Abstract: Provided is a computer-based method of aligning a plurality of molecules including: (i) providing one or more conformers for each molecule; (ii) identifying triplets for each conformer; (iii) determining a triplet type for each triplet; (iv) identifying a base triplet type; (v) rotating and translating the conformers having the base triplet type to overlay the conformers so that the triplets providing the base triplet type are superposed in the same orientation; (vi) for each overlayed conformer, determining a respective bit string fingerprint which encodes the 3D positions of the conformer's fitting points and their respective pharmacophore features relative to the triplet providing the base triplet type; and (vii) aligning the molecules by searching the bit string fingerprints for combinations of overlayed conformers, each from a different molecule, which have high concordance in terms of pharmacophore points.

Abstract: Disclosed herein is a method of finding an isotopic cluster in a polypeptide and determining the monoisotopic mass of the cluster. The method comprises an algorithm for finding an isotopic cluster based on a probabilistic model, defined by each of peaks in the isotopic cluster, and determining the monoisotopic mass of the isotopic cluster. The probabilistic model of the isotopic cluster includes characteristic functions for mass, that is, a function of the ratio of two peak intensities, and a function of the product of two ratios obtained from three peaks. These characteristic functions for mass define the shape of peaks acceptable in an actual isotopic cluster for the mass of any isotopic cluster. The algorithm of finding the isotopic cluster based on the functions uses the characteristics to score the degree of the approximation of any isotopic cluster to the spectral shape of a theoretical cluster.

Abstract: The present invention relates to the crystal structure of the insulin receptor ectodomain, to the nature of its N-linked glycans and to methods of using the crystal and related structural information to screen for and design compounds that interact with or modulate the insulin receptor and/or the closely-related insulin-like growth factor receptors or variants thereof.

Abstract: Method for the humanization of the VH and VL variable regions of an animal antibody of known sequence, humanized animal antibody obtainable according to the method, in particular anti-NGF and anti-TrkA humanized animal antibodies.

Abstract: The present invention relates to a method for reconstructing protein database for identifying a protein and a method for screening a protein using the same, more precisely a method for reconstructing protein database, and a method for identifying a protein using the same. The method for reconstructing protein database and the method for identifying the protein of the invention are very useful for the investigation of endogenous proteins and their functions and interactions, and are further effectively used for the development of diagnostic and therapeutic agents for various diseases.

Abstract: An apparatus for elemental analysis of particles such as single cells or single beads by mass spectrometry is described. The apparatus includes means for particle introduction; means to vaporize, atomize and ionize elements associated with a particle; means to separate the ions according to their mass-to-charge ratio; means to detect the separated ions, means to digitize the output of the means to detect the ions; means to transfer and/or to process and/or record the data output of the means to digitize, having means to detect the presence of a particle in a mass spectrometer; and means to synchronize one of the means for ion detection, data digitization, transfer, processing and recording with the means to detect the presence of a particle. Methods and computer readable code implementing aspects of the apparatus, and for reducing the rates of data generation, digitization, transfer, processing and recording are also described.

Abstract: Methods, systems and mediums are disclosed for aligning mass spectrometry data before the analysis of the mass spectrometry data. The mass spectrometry data may be received from a mass spectrometry machine, and re-sampled using a smooth warping function. To estimate the warping function, a synthetic signal is build using, for example, Gaussian pulses centered at a set of reference peaks. The reference peaks may be designated by users or calculated after observing a group of spectrograms. The synthetic signal is shifted and scaled so that the cross-correlation between the mass spectrometry data and the synthetic signal reaches its maximum value.

Abstract: Methods, systems and computer program products for identifying components of an unknown mixture using spectral analysis techniques. The method includes comparing the spectrum of the unknown mixture with the spectra of library compounds to obtain candidate mixture combinations. A model is generated for each of the candidate mixture combinations based on a modeling metric. A residual spectrum is computed corresponding to each of the candidate mixture combinations by removing the spectrum of each of the compounds of the candidate mixture combination from the spectrum of the unknown mixture. One or more potential compounds are identified by comparing the residual spectrum with the spectrum of library compounds. The potential compounds are added to the candidate mixture combinations to generate an updated list of the candidate mixture combinations. The search algorithm repeats the steps described above on the updated candidate mixture combinations, until a first termination condition is satisfied.

