bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics
Authors: Martínez Juan José , Melgarejo Pablo , Legua Pilar , García Francisco , Hernández Francisca
Published: January 2018

Background . Miguel Hernandez University ( Spain ) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the juice’s acidity and pH had the highest power of discrimination, and were, therefore, the most useful for genetic characterization of this pomegranate germplasm banks. This is opposed to leaf and flower characteristics, which had a low power of discrimination. This germplasm bank, more specifically, was characterized by its considerable phenotypic (and presumably genetic) diversity among pomegranate accessions, with a greater proximity existing among the varieties from the same geographical area, suggesting that over time, there had not been an exchange of plant material among the different cultivation areas. In summary, knowledge on the extent of the genetic diversity of the collection is essential for germplasm management. In this study, these data may help in developing strategies for pomegranate germplasm management and may allow for more efficient use of this germplasm in future breeding programs for this species.
Reporting quality of animal experiments of gastric cancer based on the ARRIVE guidelines
Authors: Liu Yali , Feng Yuchen , Zhang Lili , Feng Xiaohuan , Feng Qin , Luo JIngyi , Bai Zhaodi , Wu Haoyu , Tian Xin , Li Yumin
Published: January 2018

Objective: The aim of this study was to use the Animals in Research: Reporting In Vivo Experiments (ARRIVE) guidelines to evaluate the quality of reporting of recent gastric cancer animal experiments. Materials and Methods: A literature search of studies was performed using the Chinese Biomedical Literature Database, Chinese Journal Full-text Database, Chinese Scientific Journal Full-text Database, and Wanfang Database from January 2010 to December 2012. We extracted data using pre-prepared Excel data-extraction forms. Reporting quality was evaluated based on the ARRIVE guidelines. Results: Of the 1816 studies that were identified by our search, 170 were subjected to quantitative analysis using the ARRIVE guidelines. The results of the evaluation based on the ARRIVE guidelines were that 132 studies (77.61%) provided an accurate and concise description of baseline conditions and clinical conditions. Only 2 (1.18%) papers provided relevant certificates of ethical review or institutional guidelines, and 2 (1.18%) papers provided an explanation of animal experiments requiring algorithms and formulas for sample size. Forty-seven (27.65%) studies described in detail how animals were assigned to each experimental group, including the randomization procedure, 2 (1.18%) reported whether blinding was used, and 15 (8.82%) evaluated the limitations of the study. Conclusions: The reporting quality of recent animal experiments of gastric cancer is inadequate. We should improve not only the quality of the methodology but also the reporting quality of the animal experiments.
Comparison of the rate of claw horn growth and wear and sole thickness in dairy cattle housed in a free stall barn with concrete and rubber flooring
Authors: Van Amstel Sarel , Young Charles , Scully Clare , Rohrbach Barton
Published: January 2018

Background. Thin soles and resulting lameness in cows are often due to abrasive walking surfaces that cause increased wear. The aim of this project was to compare horn growth and wear and sole thickness in cows kept on rubber mats versus concrete in a free-stall barn. Methods. To examine horn growth and wear and sole thickness, we examined two groups (Group 1 kept on concrete [control] and Group 2 on rubber mats) of 12 cows each at 2-week intervals over a 12-week period. The 12 cows in each group were selected to achieve equal parity in each group, as follows: four cows, parity 1; four cows, parity 2; two cows, parity 3; and two cows, parity 4. The four cows from the parity 1 group had the most days in milk in the herd irrespective of milk production. The remaining eight cows had the fewest days in milk (most recently calved) irrespective of milk production. Results. Cows in the control group had a significant increase in claw horn growth over the study period, compared to the control group. Most of this difference in horn growth occurred during the first 2 weeks of the study. There was no significant difference in claw horn wear and sole thickness at 2 weeks or at the end of the study. There was, however, a non-significant difference in wear between cows in the 2 groups at the end of the study, with cows in the control group showing most wear. Cows in the experimental group exhibited significant increases in all parameters (claw length, wear, and growth; sole thickness) when measured at the beginning and end of the trial, whereas cows in the control group showed a significant increase in claw length and sole thickness.Discussion. These findings suggest that there was a compensatory increase in horn production in response to accelerated claw horn wear in the control group. Statistical significance in wear might have been attained between groups at the end of the study if the study had continued over a longer period.
A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A
Authors: Morrison Jessica M , Elshahed Mostafa S , Youssef Noha
Published: January 2018

