Abstract: Provided herein are compositions and methods for analyzing nucleic acids in a sample. Compositions include simple barcode sets having reduced DNA sequencing instrument-specific error rates. Methods include methods to deconvolute sequence reads from different samples.

Abstract: Disclosed is a double enzyme tandem preparation method of L-2-aminobutyric acid, and belongs to the field of bioengineering. In the disclosure, recombinant Escherichia coli expressing L-glutamate mutase and recombinant Escherichia coli expressing L-aspartate-?-decarboxylase are separately cultured to obtain L-glutamate mutase and L-aspartate-?-decarboxylase. The two enzymes are added to a reaction system at a certain mass ratio, and L-glutamate is used as a substrate to carry out an enzyme reaction to prepare the L-2-aminobutyric acid. When the dosage of the L-aspartate-?-decarboxylase is 2 mg/mL, and the reaction time is 24 h, 8.5 mmol/L L-2-aminobutyric acid is produced by conversion, with a molar conversion rate of 85.00%. Compared with a chemical production method, the method disclosed by the disclosure has a safe production process and no environmental pollution. Compared with a multi-enzyme synthesis system with threonine as a substrate, the substrate is cheaper and the process is simpler.

Abstract: Aspects of the subject disclosure may include, for example, detecting, by a substance delivery system coupled to a body part of an individual, an input signal not associated with a biological measurement of the individual, determining from the input signal, by the substance delivery system, whether delivering a dosage of a substance stored in the substance delivery system is needed and conforms to a dosage policy, and responsive to determining from the input signal that delivery of the dosage of the substance is needed and conforms to the dosage policy, initiating, by the substance delivery system, delivery of the dosage of the substance to the body part of the individual. Other embodiments are disclosed.

Abstract: A method of administering insulin includes receiving subcutaneous information for a patient at a computing device and executing a subcutaneous outpatient program for determining recommended insulin dosages. The subcutaneous outpatient program includes obtaining glucose data of the patient, aggregating glucose measurements to determine a representative aggregate glucose measurement associated with at least one scheduled glucose time interval, and determining a next recommended insulin dosage for the patient based on the representative aggregate glucose measurement and the subcutaneous information. The method also includes transmitting the next recommended insulin dosage to administration device associated with the patient.

Abstract: The present invention relates to the technical field of microbial fermentation engineering, and specifically to a method for producing psicose 3-epimerase by high-density fermentation. In view of the low expression level of psicose 3-epimerase and other problems existing in the current fermentation, by controlling the feeding rate in the fermentation process, improving the culture temperature in the middle and late stages of fermentation and other measures in the present invention, the OD value during the fermentation with recombinant Bacillus subtilis and the total enzyme activity of psicose 3-epimerase in the fermentation broth are significantly increased, the expression of psicose 3-epimerase is markedly improved, and the production cost of allulose is reduced. Therefore, the present invention has a very broad prospect of application in industry.

Abstract: Aspects of the present invention relate to compositions of bacterial isolates with probiotic activity. Aspects of the present invention also relate to compositions and methods that may confer health benefits to subjects in need thereof. This may be accomplished by administering to the subject an effective amount of the microorganism isolates and may include also administering an effective amount of a prebiotic, stabilizer, antibacterial agent, antifungal agent, and/or media component. Probiotic compositions may also be in combination with a suitable delivery system, such as a food product or a beverage, a food or beverage compositions, a food or beverage supplement or adjuvant.

Abstract: Type I interferon (IFN-I) signatures are useful in methods of diagnosing whether a subject (or patient) with IFN-I mediated disease will be responsive to treatment with an IFN-I inhibitor and treating or refraining from treating the subjects.

