Abundance of Diurnal Raptors in Relation to Prairie Dog Colonies: Implications for Bird-Aircraft Strike Hazard

Abstract: Some diurnal raptors are frequently observed at prairie dog (Cynomys sp.) colonies. As a result, some military installations have conducted prairie dog control activities to reduce the bird-aircraft strike hazard (BASH) potential of low-flying aircraft. To evaluate the validity of this management strategy, we assessed raptor associations with prairie dog colonies at 2 short-grass prairie study areas: southern Lubbock County, Texas, USA, and Melrose Bombing and Gunnery Range in east-central New Mexico, USA. We quantified diurnal raptors (i.e., Falconiformes) at plots occupied (colony plots) and unoccupied (noncolony plots) by black-tailed prairie dogs (Cynomys ludovicianus) at both sites throughout 2002. We compared the number of individual birds of a given species at colony and noncolony plots within each study area by season. Ferruginous hawks (Buteo regalis) and northern harriers (Circus cyaneus) were more abundant at colony plots, whereas Swainson's hawks (B. swainsoni) and American kestrels (Falco sparverius) were more abundant at noncolony plots. Red-tailed hawk (B. jamaicensis) abundance did not differ between the 2 plot types. Our results suggest prairie dog control as a method of reducing BASH potential may be effective at some sites but may be ineffective or even increase the BASH potential at others. Thus, bird-avoidance models assessing the BASH potential should be conducted on a site-specific basis using information on relative and seasonal abundances of individual raptor species and the relative strike risks they pose to aircraft.     

Implications of Nubian-Like Core Reduction Systems in Southern Africa for the Identification of Early Modern Human Dispersals

Lithic technologies have been used to trace dispersals of early human populations within and beyond Africa. Convergence in lithic systems has the potential to confound such interpretations, implying connections between unrelated groups. Due to their reductive nature, stone artefacts are unusually prone to this chance appearance of similar forms in unrelated populations. Here we present data from the South African Middle Stone Age sites Uitpanskraal 7 and Mertenhof suggesting that Nubian core reduction systems associated with Late Pleistocene populations in North Africa and potentially with early human migrations out of Africa in MIS 5 also occur in southern Africa during early MIS 3 and with no clear connection to the North African occurrence. The timing and spatial distribution of their appearance in southern and northern Africa implies technological convergence, rather than diffusion or dispersal. While lithic technologies can be a critical guide to human population flux, their utility in tracing early human dispersals at large spatial and temporal scales with stone artefact types remains questionable.     

Distribution-abundance relationship for passerines breeding in Tunisian oases: test of the sampling hypothesis

The positive relationship between local abundance and distribution of species is a widely recognized pattern in community ecology. However, it has been suggested that this relationship can simply be an artefact of sampling because locally rare species are less detectable then locally abundant ones, and hence their distribution can easily be underestimated. Here, we use count data to investigate the relationship between distribution and abundance of passerines breeding in a sample of oases from southern Tunisia, and we provide a test of the sampling artefact hypothesis. In particular, we checked for a difference in detection probability between localized and widespread species, and we tested if increasing the sampling effort affects the significance of the relationship. A significant positive relationship between the average local abundance of passerine species and the proportion of occupied oases was found. The use of a capture-recapture approach allowed us to estimate and to compare the detection probabilities of localized and widespread species subsets. We found that localized species were locally less detectable than widespread species, which is consistent with the main assumption of the sampling artefact hypothesis. However, increasing the detection probability of species by conducting more counts did not affect the significance of the relationship, which did not give support to the sampling artefact hypothesis. Our work implies that sampling contributed to the distribution-abundance relationship we found, but that it is unlikely that such a relationship could entirely be explained by an artefact of sampling. It also underlines the insight that can be gained by using probabilistic approaches of estimating species number and detection probability when attempting to disentangle sampling from ecological effects in community ecology studies.     

Detection and correction of probe-level artefacts on microarrays

ABSTRACT: BACKGROUND: A recent large-scale analysis of Gene Expression Omnibus (GEO) data found frequent evidence for spatial defects in a substantial fraction of Affymetrix microarrays in the GEO. Nevertheless, in contrast to quality assessment, artefact detection is not widely used in standard gene expression analysis pipelines. Furthermore, although approaches have been proposed to detect diverse types of spatial noise on arrays, the correction of these artefacts is mostly left to either summarization methods or the corresponding arrays are completely discarded. RESULTS: We show that state-of-the-art robust summarization procedures are vulnerable to artefacts on arrays and cannot appropriately correct for these. To address this problem, we present a simple approach to detect artefacts with high recall and precision, which we further improve by taking into account the spatial layout of arrays. Finally, we propose two correction methods for these artefacts that either substitute values of defective probes using probeset information or filter corrupted probes. We show that our approach can identify and correct defective probe measurements appropriately and outperforms existing tools. CONCLUSIONS: While summarization is insufficient to correct for defective probes, this problem can be addressed in a straightforward way by the methods we present for identification and correction of defective probes. As these methods output CEL files with corrected probe values that serve as input to standard normalization and summarization procedures, they can be easily integrated into existing microarray analysis pipelines as an additional pre-processing step. An R package is freely available from http://www.bio.ifi.lmu.de/artefact-correction.     

