Species diversity and arboreal structure are the main attributes that influence the community structure of forests (Magurran 1988) and hence may influence large scale carbon accumulation in humid forests over time. However anthropogenic activities can result in changes to structural components of vegetation which also influence carbon accumulation. Most studies of the relationship between biological diversity and carbon stocks or above-ground biomass (AGB) in arboreal ecosystems are based upon simple diversity indices such as species richness, Shannon Wiener index (1949), Simpson’s index (1949), and Shannon‘s evenness (Magurran 1988), which either ignore tree structure or only consider it in a limited way. Alternative structuraldiversity indexes have been developed which give a more accurate estimate of the vertical and horizontal structure of the arboreal community (Lei et al. 2009; Wang et al. 2011; Tran et al. 2013). Species abundance, stem size and height all have a direct effect on the AGB of tropical forests (Tran et al. 2013). Therefore structural indexes show a better relationship with AGB than Shannon diversity index, because they assess diversity in 2.5 cm intervals of tree trunk diameter, and combine up to three variables of community structure such as abundance, biomass and species, rather than using one variable (Tran et al. 2013). In studies of mature arboreal communities, combining both diversity and arboreal structural indexes has given stronger relationships with above-ground biomass, than when using the index individually (Tran et al. 2013).
2 StructuralDiversity in Cube-Pruning Our starting point is the cube-pruned dependency parsing model of Zhang and McDonald (2012). In that work, as here, inference is simply the Eis- ner first-order parsing model (Eisner, 1996) shown in Figure 2. In order to score higher-order fea- tures, each chart item maintains a list of signa- tures, which represent subtrees consistent with the chart item. The stored signatures are the relevant portions of the subtrees that will be part of higher- order feature calculations. For example, to score features over adjacent arcs, we might maintain ad- ditional signatures, again shown in Figure 2.
In this paper we examine the influence of critical parameters on the construction of MPSS using multidi- mensional scaling (MDS), a widely employed method for low-dimensional projection. Our analysis includes the impact of specific measures of structural similarity and the influence of the specific algorithm for MDS (either “ classical ” or “ iterative majorization, ” vide infra) on the MPSS. Further, we show that different groups of structures with common evolutionary origins are charac- terized by different levels of structuraldiversity, and that groups possessing high levels of structuraldiversity are not well captured by pairwise distances. In contrast, proximity within a MPSS predicts shared evolutionary origins of diverse groups with nearly the same efficacy as structurally self-similar groups. We also investigate the relative predictive capacities of MPSS generated using similarity scores obtained from the CE, Dali and FAT- CAT structure alignment algorithms. Finally, we investi- gate how this predictive capacity is altered by the choice of the multi-dimensional scaling algorithm.
livestock forage. As in most pastoral zones, woody taxa resources play an important role in the nourishment of livestock and meeting the needs of the human communi- ties that tend to those livestock . However, these re- sources have been progressively degraded over the last 40 years, driven by droughts, such as the large drought of the 1970s, and multiple forms of human activity. This degradation has been found to be associated with the loss of certain taxa as well as the expansion of others . Simultaneously, the average density of woody taxa in the Ferlo zone has clearly diminished over the course of the last several decades  with consequences for the quality of soil through increased erosion. Facing this situation, strategies are much needed to rehabilitate these degraded ecosystems. One such strategy is a rotational grazing approach promoted by the Senegales government to fa- cilitate the regeneration of vegetation during years in which climate conditions allow for growth and re-estab- lishment . The government has also promoted efforts to plant trees across the southern border of the Sahara desert, a pan-African project known as the Green Wall Initiative, to prevent the southwards encroachment of the desert. All of these projects have been developed with the aim of improving natural resource stocks, but have little evidence of success. In order for these strategies to work, it will be necessary to put in place a system of sustainable management that emphasizes the protection of woody taxa on fragile and vulnerable soils. This sus- tainable management requires familiarity with the precise ecological conditions under which these taxa perform best. This study aims to document the conditions under which the structuraldiversity of woody taxa changes in the Ferlo zone in order to facilitate more appropriate ma- nagement strategies.
To achieve, the National Parc of Banco has been subdivided into four (4) sectors (North, West, Central and East). Linear transects of 500 m long and 10 m wide were installed in the sectors. Along these transects, all woody species with dbh ≥ 10 cm were inventoried in the sectors. Depending on the dbh measurement, individuals were grouped into different diameter classes. The floristic inventory revealed a total of 146 woody species divided into 111 genera and belonging to 21 families. The Meliaceae family is the most abundant species. The density of the trees of the park was estimated at 257 individuals/ha with an average of 19.31 to 31.45 individuals/ha about the sector. Concerning the basal area of the PNB, it was estimated at 40.59 m²/ha. Furthermore, this study revealed the most abundant of individuals with a dbh belonging to the lower classes of diameter on those of the superior classes, with a preponderance of microphanerophytes and mesophanerophytes. Although the PNB is coveted everywhere, the results of this study reveal that it still has a relatively well-preserved structuraldiversity.
