bluuebunny/crossref_metadata_2025 huggingface dataset:
An innovative workspace for the Cherenkov Telescope Array
Authors: Costa Alessandro , Sciacca Eva , Becciani Ugo , Massimino Pietro , Riggi Simone , Sanchez David , Vitello Fabio
Published: January 2018

The Cherenkov Telescope Array (CTA) is an initiative to build the next generation, ground-based gamma-ray observatories. We present a prototype workspace developed at INAF that aims at providing innovative solutions for the CTA community. The workspace leverages open source technologies providing web access to a set of tools widely used by the CTA community. Two different user interaction models, connected to an authentication and authorization infrastructure, have been implemented in this workspace. The first one is a workflow management system accessed via a science gateway (based on the Liferay platform) and the second one is an interactive virtual desktop environment. The integrated workflow system allows to run applications used in astronomy and physics researches into distributed computing infrastructures (ranging from clusters to grids and clouds). The interactive desktop environment allows to use many software packages without any installation on local desktops exploiting their native graphical user interfaces. The science gateway and the interactive desktop environment are connected to the authentication and authorization infrastructure composed by a Shibboleth identity provider and a Grouper authorization solution. The Grouper released attributes are consumed by the science gateway to authorize the access to specific web resources and the role management mechanism in Liferay provides the attribute-role mapping.
An innovative workspace for the Cherenkov Telescope Array
Authors: Costa Alessandro , Sciacca Eva , Vitello Fabio , Becciani Ugo , Massimino Pietro , Riggi Simone , Sanchez David
Published: January 2018

The Cherenkov Telescope Array (CTA) is an initiative to build the next generation, ground-based gamma-ray observatories. We present a prototype workspace developed at INAF that aims at providing innovative solutions for the CTA community. The workspace leverages open source technologies providing web access to a set of tools widely used by the CTA community. Two different user interaction models, connected to an authentication and authorization infrastructure, have been implemented in this workspace. The first one is a workflow management system accessed via a science gateway (based on the Liferay platform) and the second one is an interactive virtual desktop environment. The integrated workflow system allows to run applications used in astronomy and physics researches into distributed computing infrastructures (ranging from clusters to grids and clouds). The interactive desktop environment allows to use many software packages without any installation on local desktops exploiting their native graphical user interfaces. The science gateway and the interactive desktop environment are connected to the authentication and authorization infrastructure composed by a Shibboleth identity provider and a Grouper authorization solution. The Grouper released attributes are consumed by the science gateway to authorize the access to specific web resources and the role management mechanism in Liferay provides the attribute-role mapping.
HUBzero and CatalyzeCare: A community driven platform for data sharing and collaboration in medical informatics research
Authors: Zentner Michael , Zink Richard
Published: January 2018

The HUBzero platform is an infrastructure enabling online scientific communities to collaborate and share information and computational resources as they explore scientific phenomena. HUBzero has been adopted by the Regenstrief Center for Healthcare Engineering (RCHE) at Purdue University to form the HUB CatalyzeCare. RCHE has formed the community REMEDI Central on their CatalyzeCare hub that has been adopted by more than 140 hospitals and records data from over 30,000 infusion pumps. Hospitals voluntarily contribute the alert streams emanating from smart intravenous pumps and their drug limit libraries to the REMEDI Central community. Infusion pumps emit an alert whenever a healthcare professional programs the pump to administer a dose to a patient outside of the bounds established by the hospital in their drug limit library. The drug limit library contains for each drug in each treatment unit (e.g. pediatrics, intensive care) a set of low and high limits for administration by bolus and continuous infusion. A practitioner’s response to an alert can be to reprogram the pump, to delay the infusion as they seek additional information from the ordering physician, or to override. Response to an individual alert can mean the difference between successful treatment, an adverse event, or even death. In the aggregate, alerts and their associated responses can represent the quality of hospital training, areas of improvement in procedures, or deficiencies in the hospital’s drug limit library. Across hospitals, the alerts and drug limit library entries provide a means of benchmarking and improvement. As part of the agreement for joining REMEDI Central, hospitals are able to benchmark against the other hospitals in the community. No hospital is anonymous. By agreement, the hospitals have determined that the value of the shared data is high enough that they willingly identify themselves. Collectively, their goal is to improve overall patient safety by creating a set of best practices regarding infusion pump alert mitigation and response. The REMEDI Central community members meet three times annually, and openly share with each other their best practices and process improvements. The REMEDI Central community is unique in that it has three key stakeholder types and provides distinct value to each. Hospital practitioners get immediate tactical feedback from REMEDI Central as it guides them on a daily basis with regard to infusion alerts. Hospital administrators gain a strategic view from being able to benchmark their practices against their peer facilities. Researchers gain access to a stream of data that would otherwise be unavailable for the purpose of developing research-based interventions in healthcare. Since practitioners are provided immediate value from their data, they are incentivized to provide their data on a regular basis. This immediate incentive is key for researchers to be able to access an up-to-date and growing database of information.
Analysis of aerobic anoxygenic phototrophic bacterial community structure in the different marine functional zones in the Zhoushan Archipelago Sea Area in summer
Authors: Zhao Benxuan , Liu Qiang , Zhao Sheng , Wu Changwen
Published: January 2018

