Abstract: The present disclosure relates to pharmaceutical compounds and compositions and methods for treating an allergy and Crohn's disease. Methods for treating an allergy can include (a) predicting potential epitopes based proteomes of microbiome and that of an allergen, (b) filtering the potential epitopes obtained in step a) to result in a list of epitopes; and (c) reengineering the list of epitopes obtained in step b) to result in the new epitope. Methods for treating Crohn's disease can include (a), identifying one or more binding regions of an HLA class II protein and/or hemagglutinin to I2 superantigen; (b) determining a first peptide sequence corresponding to the one or more binding regions, and (c) producing a peptide inhibitor having a second peptide sequence that is a mutation of the first peptide sequence, wherein the second peptide sequence has a stronger binding affinity to the I2 superantigen than the first peptide sequence.

Abstract: Methods and systems for generating agronomic indices and executing one or more actions in response to said agronomic indices at an agriculture site, the method comprising: receiving a set of samples associated with the agriculture site; generating a sample dataset upon processing the set of samples with a set of sample processing operations; generating a set of microbiome-associated features upon performing a set of transformation operations upon the sample dataset, wherein the set of microbiome-associated features comprises a first subset of taxonomic annotations, a second subset of functional annotations and a third subset of ecological indices; generating values of a set of agronomic indices based upon the set of microbiome-associated features; and executing an action for producing a desired outcome at the agriculture site, based upon the set of agronomic indices.

Abstract: Inventions provided are designed to improve states of agriculture sites and crops, in relation to agricultural inputs and management practices. Some inventions covered are able to generate agronomic indices and execute actions in response to agronomic indices at an agriculture site. An example method includes receiving samples associated with the agriculture site; generating a sample dataset upon processing the samples with a set of sample processing operations; generating a set of microbiome-associated features upon performing a set of transformation operations upon the sample dataset, wherein the set of microbiome-associated features comprises taxonomic annotations, functional annotations and ecological indices; generating values of a set of agronomic indices based upon the set of microbiome-associated features; and executing an action for producing a desired outcome at the agriculture site, based upon the set of agronomic indices.

Abstract: The invention(s) include systems and methods for receiving and processing agriculture-associated samples with sample processing architecture structured to rapidly return outputs characterizing effects of agriculture inputs and practices over time. Control instructions based upon outputs of the systems and methods are then executed for maintaining or improving performance of crops and agriculture sites (e.g., in relation to yield, in relation to nutrient characteristics) in a sustainable manner (e.g., environmentally sustainable manner). System and method outputs can further be used to affect modifications to product treatments generated by associated manufacturers.

Abstract: A method and system for evaluating and predicting a set of crop-associated features at an agriculture site, the method comprising: receiving a set of samples associated with the agriculture site; generating a sample dataset upon processing the set of samples with a set of sample processing operations; generating a set of microbiome-associated features upon performing a set of transformation operations upon the sample dataset; and returning an analysis characterizing the set of crop-associated features based upon the set of microbiome-associated features. The method can further include steps for executing an action for producing a desired outcome in relation to the agriculture site, with respect to a specific soil type and a specific crop, based upon the analysis.

Abstract: A method and system for evaluating and predicting a set of crop-associated features at an agriculture site, the method comprising: receiving a set of samples associated with the agriculture site; generating a sample dataset upon processing the set of samples with a set of sample processing operations; generating a set of microbiome-associated features upon performing a set of transformation operations upon the sample dataset; and returning an analysis characterizing the set of crop-associated features based upon the set of microbiome-associated features. The method can further include steps for executing an action for producing a desired outcome in relation to the agriculture site, with respect to a specific soil type and a specific crop, based upon the analysis.

Abstract: Methods, compositions, and systems are provided for detecting one or more a bacterial vaginosis issues by characterizing the microbiome of an individual, monitoring such effects, and/or determining, displaying, or promoting a therapy for the bacterial vaginosis issue. Methods, compositions, and systems are also provided for generating and comparing microbiome composition and/or functional diversity datasets. Methods, compositions, and systems are also provided for generating a characterization model and/or therapy model for bacterial vaginosis.

Abstract: Embodiments of a method and/or system (e.g., for improved single molecule sequencing, etc.) can include preparing a set of unique molecular identifier (UMI)-based molecules associated with a set of target nucleic acid sequences; facilitating generation of (e.g., generating, etc.) a set of tagged nucleic acid molecules based on the set of UMI-based molecules and a set of nucleic acid molecules corresponding to (e.g., including, etc.) the set of target nucleic acid sequences; and/or facilitating (e.g., performing, etc.) single molecule sequencing with the set of tagged nucleic acid molecules.

Abstract: Inventions include methods and systems for evaluation of agriculture sites and execution of actions for improving various site parameters in a sustainable manner. In embodiments, a method for characterization and improvement of an agricultural site includes: receiving a set of agriculture samples from an agriculture site or in association with an agricultural process; generating sample data upon processing the set of samples with a set of sample processing operations; generating a set of features upon performing a set of transformation operations upon the set of data streams; returning an analysis characterizing a status of the agriculture site in relation to at least one perturbation, upon processing the set of features; and executing an action for at least one of maintaining and improving the agriculture site, based upon the analysis. The inventions implement features associated with composition, network properties, and emergent properties as biomarkers for characterizing statuses of sites under analysis.

