer-assisted molecular modeling techniques, a hypothetical phencyclidine binding site model has been developed that, unlike our former hypothesis based on Dreiding models, correctly predicts the higher affinity of etoxadrol and the lesser affinity of epietoxadrol for the phencyclidine site.
Analysis of Gene Expression in <i>Escherichia coli</i> in Response to Changes of Growth-Limiting Nutrient in Chemostat Cultures (2004)

Studies of steady-state metabolic fluxes in Escherichia coli grown in nutrient-limited chemostat cultures suggest remarkable flux alterations in response to changes of growth-limiting nutrient in the medium (Hua et al., J. Bacteriol. 185:7053-7067, 2003). To elucidate the physiological adaptation of cells to the nutrient condition through the flux change and understand the molecular mechanisms underlying the change in the flux, information on gene expression is of great importance. DNA microarray analysis was performed to investigate the global transcriptional responses of steady-state cells grown in chemostat cultures with limited glucose or ammonia while other environmental conditions and the growth rate were kept constant. In slow-growing cells (specific growth rate of 0.10 h(-1)), 9.8% of a total of 4,071 genes investigated, especially those involved in amino acid metabolism, central carbon and energy metabolism, transport system and cell envelope, were observed to be differentially expressed between the two nutrient-limited cultures. One important characteristic of E. coli grown under nutrient limitation was its capacity to scavenge carbon or nitrogen from the medium through elevating the expression of the corresponding transport and assimilation genes. The number of differentially expressed genes in faster-growing cells (specific growth rate of 0.55 h(-1)), however, decreased to below half of that in slow-growing cells, which could be explained by diverse transcriptional responses to the growth rate under different nutrient limitations. Independent of the growth rate, 92 genes were identified as being differentially expressed. Genes tightly related to the culture conditions were highlighted, some of which may be used to characterize nutrient-limited growth.
Total Synthesis of the Polyether Antibiotic Lonomycin A (Emericid) (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal Synthesis of the Polyether Antibiotic Lonomycin A (Emericid)David A. Evans, Andrew M. Ratz, Bret E. Huff, and George S. SheppardCite this: J. Am. Chem. Soc. 1995, 117, 12, 3448–3467Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/ja00117a014https://doi.org/10.1021/ja00117a014research-articleACS PublicationsRequest reuse permissionsArticle Views2270Altmetric-Citations136LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Fabrication and Encapsulation of a Short‐Period Wire Grid Polarizer with Improved Viewing Angle by the Angled‐Evaporation Method (2013)

A wire grid polarizer (WGP) is fabricated by using a simplified approach with a combination of nanoimprint lithography (NIL) and angled metal deposition. The period of the imprinted polymer nanograting used in this study is 180 nm. The WGP is formed by two consecutive angled aluminium evaporation processes, essentially halving the period for the aluminium (Al) nanograting. The fabricated WGP shows good optical properties for polarized light. More importantly, because of the slight reduction of the period of the nanograting as compared with previous results, the viewing angle, which is one of the most important characters in display equipment, is extended greatly. Encapsulation of the WGP using poly(methyl methacrylate) is conducted for practical application of the WGP. The thickness of the coating is controlled to be less than 1 μm, to prevent the degradation of the optical properties of the WGP.
Optical signal eye diagram measurement with subpicosecondresolution using optical sampling (1996)

The authors have developed a novel optical waveform measurement technique that measures the waveforms of a randomly modulated optical signal with subpicosecond resolution by using sum-frequency-generation optical sampling and digital processing. With this method, the eye diagram of 10 Gbit/s optical signal is successfully measured with 0.9 ps temporal resolution and 24 dB signal-to-noise ratio.
Genome-Wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) Identifies Candidate Gene Signatures in Response to Aflatoxin Producing Fungus Aspergillus flavus (2015)

