bluuebunny/crossref_metadata_2025 huggingface dataset:
Opportunities drive the global distribution of protected areas
Authors: Baldi Germán , Texeira Marcos , Martin Osvaldo A , Grau H. Ricardo , Jobbágy Esteban G
Published: January 2018

Background. The establishment of protected areas, regarded today as a cornerstone of nature conservation, resulted from a multiple array of motivations and opportunities. We explore at global and regional levels, the current distribution of protected areas along biophysical, human, and biological gradients, and assess to what extent protection pursued (i) a balanced representation of biophysical environments, (ii) a set of preferred conditions (biological, spiritual, economical, or geopolitical) or (iii) lands where conservation opportunities exist. Methods. We described with histograms the distribution of terrestrial protected areas along physical, human, and biological independent gradients. Linear and non-linear regressions and correlations led to a general description of sign, shape, and strength of the relationships; a random forest analysis led to a importance ranking of the variables related to individual preferential motivations and opportunistic forces; and an evenness metric seized the strength of variables related to individual representative motivations. Results. We found that globally protection was primarily driven by the opportunities provided by isolation and a low population density (variable importance = 34.6 and 19.9, respectively). Preferences played a secondary role, with a bias towards tourist attractions and international borders (variable importance = 12.7 and 3.4, respectively). Opportunities shaped protection strongly in North America & Australia–NZ and Latin America & Caribbean, while the representativeness of biophysical environments was higher in Sub-Saharan Africa (1.3 times the average of other regions). Discussion. Our results suggest that in spite of being a top priority in land conservation agendas, environmental representativeness and biodiversity protection are still minor players driving protection at global and regional levels, and that the attempts to increase their relevance will necessarily have to recognize the predominant weight that other drivers are playing in the protected areas deployment.
Cost hurdles to open access publishing: A citizen scientist perspective
Authors: Ng Wenfa
Published: January 2018

Besides offering fun activities for non-scientists to explore the natural world through experiments, simulations or games, the evolving concept of citizen science is increasingly allowing some serious publication quality science to be published by the practitioners (citizen scientists) themselves. The latter is in contrast to the common perception of citizen science, where most citizen science projects such as Foldit are distribution of piecemeal segments of complex projects suitable for solution by individuals, and where the results are pooled together, or used to inform the design and direction of more complex research initiatives. Usually novices in science publishing but nonetheless aware of the importance of journal articles as the primary medium for communicating new research to the wider community (scientific and general public), citizen scientists do encounter significant challenges in science publication. One challenge is in navigating the lengthy and time-consuming peer review process of most journals. But, as benefactors of open access publishing for their scientific literature, where most journal articles are within pay walls inaccessible to citizen scientists without any research funding, open access publishing is one platform sought after or exist as an option for citizen scientists. Is the option open? Yes, at the preprint level where figshare, and PeerJ Preprints help provide an avenue for citizen scientists to have a published non peer reviewed article online, but no at the higher end gold (or immediate) open access journal article level where the manuscript needs to be peer reviewed. Even the biological sciences preprint server, bioRxiv, is closed to citizen scientists as publication on the server requires an institution affiliation with either a university or research institute. Most open access publishers (except eLife) charge a publication fee (in the hundreds to thousands of dollars per article) to defray the cost of maintaining an online presence for a peer reviewed manuscript as well as those for copyediting during final stages of journal article production. This is a significant barrier to cost constrained citizen scientists who want to contribute to the scientific discourse. For the scientific enterprise, this represent a loss, whose magnitude or severity cannot be quantified since ideas help seed new research and fields. Thus, can we as a community provide citizen scientists worldwide a chance to publish gold open access peer reviewed articles without significant cost through a competitive publication fee subsidy scheme where each application is reviewed by the national science funding agency? If the above is possible, it would open up another area where ideas from citizen scientists could percolate into the scientific mainstream, where, as always, vibrancy and diversity of ideas power science forward.
Potential connectivity among American lobster fisheries as a result of larval drift across the species’ range in eastern North America
Authors: Quinn Brady K. , Chassé Joël , Rochette Rémy
Published: January 2018

We used a bio-physical model to estimate for the first time the effect of larval drift on potential connectivity among American lobster (Homarus americanus) fisheries management areas over the geographic range of the species. The model predicted drift of larvae over distances of 50-805 km (mean = 129 km), which connected many management areas and caused marked spatial heterogeneity in retention and self-seeding versus import and export of larvae by different fisheries areas. Including mortality functions in the model resulted in less drift and settlement, and had complex effects on the amount, but not on the incidence, of connectivity among fisheries. The model’s predictions received support from comparison of predicted settlement to landings six or seven years later in some (but not all) parts of the model domain, although improvements are needed to capture spatial variability in larval release and drift across the species’ range. This information is important to lobster fisheries management, as the amount and direction of connectivity between fisheries can inform cooperative management strategies to sustain interconnected fisheries.
Potential connectivity among American lobster fisheries as a result of larval drift across the species’ range in eastern North America
Authors: Quinn Brady K. , Chassé Joël , Rochette Rémy
Published: January 2018

