Identifying and classifying biomedical perturbations in text

Molecular perturbations provide a powerful toolset for biomedical researchers to scrutinize the contributions of individual molecules in biological systems. Perturbations qualify the context of experimental results and, despite their diversity, share properties in different dimensions in ways that can be formalized. We propose a formal framework to describe and classify perturbations that allows accumulation of knowledge in order to inform the process of biomedical scientific experimentation and target analysis. We apply this framework to develop a novel algorithm for automatic detection and characterization of perturbations in text and show its relevance in the study of gene–phenotype associations and protein–protein interactions in diabetes and cancer. Analyzing perturbations introduces a novel view of the multivariate landscape of biological systems.     

Decision errors in evaluating tipping points for ecosystem resilience

When an ecosystem reaches tipping points for selected indicators, resilience to further changes in external drivers can decrease, regime shifts can occur that diminish the capacity of the ecosystem to provide ecosystem services, and the ecosystem is more vulnerable to collapse. Evaluating tipping points for resilience using crisp decision rules can result in decision errors about whether or not resilience has been compromised. The source and nature of those errors are described and a fuzzy decision rule is proposed for evaluating resilience. Decision errors are evaluated for four cases. Cases 1 through 3 (or case 4) derive conditions for evaluating decision errors when there is a single (or multiple) indicator(s). The primary sources of decision errors for the four cases are discrepancies between measured (or established) and true values of the indicators (or tipping points) and using a crisp decision rule to reach conclusions about whether or not resilience has been compromised. A fuzzy decision rule, based on fuzzy TOPSIS, is proposed that evaluates the extent to which an ecosystem is resilient. Although crisp decision rules provide unambiguous conclusions about resilience, those conclusions can be faulty, particularly when measured indicators and established tipping points deviate substantially from their true values. In contrast, the conclusions from the fuzzy decision rule are less susceptible to the decision errors and, hence, faulty decisions.     

Species richness facilitates ecosystem resilience in aquatic food webs

1. Many studies indicate that biodiversity in ecosystems affects stability, either by promoting temporal stability of ecosystem attributes or by enhancing ecosystem resistance and resilience to perturbation. The effects on temporal stability are reasonably well understood and documented but effects on resistance and resilience are not. 2. Here, we report results from an aquatic mesocosm experiment in which we manipulated the species richness and composition of aquatic food webs (macrophytes, macro‐herbivores and invertebrate predators), imposed a pulse disturbance (acidification), and monitored the resistance (initial response) and resilience (recovery) of ecosystem productivity and respiration. 3. We found that species‐rich macroinvertebrate communities had higher resilience of whole‐ecosystem respiration, but were not more resistant to perturbations. We also found that resilience and resistance were unaffected by species composition, despite the strong role composition is known to play in determining mean levels of function in these communities. 4. Biodiversity’s effects on resilience were probably mediated through complex pathways affecting phytoplankton and microbial communities (e.g. via changes in nutrient regeneration, grazing or compositional changes) rather than through simpler effects (e.g. insurance effects, enhanced facilitation) although these simpler mechanisms probably played minor roles in enhancing respiration resilience. 5. Current mechanisms for understanding biodiversity’s effects on ecosystem stability have been developed primarily in the context of single‐trophic level communities. These mechanisms may be overly simplistic for understanding the consequences of species richness on ecosystem stability in complex, multi‐trophic food webs where additional factors such as indirect effects and highly variable life‐history traits of species may also be important.     

Neural mechanisms of stress resilience and vulnerability

Exposure to stressful events can be differently perceived by individuals and can have persistent sequelae depending on the level of stress resilience or vulnerability of each person. The neural processes that underlie such clinically and socially important differences reside in the anatomical, functional, and molecular connectivity of the brain. Recent work has provided novel insight into some of the involved biological mechanisms that promises to help prevent and treat stress-related disorders. In this review, we focus on causal and mechanistic evidence implicating altered functions and connectivity of the neuroendocrine system, and of hippocampal, cortical, reward, and serotonergic circuits in the establishment and the maintenance of stress resilience and vulnerability. We also touch upon recent findings suggesting a role for epigenetic mechanisms and neurogenesis in these processes and briefly discuss promising avenues of future investigation.     

Restoration and resilience to recovery of the Lake Loosdrecht ecosystem in relation to its phosphorus flow

A reduction in external phosphorus loading since 1984 to Loosdrecht lakes system by the dephosphorization of the inlet water, yielded only minor effects in Lake Loosdrecht. This reduction measure turned out to have decreased the loading only by a factor of two. A conceptual model was constructed based on laboratory measurements to describe phosphorus flow in the lake ecosystem for the summer of 1987. The role of zooplankton and fish was more important in phosphorus recycling than diffusion at the sediment-water interface. The input and output of phosphorus of the lake were at equilibrium and therefore, further reduction in external loading was needed for recovery. The results of the conceptual model agreed well with the output of the mathematical model PCLOOS. Additional measures such as dredging, flushing, chemomanipulation, or biomanipulation would be ineffective at the present level of external loading. Only a significant further reduction in external input will restore Lake Loosdrecht's water quality over a long period of time.     