Background. The anaerobic gut fungi (phylum Neocallimastigomycota) represent a promising source of novel lignocellulolytic enzymes. Here, we report on the cloning, expression, and characterization of a glycoside hydrolase family 39 (GH39) enzyme (Bgxg1) that is highly transcribed by the anaerobic fungus Orpinomyces sp. strain C1A under different growth conditions. This represents the first study of a GH39-family enzyme from the anaerobic fungi. Methods. Using enzyme activity assays, we performed a biochemical characterization of Bgxg1 on a variety of substrates over a wide range of pH and temperature values to identify the optimal enzyme conditions and the specificity of the enzyme. In addition, substrate competition studies and comparative modeling efforts were completed. Results. Contrary to the narrow range of activities (β-xylosidase or α-L-iduronidase) observed in previously characterized GH39 enzymes, Bgxg1 is unique in that it is multifunctional, exhibiting strong β-xylosidase, β-glucosidase, β-galactosidase activities (11.5 ± 1.2, 73.4 ± 7.15, and 54.6 ± 2.26 U/mg, respectively) and a weak xylanase activity (10.8 ± 1.25 U/mg), strength determined as compared to previously characterized enzymes. Physiological characterization revealed that Bgxg1 is active over a wide range of pH (3-8, optimum 6) and temperatures (25-60°C, optimum 39°C), and possesses excellent temperature and thermal stability. Substrate competition assays suggest that all observed activities occur at a single active site. Using comparative modeling and bioinformatics approaches, we putatively identified ten amino acid differences between Bgxg1 and previously biochemically characterized GH39 β-xylosidases that we speculate could impact active site architecture, size, charge, and/or polarity. The putative contributions of these changes to the observed relaxed specificities in Bgxg1 are discussed. Discussion. Collectively, the unique capabilities and multi-functionality of Bgxg1 render it an excellent candidate for inclusion in enzyme cocktails mediating cellulose and hemicellulose saccharification from lignocellulosic biomass.
The Durand Adaptive Psychopathic Traits Questionnaire: development and preliminary validation
Authors: Durand Guillaume
Published: January 2018

In recent decades, psychopathic personality has become synonym to a pervasive personality disorder characterized by a lack of empathy, callousness, impulsivity, social deviance and aggressive behavior. However, evidences point to the existence of another form of psychopathy, which involves adaptive traits such as stress and anxiety immunity, remarkable social skills, noteworthy leadership ability, and an absence of fear. The newly developed Durand Adaptive Psychopathic Traits Questionnaire (DAPTQ) aims to assess adaptive traits known to correlate with the psychopathic personality. Validation of the questionnaire among 765 individuals from the community gave support for a 4-factor solution within the DAPTQ: Extroverted Leading, Rational Thinking, Risk Taking, and Composure. The DAPTQ and its four subscales demonstrated high internal consistency in a community sample (0.78 - 0.88) and in a clinical sample (0.79 - 0.90). Good convergent and divergent validity was established by administering the DAPTQ alongside established measures of psychopathic personality. Subscales validation against well-established personality assessments further confirm the DAPTQ’s strength. These findings indicate that the DAPTQ is a reliable and valid tool for measuring psychopathy-associated adaptive traits. Limitations of the present study and potential directives for future research are also discussed. Further studies are needed to validate the DAPTQ and its subscales against a wider range of personality traits and behaviors.
The Durand Adaptive Psychopathic Traits Questionnaire: development and preliminary validation
Authors: Durand Guillaume
Published: January 2018

