Abstract: Disclosed herein are systems and methods for determining metabolic pathway dynamics using time series multiomics data. In one example, after receiving time series multiomics data comprising time-series metabolomics data associated a metabolic pathway and time-series proteomics data associated with the metabolic pathway, derivatives of the time series multiomics data can be determined. A machine learning model, representing a metabolic pathway dynamics model, can be trained using the time series multiomics data and the derivatives of the time series multiomics data, wherein the metabolic pathway dynamics model relates the time-series metabolomics data and time-series proteomics data to the derivatives of the time series multiomics data. The method can include simulating a virtual strain of the organism using the metabolic pathway dynamics model.

Abstract: Under one aspect, a composition includes a substrate; a first polynucleotide coupled to the substrate; a second polynucleotide hybridized to the first polynucleotide; and a catalyst coupled to a first nucleotide of the second polynucleotide, the catalyst being operable to cause a chemiluminogenic molecule to emit a photon. Under another aspect, a method includes providing a catalyst operable to cause a first chemiluminogenic molecule to emit a photon; providing a substrate; providing a first polynucleotide coupled to the substrate; hybridizing a second polynucleotide to the first polynucleotide; coupling a first quencher to a first nucleotide of the second polynucleotide; and inhibiting, by the first quencher, photon emission by the first chemiluminogenic molecule.

Abstract: Provided herein are methods and compositions for treating cancers, inflammatory diseases, rasopathies, and fibrotic disease involving aberrant Ras superfamily signaling through the binding of compounds to the GTP binding domain of Ras superfamily proteins including, in certain cases, K-Ras and mutants thereof, and a novel method for assaying such compositions.

Abstract: A method of storing information using monomers such as nucleotides is provided including converting a format of information into a plurality of bit sequences of a bit stream with each having a corresponding bit barcode, converting the plurality of bit sequences to a plurality of corresponding oligonucleotide sequences using one bit per base encoding, synthesizing the plurality of corresponding oligonucleotide sequences on a substrate having a plurality of reaction locations, and storing the synthesized plurality of corresponding oligonucleotide sequences.

Abstract: The present teachings provide apparatuses and methods for automated handling of samples, e.g., biological or chemical samples. The apparatuses and the methods of the present teachings allow automated performance of various sample manipulation steps without manual intervention. In a preferred embodiment, the present teachings provide apparatuses and methods for automated enrichment of templated beads produced by PCR.

Abstract: Identifying pathways that are significantly impacted in a given condition is a crucial step in the understanding of the underlying biological phenomena. All approaches currently available for this purpose calculate a p-value that aims to quantify the significance of the involvement of each pathway in the given phenotype. These p-values were previously thought to be independent. Here, we show that this is not the case, and that pathways can affect each other's p-values through a “crosstalk” phenomenon that affects all major categories of existing methods. We describe a novel technique able to detect, quantify, and correct crosstalk effects, as well as identify novel independent functional modules. We assessed this technique on data from four real experiments coming from three phenotypes involving two species.

Abstract: The invention relates to a diagnosis and therapeutic preparation for senile dementia and an application thereof, in particular to an application of ARHGAP11A gene, SPAG7 gene and C16ORF7 gene in preparing a diagnosis and therapeutic preparation for senile dementia. In order to solve the problem that molecular markers of senile dementia are scarce at present, the inventors carried out the high-throughput sequencing on peripheral blood samples of patients with senile dementia and healthy people, selected candidate genes, and confirmed that there was a good correlation between the candidate genes and senile dementia through molecular cell experiments, which laid a foundation for clinical gene diagnosis of senile dementia.

Abstract: A method and a system for performing context-based search. The method is executed by a processing module. The method includes developing a search database, developing a search query, and retrieving at least one context-based data-record from the search database.

Abstract: Described are compositions and methods relating to modified yeast that over-express polyadenylate-binding protein (PAB1). The yeast produces a deceased amount of acetate compared to parental cells. Such yeast is particularly useful for large-scale ethanol production from starch substrates where acetate in an undesirable end product.