A fast bilateral filter with application to artefact reduction

Elastography in medical ultrasound is an imaging technique that displays information about tissue stiffness. However, elastography suffers from artefact noise that may come from two dominant sources: decorrelation error and amplitude modulation error. In order to reduce artefact and improve the quality of ultrasonic elastography, a fast bilateral filter is proposed in this study based on local histogram. The presented filter is derived from a conventional bilateral filter, and a local histogram is introduced to speed up the filter. The proposed algorithm can reduce artefact noise and, at the same time, maintain the tissue structure. Both simulation and phantom testing show that the proposed method can improve the quality of ultrasonic elastography in terms of tissue elastographic signal-to-noise ratio and elastographic contrast-to-noise ratio values.     

lumi: a pipeline for processing Illumina microarray

Illumina microarray is becoming a popular microarray platform. The BeadArray technology from Illumina makes its preprocessing and quality control different from other microarray technologies. Unfortunately, most other analyses have not taken advantage of the unique properties of the BeadArray system, and have just incorporated preprocessing methods originally designed for Affymetrix microarrays. lumi is a Bioconductor package especially designed to process the Illumina microarray data. It includes data input, quality control, variance stabilization, normalization and gene annotation portions. In specific, the lumi package includes a variance-stabilizing transformation (VST) algorithm that takes advantage of the technical replicates available on every Illumina microarray. Different normalization method options and multiple quality control plots are provided in the package. To better annotate the Illumina data, a vendor independent nucleotide universal identifier (nuID) was devised to identify the probes of Illumina microarray. The nuID annotation packages and output of lumi processed results can be easily integrated with other Bioconductor packages to construct a statistical data analysis pipeline for Illumina data. Availability: The lumi Bioconductor package, www.bioconductor.org     

Removal of Pulse Artefact from EEG Data Recorded in MR Environment at 3T. Setting of ICA Parameters for Marking Artefactual Components: Application to Resting-State Data

Simultaneous electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) allow for a non-invasive investigation of cerebral functions with high temporal and spatial resolution. The main challenge of such integration is the removal of the pulse artefact (PA) that affects EEG signals recorded in the magnetic resonance (MR) scanner. Often applied techniques for this purpose are Optimal Basis Set (OBS) and Independent Component Analysis (ICA). The combination of OBS and ICA is increasingly used, since it can potentially improve the correction performed by each technique separately. The present study is focused on the OBS-ICA combination and is aimed at providing the optimal ICA parameters for PA correction in resting-state EEG data, where the information of interest is not specified in latency and amplitude as in, for example, evoked potential. A comparison between two intervals for ICA calculation and four methods for marking artefactual components was performed. The performance of the methods was discussed in terms of their capability to 1) remove the artefact and 2) preserve the information of interest. The analysis included 12 subjects and two resting-state datasets for each of them. The results showed that none of the signal lengths for the ICA calculation was highly preferable to the other. Among the methods for the identification of PA-related components, the one based on the wavelets transform of each component emerged as the best compromise between the effectiveness in removing PA and the conservation of the physiological neuronal content.     

Non-linear analysis of epileptic seizures I. Correlation-dimension measurements for absence epilepsy and near-periodic signals

The study of six absence seizures from two patients confirmed the efficacy, in the search for low correlation dimensions, of using scaled-structure analysis, combined with the appropriate checking procedures. The analysis is directed towards characterizing an attractor not only by its correlation dimension, but also by its “quality” and by the probability for genuine identification. For near-periodic dynamics, we warn against: (1) artefacts that appear at high values of the correlation integral, in the form of apparent Grassberger-Procaccia scaling at very low values of the dimension (near-periodicity artefact); (2) erroneous interpretation of phase-randomization data, owing to destruction of the artefact by randomization rather than any evidence for low-dimensional dynamics. In single-channel analyses of two patients and six seizures altogether, high-quality attractors were found only for one seizure in two channels, at correlation dimensions 4.7 and 6, respectively. Furthermore, no attractor of measurable dimension was found from multichannel space reconstructions over durations approaching those of typical seizures. Both these results show that in an absence seizure, spatial extension of low-dimensional dynamics must be lost over such durations. Received: 27 April 1998 / Accepted in revised form: 10 November 1998     