Aflatoxins are toxic and potent carcinogenic metabolites produced from the fungi Aspergillus flavus and A. parasiticus. Aflatoxins can contaminate cottonseed under conducive preharvest and postharvest conditions. United States federal regulations restrict the use of aflatoxin contaminated cottonseed at >20 ppb for animal feed. Several strategies have been proposed for controlling aflatoxin contamination, and much success has been achieved by the application of an atoxigenic strain of A. flavus in cotton, peanut and maize fields. Development of cultivars resistant to aflatoxin through overexpression of resistance associated genes and/or knocking down aflatoxin biosynthesis of A. flavus will be an effective strategy for controlling aflatoxin contamination in cotton. In this study, genome-wide transcriptome profiling was performed to identify differentially expressed genes in response to infection with both toxigenic and atoxigenic strains of A. flavus on cotton (Gossypium hirsutum L.) pericarp and seed. The genes involved in antifungal response, oxidative burst, transcription factors, defense signaling pathways and stress response were highly differentially expressed in pericarp and seed tissues in response to A. flavus infection. The cell-wall modifying genes and genes involved in the production of antimicrobial substances were more active in pericarp as compared to seed. The genes involved in auxin and cytokinin signaling were also induced. Most of the genes involved in defense response in cotton were highly induced in pericarp than in seed. The global gene expression analysis in response to fungal invasion in cotton will serve as a source for identifying biomarkers for breeding, potential candidate genes for transgenic manipulation, and will help in understanding complex plant-fungal interaction for future downstream research.
The <i>gcvB</i> gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in <i>Escherichia coli</i> (2000)

The Escherichia coli gcvB gene encodes a small RNA transcript that is not translated in vivo. Transcription from the gcvB promoter is activated by the GcvA protein and repressed by the GcvR protein, the transcriptional regulators of the gcvTHP operon encoding the enzymes of the glycine cleavage system. A strain carrying a chromosomal deletion of gcvB exhibits normal regulation of gcvTHP expression and glycine cleavage enzyme activity. However, this mutant has high constitutive synthesis of OppA and DppA, the periplasmic-binding protein components of the two major peptide transport systems normally repressed in cells growing in rich medium. The altered regulation of oppA and dppA was also demonstrated using oppA-phoA and dppA-lacZ gene fusions. Although the mechanism(s) involving gcvB in the repression of these two genes is not known, oppA regulation appears to be at the translational level, whereas dppA regulation occurs at the mRNA level.
Mechanical Properties of Carbon Fiber-Reinforced Polymethylmethacrylate for Surgical Implant Applications (1977)

Reinforced bone cement containing a small amount of short, high-modulus carbon fibers dispersed randomly in surgical polymethylmethacrylate bone cement has been developed and successfully used in a few cases for neoplastic bone replacement. The mechanical properties of this material were evaluated with respect to the bone cement used presently in prosthetic and restorative orthopaedic surgery. Superior mechanical properties were observed in reinforced acrylic compared with unreinforced material; specifically, monotonic tensile strength increased from 28 to 38 MPa (4060 to 5510 psi) and monotonic tensile, cyclic tensile, and compressive modulii were significantly higher in reinforced acrylic. An increase of about 50 percent in fatigue strength was achieved at long lives (105 cycles), that is 15 MPa (2175 psi) as compared to 10 MPa (1450 psi) for unreinforced acrylic. Both reinforced and unreinforced surgical acrylic are porous materials by virtue of their mode of preparation, that is, operating room conditions. Additional comparative studies were performed only on carbon-reinforced full-density acrylic. The relatively small improvement in mechanical properties for these full-density systems is accounted for by poor fiber distribution. Strain-rate dependence of tensile properties studied over the 5 × 10-6 to 2 × 10-2s-1 range was found to be low for both reinforced and unreinforced porous acrylics. The fracture surfaces of the static and cyclically loaded specimens studied by scanning electron microscopy (SEM) revealed the role of intrinsic voids and the carbon fibers in the process of crack initiation and propagation.
Direct modulation of semiconductor lasers at <i>f</i>&gt;10 GHz by low-temperature operation (1984)

Using a 175-μm-long buried-heterostructure laser fabricated on a semi-insulating substrate operating at −50 °C, a direct amplitude modulation bandwidth in excess of 10 GHz has been achieved.
Bis(phosphinimino)methyl derivatives of Ca, Sr and Ba: facile access to heavier alkaline earth organometallic chemistry (2003)

A series of mononuclear and arene-soluble bis(phosphinimino)methyl derivatives of the heavier alkaline earth metals, calcium, strontium and barium, have been obtained by straightforward addition of two molar equivalents of [KN(SiMe3)2] to a mixture of [CH2(Ph2PNC6H2-Me3-2,4,6)2] and MI2 (M = Ca, Sr, Ba) in THF.
Using mutual coupling to calculate the radiation pattern for parasitic patch antennas (2004)

The far field radiation pattern of closely spaced dipoles can be calculated using mutual impedance and network equations. The definition of mutual coupling for patch antennas must be reviewed to determine the radiation pattern for parasitic patch antennas.