236 research outputs found
MICROFLUIDIC DEVICES AND METHODS OF GENERATING AND USING SAME
No full textA microfluidic device comprising a substrate having formed therein microfluidic paths, at least a portion of the microfluidic paths having attached thereto a plurality of monolayers, wherein at least a portion of the monolayers comprises a photoactivatable group capable of generating a reactive group upon exposure to a light source, the reactive group being for binding a screenable moiety
A Single-Step Photolithographic Interface for Cell-Free Gene Circuits
No full textWe have developed a biochip platform technology suitable for controlled cell-free gene expression at the micrometer scale. A new hybrid molecule, “Daisy”, was designed and synthesized to form in a single step a biocompatible
lithographic interface on silicon dioxide. A protocol is described
for the immobilization of linear DNA molecules thousands of base pairs long on Daisy-coated surfaces with submicrometer spatial resolution and up to high densities. On-chip protein synthesis can be obtained with a dynamic range of up to four ordersof magnitude and minimal nonspecific activity. En route to on-chip artificial gene circuits, a simple two-stage gene cascade was built, in which the protein synthesized at the first location diffuses to regulate the synthesis of another protein at a second location. We demonstrate the capture of proteins from crude extract onto micrometer-scale designated traps, an important step for the formation of miniaturized self-assembled protein chips. Our biochip platform can be combined with elastomeric microfluidic devices, thereby opening possibilities for isolated and confined reaction chambersand artificial cells in which the transport of products and reagents is done by diffusion and flow. The Daisy molecule and described approach enables groups not proficient in surface chemistry to construct active biochips based on cellfree gene expression
A SINGLE STEP-PLATFORM FOR ON-CHIP INTEGRATION OF BIOMOLECULES
No full textNovel compounds having a functionalized group capable of binding to a solid substrate; a photoactivatable group capable of generating a reactive group upon exposure to light and being for binding a screenable moiety; and a polymer capable of forming a monolayer on a solid substrate, and having the functionalized group and to the photoactivatable group attached thereto and processes for the preparation thereof are disclosed. Further disclosed are arrays of screenable moieties (e.g., nucleic acids, proteins, carbohydrates, substrates, chelating agents and many more) prepared using these novel compounds
ImpulseDE: detection of differentially expressed genes in time series data using impulse models.
No full textSummaryPerturbations in the environment lead to distinctive gene expression changes within a cell. Observed over time, those variations can be characterized by single impulse-like progression patterns. ImpulseDE is an R package suited to capture these patterns in high throughput time series datasets. By fitting a representative impulse model to each gene, it reports differentially expressed genes across time points from a single or between two time courses from two experiments. To optimize running time, the code uses clustering and multi-threading. By applying ImpulseDE , we demonstrate its power to represent underlying biology of gene expression in microarray and RNA-Seq data.Availability and implementationImpulseDE is available on Bioconductor ( https://bioconductor.org/packages/ImpulseDE/ )[email protected] informationSupplementary data are available at Bioinformatics online
Higher Degree Erdos-Ginzburg-Ziv Constants
No full textWe generalize the notion of Erd\H{o}s-Ginzburg-Ziv constants -- along the
same lines we generalized in earlier work the notion of Davenport constants --
to a ``higher degree" and obtain various lower and upper bounds. These bounds
are sometimes exact as is the case for certain finite commutative rings of
prime power cardinality. We also consider to what extent a theorem due
independently to W.D.~Gao and the first author that relates these two
parameters extends to this higher degree setting. Two simple examples that
capture the essence of these higher degree Erd\H{o}s-Ginzburg-Ziv constants are
the following. 1) Let denote the adic valuation of the integer
. Suppose we have integers and , then
every sequence over of length contains a
subsequence of length for which , and this is sharp. 2) Suppose
for some integer . Then every sequence over
of length contains a subsequence of length
for which . These
examples illustrate that if a sequence of elements from a finite commutative
ring is long enough, certain symmetric expressions (symmetric polynomials) have
to vanish on the elements of a subsequence of prescribed length. The
Erd\H{o}s-Ginzburg-Ziv Theorem is just the case where a sequence of length
over contains a subsequence of
length that vanishes when substituted in the linear symmetric polynomial
$a_1+\cdots+a_n.
Spatial-Aided Low-Delay Wyner-Ziv Video Coding
No full textIn distributed video coding, the side information (SI) quality plays an important role in Wyner-Ziv (WZ) frame coding. Usually, SI is generated at the decoder by the motion-compensated interpolation (MCI) from the past and future key frames under the assumption that the motion trajectory between the adjacent frames is translational with constant velocity. However, this assumption is not always true and thus, the coding efficiency for WZ coding is often unsatisfactory in video with high and/or irregular motion. This situation becomes more serious in low-delay applications since only motion-compensated extrapolation (MCE) can be applied to yield SI. In this paper, a spatial-aided Wyner-Ziv video coding (WZVC) in low-delay application is proposed. In SA-WZVC, at the encoder, each WZ frame is coded as performed in the existing common Wyner-Ziv video coding scheme and meanwhile, the auxiliary information is also coded with the low-complexity DPCM. At the decoder, for the WZ frame decoding, auxiliary information should be decoded firstly and then SI is generated with the help of this auxiliary information by the spatial-aided motion-compensated extrapolation (SA-MCE). Theoretical analysis proved that when a good tradeoff between the auxiliary information coding and WZ frame coding is achieved, SA-WZVC is able to achieve better rate distortion performance than the conventional MCE-based WZVC without auxiliary information. Experimental results also demonstrate that SA-WZVC can efficiently improve the coding performance of WZVC in low-delay application
Deterministic amplification of space bounded probabilistic algorithms
No full textThis paper initiates the study of deterministic ampli-fication of space-bounded probabilistic algorithms. The straightforward implementations of known amplification methods cannot be used for such algorithms, since they con-sume too much space. We present a new implementation of the Ajtai-Komlós-Szemerédi method, that enables to am-plify an S-space algorithm that uses r random bits and errs with probability to an O(kS)-space algorithm that uses r +O(k) random bits and errs with probability (k). This method can be used to reduce the error probability of BPL algorithms below any constant, with only a con-stant addition of new random bits. This is weaker than the exponential reduction that can be achieved for BPP algo-rithms by methods that use only O(r) random bits. How-ever, we prove that any black-box amplification method that uses O(r) random bits and makes at most p parallel simu-lations reduces the error to at most O(p). Hence, in BPL, where p should be a constant, the error cannot be reduced to less than a constant. This means that our method is op-timal with respect to black-box amplification methods, that use O(r) random bits. The new implementation of the AKS method is based on explicit constructions of constant-space online extractors and online expanders. These are extractors and expanders, for which neighborhoods can be computed in a constant space by a Turing machine with a one-way input tape.
A note on the edge cover number and independence number in hypergraphs
No full textAbstractConsider a hypergraph of rank r>2 with m edges, independence number α and edge cover number ρ. We prove the inequalityρ⩽(r-2)m+αr-1.One application of this inequality is a special case of a conjecture of Aharoni and the first author extending Ryser's Conjecture to matroids
Smaller Flight Data Recorders
No full textData captured by flight data recorders are generally stored on the system’s embedded hard disk. A common problem is the lack of storage space on the disk. This lack of space for data storage leads to either a constant effort to reduce the space used by data, or to increased costs due to acquisition of additional space, which is not always possible. File compression can solve the problem, but carries with it the potential drawback of the increased overhead required when writing the data to the disk, putting an excessive load on the system and degrading system performance. The author suggests the use of an efficient compressed file system that both compresses data in real time and ensures that there will be minimal impact on the performance of other tasks
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