Abstract: Malaria disease continues to be a major health problem worldwide due to the emergence of multidrug-resistant strains of Plasmodium falciparum. In recent days, artemisinin (ART)-based drugs and combination therapies remain the drugs of choice for resistant P. falciparum malaria. However, resistance to ART-based drugs has begun to appear in some parts of the world. Endoperoxide compounds (natural/semisynthetic/synthetic) representing a huge number of antimalarial agents possess a wide structuraldiversity with a desired antimalarial effectiveness against resistant P. falciparum malaria. The 1,2,4-trioxane ring system lacking the lactone ring that constitutes the most important endoperoxide structural scaffold is believed to be the key pharmacophoric moiety and is primarily responsible for the pharmacodynamic potential of endoperoxide-based antimalarials. Due to this reason, research into endoperoxide, particularly 1,2,4-trioxane-, 1,2,4-trioxolane- and 1,2,4,5-teraoxane-based scaffolds, has gained significant interest in recent years for developing antimalarial drugs against resistant malaria. In this paper, a comprehensive effort has been made to review the development of endoperoxide antimalarials from traditional antimalarial leads (natural/semisynthetic) and structuraldiversity of endoperoxide molecules derived from 1,2,4-trioxane-, 1,2,4-trioxolane- and 1,2,4,5-teraoxane- based structural scaffolds, including their chimeric (hybrid) molecules, which are newer and potent antimalarial agents.
Social contagion depicts a process of information (e.g., fads, opin- ions, news) diffusion in the online social networks. A recent study reports that in a social contagion process the probability of conta- gion is tightly controlled by the number of connected components in an individual’s neighborhood. Such a number is termed struc- tural diversity of an individual and it is shown to be a key predictor in the social contagion process. Based on this, a fundamental issue in a social network is to find top-k users with the highest structural diversities. In this paper, we, for the first time, study the top-k structuraldiversity search problem in a large network. Specifi- cally, we develop an effective upper bound of structuraldiversity for pruning the search space. The upper bound can be incremen- tally refined in the search process. Based on such upper bound, we propose an efficient framework for top-k structuraldiversity search. To further speed up the structuraldiversity evaluation in the search process, several carefully devised heuristic search strate- gies are proposed. Extensive experimental studies are conducted in 13 real-world large networks, and the results demonstrate the efficiency and effectiveness of the proposed methods.
dimension would accumulate in forests with little or no harvesting, where deadwood would be generated by nat- ural disturbances (Christensen et al. 2005). While unhar- vested, primary forests may have a high degree of structuraldiversity (Stiers et al. 2018), it may also be high following natural disturbances (e.g. Nagel et al. 2006; Thom and Seidl 2016). For example, windstorms or fires create deadwood, increase light conditions near the ground that influence species richness in the regen- eration layer and lead to establishment of pioneer tree species that increase tree species richness and the diver- sity of pollen and fruit production (Hooper et al. 2005; Bauhus et al. 2017b; Hilmers et al. 2018). However, many of the inventory plots without harvesting in the most recent inventory period do not represent strictly protected forest reserves, which might develop into structurally diverse stands in the long term, but merely patches that were excluded from harvesting for that period. In the state of Baden-Württemberg, the number of forest inventory plots where no trees were harvested amounted to 34% of the total number of plots. This con- trasts with an area of strictly protected reserves of only 2.8% in the state for 2012. Therefore, many of the plots without harvesting in the most recent inventory period might have been harvested in the previous period (about 76% of unharvested plots for inventory period 2002 – 2012). In addition, in the majority of strictly protected forest reserves, which cover only a small proportion of Germany ’ s total forest area (Engel et al. 2016), manage- ment has ceased only recently or a few decades ago and therefore there has been little time to develop high levels of structuraldiversity. Hence, we do not necessarily have high levels of those structural variables indicative of old and unharvested forests at zero or low levels of harvest- ing intensity. This also indicates that long-term monitor- ing is required to facilitate meaningful interpretation of the relationship between harvesting intensity and struc- tural diversity. Any short-term changes to structuraldiversity from harvesting will be more pronounced in plots harvested recently before the last inventory, whereas they will be at least partly compensated in plots harvested in the beginning of the last inventory period (see also further below).