Abstract: A computer-implemented method of analysis of melt curve data comprising the steps of: (a) parameter model fitting the melt curve data; (b) performing a principal component analysis of the melt curve data; and (c) utilizing the principal components for clustering the melt curve data into groups. Such a method allows an efficient analysis of variations in melt curve shape and position and allows to statistically quantify these variations for both supervised and unsupervised data sets. Current melt analysis methods neither allow for statistical measures of each unknown nor do they allow for the determination of unsupervised data sets (i.e., unknown number of groups present). Particularly, the method according to the invention can be advantageous for identifying a specific sequence of dsDNA in a sample after performing a polymerase chain reaction (PCR).

Abstract: Absolute quantitation of protein in a sample is provided by comparing a sum or average of the N highest ionization intensities observed for peptides of a particular protein along with a calibration standard. The calibration standard can be in the form of a table generated by prior protein peptide analysis performed using one or more pre-determined proteins. The comparison is used to determine a corresponding absolute quantity of protein based on the observed sum or average of ionization intensities. A simple conversion factor can be applied to the calibration standard value to determine the absolute quantity of protein in the sample.

Abstract: A mass spectrometry apparatus configured to allow a user to designate an upper limit value UL together with a lower limit value, as a peak sorting condition. A data processing section is operable to determine whether respective peak intensities of a plurality of peaks appearing on a mass spectrum fall within an intensity range Ath defined by upper and lower limit values UL, LL, and exclude any peak out of the intensity range Ath. The remaining ions are selected as precursor ions, for example, in descending or ascending order of peak intensity so as to perform an MS2 analysis. The upper limit UL is adequately set to allow the MS2 analysis for a sample component with a low concentration, by priority, while avoiding a sample component exhibiting a high intensity and having no need for the MS2 analysis.

Abstract: A method for calibrating an ion trap mass spectrometer is disclosed. The method includes establishing an optimal phase and amplitude-m/z relationship by acquiring peak quality data at varying values of amplitude and phase. The resonant ejection voltage applied to the electrodes of the ion trap may then be controlled during analytical scans in accordance with the established relationship between m/z and resonant ejection voltage amplitude.

Abstract: A computer-implemented system and method for determining an optimal manner of introducing and moving an introduced entity from an introduction site to a target tissue region. The method comprises: calculating a modeling value at the introduction site, the pathway to the target tissue region, and the target tissue region; calculating a diffusion value representing a concentration gradient of the introduced entity as it moves through the introduction site, the pathway, and the target tissue region; calculating a flow value representing how the introduced entity is transported through the introduction site, the pathway, and the target tissue region; and determining a time, location, and method for introducing and moving the introduced entity based on the modeling value, the diffusion value, and the flow value.

Abstract: Disclosed are methods for reliably detecting the presence of proteins, including proteins with various post-translational modifications (phosphorylation, glycosylation, methylation, acetylation, etc.) in a sample by the use of one or more capture agents that recognize and interact with recognition sequences uniquely characteristic of a protein or a set of proteins (Proteome Epitope Tags, or PETs) in the sample. Arrays comprising these capture agents or PETs are also provided.

Abstract: The present disclosure presents novel shape comparison methods. Methods for determining shape similarity between a query molecule and a target molecule and methods for screening one or more molecules in a database based on shape similarity to a query molecule are described.

Abstract: A dual-stage method is provided for identifying a microbe by, for example, its species or its subspecies. The method includes measuring a mass spectrum of the microbe using a mass spectrometer, calculating indicators for similarities between reference mass spectra in a library and the measured mass spectrum, selecting a group of reference mass spectra similar to the measured mass spectrum, determining a distinguishing weight for each mass signal of the reference mass spectra in the group, where the distinguishing weights emphasize differences between the reference mass spectra in the group, and calculating indicators for similarities between the reference mass spectra in the group and the measured mass spectrum as a function of the distinguishing weights.