Resistance and resilience of ecosystem metabolism in a flood-prone river system

1. Gross primary production (GPP) and ecosystem respiration (ER) were analysed for 18 months in two reaches of the River Thur, a prealpine river in Switzerland. The upper reach at 655 m above sea level (a.s.l.) is bedrock constrained, has a high slope (0.60%) and a catchment area of 126 km2. The lower reach at 370 m a.s.l. has a more extensive hyporheic zone, a lower slope (0.17%) and a catchment of 1696 km2.
2. In both reaches, temporal patterns of stream metabolism reflected the occurrence of bed-moving spates. Average reductions of GPP and ER by spates were 53 and 24% in the upper reach, and 37 and 14% in the lower reach, respectively. The greater resistance of ER than GPP in both reaches shifted the ecosystem metabolism towards heterotrophy (decrease of the ratio of GPP to ER (P/R)) following spates.
3. Recovery of GPP was significantly faster in the lower reach and exhibited distinct seasonal variation (positive correlation with incident light). The differences in stability (both resistance and resilience) between reaches reflected differences in geomorphic settings and disturbance regime.
4. Stepwise regression analysis was used to explore the potential influence of season, disturbance and prevailing environmental conditions on stream metabolism in each reach. Time since spate plus temperature explained 73 and 86% of variation in ER and GPP, respectively, in the upper reach and 55% of variation in ER in the lower reach. Season plus prevailing environmental conditions explained 67% of variation in GPP in the lower reach.
5. To test how the perception of stability may change with increasing scale of observation, the disturbance regimes of 12 sites were compared with the disturbance regime of the entire Thur catchment. The analysis suggests that stream metabolism at the catchment scale is far more resistant to high flow events than at the reach scale.     

Tolerance to maternal immunoglobulins: resilience of the specific T cell repertoire in spite of long-lasting perturbations

T cell tolerance is established and maintained through various mechanisms, the critical component being the persistence of the specific Ag. However, at the molecular level, the nature of the recovering TCR repertoire following breakdown of tolerance is unknown. We address this important question by following kappa light chain constant region (C kappa)-specific CD4+ T cells of kappa light chain knock-out (kappa-/-) mice born to kappa+/- mothers. These cells, which were in contact with maternal kappa+ Igs from early ontogeny until weaning, were strongly tolerized. Tolerance was reversible and waned with the disappearance of peptide C kappa 134-148 presentation in lymphoid organs, including the thymus. Whereas three specific V beta-J beta rearrangements emerged in the peptide C kappa 134-148-specific CD4+ T cell response of all regular kappa-/- mice, soon after breakdown of tolerance only one of these rearrangements was detected. The two others displayed a significant delay in reappearance and were still rare at 26 wk of age, while the control proliferative response had already recovered 3 mo earlier. At 52 wk of age, a complete recovery of the three canonical V beta-J beta rearrangements was observed. Thus, although profoundly perturbed for several months, the T cell repertoire returns to equilibrium, highlighting the resilient nature of this system.     

Resistance and resilience of microbial communities - temporal and spatial insurance against perturbations

Bacteria play fundamental roles for many ecosystem processes; however, little empirical evidence is available on how environmental perturbations affect their composition and function. We investigated how spatial and temporal refuges affect the resistance and resilience of a freshwater bacterioplankton community upon a salinity pulse perturbation in continuous cultures. Attachment to a surface avoided the flushing out of cells and enabled re-colonization of the liquid phase after the perturbation, hence serving as a temporal refuge. A spatial refuge was established by introduction of bacteria from an undisturbed reservoir upstream of the continuous culture vessel, acting analogous to a regional species pool in a metacommunity. The salinity pulse affected bacterial community composition and the rates of respiration and the pattern of potential substrate utilization as well as the correlation between composition and function. Compared with the no-refuge treatment, the temporal refuge shortened return to pre-perturbation conditions, indicating enhanced community resilience. Composition and function were less disturbed in the treatment providing a spatial refuge, suggesting higher resistance. Our results highlight that spatial and temporal dynamics in general and refuges in particular need to be considered for conceptual progress in how microbial metacommunities are shaped by perturbations.     

