A comparison of repeated soil inventory and carbon flux budget to detect soil carbon stock changes after conversion from cropland to grasslands

Assessment of soil carbon (C) stock changes over time is typically based on the application of two methods, namely (i) repeated soil inventory and (ii) determination of the ecosystem C budget or net biome productivity (NBP) by continuous measurement of CO₂ exchange in combination with quantification of other C imports and exports. Here, we applied both methods in parallel to determine C stock changes of two temperate grassland fields previously converted from long‐term cropland. The grasslands differed in management intensity with either intensive management (high fertilization, frequent cutting) or extensive management (no fertilization, less frequent cutting). Soil organic C stocks (0–45 cm depth) were quantified at the beginning (2001) and the end (2006) of a 5 year observational period using the equivalent soil mass approach. For the same period and in both fields, NBP was quantified from net CO₂ fluxes monitored using eddy covariance systems, and measured C import by organic fertilizer and C export by harvest. Both NBP and repeated soil inventories revealed a consistent and significant difference between management systems of 170 ± 48 and 253 ± 182  g C m^?2 a^?1, respectively. For both fields, the inventory method showed a tendency towards higher C loss/smaller C gain than NBP. In the extensive field, a significant C loss was observed by the inventory but not by the NBP approach. Thus neither flux measurements nor repeated soil sampling may be suitable for tracking absolute changes in SOC, but both give similar answers with respect to relative changes.     

Floristic composition,site conditions and diversity of poet’s daffodil (Narcissus radiiflorus Salisb.) hay meadows in the Venetian Pre-Alps and outer Dolomites (N-Italy): implications for conservation and restoration

Abstract

Hay meadows are an important component of the alpine landscape, which evolved over millennia of human activities. When traditionally managed, hay meadows support a rich flora and are recognized for high species diversity. However, both intensification and abandonment can lead to a loss of biodiversity in this vegetation. In this paper, the focus was on the hay meadows where Narcissus radiiflorus Salisb. forms white mosaic carpets during the blooming period. This vegetation was studied through 26 phytosociological relevés, taken in the Venetian Pre-Alps and outer Dolomites (Northern Italy). Relevés were numerically classified and analysed in their relationships with site conditions. Moreover, diversity metrics were calculated for detecting the conservation status of hay meadows subjected to different types of disturbance. The results showed that poet’s daffodils’ dominance brings together hay meadows showing a substantial range of floristic and ecologic variation and that part of the stands dominated by Narcissus radiiflorus could be referred to a habitat type regarded as prioritary for nature conservation. Moreover, management-related variations in functional diversity suggested that the best practice recommended for conservation and restoration of this habitat is the continuation of traditional late mowing. This practice will allow preserving both biodiversity and ecosystem functions and services.     

Evaluating uncertainty to improve a common monitoring method and guide management decisions for diamond-backed terrapins

Designing monitoring with adequate certainty to evaluate management actions can be challenging, especially for elusive species in relatively inaccessible habitats. The diamond-backed terrapin (Malaclemys terrapin) is considered a high priority species for management in all states within its range. Among key threats to terrapin populations is bycatch mortality in crab pots, prompting states throughout the species' range to consider crabbing regulations and creating a need for a monitoring approach able to evaluate the success of any new crabbing regulations to benefit terrapins. Because terrapins occupy extensive and often difficult to access estuarine habitat, it is hard to collect sufficient data to estimate population responses accurately and precisely for management. To assist state managers with decisions regarding monitoring bycatch reduction regulations, we modeled 12 years of terrapin capture-recapture data. We used estimates from those models to simulate capture-recapture data pre- and post-implementation of bycatch reduction that resulted in a 0.20 absolute increase in mean apparent survival probability. Results indicated weak reliability of a monitoring approach using only manual seining of tidal creeks to detect a real management effect, with a positive management effect detected at the 95% certainty level only 34% of the time. When we considered 85% and 75% certainty thresholds, we detected a positive effect on survival among 61% and 75% of simulations, respectively. Low within-year recapture probability and the effect of tide amplitude on terrapin availability indicate there is low feasibility of improving monitoring precision at a single site, requiring monitoring of more sites to improve confidence in the detection of the management effect. The number of sites monitored depends on the acceptable level of certainty. We recommend that researchers and management entities that use seining assess the level of certainty they require to evaluate management actions and increase the number of sites sampled to meet that level of certainty. Additionally, the use of multiple monitoring methods and integrated models should be explored to reduce uncertainty and to allow for easier monitoring of more populations over broader spatial scales.     

Robust Prediction of t‐Year Survival with Data from Multiple Studies

Summary Recently meta‐analysis has been widely utilized to combine information across multiple studies to evaluate a common effect. Integrating data from similar studies is particularly useful in genomic studies where the individual study sample sizes are not large relative to the number of parameters of interest. In this article, we are interested in developing robust prognostic rules for the prediction of t ‐year survival based on multiple studies. We propose to construct a composite score for prediction by fitting a stratified semiparametric transformation model that allows the studies to have related but not identical outcomes. To evaluate the accuracy of the resulting score, we provide point and interval estimators for the commonly used accuracy measures including the time‐specific receiver operating characteristic curves, and positive and negative predictive values. We apply the proposed procedures to develop prognostic rules for the 5‐year survival of breast cancer patients based on five breast cancer genomic studies.     