Abstract: Therapeutic compositions and an associated method for improving a Toll-like receptor (TLR)-related condition, including determining a set of peptide sequences associated with a microorganism-related modulator of a TLR, determining a first set of binding parameters for the set of peptide sequences in relation to the TLR, selecting a target subset of peptide sequences from the set of peptide sequences based on the first set of binding parameters, reengineering the target subset of peptide sequences based on mutating amino acid residues of the target subset of peptide sequences, determining a second set of binding parameters for the reengineered target subset of peptide sequences in relation to the TLR, and identifying a first peptide for use in a therapeutic composition for improving the TLR-related condition, based on the second set of binding parameters for the reengineered target subset of peptide sequences.

Abstract: Inventions include methods and systems for evaluation of agriculture sites and execution of actions for improving various site parameters in a sustainable manner. In embodiments, a method for characterization and improvement of an agricultural site includes: receiving a set of agriculture samples from an agriculture site or in association with an agricultural process; generating sample data upon processing the set of samples with a set of sample processing operations; generating a set of features upon performing a set of transformation operations upon the set of data streams; returning an analysis characterizing a status of the agriculture site in relation to at least one perturbation, upon processing the set of features; and executing an action for at least one of maintaining and improving the agriculture site, based upon the analysis. The inventions implement features associated with composition, network properties, and emergent properties as biomarkers for characterizing statuses of sites under analysis.

Abstract: Embodiments of a system and method for characterizing a panel of conditions associated with a set of taxa related to microorganisms can include a taxonomic database including reference microbiome features for the set of taxa associated with the panel of conditions; a handling operable to collect a container including biological material from a user, the handling system comprising a sequencer system operable to determine a microorganism sequence dataset; and a panel characterization system operable to: determine user microbiome features for the set of taxa for the user based on the microorganism sequence dataset, generate a comparison between the user microbiome features and the reference microbiome features, and determine a panel characterization for the panel of conditions for the user based on the comparison; and a treatment system operable to promote a therapy for a condition of the panel of conditions based on the panel characterization.

Abstract: Methods, compositions, and systems are provided for detecting one or more effects of antibiotic usage for an infectious disease or other health condition on the microbiome of an individual, monitoring such effects, and/or determining, displaying, or promoting a therapy for such an effect. Methods, compositions, and systems are also provided for generating and comparing microbiome composition and/or functional diversity datasets. Methods, compositions, and systems are also provided for generating a characterization model for antibiotic usage.

Abstract: Embodiments of the system and/or method can include and/or apply a magnetic device for facilitating a magnetic field for isolating the nucleic acid material from a sample, the magnetic device including a support component; and a set of magnetic pins attached to the support component and movable with at least three degrees of freedom when attached to the support component, where the set of magnetic pins provide adaptability to shapes of sample compartments of a sample container.

Abstract: Embodiments of a method and/or system, such as for characterizing at least one microorganism-related condition, can include: determining a set of associations (e.g., positive associations such as positive correlations, negative associations such as negative correlations, non-associations such as no correlation or minimal correlation, etc.) between a set of microorganism taxa and at least one microorganism-related condition; determining a set of reference features (e.g., reference abundance ranges, etc.) for the set of microorganism taxa; and determining one or more significance index metrics based on the set of associations and the set of reference features.

Abstract: A composition and a method for an antibiotic-inducing imbalance in microbiota, or specifically, a microbiota recovery composition for an antibiotic-inducing imbalance of gut microbiota are provided.

Abstract: Embodiments of a method and system for improved microbiome sequencing can include: generating guide RNA complexes for a set of targets corresponding to a set of taxa associated with the microorganism-related condition; processing the biological sample with the gRNA complexes to generate microorganism nucleic acid fragments comprising a set of end regions associated with the set of targets; ligating the set of end regions with a set of adapters sharing an adapter sequence; and amplifying the set of targets based on the ligated set of end regions and a set of primers sharing a primer sequence associated with the adapter sequence.

Abstract: The invention(s) include systems and methods for receiving and processing agriculture-associated samples with sample processing architecture structured to rapidly return outputs characterizing effects of agriculture inputs and practices over time. Control instructions based upon outputs of the systems and methods are then executed for maintaining or improving performance of crops and agriculture sites (e.g., in relation to yield, in relation to nutrient characteristics) in a sustainable manner (e.g., environmentally sustainable manner). System and method outputs can further be used to affect modifications to product treatments generated by associated manufacturers.

Abstract: The present disclosure related to a method of detecting a molecule using an antibody-DNA conjugate, and pharmaceutical compositions comprising new polypeptides and use thereof.

Abstract: Methods and systems for generating agronomic indices and executing one or more actions in response to said agronomic indices at an agriculture site, the method comprising: receiving a set of samples associated with the agriculture site; generating a sample dataset upon processing the set of samples with a set of sample processing operations; generating a set of microbiome-associated features upon performing a set of transformation operations upon the sample dataset, wherein the set of microbiome-associated features comprises a first subset of taxonomic annotations, a second subset of functional annotations and a third subset of ecological indices; generating values of a set of agronomic indices based upon the set of microbiome-associated features; and executing an action for producing a desired outcome at the agriculture site, based upon the set of agronomic indices.