Informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography and high-resolution mass spectrometry (GCxGC-HRMS)

This paper describes informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography (GCxGC) and high-resolution mass spectrometry (HRMS). GCxGC-HRMS analysis produces large data sets that are rich with information, but highly complex. The size of the data and volume of information requires automated processing for comprehensive cross-sample analysis, but the complexity poses a challenge for developing robust methods. The approach developed here analyzes GCxGC-HRMS data from multiple samples to extract a feature template that comprehensively captures the pattern of peaks detected in the retention-times plane. Then, for each sample chromatogram, the template is geometrically transformed to align with the detected peak pattern and generate a set of feature measurements for cross-sample analyses such as sample classification and biomarker discovery. The approach avoids the intractable problem of comprehensive peak matching by using a few reliable peaks for alignment and peak-based retention-plane windows to define comprehensive features that can be reliably matched for cross-sample analysis. The informatics are demonstrated with a set of 18 samples from breast-cancer tumors, each from different individuals, six each for Grades 1-3. The features allow classification that matches grading by a cancer pathologist with 78% success in leave-one-out cross-validation experiments. The HRMS signatures of the features of interest can be examined for determining elemental compositions and identifying compounds.

Eco-evolutionary Dynamics of Individual-Based Food Webs

The past decade has seen the rise of high resolution datasets. One of the main surprises of analysing such data has been the discovery of a large genetic, phenotypic and behavioural variation and heterogeneous metabolic rates among individuals within natural populations. A parallel discovery from theory and experiments has shown a strong temporal convergence between evolutionary and ecological dynamics, but a general framework to analyse from individual-level processes the convergence between ecological and evolutionary dynamics and its implications for patterns of biodiversity in food webs has been particularly lacking. Here, as a first approximation to take into account intraspecific variability and the convergence between the ecological and evolutionary dynamics in large food webs, we develop a model from population genomics and microevolutionary processes that uses sexual reproduction, genetic-distance-based speciation and trophic interactions. We confront the model with the prey consumption per individual predator, species-level connectance and prey–predator diversity in several environmental situations using a large food web with approximately 25,000 sampled prey and predator individuals. We show higher than expected diversity of abundant species in heterogeneous environmental conditions and strong deviations from the observed distribution of individual prey consumption (i.e. individual connectivity per predator) in all the environmental conditions. The observed large variance in individual prey consumption regardless of the environmental variability collapsed species-level connectance after small increases in sampling effort. These results suggest (1) intraspecific variance in prey–predator interactions has a strong effect on the macroscopic properties of food webs and (2) intraspecific variance is a potential driver regulating the speed of the convergence between ecological and evolutionary dynamics in species-rich food webs. These results also suggest that genetic–ecological drift driven by sexual reproduction, equal feeding rate among predator individuals, mutations and genetic-distance-based speciation can be used as a neutral food web dynamics test to detect the ecological and microevolutionary processes underlying the observed patterns of individual and species-based food webs at local and macroecological scales.

Del castagno e della castanicoltura nelle contrade insubriche: tentativo di una sintesi eco-storica

Il contributo ripercorre la relazione uomo-castagno partendo dalle ultime glaciazioni per arrivare ai giorni nostri, con una crescente attenzione per le contrade insubriche, dove la castanicoltura raggiunse livelli straordinari di sviluppo. Dopo una sintesi critica sui primi indizi di coltivazione, si esamina la castanicoltura nel mondo greco e romano fino all’introduzione della coltivazione del castagno nell’area insubrica. Particolare attenzione è riservata al periodo aureo tardomedievale della castanicoltura nella Svizzera italiana, comprovato con dati linguistici, con l’analisi dei sistemi produttivi (composizione varietale, tecniche di essiccazione) e delle consuetudini locali. Si indagano in seguito le ragioni e le tappe storiche del declino della castanicoltura tradizionale. Si conclude discutendo la situazione attuale e le prospettive future dei castagneti a Sud delle Alpi, confrontati con alcuni problemi incalzanti come l’invecchiamento delle ceppaie nei cedui abbandonati e la comparsa di un insidioso parassita, il cinipide galligeno.

Eco-Evolutionary Spatial Dynamics. Rapid Evolution and Isolation Explain Food Web Persistence

One of the current challenges in evolutionary ecology is understanding the long-term persistence of contemporary-evolving predator–prey interactions across space and time. To address this, we developed an extension of a multi-locus, multi-trait eco-evolutionary individual-based model that incorporates several interacting species in explicit landscapes. We simulated eco-evolutionary dynamics of multiple species food webs with different degrees of connectance across soil-moisture islands. A broad set of parameter combinations led to the local extinction of species, but some species persisted, and this was associated with (1) high connectance and omnivory and (2) ongoing evolution, due to multi-trait genetic variability of the embedded species. Furthermore, persistence was highest at intermediate island distances, likely because of a balance between predation-induced extinction (strongest at short island distances) and the coupling of island diversity by top predators, which by travelling among islands exert global top-down control of biodiversity. In the simulations with high genetic variation, we also found widespread trait evolutionary changes indicative of eco-evolutionary dynamics. We discuss how the ever-increasing computing power and high-resolution data availability will soon allow researchers to start bridging the in vivo–in silico gap.

