bluuebunny/crossref_metadata_2025 huggingface dataset:
A modeling platform for the simultaneous emergence of ecological patterns
Authors: Locey Kenneth J , Lennon Jay T.
Published: January 2018

Patterns underpin ecological theories and paradigms. While over a dozen ecological patterns are considered to be classic or even law-like, most are divided among non-overlapping theories and subfields. As a result, ecology lacks a holistic understanding for how primary patterns can emerge in unison. We developed a simulation-based platform for this purpose. The Emergence platform encodes energetic costs, ecological selection, stochasticity, and multiplicative interactions. These phenomena capture the basis of life history trade-offs, resource-limited growth, the importance of stochasticity and determinism, and the nonlinear nature of ecological dynamics. Emergence builds individual-based models from random starting conditions and allows ecological selection to operate on random variation in species traits. Emergence generates established patterns of commonness and rarity, scaling patterns from metabolic theory and biodiversity theory, growth and abundance patterns of population ecology. Our platform reveals that iconic ecological patterns that span paradigms, theories, and sub-disciplines can simultaneously emerge from random starting conditions when basic principles are observed.
Identifying frequent patterns in biochemical reaction networks - a workflow
Authors: Lambusch Fabienne , Waltemath Dagmar , Wolkenhauer Olaf , Sandkuhl Kurt , Rosenke Christian , Henkel Ron
Published: January 2018

Computational models in biology encode molecular and cell biological processes. These models often can be represented as biochemical reaction networks. Studying such networks, one is mostly interested in systems that share similar reactions and mechanisms. Typical goals of an investigation include understanding of the parts of a model, identification of reoccurring patterns, and recognition of biologically relevant motifs. The large number and size of available models, however, require automated methods to support researchers in achieving their goals. Specifically for the problem of finding patterns in large networks only partial solutions exist.

We propose a workflow that identifies frequent structural patterns in biochemical reaction networks encoded in the Systems Biology Markup Language. The workflow utilises a subgraph mining algorithm to detect frequent network patterns. Once patterns are identified, the textual pattern description can automatically be converted into a graphical representation.Furthermore, information about the distribution of patterns among the selected set of models can be retrieved.The workflow was validated with 575 models from the curated branch of BioModels. In this paper, we highlight interesting and frequent structural patterns. Further, we provide exemplary patterns that incorporate terms from the Systems Biology Ontology. Our workflow can be applied to a custom set of models or to models already existing in our graph database MaSyMoS.

The occurrences of frequent patterns may give insight into the encoding of central biological processes, evaluate postulated biological motifs, or serve as a similarity measure for models that share common structures.

Availability: https://github.com/FabienneL/BioNet-Mining[p]

Contact: fabienne.lambusch@uni-rostock.de
Emergent properties of a non-physiological computational model of tumour growth
Authors: Pantziarka Pan
Published: January 2018

NEATG is a simple non-physiological tumour growth model which displays emergent properties which are analogous to a number of characteristics common to physical tumour growth. NEATG employs a novel dual-scale evolutionary algorithm which models both cell-autonomous and non-cell autonomous behaviours. The components of the model are outlined briefly, with reference to the core algorithm and data structures. Experimental results are presented which illustrate the behaviour of the model under different evolutionary scenarios, including homeostasis, tumour growth and a number of anti-tumour interventions. In particular the system is used to explore the impact of cytotoxic interventions, (analogous to high-dose chemotherapy), with respect to adaptive responses and evolutionary change. Finally, a number of avenues for further development of the system are discussed.
Emergent properties of a non-physiological computational model of tumour growth
Authors: Pantziarka Pan
Published: January 2018

While there have been enormous advances in our understanding of the genetic drivers and molecular pathways involved in cancer in recent decades, there also remain key areas of dispute with respect to fundamental theories of cancer. The accumulation of vast new datasets from genomics and other fields, in addition to detailed descriptions of molecular pathways, cloud the issues and lead to ever greater complexity. One strategy in dealing with such complexity is to develop thought experiments which selectively focus on different levels of abstraction in order to build models to replicate salient features of the system and therefore to build hypotheses which reflect on the real system. NEATG is a simple non-physiological tumour growth model which displays emergent behaviours that correspond to a number of clinically relevant phenomena including tumour growth, intra-tumour heterogeneity, growth arrest and accelerated repopulation following cytotoxic insult. Analysis of model data suggests that the processes of cell competition and apoptosis are key drivers of these emergent behaviours. Questions are raised as to the role of cell competition and cell death in physical cancer growth and the relevance these have to cancer research in general is discussed.
Improving knowledge-creation and post-graduate education in science and medicine by means of webpendeons and meta-links
Authors: Jewett Don L
Published: January 2018

