Abstract: A method of generating a molecular structure includes generating, based on a predetermined number of a plurality of nodes, all possible two-dimensional (2D) graphs and a plurality of edges representing connections between the plurality of nodes and, for each 2D graph from among the generated 2D graphs, generating all possible molecular structures based on the 2D graph by substituting each of the plurality of nodes with a polygonal ring structure including carbon atoms and substituting the edges with bonds between polygonal ring structures. Also, a method includes substituting at least one of carbon atoms included in the polygonal ring structures with an atom other than a carbon atom.

Abstract: Systems and methods to characterize one or more microorganisms or DNA fragments thereof are disclosed. Exemplary methods and systems use comparison of DNA sequencing information to information in one or more databases to characterize the one or more microorganism or DNA fragments thereof. Exemplary systems and methods can be used in a clinical setting to provide rapid analysis of microorganisms that may be a cause of infection.

Abstract: A biological information processing apparatus and a biological information processing system. The biological information processing apparatus includes a setter configured to obtain a plurality of pieces of biological information and to set a reference used for discrimination of the plurality of pieces of biological information based on a feature amount calculated for each of the pieces of biological information, and a calculator configured to perform addition average of, among the obtained plurality of pieces of biological information, pieces of biological information that have been discriminated based on the reference. The biological information processing system includes a biological information detecting apparatus and the biological information processing apparatus.

Abstract: The present invention generally provides systems and methods for the detection, identification, or characterization of differences between properties or behavior of corresponding species in two or more mixtures comprised of molecules, including biomolecules and/or molecules able to interact with biomolecules, using techniques such as partitioning. The experimental conditions established as distinguishing between the mixtures of the molecules using the systems and methods of the invention can also be used, in some cases, for further fractionation and/or characterization of the biomolecules and/or other molecules, using techniques such as single-step or multiple-step extraction, and/or by liquid-liquid partition chromatography. The methods could also be used for discovering and identifying markers associated with specific diagnostics, and can be used for screening for such markers once discovered and identified during diagnostics screening.

Abstract: An integrated microfluidic chip, wherein at least one integrated reaction unit is provided on its substrate, and the integrated reaction unit comprises at least a sample cell (1), a mixing cell (2) and a reaction cell (3) connected through liquid channels (6). In one aspect, one end of the sample cell (1) is provided with a sample inlet (4), and the chip further comprises an internal air circulating system/circuit. One end of the internal air circulating system/circuit is connected with the mixing cell (2), while the other end comprises at least a first circulation branch circuit connected with the end of the sample cell (1) distal to the sample inlet (4).

Abstract: Method and system for storing and accessing genomic data. Genomic sequencing data are partitioned into access units of different types based on the predictability of the contained data. Access units are classified in different types and the structuring enables selective access and selective processing of genomic data.

Abstract: A method for determining a patient radiation and diagnostic study score associated with past diagnostic radiologic tests. In light of the obvious benefits of diagnostic radiology, the risks inherent in its use are often overlooked. Ionizing radiation, which is a component of much, but not all, diagnostic radiology, carries with it a small risk of inducing cancer every time it is used. This additional risk, known as “Lifetime Attributable Risk,” is layered on top of an individual's lifetime base risk of invasive cancer. The present method for determining a patient radiation and diagnostic study score provides right time, right place, and right format radiology information to assist providers in their medical decision-making. With greater awareness of recent study history, and individually contextualized risk and benefit considerations, providers are more likely to decrease their overall usage of diagnostic radiology and better counsel their patients on future risk.

Abstract: A system includes a plurality of nanopore cells. Data corresponding to nanopore states of the plurality of nanopore cells is received. The data is analyzed to determine a compressed output size of the data given at least one compression technique. It is determined whether the compressed output size exceeds a data budget. In the event it is determined that the compressed output size exceeds the data budget, the data is modified. The modified data is outputted.

Abstract: A method for calibration and/or error detection in an optical measurement device for biological samples having at least a first and a second measurement channel is described. The method comprises calculating an updated reference factor for the second measurement channel based on the first and second detection signals, comparing the updated reference factor with at least one current reference factors and depending on the result of the comparison, storing the updated reference factor as a current reference factor for use in a later measurement in the second measurement channel or keeping the current reference factors for use in a later measurement in the second measurement channel.

Abstract: Methods of predicting an in vivo serum concentration of an antibody with a post-translational modification of interest after administration of the antibody are provided, as are methods for predicting a subject's exposure to post-translational variants of the antibody. The methods include predicting a percentage of the antibody with the post-translational modification of interest using an in vivo rate constant determined for the post-translational modification, and multiplying the predicted percentage of the antibody with the post-translational modification of interest by the in vivo concentration of the antibody to determine the concentration of the antibody with the post-translational modification of interest.

