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PubMed1996

Use of IS6110 DNA fingerprinting in tracing man-to-man transmission of Mycobacterium tuberculosis in the Czech Republic.

The epidemiological relationship between tuberculosis cases in a prison and between cases within five families was investigated. Therefore, the isolated Mycobacterium tuberculosis strains were subjected to restriction fragment length polymorphism (RFLP) analysis using insertion sequence IS6110 as a probe. In case of 11 patients, the expected links of transmission were confirmed by RFLP typing. In contrast, in case of 4 patients the conclusion of classical contact tracing were not in agreement with the DNA fingerprinting results. These findings reinforce the usefulness of this recently developed technique as an additional tool in contact tracing. The IS6110DNA fingerprints of all strains investigated consisted of 7 to 13 bands and showed a high degree of polymorphism. Comparison of these fingerprints with those recorded in the Czech Republic previously, revealed the presence of a predominant DNA fingerprint type, without a known connection between the cases. Furthermore, other patterns found in the present study showed a high degree of similarity with the previously obtained fingerprints. Part of the patients were sampled twice. All of these double isolates showed identical fingerprints, confirming the previously described stability of IS6110DNA fingerprints. In contrast, from one couple of strains, isolated from husband and wife both suffering from tuberculosis, a slight change in one of the two patterns was observed. The patterns shared 10 band positions, confirming the expected relationship between these cases, but one of the patterns contained one additional band.

Contact Tracing↗
PubMedDate not supplied

Contactless optical scanning of fingerprints with 180 degrees view.

Fingerprint recognition technology is an integral part of criminal investigations. It is the basis for the design of numerous security systems in both the private and public sectors. In a recent study emulating the fingerprinting procedure with widely used optical scanners, it was found that, on average, the distance between ridges decreases about 20% when a finger is positioned on a scanner. Using calibrated silicon pressure sensors, the authors scanned the distribution of pressure across a finger, pixel by pixel, and also generated maps of the average pressure distribution during fingerprinting. Controlled loading of a finger demonstrated that it is impossible to reproduce the same distribution of pressure across a given finger during repeated fingerprinting procedures. Based on this study, a novel method of scanning the fingerprint with more than a 180 degrees view was developed. Using a camera rotated around the finger, small slices of the entire image of the finger were acquired. Equal sized slices of the image were processed with a special program assembling a more than 180 degrees view of the finger. Comparison of two images of the same fingerprint, namely the registered and actual images, could be performed by a new algorithm based on the symmetry of the correlation function. The novel method is the first contactless optical scanning technique to view 180 degrees of a fingerprint without moving the finger. In a machine which is under design, it is expected that the full view of one finger would be acquired in about a second.

Algorithms↗
PubMed1991

Differentiation of species and strains among filamentous fungi by DNA fingerprinting.

We have analyzed 11 strains and clones, representing five species (Penicillium janthinellum, P. citrioviridae, P. chrysogenum, Aspergillus niger, Trichoderma harzianum) and three genera of filamentous fungi, for the presence of hypervariable loci in their genomes by hybridization with simple repeat oligonucleotides and the DNA of phage M13. The oligonucleotide probes (CT)8, (GTG)5 and (GACA)4, as well as M13 DNA, are informative probes for fingerprinting in all genera and species tested. The probe (GATA)4 produced informative fingerprints only with the genomic DNA of A. niger. There was no similarity between the fingerprints originating from fungi of different genera and also little similarity between the fingerprints of different species belonging to the same genus. Fingerprints of strains of the same species differed only slightly from each other. Fingerprints of clones originating from one strain were identical. The results indicate that DNA fingerprinting is a powerful method to differentiate species and strains of filamentous fungi.

Aspergillus niger↗
PubMed1988

Stability of multilead ST-segment "fingerprints" over time after percutaneous transluminal coronary angioplasty and its usefulness in detecting reocclusion.

