gebhart/patrepeval huggingface dataset:
Background suppression and agent detection in multi-dimensional spaces (2006)

We describe a new method for background suppression and agent detection in principal component spaces derived from spectroscopic data to develop an improved trigger sensor for bioaerosol detection. Simulation results and laboratory data are shown.
Using budding yeast to screen for anti‐prion drugs (2005)

Prions are misfolded proteins capable of propagating their altered conformation which are commonly considered as the causative agent of transmissible spongiform encephalopathies, a class of fatal neurodegenerative diseases. Currently, no treatment for prion-based diseases is available. Recently we have developed a rapid, yeast-based, two-step assay to screen for anti-prion drugs [1]. This new method allowed us to identify several compounds that are effective in vivo against budding yeast [PSI+] and [URE3] prions but also able to promote mammalian prion clearance in three different cell culture-based assays. Taken together, these results validate our method as an economic and efficient high-throughput screening approach to identify novel prion inhibitors or to carry on comprehensive structure-activity studies for already isolated anti-mammalian prion drugs. These results suggest furthermore that biochemical pathways controlling prion formation and/or maintenance are conserved from yeast to human and thus amenable to pharmacological and genetic analysis. Finally, it would be very interesting to test active drugs isolated using the yeast-based assay in models for other diseases (neurodegenerative or not) involving amyloid fibers like Huntington's, Parkinson's or Alzheimer's diseases.
A Method to Delineate Irreversible Electroporation From Thermal Damage Validated Ex Vivo With Real-Time Temperature (2011)

Irreversible electroporation (IRE) is a new non-thermal focal tissue ablation technique that uses low-energy electric pulses to destabilize cell membranes, thus achieving tissue death [1]. The procedure is minimally invasive and is performed through small electrodes inserted into the tissue with pulse delivery of about one minute. The pulses create an electric field that induces an increase in the resting transmembrane potential (TMP) of the cells [1]. Depending on the magnitude of the induced TMP, the electric pulses can have no effect, transiently increase membrane permeability, or cause cell death [1]. Our group has confirmed the safety of the procedure in brain with three experimental dogs [2]. We also treated a canine patient with IRE and radiation therapy for a non-resectable, high-grade glioma, resulting in complete remission of the tumor at four months [3].
Cyclolinear polysiloxanes. I. Synthesis and characterization (2006)

Abstract The synthesis and characterization of two novel cyclic siloxanes, diacetoxydiethyltetramethylcyclotetrasiloxane and diacetoxytriethylpentamethylcyclopentasiloxane, and cyclolinear polymers synthesized from these monomers are presented. The cyclic siloxanes were synthesized from tetramethylcyclotetrasiloxane and pentamethylcyclopentasiloxane, respectively, by acetylation followed by ethylation. The cyclic monomers were characterized with 1 H NMR spectroscopy. Subsequently, the cyclic siloxanes were self‐condensed into cyclolinear polysiloxanes and cocondensed (extended) with silanol‐terminated polydimethylsiloxane into high‐molecular‐weight polymers containing cyclic units withlinearpolydimethylsiloxane spacers (extended cyclolinear polysiloxanes). The molecular weights of both the cyclolinear polysiloxanes and extended cyclolinear polysiloxanes were determined. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 4039‒4052, 2006
Quantum Positioning System (2004)

A quantum positioning system (QPS) is proposed that can provide a user with all four of his space-time coordinates. The user must carry a corner cube reflector, a good clock, and have a two-way classical channel of communication with the origin of the reference frame. Four pairs of entangled photons (biphotons) are sent through four interferometers: three interferometers are used to determine the user's spatial position, and an additional interferometer is used to synchronize the user's clock to coordinate time in the reference frame. The spatial positioning part of the QPS is similar to a classical time-of-arrival (TOA) system; however, a classical TOA system (such as GPS) must have synchronized clocks that keep coordinate time and, therefore, the clocks must have long-term stability, whereas in the QPS only a photon coincidence counter is needed and the clocks need only have short-term stability. Several scenarios are considered for a QPS: one is a terrestrial system and another is a space-based system composed of low-Earth orbit (LEO) satellites. Calculations indicate that for a space-based system, neglecting atmospheric effects, a position accuracy below the 1 cm level is possible for much of the region near the Earth. The QPS may be used as a primary system to define a global four-dimensional reference frame.
ChemInform Abstract: SYNTHESIS AND ANTIBACTERIAL ACTIVITY OF 1‐HYDROXY‐1‐METHYL‐1,3‐DIHYDROFURO(3,4‐B)QUINOXALINE 4,9‐DIOXIDE AND RELATED COMPOUNDS (1980)

