Rapid Identifications Research Articles

A Cloud-Based Decision Support System for Self-Healing in Distributed Automation Systems Using Fault Tree Analysis

Downtime is a key performance index for industrial automation systems. An industrial automation system achieves maximum productivity when its downtime is reduced to the minimum. One approach to minimize downtime is to predict system faults and recover from them automatically. A cloud-based decision support system is proposed for rapid problem identifications and to assist the self-management processes. By running multiple parallel simulations of control software with real-time inputs ahead of system time, faults could be detected and corrected automatically using autonomous industrial software agents. Fault trees, as well as control algorithms, are modeled using IEC 61499 function blocks that can be directly executed on both physical controllers and cloud services. A case study of water heating process is used to demonstrate the self-healing process supported by the cloud-based decision support system.

Extended Virtual Screening Strategies To Link Antiandrogenic Activities and Detected Organic Contaminants in Soils.

A tiered screening strategy based on extensive virtual fractionation and elucidation was developed to simplify identification of toxicants in complex environments. In tier1-virtual fractionation, multivariate analysis (MVA) was set up as an alternative of physical fractionation. In tier2-virtual structure elucidation, in-house quantitative structure-retention relationship (QSRR) models and toxicity simulation methods were developed to simplify nontarget identification. The efficiency of the tiered virtual strategy was tentatively verified by soil samples from a chemical park contaminated by antiandrogenic substances. Eight out of 18 sites were detected as antiandrogenic, while none of them exhibited androgenic agonist potencies. Sixty-seven peaks were selected for further identification by MVA, among which over 90% were verified in androgenic fractions in traditional effect-directed analysis (EDA). With 579 tentative structures generated by in silico fragmentation, 74% were elucidated by QSRR and 65% were elucidated by in silico toxicity prediction. All prior peaks were identified at different confidence levels with over 40% of the identified peaks above confidence level 2b, which has been increased over 40% with less than half of the time spent compared to traditional EDA. Such a combination of tiered virtual screening methods provides more efficient and rapid identifications of key toxicants at contaminated sites.

Exploring the relationship between fractal features and bacterial essential genes**Project supported by the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014FM022).

Essential genes are indispensable for the survival of an organism in optimal conditions. Rapid and accurate identifications of new essential genes are of great theoretical and practical significance. Exploring features with predictive power is fundamental for this. Here, we calculate six fractal features from primary gene and protein sequences and then explore their relationship with gene essentiality by statistical analysis and machine learning-based methods. The models are applied to all the currently available identified genes in 27 bacteria from the database of essential genes (DEG). It is found that the fractal features of essential genes generally differ from those of non-essential genes. The fractal features are used to ascertain the parameters of two machine learning classifiers: Naïve Bayes and Random Forest. The area under the curve (AUC) of both classifiers show that each fractal feature is satisfactorily discriminative between essential genes and non-essential genes individually. And, although significant correlations exist among fractal features, gene essentiality can also be reliably predicted by various combinations of them. Thus, the fractal features analyzed in our study can be used not only to construct a good essentiality classifier alone, but also to be significant contributors for computational tools identifying essential genes.

Rapid Detection of NDM, VIM, KPC and IMP Carbapenemases by Real-Time PCR

Carbapenems are the most potent beta-lactams, characterized by broad spectrum of activity against Gramnegative and Gram-positive bacteria. Unfortunately, the dynamic dispersal of carbapenem resistance among nonfermentative bacteria and Enterobacteriaceae is an over-increasing problem and might lead to dangerous limitation of treatment options. Among three different mechanisms of resistance the enzyme production is of special importance. In this case, only one small gene is enough to express carbapenem resistance. The carbapenemase genes are often a part of integrons, which carry diverse arrays of resistance gene cassettes and just one transfer event is enough to disseminate multidrug resistance. Moreover, carbapenemase genes are often located within Mobile Genetic Elements. For these reasons carbapenemases are the most epidemiologically importance. Early detection and identification of carbapenemase producers among clinical isolates can avoid nosocomial infections. We have developed a multiplex Real-Time PCR assay based on the TaqMan technology for rapid detection and identifications of the most common carbapenemases in Europe NDM, VIM, KPC and IMP. There were tested 31 isolates Enterobacteriaceae (n=15) and non-fermentative Gram-negative bacillary (n=16), which acquire NDM, VIM, KPC, IMP, GIM or OXAs carbapenemases. The whole elaborated experiment, including DNA isolation and PCR cycling, lasts up to 2 h.

