Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Amplification of the housekeeping sigma factor in Pseudomonas fluorescens CHA0 enhances antibiotic production and improves biocontrol abilities.

Pseudomonas fluorescens CHA0 produces a variety of secondary metabolites, in particular the antibiotics pyoluteorin and 2,4-diacetylphloroglucinol, and protects various plants from diseases caused by soilborne pathogenic fungi. The rpoD gene encoding the housekeeping sigma factor sigma 70 of P. fluorescens was sequenced. The deduced RpoD protein showed 83% identity with RpoD of Pseudomonas aeruginosa and 67% identity with RpoD of Escherichia coli. Attempts to inactivate the single chromosomal rpoD gene of strain CHA0 were unsuccessful, indicating an essential role of this gene. When rpoD was carried by an IncP vector in strain CHA0, the production of both antibiotics was increased severalfold and, in parallel, protection of cucumber against disease caused by Pythium ultimum was improved, in comparison with strain CHA0.

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Nonclassical measurement error with applications to labor and development issues

Zero correlation between measurement error and model error has been assumed in existing panel data models dealing specifically with measurement error. We extend this literature and propose a simple model where one regressor is mismeasured, allowing the measurement error to correlate with model error. Zero correlation between measurement error and model error is a special case in our model where correlated measurement error equals zero. We ask two research questions. First, we wonder if the correlated measurement error can be identified in the context of panel data. Second, we wonder if classical instrumental variables in panel data need to be adjusted when correlation between measurement error and model error cannot be ignored. Under some regularity conditions the answer is yes to both questions. We then propose a two-step estimation corresponding to the two questions. The first step estimates correlated measurement error from a reverse regression; and the second step estimates usual coefficients of interest using adjusted instruments.

Error estimate and control in the MSFV method for multiphase flow in porous media

n this paper the iterative MSFV method is extended to include the sequential implicit simulation of time dependent problems involving the solution of a system of pressure-saturation equations. To control numerical errors in simulation results, an error estimate, based on the residual of the MSFV approximate pressure field, is introduced. In the initial time steps in simulation iterations are employed until a specified accuracy in pressure is achieved. This initial solution is then used to improve the localization assumption at later time steps. Additional iterations in pressure solution are employed only when the pressure residual becomes larger than a specified threshold value. Efficiency of the strategy and the error control criteria are numerically investigated. This paper also shows that it is possible to derive an a-priori estimate and control based on the allowed pressure-equation residual to guarantee the desired accuracy in saturation calculation.

Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data.

Despite the central role of quantitative PCR (qPCR) in the quantification of mRNA transcripts, most analyses of qPCR data are still delegated to the software that comes with the qPCR apparatus. This is especially true for the handling of the fluorescence baseline. This article shows that baseline estimation errors are directly reflected in the observed PCR efficiency values and are thus propagated exponentially in the estimated starting concentrations as well as 'fold-difference' results. Because of the unknown origin and kinetics of the baseline fluorescence, the fluorescence values monitored in the initial cycles of the PCR reaction cannot be used to estimate a useful baseline value. An algorithm that estimates the baseline by reconstructing the log-linear phase downward from the early plateau phase of the PCR reaction was developed and shown to lead to very reproducible PCR efficiency values. PCR efficiency values were determined per sample by fitting a regression line to a subset of data points in the log-linear phase. The variability, as well as the bias, in qPCR results was significantly reduced when the mean of these PCR efficiencies per amplicon was used in the calculation of an estimate of the starting concentration per sample.

The relationship between forensic science and judicial error: a study covering error sources, bias, and remedies