Abstract Auf den im Formelschema beschriebenen Wegen wird das Halbacetal (III) dargestellt.
Using Applications of Data Versioning in Database Application Development (2004)

Database applications such as enterprise resource planning systems and customer relationship management systems are widely used software systems. Development and testing of database applications is difficult because the program execution depends on the persistent state stored in the database. In this paper we show that how versioning of the persistent data stored in the database can solve some critical problems in the development and testing of database applications can be solved by versioning the data stored in the database. Our solution framework is based on long transaction management, a well-researched branch of database systems. We also present empirical experimental results that show the proposed framework's effectiveness in practice.
Enabling Dynamic Analysis of Project Plan through Transformations into Business Processes (2011)

After winning a request for proposals and closing a deal, a business transformation services project is transitioned to the delivery team so that the delivery work can start. In an effort to minimize the delivery costs and schedules, companies are standardizing the way projects are defined and delivered. Unfortunately, it is very difficult to verify whether these standard best-practices will be successful before using them during real engagements. Project managers use tools such as Microsoft Project to build their project plans, schedules, baselines, and resources, these tools provide a rich set of functions for static analysis of project plans (e.g., discover critical path, resource contention), but little support for running dynamic "what-if" scenarios. This paper proposes two methods of enabling dynamic analysis of project plans by transforming a project plan into a business process, these business processes can be loaded and simulated into tools that support the Business Process Model and Notation (BPMN). For the purpose of this study, IBM Websphere Business Modeler (WBM) was used for running simulations. The evaluation highlights the complexity of these transformations and shows that automated tools are indeed necessary to assist people in their analysis.
Preceramic Paper‐Derived Ceramics (2008)

A novel class of preceramic paper may serve as a preform to manufacture lightweight as well as multilayer ceramic products. In this article, we discuss the formation, microstructure, and properties of preceramic papers and their conversion into ceramic materials. Oxide as well nonoxide ceramics were processed into single‐sheet, corrugated structures, and multilayer ceramics. A high filler loading and uniform distribution of ceramic fillers involves control of colloidal surface interaction including electrostatic, electrosteric, and mechanical retention. Sintering of an oxide‐loaded preceramic paper in air results in highly porous products, with the porosity shape and distribution templated by the pulp fiber used in papermaking. In the case of carbide‐loaded paper, dense composite materials are obtained by reactive infiltration processing. Anisotropic properties of machine‐fabricated preceramic paper and bonding interfaces in multilayer stacks give rise to anisotropic mechanical properties of the resulting ceramic composites. Noncatastrophic failure was observed when tensile loading stress was applied parallel to the interfaces (in‐plane loading). Applying well‐established paper processing technologies, including laminated object manufacturing, ceramic structures of complex shape and size can easily be processed, offering a high potential for economical manufacturing.
Small-Molecule Inhibitors Targeting Topoisomerase I as Novel Antituberculosis Agents (2016)

