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: Compositions and methods for producing plant-derived immunogenic compositions that confer immunity against smallpox in a subject are provided. Plants engineered to produce antigenic proteins as well as expression cassettes comprising nucleic acids encoding proteins thereof are described. Methods of immunizing subjects with plant-derived compositions are also provided.

Abstract: This disclosure is related to systems and methods for rapid determination of microorganism growth and antimicrobial agent susceptibility and/or resistance.

Abstract: There is provided a computer-implemented method for calculating a gastric emptying rate from a stomach lumen into a small intestine of a patient, comprising: using at least one processor for executing the following during an enteral tube feeding of a stomach of the patient by a feeding mechanism: analyzing outputs of at least one stomach sensor located within the stomach for detecting a stop feeding condition; pausing the enteral tube feeding in response to a detection of the stop feeding condition; after a predefined period of time, restarting the enteral tube feeding until the stop condition is redetected by an analysis of said outputs; calculating a gastric emptying rate based on an amount of feeding content delivered during a period between the restarting and the redetection; and instructing the feeding mechanism to adapt a feeding rate of the enteral tube feeding according to the gastric emptying rate.

Abstract: The present disclosure concerns methods of administering and detecting a distinguishable agent in a sample from and assessing the condition of an organ in a subject. In a particular embodiment, the present invention concerns methods of detecting and comparing the cholate shunt, in a subject, preferably in a subject with chronic hepatitis C. In certain embodiments, the methods may comprise obtaining a sample from a subject such as a blood or saliva sample after administering an oral and intravenous dose of a distinguishable agent such as cholate and analyzing the sample clearance of the distinguishable agent from the subject and comparing the clearance levels in order to assess hepatic health. In another embodiment, the methods may comprise analyzing a sample from a subject for the presence of a distinguishable agent such as cholate and applying information obtained from analyzing the presence of the distinguishable agent to determine a treatment for a medical condition of the subject.

Abstract: Methods and systems for fabricating a micro-structured biomaterial include printing a three-dimensional structure using polymerizing radiation modulated by a digital micromirror array to project microstructure patterns into a pre-polymer material to form one or more porous scaffold sheets. The microstructure patterns have a unit-cell geometry that exhibits a negative Poisson ratio that is tunable in magnitude.

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

Abstract: The invention provides methods and kits useful for predicting or assessing responsiveness of a patient having B-cell lymphoma to treatment with anti-CD40 antibodies.

Abstract: Processes, as well as associated systems and computer program (software) products, are disclosed for the biological conversion of CO into desired end products such as ethanol. The control methodologies used for these processes can advantageously result in a reduced time required for a batch operation or other initial operating period, prior to achieving a continuous operation, which may be demarcated either by the addition of fresh culture medium at a defined flow rate or by another process initiation target. The control methodologies may alternatively, or in combination, improve a process performance parameter, such as productivity of the desired end product or bacterial growth rate, during this batch operation or other initial operating period.

Abstract: The present invention provides a highly-safe information processing system that is capable of effectively using nucleotide sequence information differences between individual organisms to offer semantic information useful for each individual organism while properly preventing leakage and illegal use of nucleotide sequence information. Further, the present invention includes steps a and b. Step a is performed to acquire either encrypted nucleotide sequence-related information or cryptographic key that corresponds to positional information indicating a position within a nucleotide sequence.

Abstract: Computer systems, computer readable media, and computer methods for obtaining, calling, and assembling nucleic acid sequences are presented. In some aspects the invention includes the sequencing of template constructs that comprise double stranded portions in partially contiguous constructs, to provide for single molecule consensus sequence determination through one or both of sequencing sense and antisense strands in the same molecule.

