Detection of a genetic alteration and species identification of coho salmon (Oncorhynchus kisutch): a collaborative study

A PCR-based method for the identification of genetically modified coho salmon (Oncorhynchus kisutch) has been developed and evaluated by a collaborative study. The coho salmon contained an "all-salmon" gene-construct (OnMTGH1) consisting of the metallothionein-B-promoter fused to the full-length type-1 growth hormone gene, both from sockeye salmon (Oncorhynchus nerka). Two PCRs were performed. The first PCR served as a control for amplifiable DNA present in the sample, and at the same time as a tool for species identification by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) test. For this PCR, universal primers located in the mitochondrial cytochrome b gene were used. The second PCR, working with primers located within the construct, detected the genetic alteration. In a collaborative study with 15 laboratories, in each case the species and the genetic modification had been assigned correctly.     

Dual Grid: A New Approach for Robust Spatial Algebra Implementation

Systems of spatial data types and operations, or spatial algebras, are fundamental for the implementation of spatial database systems. Several designs of such algebras have been proposed in the last decade, and recently commercial DBMS offer such algebras in the form of extension packages (e.g., data blades). However, actual implementations are generally severely restricted when compared to designs in the literature. A main reason is that at the implementation level one cannot further ignore the problems of robustness and topological correctness arising from the discrete number representations used in computers. Therefore, implemented packages either avoid problematic operations, or accept inconsistencies and topological errors in the answers of queries due to rounding effects.The ROSE algebra [12], proposed and implemented earlier, goes a long way towards avoiding such problems, since it was defined from scratch with robustness problems in mind. It is founded on a discrete geometric basis called a realm. The ROSE algebra guarantees a correct behavior of operations and has an entirely robust implementation. Unfortunately, the realm concept and its interaction with DBMS are difficult to implement, and certain kinds of topological problems still remain.In this paper we introduce the concept of dual grid, which provides a new approach for the representation of spatial information that avoids any robustness and topological correctness problem and allows a less restrictive implementation of spatial algebras. As an example, we show how can it be used for implementing the ROSE algebra without realms, and show that such an implementation does not suffer from the side effects and disadvantages of the original realm-based one.     

Termination Criteria for DPO Transformations with Injective Matches

Reasoning about graph and model transformation systems is an important means to underpin model-driven software engineering, such as Model-Driven Architecture (MDA) and Model Integrated Computing (MIC). Termination criteria for graph and model transformation systems have become a focused area recently. This paper provides termination criteria for graph and model transformation systems with injective matches and finite input structure. It proposes a treatment for infinite sequences of rule applications, and takes attribute conditions, negative application conditions, and type constraints into account. The results are illustrated on case studies excerpted from real-world transformations, which show the termination properties of the frequently used "transitive closure" and "leaf collector" transformation idioms. An intuitive comparison with other approaches is also given.     

Ab initio determination of the framework structure of the heavy-metal oxide Cs(x)Nb2.54W2.46O14 from 100 kV precession electron diffraction data

The present work deals with the ab initio determination of the heavy metal framework in Cs(x)(Nb, W)(5)O(14) from precession electron diffraction intensities. The target structure was first discovered by Lundberg and Sundberg [Ultramicroscopy 52 (1993) 429-435], who succeeded in deriving a tentative structural model from high-resolution electron microsopy (HREM) images. The metal framework of the compound was solved in this investigation via direct methods from hk0 precession electron diffraction intensities recorded with a Philips EM400 at 100 kV. A subsequent (kinematical) least-squares refinement with electron intensities yielded slightly improved co-ordinates for the 11 heavy atoms in the structure. Chemical analysis of several crystallites by EDX is in agreement with the formula Cs(0.44)Nb(2.54)W(2.46)O(14). Moreover, the structure was independently determined by Rietveld refinement from X-ray powder data obtained from a multi-phasic sample. The compound crystallises in the orthorhombic space group Pbam with refined lattice parameters a=27.145(2), b=21.603(2), and c=3.9463(3)A. Comparison of the framework structure from electron diffraction with the result from Rietveld refinement shows an average agreement for the heavy atoms within 0.09 A.     

