gebhart/patrepeval huggingface dataset:
High-Resolution Polyacrylamide Gel Electrophoresis of Oligonucleotides Using L-Histidine Buffer (1988)

We have found that 50 mM L-histidine pH 7.6 as a buffer for gel electrophoresis greatly improves the resolution of oligonucleotides less than 70 residues long on denaturing polyacrylamide gels. The histidine buffer increases spacing between DNA bands on the gel about twofold in comparison with a standard buffer (89 mM Tris-borate, 2 mM EDTA pH 8.3). In addition, low conductivity of the histidine buffer results in a threefold reduction of the electrophoresis time. Conditions for electrophoresis were optimized by varying both histidine and acrylamide concentrations. Other polycationic compounds, such as spermidine and ethylenediamine, were also tested for improved resolution of oligonucleotides. Several hypotheses as to the factors influencing the separation of DNA on gels are presented.
Low attenuation mode converter with modal power distribution controllability by twist processing in step-index optical fibers (2017)

We proposed a short-fiber-length mode scrambler that reproduces the equilibrium mode distribution of an A3e fiber. The mode scrambler is compact, mode-controllable and has low attenuation. It is effective for not only hard plastic-clad fiber but also all step-index fibers, such as all-glass and plastic optical fibers.
Liquid Deposition Photolithography for Photonic Device Fabrication (2013)

We describe a novel fabrication method, liquid deposition photolithography (LDP), for the creation of polymer photonic devices. We demonstrate LDPs ability to fabricate photonic devices by fabricating a waveguide array and gradient index lens.
Interferometer coordinate measurement system for use in measurement and machining tools has partially reflecting boundary surfaces within its measurement head with a separation shorter than the coherence length (2004)

The invention relates to an interferometer system (41), especially for use in a co-ordinate measuring system. Said interferometer system comprises, disposed in an illumination beam path, a pair of spaced-apart boundary surfaces (52, 53). A boundary surface (53) facing an object (9) is arranged in a detection beam path, a detector (61) being additionally disposed in said detection beam path. The invention also relates to an interferometer system, especially one of the above-described type, which is provided with a speed indicating system for detecting a relative speed between the test head and the object. A frequency filter of the interferometer system is adjusted depending on the relative speed.
The Reduction of Nitrile with 2-Propanol over Hydrous Zirconium Oxide (1990)

Abstract The vapor-phase reduction of nitriles with 2-propanol proceeded efficiently over hydrous zirconium oxide to give the corresponding alcohols in high yields.
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind (2016)

To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.
TSOtool (2004)

In this paper, we describe TSOtool, a program to check thebehavior of the memory subsystem in a shared memorymultiprocessor. TSOtool runs pseudo-randomly generatedprograms with data races on a system compliant with theTotal Store Order (TSO) memory consistency model; it thenchecks the results of the program against the formal TSOspecification. Such analysis can expose subtle memory errorslike data corruption, atomicity violation and illegalinstruction ordering.While verifying TSO compliance completely is an NP-completeproblem, we describe a new polynomial timealgorithm which is incorporated in TSOtool. In spite of beingincomplete, it has been successful in detecting several bugs inthe design of commercial microprocessors and systems,during both pre-silicon and post-silicon phases of validation.
Production of Recycled Plastic Aggregates and Its Utilization in Concrete (2016)

Plastic represents an environmental issue, as only 7% of it is recycled. The plastic remaining is either burned, disposed of in an uncontrolled manner, or landfilled. Thus, to reduce the quantity of plastic that is disposed of, there is a need to increase the amount of the material that enters various product streams. This includes its use in the construction industry, and more particularly in concrete, which uses large quantities of aggregate. A novel aggregate (RPA) comprising recycled plastic was developed. The aggregate produced was lightweight, with a density ranging from 510 to 750k kg/m3 and absorption of from 2.7 to 9.81%. Other properties were comparable to aggregates of similar densities. Various composition RPA was used in concrete, and the resulting properties of both fresh and cured concrete were measured. For a given water to cement (w/c) ratio, it was possible to achieve slump of between 40 and 220 mm and fresh density of between 1,827 and 2,055 kg/m3. Further, 28-day strengths of between 14 and 18 MPa were achieved. Flexural strength was also measured. SEM analysis was undertaken to view the structure of the aggregate and the interface between the RPA and the cement matrix.
Enhancement of AlGaN/GaN high-electron mobility transistor off-state drain breakdown voltage via backside proton irradiation (2015)

