gebhart/patrepeval huggingface dataset:
Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines <i>Mycobacterium bovis</i> BCG and <i>Mycobacterium microti</i> (2002)

Although large human populations have been safely immunized against tuberculosis with two live vaccines, Mycobacterium bovis BCG or Mycobacterium microti, the vole bacillus, the molecular basis for the avirulence of these vaccine strains remains unknown. Comparative genomics has identified a series of chromosomal deletions common to both virulent and avirulent species but only a single locus, RD1, that has been deleted from M. bovis BCG and M. microti. Restoration of RD1, by gene knock-in, resulted in a marked change in colonial morphology towards that of virulent tubercle bacilli. Three RD1-encoded proteins were localized in the cell wall, and two of them, the immunodominant T-cell antigens ESAT-6 and CFP-10, were also found in culture supernatants. The BCG::RD1 and M. microti::RD1 knock-ins grew more vigorously than controls in immunodeficient mice, inducing extensive splenomegaly and granuloma formation. Increased persistence and partial reversal of attenuation were observed when immunocompetent mice were infected with the BCG::RD1 knock-in, whereas BCG controls were cleared. Knocking-in five other RD loci did not affect the virulence of BCG. This study describes a genetic lesion that contributes to safety and opens new avenues for vaccine development.
Solid state polymerization of poly(<scp>L</scp>‐lactide): Multiple‐fold increase in molecular weight via an efficient catalyst system (2011)

Abstract We report the synthesis of high molecular weight (MW), high crystallinity ( X c ) poly( L ‐lactic acid) (PLLA), with improved thermal stability, by solid state polymerization (SSP) of low MW PLLA prepolymer, pre‐PLLA. SSP enabled pre‐PLLA is synthesized by ring opening polymerization (ROP) of L ‐lactide using a ternary catalyst complex of L ‐lactide, stannous octoate, and L ‐lactic acid oligomer (OLLA). We demonstrate that this ROP, although a chain‐growth reaction, yields pre‐PLLA with end‐groups, which enable step growth SSP. MW increases ∼9 fold, with X c reaching beyond 90%, during the SSP process. Such high values of crystallinity could be due to the synchronization of the crystallization rate with that of the slower and longer lasting step‐growth SSP. Nuclear magnetic resonance spectroscopy confirms that SSP is indeed a step‐growth reaction. In comparison, Zn(OLLA) 2 only couples two pre‐PLLA chains during SSP. In addition, the radial spherulite growth rate has been quantified with annealing time of SSP synthesized PLLA. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers
Venezuelan Equine Encephalitis Virus Capsid Protein Inhibits Nuclear Import in Mammalian but Not in Mosquito Cells (2008)

Venezuelan equine encephalitis virus (VEEV) represents a continuous public health threat in the United States. It has the ability to cause fatal disease in humans and in horses and other domestic animals. We recently demonstrated that replicating VEEV interferes with cellular transcription and uses this phenomenon as a means of downregulating a cellular antiviral response. VEEV capsid protein was found to play a critical role in this process, and its approximately 35-amino-acid-long peptide, fused with green fluorescent protein, functioned as efficiently as did the entire capsid. We detected a significant fraction of VEEV capsid associated with nuclear envelope, which suggested that this protein might regulate nucleocytoplasmic trafficking. In this study, we demonstrate that VEEV capsid and its N-terminal sequence efficiently inhibit multiple receptor-mediated nuclear import pathways but have no effect on the passive diffusion of small proteins. The capsid protein of the Old World alphavirus Sindbis virus and the VEEV capsid, with a previously defined frameshift mutation, were found to have no detectable effect on nuclear import. Importantly, the VEEV capsid did not noticeably interfere with nuclear import in mosquito cells, and this might play a critical role in the ability of the virus to develop a persistent, life-long infection in mosquito vectors. These findings demonstrate a new aspect of VEEV-host cell interactions, and the results of this study are likely applicable to other New World alphaviruses, such as eastern and western equine encephalitis viruses.
Design of a Calibration Phantom for Measuring the Temporal Resolution of a Tomographic Imaging Device (2007)