Aerobic anoxygenic phototrophic bacteria (AAPB) containing bacteriochlorophyll a (BChl a) are photoheterotrophic prokaryotes that are a widely distributed functional bacterial group due to their obligately aerobic and facultative photoheterotrophic abilities. Here, we made a comparison of AAPB community structures in different marine functional zones in the surface water of the Zhoushan Archipelago Sea Area using high-throughput sequencing based on the pufM gene that encodes the M subunit of the light reaction centre complex. A total of 268,214 clean reads were obtained from the sampling stations. The sequences were divided into 5876 OTUs (97% cut-off value). Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria phyla were noted in this study. Proteobacteria phylum accounted for the major proportion and existed at all sites. Roseobacter-like AAPB was the most abundant genus, in Dongji Island (DJ) and Gouqi Island (GQ). Our results demonstrated that the structure of the AAPB community had different distribution patterns within the Zhoushan Archipelago Sea Area. Furthermore, we found that the diversity of AAPB was controlled by complex environmental factors, which might explain the difficulties encountered when predicting the distribution of total AAPB in aquatic ecosystems.
Comparing conservation monitoring approaches: traditional and environmental DNA tools for a critically endangered mammal
Authors: Qu Chanjuan , Stewart Kathryn A
Published: January 2018

While conservation management has made tremendous strides in the last few decades, the decision of knowing where and how to invest (often) small surveying budgets for biodiversity data collection remains a central hurdle for impactful conservation decision making. New analytical tools, such as environmental DNA (eDNA), are now facilitating broader biodiversity monitoring to take place at unprecedented scales, in part due to its time-efficient, and presumably cost-efficient, premise. eDNA approaches vary from conventional PCR (detecting presence/absence of species), metabarcoding (community structure), to qPCR (relative DNA abundance), and knowing when to employ these techniques over traditional sampling protocols could enable conservation practitioners to make informed trade-offs between cost, accuracy, and speed of data collection. Using 12 species-specific primers designed for conventional PCR use in eDNA analysis of the Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis), a critically endangered aquatic mammal within the Yangtze River, we validated and optimized these same primers for use in real-time Quantitative PCR (qPCR). We tested the repeatability and sensitivity of primer each to detect YFP eDNA and subsequently compared the cost of traditional visual sampling to both conventional PCR and qPCR eDNA tools. Our results suggest qPCR to be substantially more sensitive than conventional PCR eDNA analysis, although the later remains the least-expensive sampling option. Still, due to a lack of sensitivity causing an increased probability of false negatives, conventional PCR may not be the most robust sampling method for this taxa and should only be employed as a supplementary tool or when large populations are expected to be present. Alternatively, utilizing qPCR for eDNA protocols is still less-expensive than visual surveying and represents a highly repeatable and sensitive method for this behaviorally elusive species. Presenting a cost assessment of eDNA to traditional surveying practices has scarcely been discussed, while contrasting deliverables to the cost of different eDNA methods has, to date, been ignored. Yet given budgetary constraints, particularly for developing countries where low-governance and high endemism are present, we encourage managers to carefully consider the trade-offs among data accuracy, cost, coverage and speed for biodiversity collections.
Potential effects of climate change on the risk of accidents with poisonous species of the genusTityus (Scorpiones, Buthidae) in Argentina
Authors: Martinez Pablo , Andrade Mayane A , Bidau Claudio Juan
Published: January 2018

BACKGROUND: The knowledge of the factors that affect the geographic distribution of species permits us to infer where they can be found. Human beings, through the expansion of their own distribution area and their contribution to climate alteration have modified the geographic distribution of other biological species. As a consequence, the temporal pattern of co-occurrence of human beings and venomous species (scorpions, spiders, snakes) is being modified. Thus, the temporal pattern of areas with risk of accidents with such species tends to become dynamic along time. The aim of this work was to analyze the areas of occurrence of species of Tityus in Argentina and assess the impact of global climate change on their area of distribution constructing risk maps.

METHODS: Using data of occurrence of the species and climatic variables, we constructed models of species distribution (SMDs) under current and future conditions. We also created maps that allow the detection of temporal shifts in the distribution patterns of each Tityus species. Finally, we constructed risk maps for the analyzed species.

