Abstract: Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer.

Abstract: The technology described herein is directed to the diagnosis and treatment of androgen disorders and/or deficiencies, e.g. low testosterone.

Abstract: A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity in a plurality of first entities for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters. Differences in the discrete attribute values for the first entity across the second entities of a given cluster relative to the discrete attribute value for the same first entity across the other clusters are computed thereby deriving differential values. A heat map of these differential values for each first entity for each cluster is displayed to reveal the pattern in the dataset.

Abstract: Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions, including syndromes related to CNV of subchromosomal regions. In some embodiments, methods are provided for determining CNV of fetuses using maternal samples comprising maternal and fetal cell free DNA. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by removing within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples. In some embodiments, syndrome related biases in sample data are also removed to increase signal to noise ratio. Also disclosed are systems for evaluation of CNV of sequences of interest.

Abstract: Methods are described herein for small molecule biochemical profiling of an individual subject for diagnosis of a disease or disorder, facilitating diagnosis of a disease or disorder, and/or identifying an increased risk of developing a disease or disorder in the individual subject. Aberrant levels of small molecules present in a sample from an individual subject are identified and diagnostic information relevant to the individual subject is obtained based on the identified aberrant levels. The obtained diagnostic information includes one or more of an identification of at least one biochemical pathway associated with the identified subset of the small molecules having aberrant levels, an identification at least one disease or disorder associated with the identified subset of the small molecules having aberrant levels, and an identification of at least one recommended follow up test associated with the identified subset of the small molecules having aberrant levels.

Abstract: A determination device for enabling a computer to carry out a process including the steps of: obtaining an analysis result on methylation status of a CpG site located in a promoter region of at least one gene selected from HOXB4 (Homeobox B4) and ZSCAN31 (zinc finger and SCAN domain containing 31) in a DNA sample derived from a subject; and outputting a determination result as information on lung cancer in the subject based on the resulting analysis result is provided. A computer readable medium and a marker for obtaining information on lung cancer are also provided.

Abstract: A method of operation of a medical device system for determining prospective heart failure hospitalization risk. The method includes measuring one or more data observations via one or more electrodes of an implanted medical device disposed in a patient's body. The data observations are stored into memory of the implantable medical device of a patient. The data observations are transmitted to an external device. The processor of the external device parses the data observations into one or more evaluation periods. Using the number of observations in one or more evaluation periods, a look up table, stored into memory of the external device, is accessed. The look up table associates prospective heart failure hospitalization risk with the data observations noted in the evaluation period. One or more embodiments involve a weighted prospective heart failure hospitalization risk for the set of evaluation periods. The prospective heart failure hospitalization is then displayed on the graphical user interface.

Abstract: Improved methods and systems for diagnosing and for treating Cushing's syndrome and Cushing's Disease are provided herein, including methods and systems for concurrently treating Cushing's syndrome and differentially diagnosing Cushing's Disease from Ectopic Cushing's Syndrome in a patient with an established diagnosis of ACTH-dependent Cushing's syndrome. Treatment methods can use glucocorticoid receptor antagonists (GRAs), which differentially affect the ratio of cortisol to ACTH levels in patients having Cushing's Disease versus patients having Ectopic Cushing's Syndrome.

Abstract: A fitness tracking device configured to be worn by a user obtains a plurality of physical characteristics of the user including a first age and a sex of the user. The fitness tracking device maps each physical characteristic of the user to a corresponding index, wherein the first age of the user is mapped to a first age index of a first age range of a plurality of age ranges, and wherein the sex of the user is mapped to a first sex index. The fitness tracking device selects, from a memory of the fitness tracking device, a first calorimetry model of a plurality of calorimetry models, wherein the first calorimetry model is associated with each corresponding index, including the first age index and the first sex index of the user. The fitness tracking device estimates an energy expenditure rate using the first calorimetry model.

Abstract: A method and system for simulating cardiac function of a patient. A patient-specific anatomical model of at least a portion of the patient's heart is generated from medical image data. Cardiac electrophysiology potentials are calculated over a computational domain defined by the patient-specific anatomical model for each of a plurality of time steps using a patient-specific cardiac electrophysiology model. The electrophysiology potentials acting on a plurality of nodes of the computational domain are calculated in parallel for each time step. Biomechanical forces are calculated over the computational domain for each of the plurality of time steps using a cardiac biomechanical model coupled to the cardiac electrophysiology model. The biomechanical forces acting on a plurality of nodes of the computational domain are estimated in parallel for each time step. Blood flow and cardiac movement are computed at each of the plurality of time steps based on the calculated biomechanical forces.

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: 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: 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: 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: 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: 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.