gebhart/patrepeval huggingface dataset:
Efficient integration of artificial transposons into plasmid targets<i>in vitro</i>: a useful tool for DNA mapping, sequencing and genetic analysis (1994)

We have developed efficient methods for creating artificial transposons and inserting these transposons into plasmid targets in vitro, primarily for the purpose of DNA mapping and sequencing. A novel plasmid has been engineered to convert virtually any DNA sequence, or combination of sequences, into an artificial transposon; hence, custom transposons containing any desired feature can be easily designed and constructed. Such transposons are then efficiently inserted into plasmid targets, in vitro, using the integrase activity present in yeast Ty1 virus-like particles. A single in vitro integration reaction, which resembles a simple restriction digestion in the complexity of the reaction, gives rise to thousands of recoverable insertion events within DNA target molecules; this frequency approaches one insertion per phosphodiester bond in typical plasmids. Importantly, transposon insertions are recovered from all regions of DNA inserts carried on plasmid targets, indicating that integration is a random or nearly-random process. Because of its versatility, this technology offers a generalized method of generating recombinant DNA molecules of a desired structure. We have adapted this system for DNA sequencing by developing a customized artificial transposon to insert new primer binding sites into internal regions of DNA inserts carried on cloning vectors. Transposon insertions have been generated throughout several different yeast and human DNA inserts carried on plasmids, allowing the efficient recovery of sequence information from these inserts. Our results demonstrate the overall utility of this method for both small and large-scale DNA sequencing, as well as general DNA restructuring, and indicate that it could be adapted for use with a number of additional applications including functional genetic analysis.
Properties of High-Performance Fly Ash Concrete (1996)

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The Hotbox (1999)

The proliferation of multiple toolbars and UI widgets around the perimeter of application windows is an indication that the traditional GUI design of a single menubar is not sufficient to support large scale applications with numerous functions. In this paper we describe a new widget which is an enhancement of the traditional menubar which dramatically increases menu-item capacity. This widget, called the Hotbox combines several GUI techniques which are generally used independently: accelerator keys, modal dialogs, pop-up/pull down menus, radial menus, marking menus and menubars. These techniques are fitted together to create a single, easy to learn yet fast to operate GUI widget which can handle significantly more menu-items than the traditional GUI menubar. We describe the design rationale of the Hotbox and its effectiveness in a large scale commercial application. While the Hotbox was developed for a particular application domain, the widget itself and the design rationale are potentially useful in other domains.
Invited Article: Real-time sensing of flowing nanoparticles with electro-opto-mechanics (2016)

High-Q optical resonators allow label-free detection of individual nanoparticles through perturbation of optical signatures but have practical limitations due to reliance on random diffusion to deliver particles to the sensing region. We have recently developed microfluidic optomechanical resonators that allow detection of free-flowing particles in fluid media with near perfect detection efficiency, without requiring labeling, binding, or direct access to the optical mode. Rapid detection of single particles is achieved through a long-range optomechanical interaction in which modification of the resonator vibrational modes during particle transits influences the scattered light spectra from the resonator. Here, we present a hybrid electro-opto-mechanical technique for substantially increasing the bandwidth of these opto-mechano-fluidic sensors, enabling real-time operation. The demonstrated improvements are obtained through high bandwidth lock-in measurement of the optical modulation that is induced by actuating the vibrational mode electrostatically at a fixed frequency. The presented system demonstrates temporal resolution of better than 20 μs (50 000 events/s) with particle sensing resolution (i.e., the particle size noise floor) down to 490 nm, operating in the air without any stabilization or environmental control. Our technique significantly enhances the sensing capabilities of high-Q optical resonators into the mechanics domain and allows extremely high-throughput analysis of large nanoparticle populations.
A Probabilistic Approach for Detection and Removal of Rain from Videos (2011)