RESULTS: Our results predict that climate change will have an impact on the distribution of Tityus species which will clearly expand to more southern latitudes, with the exception of T. argentinus. T. bahiensis, widely distributed in Brazil, showed a considerable increase of its potential area (ca. 37%) with future climate change. The species T. confluens and T. trivittatus that cause the highest number of accidents in Argentina, showed significant changes of their distributions in future scenarios. The former fact is worrying because Buenos Aires province is the more densely populated federal district in Argentina thus liable to become the one most affected by T. trivittatus.

DISCUSSION: Then, these alterations of distributional patterns can lead to amplify the accident risk zones of venomous species, becoming an important subject of concern for public health policies.
Doing things twice: Strategies to identify studies for targeted validation
Authors: Sarma Gopal P
Published: January 2018

The “reproducibility crisis” has been a highly visible source of scientific controversy and dispute. Here, I propose and review several avenues for identifying and prioritizing research studies for the purpose of targeted validation. Of the various proposals discussed, I identify scientific data science as being a strategy that merits greater attention among those interested in reproducibility. I argue that the tremendous potential of scientific data science for uncovering high-value research studies is a significant and rarely discussed benefit of the transition to a fully open-access publishing model.
Density estimates of monarch butterflies overwintering in central Mexico
Authors: Thogmartin Wayne , Diffendorfer Jay E , Lopez-Hoffman Laura , Oberhauser Karen , Pleasants John , Semmens Brice Xavier , Semmens Darius , Taylor Orley R , Wiederholt Ruscena
Published: January 2018

Given the rapid population decline and recent petition for listing of the monarch butterfly (Danaus plexippus L.) under the Endangered Species Act, an accurate estimate of the Eastern, migratory population size is needed. Because of difficulty in counting individual monarchs, the number of hectares occupied by monarchs in the overwintering area is commonly used as a proxy for population size, which is then multiplied by the density of individuals per hectare to estimate population size. There is, however, considerable variation in published estimates of overwintering density, ranging from 6.9–60.9 million ha-1. We develop a probability distribution for overwinter density of monarch butterflies from six published density estimates. The mean density among the mixture of the six published estimates was ~27.9 million butterflies ha-1 (95% CI: 2.4–80.7 million ha-1); the mixture distribution is approximately log-normal, and as such is better represented by the median (21.1 million butterflies ha-1). Based upon assumptions regarding the number of milkweed needed to support monarchs, the amount of milkweed (Asclepias spp.) lost (0.86 billion stems) in the northern U.S. plus the amount of milkweed remaining (1.34 billion stems), we estimate >1.8 billion stems is needed to return monarchs to an average population size of 6 ha. Considerable uncertainty exists in this required amount of milkweed because of the considerable uncertainty occurring in overwinter density estimates. Nevertheless, the estimate is on the same order as other published estimates. The studies included in our synthesis differ substantially by year, location, method, and measures of precision. A better understanding of the factors influencing overwintering density across space and time would be valuable for increasing the precision of conservation recommendations.
qPortal – A science gateway for biomedical applications
Authors: Mohr Christopher , Friedrich Andreas , Wojnar David , Kenar Erhan , Polatkan Aydin Can , Codrea Marius Cosmin , Czemmel Stefan , Kohlbacher Oliver , Nahnsen Sven
Published: January 2018

Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. Nowadays, it is common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for large amounts of storage, data management, and easily accessible means of analysis. We present qPortal, a web-based science gateway providing users with an intuitive way to manage and analyze quantitative biological data. Pre-programmed analysis pipelines, quality control workflows, and visualization tools are offered to the user. Through intensive user interactions, appropriate data models have been developed. These models build the biological data management system and provide possibilities to annotate data, query existing metadata for statistics and future re-analysis on a high-performance computing system via a coupling to gUSE, a workflow management system.
Visualising higher-dimensional space-time and space-scale objects as projections to \(\mathbb{R}^3\)
Authors: Arroyo Ohori Ken , Ledoux Hugo , Stoter Jantien
Published: January 2018

Objects of more than three dimensions can be used to model geographic phenomena that occur in space, time and scale. For instance, a single 4D object can be used to represent the changes in a 3D object's shape across time or all its optimal representations at various levels of detail. In this paper, we look at how such higher-dimensional space-time and space-scale objects can be visualised as projections from \(\mathbb{R}^4\) to \(\mathbb{R}^3\). We present three projections that we believe are particularly intuitive for this purpose: (i) a simple `long axis' projection that puts 3D objects side by side; (ii) the well-known orthographic and perspective projections; and (iii) a projection to a 3-sphere (\(S^3\)) followed by a stereographic projection to \(\mathbb{R}^3\), which results in an inwards-outwards fourth axis. Our focus is in using these projections from \(\mathbb{R}^4\) to \(\mathbb{R}^3\), but they are formulated from \(\mathbb{R}^n\) to \(\mathbb{R}^{n-1}\) so as to be easily extensible and to incorporate other non-spatial characteristics. We present a prototype interactive visualiser that applies these projections from 4D to 3D in real-time using the programmable pipeline and compute shaders of the Metal graphics API.
Denitrifying bacterial communities in surface-flow constructed wetlands during different seasons : characteristics and relationships with environment factors
Authors: Wei Jiaming , Li wei , cui lijuan , lei yinru
Published: January 2018