Multilead ST-segment recordings taken during percutaneous transluminal coronary angioplasty (PTCA) could function as an individualized noninvasive template or "fingerprint," useful in evaluating transient ischemic episodes after leaving the catheterization laboratory. To evaluate the reproducibility of such ST-segment patterns over time, these changes were analyzed in patients grouped according to the time between occlusion and reocclusion. For the patients in group 1, the study required comparing their "fingerprints" in repeat balloon inflation during PTCA (reocclusion in less than 1 hour), for those in group 2, comparing ST "fingerprints" during PTCA with ST changes during spontaneous early myocardial infarction (reocclusion in 24 hours) and in group 3, comparing ST "fingerprints" with ST changes during repeat PTCA for restenosis greater than 1 month after the initial PTCA. The ST "fingerprints" among the 20 patients in group 1 were identical in 14 cases (70%) and clearly related in another 4 (20%). Of the 23 patients in group 2, 12 (52%) had the same and 8 (35%) had related patterns. Of 19 patients in group 3, 8 (42% had the same pattern and 8 (42%) had related patterns. Thus, ST fingerprints were the same or clearly related with reocclusion in the same patient from less than 1 hour to greater than 1 month after initial occlusion in 87% of patients overall, in 90% in less than 1 hour, in 87% in less than 24 hours and in 84% greater than 1 month later. Multilead pattern ST-segment "fingerprints" may serve as a noninvasive marker for detecting site-specific reocclusion.

Aged↗
PubMed1995

Predicting ligand binding to proteins by affinity fingerprinting.

BACKGROUND: There are many ways to represent a molecule's properties, including atomic-connectivity drawings, NMR spectra, and molecular orbital models. Prior methods for predicting the biological activity of compounds have largely depended on these physical representations. Measuring a compound's binding potency against a small reference panel of diverse proteins defines a very different representation of the molecule, which we call an affinity fingerprint. Statistical analysis of such fingerprints provides new insights into aspects of binding interactions that are shared among a wide variety of proteins. These analyses facilitate prediction of the binding properties of these compounds assayed against new proteins. RESULTS: Affinity fingerprints are reported for 122 structurally-diverse compounds using a reference panel of eight proteins that collectively are able to generate unique fingerprints for about 75% of the small organic compounds tested. Application of multivariate regression techniques to this database enables the creation of computational surrogates to represent new proteins that are surprisingly effective at predicting binding potencies. We illustrate this for two enzymes with no previously recognizable similarity to each other or to any of the reference proteins. Fitting of analogous computational surrogates to four other proteins confirms the generality of the method; when applied to a fingerprinted library of 5000 compounds, several sub-micromolar hits were correctly predicted. CONCLUSIONS: An affinity fingerprint database, which provides a rich source of data defining operational similarities among proteins, can be used to test theories of cryptic homology unexpected from current understanding of protein structure. Practical applications to drug design include efficient pre-screening of large numbers of compounds against target proteins using fingerprint similarities, supplemented by a small number of empirical measurements, to select promising compounds for further study.

Chromatography, Affinity↗
PubMed2004

Correction of retention time shifts for chromatographic fingerprints of herbal medicines.

In this study, the combination of chemometric resolution and cubic spline data interpolation was investigated as a method to correct the retention time shifts for chromatographic fingerprints of herbal medicines obtained by high-performance liquid chromatography-diode array detection (HPLC-DAD). With the help of the resolution approaches in chemometrics, it was easy to identify the purity of chromatographic peak clusters and then resolve the two-dimensional response matrix into chromatograms and spectra of pure chemical components so as to select multiple mark compounds involved in chromatographic fingerprints. With these mark components determined, the retention time shifts of chromatographic fingerprints might be then corrected effectively. After this correction, the cubic spline interpolation technique was then used to reconstruct new chromatographic fingerprints. The results in this work showed that, the purity identification of the chromatographic peak clusters together with the resolution of overlapping peaks into pure chromatograms and spectra by means of chemometric approaches could provide the sufficient chromatographic and spectral information for selecting multiple mark compounds to correct the retention time shifts. The cubic spline data interpolation technique was user-friendly to the reconstruction of new chromatographic fingerprints with correction. The successful application to the simulated and real chromatographic fingerprints of two Cortex cinnamomi, fifty Rhizoma chuanxiong, ten Radix angelicae and seventeen Herba menthae samples from different sources demonstrated the reliability and applicability of the approach investigated in this work. Pattern recognition based on principal component analysis for identifying inhomogenity in chromatographic fingerprints from real herbal medicines could further interpret it.

Chromatography, High Pressure Liquid↗
PubMed1998

Active drug substance impurity profiling part II. LC/MS/MS fingerprinting.