Bacterial topoisomerase functions are required for regulation of DNA supercoiling and overcoming the DNA topological barriers that are encountered during many vital cellular processes. DNA gyrase and topoisomerase IV of the type IIA bacterial topoisomerase family are important clinical targets for antibacterial therapy. Topoisomerase I, belonging to the type IA topoisomerase family, has recently been validated as a potential antitubercular target. The topoisomerase I activity has been shown to be essential for bacterial viability and infection in a murine model of tuberculosis. Mixture-based combinatorial libraries were screened in this study to identify novel bacterial topoisomerase I inhibitors. Using positional-scanning deconvolution, selective small-molecule inhibitors of bacterial topoisomerase I were identified starting from a polyamine scaffold. Antibacterial assays demonstrated that four of these small-molecule inhibitors of bacterial topoisomerase I are bactericidal against Mycobacterium smegmatis and Mycobacterium tuberculosis The MICs for growth inhibition of M. smegmatis increased with overexpression of recombinant M. tuberculosis topoisomerase I, consistent with inhibition of intracellular topoisomerase I activity being involved in the antimycobacterial mode of action.
Imaging interferometric microscopy (2008)

Imaging interferometric microscopy (IIM) is a synthetic aperture imaging approach providing resolution to the transmission medium (refractive index n) linear systems limit extending to greater, similarlambda/4n using only low-numerical-aperture (low-NA) optics. IIM uses off-axis illumination to access high spatial frequencies along with interferometric reintroduction of a zero-order reference beam on the low-NA side of the optical system. For a thin object normal to the optical axis, the frequency space limit is [(1+NA)n/lambda], while tilting the object plane allows collection of diffraction information up to the material transmission bandpass-limited spatial frequency of 2n/lambda. Tilting transforms the spatial frequencies; the algorithm to reset to the correct image frequencies is described. IIM involves combining multiple subimages; the image reconstruction procedures are discussed. A mean-square-error metric is introduced. For binary objects, sigmoidal filtering of the image provides significant resolution improvement.
Full-frame programmable spectral filters based on micro-mirror arrays (2013)

Rapidly programmable micro-mirror arrays, such as the DLP® digital micro-mirror device (DMD), have opened an exciting new arena in spectral imaging: rapidly reprogrammable, high spectral resolution, multi-band spectral filters that perform spectral processing directly in the optical hardware. Such a device is created by placing a DMD at the spectral plane of an imaging spectrometer, and using it as a spectral selector that passes some wavelengths down the optical train to the final image and rejects others. While simple in concept, realizing a truly practical DMD-based spectral filter has proved challenging. Versions described to date have been limited by the intertwining of image position and spectral propagation direction common to most imaging spectrometers, reducing these instruments to line-by-line scanning imagers rather than true spectral cameras that collect entire two-dimensional images at once. Here we report several optical innovations that overcome this limitation and allow us to construct full-frame programmable filters that spectrally manipulate every pixel, simultaneously and without spectral shifts, across a full 2D image. So far, our prototype, which can be programmed either as a matched-filter imager for specific target materials or as a fully hyperspectral multiplexing Hadamard transform imager, has demonstrated over 100 programmable spectral bands while maintaining good spatial image quality. We discuss how diffraction-mediated trades between spatial and spectral resolution determine achievable performance. Finally, we describe methods for dealing with the DLP’s 2D diffractive effects, and suggest a simple modification to the DLP that would eliminate their impact for this application.
Diacerein 1% Ointment for the Treatment of Epidermolysis Bullosa Simplex: A Randomized, Controlled Trial (2023)

Although there was no significant difference in outcomes between the groups, further study may elucidate the effects of diacerein on EBS lesions, especially in patients with severe EBS. Teng J, Paller AS, Bruckner AL, et al. Diacerein 1% ointment for the treatment of epidermolysis bullosa simplex: a randomized, controlled trial. J Drugs Dermatol. 2023;22(6):599-604. doi:10.36849/JDD.7108.
Planar optofluidic chip for single particle detection, manipulation, and analysis (2007)