Denitrification is an important part of the nitrogen cycle and the key step to removal of nitrogen in surface-flow wetlands. Denitrifying bacteria also function in denitrification. In this study, we explored space-time analysis with high-throughput sequencing to elucidate the relationships between denitrifying bacteria community structures and environmental factors during different seasons. Our results showed that along the flow direction of different processing units, there were dynamic changes in physical and chemical indicators. The bacterial abundance indexes (ACEs) in May, August, and October were 686.8, 686.8, and 996.2, respectively, whereas the Shannon-Weiner indexes were3.718, 4.303, and 4.432, respectively. Along the flow direction, the denitrifying bacterial abundance initially increased and then decreased subsequently during the same months, although diversity tended to increase. The abundance showed similar changes during the different months. Surface flow wetlands mainly contained the following denitrifying bacteria genus: unclassified Bacteria (37.12%), unclassified Proteobacteria (18.16%), Dechloromonas (16.21%), unranked environmental samples (12.51%), unclassified Betaproteobacteria (9.73%), unclassified Rhodocyclaceae (2.14%), and Rhodanobacter (1.51%). During different seasons, the same species processing units showed alternating changes, and during the same season, bacterial community structures were influenced by the second genus proportion in different processing units. ACEs were strongly correlated with temperature, dissolved oxygen, and pH. Bacterial diversity was strongly correlated with temperature, electrical conductivity, pH, and oxidation reduction potential. All denitrifying bacterial species were greatly affected by environmental factors, including temperature and pH, and the effects of electrical conductivity and oxidation reduction potential were similar.
From the desktop to the grid and cloud: conversion of KNIME workflows to WS-PGRADE
Authors: de la Garza Luis , Aicheler Fabian , Kohlbacher Oliver
Published: January 2018

Computational analyses for research usually consist of a complicated orchestration of data flows, software libraries, visualization, selection of adequate parameters, etc. Structuring these complex activities into a collaboration of simple, reproducible and well defined tasks brings down complexity and increases reproducibility. This is the basic notion of workflows. Workflow engines allow users to create and execute workflows, each having unique features. In some cases, certain features offered by platforms are royalty-based, hindering use in the scientific community. We present our efforts to convert whole workflows created in the Konstanz Information Miner Analytics Platform to the Web Services Parallel Grid Runtime and Developer Environment. We see the former as a great workflow editor due to its considerable user base and user-friendly graphical interface. We deem the latter as a great backend engine able to interact with most major distributed computing interfaces. We introduce work that provides a platform-independent tool representation, thus assisting in the conversion of whole workflows. We also present the challenges inherent to workflow conversion across systems, as well as the ones posed by the conversion between the chosen workflow engines, along with our proposed solution to overcome these challenges. The combined features of these two platforms (i.e., intuitive workflow design on a desktop computer and execution of workflows on distributed high performance computing interfaces) greatly benefit researchers and minimize time spent in technical chores not directly related to their area of research.
The isolation and identification of pathogenic fungus from the diseased Tessaratomapapillosa Drury (Hemiptera: Tessaratomidae) and their pathogenicity
Authors: Meng Xiang , Hu Junjie , Ouyang Gecheng
Published: January 2018

Background. Litchi stink-bug, Tessaratoma papillosa Drury (Hemiptera: Tessaratomidae) is a major pest on litchi and longan in Southern China. It is urgent to develop valid biological agent for control the pest and improve IPM strategy on orchard farming. Entomopathogenic fungi was regarded as avital ecological factor pressing pest populations in field, however, there were fewer searches conducted on entomopathogenic fungi against litchi stink-bug. Methods & Results. In this study, two pathogenic fungus were isolated from the adult diseased T. papillosa by normal methods and rDNA-ITS homogeneous analysis, they are identified as Paecilomyces lilacinus and Beauveria bassiana. Laboratory tests showed that the two entomopathogenic fungi both had a good lethal effect to young nymph and old nymph of T. papillosa. The toxicity determination showed that the LC50 value for Beauveria bassiana was higher than P. lilacinus. Conclusion.These pathogenic fungus did not have the risk of pollution or residue, and they can be a alternative option for integrated pest management approache.
Are anti-ganglioside antibodies associated with proventricular dilatation disease in birds?
Authors: Leal de Araujo Jeann , Tizard Ian , Guo Jianhua , Heatley J Jill , Rodrigues Hoffmann Aline , Rech Raquel R
Published: January 2018