Drug substance impurities are routinely monitored using HPLC. Because HPLC retention times can vary, uncertainty can arise as to whether a peak at a new retention time is a new impurity. When impurity standards are not available some method is needed to characterize the impurities on-line. This work sought to assess the ability of LC/MS/MS to generate characteristic impurity 'fingerprints', comprised of a precursor ion mass plus at least three product ion masses. MS/MS fingerprints of a drug substance, DuP 941, and three of its impurities were first generated using available standards. Experiments varying collision cell parameters showed that collision energy must be specified in order to reproducibly generate characteristic MS/MS fingerprints. MS/MS fingerprints were also generated on-line for seven impurities in the earliest safety lot of DuP 941. Several subsequent lots of DuP 941 were examined to see how well their impurity fingerprints matched those from the earlier lot. Fingerprint reproducibility was very good for all impurities examined, even down to 0.01 UV area percent for some impurities. MS/MS fingerprinting was able to distinguish two impurities from one another which were known to be positional isomers. It also permitted assignment of tentative structures to the drug impurities.

Chromatography, High Pressure Liquid↗
PubMed1987

Restriction enzyme fingerprinting of trimethoprim resistance plasmids.

Restriction enzyme fingerprinting was applied to 72 transferable trimethoprim resistance plasmids to examine aspects of their epidemiology and molecular relatedness. These plasmids had previously been divided into 25 groups according to differences in mol. wts and in antimicrobial resistance determinants. Restriction enzyme fingerprinting allowed the plasmids to be further divided into 44 different groups. The groups based on molecular weight and resistance patterns often, but not invariably, corresponded with those based on restriction enzyme fingerprints. Some plasmids with the same mol. wt and resistance pattern had different digest fingerprints and conversely, although more rarely, plasmids which differed in molecular weight by as much as 10 MDa or in resistance pattern by one resistance marker, had indistinguishable fingerprints. The plasmids were initially divided into three broad categories according to which restriction enzymes gave fingerprints of 6-20 fragments. These categories differed in the molecular weights of the plasmids contained, the numbers of resistance markers, and the proportions of the plasmids which carried transposon Tn7. Some plasmids were more widespread and persistent than others with the same mol. wt and resistance pattern but with a different restriction enzyme fingerprint. Thus, application of this technique has shown the trimethoprim resistance plasmids studied to be more diverse than was indicated by determination of mol. wt and resistance pattern, and has indicated changes in the plasmid pool over the 3 years during which they were collected.

Molecular Weight↗
PubMedDate not supplied

An approach to comparative analysis of chromatographic fingerprints for assuring the quality of botanical drugs.

The present study was focused on developing the chemometric methods for analysis of the chromatographic fingerprint to control the quality of botanical drugs, which has gained attention in Asia and other countries. We developed a novel approach to generate a set of fingerprint features, called Fisher components (FCs) that were extracted from the chromatographic fingerprint. The method greatly reduces the dimensionality of the fingerprint vector, and the resulting FCs still retain most discriminatory information of the original fingerprint. Choosing an example of relevance to contemporary botanical drugs, we applied the FCs to a set of Shenmai injection samples. We successfully identified the manufacturers of the samples using two classifiers, linear discriminant analysis (LDA) and k-Nearest Neighbor (k-NN) based on the FCs. We also applied a similarity assessment together with the visual analysis using the FCs to exam the products from different manufacturers. We found that the lot-to-lot consistency of products can be accurately determined using the FCs. Finally, we demonstrated that the application of chemometric methods for chromatographic fingerprinting offers reliability to detect suspected fraud samples. In summary, we demonstrated that the presented approaches could be useful to determine the identity, consistency, and authenticity of Shenmai injection through chromatographic fingerprinting. The methods are equally applicable to other botanical drugs.

Chromatography↗
PubMedDate not supplied

Fractal fingerprinting of chromatographic profiles based on wavelet analysis and its application to characterize the quality grade of medicinal herbs.

Extracting chemical fingerprints is an important step for representing and interpreting chromatographic data. In this paper, the chromatographic profile is decomposed into components at different resolution levels using wavelet analysis, then the fractal dimensions of these components are computed as the chemical fingerprints. The chromatographic fingerprint is characterized by the vector composed of these chemical fingerprints, which can represent the chemical patterns of different categories of complex samples. Computer simulations reveal that the fractal fingerprints are more stable than the original chromatographic profile data with respect to variations of peak retention time. To demonstrate the validity of this method, the evaluation of the quality of the medicinal herb Angelica sinensis (Oliv.) diels is investigated. Principal component analysis of the fractal fingerprints indicates that samples belonging to the same quality grade are clustered together, while those belonging to different quality grades are separated. Using these fractal fingerprints taken from the chromatographic scans as inputs for an artificial neural network (ANN). The quality grades of two sets of the herbs were verified by cross-validation, indicating that 96.7% of the herbs are correctly identified with respect to their quality grades evaluated by experienced experts, and 100.0% of the herbs are correctly identified with respect to their quality grades determined by pharmacodynamical evaluation.