AbstractA novel, efficient, simple, and probabilistic model based rain removal algorithm is proposed in this paper. Proposed algorithm is robust to the rain intensity variations. Probabilistic approach automatically adjust the threshold and effectively discriminate the rain pixels and non-rain moving object pixels. Discrimination between the rain and non-rain moving objects is based on the time evolution of pixels in consecutive frames. Proposed algorithm does not assume the shape, size and velocity of the raindrops and intensity of rain, which makes it robust to different rain conditions. For performance evaluation, in addition to miss and false detection a new metric temporal variance is introduced. Results show that proposed algorithm outperforms the other rain removal algorithms. Instead of working on all three color components, proposed algorithm works only on the intensity plane. Use of single plane reduces the complexity and execution time of the algorithm.
Abstract 5376: Systematic analysis of peptide linker length and liposomal polyethylene glycol coating on cellular uptake of peptide-targeted liposomal nanoparticles (2014)

Abstract In an effort to improve tumor targeting and cellular uptake of nanoparticle-based drug carriers, nanoparticles are functionalized with active targeting molecules such as antibodies, antibody fragments, small ligands, and peptides. However, active targeting approaches have not consistently shown successful outcomes. Nanoparticle design factors including: traditional methods of generating active targeting nanoparticles, PEG coatings, linkers used to conjugate targeting ligands, and various types of targeting ligands used further contribute to the inconsistencies observed with targeted nanoparticle therapies. In order to dissect the individual effects of these parameters, we employed a multifaceted synthetic strategy to prepare peptide-targeted liposomal nanoparticles with high purity, reproducibility, and precisely controlled stoichiometry of functionalities to evaluate the role of liposomal PEG coating, peptide EG-linker length, and peptide valency on cellular uptake in a systematic manner. We analyzed these parameters in two distinct disease models where the liposomes were functionalized with either HER2- or VLA-4-antagonistic peptides to target HER2-overexpressing breast cancer cells or VLA-4-overexpressing myeloma cells, respectively. When targeting peptides were tethered to nanoparticles with an EG45 (∼PEG2000) linker in a manner similar to a more traditional formulation, their cellular uptake was not enhanced compared to non-targeted versions regardless of the liposomal PEG coating used. Conversely, reduction of the liposomal PEG to PEG350 and the peptide linker to EG12 dramatically enhanced cellular uptake by ∼9-fold in breast cancer cells, while an EG6 peptide linker enhanced cellular uptake by ∼150-fold in multiple myeloma cells. Uptake efficiency is highly dependent on peptide valency, reaching a maximum and a plateau with ∼2% peptide density in the breast cancer model. Taken together, these results demonstrate the significance of using the right design elements such as the appropriate peptide EG-linker length in coordination with the appropriate liposomal PEG coating and optimal ligand density in efficient cellular uptake of liposomal nanoparticles. Citation Format: Jared Stefanick, Jonathan Ashley, Tanyel Kiziltepe, Basar Bilgicer. Systematic analysis of peptide linker length and liposomal polyethylene glycol coating on cellular uptake of peptide-targeted liposomal nanoparticles. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5376. doi:10.1158/1538-7445.AM2014-5376
The integrated swiss miniature atomic clock (2013)

The detailed design of the Swiss Miniature Atomic Clock (Swiss-MAC) was presented by CSEM in 2012. This paper describes the progress made in the meantime towards the realization of the integrated Swiss-MAC, by presenting a first prototype showing preliminary but very promising performances.
Novel method for communications using orthogonal division duplexing of signals (ODD) (2003)

