Abstract: A mobile terminal including a touch screen; and a controller configured to display a specific content on the touch screen, in response to a first force touch input satisfying a specific touch-force applied to the specific content, execute an aggregated view mode and display objects included in the specific content in an aggregated manner, in response to a first non-force touch input selecting a particular object, distinguishably display the selected particular object on the touch screen, and in response to a second force touch input satisfying the specific touch-force applied to the specific content, display related contents related to the selected particular object on the touch screen.

Abstract: The present invention provides isolated peptides or the fragments derived from SEQ ID NO: 45, which bind to an HLA antigen and induce cytotoxic T lymphocytes (CTL). The peptides may include the above mentioned amino acid sequence with substitution deletion, or addition of one, two, or several amino acids sequences. The invention also provides pharmaceutical compositions including these peptides. The peptides of this invention can be used for diagnosing or treating cancer.

Abstract: Disclosed are devices that comprise a protein, such as an antibody, placed into electronic communication with a semiconductor material, such as a carbon nanotube. The devices are useful in assessing the presence or concentration of analytes contacted to the devices, including the presence of markers for prostate cancer and Lyme disease.

Abstract: A panel of lymphoma related biomarkers are provided. The panel allows the identification of a subject at risk for a lymphoma. Further provided are methods of optimizing therapeutic efficacy associated with treatment of a lymphoma related disorder. Methods of identifying biomarkers affiliated with a condition of interest are provided.

Abstract: The present disclosure provides compositions and methods for the generation of an antibody or immunogenic composition, such as a vaccine, through epitope focusing by variable effective antigen surface concentration. Generally, the composition and methods of the disclosure comprise three steps: a “design process” comprising one or more in silico bioinformatics steps to select and generate a library of potential antigens for use in the immunogenic composition; a “formulation process”, comprising in vitro testing of potential antigens, using various biochemical assays, and further combining two or more antigens to generate one or more immunogenic compositions; and an “administering” step, whereby the immunogenic composition is administered to a host animal, immune cell, subject or patient. Further steps may also be included, such as the isolation and production of antibodies raised by host immune response to the immunogenic composition.

Abstract: Compositions which are fragrant and contain at least a member set culled from a library of compositions, each being comprised of sub-combinations of selected terpenes. Fragrances that mimic that of various states of organic and synthetic aromatics including products, processes and those from non-combusted plant products, among other things, uniquitous products, processes, medicinals, and related moieties leverage databases of all known terpene groupings are offered for consideration, and have been provided, according to the instant teachings.

Abstract: A method for manufacturing synthetic genes and combinatorial DNA and protein libraries, termed here Divide and Conquer-DNA synthesis (D&C-DNA synthesis) method. The method can be used in a systematic and automated way to synthesize any long DNA molecule and, more generally, any combinatorial molecular library having the mathematical property of being a regular set of strings. The D&C-DNA synthesis method is an algorithm design paradigm that works by recursively breaking down a problem into two or more sub-problems of the same type. The division of long DNA sequences is done in silico. The assembly of the sequence is done in vitro. The D&C-DNA synthesis method protocol consists of a tree, in which each node represents an intermediate sequence. The internal nodes are created in elongation reactions from their daughter nodes, and the leaves are synthesized directly. After each elongation only one DNA strand passes to the next level in the tree until receiving the final product.

Abstract: The present invention provides novel algorithms for designing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts. Such oligonucleotides are particularly useful as primers for reverse transcription. The invention also provides compositions containing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts.

Abstract: The disclosure relates to a method of generating a diverse set of variants to screen improved and novel properties within the variant population, a system for creating the diverse set of variants, and the variant peptides.

Abstract: Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.

Abstract: A method and an apparatus for genome assembly are provided.