A Bayesian model averaging approach for estimating the relative risk of mortality associated with heat waves in 105 U.S. cities

Estimating the risks heat waves pose to human health is a critical part of assessing the future impact of climate change. In this article, we propose a flexible class of time series models to estimate the relative risk of mortality associated with heat waves and conduct Bayesian model averaging (BMA) to account for the multiplicity of potential models. Applying these methods to data from 105 U.S. cities for the period 1987-2005, we identify those cities having a high posterior probability of increased mortality risk during heat waves, examine the heterogeneity of the posterior distributions of mortality risk across cities, assess sensitivity of the results to the selection of prior distributions, and compare our BMA results to a model selection approach. Our results show that no single model best predicts risk across the majority of cities, and that for some cities heat-wave risk estimation is sensitive to model choice. Although model averaging leads to posterior distributions with increased variance as compared to statistical inference conditional on a model obtained through model selection, we find that the posterior mean of heat wave mortality risk is robust to accounting for model uncertainty over a broad class of models.     

The immune enhancement of propolis adjuvant on inactivated porcine parvovirus vaccine in guinea pig

Two experiments were carried out. In immune response test, the immune enhancement of propolis, oilemulsion and aluminium salt were compared in guinea pig vaccinated with inactivated porcine parvovirus (PPV) vaccine. The result showed that three adjuvants could enhance antibody titer, T lymphocyte proliferation, IL-2 and IL-4 secretion of splenic lymphocyte. The action of propolis was similar to that of oilemulsion and superior to that of aluminium salt, especially in early period of vaccination propolis could accelerate antibody production. In immune protection test, the effects of three adjuvants on PPV infection were compared in guinea pig vaccinated with PPV vaccine then challenged with PPV. The result showed that propolis and oilemulsion could enhance the antibody titer, IL-2 and IL-4 content in serum and decrease the PPV content in blood and viscera. In the effect of improving cellular immune response, the propolis was the best. These results indicated that propolis possessed better immune enhancement and would be exploited into a effective adjuvant of inactivated vaccine.     

Dynamics of the active site architecture in plant-type ferredoxin-NADP reductases catalytic complexes

Kinetic isotope effects in reactions involving hydride transfer and their temperature dependence are powerful tools to explore dynamics of enzyme catalytic sites. In plant-type ferredoxin-NADP⁺ reductases the FAD cofactor exchanges a hydride with the NADP(H) coenzyme. Rates for these processes are considerably faster for the plastidic members (FNR) of the family than for those belonging to the bacterial class (FPR). Hydride transfer (HT) and deuteride transfer (DT) rates for the NADP⁺ coenzyme reduction of four plant-type FNRs (two representatives of the plastidic type FNRs and the other two from the bacterial class), and their temperature dependences are here examined applying a full tunnelling model with coupled environmental fluctuations. Parameters for the two plastidic FNRs confirm a tunnelling reaction with active dynamics contributions, but isotope effects on Arrhenius factors indicate a larger contribution for donor–acceptor distance (DAD) dynamics in the Pisum sativum FNR reaction than in the Anabaena FNR reaction. On the other hand, parameters for bacterial FPRs are consistent with passive environmental reorganisation movements dominating the HT coordinate and no contribution of DAD sampling or gating fluctuations. This indicates that active sites of FPRs are more organised and rigid than those of FNRs. These differences must be due to adaptation of the active sites and catalytic mechanisms to fulfil their particular metabolic roles, establishing a compromise between protein flexibility and functional optimisation. Analysis of site-directed mutants in plastidic enzymes additionally indicates the requirement of a minimal optimal architecture in the catalytic complex to provide a favourable gating contribution.     

Codon usage bias in human cytomegalovirus and its biological implication

Human cytomegalovirus (HCMV) infection, a worldwide contagion, causes a serious disorder in infected individuals. Analysis of codon usage can reveal much molecular information about this virus. The effective number of codon (ENC) values, relative synonymous codon usage (RSCU) values, codon adaptation index (CAI), and nucleotide contents was investigated in approximately 160 coding sequences (CDS) among 17 human cytomegalovirus genomes using the software CodonW. Linear regression analysis and logistic regression were performed to explore the preliminary data. The results showed that, overall, HCMV genomes had low codon usage bias (mean ENC = 47.619). However, the ENC of individual CDS varied widely and was distributed unevenly between host-related genes and viral-self-function genes (P = 0.002, odds ratio (OR) = 3.194), as did the GC content (P = 0.016, OR = 2.178). The ENC values correlated with CAI, GC content, and the nucleotide composing at the 3rd codon position (GC3s) (P < 0.001). There was a significant variation in the codon preference that depended on the RSCU data. The predicted ENC curve suggested that mutational pressure, rather than natural selection, was one of the main factors that determined the codon usage bias in HCMV. Among 123 genes with known function, the genes related to viral self-replication and viral–host interaction showed different ENC and CAI values, and GC and GC3s contents. In conclusion, the detailed codon usage bias theoretically revealed information concerning HCMV evolution and could be a valuable additional parameter for HCMV gene function research.     

How is Scientific Credibility Affected by Communicating Uncertainty? The Case of Endocrine Disrupter Effects on Male Fertility

Using the case of endocrine disrupter effects on male fertility, we explored how communicating uncertainty influences the credibility of the information that laypeople receive from scientists and how laypeople form judgments about the relationship between uncertainty and credibility. We found that laypeople assess the credibility of scientific information—whether or not it is accompanied by uncertainty—by referencing their “science model” and using non-scientific references (i.e., situations encountered in one's daily life, information received from other sources, one's own observations of the world, and one's education or professional experience). Scientific credibility is a mixture of (sometimes contradictory) considerations along these different axes. Previous studies have found that some scientists assume that communicating uncertainty will lower public credibility of science. Our results contradict this assumption for situations in which academic scientists communicate uncertainty, which is perceived as additional knowledge bringing a new perspective on certain information. People expect scientists to provide practical solutions and feel disillusionment when scientists lack straight answers. However, they accepted uncertainty as an intrinsic characteristic of science and a consequence of the limits to human beings’ capacity to understand the world. Further, the low credibility of industry scientists is further reinforced when they communicate uncertainty.