We used a bio-physical model to estimate for the first time the effect of larval drift on potential connectivity among American lobster (Homarus americanus) fisheries management areas over the geographic range of the species. The model predicted drift of larvae over distances of 50-805 km (mean = 129 km), which connected many management areas and caused marked spatial heterogeneity in retention and self-seeding versus export and import of larvae by different fisheries areas. Including mortality functions in the model resulted in less drift and settlement, and had complex effects on the amount, but not the incidence, of potential connectivity among fisheries. The model’s predictions received support from comparison of predicted settlement to landings six or seven years later in some (but not all) parts of the model domain. Although improvements are still needed to capture larval behaviours and spatial variability in larval release and mortality across the species’ range, this information is important to lobster fisheries management because the amount and direction of connectivity between fisheries can inform cooperative management strategies to sustain interconnected fisheries.
CATALISE: a multinational and multidisciplinary Delphi consensus study of problems with language development. Phase 2. Terminology
Authors: Bishop Dorothy V , Snowling Margaret J , Thompson Paul A , Greenhalgh Trisha ,   CATALISE-2 consortium
Published: January 2018

Background: Lack of agreement about criteria and terminology for children’s language difficulties affects access to services as well as hindering research and practice. We report the second phase of a study using an online Delphi method to address these issues. In the first phase, we focused on criteria for language disorder. Here we consider terminology. Methods: The Delphi method is an iterative process in which an initial set of statements is rated by a panel of experts, who then have the opportunity to view anonymised ratings from other panel members. On this basis they can either revise their views or make a case for their position. The statements are then revised based on panel feedback, and again rated by and commented on by the panel. In this study, feedback from a second round was used to prepare a final set of statements in narrative form. The panel included 54 individuals representing a range of professions and nationalities. Results: We achieved at least 78% agreement for 19 of 21 statements within two rounds of ratings. The term ‘Language Disorder’ was preferred to refer to a profile of difficulties that causes functional impairment in everyday life and is associated with poor prognosis. The term, ‘Developmental Language Disorder’ (DLD) was endorsed for use when the language disorder was not associated with a known biomedical aetiology. It was also agreed that (1) presence of risk factors (neurobiological or environmental) does not preclude a diagnosis of DLD, (2) DLD can co-occur with other neurodevelopmental disorders (e.g., ADHD), and (3) DLD does not require a mismatch between verbal and nonverbal ability. Conclusions: This Delphi exercise highlights reasons for disagreements about terminology for language disorders and proposes standard definitions and nomenclature.
A laid-­back trip through the Hennigian forests (Notes from Naturalists)
Authors: Mavrodiev Evgeny V , Dell Christopher A.
Published: January 2018

Binary matrix with a priori defined plesiomorphic character-­state may be re-­written as a set of branching diagrams (as a “Hennigian forest”). The last might be analyzed by the average consensus method. This procedure eventually avoids the taxon-­character matrix from the analysis of the data. Within this framework, the criteria of the best topologies based on the character-­state changes are unnecessary. The solely ‘reversal’‐based groups are always appear within the average consensus topologies despite the lack of direct evidence from the primary data.
Hard time to be parents? Sea urchin fishery shifts potential reproductive contribution of population onto the shoulders of the youngest
Authors: Loi Barbara , Guala Ivan , Pires da Silva Rodrigo , Brundu Gianni , Baroli Maura , Farina Simone
Published: January 2018