Abstract: Methods, systems, and compositions can determine gene expression level of a specified cell-type subpopulation by direct analysis of a cell mixture sample composed of multiple subpopulations of various cell-types without the need of prior separation of the component cell-type subpopulations. A target gene and a reference gene can be identified as being informative for a specific cell-type subpopulation when at least 50% of the gene's transcripts in the cell mixture are from the subpopulation. This relative expression level in the cell mixture of the informative target and reference genes can correlate to the relative expression when measured in the isolated subpopulation. Thus, a similar biomarker can be obtained without the difficult step of isolating the cells of the subpopulation.

Abstract: An embodiment of method for correcting an error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template molecule is described that comprises (a) detecting a signal generated in response to an incorporation of one or more nucleotides in a sequencing reaction; (b) generating a value for the signal; and (c) correcting the value for the phasic synchrony error using a first parameter and a second carry forward parameter.

Abstract: A method of processing sequencing data obtained with a polymer sequencing system identifies the most likely monomer sequence of a polymer, regardless of stochastic variations in recorded signals. Polymer sequencing data is recorded and two or more distinct series of pore blocking signals for a section of the polymer are recorded. A value is assigned to each series of pore blocking signals to obtain multiple trial sequences. The probability that each of the trial sequences could have resulting in all of trial sequences is calculated to determine a monomer sequence with the highest probability of resulting in all of the trial sequences, termed the first iteration sequence. The first iteration sequence is systematically altered to maximize the combined probability of the first iteration sequence leading to all the trial sequences in order to obtain a most likely sequence of monomers of the polymer.

Abstract: Methods and apparatus for analyte level estimation are provided for filtering measurement data. In an embodiment, a present predicted analyte level estimate is determined. A present corrected analyte level estimate is determined based at least in part on the determined present predicted analyte level estimate and a received present monitored analyte measurement data. One or more of the medication infusion rate or the received present monitored analyte measurement data are filtered using a rate variance filter, wherein when the medication infusion rate exceeds a predetermined threshold level, the rate variance filter is adjusted from a predetermined setting to a modified setting to be responsive to changes in the present monitored analyte measurement data after a predetermined time period lapses.

Abstract: In certain embodiments transgenic plants (e.g., transgenic tomatoes) are provided that comprise cells that express a peptide one or more domains of which comprise the amino acid sequence of an apolipoprotein or apolipoprotein mimetic peptide where the peptide has biological activity (e.g., lowers SAA, and/or increases paroxonase activity, and/or improves HDL inflammatory index, etc.) when the plant and/or the peptide is fed to a mammal.

Abstract: A compression method includes measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises at least one region associated with expected measured values and at least one region associated with unpredictable measured values; applying a first compression process to the waveform, the first compression process including an averaging of one or more frames in one or more portions of the waveform; and applying a second compression process to the waveform, the second compression process including a truncating of data corresponding to a portion of the waveform that is not related to a nucleotide incorporation component of the waveform.

Abstract: Systems, methods, and apparatus for determining at least a portion of fetal genome are provided. DNA fragments from a maternal sample (maternal and fetal DNA) can be analyzed to identify alleles at certain loci. The amounts of DNA fragments of the respective alleles at these loci can be analyzed together to determine relative amounts of the haplotypes for these loci and determine which haplotypes have been inherited from the parental genomes. Loci where the parents are a specific combination of homozygous and heterozygous can be analyzed to determine regions of the fetal genome. Reference haplotypes common in the population can be used along with the analysis of the DNA fragments of the maternal sample to determine the maternal and paternal genomes. Determination of mutations, a fractional fetal DNA concentration in a maternal sample, and a proportion of coverage of a sequencing of the maternal sample can also be provided.

Abstract: A method of producing an agent capable of eliciting immune response against White Spot Syndrome Baculovirus complex in crustaceans of Penaeidae family upon ingestion of the agent comprising the steps of introducing a vector containing genetic sequence of Seq. No 1 into an alga to transform the algae; and cultivating the transformed algae to express modified VP28 peptides according to the genetic sequence of Seq. No. 1 to obtain the agent.

Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.