An Efficient Local Search for Partial Latin Square Extension Problem

A partial Latin square (PLS) is a partial assignment of n symbols to an nxn grid such that, in each row and in each column, each symbol appears at most once. The partial Latin square extension problem is an NP-hard problem that asks for a largest extension of a given PLS. In this paper we propose an efficient local search for this problem. We focus on the local search such that the neighborhood is defined by (p,q)-swap, i.e., removing exactly p symbols and then assigning symbols to at most q empty cells. For p in {1,2,3}, our neighborhood search algorithm finds an improved solution or concludes that no such solution exists in O(n^{p+1}) time. We also propose a novel swap operation, Trellis-swap, which is a generalization of (1,q)-swap and (2,q)-swap. Our Trellis-neighborhood search algorithm takes O(n^{3.5}) time to do the same thing. Using these neighborhood search algorithms, we design a prototype iterated local search algorithm and show its effectiveness in comparison with state-of-the-art optimization solvers such as IBM ILOG CPLEX and LocalSolver.Comment: 17 pages, 2 figure

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points. The appearance of new sequencing techniques was essential to get more interpretable genomic data. In contrast to the previous short-reads, longer lengths can provide a better insight into the potential health threatening genetic abnormalities. Long-reads offer more accurate variant identification and genome assembly methods, indicating advances in nucleotide deflect-related studies. In this review, we introduce the historical background of sequencing technologies and show their benefits and limits, as well. Furthermore, we highlight the differences between short- and long-read approaches, including their unique advances and difficulties in methodologies and evaluation. Additionally, we provide a detailed description of the corresponding bioinformatics and the current applications

Efficient Multi-site Data Movement Using Constraint Programming for Data Hungry Science

For the past decade, HENP experiments have been heading towards a distributed computing model in an effort to concurrently process tasks over enormous data sets that have been increasing in size as a function of time. In order to optimize all available resources (geographically spread) and minimize the processing time, it is necessary to face also the question of efficient data transfers and placements. A key question is whether the time penalty for moving the data to the computational resources is worth the presumed gain. Onward to the truly distributed task scheduling we present the technique using a Constraint Programming (CP) approach. The CP technique schedules data transfers from multiple resources considering all available paths of diverse characteristic (capacity, sharing and storage) having minimum user's waiting time as an objective. We introduce a model for planning data transfers to a single destination (data transfer) as well as its extension for an optimal data set spreading strategy (data placement). Several enhancements for a solver of the CP model will be shown, leading to a faster schedule computation time using symmetry breaking, branch cutting, well studied principles from job-shop scheduling field and several heuristics. Finally, we will present the design and implementation of a corner-stone application aimed at moving datasets according to the schedule. Results will include comparison of performance and trade-off between CP techniques and a Peer-2-Peer model from simulation framework as well as the real case scenario taken from a practical usage of a CP scheduler.Comment: To appear in proceedings of Computing in High Energy and Nuclear Physics 200

Comprehensive DNA Methylation Analysis Reveals a Common Ten-Gene Methylation Signature in Colorectal Adenomas and Carcinomas