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: The sample plate has a principal plane in which a plurality of wells is arranged. The sample plate has a plurality of through-holes each allowing a sampling needle to pass through in a region of the principal plane where the wells are not provided, and positions of the wells and positions of the through-holes are designed such that when two pieces of the sample plates are arranged up and down with a predetermined positional relationship in a state in which respective principal planes are arranged in parallel each other, the through-holes of the sample plate arranged on an upper side is arranged at positions directly above respective wells of the sample plate arranged on a lower side.

Abstract: An image display control system includes a hardware processor that acquires data of a static image of a subject, and data of a dynamic image of the subject including a plurality of frame images, analyzes the dynamic image that is acquired, and creates analysis result data based on an analysis result, and selects, on a basis of a purpose of checking of data, at least one of the data among the data of the static image that is acquired, a part of the data of the dynamic image that is acquired, and the analysis result data that is created.

Abstract: Technology provided herein relates in part to methods, processes, machines and apparatuses for determining sequences of nucleotides for nucleic acid templates in a nucleic acid sample. The technology provide herein also relates in part to methods, processes, machines and apparatuses for counting nucleic acid templates. Nucleic acid templates of a sample are tagged with nonrandom oligonucleotide adapters that include predetermined non-randomly generated sequences. The use of these nonrandom oligonucleotide adapters provides an efficient method to reduce sequencing errors, and increase the sensitivity of detection of low-frequency single nucleotide alterations.

Abstract: Non-parametric transforms such as t-distributed stochastic neighbor embedding (tSNE) are used to analyze multi-parametric data such as data derived from flow cytometry or other particle analysis systems and methods. These transforms may be included for dimensionality reduction and identification of subpopulations (e.g., gating). By nature, non-parametric transforms cannot transform new observations without training a new transformation based on the entire dataset including the new observations. The features described parameterize non-parametric transforms using a neural network thereby allowing a small training dataset to be transformed using non-parametric techniques. The training dataset may then be used to generate an accurate parametric model for assessing additional events in a manner consistent with the initial events.

Abstract: Provided are peptide nucleic acid derivatives targeting a part of the human HIF-1? pre-mRNA. The peptide nucleic acid derivatives potently induce exon skipping to yield splice variants of HIF-1? mRNA in cells, and are useful to treat indications or conditions involving the overexpression of HIF-1?.

Abstract: A nanopore device includes an aperture and an electrode pair. A transimpedance amplifier converts a current signal IS that flows through the nanopore device into a voltage signal VS. The nanopore device measures small particles based on first data obtained by removing a DC component from the voltage signal VS and second data obtained based on the voltage signal VS from which the DC component has not been removed. Furthermore, the nanopore device is capable of monitoring the state of the nanopore device.

Abstract: Provided are methods for determining if a cannabis sample comprises hemp or marijuana, or Cannabis sativa and/or Cannabis indica as well as primers and kits for use in the methods.

Abstract: Techniques to identify a mechanism of action of a compound using network dysregulation are disclosed herein. An example method can include selecting at least a first interaction involving at least a first gene, determining a first n-dimensional probability density of gene expression levels for the first gene and one or more genes in a control state, determining a second n-dimensional probability density of gene expression levels for the first gene and one or more genes following treatment using at least one compound, estimating changes between the first probability density and the second probability density, and determining whether the estimated changes are statistically significant.

Abstract: Provided are isolated polynucleotides at least 80% identical to SEQ ID NOs: 1-479, 813-5173, 8511, 8513, 8515, 8517, 8519, 8521, 8523, 9096-9141 and 9142; and isolated polypeptides at least 80% homologous to an amino acid sequence selected from the group consisting of SEQ ID NOs: 624, 480-623, 625-812, 5174-7015, 7017-7021, 7024, 7026-8510, 8512, 8514, 8516, 8518, 8520, 8522, 8524, 9143-9177, such as the polypeptides set forth in SEQ ID NO:480-812, 5174-8510, 8512, 8514, 8516, 8518, 8520, 8522, 8524, and 9143-9177, nucleic acid constructs comprising same, transgenic cells and plants expressing same and methods of using same for increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress tolerance of a plant.