A Compendium is a scholarly publication that is a concise, yet comprehensive, evaluation of earlier work. This Article describes ways to efficiently create knowledge to be stored in Web-based Compendia. The amount and rate of Knowledge-Creation with presently-available Knowledge-Tools does not keep up with the Information-Expansion that occurs with expanded scientific and academic activity. Two issues contributing to this failure are inefficient Knowledge-Tools and insufficient numbers of human Knowledge-Compenders. WebPendeon Software will create and manage a WebSite to be used by a group of experts, in a highly-moderated special forum, to create new Knowledge by WebPending published literature about a Narrow-Topic, into an open-access online Compendium, in a MultiLevel Format. "WebPending" means Compiling, Compending, Combining, and Compacting prior literature. Repeated WebPending creates Knowledge in forms needed for easier training. The Open-Source Software described here will have considerable and immediate impact on Science and Medicine, with regard to: efficiency of Knowledge-Creation, and quality of Post-Graduate Education. The project has been designed so that it does not need continuous funding, and will make the future Web, by itself, a complete self-sustaining Knowledge-Repository that can be used more efficiently than the present Web. Open-Access WebPendeon-WebSites will be initiated and controlled by self-nominated Moderators (primarily those in Post-Graduate Education [Science and Medicine] ). Over time, a WebPendeon will dynamically change and be repeatedly peer-reviewed (post-publication). The WebPendeon/Compendium MetaData will automatically attribute Authorship of contributions and then create, save, and transmit a Chained Hash Number in the MetaData to authenticate authorship which will make plagiarism, should it occur, provable. When no longer active, the Compendium will ultimately be placed in a ActiveArchive in which the content is aging, but the MetaData is up-to-date about newer publications that have cited the ActiveArchive's content. Today's "passive" Archives can be transformed into more valuable ActiveArchives by means of the Open-Source MetaLink Software. Software for new MetaLinks will improve WebLinkages from/to each Compendium and WebPendeon. A MetaLink is a WebLink with considerable MetaData collected for Readers, conforming to the new MetaLink-Protocol, and will provide enhanced WebLinks that are available directly on a given WebSite. Unlike present "backlinks", all MetaLinks will be from Sentence-to-Sentence, even when forwards-in-time. The MetaData will contain data known to be of interest to Readers because means are provided within the Protocol for adapting the MetaData-Categories to the different needs of different fields, or to the changing needs in a changing field.
Lowland tapir distribution and habitat loss in South America
Authors: Cordeiro Jose Luis Passos , Fragoso José MV , Crawshaw Danielle , Oliveira Luiz Flamarion B
Published: January 2018

The development of species distribution models (SDMs) can help conservation efforts by generating potential distributions and identifying areas of high environmental suitability for protection. Our study presents a rigorously derived distribution and habitat map for lowland tapir in South America. We also describe the potential habitat suitability of various geographical regions and habitat loss, inside and outside of protected areas network. Two different SDM approaches, MAXENT and ENFA, produced relative different Habitat Suitability Maps for the lowland tapir. While MAXENT was efficient at identifying areas as suitable or unsuitable, it was less efficient (when compared to the results by ENFA) at identifying the gradient of habitat suitability. MAXENT is a more multifaceted technique that establishes more complex relationships between dependent and independent variables. Our results demonstrate that for at least one species, the lowland tapir, the use of a simple consensual approach (average of ENFA and MAXENT models outputs) better reflected its current distribution patterns. The Brazilian ecoregions have the highest habitat loss for the tapir. Cerrado and Atlantic Forest account for nearly half (48.19%) of the total area lost. The Amazon region contains the largest area under protection, and the most extensive remaining habitat for the tapir, but also showed high levels of habitat loss outside protected areas, which increases the importance of support for proper management.
In silico homology modelling and identification of Tousled-like kinase 1 inhibitors for glioblastoma therapy via high throughput virtual screening protein-ligand docking
Authors: Ibrahim Kamariah , Danjuma Abubakar , Ng Chyan Leong , Abdul Murad Nor Azian , Harun Roslan , Wan Ngah Wan Zurinah , Jamal Rahman
Published: January 2018

