Minimising the number of gap-zeros in binary matrices

We study a problem of minimising the total number of zeros in the gaps between blocks of consecutive ones in the columns of a binary matrix by permuting its rows. The problem is referred to as the Consecutive Ones Matrix Augmentation Problem, and is known to be NP-hard. An analysis of the structure of an optimal solution allows us to focus on a restricted solution space, and to use an implicit representation for searching the space. We develop an exact solution algorithm, which is linear-time in the number of rows if the number of columns is constant, and two constructive heuristics to tackle instances with an arbitrary number of columns. The heuristics use a novel solution representation based upon row sequencing. In our computational study, all heuristic solutions are either optimal or close to an optimum. One of the heuristics is particularly effective, especially for problems with a large number of rows

Physicochemical characterization and quantification of nanoplastics: applicability, limitations and complementarity of batch and fractionation methods

A comprehensive physicochemical characterization of heterogeneous nanoplastic (NPL) samples remains an analytical challenge requiring a combination of orthogonal measurement techniques to improve the accuracy and robustness of the results. Here, batch methods, including dynamic light scattering (DLS), nanoparticle tracking analysis (NTA), tunable resistive pulse sensing (TRPS), transmission electron microscopy (TEM), and scanning electron microscopy (SEM), as well as separation/fractionation methods such as centrifugal liquid sedimentation (CLS) and field-flow fractionation (FFF)–multi-angle light scattering (MALS) combined with pyrolysis gas chromatography mass spectrometry (pyGC–MS) or Raman microspectroscopy (RM) were evaluated for NPL size, shape, and chemical composition measurements and for quantification. A set of representative/test particles of different chemical natures, including (i) polydisperse polyethylene (PE), (ii) (doped) polystyrene (PS) NPLs, (iii) titanium dioxide, and (iv) iron oxide nanoparticles (spherical and elongated), was used to assess the applicability and limitations of the selected methodologies. Particle sizes and number-based concentrations obtained by orthogonal batch methods (DLS, NTA, TRPS) were comparable for monodisperse spherical samples, while higher deviations were observed for polydisperse, agglomerated samples and for non-spherical particles, especially for light scattering methods. CLS and TRPS offer further insight with increased size resolution, while detailed morphological information can be derived by electron microscopy (EM)–based approaches. Combined techniques such as FFF coupled to MALS and RM can provide complementary information on physical and chemical properties by online measurements, while pyGC–MS analysis of FFF fractions can be used for the identification of polymer particles (vs. inorganic particles) and for their offline (semi)quantification. However, NPL analysis in complex samples will continue to present a serious challenge for the evaluated techniques without significant improvements in sample preparation.publishedVersio

Geovisualization of forest simulation modelling results: A case study of carbon sequestration and biodiversity

Sustainable forest management requires new tools to analyze spatial and temporal forest dynamics and to examine those forest parameters that are related to sustainability. We built a prototype system for data analysis and decision-making at forest enterprise level by integrating a forest ecosystem model EFIMOD-PRO (long-term prediction of forest growth and soil development) with an interactive visualization system CommonGIS for analysis of spatially and temporally related data. Using the prototype, a case study in Central European Russia simulated four silvicultural regimes over 200 years: natural development, selective forestry, legal forestry according to the Russian forestry legislation, and illegal forest practice. Exploratory analysis of the simulation results demonstrated that (1) natural stand development is the best alternative for carbon sequestration; (2) legal forest management is the best regime for timber production; (3) selective forestry combines the advantages of two previous strategies, and can be the best strategy for implementing sustainable forest management; and (4) illegal forest practices lead to a fast decrease in forest productivity and decreasing biodiversity. Interactive and dynamic visualizations with maps and statistical graphics played a crucial role in data cleaning, model validation, and analysis of simulation results. The case study demonstrated the potential of integrating forest ecosystem models with exploratory data visualization for the analysis and expert evaluation at the local level. The prototype can be used to present ecological and silvicultural consequences of various management practices to stakeholders and differing social groups, thus stimulating effective decision-making for sustainable forestry

The Wolbachia Genome of Brugia malayi: Endosymbiont Evolution within a Human Pathogenic Nematode

Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode Brugia malayi. Although, quantitatively, the genome is even more degraded than those of closely related Rickettsia species, Wolbachia has retained more intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be Wolbachia's principal contribution to the mutualistic relationship, whereas the host nematode likely supplies amino acids required for Wolbachia growth. Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share similar metabolic trends, although their genomes show a high degree of genome shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level of repeated DNA. Both Wolbachia have lost a considerable number of membrane biogenesis genes that apparently make them unable to synthesize lipid A, the usual component of proteobacterial membranes. However, differences in their peptidoglycan structures may reflect the mutualistic lifestyle of wBm in contrast to the parasitic lifestyle of wMel. The smaller genome size of wBm, relative to wMel, may reflect the loss of genes required for infecting host cells and avoiding host defense systems. Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease

Near millimolar concentration of nucleosomes in mitotic chromosomes from late prometaphase into anaphase.

Chromosome compaction is a key feature of mitosis and critical for accurate chromosome segregation. However, a precise quantitative analysis of chromosome geometry during mitotic progression is lacking. Here, we use volume electron microscopy to map, with nanometer precision, chromosomes from prometaphase through telophase in human RPE1 cells. During prometaphase, chromosomes acquire a smoother surface, their arms shorten, and the primary centromeric constriction is formed. The chromatin is progressively compacted, ultimately reaching a remarkable nucleosome concentration of over 750 µM in late prometaphase that remains relatively constant during metaphase and early anaphase. Surprisingly, chromosomes then increase their volume in late anaphase prior to deposition of the nuclear envelope. The plateau of total chromosome volume from late prometaphase through early anaphase described here is consistent with proposals that the final stages of chromatin condensation in mitosis involve a limit density, such as might be expected for a process involving phase separation

Inventing a herbal tradition: The complex roots of the current popularity of Epilobium angustifolium in Eastern Europe

Ethnopharmacological relevance: Currently various scientific and popular sources provide a wide spectrum of ethnopharmacological information on many plants, yet the sources of that information, as well as the information itself, are often not clear, potentially resulting in the erroneous use of plants among lay people or even in official medicine. Our field studies in seven countries on the Eastern edge of Europe have revealed an unusual increase in the medicinal use of Epilobium angustifolium L., especially in Estonia, where the majority of uses were specifically related to “men's problems”. The aim of the current work is: to understand the recent and sudden increase in the interest in the use of E. angustifolium in Estonia; to evaluate the extent of documented traditional use of E. angustifolium among sources of knowledge considered traditional; to track different sources describing (or attributed as describing) the benefits of E. angustifolium; and to detect direct and indirect influences of the written sources on the currently documented local uses of E. angustifolium on the Eastern edge of Europe. Materials and methods: In this study we used a variety of methods: semi-structured interviews with 599 people in 7 countries, historical data analysis and historical ethnopharmacological source analysis. We researched historical and archival sources, and academic and popular literature published on the medicinal use of E. angustifolium in the regions of our field sites as well as internationally, paying close attention to the literature that might have directly or indirectly contributed to the popularity of E. angustifolium at different times in history. Results: Our results show that the sudden and recent popularity in the medical use of E. angustifolium in Estonia has been caused by local popular authors with academic medical backgrounds, relying simultaneously on “western” and Russian sources. While Russian sources have propagated (partially unpublished) results from the 1930s, “western” sources are scientific insights derived from the popularization of other Epilobium species by Austrian herbalist Maria Treben. The information Treben disseminated could have been originated from a previous peak in popularity of E. angustifolium in USA in the second half of the 19th century, caused in turn by misinterpretation of ancient herbals. The traditional uses of E. angustifolium were related to wounds and skin diseases, fever, pain (headache, sore throat, childbirth), and abdominal-related problems (constipation, stomach ache) and intestinal bleeding. Few more uses were based on the similarity principle. The main theme, however, is the fragmentation of use and its lack of consistency apart from wounds and skin diseases. Conclusions: Historical ethnobotanical investigations could help to avoid creating repeating waves of popularity of plants that have already been tried for certain diseases and later abandoned as not fully effective. There is, of course, a chance that E. angustifolium could also finally be proven to be clinically safe and cost-effective for treating benign prostatic hyperplasia, but this has not yet happened despite recent intensive research. Documented traditional use would suggest investigating the dermatological, intestinal anti-hemorrhagic and pain inhibiting properties of this plant, if any

2017 Research & Innovation Day Program

A one day showcase of applied research, social innovation, scholarship projects and activities.https://first.fanshawec.ca/cri_cripublications/1004/thumbnail.jp