Abstract: Applicants have discovered new methods and apparatuses for determining the fractional composition of a component in a multi-component mixture using multivariate statistical analysis of the ultrasonic frequency profile. Applicants show the use of ultrasonic spectrophonometry to determine the fractional composition of a component in a 3-component solvent mixture comprising water, ethanol and methanol as well as determination of the fractional composition of certain contaminants in water. Applicants provide a method of determining a fractional composition of a component in a multi-component mixture comprising pulsing a mixture with a source of ultrasounds, detecting “non-linear” ultrasonic spectral data propagating through the mixture and computing the fractional composition of the component.

Abstract: The present invention embraces methods for identifying compounds that modulate the activity of telomerase. Compounds of the invention are identified by designing or screening for a compound which binds to at least one amino acid residue of the TRBD, “thumb,” “finger,” and/or “palm” domain; or FP-pocket, PT-pocket or Th-pocket of telomerase and testing the compound for its ability to modulate the activity of telomerase.

Abstract: The inventors have modified the amino acid sequence of a maltogenic alpha-amylase to obtain variants with improved properties, based on the three-dimensional structure of the maltogenic alpha-amylase Novamyl. The variants have altered physicochemical properties, e.g. an altered pH optimum, improved thermostability, increased specific activity, an altered cleavage pattern or an increased ability to reduce retrogradation of starch or staling of bread.

Abstract: The invention provides methods and apparatus for analyzing a protein structure by A) receiving a reference structure (A) forming a three dimensional representation of a protein; B) substituting into the structure of (A) a pattern with amino-acids different from the one of the protein; C) optimizing the conformation of (A) substituted by pattern of (B); D) assessing the energetic compatibility (EC) of the pattern of (B) within the context of the structure of (A) being structurally optimized in (C) with respect to the pattern, by comparing the global energy of the substituted and optimized protein structure with the global energy of the non-substituted reference structure; and E) storing a value reflecting the EC of the pattern together with information related to the structure of the pattern in the form of an energetic compatibility object (ECO).

Abstract: The invention relates, in part, to the improved analysis of carbohydrates. In particular, the invention relates to the analysis of carbohydrates, such as N-glycans and O-glycans found on proteins and saccharides attached to lipids. Improved methods, therefore, for the study of glycosylation patterns on cells, tissue and body fluids are also provided. Information from the analysis of glycans, such as the glycosylation patterns on cells, tissues and in body fluids, can be used in diagnostic and treatment methods as well as for facilitating the study of the effects of glycosylation/altered glycosylation. Such methods are also provided. Methods are further provided to assess production processes, to assess the purity of samples containing glycoconjugates, and to select glycoconjugates with the desired glycosylation.

Abstract: The present invention relates generally to chemical agents useful in the prophylaxis and/or treatment of disease conditions and in particular chronic disease conditions such as inflammatory including allergic diseases, metastatic cancers and infection by pathogenic agents including bacteria, viruses or parasites. More particularly, the chemical agents contemplated by the present invention are selected from glycosaminoglycan (GAG) molecules derived from a larger GAG, GAG-like molecules which resemble GAGs in some of their characteristics but may be derived from a larger non-GAG polysaccharide and molecules having a GAG-like composite structure as well as agents which bind to the same sites as GAGs, GAG-like molecules or GAG-like composite molecules. The present invention also provides assays to identify GAG and GAG-like therapeutic agents including GAG-like composite structures as well as analogs, homologs and orthologs thereof.