Abstract: A nanopore device includes an aperture and an electrode pair. A transimpedance amplifier converts a current signal IS that flows through the nanopore device into a voltage signal VS. The nanopore device measures small particles based on first data obtained by removing a DC component from the voltage signal VS and second data obtained based on the voltage signal VS from which the DC component has not been removed. Furthermore, the nanopore device is capable of monitoring the state of the nanopore device.

Abstract: Disclosed is a novel technique of directly isolating nucleic acids from a biological sample and use of the isolated nucleic acid complexes for various applications and assays such as biobanking and sequencing.

Abstract: The present invention relates to the culture and manipulation of microorganisms for biotech applications, and is based on the discovery and characterization of spliced leader sequences identified in transcripts from Nannochloropsis species. In particular, the invention provides nucleic acid compositions comprising a SL sequence operably linked to a protein-encoding gene. Further provided are compositions and methods for enhanced gene expression in recombinant microorganisms as well as methods for identification and/or isolation of nucleic acid molecules tagged with a spliced leader sequence.

Abstract: The present invention provides a method for the in vitro formation and/or detection of paired helical filaments (PHF) of Tau protein, comprising incubating a mixture comprising a Tau protein preparation and a polyanionic co-factor for a pre-determined period of time under conditions that promote the formation of PHFs.

Abstract: A computer-implemented method includes generating, by a processor, a set of training data for each phenotype in a database including a set of subjects. The set of training data is generated by dividing genomic information of N subjects selected with or without repetition into windows, computing a distribution of genomic events in the windows for each of N subjects, and extracting, for each window, a tensor that represents the distribution of genomic events for each of N subjects. A set of test data is generated for each phenotype in the database, a distribution of genomic events in windows for each phenotype is computed, and a tensor is extracted for each window that represents a distribution of genomic events for each phenotype. The method includes classifying each phenotype of the test data with a classifier, and assigning a phenotype to a patient.

Abstract: The invention concerns the field of cell culture technology. It concerns RNA having a specific sequence, expression vectors encoding the RNA, production host cell lines comprising the RNA, and methods of producing recombinant biopharmaceutical products using engineered host cell with altered levels of the RNAs, such as small non-coding RNAs, preferably microRNAs (miRNAs). The invention also relates to engineered host cells with altered levels in one or more of the RNAs. Those cell lines have improved secretion and/or growth characteristics in comparison to control cell lines.

Abstract: Provided herein are methods and compositions for treating cancers, inflammatory diseases, rasopathies, and fibrotic disease involving aberrant Ras superfamily signaling through the binding of compounds to the GTP binding domain of Ras superfamily proteins including, in certain cases, K-Ras and mutants thereof, and a novel method for assaying such compositions.

Abstract: The present invention relates to peptides, proteins, nucleic acids and cells for use in immunotherapeutic methods. In particular, the present invention relates to the immunotherapy of cancer. The present invention furthermore relates to tumor-associated T-cell peptide epitopes, alone or in combination with other tumor-associated peptides that can for example serve as active pharmaceutical ingredients of vaccine compositions that stimulate anti-tumor immune responses, or to stimulate T cells ex vivo and transfer into patients. Peptides bound to molecules of the major histocompatibility complex (MHC), or peptides as such, can also be targets of antibodies, soluble T-cell receptors, and other binding molecules.

Abstract: Disclosed herein are compositions, probes, devices, and processes useful for detecting specific reactions and binding interactions with biological molecules. In certain embodiments, methods of binding one or more biomolecules to a solid support are disclosed. Methods of generating site-specific sequences for one or more biomolecules from a solid support are also disclosed. Biological complexes generated by these methods are also disclosed.