We present a fully planar integrated optofluidic platform that permits single particle detection, manipulation and analysis on a chip. Liquid-core optical waveguides guide both light and fluids in the same volume. They are integrated with fluidic reservoirs and solid-core optical waveguides to define sub-picoliter excitation volumes and collect the optical signal, resulting in fully planar beam geometries. Single fluorescently labeled liposomes are used to demonstrate the capabilities of the optofluidic chip. Liposome motion is controlled electrically, and fluorescence correlation spectroscopy (FCS) is used to determine concentration and dynamic properties such as diffusion coefficient and velocity. This demonstration of fully planar particle analysis on a semiconductor chip may lead to a new class of planar optofluidics-based instruments.
A prostate stem cell antigen‐derived peptide immunogenic in HLA‐A24<sup>−</sup> prostate cancer patients (2004)

The PSCA 76-84 peptide should be considered for use in clinical trials of immunotherapy for HLA-A24+ patients.
Molecular cloning approach for a putative ethylene receptor gene in <i>Arabidopsis</i> (1992)

The plant hormone ethylene is an endogenous regulator of growth and development in higher plants. This gaseous compound influences a diverse and complex range of responses during many phases of plant development and in most parts of the plant. Responses mediated by ethylene include breaking of seed dormancy, seedling growth, flower initiation, leaf abscission, senescence and fruit ripening. Ethylene biosynthesis is induced by environmental stresses such as oxygen deficiency, wounding, pathogen invasion and flooding. These stresses may result in ethylene-mediated acceleration of senescence, abscission of infected organs or induction of specific plant defence proteins.
Identification and characterization of <i>Sulfolobus solfataricus</i> <scp>D</scp>-gluconate dehydratase: a key enzyme in the non-phosphorylated Entner–Doudoroff pathway (2005)

The extremely thermoacidophilic archaeon Sulfolobus solfataricus utilizes D-glucose as a sole carbon and energy source through the non-phosphorylated Entner-Doudoroff pathway. It has been suggested that this micro-organism metabolizes D-gluconate, the oxidized form of D-glucose, to pyruvate and D-glyceraldehyde by using two unique enzymes, D-gluconate dehydratase and 2-keto-3-deoxy-D-gluconate aldolase. In the present study, we report the purification and characterization of D-gluconate dehydratase from S. solfataricus, which catalyses the conversion of D-gluconate into 2-keto-3-deoxy-D-gluconate. D-Gluconate dehydratase was purified 400-fold from extracts of S. solfataricus by ammonium sulphate fractionation and chromatography on DEAE-Sepharose, Q-Sepharose, phenyl-Sepharose and Mono Q. The native protein showed a molecular mass of 350 kDa by gel filtration, whereas SDS/PAGE analysis provided a molecular mass of 44 kDa, indicating that D-gluconate dehydratase is an octameric protein. The enzyme showed maximal activity at temperatures between 80 and 90 degrees C and pH values between 6.5 and 7.5, and a half-life of 40 min at 100 degrees C. Bivalent metal ions such as Co2+, Mg2+, Mn2+ and Ni2+ activated, whereas EDTA inhibited the enzyme. A metal analysis of the purified protein revealed the presence of one Co2+ ion per enzyme monomer. Of the 22 aldonic acids tested, only D-gluconate served as a substrate, with K(m)=0.45 mM and V(max)=0.15 unit/mg of enzyme. From N-terminal sequences of the purified enzyme, it was found that the gene product of SSO3198 in the S. solfataricus genome database corresponded to D-gluconate dehydratase (gnaD). We also found that the D-gluconate dehydratase of S. solfataricus is a phosphoprotein and that its catalytic activity is regulated by a phosphorylation-dephosphorylation mechanism. This is the first report on biochemical and genetic characterization of D-gluconate dehydratase involved in the non-phosphorylated Entner-Doudoroff pathway.
Detection of Pseudorabies Virus Infection in Subunit-Vaccinated and Nonvaccinated Pigs using a Nucleocapsid-Based Enzyme-Linked Immunosorbent Assay (1992)

