Abstract: Methods for analyzing DNA-containing samples are provided. The methods can comprise isolating a single genomic equivalent of DNA from the DNA-containing sample to provide a single isolated DNA molecule. The single isolated DNA molecule can be subjected to amplification conditions in the presence of one or more sets of unique molecularly tagged primers to provide one or more amplicons. Any spurious allelic sequences generated during the amplification process are tagged with an identical molecular tag. The methods can also include a step of determining the sequence of the one or more amplicons, in which the majority sequence for each code is selected as the sequence of the single original encapsulated target. The DNA-containing sample can be a forensic sample (e.g., mixed contributor sample), a fetal genetic screening sample, or a biological cell.

Abstract: A microfluidic assembly may include a microfluidic chip operably coupled to a device source pressure port and a device relief pressure port, first and second input reservoirs, an output reservoir, and a reservoir interface. The microfluidic chip may include a microfluidic circuit configured to support a fluid flow that includes a gas flow and a liquid flow within the microfluidic circuit. The reservoir interface may be configured to operably couple the first and second input reservoirs to the microfluidic circuit. The device source pressure port may be configured to receive a source pressure to generate the fluid flow through the microfluidic circuit and cause a mixing of liquids to form an output liquid for delivery to the output reservoir via the fluid flow. The first liquid, the second liquid, and the output liquid need not contact the device source pressure port or the device relief pressure port during the mixing.

Abstract: A microfluidic assembly may include a microfluidic chip operably coupled to a device source pressure port and a device relief pressure port, first and second input reservoirs, an output reservoir, and a reservoir interface. The microfluidic chip may include a microfluidic circuit configured to support a fluid flow that includes a gas flow and a liquid flow within the microfluidic circuit. The reservoir interface may be configured to operably couple the first and second input reservoirs to the microfluidic circuit. The device source pressure port may be configured to receive a source pressure to generate the fluid flow through the microfluidic circuit and cause a mixing of liquids to form an output liquid for delivery to the output reservoir via the fluid flow. The first liquid, the second liquid, and the output liquid need not contact the device source pressure port or the device relief pressure port during the mixing.

Abstract: An apparatus includes processing circuitry configured to execute instructions that, when executed, cause the apparatus to initialize a mixture model having a number of clusters including categorical data, iteratively update cluster assignments, evaluate cluster quality based on categorical density of the clusters, and prune clusters that have low categorical density, and determine an optimal mixture model based on the pruned clusters.

Abstract: Food products and/or pharmaceutical preparations including (i) viral neutralizing antibodies or antibody fragments anchored to a probiotic microorganism and (ii) a carrier medium for delivering the viral neutralizing antibodies or antibody fragments anchored to probiotic microorganisms to the gut of a mammal. Also provided are methods of making food products and/or pharmaceutical preparations, which can be used to treat existing viral infections or prevent the spread or transmission of viral infection.

Abstract: An apparatus includes processing circuitry configured to execute instructions that, when executed, cause the apparatus to initialize a mixture model having a number of clusters including categorical data, iteratively update cluster assignments, evaluate cluster quality based on categorical density of the clusters, and prune clusters that have low categorical density, and determine an optimal mixture model based on the pruned clusters.

Abstract: A method for synthesizing an antiserum for rapid-turnaround therapies includes collecting antibody-secreting cells from a test subject, wherein the test subject has been exposed to a target biological agent and has produced an antibody response; selecting a subset of the antibody-secreting cells, the subset of the antibody-secreting cells producing antibodies that neutralize the target biological agent; generating variable-region-coding DNA sequences from the antibodies that neutralize the target biological agent; tagging amplicons of the variable-region-coding DNA sequences with unique nucleic acid identifiers to associate the variable-region-coding DNA sequences derived from individual ones of the subset of the antibody-secreting cells; analyzing antibody-type distribution in a natural immune response; synthesizing antibodies from the variable-region-coding DNA sequences to form synthetic antibodies; and mixing the synthetic antibodies in a proportion equal to the antibody-type distribution in the natural i

Abstract: Certain embodiments of the present invention include a method for rapidly designing pharmaceutical preparations for preventing viral infection that have adapted to growth in various culturing systems but maintain antigenic similarity to the original virus. The method may include serial passaging a plurality of instances of a targeted virus strain from an infected first animal in respective droplets in second animal cells, in parallel synthesizing antibodies that neutralize the targeted virus strain in a third animal, and selecting the second animal cell-adapted viral lineages that are neutralized by the antibodies to identify second animal cell-adapted viral lineages having antigenic similarity to the targeted virus strain.

Abstract: Certain embodiments of the present invention include a method for rapidly designing pharmaceutical preparations for preventing viral infection that have adapted to growth in various culturing systems but maintain antigenic similarity to the original virus. The method may include serial passaging a plurality of instances of a targeted virus strain from an infected first animal in respective droplets in second animal cells, in parallel synthesizing antibodies that neutralize the targeted virus strain in a third animal, and selecting the second animal cell-adapted viral lineages that are neutralized by the antibodies to identify second animal cell-adapted viral lineages having antigenic similarity to the targeted virus strain.