The application of medical informatics to the veterinary management programs at companion animal practices in Alberta, Canada: a case study.

Companion animals closely share their domestic environment with people and have the potential to, act as sources of zoonotic diseases. They also have the potential to be sentinels of infectious and noninfectious, diseases. With the exception of rabies, there has been minimal ongoing surveillance of, companion animals in Canada. We developed customized data extraction software, the University of, Calgary Data Extraction Program (UCDEP), to automatically extract and warehouse the electronic, medical records (EMR) from participating private veterinary practices to make them available for, disease surveillance and knowledge creation for evidence-based practice. It was not possible to build, generic data extraction software; the UCDEP required customization to meet the specific software, capabilities of the veterinary practices. The UCDEP, tailored to the participating veterinary practices', management software, was capable of extracting data from the EMR with greater than 99%, completeness and accuracy. The experiences of the people developing and using the UCDEP and the, quality of the extracted data were evaluated. The electronic medical record data stored in the data, warehouse may be a valuable resource for surveillance and evidence-based medical research.

Using Informatics and the Electronic Medical Record to Describe Antimicrobial Use in the Clinical Management of Diarrhea Cases at 12 Companion Animal Practices

Antimicrobial drugs may be used to treat diarrheal illness in companion animals. It is important to monitor antimicrobial use to better understand trends and patterns in antimicrobial resistance. There is no monitoring of antimicrobial use in companion animals in Canada. To explore how the use of electronic medical records could contribute to the ongoing, systematic collection of antimicrobial use data in companion animals, anonymized electronic medical records were extracted from 12 participating companion animal practices and warehoused at the University of Calgary. We used the pre-diagnostic, clinical features of diarrhea as the case definition in this study. Using text-mining technologies, cases of diarrhea were described by each of the following variables: diagnostic laboratory tests performed, the etiological diagnosis and antimicrobial therapies. The ability of the text miner to accurately describe the cases for each of the variables was evaluated. It could not reliably classify cases in terms of diagnostic tests or etiological diagnosis; a manual review of a random sample of 500 diarrhea cases determined that 88/500 (17.6%) of the target cases underwent diagnostic testing of which 36/88 (40.9%) had an etiological diagnosis. Text mining, compared to a human reviewer, could accurately identify cases that had been treated with antimicrobials with high sensitivity (92%, 95% confidence interval, 88.1%-95.4%) and specificity (85%, 95% confidence interval, 80.2%-89.1%). Overall, 7400/15,928 (46.5%) of pets presenting with diarrhea were treated with antimicrobials. Some temporal trends and patterns of the antimicrobial use are described. The results from this study suggest that informatics and the electronic medical records could be useful for monitoring trends in antimicrobial use.

Mit Eco-Drive gegen Strassenlärm. Evaluation eines Interventionsprogramms zur Förderung eines leisen Fahrstils.

Strassenlärm ist diejenige Verkehrslärmquelle, die am meisten Menschen belastet. Veränderungen im Handeln der Lärmverursachenden stellen eine vielversprechende Möglichkeit dar, bisherige Lärmbekämpfungsmassnahmen zu ergänzen. Die vorliegende Studie, welche vom Schweizerischen Bundesamt für Umwelt und dem Ministerium für Umwelt, Landwirtschaft, Ernährung, Weinbau und Forsten Rheinland-Pfalz gefördert wurde, widmete sich der Frage, wie die Förderung eines leisen Fahrstils zur Bekämpfung von Strassenlärm nutzbar gemacht werden kann. Hierzu erarbeiteten wir ein Interventionsprogramm zur Förderung eines leisen Fahrstils, welches in Zusammenarbeit mit Mitarbeitenden einer Stadtverwaltung umgesetzt und evaluiert wurde. Die Ergebnisse dieser Studie deuten darauf hin, dass es sich lohnt, einen leisen Fahrstil im Rahmen der Lärmbekämpfung zu fördern; während der mehrwöchigen Durchführung des Programms konnte eine Reduktion der durchschnittlichen Drehzahl, des durchschnittlichen Treibstoffverbrauchs, des gemittelten Summenpegels des Motorengeräuschs wie auch der prozentualen Fahrzeit mit Motorengeräuschen über 60dB(A) beobachtet werden. Befragungen der TeilnehmerInnen gaben zudem Auskunft über die diesen Veränderungen zu Grunde liegende Motivstruktur. Wir präsentieren in diesem Bericht sowohl eine detaillierte Darstellung des verwendeten Interventionsprogramms, des Vorgehens bei dessen Evaluation, sowie die entsprechenden Auswertungen. Wir hoffen, dass durch diese Studie zukünftige Programme zur Förderung eines leisen Fahrstils angeregt werden und von unseren Ergebnissen profitieren können.