Bootstrap confidence intervals for principal covariates regression

Principal covariate regression (PCOVR) is a method for regressing a set of criterion variables with respect to a set of predictor variables when the latter are many in number and/or collinear. This is done by extracting a limited number of components that simultaneously synthesize the predictor variables and predict the criterion ones. So far, no procedure has been offered for estimating statistical uncertainties of the obtained PCOVR parameter estimates. The present paper shows how this goal can be achieved, conditionally on the model specification, by means of the bootstrap approach. Four strategies for estimating bootstrap confidence intervals are derived and their statistical behaviour in terms of coverage is assessed by means of a simulation experiment. Such strategies are distinguished by the use of the varimax and quartimin procedures and by the use of Procrustes rotations of bootstrap solutions towards the sample solution. In general, the four strategies showed appropriate statistical behaviour, with coverage tending to the desired level for increasing sample sizes. The main exception involved strategies based on the quartimin procedure in cases characterized by complex underlying structures of the components. The appropriateness of the statistical behaviour was higher when the proper number of components were extracted

Project scheduling with generalized precedence relations: a new method to analyze criticalities and flexibilities

In this paper, we illustrate a new method to overcome the failures of the theory proposed by Elmaghraby and Kamburowski (1992) and De Reyck (1998) for the analysis of activity criticalities and flexibilities in non-preemptive project scheduling with generalized precedence relations under unlimited resources. These failures, discussed in detail in this paper, call for a new approach to study this problem. We provide new definitions of criticalities and consequently new tools for their identification within a more general framework without ambiguities

Candecomp/Parafac with zero constraints at arbitrary positions in a loading matrix

When one interprets Candecomp/Parafac (CP) solutions for analyzing three-way data, small loadings are often ignored, that is, considered to be zero. Rather than just considering them zero, it seems better to actually model such values as zero. This can be done by successive modeling approaches as well as by a simultaneous modeling approach. This paper offers algorithms for three such approaches, and compares them on the basis of empirical data and a simulation study. The conclusion of the latter was that, under realistic circumstances, all approaches recovered the underlying structure well, when the number of values to constrain to zero was given. Whereas the simultaneous modeling approach seemed to perform slightly better, differences were very small and not substantial. Given that the simultaneous approach is far more time consuming than the successive approaches, the present study suggests that for practical purposes successive approaches for modeling zeros in the CP model seem to be indicated

Instrumental neutron activation analysis of an enriched 28Si single-crystal

The determination of the Avogadro constant plays a key role in the redefinition of the kilogram in terms of a fundamental constant. The present experiment makes use of a silicon single-crystal highly enriched in 28Si that must have a total impurity mass fraction smaller than a few parts in 109. To verify this requirement, we previously developed a relative analytical method based on neutron activation for the elemental characterization of a sample of the precursor natural silicon crystal WASO 04. The method is now extended to fifty-nine elements and applied to a monoisotopic 28Si single-crystal that was grown to test the achievable enrichment. Since this crystal was likely contaminated, this measurement tested also the detection capabilities of the analysis. The results quantified contaminations by Ge, Ga, As, Tm, Lu, Ta, W and Ir and, for a number of the detectable elements, demonstrated that we can already reach the targeted 1 ng/g detection limit.Comment: 9 pages, 1 figure, 1 tabl

Scheduling activities in project network with feeding precedence relations: an earliest start forward recursion algorithm

In some production processes, the effort associated with a certain activity for its execution can vary over time. In this case, the amount of work per time unit devoted to each activity, so as its duration, is not univocally determined. This kind of problem can be represented by an activity project network with the so-called feeding precedence relations, and activity variable execution intensity. In this paper, we propose a forward recursion algorithm able to find the earliest start and finish times of each activity, in O(m log n) time, with n and m being the number of activities and the number of precedence relations, respectively. In particular, this requires the calculation of the (optimal) execution intensity profile, for each activity, that warrants the earliest start schedule and the minimum completion time of the project

Do longer sequences improve the accuracy of identification of forensically important Calliphoridae species?

