Understanding bias in geographic range size estimates

Aim Estimates of geographic range size derived from natural history museum specimens are probably biased for many species. We aim to determine how bias in these estimates relates to range size. Location We conducted computer simulations based on herbarium specimen records from localities ranging from the southern United States to northern Argentina. Methods We used theory on the sampling distribution of the mean and variance to develop working hypotheses about how range size, defined as area of occupancy (AOO), was related to the inter-specific distribution of: (1) mean collection effort per area across the range of a species (MC); (2) variance in collection effort per area across the range of a species (VC); and (3) proportional bias in AOO estimates (PBias: the difference between the expected value of the estimate of AOO and true AOO, divided by true AOO). We tested predictions from these hypotheses using computer simulations based on a dataset of more than 29,000 herbarium specimen records documenting occurrences of 377 plant species in the tribe Bignonieae (Bignoniaceae). Results The working hypotheses predicted that the mean of the inter-specific distribution of MC, VC and PBias were independent of AOO, but that the respective variance and skewness decreased with increasing AOO. Computer simulations supported all but one prediction: the variance of the inter-specific distribution of VC did not decrease with increasing AOO. Main conclusions Our results suggest that, despite an invariant mean, the dispersion and symmetry of the inter-specific distribution of PBias decreases as AOO increases. As AOO increased, range size was less severely underestimated for a large proportion of simulated species. However, as AOO increased, range size estimates having extremely low bias were less common.

Evolution of pi(0) Suppression in Au plus Au Collisions from root s(NN)=39 to 200 GeV

Neutral-pion pi(0) spectra were measured at midrapidity (vertical bar y vertical bar < 0.35) in Au + Au collisions at root s(NN) = 39 and 62.4 GeV and compared with earlier measurements at 200 GeV in a transverse-momentum range of 1 < p(T) < 10 GeV/c. The high-p(T) tail is well described by a power law in all cases, and the powers decrease significantly with decreasing center-of-mass energy. The change of powers is very similar to that observed in the corresponding spectra for p + p collisions. The nuclear modification factors (RAA) show significant suppression, with a distinct energy, centrality, and p(T) dependence. Above p(T) = 7 GeV/c, R-AA is similar for root sNN = 62.4 and 200 GeV at all centralities. Perturbative-quantum-chromodynamics calculations that describe R-AA well at 200 GeV fail to describe the 39 GeV data, raising the possibility that, for the same p(T) region, the relative importance of initial-state effects and soft processes increases at lower energies. The p(T) range where pi(0) spectra in central Au + Au collisions have the same power as in p + p collisions is approximate to 5 and 7 GeV/c for root sNN = 200 and 62.4 GeV, respectively. For the root sNN = 39 GeV data, it is not clear whether such a region is reached, and the x(T) dependence of the x(T)-scaling power-law exponent is very different from that observed in the root sNN = 62 and 200 GeV data, providing further evidence that initial-state effects and soft processes mask the in-medium suppression of hardscattered partons to higher p(T) as the collision energy decreases.

Measurement of Direct Photons in Au plus Au Collisions at root s(NN)=200 GeV

We report the measurement of direct photons at midrapidity in Au + Au collisions at root s(NN) = 200 GeV. The direct photon signal was extracted for the transverse momentum range of 4 GeV/c < pT < 22 GeV/c, using a statistical method to subtract decay photons from the inclusive photon sample. The direct photon nuclear modification factor R-AA was calculated as a function of p(T) for different Au + Au collision centralities using the measured p + p direct photon spectrum and compared to theoretical predictions. R-AA was found to be consistent with unity for all centralities over the entire measured pT range. Theoretical models that account for modifications of initial direct photon production due to modified parton distribution functions in Au and the different isospin composition of the nuclei predict a modest change of R-AA from unity. They are consistent with the data. Models with compensating effects of the quark-gluon plasma on high-energy photons, such as suppression of jet-fragmentation photons and induced-photon bremsstrahlung from partons traversing the medium, are also consistent with this measurement.

Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes

Paraleia was originally described by Tonnoir for P. fulvescens, known from Australia. More recently, eleven Neotropical species were added to the genus-nine of which are from Chile and southern Argentina, one from Bolivia, and one from Peru. This distribution pattern is typical of many mycetophilid genera. Six new Neotropical species of Paraleia from the Andean Colombia and Ecuador are herein described. Male terminalia of P. bolivari sp. n., P. denticulata sp. n., P. fumosa sp. n., and P. tonnoiri sp. n., as well as female terminalia of P. bolivari sp. n., P. denticulata sp. n., P. fumosa sp. n., P. nidorosa sp. n., P. sharkeyi sp. n., and Paraleia sp. are illustrated. High-resolution photos of wings for all species are presented. An identification key for world species of Paraleia is provided.

Direct photon production in p plus p collisions at root s=200 GeV at midrapidity

The differential cross section for the production of direct photons in p + p collisions at root s = 200 GeV at midrapidity was measured in the PHENIX detector at the Relativistic Heavy Ion Collider. Inclusive direct photons were measured in the transverse momentum range from 5: 5-25 GeV/c, extending the range beyond previous measurements. Event structure was studied with an isolation criterion. Next-to-leading-order perturbative-quantum-chromodynamics calculations give a good description of the spectrum. When the cross section is expressed versus x(T), the PHENIX data are seen to be in agreement with measurements from other experiments at different center-of-mass energies.

Seroprevalence and isolation of Toxoplasma gondii from free-range chickens from Espirito Santo state, southeastern Brazil

Prevalence of Toxoplasma gondii infection in 510 free-range (FR) chickens (380 from 33 small farms, and 130 from a slaughter house for FR chickens) from Espirito Santo state, southeastern Brazil, was investigated. Antibodies to T. gondii were sought using commercial indirect haemagglutination (IHAT, Imuno-HAI Toxo (R), Wama Diagnostica, Sao Paulo, Brazil, cut-off 1:16) and the modified agglutination test (MAT, cut-off 1:25) tests. Attempts were made to isolate viable T. gondii from seropositive chickens by bioassay in mice. Pooled samples of brain, heart and quadriceps muscle of one thigh (total 40 g) from 64 chickens with IHAT titers of >= 1:16 were minced, digested in pepsin and bioassayed in mice. Antibodies to T. gondii were found in 40.4% (206/510) FR chickens by IHAT (titer >= 1:16) and 38.8% (198/510) by MAT (titer >= 1:25); concordance between IHAT and MAT was 81.6% (kappa index = 0.614). Viable T. gondii was isolated (designated TgCkBr234-281) from 48 of 64(75%) seropositive (IHAT titers >= 1:32) FR chickens. Most isolates of T. gondii were virulent for mice; 100% of mice inoculated with 44 of 48 isolates died of toxoplasmosis within 30 days post inoculation (p.i). An epidemiological investigation revealed that people living in rural areas have little knowledge about the parasite and about the risk of acquiring it from raw meat. Results indicated that the locally available IHAT was useful for screening of chicken sera for T. gondii antibodies. (C) 2012 Elsevier B.V. All rights reserved.

Quantification of Short and Medium Range Order in Mixed Network Former Glasses of the System GeO2-NaPO3: A Combined NMR and X-ray Photoelectron Spectroscopy Study

Glasses in the system xGeO(2)-(1-x)NaPO3 (0 <= x <= 0.50) were prepared by conventional melting quenching and characterized by thermal analysis, Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), and P-31 nuclear magnetic resonance (MAS NMR) techniques. The deconvolution of the latter spectra was aided by homonuclear J-resolved and refocused INADEQUATE techniques. The combined analyses of P-31 MAS NMR and O-1s XPS lineshapes, taking charge and mass balance considerations into account, yield the detailed quantitative speciations of the phosphorus, germanium, and oxygen atoms and their respective connectivities. An internally consistent description is possible without invoking the formation of higher-coordinated germanium species in these glasses, in agreement with experimental evidence in the literature. The structure can be regarded, to a first approximation, as a network consisting of P-(2) and P-(3) tetrahedra linked via four-coordinate germanium. As implied by the appearance of P-(3) units, there is a moderate extent of network modifier sharing between phosphate and germanate network formers, as expressed by the formal melt reaction P-(2) + Ge-(4) -> P-(3) + Ge-(3). The equilibrium constant of this reaction is estimated as K = 0.52 +/- 0.11, indicating a preferential attraction of network modifier by the phosphorus component. These conclusions are qualitatively supported by Raman spectroscopy as well as P-31{Na-23} and P-31{Na-23} rotational echo double resonance (REDOR) NMR results. The combined interpretation of O-1s XPS and P-31 MAS NMR spectra shows further that there are clear deviations from a random connectivity scenario: heteroatomic P-O-Ge linkages are favored over homoatomic P-O-P and Ge-O-Ge linkages.

Cold-Nuclear-Matter Effects on Heavy-Quark Production in d+Au Collisions at root S-NN=200 GeV

The PHENIX experiment has measured electrons and positrons at midrapidity from the decays of hadrons containing charm and bottom quarks produced in d + Au and p + p collisions at root S-NN = 200 GeV in the transverse-momentum range 0.85 <= p(T)(e) <= 8.5 GeV/c. In central d + Au collisions, the nuclear modification factor R-dA at 1.5 < p(T) < 5 GeV/c displays evidence of enhancement of these electrons, relative to those produced in p + p collisions, and shows that the mass-dependent Cronin enhancement observed at the Relativistic Heavy Ion Collider extends to the heavy D meson family. A comparison with the neutral-pion data suggests that the difference in cold-nuclear-matter effects on light- and heavy-flavor mesons could contribute to the observed differences between the pi(0) and heavy-flavor-electron nuclear modification factors R-AA. DOI: 10.1103/PhysRevLett.109.242301

Cross sections and double-helicity asymmetries of midrapidity inclusive charged hadrons in p plus p collisions at root s = 62.4 GeV

Unpolarized cross sections and double-helicity asymmetries of single-inclusive positive and negative charged hadrons at midrapidity from p + p collisions at root s = 62.4 GeV are presented. The PHENIX measurement of the cross sections for 1.0 < p(T) < 4.5 GeV/c are consistent with perturbative QCD calculations at next-to-leading order in the strong-coupling constant, alpha(s). Resummed pQCD calculations including terms with next-to-leading-log accuracy, yielding reduced theoretical uncertainties, also agree with the data. The double-helicity asymmetry, sensitive at leading order to the gluon polarization in a momentum-fraction range of 0.05 less than or similar to x(gluon) less than or similar to 0.2, is consistent with recent global parametrizations disfavoring large gluon polarization.

Non-mean-field effects in systems with long-range forces in competition

We investigate the canonical equilibrium of systems with long-range forces in competition. These forces create a modulation in the interaction potential and modulated phases appear at the system scale. The structure of these phases differentiate this system from monotonic potentials, where only the mean-field and disordered phases exist. With increasing temperature, the system switches from one ordered phase to another through a first-order phase transition. Both mean-field and modulated phases may be stable, even at zero temperature, and the long-range nature of the interaction will lead to metastability characterized by extremely long time scales.

Entanglement entropy in long-range harmonic oscillators

We study the Von Neumann and Renyi entanglement entropy of long-range harmonic oscillators (LRHO) by both theoretical and numerical means. We show that the entanglement entropy in massless harmonic oscillators increases logarithmically with the sub-system size as S - c(eff)/3 log l. Although the entanglement entropy of LRHO's shares some similarities with the entanglement entropy at conformal critical points we show that the Renyi entanglement entropy presents some deviations from the expected conformal behaviour. In the massive case we demonstrate that the behaviour of the entanglement entropy with respect to the correlation length is also logarithmic as the short-range case. Copyright (c) EPLA, 2012

Suitability of distance metrics as indexes of home-range size in tropical rodent species

Estimators of home-range size require a large number of observations for estimation and sparse data typical of tropical studies often prohibit the use of such estimators. An alternative may be use of distance metrics as indexes of home range. However, tests of correlation between distance metrics and home-range estimators only exist for North American rodents. We evaluated the suitability of 3 distance metrics (mean distance between successive captures [SD], observed range length [ORL], and mean distance between all capture points [AD]) as indexes for home range for 2 Brazilian Atlantic forest rodents, Akodon montensis (montane grass mouse) and Delomys sublineatus (pallid Atlantic forest rat). Further, we investigated the robustness of distance metrics to low numbers of individuals and captures per individual. We observed a strong correlation between distance metrics and the home-range estimator. None of the metrics was influenced by the number of individuals. ORL presented a strong dependence on the number of captures per individual. Accuracy of SD and AD was not dependent on number of captures per individual, but precision of both metrics was low with numbers of captures below 10. We recommend the use of SD and AD instead of ORL and use of caution in interpretation of results based on trapping data with low captures per individual.

Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range

Abstract Background Citrus bacterial canker is a disease that has severe economic impact on citrus industries worldwide and is caused by a few species and pathotypes of Xanthomonas. X. citri subsp. citri strain 306 (XccA306) is a type A (Asiatic) strain with a wide host range, whereas its variant X. citri subsp. citri strain Aw12879 (Xcaw12879, Wellington strain) is restricted to Mexican lime. Results To characterize the mechanism for the differences in host range of XccA and Xcaw, the genome of Xcaw12879 that was completed recently was compared with XccA306 genome. Effectors xopAF and avrGf1 are present in Xcaw12879, but were absent in XccA306. AvrGf1 was shown previously for Xcaw to cause hypersensitive response in Duncan grapefruit. Mutation analysis of xopAF indicates that the gene contributes to Xcaw growth in Mexican lime but does not contribute to the limited host range of Xcaw. RNA-Seq analysis was conducted to compare the expression profiles of Xcaw12879 and XccA306 in Nutrient Broth (NB) medium and XVM2 medium, which induces hrp gene expression. Two hundred ninety two and 281 genes showed differential expression in XVM2 compared to in NB for XccA306 and Xcaw12879, respectively. Twenty-five type 3 secretion system genes were up-regulated in XVM2 for both XccA and Xcaw. Among the 4,370 common genes of Xcaw12879 compared to XccA306, 603 genes in NB and 450 genes in XVM2 conditions were differentially regulated. Xcaw12879 showed higher protease activity than XccA306 whereas Xcaw12879 showed lower pectate lyase activity in comparison to XccA306. Conclusions Comparative genomic analysis of XccA306 and Xcaw12879 identified strain specific genes. Our study indicated that AvrGf1 contributes to the host range limitation of Xcaw12879 whereas XopAF contributes to virulence. Transcriptome analyses of XccA306 and Xcaw12879 presented insights into the expression of the two closely related strains of X. citri subsp. citri. Virulence genes including genes encoding T3SS components and effectors are induced in XVM2 medium. Numerous genes with differential expression in Xcaw12879 and XccA306 were identified. This study provided the foundation to further characterize the mechanisms for virulence and host range of pathotypes of X. citri subsp. citri.

Increased coherence among striatal regions in the theta range during attentive wakefulness

The striatum, the largest component of the basal ganglia, is usually subdivided into associative, motor and limbic components. However, the electrophysiological interactions between these three subsystems during behavior remain largely unknown. We hypothesized that the striatum might be particularly active during exploratory behavior, which is presumably associated with increased attention. We investigated the modulation of local field potentials (LFPs) in the striatum during attentive wakefulness in freely moving rats. To this end, we implanted microelectrodes into different parts of the striatum of Wistar rats, as well as into the motor, associative and limbic cortices. We then used electromyograms to identify motor activity and analyzed the instantaneous frequency, power spectra and partial directed coherence during exploratory behavior. We observed fine modulation in the theta frequency range of striatal LFPs in 92.5 ± 2.5% of all epochs of exploratory behavior. Concomitantly, the theta power spectrum increased in all striatal channels (P < 0.001), and coherence analysis revealed strong connectivity (coefficients >0.7) between the primary motor cortex and the rostral part of the caudatoputamen nucleus, as well as among all striatal channels (P < 0.001). Conclusively, we observed a pattern of strong theta band activation in the entire striatum during attentive wakefulness, as well as a strong coherence between the motor cortex and the entire striatum. We suggest that this activation reflects the integration of motor, cognitive and limbic systems during attentive wakefulness.