Soil organic carbon in the rocky desert of northern Negev (Israel)

Purpose

So far, the soil organic carbon (SOC) literature is dominated by studies in the humid environments with huge stocks of vulnerable carbon. Limited attention has been given to dryland ecosystems despite being often considered to be highly sensitive to environmental change. Thus, there is insufficient research about the spatial patterns of SOC stocks and the interaction between soil depth, ecohydrology, geomorphic processes, and SOC stocks. This study aimed at identifying the relationship between surface characteristics, vegetation coverage, SOC, and SOC stocks in the arid northern Negev in Israel.

Materials and methods

The study site Sede Boker is ideally suited because of well-researched but variable ecohydrology. For this purpose, we sampled five slope sections with different ecohydrologic characteristics (e.g., soil and vegetation) and calculate SOC stocks. To identify controlling factors of SOC stocks on rocky desert slopes, we compared soil properties, vegetation coverage, SOC concentration, and stocks between the five ecohydrologic units.

Results and discussion

The results show that in Sede Boker, rocky desert slopes represent a significant SOC pool with a mean SOC stock of 0.58?kg?C?m^?2 averaged over the entire study area. The spatial variability of the soil coverage represents a strong control on SOC stocks, which varies between zero in uncovered areas and 1.54?kg?C?m^?2 on average in the soil-covered areas. Aspect-driven changes of solar radiation and thus of water availability are the dominant control of vegetation coverage and SOC stock in the study area.

Conclusions

The data indicate that dryland soils contain a significant amount of SOC. The SOC varies between the ecohydrologic units, which reflect (1) aspect-driven differences, (2) microscale topography, (3) soil formation, and (4) vegetation coverage, which are of greatest importance for estimating SOC stocks in drylands.     

Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension

Background

Biomedical scientists need to access figures to validate research facts and to formulate or to test novel research hypotheses. However, figures are difficult to comprehend without associated text (e.g., figure legend and other reference text). We are developing automated systems to extract the relevant explanatory information along with figures extracted from full text articles. Such systems could be very useful in improving figure retrieval and in reducing the workload of biomedical scientists, who otherwise have to retrieve and read the entire full-text journal article to determine which figures are relevant to their research. As a crucial step, we studied the importance of associated text in biomedical figure comprehension.

Methods

Twenty subjects evaluated three figure-text combinations: figure+legend, figure+legend+title+abstract, and figure+full-text. Using a Likert scale, each subject scored each figure+text according to the extent to which the subject thought he/she understood the meaning of the figure and the confidence in providing the assigned score. Additionally, each subject entered a free text summary for each figure-text. We identified missing information using indicator words present within the text summaries. Both the Likert scores and the missing information were statistically analyzed for differences among the figure-text types. We also evaluated the quality of text summaries with the text-summarization evaluation method the ROUGE score.

Results

Our results showed statistically significant differences in figure comprehension when varying levels of text were provided. When the full-text article is not available, presenting just the figure+legend left biomedical researchers lacking 39–68% of the information about a figure as compared to having complete figure comprehension; adding the title and abstract improved the situation, but still left biomedical researchers missing 30% of the information. When the full-text article is available, figure comprehension increased to 86–97%; this indicates that researchers felt that only 3–14% of the necessary information for full figure comprehension was missing when full text was available to them. Clearly there is information in the abstract and in the full text that biomedical scientists deem important for understanding the figures that appear in full-text biomedical articles.

Conclusion

We conclude that the texts that appear in full-text biomedical articles are useful for understanding the meaning of a figure, and an effective figure-mining system needs to unlock the information beyond figure legend. Our work provides important guidance to the figure mining systems that extract information only from figure and figure legend.