HBGC123D: a high-performance computer model of coupled hydrogeological and biogeochemical processes

Groundwater flow and transport models have been used to assist management of subsurface water resources and water quality. The needs of more efficient use of technical and financial resources have recently motivated the development of more effective remediation techniques and complex models of coupled hydrogeological and biogeochemical processes. We present a high-performance computer model of the coupled processes, HBGC123D. The model uses a hybrid Eulerian–Lagrangian finite element method to solve the solute transport equation and a Newton's method to solve the system of nonlinear, mixed kinetics and equilibrium reaction equations. Application of the model to a laboratory soil column with multispecies tracer injection suggests that one may use the model to derive important parameters of subsurface solute fate and transport. These parameters may be used for predictive purpose in similar field problems. To this end, we present a three-dimensional, hypothetical bioremediation simulation on an aquifer contaminated by CoNTA. The simulation suggests that, using oxygen alone to stimulate the biodegradation of the contaminant, one may reduce the waste to 40% in 10 years. Using a refined mesh of this three-dimensional model, we also conduct a performance study of HBGC123D on an array of SGI Origin 2000 distributed shared-memory processors. Both the computational kernels and the entire model show very good performance up to 32 processors. The CPU time is essentially reduced by 20-fold using 64 processors. This result suggests that HBGC123D may be a useful tool in assisting environmental restoration efforts such as waste site characterization and remediation.     

On-the-Fly Processing of Generalized Lumigraphs

We introduce a flexible and powerful concept for reconstructing arbitrary views from multiple source images on the fly. Our approach is based on a Lumigraph structure with per-pixel depth values, and generalizes the classical two-plane parameterized light fields and Lumigraphs. With our technique, it is possible to render arbitrary views of time-varying, non-diffuse scenes at interactive frame rates, and it allows using any kind of sensor that yields images with dense depth information. We demonstrate the flexibility and efficiency of our approach through various examples.     

Using model checking to identify errors in intrusion detection signatures

Most intrusion detection systems deployed today apply misuse detection as analysis method. Misuse detection searches for attack traces in the recorded audit data using predefined patterns. The matching rules are called signatures. The definition of signatures is up to now an empirical process based on expert knowledge and experience. The analysis success and accordingly the acceptance of intrusion detection systems in general depend essentially on the topicality of the deployed signatures. Methods for a systematic development of signatures have scarcely been reported yet, so the modeling of a new signature is a time-consuming, cumbersome, and error-prone process. The modeled signatures have to be validated and corrected to improve their quality. So far only signature testing is applied for this. Signature testing is still a rather empirical and time-consuming process to detect modeling errors. In this paper, we present the first approach for verifying signature specifications using the Spin model checker. The signatures are modeled in the specification language EDL, which leans on colored Petri nets. We show how the signature specification is transformed into a Promela model and how characteristic specification errors can be found by Spin.     

泥炭栽培基质是欧洲可持续园艺业的前提

过去被当作废物的泥炭今天成为最有前途的栽培基质。在欧洲和其它现代园艺业盛行的国家里，以泥炭为主要成分的栽培基质广泛应用于各种作物栽培。栽培基质作为标准生产资料，和设施农业中计算机自动施肥、小气候控制和杀灭病虫害一样，在实现现代园艺业可持续发展中起着重要的作用。一些欧洲国家已经制定了泥炭栽培基质的国家质量标准，一些公司还制定了自己的企业标准，也有一些公司执行ISO条款。这些产品都在向着CEN标准迈进，并将成为欧洲产品标准。在一些地区和国家，以生活废弃物、工业副产品制成的栽培基质在不断地推向市场的同时，新的标准也在不断地制定。最近起草的一个鼓励利用堆肥的法令中，其中一项就是关于减少泥炭利用的。泥炭业界必须意识到这些发展变化与资源安全息息相关，必须意识到其它替代材料的有利和不利的一面，意识到它们物理、化学、生物性质以及对社会政治和自然环境的利弊影响。     

Die Macht der Bilder oder Everybody’s gonna be a Star for 15/10 of a Second

Nahezu alle Lebensvorg?nge und -bereiche werden heute weltweit verbildlicht. Videokameras, die unser Verhalten im ?ffentlichen und nicht-?ffentlichen Bereich aufzeichnen, Google, das unsere H?user filmt und sie weltweit zug?nglich macht; Facebook, das unsere Fotos scannt und unsere Gesichter identifiziert. Das nationale Datenschutzrecht und insbesondere das Unionsrecht lassen bislang überzeugende Antworten auf diese Verbildlichung des Alltags vermissen, Bilder werden als „normale“ personenbezogene Daten eingeordnet. Im Entwurf der Europ?ischen Kommission für eine Datenschutzgrundverordnung (DS-GVO) ist im Gegensatz etwa zum deutschen Recht die Videoüberwachung explizit nicht geregelt. Jedoch kommt Bildern eine besondere Macht zu. Sie wirkt sich deutlich auf die Pers?nlichkeitsrechte betroffener Personen aus. Mit den neuen Facetten der Macht der Bilder befasst sich der folgende Beitrag.