Abstract: The present disclosure teaches that the recombination of homologous sequences of P450 enzymes, with the aid of SCHEMA to predict a resulting protein structure, is able to generate libraries of chimeras with significant functional diversity. Additionally, the members of these libraries demonstrate superior or unexpected new properties, which correlate with other factors that are observable in the library. Thus, the making of libraries of optimized P450 enzymes, the analysis of libraries to identify an optimized subset, and the optimized chimeras with improved or altered functionalities are all taught in the present disclosure.

Abstract: Method to create in silico protein mutants with improved expression level in an expression host compared to an original protein. The mutants retain unaltered or minimally altered function and specific activity that is at the same or higher level compared to the original protein. The method also allows predicting one or more optimal expression host(s) for the given protein and mutants for maximum production level in the predicted optimal host(s). The method is based on optimizing protein sequence parameters that are important for protein expression, such as amino acid composition, guanine-cytosine (GC) content, RNA secondary structure, amount of charged amino acids on the surface, and length of the protein, among other parameters.

Abstract: The present invention provides the means for producing libraries of peptide structures for drug screening applications that are capable of folding or assuming their native conformations independently of artificial scaffolds or flanking sequences in the proteins from which they are derived. The libraries can be highly diverse such that they are representative of the repertoire of protein structures existing in nature. The libraries can also be non-redundant or normalized such that the bias towards specific structures existing in source data sets and/or in nature is/are removed. In a particularly preferred embodiment, the present invention provides 30,000 independent fold structures produced by this method. The present invention also provides computer-readable media and systems comprising structural data in relation to the peptide libraries, and methods for displaying and screening the libraries.

Abstract: The present invention overcomes the inadequacies inherent in the known methods for generating libraries of antibody-encoding polynucleotides by specifically designing the libraries with directed sequence and length diversity.

Abstract: Computer processing methods and/or systems for minimizing and/or optimizing data strings in accordance with rules and options. Minimized data strings can represent data sequences important in certain biologic analyses and/or syntheses. In specific embodiments, a request is generated by a user at a client system and received by a server system. The server system accesses initial data indicated or provided by the client system. The server system then performs an analysis to minimize the data needed for further reactions. In specific embodiments, a server can use proprietary methods or data at the server side while protecting those proprietary methods and data from access by the client system.

Abstract: The invention provides for methods and systems for engineering target proteins, based on protein sequence characteristics that influence the likelihood of obtaining a crystal suitable for X-ray structure solution, to improve protein crystallization, as well as related material.

Abstract: The present invention is relevant to proteins and novel methods of protein evolution. The present invention further relates to methods of identifying and mapping mutant polypeptides formed from, or based upon, a template polypeptide.

Abstract: Motility contrast imaging (MCI) is a depth-resolved holographic technique to extract cellular and subcellular motion inside tissue. The holographic basis of the measurement technique makes it highly susceptible to mechanical motion. The motility contrast application, in particular, preferably includes increased mechanical stability because the signal is based on time-varying changes caused by cellular motion, not to be confused with mechanical motion of the system. The use of the resulting spectrogram response signatures, or “fingerprint” data, of known compounds is disclosed to screen new compounds for leads as to those having potentially beneficial mechanisms of action. The “fingerprint” data of known toxic compounds can be used to screen new compounds for toxicity.

Abstract: The invention provides systems and methods for improved peptide screening library design. In some implementations the systems and methods utilize screening data relating to a plurality of peptides used in a peptide screen against a target molecule to construct a consensus binding sequence alignment using least a subset of the plurality of peptides. For one or more positions of the sequence alignment an observed distance matrix is constructed, the matrix describing a distance between the relative binding activity of pairwise comparisons of each amino acid in a given position. The observed distance matrix is then compared to a plurality of molecular field-based amino acid substitution matrices so as to identify one or more preferred amino acids for use in the design of novel predicted binding peptide sequences for a subsequent peptide screen.