Background. In Sardinia, as in other regions of the Mediterranean Sea, sustainable fisheries of the sea urchin Paracentrotus lividus have become a necessity. At harvesting sites, the systematic removal of large individuals (diameter ≥ 50 mm) seriously compromises the biological and ecological functions of sea urchin populations. Specifically, in this study, we compared the reproductive potential of the populations from two Mediterranean coastal sites which have different levels of protection. The sites were Su Pallosu, where fishing pressure is high (take zone) and at Tavolara-Punta Coda Cavallo Marine Protected Area (no-take zone) where the pressure is negligible. Methods. Reproductive potential was estimated by calculating Gonadosomatic Index (GSI) from June 2013 to May 2014 both for individuals of commercial size (diameter without spines, TD ≥ 50 mm) and the undersized ones with gonads (30 ≤ TD < 40 mm and 40 ≤ TD < 50 mm). Gamete Output was calculated for the commercial-size class and the undersized individuals with fertile gonads (40 ≤ TD < 50 mm) in relation to their natural density (Gamete Output per m2). Results. The reproductive potential of populations was slightly different at the beginning of the sampling period but it progressed at different rates with an early spring spawning event in the take zone and two gamete depositions in early and late spring in the no-take zone. For each fertile size class, GSI values changed significantly during the year of our study and between the two levels of protection. Although the multiple spawning events determined a two-fold higher total Gamete Output of population (popTGO) in the no-take zone, the population Mean Gamete Output (popMGO) was similar in the two zones. In the take zone, the commercial-sized individuals represented approximatively 5% of the population, with almost all the individuals smaller than 60 mm producing an amount of gametes nearly three times lower than the undersized ones. Conversely, the high density of the undersized individuals released a similar amount of gametes to the commercial-size class in the no-take zone. Discussion. Overall, the lack of the commercial-size class in the take zone does not seem to be very alarming for the self-supporting capacity of the population, and the reproductive potential contribution seems to depend more on the total density of fertile sea urchins than on their size. However, since population survival in the take zone is supported by the high density of undersized sea urchins between 30 and 50 mm, management measures should be addressed to maintain this size and to shed light on the source of the larval supply.
From science gateways to commercial solutions
Authors: Kiss Tamas , Terstyanszky Gabor
Published: January 2018

The European CloudSME project that incorporated 24 European SMEs, besides five academic partners, has finished its funded phase in March 2016. This presentation will provide a summary of the results of the project, and will analyze the challenges and differences when developing “SME Gateways”, when compared to “Science Gateways”. CloudSME started in 2013 with the aim to develop a cloud-based simulation platform for manufacturing and engineering SMEs. The project was based around industry use-cases, five of which were incorporated in the project from the start, and seven additional ones that were added as an outcome of an open call in January 2015. CloudSME utilized science gateway related technologies, such as the commercial CloudBroker Platform and the WS-PGRADE/gUSE Gateway Framework that were developed in the preceding SCI-BUS project. As most important outcome, the project successfully implemented 12 industry quality demonstrators that showcase how SMEs in the manufacturing and engineering sector can utilize cloud-based simulation services. Some of these solutions are already market-ready and currently being rolled out by the software vendor companies. Some others require further fine-tuning and the implementation of commercial interfaces before being put into the market.

The CloudSME use-cases came from a very wide application spectrum. The project implemented, for example, an open marketplace for micro-breweries to optimize their production and distribution processes, an insole design validation service to be used by podiatrists and shoe manufacturers, a generic stock management solution for manufacturing SMEs, and also several “classical” high-performance computing case-studies, such as fluid dynamics simulations for model helicopter design, and dual-fuel internal combustion engine simulation. As the project generated significant impact and interest in the manufacturing sector, 10 CloudSME stakeholders established a follow-up company called CloudSME UG for the future commercialization of the results.

Besides the success stories, this talk would also like to highlight the difficulties when transferring the outcomes of an academic research project to real commercial applications. The different mindset and approach of academic and industry partners presented a real challenge for the CloudSME project, with some interesting and valuable lessons learnt. The academic way of supporting SMEs did not always work well with the rather different working practices and culture of many participants. Also, the quality of support regarding operational solutions required by the SMEs is well beyond the typical support services academic institutions are prepared for. Finally, a clear lack of trust in academic solutions when compared to commercial solutions was also imminent. The talk will highlight some of these challenges underpinned by the implementation of the CloudSME use-cases.
Early to Middle Miocene shallow-water corals from La Guajira, Colombia
Authors: Flórez Paola , Zapata-Ramírez Paula Andrea , Jaramillo Carlos , Klaus James S
Published: January 2018

Here we describe and illustrate 31 Miocene corals species from the Siamaná and Jimol Formations that were collected over two expeditions in the Guajira basin, Colombia during 2011 and 2014. Corals include 25 species, derived from 15 different genera and 12 families. Six of them remain with open nomenclature. From the 25 species found in the study area, 88% are extinct and the remaining under endanger status. Most of the species are hermatypic components of the Scleractinian order, with the exception of a member of the Milleporidae family. The corals described are composed of typical taxa from the Oligocene-Miocene transition, during which they were important components in building fringing and patch reefs in the circum-Caribbean/Gulf of Mexico region. The presence of typical Oligocene coral taxa such as Agathiphyllia spp., Antiguastrea sp., and Diploastrea spp. from La Guajira extend the distribution of these genera into the Miocene, adding a more recent geological presence in the Southern Caribbean. Coral assemblages suggest a development in clear, calm and shallow waters, under oligotrophic conditions and only moderate physical disturbance. Our descriptions represent the first effort to characterize the taxonomy of fossilized corals in Colombia.
Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminants
Authors: Opazo Juan C , Zavala Kattina , Krall Paola , Arias Rodrigo A
Published: January 2018