Background: Glioblastoma multiforme (GBM) is a grade IV brain tumor that arises from star-shaped glial cells supporting neural cells called astrocytes. The survival of GBM patients remains poor despite many specific molecular targets that have been developed and used for therapy. Tousled-like kinase 1 (TLK1), a serine-threonine kinase, was identified to be overexpressed in cancers such as GBM. TLK1 plays an important role in controlling chromosomal aggregation, cell survival and proliferation. In vitro studies suggested that TLK1 is a potential target for some cancers; hence, the identification of suitable molecular inhibitors for TLK1 is warranted as a new therapeutic agents in GBM. To date, there is no structure available for TLK1. In this study, we aimed to create a homology model of TLK1 and to identify suitable molecular inhibitors or compounds that are likely to bind and inhibit TLK1 activity via in silico high-throughput virtual screening (HTVS) protein-ligand docking. Methods: 3D homology models of TLK1 were derived from various servers including HOmology ModellER, i-Tasser, Psipred and Swiss Model. All models were evaluated using Swiss Model Q-Mean server. Only one model was selected for further analysis. Further validation was performed using PDBsum, 3d2go, ProSA, Procheck analysis and ERRAT. Energy minimization was performed using YASARA energy minimization server. Subsequently, HTVS was performed using Molegro Virtual Docker 6.0 and candidate ligands from ligand.info database. Ligand-docking procedures were analyzed at the putative catalytic site of TLK1. Drug-like molecules were filtered using FAF-Drugs3, which is an ADME-Tox filtering program. Results and conclusion: High quality homology models were obtained from the Aurora B kinase (PDB ID:4B8M) derived from Xenopus levias structure that share 33% sequence identity to TLK1. From the HTVS ligand-docking, two compounds were identified to be the potential inhibitors as it did not violate the Lipinski rule of five and the CNS-based filter as a potential drug-like molecule for GBM.
Biodiversity collapse in a phase transition between neutral and niche communities
Authors: Saravia Leonardo A , Momo Fernando R
Published: January 2018

The dynamics of ecological communities can be described by two contrasting models: the first assumes that the individuals of all species are identical and do not have competitive interactions. The second assumes that species are different, adapted to particular habitat conditions, and have strong interactions. These represent extremes of a continuum: the neutral and the niche models of community organization. Real communities are actually a mixture of both types of dynamics. Here we study the simplest model of neutral-niche communities where niche dynamics is represented as a competitive hierarchy. The competition intensity is defined as a parameter that modulates the transition between these extremes. We use a stochastic cellular automata to show that there is a phase transition between the neutral and niche model with a spanning patch formed by the most abundant species. We measure the diversity as the Shannon index and the richness as the number of species. The transition implies a sharp fall of species diversity but the richness shows a gentle decline with increasing competitive intensity. As this kind of multi-species critical transition have not been described previously, we suggest new early warning signals: the rate of exponential decay in the patch distribution of the non-dominant species. This rate decreases when the community approaches the critical point and increases when the community crosses it. As an example we apply the early warnings to the Barro Colorado Tropical forest, which as expected, result to be far from a critical transition. The model shows that the critical point occur at a very low value of competitive intensity. Low values of competitive intensity were also reported for different high diversity real communities suggesting the possibility that this kind of communities are located near the critical point. This transition could happen before habitat destruction or degradation affect the community in response to changes in environmental conditions like the ones produced by climate change or exotic species invasions.
Biodiversity collapse and early warning indicators in a spatial phase transition between neutral and niche communities
Authors: Saravia Leonardo A , Momo Fernando R
Published: January 2018

The dynamics of ecological communities have been described by neutral and niche theories that are now increasingly integrated into unified models. It is known that a critical transition exists between these two states, but the spatial aspect of this transition has not been studied. Our aim is to study the spatial aspect of the transition and propose early warning signals to detect it. We used a stochastic, spatially explicit model that spans a continuum from neutral to niche communities, and is driven by the intensity of hierarchical competition. The transition is indicated by the emergence of a large patch formed by one species that connects the whole area. The properties of this patch can be used as early warning indicators of a critical transition. If competition intensity increases beyond the critical point, our model shows a sudden decrease of the Shannon diversity index and a gentle decline in species richness. The critical point occurs at a very low value of competitive intensity, with the rate of migration from the metacommunity greatly influencing the position of this critical point. As an example, we apply our new method of early warning indicators to the Barro Colorado Tropical forest, which, as expected, appears to be far from a critical transition. Low values of competitive intensity were also reported by previous studies for different high-diversity real communities, suggesting that these communities are located before the critical point. A small increase of competitive interactions could push them across the transition, however, to a state in which diversity is much lower. Thus this new early warnings indicator could be used to monitor high diversity ecosystems that are still undisturbed.
A trait based approach to bacterial biofilms in soil
Authors: Lennon Jay T , Lehmkuhl Brent K
Published: January 2018

