Planning tendon paths using an interactive graphic workstation

This study provides a technique to be used for planning tendon paths in thumb reconstruction surgery. All mathematical modeling computations are performed on a VAX 11/750 host computer and the graphic manipulation is carried out by the Evans & Sutherland PS390 color display system. The results of the simulation are stored in a log file, including the rotation angles of the joints and the location of the pulley and the insertion points as a record of the tendon transfer design for a specific hand. The methods are based on the modeling of two separate types of tendon paths that consist of straight line segments and curved segments that follow bone contours. The method further assumes that the path of the tendon will always evolve to a planar curve. By integrating this technique with an existing kinematic model of the hand derived from CT-scans, a clinically relevant method has been developed.     

Planning and design of ecological networks in urban areas

Urban ecological networks are defined differently in ecology, urban planning and landscape ecology, but they all have linearity and linkage in common. Early urban representations evolved from the constraints of deep ecological structure in the landscape to built elements that must work around natural linear obstacles—rivers, coastlines, dunes, cliffs, hills and valley swamps. Village commons were linked by roads. The Industrial Revolution led to accelerating urban growth, where the role of open space focussed on public health and transport. The Renaissance, Baroque and Picturesque movements accentuated networks in wooded parks, boulevards and sweeping riverine vistas. These provided a new aesthetic and sense of grandeur in the urban centres of European empires and later their colonies. Grafted onto this visual connectivity has been an awakened ecological understanding of spatial dynamics. The emergent notion of ecological corridor functionality provided support for green linear features, although initially this was based on untested theory. The idea of organisms moving along green highways seemed logical, but only recently has unequivocal empirical evidence emerged that demonstrates this functionality. Nevertheless, the main role of corridors may be to provide habitat rather than to act as connectors of nodal habitats. Most organisms can utilise stepping stones, and these may accommodate desired meta-populations while deterring pest movement. Swale drains and treatment wetlands provide riparian services and serve as biodiversity corridors. However, to most people the obvious function is visual—providing green fingers through what would otherwise be urban grey. The health benefits of these are have been demonstrated to be psychological as much as biophysical.     

Successful city dwellers: a comparative study of the ecological characteristics of urban birds in the Western Palearctic

Numerous species have adapted to the proximity of humans, and this feature is no clearer than among species that have invaded towns and cities. The characteristics of species that have successfully managed to expand their range into urban areas remain largely unexplored, although they are of general interest in a world that is increasingly urbanised. I hypothesised that widely distributed species with high dispersal abilities, species with a high rate of innovation, a high level of risk-taking, and a fast life history would have a selective advantage in habitats influenced by humans. Consistent with this hypothesis, in a comparative analysis of 39 independent evolutionary events of urbanisation of birds in the Western Palearctic (thus taking the fact that closely related species that have become urbanised are caused by common phylogenetic descent rather than convergent evolution), bird species that adapted to urban habitats were characterised by large breeding ranges, high propensity for dispersal, high rates of feeding innovation (novel ways of acquiring food), short flight distances when approached by a human, and a life history characterised by high annual fecundity and high adult survival rate. Urban species may be disproportionately resistant to parasitism and predation because they had disproportionately strong immune responses, as reflected by the size of the bursa of Fabricius, and a history of weak predation-mediated natural selection, as reflected by the force required to remove feathers from the rump. Urban species had high overall ecological success as indicated by large range size and population size and high population density. This suggests that a suite of ecological features providing them with general ecological success characterises species of birds that have successfully invaded urban environments. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identifying the ecological causes of long-term declines of wetland-dependent birds in an urbanizing landscape