Understanding the processes that give rise to genomic variability in extant species is an active area of research within evolutionary biology. With the availability of whole genome sequences, it is possible to quantify different forms of variability such as variation in gene copy number, which has been described as an important source of genetic variability and in consequence of phenotypic variability. Most of the research on this topic has been focused on understanding the biological significance of gene duplication, and less attention has been given to the evolutionary role of gene loss. Gremlin 2 is a member of the DAN gene family and plays a significant role in tooth development by blocking the ligand-signaling pathway of BMP2 and BMP4. The goal of this study was to investigate the evolutionary history of gremlin 2 in cetartiodactyl mammals, a group that possesses highly divergent teeth morphology. Results from our analyses indicate that gremlin 2 has experienced a mixture of gene loss, gene duplication, and rate acceleration. Although the last common ancestor of cetartiodactyls possessed a single gene copy, pigs and camels are the only cetartiodactyl groups that have retained gremlin 2. According to the phyletic distribution of this gene and synteny analyses, we propose that gremlin 2 was lost in the common ancestor of ruminants and cetaceans between 56.3 and 63.5 million years ago as a product of a chromosomal rearrangement. Our analyses also indicate that the rate of evolution of gremlin 2 has been accelerated in the two groups that have retained this gene. Additionally, the lack of this gene could explain the high diversity of teeth among cetartiodactyl mammals; specifically, the presence of this gene could act as a biological constraint. Thus, our results support the notions that gene loss is a way to increase phenotypic diversity and that gremlin 2 is a dispensable gene, at least in cetartiodactyl mammals.
Virtual research environments as-a-service by gCube
Authors: Assante Massimiliano , Candela Leonardo , Castelli Donatella , Coro Gianpaolo , Lelii Lucio , Pagano Pasquale
Published: January 2018

Science is in continuous evolution and so are the methodologies and approaches scientists tend to apply by calling for appropriate supporting environments. This is in part due to the limitations of the existing practices and in part due to the new possibilities offered by technology advances. gCube is a software system promoting elastic and seamless access to research assets (data, services, computing) across the boundaries of institutions, disciplines and providers to favour collaborative-oriented research tasks. Its primary goal is to enable Hybrid Data Infrastructures facilitating the dynamic definition and operation of Virtual Research Environments. To this end, it offers a comprehensive set of data management commodities on various types of data and a rich array of ``mediators'' to interface well-established Infrastructures and Information Systems from various domains. Its effectiveness has been proved by operating the D4Science.org infrastructure and serving concrete, multidisciplinary, challenging, and large scale scenarios. This paper gives an overview of the gCube system.
Exiguobacterium pavilionensis str. N139, a halotolerant, UV-B and metal resistant bacteria from a high-altitude Andean lake
Authors: Gutiérrez-Preciado Ana , Vargas-Chávez Carlos , Reyes-Prieto Mariana , Ordoñez Omar F , Santos-García Diego , Rosas-Pérez Tania , Valdivia-Anistro Jorge , Rebollar Eria A , Saralegui Andrés , Moya Andrés , Merino Enrique , Farías María Eugenia , Latorre Amparo , Souza Valeria
Published: January 2018

We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three megaplasmids. The genome analysis suggests the presence of enzymes that confer E. pavilionensis str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals and high ultraviolet B radiation. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina .
Effects of enhanced hydrological connectivity on Mediterranean salt marsh fish assemblages with emphasis on the endangered Spanish toothcarp (Aphanius iberus)
Authors: Prado Patricia , Alcaraz Carles , Jornet Lluis , Caiola Nuno Alberto , Ibáñez Carles
Published: January 2018

