Source tree composition

Dividing software systems in components improves software reusability as well as software maintainability. Components live at several levels, we concentrate on the implementation level where components are formed by source files, divided over directory structures. Such source code components are usually strongly coupled in the directory structure of a software system. Their compilation is usually controlled by a single global build process. This entangling of source trees and build processes often makes reuse of source code components in different software systems difficult. It also makes software systems inflexible because integration of additional source code components in source trees and build processes is difficult. This paper's subject is to increase software reuse by decreasing coupling of source code components. It is achieved by automized assembly of software systems from reusable source code components and involves integration of source trees, build processes, and configuration processes. Application domains include generative programming, product-line architectures, and commercial off-the-shelf (COTS) software engineering

Fast and scalable inference of multi-sample cancer lineages.

Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building methods are required for cancer phylogeny reconstruction. We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples. LICHeE is open source and available at http://viq854.github.io/lichee

Scaling from single-point sap velocity measurements to stand transpiration in a multi-species deciduous forest: uncertainty sources, stand structure effect, and future scenarios impacts

ABSTRACT A major challenge in studies estimating stand water use in mixed-species forests is how to effectively scale data from individual trees to the stand. This is the case for forest ecosystems in the northeastern USA where differences in water use among species and across different size classes have not been extensively studied, despite their relevance for a wide range of ecosystem services. Our objectives were to assess the importance of different sources of variability ontranspiration upscaling and explore the potential impacts of future shifts in species composition on forest water budget. We measured sap velocity in five tree species (Fagus grandiflora, Acer rubrum, A. saccharum, Betula alleghaniensis, B. papyrifera) in a mature and young stand in NH (USA). Our results showed that the greatest potential source of error was radial variability and that tree size was more important than species in determining sap velocity. Total sapwood area was demonstrated to exert a strong controlling influence on transpiration, varying depending on tree size and species. We conclude that the effect of potential species shifts on transpirationwill depend on the sap velocity, determined mainly by radial variation and tree size, but also on the sapwood area distribution in the stand

Scaling from single-point sap velocity measurements to stand transpiration in a multi-species deciduous forest: uncertainty sources, stand structure effect, and future scenarios impacts

ABSTRACT A major challenge in studies estimating stand water use in mixed-species forests is how to effectively scale data from individual trees to the stand. This is the case for forest ecosystems in the northeastern USA where differences in water use among species and across different size classes have not been extensively studied, despite their relevance for a wide range of ecosystem services. Our objectives were to assess the importance of different sources of variability ontranspiration upscaling and explore the potential impacts of future shifts in species composition on forest water budget. We measured sap velocity in five tree species (Fagus grandiflora, Acer rubrum, A. saccharum, Betula alleghaniensis, B. papyrifera) in a mature and young stand in NH (USA). Our results showed that the greatest potential source of error was radial variability and that tree size was more important than species in determining sap velocity. Total sapwood area was demonstrated to exert a strong controlling influence on transpiration, varying depending on tree size and species. We conclude that the effect of potential species shifts on transpirationwill depend on the sap velocity, determined mainly by radial variation and tree size, but also on the sapwood area distribution in the stand

Climate tolerances and trait choices shape continental patterns of urban tree biodiversity

Aim: We propose and test a climate tolerance and trait choice hypothesis of urban macroecological variation in which strong filtering associated with low winter temperatures restricts urban biodiversity while weak filtering associated with warmer temperatures and irrigation allows dispersal of species from a global source pool, thereby increasing urban biodiversity. Location: Twenty cities across the USA and Canada. Methods: We examined variation in tree community taxonomic diversity, origins and production of an aesthetic ecosystem service trait in a cross-section of urban field surveys. We correlated urban tree community composition indicators with a key climate restriction, namely mean minimum winter temperature, and evaluated alternative possible drivers: precipitation, summer maximum temperature, population size and the percentage of adults with a college education. Results: Species accumulation curves differed substantially among cities, with observed richness varying from 22 to 122 species. Similarities in tree communities decreased exponentially with increases in climatic differences. Ordination of tree communities showed strong separation among cities with component axes correlated with minimum winter temperature and annual precipitation. Variation among urban tree communities in richness, origins and the provisioning of an aesthetic ecosystem service were all correlated with minimum winter temperature. Main conclusions: The urban climate tolerance and trait choice hypothesis provides a coherent mechanism to explain the large variation among urban tree communities resulting from an interacting environment, species and human decisions. Reconciling the feedbacks between human decision making and biophysical limitations provides a foundation for an urban ecological theory that can better understand and predict the dynamics of other linked biotic communities, associated ecosystem dynamics and resulting services provided to urban residents

Mapping the species richness and composition of tropical forests from remotely sensed data with neural networks

The understanding and management of biodiversity is often limited by a lack of data. Remote sensing has considerable potential as a source of data on biodiversity at spatial and temporal scales appropriate for biodiversity management. To-date, most remote sensing studies have focused on only one aspect of biodiversity, species richness, and have generally used conventional image analysis techniques that may not fully exploit the data's information content. Here, we report on a study that aimed to estimate biodiversity more fully from remotely sensed data with the aid of neural networks. Two neural network models, feedforward networks to estimate basic indices of biodiversity and Kohonen networks to provide information on species composition, were used. Biodiversity indices of species richness and evenness derived from the remotely sensed data were strongly correlated with those derived from field survey. For example, the predicted tree species richness was significantly correlated with that observed in the field (r=0.69, significant at the 95% level of confidence). In addition, there was a high degree of correspondence (?83%) between the partitioning of the outputs from Kohonen networks applied to tree species and remotely sensed data sets that indicated the potential to map species composition. Combining the outputs of the two sets of neural network based analyses enabled a map of biodiversity to be produce