Abstract: A method that identifies common peaks among unidentified peaks in the data from different LC-MS or LC-MS/MS runs is provided. The method employs an algorithm, herein referred to as “Precision Peak Matching (PPM).” The different runs can be from different laboratories, instruments, and biological samples that result in a significant variability in the data. PPM allows estimation and control of precision, defined as the fraction of truly identical peptide pairs among all pairs retrieved, in the matching process. PPM finds the maximal number of peptide pairs at a prescribed precision, thereby allowing quantitative control over the trade off between the number of true pairs missed, and false pairs found. PPM finds common peptides from a database of LC-MS runs of heterogeneous origins, and at the specified precision. PPM fills a much-needed role in proteomics by extracting useful information from disparate LC-MS databases in a statistically rigorous and interpretable manner.

Abstract: A method that identifies common peaks among unidentified peaks in the data from different LC-MS or LC-MS/MS runs is provided. The method employs an algorithm, herein referred to as “Precision Peak Matching (PPM).” The different runs can be from different laboratories, instruments, and biological samples that result in a significant variability in the data. PPM allows estimation and control of precision, defined as the fraction of truly identical peptide pairs among all pairs retrieved, in the matching process. PPM finds the maximal number of peptide pairs at a prescribed precision, thereby allowing quantitative control over the trade off between the number of true pairs missed, and false pairs found. PPM finds common peptides from a database of LC-MS runs of heterogeneous origins, and at the specified precision. PPM fills a much-needed role in proteomics by extracting useful information from disparate LC-MS databases in a statistically rigorous and interpretable manner.

Abstract: A chromatograph mass spectrometer is provided for obtaining the information pertinent to a structural analysis, with a simple operation, on a compound series including a plurality of compounds whose structures and characters are similar. First, based on the data obtained by a normal LC/MS analysis, a two-dimensional isointensity line graph is created and displayed with a retention time and a mass-to-charge ratio on the two axes and with a signal intensity represented in contour (S1 and S2). When the operator specifies a desired range by a drag operation or the like by a mouse (S3), peaks included in the range specified are extracted and based on the peaks, precursor ions are selected (S4 through S6). Then a schedule is created so that an MS2 analysis is performed for the precursor ions selected in the course of an LC/MS analysis for the sample to be targeted (S7).

Abstract: The object of the present invention is to provide a method for identifying a nucleotide sequence necessary for expressing affinity for a target substance with respect to a nucleotide sequence of a nucleic acid molecule such as an aptamer having such affinity for the target substance, based on similarity between nucleotide sequences and an evaluated value of the affinity of the nucleotide sequence, and a method for predicting a secondary structure of the nucleic acid molecule including the identified nucleotide sequence. The method of present invention includes the steps of extracting a single-stranded region by excluding based capable of forming a stem structure from the nucleotide sequence of the nucleic acid molecule; and searching a motif sequence from the single-stranded region, based on an evaluated value of the affinity.

Abstract: The present invention provides a method for configuring a pattern recognizer using versatile, readily available data, comprehensive protein data, and comprehensive chemical data, as well as a method for predicting an unknown interaction of a pair by using the pattern recognizer-configuring method. An interaction such as the coupling between a protein and a chemical is used as an index; at least one of four parameters is vectorized; a vector containing elements of the vector derived from each protein and elements of the vector derived from each chemical paired with the protein is created; and a support vector machine (SVM) is applied to this vector and trained to learn them, where the pattern recognizer is configured so as to discriminate between a class to which the first pair belong and a class to which the second pair belong.

Abstract: When a target substance's composition formula is deduced by using a mass spectrometer, if the target substance's composition formula is deduced based on an MSn spectrum and candidates are found, a composition formula candidate list including all the composition formula candidates is created, and the list is displayed in a list format. The composition formula candidates are narrowed down based on the MSn spectrum by an MS2 analysis or MS3 analysis. If there is a candidate to be excluded, the composition formula candidate list is updated, and the excluded candidate is moved to the exclusion list. Accompanying this, a composition formula candidate table is displayed in a list format on the display window. In this table, the composition formula candidates included in the exclusion list and the remaining composition formula candidates in the composition formula candidate list are simultaneously displayed with different colors so that they are visually discriminable.

