Level-wise node size distribution of randomly generated regular trees

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The use of classification and regression trees to predict the likelihood of seasonal influenza.

Background Individual signs and symptoms are of limited value for the diagnosis of influenza. Objective To develop a decision tree for the diagnosis of influenza based on a classification and regression tree (CART) analysis. Methods Data from two previous similar cohort studies were assembled into a single dataset. The data were randomly divided into a development set (70%) and a validation set (30%). We used CART analysis to develop three models that maximize the number of patients who do not require diagnostic testing prior to treatment decisions. The validation set was used to evaluate overfitting of the model to the training set. Results Model 1 has seven terminal nodes based on temperature, the onset of symptoms and the presence of chills, cough and myalgia. Model 2 was a simpler tree with only two splits based on temperature and the presence of chills. Model 3 was developed with temperature as a dichotomous variable (≥38°C) and had only two splits based on the presence of fever and myalgia. The area under the receiver operating characteristic curves (AUROCC) for the development and validation sets, respectively, were 0.82 and 0.80 for Model 1, 0.75 and 0.76 for Model 2 and 0.76 and 0.77 for Model 3. Model 2 classified 67% of patients in the validation group into a high- or low-risk group compared with only 38% for Model 1 and 54% for Model 3. Conclusions A simple decision tree (Model 2) classified two-thirds of patients as low or high risk and had an AUROCC of 0.76. After further validation in an independent population, this CART model could support clinical decision making regarding influenza, with low-risk patients requiring no further evaluation for influenza and high-risk patients being candidates for empiric symptomatic or drug therapy.

Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling.

In this paper we included a very broad representation of grass family diversity (84% of tribes and 42% of genera). Phylogenetic inference was based on three plastid DNA regions rbcL, matK and trnL-F, using maximum parsimony and Bayesian methods. Our results resolved most of the subfamily relationships within the major clades (BEP and PACCMAD), which had previously been unclear, such as, among others the: (i) BEP and PACCMAD sister relationship, (ii) composition of clades and the sister-relationship of Ehrhartoideae and Bambusoideae + Pooideae, (iii) paraphyly of tribe Bambuseae, (iv) position of Gynerium as sister to Panicoideae, (v) phylogenetic position of Micrairoideae. With the presence of a relatively large amount of missing data, we were able to increase taxon sampling substantially in our analyses from 107 to 295 taxa. However, bootstrap support and to a lesser extent Bayesian inference posterior probabilities were generally lower in analyses involving missing data than those not including them. We produced a fully resolved phylogenetic summary tree for the grass family at subfamily level and indicated the most likely relationships of all included tribes in our analysis.

Biophysical requirements of power-supply systems: nuclear energy and fossil energy

The report presents a grammar capable of analyzing the process of production of electricity in modular elements for different power-supply systems, defined using semantic and formal categories. In this way it becomes possible to individuate similarities and differences in the process of production of electricity, and then measure and compare “apples” with “apples” and “oranges” with “oranges”. For instance, when comparing the various unit operations of the process of production of electricity with nuclear energy to the analogous unit operations of the process of production of fossil energy, we see that the various phases of the process are the same. The only difference is related to characteristics of the process associated with the generation of heat which are completely different in the two systems. As a matter of facts, the performance of the production of electricity from nuclear energy can be studied, by comparing the biophysical costs associated with the different unit operations taking place in nuclear and fossil power plants when generating process heat or net electricity. By adopting this approach, it becomes possible to compare the performance of the two power-supply systems by comparing their relative biophysical requirements for the phases that both nuclear energy power plants and fossil energy power plants have in common: (i) mining; (ii) refining/enriching; (iii) generating heat/electricity; (iv) handling the pollution/radioactive wastes. This report presents the evaluation of the biophysical requirements for the two powersupply systems: nuclear energy and fossil energy. In particular, the report focuses on the following requirements: (i) electricity; (ii) fossil-fuels, (iii) labor; and (iv) materials.

Description of Pintomyia (Pifanomyia) falcaorum sp. n. (Diptera: Psychodidae: Phlebotominae), a Fossil Sand Fly from Dominican Amber

A new species of sand fly, Pintomyia (Pifanomyia) falcaorum is described from an amber originated from the northern mountain range of Dominican Republic. The male sand fly specimen is well preserved and most features used in Phlebotominae taxonomy are seen with remarkable clarity.

The fossil tabanids (Diptera Tabanidae): when they began to appreciate warm blood and when they began transmit diseases?