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

High-throughput molecular technologies can profile microbial communities at high resolution even in complex environments like the intestinal microbiota. Recent improvements in next-generation sequencing technologies allow for even finer resolution. We compared phylogenetic profiling of both longer (454 Titanium) sequence reads with shorter, but more numerous, paired-end reads (Illumina). For both approaches, we targeted six tandem combinations of 16S rRNA gene variable regions, in microbial DNA extracted from a human faecal sample, in order to investigate their limitations and potentials. In silico evaluations predicted that the V3/V4 and V4/V5 regions would provide the highest classification accuracies for both technologies. However, experimental sequencing of the V3/V4 region revealed significant amplification bias compared to the other regions, emphasising the necessity for experimental validation of primer pairs. The latest developments of 454 and Illumina technologies offered higher resolution compared to their previous versions, and showed relative consistency with each other. However, the majority of the Illumina reads could not be classified down to genus level due to their shorter length and higher error rates beyond 60 nt. Nonetheless, with improved quality and longer reads, the far greater coverage of Illumina promises unparalleled insights into highly diverse and complex environments such as the human gut.     

Culture and cognition in the Acheulian industry: a case study from Gesher Benot Ya'aqov

The Acheulian presence in the Dead Sea Rift and its environs is characterized by the discontinuity of its cultural manifestations. Nevertheless, the long stratigraphic sequences of the Acheulian Technocomplex provide a unique opportunity for synergetic examination along a temporal trajectory. Hominin cognitive and cultural behaviour are studied at Gesher Benot Ya'aqov through analyses of lithic, palaeontological and palaeobotanical assemblages, as well as the Early-Middle Pleistocene environment, ecology and climate. The study attempts to reconstruct reduction sequences of some major artefact groups at the site, which include raw material acquisition, production, technology, typology, usage and discard. Experimental archaeology illustrates artefact mobility on the palaeo-landscape. Strategies of biomass-exploitation are studied in detail, with other aspects yielding additional information on hominin subsistence and adaptive responses to their environment. The cultural marker of fire and the spatial association of selected categories of finds are integrated in the general synthesis, allowing reconstruction of the cultural and cognitive realm of Acheulian hominins. The synthesis attempts to reassess the abilities, social structure, subsistence and adaptability to the changing environment of hominins in the Levantine Corridor.     

Parasitism and the burrowing depth of the beach hopper Talorchestia quoyana (Amphipoda: Talitridae)

Talitrid amphipods spend their days burrowed in sand to avoid predators as well as desiccation and heat stress, although other factors may influence burrowing depth. We investigated the potential role of mermithid nematode parasites in determining burrowing depth in the amphipod Talorchestia quoyana. Mermithids grow as parasites inside amphipods until they reach adulthood, when they must emerge from their host into moist sand to complete their life cycle and reproduce. When allowed to burrow to a depth of their choice in experimental situations, large amphipods burrowed deeper than small ones. In addition, deep-burrowing amphipods were more likely to be infected by mermithid nematodes, and harboured longer worms, on average, than amphipods that burrowed close to the sand surface. This last result is not an artefact of the larger size of deep-burrowing amphipods: the increase in worm length with increasing depth was found after statistical correction for host size. In other words, amphipods that burrowed deeper harboured longer worms than expected based on their body size, whereas those that stayed near the surface of the sand column harboured worms shorter than one would expect based on host size. This implies that the greater burrowing depth of infected amphipods is a consequence, and not a cause, of infection. These results emphasize the importance of parasitism as a determinant of the small-scale spatial distribution of their hosts.     

Le travail des matières d’origine dure animale dans le Magdalénien Morave : l’exemple des aiguilles à chas

Needles made from hard animal tissues are a stereotyped artefact; they have been found in six caves of the Moravian Karst / Czech Republic (Pekárna, ?itného, K?lna, Bý?í skála, Verun?ina, K?í?ova) containing Magdalenian layers. The paper deals with the technology of the production of these objects on the example of the Pekárna cave that has provided a lot of these artefacts in various degrees of wear, fragments, exploitation matrices and uncompleted needles. By the mean of spatial analysis we try to reconstitute the original context in the cave and insert the concerned artefact into the frame of the exploitation, treatment and utilisation of hard animal tissues by Magdalenian hunters in Moravia.     

Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data

Background  

A key stage for all microarray analyses is the extraction of feature-intensities from an image. If this step goes wrong, then subsequent preprocessing and processing stages will stand little chance of rectifying the matter. Illumina employ random construction of their BeadArrays, making feature-intensity extraction even more important for the Illumina platform than for other technologies. In this paper we show that using raw Illumina data it is possible to identify, control, and perhaps correct for a range of spatial-related phenomena that affect feature-intensity extraction.     

