bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbes in deionized water: Implications for maintenance of laboratory water production system
Authors: Ng Wenfa
Published: January 2018

Microbes, with their diverse metabolic capabilities and great adaptability, occupy almost every conceivable ecological niche on Earth – thus, could they survive in the oligotrophic (i.e., nutrient-poor) deionized (DI) water that we use for our experiments? Observations of white cauliflower-like lumps and black specks in salt solutions after months of storage in plastic bottles prompted the inquisition concerning the origin and nature of the “contaminants.” Hypothesising that the “contaminants” may be microbes from DI water, a series of growth experiments was conducted to detect and profile the microbial diversity in fresh DI water - produced on a just-in-time basis by a filter-cum-ion-exchange system with tap water as feed. While microbes could also be present on the surfaces and headspace of the unsterilized polyethylene bottles, investigating whether microbes are present in freshly produced DI water provides a more stringent performance test of the production system. Inoculation of DI water on R2A agar followed by multi-day aerobic cultivation revealed the presence of a wide variety of microbes (total viable cell concentration of ~103 colony forming units (CFU) per mL) with differing pigmentations, growth rates as well as colony sizes and morphologies. Additionally, greater abundance and diversity of microbes was recovered at 30 oC relative to 25 and 37 oC; most probably due to adaptation of microbes to tropical ambient water temperatures of 25 to 30 oC. Comparative experiments with tap water as inoculum recovered a significantly smaller number and diversity of microbes; thereby, suggesting that monochloramine residual disinfectant in tap water was effective in inhibiting cell viability. In contrast, possible removal of monochloramine by adsorption onto ion-exchange resins – and thus, alleviation of a source of environmental stress - might explain the observed greater diversity and abundance of viable microbes in DI water. Collectively, this study confirmed the presence of microbes in fresh DI water – and suggested a possible source for the “contaminants” in prepared salt solutions. Propensity of microbes for forming biofilm on various surfaces suggested that intermittent flow in just-in-time DI water production provided opportunities for cell attachment and biofilm formation in the system during water stagnation, and subsequent dislodgement and resuspension of cells upon water flow. Thus, regular maintenance and cleaning of the production system should help reduce DI water’s microbial load. Additionally, simple and low-cost culture experiments on agar medium can provide a qualitative and semi-quantitative estimate of microbial diversity and viable cell concentration in DI water, respectively; which, along with regular monitoring of water resistivity or conductivity, comprise a trio of tests useful for detecting possible contamination or, deterioration of DI water’s chemical and microbiological quality.
Microbes in deionized water: Implications for maintenance of laboratory water production system
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Microbes, with their diverse metabolic capabilities and great adaptability, occupy almost every conceivable ecological niche on Earth – thus, could they survive in the oligotrophic (i.e., nutrient-poor) deionized (DI) water that we use for our experiments? Observations of white cauliflower-like lumps and black specks in salt solutions after months of storage in plastic bottles prompted the inquisition concerning the origin and nature of the “contaminants”. Hypothesizing that the “contaminants” may be microbes from DI water, a series of growth experiments was conducted to detect and profile the microbial diversity in fresh DI water - produced on a just-in-time basis by a filter-cum-ion-exchange system with tap water as feed. While microbes could also be present on the surfaces and headspace of the unsterilized polyethylene bottles, investigating whether microbes are present in freshly produced DI water provides a more stringent performance test of the production system. Inoculation of DI water on R2A agar followed by multi-day aerobic cultivation revealed the presence of a wide variety of microbes (total viable cell concentration of ~103 colony forming units (CFU) per mL) with differing pigmentations, growth rates as well as colony sizes and morphologies. Additionally, greater abundance and diversity of microbes was recovered at 30 oC relative to 25 and 37 oC; most probably due to adaptation of microbes to tropical ambient water temperatures of 25 to 30 oC. Comparative experiments with tap water as inoculum recovered a significantly smaller number and diversity of microbes; thereby, suggesting that monochloramine residual disinfectant in tap water was effective in inhibiting cell viability. In contrast, possible removal of monochloramine by adsorption onto ion-exchange resins – and thus, alleviation of a source of environmental stress - might explain the observed greater diversity and abundance of viable microbes in DI water. Collectively, this study confirmed the presence of microbes in fresh DI water – and suggested a possible source of the “contaminants” in prepared salt solutions. Propensity of microbes for forming biofilm on various surfaces suggested that intermittent flow in just-in-time DI water production provided opportunities for cell attachment and biofilm formation in the system during water stagnation, and subsequent dislodgement and resuspension of cells upon water flow. Thus, regular maintenance and cleaning of the production system should help reduce DI water’s microbial load. Additionally, simple and low-cost culture experiments on agar medium can provide a qualitative and semi-quantitative estimate of microbial diversity and viable cell concentration in DI water, respectively, and along with regular monitoring of water resistivity or conductivity, comprise a trio of tests useful for detecting possible contamination, or deterioration of DI water’s chemical and microbiological quality.
The Clawpack 5.x software
Authors: Mandli Kyle T , Ahmadia Aaron J , Berger Marsha , Calhoun Donna , George David L , Hadjimichael Yiannis , Ketcheson David I , Lemoine Grady I , LeVeque Randall J
Published: January 2018

