Abstract: The present invention relates to methods for the specific lysis of eukaryotic cells in a sample containing microorganisms such as bacterium and fungus by incubating the sample in a buffer of around pH 9 that contains a non-ionic detergent.

Abstract: A computing system comprising a central processing unit (CPU), and memory coupled to the CPU and having stored therein instructions that, when executed by the computing system, cause the computing system to execute operations to generate a radiation treatment plan. The operations include accessing a minimum prescribed dose to be delivered into and across the target, determining a number of beams and directions of the beams, and determining a beam energy for each of the beams, wherein the number of beams, the directions of the beams, and the beam energy for each of the beams are determined such that the entire target receives the minimum prescribed dose. A quantitative time-dependent model-based charged particle pencil beam scanning optimization is then implemented for FLASH therapy.

Abstract: Provided herein are methods and compositions to classify DLBCL subtypes using quantitative RT-PCR.

Abstract: A computing system comprising a central processing unit (CPU), and memory coupled to the CPU and having stored therein instructions that, when executed by the computing system, cause the computing system to execute operations to generate a radiation treatment plan. The operations include accessing a minimum prescribed dose to be delivered into and across the target, determining a number of beams and directions of the beams, and determining a beam energy for each of the beams, wherein the number of beams, the directions of the beams, and the beam energy for each of the beams are determined such that the entire target receives the minimum prescribed dose. A quantitative time-dependent model-based charged particle pencil beam scanning optimization is then implemented for FLASH therapy.

Abstract: Embodiments of the present invention provide an integrated solution to radiotherapy treatment planning that enables accurate recording and accumulation of physical parameters as input (e.g., dose, dose rate, irradiation time per voxel, etc.). User-defined functions are evaluated to correlate the input parameters with 4D biological outcomes. The resulting biological parameters can be visualized as a biological outcome map to evaluate decisions, support decisions, and optimize decisions regarding the parameters of the radiotherapy treatment plan, for example, for supporting clinical trials and related clinical research.

Abstract: Embodiments of the present invention provide an integrated solution to radiotherapy treatment planning that enables accurate recording and accumulation of physical parameters as input (e.g., dose, dose rate, irradiation time per voxel, etc.). User-defined functions are evaluated to correlate the input parameters with 4D biological outcomes. The resulting biological parameters can be visualized as a biological outcome map to evaluate decisions, support decisions, and optimize decisions regarding the parameters of the radiotherapy treatment plan, for example, for supporting clinical trials and related clinical research.

Abstract: A computing system comprising a central processing unit (CPU), and memory coupled to the CPU and having stored therein instructions that, when executed by the computing system, cause the computing system to execute operations to generate a radiation treatment plan. The operations include accessing a minimum prescribed dose to be delivered into and across the target, determining a number of beams and directions of the beams, and determining a beam energy for each of the beams, wherein the number of beams, the directions of the beams, and the beam energy for each of the beams are determined such that the entire target receives the minimum prescribed dose. A quantitative time-dependent model-based charged particle pencil beam scanning optimization is then implemented for FLASH therapy.

Abstract: Provided herein are methods and compositions to classify DLBCL subtypes using quantitative RT-PCR.

Abstract: Provided herein are methods and compositions for detecting gene fusions, e.g., relevant to cancer. The present methods and compositions can be used to detect gene fusions with very high sensitivity and specificity. The present methods and compositions can detect gene fusions, e.g., in free circulating tumor RNA from a plasma sample.

Abstract: Provided herein are methods and compositions to classify DLBCL subtypes using quantitative RT-PCR.

Abstract: Provided herein are methods and compositions to classify DLBCL subtypes using quantitative RT-PCR.

Abstract: Provided herein are methods and compositions for detecting gene fusions, e.g., relevant to cancer. The present methods and compositions can be used to detect gene fusions with very high sensitivity and specificity. The present methods and compositions can detect gene fusions, e.g., in free circulating tumor RNA from a plasma sample.

Abstract: The invention provides methods and kits for detecting and/or measuring receptor homodimers on a cell surface membrane. In one aspect, the methods employ pairs of probes comprising binding compounds and a cleaving probe, such that at least one binding compound binds specifically to the same epitope of a membrane-bound analyte as the cleaving probe. The binding compound includes one or more molecular tags attached through a cleavable linkage, and the cleaving probe includes a cleavage-inducing moiety that can cleave the linkage when within a defined proximity thereto. Binding of the two probes to a homodimer of a cell surface molecules results in release of molecular tags from the binding compounds, providing a measure of formation of the homodimeric complex.