Algorithms↗
PubMed2003

Mini-fingerprints for virtual screening: design principles and generation of novel prototypes based on information theory.

Binary fingerprint representations of molecular structure and properties are convenient computational tools for similarity searching in compound databases and virtual screening (VS). We are investigating the design of relatively simple fingerprints for the identification of molecules having similar biological activity and recognition of remote similarity relationships. Since our designs are considerably shorter than other fingerprints used in VS, we have previously termed them "mini-fingerprints" (MFPs). A key aspect of the design strategy is the identification of suitable molecular descriptors. Whereas our initial fingerprint designs have relied on descriptor combinations that performed well in compound classification according to biological activity, second generation MFPs encode combinations of descriptors with high information content in large compound databases and high frequency of occurrence in drug-like molecules. Thus, the design of these new fingerprints does not depend on the analysis of specific classes of bioactive compounds, but rather on descriptor information content in large compound databases. Systematic evaluation of fingerprint performance in VS test calculations demonstrates that these new prototypes perform better than previously generated MFPs. The analysis described herein provides an example for the development of search tools for VS.

Environmental Pollutants↗
PubMed2007

Pores and ridges: high-resolution fingerprint matching using level 3 features.

Fingerprint friction ridge details are generally described in a hierarchical order at three different levels, namely, Level 1 (pattern), Level 2 (minutia points), and Level 3 (pores and ridge contours). Although latent print examiners frequently take advantage of Level 3 features to assist in identification, Automated Fingerprint Identification Systems (AFIS) currently rely only on Level 1 and Level 2 features. In fact, the Federal Bureau of Investigation's (FBI) standard of fingerprint resolution for AFIS is 500 pixels per inch (ppi), which is inadequate for capturing Level 3 features, such as pores. With the advances in fingerprint sensing technology, many sensors are now equipped with dual resolution (500 ppi/1,000 ppi) scanning capability. However, increasing the scan resolution alone does not necessarily provide any performance improvement in fingerprint matching, unless an extended feature set is utilized. As a result, a systematic study to determine how much performance gain one can achieve by introducing Level 3 features in AFIS is highly desired. We propose a hierarchical matching system that utilizes features at all the three levels extracted from 1,000 ppi fingerprint scans. Level 3 features, including pores and ridge contours, are automatically extracted using Gabor filters and wavelet transform and are locally matched using the Iterative Closest Point (ICP) algorithm. Our experiments show that Level 3 features carry significant discriminatory information. There is a relative reduction of 20 percent in the equal error rate (EER) of the matching system when Level 3 features are employed in combination with Level 1 and 2 features. This significant performance gain is consistently observed across various quality fingerprint images.

Algorithms↗
PubMed1988

Assessment of clonality in gastrointestinal cancer by DNA fingerprinting.

DNA fingerprinting with three different probes (33.15, 33.6, and alpha-globin 3'HVR) was investigated as a method for the determination of clonality in gastrointestinal tumors. In 29/44 carcinomas the tumor DNA showed clonal somatic mutations that were not seen in the corresponding peripheral blood and normal mucosa samples. The changes consisted of either novel fingerprint bands, losses of bands, or both. The probe 33.15 yielded the highest rate of abnormal DNA fingerprints (21/44 carcinomas). Sequential use of the probes increased the number of cases where clonal fingerprint markers could be detected. One out of five colorectal adenomas also showed a clonal loss of a fingerprint band. In two cases of gastric cancer, DNA from the metastatic tumor had a different DNA fingerprint from that found in the primary carcinoma. DNA fingerprinting offers a novel approach to determining clonality in tumors and may prove useful for the study of tumor progression.

Cloning, Molecular↗
PubMed2002

Digital analysis of cDNA abundance; expression profiling by means of restriction fragment fingerprinting.

