Abstract: A modeling and simulation environment enables a user to create a model of a stiff chemical or biological system. The stiff chemical or biological system refers to a system that includes at least two or more different time scales of the chemical or biochemical reactions. The modeling and simulation environment also enables the user to solve the stiff chemical or biological system using a leaping algorithm. The leaping algorithm may leap over simulation of the reactions occurring in the time interval to accelerate the simulation of the chemical or biological system. The algorithm maximizes the size of the time interval by adjusting the size of the time interval using a bracketing algorithm.

Abstract: Clinical information, molecular information and/or computer-generated morphometric information is used in a predictive model for predicting the occurrence of a medical condition. In an embodiment, a model predicts whether a patient is likely to have a favorable pathological stage of prostate cancer, where the model is based on features including one or more (e.g., all) of preoperative PSA, Gleason Score, a measurement of expression of androgen receptor (AR) in epithelial and stromal nuclei and/or a measurement of expression of Ki67-positive epithelial nuclei, a morphometric measurement of a ratio of area of epithelial nuclei outside gland units to area of epithelial nuclei within gland units, and a morphometric measurement of area of epithelial nuclei distributed away from gland units. In some embodiments, quantitative measurements of protein expression in cell lines are utilized to objectively assess assay (e.g.

Abstract: The methods and systems of the present invention are useful in the diagnosis of inflammatory bowel disease (IBD) and in the prognosis of IBD progression and disease complications. With the present invention, it is possible to predict outcome of disease and patients who will have a particular risk of disease complications and/or progression to surgery.

Abstract: Methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer.

Abstract: Systems, methods, and devices for intercommunication between a medical sensor and an electronic patient monitor are provided. For example, one embodiment of a system for communicably coupling a medical sensor to an electronic patient monitor may include a sensor-side communication connector and a monitor-side communication connector. The sensor-side communication connector may be capable of receiving a raw physiological measurement signal from the medical sensor, and the monitor-side communication connector may be capable of providing a digital physiological measurement signal based at least in part on the raw physiological measurement signal to the electronic patient monitor via a data link.

Abstract: Systems, methods, and devices for intercommunication between a medical sensor and an electronic patient monitor are provided. For example, one embodiment of a system for communicably coupling a medical sensor to an electronic patient monitor may include a sensor-side communication connector and a monitor-side communication connector. The sensor-side communication connector may be capable of receiving a raw physiological measurement signal from the medical sensor, and the monitor-side communication connector may be capable of providing a digital physiological measurement signal based at least in part on the raw physiological measurement signal to the electronic patient monitor via a data link.

Abstract: In a biological sample analyzing apparatus and method, an assay sample is prepared by mixing a reagent with a biological sample which may contain assay material. Then, a first information relating to the assay material is collected from the assay sample, and when the first information satisfies predetermined condition, the assay material is analyzed based on the first information. However, when the first information does not satisfy the predetermined condition, a second information related to the assay material is collected from the assay sample, and the assay material is analyzed based on the second information.

Abstract: Systems, methods, and devices for intercommunication between a medical sensor and an electronic patient monitor are provided. For example, one embodiment of a system for communicably coupling a medical sensor to an electronic patient monitor may include a sensor-side communication connector and a monitor-side communication connector. The sensor-side communication connector may be capable of receiving a raw physiological measurement signal from the medical sensor, and the monitor-side communication connector may be capable of providing a digital physiological measurement signal based at least in part on the raw physiological measurement signal to the electronic patient monitor via a data link.

Abstract: A method and/or system for analyzing data using population clustering through density based merging.

Abstract: The current invention is directed to methods for noninvasive detection of fetal genetic abnormalities by large-scale sequencing of nucleotides from maternal biological sample. Further provided are methods to remove GC bias from the sequencing results according to the difference in GC content of a chromosome. The current invention not only makes the detection much more accurate but also represents a comprehensive method for fetal aneuploidy detection including sex chromosome disorders such as XO, XXX, XXY, and XYY, etc.

Abstract: A noninvasive patient-specific method is provided to aid in the analysis, diagnosis, prediction or treatment of hemodynamics of the cardiovascular system of a patient. Coronary blood flow and pressure can be predicted using a 3-D patient image-based model that is implicitly coupled with a model of at least a portion of the remaining cardiovascular system. The 3-D patient image-based model includes at least a portion of the thoracic aorta and epicardial coronaries of the patient. The shape of one or more velocity profiles at the interface of the models is enforced to control complex flow features of recirculating or retrograde flow thereby minimizing model instabilities and resulting in patient-specific predictions of coronary flow rate and pressure. The invention allows for patient-specific predictions of the effect of different or varying physiological states and hemodynamic benefits of coronary medical interventions, percutaneous coronary interventions and surgical therapies.

