Abstract: Embodiments include a system for providing blood flow information for a patient. The system may include at least one computer system including a touchscreen. The at least one computer system may be configured to display, on the touchscreen, a three-dimensional model representing at least a portion of an anatomical structure of the patient based on patient-specific data. The at least one computer system may also be configured to receive a first input relating to a first location on the touchscreen indicated by at least one pointing object controlled by a user, and the first location on the touchscreen may indicate a first location on the displayed three-dimensional model. The at least one computer system may be further configured to display first information on the touchscreen, and the first information may indicate a blood flow characteristic at the first location.

Abstract: Telenostics style prognostication algorithms are used in medical prognosis to predict the mean time to an unacceptable result, such as death, or the mean time to a cure or partial cure.

Abstract: Methods and materials for measuring the composition of plant biomass and predicting the efficiency of conversion of such biomass to various end products under various processing conditions are disclosed. For example, methods and materials for identifying plant material having higher levels of accessible carbohydrate, as well as materials and methods for processing plant material having higher levels of accessible carbohydrate are disclosed. Also disclosed are computer-implemented methods and systems that provide improved economic efficiencies to biorefineries.

Abstract: A computer system for recommending an optimal treatment protocol comprising a model of biological processes related to a disease. A treatment protocol generator generates a plurality of treatment protocols for treating a disease using drugs. A selector selects an optimal treatment protocol from the plurality of treatment protocols based on model. The model further comprises a pharmacokinetics macro module adapted to analyze interactions between a ligand and a population of target cells at a tissue level. The model further comprises a pharmacokinetics micro module adapted to analyze interactions between the ligand and a cell at an individual cell level. The pharmacokinetics micro module is adapted to model behavior of the ligand and receptors related to single cell level of ligand-cell interactions, as a stochastic process.

Abstract: System, methods, and apparatuses produce simulated human physiological waveforms such as electrocardiograph (ECG) and blood pressure signals where the microcontroller and/or digital-to-analog converters may be switched to a lower power-consuming state by programmable instructions and switched on in response to a programmable sleep timer.

Abstract: A system and method for predicting the onset of glaucoma uses a Finite Element Model (FEM) to obtain a response profile of the Optical Nerve Head (ONH) inside an eye. To do this, the FEM is programmed with data from first and second images of the ONH that are respectively taken at the beginning and the end of an imposed pressure differential (e.g. over a range of about 8kPa). The FEM is then subjected to a sequence of pressure increments and the resultant profile is compared with empirical data to predict an onset of glaucoma.

Abstract: The present invention relates to cGMP protein kinase (PKG) and regulatory domains and methods of use thereof. The structural determination of PKG domains is also described. cGMP independent PKG activators and uses thereof are also described.

Abstract: An object correcting method includes disposing multiple sample objects at different positions on a display screen, the sample objects having respective attributes characteristic thereof; obtaining the position of a point on the display screen specified by a user; changing the attribute of a target object by calculating an interpolated value of the attributes of the sample objects based on the positions at which the sample objects are disposed and the position of the point and replacing the value of at least one of the parameters of the attribute of the target object with the calculated interpolated value; and correcting the target object based on the changed attribute thereof.

Abstract: This invention concerns methods of identifying genetic alterations with which a microbe can be used to produce fatty acids at a large amount for making biofuels. Also disclosed are microbes with such genetic alterations and uses thereof.

Abstract: A method and a device are disclosed for an electronic neuron emulator for representing both passive and active electrical properties of a live neuron. The currents used to generate action potentials are derived from a pre-charged capacitor. The present invention provides for a more physiological state for testing neuroscience instruments such as the single-electrode voltage clamp and the patch clamp. The device can also include multiple pre-charged capacitors to represent ionic channels with more accurate physiologically parameters.

Abstract: The present invention relates to a method of designing an inhibitor of the binding of HIV (human immunodeficiency virus) glycoprotein (gp)120 to a CD4-receptor or to the integrin alpha4 beta7 (a4b7). The inhibitor interacts with at least two amino acid residues comprised in six motifs within the 3-dimensional structure of gp120. Also provided are compounds, pharmaceutical compositions thereof and uses thereof in the development of an inhibitor of the binding of a HIV gp120 to a CD4-receptor or an integrin alpha4 beta7 (a4b7). The inhibitors are useful for the prevention or treatment of an HIV infection and/or diseases associated with an HIV infection.