Clawpack is a software package designed to solve nonlinear hyperbolic partial differential equations using high-resolution finite volume methods based on Riemann solvers and limiters. The package includes a number of variants aimed at different applications and user communities. Clawpack has been actively developed as an open source project for over 20 years. The latest major release, Clawpack 5, introduces a number of new features and changes to the code base and a new development model based on GitHub and Git submodules. This article provides a summary of the most significant changes, the rationale behind some of these changes, and a description of our current development model.
Accessing biological data with semantic web technologies
Authors: Willighagen Egon
Published: January 2018

Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness show advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows.

Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be use in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library.

Results. We here present two examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart and converts this into a RDF data set. The second example runs a query on an experimental remote SPARQL end point provided by Uniprot, and searches textual annotations of proteins encoded by the BRCA1 gene.

Discussion. The two provided library bring basic semantic web technologies to R. While only a subset of Apache Jena is currently exposed, it provides key methods to deal with RDF data and resources. The libraries are freely available from the CRAN under the Affero GNU Public License version 3: http://cran.r-project.org/web/packages/rrdf/.
Accessing biological data in R with semantic web technologies
Authors: Willighagen Egon
Published: January 2018

Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness show advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows.

Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be use in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library.

Results. We here present two examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart and converts this into a RDF data set. The second example runs a query on an experimental remote SPARQL end point provided by Uniprot, and searches textual annotations of proteins encoded by the BRCA1 gene. The third example shows how the package can be used to handle RDF returned by OpenTox web services.

Discussion. The two provided library bring basic semantic web technologies to R. While only a subset of Apache Jena is currently exposed, it provides key methods to deal with RDF data and resources. The libraries are freely available from the CRAN under the Affero GNU Public License version 3: http://cran.r-project.org/web/packages/rrdf/.
CIA; assessment of Atlantic herring spawning beds as an example of effective transboundary co-operation
Authors: Latto Philip L , Reach Ian S , Warner Iain , Russell Mark
Published: January 2018

In the UK, Cumulative Impact Assessment (CIA) has become a staple component of the licensing and regulatory assessment process. CIA considers the prospective impacts originating from new developments alongside impacts arising from existing activities. This assessment provides a representation of the disturbance experienced within UK waters, yet international transboundary effects are often overlooked or data is not freely available. An assessment of Atlantic herring Clupea harengus spawning beds was conducted. Seabed sediment maps, fisheries information and larval survey data were used to identify likely spawning sites. Interactions with seabed user activities and cumulative effects were then assessed for UK waters only. This methodology and the subsequent assessment have informed revised ICES management advice on activities interacting with spawning beds. The benefit of assessing single species interactions with developments is recognised, and the need for expanding the assessment to transcend territorial boundaries accepted. To extend this assessment to cover the geographic range of a mobile species such as Atlantic herring requires more data than considered previously. A proposed wider mapping project seeks to include data from fisheries, renewable energy companies, dredging companies, and statistics and mapping experts. This co-ordination between sea users and policy makers will allow a more robust assessment of the interaction of Atlantic herring with marine activities. Extending beyond this initial single species assessment it is suggested that there is a requirement for the quantifiable assessment of other individual transboundary receptors such as habitats, and mobile species such as birds and mammals. This can only be achieved through effective co-operation and free data exchange between developers and policy makers. Without clear co-ordination and the inclusion of all parameters in a CIA the true extent of impacts on the receptor cannot be determined.
Variation in energy intake of female chimpanzees: comparing estimates based on food item versus energy ingestion rates
Authors: Uwimbabazi Moreen , Wrangham Richard W , Machanda Zarin P , Conklin-Brittain Nancy L , Rothman Jessica M , Basuta Gilbert I
Published: January 2018

