gebhart/patrepeval huggingface dataset:
Discovery of a Highly Selective and Efficient Reagent for Formation of Intramolecular Disulfide Bonds in Peptides (2000)

We have discovered that trans-[Pt(en)2Cl2]2+ (en = ethylenediamine) is a highly selective and efficient reagent for the quantitative formation of intramolecular disulfide bonds in peptides. A series of 14 dithiol peptides which form disulfide-containing rings ranging in size from 14 to 53 atoms were used to characterize the reagent. The dithiol peptides are cleanly and rapidly converted to their disulfide forms by a slight excess of the platinum complex under mild reaction conditions (slightly acidic and neutral media). For all the dithiol peptides studied, including a penicillamine-derived peptide, the oxidation yields range from 97% to 100%. No side reactions were observed, including no oxidation of the methionine side chain. The reaction kinetics for oxidation of reduced pressinoic acid were found to be second order overall: rate = k‘[Pt(IV)][dithiol peptide], where k‘ is a pH-dependent second-order rate constant. Values of 0.60 ± 0.01, 3.5 ± 0.2, and 22 ± 1 M-1 s-1 were determined for k‘ at pH 3.0, 4.0, and 5.0, respectively (25 °C and 0.45 M ionic strength). A reaction mechanism for oxidation of dithiol peptides by [Pt(en)2Cl2]2+ is proposed. [Pt(en)2Cl2]2+ and its reduction product [Pt(en)2]2+ are essentially substitution inert under the conditions used for disulfide formation, they are nontoxic, and they are readily separated from peptides by HPLC. The characteristics of [Pt(en)2Cl2]2+ and its reaction properties with dithiol peptides suggest that [Pt(en)2Cl2]2+ is a universal reagent for the rapid and quantitative formation of intramolecular disulfide bonds in peptides.
Wafer-Scale High-Throughput Ordered Growth of Vertically Aligned ZnO Nanowire Arrays (2010)

This article presents an effective approach for patterned growth of vertically aligned ZnO nanowire (NW) arrays with high throughput and low cost at wafer scale without using cleanroom technology. Periodic hole patterns are generated using laser interference lithography on substrates coated with the photoresist SU-8. ZnO NWs are selectively grown through the holes via a low-temperature hydrothermal method without using a catalyst and with a superior control over orientation, location/density, and as-synthesized morphology. The development of textured ZnO seed layers for replacing single crystalline GaN and ZnO substrates extends the large-scale fabrication of vertically aligned ZnO NW arrays on substrates of other materials, such as polymers, Si, and glass. This combined approach demonstrates a novel method of manufacturing large-scale patterned one-dimensional nanostructures on various substrates for applications in energy harvesting, sensing, optoelectronics, and electronic devices.
Safe constraint queries (1998)

Article Free Access Share on Safe constraint queries Authors: Michael Benedikt Bell Laboratories, 1000 E Warrenville Rd., Naperville, IL Bell Laboratories, 1000 E Warrenville Rd., Naperville, ILView Profile , Leonid Libkin Bell Laboratories, 600 Mountain Avenue, Murray Hill, NJ Bell Laboratories, 600 Mountain Avenue, Murray Hill, NJView Profile Authors Info & Claims PODS '98: Proceedings of the seventeenth ACM SIGACT-SIGMOD-SIGART symposium on Principles of database systemsMay 1998 Pages 99–108https://doi.org/10.1145/275487.275499Published:01 May 1998Publication History 20citation234DownloadsMetricsTotal Citations20Total Downloads234Last 12 Months6Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Surgical motion task performance in a hand eye colocated digital stereo microcsope (2013)

The effect of hand-eye colocation in performing dexterous fine movements such as microsurgical manipulation is studied under a novel digital stereo microscope. Hand motion data is captured under conditions of hand-eye colocation and separation. Both configurations are tested with monoscopic and stereoscopic vision. A set of microsurgical task abstractions are created to reduce the effect of prior expertise. Finally the captured motion data is analyzed to determine the effect of colocation and stereopsis for surgical motion tasks.
Structure-Activity Study of the Lantibiotic Mutacin II from <i>Streptococcus mutans</i> T8 by a Gene Replacement Strategy (1998)