Abstract: According to one embodiment, a genotype estimation device includes: an acquirer configured to acquire a clustering strength of genotype data of a plurality of specimens including an unknown specimen whose genotype is not known and known specimens whose genotypes are known; and an estimator configured to estimate the genotype of the unknown specimen on the basis of the genotype data in response to the clustering strength being larger than a first threshold, and output an estimation result.

Abstract: Systems and methods for protecting information stored in private references that are available to be queried—e.g., graph-based sequence references that users query through an interface, providing short reads to obtain the results of an alignment against the reference sequence—analyze the query and/or alignment results to determine whether the query represents an attack. The analysis may be performed before returning results to a user, and in some cases before performing the alignment.

Abstract: Techniques to suggest alternative chemical compounds that can be used to recreate or mimic a target flavor using artificial intelligence are disclosed. A neural network based model is trained on source chemical compounds and their corresponding flavors and odors. The neural network-based model learns compound embeddings of the source chemical compounds and a target chemical compound of a food item. From the compound embeddings, one or more chemical compounds that are closest to the target chemical compound may be determined by a distance metric. Each suggested chemical compound is an alternative that can be used to recreate functional features of the target chemical compound.

Abstract: A cell modification device, comprising a centrifugation chamber with at least one cell modifying surface with a normal vector having an angle of 135-45° to the rotational axis of the centrifugation chamber, wherein the centrifugation chamber comprises at least one input/output port and the cells to be modified are immobilized at the cell modifying surfaces by the rotation of the centrifugation chamber at 2 to 2000 g. In an embodiment, the device is used as a point-of-care and/or portable device. Further, the present disclosure describes software that, when executed by a processor, causes the device to perform the disclosed functions.

Abstract: A method and system for automated disease progression modeling and therapy optimization for an individual patient is disclosed. A current condition of the patient is modeled using a state-variable model in which a plurality of state variables in a state vector represent a plurality of characteristics of the patient. Disease progression for the patient is predicted based on the state variables of the patient. An optimization is performed to determine an optimal therapy type and an optimal therapy timing for the patient based on the predicted disease progression for the patient.

Abstract: Methods and systems are provided for determining a variant of interest by analyzing sizes and sequences of cfDNA fragments obtained from a test sample. The methods and systems provided herein implement processes that synergistically combine size and sequence information, thereby improving specificity and sensitivity of assays over conventional methods.

Abstract: A method for detecting false positive variant calls in a next generation sequencing analysis pipeline involves obtaining a plurality of read pileup windows associated with a first sample genome. The method also involves obtaining, for each reference nucleotide position represented in the plurality of read pileup windows, a label indicating that the reference nucleotide position is either (i) a known variant or (ii) a non-variant. The method further involves training a neural network based on data indicative of the plurality of read pileup windows and the labels. Additionally, the method involves receiving a read pileup window associated with a second sample genome. Further, the method involves determining, using the trained neural network, a likelihood that the read pileup window associated with the second sample genome represents a variant.

Abstract: The present invention provides a device, method, and program for detection of a biomarker candidate that may be used in a diagnosis of a pre-disease state indicating a transition from a healthy state to a disease state. Biological samples are collected from a subject to be measured at different times. Statistical data is obtained by aggregating measurement data obtained in measurement on collected biological samples. Thereafter, a process of obtaining high-throughput data (s1), a process of choosing differential biological molecules (s2), a process of clustering (s3), a process of choosing a DNB candidate (s4), and a process of identifying a DNB by significance analysis (s5) are carried out.

Abstract: The present disclosure provides a method for identifying and quantifying sulfated glycosaminoglycans, including for example heparin, by passing a sample through nanopores. The glycosaminoglycans sample is measured in microliter quantities, at nanomolar concentrations with detection of impurities below 0.5%, and a dynamic range over five decades of magnitude with a trained machine learning algorithm.

Abstract: The present disclosure provides systems and methods for determining effects of genetic variants on selection of polyadenylation sites (PAS) during polyadenylation processes. In an aspect, the present disclosure provides a polyadenylation code, a computational model that can predict alternative polyadenylation patterns from transcript sequences. A score can be calculated that describes or corresponds to the strength of a PAS, or the efficiency in which it is recognized by the 3?-end processing machinery. The polyadenylation model may be used, for example, to assess the effects of anti-sense oligonucleotides to alter transcript abundance. As another example, the polyadenylation model may be used to scan the 3?-UTR of a human genome to find potential PAS.