The Linux kernel as flexible product-line architecture

The Linux kernel source tree is huge ($>$ 125 MB) and inflexible (because it is difficult to add new kernel components). We propose to make this architecture more flexible by assembling kernel source trees dynamically from individual kernel components. Users then, can select what component they really need. Hardware vendors can easily support the Linux platform by providing additional separately developed kernel components. We demonstrate how the kernel's build process can be setup for this approach and how individual build processes look like. We use a technique called source tree composition to assemble source trees of components. We demonstrate how it is automated by the tool autobundle. We also propose a kernel component base as central repository of kernel components. It forms a central meeting point for kernel developers and users

Honey volatiles as a fingerprint for botanical origin: a review on their occurrence on monofloral honeys

Honeys have specific organoleptic characteristics, with nutritional and health benefits, being highly appreciated by consumers, not only in food but also in the pharmaceutical and cosmetic industries. Honey composition varies between regions according to the surrounding flora, enabling its characterization by source or type. Monofloral honeys may reach higher market values than multifloral ones. Honey's aroma is very specific, resulting from the combination of volatile compounds present in low concentrations. The authentication of honey's complex matrix, according to its botanical and/or geographical origin, represents a challenge nowadays, due to the different sorts of adulteration that may occur, leading to the search for reliable marker compounds for the different monofloral honeys. The existing information on the volatiles of monofloral honeys is scarce and disperse. In this review, twenty monofloral honeys and honeydews, from acacia, buckwheat, chestnut, clover, cotton, dandelion, eucalyptus, fir tree, heather, lavender, lime tree, orange, pine, rape, raspberry, rhododendron, rosemary, strawberry tree, sunflower and thyme, were selected for volatile comparison purposes. Taking into consideration the country of origin, the technique of isolation and analysis, the five main volatiles from each of the honeys are compared. Whereas some compounds were found in several types of monofloral honey, and thus not considered good volatile markers, some monofloral honeys revealed characteristic volatile compounds independently of their provenance.Funding: SFRH/BD/117013/2016, UID/AGR/00690/2019, UID/AMB/50017/2019, MED (UIDB/05183/2020), FEDER, PT2020 PACompete 2020info:eu-repo/semantics/publishedVersio

Lignin engineering in forest trees

Wood is a renewable resource that is mainly composed of lignin and cell wall polysaccharides. The polysaccharide fraction is valuable as it can be converted into pulp and paper, or into fermentable sugars. On the other hand, the lignin fraction is increasingly being considered a valuable source of aromatic building blocks for the chemical industry. The presence of lignin in wood is one of the major recalcitrance factors in woody biomass processing, necessitating the need for harsh chemical treatments to degrade and extract it prior to the valorization of the cell wall polysaccharides, cellulose and hemicellulose. Over the past years, large research efforts have been devoted to engineering lignin amount and composition to reduce biomass recalcitrance toward chemical processing. We review the efforts made in forest trees, and compare results from greenhouse and field trials. Furthermore, we address the value and potential of CRISPR-based gene editing in lignin engineering and its integration in tree breeding programs

Diversity for chemical composition in a collection of different varietal types of tree tomato (Solanum betaceum Cav.), an Andean exotic fruit

[EN] We evaluated 23 tree tomato (Solanum betaceum) accessions from five cultivar groups and one wild relative (Solanum cajanumense) for 26 composition traits. For all traits we found highly significant differences (P < 0.001) among the materials studied. The high diversity found within S. betaceum for composition traits was matched by a high diversity within each of the cultivar groups. We found that sucrose and citric acid were the most important soluble sugar and organic acid, respectively, in tree tomato. Fruit in the anthocyanin pigmented (purple) group had a carotenoid content similar to that in the yellow-orange cultivar groups. Total phenolic content was significantly correlated (r = 0.8607) with antioxidant activity. Analyses of mineral content showed that tree tomato is a good source of K, Mg, and Cu. Multivariate principal components analysis (PCA) confirmed that an important diversity exists within each cultivar group. The results we have obtained indicate that the high diversity found within the tree tomato could be exploited for selection and breeding for developing the tree tomato as a commercial crop. (C) 2014 Elsevier Ltd. All rights reserved.This work was partially financed by the Ecuadorian Secretaria Nacional de Educacion Superior, Ciencia, Tecnologia e Innovacion from Ecuador (SENESCYT).Acosta-Quezada, P.; Raigón Jiménez, MD.; Riofrío-Cuenca, T.; García Martínez, MD.; Plazas Ávila, MDLO.; Burneo, J.; Figueroa, JG.... (2015). Diversity for chemical composition in a collection of different varietal types of tree tomato (Solanum betaceum Cav.), an Andean exotic fruit. Food Chemistry. 169:327-335. doi:10.1016/j.foodchem.2014.07.152S32733516