This paper describes the design and development of a calibration phantom to be used to aid in the calculation of the temporal resolution of tomographic imaging devices. Current practice for characterizing the dynamic response of a tomographic imaging device, such as a computed tomography or magnetic resonance imaging machine, uses image acquisition time as a surrogate for temporal resolution. At present, no standard method for describing the temporal resolution of a tomographic imaging device exists. Similar to the spatial modulation transfer function (MTF) used for characterizing spatial resolution, the concept of temporal MTF (t-MTF) can be used to enable characterization of temporal resolution. A scanner’s t-MTF represents the percentage amplitude modulation transfer in the image as a function of the input frequency. The calibration phantom uses slotted disks, each mounted to the rotating ring gear of a planetary gear assembly. The sun gears of each planetary gear set are driven from a common shaft to create differential speed sectors, allowing for about two decades of input frequencies to be obtained using a single motor and driveshaft. Preliminary results show a monotonic decline in the modulation transfer as the input frequency is increased. As expected, there is more modulation transfer at lower frequency and less modulation transfer at high frequency. Analogous to the spatial resolution, one can define the frequency for which there is 10% modulation transfer as the temporal resolution of a scanner.
Recombinant Paraprobiotics as a New Paradigm for Treating Gastrointestinal Nematode Parasites of Humans (2020)

Abstract Gastrointestinal nematodes (GINs) of humans, e.g ., hookworms, negatively impact childhood growth, cognition, nutrition, educational attainment, income, productivity, and pregnancy. Hundreds of millions of people are targeted with mass drug administration (MDA) of donated benzimidazole (BZ) anthelmintics. However, BZ efficacy against GINs is suboptimal, and reduced/low efficacy has been seen. Developing an anthelmintic for human MDA is daunting: it must be safe, effective, inexpensive, stable without a cold chain, and massively scalable. Bacillus thuringiensis (Bt) crystal protein 5B (Cry5B) has anthelmintic properties that could fill this void. Here we develop an API (Active Pharmaceutical Ingredient) form of Bt Cry5B compatible with MDA. We expressed Cry5B in asporogenous Bt during vegetative phase, forming cytosolic crystals. These Ba cteria with C ytosolic C rystals (BaCC) were rendered inviable (inactivated BaCC or IBaCC) with food-grade essential oils. IBaCC potency was validated in vitro against nematodes. IBaCC was also potent in vivo against human hookworm infections in hamsters. IBaCC production was successfully scaled to 350 liters at a contract manufacturing facility. A simple fit-for-purpose formulation to protect against stomach digestion and powdered IBaCC were successfully made and used against GINS in hamsters and mice. A pilot histopathology study and blood chemistry workup showed that five daily consecutive doses of 200 mg/kg Cry5B IBaCC (the curative single dose is 40 mg/kg) was non-toxic and completely safe. IBaCC is a safe, inexpensive, highly effective, easy-to-manufacture, and scalable anthelmintic that is practical for MDA and represents a new paradigm for treating human GINs.
High-speed all-optical switching experiment in Mach–Zehnder configuration using GaAs waveguide (1993)

We report the results of a high-speed all-optical switching experiment in Mach–Zehnder configuration using a GaAs waveguide. The all-optical switching is based on the nonlinear refractive index change induced by the band-filling effect in the GaAs waveguide. To achieve high-speed operation without being limited by the slow carrier relaxation time, a dc electric field is externally applied to the nonlinear waveguide to sweep carriers away from the light guiding region. The FWHM (full width at half maximum) of the switching waveform without the externally applied electric field is about 800–900 ps. As the electric field is increased, the FWHM is reduced to about 80–90 ps.
Tutorial: polarization mode dispersion impairment in lightwave transmission systems (2003)