Abstract: The present invention provides nucleic acids, vectors, host cells, methods and compositions to confer and/or augment immune responses mediated by cellular immunotherapy, such as by adoptively transferring CD8+ central memory T cells or combinations of central memory T cells with CD4+ T cells that are genetically modified to express a chimeric receptor under the control of an inducible promoter. In some alternatives the genetically modified host cell comprises a nucleic acid comprising a polynucleotide coding for a chimeric antigen receptor comprising a ligand binding domain, a polynucleotide comprising a spacer region, a polynucleotide comprising a transmembrane domain, and a polynucleotide comprising an intracellular signaling domain under the control of a drug inducible promoter. Controlling the expression of the chimeric receptor provides for the ability to turn expression on and off depending on the status of the patient.

Abstract: A method of treating a subject suffering from cancer includes administering an effective amount of a RNA molecule to the subject, wherein the RNA molecule is isolated or derived from a plant of the genus Taxus. A method of inhibiting growth or proliferation of cancer cells includes contacting cancer cells with the RNA molecule; and a pharmaceutical composition for treating cancer includes the RNA molecule and a pharmaceutically tolerable excipient. Also a double-stranded RNA molecule and a recombinant vector include the double-stranded RNA molecule.

Abstract: Methods, compositions and kits are provided to amplify the amount of genomic methylated DNA can by subsequently analyzed and/or sequenced. It has particular use with small amounts of DNA, including, but not limited to cell free DNA samples. In some embodiments, the ratio of polymerase and methyltransferase is controlled in order to provide maximum yields. In some embodiments, a dual primase/polymerase is used.

Abstract: Disclosed herein are methods of detecting a target RNA, methods of diagnosing an individual with a disease or condition when a target RNA associated with the disease or condition is detected, and methods of conveying via a communication medium data from the detection of a target RNA.

Abstract: An engineered payload-delivery system includes a target cell binding unit, covalently bound to a pore forming unit, and a payload portion adapted with a region capable of non-covalently binding to the pore forming unit. The pore forming unit is derived from a particular sub-serotype of Clostridium toxin, while the payload region is derived from a different sub-serotype of Clostridium toxin. The disclosed chimeric protein-based composition is capable of specifically delivering payload to neural cells.

Abstract: Disclosed are compositions, methods and kits for determining the presence, absence, amount, copy number, or other characteristics of one or more polynucleotide sequences in two or more samples and use thereof in genotyping, evaluation of copy number variation, expression analysis, determination of splice variants and fusion genes, and other genetic analyses.

Abstract: A system for DNA gene assembly that utilizes a DNA symbol library and a DNA linker library. The symbol library has a number of DNA symbols each having a first overhanging end and a second overhanging end different than and non-complimentary to the first end, the first and second ends being the same nucleotides for each DNA symbol. The linker library has pairs of DNA linkers, a first linker of a pair having a first overhanging end and a second overhanging end and a second linker of the pair having a first overhanging end and a second overhanging end, the first end of the first linker being the same nucleotides for each first linker and the second end of the second linker being the same nucleotides for each second linker, wherein the second end of the first linker and the first end of the second linker have complementary nucleotides. The first linker joins to the first end of a DNA symbol and the second linker joins to the second end of another DNA symbol.

Abstract: A method for designing all coverage of valid primer pairs, which satisfy various filtering constraints provided by users with respect to a given sequence database and has validated specificity to given sequences, is provided. By screening all suitable primer pairs present on a given DNA sequence database without omitting any one primer pair and also screening all primers having a coverage of 1 or more as well as primers having a coverage of 1, a user can be allowed to give rankings to the primers in order to easily select the primers having a high success rate in biological experiments from the resulting primers.

Abstract: Cells, including stem cells, comprising an autobioluminescent phenotype, wherein the cells emit a luminescent signal in the absence of an exogenous luminescent stimulator, are provided. The luminescent signal may be constitutive, inducible, repressible, or tissue-specific. The cells express a synthetically engineered bacterial luciferase (lux) cassette, i.e., the luxCDABEfrp gene cassette. The cells may comprise luxA, luxB, luxC, luxD, luxE, and flavin reductase. The cells may each express a combined expression level of luxC, luxD, luxE, and flavin reductase that is from ten to forty times greater than a combined expression level of luxA and luxB. Further, methods of making and using the cells comprising an autobioluminescent phenotype are disclosed herein.