Abstract: A mass-spectral method is disclosed for determining whether breast cancer patient is likely to benefit from a combination treatment in the form of administration of a targeted anti-cancer drug in addition to an endocrine therapy drug. The method obtains a mass spectrum from a blood-based sample from the patient. The spectrum is subject to one or more predefined pre-processing steps. Values of selected features in the spectrum at one or more predefined m/z ranges are obtained. The values are used in a classification algorithm using a training set comprising class-labeled spectra and a class label for the sample is obtained. If the class label is “Poor”, the patient is identified as being likely to benefit from the combination treatment. In a variation, the “Poor” class label predicts whether the patient is unlikely to benefit from endocrine therapy drugs alone, regardless of the patient's HER2 status.

Abstract: Markers and methods useful for assessing coronary artery disease in a subject are provided, along with kits for measuring their expression. Also provided are predictive models, based on the markers, as well as computer systems, and software embodiments of the models for scoring and optionally classifying samples.

Abstract: The invention relates to methods for the early diagnosis of Acute Coronary Syndrome.

Abstract: Genetic sequence data occurring in genome sequences is represented for efficient access of the sequence information in a defined storage scheme. A described replet-sequence matrix data structure allows the compression and efficient access of sequence information. The data structure allows the dynamic change of ontology: the replet-information table can evolve by adding, updating, removing replets, and the set of replets present in the table represent the ontology at the moment. The data structure enables the sequence information to be processed in parallel, and also enables multiple views of the sequence data to exist along with replet specific information.

Abstract: Systems and methods automatically assemble a set of read sequences into one or more larger nucleotide sequences using a set of comparing sequences as a template. The sequences of each set are divided into smaller mer sequences and sorted to arrange the mer sequences in order, and the sets of mers originating from the read sequence set and the comparing sequence set are compared pairwise to determine matching regions between the sequences of the read sequence set and the sequences of the comparing set. The sorting of the sequence sets prior to the pairwise comparison reduces the amount of volatile memory required to assemble the read sequence set and also reduces the overall time to assemble the read sequence set into one or more larger nucleotide sequences.

Abstract: A system and device are provided which include a gene regulatory system controlling expression of one or more expression cassettes present in or released by the device, by emitting one or more stimulations. An expression cassette includes a regulatable transcription control element that is responsive to the emitted stimulations linked to an open reading frame of interest. The system optionally includes a sensor to sense a parameter indicative of a need, a telemetry module to receive an external command, or a programmable device, for regulating gene expression of the open reading frame.

Abstract: A method for determining bias across two domains comprising gene expression data. The method can comprise (a) providing a first domain and a second domain; (b) obtaining information indicative of a bias within the first domain; (c) obtaining information indicative of a bias within the second domain; and (d) using the information indicative of the bias within the first domain and the information indicative of the bias within the second domain to produce an indication of bias across the two domains.

Abstract: Provided is a method for improving useful substance-producing organisms using metabolic flux analysis, and more particularly a method for improving a host organism producing a useful substance, the method including: calculating a maximum flux value corresponding to the theoretical maximum yield of the useful substance in the metabolic network model of the host organism for producing useful substance, and calculating the optimum value of metabolic flux associated with useful substance production in the metabolic network when the value of cell growth-associated metabolic flux is the maximum under the condition where fermentation data are applied or not applied; selecting metabolic fluxes whose absolute values increase from the range between the maximum value and the optimum value; screening genes associated with the selected metabolic fluxes; and introducing and/or amplifying the selected genes in the host organism. Production of the useful substance can be effectively improved by using the method.

Abstract: The present invention identifies genes whose gene products are differentially expressed in lymphedema tissues, particularly cutaneous tissue involved in whole organ response to lymphedema. The invention provides methods for diagnosing or assessing an individual's susceptibility to lymphedema. Also provided are therapeutic methods for treating a patient or methods for prophylactically treating an individual susceptible to lymphedema. Additionally, the invention describes screening methods for identifying agents that can be administered to treat individuals that have or at risk of developing lymphedema.