Fiber PMD can cause a variety of impairments in optical fiber transmission systems. First, a single digital transmission channel suffers impairment due to intersymbol interference (ISI). The ISI impairment is caused by the differential group delay (DGD) between the two pulses propagating in the fiber when the input polarization of the signal does not match the principal state of polarization of the fiber. The first-order PMD impairment caused by this effect can be expressed as a power penalty proportional to the square of the instantaneous DGD to bit-interval ratio and the dimensionless A-parameter that depends on the pulse shape, modulation format, and receiver characteristics such as the response of the electrical filter. We will discuss measurements, emulations and simulations of these penalties and the associated A-parameter.
Efficient, Real-Time Global Spectral and Broadband Irradiance Acquisition (2018)

Two global solar spectral irradiance meters (SolarSIM-Gs) were deployed and tested at the National Renewable Energy Laboratory in Golden, USA from 18 September to 6 October 2017. The instruments were installed in the global horizontal orientation at the Solar Radiation Research Laboratory and their measurements were compared against colocated secondary reference spectroradiometers and secondary standard pyranometers. The SolarSIM-Gs' spectral global horizontal irradiance (GHI) accuracy was shown to be <; 5% on average per wavelength in the 290-1650 nm range for over 1,900 analyzed spectra. The broadband GHI measurement accuracy for two instruments was shown to have mean bias and standard deviation of 0.97, 1.23 W/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and 5.27, 5.65 W/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , respectively, for over 10,000 analyzed data points.
Incident angle-dependent gain correction for reflection images on ultrasound computed tomography (2020)

We are performing clinical studies on breast cancer examinations at Hokkaido University Hospital with an ultrasound computed tomography (USCT) system. Our studies have revealed that some reflection images exhibit intensity inhomogeneity because ultrasound waves, shot by a 1-D ring array transducer, go non-vertically into the object surface. This trend significantly increases the burden of interpretation. Therefore, we developed a calibration method to remove this heterogeneity based on the distribution of the incident angle of waves that are estimated from the slope of the subject surface morphologically extracted from multi-slice reflection images. Results showed that applying this correction method to clinical images enabled the image contrast and uniformity to be successfully recovered.
Combined coal gasifer and fuel cell system and method (1990)

This patent describes a coal gasification and fuel cell system. It comprises: in combination coal gasification means for endothermically reacting coal or coal char in the presence of a catalyst, an external source of heat and steam for producing a stream of gaseous products containing carbon dioxide and hydrogen at a temperature in the range of about 1150{degrees} to 1050{degrees} F., a molten carbonate fuel cell means having anode means and cathode means, conduit means connecting the gasification means to the fuel cell means. Gas separating means in the conduit means for separating the carbon dioxide from the hydrogen, the conduit means comprising a first conduit means coupling the gas separating means and the anode means for conveying hydrogen.
Multi-tube once-through boiler (1990)

A multi-tube once-through boiler is provided, having a quadrangular type of boiler body, comprising a feed path for combustion air, a combustion chamber, and an exhaust gas channel passing through a flue. The feed path, combustion chamber, and exhaust gas channel are aligned in substantially the same plane along the lateral walls of the boiler body. A burner duct forming part of the feed path and a blower for use with the boiler are disposed in any desired regions of the lateral wall portions defining the width of the boiler body. The boiler body includes a water tube assembly arranged such that combustion gas flows crosswide to the tubes. A burner is disposed closely adjacent to the first water tube row in the water tube assembly. According to another aspect of the invention, a multi-tube once-through boiler has a quadrangular type body installed on a bed together with ancillary parts. A frame formed of a required number of substantially vertically or horizontally extending connecting members define a plurality of receiving compartments for the boiler unit. Front and lateral sealing panels are provided for closing an opening in the front surface of the receiving compartments and in each lateral surface of the structure. 14 figs.
Estimation of intraocular lens position from full crystalline lens geometry: towards a new generation of intraocular lens power calculation formulas (2018)