Many wetland-dependent birds are thought to be experiencing significant population declines, although population trend data for this suite of birds are rare and the causes of declines poorly understood. We used a 26-year dataset (1980–2005) of wetland bird abundance and distribution among 196 wetlands in northeastern Illinois (i.e., Chicago and its suburbs) to evaluate population trends and identify underlying ecological causes. We used aerial photography and GIS to quantify wetland habitat structure (i.e., the extent of emergent vegetation) and changes in surrounding land use. We then evaluated how changes in land use affected the structure of wetlands and ultimately wetland bird populations. Of the 12 species analyzed, seven experienced significant declines, three showed non-significant declines, and two experienced significant increases. Population declines could not be attributed to wetland loss because none of our wetlands were destroyed. Concurrent research at these wetlands also suggests that neither low adult survival nor poor reproductive success were responsible for the declines. Increased development within 2 km of wetlands, however, was associated with extreme changes in the structure of wetlands. Wetlands tended either to lose much of their vegetation and become open ponds, or become rank stands of dense vegetation. Both changes made wetlands less suitable for many wetland birds. While “no net loss” legislation may protect wetlands from being filled or drained, development near wetlands appears to be altering hydrology, resulting in habitat degradation and population declines of several wetland-dependent bird species.     

Strong, long-term temporal dynamics of an ecological network

Nature is organized into complex, dynamical networks of species and their interactions, which may influence diversity and stability. However, network research is, generally, short-term and depict ecological networks as static structures only, devoid of any dynamics. This hampers our understanding of how nature responds to larger disturbances such as changes in climate. In order to remedy this we studied the long-term (12-yrs) dynamics of a flower-visitation network, consisting of flower-visiting butterflies and their nectar plants. Global network properties, i.e. numbers of species and links, as well as connectance, were temporally stable, whereas most species and links showed a strong temporal dynamics. However, species of butterflies and plants varied bimodally in their temporal persistance: Sporadic species, being present only 1-2(-5) years, and stable species, being present (9-)11-12 years, dominated the networks. Temporal persistence and linkage level of species, i.e. number of links to other species, made up two groups of species: Specialists with a highly variable temporal persistence, and temporally stable species with a highly variable linkage level. Turnover of links of specialists was driven by species turnover, whereas turnover of links among generalists took place through rewiring, i.e. by reshuffling existing interactions. However, in spite of this strong internal dynamics of species and links the network appeared overall stable. If this global stability-local instability phenomenon is general, it is a most astonishing feature of ecological networks.     

Drug off-target effects predicted using structural analysis in the context of a metabolic network model

Recent advances in structural bioinformatics have enabled the prediction of protein-drug off-targets based on their ligand binding sites. Concurrent developments in systems biology allow for prediction of the functional effects of system perturbations using large-scale network models. Integration of these two capabilities provides a framework for evaluating metabolic drug response phenotypes in silico. This combined approach was applied to investigate the hypertensive side effect of the cholesteryl ester transfer protein inhibitor torcetrapib in the context of human renal function. A metabolic kidney model was generated in which to simulate drug treatment. Causal drug off-targets were predicted that have previously been observed to impact renal function in gene-deficient patients and may play a role in the adverse side effects observed in clinical trials. Genetic risk factors for drug treatment were also predicted that correspond to both characterized and unknown renal metabolic disorders as well as cryptic genetic deficiencies that are not expected to exhibit a renal disorder phenotype except under drug treatment. This study represents a novel integration of structural and systems biology and a first step towards computational systems medicine. The methodology introduced herein has important implications for drug development and personalized medicine.     

Lower extremity joint torque predicted by using artificial neural network during vertical jump

The purpose of this study was to develop an artificial neural network (ANN) for predicting lower extremity joint torques using the ground reaction force (GRF) and related parameters derived by the GRF during counter-movement jump (CMJ) and squat jump (SJ). Ten student athletes performed CMJ and SJ. Force plate and kinematic data were recorded. Joint torques were calculated using inverse dynamics and ANN. We used a fully connected, feed-forward network. The network comprised of one input layer, one hidden layer and one output layer. It was trained by error back-propagation algorithm using Steepest Descent Method. Input parameters of the ANN were GRF measurements and related parameters. Output parameters were three lower extremity joint torques. ANN model fitted well with the results of the inverse dynamics output. Our observations indicate that the model developed in this study can be used to estimate three lower extremity joint torques for CMJ and SJ based on ground reaction force data and related parameters.     