Anaerobic digestion (AD) is a very complex biological process. Despite being so widely used around the world, the microbial ecology of this process is very poorly understood (Nelson et al., 2010; Amha et al., 2018). Unfolding and proper understanding of the complex structuraldiversity is very important in understanding functional relationship between the various metabolic groups of microorganisms (hydrolytic, acidogenic, acetogenic and methanogenic). Understanding this synergy will help improve and optimize the process of AD thereby making it more effective (Manyi-Loh et al., 2013; Amha et al., 2018). Most of the microorganisms involved in AD are anaerobes and their cultivation in the laboratory is one of the most challenging areas of microbial research (Mori and Kamagata, 2014). Before the advent of molecular tools such as metagenomics, microbial ecology of various environments including those of the anaerobic world were largely elusive (Edet et al., 2017a; Edet et al., 2017b; Edet et al., 2018a; Edet et al., 2018b; Mori and Kamagata, 2014). Metagenomics, a culture-independent method allows for the direct examination of microbial community structure and function in an ecosystem using various bioinformatics pipelines (Edet et al., 2017a; Manyi-Loh et al., 2013). Application of omics-based studies have revealed a number of things previously unknown to the anaerobic microbial world such as new taxa and their roles in Anaerobic digester has emerged as a technology of choice in management of waste and production of biogas. However, the microbial ecology of digesters utilizing various substrates are very poorly understood. The ecology of anaerobic digester utilizing Citrullus lanatus fruit waste was analyzed using metagenomics. Slurry substrate sample was collected from a functional digester
ecological problems such as calamities. The quanti- fication of the diversity through the mathematic for- mulas allows us to evaluate this problem objectively and to better understand the relations of a given for- est ecosystem. A remarkable part of their diversity is structuraldiversity, which according to some authors is defined as specific arrangement of the components in the system (Gadow 1999) or as their positioning and mutual connections (Heupler 1982 in Lübbers 1999). According to Zenner (1999) the structure can be characterized horizontally, i.e. the spatial distribution of the trees, and vertically in their height differentiation. Lübbers (1999) added the amount and form of dead wood to these attributes. Gadow and Hui (1999) defined the structure as spatial dis- tribution, mutual position and height differentiation of the trees in a forest ecosystem. For the mathematic
Results: Here we developed an index of structuraldiversity based on National Forest Inventory (NFI) data of Baden- Württemberg, Germany, a state with 1.3 million ha of diverse forest types in different ownerships. Based on a literature review, 11 aspects of structuraldiversity were identified a priori as crucially important to describe structuraldiversity. An initial comprehensive list of 52 variables derived from National Forest Inventory (NFI) data related to structuraldiversity was reduced by applying five selection criteria to arrive at one variable for each aspect of structuraldiversity. These variables comprise 1) quadratic mean diameter at breast height (DBH), 2) standard deviation of DBH, 3) standard deviation of stand height, 4) number of decay classes, 5) bark-diversity index, 6) trees with DBH ≥ 40 cm, 7) diversity of flowering and fructification, 8) average mean diameter of downed deadwood, 9) mean DBH of standing deadwood, 10) tree species richness and 11) tree species richness in the regeneration layer. These variables were combined into a simple, additive index to quantify the level of structuraldiversity, which assumes values between 0 and 1. We applied this index in an exemplary way to broad forest categories and ownerships to assess its feasibility to analyse structuraldiversity in large-scale forest inventories.
DISCUSSION AND CONCLUSION The bedrock of the spruce natural forest in Nef- cerka NNR in TANAP is built of a crystalline com- plex. Its structure is determined to a great extent by the soil type – ranker soil, which contributes to the diversity of this virgin forest from the aspect of irregular nutrient supply. In comparison with the structuraldiversity of the virgin forest Babia hora (Vorčák et al. 2006) determined by Jaehne and Dohrenbusch index (1997), the structural diver- sity of the spruce virgin forest in Nefcerka NNR is slightly lower, in the growth stage even remark- ably lower. The reason is better soil (flysch) in the Babia hora NNR, higher number of individuals per unit area with greater height differentiation hav- ing nearly a character of unnatural forest structure (Saniga 2007). In the complex mathematic formula of Jaehne and Dohrenbusch index (1997), great support is given to the vertical structure index. In the formula, 3 thickest and 3 thinnest trees are involved, which logically gives lower values of this complex index with the lower number of trees in Nefcerka NNR. The information given by the index concerned is more important for the virgin forests in lower forest vegetation levels, where the diameter and height differentiation is greater and tree species structure is richer. Structuraldiversity qualified by the three indices confirmed the highest structuraldiversity in the growth stage and its increase with the ascending altitude.
