Abstract: A method and system for detecting and removing EEG artifacts is disclosed herein. Each source of a plurality of sources for an EEG signal is separated for a selected artifact type. Each source of the plurality of sources is reconstituted into a recorded montage and an optimal reference montage for recognizing the selected artifact type of each source. The sources with artifacts are removed and the remaining sources are reconstituted into a filtered montage for the EEG signal.

Abstract: Methods for identifying patients with anemia, distinguishing thalassemia-trait anemia from iron-deficiency anemia, and identifying pre-anemic patients several weeks before anemia becomes clinically detectable. Also, methods for detecting blood doping in athletes and for optimizing therapy with erythropoiesis stimulating agents or iron supplementation. Computer-readable storage devices and systems, e.g., for use in the described methods.

Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Abstract: Systems, computer program products, and methods for using a flow cell array are provided herein. A computer program product includes a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a device to cause the device to determine placement of multiple reaction site openings, wherein each reaction site opening is connected to a first sub-surface channel; connect the first sub-surface channel to two or more additional sub-surface channels by multiple vias; and provide a material for multiple reaction sites, wherein an overlap of the multiple reaction site openings and the material delineate the multiple reaction sites.

Abstract: A method of tuning the performance of a synthetic gene circuit comprising a plurality of genes is disclosed. The method includes quantifying, for each gene, a relative gene expression metric. The metric is quantified by determining a number of nucleotides in a 5? adjacent transcriptional region (ATR) of the gene, a number of nucleotides in a 3? ATR, a minimum free energy of a mRNA secondary structure around a ribosome binding site of the gene, a total folding energy for the 5? ATR, and a folding energy for the first 100 nucleotides of the 3? ATR, and then summing sequence-dependent energy changes, the terms including scaling coefficients and an average energy cost for synthesizing a nucleotide. The method further includes simulating, through application of the relative gene expression metrics of the plurality of genes to a deterministic model, the performance of an intended function of the synthetic gene circuit.

Abstract: Systems, computer program products, and methods for using a flow cell array are provided herein. A system includes at least one processor coupled to a memory and configured for determining placement of multiple reaction site openings, wherein each reaction site opening is connected to a first sub-surface channel; connecting the first sub-surface channel to two or more additional sub-surface channels by multiple vias; and providing a material for multiple reaction sites, wherein an overlap of the multiple reaction site openings and the material delineate the multiple reaction sites.

Abstract: Apparatus, computer program products, and methods for using a flow cell array are provided herein. A computer program product includes a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a device to cause the device to determine placement of one or more reaction sites on a first component; provide a material for the reaction sites in one or more surface channels of the first component; connect the first component to a second component to form an array, wherein the surface channels of the first component connect the reaction sites with one or more vias, and wherein the second component comprises the vias connected to multiple sub-surface channels; and align the surface channels of the first component with the vias of the second component to form a connection between the first component and the second component.

Abstract: Systems, computer program products, and methods for using a flow cell array are provided herein. A system includes at least one processor coupled to a memory and configured for delivering multiple items of chemical matter independently to multiple reaction sites of a flow cell array across multiple distinct instances of time; imaging multiple parallel chemical reactions at the multiple reaction sites of the flow cell array; and recording an emission from each of the multiple chemical reactions site.

Abstract: A method of treating senescence in a subject can include applying a senoremediation drug treatment protocol to the subject in order to rescue one or more first cells in the subject, wherein the senoremediation drug treatment protocol is derived from a computational transcriptome analysis of the tissue or organ of the subject. The method can include applying a senolytic drug treatment protocol to the subject in order to remove one or more second cells in the subject. The method can include introducing stem cells into a tissue and/or organ of the subject in order to rejuvenate one or more tissue cells in the tissue and/or one or more organ cells in the organ. The method can include carrying out a reinforcement step that includes one or more actions that prevent further senescence or degradation of the tissue or organ.

Abstract: The subject disclosure presents systems and computer-implemented methods for providing reliable risk stratification for early-stage cancer patients by predicting a recurrence risk of the patient and to categorize the patient into a high or low risk group. A series of slides depicting serial sections of cancerous tissue are automatically analyzed by a digital pathology system, a score for the sections is calculated, and a Cox proportional hazards regression model is used to stratify the patient into a low or high risk group. The Cox proportional hazards regression model may be used to determine a whole-slide scoring algorithm based on training data comprising survival data for a plurality of patients and their respective tissue sections. The coefficients may differ based on different types of image analysis operations applied to either whole-tumor regions or specified regions within a slide.

Abstract: A specimen analyzer includes: an analysis unit which analyzes a specimen collected from a subject and generates an analysis result including a component amount in the specimen; an output unit which outputs the analysis result; and a controller which causes the output unit to output or not to output the component amount based on a comparison between the component amount and a determination reference value.

