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: Method and system for quantifying target nucleic acids using real-time amplification and internal calibration adjustment. The approach employs a single fixed data point in combination with a single adjustment calibrator amplified on the instrument that is to be calibrated for approximating a complete calibration curve.

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: Method and system for quantifying target nucleic acids using real-time amplification and internal calibration adjustment. The invention employs dual reference calibration curves for approximating a complete calibration curve from only a single adjustment calibrator amplified on the instrument that is to be calibrated.

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 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: 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: A compression method includes: measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises a plurality of measured values and the chemical event is indicative of a number of nucleotide incorporations in a genetic sequencing reaction; applying a first compression process to the waveform, the first compression process including a truncating of data corresponding to a portion of the waveform that is not related to nucleotide incorporations in the genetic sequencing reaction; and applying a second compression process to the waveform, the second compression process including a data substitution process that replaces at least a portion of the waveform with a plurality of coefficients representative of the portion of the waveform.

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: 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: 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: Methods, libraries, and kits for nucleotide sequencing are provided.

Abstract: A method, a program, and a device for evaluating food preference of pets that do not require humans to eat a pet food itself. The preference of pets can be evaluated by conducting sensory analysis on selected palatants contained in a pet food by humans. Accordingly, highly precise prediction of the preference can be made by a simple and intuitive method based on sensory attributes for human. Further, humans are not required to eat a pet food itself because the humans may conduct sensory analysis on selected palatants contained in the pet food.

Abstract: According to one aspect, a method for predicting the likelihood of survival of a particular individual with favorable neurological function during a cardiopulmonary resuscitation (CPR) procedure includes obtaining an electroencephalogram (EEG) signal of the particular individual during the CPR procedure. The method also includes obtaining a non-invasive measure of circulation of the particular individual during the CPR procedure and generating a prediction for the likelihood of survival of the particular individual with favorable neurological function based on the EEG signal and the non-invasive measure of circulation.

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: Nucleic acid expression constructs are provided and, more particularly, nucleic acid constructs for expression of human alpha-galactosidase in plant cells, cells expressing the nucleic acid construct, producing the human alpha-galactosidase and uses thereof.