The identification of Parrot bornaviruses in psittacine birds with proventricular dilatation disease (PDD) has not been sufficient to explain the pathogenesis of this fatal disease since not all infected birds develop clinical signs. One hypothesis suggests that PaBV could trigger the production of autoantibodies targeting neuronal gangliosides. These are major neuronal antigens, and PDD might therefore resemble Guillain-Barré Syndrome (GBS) in its pathogenesis. Experimental inoculation of pure gangliosides and brain-derived ganglioside extracts were used in two different immunization studies. A preliminary study on seven healthy chickens (Gallus gallus domesticus) was performed using a group of four chickens inoculated with a brain ganglioside extract in Freund’s complete adjuvant (FCA) and a control group comprised by three chickens inoculated only with phosphate-buffered saline (PBS). A second study with five healthy quaker parrots (Myiopsitta monachus) was comprised of three groups. Two quaker parrots received purified gangliosides in FCA, two received a crude brain extract in FCA, and one control quaker parrot received FCA alone. In the preliminary study, one chicken developed ataxia and weakness. None of the quaker parrots had any clinical signs that could resemble PDD or GBS. None of the chickens or quaker parrots presented any gross lesions. The chicken with clinical signs had a perivascular and perineural lymphocytic infiltrate in the proventriculus. Two of the quaker parrots (one from each treatment group) developed mild lymphoplasmacytic encephalitis and myelitis. Our results suggest that autoantibodies against gangliosides in birds are not associated with a condition resembling PDD.
Halkieriid-like animals in the Late Ordovician?
Authors: Mazurek Dawid
Published: January 2018

The recent description of the Tremadocian halkieriid-like stem aculiferan, Calvapilosa kroegeri, could shed new light on some enigmatic Ordovician fossils known only by their disarticulated plates. Specifically, Conchopeltis alternata could be interpreted as a plate of sclerite-bearing stem aculiferan. Comparison is based on a similarity of conchs and reinterpretation of Conchopeltis tentacles as sclerites. This is a highly speculative idea, nevertheless, I think it may have some merit and ignite a discussion, but a reevaluation of Conchopeltis and some shelly taxa, like Scenella, is required.
Ranking of critical species to preserve the functionality of mutualistic networks using the k-core decomposition
Authors: García-Algarra Javier , Pastor Juan Manuel , Iriondo José María , Galeano Javier
Published: January 2018

Mutualistic communities play an important role in biodiversity preservation. They are modeled as bipartite networks and measurements of centrality and degree help to order species and their relative importance for network robustness. Identifying the most endangered ones or those more prone to trigger cascade extinctions is essential to define conservation policies. In this work, we explain how a classical graph analysis tool, the k-core decomposition, provides new ranking magnitudes that reach outstanding performance for these purposes.
Modeling covalent-modifier drugs
Authors: Awoonor-Williams Ernest , Walsh Andrew G , Rowley Christopher N
Published: January 2018

In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly. Computer modeling is widely used in drug discovery, but different computational methods must be used to model covalent modifiers because of the chemical bonds formed. Structural and bioinformatic analysis has identified sites of modification that could yield selectivity for a chosen target. Docking methods, which are used to rank binding poses of large sets of inhibitors, have been augmented to support the formation of protein--ligand bonds and are now capable of predicting the binding pose of covalent modifiers accurately. The pKa's of amino acids can be calculated in order to assess their reactivity towards electrophiles. QM/MM methods have been used to model the reaction mechanisms of covalent modification. The continued development of these tools will allow computation to aid in the development of new covalent modifier drugs.
Aesthetic local search of wind farm layouts
Authors: Mayo Michael , Daoud Maisa
Published: January 2018

The visual impact of wind farm layouts has seen little consideration in the literature on the wind farm layout optimisation problem to date. Most existing algorithms focus on optimising layouts for power or cost of energy alone. In this paper, we consider the geometry of wind farm layouts and whether it is possible to bi-optimise a layout for both energy efficiency and the degree of visual impact that the layout exhibits. We develop a novel optimisation approach for solving the problem, with our approach towards measuring mathematically the degree of visual impact drawing inspiration from the field of architecture. To evaluate our ideas, we demonstrate them on three benchmark problems for the wind farm layout optimisation problem in conjunction with two recently published stochastic local search algorithms. Optimal patterned layouts are shown to be very close in terms of energy efficiency to optimal non-patterned layouts.
De novo characterization of Platycladus orientalis transcriptome and analysis of its gene expression during aging
Authors: Chang Ermei , Yao Xiamei , Zhang Jin , Deng Nan , Jiang Zeping , Shi Shengqing
Published: January 2018

