Multilevel Selection in Models of Prebiotic Evolution: Compartments and Spatial Self-organization

In this paper we explore the impact of new levels ofselection in models of early evolution.We contrast two types of higher levels of selection. On the one hand we look at spatially explicitmodels of replicators in which, by a process of self-organization, new levels of selection ariseas large scale spatial patterns with a dynamics of their own. Alternatively externally imposedlevels of selection above the basic replicators are created by enclosing the replicators in vesicles.In this paper we first review some results on the impact of emerging higher levels of selection onthe evolutionary persistence of interacting co-evolvingreplicator systems. Moreover, we presenta vesicle model, which can potentially integrate emerging and imposed levels of selection. We use the models to examinethe classical problem information integration in early evolution.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1023/A:1025754907141     

Competing Models of Stability in Complex, Evolving Systems: Kauffman vs. Simon

I criticize Herbert Simon's argument for the claim that complex natural systems must constitute decomposable, mereological or functional hierarchies. The argument depends on certain assumptions about the requirements for the successful evolution of complex systems, most importantly, the existence of stable, intermediate stages in evolution. Simon offers an abstract model of any process that succeeds in meeting these requirements. This model necessarily involves construction through a decomposable hierarchy, and thus suggests that any complex, natural, i.e., evolved, system is constituted by a decomposable hierarchy. I argue that Stuart Kauffman's recent models of genetic regulatory networks succeed in specifying processes that could meet Simon's requirements for evolvability without requiring construction through a decomposable hierarchy. Since Kauffman's models are at least as plausible as Simon's model, Simon's argument that complex natural systems must constitute decomposable, mereological or functional hierarchies does not succeed.     

Indigenous Land Use in the Ecuadorian Amazon: A Cross-cultural and Multilevel Analysis

Among the remaining tropical forests of lowland Latin America, many are inhabited by indigenous peoples, and the sustainability of their land uses is a point of heated debate in the conservation community. Numerous small-scale studies have documented changes in indigenous land use in individual communities in the context of expanding frontier settlements and markets, but few studies have included larger populations or multiple ethnic groups. In this paper we use data from a regional-scale survey of five indigenous populations in the Northern Ecuadorian Amazon to describe their agricultural land use practices and investigate the factors that affect those practices. We find the areas cultivated by indigenous households to be small compared to those of nearby mestizo colonists, but a large proportion of indigenous cultivated area is in commercial land uses. We also construct multilevel statistical models to investigate the household and community-level factors that affect indigenous land use. The results reveal significant influences on cultivated area from contextual factors such as access to markets, oil company activities, and the land tenure regime, as well as from household characteristics such as demographic composition, participation in alternative livelihood activities, and human, social and physical capitals. Overall the results are most consistent with market integration as an underlying driver of land use change in indigenous territories of the study area.

On the Use of Enterprise Models

This paper presents the results of a field study designed to determine how enterprise models are used. The paper begins with an introduction to enterprise models then provides an overview of the survey method used. No known empirical studies have been conducted to determine how enterprise models actually are used by industry. The research is designed to answer this question. A screening sample and complete web-based survey of 72 enterprise modelers was conducted. The primary research question of this survey was on the use of enterprise models, with particular focus on the three dimensions of living models: scope, enactment, and dynamicity. Half the respondents claim that their enterprise models were of their entire division, multiple divisions, and even multiple enterprises. It is encouraging to see that enterprise models are used on such a wide scope. The enactment of the enterprise models was not as large as was expected. Of the respondents, 75% claimed that their models did not receive information from the enterprise more frequently than quarterly. The same was true for how often the models provided information to the enterprise. Seventy-five percent did not update their models more than five times (although, 32% did update the model three to five times). Finally, additional areas of research are proposed.     

Use of Public Oral Health Services by the Adult Population: A Multilevel Analysis

Background

It is important to assess context to explain inequalities in oral health, particularly with regard to the type of service used; thus, this study aimed to identify the social determinants of public dental service use by adults and to assess whether, beyond the level individual, existing inequalities are also expressed in the context in which individuals are embedded.

Methods

A multilevel analysis with three levels of aggregation of variables was performed. The individual variables were derived from the database of the SB Minas Gerais project—a survey of oral health status of the population of Minas Gerais, a state of the Brazilian Southeast region. The variable at the neighborhood level came from the Census of 2010. The variables at the municipal level were obtained from available public databases relating to oral health services. At the municipal level, the Human Development Index (HDI) variable was chosen to represent quality of life in the municipalities.