The potential of a pseudorabies virus (PRV) nucleocapsid protein (NC)-based enzyme-linked immunosorbent assay (ELISA) as a screening assay for PRV infection in subunit-vaccinated and nonvaccinated pigs was studied. The NC-ELISA compared favorably to a commercial ELISA for detecting PRV infection in nonvaccinated pigs. Virus-specific antibody was first detected by the NC-ELISA between days 14 and 21 in 5 pigs challenged intranasally with 10(4) PFU of virus. Antibody continued to be detected in these pigs through day 42, when the experiment was terminated. The NC-ELISA also detected antibody in 23 of 24 pigs from PRV-infected herds. In contrast, the commercial ELISA detected antibody 1 week earlier than the NC-ELISA in experimentally infected pigs but failed to detect antibody in 3 naturally exposed pigs that were identified by the NC-ELISA. Infection in these animals was confirmed by radioimmunoprecipitation analysis. The potential usefulness of the NC-ELISA for detecting infection in vaccinated pigs was also evaluated. The nucleocapsid-specific antibody responses of 10 PRV envelope glycoprotein subunit-vaccinated pigs were monitored prior to and following nasal exposure to a low dose (10(2.3) PFU) of PRV. Sera were collected periodically for 113 days after infection. Nucleocapsid-specific antibody responses measured by the NC-ELISA remained below the positive threshold before challenge but increased dramatically following virus exposure. Maximum ELISA responses were obtained on day 32 postchallenge (p.c.). Mean ELISA responses decreased thereafter but remained well above the positive threshold on day 113 p.c. PRV nucleocapsid protein can be used effectively as antigen in the ELISA for detecting PRV infection in both nonvaccinated and subunit-vaccinated pigs.
Fiber spinning for reducing polarization mode dispersion in single-mode fibers: theory and applications (2003)

This paper surveys recent progress in fiber spinning technology for reducing polarization mode dispersion with the focus on theoretical understanding of fiber spinning mechanism and features of spun fibers, as well as their applications in fiber spin profiles designs. First, a brief introduction to the requirements of fiber PMD for high-speed optical fiber communications systems is given. Further discussion covers several spin technologies, including preform spinning and fiber spinning. Different theoretical approaches for modeling fiber spinning are reviewed with the emphasis on the coupled-mode formalism. The coupled-mode theory is then applied to different fiber spin profile designs, including constant, sinusoidal and frequency and amplitude modulated spin profiles. Main features of these spin profiles, such as PMD reduction dependence on fiber beatlength and sensitivity to spin parameters, are compared. Scaling properties of spun fibers, which show different behaviors from unspun fibers, are also discussed.
Multiple Degree-of-Freedom Control of a Flapping-Wing Micro Air Vehicle with Power and Control Actuators (2010)

Flapping wing micro air vehicles have received a great deal of interest from the research community due to their potential to achieve insect-like maneuverability. The ability to mimic the flight behavior of insects could enable such a vehicle to perform missions which larger, fixed wing vehicles are unable to perform, such as intelligence, surveillance, and reconnaissance in urban environments and confined locations. The Harvard Microrobotics Lab developed the world’s first robotic insect capable of vertical takeoff. This vehicle used a single piezoelectric actuator to drive the motion of both wings symmetrically in order to generate average lift which exceeded the vehicle’s weight. There was no mechanism to produce body torques or forces in the horizontal or lateral directions. Upon extending this work, the Harvard Microrobotics Lab has modified this configuration to include not only a single power actuator, but also control actuators for each wing, with the goal of generating body torques. The power actuator provides the mechanical power for flapping, while the control actuators cause a small displacement of the wing root which changes the wing kinematics, such that pitch and yaw torques can be generated. This work utilizes the power
Fabry-Perot Cavity antenna system with beam-splitting of near-field radiation (2016)

This paper describes the design and behavior of a Fabry-Perot Cavity (FPC) antenna system with split beam in the near-field and decreased beamwidth of the far-field pattern. The FPC antenna system is a coplanar waveguide (CPW)-fed slot antenna with 9 × 27 rectangular aperture unit cells in the frequency selective surface (FSS) oriented in horizontal and vertical directions. The far-field response has 3dB beamwidth of 21° and gain of 12.84 dBi at 11.2 GHz.