Species identification is a crucial step in forensic entomology. In several cases the calculation of the larval age allows the estimation of the minimum Post-Mortem Interval (mPMI). A correct identification of the species is the first step for a correct mPMI estimation. To overcome the difficulties due to the morphological identification especially of the immature stages, a molecular approach can be applied. However, difficulties in separation of closely related species are still an unsolved problem. Sequences of 4 different genes (COI, ND5, EF-1\u3b1, PER) of 13 different fly species collected during forensic experiments (Calliphora vicina, Calliphora vomitoria, Lucilia sericata, Lucilia illustris, Lucilia caesar, Chrysomya albiceps, Phormia regina, Cynomya mortuorum, Sarcophaga sp., Hydrotaea sp., Fannia scalaris, Piophila sp., Megaselia scalaris) were evaluated for their capability to identify correctly the species. Three concatenated sequences were obtained combining the four genes in order to verify if longer sequences increase the probability of a correct identification. The obtained results showed that this rule does not work for the species L. caesar and L. illustris. Future works on other DNA regions are suggested to solve this taxonomic issue

Specific LTR-Retrotransposons Show Copy Number Variations between Wild and Cultivated Sunflowers

The relationship between variation of the repetitive component of the genome and domestication in plant species is not fully understood. In previous work, variations in the abundance and proximity to genes of long terminal repeats (LTR)-retrotransposons of sunflower (Helianthus annuus L.) were investigated by Illumina DNA sequencingtocompare cultivars and wild accessions. In this study, we annotated and characterized 22 specific retrotransposon families whose abundance varies between domesticated and wild genotypes. These families mostly belonged to the Chromovirus lineage of the Gypsy superfamily and were distributed overall chromosomes. They were also analyzed in respect to their proximity to genes. Genes close to retrotransposon were classified according to biochemical pathways, and differences between domesticated and wild genotypes are shown. These data suggest that structural variations related to retrotransposons might have occurred to produce phenotypic variation between wild and domesticated genotypes, possibly by affecting the expression of genes that lie close to inserted or deleted retrotransposons and belong to specific biochemical pathways as those involved in plant stress responses

Genome-wide analysis of LTR retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.)

Background: Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels. Results: After determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species. Conclusions: This large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial habit of that species

Comparative genome-wide analysis of repetitive DNA in the genus Populus L.

Genome skimming was performed, using Illumina sequence reads, in order to obtain a detailed comparative picture of the repetitive component of the genome of Populus species. Read sets of seven Populus and two Salix species (as outgroups) were subjected to clustering using RepeatExplorer (Novák et al. BMC Bioinformatics 11:378 2010). The repetitive portion of the genome ranged from 33.8 in Populus nigra to 46.5% in Populus tremuloides. The large majority of repetitive sequences were long terminal repeat-retrotransposons. Gypsy elements were over-represented compared to Copia ones, with a mean ratio Gypsy to Copia of 6.7:1. Satellite DNAs showed a mean genome proportion of 2.2%. DNA transposons and ribosomal DNA showed genome proportions of 1.8 and 1.9%, respectively. The other repeat types accounted for less of 1% each. Long terminal repeat-retrotransposons were further characterized, identifying the lineage to which they belong and studying the proliferation times of each lineage in the different species. The most abundant lineage was Athila, which showed large differences among species. Concerning Copia lineages, similar transpositional profiles were observed among all the analysed species; by contrast, differences in transpositional peaks of Gypsy lineages were found. The genome proportions of repeats were compared in the seven species, and a phylogenetic tree was built, showing species separation according to the botanical section to which the species belongs, although significant differences could be found within sections, possibly related to the different geographical origin of the species. Overall, the data indicate that the repetitive component of the genome in the poplar genus is still rapidly evolving