Proton irradiation from the backside of the samples were employed to enhance off-state drain breakdown voltage of AlGaN/GaN high electron mobility transistors (HEMTs) grown on Si substrates. Via holes were fabricated directly under the active area of the HEMTs by etching through the Si substrate for subsequent backside proton irradiation. By taking the advantage of the steep drop at the end of proton energy loss profile, the defects created by the proton irradiation from the backside of the sample could be precisely placed at specific locations inside the AlGaN/GaN HEMT structure. There were no degradation of drain current nor enhancement of off-state drain voltage breakdown voltage observed for the irradiated AlGaN/GaN HEMTs with the proton energy of 225 or 275 keV, for which the defects created by the proton irradiations were intentionally placed in the GaN buffer. HEMTs with defects placed in the 2 dimensional electron gas (2DEG) channel region and AlGaN barrier using 330 or 340 keV protons not only showed degradation of drain current, but also exhibited improvement of the off-state drain breakdown voltage. FLOODS TCAD finite-element simulations were performed to confirm the hypothesis of a virtual gate formed around the 2DEG region to reduce the peak electric field around the gate edges and increase the off-state drain breakdown voltage.
Overview of Nearfield Acoustical Holography Technologies (2004)

This paper describes how nearfield acoustical holography (NAH) allows for reconstructing acoustic quantities such as the acoustic pressure, intensity, and power radiated from a finite object into 3D space based on the acoustic pressures measured on 2D surface. Since NAH provides complete acoustic information cost effectively, it has drawn a great deal of attention in the diagnostics of noise and vibration sources. Three major NAH methods are reviewed and their advantages and disadvantages are compared. While planar NAH is easy to implement, its applications are limited to planar surfaces in a free field only. The Inverse Boundary Element Method (IBEM) is suitable for an arbitrary source surface, but it is difficult to implement due to its strict requirements and intensive computations. The Helmholtz Equation Least Squares (HELS) provides a compromise in reconstruction of acoustic radiation from an arbitrary object by providing an approximate solution using the fewest measurements. Moreover, it is easy to implement, offers great flexibility in measurements and reconstruction, and is very fast. As such, it enables one to obtain a satisfactory reconstruction in the most cost-effective manner.
Structured set partitions for high-order partial response channels (2003)

Multilevel modulation codes for partial response (PR) channels can be constructed using a structured set partition (SSP) of channel output words, and a set of block codes with different error correcting capabilities. We present SSP for the classical and modified E/sup 2/PR4 channels. The coding gain 3.5 dB can be achieved at the linear density 2.8 for ME/sup 2/PR channel with the target [5,4,-3,-4,-2] given by Sawaguchi et al. (see Proc. GLOBCOM-98, 1998).
MASH-Based Divider Controllers for Mitigation of Wandering Spurs in a Fractional-<i>N</i> Frequency Synthesizer (2020)

The divider controller can contribute significantly to the phase noise and spur pattern in the output of a nonlinear fractional-N frequency synthesizer. A type of time-varying spurs caused by a MASH DDSM divider controller, termed wandering spurs, has been observed in simulations and measurements of real synthesizers. In this work, we propose and analyze several MASH-based divider controller architectures that mitigate wandering spurs in a fractional-N frequency synthesizer.
Envelope modulated x-ray grating interferometry (2022)

X-ray dark-field and phase contrast imaging using grating interferometry (GI) have demonstrated great potential for medical and industrial applications. GI relies on the fabrication of high-quality absorption gratings, which has revealed to be quite challenging. This paper proposes an interferometer for dark-field and differential phase contrast imaging using a single phase-shifting element. This proposal simplifies the setup without penalizing the image quality. The proposed interferometer consists of a single dual-period phase grating having two distinct periods, which generates intensity modulation with a period large enough to be resolved directly by the detector. This makes the proposed GI system easily adaptable as there are no stringent alignment requirements. We show the utility of this method for a possible diagnostic task by imaging smoked murine lung samples. The simplicity of the proposed setup compared to a conventional Talbot(-Lau) interferometer suggests that it could be easily and widely used for a variety of applications.
Global Transposon Mutagenesis and a Minimal Mycoplasma Genome (1999)

Mycoplasma genitalium with 517 genes has the smallest gene complement of any independently replicating cell so far identified. Global transposon mutagenesis was used to identify nonessential genes in an effort to learn whether the naturally occurring gene complement is a true minimal genome under laboratory growth conditions. The positions of 2209 transposon insertions in the completely sequenced genomes of M. genitalium and its close relative M. pneumoniae were determined by sequencing across the junction of the transposon and the genomic DNA. These junctions defined 1354 distinct sites of insertion that were not lethal. The analysis suggests that 265 to 350 of the 480 protein-coding genes of M. genitalium are essential under laboratory growth conditions, including about 100 genes of unknown function.
Copper‐Catalyzed Enantioselective Markovnikov Protoboration of α‐Olefins Enabled by a Buttressed N‐Heterocyclic Carbene Ligand (2017)