Microarray analysis of promoter hypermethylation provides insight into the role and extent of DNA methylation in the development of colorectal cancer (CRC) and may be co-monitored with the appearance of driver mutations. Colonic biopsy samples were obtained endoscopically from 10 normal, 23 adenoma (17 low-grade (LGD) and 6 high-grade dysplasia (HGD)), and 8 ulcerative colitis (UC) patients (4 active and 4 inactive). CRC samples were obtained from 24 patients (17 primary, 7 metastatic (MCRC)), 7 of them with synchronous LGD. Field effects were analyzed in tissues 1 cm (n = 5) and 10 cm (n = 5) from the margin of CRC. Tissue materials were studied for DNA methylation status using a 96 gene panel and for KRAS and BRAF mutations. Expression levels were assayed using whole genomic mRNA arrays. SFRP1 was further examined by immunohistochemistry. HT29 cells were treated with 5-aza-2' deoxycytidine to analyze the reversal possibility of DNA methylation. More than 85% of tumor samples showed hypermethylation in 10 genes (SFRP1, SST, BNC1, MAL, SLIT2, SFRP2, SLIT3, ALDH1A3, TMEFF2, WIF1), whereas the frequency of examined mutations were below 25%. These genes distinguished precancerous and cancerous lesions from inflamed and healthy tissue. The mRNA alterations that might be caused by systematic methylation could be partly reversed by demethylation treatment. Systematic changes in methylation patterns were observed early in CRC carcinogenesis, occuring in precursor lesions and CRC. Thus we conclude that DNA hypermethylation is an early and systematic event in colorectal carcinogenesis, and it could be potentially reversed by systematic demethylation therapy, but it would need more in vitro and in vivo experiments to support this theory

Constraint Solving on Bounded String Variables

Abstract Constraints on strings of unknown length occur in a wide variety of real-world problems, such as test case generation, program analysis, model checking, and web security. We describe a set of con-straints sufficient to model many standard benchmark problems from these fields. For strings of an unknown length bounded by an integer, we describe propagators for these constraints. Finally, we provide an experi-mental comparison between a state-of-the-art dedicated string solver, CP approaches utilising fixed-length string solving, and our implementation extending an off-the-shelf CP solver.

Complete genes may pass from food to human blood

Our bloodstream is considered to be an environment well separated from the outside world and the digestive tract. According to the standard paradigm large macromolecules consumed with food cannot pass directly to the circulatory system. During digestion proteins and DNA are thought to be degraded into small constituents, amino acids and nucleic acids, respectively, and then absorbed by a complex active process and distributed to various parts of the body through the circulation system. Here, based on the analysis of over 1000 human samples from four independent studies, we report evidence that meal-derived DNA fragments which are large enough to carry complete genes can avoid degradation and through an unknown mechanism enter the human circulation system. In one of the blood samples the relative concentration of plant DNA is higher than the human DNA. The plant DNA concentration shows a surprisingly precise log-normal distribution in the plasma samples while non-plasma (cord blood) control sample was found to be free of plant DNA

Fauna Europaea: Diptera -Brachycera

Link to publication Citation for published version (APA): Pape, T., Beuk, P., Pont, A. C., Shatalkin, A. I., Ozerov, A. L., Woźnica, A. J., ... de Jong, Y. (2015). Fauna Europaea: 3, [e4187]. https://doi.org/10.3897/BDJ.3.e4187 General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. Abstract Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant multicellular European terrestrial and freshwater animals and their geographical distribution at the level of countries and major islands (east of the Urals and excluding the Caucasus region). The Fauna Europaea project comprises about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. Fauna Europaea represents a huge effort by more than 400 contributing taxonomic specialists throughout Europe and is a unique (standard) reference suitable for many user communities in science, government, industry, nature conservation and education. The Diptera-Brachycera is one of the 58 Fauna Europaea major taxonomic groups, and data have been compiled by a network of 55 specialists. Within the two-winged insects (Diptera), the Brachycera constitute a monophyletic group, which is generally given rank of suborder. The Brachycera may be classified into the probably paraphyletic 'lower brachyceran grade' and the monophyletic Eremoneura. The latter contains the Empidoidea, the Apystomyioidea with a single Nearctic species, and the Cyclorrhapha, which in turn is divided into the paraphyletic 'aschizan grade' and the monophyletic Schizophora. The latter is traditionally divided into the paraphyletic 'acalyptrate grade' and the monophyletic Calyptratae. Our knowledge of the European fauna of Diptera-Brachycera varies tremendously among families, from the reasonably well known hoverflies (Syrphidae) to the extremely poorly known scuttle flies (Phoridae). There has been a steady growth in our knowledge of European Diptera for the last two centuries, with no apparent slow down, but there is a shift towards a larger fraction of the new species being found among the families of the nematoceran grade (lower Diptera), which due to a larger number of small-sized species may be considered as taxonomically more challenging. Most of Europe is highly industrialised and has a high human population density, and the more fertile habitats are extensively cultivated. This has undoubtedly increased the extinction risk for numerous species of brachyceran flies, yet with the recent re-discovery of Thyreophora cynophila (Panzer), there are no known cases of extinction at a European level. However, few national Red Lists have extensive information on Diptera. For the Diptera-Brachycera, data from 96 families containing 11,751 species are included in this paper