Summary : Forensic science - both as a source of and as a remedy for error potentially leading to judicial error - has been studied empirically in this research. A comprehensive literature review, experimental tests on the influence of observational biases in fingermark comparison, and semistructured interviews with heads of forensic science laboratories/units in Switzerland and abroad were the tools used. For the literature review, some of the areas studied are: the quality of forensic science work in general, the complex interaction between science and law, and specific propositions as to error sources not directly related to the interaction between law and science. A list of potential error sources all the way from the crime scene to the writing of the report has been established as well. For the empirical tests, the ACE-V (Analysis, Comparison, Evaluation, and Verification) process of fingermark comparison was selected as an area of special interest for the study of observational biases, due to its heavy reliance on visual observation and recent cases of misidentifications. Results of the tests performed with forensic science students tend to show that decision-making stages are the most vulnerable to stimuli inducing observational biases. For the semi-structured interviews, eleven senior forensic scientists answered questions on several subjects, for example on potential and existing error sources in their work, of the limitations of what can be done with forensic science, and of the possibilities and tools to minimise errors. Training and education to augment the quality of forensic science have been discussed together with possible solutions to minimise the risk of errors in forensic science. In addition, the time that samples of physical evidence are kept has been determined as well. Results tend to show considerable agreement on most subjects among the international participants. Their opinions on possible explanations for the occurrence of such problems and the relative weight of such errors in the three stages of crime scene, laboratory, and report writing, disagree, however, with opinions widely represented in existing literature. Through the present research it was therefore possible to obtain a better view of the interaction of forensic science and judicial error to propose practical recommendations to minimise their occurrence. Résumé : Les sciences forensiques - considérés aussi bien comme source de que comme remède à l'erreur judiciaire - ont été étudiées empiriquement dans cette recherche. Une revue complète de littérature, des tests expérimentaux sur l'influence du biais de l'observation dans l'individualisation de traces digitales et des entretiens semi-directifs avec des responsables de laboratoires et unités de sciences forensiques en Suisse et à l'étranger étaient les outils utilisés. Pour la revue de littérature, quelques éléments étudies comprennent: la qualité du travail en sciences forensiques en général, l'interaction complexe entre la science et le droit, et des propositions spécifiques quant aux sources d'erreur pas directement liées à l'interaction entre droit et science. Une liste des sources potentielles d'erreur tout le long du processus de la scène de crime à la rédaction du rapport a également été établie. Pour les tests empiriques, le processus d'ACE-V (analyse, comparaison, évaluation et vérification) de l'individualisation de traces digitales a été choisi comme un sujet d'intérêt spécial pour l'étude des effets d'observation, due à son fort recours à l'observation visuelle et dû à des cas récents d'identification erronée. Les résultats des tests avec des étudiants tendent à prouver que les étapes de prise de décision sont les plus vulnérables aux stimuli induisant des biais d'observation. Pour les entretiens semi-structurés, onze forensiciens ont répondu à des questions sur des sujets variés, par exemple sur des sources potentielles et existantes d'erreur dans leur travail, des limitations de ce qui peut être fait en sciences forensiques, et des possibilités et des outils pour réduire au minimum ses erreurs. La formation et l'éducation pour augmenter la qualité des sciences forensiques ont été discutées ainsi que les solutions possibles pour réduire au minimum le risque d'erreurs en sciences forensiques. Le temps que des échantillons sont gardés a été également déterminé. En général, les résultats tendent à montrer un grand accord sur la plupart des sujets abordés pour les divers participants internationaux. Leur avis sur des explications possibles pour l'occurrence de tels problèmes et sur le poids relatif de telles erreurs dans les trois étapes scène de crime;', laboratoire et rédaction de rapports est cependant en désaccord avec les avis largement représentés dans la littérature existante. Par cette recherche il était donc possible d'obtenir une meilleure vue de l'interaction des sciences forensiques et de l'erreur judiciaire afin de proposer des recommandations pratiques pour réduire au minimum leur occurrence. Zusammenfassung : Forensische Wissenschaften - als Ursache und als Hilfsmittel