Abstract: Provided are systems and methods for generating context-specific, field based amino acid substitution matrices. In some implementations, the systems and methods utilize a set of characteristics including sequence length, sequence, variable position, backbone conformation, sidechain conformation, and charge and/or ionization state to construct a number of instantiated virtual peptide variants that vary an amino acid at the variable position. Molecular fields are then calculated for each instantiated variant. The fields for each variant are then compared to one another in a pairwise fashion. Values representing the similarity of the fields resulting from the comparison are then assembled into an amino acid substitution matrix.

Abstract: Aspects of the invention relate to methods, compositions and algorithms for designing and producing a target nucleic acid. The method can include: (1) providing a plurality of blunt-end double-stranded nucleic acid fragments having a restriction enzyme recognition sequence at both ends thereof; (2) producing via enzymatic digestion a plurality of cohesive-end double-stranded nucleic acid fragments each having two different and non-complementary overhangs; (3) ligating the plurality of cohesive-end double-stranded nucleic acid fragments with a ligase; and (4) forming a linear arrangement of the plurality of cohesive-end double-stranded nucleic acid fragments, wherein the unique arrangement comprises the target nucleic acid.

Abstract: A data base of species specific nucleotide sequences (SSN) is created. The chemically synthesized sequences are used as DNA sequencing primers. Different mixes of DNA primers allow for the rapid and unique identification of any pathogen previously identified in the species specific data base. Staphylococcus simulans can be identified as the causative agent of Interstitial Cystitis using the unique SSN sequence 5? ATG GAT GTT TCA AAA AAA GTA GCT 3? coding for pre-prolysostaphin using it as a differential DNA primer in a mix set of pathogenic SSN sequence primers.

Abstract: Described herein is a discovery Platform Technology for analyzing a biological system or process (e.g., a disease condition, such as cancer) via model building.

Abstract: This invention provides methods and systems for identifying and typing toxicity of chemical compositions, as well as for screening new compositions for toxicity. The invention involves detecting alterations in gene or protein expression and hence establishing molecular profiles in isolated mammalian LSCs contacted with various chemical compositions of known and unknown toxicities, and correlating the molecular profiles with toxicities of the chemical compositions.

Abstract: The present invention concerns the design and construction of diverse peptide and polypeptide libraries. In particular, the invention concerns methods of analytical database design for creating datasets using multiple relevant parameters as filters, and methods for generating sequence diversity by directed multisyntheses oligonucleotide synthesis. The present methods enable the reduction of large complex annotated databases to simpler datasets of related sequences, based upon relevant single or multiple key parameters that can be individually directly defined. The methods further enable the creation of diverse libraries based on this approach, using multisynthetic collections of discrete and degenerate oligonucleotides to capture the diverse collection of sequences, or portions thereof.

Abstract: Disclosed is a method of iteratively optimizing two (or more) interrelated sets of probes for the multi-step analysis of sets of designated sequences, each such sequence requiring, for conversion, at least one conversion probe (“primer”), and each converted sequence requiring, for detection, at least one capture probe. The iterative method disclosed herein for the concurrent optimization of primer and probe selection invokes fast logical string matching functions to perform a complete cross-correlation of probe sequences and target sequences. The score function assigns to each probe-target alignment a “degree of matching” score on the basis of position-weighted Hamming distance functions introduced herein. Pairs of probes in the final selection may differ in several positions, while other pairs of probes may differ in only a single position. Not all such positions are of equal importance, and a score function is introduced, reflecting the position of the mismatch within the probe sequence.

Abstract: Rotamer libraries and methods of use thereof are provided.

Abstract: The invention utilizes clinical features of diseases with a genetic background to define logical panels of diseases which have shared signs or symptoms. The invention includes methods for collecting data for use in determining a cause or risk factor for disease and includes micro arrays for use in detecting mutations associated with the diseases set forth in the panel.

Abstract: Embodiments of the invention provides methods, computer software products and systems for arranging polymers during combinatorial polymer synthesis so that the border or edge between synthesis site is minimized. In one embodiment, travelling salesman algorithm is used to minimize the edges. In another embodiment, a locally greedy optimization method is provided. In addition, methods and software products are provided for solving the robust arrangement problem for multi-probe gene expression arrays.