The influence of curing conditions on properties of electrically conductive adhesives

Práce se věnuje problematice elektricky vodivých lepidel, která se používají jako alternativa k pájeným spojům. Práce je zaměřena na analýzu vlivu podmínek vytvrzování na elektrické a mechanické vlastnosti elektricky vodivých lepidel. Vzorky spojů vytvořených elektricky vodivým lepením byly vytvrzovány jednak za podmínek doporučených výrobcem ale také v prodloužených časech. Průběžně byly sledovány změny parametrů spojů v průběhu času vytvrzování. Měřily se parametry jako elektrický odpor a střihová síla lepených spojů. Byl také analyzován vliv různých doporučených kombinací podmínek vytvrzování. Jev dodatečného vytvrzení byl zjištěn během prodloužené doby vytvrzování.The work is focused on problematic of electrically conductive adhesives. These are used as an alternative to solder joints. Goal of work was concentrated to analysis of influence of curing conditions on electric and mechanical properties of electrically conductive adhesives. Samples of joins realized by electrically conductive adhesives were cured at conditions recommended by producer as well as in extended time. Changes in parameters over time have been monitored continuously. Electrical resistance and tear out force of adhesive joints were measured. Influence of different recommended curing conditions was analyzed too. The effect of post-curing or degradation of binders may appear during curing process

Lichens-a new source or yet unknown host of herbaceous plant viruses?

Abstract Lichens are symbiotic associations of fungi with green algae or cyanobacteria. They have arisen independently several times within the Ascomycota and Basidiomycota. This symbiosis became with time one of the most successful life forms on Earth. Outside of the symbiotic algae and fungi, there are endophytic fungi, other algae, and lichen-associated bacteria present within lichen thalli. Till now, no lichen-specific pathogens have been reported among bacteria and viruses. Around 15 dsRNA viruses are known from Eurotiomycetes and another dsRNA and reverse transcribed ssRNA viruses from Dothideomycetes containing some lichenized fungal lineages. Algal viruses have been identified from less than 1 % of known eukaryotic algal species but no virus has been found in Trebouxia or in Trentepohlia (Chlorophyta, Pleurastrophyceae, Pleurastrales), the most common green lichen photobionts. On the other hand, dsDNA viruses infecting related Chlorella algae are well known from freshwater phytoplankton. However, high-molecular weight dsRNA isolated from different lichen thalli indicated to us presence of ss or dsRNA viruses. A PCRbased search for viruses with genus-specific and speciesspecific primers resulted in amplification of genome segments highly identical with those of plant cytorhabdoviruses and with Apple mosaic virus (ApMV). The nucleotide sequence of the putative lichen cytorhabdovirus showed high identity (98 %) with Ivy latent cytorhabdovirus. The nucleotide sequences of six Apple mosaic virus isolates from lichens showed high similarity with ApMV isolates from apple and pear hosts. The lichen ApMV isolates were mechanically transmitted to an herbaceous host and detected positive in ELISA 14 days thereafter, which support its infectivity on plants. We prepared axenic cultures of photobionts identified as Trebouxia sp. from this ApMVpositive lichen samples. All these cultures were positive for ApMV in RT-PCR test. We suggest that lichens as a whole (or their photobionts, more specifically) could serve as reservoirs for viruses, despite the fact that the way of transmission between different organisms is not Eur J Plant Patho