Different food items can provide calories at different rates, yet nutritional studies of primates are generally based on the proportion of time spent eating different foods. Accordingly, estimates of energy intake are potentially wrong. To assess the importance of this problem we observed 15 female chimpanzees from the Kanyawara chimpanzee community in Kibale National Park, Uganda for 15 months. Feeding rates were recorded and nutritional analyses assembled for 90 food types. Across all foods the mean estimated rate of energy ingestion was 8.8±7.6 Kcal/minute. Energy ingestion rates varied among food types (F8,82,=2.24, p<0.05), being higher for ripe fruits (12.2±8.7Kcals/min) than for young leaves (7.8±7.9Kcals/minute), piths (6.0±5.2Kcal/min) or seeds (2.8±1.9Kcal/min). Energy ingestion rates estimated assuming high %NDF fermentation (54.3%) were significantly higher than the rates at zero (0%) fermentation (t=6.14, p<0.01). At 54.3% NDF fermentation, estimated energy ingestion rate rose by 20.5% for ripe fruits (9.7 to 12.2 kcal/min), and by 39.7% for young leaves (4.7 to 7.8 kcal/min). Chimpanzees spent a mean of 314±89 minutes feeding daily, indicating that daily energy intake averaged to 2433 ±1221 Kcal. When chimpanzees spent >60% of feeding time on ripe fruits (N=74 days), the average energy intake (2494 Kcal) was significantly higher than when they spent >60% of feeding time on herbaceous vegetation (1774 Kcal, N=39 days) (F1,111=9.20, p<0.01). Our results highlight the value of using feeding rates to understand chimpanzee nutrition, and suggest that seasonal fluctuation in nutrient intake is more pronounced than indicated by variation in feeding time.
Predictive analytics using a novel simulation application: Validation of an effective decision support tool for Emergency Department flow
Authors: Hurwitz Joshua E , Lopiano Kenneth K , Bohrmann Thomas F , Swan Wendy , Falgiani Michael , Tyndall J Adrian
Published: January 2018

Objectives: To develop a scalable software application that can predict the effects of operational decisions in a variety of emergency care environments. Validate the ability of the application's core simulation model to recreate and predict site-specific patient flow at both a large academic center and a freestanding ED. Evaluate the utility of the application for use by ED managers to inform operational decisions.

Methods: The application was developed through a public-private partnership between University of Florida Health and Roundtable Analytics, Inc., supported by a National Science Foundation Small Business Technology Transfer (STTR) grant. The core simulation model was parameterized using site-specific data and Monte Carlo studies were performed to validate its ability to predict the effects of management interventions at two EDs. At one ED, the medical director conducted simulation studies to evaluate the sustainability of the current operational strategy and predict the effects of specific interventions. After implementation, the fidelity of the model's predictions was evaluated.

Results: The application was successfully built and deployed at two qualitatively distinct EDs. When equipped with site-specific parameters, the model accurately recreated the each ED's throughput and faithfully predicted the effects of specific management interventions. One ED model also identified a point when increasing arrivals dictate that the current operational strategy will become less effective than an alternative strategy. As actual arrivals approached this point, decision-makers used the application to simulate a variety different interventions and incorporated this information in their decision to implement a new strategy. The observed outcomes resulting from this intervention fell within the range of predictions from the model. An online demonstration of this application is available at http://solutions.roundtableanalytics.com/Emergency-Department-Simulation/

Conclusion: This application overcomes technical barriers to entry that have kept simulation modeling out of the hands of key decision-makers. Using this technology, ED managers with no programming experience were able to conduct simulation studies customized to their ED. Moreover, the incorporation of these results by decision-makers had a direct positive impact on ED operations. The effective use of simulation modeling promises to replace inefficient trial-and-error approaches and become a useful and accessible tool for healthcare managers challenged to make operational decisions in environments of increasingly scarce resources.
Syzygium (Myrtaceae): Monographing a taxonomic giant via 22 coordinated regional revisions
Authors: Ahmad Berhaman , Baider Claudia , Bernardini Benedetta , Biffin Edward , Brambach Fabian , Burslem David , Byng James W , Christenhusz Maarten , Florens F. B. Vincent , Lucas Eve , Ray Avik , Ray Rajasri , Smets Erik , Snow Neil , Strijk Joeri S , Wilson Peter G. ,   Syzygium Working Group
Published: January 2018

Syzygium Gaertn. is the largest woody genus of flowering plants in the world. Unpublished but extensive recent herbarium surveys suggest 1200‒1800 species distributed throughout the Old World tropics and subtropics (Table 1). Until recently, Syzygium exemplified a recurring taxonomic impediment among megadiverse genera, wherein few taxonomists worked on the group in any sustained manner, a majority of the herbarium specimens remained undetermined or misidentified, few if any attempts were made to look at the genus globally, and limited or no molecular studies were available to provide a predictive phylogenetic context of the genus. The situation with Syzygium has slowly begun to change as allied genera have been absorbed into the genus (Biffin et al., 2006; Craven & Biffin, 2010), and predictive phylogenetically-based infrageneric classifications are emerging. Taxonomic outputs on Syzygium also have been increasing across its range with the description of new species, resolution of nomenclatural and typification issues, and some regional revisions being initiated or updated. However, virtually all regional treatments (which some areas lack) need urgent revision because they are severely outdated, have limited molecular sampling and are error-ridden. We are coordinating a genus-wide taxonomic update of Syzygium through a series of 22 regional revisions, including 9 in the Flora Malesiana region (Figure 1). Each treatment will include a phylogenetic framework with species descriptions, type information, synonymy, distributions, ecological notes, and keys. Field images (Figure 2) and/or line drawings will be included with the goal of every species being illustrated. This working group has been formed to encourage a coordinated effort to document this unwieldy taxonomic giant and regional botanists working on the group are encouraged to be involved. A robust taxonomy of the genus is a prerequisite for testing the many complex questions about evolution and ecology that Syzygium could help address.
The fractal dimension of the tree of life
Authors: Ma Bin , Lv Xiaofei , Gong Jun
Published: January 2018