Automated leaf physiognomic character identification from digital images

AbstractResearch into the relationship between leaf form and climate over the last century has revealed that, in many species, the sizes and shapes of leaf characters exhibit highly structured and predictable patterns of variation in response to the local climate. Several procedures have been developed that quantify covariation between the relative abundance of plant character states and the states of climate variables as a means of estimating paleoclimate parameters. One of the most widely used of these is the Climate Leaf Analysis Multivariate Program (CLAMP). The consistency, accuracy and reliability with which leaf characters can be identified and assigned to CLAMP character-state categories is critical to the accuracy of all CLAMP analyses. Here we report results of a series of performance tests for an image-based, fully automated at the point of use, leaf character scoring system that can be used to generate CLAMP leaf character state data for: leaf bases (acute, cordate and round), leaf apices (acute, attenuate), leaf shapes (ovate, elliptical and obovate), leaf lobing (unlobed, lobed), and leaf aspect ratios (length/width). This image-based system returned jackknifed identification accuracy ratios of between 87% and 100%. These results demonstrate that automated image-based identification systems have the potential to improve paleoenvironmental inferences via the provision of accurate, consistent and rapid CLAMP leaf-character identifications. More generally, our results provide strong support for the feasibility of using fully automated, image-based morphometric procedures to address the general problem of morphological character-state identification.

Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome.

We describe the utility of integrated strategies that employ both translation of ENCODE data and major proteomic technology pillars to improve the identification of the "missing proteins", novel proteoforms, and PTMs. On one hand, databases in combination with bioinformatic tools are efficiently utilized to establish microarray-based transcript analysis and supply rapid protein identifications in clinical samples. On the other hand, sequence libraries are the foundation of targeted protein identification and quantification using mass spectrometric and immunoaffinity techniques. The results from combining proteoENCODEdb searches with experimental mass spectral data indicate that some alternative splicing forms detected at the transcript level are in fact translated to proteins. Our results provide a step toward the directives of the C-HPP initiative and related biomedical research.

An integrated approach for structural damage identification using wavelet neuro-fuzzy model

Structural damage can be identified by processing structural vibration response signals and excitation data, and thus the suitability of signal processing methods is essential to structural damage identification. To explore an intelligent signal processing method for structural damage identification, the paper integrated wavelet real-time filtering algorithm, Adaptive Neruo-Fuzzy Inference System (ANFIS) and interval modeling technique to process structural response signals and excitation data. With Wavelet Transform (WT) algorithm filtering random noise, ANFIS was found to model the structural behavior properly and interval modeling technique to quantify damage index accurately. The rapid identifications of several unknown damages and small damages indicate the efficiency of this integrated method. The comparison of these results and some other signal processing methods shows that, the proposed method can be used to identify both the time and the location when the structural damage occurs unexpectedly.

Prenatal and post-natal screening of β-thalassemia and hemoglobin E genes in Thailand using denaturing high performance liquid chromatography

We have developed methods based on PCR and denaturing high performance liquid chromatography (DHPLC) for rapid identifications of common β-thalassemia mutations found in Thailand. The β-globin gene was separately amplified by PCR on four different fragments covering eight most common β-thalassemia mutations including nucleotide -28 A-G, codon 17 (A-T), IVSI-1 (G-T), IVSI-5 (G-C), codon 26 (G-A or Hb E), codons 41/42 (-TTCT), codons 71/72 (+A) and IVSII-654 (C-T). After PCR amplification, heteroduplex was generated by denaturation at 95 °C for 5 min followed by a slow reduction in temperature to 25 °C at 0.03 °C/s. Analysis of heteroduplex was done on an automated WAVE Nucleic Acid Fragment Analysis System. Specific DHPLC profile for each mutation was demonstrated which could be used in screening for all eight β-thalassemia mutations. Further validation was done on 42 pre- and post-natal DNA samples which demonstrated 100 % accuracy as compared to the result obtained with conventional PCR assays. In a remaining case with an unknown mutation, a different DHPLC profile was noted on one of the amplified fragment. Further DNA sequencing of this fragment revealed a T-G transversion at the IVSI-116, a previously un-described mutation in Thai population. The DHPLC assay developed should prove useful for rapid screening of known and unknown β-thalassemia mutations during carrier screening and pre-natal diagnosis which would facilitate an ongoing prevention and control program of thalassemia.