Tick infestation on birds in an urban Atlantic Forest fragment in north-eastern Brazil

Birds are important hosts for various tick species, playing a significant role in their biological life cycle and dispersion. In this study, we investigated tick infestations on birds trapped in an urban remnant of Atlantic Forest in Pernambuco state, Brazil. From February 2015 to March 2017, 541 birds belonging to 52 species were trapped with mist nets and examined for ectoparasites. Birds trapped in the late successional forest were significantly more infested than birds trapped in the early successional forest. In the same way, ectoparasite infestation varied significantly according to bird weight and collection plot. Overall, 198 birds (36.6%) belonging to 27 species were parasitized by ectoparasites (i.e., ticks, lice and/or mites). Ectoparasites were effectively collected from 111 birds, of which 99 belonging to 20 species were infested by ticks (n?=?261), namely, Amblyomma longirostre (13 nymphs), Amblyomma nodosum (21 nymphs), Amblyomma varium (one nymph), and Amblyomma spp. (five nymphs and 221 larvae). Most of the ticks (>?90%) were collected from Passeriformes. This study provides the second record of A. varium in Pernambuco state and confirms that birds, especially Passeriformes, are important hosts for larvae and nymphs of Amblyomma spp. in the Atlantic Forest biome of Pernambuco.

     

Nest biology of urban populations of cavity-nesting birds

Nesting features of four species of cavity-nesting birds—common starling (Sturnus vulgaris L.), great tit (Parus major L.), common redstart (Phoenicurus phoenicurus L.), and pied flycatcher (Ficedula hypoleuca Pall.)—have been studied in city. Under urban conditions, number of eggs in a nest of a redstart is significantly larger, while for great tit and pied flycatcher it is significantly smaller; differences between the populations of starling are insignificant. Success of reproduction for the cavity-nesters is significantly higher in a city and exceeds the reference value for all the species by 10–20%. The number of chicks per a reproduction attempt is also higher in city for all the species. Starling population in city exceeds the reference population in the success of reproduction mainly due to a decrease in the percentage of abandoned eggs. The main reasons for an increase in the reproduction success of other species at the urbanized locality are weakened pressure of predators and a decrease in the percentage of abandoned broods.     

Synchronicity of movement paths of barren-ground caribou and tundra wolves

Movement patterns of highly mobile animals can reveal life history strategies and ecological relationships. We hypothesized that wolves (Canis lupus) would display similar movement patterns as their prey, barren-ground caribou (Rangifer tarandus groenlandicus), and that movements of the two species would co-vary with season. We tested for interspecific movement dynamics using animal locations from wolves and caribou monitored concurrently from mid-October to June, across the Northwest Territories and Nunavut, Canada. We used a correlated random walk as a null model to test for pattern in movements and the bearing procedure to detect whether movements were consistently directional. There was a statistical difference between the movements of caribou and wolves (F _1,9 = 13.232, P = 0.005), when compared to a correlated random walk, and a significant interaction effect between season and species (F _1,9 = 6.815, P = 0.028). During winter, the movements of caribou were strongly correlated with the 80°–90° ( $\overline{X}$ X ¯ r = 0.859, SE = 0.065) and 270°–280° ( $\overline{X}$ X ¯ r = 0.875, SE = 0.059) bearing classes suggesting an east–west movement gradient. Wolf movements during winter showed large variation in direction, but were generally east to west. Peak mean correlation for caribou movements during spring was distinct at 40°–50° ( $\overline{X}$ X ¯ r = 0.978, SE = 0.006) revealing movement to the north-east calving grounds. During spring, wolf movements correlated with the 80°–90° ( $\overline{X}$ X ¯ r = 0.861, SE = 0.043) and 270°–280° ( $\overline{X}$ X ¯ r = 0.850, SE = 0.064) bearing class. Directionality of movement suggested that during winter, caribou and wolves had a similar distribution at the large spatial scales we tested. During spring migration, however, caribou and wolves employed asynchronous movement strategies. Our findings demonstrate the utility of the correlated random walk and bearing procedure for quantifying the movement patterns of co-occurring species.     