Abstract: The present disclosure provides isolated nucleic acid sequences encoding a monomeric green/yellow fluorescent proteins, and fragments and derivatives thereof. Also provided is a method for engineering the nucleic acid sequence, a vector comprising the nucleic acid sequence, a host cell comprising the vector, and use of the vector in a method for expressing the nucleic acid sequence. The present invention further provides an isolated nucleic acid, or mimetic or complement thereof, that hybridizes under stringent conditions to the nucleic acid sequence. Additionally, the present invention provides a monomeric green/yellow fluorescent protein encoded by the nucleic acid sequence, as well as derivatives, fragments, and homologues thereof. Also provided is an antibody that specifically binds to the green/yellow fluorescent protein.

Abstract: The current invention reports a method for producing an antibody comprising the steps of a) providing a plurality of hybridoma cells each expressing an antibody, b) determining the time dependent amount of said antibody bound to the respective antigen by surface plasmon resonance at different temperatures and different antibody concentrations, c) calculating with the time dependent amount determined in b) based on equations (II) to (XIII) at least the thermodynamic parameters (i) standard association binding entropy formula (A), (ii) standard dissociation binding entropy formula (B), (iii) standard binding entropy (?S°), (iv) free standard binding enthalpy (?G°), (v) standard dissociation free binding enthalpy formula (C), (vi) standard association free binding enthalpy formula (D), (vii) ?T?S°, (viii) dissociation rate constant kd, (ix) equilibrium binding constant KD, and (x) association rate constant ka, d) selecting a hybridoma cell producing an antibody with at least two of the following: i) a standard a

Abstract: We have created novel engineered genetic counter designs and methods of use thereof that utilize DNA recombinases to provide modular systems, termed single invertase memory modules (SIMMs), for encoding memory in cells and cellular systems. Our designs are easily extended to compute to high numbers, by utilizing the >100 known recombinases to create subsequent modules. Flexibility in our engineered genetic counter designs is provided by daisy-chaining individual modular components, i.e., SIMMs together. These modular components of the engineered genetic counters can be combined in other network topologies to create circuits that perform, amongst other things, logic and memory. Our novel engineered genetic counter designs allow for the maintenance of memory and provide the ability to count between discrete states by expressing the recombinases between their cognate recognition sites.

Abstract: The attached disclosure provides a systems approach based on mathematical modelling of the kinetics of essential biochemical pathways involved in organ homeostasis. When this in silico model is coupled with in-vitro and/or in-vivo measurements to quantify drug-induced perturbations, a powerful platform that allows accurate and mechanistic-level prediction of drug-induced organ injury can be generated. The method described in this disclosure demonstrates that several physiological situations can also be accurately modelled in addition to the effect of perturbations induced by drugs. It can also be used along with high-throughput “omics” data to generate testable hypotheses leading to informed decision-making in drug development.

Abstract: Techniques for reconstructing evolutionary data of a set of genomic data are provided. The techniques include obtaining a set of genomic data, determining a chronological order of one or more mutations within the set of genomic data, determining a chronological order of one or more recombinations within the set of genomic data, determining a position of each recombination within the set of genomic data, and combining the chronological order of the one or more mutations, the chronological order of the one or more recombinations and the position of each recombination to reconstruct evolutionary data of the set of genomic data.

Abstract: A method of creating a model of an organ, includes creating a shape model, including a blood vessel structure, of the organ based on three-dimensional (3D) images of the organ, and compartmentalizing the shape model into areas based on an influence of a blood vessel tree with respect to a deformation of the shape model, the blood vessel tree indicating the blood vessel structure. The method further includes deforming the blood vessel structure of the shape model to fit a blood vessel structure of a two-dimensional (2D) image of the organ, and creating the model of the organ based on the deformed blood vessel structure and the areas.