Evaluation of the Bruker Biotyper and Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems for Identification of Nonfermenting Gram-Negative Bacilli Isolated from Cultures from Cystic Fibrosis Patients

The Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) instruments were evaluated for the identification of nonfermenting gram-negative bacilli (NFGNB) by a blinded comparison to conventional biochemical or molecular methods. Two hundred NFGNB that were recovered from cultures from cystic fibrosis patients in the University of Iowa Health Care (UIHC) Microbiology Laboratory between 1 January 2006 and 31 October 2010 were sent to Mayo Clinic for analysis with the Bruker Biotyper (software version 3.0) and to bioMérieux for testing with Vitek MS (SARAMIS database version 3.62). If two attempts at direct colony testing failed to provide an acceptable MALDI-TOF identification, an extraction procedure was performed. The MS identifications from both of these systems were provided to UIHC for comparison to the biochemical or molecular identification that had been reported in the patient record. Isolates with discordant results were analyzed by 16S rRNA gene sequencing at UIHC. After discrepancy testing, the Bruker Biotyper result agreed with the biochemical or molecular method, with 72.5% of isolates to the species level, 5.5% to the complex level, and 19% to the genus level (3% not identified). The level of agreement for Vitek MS was 80% species, 3.5% complex, 6% genus, and 3.5% family (7% not identified). Both MS systems provided rapid (≤3 min per isolate) and reliable identifications. The agreement of combined species/complex/genus-level identification with the reference method was higher for the Bruker Biotyper (97% versus 89.5%, P = 0.004) but required an extraction step more often. Species-level agreement with the reference method was similar for both MS systems (72.5% and 80%, P = 0.099).

A Single-Laboratory Validated Method for the Generation of DNA Barcodes for the Identification of Fish for Regulatory Compliance

The U.S. Food and Drug Administration is responsible for ensuring that the nation's food supply is safe and accurately labeled. This task is particularly challenging in the case of seafood where a large variety of species are marketed, most of this commodity is imported, and processed product is difficult to identify using traditional morphological methods. Reliable species identification is critical for both foodborne illness investigations and for prevention of deceptive practices, such as those where species are intentionally mislabeled to circumvent import restrictions or for resale as species of higher value. New methods that allow accurate and rapid species identifications are needed, but any new methods to be used for regulatory compliance must be both standardized and adequately validated. "DNA barcoding" is a process by which species discriminations are achieved through the use of short, standardized gene fragments. For animals, a fragment (655 base pairs starting near the 5' end) of the cytochrome c oxidase subunit 1 mitochondrial gene has been shown to provide reliable species level discrimination in most cases. We provide here a protocol with single-laboratory validation for the generation of DNA barcodes suitable for the identification of seafood products, specifically fish, in a manner that is suitable for FDA regulatory use.

DNA barcoding demystified

Only 10% of the earth’s biota has been described despite250 yearsoftaxonomicresearch(Wilson2000).Thisisinlargepart a reflection of the extent and complexity of biologicaldiversity,butitisalsotruethattraditionaltaxonomictechniquesare labourious and highly specialised, and taxonomic expertiseis very thinly spread across the myriad groups of life (Scotland

Maternal identification of hybrid eggs in Hexagrammos spp. by means of multiplex amplified product length polymorphism of mitochondrial DNA

Hybridization has been frequently observed among 3 species of greenlings (genus Hexagrammos) common in waters off Japan. In order to estimate the frequency of hybridization events from egg masses collected from male territories, efficient maternal identification of numerous egg masses is required. A novel streamlined approach for maternal identification of 3 Hexagrammos spp. was developed using multiplex amplified product length polymorphism (APLP) analysis of the mitochondrial cytochrome b (Cytb) and the 12S and 16S ribosomal RNA (12-16S rRNA) regions. Concurrent use of species-specific primer sets permits the amplification of different-sized PCR products, diagnosing each species through one procedure of PCR in a single reaction tube. The APLP method produced more rapid, reliable, and cost-efficient species identifications compared to those from an established restriction fragment length polymorphism (RFLP) protocol.

