Analysis of AIS Data of the Recluse Oil Field, Recluse, Wyoming

Airborne Imaging Spectrometer (AIS) data were flown over the Recluse, Wyoming oil field on September 9, 1984. Processing software was developed at Earth Satellite Corporation (EarthSat) for interactive analysis of the AIS data. EarthSat's AIS processing capabilities include destriping, solar irradiance corrections, residual calculations, geometric resampling, equal energy normalization, interactive spectral classifications and a variety of compressive algorithms to reduce the data to 8-bit format with a minimum of information loss. The in-house photolab facilities of EarthSat can routinely produce high-quality color renditions of the enhanced AIS data. A total of 80 lithologic samples were collected under the AIS flight lines. Correlation (within the atmospheric windows) between the laboratory and the AIS spectra of sample sites was generally poor. Reasonable correlation was only possible in large, freshly plowed fields. Mixed pixels and contrast between the natural and sample's surfaces were believed responsible for the poor correlation. Finally, a drift of approximately three channels was observed in the diffraction grating position within the 1.8 to 2.1 micron quadrant

The Bases of Association Rules of High Confidence

We develop a new approach for distributed computing of the association rules of high confidence in a binary table. It is derived from the D-basis algorithm in K. Adaricheva and J.B. Nation (TCS 2017), which is performed on multiple sub-tables of a table given by removing several rows at a time. The set of rules is then aggregated using the same approach as the D-basis is retrieved from a larger set of implications. This allows to obtain a basis of association rules of high confidence, which can be used for ranking all attributes of the table with respect to a given fixed attribute using the relevance parameter introduced in K. Adaricheva et al. (Proceedings of ICFCA-2015). This paper focuses on the technical implementation of the new algorithm. Some testing results are performed on transaction data and medical data.Comment: Presented at DTMN, Sydney, Australia, July 28, 201

Confinement effects in a guided-wave interferometer with millimeter-scale arm separation

Guided-wave atom interferometers measure interference effects using atoms held in a confining potential. In one common implementation, the confinement is primarily two-dimensional, and the atoms move along the nearly free dimension under the influence of an off-resonant standing wave laser beam. In this configuration, residual confinement along the nominally free axis can introduce a phase gradient to the atoms that limits the arm separation of the interferometer. We experimentally investigate this effect in detail, and show that it can be alleviated by having the atoms undergo a more symmetric motion in the guide. This can be achieved by either using additional laser pulses or by allowing the atoms to freely oscillate in the potential. Using these techniques, we demonstrate interferometer measurement times up to 72 ms and arm separations up to 0.42 mm with a well controlled phase, or times of 0.91 s and separations of 1.7 mm with an uncontrolled phase.Comment: 14 pages, 6 figure

Methods for Scarless, Selection-Free Generation of Human Cells and Allele-Specific Functional Analysis of Disease-Associated SNPs and Variants of Uncertain Significance.

With the continued emergence of risk loci from Genome-Wide Association studies and variants of uncertain significance identified from patient sequencing, better methods are required to translate these human genetic findings into improvements in public health. Here we combine CRISPR/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) genotyping technology to create scarless isogenic cell models of cancer variants in ~1 month. We successfully modeled two novel variants previously identified by our lab in the PALB2 gene in HEK239 cells, resulting in isogenic cells representing all three genotypes for both variants. We also modeled a known functional risk SNP of colorectal cancer, rs6983267, in HCT-116 cells. Cells with extremely low levels of gene editing could still be identified and isolated using this approach. We also introduce a novel molecular assay, ChIPnQASO (Chromatin Immunoprecipitation and Quantitative Allele-Specific Occupation), which uses the same technology to reveal allele-specific function of these variants at the DNA-protein interaction level. We demonstrated preferential binding of the transcription factor TCF7L2 to the rs6983267 risk allele over the non-risk. Our pipeline provides a platform for functional variant discovery and validation that is accessible and broadly applicable for the progression of efforts towards precision medicine

Transcription activator like effector (TALE)-directed piggyBac transposition in human cells.

Insertional therapies have shown great potential for combating genetic disease and safer methods would undoubtedly broaden the variety of possible illness that can be treated. A major challenge that remains is reducing the risk of insertional mutagenesis due to random insertion by both viral and non-viral vectors. Targetable nucleases are capable of inducing double-stranded breaks to enhance homologous recombination for the introduction of transgenes at specific sequences. However, off-target DNA cleavages at unknown sites can lead to mutations that are difficult to detect. Alternatively, the piggyBac transposase is able perform all of the steps required for integration; therefore, cells confirmed to contain a single copy of a targeted transposon, for which its location is known, are likely to be devoid of aberrant genomic modifications. We aimed to retarget transposon insertions by comparing a series of novel hyperactive piggyBac constructs tethered to a custom transcription activator like effector DNA-binding domain designed to bind the first intron of the human CCR5 gene. Multiple targeting strategies were evaluated using combinations of both plasmid-DNA and transposase-protein relocalization to the target sequence. We demonstrated user-defined directed transposition to the CCR5 genomic safe harbor and isolated single-copy clones harboring targeted integrations

Doppler-free laser spectroscopy of buffer gas cooled molecular radicals

We demonstrate Doppler-free saturated absorption spectroscopy of cold molecular radicals formed by laser ablation inside a cryogenic buffer gas cell. By lowering the temperature, congested regions of the spectrum can be simplified, and by using different temperatures for different regions of the spectrum a wide range of rotational states can be studied optimally. We use the technique to study the optical spectrum of YbF radicals with a resolution of 30 MHz, measuring the magnetic hyperfine parameters of the electronic ground state. The method is suitable for high resolution spectroscopy of a great variety of molecules at controlled temperature and pressure, and is particularly well-suited to those that are difficult to produce in the gas phase.Comment: 11 pages, 4 figure

Chimeric piggyBac transposases for genomic targeting in human cells.

Integrating vectors such as viruses and transposons insert transgenes semi-randomly and can potentially disrupt or deregulate genes. For these techniques to be of therapeutic value, a method for controlling the precise location of insertion is required. The piggyBac (PB) transposase is an efficient gene transfer vector active in a variety of cell types and proven to be amenable to modification. Here we present the design and validation of chimeric PB proteins fused to the Gal4 DNA binding domain with the ability to target transgenes to pre-determined sites. Upstream activating sequence (UAS) Gal4 recognition sites harbored on recipient plasmids were preferentially targeted by the chimeric Gal4-PB transposase in human cells. To analyze the ability of these PB fusion proteins to target chromosomal locations, UAS sites were randomly integrated throughout the genome using the Sleeping Beauty transposon. Both N- and C-terminal Gal4-PB fusion proteins but not native PB were capable of targeting transposition nearby these introduced sites. A genome-wide integration analysis revealed the ability of our fusion constructs to bias 24% of integrations near endogenous Gal4 recognition sequences. This work provides a powerful approach to enhance the properties of the PB system for applications such as genetic engineering and gene therapy