Hormones in the city: endocrine ecology of urban birds

Urbanization dramatically changes the landscape, presenting organisms with novel challenges and often leading to reduced species diversity. Urban ecologists have documented numerous biotic and abiotic consequences of urbanization, such as altered climate, species interactions, and community composition, but we lack an understanding of the mechanisms underlying organisms' responses to urbanization. Here, I review findings from the nascent field of study of the endocrine ecology of urban birds. Thus far, no clear or consistent patterns have been revealed, but we do have evidence that urban habitat can shape endocrine traits, and that those traits might contribute to adaptation to the urban environment. I suggest strong approaches for future work addressing exciting questions about the role of endocrine traits in mediating responses to urbanization within species across the globe.     

Behavioural and ecological correlates of natural hybridization in birds

Hybridization and speciation are central to evolutionary biology. Although birds have been studied more thoroughly than any other vertebrate class, there have still been few macro-evolutionary analyses. Here, I present results based on 65 phylogenetically independent hybrid types from the western Palearctic, focusing on behavioural and ecological correlates of hybridization. The main results are as follows. (1) Hybrids that are easier to detect were more often reported. (2) A positive correlation exists between population size (mean of both parent species) and the number of hybrids. After accounting for these confounding variables in a General Linear Model, I found (3) that sympatric species pairs produced fewer hybrids than did parapatric species pairs and (4) pairs with at least one of the parent species reported as endangered produced a greater number of hybrids whereas (5) species pairs with high male parental (paternal) care produced fewer hybrids. Other variables were excluded by a stepwise procedure in the following order: sexual dichromatism; body weight differences; publication bias. Phylogenetic information was available for a small number of hybrids but did not influence the results.     

Assessment of urban allergophytes using an allergen index

Utilizing data on the biological andphenological characteristics of allergophytesin various urban ecosystems of central Italyand taking into consideration some allergologiccharacteristics of their pollens, an allergenindex (A.I.) is proposed. On the basis of thisindex, plants are grouped into stronglyallergenic (A.I. = 7–10), moderately allergenic(A.I. = 4–6), and slightly allergenic or ofuncertain effect (A.I. 3). The index can beused to conduct a rapid survey of a city'sphytoallergenic potential. Follow-up assessmentof allergophyte distribution through selectivefloristic cartography and identification of themaximum pollen production period can facilitatepreventative treatment and lessen thesymptomatology of pollinosis in the humanpopulation.     

Coupled myosin VI motors facilitate unidirectional movement on an F-actin network

Unconventional myosins interact with the dense cortical actin network during processes such as membrane trafficking, cell migration, and mechanotransduction. Our understanding of unconventional myosin function is derived largely from assays that examine the interaction of a single myosin with a single actin filament. In this study, we have developed a model system to study the interaction between multiple tethered unconventional myosins and a model F-actin cortex, namely the lamellipodium of a migrating fish epidermal keratocyte. Using myosin VI, which moves toward the pointed end of actin filaments, we directly determine the polarity of the extracted keratocyte lamellipodium from the cell periphery to the cell nucleus. We use a combination of experimentation and simulation to demonstrate that multiple myosin VI molecules can coordinate to efficiently transport vesicle-size cargo over 10 µm of the dense interlaced actin network. Furthermore, several molecules of monomeric myosin VI, which are nonprocessive in single molecule assays, can coordinate to transport cargo with similar speeds as dimers.     