One of the greatest challenges of living in the soil environment is that microorganisms must contend with fluctuations in water availability. Biofilm production is a trait that may helps bacteria persist through moisture conditions that are suboptimal for growth and reproduction. Using an alginate knockout of Pseudomonas aeruginosa, we demonstrate that biofilm production increased survivorship and created a more favorable moisture niche. Although biofilm production is assumed to incur a fitness cost, we were unable to detect a trade-off along a moisture gradient. In addition to increasing desiccation tolerance, biofilm production altered the soil environment in ways that were consistent with niche construction. Specifically, biofilm production increased soil water retention, but this did not facilitate the growth of an unrelated, desiccation-sensitive soil bacterium. In sum, our findings suggest that biofilm production is a response and effect trait that may influence the distribution and abundance of microorganisms in soil environments.
A trait-based approach to bacterial biofilms in soil
Authors: Lennon Jay T , Lehmkuhl Brent K
Published: January 2018

A trait-based approach focuses on attributes of taxa that influence the structure and function of communities. Biofilm production is a trait that is common among microorganisms in a wide range of environmental, engineered, and host-associated ecosystems. In this study, we present experimental evidence linking biofilm production to moisture availability, which is one of the greatest challenges for microorganisms living in the soil environment. Using Pseudomonas aeruginosa as a model system, first, we demonstrate that biofilm production is a response trait that affects bacterial performance under dry conditions. In addition to increasing survivorship, biofilm production affected the desiccation phenotype by shifting the niche space and reducing the minimum water potential needed to sustain a net-positive growth rate (Ψ*). Although the allocation of resources to biofilms is thought to be costly, we found we no evidence to support a hypothesized trade-off between bacterial fitness and biofilm production along a moisture gradient. Second, we demonstrated that biofilm production is an effect trait. Specifically, biofilm production increased soil water retention in soils that were exposed to a series of drying and rewetting cycles. Although this form of niche construction via the release of public goods should affect species interactions, we found no evidence that biofilm production modified the performance of another soil bacterium. Together, our results support the view that biofilm production is an important functional trait that may contribute to the distribution, abundance, and functioning of microorganisms in soil environments.
Phylogenetic analysis and population genetic study of Plotosus canius (Siluriformes, Plotosidae) from Malaysian coastal waters
Authors: Khalili Samani Nima , Esa Yuzine , Mohd Ikhsan Natrah Fatin , Amin Nurul
Published: January 2018

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental researches on biological characteristics of P.canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P.canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395 to 0.771 and 0.033 to 0.65 respectively, which pointed out the unlikelihood of mutation effects on gene flow. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (H0) value of 0.2168, which was lower than the standard heterozygosity in marine populations (H0= 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940 at which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P.canius, and should be necessary highlighted for appropriate management and conservation of species. Though, further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of more COI genes and nuclear hypervariable markers.
Aboveground and belowground arthropod communities experience different relative influences of stochastic and deterministic assembly processes following disturbance
Authors: Ferrenberg Scott , Martinez Alexander S. , Faist Akasha M.
Published: January 2018

Background. Understanding patterns of biodiversity is a longstanding challenge in ecology. Similar to other biotic groups, arthropod community structure can be shaped by deterministic and stochastic processes, with limited understanding of what moderates the relative influence of these processes. Disturbances have been noted to alter the relative influence of deterministic and stochastic processes on community assembly in various study systems, implicating ecological disturbances as a potential moderator of these forces. Methods. Using a disturbance gradient along a 5-year chronosequence of insect-induced tree mortality in a subalpine forest of the southern Rocky Mountains, Colorado, USA, we examined changes in community structure and relative influences of deterministic and stochastic processes in the assembly of aboveground (surface and litter-active species) and belowground (species active in organic and mineral soil layers) arthropod communities. Arthropods were sampled for all years of the chronosequence via pitfall traps (aboveground community) and modified Winkler funnels (belowground community) and sorted to morphospecies. Community structure of both communities were assessed via comparisons of morphospecies diversity and assemblages. Assembly processes were inferred from a mixture of linear models and matrix correlations testing for community associations with environmental properties, and from null-deviation models calculated from observed vs. expected levels of species turnover (Beta diversity) among samples. Results. Tree mortality altered community structure in both aboveground and belowground arthropod communities, but null models suggested that aboveground communities experienced greater relative influences of deterministic processes, while the relative influence of stochastic processes increased for belowground communities. Additionally, Mantel tests and linear regression models revealed significant associations between the aboveground arthropod communities and vegetation and soil properties, but no significant association among belowground arthropod communities and environmental factors. Discussion. Our results suggest context-dependent influences of stochastic and deterministic community assembly processes across different fractions of a ground-dwelling arthropod community following a disturbance. This variation in assembly may be linked to contrasting ecological strategies and dispersal rates within above- and below-ground communities. Our findings add to a growing body of evidence indicating concurrent influences of different processes in community assembly, and highlight the need to consider potential variation across different fractions of biotic communities when testing community ecology theory.
Declarative and Sequential learning in Spanish-speaking children with Language Impairment
Authors: Roa-Rojas Paloma , Silva-Pereyra Juan , Jackson-Maldonado Donna , Villa-Rodríguez Miguel M. A. , Gillon-Dowens Margaret
Published: January 2018