Abstract: Computer methods and systems for quantifying a nucleic acid sample comprising nucleic acid of one or more contributors to: receive nucleic acid sequence reads obtained from the nucleic acid sample and mapped to alleles at polymorphism loci; determine, using the nucleic acid sequence reads, allele counts for each of the alleles at the polymorphism loci; use a probabilistic mixture model that applies a probabilistic mixture model to the allele counts, and that uses probability distributions to model the allele counts at the polymorphism loci; quantify, using the probabilistic mixture model, one or more fractions of nucleic acid of the one or more contributors in the nucleic acid sample; determine a probability that a specific contributor among the one or more contributors has a specific genotype; and call, based on the posterior probability, that the nucleic acid sample includes nucleic acid from the specific contributor.

Abstract: Exemplary embodiments for a multiprocessor pipeline architecture that converts signals from sequencing sample acquisition into sequence data, comprising: a custom coprocessor card configured to directly receive a stream of serialized sensor data generated by an image sensor, wherein the sensor data represents frame-by-frame intensity values for pixels comprising the image sensor, wherein the image sensor captures images of light emitted from a plurality of reaction cells of a removable integrated sequencing chip; a first coprocessor that continually receives the stream of serialized sensor data and transposes the frame-by-frame intensity values into reaction cell chunks, each of the reaction cell chunks representing movie data of the pixel intensity values of a corresponding reaction cell across the frames over a predetermined time window; a buffer that repeatedly receives the reaction cell chunks and stores in contiguous memory locations the reaction cell chunks for each respective reaction cell over a large

Abstract: Systems and methods include a computer-implemented method for random selection and use of observation cells. Observation cells are randomly selected from a model of process-based reactive transport modeling (RTM). The observation cells are incorporated into a neural network for proxy modeling. A set of parameter-specific proxy models represented by a neural network is trained. Each parameter-specific proxy model corresponds to a specific RTM parameter from a set of RTM parameters. Blind tests are performed using the set of parameter-specific proxy models, where each blind test tests a specific one of the parameter-specific proxy models. Predictions are generated using the set of parameter-specific proxy models. 3-dimensional interpolation the observation cells is performed.

Abstract: In accordance with embodiments, a computing device of a processing system performs a seed search of a short read (SR) against a reference sequence using a Burrows Wheeler Transform (BWT) algorithm to determine a seed. During the seed search one or more seed candidates in the reference sequence are determined. If the number of matches is less than or equal to a predefined threshold value the seed search using the BWT algorithm is stopped. Each seed candidate is extended to a respective extended seed candidate equal in length to the SR. bp-to-bp comparisons are performed between a remaining bp sequence of the SR after the matching bp and a corresponding remaining bp sequence in each extended seed candidate. An extended seed candidate that exactly matches the SR in the bp-to-bp comparisons is outputted as the seed.

Abstract: Techniques for predicting a protein sequence are described. An exemplary method includes receiving a request to predict a missing area of a protein's primary sequence and a corresponding three-dimensional position of the missing area; applying a machine learning model to backbone Cartesian coordinates of the protein's primary sequence and a protein vector of a representation of the protein's primary sequence including the missing area to predict a missing area of the protein primary sequence and a corresponding three-dimensional position for the missing area, wherein the machine learning model is selected from the group consisting of: an attention-based machine learning model, a bidirectional long short term memory-based model, and a convolutional neural network-based model; and outputting a result of the machine learning model.

Abstract: In comparison to conventional sequencing pileup algorithms, the process described herein generates sequencing pileups that contains additional information not typically reported by conventional algorithms while also consuming fewer computational resources (e.g., time, processing power, and memory). First, each of a FASTA reference genome and BAM sequence read files are converted to an internal representation. This enables the rapid iteration across nucleotide bases of the sequence reads to determine support characteristics that summarize information of nucleic acid molecules corresponding to positions across the reference genome. Next, the support characteristics of positions across the reference genome are stored through a memory allocation process that utilizes a first and a second temporary storage. This enables the convenient freeing of one temporary storage while the other temporary storage is being used.