ABSTRACT Mutacin II, elaborated by group II Streptococcus mutans , is a ribosomally synthesized and posttranslationally modified polypeptide antibiotic containing unusual thioether and didehydro amino acids. To ascertain the role of specific amino acid residues in mutacin II antimicrobial activity, we developed a streptococcal expression system that facilitates the replacement of the mutA gene with a single copy of a mutated variant gene. As a result, variants of mutacin II can be designed and expressed. The system was tested by constructing the following mutant peptides: ΔN1, V7A, P9A, T10A, T10S, C15A, C26A, and C27A. All of these mutacin II variants except ΔN1 and T10A, which were not secreted, were isolated, and their identities were verified by mass spectrometry. Variants P9A, C15A, C26A, and C27A failed to exert antimicrobial activity. Because the P9A and T10A variants comprise the “hinge” region of mutacin II, these observations suggest that in addition to the thioether and didehydro amino acids, the hinge region is essential for biological activity and biosynthesis or export of the peptide. Tandem mass spectrometry of the N-terminal part of the wild-type molecule and its C15A variant confirmed that the threonine at position 10 is dehydrated and present as a didehydrobutyrine residue. This analysis of the active T10S variant further suggested that a didehydro amino acid at this position is specific for antimicrobial activity and that the biosynthetic machinery does not discriminate between threonine and serine. In contrast, the lack of production of mutacin variants with alanine substituted for threonine at position 10, as well as the deletion of asparagine at the N terminus (ΔN1), indicates that specific residues in the propeptide may be crucial for certain steps in the biosynthetic pathway of this lantibiotic.
Hierarchical N-port memory architecture based on 1-port memory cells (1997)

The new hierarchical N-port memory architecture features parallel read/write access with low access conflict probability from all ports, although only 1-port memory cells are used. A simple, effective circuit is proposed for conflict handling and monitoring. In comparison with conventional implementation of all N ports in each memory cell, substantial memory area reductions between 28 % (2 ports) and 68 % (16 ports) can be realized, while access times are nearly equivalent. The architecture is a generalization of the previous state of the art and is applicable for all types of dynamic, static and non-volatile memory.
Autonomous smart sensor network for full-scale structural health monitoring (2010)

The demands of aging infrastructure require effective methods for structural monitoring and maintenance. Wireless smart sensor networks offer the ability to enhance structural health monitoring (SHM) practices through the utilization of onboard computation to achieve distributed data management. Such an approach is scalable to the large number of sensor nodes required for high-fidelity modal analysis and damage detection. While smart sensor technology is not new, the number of full-scale SHM applications has been limited. This slow progress is due, in part, to the complex network management issues that arise when moving from a laboratory setting to a full-scale monitoring implementation. This paper presents flexible network management software that enables continuous and autonomous operation of wireless smart sensor networks for full-scale SHM applications. The software components combine sleep/wake cycling for enhanced power management with threshold detection for triggering network wide tasks, such as synchronized sensing or decentralized modal analysis, during periods of critical structural response.
Emergent Properties of Reduced-Genome <i>Escherichia coli</i> (2006)

With the use of synthetic biology, we reduced the Escherichia coli K-12 genome by making planned, precise deletions. The multiple-deletion series (MDS) strains, with genome reductions up to 15%, were designed by identifying nonessential genes and sequences for elimination, including recombinogenic or mobile DNA and cryptic virulence genes, while preserving good growth profiles and protein production. Genome reduction also led to unanticipated beneficial properties: high electroporation efficiency and accurate propagation of recombinant genes and plasmids that were unstable in other strains. Eradication of stress-induced transposition evidently stabilized the MDS genomes and provided some of the new properties.
Structural Investigations of AMS-n Mesoporous Materials by Transmission Electron Microscopy (2004)