A discussion of the known fossil tabanids (Diptera Tabanidae) is presented based on fossil evidence. This includes the origin of the hemathophagy in the Brachycera, more specifically for tabanids. Several tabanid species in the extant fauna are vectors for disease-producing organisms that affect humans and animals. Bacteria, viruses, rickettsiae, protozoa, and filarial worms can be transmitted by them, causing such diseases as anthrax, tularemia, anaplasmosis, various forms of trypanosomiasis, Q fever, and filariasis. However, if tabanids are directly responsible for all of these diseases is not consensual and the known fossil evidence is presented here.

Fossil psychodoid flies and their relation to parasitic diseases

Psychodid sand flies are blood-sucking fly vectors of several parasitic diseases. The oldest definitive record of this group is from the Lower Cretaceous amber of Lebanon (circa -135 to -125 My), but the high diversity within this group supports the idea that the psychodoids originated much earlier in history. The palaeontology demonstrates that the Lower Cretaceous representatives of the different subfamilies of Psychodidae had similar morphology and were blood-feeders, which supports Hennig's hypothesis on the ground plan structure of this family. Historical relationship between sand flies and diseases is unclear up to the present time, but this relationship could be as old as the origin of psychodoids because of the blood-feeding life mode.

Relationships of new world Phlebotomine sand flies (Diptera: Psychodidae) based on fossil evidence

The fossil record and systematics of phlebotomid sand flies, vectors of leishmaniasis and arbovirus in several regions of the world, strongly support that living genera existed long before the Oligocene (38 million years, myr). A common Phlebotominae ancestor was present in the Triassic period before the separations of continents (248 myr).

Palaeoenvironment and palaeoclimate of the Middle Miocene lake in the Steinheim basin, SW Germany: A reconstruction from C, O, and Sr isotopes of fossil remains

A differentiated reconstruction of palaeolimnologic, -environmental, and -climatic conditions is presented for the Middle Miocene long-term freshwater lake (14.3 to 13.5 Ma) of the Steinheim basin, on the basis of a combined C, 0, and Sr isotope study of sympatric skeletal fossils of aquatic and terrestrial organisms from the lake sediments. The oxygen isotope composition for lake water of the Steinheim basin (delta O-18(H2O) = +2.0 +/- 0.4 parts per thousand VSMOW, n = 6) was reconstructed from measurements of delta O-18(PO4) of aquatic turtle bones. The drinking water calculated from the enamel of large mammals (proboscideans, rhinocerotids, equids, cervids, suids) has delta O-18(H2O) values (delta(OH2O)-O-18 = -5.9 +/- 1.7 parts per thousand VSMOW, n = 31) typical for Middle Miocene meteoric water of the area. This delta O-18(H2O) value corresponds to a mean annual air temperature (MAT) of 18.8 +/- 3.8 degrees C, calculated using a modem-day delta(OH2O)-O-18-MAT relation. Hence, large mammals did not use the lake water as principal drinking water. In contrast, small mammals, especially the then abundant pika Prolagus oeningensis drank from O-18-enriched water sources (delta O-18(H2O) = +2.7 +/- 2.3 parts per thousand VSMOW, n = 7), such as the lake water. Differences in Sr and 0 isotopic compositions between large and small mammal teeth indicate different home ranges and drinking behaviour and support migration of some large mammals between the Swabian Alb plateau and the nearby Molasse basin, while small mammals ingested their food and water locally. Changes in the lake level, water chemistry, and temperature were inferred using isotopic compositions of ostracod and gastropod shells from a composite lake sediment profile. Calcitic ostracod valves (Ilyocypris binocularis; delta O-18 = +1.7 +/- 1.2 parts per thousand VPDB, delta C-18 = -0.5 +/- 0.9 parts per thousand, VPDB, n = 68) and aragonitic, gastropod shells (Gyraulus spp.; delta O-18 = +2.0 +/- 13 parts per thousand VPDB, delta C-13 = -1.1 +/- 1.3 parts per thousand VPDB, n = 89) have delta O-18 and delta C-13 values similar to or even higher than those of marine, carbonates. delta C-13 values:of the biogenic carbonates parallel lake level fluctuations while delta O-18 values scatter around +2 +/- 2 parts per thousand and reflect the short term variability of meteoric water inflow vs. longer term evaporation. Sr-87/Sr-86 ratios of aragonitic Gyraulus spp. gastropod shells parallel the lake level fluctuations, reflecting variable inputs of groundwater and surface waters. Using a water delta O-18(H2O) value of +2.0 parts per thousand VSMOW, water temperatures calculated from skeletal tissue delta O-18 values of ostracods are 16.7 +/- 5.0 degrees C, gastropods 20.6 +/- 5.6 degrees C, otoliths 21.8 +/- 1.4 degrees C, and fish teeth 17.0 +/- 2.7 degrees C. The calculated MAT (similar to 19 degrees C), lake water temperatures (similar to 17 to 22 degrees C) and the O-18-enriched water compositions are indicative of warm-temperate climatic conditions, possibly with a high humidity during this period. Vegetation in the area surrounding the basin was largely of the C-3-type, as indicated by carbon isotopic compositions of tooth enamel from large mammals (delta C-13 = -11.1 +/- 1.1 parts per thousand VPDB, n = 40). (c) 2006 Elsevier B.V. All rights reserved.