Abstract: A computer-implemented system and method for improving glucose management through modeling of circadian profiles is provided. Meal period data is assembled, which includes, for each stated period, at least two measurements of pre-meal and post-meal self-measured blood glucose. Diabetes medication dosed over the periods is identified. The assembled meal period data and the medication are organized into a circadian profile for a diabetic patient. A model including expected blood glucose values and their predicted errors at each period is created from the blood glucose measurements and is visualized in a log-normal distribution. Target ranges for blood glucose at each period are determined and superimposed over the expected blood glucose values. Pharmacodynamics of the medication are obtained. An incremental change in dosing of the medication is propagated over a model day and the expected blood glucose values and their predicted errors are adjusted in response to the incremental dosing change.

Abstract: Provided herein are methods, compositions, and kits for determining cell signaling profiles in normal cells and comparing the cell signaling profiles of normal cells to cell signaling profiles from a test sample.

Abstract: Methods, computer systems, and computer program products for biopolymer engineering. A variant set for a biopolymer of interest is constructed by identifying, using a plurality of rules, a plurality of positions in the biopolymer of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions, and the substitutions for each respective position in the plurality of positions collectively defined a biopolymer sequence space. A variant set comprising a plurality of variants of the biopolymer of interest is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-actively relationship is modeled between (i) one or more substitutions at one or more positions of the biopolymer of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set.

Abstract: A computer-implemented system and method for improving glucose management through cloud-based modeling of circadian profiles is provided. For each daily meal period, two sets of pre- and post-meal period data that include a blood glucose level and a diabetes medication dosing are stored into a circadian profile for a diabetic patient in a cloud computing infrastructure. Predicted blood glucose is modeled over the infrastructure and the access will be validated. A model, including expected blood glucose values and their predicted errors is created from the blood glucose levels in each profile and visualized in a log-normal distribution. Target ranges for blood glucose are determined and superimposed over the expected values. Pharmacodynamics of the medication are obtained. An incremental change in dosing of the medication is propagated over a model day and the expected blood glucose values and their predicted errors are adjusted in response to the incremental dosing change.

Abstract: A blood glucose meter and computer-implemented method for improving glucose management through modeling of circadian profiles is provided. For each daily meal period, two sets of pre- and post-meal period data are collected into a circadian profile and stored on a glucose meter, including a level of blood glucose of a diabetic patient and a dosage of diabetes medication. A model of predicted blood glucose for the patient is created from the blood glucose levels in each record as expected blood glucose values and predicted errors and visualized in a log-normal distribution. Target ranges for blood glucose at each meal period are determined and superimposed over the expected blood glucose values. Pharmacodynamics of the medication are obtained. An incremental change in dosing of the medication is propagated over a model day and the expected blood glucose values and their predicted errors are adjusted in response to the incremental dosing change.

Abstract: A process and apparatus are provided for manufacturing complex parts and devices which utilize a CAD environment to design a part or device to be created (FIG. 1); Boolean, scaling, smoothing, mirroring, or other operations to modify the CAD design; a software interface to convert the CAD designed part (Data Process System) or device into a heterogeneous material and multi-part assembly model (Design Input Model) which can be used for multi-nozzle printing; and a multi-nozzle system to print the designed part or device using different, specialized nozzles (Tissue substitutes).

Abstract: Provided are methods for identifying and/or designing inhibitors of Staphylococcus aureus biological activity. Also provided is a computer readable medium encoded with instructions executable by a CPU for performing the functions of identifying or designing inhibitors of Staphylococcus aureus biological activity, and a system comprising the computer readable medium and a CPU. Also provided are compounds identified and/or designed by the methods, methods of treatment including the compounds, methods of inhibiting S. aureus using the compounds, medicaments including the compounds for use in the treatment of S. aureus infection, or conditions related to S. aureus infection, and pharmaceutical compositions including the compounds. Methods for identifying a bacterial cell that is resistant to methicillin are also provided.

Abstract: Systems and methods for modifying a medical model of a physical system is disclosed. One disclosed system includes a graphical user interface configured to display at least one parameter associated with the medical model and receive a modification of the at least one parameter. The system also includes a processor configured to receive the modification of the at least one parameter from the graphical user interface and execute a simulation of a part of the medical model including the modification of the at least one parameter.

