OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data

<p>Abstract</p> <p>Background</p> <p>Today, data evaluation has become a bottleneck in chromatographic science. Analytical instruments equipped with automated samplers yield large amounts of measurement data, which needs to be verified and analyzed. Since nearly every GC/MS instrument vendor offers its own data format and software tools, the consequences are problems with data exchange and a lack of comparability between the analytical results. To challenge this situation a number of either commercial or non-profit software applications have been developed. These applications provide functionalities to import and analyze several data formats but have shortcomings in terms of the transparency of the implemented analytical algorithms and/or are restricted to a specific computer platform.</p> <p>Results</p> <p>This work describes a native approach to handle chromatographic data files. The approach can be extended in its functionality such as facilities to detect baselines, to detect, integrate and identify peaks and to compare mass spectra, as well as the ability to internationalize the application. Additionally, filters can be applied on the chromatographic data to enhance its quality, for example to remove background and noise. Extended operations like do, undo and redo are supported.</p> <p>Conclusions</p> <p>OpenChrom is a software application to edit and analyze mass spectrometric chromatographic data. It is extensible in many different ways, depending on the demands of the users or the analytical procedures and algorithms. It offers a customizable graphical user interface. The software is independent of the operating system, due to the fact that the Rich Client Platform is written in Java. OpenChrom is released under the Eclipse Public License 1.0 (EPL). There are no license constraints regarding extensions. They can be published using open source as well as proprietary licenses. OpenChrom is available free of charge at <url>http://www.openchrom.net</url>.</p

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

BACKGROUND: Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas. RESULTS: An algorithm for filtering molecular formulas is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds. Formulas are ranked according to their isotopic patterns and subsequently constrained by presence in public chemical databases. The seven rules were developed on 68,237 existing molecular formulas and were validated in four experiments. First, 432,968 formulas covering five million PubChem database entries were checked for consistency. Only 0.6% of these compounds did not pass all rules. Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions. Thirdly 6,000 pharmaceutical, toxic and natural compounds were selected from DrugBank, TSCA and DNP databases. The correct formulas were retrieved as top hit at 80–99% probability when assuming data acquisition with complete resolution of unique compounds and 5% absolute isotope ratio deviation and 3 ppm mass accuracy. Last, some exemplary compounds were analyzed by Fourier transform ion cyclotron resonance mass spectrometry and by gas chromatography-time of flight mass spectrometry. In each case, the correct formula was ranked as top hit when combining the seven rules with database queries. CONCLUSION: The seven rules enable an automatic exclusion of molecular formulas which are either wrong or which contain unlikely high or low number of elements. The correct molecular formula is assigned with a probability of 98% if the formula exists in a compound database. For truly novel compounds that are not present in databases, the correct formula is found in the first three hits with a probability of 65–81%. Corresponding software and supplemental data are available for downloads from the authors' website

Comparison of DNA histograms by standard flow cytometry and image cytometry on sections in Barrett's adenocarcinoma

<p>Abstract</p> <p>Background</p> <p>The purpose of this study was to compare DNA histograms obtained by standard flow cytometry (FC) and high fidelity image cytometry on sections (ICS) in normal gastrointestinal mucosa and Barrett's adenocarcinoma (BAC).</p> <p>Methods</p> <p>Archival formalin-fixed paraffin-embedded tissue blocks of 10 normal controls from 10 subjects and 42 BAC tissues from 17 patients were examined. DNA FC was performed using standard techniques and ICS was carried out by Automated Cellular Imaging System (ACIS). DNA ploidy histograms were classified into diploid with peak DNA index (DI) at 0.9–1.1, and aneuploid with peak DI > 1.1. DI values of aneuploid peaks were determined. Additionally, for DNA ICS, heterogeneity index (HI) representing DNA content heterogeneity, and histograms containing cells with DI > G2 were also identified.</p> <p>Results</p> <p>All control samples were diploid by both FC and ICS analyses. In BAC, FC showed diploid peaks in 29%, diploid peaks with additional aneuploid or tetraploid peaks in 57%, and 14% of the samples, respectively. In contrast, ICS showed aneuploid peaks in all the cases with peak DI > 1.25; 37 cases had peak DI between 1.25 and 2.25; and 5 cases had peak DI > 2.25. HI values (mean ± SD) were 11.3 ± 1.1 in controls and 32.4 ± 8.5 in BAC (p < 0.05). Controls had no G2 exceeding cells. However, 19/37 (51%) of the cases with primary peak DI < 2.25 had cells exceeding 9N.</p> <p>Conclusion</p> <p>ICS detects DNA aneuploidy in all BAC samples while FC missed the diagnosis of aneuploidy in 29%. In addition, ICS provides more information on HI and G2 exceeding rates.</p