Aquatic biodiversity in forests: a weak link in ecosystem services resilience

The diversity of aquatic ecosystems is being quickly reduced on many continents, warranting a closer examination of the consequences for ecological integrity and ecosystem services. Here we describe intermediate and final ecosystem services derived from aquatic biodiversity in forests. We include a summary of the factors framing the assembly of aquatic biodiversity in forests in natural systems and how they change with a variety of natural disturbances and human-derived stressors. We consider forested aquatic ecosystems as a multi-state portfolio, with diverse assemblages and life-history strategies occurring at local scales as a consequence of a mosaic of habitat conditions and past disturbances and stressors. Maintaining this multi-state portfolio of assemblages requires a broad perspective of ecosystem structure, various functions, services, and management implications relative to contemporary stressors. Because aquatic biodiversity provides multiple ecosystem services to forests, activities that compromise aquatic ecosystems and biodiversity could be an issue for maintaining forest ecosystem integrity. We illustrate these concepts with examples of aquatic biodiversity and ecosystem services in forests of northwestern North America, also known as Northeast Pacific Rim. Encouraging management planning at broad as well as local spatial scales to recognize multi-state ecosystem management goals has promise for maintaining valuable ecosystem services. Ultimately, integration of information from socio-ecological ecosystems will be needed to maintain ecosystem services derived directly and indirectly from forest aquatic biota.     

Swimming against the tide: resilience of a riverine turtle to recurrent extreme environmental events

Extreme environmental events (EEEs) are likely to exert deleterious effects on populations. From 1996 to 2012 we studied the nesting dynamics of a riverine population of painted turtles (Chrysemys picta) that experienced seven years with significantly definable spring floods. We used capture–mark–recapture methods to estimate the relationships between more than 5 m and more than 6 m flood events and population parameters. Contrary to expectations, flooding was not associated with annual differences in survival, recruitment or annual population growth rates of the adult female segment of the population. These findings suggest that female C. picta exhibit resiliency to key EEE, which are expected to increase in frequency under climate change.     

Analysis and evaluation of ecosystem resilience: an economic perspective with an application to the Venice lagoon

This paper focuses on the analysis and evaluation of resilience anchored in an economic perspective. Resilience, as well as most of the benefits provided by ecosystems, is not priced on current markets. However, this does not mean that resilience is of no value for humans. On the contrary, the interest of using an economic perspective, and the respective scientific methodology, will be put forward in terms of resilience relevance for ecosystem functioning, and its impact on human welfare. The economic perspective is anchored in an anthropocentric analysis evaluating resilience in terms of provision of natural capital benefits. These in turn are interpreted as insurance against the risk of ecosystem malfunctioning and the consequent interruption of the provision of goods and services to humans. For this analysis, we make use of a conceptual framework that identifies and describes the different value components of resilience. Finally, we present an illustration that discusses the economic analysis of resilience benefits in the context of the Venice Lagoon.     

Herbivory, connectivity, and ecosystem resilience: response of a coral reef to a large-scale perturbation

Coral reefs world-wide are threatened by escalating local and global impacts, and some impacted reefs have shifted from coral dominance to a state dominated by macroalgae. Therefore, there is a growing need to understand the processes that affect the capacity of these ecosystems to return to coral dominance following disturbances, including those that prevent the establishment of persistent stands of macroalgae. Unlike many reefs in the Caribbean, over the last several decades, reefs around the Indo-Pacific island of Moorea, French Polynesia have consistently returned to coral dominance following major perturbations without shifting to a macroalgae-dominated state. Here, we present evidence of a rapid increase in populations of herbivorous fishes following the most recent perturbation, and show that grazing by these herbivores has prevented the establishment of macroalgae following near complete loss of coral on offshore reefs. Importantly, we found the positive response of herbivorous fishes to increased benthic primary productivity associated with coral loss was driven largely by parrotfishes that initially recruit to stable nursery habitat within the lagoons before moving to offshore reefs later in life. These results underscore the importance of connectivity between the lagoon and offshore reefs for preventing the establishment of macroalgae following disturbances, and indicate that protecting nearshore nursery habitat of herbivorous fishes is critical for maintaining reef resilience.     

基于地理信息系统的青藏铁路穿越区生态系统恢复力评价

在明晰生态系统恢复力基本定义及其影响因子性质的基础上,基于地理信息系统(GIS)、均方差决策法和突变级数法,选择物种多样性、群落覆盖度以及群落生物量为指标对青藏铁路穿越区生态系统恢复力进行了定量评估.结果表明:研究区恢复力高值区位于祁连山草甸草原、湟水谷地的针叶林和落叶阔叶林以及唐古拉山以南的嵩草沼泽草甸,而最低值位于柴达木盆地中部和昆仑山山麓.研究区绝大部分区域的生态系统具有强或中等恢复力,整体趋势表现为:在高原面上(昆仑山以南),铁路以北区域的生态系统恢复力等级普遍较低,而在柴达木盆地以东尤其是青海湖地区,表现为铁路以南地区的恢复力等级普遍小于铁路以北地区.通过对生态系统恢复力的评价研究可以找出生态恢复建设的薄弱环节,并确定从哪些方面入手进行恢复更有效,进而可结合脆弱性评价为区域开发提供科学依据,以期避免或尽量减少人为扰动对环境造成的不利影响.