A network-based measure of functional diversity in food webs.

Biodiversity is measured from various perspectives. One of them, functional diversity, quantifies the heterogeneity in species traits and roles in an ecosystem. One important aspect of species roles is their interactions with other species, i.e. their network role. We therefore investigate here functional diversity from the network perspective. Species differ in their network positions in a food web, having different interaction patterns. We developed a measure for quantifying the diversity in species interaction patterns in a food web. We examined the relationship between interaction diversity and several global network properties for 92 food webs. Our results showed that high interaction diversity occurs in sparsely connected and less cohesive food webs. High interaction diversity also occurred in food webs with more clusters and high network modularity. We also quantified several conventional functional diversity indices and demonstrate that they show little or no correlation with interaction diversity. Our proposed diversity index therefore provides a measure complementary to current concepts of functional diversity.

A continuum of biological adaptations to environmental fluctuation.

Bet-hedging-a strategy that reduces fitness variance at the expense of lower mean fitness among different generations-is thought to evolve as a biological adaptation to environmental unpredictability. Despite widespread use of the bet-hedging concept, most theoretical treatments have largely made unrealistic demographic assumptions, such as non-overlapping generations and fixed or infinite population sizes. Here, we extend the concept to consider overlapping generations by defining bet-hedging as a strategy with lower variance and mean per capita growth rate across different environments. We also define an opposing strategy-the rising-tide-that has higher mean but also higher variance in per capita growth. These alternative strategies lie along a continuum of biological adaptions to environmental fluctuation. Using stochastic Lotka-Volterra models to explore the evolution of the rising-tide versus bet-hedging strategies, we show that both the mean environmental conditions and the temporal scales of their fluctuations, as well as whether population dynamics are discrete or continuous, are crucial in shaping the type of strategy that evolves in fluctuating environments. Our model demonstrates that there are likely to be a wide range of ways that organisms with overlapping generations respond to environmental unpredictability beyond the classic bet-hedging concept.

A novel 3D-printed computer-assisted piezocision guide for surgically facilitated orthodontics.

Surgical interventions on the alveolar ridges aimed at facilitating orthodontic tooth movement have been extensively reported. However, unexpected events or complications still occur in daily practice. The purpose of this report was to present a novel 3-dimensional (3D) computer-assisted piezocision guide (CAPG) designed to be translucent for increased visibility, rigid for enhanced support during guidance, and porous for profuse irrigation during procedure. Such a design can function to minimize the risk of surgical complications. In this case, we present a novel 3D-printed CAPG to facilitate a minimally invasive periodontal accelerated osteogenic orthodontics (PAOO) procedure with a guide that provides accuracy, adequate visibility, and greater access for the coolant to reach the surgery site. By navigating the cone-beam computed tomography data, we precisely know the cortical bone thickness, root direction, and interrelations between anatomic structures in an individual situation, which allows us to design our cutting slot for the required length and depth according to the operator's knowledge. Finally, 3D printing was applied, transferring our surgical plan to fabricate the CAPG. Moreover, the well designed pores on the CAPG allow effective irrigation during the piezocision procedure. This minimally invasive procedure was uneventful, and no devitalized tooth or alveolar bone was found.

Drastic population fluctuations explain the rapid extinction of the passenger pigeon.

