Abundance Estimation With a Transient Model Under the Robust Design

Abstract: A common situation in capture-mark-recapture (CMR) studies on birds and other organisms is to capture individuals not belonging to the studied population only present during the short time of the capture session. Presence of such transient individuals affects demographic parameter estimation from CMR data. Methods exist to reduce biases on survival estimates in the presence of transients and have been shown to be particularly efficient within the Robust Design framework (several secondary capture sessions within a short time interval during which the studied population can be assumed closed). We present a new model to estimate population size accounting for transients. We first used simulated data to show that the method reduces positive biases due to transients. In a second step, we applied the method to a real CMR dataset on a reed warbler (Acrocephalus scirpaceus) population. Population size estimates are reduced by up to 50% when correcting for the presence of transients. Many field studies on managed animal populations use capture-recapture methodology to obtain crucial parameters of the focal population demography. The resulting data sets are used either to estimate population size ignoring the presence of transients, or to estimate vital rates, accounting for transients but overlooking abundance estimation. Our method conciliates these 2 approaches.     

Computational approaches from polymer physics to investigate chromatin folding

Microscopy and sequencing-based technologies are providing increasing insights into chromatin architecture. Nevertheless, a full comprehension of chromosome folding and its link with vital cell functions is far from accomplished at the molecular level. Recent theoretical and computational approaches are providing important support to experiments to dissect the three-dimensional structure of chromosomes and its organizational mechanisms. Here, we review, in particular, the String&Binders polymer model of chromatin that describes the textbook scenario where contacts between distal DNA sites are established by cognate binders. It has been shown to recapitulate key features of chromosome folding and to be able at predicting how phenotypes causing structural variants rewire the interactions between genes and regulators.     

Predictive modeling for allopatric Strix (Strigiformes: Strigidae) owls in South America: determinants of their distributions and ecological niche‐based processes

Strix (Strigidae) is a worldwide genus of 17 owl species typical of forested habitats, including Rusty‐barred Owls (S. hylophila), Chaco Owls (S. chacoensis), and Rufous‐legged Owls (S. rufipes) in South America. These species are distributed allopatrically, but the ecological traits that determine their distributions remain largely unknown and their phylogenetic relationships are unclear. We used species distribution models (SDMs) to identify variables explaining their distribution patterns and test hypotheses about ecological divergence and conservatism based on niche overlap analysis. For Rusty‐barred Owls and Chaco Owls, climatic factors related to temperature played a major role, whereas a rainfall variable was more important for Rufous‐legged Owls. When niche overlaps were compared, accounting for regional similarities in the habitat available to each species, an ecological niche divergence process was supported for Chaco Owl‐Rusty‐barred Owl and Chaco Owl‐Rufous‐legged Owl, whereas a niche conservatism process was supported for Rusty‐barred Owl‐Rufous‐legged Owl. Different ecological requirements support current species delimitation, but they are in disagreement with the two main hypotheses currently envisaged about their phylogenetic relationships (Chaco Owls as the sister taxa of either Rufous‐legged Owls or Rusty‐barred Owls) and support a new phylogenetic hypothesis (Rufous‐legged Owls as sister taxa of Rusty‐barred Owls). Our findings suggest that speciation of Rusty‐barred Owls and Rufous‐legged Owls was a vicariant event resulting from Atlantic marine transgressions in southern South America in the Miocene, but their niche was conserved because habitat changed little in their respective ranges. In contrast, Chaco Owls diverged ecologically from the other two species as a result of their adaptations to the habitat they currently occupy. Ecological and historical approaches in biogeography can be embedded to explain distribution patterns, and results provided by SDMs can be used to infer historical and ecological processes in an integrative way.     

Performance of the marginal structural models under various scenarios of incomplete marker's values: A simulation study

Marginal structural models (MSMs) have been proposed for estimating a treatment's effect, in the presence of time‐dependent confounding. We aimed to evaluate the performance of the Cox MSM in the presence of missing data and to explore methods to adjust for missingness. We simulated data with a continuous time‐dependent confounder and a binary treatment. We explored two classes of missing data: (i) missed visits, which resemble clinical cohort studies; (ii) missing confounder's values, which correspond to interval cohort studies. Missing data were generated under various mechanisms. In the first class, the source of the bias was the extreme treatment weights. Truncation or normalization improved estimation. Therefore, particular attention must be paid to the distribution of weights, and truncation or normalization should be applied if extreme weights are noticed. In the second case, bias was due to the misspecification of the treatment model. Last observation carried forward (LOCF), multiple imputation (MI), and inverse probability of missingness weighting (IPMW) were used to correct for the missingness. We found that alternatives, especially the IPMW method, perform better than the classic LOCF method. Nevertheless, in situations with high marker's variance and rarely recorded measurements none of the examined method adequately corrected the bias.     