Abstract: Methods and systems may provide for cognitive decline prediction or assessment. Baseline and follow-up inertial sensor data may be received from one or more inertial sensors attached to a person. Baseline and follow-up data indicative of cognitive decline may be received from the person. An indication of cognitive decline may be determined based on the baseline and follow-up cognitive decline data. A classifier function for predicting cognitive decline may be trained with the baseline inertial sensor data and the indication of cognitive decline. A classifier function for assessing cognitive decline may be trained with the baseline inertial sensor data, a difference between the baseline inertial sensor data and follow-up inertial sensor data, and the indication of cognitive decline.

Abstract: Methods, computer systems, and computer program products for biopolymer engineering. A variant set for a biopolymer of interest is constructed by identifying, using a plurality of rules, a plurality of positions in the biopolymer of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions and the substitutions for each respective position in the plurality of positions collectively define a biopolymer sequence space. A variant set comprising a plurality of variants of the biopolymer of interest is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-activity relationship is modeled between (i) one or more substitutions at one or more positions of the biopolymer of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set.

Abstract: A diabetes care management system for managing blood glucose levels associated with diabetes comprising a computing device and an insulin delivery device.

Abstract: System and method for managing fermentation feed in a biofuel production process, comprising a dynamic multivariate predictive model-based controller coupled to a dynamic multivariate predictive model. The model is executable to: receive process information, including water inventory and biomass information, from the biofuel production process; receive a specified objective for the fermentation feed specifying a target biomass concentration; and generate model output comprising target values for a plurality of manipulated variables of the biofuel production process, including target flow rates of water and/or biomass contributing to the fermentation feed in accordance with the specified objective.

Abstract: A system and method for automatically analyzing impedance and pH data from an esophageal probe includes a data collection system that collects and stores the output from the sensors for a certain period of time to locate reflux episodes in the waveforms. The data analysis system uses wavelet analysis to assist in locating bolus entry and exit points in the waveforms and to smooth waveforms for additional analysis. It also distinguishes between candidate acid reflux episodes and candidate non-acid reflux episodes for determining actual acid reflux episodes and non-acid reflux episodes, and it distinguishes between, and provides different signal processing for, signals from patients that have healthy esophageal tissue and those that have diseased esophageal tissue.

Abstract: A method of determining an allelic type of a specific individual, comprising: accessing a database of genetic information on a plurality of individuals, the genetic information comprising: the allelic type of each individual; and the type of each of a plurality of genetic markers for each individual; categorizing the data in the database into a plurality of groups of individuals, such that all individuals having the same allelic type are in the same group, and each group represents a different allelic type; inputting data comprising the type of each of a plurality of genetic markers of the specific individual having an unknown allelic type; specifying a set of genetic markers for which type information is known both for the individuals in the database and for the specific individual; applying a population genetic model to calculate the likelihood of sampling, from some or all of the groups in turn, the input type data of the specified set of genetic markers for the specific individual; and determining the

Abstract: A method for preoperatively characterizing an individual patient's biomechanic function in preparation of implanting a prosthesis is provided. The method includes subjecting a patient to various activities, recording relative positions of anatomy during said various activities, measuring force environments responsive to said patient's anatomy and affected area during said various activities, characterizing the patient's biomechanic function from said relative positions and corresponding force environments, inputting the measured force environments, relative positions of knee anatomy, and patient's biomechanic function characterization into one or more computer simulation models, inputting a computer model of the prosthesis into said one or more computer simulation models, and manipulating the placement of the prosthesis in the computer simulation using said patient's biomechanic function characterization and said computer model of the prosthesis to approximate a preferred biomechanical fit of the prosthesis.

Abstract: A method for producing a custom resection jig for a current patient scheduled to receive total knee arthroplasty using outcomes analysis comprising the steps of maintaining a database on a computer system of (1) prior patient bone morphology, (2) along with anatomical and mechanical bone alignment data and (3) data defining a custom resection jig design with a generally transverse resection window operable to guide a surgeon's transverse bone cut for prior patients that have received total knee arthroplasty and a post-surgery medically recognized scoring register greater or equal to a predetermined highly successful score value for a total knee arthroplasty procedure using prior success data to guide production of a current patient custom jig resection windows.