The structure pattern of the tree of life clues on the key ecological issues; hence knowing the fractal dimension is the fundamental question in understanding the tree of life. Yet the fractal dimension of the tree of life remains unclear since the scale of the tree of life has hypergrown in recent years. Here we show that the tree of life displays a consistent power-law rules for inter- and intra-taxonomic levels. The values of fractal dimension for both inter- and intra-taxonomic levels were different among different kingdoms. The distribution of taxa size is governed by fractal diversity but skewed by overdominating taxa with low frequency; the proportion of subtaxa in taxa with small and large sizes was greater than in taxa with intermediate size. Our results suggest that the abundance of subtaxa in taxa with small and large sizes can be predicted with fractal dimension for the accumulating taxa abundance rather than the taxa abundance. These results emphasize the need for further theoretical studies, as well as predictive modelling, to interpret the different fractal dimension for different taxonomic groups.
The fractal dimension of the tree of life
Authors: Ma Bin , Lv Xiaofei , Gong Jun
Published: January 2018

The structure pattern of the tree of life clues on the key ecological issues; hence knowing the fractal dimension is the fundamental question in understanding the tree of life. Yet the fractal dimension of the tree of life remains unclear since the scale of the tree of life has hypergrown in recent years. Here we show that the tree of life display a consistent power-law rules for inter- and intra-taxonomic levels, but the fractal dimensions were different among different kingdoms. The fractal dimension of hierarchical structure (Dr) is 0.873 for the entire tree of life, which smaller than the values of Dr for Animalia and Plantae but greater than the values of Dr for Fungi, Chromista, and Protozoa. The hierarchical fractal dimensions values for prokaryotic kingdoms are lower than for other kingdoms. The Dr value for Viruses was lower than most eukaryotic kingdoms, but greater than prokaryotes. The distribution of taxa size is governed by fractal diversity but skewed by overdominating taxa with large subtaxa size. The proportion of subtaxa in taxa with small and large sizes was greater than in taxa with intermediate size. Our results suggest that the distribution of subtaxa in taxa can be predicted with fractal dimension for the accumulating taxa abundance rather than the taxa abundance. Our study determined the fractal dimensions for inter- and intra-taxonomic levels of the present tree of life. These results emphases the need for further theoretical studies, as well as predictive modelling, to interpret the different fractal dimension for different taxonomic groups and skewness of taxa with large subtaxa size.
Variation of pyrrolizidine alkaloids in Senecio vulgaris plants from native and invasive ranges
Authors: Cheng Dandan , Nguyen Viet-Thang , Ndihokubwayo Noel
Published: January 2018

Pyrrolizidine alkaloids (PAs), a typical kind of secondary metabolites in plants, have important roles on defense against herbivores and pathogens; however, specialist herbivores adapted to PAs can use them as cues for oviposition and feeding. Thus, in the native ranges, PA diversity and concentration in plants were selected by the balance between pressure from generalist and specialist herbivores. In introduced ranges, where the specialist herbivores are absent, the introduced plants could increase concentration and diversity of PAs. This predication is deduced from the Shift Defense Hypothesis (SDH). In this research, we investigated whether there were any differences between native and invasive Senecio vulgaris plants (from Europe and China, respectively) with regards to the PA composition and concentration. We grew the native and invasive S. vulgaris plants in an identical condition and harvested them when they started to bloom. Their roots and shoots were separately harvested and dried. PA composition and concentration from powder of the shoots and roots were detected by using liquid chromatography – tanderm mass spectrometry (LC-MS/MS). We identified 14 PAs which belongs to the structural group senecionine – like PAs. Most of them occurred in both the native and invasive S. vulgaris plants, except the usaramine N – oxide that was only found in the native ones. From the 14 PAs identified, only riddelliine N – oxide had significantly higher present frequency in the invasive plants than in the native plants. The invasive S. vulgaris plants had significantly lower concentration of 3 individual PAs (seneciphylline N – oxide, spartioidine and spartioidine N – oxide) than the native ones. These results demonstrated that PA diversity and concentration of some individual PAs tended to reduce in the invasive range of S. vulgaris. This is contrary to the predictions of the SDH that the invasive plants would produce more qualitative defense than the native ones, and it is probably an evidence that a little trade – off between defense and growth happened to the S. vulgaris in China.
Automated annotation of corals in natural scene images using multiple texture representations
Authors: Blanchet Jean-Nicola , Déry Sébastien , Landry Jacques-André , Osborne Kate
Published: January 2018