The hydrological connectivity between the salt marsh and the sea was partially restored in a Mediterranean wetland containing isolated ponds resulting from former salt extraction and aquaculture activities. A preliminary assessment provided evidence that ponds farther from the sea hosted very large numbers of the endangered Spanish toothcarp, Aphanius iberus, suggesting that individuals had been trapped and consequently reach unnaturally high densities. In order to achieve both habitat rehabilitation and toothcarp conservation, efforts were made to create a gradient of hydrologically connected areas, including isolated fish reservoirs, semi-isolated, and connected salt marsh–sea areas that could allow migratory movements of fish and provide some protection for A. iberus. The fish community was monitored prior to, and for three years after rehabilitation. Results showed an increase in the number of fish species within semi-isolated areas (Zone A), relative to connected areas (Zone B), while at the assemblage level, structural differences between zones were higher than interannual variability. GLMs evidenced that distance to the sea was the most important variable explaining the local diversity of the fish community after restoration, with occasional influence of other factors such as temperature, and depth. The abundance of A. iberus was consistently higher in semi-isolated areas at greater distances from the sea, but a decline occurred in both zones and in isolated reservoir ponds after restoration efforts, which may be attributable to dispersal to adjacent habitats, and to interannual differences in recruitment success. A negative effect of restoration works on fish population cannot be excluded, but the final outcome of the intervention likely needs a longer period .
Seizures and Amyloid-β induce similar changes in neuronal network metabolic parameters in mouse hippocampal slices
Authors: Ivanov Anton , Malkov Anton E , Buldakova Svetlna , Zilberter Misha , Zilberter Yuri
Published: January 2018

Major risk factors for neurodegenerative diseases share brain hypometabolism as one common outcome. In turn, many neurodegenerative pathologies result in brain hypometabolism; both epilepsy and Alzheimer's disease are characterised by disruptions in glucose metabolism. However, the causative link between energy shortage and neuronal pathologies in these disease has remained elusive. Using real-time brain slice recordings of energy metabolism parameter (NAD(P)H, FAD, pO2 and extracellular glucose) transients in response to network activation, we found that induced epileptic seizures and amyloid-beta peptide both result in similar and long-lasting disruptions of neuronal energy metabolism, suggesting a common path of action. In addition, we found that in both cases, subsequent addition of pyruvate, the principal mitochondrial fuel possessing multiple neuroprotective properties, completely normalised the disputed energy state. Our data suggests that energy metabolism disruptions underlie the initiation and progression of neurodegenerative diseases.
Interoperability and FAIRness through a novel combination of Web technologies
Authors: Wilkinson Mark D , Verborgh Ruben , Bonino da Silva Santos Luiz Olavo , Clark Tim , Swertz Morris A , Kelpin Fleur D.L. , Gray Alasdair J. G. , Schultes Erik A. , van Mulligen Erik M. , Ciccarese Paolo , Kuzniar Arnold , Gavai Anand , Thompson Mark , Kaliyaperumal Rajaram , Bolleman Jerven T. , Dumontier Michel
Published: January 2018

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs.
Dynamics of resource allocation in Biological Systems II: On cancer cell metabolism
Authors: Jeff-Eke Imadol V
Published: January 2018

Here we shall apply the approach presented in the paper Dynamics of resource allocation in biological systems in considering resource allocation in cancer cell metabolism, specifically, aerobic glycolysis (Warburg effect). Aerobic glycolysis, the metabolic phenomenon of cells utilizing glucose fermentation to lactate even under conditions of ample oxygen availability. We shall consider resource reallocations between processes of two hypothetical cells: a cancer cell and a normal cell. Specifically, we consider reallocation of resources between cancer-related processes of a cancer cell, normal processes of same cancer cell, and processes of a normal cell in attempts to satisfy the high resource requirements for cancer-related processes. In doing this, we draw inferences from the initial work and state hypotheses as pertains to cancer cell metabolism. From this hypotheses, we shall attempt explanation of Aerobic glycolysis. We end by considering genomic instability as a derivation of cancer cell metabolism.
Multiple stressors threaten an important coastal foundation species
Authors: Lefcheck Jonathan S , Wilcox David J , Murphy Rebecca R , Marion Scott R , Orth Robert J
Published: January 2018

Interactions among global change stressors and their effects at large scales are often proposed but seldom evaluated, in part due to lack of comprehensive, sufficiently long-term, and spatially-extensive datasets. Seagrasses, which provide nursery habitat, improve water quality, and constitute a globally-important carbon sink, are among the most vulnerable habitats on the planet. Here, we unite 31-years of high-resolution aerial monitoring and water quality data to elucidate the patterns and drivers of eelgrass (Zostera marina) abundance in Chesapeake Bay, USA, one of the largest and most valuable estuaries in the world, with an unparalleled history of regulatory efforts. We show that eelgrass cover has declined 29% in total since 1991, with wide-ranging and severe ecological and economic consequences. We go on to identify an interaction between decreasing water clarity and warming temperatures as the primary driver of this trend. Declining clarity has gradually reduced eelgrass over the past two decades, primarily in deeper beds where light is already limiting. In shallow beds, however, reduced visibility exacerbates the physiological stress of acute warming, leading to recent instances of decline approaching 80%. While degraded water quality has long been known to influence underwater grasses worldwide, we demonstrate a clear and rapidly emerging interaction with climate change. We highlight the urgent need to integrate a broader perspective into local water quality management, in the Chesapeake Bay and in the many other coastal systems facing similar stressors.
Validation of the Actibelt® speed measurement in patients with dizziness and vertigo
Authors: Rampmaier Valentin , Schenkel Fabian , Daumer Martin , Schniepp Roman
Published: January 2018