A novel synthesis route for mesoporous silicates using anionic surfactants has been recently reported. It was advanced that materials synthesized using anionic surfactants and aminosilane groups as co-structure directing agents led to the synthesis of highly ordered, novel mesoporous materials with unprecedented structural properties. Here we present an in-depth high-resolution transmission electron microscopy (HRTEM) investigation on the structural characteristics of these novel mesoporous solids denoted AMS-n (anionic mesoporous silicas). These materials show increased order in comparison with conventional mesoporous structures as a result of the long-range periodicity of structural modulations. Structural defects formed in these materials are investigated using electron diffraction (ED) and Fourier transform (FT) diffractograms. In addition we present a new cubic mesostructure AMS-8 (space group Fd3̄m). These new materials show promising new pore connectivities and morphologies making them ideal for applications ranging from catalysts' supports to gas separation, and from nanodevices to drug delivery.
A semi-fragile lossless digital watermarking scheme based on integer wavelet transform (2005)

In this paper, a new semi-fragile lossless digital watermarking scheme based on integer wavelet transform (IWT) is presented. Data are embedded into some IWT coefficients. The wavelet family applied is the 5/3 filter bank which serves as the default transformation in the JPEG2000 standard for image lossless compression. As a result, the proposed scheme can be integrated into the JPEG2000 standard smoothly. Different from the only existing semi-fragile lossless watermarking scheme, instead of using modulo 256 addition, this method takes special measures that prevents overflow/underflow (one of critical issue for lossless watermarking) and hence does not suffer from annoying salt-and-pepper noise. The exact cover media can be losslessly recovered if the stegoimage has not been altered. Furthermore, the hidden data can be extracted with no error even after incidental alterations, including compression, have been applied to the stegoimage (thus named after "semi-fragile").
Singlemode lightwave transmission in SOI-type photonic-crystal line-defect waveguides with phase-shifted holes (2002)

Singlemode lightwave transmission was observed in novel line-defect photonic-crystal (PC) waveguides. The waveguide structure is constructed by adding phase-shifted holes in an ordinary missing-hole line defect. This device permits a fine singlemode lightwave transmission even though the waveguide structure is fabricated on silicon-on-insulator (SOI) substrate, which seriously promotes off-plane leakage of waveguiding modes.
Stator Inter-turn Fault Detection of Synchronous Machines Using Field Current Signature Analysis (2006)

Our recent observations suggested that harmonics in the field current are very promising to detect stator inter-turn faults in synchronous machines. So far, an increase in some of the even harmonics in the field current has been reported to detect such faults. However no explanation has been provided for the cause of these harmonics. Moreover, the even harmonics can significantly increase with supply unbalance as well as time harmonics, which can lead to a serious confusion. Hence, in this study, an in-depth investigation was conducted to determine the origin of various harmonic components in the field current and their feasibility to detect stator faults. It was found that, owing to structural asymmetries of the field winding, some of these components clearly increased with stator inter-turn fault. The findings are helpful to detect faults involving few turns without ambiguity, in spite of with supply unbalance and time harmonics. Both simulation and experimental results are presented in this paper. The diagnosis results have also been verified using a rotor-mounted search-coil, which can also be used to detect even a one-turn stator fault very effectively
Simultaneous Atrial and Ventricular Electrogram Transmission Via a Specialized Single Lead System (1984)

No telemetrically monitorable pacemakers are capable of detecting and transmitting the complete electrogram (EGM) during normal and paced rhythms, although some are capable of detecting and transmitting either the P- or R-wave. A new lead and telemetry-pacemaker system has been developed that permits the transmission of the complete EGM and is not adversely affected by pacemaker outputs or after-potentials. Electrodes are placed in the right ventricle and atrium to optimize EGM detection. These A-V data probe electrodes are electrically separate from the pacing-sensing electrodes but are structurally part of a coaxial ventricular lead that is no larger than a conventional bipolar lead (2.3 mm). The telemetry system is also compatible with telephone monitoring systems. The system has consistently demonstrated its ability to detect accurately the EGM during normal sinus rhythms and does not affect atrial, ventricular, or A-V sequential pacing. In addition, this system can detect and transmit EGM abnormalities, including ectopic beats, retrograde conduction, and ischemic changes. A-V data leads with telemetry monitored VVI pacemakers have been implanted in dogs for over two years. This system will provide the means to detect and telemetrically record noninvasively the entire normal and abnormal EGM, even in pacer dependent patients. (PACE, Vol. 7, November-December, 1984).
<i>Rht18</i> Semidwarfism in Wheat Is Due to Increased <i>GA 2-oxidaseA9</i> Expression and Reduced GA Content (2018)