Current coral reef health monitoring programs rely on biodiversity data obtained through the acquisition and annotation of underwater photographs. Manual annotation of these photographs is a necessary step, but has become problematic due to the high volume of images and the lack of available human resources. While automated and reliable multi-spectral annotation methods exist, coral reef images are often limited to visible light, which makes automation difficult. Much of the previous work has focused on popular texture recognition methods, but the results remain unsatisfactory when compared to human performance for the same task. In this work, we present an improved automatic method for coral image annotation that yields consistent accuracy improvements over existing methods. Our method builds on previous work by combining multiple feature representations. We demonstrate that the aggregation of multiple methods outperforms any single method. Furthermore, our proposed system requires virtually no parameter tuning, and supports rejection for improved results. Firstly, the complex texture diversity of corals is handled by combining multiple feature representations: local binary patterns, hue and opponent angle histograms, textons, and deep convolutional activation feature. Secondly, these multiple representations are aggregated using a score-level fusion of multiple support vector machines. Thirdly, rejection can optionally be applied to enhance classification results, and allows efficient semi-supervised image annotation in collaboration with human experts.
Morphological evidence for introgressive hybridization between Feirana quadranus and Feirana taihangnica in Tsinling Mountains, China
Authors: Song Yang , Sui Xin , Bian Yuhong , Zhang Junfang , Zheng Junqiang , Li Pipeng
Published: January 2018

Background. Feirana quadranus and Feirana taihangnica, two species of frogs inhabiting in waterbodies in the Tsinling Mountains, China, are believed to be sister species that diverged 46,000 years ago. In their sympatric area, morphological variations found between the two species imply that the two species had inter-bred. Additionally, F. taihangnica’s polyandrous breeding behavior, without amplexus, would not hinder the potential hybridization. Methods. To verify the hybridization, 117 specimens of F. quadranus and F. taihangnica were collected from eight sampling sites in their sympatric area, and 110 of the specimens were classified morphologically into VV, vw&wv, and ww, representing the putative parental and suspected hybrid types. Their maternal bloodlines were identified using a phylogenetic tree based on a region of the mitochondrial 16S rRNA gene. In total, 34 morphometric indices were selected to analyze the morphological variation between 16S-types or among morphotypes. A principal component analysis (PCA) and linear discriminant analysis (LDA) were conducted on total or partial indices for females, males, and total specimens, as well as simulated populations with falsified morphotypes. The most important indices for differentiation among morphotypes were revealed with the assistance of heat-maps. Results. In the mitochondrial DNA tree, most of the VV were in the same clade as the reference F. quadranus, labeled as Q, while most of the ww and vw&wv were grouped with the reference F. taihangnica, labeled as T. According to the PCA, there was a clear differentiation between VV and ww, while vw&wv specimens were in the middle area close to ww. According to the LDA, VV, vw&wv, and ww were clustered into three separate groups. An ambiguous differentiation between Q and T was shown both in mtDNA tree and in multivariate analyses. Seven of the specimens with conflicting classifications blurred the morphological boundary between Q and T. In both the PCA and LDA, indices that were based on the extent of bumps and skin coloration discriminated VV, vw&wv, and ww better than ratio indices that were derived from measurements. Discussion. The distribution of VV, vw&wv, and ww in multivariate spaces, especially vw&wv being scattered between VV and ww, demonstrated an introgressive hybridization pattern. The extents of bumps in the shape of an inverted "V" between the shoulder blades, spot pattern on the back, and large bumps above the anal region were the most important characteristics for differentiating between three morphotypes or between F. quadranus and F. taihangnica.
Heterochronic shifts in germband movements contribute to the rapid embryonic development of the coffin fly Megaselia scalaris
Authors: Wotton Karl R
Published: January 2018

The coffin fly, Megaselia scalaris, is a species of medical and forensic importance and is increasingly being used for the study of genetics. Postmortem interval can be estimated based on the life stage of M. scalaris recovered from corpses, therefore many studies have addressed the duration of each life stage. These studies demonstrate that embryogenesis completes significantly faster in M. scalaris than in the congener Megaselia abdita and faster even than the 24 hours needed for Drosophila melanogaster embryogenesis. However, until now it has been unclear if this increased speed is achieved by reducing developmental time across all embryonic stages or by the acceleration of individual stages and processes. Furthermore, the large difference in developmental time between the Megaselia species suggests that the staging scheme developed for M. abdita will not be directly applicable to M. scalaris. Here I use time-lapse imaging to create a staging scheme for M. scalaris embryogenesis. Comparison of stages between D. melanogaster and both Megaselia species reveals heterochronic shifts, increased coordination of morphogenetic movements and compression of individual stages all contribute to the rapid development of M. scalaris.
Tree seedling establishment among C4 grasses
Authors: February Edmund C , Lewis Joel R
Published: January 2018