While the term ‘psychopathy’ is embedded with negativity, evidences point to the existence of another form of psychopathy, which involves adaptive traits such as stress and anxiety immunity, remarkable social skills, noteworthy leadership ability, and an absence of fear. The newly developed Durand Adaptive Psychopathic Traits Questionnaire (DAPTQ) aims to assess adaptive traits known to correlate with the psychopathic personality. Validation of the questionnaire among 765 individuals from the community gave support for a 4-factor solution within the DAPTQ: Extroverted Leading, Rational Thinking, Risk Taking, and Composure. The DAPTQ and its four subscales demonstrated high internal consistency in a community sample (0.78 - 0.88). Good convergent and divergent validity was established by administering the DAPTQ alongside established measures of psychopathic personality. Subscales validation against well-established personality assessments further confirm the DAPTQ’s strength. These findings indicate that the DAPTQ is a reliable and valid tool for measuring psychopathy-associated adaptive traits. Limitations of the present study and potential directives for future research are also discussed. Further studies are needed to validate the DAPTQ and its subscales against a wider range of personality traits and behaviors.
SymPy: Symbolic computing in Python
Authors: Meurer Aaron , Smith Christopher P , Paprocki Mateusz , Čertík Ondřej , Rocklin Matthew , Kumar AMiT , Ivanov Sergiu , Moore Jason K , Singh Sartaj , Rathnayake Thilina , Vig Sean , Granger Brian E , Muller Richard P , Bonazzi Francesco , Gupta Harsh , Vats Shivam , Johansson Fredrik , Pedregosa Fabian , Curry Matthew J , Saboo Ashutosh , Fernando Isuru , Kulal Sumith , Cimrman Robert , Scopatz Anthony
Published: January 2018

SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become the standard symbolic library for the scientific Python ecosystem. This paper presents the architecture of SymPy, a description of its features, and a discussion of select domain specific submodules. The supplementary materials provide additional examples and further outline details of the architecture and features of SymPy.
Bacteria surface charge in “layers”: revealed by wash buffers of different ionic strength
Authors: Ng Wenfa
Published: January 2018

Bacteria surface charge derives its meaning from the cell’s environment; thus, there is no one specific surface charge. Determining the surface charge of bacteria in its native environment requires measuring the proxy variable, zeta potential, using cells obtained from field studies. However, lack of adequate cell mass and concerns over measurement of a mixed species consortia rather than a specific species meant that bacteria surface charge measurement require biomass obtained from laboratory shake flask pure culture. Often grown in rich medium where myriad proteins and ions nonspecifically adsorbed on the cell envelope or peptidoglycan layer, standard procedures for preparing the cell mass require repeated steps of washing and centrifugation with various wash buffers, the efficacies of which are poorly understood. This report describes a systematic study on how wash buffers of different composition and salinity affect the efficiency of removing nonspecifically adsorbed biomolecules and ions from Escherichia coli DH5a (ATCC 53868) cultured aerobically (shake flask, 37 oC and 230 rpm) in LB Lennox medium. Using zeta potential-pH profiles over pH 1 to 12 as readout, proxy measurement of wash buffers’ efficacies showed that efficiency of removing nonspecifically adsorbed ions and metabolites positively correlates with wash buffer ionic strength. More importantly, 0.15M ionic strength (i.e., 9 g/L NaCl and phosphate buffer saline) seems to be the minimum below which there appeared to be little removal of nonspecifically adsorbed biomolecules (deionized water wash as control). On the other hand, high ionic strength of 0.6M (0.1M sodium citrate) significantly changed the point of zero charge (pHzpc), a reference marker for the removal of ions intrinsic to the cell envelope; thus, indicating significant cell surface damage. Collectively, results obtained provided important pointers for wash buffer choice concerning preservation of cell envelope integrity. Finally, is there a true cell surface charge? Yes, but how to define it? How many “layers” of adsorbed biomolecules? Philosophically, cells in culture broth are coated with layers of metabolites, proteins and ions; hence, desire to reveal the true surface charge is essentially a decoating process, where wash buffers of increasing ionic strength could remove each layer through charge screening. Where is the endpoint? This research suggests that ionic strength of wash buffers chosen should be similar to that of the environment the research is seeking to address. Imagine a single bacterium suspended in LB medium, what is its relevant surface charge? It is the one where the loosely associated ions and metabolites can be removed, similar to the constant adsorption and desorption processes that the cell experiences in its growth environment. Thus, deionized water wash provides a good estimate of the bacteria surface charge as grown in specific medium.
Aquatic insects dealing with dehydration: do desiccation resistance traits differ in species with contrasting habitat preferences?
Authors: Pallarés Susana , Velasco Josefa , Millán Andrés , Bilton David T. , Arribas Paula
Published: January 2018