Ki-67 expression predicts locoregional recurrence in stage I oral tongue carcinoma

Oral tongue squamous cell carcinoma (OTSCC) is an aggressive cancer associated with poor prognosis. Methods for determining the aggressiveness of OTSCC from analysis of the primary tumour specimen are thus highly desirable. We investigated whether genomic instability and proliferative activity (by means of Ki-67 activity) could be of clinical use for prediction of locoregional recurrence in 76 pretreatment OTSCC paraffin samples (stage I, n=22; stage II, n=33; stage III, n=8; stage IV, n=13). Eleven surgical tumour specimens were also analysed for remnants of proliferative activity after preoperative radiotherapy. Ninety-seven percent of cases (n=72) were characterised as being aneuploid as measured by means of image cytometry. Preoperative radiotherapy (50–68 Gy) resulted in significant reduction of proliferative activity in all patients for which post-treatment biopsies were available (P-value=0.001). Proliferative activity was not associated with response to radiation in stage II patients. However, we report a significant correlation between high proliferation rates and locoregional recurrences in stage I OTSCC patients (P-value=0.028). High-proliferative activity is thus related to an elevated risk of recurrence after surgery alone. We therefore conclude that Ki-67 expression level is a potentially useful clinical marker for predicting recurrence in surgically treated stage I OTSCC

Barriers and enablers for participation in healthy lifestyle programs by adolescents who are overweight: a qualitative study of the opinions of adolescents, their parents and community stakeholders

Background: Overweight or obesity during adolescence affects almost 25% of Australian youth, yet limited research exists regarding recruitment and engagement of adolescents in weight-management or healthy lifestyle interventions, or best-practice for encouraging long-term healthy behaviour change. A sound understanding of community perceptions, including views from adolescents, parents and community stakeholders, regarding barriers and enablers to entering and engaging meaningfully in an intervention is critical to improve the design of such programs. Methods: This paper reports findings from focus groups and semi-structured interviews conducted with adolescents (n=44), parents (n=12) and community stakeholders (n=39) in Western Australia. Three major topics were discussed to inform the design of more feasible and effective interventions: recruitment, retention in the program and maintenance of healthy change. Data were analysed using content and thematic analyses.Results: Data were categorised into barriers and enablers across the three main topics. For recruitment, identified barriers included: the stigma associated with overweight, difficulty defining overweight, a lack of current health services and broader social barriers. The enablers for recruitment included: strategic marketing, a positive approach and subsidising program costs. For retention, identified barriers included: location, timing, high level of commitment needed and social barriers. Enablers for retention included: making it fun and enjoyable for adolescents, involving the family, having an on-line component, recruiting good staff and making it easy for parents to attend. For maintenance, identified barriers included: the high degree of difficulty in sustaining change and limited services to support change. Enablers for maintenance included: on-going follow up, focusing on positive change, utilisation of electronic media and transition back to community services. Conclusions: This study highlights significant barriers for adolescents and parents to overcome to engage meaningfully with weight-management or healthy lifestyle programs. A number of enablers were identified to promote ongoing involvement with an intervention. This insight into specific contextual opinions from the local community can be used to inform the delivery of healthy lifestyle programs for overweight adolescents, with a focus on maximising acceptability and feasibility

Systematic NMR Analysis of Stable Isotope Labeled Metabolite Mixtures in Plant and Animal Systems: Coarse Grained Views of Metabolic Pathways