Semidwarfing genes have improved crop yield by reducing height, improving lodging resistance, and allowing plants to allocate more assimilates to grain growth. In wheat (<i>Triticum aestivum</i>), the <i>Rht18</i> semidwarfing gene was identified and deployed in durum wheat before it was transferred into bread wheat, where it was shown to have agronomic potential. <i>Rht18</i>, a dominant and gibberellin (GA) responsive mutant, is genetically and functionally distinct from the widely used GA-insensitive semidwarfing genes <i>Rht-B1b</i> and <i>Rht-D1b</i> In this study, the <i>Rht18</i> gene was identified by mutagenizing the semidwarf durum cultivar Icaro (<i>Rht18</i>) and generating mutants with a range of tall phenotypes. Isolating and sequencing chromosome 6A of these "overgrowth" mutants showed that they contained independent mutations in the coding region of <i>GA2oxA9</i><i>GA2oxA9</i> is predicted to encode a GA 2-oxidase that metabolizes GA biosynthetic intermediates into inactive products, effectively reducing the amount of bioactive GA (GA<sub>1</sub>). Functional analysis of the GA2oxA9 protein demonstrated that GA2oxA9 converts the intermediate GA<sub>12</sub> to the inactive metabolite GA<sub>110</sub> Furthermore, <i>Rht18</i> showed higher expression of <i>GA2oxA9</i> and lower GA content compared with its tall parent. These data indicate that the increased expression of <i>GA2oxA9</i> in <i>Rht18</i> results in a reduction of both bioactive GA content and plant height. This study describes a height-reducing mechanism that can generate new genetic diversity for semidwarfism in wheat by combining increased expression with mutations of specific amino acid residues in <i>GA2oxA9</i>.
X-ray tensor tomography (2014)

Here we introduce a new concept for x-ray computed tomography that yields information about the local micro-morphology and its orientation in each voxel of the reconstructed 3D tomogram. Contrary to conventional x-ray CT, which only reconstructs a single scalar value for each point in the 3D image, our approach provides a full scattering tensor with multiple independent structural parameters in each volume element. In the application example shown in this study, we highlight that our method can visualize sub-pixel fiber orientations in a carbon composite sample, hence demonstrating its value for non-destructive testing applications. Moreover, as the method is based on the use of a conventional x-ray tube, we believe that it will also have a great impact in the wider range of material science investigations and in future medical diagnostics.
Fluctuation spectroscopy in low-coherence dynamic light scattering of tissue responding to pharmacologicals (2010)

Motility contrast imaging (MCI) detects dynamic speckle from living tissue using digital holography. It detects sub-cellular motion in living tissue as a fully endogenous imaging contrast agent. Three-dimensional imaging assays of anti-mitotic cancer drugs extract label-free functional signatures in tumors.
Cost-based optimization of decision support queries using transient-views (1998)

Next generation decision support applications, besides being capable of processing huge amounts of data, require the ability to integrate and reason over data from multiple, heterogeneous data sources. Often, these data sources differ in a variety of aspects such as their data models, the query languages they support, and their network protocols. Also, typically they are spread over a wide geographical area. The cost of processing decision support queries in such a setting is quite high. However, processing these queries often involves redundancies such as repeated access of same data source and multiple execution of similar processing sequences. Minimizing these redundancies would significantly reduce the query processing cost. In this paper, we (1) propose an architecture for processing complex decision support queries involving multiple, heterogeneous data sources; (2) introduce the notion of transient-views — materialized views that exist only in the context of execution of a query — that is useful for minimizing the redundancies involved in the execution of these queries; (3) develop a cost-based algorithm that takes a query plan as input and generates an optimal “covering plan”, by minimizing redundancies in the original plan; (4) validate our approach by means of an implementation of the algorithms and a detailed performance study based on TPC-D benchmark queries on a commercial database system; and finally, (5) compare and contrast our approach with work in related areas, in particular, the areas of answering queries using views and optimization using common sub-expressions. Our experiments demonstrate the practicality and usefulness of transient-views in significantly improving the performance of decision support queries.
Active-Impedance Control of a Lower-Limb Assistive Exoskeleton (2007)

