Near MDS poset codes and distributions

We study $q$-ary codes with distance defined by a partial order of the coordinates of the codewords. Maximum Distance Separable (MDS) codes in the poset metric have been studied in a number of earlier works. We consider codes that are close to MDS codes by the value of their minimum distance. For such codes, we determine their weight distribution, and in the particular case of the "ordered metric" characterize distributions of points in the unit cube defined by the codes. We also give some constructions of codes in the ordered Hamming space.Comment: 13 pages, 1 figur

Temporal patterns of gene expression via nonmetric multidimensional scaling analysis

Motivation: Microarray experiments result in large scale data sets that require extensive mining and refining to extract useful information. We have been developing an efficient novel algorithm for nonmetric multidimensional scaling (nMDS) analysis for very large data sets as a maximally unsupervised data mining device. We wish to demonstrate its usefulness in the context of bioinformatics. In our motivation is also an aim to demonstrate that intrinsically nonlinear methods are generally advantageous in data mining. Results: The Pearson correlation distance measure is used to indicate the dissimilarity of the gene activities in transcriptional response of cell cycle-synchronized human fibroblasts to serum [Iyer et al., Science vol. 283, p83 (1999)]. These dissimilarity data have been analyzed with our nMDS algorithm to produce an almost circular arrangement of the genes. The temporal expression patterns of the genes rotate along this circular arrangement. If an appropriate preparation procedure may be applied to the original data set, linear methods such as the principal component analysis (PCA) could achieve reasonable results, but without data preprocessing linear methods such as PCA cannot achieve a useful picture. Furthermore, even with an appropriate data preprocessing, the outcomes of linear procedures are not as clearcut as those by nMDS without preprocessing.Comment: 11 pages, 6 figures + online only 2 color figures, submitted to Bioinformatic

Early-Middle Pleistocene benthic turnover and oxygen isotope stratigraphy from the Central Mediterranean (Valle di Manche, Crotone Basin, Italy): data and trends

Ostracod faunal turnover and oxygen isotope data (foraminifera) along the Valle di Manche (VdM) section are herein compiled. Specifically, the material reported in this work includes quantitative palaeoecological data and patterns of ostracod fauna framed within a high-resolution oxygen isotope stratigraphy (δ18O) from Uvigerina peregrina. In addition, the multivariate ostracod faunal stratigraphic trend (nMDS axis-1 sample score) is calibrated using bathymetric distributions of extant molluscs sampled from the same stratigraphic intervals along the VdM section. Data and analyses support the research article “Dynamics of benthic marine communities across the Early-Middle Pleistocene boundary in the Mediterranean region (Valle di Manche, Southern Italy): biotic and stratigraphic implications” Rossi et al. [1]

Evaluation of Potential Translocation Sites for an Imperiled Cyprinid, the Hornyhead Chub

Translocation of isolated species into suitable habitats may help to secure vulnerable, geographically limited species. Due to the decline of Wyoming Hornyhead Chub Nocomis biguttatus, conservation actions, such as the translocation of populations within the plausible historical range, are being considered to improve population redundancy and resiliency to disturbance events. Translocation of Wyoming Hornyhead Chub must be rigorously evaluated because a hatchery stock does not exist, so all fish used in translocations will come from the wild population. We present an approach to identify the best available translocation sites prior to translocation efforts taking place. We evaluated fish community composition and habitat conditions at 54 potential translocation sites for Hornyhead Chub within 12 streams of the North Platte River basin of Wyoming. We used two analyses to identify translocation sites that were most similar to currently occupied Hornyhead Chub sites on the Laramie River: hurdle models to predict hypothetical abundance of Hornyhead Chub at translocation sites and nonmetric multidimensional scaling with fish community and habitat conditions. Presence and abundance of Hornyhead Chub were positively related to a lack of nonnative predators and to habitat features characteristic of backwater and velocity refuge habitats (e.g., minimum water velocity and width-to-depth ratio). We used a rank scoring system to weight the outcomes of each analysis, and the highest-ranking translocation sites occurred at a historically occupied locality, the Sweetwater River. Our approach may be appropriate for other at-risk species with isolated distributions and little historical data

Terrestrial climate variability and seasonality changes in the Mediterranean region between 15 000 and 4000 years BP deduced from marine pollen records

Pollen-based climate reconstructions were performed on two high-resolution pollen marines cores from the Alboran and Aegean Seas in order to unravel the climatic variability in the coastal settings of the Mediterranean region between 15 000 and 4000 years BP (the Lateglacial, and early to mid-Holocene). The quantitative climate reconstructions for the Alboran and Aegean Sea records focus mainly on the reconstruction of the seasonality changes (temperatures and precipitation), a crucial parameter in the Mediterranean region. This study is based on a multi-method approach comprising 3 methods: the Modern Analogues Technique (MAT), the recent Non-Metric Multidimensional Scaling/Generalized Additive Model method (NMDS/GAM) and Partial Least Squares regression (PLS). The climate signal inferred from this comparative approach confirms that cold and dry conditions prevailed in the Mediterranean region during the Oldest and Younger Dryas periods, while temperate conditions prevailed during the Bølling/Allerød and the Holocene. Our records suggest a West/East gradient of decreasing precipitation across the Mediterranean region during the cooler Late-glacial and early Holocene periods, similar to present-day conditions. Winter precipitation was highest during warm intervals and lowest during cooling phases. Several short-lived cool intervals (i.e. Older Dryas, another oscillation after this one (GI-1c2), Gerzensee/Preboreal Oscillations, 8.2 ka event, Bond events) connected to the North Atlantic climate system are documented in the Alboran and Aegean Sea records indicating that the climate oscillations associated with the successive steps of the deglaciation in the North Atlantic area occurred in both the western and eastern Mediterranean regions. This observation confirms the presence of strong climatic linkages between the North Atlantic and Mediterranean regions

Alkane hydroxylase genes in psychrophile genomes and the potential for cold active catalysis.

BackgroundPsychrophiles are presumed to play a large role in the catabolism of alkanes and other components of crude oil in natural low temperature environments. In this study we analyzed the functional diversity of genes for alkane hydroxylases, the enzymes responsible for converting alkanes to more labile alcohols, as found in the genomes of nineteen psychrophiles for which alkane degradation has not been reported. To identify possible mechanisms of low temperature optimization we compared putative alkane hydroxylases from these psychrophiles with homologues from nineteen taxonomically related mesophilic strains.ResultsSeven of the analyzed psychrophile genomes contained a total of 27 candidate alkane hydroxylase genes, only two of which are currently annotated as alkane hydroxylase. These candidates were mostly related to the AlkB and cytochrome p450 alkane hydroxylases, but several homologues of the LadA and AlmA enzymes, significant for their ability to degrade long-chain alkanes, were also detected. These putative alkane hydroxylases showed significant differences in primary structure from their mesophile homologues, with preferences for specific amino acids and increased flexibility on loops, bends, and α-helices.ConclusionA focused analysis on psychrophile genomes led to discovery of numerous candidate alkane hydroxylase genes not currently annotated as alkane hydroxylase. Gene products show signs of optimization to low temperature, including regions of increased flexibility and amino acid preferences typical of psychrophilic proteins. These findings are consistent with observations of microbial degradation of crude oil in cold environments and identify proteins that can be targeted in rate studies and in the design of molecular tools for low temperature bioremediation