Abstract: Provided are methods of simulating tissue healing. The methods comprise using a mechanistic computer model of the interrelated effects of inflammation, tissue damage or dysfunction and tissue healing to predict an outcome of healing of damaged tissue in vivo, thereby predicting the outcome of healing of damaged tissue in vivo. Implementations of these methods on a computing device also are provided. Non-limiting examples of diseases and/or conditions that are amenable to simulation according to the methods described herein include: a diabetes, diabetic foot ulcers, necrotizing enterocolitis, ulcerative colitis, Crohn's disease, inflammatory bowel disease, restenosis (post-angioplasty or stent implantation), incisional wounding, excisional wounding, surgery, accidental trauma, pressure ulcer, stasis ulcer, tendon rupture, vocal fold phonotrauma, otitis media and pancreatitis.

Abstract: A system, method, and article for diagnosing a test set of biological cells. For example, in one embodiment a normal set of cells is characterized using flow cytometry. A centroid and radius are defined for a set of clusters in an n-dimensional space corresponding to a normal maturation for a cell lineage in the normal set of cells. A test set of cells is characterized using flow cytometry and the characterization is compared to the set of clusters.

Abstract: Provided herein are methods and computer-implemented systems for using computer simulations to predict likelihood of a cell population associated with a pathophysiological condition acquiring resistance to a therapeutic agent, to screen for therapeutic agents effective to suppress acquisition of resistance within a cell population and to treat the pathophysiological conditions associated therewith. The computer simulation comprises at least an input/out system and a mathematical model, including operably linked equations, parameter values and constant values, of growth response over a period of time of a cell population in contact with an therapeutic agent. Also provide is a method for determining a best-fit mathematical model of adaptation of a microbial population to a therapeutic agent over time and using the model to simulate microbial population behavior to a therapeutic agent.

Abstract: A system operating in a plurality of modes to provide an integrated analysis of molecular data, imaging data, and clinical data associated with a patient includes a multi-scale model, a molecular model, and a linking component. The multi-scale model is configured to generate one or more estimated multi-scale parameters based on the clinical data and the imaging data when the system operates in a first mode, and generate a model of organ functionality based on one or more inferred multi-scale parameters when the system operates in a second mode. The molecular model is configured to generate one or more first molecular findings based on a molecular network analysis of the molecular data, wherein the molecular model is constrained by the estimated parameters when the system operates in the first mode.

Abstract: A blood sugar condition is estimated by measuring a urine sugar value, discriminating whether it is less than a discriminating method classification boundary value, when it is less, obtaining an averaged value of measured urine sugar values during a past predetermined period of time, measured at the same time of day as the latest measurement, calculating the difference between the averaged and measured urine sugar values, when the difference is not less than a positive discriminating reference difference, discriminating as being a blood sugar value decrease, when the measured value is not less than the discriminating method classification boundary value, obtaining an averaged value of all measured values during the past predetermined period of time, calculating a ratio between the measured and averaged values, and, when the ratio is not greater than a first discriminating reference ratio, discriminating as being the blood sugar value decrease.

Abstract: A method of generating a computerized bone model representative of at least a portion of a patient bone in a pre-degenerated state. The method includes: generating at least one image of the patient bone in a degenerated state; identifying a reference portion associated with a generally non-degenerated portion of the patient bone; identifying a degenerated portion associated with a generally degenerated portion of the patient bone; and using information from at least one image associated with the reference portion to modify at least one aspect associated with at least one image associated the generally degenerated portion. The method may further include employing the computerized bone model representative of the at least a portion of the patient bone in the pre-degenerated state in defining manufacturing instructions for the manufacture of a customized arthroplasty jig.

Abstract: Methods, systems, and apparatus for accurately determining a proportion (ratio) of two analytes is provided, as well as provide a concentration of a first analyte from a determined concentration of a second analyte and from a proportion of the analytes to each other. In one aspect, a surface model (called a “dose surface” herein) relating the concentrations of the two analytes to the proportion can be used to obtain accurate values for one of the variables (e.g. a concentration or the proportion) when the other two variables have previously been obtained. The dose surface can be a three-dimensional surface and be non-linear. The dose surface model can include multiple regression functions. For example, measured responses can be individually converted to concentrations using two dose-response curves, and the concentrations can be input to a dose surface function to obtain the proportion.