Background. Desiccation resistance shapes the distribution of terrestrial insects at multiple spatial scales. However, responses to desiccation stress have been poorly studied in aquatic groups, despite their potential role in constraining their distribution and diversification, particularly in arid and semi-arid regions. Methods. We examined desiccation resistance in adults of four congeneric water beetle species (Enochrus, family Hydrophilidae) with contrasting habitat specificity (lentic vs lotic systems and different salinity optima from fresh- to hypersaline waters).We measured survival, recovery capacity and key traits related to desiccation resistance (fresh mass, % water content, % cuticle content and water loss rate) under controlled exposure to desiccation, and explored their variability within and between species. Results. Meso- and hypersaline species were more resistant to desiccation than freshwater and hyposaline ones, showing significantly lower water loss rates and higher water content. No clear patterns in desiccation resistance traits were observed between lotic and lentic species. Intraspecifically, water loss rate was positively related to specimens’ initial % water content, but not to fresh mass or % cuticle content, suggesting that the dynamic mechanism controlling water loss is mainly regulated by the amount of body water available. Discussion. Our results support previous hypotheses suggesting that the evolution of desiccation resistance is associated with the colonization of saline habitats by aquatic beetles. The interespecific patterns observed in Enochrus also suggest that freshwater species may be more vulnerable than saline ones to drought intensification expected under climate change in semi-arid regions such as the Mediterranean Basin.
An optimized approach to germ-free rearing in the jewel wasp Nasonia
Authors: Shropshire J. Dylan , van Opstal Edward J. , Bordenstein Seth R.
Published: January 2018

The initial development of the Nasonia in vitro germ-free rearing system in 2012 enabled investigations of Nasonia-microbiota interactions and real-time visualization of metamorphosis. However, the use of antibiotics, bleach, and fetal bovine serum in this in vitro rearing system introduced artifacts relative to conventional rearing of Nasonia. Here, we optimize the germ-free rearing procedure by using filter sterilization in lieu of antibiotics and by removing residual bleach and fetal bovine serum. Comparison of these methods reveals no influence on larval survival or growth, and a 52% improvement in adult production. Additionally, adult males produced in the new germ-free system are similar in size to conventionally reared males. Experimental implications of these changes are discussed.
Coupling spatiotemporal community assembly processes to changes in microbial metabolism
Authors: Graham Emily , Crump Alex R. , Resch Charles T , Fansler Sarah , Arntzen Evan , Kennedy David , Fredrickson Jim K , Stegen James C.
Published: January 2018

Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally-explicit multivariate statistics. We demonstrate that multiple selective pressures—imposed by sediment and porewater physicochemistry—integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally-stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.
The potential of bacteriocin AS-48 in the control of Propionibacterium acnes
Authors: Cebrián Rubén , Arévalo Sergio , Ananou Samir , Arias-Santiago Salvador , Riazzo Cristina , Rojo Maria Dolores , Bermudez-Ruiz Maria Pilar , Valdivia Eva , Martinez-Bueno Manuel , Maqueda Mercedes
Published: January 2018

Background Global reports show that the antimicrobial-resistance of Propionibacterium acnes isolated from patients with acne vulgaris is becoming a large problem, making it necessary to find new therapeutic drugs.

Methods In this study, 23 clinical isolates of P. acnes have been identified by MaldiToff and specific PCR. The susceptibility of theses strains to antibiotics (clindamicin, erytromycin and tetracicline) and to bacteriocin (AS-48) has been established, using the CECT 5684 strain as reference. Moreover, we have investigated the potential of several chemical compounds to bolster the activity of AS-48. Finally, the effectivity of four different formulations containing AS-48 and lysozyme have been evaluated on the surface of swine-ear skin previously inoculated with P. acnes CECT5684 strain.