Walking velocity is an important control variable in gait disorders due to sensory or cerebellar disfunction. Non-preferred walking speeds are closely linked to a higher risk of falls. A compensation strategy of patients to avoid these speed sectors can be assumed. So far speed measurements are only possible in a laboratory environment. Actibelt® is a promising tool that allows speed estimation based on accelerometer data. The used algorithms have not been validated for patients with sensory or cerebellar disorders.
Daggers, swords, scythes and sickles: Pachycormid fins as ecological predictors
Authors: Liston Jeff , Maltese Anthony
Published: January 2018

Pachycormids occupy a key position within Actinopterygii, as part of the Holostei- Teleostei Transition, although their precise position in this hierarchy has been fought over for some years. Discoveries in the last three years have expanded our global knowledge of the diversity, distribution and success of this group, continuing the recent 'Pachycormid Renaissance'. However, clarity over the definitions of pachycormid taxa has been undermined by the number of type specimens destroyed during World War II, introducing a need for neotype material to be identified (e.g. Asthenocormus titanius, Hypsocormus macrodon), and comparative work has revealed how poorly constrained a number of historical genera are, particularly those of the Toarcian (Early Jurassic) Holzmaden shale fauna that were the foundation of Arthur Smith Woodward's family Pachycormidae in 1895. These historical problems with descriptions and material have undermined confidence in recent phylogenetic analyses. The characteristic unusually long pectoral fins appear to have developed in conjunction with otherwise reduced skeletal ossification to counteract buoyancy problems in a group lacking a gas bladder. A sample of over 90 specimens from 16 recognised pachycormid genera was assessed, demonstrating that the ubiquitously stated 'scythe'-like pectoral fin is not a pachycormid synapomorphy: three clear and distinct pectoral fin structural morphotypes emerged, reflecting a diversity of pachycormid lifestyles that changed throughout the Mesozoic, from agile pursuit predator to slow-cruising suspension feeder. Those morphotypes closely mirror modern fuel-saving wingtip designs from today's aerodynamicists, converging on similar solutions to these enigmatic and fascinating fish some 160 million years later.
Crowdsourcing the discovery of software repositories in an educational environment
Authors: Ma Yuxing , Dey Tapajit , Smith Jarred M , Wilder Nathan , Mockus Audris
Published: January 2018

In software repository mining, it's important to have a broad representation of projects. In particular, it may be of interest to know what proportion of projects are public. Discovering public projects can be easily parallelized but not so easy to automate due to a variety of data sources. We evaluate the research and educational potential of crowd-sourcing such research activity in an educational setting. Students were instructed on three ways of discovering the projects and assigned a task to discover the list of public projects from top 45 forges with each student assigned to one forge. Students had to discover as many of the projects as they could using the method of their choice and provide a market-research report for a fictional customer based on the attribute they selected. A subset of the results was sampled and verified for accuracy. We found that many of the public forges do not host public projects, that a substantial fraction of forges do not provide APIs and the APIs vary dramatically among the remaining forges. Some forges have been discontinued and others renamed, making the discovery task into an archaeological exercise. The students' findings raise a number of new research questions and demonstrate the teaching potential of the approach. The accuracy of the results obtained, however, was low, suggesting that crowd-sourcing would require at least two or more likely a larger number of investigators per forge or a better way to gauge investigator skill. We expect that these lessons will be helpful in creating education-sourcing efforts in software data discovery.
The piglet case: commensalism as a distinct category of intraspecific animal relationships
Authors: Skok Janko
Published: January 2018

1. Interspecific relationships, termed symbiosis, are considered very diverse, while intraspecific relationships have just two categories.

2. The present classification fails to define all interactions among members of the same species, as demonstrated by observations of suckling behaviour in pigs.

