Abstract: An exemplary system, method and computer-accessible medium for multiplexing base-calling of a plurality of nucleic acid molecules in the same flow cell is provided. When multiplexing for just two nucleic acid molecules, it can operate by selecting a first base call for a first nucleic acid molecule and a second base call for a second nucleic acid molecule, after having placed them in the same flow cell and obtaining the combined raw intensity output. It can use as prior the appropriate reference genome sequences from which the nucleic acid molecules can be derived in order to create a score function, which can additionally be constrained by various penalty functions. It can derive accuracy and speed by using a branch and bound strategy as well as by performing alignment and base-calling in one step per cycle.

Abstract: An exemplary system, method, and computer-accessible medium for recommending a model(s), can include, for example, receiving a plurality of test models including the model(s), determining if each of the test models has at least one verifier associated therewith, and recommending the model(s) based on the determination. An indication of a stake associated with each of the test models can be received. The stake can be a financial stake or a reputation stake. The financial stake can be a cryptocurrency. At least one of the test models can be analyzed using a machine learning procedure, which can be a convolutional neural network or a recurrent neural network. At least one of the test models can be analyzed using an empirical Bayes procedure. A particular model can be removed if the particular model(s) does not have a verifier(s) associated therewith.

Abstract: Described herein are real-time musical translation devices (RETMs) and methods of use thereof. Exemplary uses of RETMs include optimizing the understanding and/or recall of an input message for a user and improving a cognitive process in a user.

Abstract: Exemplary system, method, and computer-accessible medium for transmitting or generating an encrypted message(s) to or for a receiver(s) from a sender(s), can be provided, which can include, for example, generating an electronic public key(s) and an electronic private key(s) for the sender(s), generating first information based on (i) data of the sender(s), (ii) a state(s) of the sender(s), and/or (iii) a type of the sender(s), electronically selecting an electronic message signal(s) and a time stamp(s) based on the first information, generating a message(s) based on the electronic message signal(s) and the time stamp(s), generating the encrypted message(s) by encrypting the message(s) using the electronic private key(s), and transmitting the encrypted message(s) to the receiver(s).

Abstract: An exemplary system, method, and computer-accessible medium for recommending a model(s), can include, for example, receiving a plurality of test models including the model(s), determining if each of the test models has at least one verifier associated therewith, and recommending the model(s) based on the determination. An indication of a stake associated with each of the test models can be received. The stake can be a financial stake or a reputation stake. The financial stake can be a cryptocurrency. At least one of the test models can be analyzed using a machine learning procedure, which can be a convolutional neural network or a recurrent neural network. At least one of the test models can be analyzed using an empirical Bayes procedure. A particular model can be removed if the particular model(s) does not have a verifier(s) associated therewith.

Abstract: An exemplary embodiment of system, method and computer-accessible medium can be provided to reconstruct models based on the probabilistic notion of causation, which can differ fundamentally from that can be based on correlation. A general reconstruction setting can be complicated by the presence of noise in the data, owing to the intrinsic variability of biological processes as well as experimental or measurement errors. To gain immunity to noise in the reconstruction performance, it is possible to use a shrinkage estimator. On synthetic data, the exemplary procedure can outperform currently known procedures and, for some real cancer datasets, there are biologically significant differences revealed by the exemplary reconstructed progressions. The exemplary system, method and computer accessible medium can be efficient even with a relatively low number of samples and its performance quickly converges to its asymptote as the number of samples increases.

Abstract: Exemplary methods, procedures, computer-accessible medium, and systems for base-calling, aligning and polymorphism detection and analysis using raw output from a sequencing platform can be provided. A set of raw outputs can be used to detect polymorphisms in an individual by obtaining a plurality of sequence read data from one or more technologies (e.g., using sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, Sanger sequencing, etc.). For example, provided herein are exemplary methods, procedures, computer-accessible medium and systems, which can include and/or be configured for obtaining raw output from a sequencing platform configured to be used for reading fragment(s) of genomes, obtaining reference sequences for the genomes obtained independently from the raw output, and generating a base-call interpretation and/or alignment using the raw output and the reference sequences.

