gebhart/patrepeval huggingface dataset:
Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing (2004)

Pash is a computer program for efficient, parallel, all-against-all comparison of very long DNA sequences. Pash implements Positional Hashing, a novel parallelizable method for sequence comparison based on k-mer representation of sequences. The Positional Hashing method breaks the comparison problem in a unique way that avoids the quadratic penalty encountered with other sensitive methods and confers inherent low-level parallelism. Furthermore, Positional Hashing allows one to readily and predictably trade between sensitivity and speed. In a simulated comparison task, anchoring computationally mutated reads onto a genome, the sensitivity of Pash was equal to or greater than that of BLAST and BLAT, with Pash outperforming these programs as the reads became shorter and less similar to the genome. Using modest computing resources, we employed Pash for two large-scale sequence comparison tasks: comparison of three mammalian genomes, and anchoring millions of chimpanzee whole-genome shotgun sequencing reads onto the human genome. The results of these comparisons by Pash agree with those computed by other methods that use more than an order of magnitude more computing resources. These results confirm the sensitivity of Positional Hashing.
Evaluation of a Cytolethal Distending Toxin (<i>cdt</i>) Gene‐Based Species‐Specific Multiplex PCR Assay for the Identification of <i>Campylobacter</i> Strains Isolated from Poultry in Thailand (2007)

We have recently developed a cytolethal distending toxin (cdt) gene-based species-specific multiplex PCR assay for identifying Campylobacter jejuni, C. coli and C. fetus. In the present study, the applicability of this assay was evaluated with 34 Campylobacter-like organisms isolated from poultry in Thailand for species identification and was compared with other assays including API Campy, 16S rRNA gene sequence, and hippuricase (hipO) gene detection. Of the 34 strains analyzed, 20, 10 and 1 were identified as C. jejuni, C. coli, and Arcobacter cryaerophilus, respectively, and 3 could not be identified by API Campy. However, 16S rRNA gene analysis, showed that all 34 strains are C. jejuni/coli. To discriminate between these 2 species, the hipO gene, which is specifically present in C. jejuni, was examined by PCR and was detected in 20 strains, which were identified as C. jejuni by API Campy but not in the remaining 14 strains. Collective results indicated that 20 strains were C. jejuni whereas the 14 strains were C. coli. When the cdt gene-based multiplex PCR was employed, however, 19, 20 and 19 strains were identified as C. jejuni while 13, 14 and 13 were identified as C. coli by the cdtA, cdtB and cdtC gene-based multiplex PCR, respectively. Pulsed-field gel electrophoresis revealed that C. jejuni and C. coli strains analyzed are genetically diverse. Taken together, these data suggest that the cdt gene-based multiplex PCR, particularly cdtB gene-based multiplex PCR, is a simple, rapid and reliable method for identifying the species of Campylobacter strains.
Targeted axonal import (TAxI) peptide delivers functional proteins into spinal cord motor neurons after peripheral administration (2016)

A significant unmet need in treating neurodegenerative disease is effective methods for delivery of biologic drugs, such as peptides, proteins, or nucleic acids into the central nervous system (CNS). To date, there are no operative technologies for the delivery of macromolecular drugs to the CNS via peripheral administration routes. Using an in vivo phage-display screen, we identify a peptide, targeted axonal import (TAxI), that enriched recombinant bacteriophage accumulation and delivered protein cargo into spinal cord motor neurons after intramuscular injection. In animals with transected peripheral nerve roots, TAxI delivery into motor neurons after peripheral administration was inhibited, suggesting a retrograde axonal transport mechanism for delivery into the CNS. Notably, TAxI-Cre recombinase fusion proteins induced selective recombination and tdTomato-reporter expression in motor neurons after intramuscular injections. Furthermore, TAxI peptide was shown to label motor neurons in the human tissue. The demonstration of a nonviral-mediated delivery of functional proteins into the spinal cord establishes the clinical potential of this technology for minimally invasive administration of CNS-targeted therapeutics.
Atmospheric aerosol concentration measurements: A comparison between a tapered-element oscillating microbalance and an aerosol time-of-flight mass spectrometer (1998)

Throughout the previous decade, various epidemiological studies have shown that human morbidity and mortality are correlated with concentration levels of ambient aerosols. As a result, more detailed information is desired for atmospheric aerosols. Using aerosol time-of-flight mass spectrometry, additional information for atmospheric aerosols is available on a single particle basis. Chemically unique particle types are identified in ambient outdoor aerosols, making it possible to determine the source of single airborne particles. In addition to chemical information, measurements are also made of single particle size and aerosol size distributions. Because aerosol time-of-flight mass spectrometry performs its measurements in real-time, aerosol concentration measurements may be extracted from the single particle data. Number concentration measurements of atmospheric aerosols are performed and compared with mass concentration measured by a tapered-element oscillating microbalance. Aerosol time-of-flight mass spectrometry was designed to perform chemical analysis on single particles. As a result, the sampling efficiencies for ambient aerosols are less than instruments that are designed specifically for concentration measurements. However, relative variations in aerosol concentration correlate well between an aerosol time-of-flight mass spectrometer and a tapered-element oscillating microbalance for hourly measurements
Determination of burn depth by phase-resolved polarization-sensitive optical coherence tomography (2004)