The coexistence of leguminous trees and C4 grasses in African savanna remains poorly understood. Trees are able to establish among grasses despite grasses being competitively superior for below ground resources. Here we test the hypothesis that trees are only able to establish when grass biomass has been reduced. We do this at four locations in Limpopo Province South Africa where we locate young seedlings of Senegalia nigrescens. Where we found seedlings we determine grass species composition as well as grass percentage canopy cover, height above ground, and root length. We also make determinations of grass characteristics at two locations where we found no seedlings. For seedlings we determine rooting depth, plant height and stem diameter. To confirm that these are indeed young seedlings, less than a year old, we compare root length and plant height with that of seedlings germinated and grown for 77 days in a greenhouse. Our results show that where seedlings are present grasses are dominated by short-lived species such as Aristida congesta and Enneapogan cenchroides. These species are often found in disturbed soils and would increase with overgrazing. On those sites with no seedlings grass species composition is dominated by perennial species such as Panicum maximum, Panicum coloratum and Cenchrus ciliarus that would decrease with overgrazing and/or repeated burning. The perennial species have a 90-100% canopy cover while the short-lived species have a much lower canopy cover of less than 50%. Within 77 days of germinating tree seedlings are able to develop a root system that is deeper than the short-lived grasses but not deeper than the perennial grasses. These results demonstrate that tree seedlings are only able to establish among grasses if there are gaps in both grass canopy and root mass resulting from increased herbivory, frequent fire or extended drought.
Are sites with multiple single nucleotide variants in cancer genomes a consequence of drivers, hypermutable sites or sequencing errors?
Authors: Smith Thomas C A , Carr Antony M , Eyre-Walker Adam C
Published: January 2018

Across indepedent cancer genomes it has been observed that some sites have been recurrently hit by single nucleotide variants (SNVs). Such recurrently hit sites might be either i) drivers of cancer that are postively selected during oncogenesis, ii) due to mutation rate variation, or iii) due to sequencing and assembly errors. We have investigated the cause of recurrently hit sites in a dataset of >3 million SNVs from 507 complete cancer genome sequences. We find evidence that many sites have been hit significantly more often than one would expect by chance, even taking into account the effect of the adjacent nucleotides on the rate of mutation. We find that the density of these recurrently hit sites is higher in non-coding than coding DNA and hence conclude that most of them are unlikely to be drivers. We also find that most of them are found in parts of the genome that are not uniquely mappable and hence are likly to be due to mapping errors. In support of the error hypothesis, we find that recurently hit sites are not randomly distributed across sequences from different laboratories. We fit a model to the data in which the rate of mutation is constant across sites but the rate of error varies. This model suggests that ~4% of all SNVs are error in this dataset, but that the rate of error varies by thousands-of-fold.
Talk the talk and walk the walk. Evaluation of autonomy in aging and Alzheimer Disease by simulating instrumental activities of daily living: The S-IADL
Authors: Quaglino Véronique , Gounden Yannick , Lacot Emilie , Couvillers Frédérique , Lions Amandine , Hainselin Mathieu
Published: January 2018

The autonomy of individuals is linked to the achievement of instrumental activities of daily living that require complex behavior. In elderly, the assessment of autonomy is usually based on questionnaires that have strong subjective constraints. Considering this fact, we tested on elderly healthy adults and Alzheimer disease patients, a new measure, the S-IADL (Simulation of Instrumental Activities for Daily Living) to assess the ability to perform effectively activities of daily living. The S-IADL shares many items with the well-known IADL questionnaire proposed by Lawton and Brody (1969). However, as opposed to the IADL, the assessment of autonomy is not based on the completion of a questionnaire but requires the realization or simulation of various activities of daily living. Eighty-three participants (69 healthy elderly, and 14 Alzheimer Disease patients) filled in the IADL and performed the S-IADL assessment. Results revealed that like the IADL, the S-IADL is able to identify AD patients who are likely to encounter difficulties in performing everyday activities, and no major differences were found between the IADL and the S-IADL. However, this preliminary study reveals some advantages for privileging new tool based on simulation of activities in functional evaluation particularly in specific situation. Finally, we discuss of the main limits of the S-IADL that should be investigated prior to its utilization by clinicians.
Defining ecologically-relevant scales for spatial protection using long-term data on an endangered seabird and local prey availability
Authors: Sherley Richard B , Botha Philna , Underhill Les G , Ryan Peter G , van Zyl Danie , Cockcroft Andrew C , Crawford Robert JM , Dyer Bruce M , Cook Timothée R
Published: January 2018