     

Evolutionary analysis of herbivorous insects in natural and agricultural environments

Herbivorous insects offer a remarkable example of the biological diversity that formed the foundation for Darwin's theory of evolution by natural selection. The ability of insects to evolve resistance rapidly to insecticides and host‐plant resistance present a continual challenge for pest management. This paper considers the manner in which genetic constraints, host‐plant availability and trade‐offs affect the evolution of herbivorous insects in natural and agricultural environments, and the extent to which lessons learned from studying natural systems may be applied to improve insect resistance management in agricultural systems. Studies on the genetic architecture of adaptation by herbivores to host plants and to insecticides are reviewed. The genetic basis of resistance is an important component of simulation models that predict the evolution of resistance. These models often assume monogenic resistance, but available data suggest that this assumption may be overly narrow and that modeling of resistance as oligogenic or polygenic may be more appropriate. As omics (e.g. genomics and proteomics) technologies become more accessible, a better understanding of the genetic basis of resistance will be possible. Trade‐offs often accompany adaptations by herbivores. Trade‐offs arise when the benefit of a trait, such as the ability to feed on a novel host plant or to survive in the presence of an insecticide, is counterbalanced by fitness costs that decrease fitness in the absence of the selective agent. For resistance to insecticides, and resistance to insecticidal transgenic crops in particular, fitness costs may act as an evolutionary constraint and delay or prevent the evolution of resistance. An important observation is that certain ecological factors such as host plants and entomopathogens can magnify fitness costs, which is termed ecological negative cross‐resistance. The application of omics technologies may allow for more efficient identification of factors that will impose ecological negative cross‐resistance, thereby bolstering insect resistance management. Copyright © 2009 Society of Chemical Industry     

A comparative review of fisheries management experiences in the European Union and in other countries worldwide: Iceland,Australia, and New Zealand

This study compares the details and performance of fisheries management between the EU and a selection of other countries worldwide: Iceland, New Zealand, and Australia, which are considered in many respects to be among the most advanced in the world in fisheries management. Fisheries management in the EU, Iceland, Australia, and New Zealand has developed following different paths, despite being based on similar instruments and principles. Iceland, Australia, and New Zealand have been at the forefront of developing management practices such as stakeholder involvement, legally binding management targets (Australia, New Zealand), individual transferable quotas, and discard bans (Iceland, New Zealand). The EU has since the beginning of the 21st century taken significant steps to better involve stakeholders and establish quantitative targets through management plans, and a landing obligation is gradually being implemented from 2015 onward. The management of domestic fisheries resources in Australia, New Zealand, and Iceland has, overall, performed better than in the EU, in terms of conservation and economic efficiency. It should, however, be stressed that, compared to Australia, New Zealand, and Iceland, (i) initial over‐capacity was more of an issue in the EU when management measures became legally binding and also that (ii) EU has been progressive in developing common enforcement standards, on stocks shared by sovereign nations. The situation of EU fisheries has substantially improved over the period 2004–2013 in the northeast Atlantic, with fishery status getting close to that in the other jurisdictions, but the lack of recovery for Mediterranean fish stocks remains a concern.     

Ancient noncoding elements conserved in the human genome

Cartilaginous fishes represent the living group of jawed vertebrates that diverged from the common ancestor of human and teleost fish lineages about 530 million years ago. We generated approximately 1.4x genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost fishes and human. The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression.     

The TREC 2004 genomics track categorization task: classifying full text biomedical documents

Background

The TREC 2004 Genomics Track focused on applying information retrieval and text mining techniques to improve the use of genomic information in biomedicine. The Genomics Track consisted of two main tasks, ad hoc retrieval and document categorization. In this paper, we describe the categorization task, which focused on the classification of full-text documents, simulating the task of curators of the Mouse Genome Informatics (MGI) system and consisting of three subtasks. One subtask of the categorization task required the triage of articles likely to have experimental evidence warranting the assignment of GO terms, while the other two subtasks were concerned with the assignment of the three top-level GO categories to each paper containing evidence for these categories.

Results

The track had 33 participating groups. The mean and maximum utility measure for the triage subtask was 0.3303, with a top score of 0.6512. No system was able to substantially improve results over simply using the MeSH term Mice. Analysis of significant feature overlap between the training and test sets was found to be less than expected. Sample coverage of GO terms assigned to papers in the collection was very sparse. Determining papers containing GO term evidence will likely need to be treated as separate tasks for each concept represented in GO, and therefore require much denser sampling than was available in the data sets.The annotation subtask had a mean F-measure of 0.3824, with a top score of 0.5611. The mean F-measure for the annotation plus evidence codes subtask was 0.3676, with a top score of 0.4224. Gene name recognition was found to be of benefit for this task.