Solution-based targeted genomic enrichment for precious DNA samples

ABSTRACT: BACKGROUND: Solution-based targeted genomic enrichment (TGE) protocols permit selective sequencing of genomic regions of interest on a massively parallel scale. These protocols could be improved by: 1) modifying or eliminating time consuming steps; 2) increasing yield to reduce input DNA and excessive PCR cycling; and 3) enhancing reproducible. RESULTS: We developed a solution-based TGE method for downstream Illumina sequencing in a non-automated workflow, adding standard Illumina barcode indexes during the post-hybridization amplification to allow for sample pooling prior to sequencing. The method utilizes Agilent SureSelect baits, primers and hybridization reagents for the capture, off-the-shelf reagents for the library preparation steps, and adaptor oligonucleotides for Illumina paired-end sequencing purchased directly from an oligonucleotide manufacturing company. CONCLUSIONS: This solution-based TGE method for Illumina sequencing is optimized for small- or medium-sized laboratories and addresses the weaknesses of standard protocols by reducing the amount of input DNA required, increasing capture yield, optimizing efficiency, and improving reproducibility.     

Investigating species–environment relationships at multiple scales: Differentiating between intrinsic scale and the modifiable areal unit problem

In ecology, multi-scale analyses are commonly performed to identify the scale at which a species interacts with its environment (intrinsic scale). This is typically carried out using multi-scale species–environment models that compare the relationship between ecological attributes (e.g., species diversity) measured with point data to environmental data (e.g. vegetation cover) for the surrounding area within buffers of multiple sizes. The intrinsic scale is identified as the buffer size at which the highest correlation between environmental and ecological variables occurs. We present the first investigation of how the spatial resolution of remote sensing environmental data can influence the identification of the intrinsic scale using multi-scale species–environment models. Using the virtual ecologist approach we tested this influence using vegetation cover spatial data and a simulated species–environment relationship derived from the same spatial data. By using a simulation model there was a known truth to use as a benchmark to measure accuracy. Our findings indicate that by varying the spatial resolution of the environmental data, the intrinsic scale may be incorrectly identified. In some cases, the errors in the intrinsic scale identified were close to the maximum value possible that could be measured by this experiment. Consequently, multi-scale ecological analyses may not be suitable for distinguishing scale patterns caused by the relationship between an organism and its environment from scale patterns caused by the effect of changing spatial resolution: a phenomenon referred to as the modifiable areal unit problem (MAUP). Thus, observed scale-dependent ecological patterns may be an artefact of the observation of ecological data, not the ecological phenomenon. This study concludes with some suggestions for future work to quantify the effect of the MAUP on multi-scale studies and develop generalisations that can be used to assess when multi-scale analyses have the potential to produce spurious results.     

Model-based variance-stabilizing transformation for Illumina microarray data

Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit the performance of subsequent statistical modeling and inference. Due to the often limited number of technical replicates for Affymetrix and cDNA arrays, achieving variance stabilization can be difficult. Although the Illumina microarray platform provides a larger number of technical replicates on each array (usually over 30 randomly distributed beads per probe), these replicates have not been leveraged in the current log2 data transformation process. We devised a variance-stabilizing transformation (VST) method that takes advantage of the technical replicates available on an Illumina microarray. We have compared VST with log2 and Variance-stabilizing normalization (VSN) by using the Kruglyak bead-level data (2006) and Barnes titration data (2005). The results of the Kruglyak data suggest that VST stabilizes variances of bead-replicates within an array. The results of the Barnes data show that VST can improve the detection of differentially expressed genes and reduce false-positive identifications. We conclude that although both VST and VSN are built upon the same model of measurement noise, VST stabilizes the variance better and more efficiently for the Illumina platform by leveraging the availability of a larger number of within-array replicates. The algorithms and Supplementary Data are included in the lumi package of Bioconductor, available at: www.bioconductor.org.     

Mechanisms linking diversity,productivity and invasibility in experimental bacterial communities

Decreasing species diversity is thought to both reduce community productivity and increase invasibility to other species. However, it remains unclear whether identical mechanisms drive both diversity-productivity and diversity-invasibility relationships. We found a positive diversity-productivity relationship and negative diversity-invasibility and productivity-invasibility relationships using microcosm communities constructed from spatial niche specialist genotypes of the bacterium Pseudomonas fluorescens. The primary mechanism driving these relationships was a dominance (or selection) effect: more diverse communities were more likely to contain the most productive and least invasible type. Statistical elimination of the dominance effect greatly weakened the diversity-invasibility relationship and eliminated the diversity-productivity relationship, but also revealed the operation of additional mechanisms (niche complementarity, positive and negative interactions) for particular combinations of niche specialists. However, these mechanisms differed for invasibility and productivity responses, resulting in the invasibility-productivity relationship changing from strongly negative to weakly positive. In the absence of the dominance effect, which may be an experimental artefact, decreasing diversity can have unexpected or no effects on ecosystem properties.