3. Supporting latest findings on the suckling behaviour of piglets, I propose an extension of the classification for existing intraspecific animal relationships by adding a new distinct category: commensalism.
Prediction of pKa values for drug-like molecules using semiempirical quantum chemical methods
Authors: Jensen Jan H.
Published: January 2018

Rapid yet accurate pKa prediction for drug-like molecules is a key challenge in computational chemistry. This study uses PM6-DH+/COSMO, PM6/COSMO, PM7/COSMO, PM3/COSMO, AM1/COSMO, PM3/SMD, AM1/SMD, and DFTB3/SMD to predict the pKa values of 53 amine groups in 48 drug-like compounds. The approach uses an isodesmic reaction where the pKa value is computed relative to a chemically related reference compound for which the pKa value has been measured experimentally or estimated using a standard empirical approach. The AM1- and PM3-based methods perform best with RMSE values of 1.4 - 1.6 pH units that have uncertainties of 0.3-0.4 pH units, which make them statistically equivalent. However, for all but PM3/SMD and AM1/SMD the RMSEs are dominated by a single outlier, cefadoxil, caused by proton transfer in the zwitterionic protonation state. If this outlier is removed, the RMSE values for PM3/COSMO and AM1/COSMO drop to 1.0 ± 0.2 and 1.1 ± 0.3, while PM3/SMD and AM1/SMD remain at 1.5 ± 0.4 and 1.6 ± 0.4 pH units, making the COSMO-based predictions statistically better than the SMD-based predictions. So for pKa calculations where a zwitterionic state is not involved or proton transfer in a zwitterionic state is not observed then PM3/COSMO or AM1/COSMO is the best pKa prediction method, otherwise PM3/SMD or AM1/SMD should be used. Thus, fast and relatively accurate pKa prediction for 100-1000s of drug-line amines is feasible with the current setup and relatively modest computational resources.
Barriers to the use of personal health records by patients: A structured review
Authors: Showell Chris
Published: January 2018

Introduction:

An increasing focus on personal electronic health records (PHRs) offers healthcare benefits for patients, particularly those in undeserved and marginalised populations, who are at risk of receiving less effective healthcare, and may have worse health outcomes. However, PHRs are likely to favour text, technical and health literate users, and be less suitable for disadvantaged patients. These concerns have prompted this review of the literature, which seeks evidence about barriers to the adoption and continued use of PHRs, the nature of the evidence for those barriers, and the stage of PHR implementation where particular barriers apply.

Methods:

Searches in PubMed, Embase, CINAHL and ProQuest databases were used to retrieve articles published in English after 2003 in a refereed journal or presented in a refereed conference or scientific meeting. After screening to remove items which were out of scope, the phase of the PHR implementation, the type of investigation, and PHR barriers were categorised using thematic coding.

Results:

The search retrieved 439 items; screening identified 40 in-scope publications, which provided evidence of 21 identified barriers to patient adoption and continued use of PHRs, categorised here as Individual, Demographic, Capability, Health-related, PHR or Attitudinal factors. Barriers were identified in most phases of PHR implementation, and in most types of study. A secondary outcome identified that eleven of the publications may have introduced a bias by excluding participants who were less affluent, less capable, or marginalised.

Conclusions:

PHR barriers can interfere with the decision to start using a PHR, with the adoption process, and with continued use, and the impact of particular barriers may vary at different phases of PHR adoption. The complex interrelationships which exist between many of the barriers is suggested in some publications, and emerges more clearly from this review. Many PHR barriers appear to be related to low socioeconomic status. A better understanding is needed of how the effect of barriers is manifested, how that that effect can be countered, and how planning and implementation of PHR initiatives can make allowance for patient level barriers to PHR adoption and use, with appropriate actions to mitigate the effect of those barriers for more disadvantaged patients.
A comparison of anesthesia techniques for entomological experimentation: Longevity of the leaf-mining fly pest Scaptomyza flava Fallén (Drosophilidae)
Authors: Rayl Ryan J , Wratten Steve D
Published: January 2018

Historically, handling insects usually involved their being killed as early studies used these organisms for work on genetics, physiology and/or pesticide bioassays. With the advancement of these research topics, the development of behavioral studies and the sensitivity of culturally important, threatened or endangered species, approaches that focus on non-lethal preparation of the insects for experimentation have become important. Anesthesia has been used as one of these non-lethal approaches to provide researchers flexibility when designing experiments. Two common anesthetics used for insect experimentation are carbon dioxide and chilling. These anesthetics have been used frequently in the literature but their sub-lethal effects on insects are poorly studied. Another that has potential for experimental use is triethylamine (TEA). This chemical shows promise because of its ease of use and potency as an insect anesthetic, but evidence, if any, of the sub-lethal effects is almost non-existent in the literature. A series of experiments was carried out to find the optimal exposure times and/or concentrations for each of these three approaches. Once an optimal treatment was found for each approach, these were compared to each other in a subsequent experiment. It was found that TEA is a far superior anesthetic when recording/observing fly longevity.
Making inference from wildlife collision data: inferring predator absence from prey strikes
Authors: Caley Peter , Hosack Geoffrey R , Barry Simon C
Published: January 2018