Why can't we analyze a whole proteome by MS? | Finding palmitoyl proteins | Phosphoproteomics of a signal transduction pathway | A step towards proteomics on a chip | Dynamic proteomics of single cells | Cancer proteins are connected differently | TOOLbox: PROMPT for comparisons | msInspect | Rapid peptide identifications | MeMo for metabolomics data

Why can't we analyze a whole proteome by MS? | Finding palmitoyl proteins | Phosphoproteomics of a signal transduction pathway | A step towards proteomics on a chip | Dynamic proteomics of single cells | Cancer proteins are connected differently | TOOLbox: PROMPT for comparisons | msInspect | Rapid peptide identifications | MeMo for metabolomics data

Automated integration of monolith‐based protein separation with on‐plate digestion for mass spectrometric analysis of esophageal adenocarcinoma human epithelial samples

A unique approach of automating the integration of monolithic capillary HPLC-based protein separation and on-plate digestion for subsequent MALDI-MS analysis has been developed. All liquid-handling procedures were performed using a robotic module. This automated high-throughput method minimizes the amount of time and extensive labor required for traditional in-solution digestion followed by exhaustive sample cleanup and analysis. Also, precise positioning of the droplet from the capillary HPLC separation onto the MALDI plate allows for preconcentration effects of analytes for improved sensitivity. Proteins from primary esophageal Barrett's adenocarcinoma tissue were prefractionated by chromatofocusing and analyzed successfully by this automated configuration, obtaining rapid protein identifications through PMF and sequencing analyses with high sequence coverage. Additionally, intact protein molecular weight values were obtained as a means to further confirm protein identification and also to identify potential sequence modifications of proteins. This simple and rapid method is a highly versatile and robust approach for the analysis of complex proteomes.

DNA Barcoding Applied to Invasive Leafminers (Diptera: Agromyzidae) in the Philippines

DNA barcoding involves the sequencing of a single gene region from all species to provide a means for identifying all of life. Although appealing to many scientists, this idea has caused considerable controversy among systematists. We applied a DNA barcoding approach to outbreak populations of invasive Liriomyza spp. leafminer pests in the Philippines to explore the use of barcoding in a relatively well studied, economically important group. We sequenced a 527-bp portion of mitochondrial cytochrome oxidase I (COI) from 258 leafminers from 26 plant host species in the Philippines. Neighbor-joining and parsimony analysis were used to compare COI sequences from the Philippines to an extensive database of COI sequences previously obtained from samples of the invasive leafminers Liriomyza huidobrensis (Blanchard), Liriomyza trifolii (Burgess), and Liriomyza sativae Blanchard from locations around the world. We conclude that although a DNA barcoding approach can provide rapid species identifications, in certain instances it is likely to either overestimate or underestimate the number of species present. Only when placed within the context of considerable other data can DNA barcoding be fully interpreted and used. For economically and medically important species, which can be well studied, DNA barcoding offers a powerful means for rapid identifications.

The Promise of DNA Barcoding for Taxonomy

DNA barcoding is a novel system designed to provide rapid, accurate, and automatable species identifications by using short, standardized gene regions as internal species tags. As a consequence, it will make the Linnaean taxonomic system more accessible, with benefits to ecologists, conservationists, and the diversity of agencies charged with the control of pests, invasive species, and food safety. More broadly, DNA barcoding allows a day to be envisioned when every curious mind, from professional biologists to schoolchildren, will have easy access to the names and biological attributes of any species on the planet. In addition to assigning specimens to known species, DNA barcoding will accelerate the pace of species discovery by allowing taxonomists to rapidly sort specimens and by highlighting divergent taxa that may represent new species. By augmenting their capabilities in these ways, DNA barcoding offers taxonomists the opportunity to greatly expand, and eventually complete, a global inventory of life’s diversity. Despite the potential benefits of DNA barcoding to both the practitioners and users of taxonomy, it has been controversial in some scientific circles (Wheeler, 2004; Will and Rubinoff, 2004; Ebach and Holdredge, 2005; Will et al., 2005). A few have even characterized DNA barcoding as being “anti-taxonomy,” arguing that its implementation will signal the death of a system 250 years in the making. We feel that this opposition stems from misconceptions about the DNA barcoding effort. As such, we welcome this opportunity to clarify both the rationale and potential impacts of DNA barcoding. In responding to this set of questions, we emphasize the multiple positive impacts of this approach for taxonomy and biodiversity science.