In a cataract surgery, the opacified crystalline lens is replaced by an artificial intraocular lens (IOL). To optimize the visual quality after surgery, the intraocular lens to be implanted must be selected preoperatively for every individual patient. Different generations of formulas have been proposed for selecting the intraocular lens dioptric power as a function of its estimated postoperative position. However, very few formulas include crystalline lens information, in most cases only one-dimensional. The present study proposes a new formula to preoperatively estimate the postoperative IOL position (ELP) based on information of the 3-dimensional full shape of the crystalline lens, obtained from quantitative eye anterior segment optical coherence tomography imaging. Real patients were measured before and after cataract surgery (IOL implantation). The IOL position and the postoperative refraction estimation errors were calculated by subtracting the preoperative estimations from the actual values measured after surgery. The proposed ELP formula produced lower estimation errors for both parameters -ELP and refraction- than the predictions obtained with standard state-of-the-art methods, and opens new avenues to the development of new generation IOL power calculation formulas that improve refractive and visual outcomes.
Comparison of Polar Decoders with Existing Low-Density Parity-Check and Turbo Decoders (2017)

Polar codes are a recently proposed family of provably capacity-achieving error-correction codes that received a lot of attention. While their theoretical properties render them interesting, their practicality compared to other types of codes has not been thoroughly studied. Towards this end, in this paper, we perform a comparison of polar decoders against LDPC and Turbo decoders that are used in existing communications standards. More specifically, we compare both the error-correction performance and the hardware efficiency of the corresponding hardware implementations. This comparison enables us to identify applications where polar codes are superior to existing error-correction coding solutions as well as to determine the most promising research direction in terms of the hardware implementation of polar decoders.
Experimental Mitigation of Atmospheric Turbulence Effect Using Pre-Signal Combining for Uni- and Bi-Directional Free-Space Optical Links With Two 100-Gbit/s OAM-Multiplexed Channels (2019)

In this paper, we experimentally demonstrate the mitigation of atmospheric turbulence effects using phase patterns that apply the inverse transmission matrix for pre-compensation in the 200-Gbit/s free-space orbital angular momentum (OAM) multiplexed optical link. In this link, two OAM channels are multiplexed, each carrying a 100-Gbit/s quadrature-phase shift keying (QPSK) signal. In the uni-directional (forward) link, a combination of two OAM modes is generated using a designed phase pattern in each of the two channels. After the two channels are multiplexed, each OAM mode will carry the combination of signals from both channels. Such beams could perform the inverse function of turbulence-induced crosstalk. We explore the link performances including crosstalk and bit error rate (BER) under 6 different turbulence realizations with a Fried parameter of 1-mm. We find the following: (a) the inter-channel crosstalk is reduced by up to 21 dB; (b) the inter-channel crosstalk is below -10 dB for the 6 turbulence realizations when the compensation is applied; (c) a BER below the FEC limit could be realized for the 6 turbulence realizations with an optical signal-to-noise ratio (OSNR) of 16.8 dB for the uni-directional link with the compensation. Moreover, the post-compensation is also investigated for the two 100-Gbit/s OAM-multiplexed backward channels in the bi-directional link. For the backward channels, the phase patterns are used to mitigate turbulence-induced crosstalk at the receiver for backward channels, and the inter-channel crosstalk is reduced by up to 16 dB.
Transposition of the <i>Tol2</i> Element, an <i>Ac</i>-Like Element From the Japanese Medaka Fish <i>Oryzias latipes</i>, in Mouse Embryonic Stem Cells (2004)