BACKGROUND: Metabolic phenotyping has become an important 'bird's-eye-view' technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of 'top-down' chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems. METHODOLOGY/PRINCIPAL FINDINGS: The analysis method includes a stable isotope labeling technique for use in living organisms; a systematic method for simultaneously identifying a large number of metabolites by using a newly developed HSQC-based metabolite chemical shift database combined with heteronuclear multidimensional NMR spectroscopy; Principal Components Analysis; and a visualization method using a coarse-grained overview of the metabolic system. The database contains more than 1000 (1)H and (13)C chemical shifts corresponding to 142 metabolites measured under identical physicochemical conditions. Using the stable isotope labeling technique in Arabidopsis T87 cultured cells and Bombyx mori, we systematically detected >450 HSQC peaks in each (13)C-HSQC spectrum derived from model plant, Arabidopsis T87 cultured cells and the invertebrate animal model Bombyx mori. Furthermore, for the first time, efficient (13)C labeling has allowed reliable signal assignment using analytical separation techniques such as 3D HCCH-COSY spectra in higher organism extracts. CONCLUSIONS/SIGNIFICANCE: Overall physiological changes could be detected and categorized in relation to a critical developmental phase change in B. mori by coarse-grained representations in which the organization of metabolic pathways related to a specific developmental phase was visualized on the basis of constituent changes of 56 identified metabolites. Based on the observed intensities of (13)C atoms of given metabolites on development-dependent changes in the 56 identified (13)C-HSQC signals, we have determined the changes in metabolic networks that are associated with energy and nitrogen metabolism

Pathologic mitoses and pathology of mitosis in tumorigenesis

The gist of my hypothesis (.. is) a certain abnormal chromatin constitution. Each process, which brings about this chromatin constitution, would result in the origin of a malignant tumour. Certainly, I consider irregularities with mitosis as the normal mode of the origin of an incorrectly assembled nucleus. This statement by Boveri (1914) has considered earlier observations of asymmetric divisions in human cancers (Hansemann, 1890). The hypothesis is based on the understanding of mitosis as an equational bipartition of the hereditary substance (Flemming, 1879; Roux, 1883). Latest since it was known that genes are located on chromosomes (Sturtevant, 1913), their balanced transport in anaphase appeared as a condition of correct somatic proliferation. True mitoses guarantee the constancy of terminally differentiated tissues. Politzer (1934) has performed X-ray experiments to investigate abnormal karyokinesis with regard to anomalous chromatin condensation, chromosome breakage, spindle malformation, and failure in cytokinesis. On the basis of light microscopy, further significant progress in understanding the pathology of mitosis was not possible. Tumour cases with reduced chromosome numbers seduced to the idea that mitotic activity is rather under cytoplasmic than under nuclear control (Koller, 1947)

Defining the rest interval associated with the main sleep period in actigraph scoring

Chin Moi Chow,1 Shi Ngar Wong,1 Mirim Shin,1 Rebecca G Maddox,2 Kristy-Lee Feilds,3 Karen Paxton,4 Catherine Hawke,4 Philip Hazell,3 Katharine Steinbeck5 1Discipline of Exercise and Sport Science, Faculty of Health Sciences, 2Sydney Medical School, 3Discipline of Psychiatry, 4School of Rural Health, 5Discipline of Paediatrics and Child Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia Abstract: Actigraphy is increasingly used for sleep monitoring. However, there is a lack of standardized methodology for data processing and analysis, which often makes between study comparisons difficult, if not impossible, and thus open to flawed interpretation. This study evaluated a manual method for detection of the rest interval in actigraph data collected with Actiwatch 2. The rest interval (time in bed), defined as the bedtime and rise time and set by proprietary software, is an essential requirement for the estimation of sleep indices. This study manually and systematically detected the rest interval of 187 nights of recording from seven healthy males and three females, aged 13.5&plusmn;0.7 (mean &plusmn; standard deviation) years. Data were analyzed for agreement between software default algorithm and manual scoring. Inter-rater reliability in manual scoring was also tested between two scorers. Data showed consistency between default settings and manual scorers for bedtime and rise time, but only moderate agreement for the rest interval duration and poor agreement for activity level at bedtime and rise time. Manual detection of rest intervals between scorers showed a high degree of agreement for all parameters (intraclass correlations range 0.864 to 0.995). The findings demonstrate that the default algorithm on occasions was unable to detect rest intervals or set the exact interval. Participant issues and inter-scorer issues also made difficult the detection of rest intervals. These findings have led to a manual detection protocol to define bedtime and rise time, supplemented with an event diary. Keywords: actigraph recording, activity level, light leve