Platycladus orientalis in China has a lifespan of one to several thousands of years. The long lifespans of trees have attracted interest in aging at the molecular level. There is little information on how the global process is controlled. In this study, the MDA content, SOD and POD activities were higher in ancient P. orientalis than in 20-year-old Platycladus orientalis, and the content of protein showed the inverse trend. We obtained 48,044 unigenes having an average length of 896 bp from pooled samples of P. orientalis by transcriptome sequencing. Microarray analysis produced a high-resolution age-course profile of gene expression levels in different age of P. orientalis. In total, 418 differentially expressed genes were identified. The use of highly informative clustering revealed distinct time points at which oxidation reduction and photosynthesis pathways changed. Eight clusters with distinctive expression patterns were identified, the expression of metabolism, photosynthesis, oxidation reduction and transporters related genes were downregulated and protein synthesis, transcription, signal transduction and senescence related genes were upregulated with increasing age. Total chlorophyll, chlorophyll a, and chlorophyll b levels were decreased steadily with age. This study discovery of potential candidate genes affecting photosynthesis in different P. orientalis ages and at senescence, and for identification of the functions of genes involved in regulation of photosynthesis. This work also suggests that improving photosynthetic efficiency under field conditions will require the consideration of multiple factors, such as stress responses.
Druggability analysis of membrane proteins by DoGSiteScorer
Authors: Zhang Ning , Li Daiwei
Published: January 2018

Membrane proteins are the most medicinally important yet to be fully exploited pharmaceutical targets. Here druggability analyses are conducted on three different membrane proteins, namely, the human P2Y12 receptor, glycoprotein-41 that mediates the HIV-1 virus entry and membrane fusion, and phospholamban that regulates the Ca2+ pump in cardiac muscle cells. DoGSiteScorer, a grid-based bioinfromatic technology, is able to identify the binding pockets of all three membrane proteins, and the results were in great agreements with the available crystal structure of P2Y12 receptor-ligand complex. This druggability analysis is especially helpful in cases where the crystal structures of membrane protein-ligand complexes are still difficult to obtain. Better understanding of the druggable pockets of membrane proteins also requires including the membrane environment.
High or low? Comparing high and low-variability phonetic training in adult and child second language learners
Authors: Giannakopoulou Anastasia , Brown Helen , Clayards Meghan , Wonnacott Elizabeth
Published: January 2018

Background. High talker variability (i.e. multiple voices in the input) has been found effective in training non-native phonetic contrasts in adults. A small number of studies suggest that children also benefit from high-variability phonetic training with some evidence that they show greater learning (more plasticity) than adults given matched input, although results are mixed. However no study has directly compared the effectiveness of high versus low talker variability in children. Methods. Native Greek speaking 8-year-olds (N=52), and adults (N=41) were exposed to the English /i/-/ɪ/ contrast in ten training sessions through a computerized word-learning game. Pre- and post-training tests examined discrimination of the contrast as well as lexical learning. Participants were randomly assigned to high (4 talkers) or low (1 talker) variability training conditions. Results. Both age groups improved during training, and both improved more while trained with a single talker. Results of a 3-interval oddity discrimination test did not show the predicted benefit of high-variability in training in either age group. Instead, children showed an effect in the reverse direction – i.e. reliably greater improvements in discrimination following single talker training, even for untrained generalization items, although the result is qualified by (accidental) differences in participant groups at pre-test. Adults showed a numeric advantage for high-variability but were inconsistent with respect to voice and word novelty. In addition, no effect of variability was found for lexical learning. There was no evidence of greater plasticity for phonetic learning in child learners. Discussion. This paper adds to the handful of studies demonstrating that, like adults, child learners can improve their discrimination of a phonetic contrast via computerized training. There was no evidence of a benefit of training with multiple talkers, either for discrimination or word learning. The results also do not support the findings of greater plasticity in child learning found in a previous paper (Giannakopoulou et al., 2013a). We discuss these results in terms of various differences between training and test tasks used in the current work compared with previous literature.
Optimizing pedigrees: Using a biasing system to determine likely inheritance systems
Authors: Ang Justin
Published: January 2018

Pedigrees, though straightforward and versatile, lack the ability to tell us information about many individuals. Though numerical systems have been developed, there has yet to be a system that tells us the probabilities of a pedigree following certain inheritance systems. My system intends to do that by creating a ﬂexible numerical system, which can then be tested for variance. In order to do so, my system attempts to adapt inheritance system to known pedigree data. Then, it calculates the diﬀerence between the calculated values and the known pedigree data. It aggregates these values, then it uses a chi-squared analysis in order to determine how likely said inheritance system is to match the pedigree. This is done for many diﬀerent systems, until we have a general idea of which systems are probable and which are not.
Optimizing pedigrees: Using a biasing system to determine likely inheritance systems
Authors: Ang Justin
Published: January 2018