Human activities are important drivers of marine ecosystem functioning. However, teasing apart the synergistic effects of fishing and environmental variability on the prey base of non-target predators is difficult, often because estimates of prey availability on appropriate scales are lacking. Hence, understanding the links between direct measures of prey abundance and population change can help integrate the needs of non-target predators into fisheries management. Here we investigated the local population response (number of breeders) of bank cormorants Phalacrocorax neglectus, an Endangered seabird, to the availability of its prey, the heavily-fished West Coast rock lobster Jasus lalandii. Using Bayesian state-space modelled counts of cormorants at three colonies, 22 years of fisheries-independent data on local lobster abundance and generalized additive modelling, we determined the spatial-scale pertinent to these relationships in areas of differing lobster abundance. Cormorant numbers responded positively to rock lobster availability in the regions of intermediate and high abundance, but not where regime shifts and fishing pressure have made rock lobster scarce. However, the spatial scale (30 km) at which the relationships were strongest was greater than the cormorants’ foraging range when breeding. Prey availability in the non-breeding season, prey switching and prey ecology can all influence neritic seabirds and should be considered in marine spatial planning. Crucially, though, our results highlight the potential for small-scale marine protected areas (MPAs) to benefit top predators over their full-life cycle by protecting their prey. Precautionary implementation of MPAs, with robust assessment and adaptive-management, could protect predators and their prey without negatively impacting dependent fisheries.
What the future held: Childhood psychosocial adversity is associated with health deterioration through adulthood in a cohort of British women
Authors: Nettle Daniel
Published: January 2018

Childhood psychosocial adversity is associated with accelerated onset of reproductive effort in women. Adaptive explanations for this phenomenon are built on the assumption that greater childhood psychosocial adversity is statistically associated with having a shorter period of healthy adult life during which reproduction will be possible. However, this critical assumption is never actually tested using individual-level longitudinal data. In this study, we revisit a large, longitudinally studied cohort of British women. In an earlier study, we showed that a simple index of psychosocial adversity in the first seven years of life predicted age at first pregnancy in a dose-dependent manner. Here, we show that the same index of adversity predicts accelerated deterioration of health across the potentially reproductive period, and increased levels of the inflammatory biomarker c-reactive protein at age 44. These associations are robust to controlling for adult socioeconomic position, and do not appear to be a consequence of accelerated reproductive strategy, smoking, or BMI. We argue that childhood psychosocial adversity may lead to the lasting embedding of somatic damage that accelerates age-related physical decline. This provides a compelling adaptive rationale for the accelerated reproductive schedules observed in women who experience childhood psychosocial adversity.
Association between In-scanner Head Motion with Cerebral White Matter Microstructure: A Multiband Diffusion-weighted MRI study
Authors: Kong Xiang-zhen
Published: January 2018

Diffusion-weighted MRI (DW-MRI) has emerged as a promising neuroimaging technique used to depict the biological microstructural properties of the human brain white matter. However, like any other MRI technique, DW-MRI remains subject to head motion during scanning. The association between motion and diffusion metrics is rarely understood. Previous studies have indicated that there are some regions showing significant relationship with diffusion metrics from traditional DW-MRI data with relative few gradient directions (e.g., 30 directions). As imaging techniques improves, additional gradient directions can be acquired in the same scan duration without a significant loss in spatial resolution. The current study examined the association between motion and diffusion metrics with the standard pipeline, tract-based spatial statistics (TBSS), with a multiband diffusion data (i.e., 137 directions). The diffusion metrics used in this study not only the included the commonly used metrics (i.e., FA and MD) in DW-MRI studies, but also a newly proposed inter-voxel metric, local diffusion homogeneity (LDH). The positive association was observed with MD, while the negative association with LDH. No significant association between motion and FA was observed. These results indicate that there is a similar link between motion and diffusion metrics in the multiband diffusion data. Finally, the motion-diffusion association is discussed.
Pseudo amino acid composition improves antifreeze protein prediction
Authors: Mondal Sukanta , Pai Priyadarshini P.
Published: January 2018