Abstract: A method of diagnosing, predicting, or prognosticating about a disease that includes obtaining experimental data, wherein the experimental data is high dimensional data, filtering the data, reducing the dimensionality of the data through use of one or more methods, training a supervised pattern recognition method, ranking individual data points from the data, wherein the ranking is dependent on the outcome of the supervised pattern recognition method, choosing multiple data points from the data, wherein the choice is based on the relative ranking of the individual data points, and using the multiple data points to determine if an unknown set of experimental data indicates a diseased condition, a predilection for a diseased condition, or a prognosis about a diseased condition.

Abstract: Methods and compositions are provided for creating a binding protein that recognizes a rationally chosen recognition sequence in which a first amino acid has been substituted for a second amino acid using site-directed mutagenesis of a member protein of a set of proteins at an identified position or positions correlated with recognition of a chosen specified target module in the recognition sequence. A system is provided for automating the storage and manipulation of the correlations between positions and types of amino acid residues in the binding protein with specific modules at specified positions in the target recognition sequence and for designing and creating proteins with novel specificities.

Abstract: Ambulatory or in-hospital monitoring of patients is provided with early warning and prioritization, enabling proactive intervention and amelioration of both costs and risks of health care. Multivariate physiological parameters are estimated by empirical model to remove normal variation. Residuals are tested using a multivariate probability density function to provide a multivariate health index for prioritizing medical effort.

Abstract: A system and method are described for determining candidate fiducial marker locations in the vicinity of a lesion. Imaging information and data are input or received by the system and candidate marker locations are calculated and displayed to the physician. Additionally, interactive feedback may be provided to the physician for manually selected or identified sites. The physician may thus receive automatic real time feedback for a candidate fiducial marker location and adjust or accept a constellation of fiducial marker locations. 3D renderings of the airway tree, lesion, and marker constellations may be displayed.

Abstract: A method and apparatus are provided to determine a focus of high-intensity focused ultrasound (HIFU). The method and apparatus include designating an initial location of an observation point on a three-dimensional (3-D) organ model. The method and apparatus also include determining a first location to which the observation point has moved as a result of a change in a form of the 3-D organ model, and transmitting the ultrasound to the observation point. The method and apparatus further determine a displacement of the observation point through a time taken to receive a reflected wave from the observation point, determine a second location of the observation point using the obtained displacement, and process the first and second locations to determine a final location to which the observation point has moved. The method and apparatus include determining the focus of the HIFU based on the determined final location of the observation point.

Abstract: Systems and method for determining variants can receive mapped reads, align flow space information to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be evaluated in a context specific manner. A list of probable variants can be provided.

Abstract: Disclosed is number coding of pairs (“doublets”) or small sets (“multiplets”) of solid phase carriers which provides distinguishable subtypes of a given type of such carriers, where each carrier type is distinguishable on the bases of a different code. Such number coding is useful for augmenting a coding system, such as a color code, and thereby effectively multiplying the number of “colors” (distinguishable sub-types). It can be applied, for example, to determine whether a sample is homozygous or heterozygous at a number of different sites for one of two different alleles, where the same color code is applied for each of the two alleles, and the alleles with the same color code are distinguished by knowing how many carriers are associated with molecules which detect each different allele.

Abstract: A method for monitoring blood glucose (bG) levels of a diabetic user. The method may be implemented on a non-transitory computer readable medium adapted to run on a processing subsystem, the processing subsystem forming a portion of a handheld diabetes management device for monitoring the bG levels of a diabetic user and determining a correction bolus to be provided to the user. The method may comprise using a memory to store information in a plurality of different time blocks. The information may include a plurality of differing user defined health events that each include a predetermined associated percentage value set by the user by which a correction bolus calculation will be modified to account for one of an increase or a decrease in insulin associated with each one of the defined health events. The processing subsystem may be used to communicate with the memory and to obtain the information and to calculate therefrom the correction bolus.

Abstract: Virus-like particle (hereinafter sometimes VLP)-based strategies for developing vaccines against human viruses. Computer models of the VLPs are modified by the addition to the computer models of computer models of viral materials of the viruses against which the vaccines are being developed.

Abstract: Methods of identifying RNA-protein interaction sites are provided. Systems for identifying RNA-protein interaction sites are provided. Systems for identifying secondary structures are provided. Methods of identifying secondary structures are provided. Methods of identifying RNA-binding proteins are provided.