Abstract The Tol2 transposable element of the Japanese medaka fish belongs to the hAT family of transposons including hobo of Drosophila, Ac of maize, and Tam3 of snapdragon. To date, Tol2 is the only natural transposon in vertebrates that has ever been shown to encode a fully functional transposase. It has not been known, however, whether Tol2 can transpose in vertebrates other than fish. We report here transposition of Tol2 in mouse embryonic stem (ES) cells. We constructed a transposon donor plasmid containing a nonautonomous Tol2 element with the neomycin resistance gene and a helper plasmid capable of expressing the transposase and introduced the donor plasmid with various amounts of the helper plasmid by electroporation into mouse ES cells. The number of G418-resistant ES colonies increased as the amount of helper plasmid was increased, in a dose-dependent manner, indicating that the transposase activity elevated the integration efficiency. These G418-resistant ES colonies were cloned and the structure of the junction of the integrated Tol2 element and the genomic DNA was analyzed by inverse PCR. In those clones, Tol2 was surrounded by mouse genomic sequences and an 8-bp direct repeat was created adjacent to both ends of Tol2, indicating that Tol2 was integrated in the genome through transposition. The Tol2 transposon system is thus active in mouse as well as in fish. We propose that it should be used as a genetic tool to develop novel gene transfer, transgenesis, and mutagenesis methods in mammals.
Few-mode fibers for mode-division multiplexing (2013)

The design of few-mode fibers will be discussed from the point of view of key attributes and fundamental limitations. We will consider the maximum number of modes that might be supported in a practical fiber.
Ubiquitination and its consequences for mammalian spermatogenesis, epididymal sperm maturation, fertilization and pre-implantation embryonic development (2005)

The ubiquitin-proteasome pathway is a substrate specific system for ATP-dependent proteolytic degradation of damaged, improperly postranslationally modified or outlived proteins. Ubiquitination is achieved through the covalent ligation of an 8.5 kDa ubiquitin to the substrate Lys-residue. Ensuing formation of a long polyubiquitin chain targets the ubiquitinated substrate towards 26S proteasome, a multi-subunit protease complex. Disproportionate to the impact of ubiquitin research on general areas of cell biology and medicine, little attention had been paid until recently, to protein ubiquitination within the male and female reproductive system. Recent research implicates the ubiquifin system in control of mammalian reproductive processes at distinct developmental steps including spermatogenesis in the testis, sperm maturation in the epididymis, penetration of zona pellucida during fertilization, pronuclear development, blastocyst differentiation and implantation embryo. This research opens new opportunities in the area of assisted reproductive technology including human infertility diagnostics and treatment, fertility evaluation in male farm animals and laboratory rodents, contraceptive development, embryo transfer technology in farm animals, somatic cell nuclear transfer for the production of transgenic animals and stem cell technology.
Milk Production and Composition in Cows and Goats Fed α-Ketoisocaproate (1988)

To examine whether alpha-ketoisocaproate supplementation affects milk production, 10 goats were fed either 0 or 1.1% calcium-alpha-ketoisocaproate for 2 wk and 12 cows were fed either 0 or .75% Na alpha-ketoisocaproate for 3 wk. Supplementation with alpha-ketoisocaproate increased milk fat content, milk fat yield, and 4% FCM yield in cows by an average of 5, 10, and 8%, respectively, for the treatment period. In cows, response of milk fat yield to alpha-ketoisocaproate was 120 g during wk 1 of treatment but diminished to 55 g by wk 3. Milk yield and milk protein yield tended to be greater in cows fed alpha-ketoisocaproate, but milk production efficiency and body weight were not altered by treatment in either species. Supplementation with alpha-ketoisocaproate had no significant effect on fatty acid composition of milk but tended to increase the percentage of C10 and C12 fatty acids. In goats, supplementation with alpha-ketoisocaproate had no significant effect on milk production or composition, but trends toward increased milk fat and protein content were observed. Results indicate that alpha-ketoisocaproate acutely stimulates milk fat production in lactating cows and that this effect seems to diminish with time.
Fraud detection (2002)

Fraud is the deliberate use of deception to conduct illicit activities. Automatic fraud detection involves scanning large volumes of data to uncover patterns of fradulent usage, and as such it is well suited to data mining techniques. We present three general types of fraud that have been addressed in data mining research, and we summarize the approaches taken. We also discuss general characteristics of fraud detection problems that make them difficult, as well as system integration issues for automatic fraud detection systems.