Experimental evidence for an impact of anthropogenic noise on dawn chorus timing in urban birds

Many animal species are living in urban areas, where they encounter human‐altered environmental conditions. Artificial light and traffic noise are two of the most prominent anthropogenic factors, both of which potentially affect animal life. Here we studied the changes in traffic noise conditions over the morning in the urban bird habitat of the city of Seville, Spain. We tested experimentally whether noise from human activities can cause a shift in the timing of birdsong activity. Our data revealed that noise conditions vary markedly among our replicate set of twelve streets. Relatively quiet streets show low base‐line amplitude levels early in the morning, with frequent events of brief noise bursts, followed by a strong rise in noise levels. Relatively noisy streets have high base‐line amplitude levels from a much earlier start in the morning. Experimental exposure data revealed a noise‐related earlier start of dawn singing for two out of six species: the spotless starling Sturnus unicolor and the house sparrow Passer domesticus. Our experiment did not cover earlier singing species and revealed no impact for species with more‐variable starting times of the dawn singing. Our study provides more insight into the intertwinings of bird and human behavior and confirms the potential for experimental approaches to successfully tackle questions related to the impact of anthropogenic factors on animal life in cities.     

Equivalence of grasslands in an ecological network and a World Heritage Site

Ecological networks (ENs) of indigenous vegetation among commercial forestry plantations have been implemented to offset the negative effects of the alien plantation trees on local biodiversity. However, it is not known whether these ENs are equivalent to protected areas (PAs) in terms of their grassland biodiversity. To address this knowledge gap, we investigated how well grassland plant species richness and composition in an EN corresponds to similar habitats in an adjacent PA. This took place in grasslands on the east coast of South Africa, and was done at four paired sites using ten replicates at each of the eight sites. Pairwise comparisons (EN vs. PA) of plant species composition yielded statistically smaller differences than comparisons between different pairs of sites within either the EN or PA, illustrating considerable turnover of species whether or not they were in an EN or PA. Overall, there were fewer plant species in the EN for three of the four pairs of sites. Nevertheless, plant species composition was similar in each pair of sites. The grassland EN was also characterized by greater maximum vegetation height and less green vegetation cover. When differences between the EN and a PA were viewed against the natural variation of abiotic and biotic conditions across the landscape, they were small. We conclude that ENs of natural habitat contribute substantially to biodiversity conservation in transformed, commercially-productive landscapes, are almost as good as PAs for maintaining grassland plant diversity.     

Age at the onset of senescence in birds and mammals is predicted by early-life performance

Life-history theory predicts that traits involved in maturity, reproduction and survival correlate along a fast–slow continuum of life histories. Evolutionary theories and empirical results indicate that senescence-related traits vary along this continuum, with slow species senescing later and at a slower pace than fast species. Because senescence patterns are typically difficult to estimate from studies in the wild, here we propose to predict the associated trait values in the frame of life-history theory. From a comparative analysis based on 81 free-ranging populations of 72 species of birds and mammals, we find that a nonlinear combination of fecundity, age at first reproduction and survival over the immature stage can account for ca two-thirds of the variance in the age at the onset of actuarial senescence. Our life-history model performs better than a model predicting the onset based on generation time, and it only includes life-history traits during early life as explanatory variables, i.e. parameters that are both theoretically expected to shape senescence and are measurable within relatively short studies. We discuss the good-fit of our life-history model to the available data in the light of current evolutionary theories of senescence. We further use it to evaluate whether studies that provided no evidence for senescence lasted long enough to include the onset of senescence.     

A predicted protein-protein interaction network of the filamentous fungus Neurospora crassa

The filamentous fungus Neurospora crassa is a leading model organism for circadian clock studies. Computational identification of a protein-protein interaction (PPI) network (also known as an interactome) in N. crassa can provide new insights into the cellular functions of proteins. Using two well-established bioinformatics methods (the interolog method and the domain interaction-based method), we predicted 27,588 PPIs among 3006 N. crassa proteins. To the best of our knowledge, this is the first identified interactome for N. crassa, although it remains problematic because of incomplete interactions and false positives. In particular, the established PPI network has provided clues to further decipher the molecular mechanism of circadian rhythmicity. For instance, we found that clock-controlled genes (ccgs) are more likely to act as bottlenecks in the established PPI network. We also identified an important module related to circadian oscillators, and some functional unknown proteins in this module may serve as potential candidates for new oscillators. Finally, all predicted PPIs were compiled into a user-friendly database server (NCPI), which is freely available at .