Abstract: The present invention is in the field of recombinant biotechnology, in particular in the field of protein expression. The invention generally relates to methods of increasing the expression level of a protein of interest of a bacterial host cell in a production process. The invention relates particularly to improving the capacity of a bacterial host cell to express a protein of interest by expressing a phage protein during the production process which inhibits growth of the bacterial host cell. Decoupling growth of the bacterial host cell of manufacturing of the protein of interest during the production process reduces (i) the metabolic burden, (ii) oxygen demand, (iii) metabolic heat development, and (iv) avoids stress response caused by heterologous protein expression and thereby increases the capacity of a host cell to produce the protein of interest.

Abstract: A microfluidic device (1) comprising, a pallet, having a first surface (4a) and second, opposite, surface (4b); the first surface (4a) having defined therein, a main channel (5), and one or more inlet subsidiary channels (6a,6b) each of which is in fluid communication with the main channel (5) at a first junction (7) which is located at one end of the main channel (5), and corresponding one or more outlet subsidiary channels (8a,8b) each of which is in fluid communication with the main channel (5) at a second junction (9) which is located an second, opposite, end of the main channel (5); wherein the depth (‘d’) of the one or more inlet subsidiary channels (6a,6b) and the depth (‘?’) of the one or more outlet subsidiary channels (8a,8b) is less than the depth (‘f) of the main channel (5) so that there is step (106a,106b, 108a, 108b) defined at the first junction (7) and at the second junction (9); the second, opposite, surface (4b) having defined therein a groove (15) which can receive a means for generating a

Abstract: Provided are methods for multiplex polymerase chain reaction (PCR) amplification of short tandem repeat (STR) loci that can be used to rapidly generate a highly specific STR profile from target nucleic acids. The resulting STR profiles are useful for human identification purposes in law enforcement, homeland security, military, intelligence, and paternity testing applications.

Abstract: Methods for in vitro transcription and translation using a double-stranded concatemeric DNA in a eukaryotic cell-free expression system are provided. The method includes the steps of (a) contacting a double-stranded concatemeric DNA with a eukaryotic cell-free expression system, and (b) expressing a protein in vitro from the double-stranded concatemeric DNA in the eukaryotic cell-free expression system. The double-stranded concatemeric DNA includes a plurality of tandem repeat sequences. The plurality of tandem repeat sequences includes an expression sequence including a promoter, a cap-independent translation element (CITE), and an open reading frame. A final concentration of the double-stranded concatemeric DNA in the eukaryotic cell-free expression system is in a range from about 0.1 ng/?L to about 35 ng/?L. A RCA product DNA may be used as the double stranded concatemer DNA for the methods.

Abstract: This invention provides methods and systems for measuring the concentration of multiple nucleic acid sequences in a sample. The nucleic acid sequences in the sample are simultaneously amplified, for example, using polymerase chain reaction (PCR) in the presence of an array of nucleic acid probes. The amount of amplicon corresponding to the multiple nucleic acid sequences can be measured in real-time during or after each cycle using a real-time microarray. The measured amount of amplicon produced can be used to determine the original amount of the nucleic acid sequences in the sample. Also provided herein are biosensor arrays, systems and methods for affinity based assays that are able to simultaneously obtain high quality measurements of the binding characteristics of multiple analytes, and that are able to determine the amounts of those analytes in solution. The invention also provides a fully integrated bioarray for detecting real-time characteristics of affinity based assays.

Abstract: Methods and compositions are provided for engineering microorganisms, which permit enhanced H2 production. The methods and compositions provided include novel chimeric gene constructs encoding H2-forming H2ase and maturation proteins, allowing for generation of H2 continuously in large quantities. In one illustrated embodiment, novel engineered algae are provided with increased levels of H2 production.