Abstract: Disclosed is a sample processing apparatus, comprising: a sample processing unit for processing a sample with an auxiliary item used to process the sample; an output device for outputting a processing result by the sample processing unit; and a controller for determining whether or not the auxiliary item is appropriate for the sample processing by sample processing unit, and controlling, when determining that the auxiliary item is not appropriate for the sample processing by the sample processing unit, the output device so as to output the processing result and reliability information showing that the processing result has a low reliability. Also disclosed is a method for outputting the processing result by the sample processing apparatus and a computer program product.

Abstract: A real time gamma-ray signature/source identification method and system using principal components analysis (PCA) for transforming and substantially reducing one or more comprehensive spectral libraries of nuclear materials types and configurations into a corresponding concise representation/signature(s) representing and indexing each individual predetermined spectrum in principal component (PC) space, wherein an unknown gamma-ray signature may be compared against the representative signature to find a match or at least characterize the unknown signature from among all the entries in the library with a single regression or simple projection into the PC space, so as to substantially reduce processing time and computing resources and enable real-time characterization and/or identification.

Abstract: The present invention relates to a method for identifying compounds that modulate the activity of sirtuin deacetylase protein family members. Compounds of the invention are identified by designing or screening for a compound which binds to at least one amino acid residue of the newly identified nicotinamide inhibition and base exchange site of Sir2 and testing the compound for its ability to modulate the activity of the Sir2 protein. Compositions and methods for preventing or treating diseases or disorders associated with Sir2 are also provided.

Abstract: A method of identifying a drug candidate to a target protein for inhibiting shikimate pathway comprising (a) performing a molecular program for computing a molecule conformation and orientation relative to an active site of the target protein and selecting top-rank molecules, (b) generating protein-molecule interacting profiles and identifying conserved interactions and pharmacophore spots, (c) developing homologous pharmacophore models for identifying pharmacophore hot spots, (d) rescoring molecules selected from step (a) by their homologous pharmacophore scores, (e) selecting potential molecules having the highest homologous pharmacophore scores, and (f) acquiring corresponding real compounds of the potential molecules selected from step (c) and identifying their inhibitory activity on the target protein by bioassay.

Abstract: A method is disclosed for generating a mass spectrum, e.g. for Fourier transform mass spectrometry, having improved resolving power. The method includes steps of acquiring a plurality of mass spectra from a mass spectrometer using image current detection determining the centroids of at least some of the peaks which have a sufficient signal-to-noise (S/N) ratio so that the variation of the centroid of each such peak from the plurality of mass spectra is significantly lower than the full-width at half-maximum, dM, of the peak in the m/z domain; and generating a histogram of the centroids determined from the plurality of acquired mass spectra thereby forming a composite mass spectrum. The resultant composite mass spectrum comprises peaks having full-width at half-maximum, dMC, significantly narrower than the peak width, dM, of the corresponding peaks in the plurality of acquired mass spectra.

Abstract: The process of modeling a complex two-dimensional periodic structure is improved by selectively truncating the Fourier expansion used in the calculation of resulting scatter signature from the model. The Fourier expansion is selectively truncated by determining the contribution for each harmonic order in the Fourier transform of the permittivity function and retaining the harmonic orders with a contribution that is above a threshold. The Fourier space may be compressed so that only the selected harmonic orders are used, thereby reducing the required memory and calculation times. The compressed Fourier space may be used in a real-time analysis of a sample or to generate a library that is used in the analysis of a sample.

Abstract: A method for controlling fluid injection parameters to improve well interactions and control hydrofracture geometries is provided. The method incorporates a systematic, transient analysis process for determining the formation effective displacement, stress and excess pore pressure field quantities at any depth within a stratified subterranean formation resulting from the subsurface injection of pressurized fluids.