To assess the role of human disturbances in species' extinction requires an understanding of the species population history before human impact. The passenger pigeon was once the most abundant bird in the world, with a population size estimated at 3-5 billion in the 1800s; its abrupt extinction in 1914 raises the question of how such an abundant bird could have been driven to extinction in mere decades. Although human exploitation is often blamed, the role of natural population dynamics in the passenger pigeon's extinction remains unexplored. Applying high-throughput sequencing technologies to obtain sequences from most of the genome, we calculated that the passenger pigeon's effective population size throughout the last million years was persistently about 1/10,000 of the 1800's estimated number of individuals, a ratio 1,000-times lower than typically found. This result suggests that the passenger pigeon was not always super abundant but experienced dramatic population fluctuations, resembling those of an "outbreak" species. Ecological niche models supported inference of drastic changes in the extent of its breeding range over the last glacial-interglacial cycle. An estimate of acorn-based carrying capacity during the past 21,000 y showed great year-to-year variations. Based on our results, we hypothesize that ecological conditions that dramatically reduced population size under natural conditions could have interacted with human exploitation in causing the passenger pigeon's rapid demise. Our study illustrates that even species as abundant as the passenger pigeon can be vulnerable to human threats if they are subject to dramatic population fluctuations, and provides a new perspective on the greatest human-caused extinction in recorded history.

On the centrality and uniqueness of species from the network perspective.

Identifying important species for maintaining ecosystem functions is a challenge in ecology. Since species are components of food webs, one way to conceptualize and quantify species importance is from a network perspective. The importance of a species can be quantified by measuring the centrality of its position in a food web, because a central node may have greater influence on others in the network. A species may also be important because it has a unique network position, such that its loss cannot be easily compensated. Therefore, for a food web to be robust, we hypothesize that central species must be functionally redundant in terms of their network position. In this paper, we test our hypothesis by analysing the Prince William Sound ecosystem. We found that species centrality and uniqueness are negatively correlated, and such an observation is also carried over to other food webs.

The response patterns of young bicyclists to a right-turning motorcycle: a simulator study.

This study was designed to assess how bicyclists (30 men, 30 women) responded to right-turning motorised vehicles, which is a risky situation for bicyclists, and employed a scenario in which a motorcycle made a right turn in front of a bicyclist. The factors of speed difference and cut-in time gap were generated to objectively investigate steering control, speed, and the associated collisions in a bicycle simulator. There was no effect for sex, but as expected, for shorter cut-in time gaps, the steering angles were smaller (deflected to the right to avoid the passing motorcycle), the speeds were lower, and the variations in the steering angle and speed were larger. Variations in the steering angle and speed were unexpectedly lower for larger speed differences than for smaller speed differences. Response patterns comprised 5 patterns: early response and quickly depress the brake, last-moment response and slowly depress the brake, late response and quickly depress the brake, very late response and quickly depress the brake, and no response. Larger speed differences and the no-response pattern resulted in two collisions. Individuals with less experience may not have associated speed differences with potential dangers.

Quantifying the interaction structure and the topological importance of species in food webs: a signed digraph approach.

Due to the structural complexity of nature, it is not always easy to identify topologically importance species in an ecosystem. In the past decade, several studies in ecology have developed methods for measuring species importance basing on direct and indirect inter-specific interactions. Here, by extending a previously developed methodology, we present an approach that can quantify the interaction structure of a food web and consequently the topological importance of species when the food web is viewed as a signed digraph. The basic principle behind our approach is to determine the sign and strength of direct and indirect interactions for all pathways up to a predefined number of steps. Our approach mainly differs from the previous methodology in that we are able to quantify the strength of inter-specific interaction as well as in what way species interact with each other, as it can explicitly quantify a wide range of ecological interactions such as cascading effect, indirect food supply effect, apparent and exploitive competitions in the same framework. This then allows us to quantify the topological importance of a species and examine whether it is a predominately positive or negative interactor in a food web. Furthermore, our analysis reveals that positive and negative effects from one species on others eventually cancel each other out for longer pathways resulting in stable interaction structure. Applications of our methodology include providing a more informative index for conservation biologists, and the potential use of interaction structure derived from our approach in food web robustness studies is also discussed.

Cordyceps sinensis health supplement enhances recovery from taxol-induced leukopenia.