Reported is a highly enantioselective copper-catalyzed Markovnikov protoboration of unactivated terminal alkenes. A variety of simple and abundant feedstock α-olefins bearing a diverse array of functional groups and heterocyclic substituents can be used as substrates, and the reaction proceeds under mild reaction conditions at ambient temperature to provide expedient access to enantioenriched alkylboronic esters in good regioselectivity and with excellent enantiocontrol. Critical to the success of the protocol was the development and application of a novel, sterically hindered N-heterocyclic carbene, (R,R,R,R)-ANIPE, as the ligand for copper.
AI-augmented time stretch microscopy (2017)

Cell reagents used in biomedical analysis often change behavior of the cells that they are attached to, inhibiting their native signaling. On the other hand, label-free cell analysis techniques have long been viewed as challenging either due to insufficient accuracy by limited features, or because of low throughput as a sacrifice of improved precision. We present a recently developed artificial-intelligence augmented microscope, which builds upon high-throughput time stretch quantitative phase imaging (TS-QPI) and deep learning to perform label-free cell classification with record high-accuracy. Our system captures quantitative optical phase and intensity images simultaneously by frequency multiplexing, extracts multiple biophysical features of the individual cells from these images fused, and feeds these features into a supervised machine learning model for classification. The enhanced performance of our system compared to other label-free assays is demonstrated by classification of white blood T-cells versus colon cancer cells and lipid accumulating algal strains for biofuel production, which is as much as five-fold reduction in inaccuracy. This system obtains the accuracy required in practical applications such as personalized drug development, while the cells remain intact and the throughput is not sacrificed. Here, we introduce a data acquisition scheme based on quadrature phase demodulation that enables interruptionless storage of TS-QPI cell images. Our proof of principle demonstration is capable of saving 40 TB of cell images in about four hours, i.e. pictures of every single cell in 10 mL of a sample.
Bile Salts and Glycine as Cogerminants for <i>Clostridium difficile</i> Spores (2008)

Spore formation by Clostridium difficile is a significant obstacle to overcoming hospital-acquired C. difficile-associated disease. Spores are resistant to heat, radiation, chemicals, and antibiotics, making a contaminated environment difficult to clean. To cause disease, however, spores must germinate and grow out as vegetative cells. The germination of C. difficile spores has not been examined in detail. In an effort to understand the germination of C. difficile spores, we characterized the response of C. difficile spores to bile. We found that cholate derivatives and the amino acid glycine act as cogerminants. Deoxycholate, a metabolite of cholate produced by the normal intestinal flora, also induced germination of C. difficile spores but prevented the growth of vegetative C. difficile. A model of resistance to C. difficile colonization mediated by the normal bacterial flora is proposed.
Study of Plunge Stage for a Hybrid Friction Stir Welding Process Based on Electro-Plastic Effect (2015)

In this study, an electrically assisted friction stir welding (FSW) system has been designed and developed. Additional electrodes are assembled and stay in the close proximity of the tool as the tool translates along the weldline. Plunge stage of FSW process has been studied for both aluminum alloy Al 6061 and TRIP 780 steel based on this developed experimental configuration. An effective axial force reduction can be consistently observed after application of a continuous current. In order to compare the relative significance of the associated resistance thermal effect, the workpiece has been preheated to approximately same temperature and it can be shown that around 2/3 of the force reduction can be contributed to the electricity itself. Microstructure of the cross sections for Al 6061 plunge specimens indicated an enhanced dynamic recrystallization process under the influence of current. This phenomenon was not obvious on steel, which is probably due to the higher Joule heating temperature and consequently accelerated grain growth. On the other hand, thermal mechanically affected zone of steel suggested a retarded martensitic phase transformation with electrical current applied.
Effects of Dietary Supplementation of Rumen-Protected Conjugated Linoleic Acid in Dairy Cows during Established Lactation (2002)