Abstract: Method for studying constituents of individual molecular complexes by labelling the molecules belonging to the same complex with at least one set of molecular constructs, wherein each set member includes a Unique Identifying Sequence (UIS), which is a nucleic acid sequence unique for each set member, and at least one Common Tag Sequence (CTS), which is a nucleic acid sequence common to all set members, by: attaching the molecular construct to the complex by ligating or hybridizing the molecular construct to a nucleic acid molecule of the complex, or ligating or hybridizing the tag to a nucleic acid linked to an affinity binder that binds specifically to a constituent of the complex; labelling the molecules belonging to the same complex using the molecular construct tags as primers or templates in a nucleic acid polymerization reaction; and analyzing the composition of the complex by analyzing combinations of UISs and CTSs.

Abstract: Multiplex immunoassays utilize the differential affinities among the conjugation pairs between the capture ligands and target analytes are proposed. Window magnetic-assisted rapid aptamer selection (window-MARAS) methods for selecting aptamers with desirable affinity toward the target analytes and methods for generating reagents for multiplex immunoassays or multiplex detection in one assay by utilizing the selected aptamers as capture ligands in reagents are described and used to demonstrate the feasibility of multiplex immunoassays based on the differential affinity of conjugation pairs between the capture ligands and target analytes.

Abstract: The present invention relates to a new method for the production of a molecule of interest by conversion of a source of carbon in a fermentative process comprising culturing a microorganism genetically modified for the production of molecule of interest, wherein said microorganism comprises functional genes coding PTS carbohydrate utilization system and wherein the expression of proteins regulated the expression of phosphoenolpyruvate synthase (PPS) is down-regulated. The present invention also relates to the genetically modified microorganism used in the method of the invention.

Abstract: The problem of the present invention is to provide a method for preserving mammalian cells over a long period of time using a solution for cell transplantation, capable of effectively suppressing cell death when the mammalian cells have been preserved, and the solution for cell transplantation. The present invention is characterized in that mammalian cells are preserved in a physiological aqueous solution for cell transplantation, comprising 2.0 to 6.0% (w/v) of trehalose, a derivative thereof, or a salt of trehalose or the derivative (a trehalose) and 4.0 to 7.0% (w/v) of dextran, a derivative thereof, or a salt of dextran or the derivative (a dextran). The effects of a trehalose and a dextran contained in the physiological aqueous solution for cell transplantation can suppress a decrease in the cell survival rate when mammalian cells are preserved for a long period of time (at least 14 days).

Abstract: The invention relates to carbon nanotube-containing composites as biosensors to detect the presence of target clinical markers, methods of their preparation and uses in the medical field. The invention is particularly suitable for the detection in patient biological specimens of bone markers and tissue markers. The biosensors of the invention include carbon nanotubes deposited on a substrate, gold nanoparticles deposited on the carbon nanotubes and, binder material and biomolecule deposited on the gold-coated carbon nanotubes. The biomolecule is selected to interact with the target clinical markers. The biosensor can be used as an in-situ or an ex-situ device to detect and measure the presence of the target clinical markers.

Abstract: Biosensors and methods for localized surface plasmon resonance biosensing are disclosed. The biosensor can include a substrate having a substrate surface to which a plurality of localized surface plasmon resonance (LSPR) antennae are affixed. The LSPR antennae can be affixed via an affixation surface of the LSPR antenna. The LSPR antennae can have a functional surface opposite the affixation surface. Each functional surface can be functionalized by a plurality of single-stranded DNA.

Abstract: Disclosed is a new process for the production of recombinant proteins, by transient transfection of suspension-grown human embryonic kidney cells (293 cell line and its genetic variants) with an expression vector, using polyethylenimine (PEI) as a transfection reagent. In a preferred embodiment, the process uses 293E cells expressing the Epstein-Barr virus (EBV) EBNA 1 protein, in combination with an oriP-based episomal expression vector having an improved cytomegalovirus expression cassette comprising the CMV5 promoter. The process combines in a single step the cell growth, transfection and protein expression, is carried out without changing the culture medium, and allows to achieve high expression levels in a short period of time. The process may be carried out in a serum-free, low-protein culture medium, is easily scalable, compatible with continuous production processes, and fully adapted to high-throughput production of milligram quantities of recombinant proteins.