As mobile radio systems expand their role in global communications, there is a need for both increased efficiency and an ability to operate in a variety of arbitrary unpaired spectrum assignments. While traditional mobile systems are mostly operated with separated transmit and receive spectrum assignments, these assignments are becoming more difficult to find for new systems among the crowded radio spectrum. Developing a radio system that is suitable for an unpaired spectrum assignment and that can also provide rapid availability of channel information for adaptive transmissions is thus a significant goal. The paper introduces a novel concept, which we refer to as orthogonal division duplexing (ODD), to address these issues. The ODD technique interleaves multiple orthogonal carriers in the same band for transmission and reception. These orthogonal carriers are produced using techniques similar to those used for OFDM. Using the same channel for both transmission and reception enables the channel conditions to be rapidly and accurately estimated by each transceiver, eliminating the delays or errors associated with traditional channel reporting techniques. The ODD transmission system is particularly well suited to multimedia high-speed mobile communications and may be designed to be adaptable to asymmetric traffic flows.
Correlation and classification of single kernel fluorescence hyperspectral data with aflatoxin concentration in corn kernels inoculated with<i>Aspergillus flavus</i>spores (2010)

The objective of this study was to examine the relationship between fluorescence emissions of corn kernels inoculated with Aspergillus flavus and aflatoxin contamination levels within the kernels. Aflatoxin contamination in corn has been a long-standing problem plaguing the grain industry with potentially devastating consequences to corn growers. In this study, aflatoxin-contaminated corn kernels were produced through artificial inoculation of corn ears in the field with toxigenic A. flavus spores. The kernel fluorescence emission data were taken with a fluorescence hyperspectral imaging system when corn kernels were excited with ultraviolet light. Raw fluorescence image data were preprocessed and regions of interest in each image were created for all kernels. The regions of interest were used to extract spectral signatures and statistical information. The aflatoxin contamination level of single corn kernels was then chemically measured using affinity column chromatography. A fluorescence peak shift phenomenon was noted among different groups of kernels with different aflatoxin contamination levels. The fluorescence peak shift was found to move more toward the longer wavelength in the blue region for the highly contaminated kernels and toward the shorter wavelengths for the clean kernels. Highly contaminated kernels were also found to have a lower fluorescence peak magnitude compared with the less contaminated kernels. It was also noted that a general negative correlation exists between measured aflatoxin and the fluorescence image bands in the blue and green regions. The correlation coefficients of determination, r(2), was 0.72 for the multiple linear regression model. The multivariate analysis of variance found that the fluorescence means of four aflatoxin groups, <1, 1-20, 20-100, and >or=100 ng g(-1) (parts per billion), were significantly different from each other at the 0.01 level of alpha. Classification accuracy under a two-class schema ranged from 0.84 to 0.91 when a threshold of either 20 or 100 ng g(-1) was used. Overall, the results indicate that fluorescence hyperspectral imaging may be applicable in estimating aflatoxin content in individual corn kernels.
Evaluation of a Transparent Wall System for Residential Construction (2014)

A new type of transparent panelized wall system for residential construction has recently been developed that can be used as an alternative to typical wood-frame and other light-frame wall systems. The new wall system is a prefabricated wall panel consisting of a structural steel back-up frame, transparent polycarbonate sheathing, and a curtain-wall system that may contain an integrated photovoltaic glazing panel. In this paper, after an introduction to the structural and architectural aspects of system, the thermal and energy performance aspects of this wall system are evaluated based on several criteria. The current configuration of the wall system shows an overall U-factor of 1.585 W/m 2 k. The material and systems analysis using a combination of life-cycle assessment and embodied energy are discussed as well. The embodied energy of the system turns out to be approximately two and a half times that of conventional wood-frame system. The paper provides some concluding remarks regarding the sustainability aspects.
Heterogeneous Catalyzed Chemoselective Reductive Amination of Halogenated Aromatic Aldehydes (2021)

