Abstract: A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.

Abstract: A mirror system includes a visual display disposed to convey information and images during an active period; and the visual display disposed to provide a reflected image during an inactive period; a multi-spectral 3D camera including a high definition video camera and an infrared camera; and a processor coupled to the visual display and the multi-spectral 3D camera.

Abstract: A screening method evaluates influence of a cytotoxic factor on lymphoid cells. The method includes administering or irradiating lymphoid cells with the cytotoxic factor that injures the lymphoid cells; incubating the lymphoid cells to which the cytotoxic factor is administered or irradiated for a selected time; measuring a cell size of the lymphoid cells after the incubation; and determining influence of the cytotoxic factor on the lymphoid cells based on a change of the cell size. According to this method, influence of radiation or a drug, or efficacy of radiation, a radiation-protecting agent, an antioxidant, a radiation-sensitizing agent, a drug, or ultraviolet rays can be evaluated economically and objectively in a short period of time.

Abstract: A computer-implemented method for processing and/or analyzing nucleic acid sequencing data comprises receiving a first data input and a second data input. The first data input comprises untargeted sequencing data generated from a first nucleic acid sample obtained from a subject. The second data input comprises target-specific sequencing data generated from a second nucleic acid sample obtained from the subject. Next, with the aid of a computer processor, the first data input and the second data input are combined to produce a combined data set. Next, an output derived from the combined data set is generated. The output is indicative of the presence or absence of one or more polymorphisms of the first nucleic acid sample and/or the second nucleic acid sample.

Abstract: A method of screening biologically active agent based on the analysis of complex biological responses in culture. Methods for selecting cells and culture conditions for such screens are provided, as well as the identification of an optimized set of discrete parameters to be measured, and the use of biomap analysis for rapid identification and characterization of drug candidates, genetic sequences acting pathways, and the like. A feature of the invention is simultaneous screening of a large number of cellular pathways, and the rapid identification of compounds that cause cellular responses.

Abstract: The invention provides a method and system combining functional genomic and genetic, proteomic, anatomic neuroimaging, functional neuroimaging, behavioral and clinical measurements and data analyses for autism pediatric population screening, diagnosis or prognosis. More specifically, the invention provides a weighted gene and feature test for autism which uses a weighted gene signature matrix for comparison to a reference database of healthy and afflicted individuals. The invention also provides normalized gene expression value signatures for comparison to a reference database.

Abstract: Methods and apparatus for providing data processing and control for use in a medical communication system are provided.

Abstract: Method of analyzing signal data from a biosensor including a detection device having an array of light detectors. The method includes obtaining signal data from the light detectors. The signal data includes light scores that are based on an amount of light detected by the light detectors during a plurality of imaging events. The method also includes analyzing the light scores from a group of light detectors for each of the plurality of the imaging events. The method also includes determining respective crosstalk functions of the light detectors in the group. Each of the crosstalk functions for a corresponding light detector is based on the amount of light detected by other light detectors in the group. The method also includes analyzing the signal data for each of the imaging events using the crosstalk functions to determine characteristics of the analytes-of-interest.

Abstract: Systems, methods, and apparatuses for performing a prenatal diagnosis of a sequence imbalance are provided. A shift (e.g. to a smaller size distribution) can signify an imbalance in certain circumstances. For example, a size distribution of fragments of nucleic acids from an at-risk chromosome can be used to determine a fetal chromosomal aneuploidy. A size ranking of different chromosomes can be used to determine changes of a rank of an at-risk chromosome from an expected ranking. Also, a difference between a statistical size value for one chromosome can be compared to a statistical size value of another chromosome to identify a significant shift in size. A genotype and haplotype of the fetus may also be determined using a size distribution to determine whether a sequence imbalance occurs in a maternal sample relative to a genotypes or haplotype of the mother, thereby providing a genotype or haplotype of the fetus.

Abstract: The invention provides methods of using sequence based analysis and rational strategies to modify and improve the structural and biophysical properties of single chain antibodies (scFvs), including stability, solubility, and antigen binding affinity. These methods and strategies can be used individually or in combination. The methods of the present invention also include the use of a database comprising scFv sequences from an experimentally screened scFv library of antibodies that have been selected to have superior solubility and stability. The invention also provides methods of using the properties found for these selected antibodies in a general approach for reshaping scFv antibodies to improve stability and solubility properties of a single chain antibody fragment.

Abstract: Embodiments of the invention are directed to methods of diagnosing eosinophilic esophagitis (EoE), or remission therefrom in a subject, wherein the methods include applying a sample from the subject to a diagnostic panel that contains selected markers for EoE, analyzing to obtain relatedness information relative to an EoE cohort and making a determination as to the EoE status of the subject, wherein an analysis indicating grouping with an EoE cohort or a quantitative score similar to that of an EoE cohort are indicative of EoE in the subject. Embodiments of the invention are also directed to methods of monitoring the pathological development or medical prognosis of EoE in a subject.