Abstract: A method for matching a precursor ion with one or more related product ions includes providing input data sets obtained from sample injections, each of the data sets including a precursor ion and one or more product ions, normalizing the input data sets in accordance with a single retention time for the precursor ion, determining which product ions are within a predetermined retention time window with respect to the single retention time, and, if a product ion is within the predetermined retention time window for a specified number of the input data sets, determining that the product ion is related to the precursor having the single retention time. An apparatus for analyzing a sample includes a chromatography module, a mass-spectrometry module in communication with the chromatography module, and a control unit in communication with the chromatography module and the mass-spectrometry module.

Abstract: The invention provides methods and apparatus for characterizing complex polymeric mixture of interest. Candidate solutions are eliminated from a solution space using one or more experimental measurements of a polymeric mixture of interest. The elimination step can be repeated one or more times using different experimental measurements produced by various chemical and physical protocols, so that the remaining candidate solutions converge to describe the actual polymeric mixture under investigation. Once the composition of the complex polymeric mixture has been characterized, the information thus generated can be used to facilitate, for example, the manufacture of a bio-equivalent of the complex polymeric mixture.

Abstract: The invention relates to a method for identifying a strain isolated from a clinical sample, at the species and/or subspecies level, using MALDI-TOF-MS analysis comprising a step of classifying the germ in a group before performing the MALDI-TOF-MS analysis.

Abstract: The present invention is directed to methods of merging spectral data resulting from collision fragmentation processes, such as, for example, Pulsed Q Dissociation (PQD), high-energy collision-induced dissociation (HCD), electron transfer disassociation (ETD), collision-induced dissociation (CID), and photo-dissociation processes, such as, but not limited to, infrared multi-photon photo-dissociation (IRMPD), to provide the desired qualitative and quantitative information on a single peptide. By merging such ETD, CID, or IRMPD scans with corresponding HCD scans that are obtained on the same precursor, the quality of the resulting spectrum is increased so as to provide more confident identification of peptides and correspondingly the quantification is enhanced because the HCD method of the MS/MS spectrum produces higher abundances of detectable reporter ions. Such methods, as disclosed herein, are especially applicable for peptides which experience predominant neutral loss in the ion trap, e.g., phosphorylated.

Abstract: The process of determining similarities of signals resulting from a sample analysis step using the same type of measuring device, characterized by the fact that it comprises a step of determining a value for each parameter of an uncertainty model related to said signals by processing homologous characteristic elements in at least two signals derived from the analysis of similar samples, and a step of determining a measurement of similarity between signals based on each parameter value of the said uncertainty model and of homologous characteristic elements in the different signals whose similarity is being measured.

Abstract: A computer-implemented method for calculating a value representative of interaction (VRI) of a proposed ligand with a specified receptor. Hydrophobic interactions between one or more ligand atoms and one or more receptor atoms are scored by a method that awards a bonus for the presence of hydrophobic enclosure of one or more ligand atoms by the receptor. Also, charge-charge hydrogen bonds between a ligand and a receptor are scored by setting a default value for a charge-charge hydrogen bond and awarding a bonus above the default value when one or more specialized predetermined charge-charge hydrogen bond criteria is satisfied. Various charge-charge hydrogen bond criteria are used. Zwitterions, charge, salvation, geometry and electrostatic energy are accounted for.

Abstract: A system is provided wherein spectrometer measurements, and/or measurements from other analytical instruments, are transmitted to a processing station which determines the component substances of the sample(s) subjected to the measurements. The names of the component substances are then inserted into database search queries related to matters such as handling precautions, causes/sources of the substances, remedies and neutralizing agents for the substances, regulations related to the substances, etc. The results of the search queries are then provided to the personnel who made the measurements, preferably wirelessly and almost immediately after the measurements were made. The system therefore provides nearly immediate guidance as to what substances are present and how to handle them, which can be useful for inexperienced personnel in hazardous response, contraband detection, industrial process control, and other situations.