Abstract The chemoselective conversion of a specific functional group in a multifunctional substrate is of great importance in the chemical industry to obtain cost efficient, sustainable and waste free processes. This work focuses on the chemoselective amination of halogenated aromatic aldehydes with dimethyl amine towards halogenated aromatic amines, a raw material used in the production of for example agrochemical active ingredients. It was found that by combining palladium, a metal known for dehalogenation reactions, and copper, known for its direct hydrogenation of aldehydes to alcohols, in one heterogeneous bimetallic catalyst, a synergistic effect is obtained. By depositing copper onto a palladium on carbon catalyst with a Cu/Pd ratio of at least 1 : 1, the yield could be increased from 66 % (Pd/C) to 98 % (PdCu/C). Moreover, this highly active and stable catalyst also showed suppressed dehalogenation side‐reactions in several other chemical conversions such as hydrogenation of nitro functional groups and hydrogenation of aldehydes.
Ganglion Dynamics and Its Implications to Geologic Carbon Dioxide Storage (2012)

Capillary trapping of a nonwetting fluid phase in the subsurface has been considered as an important mechanism for geologic storage of carbon dioxide (CO(2)). This mechanism can potentially relax stringent requirements for the integrity of cap rocks for CO(2) storage and therefore can significantly enhance storage capacity and security. We here apply ganglion dynamics to understand the capillary trapping of supercritical CO(2) (scCO(2)) under relevant reservoir conditions. We show that, by breaking the injected scCO(2) into small disconnected ganglia, the efficiency of capillary trapping can be greatly enhanced, because the mobility of a ganglion is inversely dependent on its size. Supercritical CO(2) ganglia can be engineered by promoting CO(2)-water interface instability during immiscible displacement, and their size distribution can be controlled by injection mode (e.g., water-alternating-gas) and rate. We also show that a large mobile ganglion can potentially break into smaller ganglia due to CO(2)-brine interface instability during buoyant rise, thus becoming less mobile. The mobility of scCO(2) in the subsurface is therefore self-limited. Vertical structural heterogeneity within a reservoir can inhibit the buoyant rise of scCO(2) ganglia. The dynamics of scCO(2) ganglia described here provides a new perspective for the security and monitoring of subsurface CO(2) storage.
THF co-solvent enhances hydrocarbon fuel precursor yields from lignocellulosic biomass (2013)

A novel single phase co-solvent system using tetrahydrofuran (THF) promotes hydrolysis of maple wood to sugars, sugar dehydration, and lignin extraction simultaneously and achieves higher overall yields of the fuel precursors furfural, 5-hydroxymethylfurfural (HMF), and levulinic acid (LA) than previously reported from biomass. In a one-pot reaction, we obtained yields of 86% furfural, 21% HMF, and 40% LA in the liquid phase and over 90% extraction of lignin as a solid powder. The co-solvent reaction also produced a glucan-rich residue that is highly digestible by enzymes for biological conversion to ethanol or further thermochemical reaction to additional HMF and levulinic acid. These findings enable an integrated conversion platform in which THF is both a co-solvent and final co-product to enhance production of fuel precursors for catalytic upgrading to renewable liquid hydrocarbons fuels.
An exploratory study of area-efficient vortex flap concepts (1983)

The potential of planform modification and hinge-line relocation to improve the thrust efficiency of vortex flaps was experimentally investigated on a 60-deg cropped delta wing model. Spanwise segmentation of the flap, together with chord-tailoring of the segments, allowed the vortex to be maintained on the outboard flap surfaces to higher angles of attack. In addition, location of the flap hinge aft of and underneath the wing leading edge generated substantial thrust from the vortex suction acting on the leading-edge lower surface. A combination of these beneficial effects allowed the flap/wing area to be reduced from 11.4 percent of the continuous flap to 6.3 percent of segmented flap, essentially without detriment to the incremental lift-to-drag ratio due to flap addition in the lift coefficient range 0.5-0.7 based on the basic wing area.
Innovation for forming aluminum alloy thin shells at ultra-low temperature by the dual enhancement effect (2022)