Abstract: Methods are provided for detecting the formation of complexes of molecules, especially proteins, in a sample, such as a cell or tissue lysate. In one aspect, a cleaving probe specific for a first protein in a complex and one or more binding compounds specific for one or more second proteins in a complex are provided. Upon binding, the cleaving probe is induced to generate an active species, such as singlet oxygen, that cleaves molecular tags attached to the binding compounds only in the local region of the cleaving probe. The released molecular tags are separated from the assay mixture and from one another to provide a readout that is related to the number and types of proteins present in the complex.

Abstract: Methods for measuring hetero- and homodimerization of HIV reverse transcriptase (HIV RT) are provided using pairs of tagged probes and cleaving probes. The methods can be used, for example, to screen for modulators of HIV RT dimerization. Also provided are methods of determining whether a compound modulates HIV RT. Further provided are methods of determining whether a compound modulates formation of a complex between a p66 and p51, p66 and p66, or p51 and p55 subunits polypeptides of HIV RT.

Abstract: The invention is directed to a new class of biomarker in patient samples comprising dimers of ErbB cell surface membrane receptors. In one aspect, the invention includes a method of determining the status of a disease or healthful condition by correlating such condition to amounts of one or more dimers of ErbB cell surface membrane receptors measured directly in a patient sample, in particular a fixed tissue sample. In another aspect, the invention includes a method of determining a status of a cancer in a specimen from an individual by correlating measurements of amounts of one or more dimers of ErbB cell surface membrane receptors in cells of the specimen to such status, including presence or absence of a pre-cancerous state, presence or absence of a cancerous state, prognosis of a cancer, or responsiveness to treatment.

Abstract: The invention is directed to a new class of biomarker in patient samples comprising dimers of ErbB cell surface membrane receptors. In one aspect, the invention includes a method of determining the status of a disease or healthful condition by correlating such condition to amounts of one or more dimers of ErbB cell surface membrane receptors measured directly in a patient sample, in particular a fixed tissue sample. In another aspect, the invention includes a method of determining a status of a cancer in a specimen from an individual by correlating measurements of amounts of one or more dimers of ErbB cell surface membrane receptors in cells of the specimen to such status, including presence or absence of a pre-cancerous state, presence or absence of a cancerous state, prognosis of a cancer, or responsiveness to treatment.

Abstract: The invention provides methods and kits for detecting and/or measuring receptor homodimers on a cell surface membrane. In one aspect, the methods employ pairs of probes comprising binding compounds and a cleaving probe, such that at least one binding compound binds specifically to the same epitope of a membrane-bound analyte as the cleaving probe. The binding compound includes one or more molecular tags attached through a cleavable linkage, and the cleaving probe includes a cleavage-inducing moiety that can cleave the linkage when within a defined proximity thereto. Binding of the two probes to a homodimer of a cell surface molecules results in release of molecular tags from the binding compounds, providing a measure of formation of the homodimeric complex.

Abstract: The invention is directed to a new class of biomarker in patient samples comprising dimers of cell surface membrane receptors. In one aspect, the invention includes a method of determining the status of a disease or healthful condition by correlating such condition to amounts of one or more dimers of cell surface membrane receptors measured directly in a patient sample, in particular a fixed tissue sample. In another aspect, the invention includes a method of determining a status of a cancer in a specimen from an individual by correlating measurements of amounts of one or more dimers of cell surface membrane receptors in cells of the specimen to such status, including presence or absence of a pre-cancerous state, presence or absence of a cancerous state, prognosis of a cancer, or responsiveness to treatment. Preferably, methods of the invention are implemented by using sets of binding compounds having releasable molecular tags that are specific for multiple components of one or more types of receptor dimers.

Abstract: The invention is directed to a new class of biomarker in patient samples comprising dimers of ErbB cell surface membrane receptors. In one aspect, the invention includes a method of determining the status of a disease or healthful condition by correlating such condition to amounts of one or more dimers of ErbB cell surface membrane receptors measured directly in a patient sample, in particular a fixed tissue sample. In another aspect, the invention includes a method of determining a status of a cancer in a specimen from an individual by correlating measurements of amounts of one or more dimers of ErbB cell surface membrane receptors in cells of the specimen to such status, including presence or absence of a pre-cancerous state, presence or absence of a cancerous state, prognosis of a cancer, or responsiveness to treatment.