This study aimed to evaluate the ability of the health food supplement Cordyceps sinensis (CS) to ameliorate suppressive effects of chemotherapy on bone marrow function as a model for cancer treatment. Mice were treated with Taxol (17 mg/kg body wt) one day before oral administration of a hot-water extract of CS (50 mg/kg daily) that was given daily for 3 weeks. White blood cell counts in peripheral blood of mice receiving Taxol were at 50% of normal levels on day 28 but had recovered completely in mice treated with CS. In vitro assays showed that CS enhanced the colony-forming ability of both granulocyte macrophage colony forming unit (GM-CFU) and osteogenic cells from bone marrow preparations and promoted the differentiation of bone marrow mesenchymal stromal cells into adipocytes, alkaline phosphatase-positive osteoblasts, and bone tissue. This result could be attributed to enhanced expression of Cbfa1 (core binding factor a) and BMP-2 (bone morphogenetic protein) with concurrent suppression of ODF (osteoclast differentiation factor/RANK [receptor activator of NF-kappaB]) ligand. In summary, CS enhances recovery of mice from leukopenia caused by Taxol treatment. It appears to do so by protecting both hematopoietic progenitor cells directly and the bone marrow stem cell niche through its effects on osteoblast differentiation.

A network perspective on the topological importance of enzymes and their phylogenetic conservation.

BACKGROUND: A metabolic network is the sum of all chemical transformations or reactions in the cell, with the metabolites being interconnected by enzyme-catalyzed reactions. Many enzymes exist in numerous species while others occur only in a few. We ask if there are relationships between the phylogenetic profile of an enzyme, or the number of different bacterial species that contain it, and its topological importance in the metabolic network. Our null hypothesis is that phylogenetic profile is independent of topological importance. To test our null hypothesis we constructed an enzyme network from the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. We calculated three network indices of topological importance: the degree or the number of connections of a network node; closeness centrality, which measures how close a node is to others; and betweenness centrality measuring how frequently a node appears on all shortest paths between two other nodes. RESULTS: Enzyme phylogenetic profile correlates best with betweenness centrality and also quite closely with degree, but poorly with closeness centrality. Both betweenness and closeness centralities are non-local measures of topological importance and it is intriguing that they have contrasting power of predicting phylogenetic profile in bacterial species. We speculate that redundancy in an enzyme network may be reflected by betweenness centrality but not by closeness centrality. We also discuss factors influencing the correlation between phylogenetic profile and topological importance. CONCLUSION: Our analysis falsifies the hypothesis that phylogenetic profile of enzymes is independent of enzyme network importance. Our results show that phylogenetic profile correlates better with degree and betweenness centrality, but less so with closeness centrality. Enzymes that occur in many bacterial species tend to be those that have high network importance. We speculate that this phenomenon originates in mechanisms driving network evolution. Closeness centrality reflects phylogenetic profile poorly. This is because metabolic networks often consist of distinct functional modules and some are not in the centre of the network. Enzymes in these peripheral parts of a network might be important for cell survival and should therefore occur in many bacterial species. They are, however, distant from other enzymes in the same network.

Metapopulation dynamics of Escherichia coli O157 in cattle: an exploratory model.

Livestock movement is thought to be a risk factor for the transmission of infectious diseases of farm animals. Simple mathematical models were constructed for the transmission of Escherichia coli serogroup O157 between Scottish cattle farms, and the models were used in a preliminary exploration of factors contributing to the levels of infection reported in the field. The results suggest that cattle movement can make a significant contribution to the observed prevalence of E. coli O157-positive farms, but is not by itself sufficient for the persistence of E. coli O157. The results also suggest that cattle movements involving infected farms with cattle shedding an exceptional amount of E. coli O157, 'super-shedders', also make a substantial contribution to the prevalence of infected farms. Simulations indicate that E. coli O157 could have reached the currently observed prevalence levels in less than a decade. Implications and findings from our models are discussed in relation to possible control of E. coli O157 in Scottish cattle.

Investigation of photoneutron dose equivalent from high-energy photons in radiotherapy.