Abstract: The invention provides methods for producing a replication competent chimeric human immunodeficiency virus (HIV) that optionally contains a heterologous reporter gene, and methods for generating these viruses. The invention's recombinant viruses are useful in the determination of, for example, antiretroviral drug susceptibility, HIV drug resistance, HIV phenotyping, HIV genotyping, HIV fitness, HIV tropism or coreceptor usage, HIV serum neutralization, and for HIV vaccine development, HIV vector development, and HIV virus production.

Abstract: Methods and systems are provided for constructing recombinant antibody libraries based on three-dimensional structures of antibodies from various species including human. In one aspect, a library of antibodies with diverse sequences is efficiently constructed in silico to represent the structural repertoire of the vertebrate antibodies. Such a functionally representative library provides a structurally diverse and yet functionally more relevant source of antibody candidates which can then be screened for high affinity binding to a wide variety of target molecules, including but not limited to biomacromolecules such as protein, peptide, and nucleic acids, and small molecules.

Abstract: The system relates to filed-programmable lab-on-chip (FPLOC) microfluidic operations, fabrications, and programming based on Microelectrode Array Architecture are disclosed herein. The FPLOC device by employing the microelectrode array architecture may include the following: (a) a bottom plate comprising an array of multiple microelectrodes disposed on a top surface of a substrate covered by a dielectric layer; wherein each of the microelectrode is coupled to at least one grounding elements of a grounding mechanism, wherein a hydrophobic layer is disposed on the top of the dielectric layer and the grounding elements to make hydrophobic surfaces with the droplets; (b) a field programmability mechanism for programming a group of configured-electrodes to generate microfluidic components and layouts with selected shapes and sizes; and, (c) a FPLOC functional block, comprising: (i) I/O ports; (ii) a sample preparation unit; (iii) a droplet manipulation unit; (iv) a detection unit; and (iv) a system control unit.

Abstract: A method is provided allowing for automatic selection of enzymes to be used in protocols such as methylation profiling, chip-on-chip, and comparative genomic hybridization experiments. The method may also maximize the space on a micro array for a given experiment. This means that the results from the micro array are improved. The method also improves zero-in and focus of significant patterns on a micro array. This enhances the ability to distinguish two separate classes of samples, e.g. tumour vs. normal, aggressive vs. non-aggressive, male vs. female, etc. Furthermore, a computer readable medium and a device are also provided.

Abstract: Methods for determining the compatibility of a plurality of fluid samples of different lubricating oil compositions with elastomers is provided. Each sample includes one or more base oils of lubricating viscosity and one or more lubricating oil additives. The methods can advantageously be optimized using combinatorial chemistry, in which a database of combinations of lubricating oil compositions are generated. As market conditions vary and/or product requirements or customer specifications change, conditions suitable for forming desired products can be identified with little or no downtime.

Abstract: The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

Abstract: Aspects of the invention relate to variant proteins and methods for designing and using the same. In some embodiments, the invention relates to methods for determining a functional variant of a protein that is restricted by one or more known legal rights, such as patent rights. Functional variants according to this invention are free of such restrictions.

Abstract: The present invention provides a methodology for efficiently generating and screening protein libraries for optimized proteins with desirable biological functions, such as improved binding affinity towards biologically and/or therapeutically important target molecules. The process is carried out computationally in a high throughput manner by mining the ever-expanding databases of protein sequences of all organisms, especially human.

Abstract: Combinations, called matrices with memories, of matrix materials with remotely addressable or remotely programmable recording devices that contain at least one data storage unit are provided. The matrix materials are those that are used in as supports in solid phase chemical and biochemical syntheses, immunoassays and hybridization reactions. The matrix materials may additionally include fluophors or other luminescent moieties to produce luminescing matrices with memories. The data storage units are non-volatile antifuse memories or volatile memories, such as EEPROMS, DRAMS or flash memory. By virtue of this combination, molecules and biological particles, such as phage and viral particles and cells, that are in proximity or in physical contact with the matrix combination can be labeled by programming the memory with identifying information and can be identified by retrieving the stored information. Combinations of matrix materials, memories, and linked molecules and biological materials are also provided.