BACKGROUND: Gene expression profiling among different tissues is of paramount interest in various areas of biomedical research. We have developed a novel method (DADA, Digital Analysis of cDNA Abundance), that calculates the relative abundance of genes in cDNA libraries. RESULTS: DADA is based upon multiple restriction fragment length analysis of pools of clones from cDNA libraries and the identification of gene-specific restriction fingerprints in the resulting complex fragment mixtures. A specific cDNA cloning vector had to be constructed that governed missing or incomplete cDNA inserts which would generate misleading fingerprints in standard cloning vectors. Double stranded cDNA was synthesized using an anchored oligo dT primer, uni-directionally inserted into the DADA vector and cDNA libraries were constructed in E. coli. The cDNA fingerprints were generated in a PCR-free procedure that allows for parallel plasmid preparation, labeling, restriction digest and fragment separation of pools of 96 colonies each. This multiplexing significantly enhanced the throughput in comparison to sequence-based methods (e.g. EST approach). The data of the fragment mixtures were integrated into a relational database system and queried with fingerprints experimentally produced by analyzing single colonies. Due to limited predictability of the position of DNA fragments on the polyacrylamid gels of a given size, fingerprints derived solely from cDNA sequences were not accurate enough to be used for the analysis. We applied DADA to the analysis of gene expression profiles in a model for impaired wound healing (treatment of mice with dexamethasone). CONCLUSIONS: The method proved to be capable of identifying pharmacologically relevant target genes that had not been identified by other standard methods routinely used to find differentially expressed genes. Due to the above mentioned limited predictability of the fingerprints, the method was yet tested only with a limited number of experimentally determined fingerprints and was able to detect differences in gene expression of transcripts representing 0.05% of the total mRNA population (e.g. medium abundant gene transcripts).

Journal Article↗
PubMed2006

Artificial fingerprint recognition by using optical coherence tomography with autocorrelation analysis.

Fingerprint recognition is one of the most widely used methods of biometrics. This method relies on the surface topography of a finger and, thus, is potentially vulnerable for spoofing by artificial dummies with embedded fingerprints. In this study, we applied the optical coherence tomography (OCT) technique to distinguish artificial materials commonly used for spoofing fingerprint scanning systems from the real skin. Several artificial fingerprint dummies made from household cement and liquid silicone rubber were prepared and tested using a commercial fingerprint reader and an OCT system. While the artificial fingerprints easily spoofed the commercial fingerprint reader, OCT images revealed the presence of them at all times. We also demonstrated that an autocorrelation analysis of the OCT images could be potentially used in automatic recognition systems.

Algorithms↗
PubMed2001

[Fingerprints of Radix Salviae Miltiorrhizae].

OBJECTIVES: To establish fingerprints of the Radix Salviae Miltiorrhizae from Shangluo Dansben Base of Tasly Group Co. Ltd., and to compare the fingerprints with fingerprints of Radix Salviae Miltiorrhizae from Tianjin market of medicinal materials. METHOD: By HPLC to establish fingerprint of water-soluble extract of Radix Salviae Miltiorrhizae. CONCLUSION: The fingerprints of 10 batches of Radix Salviae Miltiorrhizae from Shangluo conformed to the requirements of fingerprints of Chinese medicinal materials issued by State Drug Administration in 2000. And there were obvious differences between the fingerprints of Radix Salviae Miltiorrhizae from Shangluo and from Tianjin market of medicinal materials.

Chromatography, High Pressure Liquid↗
PubMed2003

Optimization and initial evaluation of 1,2-indandione as a reagent for fingerprint detection.

1,2-Indandione has been used to develop fluorescent fingerprints on porous materials such as paper. The compound reacts with amino acid residues to produce highly fluorescent fingerprint ridges. An optimized formulation and treatment protocol for using the reagent is presented here. The reagent is applied as a solution in HFE7100 containing acetic acid and ethyl acetate. Treated articles are heated at 100 degrees C for 10 min at ambient humidity and stored in the dark before recording the fingerprints using fluorescence photography or digital imaging. Photodecomposition of the fluorescent fingerprints has been observed. Storage in the dark reduces degradation, extending the lifetime of the fingerprints. Other chemical methods to stabilize the fingerprints proved unsuccessful. Comparisons of the performance of 1,2-indandione with DFO in CFC113 performed on a limited range of substrates indicated that the reagent might be an effective method for the development of latent fingerprints despite the new reagent producing less intense fluorescence.

Aza Compounds↗
PubMed2003

Enhancing contrast of fingerprints on plastic tape.

Many of the currently available fingerprinting methods have limited ability to visualize fingerprints on plastic tape without expensive equipment or significant handling of the sample. This is especially true for visualizing fingerprints on black electrical tape. This study sought a hands-off method to produce easy visualization of fingerprints on different types of plastic tape, including black electrical tape, without the need for expensive equipment. The methods selected were to sublime disperse dyes into the tape, both with and without the fuming of cyanoacrylate, everywhere except for where the fingerprint was applied. The resulting color contrasts provided enough differentiation to visualize fingerprints on plastic tape under ambient light. Sequential fuming with cyanoacrylate followed by disperse dyes provided the best visualizations on all tapes, and cyanoacrylate followed by disperse yellow 211 clearly visualized fingerprints on black electrical tape.

Anthraquinones↗