Spatial distribution of photoneutron dose equivalent during radiotherapy at different beam size, depth, and distance from a 15 MV linear accelerator was investigated with bubble detectors in a water phantom. The photoneutron dose equivalent was mainly from fast neutrons, and decreased with distance at a fixed field and with depth. Besides, photoneutron dose equivalent was slightly affected by beam size due to the variation of tungsten area exposed in the beam direction and photoneutrons occurred at the jaws. Fast photoneutron dose equivalent of shallow critical organs was represented still considerably outside the beam size.

Protection against radiation-induced bone marrow and intestinal injuries by Cordyceps sinensis, a Chinese herbal medicine.

Bone marrow and intestinal damage limits the efficacy of radiotherapy for cancer and can result in death if the whole body is exposed to too high a dose, as might be the case in a nuclear accident or terrorist incident. Identification of an effective nontoxic biological radioprotector is therefore a matter of some urgency. In this study, we show that an orally administered hot-water extract from a Chinese herbal medicine, Cordyceps sinensis (CS), protects mice from bone marrow and intestinal injuries after total-body irradiation (TBI). CS increased the median time to death from 13 to 20 days after 8 Gy TBI and from 9 to 18 days after 10 Gy TBI. Although CS-treated mice receiving 10 Gy TBI survived intestinal injury, most died from bone marrow failure, as shown by severe marrow hypoplasia in mice dying between 18 and 24 days. At lower TBI doses of 5.5 and 6.5 Gy, CS protected against bone marrow death, an effect that was confirmed by the finding that white blood cell counts recovered more rapidly. In vitro, CS reduced the levels of free radical species (ROS) within cells, and this is one likely mechanism for the radioprotective effects of CS, although probably not the only one.

Seasonal and daily climate variation have opposite effects on species elevational range size.

The climatic variability hypothesis posits that the magnitude of climatic variability increases with latitude, elevation, or both, and that greater variability selects for organisms with broader temperature tolerances, enabling them to be geographically widespread. We tested this classical hypothesis for the elevational range sizes of more than 16,500 terrestrial vertebrates on 180 montane gradients. In support of the hypothesis, mean elevational range size was positively correlated with the scope of seasonal temperature variation, whereas elevational range size was negatively correlated with daily temperature variation among gradients. In accordance with a previous life history model and our extended versions of it, our findings indicate that physiological specialization may be favored under shorter-term climatic variability.

Compartmental responses after thoracic irradiation of mice: strain differences.

PURPOSE: To examine and compare the molecular and cellular processes leading to radiation fibrosis and pneumonitis in C57BL/6J and C3H/HeN mice. METHODS AND MATERIALS: At indicated times after various doses of thoracic irradiation, the cell populations obtained by bronchoalveolar lavage of C57BL/6J mice were differentially analyzed by cytology and assessed by RNase protection (RPA) assay for levels of cytokines and related genes. The molecular responses in bronchial alveolar lavage (BAL) populations were compared with those in whole lung of C57BL/6J mice and with those of C3H/HeN mice. The former strain develops late radiation fibrosis, whereas the latter develop subacute radiation pneumonitis. RESULTS: In C57BL/6J mice, a decrease in the total number of BAL cells was found 1 week after 6, 12, or 20 Gy thoracic irradiation with a subsequent dose-dependent increase up to 6 months. After 12 and 20 Gy, large, foamy macrophages and multinucleated cells became evident in BAL at 3 weeks, only to disappear at 4 months and reappear at 6 months. This biphasic response was mirrored by changes expression of mRNA for proinflammatory cytokines and the Mac-1 macrophage-associated antigen. As with BAL, whole lung tissue also showed biphasic cytokine and Mac-1 mRNA responses, but there were striking temporal differences between the two compartments, with changes in whole lung tissue correlating better than BAL with the onset of fibrosis in this strain. The radiation-induced proinflammatory mRNA responses had strain-dependent and strain-independent components. Thoracic irradiation of C3H/HeN induced similar increases in tumor necrosis factor (TNF)-alpha, interleukin (IL)-1alpha/beta, and interferon (IFN)-gamma mRNA expression in lung as it did in C57BL/6J mice during the "presymptom" phase at 1-2 months. However, immediately preceding and during the pneumonitic time period at 3-4 months, TNF-alpha and IL-1alpha/beta mRNAs were highly upregulated in C3H/HeN mice, which develop pneumonitis, but not in C57BL/6J mice, which do not. At the onset of radiation fibrosis in C57BL/6J mice (5-6 months), irradiated lungs had increased levels of IL-1alpha/beta and IFN-gamma mRNA expression, but the TNF-alpha response was, notably, still muted. CONCLUSIONS: The major molecular and cellular events in lungs of C57BL/6J and C3H/HeN mice, which develop late fibrosis and subacute pneumonitis after thoracic irradiation respectively, take place within the interstitium and are not reflected within BAL populations. The initial proinflammatory responses are similar in the two strains, but later responses reflect the latent time to lesion development. TNF-alpha expression at 3-4 months may be important in radiation-induced pneumonitis, and its downregulation is important in avoiding this radiation-induced complication.