Comparison of two PCR methods for rapid identification of Leptospira genospecies interrogans

Based on (i) an analysis of Leptospira 16S rDNA sequences determined by us and of those from databases and (ii) a previously published finding that restriction fragment length polymorphisms (RFLPs) within the Leptospira 16S and 23S rDNA were detected by nine restriction enzymes and these RFLPs allowed categorisation of Leptospira into eight genospecies, we predicted that one particular DdeI restriction site polymorphism within 16S rDNA could be independently used for identifications of Leptospira strains belonging to the genospecies interrogans. Two PCR-based methods, namely allele-specific amplification (ASA) and PCR-RFLP, were tested for the rapid detection of the DdeI restriction site polymorphism. One or two representative strains from each of nine genospecies were tested by ASA, whereas 73 strains from nine genospecies and two field isolates were tested by PCR-RFLP. Our experiments showed that the ASA method was not as specific as intended, but the PCR-RFLP method was useful for rapid identifications of the genospecies interrogans. We have not only confirmed a previous finding and extended the number of samples particularly from the genospecies biflexa, weilii, and inadai, but also simplified a previous PCR-RFLP protocol.

Mass spectrometry and proteomics.

the 15th asilomar conference on Mass Spectrometry this October was devoted to the role of mass spectrometry (MS) in proteomics. The Asilomar Conference site is in a picturesque national park in Pacific Grove, CA, overlooking the Pacific Ocean. The conference aims to bring together scientists from a

Usefulness of rapid antigen detection for the diagnosis of systemic infections due to Haemophilus influenzae

Twenty-eight cases of systemic infections due to Haemophilus influenzae diagnosed from October 1988 to December 1998 were analyzed retrospectively. The clinical manifestations were 13 meningitis (15 episodes), 9 septic arthritis, 4 acute epiglottitis, 1 septicemia and 1 lung abscess. In the 15 meningitis episodes, 13 had positive CSF culture results, and the other 2 episodes of pretreated with antibiotics were diagnosed by H. influenzae type b (Hib) antigen detection by using concentrated urine specimens. In the 9 septic arthritis cases, 6 had positive synovial fluid culture results. Of the 3 cases with negative results on Gram stain and on synovial fluid and blood cultures, etiological diagnosis was established by Hib antigen detection in synovial fluid. Results of Hib antigen detection were positive in all 8 cases (100%). In 6 of these 8 cases, antimicrobial therapy was started by the results of antigen detection. In the 4 acute epiglottitis, 2 had positive blood culture results, and the other 1 case was diagnosed by Hib antigen detection by using concentrated urine specimen. In 3 of these 4 cases, H. influenzae strains isolated from nasopharyngeal swab or aspirated sputum were serotyped as type b. In this study, rapid antigen detection has several advantages in the rapid laboratory diagnosis of systemic infections due to Haemophilus influenzae. 1. The detection of Hib antigen is the only way to diagnose bacterial etiology of infection in patients who had received partially treatment with antimicrobials. Urine is as an appropriate specimen for antigen testing as CSF in patients with suspected Hib meningitis. Moreover, to detect Hib antigen in synovial fluid is clinically useful in septic arthritis. 2. Both the antigen detection and Gram stain made the rapid presumptive identifications and effected therapeutic decision making. 3. Antigen detection methods have also been used in serotyping of clinical isolates. We conclude that rapid antigen detection is a very useful tool for the rapid etiological diagnosis and guideline for the choice of antimicrobials in systemic infections due to Hib. It is necessary to diagnose bacterial etiology as a routine procedure using not only Gram stain and culture but also rapid antigen detection technique in patients with suspected Hib systemic infection.

DNA Probes Can Be Used To Discriminate between Tephritid Species at all Stages of the Life Cycle (Diptera: Tephritidae)

We isolated DNA sequences from the genomes of three Tephritid species. These can be used as probes to make rapid and reliable species identifications using material from any stage of the life cycle. The three Tephritid species are the Mediterranean fruit fly, Ceratitis capitata (Weidemann); the oriental fruit fly, Bactrocera dorsalis (Hendel), and the melon fly, Bactrocera cucurbitae (Coquillett). These isolated DNA sequences can be used to probe specimen material such as single eggs, larvae, or adult body parts on dot blots or squash blots to determine rapidly which species are present when infestations are found. The actual species identifications are made either on the basis of a direct positive result with a particular probe or by the process of elimination from multiple probings. The availability of species-specific DNA probes for use on minimal amounts of material from any stage of the life cycle or body part can facilitate greatly the identification of specimens which are otherwise indistinguishable or unsuitable for classification on the basis of morphological criteria. This technique also allows material to be analyzed immediately, which obviates the need for rearing and handling of material collected at immature stages. Although these probes have been developed for the three Tephritid species described here, the methods used are applicable to any group of organisms.