A phase-resolved polarization sensitive optical coherence tomography (PS-OCT) system was used to determine the burn depth of in vivo tissue non-invasively. The phase retardation information was obtained by processing the analytical interference fringe signals from two perpendicular polarization-detection channels. From the birefringence images for the four reference polarization states, the birefringence reduction in the rat skin due to thermal damage can be measured. The determined burn depth showed good agreement with histological result.
Poly(ethylene terephthalate) crystallization as a method for microlithography (1990)

Abstract Thermal lithography on poly(ethylene terephthalate) (PET) is carried out by inducing crystallization through selective exposure of amorphous films to Infrared radiation. The obtained images can be smaller than the wavelength of the CO2 laser light. This circumvention of the diffraction limit is accomplished by taking advantage of the non‐linear temperature dependence of the crystallization rate. The optical marking process is reversible through simple melting of the crystalline images. The complementary process, selective melting of an initially crystalline film, can also be accomplished. The use as a heat sink of a mask which forms the image pattern is demonstrated.
Recombinant Canine Coronaviruses Related to Transmissible Gastroenteritis Virus of Swine Are Circulating in Dogs (2008)

Four canine coronavirus type II (CCoV-II) strains were identified in the guts and internal organs of pups which had died of acute gastroenteritis. The CCoV-II strains were strictly related to porcine transmissible gastroenteritis virus (TGEV) in the N-terminal domain of the spike protein, whereas in the other parts of the genome, a higher genetic relatedness to recent CCoV-II isolates was observed. Experimental infection of dogs with a TGEV-like isolate induced mild gastroenteritis without any systemic involvement. By virus neutralization tests, antigenic differences between reference and TGEV-like CCoVs were found. Our data support the potential recombinant origin of the TGEV-like CCoVs.
Polyaromatics with Terminal or Pendant Styrene Groups (1985)

Synthetic methods for the preparation of α,ω-bis(vinyl-benzyl) polyaromatic oligomers, and polyaromatics with pendant substituted styrene-type vinyl groups are presented. In the first case, the synthesis involves a quantitative etherification of an α,ω-bis(hydroxyphenyl) oligomer with chloromethylstyrene in the presence of tetrabutylammonium hydrogen sulfate as phase transfer catalyst. In the second case, the method entails a phase transfer catalyzed Wittig vinylation of polyaromatics containing pendant phosphonium salt groups from precursor chloromethylated or bromomethylated polymers. Examples are presented for α,ω-bis(hydroxyphenyl) aromatic polyether sulfone and poly(2,6-dimethyl-1,4-phenylene oxide). Both terminally and pendantly functionalized oligomers show very high thermal curing reactivity and can be used to tailor the properties of the final networks.
Arabinogalactan: a new ophthalmic vehicle for dry eye protection and treatment of corneal lesions (2007)

Abstract Purpose: Dry eye syndrome and contact lens wearing may lead to desiccation of the corneal epithelium with abrasions and increased incidence of infectious diseases. Therefore, it is important a rapid regeneration when epithelium is compromised. Aim of the present investigation was to demonstrate that Arabinogalactan (AG), a natural polysaccharide from Larch tree, was well tolerated after ocular administration and exerted a corneal protective action. Methods: AG formulation was then subjected to specific investigations. Results: Rheological measurements highlighted a newtonian non‐viscous behavior of AG aqueous dispersions at concentration up to 10% with η value of 1.6 mPas. The rheological evaluation of mucoadhesive properties showed strong interactions with mucin, property useful to retain the formulation on the eye surface. 5.0% AG dispersion exerted a significant increase in healing rate of experimental corneal wound in rabbits since 27 h after the first treatment. The corneal re‐epithelization process produced a tissue stratification in the same features of native epithelium, restoring the normal multilayered architecture of the rabbit corneal epithelium. Finally, studies of cell proliferation on rabbit corneal epithelial cell culture were carried out. Solutions at AG concentrations from 5x10‐3 to 1% enhanced the proliferation of the cells culture, showing cell viability values of 180% respect to the control after 48 hs exposure time. Conclusions: These findings suggest that AG may be a new potential artificial tear for the prevention and the treatment of corneal wounds in dry eye syndrome and in contact lens induced abrasions since it do not interfere with vision because of its non‐viscous feature.
Effect of processing conditions on the properties of high molecular weight conductive polyaniline fiber (2000)