Pedigrees, though straightforward and versatile, lack the ability to tell us information about many individuals. Though numerical systems have been developed, there is currently no system to quantify the probability of a pedigree following certain inheritance systems. My system intends to fulfill that chasm by creating a flexible numerical system and testing it for variance. First, my system attempts to adapt inheritance system to known pedigree data. Then, it calculates the difference between the calculated values and the known pedigree data. It aggregates these values, then it uses a chi-squared analysis in order to determine the likelihood of said inheritance system. This is done for many different systems, until we have a general idea of which systems are probable and which are not.
A review of R for Data Science: key elements and a critical analysis
Authors: Lortie Christopher J
Published: January 2018

A detailed review of a recent data science book by Hadley Wickham and Garrett Grolemund is developed herein. Technical book reviews should provide a guide to the readers, a sense of the appropriate audience, the specifics of the software/language, and identify critical thinking questions that emerge through reading the specifics of these books. This is a pre-print, extended version of a review of 'R for Data Science', and it provides a relatively comprehensive framing of this particular book. The context and background of the authors is introduced, key elements of this book - primarily the workflow proposed and the value of the tidyverse - are summarized, and a critical analysis of the book was done. The following critical questions were addressed in the review.

(1) Does this book (or any data science book for that matter) effectively communicate basic versus advanced data science concepts to the reader?

(2) Does this book extend or improve upon previous resources particularly for the individual in- terested in using and learning data science to do statistics in R?

(3) Can this book be read as a general data science book and by extension how much is this an R versus RStudio book?

The importance of reading a book associated with tools one uses in computer science such as R versus rapid, online solution-based reading is very effectively established in 'R for Data Science'. Time spent with a technical book providing the big picture for the tools one uses to solve problems in R is important for deeper learning and insights.
Effects of exposure to atrazine on retinoid signaling in zebrafish
Authors: Fan Yu , Liu Haixing , Xu Pengxing , Zhang Weizhi
Published: January 2018

Atrazine is a widely used herbicide developed for use in range and pastureland. It is present in many surface waters, contaminating nontarget organisms due to its persistence. In this study, the effects of acute exposure to atrazine on retinoid signaling were investigated in zebrafish. Zebrafish embryos were exposed to atrazine from 6 hours post-fertilization (hpf) to 120 hpf. The contents of retinal and retinoic acid were decreased significantly. The mRNA expression levels of retinal dehydrogenase (raldh2), retinol dehydrogenase (rdh1), retinol binding protein (rbp1a), retinoic acid receptor subunit (raraa), and cellular retinoic acid binding protein (crabp1a and crabp2a) were significantly reduced, which indicated that retinoid signaling was interrupted. However, the transcriptional levels of five opsin genes (zfrho, zfuv, zfred, zfblue, and zfgr1) were increased. These results indicated that exposure to atrazine could inhibit retinoid signaling and impair the eye development of zebrafish larvae.
Missing, delayed, and old: A status review of ESA recovery plans
Authors: Malcom Jacob , Li Ya-Wei
Published: January 2018

Recovery planning is an essential part of implementing the U.S. Endangered Species Act (ESA), but conservationists and government agencies recognize many problems with the planning process. Common criticisms are that too many species lack recovery plans, plans take too long to write, and they are rarely updated to include new information. Using data from all U.S. domestic and transboundary ESA-listed species—most of which are required to have recovery plans—we quantify basic characteristics of ESA recovery planning over the past 40 years. We show that nearly 1/4 of eligible listed species (n = 1,503) lack recovery plans; the average recovery plan has taken >5 years to finalize after listing; half of recovery plans are 19 or more years old; and there is significant variation among regions and between agencies in plan completion rates and time-to-completion. These results are not unexpected given dwindling budgets and an increasing number of species to protect, but underscore the need for systematic improvements to recovery planning. We discuss solutions that may address some of the shortcomings we identify here, including a transition to dynamic, web-based recovery plans.
Changes in the spatial and temporal pattern of natural forest cover on Hainan Island from the 1950s to the 2010s：implications for natural forest conservation and management
Authors: Lin Siliang , Jiang Yaozhu , He Jiekun , Ma Guangzhi , Xu Yang , Jiang Haisheng
Published: January 2018