Language Impairment (LI) is a developmental disorder that mainly manifests impaired language learning and processing. Evidence, largely from English-speaking population studies, has shown that children with LI compared to typically developing (TD) children have low scores in sequential learning tasks but similar performance in declarative learning tasks. According to the declarative/procedural model, LI children compensate for their deficiency in syntactic skills (i.e., deficits in the procedural memory system) by using the declarative memory system (indispensable for vocabulary acquisition). Although there are specific deficits in children with LI depending on the language they speak, it is assumed that this model can explain the shortcomings of such pathology regardless of the language spoken. In the current study, we compared the performance of fifteen school-aged Mexican Spanish-speaking children with LI and twenty TD children during sequential and declarative learning tasks and then analyzed the relationship between their performance in these tasks and their abilities in syntax and semantics. Children with LI displayed lower scores than normal children in the sequential learning task, but no differences were found in declarative learning performance with verbal or visual stimuli. No significant correlations were observed in children with LI between their performance in sequential learning and their abilities in semantics and no significant correlations were observed in TD children between their performance in sequential learning and their abilities in syntax. In contrast, for children with LI, a significant correlation between their performance in declarative learning and their abilities in semantics was observed and for the group of TD children a significant correlation between their performance in declarative learning and their abilities in syntax was observed. This study shows that Spanish-speaking children with LI display a pattern of learning impairment that supports the declarative/procedural model hypothesis. However, they display poor verbal declarative learning skills, probably due to low verbal working memory capacity.
A new GRASP metaheuristic for biclustering of gene expression data
Authors: Ferone Daniele , Facchiano Angelo , Marabotti Anna , Festa Paola
Published: January 2018

The term biclustering stands for simultaneous clustering of both genes and conditions. This task has generated considerable interest over the past few decades, particularly related to the analysis of high-dimensional gene expression data in information retrieval, knowledge discovery, and data mining [1]. Since the problem has been shown to be NP-complete, we have recently designed and implemented a GRASP metaheuristic [2,3,4]. The greedy criterion used in the construction phase uses the Euclidean distance to build spanning trees of the graph representing the input data matrix. Once obtained a complete solution, the local search procedure tries to both enlarge the current solution and to improve its H-score exchanging rows and columns. The proposed approach has been tested on 5 synthetic datasets [5]: 1) constant biclusters; 2) constant, upregulated biclusters; 3) shift-scale biclusters; 4) shift biclusters, and 5) scale biclusters. Compared with state-of-the-art competitors, its behaviour is excellent on shift datasets and is very good on all other datasets except for scaled ones. In order to improve its behaviour on scaled data as well and to reduce running times, we have designed and preliminarily tested a variant of the existing GRASP, whose local search phase returns an approximate local optimal solution. The resulting algorithm promises to be a more efficient, general, and robust method for the biclustering of all kinds of possible biological data.
The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China
Authors: Duan Ren-Yan , Kong Xiao-Quan , Huang Min-Yi , Varela Sara , Ji Xiang
Published: January 2018

Many studies predict that climate change will cause species movement and turnover, but few studies have considered the effect of climate change on range fragmentation for current species and/or populations. We used MaxEnt to predict suitable habitat, fragmentation and turnover for 134 amphibian species in China under 40 future climate change scenarios spanning four pathways (RCP2.6, RCP4.5, RCP6 and RCP8.5) and two time periods (the 2050s and 2070s). Our results show that climate change will cause a major shift in the spatial patterns of amphibian diversity. Suitable habitats for over 90% of species will be located in the north of the current range, for over 95% of species in higher altitudes, and for over 75% of species in the west of the current range. The distributions of species predicted to move westwards, southwards and to higher altitudes will contract, while the ranges of the species not showing these trends will expand. Amphibians will lose 20% of their original ranges on average; the distribution outside current ranges will increase by 15%. Climate change will likely modify the spatial configuration of climatically suitable areas. Changes in area and fragmentation of climatically suitable patches are related, which means that species may be simultaneously affected by different stressors as a consequence of climate change.
Looking upstream: enhancers of child nutritional status in post-flood rural settings
Authors: Rodriguez-Llanes Jose Manuel , Ranjan-Dash Shishir , Mukhopadhyay Alok , Guha-Sapir Debarati
Published: January 2018