Abstract: Exemplary methods, procedures, computer-accessible medium, and systems for base-calling, aligning and polymorphism detection and analysis using raw output from a sequencing platform can be provided. A set of raw outputs can be used to detect polymorphisms in an individual by obtaining a plurality of sequence read data from one or more technologies (e.g., using sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, Sanger sequencing, etc.). For example, provided herein are exemplary methods, procedures, computer-accessible medium and systems, which can include and/or be configured for obtaining raw output from a sequencing platform configured to be used for reading fragment(s) of genomes, obtaining reference sequences for the genomes obtained independently from the raw output, and generating a base-call interpretation and/or alignment using the raw output and the reference sequences.

Abstract: Exemplary system, method, and computer-accessible medium for transmitting or generating an encrypted message(s) to or for a receiver(s) from a sender(s), can be provided, which can include, for example, generating an electronic public key(s) and an electronic private key(s) for the sender(s), generating first information based on (i) data of the sender(s), (ii) a state(s) of the sender(s), and/or (iii) a type of the sender(s), electronically selecting an electronic message signal(s) and a time stamp(s) based on the first information, generating a message(s) based on the electronic message signal(s) and the time stamp(s), generating the encrypted message(s) by encrypting the message(s) using the electronic private key(s), and transmitting the encrypted message(s) to the receiver(s).

Abstract: Exemplary embodiments of the present disclosure relate generally to methods, computer-accessible medium and systems for assembling haplotype and/or genotype sequences of at least one genome, which can be based upon, e.g., consistent layouts of short sequence reads and long-range genome related data. For example, a processing arrangement can be configured to perform a procedure including, e.g., obtaining randomly located short sequence reads, using at least one score function in combination with constraints based on, e.g., the long range data, generating a layout of randomly located short sequence reads such that the layout is globally optimal with respect to the score function, obtained through searching coupled with score and constraint dependent pruning to determine the globally optimal layout substantially satisfying the constraints, generating a whole and/or a part of a genome wide haplotype sequence and/or genotype sequence, and converting a globally optimal layout into one or more consensus sequences.

Abstract: An exemplary system, method and computer-accessible medium for multiplexing base-calling of a plurality of nucleic acid molecules in the same flow cell is provided. When multiplexing for just two nucleic acid molecules, it can operate by selecting a first base call for a first nucleic acid molecule and a second base call for a second nucleic acid molecule, after having placed them in the same flow cell and obtaining the combined raw intensity output. It can use as prior the appropriate reference genome sequences from which the nucleic acid molecules can be derived in order to create a score function, which can additionally be constrained by various penalty functions. It can derive accuracy and speed by using a branch and bound strategy as well as by performing alignment and base-calling in one step per cycle.

Abstract: The present invention provides methods of detecting a nucleic acid analyte in a sample. The methods generally involve modifying immobilized nucleic acids from a sample onto an insoluble support in a substantially elongated configuration, where modification generates an identifying feature that identifies the analyte; and detecting the identifying feature(s) using scanning probe microscopy, to detect the analyte. The present invention further provides a method for assigning a profile of a feature to a nucleic acid. The present invention further provides a computer program product for use in a subject method. The present invention further provides a system for detecting a nucleic acid in a sample; and a system for assigning a profile of a feature to a nucleic acid. The present invention further provides a method for immobilizing a nucleic acid onto an insoluble support; and further provides insoluble support having nucleic acid(s) immobilized thereon.

Abstract: An exemplary system method, and computer-accessible medium for initiating a protocol(s) can be provided, which can include, for example, generating a digitally encrypted perishable object(s), distributing the digitally encrypted perishable object(s) to a cyber-physical entity(s), determining if the cyber-physical entity(s) has received the digitally encrypted perishable object(s), and initiating at a predetermined protocol(s) based on the determination.