The study of the past, present, and future state and dynamics of the tropical natural forest cover (NFC) might help to better understand the pattern of deforestation and fragmentation as well as the influence of social and natural processes. The obtained information will support the development of effective conservation policies and strategies. In the present study, we used historical data of the road network, topography, and climatic productivity to reconstruct NFC maps of Hainan Island, China, from the 1950s to the 2010s, using the random forest algorithm. We investigated the spatial and temporal patterns of NFC change from the 1950s to the 2010s and found that it was highly dynamic in both space and time. Our data showed that grid cells with low NFC were more vulnerable to NFC decrease, suggesting that conservation actions regarding natural forests need to focus on regions with low NFC and high ecological value. We also identified the hot-spots of NFC change, which provides insights into the dynamic changes of natural forests over time.
Microsatellite markers for Sturnira parvidens (Illumina paired-end sequences), and cross species amplification with other bats of the genus
Authors: Gutiérrez Edgar G , Hernández Canchola Giovani , León Paniagua Livia S , Martínez Méndez Norberto , Ortega Jorge
Published: January 2018

Background. Sturnira is one of the most species-richness in the Neotropic, and it is found from Mexico, Lesser Antilles to Argentina. Genus forms a well-supported monophyletic clade with at least twenty-one recognized species, and several under taxonomic review. Sturnira parvidens is a widespread frugivorous bat of the deciduous forest in the Neotropics, highly abundant, and a major component in the fruit dispersal to regenerate ecosystems. It can be consider a non-model organism to isolate and characterize polymorphic microsatellites.Methods. We used a technique based on Illumina paired-end sequencing of a library highly enriched for microsatellite repeats to develop loci for S. parvidens. We analyzing millions of resulting reads with specific software to extract those reads that contained di-, tri-, tetra-, penta-, and hexanucleotide microsatellites.Results. We select and test 14 polymorphic (di, tri, and tetra) microsatellites. All markers were genotyped on 26 different individuals from distinct locations of its distributional area. We observed medium–high genetic variation across most loci, but only 12 were functional polymorphic. Levels of expected heterozygosity across all markers was high to medium (mean HE = 0.79, mean HO = 0.72). We probed ascertainment bias in twelve bats of the genus, obtaining null/monomorphic/polymorphic amplifications.Discussion. Illumina paired-end sequencing system is capable to identify massive microsatellite loci, expending few time, reducing costs, and providing a large amount of data. Described polymorphic loci for S. parvidens particularly, and the genus, could be suitable for further genetic analysis, including taxonomic inconsistencies, parenting/relatedness analysis, and population genetics assessments.
A public dataset of running biomechanics and the effects of running speed on lower extremity kinematics and kinetics
Authors: Fukuchi Reginaldo K , Fukuchi Claudiane A , Duarte Marcos
Published: January 2018

Background. The goals of this study were (1) to present the set of data evaluating running biomechanics (kinematics and kinetics), including data on running habits, demographics, and levels of muscle strength and flexibility made available at Figshare (DOI: 10.6084/m9.figshare.4543435); and (2) to examine the effect of running speed on selected gait-biomechanics variables related to both running injuries and running economy. Methods. The lower-extremity kinematics and kinetics data of 28 regular runners were collected using a three-dimensional (3D) motion-capture system and an instrumented treadmill while the subjects ran at 2.5 m/s, 3.5 m/s, and 4.5 m/s wearing standard neutral shoes. Results. A dataset comprising raw and processed kinematics and kinetics signals pertaining to this experiment is available in various file formats. In addition, a file of metadata, including demographics, running characteristics, foot-strike patterns, and muscle strength and flexibility measurements is provided. Overall, there was an effect of running speed on most of the gait-biomechanics variables selected for this study. However, the foot-strike patterns were not affected by running speed. Discussion. Several applications of this dataset can be anticipated, including testing new methods of data reduction and variable selection; for educational purposes; and answering specific research questions. This last application was exemplified in the study’s second objective.
High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis
Authors: Arocha-Garza Hector Fernando , Canales-Del Castillo Ricardo , Eguiarte Luis E. , Souza Valeria , De la Torre-Zavala Susana
Published: January 2018

The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media. The 16S rDNA of putative Actinobacteria were sequenced using both bacteria universal and phylum-specific primer pairs. Phylogenetic reconstructions were performed to analyze OTUs clustering and taxonomic identification of the isolates in an evolutionary context, using validated type species of Streptomyces from previously phylogenies as a reference. Rarefaction analysis for total Actinobacteria and for Streptomyces isolates were performed to estimate species´ richness in the intermediate lagoon (IL) in the oligotrophic Churince system. A total of 350 morphologically and nutritionally diverse isolates were successfully cultured and characterized as members of the Phylum Actinobacteria. 105 from the total isolates were successfully subcultured, processed for DNA extraction and 16S-rDNA sequenced. All strains belong to the order Actinomycetales, encompassing 11 genera of Actinobacteria; the genus Streptomyces was found to be the most abundant taxa in all the media tested throughout the 3-year sampling period. Phylogenetic analysis of our isolates and another 667 reference strains of the family Streptomycetaceae shows that our isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.