Abstract: Disclosed are systems and methods for developing diagnostic tests (e.g., detection, screening, monitoring, and prognostic tests) based on biomarker information from legacy clinical sample sets, for which only small sample volumes (e.g., about 0.05 to about 1.0 mL or less per sample) are typically available. For example, biomarkers (e.g., about 10, 50, 100, 150, 200, 300, or more) may be detected in the clinical samples through the use of single molecule detection and each biomarker may be detected in an assay that includes about 1 ?L or less of a legacy clinical sample.

Abstract: A method and a system for selecting a set of FISH probe oligonucleotide sequences from a plurality of overlapping tiled candidate FISH probe oligonucleotide sequences are provided. A composition that includes FISH probes with sequences from the set of FISH probe oligonucleotide sequences is also provided.

Abstract: The disclosure relates to a method of generating a diverse set of variants to screen improved and novel properties within the variant population, a system for creating the diverse set of variants, and the variant peptides.

Abstract: Methods and systems for providing biological results in the form of systematically varied libraries of sequences or as data representing sequences or physical preparations of systematically varied libraries and/or selections from systematically varied libraries.

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: The present invention provides kits and methods for the diagnosis, prognosis and prediction of sepsis in a subject or for the differentiation between sepsis and SIRS in a subject, the method comprising(a) measuring the level of pro-hepcidin (pro-HEPC) in a biological sample taken from said subject, (b) measuring the level of at least one further biomarker selected from the group consisting of soluble TNF-receptor 2 (sTNFR2), Pentraxin-3 (PTX-3), Macrophage Colony-Stimulating Factor (MCSF), pro-Brain Natriuretic Protein (pro-BNP), one or more members of the Histone protein family, Procalcitonin (PCT) and c-Reactive Protein (CRP) in a biological sample from said subject, (c) using said measurements obtained in steps (a) and (b) to create a profile for said biomarkers and (d) comparing said profile with a reference biomarker profile obtained form a patient having SIRS or from a healthy subject.

Abstract: Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or comparative genome hybridization microarray, comprising selecting a plurality of potential target sequences, generating a plurality of candidate probes from the target sequences, filtering the plurality of candidate probes by analyzing candidate probes for selected probe properties in silico. Microarrays comprising probes selected by the methods of the invention are particularly useful for comparative genome hybridization and location analysis.

Abstract: A method of analyzing wound samples is provided. The analysis typically involves the use of mass spectrometry.

Abstract: Systems and methods for using the same to obtain a chemical array layout are provided. Also provided are computer program products for executing the subject methods.

Abstract: A biomolecular assay includes a substrate with a metallic layer on at least one surface thereof. The metallic film includes nanocavities. The nanocavities are configured to enhance signals that are representative of the presence or amount of one or more analytes in a sample or sample solution, and may be configured to enhance the signal by a factor of about two or more or by a factor of about three or more. Such signal enhancement may be achieved with nanocavities that are organized in an array, randomly positioned nanocavities, or nanocavities that are surrounded by increased surface area features, such as corrugation or patterning, or nanocavities that have quadrilateral or triangular shapes with tailored edge lengths, or with a plurality of nanoparticles. Methods for fabricating biomolecular substrates and assay techniques in which such biomolecular substrates are used are also disclosed.

Abstract: Systems and methods collect and screen a biological material to facilitate its selection and use for therapeutic and/or research purposes. The systems and methods take into account both objective and semi-objective attributes manifest in a biological material, such as genetic, phenotypic, clinical, and genealogic attributes. The diverse array of the objective and semi-objective attributes enhances the level of confidence that the biological material can be best matched with a particular research or therapeutic purpose.