The ability to halt Xrn1 and potentially other cellular exori- bonucleases is shared across the ﬂavivirus genus, although the RNA structural determinants of this function have diverged. Speciﬁcally, comparing the structural characteristics of the Xrn1- resistant elements from some members of the NKVFVs and the TBFVs with those from the MBFVs reveals obvious differences. Although the experimentally-supported secondary structure models of these diverse xrRNAs all contain three-way helical junctions, they are only superﬁcially similar when compared with known RNA three-way junctions 37 . In addition, the distance (in terms of sequence length) between the sequences involved in a putative long-range base pairing interaction is longer than is typical for the MBFVs 25 . Likewise, the halt point for the exori- bonuclease in the tested NKVFV and TBFV xrRNAs lies within a helical element and only 5–6 nucleotides upstream of the junc- tion. This is potentially signiﬁcant because as the enzyme approaches, it will unwind these helical elements, with the effect of further increasing the amount of single-stranded RNA between the structure and the long-range base pairing. Furthermore, at the moment the enzyme halts, the 5–6 nucleotides between the junction and the halt point will be single-stranded and inside the enzyme, suggesting a different RNA structure-based mechanism of halting Xrn1. Although it is possible that these divergent secondary structures and sequences may possess three- dimensional folds or topologies similar to those from the MBFV, it is premature to make this prediction; it is just as pos- sible that they use a different tertiary structure and strategy to block Xrn1. These observations suggest there are at least two secondary structural classes of xrRNAs within the ﬂavivirus genus: the well-characterized class typiﬁed by the MBFVs and ISFVs (Class 1) and the class found in the TBFV and some of the NKVFVs (Class 2) (Fig. 6a).
To provide an atomistic interpretation of the cryo-ET density for each topoisomer and to explore how localized distortions may alter the structural properties of DNA, we performed explicitly solvated MD simulations (Supplementary Movie 6–9). Because the inclusion of solvent molecules in the calculations slows down conﬁgurational sampling, these simulations were performed starting from conformers most commonly observed in the continuum solvent MD. The explicit solvent simulations allowed increased conformational diversity and could be directly ﬁtted to the cryo-ET density maps (Fig. 3b and Supplementary Movie 10–13). Whereas restraints were imposed on the hydrogen bond interactions between complementary base pairs in the simulations in implicit solvent, these restrictions were removed for simulations in explicit solvent. This removal of restraints allowed single-stranded regions to form within the minicircles under sufﬁciently high levels of torsional or bending stress. Accordingly, in simulations of the DLk ¼ 3 topoisomer, a kink emerged at the apex of a highly writhed minicircle, where b
same orientation. Both have evolved to provide scaffolds for a comparable set of diverse biochemical functions, including RNA-binding, small-molecule or solute recog- nition, protein-binding, supporting Fe-S clusters (ferre- doxins) and providing the skeleton for active sites of very different enzymes. Both of these folds also appear to have undergone extensive adaptive radiation even prior to LUCA after starting off as domains with primitive roles related to RNA metabolism . These two folds differ from the ancient α/β3-layered sandwich domains like the Rossmannoid and P-loop NTPase domains, which appear to have begun their existence as enzymatic domains and more-or-less retained a conserved set of basic biochemical activities throughout their evolution [121,122]. The versa- tility of the β-GF and RRM-like folds in providing scaf- folds for both enzymatic and diverse non-enzymatic function might be attributable in part to two major fac- tors: 1) an issue of contingency – these folds simply arose very early in evolution and had the time to colonize numerous functional roles. 2) Favorable structures – their relatively large sheet that is exposed on one side provides an interface for diverse interactions, especially in the form of binding various substrates. Sequence alteration to this binding surface, without disrupting the overall scaffold, could easily allow the emergence of a great diversity of new interactions. Secondly, the presence of the large sheet with just a single helical segment also favors formation of barrel-like structures, thereby opening new faces for inter- actions.
Since monoterpenes are excellent starting materials for the synthesis of enantiomeric alicyclic compounds, our aim was to synthetize new α-pinane-based optically active 1,3- amino alcohols and 1,3-diamines and to apply them as catalysts in the enantioselective addition of diethylzinc to various aldehydes. The major advantage of the chosen α-pinene over other monoterpenes is that both enantiomeric forms are commercially available in bulk. Moreover, due to the highly constrained bicyclic pinane skeleton, a high degree of chiral information transfer can be expected in asymmetric transformations. Besides the synthesis of optically pure 1,3-amino alcohols, an additional aim was to develop a simple and short procedure for the synthesis of alicyclic N-substituted 1,3-amino alcohols, since the prepara- tion of such compounds with increased diversity usually requires a time-consuming multistep process.