Short-term studies (< 5 d) involving abomasal infusion of a mixture of CLA isomers or pure trans-10, cis-12 CLA have demonstrated that supplements of conjugated linoleic acids (CLA) reduce milk fat synthesis during established lactation in dairy cows. Our objective was to assess longer term effects of supplementation during established lactation using a dietary supplement of rumen-protected CLA. Thirty Holstein cows were blocked by parity and received a dietary fat supplement of either Ca-salts of palm oil fatty acids (control) or a mixture of Ca-salts of palm oil fatty acids plus Ca-salts of CLA (CLA treatment). Supplements provided about 90 g/d of fatty acids and were topdressed on the TMR. The CLA supplement provided 30.4 g/d of CLA in which the predominant isomers were: trans-8, cis-10 (9.2%), cis-9, trans-11 (25.1%), trans-10, cis-12 (28.9%), and cis-11, trans-13 (16.1%). All cows were pregnant; treatments were initiated on d 79 of pregnancy (approximately 200 d prepartum) and continued for 140 d until dry off. Twenty-three cows completed the study; those receiving CLA supplement had a lower milk fat test (2.90 versus 3.80%) and a 23% reduction in milk fat yield (927 versus 1201 g/d). Intake of DM, milk yield, and the yield and content of true protein and lactose in milk were unaffected by treatment. Milk fat analysis indicated that the CLA supplement reduced the secretion of fatty acids of all chain lengths. However, effects were proportionally greater on short and medium chain fatty acids, thereby causing a shift in the milk fatty acid composition to a greater content of longer-chain fatty acids. Changes in body weight gain, body condition score, and net energy balance were not significant and imply no differences in cows fed the CLA supplement in replenishment of body reserves in late lactation. Likewise, maintenance of pregnancy, gestation length, and calf birth weight were unaffected by treatment. Overall, feeding a dietary supplement of rumen-protected CLA to pregnant cows over the last 140 d of the lactation cycle resulted in a marked reduction in milk fat content and yield, and a shift in milk fatty acid composition, but other milk components, DMI, maintenance of pregnancy, and cow well-being were unaffected.
Natural color reproduction system for telemedicine (2002)

The color information of a patient image is quite important in telemedicine systems, but is not correctly reproduced by conventional color imaging systems. In this paper, we present a natural color reproduction system for telemedicine. In this system, the illumination difference between the image capturing site and observation site is corrected using a multispectral image, and the color image is displayed on a calibrated display device. For improvement of the color reproduction accuracy, the principal components of spectral reflectances are utilized in the color measurement. The accuracy of color reproduction in the developed system is experimentally evaluated. As a result, it is confirmed that the system realizes good accuracy in the color reproduction of human skin from a five band multispectral image.
Lanelok: Detection Of Lane Boundaries And Vehicle Tracking Using Image-Processing Techniques - Part I: Hough-Transform, Region-Tracing And Correlation Algorithms (1990)

The purpose of this study was to develop image-processing techniques for detecting lane boundaries and vehicle tracking using an on-board video camera. It resulted in several algorithms which process the image of the road scene to extract the position of lane markers and estimate the position of the lane boundaries and the position of the vehicle within the lane. The following algorithms were developed to process the camera's output: a Hough-transform algorithm, a region-tracing algorithm, and a vehicle-tracking algorithm. These algorithms were successfully tested on 3000 real road images, including some with missing and discontinuous markers. This capability to estimate lane boundaries will play a key role in the development of advanced automotive functions such as collision warning, collision avoidance and automatic vehicle-guidance.
Feasibility of transcranial photoacoustic imaging for interventional guidance of endonasal surgeries (2014)

Endonasal surgeries to remove pituitary tumors incur the deadly risk of carotid artery injury due to limitations with real-time visualization of blood vessels surrounded by bone. We propose to use photoacoustic imaging to overcome current limitations. Blood vessels and surrounding bone would be illuminated by an optical fiber attached to the endonasal drill, while a transducer placed on the pterional region outside of the skull acquires images. To investigate feasibility, a plastisol phantom embedded with a spherical metal target was submerged in a water tank. The target was aligned with a 1-mm optical fiber coupled to a 1064nm Nd:YAG laser. An Ultrasonix L14-5W/60 linear transducer, placed approximately 1 cm above the phantom, acquired photoacoustic and ultrasound images of the target in the presence and absence of 2- and 4-mm-thick human adult cadaveric skull specimens. Though visualized at 18 mm depth when no bone was present, the target was not detectable in ultrasound images when the 4-mm thick skull specimen was placed between the transducer and phantom. In contrast, the target was visible in photoacoustic images at depths of 17-18 mm with and without the skull specimen. To mimic a clinical scenario where cranial bone in the nasal cavity reduces optical transmission prior to drill penetration, the 2-mm-thick specimen was placed between the phantom and optical fiber, while the 4-mm specimen remained between the phantom and transducer. In this case, the target was present at depths of 15-17 mm for energies ranging 9-18 mJ. With conventional delay-and-sum beamforming, the photoacoustic signal-tonoise ratios measured 15-18 dB and the contrast measured 5-13 dB. A short-lag spatial coherence beamformer was applied to increase signal contrast by 11-27 dB with similar values for SNR at most laser energies. Results are generally promising for photoacoustic-guided endonasal surgeries.