gegen Fehler, die möglicherweise zu Justizirrtümern führen könnten - sind hier empirisch erforscht worden. Die eingestzten Methoden waren eine Literaturübersicht, experimentelle Tests über den Einfluss von Beobachtungseffekten (observer bias) in der Individualisierung von Fingerabdrücken und halbstandardisierte Interviews mit Verantwortlichen von kriminalistischen Labors/Diensten in der Schweiz und im Ausland. Der Literaturüberblick umfasst unter anderem: die Qualität der kriminalistischen Arbeit im Allgemeinen, die komplizierte Interaktion zwischen Wissenschaft und Recht und spezifische Fehlerquellen, welche nicht direkt auf der Interaktion von Recht und Wissenschaft beruhen. Eine Liste möglicher Fehlerquellen vom Tatort zum Rapportschreiben ist zudem erstellt worden. Für die empirischen Tests wurde der ACE-V (Analyse, Vergleich, Auswertung und Überprüfung) Prozess in der Fingerabdruck-Individualisierung als speziell interessantes Fachgebiet für die Studie von Beobachtungseffekten gewählt. Gründe sind die Wichtigkeit von visuellen Beobachtungen und kürzliche Fälle von Fehlidentifizierungen. Resultate der Tests, die mit Studenten durchgeführt wurden, neigen dazu Entscheidungsphasen als die anfälligsten für Stimuli aufzuzeigen, die Beobachtungseffekte anregen könnten. Für die halbstandardisierten Interviews beantworteten elf Forensiker Fragen über Themen wie zum Beispiel mögliche und vorhandene Fehlerquellen in ihrer Arbeit, Grenzen der forensischen Wissenschaften und Möglichkeiten und Mittel um Fehler zu verringern. Wie Training und Ausbildung die Qualität der forensischen Wissenschaften verbessern können ist zusammen mit möglichen Lösungen zur Fehlervermeidung im selben Bereich diskutiert worden. Wie lange Beweismitten aufbewahrt werden wurde auch festgehalten. Resultate neigen dazu, für die meisten Themen eine grosse Übereinstimmung zwischen den verschiedenen internationalen Teilnehmern zu zeigen. Ihre Meinungen über mögliche Erklärungen für das Auftreten solcher Probleme und des relativen Gewichts solcher Fehler in den drei Phasen Tatort, Labor und Rapportschreiben gehen jedoch mit den Meinungen, welche in der Literatur vertreten werden auseinander. Durch diese Forschungsarbeit war es folglich möglich, ein besseres Verständnis der Interaktion von forensischen Wissenschaften und Justizirrtümer zu erhalten, um somit praktische Empfehlungen vorzuschlagen, welche diese verringern. Resumen : Esta investigación ha analizado de manera empírica el rol de las ciencias forenses como fuente y como remedio de potenciales errores judiciales. La metodología empleada consistió en una revisión integral de la literatura, en una serie de experimentos sobre la influencia de los sesgos de observación en la individualización de huellas dactilares y en una serie de entrevistas semiestructuradas con jefes de laboratorios o unidades de ciencias forenses en Suiza y en el extranjero. En la revisión de la literatura, algunas de las áreas estudiadas fueron: la calidad del trabajo en ciencias forenses en general, la interacción compleja entre la ciencia y el derecho, así como otras fuentes de error no relacionadas directamente con la interacción entre derecho y ciencia. También se ha establecido una lista exhaustiva de las fuentes potenciales de error desde la llegada a la escena del crimen a la redacción del informe. En el marco de los tests empíricos, al analizar los sesgos de observación dedicamos especial interés al proceso de ACE-V (análisis, comparación, evaluación y verificación) para la individualización de huellas dactilares puesto que este reposa sobre la observación visual y ha originado varios casos recientes de identificaciones erróneas. Los resultados de las experimentaciones realizadas con estudiantes sugieren que las etapas en las que deben tornarse decisiones son las más vulnerables a lös factores que pueden generar sesgos de observación. En el contexto de las entrevistas semi-estructuradas, once científicos forenses de diversos países contestaron preguntas sobre varios temas, incluyendo las fuentes potenciales y existehtes de error en su trabajo, las limitaciones propias a las ciencias forenses, las posibilidades de reducir al mínimo los errores y las herramientas que podrían ser utilizadas para ello. Se han sugerido diversas soluciones para alcanzar este objetivo, incluyendo el entrenamiento y la educación para aumentar la calidad de las ciencias forenses. Además, se ha establecido el periodo de conservación de las muestras judiciales. Los resultados apuntan a un elevado grado de consenso entre los entrevistados en la mayoría de los temas. Sin embargo, sus opiniones sobre las posibles causas de estos errores y su importancia relativa en las tres etapas de la investigación -la escena del crimen, el laboratorio y la redacción de informe- discrepan con las que predominan ampliamente en la literatura actual. De este modo, esta investigación nos ha permitido obtener una mejor imagen de la interacción entre ciencias forenses y errores judiciales, y comenzar a formular una serie de recomendaciones prácticas para reducirlos al minimo.