Background. Child undernutrition and flooding are highly prevalent public health issues in many developing countries. Yet we have little understanding of preventive strategies for effective coping in these circumstances. Education has been recently highlighted as key to reduce the societal impacts of extreme weather events under climate change, but there is a lack of studies assessing to what extent parental education may prevent post-flood child undernutrition. Methods and materials. One year after large floods in 2008, we conducted a two-stage cluster population-based survey of 6–59 months children inhabiting flooded and non-flooded communities of Jagatsinghpur district, Odisha (India), and collected anthropometric measurements on children along with child, parental and household level variables through face-to-face interviews. Using multivariate logistic regression models, we examined separately the effect of maternal and paternal education and other risk factors (mainly income, socio-demographic, and child and mother variables) on stunting and wasting in children from households inhabiting recurrently flooded communities (2006 and 2008; n = 299). As a comparison, separate analyses on children in non-flooded communities were carried out (n = 385). All analyses were adjusted by income as additional robustness check. Results. Overall, fathers with at least completed middle education (up to 14 years of age and compulsory in India) had an advantage in protecting their children from child wasting and stunting. For child stunting, the clearest result was a 100 to 200% lower prevalence associated with at least paternal secondary schooling (compared to no schooling) in flooded-areas. Again, only in flooded communities, an increase in per capita annual household income of 1,000 rupees was associated to a 4.7–4.9% lower prevalence of child stunting. For child wasting and only in flooded areas, delayed motherhood was associated to better nutritional outcomes (3.4% lower prevalence per year). In flooded communities, households dedicated to activities other than agriculture, a 50 to 51% lower prevalence of child wasting was estimated, suggesting farmers and fishermen as the most vulnerable livelihoods under flooding. In flooded areas, lower rank castes were at higher odds of both child wasting and stunting. Conclusions. In the short-term, protracted nutritional response in the aftermath of floods should be urgently implemented and target agricultural livelihoods and low-rank castes. Education promotion and schooling up to 14 years should have positive impacts on improving children nutritional health in the long run, especially under flooding. Policies effectively helping sustainable livelihood economic development and delayed motherhood are also recommended.
Tracking white sharks in a dynamic system at the southern tip of Africa
Authors: Jewell Oliver JD , Edwards David
Published: January 2018

Sharks and rays are among the most important of marine megafauna as they are ecologically vital predators. However, most species are threatened and over exploited. Identifying core-habitats and movement patterns within aggregation areas is critical for conservation and management efforts. White sharks are threatened globally and considered at risk of extinction. South Africa hosts the largest known concentration of the species with several documented coastal aggregations. This digital object details the various types of biotelemetry used to collect movement data from sharks as well as deployment methods and data analysis, with specific emphasis on active acoustic transmitters and manual tracking of individual sharks in Gansbaai, Western Cape (as in Jewell et al., 2014).
Do the impacts of an ecosystem engineer vary along an environmental gradient? Tests with the leaf-cutter ant Atta laevigata in a Neotropical savanna
Authors: Costa Alan N , Bruna Emilio M , Vasconcelos Heraldo L
Published: January 2018

Background. Species that transform habitats in ways that influence other species are known as Ecosystem Engineers. While the impacts of many engineers have been well described, our understanding of how these impacts vary along or alter environmental gradients remains limited. While disentangling the effects of gradients and engineers on biodiversity is complicated – the gradients themselves can be altered by engineers – doing so is necessary to advance models of ecosystem engineering. We used leaf-cutter ants (Atta spp.), a major engineer in the Neotropics, as a model system with which to investigate the relative influence of gradients and engineers on the abundance and diversity of seedlings. Methods. We conducted our research South Americas Cerrado (savanna woodlands). We used a survey of seedlings along a canopy cover gradient and data on environmental conditions previously shown to influence seedling establishment that were collected at different distances from ant colonies to fit statistical models addressing the following questions: Do the environmental conditions previously shown to influence seedling establishment vary with canopy cover? Does A. laevigata alter canopy cover and related environmental conditions influencing seedling establishment? What is the spatial extent of Atta impact on the gradient and environmental conditions, and how does this vary along the canopy cover gradient? Do A. laevigata and canopy cover act independently or in synergy to influence seedling abundance and species richness? Results. We found that the environmental conditions varied in concert with canopy cover, but that ants are not modifying canopy cover. However, ants are modifying environmental conditions, with the magnitude and spatial extent of changes consistent across the gradient. In contrast to prior studies, we found that seedling abundance and diversity were independent of canopy-related environmental conditions. Proximity to leaf-cutter nests had the strongest effect on diversity and richness. Discussion. Atta laevigata engineers environmental conditions in the Cerrado, with strong but spatially restricted consequences for seedling communities. We hypothesize that ants indirectly reduce seedling establishment by increasing rates of seed dessication and reduce seedling growth and survivorship. As such the indirect reduction of seedling abundance due to engineering could exacerbate the direct reduction due to herbivory. The effects of Atta appear restricted to the nest mound, but they could be long-lasting because mounds persist long after a colony has died or migrated. These results underscore the hypothesis that Atta plays a dominant role in Cerrado plant demography, and that its footprint may increase dramatically in coming decades due to ongoing transformations of the Cerrado.
Vaccine coverage and the cost effectiveness of dengue vaccine in South East Asia
Authors: Polwiang Sittisede
Published: January 2018

