Abstract: A system can be configured to generate and analyze one or more candidate logistics maps based on a set of input parameters and a baseline map of a logistics facility. The system can identify modifications strategies, resource limits, regions of interest, mapping constraints through analysis of the input parameters and the baseline map. The generated candidate maps and the baseline map can be implemented in virtual environments that are configured to replicate one or more operations associated with the baseline map, such as item distribution, item retrieval, and reorganization operations. The virtual environment can further simulate the resource limits associated with the baseline map and compare performance indicators from simulation of the baseline map to performance indicators from simulation of the candidate maps to identify viable improvements over existing logistics solutions.

Abstract: Systems and methods are provided for multi-style portfolio cash flow enhancement. The systems and methods include identifying a first set of one or more investment sleeves within an investment account as underweighted relative to a desired target and identifying a second set of one or more investment sleeves within the investment account as overweighted relative to the desired target, where the investment account includes a plurality of investment sleeves and where each investment sleeve includes at least one asset.

Abstract: A system and method for identifying a candidate set of at least one buy order associated with an investment account, determining a back out target value that identifies a fiscal amount by which the candidate set must to be reduced, and progressively decrementing a respective initial asset quantity of one or more buy orders of the candidate set until the back out target value is achieved at a final asset quantity of the one or more buy orders. The candidate set of buy orders can then be modified by replacing the respective initial asset quantity with the respective final asset quantity for at least one of the one or more buy orders. The modified candidate set of buy orders can then be provided for trade execution.

Abstract: A system and method for identifying a candidate set of one or more buy orders associated with an investment account, ordering the buy orders in the candidate set into a chain, determining a back out target value that identifies a fiscal amount by which the candidate set must be reduced, and decrementing an initial asset quantity of one or more successive non-zero quantity buy orders in the chain by a fixed integer quantity to a final asset quantity until the back out target value is achieved. The candidate set of buy orders can then be modified by replacing the respective initial asset quantity with the respective final asset quantity for at least one of the one or more buy orders. The modified candidate set of buy orders can then be provided for trade execution.

Abstract: In accordance with the present invention, methods are presented for labeling a cDNA strand with a labeled ribonucleotide base precursor which upon exposure to Mg2+, heat and base cleaves the cDNA at each place of incorporation of an RNA. In accordance with an aspect of the present invention, compounds selected from the group consisting of are incorporated into the growing strand of a cDNA by a reverse transcriptase or a mutant reverse transcriptase. After subject the strands to Mg2+, base and heat, the 3? OH causes cleavage of the cDNA leaving a 2?OH phosphate with a biotin label. The biotin provides a label which may be bound to streptavidin and thereafter hybridized to a nucleic acid array.

Abstract: In one aspect of the present invention polymers are used to create films providing three-dimensional array substrates. The films were stable and presented good hydroxyl group numbers as compared with arrays without polymer films. It is an object of the present invention that three dimensional arrays substrates provide a means to obtain higher density polymer arrays.

Abstract: In one aspect of the invention, a method is provided for end-labeling RNA (total RNA, mRNA, cRNA or fragmented RNA). In one aspect of the present invention, T4 RNA ligase is used to attach a 3?-labeled AMP or CMP donor to an RNA acceptor molecule. In another embodiment, a pyrophosphate molecule 3?-AppN-3?-linker-detectable moiety is used as donor molecule.

Abstract: VLSIPS™ manufacturing processes are of increasing commercial importance. The present invention provides methods and compositions for monitoring the efficiency and quality of polymer synthesis in VLSIPS™ arrays. Methods for monitoring polymer synthesis in an array on a substrate are provided. Mono-isomeric labels for the labeling of synthetic polymer arrays are provided. Methods and compositions for post-synthetically labeling polymers in polymer arrays are also provided.

Abstract: In accordance with the present invention, method are presented for labeling a cDNA strand with a photochemical cleavable reagent which upon exposure to electromagnetic radiation of particular reagent to create abasic DNA sites. According to one aspect of the present invention, DNA at the abasic sites, also known a chemical lactone group, is cleaved with an endonuclease, for example an endonuclease IV, which cleaves the DNA and leaves a free 3? OH group. This free 3? OH group is then labeled with a terminal transferase to provide a detectable moiety.

Abstract: Methods are provided for detecting hybridization of a polynucleotide to a nucleic acid array by chemically modifying the polynucleotide to contain a detectable label. According to one aspect of the present invention, a method is provided for detecting the presence of a mRNA in a nucleic acid sample, the method having the steps of providing a mRNA sample and azido modified nucleotides, hybridizing a primer to the mRNA, reversed transcribing the mRNA to provide azido modified DNA, followed by reacting the azido groups with a detectable label, hybridizing the labeled RNA to a nucleic acid array and detecting the presence of the mRNA.

Abstract: Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. The heterocyclic derivative containing compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.

Abstract: Methods for fragmenting and labeling nucleic acids for hybridization analysis are disclosed. In one aspect of the invention, methods and compositions are provided for fragmenting nucleic acid samples by exposure to acidic conditions to generate abasic positions and then cleavage of the abasic sites by, for example, an apurinic/apyrimidinic endonuclease. The resulting fragments may be end labeled and analyzed by hybridization to an array of nucleic acid probes.

Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.

Abstract: Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. The heterocyclic derivative containing compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.

Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.

Abstract: In one aspect of the invention, methods and compositions are provided for fragmenting nucleic acid samples. Fragmented nucleic acid samples may be used for hybridization with microarrays.

Abstract: Novel compounds are provided, which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Y, wherein Y is a chemical structure as shown in FIG. 1. Also provided is a method of forming, from component molecules, a plurality of compounds on a support, each compound occupying a separate predefined region of the support, using the protected compounds described above.

Abstract: Methods are provided for post incorporation labeling of a nucleic acid, including for example cRNA, labeled with nucleotide analogs having a formula selected from the group consisting of wherein A is H or a functional group that permits the attachment of the nucleic acid labeling compound to a nucleic acid; Y and Z are independently H or OH; L is linker group; and P is a connecting group. After incorporation of the nucleic acid (including cRNA) with the above nucleotide analogs, the nucleic acid is labeled with a detectable group reagent wherein said detetable group reagent comprises a chemical moiety which is capable of specifically reacting with said P group to allow coupling of the detectable group to said primed cRNA. Compounds comprising nucleotide analogs are also presented in accordance with the present invention. Methods are also presented for incorporating these compounds into nucleic acids and subsequently labeling the incorporated nucleotide analog with detectable moiety reagent.

Abstract: Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. Methods for making such heterocyclic compounds are also disclosed. The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.

Abstract: Novel compounds are provided which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Y, wherein: Y is a chemical structure as shown in FIG. 1. Also provided is a method of forming, from component molecules, a plurality of compounds on a support, each compound occupying a separate predefined region of the support, using the protected compounds described above.