CXCR4-activated astrocyte glutamate release via TNFalpha: amplification by microglia triggers neurotoxicity.

Astrocytes actively participate in synaptic integration by releasing transmitter (glutamate) via a calcium-regulated, exocytosis-like process. Here we show that this process follows activation of the receptor CXCR4 by the chemokine stromal cell-derived factor 1 (SDF-1). An extraordinary feature of the ensuing signaling cascade is the rapid extracellular release of tumor necrosis factor-alpha (TNFalpha). Autocrine/paracrine TNFalpha-dependent signaling leading to prostaglandin (PG) formation not only controls glutamate release and astrocyte communication, but also causes their derangement when activated microglia cooperate to dramatically enhance release of the cytokine in response to CXCR4 stimulation. We demonstrate that altered glial communication has direct neuropathological consequences and that agents interfering with CXCR4-dependent astrocyte-microglia signaling prevent neuronal apoptosis induced by the HIV-1 coat glycoprotein, gp120IIIB. Our results identify a new pathway for glia-glia and glia-neuron communication that is relevant to both normal brain function and neurodegenerative diseases.

Novel microsatellite loci for Sebaea aurea (Gentianaceae) and cross-amplification in related species.

Premise of the study: Microsatellite loci were developed in Sebaea aurea (Gentianaceae) to investigate the functional role of diplostigmaty (i.e., the presence of additional stigmas along the style). Methods and Results: One hundred seventy-four and 180 microsatellite loci were isolated through 454 shotgun sequencing of genomic and microsatellite-enriched DNA libraries, respectively. Sixteen polymorphic microsatellite loci were characterized, and 12 of them were selected to genotype individuals from two populations. Microsatellite amplification was conducted in two multiplex groups, each containing six microsatellite loci. Cross-species amplification was tested in seven other species of Sebaea. The 12 novel microsatellite loci amplified only in the two most closely related species to S. aurea (i.e., S. ambigua and S. minutiflora) and were also polymorphic in these two species. Conclusions: These results demonstrate the usefulness of this set of newly developed microsatellite loci to investigate the mating system and population genetic structure in S. aurea and related species.

Description of microsatellite markers and genotyping performances using feathers and buccal swabs for the Ivory gull (Pagophila eburnea).

We report 22 new polymorphic microsatellites for the Ivory gull (Pagophila eburnea), and we describe how they can be efficiently co-amplified using multiplexed polymerase chain reactions. In addition, we report DNA concentration, amplification success, rates of genotyping errors and the number of genotyping repetitions required to obtain reliable data with three types of noninvasive or nondestructive samples: shed feathers collected in colonies, feathers plucked from living individuals and buccal swabs. In two populations from Greenland (n=21) and Russia (Severnaya Zemlya Archipelago, n=21), the number of alleles per locus varied between 2 and 17, and expected heterozygosity per population ranged from 0.18 to 0.92. Twenty of the markers conformed to Hardy-Weinberg and linkage equilibrium expectations. Most markers were easily amplified and highly reliable when analysed from buccal swabs and plucked feathers, showing that buccal swabbing is a very efficient approach allowing good quality DNA retrieval. Although DNA amplification success using single shed feathers was generally high, the genotypes obtained from this type of samples were prone to error and thus need to be amplified several times. The set of microsatellite markers described here together with multiplex amplification conditions and genotyping error rates will be useful for population genetic studies of the Ivory gull.

Imaging for clarification of accusation of treatment error

In the assessment of medical malpractice imaging methods can be used for the documentation of crucial morphological findings which are indicative for or against an iatrogenically caused injury. The clarification of deaths in this context can be usefully supported by postmortem imaging (primarily native computed tomography, angiography, magnetic resonance imaging). Postmortem imaging offers significant additional information compared to an autopsy in the detection of iatrogenic air embolisms and documentation of misplaced medical aids before dissection with an inherent danger of relocation. Additional information is supplied by postmortem imaging in the search for sources of bleeding as well as the documentation of perfusion after cardiovascular surgery. Key criteria for the decision to perform postmortem imaging can be obtained from the necessary preliminary inspection of clinical documentation.

Valeur prédictive de la surexpression/ amplification de Her2/neu pour un traitement ciblé du cancer du sein [Predictive value of Her2/neu expression/amplification for the targeted treatment of breast cancer]

Her2/neu is a tyrosine kinase receptor which stimulates cell growth. The receptor is overexpressed in about 20% of breast cancers. Her2/neu expression is an indicator of poor prognosis but also the target of the treatment of breast cancer using humanised anti-Her2/ neu antibodies. Only cancers overexpressing the protein will respond to this therapy, but which has significant (cardiac) side effects and is expensive. It is therefore important to test for the overexpression of the protein on breast cancer cells. This paper discusses how this can be done and ongoing research into new therapeutic options targeting the involved signaling pathways.

Error and attack tolerance of layered complex networks.

Many complex systems may be described by not one but a number of complex networks mapped on each other in a multi-layer structure. Because of the interactions and dependencies between these layers, the state of a single layer does not necessarily reflect well the state of the entire system. In this paper we study the robustness of five examples of two-layer complex systems: three real-life data sets in the fields of communication (the Internet), transportation (the European railway system), and biology (the human brain), and two models based on random graphs. In order to cover the whole range of features specific to these systems, we focus on two extreme policies of system's response to failures, no rerouting and full rerouting. Our main finding is that multi-layer systems are much more vulnerable to errors and intentional attacks than they appear from a single layer perspective.