Abstract: The invention includes methods for aligning reads (e.g., nucleic acid reads, amino acid reads) to a reference sequence construct, methods for building the reference sequence construct, and systems that use the alignment methods and constructs to produce sequences. The method is scalable, and can be used to align millions of reads to a construct thousands of bases or amino acids long. The invention additionally includes methods for identifying a disease or a genotype based upon alignment of nucleic acid reads to a location in the construct.

Abstract: Disclosed are methods of predicting the likelihood of long-term survival without recurrence of breast cancer for a subject having estrogen receptor-positive (ER+) breast cancer treated with adjuvant endocrine monotherapy. In various embodiments, these methods comprise performing a gene expression profile of a breast tissue sample of substantially all of the genes of the “CADER set” described herein; calculating a risk score using a regression model; and applying a double median cutoff classification to assign the subject to a sensitive, indeterminate or resistant group, wherein assignment to a sensitive group predicts longer relapse-free survival compared to the median relapse-free survival of ER+ breast cancer patients treated with adjuvant endocrine monotherapy.

Abstract: The present disclosure provides a method for enriching for multiple genomic regions using a first bait set that selectively hybridizes to a first set of genomic regions of a nucleic acid sample and a second bait set that selectively hybridizes to a second set of genomic regions of the nucleic acid sample. These bait set panels can selectively enrich for one or more nucleosome-associated regions of a genome, said nucleosome-associated regions comprising genomic regions having one or more genomic base positions with differential nucleosomal occupancy, wherein the differential nucleosomal occupancy is characteristic of a cell or tissue type of origin or disease state.

Abstract: Disclosed are methods and tools for rapidly aligning reads to a reference sequence. These methods and tools employ Bloom filters or similar set membership testers to perform the alignment. The reads may be short sequences of nucleic acids or other biological molecules and the reference sequences may be sequences of genomes, chromosomes, etc. The Bloom filters include a collection of hash functions, a bit array, and associated logic for applying reads to the filter. Each filter, and there may be multiple of these used in a particular application, is used to determine whether an applied read is present in a reference sequence. Each Bloom filter is associated with a single reference sequence such as the sequence of a particular chromosome. In one example, chromosomal abundance is determined by aligning reads from a sequencer to multiple chromosomes, each having an associated Bloom filter or other set membership tester.

Abstract: Response to treatment of an inflammatory condition can be predicted based on characteristics of one or more markers from a subject. The markers can include expressions of nucleotide sequences identified herein and of combinations thereof. A response value can be calculated based on characteristics (e.g., expression levels) of one or more of the markers, as well as other characteristics of the subject, such as baseline clinical data. The treatment can be administered when the response value is beyond a threshold.

Abstract: Provided is an open diatom cultivation method where continuous production of one or more selected diatom species achieve dominancy in the production system and that dominancy is maintained. The algae culture solution containing diatoms is first introduced to an open microalgae culture system. Then, carbon dioxide and nutrient salts are added to form a culture solution for diatom cultivation. The method enables industrial scale cultivation of diatoms at economically competitive production cost, with a high cultivation density and for a high production volume. The method also enables continuous stable production of selected diatoms and solves the difficult problem of controlling invading algae by always using the most competitive of local diatoms without imposing a selected algae which may be superior in some localities and under some climate conditions.

Abstract: The present invention relates to a microorganism, a microbial phosphate fertilizer and a method for manufacturing the microbial phosphate fertilizer, wherein the microorganism is Streptomyces cellulosae with Accession number CGMCC No. 2167 or Aspergillus versicolor with Accession number CGMCC No. 2171. The microbial phosphate fertilizer of the present invention comprises a fermentation product of the microbial composition consisting of the following four microorganisms: Bacillus subtilis strain WH2, Bacillus licheniformis strain WH4, Streptomyces cellulosae strain WH9 and Aspergillus versicolor strain WH13. A method for manufacturing the microbial phosphate fertilizer is also provided, wherein the manufacture of the microbial phosphate fertilizer may involve the use of ground phosphate rock having 8%-12% P2O5.

Abstract: A method of discovering one or more patterns in two sequences of symbols S1 and S2 includes the formation, for each sequence, of a master offset table that groups for each symbol the position in the sequence occupied by each occurrence of that symbol. The difference in position between each occurrence of a symbol in one of the sequences and each occurrence of that same symbol in the other sequence is determined and a Pattern Map is formed. For each given value of a difference in position the Pattern Map lists the position in the first sequence of each symbol therein that appears in the second sequence at that difference in position. The collection of the symbols tabulated for each value of difference in position thereby defines a parent pattern in the first sequence that is repeated in the second sequence.

Abstract: It is the aim of the invention to provide a technology for the stimulation of the crystallization of biomolecules contained in a liquid solution that leads to significant improvements in the reliability of crystal growth processes and shortens the time and the number of attempts to grow a certain biomolecule crystal, also under the condition that only very small amounts of the biomolecules are available.