Background: Dengue is one of the most important vector-borne diseases, nearly 400000 reported cases in South East Asia and more than 2000 fatalities annually. The first of dengue vaccine called Dengvaxia by the French company, Sanofi Pasteur, was recently approved in Mexico, Brazil and the Philippines to be used for persons who are 9-45 years of age. Objective: The objective of this study was to estimate the effective of a vaccine to dengue transmission and the cost-effectiveness of the vaccine in South East Asia (SEA). Methods: The simulation and analysis was carried out using a mathematical model for dengue transmission. The vaccine was given to a certain part of population in the community and the number of dengue infections and incidences was then calculated. The cost effective price of the vaccine was measured as disability adjusted life years (DALYs) averted, and the incremental cost-effectiveness ratio (ICER) of the vaccination was expressed in 2015 US dollars per DALY averted for the countries in SEA. Results: The herd immunity was observed in the model simulation. The number of dengue incidences was declined with increased vaccine coverage in the community. If a vaccination program would be implemented the highly cost effective of vaccine per person should be 25-28 US dollars in SEA country on the average. Conclusions: Our results describe effects of the dengue vaccination to infections and incidences. The price of the vaccine has been calculated and and it is different in each SEA country due to several factors such as the number of incidences, the GDP per capita, the hospital costs and the DALYs.
Canonical instabilities of autonomous vehicle systems
Authors: Wallace Rodrick
Published: January 2018

Formal argument suggests that command, communication and control systems can remain stable in the sense of the Data Rate Theorem that mandates the minimum rate of control information required to stabilize inherently unstable 'plants', but may nonetheless, under fog-of-war demands, collapse into dysfunctional modes at variance with their fundamental mission. We apply the theory to autonomous ground vehicles under intelligent traffic control in which swarms of interacting, self-driving devices are inherently unstable as a consequence of the basic irregularity of the road network. It appears that such 'V2V/V2I' systems will experience large-scale failures analogous to the vast propagating fronts of power network blackouts, and possibly less benign, but more subtle patterns of `psychopathology' at various scales.
BMPR1A signalling is linked to tumour progression in dedifferentiated liposarcomas: lessons for rhBMP2 use in spinal surgery
Authors: O'Neill Hannah L , Cassidy Amy P , Harris Olivia B , Cassidy John W
Published: January 2018

Bone Morphogenic Protein 2 (BMP2) is a multipurpose cytokine, important in the development of bone and cartilage, and with a role in tumour initiation and progression. Because of BMP2’s osteogenic properties, a recombinant human version (rhBMP2) has found utility as an adjuvant therapy during surgery for spinal fusions. However, the results of large-scale meta-analysis has highlighted the potential of rhBMP2 to promote new tumour formation, leading to an FDA black box warning. BMP2 signal transduction is dependent on two distinct classes of serine/threonine kinase known as the type I and type II receptors. Although the type I receptors (BMPR1A and BMPR1B) are largely thought to have overlapping functions, we find tissue and cellular compartment specific patterns of expression, suggesting potential for distinct BMP2 signalling outcomes dependent on tissue type. Herein, we utilise large publicly available datasets from The Cancer Genome Atlas (TCGA) and Protein Atlas to define a novel role for BMPR1A-biased BMP2 signalling in soft tissue sarcomas. Using disease free survival as our primary endpoint, we find this BMPR1A-biased BMP2 signalling confers poor overall prognosis compared both to patients with BMPR1B-biased and to the sarcoma dataset as a whole. Through further annotation of the TCGA sarcoma dataset, we localise this effect to dedifferentiated liposarcomas but find overall BMP2/BMP receptor expression is equal across subsets. Finally, through gene set enrichment analysis we link this effect to increased transcriptional activity of the matrisome and general extracellular matrix remodelling. Our study highlights the importance of continued research into the tumorigenic properties of BMP2, the need for extensive patient follow-up and the potential disadvantages of rhBMP2 use. For the first time, we identify BMPR1A-biased BMP2 signalling as a biomarker of disease relapse in dedifferentiated liposarcomas.
Open computational landscape genetics
Authors: Joost Stéphane , Duruz Solange , Rochat Estelle , Widmer Ivo
Published: January 2018