Abstract: A method includes receiving electroencephalographic (EEG) signal data recordings collected from a plurality of individuals via at least one EEG monitoring device. An optimized plurality of wavelet packet atoms is constructed based on the EEG signal data recordings and a mother wavelet. The optimized plurality of wavelet packet atoms is reordered to obtain an optimal reordered set of wavelet packet atoms. The optimal reordered set of wavelet packet atoms is normalized to obtain an optimal normalized set of wavelet packet atoms that is representative of brain activities of the plurality of individuals. A particular EEG signal data recording of a particular individual is received, which is projected onto the optimal normalized set of wavelet packet atoms to obtain an individual-specific set of projections for the particular individual on the optimal normalized set of wavelet packet atoms.

Abstract: Methods and systems for processing a plurality of sample reads for genome sequencing include, for each sample read of the plurality of sample reads, comparing substring sequences from the sample read to reference sequences representing different portions of a reference genome. One or more reference sequences are identified that match one or more of the compared substring sequences, and a probabilistic location within the reference genome is determined for the sample read based on the one or more identified reference sequences. The reference genome is partitioned for reference-aligned genome sequencing based on the determined probabilistic locations of the respective sample reads.

Abstract: The present invention provides a powerful tool to identify personalized therapeutic strategies. In particular, the invention provides methods for determining therapeutically targetable dominant signaling pathways in a cancer sample from a subject affected with a solid cancer, determining a treatment protocol for the subject, selecting a subject for a therapy, determining whether the subject is susceptible to benefit from a therapy, predicting clinical outcome of the subject, treating the subject and/or predicting the sensitivity of a solid cancer to a therapy.

Abstract: Technologies are provided for an improved classifier apparatus and processes for improving the accuracy of classification technology including example applications of such classifiers. A process includes applying clustering to variables contributing to the classification task. The clusters may be represented in a 1-dimensional, 2-dimensional, or 3-dimensional matrix that is a spatial abstraction of the interrelationships. A convolutional transformation may be applied to the matrix so as to reduce the effective dimensionality of the classification problem and improve the signal-to-noise ration. A deep learning neural network method may be applied to the transformed network to generate an improved classification model, which may be utilized by a decision support tool. One embodiment comprises a decision support tool for detecting risk of venous thrombosis and venous thromboembolism (VTE) in a patient, based on phenotype and genomics information.

Abstract: Method and apparatus for the coding and selective access of compressed genomic sequence data produced by genomic sequencing machines. The coding process is based on aligning sequence reads with respect to pre-existing or constructed reference sequences, on classifying and coding the sequence reads by means of sets of descriptors, and further partitioning the descriptor sets into access units of different types. Efficient selective access to specific genomic regions with the guarantee of retrieving all sequence reads mapped to those regions, is provided by: signaling the type of data mapping configuration used to store or transmit the descriptor sets, determining the minimum number of access units that need to be retrieved and decoded to access a genomic region, providing a master index table that contain all information for optimizing the data access process.

Abstract: Systems and methods providing a clotting factor VIII dosing regimen are disclosed. The systems and methods include determining an estimated pharmacokinetic profile of a patient using a Bayesian model of pharmacokinetic profiles of sampled patients. The systems and methods can determine a first dosing regimen for a first dosing interval including (i) a first dosage and (ii) a first therapeutic plasma protein level in the patient varying over time based at least upon the estimated pharmacokinetic profile. The systems and methods can determine a second dosing regimen for a second dosing interval including (i) a second dosage and (ii) a second therapeutic plasma protein level in the patient varying over time. The estimated pharmacokinetic profile can be adjusted based on previous patient treatments. Further, a user can select which days a dosage is to be applied such that the protein level does not fall below a target trough.

Abstract: Disclosed are systems, devices, and methods for planning a procedure for treatment of tissue in a patient's lungs. An exemplary method includes generating a three-dimensional (3D) model of the patient's lungs, displaying the 3D model of the patient's lungs, selecting a target location in the tissue of the patient's lungs as displayed on the 3D model, identifying a point on a pleural surface of the patient's lungs with access to the target location, determining an access path between the target location and the identified point on the pleural surface, calculating a risk of injury to intervening structures between the identified point on the pleural surface and the target location, based on the determined access path, and displaying the access path and the calculated risk of injury for the access path on the 3D model.