Inferring microbial interaction network from microbiome data using RMN algorithm.

BACKGROUND: Microbial interactions are ubiquitous in nature. Recently, many similarity-based approaches have been developed to study the interaction in microbial ecosystems. These approaches can only explain the non-directional interactions yet a more complete view on how microbes regulate each other remains elusive. In addition, the strength of microbial interactions is difficult to be quantified by only using correlation analysis. RESULTS: In this study, a rule-based microbial network (RMN) algorithm, which integrates regulatory OTU-triplet model with parametric weighting function, is being developed to construct microbial regulatory networks. The RMN algorithm not only can extrapolate the cooperative and competitive relationships between microbes, but also can infer the direction of such interactions. In addition, RMN algorithm can theoretically characterize the regulatory relationship composed of microbial pairs with low correlation coefficient in microbial networks. Our results suggested that Bifidobacterium, Streptococcus, Clostridium XI, and Bacteroides are essential for causing abundance changes of Veillonella in gut microbiome. Furthermore, we inferred some possible microbial interactions, including the competitive relationship between Veillonella and Bacteroides, and the cooperative relationship between Veillonella and Clostridium XI. CONCLUSIONS: The RMN algorithm provides the reconstruction of gut microbe networks, and can shed light on the dynamical interactions of microbes in the infant intestinal tract.

Analysing the Unequal Effects of Positive and Negative Information on the Behaviour of Users of a Taiwanese On-Line Bulletin Board.

The impact of social influence causes people to adopt the behaviour of others when interacting with other individuals. The effects of social influence can be direct or indirect. Direct social influence is the result of an individual directly influencing the opinion of another, while indirect social influence is a process taking place when an individual's opinion and behaviour is affected by the availability of information about others' actions. Such indirect effect may exhibit a more significant impact in the on-line community because the internet records not only positive but also negative information, for example on-line written text comments. This study focuses on indirect social influence and examines the effect of preceding information on subsequent users' opinions by fitting statistical models to data collected from an on-line bulletin board. Specifically, the different impacts of information on approval and disapproval comments on subsequent opinions were investigated. Although in an anonymous situation where social influence is assumed to be at minimum, our results demonstrate the tendency of on-line users to adopt both positive and negative information to conform to the neighbouring trend when expressing opinions. Moreover, our results suggest unequal effects of the local approval and disapproval comments in affecting the likelihood of expressing opinions. The impact of neighbouring disapproval densities was stronger than that of neighbouring approval densities on inducing subsequent disapproval relative to approval comments. However, our results suggest no effects of global social influence on subsequent opinion expression.

Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters.