Wildlife collision data are ubiquitous, though challenging for making ecological inference due to typically irreducible uncertainty relating to the sampling process. We illustrate a new approach that is useful for generating inference from predator data arising from wildlife collisions. By simply conditioning on a second prey species sampled via the same collision process, and by using a biologically realistic numerical response functions, we can produce a coherent numerical response relationship between predator and prey. This relationship can then be used to make inference on the population size of the predator species, including the probability of extinction. The statistical conditioning enables us to account for unmeasured variation in factors influencing the runway strike incidence for individual airports and to enable valid comparisons. A practical application of the approach for testing hypotheses about the distribution and abundance of a predator species is illustrated using the hypothesized red fox incursion into Tasmania, Australia. We estimate that conditional on the numerical response between fox and lagomorph runway strikes on mainland Australia, the predictive probability of observing no runway strikes of foxes in Tasmania after observing 15 lagomorph strikes is 0.001. We conclude there is enough evidence to safely reject the null hypothesis that there is a widespread red fox population in Tasmania at a population density consistent with prey availability. The method is novel and has potential wider application.
Jupyter notebooks in science gateways
Authors: Zonca Andrea
Published: January 2018

Jupyter Notebooks empower scientists to create executable documents that include text, equations, code and figures. Notebooks are a simple way to create reproducible and shareable workflows. The Jupyter developers have also released a multi-user notebook environment: Jupyterhub. Jupyterhub provides an extensible platform for handling user authentication and spawning the Notebook application to each user. I developed a plugin for Jupyterhub to spawn notebooks on a Supercomputer and integrated the authentication with CILogon and XSEDE. Scientists can authenticate on their browser and connect to a Jupyter Notebook instance running on the computing node of a Supercomputer, in my test deployment SDSC Comet. Jupyterhub can benefit Science Gateways by providing an expressive interface to a centralized environment with many software tools pre-installed and allow scientists to access Gateway functionality via web API. Scientists can then define their own workflows with maximum flexibility: they can mix data processing with a programming language of their choice, e.g. Python, R or Julia, add their own software modules and call the Gateway web API for the more resource-intensive operations. Workflows written as notebooks and executed in such a standard environment boost reproducibility with minimal effort from the scientists. Such notebooks can be both attached to publications to ensure reproducibility of past research and also modified and improved by other interested research groups. In this talk I will introduce the functionalities of Jupyterhub, give an overview of the architecture of the interface with XSEDE authentication and with Comet and finally different scenarios where Jupyter Notebooks can be integrated into Science Gateways.
External kinetics of the kettlebell snatch in trained athletes
Authors: Ross James A , Keogh Justin W L , Wilson Cameron J , Lorenzen Christian
Published: January 2018

Background. Kettlebell lifting has gained increased popularity as both a form of resistance training and as a sport, despite the paucity of literature validating its use as a training tool. Kettlebell sport requires participants to complete the kettlebell snatch continuously over prolonged periods of time. Kettlebell sport and weightlifting involve similar exercises, however their traditional uses suggest they are better suited to training different fitness qualities. This study examined the three dimensional ground reaction force (GRF) and force applied to the kettlebell over a six minute kettlebell snatch set in 12 kettlebell trained males.

Methods. During this set, VICON was used to record the kettlebell trajectory with nine infrared cameras while the GRF of each leg was recorded with a separate AMTI force plate. Over the course of the set, an average of 13.9 ± 3.3 repetitions per minute were performed with a 24 kg kettlebell. Significance was evaluated with a two-way ANOVA and paired t-tests, whilst Cohen’s F (ESF) and Cohen’s D (ESD) were used to determine the magnitude.

Results. The applied force at the point of maximum acceleration was 814 ± 75 N and 885 ± 86 N for the downwards and upwards phases, respectively. The absolute peak resultant bilateral GRF was 1746 ± 217 N and 1768 ± 242 N for the downwards and upwards phases, respectively. Bilateral GRF of the first and last 14 repetitions was found to be similar, however there was a significant difference in the peak applied force (F (1.11) = 7.42, p = 0.02, ESF = 0.45). Unilateral GRF was found have a significant difference for the absolute anterior-posterior (F (1.11) = 885.15 p < 0.0001, ESF = 7.00) and medio-lateral force vectors (F (1.11) = 5.31, p = 0.042, ESF = 0.67).

Discussion. Over the course of a single repetition there were significant differences in the GRF and applied force at multiple points of the kettlebells trajectory. The kettlebell snatch loads each leg differently throughout a repetition and performing the kettlebell snatch for six minutes will result in a reduction in peak applied force.