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  • Ruusuvuori, Johanna; Peräkylä, Anssi (ROUTLEDGE, 2009)
  • Peräkylä, Anssi; Ruusuvuori, Johanna (Peter Lang, 2006)
  • Zubizarreta-Gerendiain, Ane; Pellikka, Petri; Garcia-Gonzalo, Jordi; Ikonen, Veli-Pekka; Peltola, Heli (Finnish Society of Forest Science, 2012)
  • Berzins,-A; Horman,-A; Lunden,-J; Korkeala,-H (Amsterdam, Netherlands: Elsevier., 2007)
    A total of 312 samples of sliced, vacuum packaged, cold-smoked pork from 15 meat processing plants in Latvia and Lithuania, obtained over a 15-month period from 2003 until 2004, were analyzed for the presence of Listeria monocytogenes at the end of their shelf-life. Overall, 120 samples (38%) tested positive for L. monocytogenes. Despite the long storing period, the levels of L. monocytogenes in cold-smoked pork products were low. Manufacturing processes were studied at seven meat processing plants. A new approach with a logistic multivariable regression model was applied to identify the main factors associated with L. monocytogenes contamination during the manufacturing of cold-smoked pork products. Brining by injection was a significant factor (odds ratio 10.66; P<0.05) for contamination of product with L. monocytogenes. Moreover, long cold-smoking times (>=12 h) had a significant predictive value (odds ratio 24.38; P<0.014) for a sample to test positive for L. monocytogenes. Pulsed-field gel electrophoresis results indicated that various sources of L. monocytogenes contamination existed over periods of time in several meat processing plants. In two meat processing plants, persistent L. monocytogenes strains belonging to serotypes 1/2a and 1/2c were found.
  • Almeda-Valdes, Paloma; Cuevas-Ramos, Daniel; Mehta, Roopa; Muñoz-Hernandez, Liliana; Cruz-Bautista, Ivette; Perez-Mendez, Oscar; Tusie-Luna, Maria T; Gomez-Perez, Francisco J; Pajukanta, Päivi; Matikainen, Niina; Taskinen, Marja-Riitta; Aguilar-Salinas, Carlos A (BioMed Central Ltd, 2014)
    Abstract Background Alterations in postprandial metabolism have been described in familial combined hyperlipidemia (FCH); however, their underlying mechanisms are not well characterized. We aimed to identify factors related to the magnitude of postprandial lipemia and apolipoprotein (apo) A-V levels in subjects with FCH. Methods FCH cases (n&#8201;=&#8201;99) were studied using a standardized meal test. Abdominal obesity was assessed using the waist to hip ratio (WHR). A linear regression model was performed to investigate the variables associated with the triglycerides incremental area under the curve (iAUC). Independent associations between metabolic variables and apo A-V iAUC were also investigated in a randomly selected subgroup (n&#8201;=&#8201;44). The study sample was classified according to the presence of fasting hypertriglyceridemia (&#8805;150&#160;mg/dL) and abdominal obesity (WHR &#8805;0.92 in men and &#8805;0.85 in women) to explore differences in parameters. Results The fasting apo B-48 levels (r&#8201;=&#8201;0.404), and the WHR (r&#8201;=&#8201;0.359) were independent factors contributing to the triglycerides iAUC (r2&#8201;=&#8201;0.29, P&#8201;&lt;&#8201;0.001). The triglycerides iAUC was independently associated with the apo A-V iAUC (r2&#8201;=&#8201;0.54, P&#8201;&lt;&#8201;0.01). Patients with both hypertriglyceridemia and abdominal obesity showed the most robust triglycerides and apo A-V postprandial responses. Conclusions In patients with FCH the fasting apo B-48 level is the main factor associated with postprandial lipemia. Abdominal obesity also contributes to the magnitude of the postprandial response.The triglycerides postprandial increment is the principal factor associated with the apo A-V postprandial response.
  • Simonen, Outi; Viitanen, Elina; Blom, Marja (EMERALD GROUP PUBLISHING LIMITED, 2012)
  • Räsänen, Pajari (Gaudeamus Helsinki University Press, 2010)
  • Kasari, Melissa; Toivonen, Hannu; Hintsanen, Petteri (2010)
  • Hintsanen, Petteri; Toivonen, Hannu; Sevon, Petteri (2010)
  • Åstrand, Matti; Suomela, Jukka (2010)
    We present a distributed algorithm that finds a maximal edge packing in O(Δ + log* W) synchronous communication rounds in a weighted graph, independent of the number of nodes in the network; here Δ is the maximum degree of the graph and W is the maximum weight. As a direct application, we have a distributed 2-approximation algorithm for minimum-weight vertex cover, with the same running time. We also show how to find an f-approximation of minimum-weight set cover in O(f2k2 + fk log* W) rounds; here k is the maximum size of a subset in the set cover instance, f is the maximum frequency of an element, and W is the maximum weight of a subset. The algorithms are deterministic, and they can be applied in anonymous networks.
  • Lemström, Kjell; Mikkilä, Niko; Mäkinen, Veli (2008)
    We consider two content-based music retrieval problems where the music is modeled as sets of points in the Euclidean plane, formed by the (on-set time, pitch) pairs. We introduce fast filtering methods based on indexing the underlying database. The filters run in a sublinear time in the length of the database, and they are lossless if a quadratic space may be used. By taking into account the application, the search space can be narrowed down, obtaining practically lossless filters using linear size index structures. For the checking phase, which dominates the overall running time, we exploit previously designed algorithms suitable for local checking. In our experiments on a music database, our best filter-based methods performed several orders of a magnitude faster than previous solutions.