Abstract: Certain embodiments of the present invention include a method for rapidly designing pharmaceutical preparations for preventing viral infection that have adapted to growth in various culturing systems but maintain antigenic similarity to the original virus. The method may include serial passaging a plurality of instances of a targeted virus strain from an infected first animal in respective droplets in second animal cells, in parallel synthesizing antibodies that neutralize the targeted virus strain in a third animal, and selecting the second animal cell-adapted viral lineages that are neutralized by the antibodies to identify second animal cell-adapted viral lineages having antigenic similarity to the targeted virus strain.

Abstract: A method for synthesizing an antiserum for rapid-turnaround therapies includes collecting antibody-secreting cells from a test subject, wherein the test subject has been exposed to a target biological agent and has produced an antibody response; selecting a subset of the antibody-secreting cells, the subset of the antibody-secreting cells producing antibodies that neutralize the target biological agent; generating variable-region-coding DNA sequences from the antibodies that neutralize the target biological agent; tagging amplicons of the variable-region-coding DNA sequences with unique nucleic acid identifiers to associate the variable-region-coding DNA sequences derived from individual ones of the subset of the antibody-secreting cells; analyzing antibody-type distribution in a natural immune response; synthesizing antibodies from the variable-region-coding DNA sequences to form synthetic antibodies; and mixing the synthetic antibodies in a proportion equal to the antibody-type distribution in the natural i

Abstract: Certain embodiments of the present invention include a method for rapidly designing pharmaceutical preparations for preventing viral infection that have adapted to growth in various culturing systems but maintain antigenic similarity to the original virus. The method may include serial passaging a plurality of instances of a targeted virus strain from an infected first animal in respective droplets in second animal cells, in parallel synthesizing antibodies that neutralize the targeted virus strain in a third animal, and selecting the second animal cell-adapted viral lineages that are neutralized by the antibodies to identify second animal cell-adapted viral lineages having antigenic similarity to the targeted virus strain.

Abstract: Food products and/or pharmaceutical preparations including (i) viral neutralizing antibodies or antibody fragments anchored to a probiotic microorganism and (ii) a carrier medium for delivering the viral neutralizing antibodies or antibody fragments anchored to probiotic microorganisms to the gut of a mammal. Also provided are methods of making food products and/or pharmaceutical preparations, which can be used to treat existing viral infections or prevent the spread or transmission of viral infection.

Abstract: Methods for analyzing DNA-containing samples are provided. The methods can comprise isolating a single genomic equivalent of DNA from the DNA-containing sample to provide a single isolated DNA molecule. The single isolated DNA molecule can be subjected to amplification conditions in the presence of one or more sets of unique molecularly tagged primers to provide one or more amplicons. Any spurious allelic sequences generated during the amplification process are tagged with an identical molecular tag. The methods can also include a step of determining the sequence of the one or more amplicons, in which the majority sequence for each code is selected as the sequence of the single original encapsulated target. The DNA-containing sample can be a forensic sample (e.g., mixed contributor sample), a fetal genetic screening sample, or a biological cell.

Abstract: The present invention is based on the discovery that drug resistance in microorganisms can be rapidly and accurately determined using mass spectrometry. A mass spectrum of an intact microorganism or one or more isolated biomarkers from the microorganism grown in drug containing, isotopically-labeled media is compared with a mass spectrum of the intact microorganism or one or more isolated biomarkers from the microorganism grown in non-labeled media without the drug present. Drug resistance is determined by predicting and detecting a characteristic mass shift of one or more biomarkers using algorithms. The characteristic mass shift is indicative that the microorganism is growing in the presence of the drug and incorporating the isotopic label into the one or more biomarkers, resulting in change in mass.

Abstract: The present invention is based on the discovery that drug resistance in microorganisms can be rapidly and accurately determined using mass spectrometry. A mass spectrum of an intact microorganism or one or more isolated biomarkers from the microorganism grown in drug containing, isotopically-labeled media is compared with a mass spectrum of the intact microorganism or one or more isolated biomarkers from the microorganism grown in non-labeled media without the drug present. Drug resistance is determined by predicting and detecting a characteristic mass shift of one or more biomarkers using algorithms. The characteristic mass shift is indicative that the microorganism is growing in the presence of the drug and incorporating the isotopic label into the one or more biomarkers, resulting in change in mass.

Abstract: Techniques for automatically analyzing a biological sample with a microscope include obtaining a first digital image of a first field of view of the biological sample. Cell data and anomalous data are automatically determined. Cell data indicates an area co-located in the first digital image with a cell set of one or more cells of a particular type. Anomalous data indicates an area co-located in the first digital image with an anomalous set of zero or more particular objects that are anomalous to normal cells of the particular type. The cell data and the anomalous data are automatically combined to determine the particular objects inside the cell set in the first digital image. An analytical result for the biological sample is generated based on the particular objects inside the cell set. These techniques allow the automated classification and quantification of malaria in microscope views of blood smears, among other diseases.

Abstract: A simple statistical model that predicts the distribution of false matches between peaks in matrix-assisted laser desorption/ionization mass spectrometry data and proteins in proteome databases is derived and validated. Given the cluttered and incomplete nature of the data, it is likely that neither simple ranking, nor simple hypothesis testing will be sufficient for truly robust microorganism identification over a large number of candidate microorganisms. In an effort to increase robust microorganism identification, the proteome databases are restricted to include data related to a given set of proteins, and not all proteins. By removing data from the proteome databases, the model is made more robust, i.e., there is a decrease in the number of false matches.