Antifreeze proteins (AFP) in living organisms play a key role in their tolerance to extremely cold temperatures and have wide range of biotechnological applications. But on account of diversity, their identification has been challenging to biologists. Earlier work explored in this area did not cover introduction of sequence order information, known to represent important properties of various proteins and protein systems for prediction of their attributes. In this study, the effect of Chou's pseudo amino acid composition that presents sequence order of proteins was systematically explored using support vector machines for AFP prediction. Our findings suggest that introduction of sequence order information helps identify AFPs with an accuracy of 84.75% on independent test dataset, outperforming approaches such as AFP-Pred and iAFP. The relative performance calculated using Youden’s Index (Sensitivity + Specificity -1) was found to be 0.71 for our predictor (AFP-PseAAC), 0.48 for AFP-Pred and 0.05 for iAFP. We hope this novel prediction approach will aid in AFP based research for biotechnological applications.
The pupillary light response reflects eye-movement preparation
Authors: Mathôt Sebastiaan , van der Linden Lotje , Grainger Jonathan , Vitu Françoise
Published: January 2018

When the eyes are exposed to an increased influx of light, the pupils constrict. The pupillary light response (PLR) is traditionally believed to be purely reflexive and not susceptible to cognitive influences. In contrast to this traditional view, we report here that preparation of a PLR occurs in parallel with preparation of a saccadic eye movement towards a bright (or dark) stimulus, even before the eyes set in motion. Participants fixated a central gray area and made a saccade towards a peripheral target. Using gaze-contingent display changes, we manipulated whether or not the brightness of the target background was the same during and after saccade preparation. More specifically, on some trials we changed the brightness of the target background as soon as the eyes set in motion, thus dissociating the preparatory PLR (i.e. to the brightness of the target background before the saccade) from the 'regular' PLR (i.e. to the brightness after the saccade). We show that a PLR to the brightness of the to-be-fixated target background is prepared before the eyes set in motion. This reduces the latency of the PLR by approximately 100 ms. We link our findings to the pre-saccadic shift of attention: The pupil prepares to adjusts its size to the brightness of a to-be-fixated stimulus as soon as attention covertly shifts towards that stimulus, about 100 ms before a saccade is executed. Our findings illustrate that the PLR is a dynamic movement that is tightly linked to visual attention and eye-movement preparation.
How the flow and processing of information shapes the cerebrum
Authors: de Lussanet Marc HE
Published: January 2018

The cerebrum of mammals spans a vast range of sizes and yet has a very regular structure. The amount of folding of the cortical surface and the proportion of white matter gradually increase with size, but the underlying mechanisms remain elusive. Here, two laws are derived to fully explain these cerebral scaling relations. The two general laws are derived from the notion that total processing power of the cortex is determined by the total cortical surface (i.e., the number of neurons), whereas the most efficient over-all flow of information is governed by the size of local networks (cortical columns). Since information is transferred by axonal connections which have a definite volume, a trade-off can be formulated from theoretical considerations between local, inter-gyral information transfer and long-range information transfer. It can be shown that this trade-off is governed by a single parameter describing the size of local networks, \(t_{local}\). Despite having just one free parameter, the first law fits the mammalian cerebrum better than any existing function, both across species and within humans. According to the second law, the scaling of white matter volume is also determined by the information principles. It follows that large cerebrums have much local processing and little global information flow. Moreover, paradoxically, a further increase in long-range connections would decrease the efficiency of information flow. These theoretical scaling principles help to compare the cerebrums across mammals regardless their size.
Swedish high-school pupils’ attitudes towards drugs in relation to drug usage, impulsiveness and other risk factors
Authors: Mousavi Fariba , Garcia Danilo , Archer Trevor , Ewalds-Kvist Béatrice
Published: January 2018

Background: Illicit drug use influences people’s lives and elicits unwanted behaviour. Current research shows that there is an increase in young people’s drug use in Sweden. Therefore, this study aimed at investigating high-school students’ attitudes, impulsiveness and gender differences linked to drug use. Also risk and protective factors relative to drug use were in focus of interest. Method: High school pupils (n = 146), aged 17- 21 years, responded to the Adolescent Health and Development Inventory, Barratt Impulsiveness Scale (BIS-11) and Knowledge, and the Attitudes and Beliefs (KAB). Direct logistic, multiple regression analyses, and Multivariate Analysis of Variance were used to analyse the data. Results: Positive Attitudes towards drugs was predicted by risk factors, odds ratio = 37.31. Risk factors, odds ratio = 46.89, and positive attitudes towards drugs, odds ratio = 4.63, predicted drug usage. Family, friends and individual as risk factors was positively related to impulsiveness among drug users. Moreover, although males reported using drugs to a greater extent, but female expressed more positive attitude towards drugs and even reported more impulsiveness than male students. Conclusion: Positive attitudes towards drugs among adolescents seem to be part of a vicious circle including risk factors, such as friendly drug environments (e.g., friends who use drugs) and unsupportive family environments, and impulsiveness. Even pro-drug attitudes were interpreted as a sign of a social change defined as altered norms, values and symbols of the society. This study reinforces the idea that research must focus on gender differences relative to pro-drug attitudes along with testing for differences in the predictors of girls’ and boys’ delinquency and impulsiveness.