Abstract Integral thin shells made of high strength aluminum alloys are urgently needed in new generation transportation equipment. There are challenges to overcoming the co-existing problems of wrinkling and splitting by the cold forming and hot forming processes. An innovative technology of ultra-low temperature forming has been invented for aluminum alloy thin shells by the new phenomenon of ‘dual enhancement effect’. That means plasticity and hardening are enhanced simultaneously at ultra-low temperatures. In this perspective, the dual enhancement effect is described, and the development, current state and prospects of this new forming method are introduced. This innovative method can provide a new approach for integral aluminum alloy components with large size, ultra-thin thickness, and high strength. An integral tank dome of rocket with 2 m in diameter was formed by using a blank sheet with the same thickness as the final component, breaking through the limit value of thickness-diameter ratio.
Engineering resistance against <i>Tomato yellow leaf curl virus</i> via the CRISPR/Cas9 system in tomato (2017)

Abstract CRISPR/Cas systems confer molecular immunity against phages and conjugative plasmids in prokaryotes. Recently, CRISPR/Cas9 systems have been used to confer interference against eukaryotic viruses. Here, we engineered Nicotiana benthamiana and tomato (Solanum lycopersicum) plants with the CRISPR/Cas9 system to confer immunity against the Tomato yellow leaf curl virus (TYLCV). Targeting the TYLCV genome with Cas9-single guide RNA at the sequences encoding the coat protein (CP) or replicase (Rep) resulted in efficient virus interference, as evidenced by low accumulation of the TYLCV DNA genome in the transgenic plants. The CRISPR/Cas9-based immunity remained active across multiple generations in the N. benthamiana and tomato plants. Together, our results confirmed the efficiency of the CRISPR/Cas9 system for stable engineering of TYLCV resistance in N. benthamiana and tomato, and opens the possibilities of engineering virus resistance against single and multiple infectious viruses in other crops.
Convective clouds modelling and tracking by an airborne radar (2008)

A method for modelling and tracking convective clouds within radar images is described. Clouds are non-rigid heterogeneous objects; a good representation of the weather scene is performed by extracting skeletal lines of the 2-dimensional grayscale pictures. Skeletons are reduced to sets of segments within a graph structure and tracked among successive pictures by means of relaxation labelling processes. We present preliminary results of our method on airborne weather radar data. The conventional morphological skeleton constraint -i.e., to be centered in relation to the object boundaries- is here replaced by attachment to the gray levels local maxima. The resulting skeletal line is forced to go through each intense convective cell, and links neighboring ones into a global structure. Moreover, each feature point can be labelled and enriched by meteorological information. Such pattern is particularly suitable for weather nowcasting, since the user (for example, an aircraft's crew) is specially interested in the convective cells evolution.
Non-contact micromanipulation using an ultrasonic standing wave field (2002)

Transportation of particles using acoustic radiation pressure in water is studied to develop non-contact micromanipulation technique. The radiation pressure traps particles suspended in water to form agglomeration every half wavelength in a standing wave field. Using two sets of standing wave fields crossing to each other, the shape of agglomeration was varied. Applying focused acoustic radiation pressure of traveling wave, a limited part of trapped particles was transported for long distance. Using a concave transducer to generate a standing wave, trapped particles were transported stably along the sound beam axis by changing the ultrasonic frequency. The resolution of transportation to the order of submicron is possible to achieve. Furthermore, the column of trapped particles was separated and transported oppositely by using an appropriate value of frequency increment. Although intense ultrasound generates acoustic streaming, it was possible to avoid its influence using a burst wave.
46‐4: <i>Distinguished Student Paper</i>: Perspective Correct Occlusion‐Capable Augmented Reality Displays using Cloaking Optics Constraints (2017)

Perspective‐correct occlusion‐capable augmented reality displays are generalized using an optical cloak constraint for ray transfer analysis or simulations; any ray entering the optical system exits at the height and angle as if it passed through empty space. We analyze several systems with two‐, three‐, and four‐lens groups in inline, folded, and looped configurations. We design and demonstrate a four‐lens folded optical cloak and a three‐lens inverted cloak with an erecting prism.