Conclusion

Automated classification of documents for GO annotation is a challenging task, as was the automated extraction of GO code hierarchies and evidence codes. However, automating these tasks would provide substantial benefit to biomedical curation, and therefore work in this area must continue. Additional experience will allow comparison and further analysis about which algorithmic features are most useful in biomedical document classification, and better understanding of the task characteristics that make automated classification feasible and useful for biomedical document curation. The TREC Genomics Track will be continuing in 2005 focusing on a wider range of triage tasks and improving results from 2004.

     

Modeling top height growth of red alder plantations

Height growth equations for dominant trees are needed for growth and yield projections, to determine appropriate silvicultural regimes, and to estimate site index. Red alder [Alnus rubra Bong.] is a fast-growing hardwood species that is widely planted in the Pacific Northwest, USA. However, red alder dominant height growth equations used currently have been determined using stem analysis trees from natural stands rather than repeated measurements of stand-level top height from plantations, which may cause them to be biased. A regional dataset of red alder plantations was complied and used to construct a dynamic base-age invariant top height growth equation. Ten anamorphic and polymorphic Generalized Algebraic Difference Approach (GADA) forms were fit using the forward difference approach. The Chapman–Richards anamorphic and Schumacher anamorphic model forms were the only ones with statistically significant parameters that yielded biologically reasonable predictions across a full range of the available data. The Schumacher model form performed better on three independent datasets and, therefore, was selected as the final model. The resulting top height growth equations differed appreciably from tree-level dominant height growth equations developed using data from natural stands, particularly at the younger ages and on lower site indices. Both the rate and shape parameters of the Schumacher function were not influenced by initial planting density. However, this analysis indicates that the asymptote, which is related to site index, may be reduced for plantations with initial planting density below 500 trees ha⁻¹. The final equation can be used for predictions of top height (and thus) site index for red alder plantations across a range of different growing conditions.     

Sources of within- and between-stand variability in specific leaf area of three ecologically distinct conifer species

Specific leaf area (SLA) is an important ecophysiological variable, but its variability within and between stands has rarely been simultaneously examined and modeled across multiple species. Extensive datasets on SLA in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco), hybrid spruce (Picea engelmannii Parry × Picea glauca (Moench) Voss × Picea sitchensis (Bong.) Carr.), and ponderosa pine (Pinus ponderosa Dougl. ex P. & C. Laws.) were used to estimate variability of SLA within a canopy and its relationship to tree- and stand-level covariates, and to predict SLA at various locations in tree crowns. Also, in the case of hybrid spruce, variation in SLA due to different relative horizontal lengths from the bole was examined. In all species, SLA systematically increased from tree tip to crown base and decreased with foliage age class. Cardinal direction did not have a highly significant influence in either Douglas-fir or hybrid spruce, but SLA did significantly decrease from branch tip to bole in hybrid spruce. Tree- and stand-level (e.g. density, site index) factors had relatively little influence on SLA, but stand age did have a significant positive influence. For ponderosa pine, a significant relationship between canopy mean current-year SLA and carbon isotope discrimination was also found, suggesting the importance of water stress in this species. An equation was fitted to estimate SLA at various points in the canopy for each species and foliage age class using absolute height in the canopy, relative vertical height in the tree, and stand age.     

Effect of wide spacing on tree growth, branch and sapwood properties of young Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] in south-western Germany

The influence of stand density on Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] is conceptually understood, but for wide spacings not well quantified, particularly in Europe. This study used 41 trees from 7 different locations in south-western Germany to compare important tree- and branch-level attributes across three different densities, namely 100, 200, and 1,200 stems ha⁻¹. In general, there were only a few tree and branch attributes that were significantly different between the 100 and 200 ha⁻¹ densities. Crown projection area and diameter of the thickest branches were the most important differences between the 100 and 200 ha⁻¹ densities. The most obvious and significant differences in this study were between 100 and 1,200 ha⁻¹ densities, where nearly every examined tree and branch attributes were statistically significant. However, relative sapwood area, the number of branches, branch angle, and the occurrence of spike knots were insensitive to stand density. Although the two lowest stand densities in this study represent rather extremely wide spacings, these results still have important implications for the development of effective thinning regimes for Douglas-fir in south-western Germany. Important management recommendations from this study include thinned stands should be maintained to at least 200 stems ha⁻¹ to maintain high log quality and stand stability. Furthermore, even at stand densities exceeding more than 1,200 trees ha⁻¹ planted trees, artificial pruning may even be necessary to produce high quality logs.