Polyaniline–emeraldine base (EB) fiber with excellent mechanical and electrical properties have been spun from highly concentrated (20% w/w), EB/N-methyl-2-pyrrolidinone (NMP)/2-methylaziridine (2 MA) solution. These solutions had gelation times, which varied from hours to days depending on the molar ratio of 2 MA to EB tetramer repeating unit in the N-methyl-2-pyrrolidinone (NMP) solvent. To better compare the mechanical and electrical properties, dense films were also prepared by thermal evaporation of less concentrated solution (1% w/w). Both fibers and films were amenable to thermal stretching with maximum draw ratios of 4 : 1 and these stretched samples exhibited the greatest tensile strength overall. Wide-angle X-ray diffraction (WAXD) of as-spun and 4-times stretched fiber showed a completely amorphous structure. Fiber subjected to heat treatment at 250 °C under N2 flux for 2 h displayed further improvements in mechanical properties because of crosslinking between the polymer chains. Fibers and films were later doped by immersion in a variety of aqueous acid solutions. Room temperature DC conductivities for the doped samples ranged from 6 × 10−4 to 45 S/cm depending on the specific choice of acid. Scanning electron microscopy of fiber samples shows the presence of macrovoid formation during fiber spinning. Continued refinement of the processing parameters and fiber post-treatment, to enhance chain alignment and increase fiber density, will likely lead to additional improvements in the fiber mechanical and electrical properties. Characterization of emeraldine base (EB) powder, solution, films, and fibers by UV-Vis, DSC, TGA, and WAXD were also performed. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 194–204, 2000
Radio and Computing Resource Allocation in Co-Located Edge Computing: A Generalized Nash Equilibrium Model (2021)

Mobile Network Operators (MNO) can reduce their Capital and Operational Expenditure (CAPEX) and (OPEX) with the help of tower sharing approach by utilizing the physical infrastructure equipped by a third party tower provider to expand their network coverage. Moreover, Computing Resource Providers (CRP) are also setting up their micro-datacenters at tower stations to provide the Multi-access Edge Computing (MEC) services by cooperating with tower providers. Since both the communication and computing services contribute to the task offloading in MEC, the resource allocation has become a challenging problem. In this paper, we formulate the joint uplink, downlink, and computing resources allocation problem in which the objectives of both MNOs and CRP are to minimize their OPEX. The task offloading is modeled as a network of queues where the end-to-end latency is calculated based on the performance of the queue network. Then, the formulated problem is transformed into a Generalized Nash Equilibrium Problem (GNEP) to capture the conflicting interests in the resource allocation among MNOs and CRP. To solve the formulated GNEP efficiently, two decentralized algorithms are proposed by introducing the penalty parameters to the coupling constraints. In addition, the convergence and performance of the algorithms on different parameters are analyzed.
Control of Tower Cranes With Double-Pendulum Payload Dynamics (2010)

The usefulness of cranes is limited because the payload is supported by an overhead suspension cable that allows oscillation to occur during crane motion. Under certain conditions, the payload dynamics may introduce an additional oscillatory mode that creates a double pendulum. This paper presents an analysis of this effect on tower cranes. This paper also reviews a command generation technique to suppress the oscillatory dynamics with robustness to frequency changes. Experimental results are presented to verify that the proposed method can improve the ability of crane operators to drive a double-pendulum tower crane. The performance improvements occurred during both local and teleoperated control.
Segmentation and automated measurement of chronic wound images: probability map approach (2014)

estimated 6.5 million patients in the United States are affected by chronic wounds, with more than 25 billion US dollars and countless hours spent annually for all aspects of chronic wound care. There is need to develop software tools to analyze wound images that characterize wound tissue composition, measure their size, and monitor changes over time. This process, when done manually, is time-consuming and subject to intra- and inter-reader variability. In this paper, we propose a method that can characterize chronic wounds containing granulation, slough and eschar tissues. First, we generate a Red-Yellow-Black-White (RYKW) probability map, which then guides the region growing segmentation process. The red, yellow and black probability maps are designed to handle the granulation, slough and eschar tissues, respectively found in wound tissues, while the white probability map is designed to detect the white label card for measurement calibration purpose. The innovative aspects of this work include: 1) Definition of a wound characteristics specific probability map for segmentation, 2) Computationally efficient regions growing on 4D map; 3) Auto-calibration of measurements with the content of the image. The method was applied on 30 wound images provided by the Ohio State University Wexner Medical Center, with the ground truth independently generated by the consensus of two clinicians. While the inter-reader agreement between the readers is 85.5%, the computer achieves an accuracy of 80%.
The Use, in Diabetic Rats and Monkeys, of Artificial Capillary Units Containing Cultured Islets of Langerhans (Artificial Endocrine Pancreas) (1977)