We propose a novel control method for lower-limb assist that produces a virtual modification of the mechanical impedance of the human limbs. This effect is accomplished by making the exoskeleton display active impedance properties. Active impedance control emphasizes control of the exoskeleton's dynamics and regulation of the transfer of energy between the exoskeleton and the user. Its goal is improving the dynamic response of the human limbs without sacrificing the user's control authority. The proposed method is an alternative to myoelectrical exoskeleton control, which is based on estimating muscle torques from electromyographical (EMG) activity. Implementation of an EMG-based controller is a complex task that involves modeling the user's musculoskeletal system and requires recalibration. In contrast, active impedance control is less dependent on estimation of the user's attempted motion, thereby avoiding conflicts resulting from inaccurate estimation. In this paper we also introduce a new form of human assist based on improving the kinematic response of the limbs. Reduction of average muscle torques is a common goal of research in human assist. However, less emphasis has been placed so far on improving the user's agility of motion. We aim to use active impedance control to attain such effects as increasing the user's average speed of motion, and improving their acceleration capabilities in order to compensate for perturbations from the environment.
Differentiation of Mycobacterial Species by PCR-Restriction Analysis of DNA (342 Base Pairs) of the RNA Polymerase Gene ( <i>rpoB</i> ) (2001)

PCR amplification-restriction analysis (PRA) of rpoB DNA (342 bp), which comprises the Rif(r) region, was used for the differential identification of 49 mycobacteria. The DNA had been used previously for the identification of mycobacterial species by comparative sequence analysis (B. J. Kim et al., J. Clin. Microbiol. 37:1714-1720, 1999). Digestion with four restriction enzymes (HaeIII, HindII, MvaI, and AccII), which were selected on the basis of rpoB DNA sequences, generated distinctive PRA patterns that allowed not only the reference strains but also the clinical isolates of mycobacteria to be distinguished. Both rapidly and slowly growing mycobacteria were distinctly differentiated by HaeIII digestion of the amplified rpoB DNA. By HindII digestion the Mycobacterium tuberculosis complex was distinguished from the other mycobacteria. Furthermore, six subspecies of Mycobacterium kansasii (subspecies I to VI) as well as the closely related Mycobacterium gastri, and other closely related species, were distinguished by simultaneous digestion of MvaI and AccII. According to the rpoB PRA scheme, 240 strains of clinical isolates could be identified. It was also possible to detect and identify M. tuberculosis directly from sputa and bronchoalveolar lavage specimens. These results suggest that PRA of rpoB DNA is a simple and feasible method not only for the differentiation of culture isolates but also for the rapid detection and identification of pathogenic mycobacteria in primary clinical specimens.
<title>Fiber Interferometer Gyroscope</title> (1978)

A one-axis, fiber optic interferometer gyro has been constructed and tested. The device, based on a 670 meter length of single-mode optical fiber, uses a GaAlAs laser as a source, and phase sensitive synchronous detection to measure fringe shifts as a function of rotation rate. Using a calibrated rate table, rotation rates from 0 to 110 deg/sec have been measured. The device easily measures rates as low as 0.05 deg/sec with a signal-to-noise ratio of ten. Error sources and potential improvements will be discussed.
Integrated Thermal Stabilization of a Microring Modulator (2013)

An integrated silicon photodiode and heater are used to thermally stabilize a microring modulator, interfacing with external feedback circuitry to provide error-free microring modulator operation under thermal fluctuations that would normally render it inoperable.