Geographical Information Systems (GIS) are considered to be applications-led technology. Consequently, geographic information scientists commonly find themselves as guest in host disciplines in order to best exploit spatial analysis tools and methods, appropriately guided by experts in the field. An example is population genetics in evolutionary biology. Genetic information being linked to living organisms can be partially characterized by geographic coordinates. A research field named landscape genetics emerged at the intersection of genetics, environmental and geographic information science. Geocomputation and programming efforts carried out with the help of open sources technologies and dedicated to the analysis of genetic data gather together a key scientific community whose goal is to extract new knowledge from the present data tsunami caused by the advent of high throughput molecular data and of new sources of high resolution environmental data. While the level of sophistication of the population genetics functions included in the analytical frameworks developed until now are cutting-edge, advanced geo-competences are also required to reinforce the spatial side of this discipline. They will be particularly useful in conservation programmes for wildlife preservation, but also in farm animal genetic resources conservation.
Gender bias in open source: Pull request acceptance of women versus men
Authors: Terrell Josh , Kofink Andrew , Middleton Justin , Rainear Clarissa , Murphy-Hill Emerson , Parnin Chris
Published: January 2018

Biases against women in the workplace have been documented in a variety of studies. This paper presents the largest study to date on gender bias, where we compare acceptance rates of contributions from men versus women in an open source software community. Surprisingly, our results show that women's contributions tend to be accepted more often than men's. However, when a woman's gender is identifiable, they are rejected more often. Our results suggest that although women on GitHub may be more competent overall, bias against them exists nonetheless.
Changes to coral health and metabolic activity under oxygen deprivation
Authors: Murphy James WA , Richmond Robert H
Published: January 2018

Scleractinian corals play a critical role in tropical marine ecosystems by providing essential structure and food for coral reef inhabitants. However, recent investigations have found an alarming increase in coral losses from a variety of stressors, which threatens the general health and resilience of tropical coastal ecosystems. The effect of oxygen deprivation on the health of Hawaiian corals based on local drivers is of particular concern. On Hawaiian reefs, the fast-growing, invasive algae Gracilaria salicornia overgrows coral heads, restricting water flow and light, thereby smothering corals. Field data shows hypoxic conditions (dissolved oxygen (DO2) < 2 mg/L) occurring underneath algal mats at night, and concurrent bleaching and partial tissue loss of shaded corals. This study evaluates changes in coral health and metabolism through the replication of hypoxic conditions in a laboratory setting in order to limit the contribution of additional environmental variables to health shifts. Analyses of metabolic stress were accomplished through the quantification of lactate dehydrogenase and opine dehydrogenase activities. Through experimentation, treatment corals were observed to exhibit significant increases in alanopine and strombine dehydrogenase activities (ADH and SDH, respectively), but little to no lactate or octopine dehydrogenase activity. These findings indicate that not only is hypoxia a major source of increased coral stress, which occurs in response to invasive algae mat smothering, but provide novel insight into coral metabolic shifts in extremely low-oxygen environments and point to ADH and SDH as possible tools for hypoxia mitigation.
Functional analysis of the COBRA-like family
Authors: Sorek Nadav , Ryan Andrew , Carroll Andrew , Somerville Chris
Published: January 2018

The COBRA protein is found only in higher plants and algae, and has been implicated in cellulose synthesis, but its specific function remains unknown. To shed light on COBRA function we tested the ability of putative Arabidopsis COBRA orthologs to complement mutations in the COBRA gene. We expanded the previously published phylogenetic analysis and found that COBRA genes can be grouped into five clades. Representative COBRA genes from the different clades were expressed in a cobra mutant background. Surprisingly, none of the COBRA-LIKE genes was able to complement cobra, including the closest homolog which we found to bind cellulose with the same avidity as COBRA. We hypothesize that the lack of ability of the COBRA-LIKE genes to complement the cobra mutant is due to an unidentified binding interaction that is sensitive to the structure of the COBRA-LIKE proteins. However, membrane-based yeast two hybrid assays failed to identify positive interactors for COBRA.