Abstract: A method for detecting rare genomic variants in a population of cells is disclosed. The method can detect de novo mutations in bacteria and analyze the impact of various physiological conditions on mutation rate, even though such effects would be too subtle to detect using other methods. The method can be used for detection of low-frequency subpopulations in the microbiome or in cancer.

Abstract: The present disclosure relates to exemplary embodiments of method, computer-accessible medium, system and software arrangements for, e.g., Cancer Hallmark Automata, a formalism to model the progression of cancers through discrete phenotypes (so-called hallmarks). The precise computational model described herein includes the automatic verification of progression models (e.g., consistency, causal connections, etc.), classification of unreachable or unstable states (e.g., “anti-hallmarks”) and computer-generated (individualized or universal) therapy plans. Exemplary embodiments abstractly model transition timings between hallmarks as well as the effects of drugs and clinical tests, and thus allows formalization of temporal statements about the progression as well as notions of timed therapies. Certain exemplary models discussed herein can be based on hybrid automata (e.g., with multiple clocks), for which relevant verification and planning algorithms exist.

Abstract: The present invention provides methods of detecting a nucleic acid analyte in a sample. The methods generally involve modifying immobilized nucleic acids from a sample onto an insoluble support in a substantially elongated configuration, where modification generates an identifying feature that identifies the analyte; and detecting the identifying feature(s) using scanning probe microscopy, to detect the analyte. The present invention further provides a method for assigning a profile of a feature to a nucleic acid. The present invention further provides a computer program product for use in a subject method. The present invention further provides a system for detecting a nucleic acid in a sample; and a system for assigning a profile of a feature to a nucleic acid. The present invention further provides a method for immobilizing a nucleic acid onto an insoluble support; and further provides insoluble support having nucleic acid(s) immobilized thereon.

Abstract: A method for detecting rare genomic variants in a population of cells is disclosed. The method can detect de novo mutations in bacteria and analyze the impact of various physiological conditions on mutation rate, even though such effects would be too subtle to detect using other methods. The method can be used for detection of low-frequency subpopulations in the microbiome or in cancer.

Abstract: Exemplary embodiments of the present disclosure can include, for example, an atomic force microscopy (AFM) system, including a cantilever(s), an optical pickup unit(s) (OPU(s)) including a laser positioned over the cantilever(s), and a power source providing noise with a noise level that is below 300 Picometers. The noise level of the power source can be below 200 Picometers. A digitizing arrangement can be included which can be associated with the OPU. The digitizing arrangement(s) can have a bandwidth of about 2 MHZ. The OPU(s) can have a detection bandwidth of at least 80 MHZ. The exemplary apparatus can be combined with a chemical protocol and statistical signal processing and image analysis procedures to map DNA at high speed and accuracy.

Abstract: An exemplary embodiment of system, method and computer-accessible medium can be provided to reconstruct models based on the probabilistic notion of causation, which can differ fundamentally from that can be based on correlation. A general reconstruction setting can be complicated by the presence of noise in the data, owing to the intrinsic variability of biological processes as well as experimental or measurement errors. To gain immunity to noise in the reconstruction performance, it is possible to use a shrinkage estimator. On synthetic data, the exemplary procedure can outperform currently known procedures and, for some real cancer datasets, there are biologically significant differences revealed by the exemplary reconstructed progressions. The exemplary system, method and computer accessible medium can be efficient even with a relatively low number of samples and its performance quickly converges to its asymptote as the number of samples increases.

Abstract: Exemplary systems, methods and computer-accessible mediums can receive first data related to at least one first string arranged in a directed acyclic graph, compress the first data into second data, and can search the second data for a match of at least one second string. A node of the directed acyclic graph can encode at least one substring, and an edge of the directed acyclic graph can encode instructions for concatenating substrings.