Results

In the final model, the following individual variables were associated with greater use of public dental services: lower income (PR = 1.98, 95% CI = 1.53; 2.58), higher number of residents at home (PR = 1.37, 95% CI = 1.11; 1.68) and higher number of teeth requiring treatment (PR = 1.49, 95% CI = 1.20; 1.84). With regard to context variables, a poorer infrastructure (PR = 0.62, 95% CI = 0.40; 0.96) leads to a lower use of public services.

Conclusion

The use of public services is associated with family income, how this income is divided in households, the need for treatment presented by the individual and the organization of the existing oral health service infrastructure in the municipality.     

Multilevel Effects of Wealth on Women's Contraceptive Use in Mozambique

Objective

This paper analyzes the impact of wealth on the use of contraception in Mozambique unmixing the contextual effects due to community wealth from the individual effects associated with the women''s situation within the community of residence.

Methods

Data from the 2011 Mozambican Demographic and Health Survey on women who are married or living together are analyzed for the entire country and also for the rural and urban areas separately. We used single level and multilevel probit regression models.

Findings

A single level probit regression reveals that region, religion, age, previous fertility, education, and wealth impact contraceptive behavior. The multilevel analysis shows that average community wealth and the women’s relative socioeconomic position within the community have significant positive effects on the use of modern contraceptives. The multilevel framework proved to be necessary in rural settings but not relevant in urban areas. Moreover, the contextual effects due to community wealth are greater in rural than in urban areas and this feature is associated with the higher socioeconomic heterogeneity within the richest communities.

Conclusion

This analysis highlights the need for the studies on contraceptive behavior to specifically address the individual and contextual effects arising from the poverty-wealth dimension in rural and urban areas separately. The inclusion in a particular community of residence is not relevant in urban areas, but it is an important feature in rural areas. Although the women''s individual position within the community of residence has a similar effect on contraceptive adoption in rural and urban settings, the impact of community wealth is greater in rural areas and smaller in urban areas.     

Use of NHANES Data to Link Chemical Exposures to Chronic Diseases: A Cautionary Tale

Background

The National Health and Nutrition Examination Survey (NHANES) is one example of cross-sectional datasets that have been used to draw causal inferences regarding environmental chemical exposures and adverse health outcomes. Our objectives were to analyze four NHANES datasets using consistent a priori selected methods to address the following questions: Is there a consistent association between urinary bisphenol A (BPA) measures and diabetes, coronary heart disease (CHD), and/or heart attack across surveys? Is NHANES an appropriate dataset for investigating associations between chemicals with short physiologic half-lives such as BPA and chronic diseases with multi-factorial etiologies? Data on urinary BPA and health outcomes from 2003–2004, 2005–2006, 2007–2008, and 2009–2010 were available.

Methodology and Findings

Regression models were adjusted for creatinine, age, gender, race/ethnicity, education, income, smoking, heavy drinking, BMI, waist circumference, calorie intake, family history of heart attack, hypertension, sedentary time, and total cholesterol. Urinary BPA was not significantly associated with adverse health outcomes for any of the NHANES surveys, with ORs (95% CIs) ranging from 0.996 (0.951–1.04) to 1.03 (0.978–1.09) for CHD, 0.987 (0.941–1.04) to 1.04 (0.996–1.09) for heart attack, and 0.957 (0.899–1.02) to 1.01 (0.980–1.05) for diabetes.

Conclusions

Using scientifically and clinically supportable exclusion criteria and outcome definitions, we consistently found no associations between urinary BPA and heart disease or diabetes. These results do not support associations and causal inferences reported in previous studies that used different criteria and definitions. We are not drawing conclusions regarding whether BPA is a risk factor for these diseases. We are stating the opposite–that using cross-sectional datasets like NHANES to draw such conclusions about short-lived environmental chemicals and chronic complex diseases is inappropriate. We need to expend resources on appropriately designed epidemiologic studies and toxicological explorations to understand whether these types of chemicals play a causal role in chronic diseases.     

