Capture and Release Gels for Optimized Storage (CaRGOS)

Unassisted, the lifetime of many proteins outside their natural environment is very short. Scientists generally need to extract the sample, often in remote locations, and then transport, isolate, and store such biospecimens relatively far from the point of origin in order to study them. Currently, the most commonly used methods for storage of biospecimens are cryopreservation or refrigeration which, though effective, have their fair share of flaws. Cryopreservation and refrigeration-based storage of biospecimens requires a great deal of space and other resources to be effective. Furthermore, the hardware required for cold storage does not transport well. These factors make such storage methods impractical for use in the field and even some laboratories[1-3]. Due to repeated strain on biomolecules from crystallization, rapid degradation occurs after repeated freezing and thawing; this problem could be avoided by storing specimens at ambient temperatures. Herein, we report a novel method for long-term room-temperature aqueous biomolecule storage utilizing rapidly fabricated silica sol-gel networks. By adjusting solution conditions such as acidity, salinity, buffer concentration, and silica density, it is possible to tailor sol-gel chemistry to create hospitable silica structures to support a variety of biomolecules. We have demonstrated the preservation of RNA and Hemoglobin samples for up to 28 days and 31 days respectively, under ambient conditions, using this technique. Upon coupling the amenability of the sol-gel structure with a contemporary rapid synthesis method, silica sol-gels become Capture and Release Gels for Optimized Storage(CaRGOS)

Successful ATAC-Seq From Snap-Frozen Equine Tissues

An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin to characterize tissue specificity of genome function for prioritized tissues have been performed. Due to the logistics of tissue collection and storage, extracting nuclei from a large number of tissues for ATAC-seq at the time of collection is not always practical. To assess the feasibility of using stored frozen tissues for ATAC-seq and to provide a guideline for the equine FAANG project, we compared ATAC-seq results from nuclei isolated from frozen tissue to cryopreserved nuclei (CN) isolated at the time of tissue harvest in liver, a highly cellular homogenous tissue, and lamina, a relatively acellular tissue unique to the horse. We identified 20,000– 33,000 accessible chromatin regions in lamina and 22–61,000 in liver, with consistently more peaks identified using CN isolated at time of tissue collection. Our results suggest that frozen tissues are an acceptable substitute when CN are not available. For more challenging tissues such as lamina, nuclei extraction at the time of tissue collection is still preferred for optimal results. Therefore, tissue type and accessibility to intact nuclei should be considered when designing ATAC-seq experiments

A Recurrent Neural Network Survival Model: Predicting Web User Return Time

The size of a website's active user base directly affects its value. Thus, it is important to monitor and influence a user's likelihood to return to a site. Essential to this is predicting when a user will return. Current state of the art approaches to solve this problem come in two flavors: (1) Recurrent Neural Network (RNN) based solutions and (2) survival analysis methods. We observe that both techniques are severely limited when applied to this problem. Survival models can only incorporate aggregate representations of users instead of automatically learning a representation directly from a raw time series of user actions. RNNs can automatically learn features, but can not be directly trained with examples of non-returning users who have no target value for their return time. We develop a novel RNN survival model that removes the limitations of the state of the art methods. We demonstrate that this model can successfully be applied to return time prediction on a large e-commerce dataset with a superior ability to discriminate between returning and non-returning users than either method applied in isolation.Comment: Accepted into ECML PKDD 2018; 8 figures and 1 tabl

Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads

The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight\u27s half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects\u27 and Twilight\u27s genome or due to errors in the reference. EquCab2 is regarded as The Twilight Assembly. The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo\u27s BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies between new, high throughput genomic sequence data generated for Twilight and the EquCab2 reference assembly. Most of these represent errors in the assembly, while approximately 10,000 are demonstrated to be contributions from another horse. Other results are presented that include the binary alignment map file of the mapped Sanger reads, a list of variants identified as discrepancies between the source data and resulting reference, and a BED annotation file that lists the regions of the genome whose consensus was likely derived from low coverage alignments

Revealing three-dimensional structure of individual colloidal crystal grain by coherent x-ray diffractive imaging

We present results of a coherent x-ray diffractive imaging experiment performed on a single colloidal crystal grain. The full three-dimensional (3D) reciprocal space map measured by an azimuthal rotational scan contained several orders of Bragg reflections together with the coherent interference signal between them. Applying the iterative phase retrieval approach, the 3D structure of the crystal grain was reconstructed and positions of individual colloidal particles were resolved. As a result, an exact stacking sequence of hexagonal close-packed layers including planar and linear defects were identified.Comment: 8 pages, 5 figure

Survival Benefit-Based Deceased-Donor Liver Allocation

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74806/1/j.1600-6143.2009.02571.x.pd

Comparison of the equine reference sequence with its Sanger source data and new Illumina reads

The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight's half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects' and Twilight's genome or due to errors in the reference. EquCab2 is regarded as "The Twilight Assembly." The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo's BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies between new, high throughput genomic sequence data generated for Twilight and the EquCab2 reference assembly. Most of these represent errors in the assembly, while approximately 10,000 are demonstrated to be contributions from another horse. Other results are presented that include the binary alignment map file of the mapped Sanger reads, a list of variants identified as discrepancies between the source data and resulting reference, and a BED annotation file that lists the regions of the genome whose consensus was likely derived from low coverage alignments

Limits on Production of Magnetic Monopoles Utilizing Samples from the DO and CDF Detectors at the Tevatron

We present 90% confidence level limits on magnetic monopole production at the Fermilab Tevatron from three sets of samples obtained from the D0 and CDF detectors each exposed to a proton-antiproton luminosity of $\sim175 {pb}^{-1}$ (experiment E-882). Limits are obtained for the production cross-sections and masses for low-mass accelerator-produced pointlike Dirac monopoles trapped and bound in material surrounding the D0 and CDF collision regions. In the absence of a complete quantum field theory of magnetic charge, we estimate these limits on the basis of a Drell-Yan model. These results (for magnetic charge values of 1, 2, 3, and 6 times the minimum Dirac charge) extend and improve previously published bounds.Comment: 18 pages, 17 figures, REVTeX

Estimation of loan portfolio risk on the basis of Markov chain model

A change of shares of credits portfolio is described by Markov chain with discrete time. A credit state is determined on as an accessory to some group of credits depending on presence of indebtedness and its terms. We use a model with discrete time and fix the system state through identical time intervals - once a month. It is obvious that the matrix of transitive probabilities is known incompletely. Various approaches to the matrix estimation are studied and methods of forecast the portfolio risk are proposed. The portfolio risk is set as a share of problematic loans. We propose a method to calculate necessary reserves on the base of the considered model. © 2013 IFIP International Federation for Information Processing.German Sci. Found. (DFG) Eur. Sci. Found. (ESF);Natl. Inst. Res. Comput. Sci. Control France (INRIA);DFG Research Center MATHEON;Weierstrass Institute for Applied Analysis and Stochastics (WIAS);European Patent Offic