Abstract: A method of distinguishing nucleotide sequences for different nucleic acid molecules including the steps of (a) mixing a plurality of different nucleic acid molecules with polymerase molecules and nucleotide molecules, wherein the different nucleic acid molecules are attached to a surface in the form of an array of nucleic acid features; (b) determining a transient state of the polymerase molecules at the nucleic acid features; and (c) identifying a subset of nucleic acid features that correctly incorporate the nucleotide molecules based on the transient state of the polymerase molecules at the nucleic acid features, thereby distinguishing the nucleotide sequences for the different nucleic acid molecules.

Abstract: The present invention relates to methods for the analysis of nucleic acids present in biological samples, and more specifically to normalize a high resolution melt curve to assist in the identification of one or more properties of the nucleic acids. The present invention provides methods and systems that incorporate a background identification algorithm according to invention principles using raw melt curve data to identify reactions that are unrelated actual DNA melt reactions. Furthermore, a web-based application for analyzing experimental data is provided. The raw experimental data obtained from a variety of instruments is processed and analyzed on a server and presented to a user through a user interface (UI).

Abstract: A fractional concentration of clinically-relevant DNA in a mixture of DNA from a biological sample is determined based on amounts of DNA fragments at multiple sizes. For example, the fractional concentration of fetal DNA in maternal plasma or tumor DNA in a patient's plasma can be determined. The size of DNA fragments in a sample is shown to be correlated with a proportion of fetal DNA and a proportion of tumor DNA, respectively. Calibration data points (e.g., as a calibration function) indicate a correspondence between values of a size parameter and the fractional concentration of the clinically-relevant DNA. For a given sample, a first value of a size parameter can be determined from the sizes of DNA fragments in a sample. A comparison of the first value to the calibration data points can provide the estimate of the fractional concentration of the clinically-relevant DNA.

Abstract: Methods and systems are presented for analyzing the blood of a living being. Equations are presented for volume-aware extension of the concept of Hematocrit. A method for calculating these volume-aware measures and using said measures to evaluate and guide possible treatments is described. A system comprising an automated analyzer and a processor and other components is described which can carry out said calculations. Methods of treatment for volume abnormalities are described which are guided by the volume-aware Hct measures. In one exemplary embodiment, a method of treatment for plasma volume excess using ultrafiltration is described. In another exemplary embodiment, a method of treatment for red cell volume excess using erythrocytapheresis is described.

Abstract: A method for increasing the veracity of classification by detecting protein YKL-40 and MASP2 levels in the samples, comprises detecting the content of the YKL-40 and MASP2 in the samples; the ratio of the content of YKL-40 to the that of MASP2 acted as variable, receiving the ROC curve according to the sensitivity and specialty of the difference threshold value to the diagnosis for the cancer, calculating an area under the curve AUC; classifying the samples according to the value of the AUC, sensitivity and specialty. And a kit for detecting the protein YKL-40 and MASP2 levels in the samples.

Abstract: The present invention relates to a method and a system for selecting an anticancer agent based on protein damage information of an individual by using individual genome sequencing. The method and the system, according to the present invention, are highly reliable and widely applicable techniques capable of predicting side effects or risks of specific drugs, in other words, anticancer agents, for each individual by performing sequence analysis of an exon part of a gene that codes various proteins involved in pharmacokinetics or pharmacodynamics of anticancer agents.

Abstract: A system is disclosed that enables the automated measurement of cellular mechanical parameters at high throughputs. The microfluidic device uses intersecting flows to create an extensional flow region where the cells undergo controlled stretching. Cells are focused into streamlines prior to entering the extensional flow region. In the extensional region, each cell's deformation is measured with an imaging device. Automated image analysis extracts a range of independent biomechanical parameters from the images. These may include cell size, deformability, and circularity. The single cell data that is obtained may then be used to in a variety of ways. Scatter density plots of deformability and circularity may be developed and displayed for the user. Mechanical parameters such as deformability and circularity may be gated or thresholded to identify certain cells of interest or sub-populations of interest. Similarly, the mechanical data obtained using the device may be used as cell signatures.

Abstract: In some embodiments, systems and methods for storing and/or retrieving digital information in a nucleic acid library are provided. In some embodiments, an integrated system comprising a nucleic acid synthesis device, a nucleic acid sequencing device, a computing device, and a nucleic acid library is provided. In some embodiments, a write request that associates a value with a key is received by the system, the system synthesizes nucleic acid molecules associated with the request, and stores the nucleic acid molecules in the nucleic acid library. In some embodiments, a read request for a key is received by the system, and the system sequences nucleic acid molecules from the nucleic acid library that are associated with the key.

Abstract: Utilizing a computing device to assist in repurposing of a pharmaceutical. An identification of a pharmaceutical for repurposing study is received by a computing device. A pharmaceutical expression signature is retrieved based upon the identification of the pharmaceutical, the pharmaceutical expression signature indicating differential expressions of a plurality of biomolecules regulated by the pharmaceutical. A plurality of disease expression signatures are retrieved from a disease omics database, each disease expression signature indicating differential expressions of a plurality of biomolecules affected by a disease. A pharmaceutical vector is generated based upon the pharmaceutical expression signature for the pharmaceutical. A plurality of disease vectors are generated based upon the plurality of disease expression signatures for each disease.