Multilevel Selection in Models of Prebiotic Evolution II: A Direct Comparison of Compartmentalization and Spatial Self-Organization

Multilevel selection has been indicated as an essential factor for the evolution of complexity in interacting RNA-like replicator systems. There are two types of multilevel selection mechanisms: implicit and explicit. For implicit multilevel selection, spatial self-organization of replicator populations has been suggested, which leads to higher level selection among emergent mesoscopic spatial patterns (traveling waves). For explicit multilevel selection, compartmentalization of replicators by vesicles has been suggested, which leads to higher level evolutionary dynamics among explicitly imposed mesoscopic entities (protocells). Historically, these mechanisms have been given separate consideration for the interests on its own. Here, we make a direct comparison between spatial self-organization and compartmentalization in simulated RNA-like replicator systems. Firstly, we show that both mechanisms achieve the macroscopic stability of a replicator system through the evolutionary dynamics on mesoscopic entities that counteract that of microscopic entities. Secondly, we show that a striking difference exists between the two mechanisms regarding their possible influence on the long-term evolutionary dynamics, which happens under an emergent trade-off situation arising from the multilevel selection. The difference is explained in terms of the difference in the stability between self-organized mesoscopic entities and externally imposed mesoscopic entities. Thirdly, we show that a sharp transition happens in the long-term evolutionary dynamics of the compartmentalized system as a function of replicator mutation rate. Fourthly, the results imply that spatial self-organization can allow the evolution of stable folding in parasitic replicators without any specific functionality in the folding itself. Finally, the results are discussed in relation to the experimental synthesis of chemical Darwinian systems and to the multilevel selection theory of evolutionary biology in general. To conclude, novel evolutionary directions can emerge through interactions between the evolutionary dynamics on multiple levels of organization. Different multilevel selection mechanisms can produce a difference in the long-term evolutionary trend of identical microscopic entities.     

Evaluation of Constant Thickness Cartilage Models vs. Patient Specific Cartilage Models for an Optimized Computer-Assisted Planning of Periacetabular Osteotomy

Modern computerized planning tools for periacetabular osteotomy (PAO) use either morphology-based or biomechanics-based methods. The latter relies on estimation of peak contact pressures and contact areas using either patient specific or constant thickness cartilage models. We performed a finite element analysis investigating the optimal reorientation of the acetabulum in PAO surgery based on simulated joint contact pressures and contact areas using patient specific cartilage model. Furthermore we investigated the influences of using patient specific cartilage model or constant thickness cartilage model on the biomechanical simulation results. Ten specimens with hip dysplasia were used in this study. Image data were available from CT arthrography studies. Bone models were reconstructed. Mesh models for the patient specific cartilage were defined and subsequently loaded under previously reported boundary and loading conditions. Peak contact pressures and contact areas were estimated in the original position. Afterwards we used a validated preoperative planning software to change the acetabular inclination by an increment of 5° and measured the lateral center edge angle (LCE) at each reorientation position. The position with the largest contact area and the lowest peak contact pressure was defined as the optimal position. In order to investigate the influence of using patient specific cartilage model or constant thickness cartilage model on the biomechanical simulation results, the same procedure was repeated with the same bone models but with a cartilage mesh of constant thickness. Comparison of the peak contact pressures and the contact areas between these two different cartilage models showed that good correlation between these two cartilage models for peak contact pressures (r = 0.634 ∈ [0.6, 0.8], p < 0.001) and contact areas (r = 0.872 > 0.8, p < 0.001). For both cartilage models, the largest contact areas and the lowest peak pressures were found at the same position. Our study is the first study comparing peak contact pressures and contact areas between patient specific and constant thickness cartilage models during PAO planning. Good correlation for these two models was detected. Computer assisted planning with FE modeling using constant thickness cartilage models might be a promising PAO planning tool when a conventional CT is available.     

Pre‐ to Postoperative Physical Activity Changes in Bariatric Surgery Patients: Self Report vs. Objective Measures

Bariatric surgery patients report significant pre‐ to postoperative increases in physical activity (PA). However, it is unclear whether objective measures would corroborate these changes. The present study compared self‐reported and accelerometer‐based estimates of changes in moderate‐to‐vigorous intensity PA (MVPA) from pre‐ (pre‐op) to 6 months postsurgery (post‐op). Twenty bariatric surgery (65% laparoscopic‐adjustable gastric banding, 35% gastric bypass) patients (46.2 ± 9.8 years, 88% female, pre‐op BMI = 50.8 ± 9.7 kg/m²) wore RT3 accelerometers as an objective measure of MVPA and completed the Paffenbarger Physical Activity Questionnaire (PPAQ) as a subjective measure before and 6 months after bariatric surgery. Time (min/week) spent in MVPA was calculated for the PPAQ and RT3 (≥1‐min and ≥10‐min bouts) at pre‐op and post‐op. Self‐reported MVPA increased fivefold from pre‐op to post‐op (44.6 ± 80.8 to 212.3 ± 212.4 min/week; P < 0.005). By contrast, the RT3 showed nonsignificant decreases in MVPA for both ≥1‐min (186.0 ± 169.0 to 151.2 ± 118.3 min/week) and ≥10‐min (41.3 ± 109.3 to 39.8 ± 71.3 min/week) bouts. At pre‐op, the percentage of participants who accumulated ≥150‐min/week of MVPA in bouts ≥10‐min according to the PPAQ and RT3 was identical (10%). However, at post‐op, 55% of participants reported compliance with the recommendation compared to 5% based on RT3 measurement (P = 0.002). Objectively‐measured changes in MVPA from pre‐op to 6 months post‐op appear to be much smaller than self‐reported changes. Further research involving larger samples is needed to confirm these findings and to determine whether self‐report and objective PA measures are differentially associated with surgical weight loss outcomes.     