BACKGROUND: A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system's dynamics. RESULTS: We demonstrate our methodology on a prototype biological system of perfect adaptation dynamics, namely the chemotaxis model for Escherichia coli. Our results agreed well with those derived from experimental data and theoretical studies in the literature. Using this model system, we showed that there are motifs in kinetic parameters and that these motifs are governed by constraints of the specified system dynamics. CONCLUSIONS: A systematic approach based on enrichment statistical tests has been developed to elucidate the relationships between model parameters and the roles they play in affecting system dynamics of a prototype biological network. The proposed approach is generally applicable and therefore can find wide use in systems biology modeling research.

Osteogenic activity of nanonized pearl powder/poly (lactide-co-glycolide) composite scaffolds for bone tissue engineering.

Numerous materials have been proposed for bone tissue engineering. In this study, a newly designed hybrid composite scaffold composed of poly (D,L-lactide-co-glycolide) and a naturally bioceramic hybrid material, nanonized pearl powder, were prepared and the biological activities and physical properties of the scaffold for bone tissue engineering were evaluated. It is a composite consisting calcium carbonate crystal in an aragonite structure, embedded in an organic matrix. Peral contains one or more signal molecules capable of stimulating bone formation. The nanonized pearl powder is considered as a promising osteoinductive biomaterial. This biomaterial is biocompatible and shows osteogenic activity. In this study, the designed biohybrid of nanonized pearl powder/poly (lactide-co-glycolide) (NPP/PLGA) biocomposite scaffolds would employ biodegradable material as MC3T3-E1 cells seeded scaffolds. Therefore, the biocomposite scaffolds would be used to culture with MC3T3-E1 cells under spinner bioreactor in vitro. Furthermore, it also detailed how these tissues were characterized, qualitatively and quantitatively, with scanning electron microscopy and biochemical testing. The identity and the mode of action of these molecules on the osteoblast differentiation were analyzed. This study indicates that the efficiency of nanonized pearl powders in bone cell differentiation are certainly different from that of proteins. Further sudy will look forward to manufacturing the promising new generation bone substitute, three dimensional biocomposite scaffolds to replace the implant and autogeneous bone graft, which combines basic research and clinical application.

Studying protein-protein interaction networks: a systems view on diseases.

In order to better understand several cellular processes, it is helpful to study how various components make up the system. This systems perspective is supported by several modelling tools including network analysis. Networks of protein-protein interactions (PPI networks) offer a way to depict, visualize and quantify the functioning and relative importance of particular proteins in cell function. The toolkit of network analysis ranges from the local indices describing individual proteins (as network nodes) to global indicators of system architecture, describing the total interaction system (as the whole network). We briefly introduce some of these network indices and present a case study where the connectedness and potential functional relationships between certain disease proteins are inferred. We argue that network analysis can be used, in general, to improve databases, to infer novel functions, to quantify positional importance and to support predictions in pathogenesis studies. The systems perspective and network analysis can be of particular importance in studying diseases with complex molecular processes.

Inferring pleiotropy by network analysis: linked diseases in the human PPI network.

BACKGROUND: Earlier, we identified proteins connecting different disease proteins in the human protein-protein interaction network and quantified their mediator role. An analysis of the networks of these mediators shows that proteins connecting heart disease and diabetes largely overlap with the ones connecting heart disease and obesity. RESULTS: We quantified their overlap, and based on the identified topological patterns, we inferred the structural disease-relatedness of several proteins. Literature data provide a functional look of them, well supporting our findings. For example, the inferred structurally important role of the PDZ domain-containing protein GIPC1 in diabetes is supported despite the lack of this information in the Online Mendelian Inheritance in Man database. Several key mediator proteins identified here clearly has pleiotropic effects, supported by ample evidence for their general but always of only secondary importance. CONCLUSIONS: We suggest that studying central nodes in mediator networks may contribute to better understanding and quantifying pleiotropy. Network analysis provides potentially useful tools here, as well as helps in improving databases.