Abstract: Generally, the present invention provides a number of procedures to spatially profile proteins by using hydrophobic moments. In all procedures, a hydrophobicity distribution of a protein is shifted and normalized. In one procedure, a shape or profile of a curve of a second-order moment of hydrophobicity is determined. A second procedure involves determining one or more ratios, such as the ratio of a distance at which the second order moment of hydrophobicity vanishes to the distance at which a zero-order moment of hydrophobicity vanishes. The distance at which a peak occurs in a profile of the zero- or second-order moment of hydrophobicity can also be used for comparison. For many of these procedures, a surface or profiling contour can be chosen and used to accumulate hydrophobicities and to determine the moments. These procedures can be combined to provide a good mathematical determination of whether a protein belongs to a particular class of proteins.

Abstract: Techniques for analyzing protein structures, such as a tertiary protein structure, are provided. A centroid of the residue centroids is calculated. The centroid of the residue centroids is used as a spatial origin of a global linear hydrophobic moment. The correlation between residue centroid magnitude and residue solvent accessibility is enhanced. The global linear hydrophobic moment is defined, wherein each of the residue centroids contributes a magnitude and direction to the global linear hydrophobic moment. A method for comparing at least two tertiary protein structures is also disclosed.

Abstract: A system and method generate a structure activity relationship model to determine whether unknown chemical compounds are of a desired classification where the structure activity relationship model is based on a set of known chemical compounds having known structural and/or biological descriptors. A system and method utilize a structure activity relationship model to determine whether unknown chemical compounds are of the desired classification, where descriptors of the known chemical compounds are compared to structural and/or biological descriptors of the unknown chemical compounds to determine whether the test chemical compounds are of the desired classification. A system and method generate a structure activity relationship model to study how particular agents may induce disease or act as therapeutic agents. The model may also be used to study how groups of agents induce disease or act as therapeutic agents and to study the etiology and treatment of disease in general.

Abstract: The present invention relates to FGFR pharmacophores, and in particular to compounds which are capable of binding to FGFR with greater affinity than their binding to VEGFR and methods of identifying such compounds using the pharmacophore. The present invention further relates to compositions, methods and uses of the compounds and the pharmacophores disclosed herein.

Abstract: Candidate structures for nanocrystal and other specimens are obtained based on a specimen complex spectrum that is determined as a Fourier transform of a phase-contrast electron micrograph. The specimen can also be assessed based on an amplitude portion of the complex spectrum using a lattice-fringe fingerprint. In some examples, the specimen complex spectrum is compensated based on an electron microscope transfer function, a specimen tilt, or based on other crystallographic compensation. Amplitude or phase portions of the compensated complex spectrum can be compared with reference structures stored in one or more reference structure databases.

Abstract: A computer system (100), an ingredient manufacturer system (200), and composition manufacturers can be connected online, and a system of the ingredient manufacturer obtains composition information from a system (300), and provides it for the system (100). At this time, an estimated product property and production cost can be provided.

Abstract: A computer-implemented molecular design method constructs and stores a data structure including an atomic data structure, a bond axis data structure, a molecular data structure, an auxiliary data structure, and an event data structure, with respect to data of a given three-dimensional (3D) molecular structure. A partial structure that is a modifying target is determined using the data structure, based on an atom or bond axis that is specified. A modified 3D molecular structure in which the partial structure has been subjected to a modifying operation is specified. An Undo or Redo operation is performed on the specified modifying operation using the data structure.

Abstract: A process, apparatus, and method for computerized detection, tracking, and feedback control of nutritional supplements in an animal, including humans relies on Raman scattering effects on skin or other tissues to determine the content of carotenoids or other nutrients as evidenced in that skin. Serum levels of nutrients may vary dramatically with time, but skin tissues may average such nutrition over time. Skin and other tissues may be scanned with light to produce accurate measurements of carotenoids or other nutrients accumulated in the skin based on the Raman scattering affect of those nutrients in the skin. A score can be derived from a properly calibrated bio-photonic scanner to reflect an averaged effective uptake of the detected nutrient (e.g. such as the carotenoid example).