Aggregated proteoglycan synthesis in organ cultures of human nucleus pulposus.

Proteoglycans isolated under associative conditions in the presence of protease inhibitors from human nucleus pulposus contained 17% aggregate and 83% non-aggregating monomer (Kav = 0.5 on Sepharose CL-2B). Isolated aggregate after reduction and alkylation was resolved into two components (Kav = 0.15 and 0.43) on Sepharose CL-2B. Labeled proteoglycans isolated from parallel samples pulsed with [35S]sulfate and chased for up to 18 h were present largely as aggregated material (up to 78%). Reduction and alkylation of the labeled samples gave a labeled proteoglycan monomer with Kav = 0.15. Both the labeled and unlabeled chondroitin sulfate chains had the same distribution on Sepharose CL-6B and equivalent molecular weights (Mr = 2.0 x 10(3)). After chondroitinase ABC digestion, the unlabeled keratan sulfate-protein core was polydisperse with a Kav = 0.38 on Sepharose CL-4B while the labeled keratan sulfate-protein core had a Kav = 0.05. This indicates that the newly synthesized proteoglycan had a large core protein and suggests that the proteoglycans present in nucleus pulposus are originally synthesized as large molecular weight, aggregating proteoglycans.     

Clarifying the regulation of genome editing in Australia: situation for food

Transgenic Research -     

Models of Cadmium Accumulation and Toxicity to Hyalella azteca during 7- and 28-Day Exposures

The inhibition of Cd accumulation by Ca in the amphipod Hyalella azteca in short-term (7-d) exposures appears to follow anti-competitive, rather than competitive, inhibition. Increasing Ca reduces Cd accumulation more at high than at low Cd concentrations. Cadmium accumulation and toxicity in chronic exposures can be predicted using the 7-d model to which the effects of acclimation, Cd inhibition of acclimation, and growth dilution are added. The resultant model is complex and species-specific, making it unwieldy for direct application in water quality guideline or criteria development. However, it does demonstrate that a mechanistic explanation of the relationship between short- and long-term accumulation and toxicity is possible, as well as suggest why the acute-to-chronic ratio changes with water chemistry. It is not, therefore, appropriate to estimate chronic Cd toxicity to H. azteca from acute toxicity assuming a constant acute-to-chronic ratio. The standard Biotic Ligand Model (BLM) can also be fit to the chronic bioaccumulation and toxicity data. This may be a more practical approach to guideline or criteria development, provided it is understood that this is an empirical fit of the model and that the underlying mechanisms are far more complex than those invoked in the standard BLM.     

A Multilevel Analysis of the Impact of Land Use on Interannual Land-Cover Change in East Africa

Abstract The aim of this study was to characterize the short-term land-cover change processes that were detected in Eastern Africa, based on a set of change metrics that allow for the quantification of interannual changes in vegetation productivity, changes in vegetation phenology and a combination of both. We tested to what extent land use, fire activity and livestock grazing modified the vegetation response to short-term rainfall variability in East Africa and how this is reflected in change metrics derived from MODerate Imaging Spectrometer (MODIS) time series of remote sensing data. We used a hierarchical approach to disentangle the contribution of human activities and climate variability to the patterns of short-term vegetation change in East Africa at different levels of organization. Our results clearly show that land use significantly influences the vegetation response to rainfall variability as measured by time series of MODIS data. Areas with different types of land use react in a different way to interannual climate variability, leading to different values of the change indices depending on the land use type. The impact of land use is more reflected in interannual variability of vegetation productivity and overall change in the vegetation, whereas changes in phenology are mainly driven by climate variability and affect most vegetation types in similar ways. Our multilevel approach led to improved models and clearly demonstrated that climate influence plays at a different scale than land use, fire and herbivore grazing. It helped us to understand dynamics within and between biomes in the study area and investigate the relative importance of different factors influencing short-term variability in change indices at different scales.     

New Views of Old Proteins: Clarifying the Enigmatic Proteome

All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.