A unit was constructed that consisted of a core of hollow fibers through which low-molecular-weight substances, such as glucose and insulin, could pass freely but were impermeable to high-molecular-weight proteins, such as antibodies. Islets of Langerhans from normal rats were planted in the space surrounding the fibers, and either blood or nutrient medium was circulated through the fibers themselves. In experiments with animals, the units were attached to the vascular system of diabetic rats and monkeys. Blood glucose concentrations in the rats were reduced to nondiabetic levels within one hour and were maintained for the duration of the experiments. In monkeys the blood glucose level declined from 210 mg./100 ml. to 90 mg./100 ml. in four hours and insulin in the serum rose to 93 muU./ml. in one-half hour. Also, we have found that islets from monkeys cultivated in the artificial endocrine pancreas (AEP) continue to release insulin into circulating tissue culture medium for over eight months.
The wheat <i>Sr22</i>, <i>Sr33</i>, <i>Sr35</i> and <i>Sr45</i> genes confer resistance against stem rust in barley (2020)

In the last 20 years, stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has re-emerged as a major threat to wheat and barley production in Africa and Europe. In contrast to wheat with 60 designated stem rust (Sr) resistance genes, barley's genetic variation for stem rust resistance is very narrow with only ten resistance genes genetically identified. Of these, only one complex locus consisting of three genes is effective against TTKSK, a widely virulent Pgt race of the Ug99 tribe which emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheat Sr genes effective against race TTKSK. Sr22, Sr33, Sr35 and Sr45 were transformed into barley cv. Golden Promise using Agrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogen Puccinia hordei, indicating that the resistance conferred by these wheat Sr genes was specific for Pgt. Furthermore, these transgenic plants did not display significant adverse agronomic effects in the absence of disease. Cloned Sr genes from wheat are therefore a potential source of resistance against wheat stem rust in barley.
Distortion-aware MIMO link adaptation for enhanced multimedia communications (2010)

In wireless multimedia communications, optimizing the quality of user experience is a major design goal, which is often quantified by the end-to-end distortion between the actual multimedia source at the encoder and its reconstructed version at the decoder. Joint source-channel coding (JSCC) techniques aim to optimize codec and radio system parameters in order to minimize end-to-end distortion and yield enhanced quality of user experience when compared with separate source-channel coding techniques. With the motivation of applying JSCC-based cross-layer optimizations to PHY/MAC layer design for practical wireless systems, this paper proposes new techniques for MIMO link adaptation toward enhanced multimedia communications. In particular, we propose new distortion-aware MIMO link adaptation techniques toward the selection of modulation and coding schemes (MCS) and MIMO space-time modulation (including MIMO diversity and spatial multiplexing) schemes with the objective of minimizing end-to-end distortion, different from classical approaches that aimed for other optimizations such as maximizing spectral efficiency or goodput. Furthermore, we investigate the performance of distortion-aware MIMO link adaptation in realistic link-level simulation (LLS) and system-level simulation (SLS) environments based on orthogonal frequency division multiplexing (OFDM) under broadband frequency-selective fading with special focus on multicast broadcast services (MBS), and demonstrate their advantages over goodput-maximizing MIMO link adaptation techniques in terms of reduced end-to-end distortion and higher peak signal-to-noise ratio (PSNR).
Using dynamic buffer limiting to protect against belligerent flows in high-speed networks (2005)

Conventional QoS mechanisms have focused primarily on providing better than normal service for some flows over others. With networks moving to much higher speeds and reasonable provisioning, best efforts access to network resources is adequate for common applications except when a belligerent flow attempts to consume an excessive amount of bandwidth. Any mechanism that attempts to contain such a flow must be able to operate at wirespeed in hardware. In this environment, conventional QoS mechanisms are not sufficient, either because they do not have mechanisms to contain these belligerent flows or because they are not practical to implement in hardware. In this paper we describe dynamic buffer limiting (DBL), a buffer and queue management mechanism designed to recognize and handle belligerent flows at very high speed and suitable for hardware implementation.
Space-time-Doppler block coding for correlated time-selective fading channels (2005)

Coping with time-selective fading channels is challenging but also rewarding, especially with multiantenna systems, where joint space-Doppler diversity and coding gains can be collected to enhance performance of wireless mobile links. These gains have not been quantified, and space-time coded systems maximizing joint space-Doppler benefits have not been designed. Based on a parsimonious basis expansion model for the underlying time-selective (and possibly correlated) channels, we quantify these gains in closed form. Furthermore, we develop space-time-Doppler coded systems that guarantee the maximum possible space-Doppler diversity, along with the largest coding gains within all linearly coded systems. Our three novel designs exploit knowledge of the maximum Doppler spread, and each offers a uniquely desirable tradeoff, including high spectral efficiency, low decoding complexity, and high performance. Our analytical results are confirmed by simulations and reveal the relative of merits of our three designs in comparison with an existing approach.