Ruptured fission yeast walls

Distributions of rupture sites of fission yeast cells ruptured by glass beads have been related to a new morphometric analysis. As shown previously (Johnson et al.,Cell Biophysics, 1995), ruptures were not randomly distributed nor was their distribution dictated by geometry, rather, ruptures at the extensile end were related to cell length just as the rate of extension is related to cell length. The extension patterns of early log, mid-log, late log, and stationary phase cells from suspension cultures were found to approximate the linear growth patterns of Kubitschek and Clay (1986). The median length of cells was found to decline through the log phase in an unbalanced manner.     

Climatic patterns in the establishment of wintering areas by North American migratory birds

Long‐distance migration in birds is relatively well studied in nature; however, one aspect of this phenomenon that remains poorly understood is the pattern of distribution presented by species during arrival to and establishment of wintering areas. Some studies suggest that the selection of areas in winter is somehow determined by climate, given its influence on both the distribution of bird species and their resources. We analyzed whether different migrant passerine species of North America present climatic preferences during arrival to and departure from their wintering areas. We used ecological niche modeling to generate monthly potential climatic distributions for 13 migratory bird species during the winter season by combining the locations recorded per month with four environmental layers. We calculated monthly coefficients of climate variation and then compared two GLM (generalized linear models), evaluated with the AIC (Akaike information criterion), to describe how these coefficients varied over the course of the season, as a measure of the patterns of establishment in the wintering areas. For 11 species, the sites show nonlinear patterns of variation in climatic preferences, with low coefficients of variation at the beginning and end of the season and higher values found in the intermediate months. The remaining two species analyzed showed a different climatic pattern of selective establishment of wintering areas, probably due to taxonomic discrepancy, which would affect their modeled winter distribution. Patterns of establishment of wintering areas in the species showed a climatic preference at the macroscale, suggesting that individuals of several species actively select wintering areas that meet specific climatic conditions. This probably gives them an advantage over the winter and during the return to breeding areas. As these areas become full of migrants, alternative suboptimal sites are occupied. Nonrandom winter area selection may also have consequences for the conservation of migratory bird species, particularly under a scenario of climate change.     

Rate transition and regulatory coupling in endocytosis of interferon-alpha and tumor necrosis factor-alpha in human epithelial tumor cells.

The time-dependent concentrations of interferon-alpha and tumor necrosis factor-alpha associated with the membrane and internalized by cells contain information on the kinetics of endocytosis and their cellular processing. This information can be reduced quantitatively by application of the respective compartmental models. In our studies of human epithelial tumor cells interacting with human interferon-alpha and human tumor necrosis factor-alpha, we accounted only for actual endocytosis and elimination of the tracer from cells by a novel method sensitive to changes in the rate of endocytosis, to the delay in tracer elimination, and to the nonlinear regulatory coupling between endocytosis and the internalized ligand. Data reduced by this method resulted in best-fit parameter values statistically superior to values obtained by previous methods (Bajzer et al., 1989). The results indicate a change with time in the rate of endocytosis of tumor necrosis factor-alpha and the inhibition of endocytosis by the endocytosed ligand-receptor complex. We conclude that sorting and processing of interferon-alpha and tumor necrosis factor-alpha are restricted by the type of both the receptor and the cell.     

Transitions: Homo erectus and the Acheulian: the Ethiopian sites of Gadeb and the Middle Awash

Significant differences in activity-site patterning and artifact composition at Middle Pleistocene localities in Ethiopia's high plains and Afar Rift are indications of both single-episode, small-site residues from small groups and multi-purpose, multiple occupation sites from which larger, temporary groupings might be inferred. Reconstructions of palaeo-environments and geography show that large assemblages relate to relatively stable topography, such as stream channels or lake margins, while small assemblages are more common in deltaic situations of rapid sedimentation and burial in the Rift that preclude possibility of reoccupation. A model for Acheulian socio-economic behaviour within the drier African savanna, based (in part) on chimpanzee behaviour in open savanna habitats, is proposed. This takes the form of organization into relatively extensive territories, each with several more closed-vegetation core areas, of limited extent close to permanent water, surrounded by more extensive areas of drier, open savanna, regularly exploited and patrolled by small groups. Movement from one core area to another was rapid and made together as a group, to minimize danger from large predators and competition from other hominid groups.