  • Arroyuelo, Diego; Claude, Francisco; Maneth, Sebastian; Mäkinen, Veli; Navarro, Gonzalo; Nguyen, Kim; Sirén, Jouni; Välimäki, Niko (2010)
    A large fraction of an XML document typically consists of text data. The XPath query language allows text search via the equal, contains, and starts-with predicates. Such predicates can be efficiently implemented using a compressed self-index of the document's text nodes. Most queries, however, contain some parts querying the text of the document, plus some parts querying the tree structure. It is therefore a challenge to choose an appropriate evaluation order for a given query, which optimally leverages the execution speeds of the text and tree indexes. Here the SXSI system is introduced. It stores the tree structure of an XML document using a bit array of opening and closing brackets plus a sequence of labels, and stores the text nodes of the document using a global compressed self-index. On top of these indexes sits an XPath query engine that is based on tree automata. The engine uses fast counting queries of the text index in order to dynamically determine whether to evaluate top-down or bottom-up with respect to the tree structure. The resulting system has several advantages over existing systems: (1) on pure tree queries (without text search) such as the XPathMark queries, the SXSI system performs on par or better than the fastest known systems MonetDB and Qizx, (2) on queries that use text search, SXSI outperforms the existing systems by 1-3 orders of magnitude (depending on the size of the result set), and (3) with respect to memory consumption, SXSI outperforms all other systems for counting-only queries.
  • Kalendar, Ruslan; Lee, David; Schulman, Alan (Humana Press, 2014)
    This chapter introduces the software FastPCR as an integrated tools environment for PCR primer and probe design. It also predicts oligonucleotide properties based on experimental studies of PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, group-specific, unique, and overlap extension PCR for multi-fragment assembly in cloning, as well as bisulphite modification assays. It includes a programme to design oligonucleotide sets for long sequence assembly by the ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with GC or AT skew, of CG content and purine-pyrimidine skew, and of linguistic sequence complexity. It also permits generation of random DNA sequence and analysis of restriction enzymes of all types. It finds or creates restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It generates consensus sequences and analyses sequence conservation. It performs efficient and complete detection of various repeat types and displays them. FastPCR allows for sequence file batch processing, which is essential for automation. The FastPCR software is available for download at and online version at
  • Salmela, Leena; Mäkinen, Veli; Välimäki, Niko; Ylinen, Johannes; Ukkonen, Esko (Oxford University Press, 2011)
  • Tervahattu, H.; Juhanoja, J.; Vaida, V.; Tuck, A. F.; Niemi, J. V.; Kupiainen, K.; Kulmala, M.; Vehkamäki, H. (American Geophysical Union, 2005)
    Surface analyses of atmospheric aerosols from different continental sources, such as forest fires and coal and straw burning, show that organic surfactants are found on such aerosols. The predominant organic species detected by time-of-flight secondary ion mass spectrometry on the sulfate aerosols are fatty acids of different carbon chain length up to the C32 acid. These observations are consistent with literature accounts of functional group analysis of bulk samples, but this is the first direct evidence of fatty acid films on the surface of sulfate aerosols. Surface analysis leads to the conclusion that fatty acid films on continental aerosols may be more common than has been previously suggested.
  • Solonen, T.; Lodenius, M. (Nordic Ecological Society Oikos, 1990)
  • Rein, Alexander-Derek; Münch, Jürgen (2013)
    As development teams’ resources are limited, selecting the right features is of utmost importance. Often, features are considered right if they result in increased business value at acceptable implementation cost. Predicting implementation cost and prioritizing features is well documented in literature. However, there has only been little work on the prediction of business value. This article presents an approach for feature proioritization that is based on mock-purchases. Considering several limitations, the approach allows key stakeholders to depict the real business value of a feature without having to implement it. Hence, the approach allows feature prioritization based on facts rather than on predictions. The approach was evaluated with a smartphone application. The business value of two features which were subjectively considered to be equally important was investigated. Moreover, the users were assigned different price categories for the features. Combined with live customer feedback, the approach allows us to identify an adequate pricing for the features. The study yielded insightful results as it showed which of the features incorporates higher revenue as well as how users react to the approach. It contributes to the body of knowledge in requirements en- gineering and software engineering as it enables practitioners to select features based on facts rather than predictions and to find ideal price points.
  • Kauppi, P.E. (IIASA, 1982)
  • Voutilainen, Atro; Linden, Krister (2011)
    Researchers and developers in academia and industry would benefit from a facility that enables them to easily locate, licence and use the kind of empirical data they need for testing and refining their hypotheses and to deposit and disseminate their data e.g. to support replication and validation of reported scientific experiments. To answer these needs initially in Finland, there is an ongoing project at University of Helsinki and its collaborators to create a user-friendly web service for researchers and developers in Finland and other countries. In our talk, we describe ongoing work to create a palette of extensive but easily available Finnish language resources and technologies for the research community, including lexical resources, wordnets, morphologically tagged corpora, dependency syntactic treebanks and parsebanks, open-source finite state toolkits and libraries and language models to support text analysis and processing at customer site. Also first publicly available results are presented.