The serine repeat antigen (SERA) gene family phylogeny in Plasmodium: the impact of GC content and reconciliation of gene and species trees.

Plasmodium falciparum is the parasite responsible for the most acute form of malaria in humans. Recently, the serine repeat antigen (SERA) in P. falciparum has attracted attention as a potential vaccine and drug target, and it has been shown to be a member of a large gene family. To clarify the relationships among the numerous P. falciparum SERAs and to identify orthologs to SERA5 and SERA6 in Plasmodium species affecting rodents, gene trees were inferred from nucleotide and amino acid sequence data for 33 putative SERA homologs in seven different species. (A distance method for nucleotide sequences that is specifically designed to accommodate differing GC content yielded results that were largely compatible with the amino acid tree. Standard-distance and maximum-likelihood methods for nucleotide sequences, on the other hand, yielded gene trees that differed in important respects.) To infer the pattern of duplication, speciation, and gene loss events in the SERA gene family history, the resulting gene trees were then "reconciled" with two competing Plasmodium species tree topologies that have been identified by previous phylogenetic studies. Parsimony of reconciliation was used as a criterion for selecting a gene tree/species tree pair and provided (1) support for one of the two species trees and for the core topology of the amino acid-derived gene tree, (2) a basis for critiquing fine detail in a poorly resolved region of the gene tree, (3) a set of predicted "missing genes" in some species, (4) clarification of the relationship among the P. falciparum SERA, and (5) some information about SERA5 and SERA6 orthologs in the rodent malaria parasites. Parsimony of reconciliation and a second criterion--implied mutational pattern at two key active sites in the SERA proteins-were also seen to be useful supplements to standard "bootstrap" analysis for inferred topologies.

Description of Pintomyia (Pifanomyia) brazilorum sp. nov. a new fossil species from the Dominican Republic (Diptera: Psychodidae: Phlebotominae)

A sand fly fossil was found in amber, a vegetal resin, which allows all the external phlebotomine structures to be seen. The piece that contains the new species is 14 mm long ´ 8 mm wide ´ 3 mm high. All the structures from the head, thorax, and abdomen were examined under the microscope and measured with a calibrated micrometric eye-piece. The morphological aspects of the new species suggest its inclusion in the Pintomyia genus, Pifanomyia subgenus though it is not possible to include it in any of the series known for this subgenus. The presence of two atrophied spines on the gonostyles and gonocoxites without tufts of setae permit the exclusion of the new species from the other species of the subgenus Pifanomyia. The new species is named Pintomyia (Pifanomyia) brazilorum sp. nov.

Early Cretaceous trypanosomatids associated with fossil sand fly larvae in Burmese amber

Early Cretaceous flagellates with characters typical of trypanosomatids were found in the gut of sand fly larvae, as well as in surrounding debris, in Burmese amber. This discovery supports a hypothesis in which free-living trypanosomatids could have been acquired by sand fly larvae in their feeding environment and then carried transtadially into the adult stage. At some point in time, specific genera were introduced into vertebrates, thus establishing a dixenous life cycle.

Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism.

The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).

Description of Micropygomyia brandaoi sp. n. (Diptera: Psychodidae: Phlebotominae), a fossil phlebotomine from the Dominican Republic

The description of Micropygomyia brandaoi, a new species of fossil phlebotomine sand fly, is based on one male specimen obtained from Dominican amber of the Miocene period (20 million years). In this new species, the fifth palpal segment is long, the coxite lacks a setal tuft and the style shows four well-developed spines. This set of characters allowed us to place the new species in the genus Micropygomyia Barretto.

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.

Phylogenomic databases provide orthology predictions for species with fully sequenced genomes. Although the goal seems well-defined, the content of these databases differs greatly. Seven ortholog databases (Ensembl Compara, eggNOG, HOGENOM, InParanoid, OMA, OrthoDB, Panther) were compared on the basis of reference trees. For three well-conserved protein families, we observed a generally high specificity of orthology assignments for these databases. We show that differences in the completeness of predicted gene relationships and in the phylogenetic information are, for the great majority, not due to the methods used, but to differences in the underlying database concepts. According to our metrics, none of the databases provides a fully correct and comprehensive protein classification. Our results provide a framework for meaningful and systematic comparisons of phylogenomic databases. In the future, a sustainable set of 'Gold standard' phylogenetic trees could provide a robust method for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure.