Assessing the effect of sound file compression and background noise on measures of acoustic signal structure

The study of animal acoustic signals is a central tool for many fields in ecology and evolution, but the diversity of analytical methods and sources of animal sound recordings poses important challenges for carrying out robust acoustic analyses. Sound file compression and background noise may both affect acoustic analysis, although little attention has been paid to their respective effects. We evaluated the effect of these factors by assessing the systematic deviation (i.e. bias) and measurement error (i.e. precision) that they generate on spectrographic parameters and two (dis)similarity methods (dynamic time warping on frequency contours and cross-correlation), which represent the most common methods currently used for quantitative characterization of acoustic signals. Measurements were taken across a wide range of signals from a diverse group of bird species, and compared between uncompressed files and decompressed files obtained from mp3-encoded files generated using the two most common mp3 encoders (Fraunhofer and LAME). Measurements were also compared across a range of synthetically-generated background noise levels. Compression did not significantly bias any of the acoustic or similarity measurements. However, the precision of acoustic parameters representing single extreme values (e.g. peak frequency) as well as dynamic time warping distances, was strongly affected by compression. High background noise biased most energy distribution-related parameters (e.g. spectral entropy) and affected the precision of most acoustic parameters and dynamic time warping. Overall, compression and background noise did have considerable effects on acoustic analyses. We provide recommendations to avoid potential pitfalls and maximize the information that can be reliably obtained.     

Relative contribution of rainfall and coconut hybrids to the abundance and composition of the Auchenorrhyncha community as potential vectors of phytoplasmas in the state of Sergipe,Brazil

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Identification of flavonoids as regulators of YbeY activity in Liberibacter asiaticus

Liberibacter asiaticus is the prevalent causative pathogen of Huanglongbing or citrus greening disease, which has resulted in a devastating crisis in the citrus industry. A thorough understanding of this pathogen's physiology and mechanisms to control cell survival is critical in the identification of therapeutic targets. YbeY is a highly conserved bacterial RNase that has been implicated in multiple roles. In this study, we evaluated the biochemical characteristics of the L. asiaticus YbeY (CLIBASIA_01560) and assessed its potential as a target for antimicrobials. YbeY_Las was characterized as an endoribonuclease with activity on 3′ and 5′ termini of 16S and 23S rRNAs, and the capacity to suppress the E. coli ΔybeY phenotype. We predicted the YbeY_Las protein:ligand interface and subsequently identified a flavone compound, luteolin, as a selective inhibitor. Site-directed mutagenesis was subsequently used to identify key residues involved in the catalytic activity of YbeY_Las. Further evaluation of naturally occurring flavonoids in citrus trees indicated that both flavones and flavonols had potent inhibitory effects on YbeY_Las. Luteolin was subsequently examined for efficacy against L. asiaticus in Huanglongbing-infected citrus trees, where a significant reduction in L. asiaticus gene expression was observed.     

Riparian zone as a main determinant of the structure of lizard assemblages in upland Amazonian forests

The use of lizards as model organisms in ecological studies is based on their success in occupying a great diversity of habitats, and some species are closely tied to the environment, which is disadvantaged by the legislation of several countries concerning land use. Our aim was to relate lizard species distribution patterns in rainforest environments to variation in environmental gradients, and provide ecologically based metrics for establishing buffer zones around streams. Lizards were sampled three times in 41 standardised transects near Manaus, Brazil, only in dry season, with Time Limited Visual Search associated with raking through leaf litter. We recorded 20 species from 10 families and used non‐metric multidimensional scaling to reduce the dimensionality of quantitative and qualitative compositions of species. Multiple linear regression models indicated that the environmental gradients distance to nearest stream, extent of canopy openness, vegetation density and slope did not significantly influence assemblage species distribution, with an indication of effect of litter depth. By means of piecewise linear regression, the use of riparian zone was estimated at ~190 m from quantitative species composition and ~211 m from qualitative species composition. Five species occurred only in the riparian zone. Our results suggest that conservation of the entire riparian lizard assemblage in Amazonian rainforest is likely to require protection of at least a 211 m buffer on either side of streams.     

Contrasting responses of plants and pollinators to woodland disturbance

Preserving species diversity is critical to ensure ecosystem functioning; however, different components of diversity might respond to human disturbance in different ways. Similarly, trophic levels might have uncoupled responses to the same disturbance, thus ameliorating or aggravating the persistence of ecological communities. In this study, we analysed how the density, richness and evenness of flowers and pollinators respond to four levels of woodland thinning intensity (0, 30, 50 and 70% of woodland basal area removed) over 2 years in three contrasting sites. We found a mismatch in the response of flowers and pollinators to thinning. Flower density and richness had disparate responses, depending on the site and year, while evenness did not change with thinning. In contrast, pollinator density and richness, but not evenness, consistently increased with thinning among years and sites. These results suggest that thinning has a great influence on pollinators through changes in abiotic conditions and, perhaps, flower attractiveness rather than through small‐scale changes in flower density and richness. At the site where tree flowers were absent, bee pollinator community composition was impoverished, suggesting that trees provide important floral resources to pollinators. Our findings indicate that disturbance may diminish local plant abundance and richness, but pollinator abundance and richness are enhanced after intense thinning at small scales.     

The growth ring concept: seeking a broader and unambiguous approach covering tropical species

The concept of growth rings is little discussed in the literature and their treatment remains somewhat confusing in terms of the diversity of structures described. This situation has a major impact on the study of growth rings in tropical species, in which variations and complexity are greater and accuracy of identification less good. The rigid conceptual delimitations used by dendrochronologists and wood anatomists of temperate regions cannot be applied to the study of growth rings in most tropical species, which has led to neglect of this subject. With the objective of discussing the concept of growth rings, the present study consists of a survey of anatomical, periodicity, causal and evolutionary aspects of the treatment of these structures as evidenced in previous studies, and the evaluation of their application and limitations to the development of this concept. Anatomical aspects arise through radial integrity, or the presence of early and late wood; the degree of distinction of the rings, which may vary from well to poorly defined; and tangential continuity, meaning that rings may form a complete circle in the transverse section of the trunk, or instead be tangentially discontinuous, lens‐shaped or in wedges. In addition there are a diversity of anatomical markers which enable us to recognize growth rings. Regarding periodicity, the rings may be annual, infra‐annual or supra‐annual. Causal aspects include genetic, endogenous and environmental components. Evolutionary aspects continue to be insufficiently investigated, and although most comparative studies treat growth rings recognized by different markers as though they were a single character, it remains questionable whether they can be regarded as homologous or the result of homoplasy. We conclude that the elaboration of a robust but broad definition which can include all the variation observed in growth rings of tropical species is a complex task, which is only possible by overcoming the restrictions adopted by dendrochronologists and wood anatomists of temperate regions for whom growth rings are essentially annual, strongly demarcated, tangentially continuous and restricted to the most pronounced markers.     

Stress distribution of three-unit fixed partial prostheses (conventional and pontic) supported by three or two implants: 3D finite element analysis of ductile materials

In implantology, when financial or biological feasibility limitations appear, it is necessary to use prostheses with geometries that deviate from the conventional, with a pontic in the absence of an intermediate implant. The aim of this study was analyze and understand the general differences in the stresses generated in implants, components and infrastructures according to the configuration of the prosthesis over three or two implants. Thus, this paper analyzes the von Mises equivalent stresses (VMES) of ductile materials on their external surfaces. The experimental groups: Regular Splinted Conventional Group (RCG), which had conventional infrastructures on 3 regular-length Morse taper implants (4x11?mm); Regular Splinted Pontic Group (RPG), which had infrastructures with intermediate pontics on 2 regular-length Morse taper implants (4x11?mm). The simulations of the groups were created with Ansys Workbench 10.0 software. The results revealed that the RPG presented greater areas of possible fragility due to higher stress concentrations, for example, in the cervical area of the union between the implant and component the top platform of the abutment, as well as greater coverage of the stress by the cervical implant threads. The RPG infrastructure was also more affected by stresses in the connection areas between the prostheses and on the occlusal surface. There is an advantage to using prostheses supported by a greater number of implants (RCG) because this decreases the stress in the analyzed structures and consequently improves stress dissipation to the supporting bone, which would preserve the system.     

Habitat use of the ocelot (Leopardus pardalis) in Brazilian Amazon

Amazonia forest plays a major role in providing ecosystem services for human and sanctuaries for wildlife. However, ongoing deforestation and habitat fragmentation in the Brazilian Amazon has threatened both. The ocelot is an ecologically important mesopredator and a potential conservation ambassador species, yet there are no previous studies on its habitat preference and spatial patterns in this biome. From 2010 to 2017, twelve sites were surveyed, totaling 899 camera trap stations, the largest known dataset for this species. Using occupancy modeling incorporating spatial autocorrelation, we assessed habitat use for ocelot populations across the Brazilian Amazon. Our results revealed a positive sigmoidal correlation between remote‐sensing derived metrics of forest cover, disjunct core area density, elevation, distance to roads, distance to settlements and habitat use, and that habitat use by ocelots was negatively associated with slope and distance to river/lake. These findings shed light on the regional scale habitat use of ocelots and indicate important species–habitat relationships, thus providing valuable information for conservation management and land‐use planning.