Automated extraction of DNA from blood and PCR setup using a Tecan Freedom EVO liquid handler for forensic genetic STR typing of reference samples

We have implemented and validated automated protocols for DNA extraction and PCR setup using a Tecan Freedom EVO liquid handler mounted with the Te-MagS magnetic separation device (Tecan, M?nnedorf, Switzerland). The protocols were validated for accredited forensic genetic work according to ISO 17025 using the Qiagen MagAttract DNA Mini M48 kit (Qiagen GmbH, Hilden, Germany) from fresh whole blood and blood from deceased individuals. The workflow was simplified by returning the DNA extracts to the original tubes minimizing the risk of misplacing samples. The tubes that originally contained the samples were washed with MilliQ water before the return of the DNA extracts. The PCR was setup in 96-well microtiter plates. The methods were validated for the kits: AmpF?STR Identifiler, SGM Plus and Yfiler (Applied Biosystems, Foster City, CA), GenePrint FFFL and PowerPlex Y (Promega, Madison, WI). The automated protocols allowed for extraction and addition of PCR master mix of 96 samples within 3.5h. In conclusion, we demonstrated that (1) DNA extraction with magnetic beads and (2) PCR setup for accredited, forensic genetic short tandem repeat typing can be implemented on a simple automated liquid handler leading to the reduction of manual work, and increased quality and throughput.     

DYFRAM: dynamic fragmentation and replica management in distributed database systems

In distributed database systems, tables are frequently fragmented and replicated over a number of sites in order to reduce network communication costs. How to fragment, when to replicate and how to allocate the fragments to the sites are challenging problems that has previously been solved either by static fragmentation, replication and allocation, or based on a priori query analysis. Many emerging applications of distributed database systems generate very dynamic workloads with frequent changes in access patterns from different sites. In such contexts, continuous refragmentation and reallocation can significantly improve performance. In this paper we present DYFRAM, a decentralized approach for dynamic table fragmentation and allocation in distributed database systems based on observation of the access patterns of sites to tables. The approach performs fragmentation, replication, and reallocation based on recent access history, aiming at maximizing the number of local accesses compared to accesses from remote sites. We show through simulations and experiments on the DASCOSA distributed database system that the approach significantly reduces communication costs for typical access patterns, thus demonstrating the feasibility of our approach.     

Domain science and engineering from computer science to the sciences of informatics. Part I: Engineering

In this paper, we wish to advocate that departments of computer science put emphasis on teaching programming and software engineering based on formal methods; and more emphasis on research into formal methods for the trustworthy development of software. We also wish to advocate that the concepts of domain science and domain engineering become an indispensable part of the science of informatics and of software engineering.     

Eigenvectors of directed graphs and importance scores: dominance,T-Rank,and sink remedies

We study the properties of the principal eigenvector for the adjacency matrix (and related matrices) for a general directed graph. In particular—motivated by the use of the eigenvector for estimating the “importance” of the nodes in the graph—we focus on the distribution of positive weight in this eigenvector, and give a coherent picture which builds upon and unites earlier results. We also propose a simple method—“T-Rank”—for generating importance scores. T-Rank generates authority scores via a one-level, non-normalized matrix, and is thus distinct from known methods such as PageRank (normalized), HITS (two-level), and SALSA (two-level and normalized). We show, using our understanding of the principal eigenvector, that T-Rank has a much less severe “sink problem” than does PageRank. Also, we offer numerical results which quantify the “tightly-knit community” or TKC effect. We find that T-Rank has a stronger TKC effect than PageRank, and we offer a novel interpolation method which allows for continuous tuning of the strength of this TKC effect. Finally, we propose two new “sink remedies”, i.e., methods for ensuring that the principal eigenvector is positive everywhere. One of our sink remedies (source pumping) is unique among sink remedies, in that it gives a positive eigenvector without rendering the graph strongly connected. We offer a preliminary evaluation of the effects and possible applications of these new sink remedies.     

Optimal Sparse Matrix Dense Vector Multiplication in the I/O-Model

We study the problem of sparse-matrix dense-vector multiplication (SpMV) in external memory. The task of SpMV is to compute y:=Ax, where A is a sparse N×N matrix and x is a vector. We express sparsity by a parameter k, and for each choice of k consider the class of matrices where the number of nonzero entries is kN, i.e., where the average number of nonzero entries per column is k.     

Control strategies used by experienced marine navigators: observation of verbal conversations during navigation training

This article investigates the relationship between the control situation framework, as presented by Bjørkli et al. (Cogn Technol Work 9:67–80, 2007), and observed operator action and communication in high-speed craft operation in the Norwegian Royal Navy. The reported data include two series of events during sailing in the Norwegian archipelago where uncertainty of ship position, challenges of manoeuvring and navigation strategies are addressed. The results indicate that the navigators perform actions and communicate in accordance with the key features of the control situation framework, and thus adapt to the interrelation between control possibilities and control requirements. The navigators were guided by explicit knowledge of the functional characteristics of psychical and temporal dynamics, which were actualized in manoeuvring. It indicates that the control situation framework can be used to describe the models the operators use.     

Predicting Articulated Human Motion from Spatial Processes

We present a probabilistic interpretation of inverse kinematics and extend it to sequential data. The resulting model is used to estimate articulated human motion in visual data. The approach allows us to express the prior temporal models in spatial limb coordinates, which is in contrast to most recent work where prior models are derived in terms of joint angles. This approach has several advantages. First of all, it allows us to construct motion models in low dimensional spaces, which makes motion estimation more robust. Secondly, as many types of motion are easily expressed in spatial coordinates, the approach allows us to construct high quality application specific motion models with little effort. Thirdly, the state space is a real vector space, which allows us to use off-the-shelf stochastic processes as motion models, which is rarely possible when working with joint angles. Fourthly, we avoid the problem of accumulated variance, where noise in one joint affects all joints further down the kinematic chains. All this combined allows us to more easily construct high quality motion models. In the evaluation, we show that an activity independent version of our model is superior to the corresponding state-of-the-art model. We also give examples of activity dependent models that would be hard to phrase directly in terms of joint angles.     

Efficient search based on content similarity over self-organizing P2P networks

The advent of the World Wide Web has made an enormous amount of information available to everyone and the widespread use of digital equipment enables end-users (peers) to produce their own digital content. This vast amount of information requires scalable data management systems. Peer-to-peer (P2P) systems have so far been well established in several application areas, with file-sharing being the most prominent. The next challenge that needs to be addressed is (more complex) data sharing, management and query processing, thus facilitating the delivery of a wide spectrum of novel data-centric applications to the end-user, while providing high Quality-of-Service. In this paper, we propose a self-organizing P2P system that is capable to identify peers with similar content and intentionally assign them to the same super-peer. During content retrieval, fewer super-peers need to be contacted and therefore efficient similarity search is supported, in terms of reduced network traffic and contacted peers. Our approach increases the responsiveness and reliability of a P2P system and we demonstrate the advantages of our approach using large-scale simulations.     

Musculoskeletal complaints among nurses related to patient handling tasks and psychosocial factors--based on logbook registrations

The aims were to evaluate the inter-method reliability of a registration sheet for patient handling tasks, to study the day-to-day variation of musculoskeletal complaints (MSC) and to examine whether patient handling tasks and psychosocial factors were associated with MSC.Nurses (n = 148) fulfilled logbooks for three consecutive working days followed by a day off. Low back pain (LBP), neck/shoulder pain (NSP), knee pain (KP), psychosocial factors (time pressure, stress, conscience of the quality of work) and patient transfers and care tasks were reported.The logbook was reliable for both transfer and care tasks. The numbers of nurses reporting MSC and the level of pain increased significantly during the three working days (15%-30% and 17%-37%, respectively) and decreased on the day off. Stress and transfer task were associated with LPB and transfer tasks were associated with KP.Our results confirm a relationship between work factors and MSC and indicate that logs could be one way to obtain a better understanding of the complex interaction of various nursing working conditions in relation to MSC.