Results. The results presented in this work probe that AS-48 has a significant bactericidal activity against the 23 clinical isolates of P. acnes, including isolates resistant to one or more common antibiotics used in the treatment of acne. Antibacterial synergy of AS-48 with other chemical compounds has been demonstrated, as was the effect of lysozyme and to a lesser extent with palmitic acid. Likewise, the use of a combination therapy into a cream formulation, resulted in large decrease in the number of viable P. acnes counts in an experiemental model.

Conclusion. Once more these studios support that compositions comprising bacteriocins displaying antibacterial activity, must be considered an approach for medical and pharmaceutical purposes. These applications are particularly promising in light of emerging antibiotic resistance across bacteria involved in treatment of dermatological disease as acne vulgaris.
Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content by Genotyping-By-Sequencing (GBS) in teleost Larimichthys crocea
Authors: Xiao Shijun , Wang Panpan , Dong Linsong , Zhang Yaguang , Han Zhaofang , Wang Qiurong , Wang Zhiyong
Published: January 2018

Whole-genome single-nucleotide polymorphism (SNP) markers are valuable genetic resources for the association and conservation studies. Genome-wide SNP development in many teleost species are still challenging because of the genome complexity and the cost of re-sequencing. GBS provided an efficient reduced representative method to squeeze cost for SNP detection; however, most of recent GBS applications were reported on plant organisms. In this work, we used an EcoRI-NlaIII based GBS protocol to teleost large yellow croaker, an important commercial fish in China and East-Asia, and reported the first whole-genome SNP development for the species. 69,845 high quality SNP markers that evenly distributed along genome were detected in at least 80% of 500 individuals. Nearly 95% randomly selected genotypes were successfully validated by SequenomMassARRAYassay. The association studies with the muscle EPA and DHA content discovered 39 significant SNP markers, contributing as high up to ~63% genetic variance that explained by all markers. Functional genes that involved in fat digestion and absorption pathway were identified, such as APOB, CRAT and OSBPL10. Notably, PPT2 Gene, previously identified in the association study of the plasma n-3 and n-6 polyunsaturated fatty acid level in human, was re-discovered in large yellow croaker. Our study verified that EcoRI-NlaIII based GBS could produce quality SNP markers in a cost-efficient manner in teleost genome. The developed SNP markers and the EPA/DHA associated SNP loci provided invaluable resources for the population structure, conservation genetics and genomic selection of large yellow croaker and other fish organisms.
Using Python® language for the validation of the CCI soil moisture products via SM2RAIN
Authors: Ciabatta Luca , Massari Christian , Brocca Luca , Reimer Christoph , Hann Sebastian , Dorigo Wouter , Wagner Wolfgang
Published: January 2018

Remote sensing techniques provide a new way to obtain hydrological variables (i.e. rainfall and soil moisture), mainly in poorly instrumented areas that are fundamental for natural hazard assessment and mitigation. The even increasing availability of satellite derived products characterized by high temporal and spatial coverage requires the development of techniques and instruments for big data volume managing. Moreover, the use of open source systems is highly encouraged in order to increase their use by the scientific community. In this study, the application of the SM2RAIN algorithm to the CCI soil moisture product is proposed as case study. A number of Python® classes and methods have been developed for this purpose, with the aim of creating an open-source web validation tool for SM dataset, within the Earth Observation Data Centre for Water Resources Monitoring (EODC).
LISAM: an open source GIS-based model for liveability spatial assessment
Authors: Antognelli Sara , Vizzari Marco
Published: January 2018

Ecosystem Services (ES) and Urban Services (US) influence place liveability in a comparable manner. Consequently, assessing landscape liveability considering both types of services can result effective for landscape planning and policy-making purposes. Since liveability depends also on local population preferences and perceptions, stakeholder involvement results essential for a more coherent liveability assessment. In this study a Spatial Multicriteria Decision Aiding (S-MCDA) approach guided the development of a LIveability Spatial Assessment Model (LISAM). Using a combination of GIS techniques (Euclidean distance, kernel density estimation, network analysis, viewshed analysis), consistent and comparable ES and US spatial indices were calculated in a study area located in central Italy. The indices were implemented in open-source geo-spatial software (QGIS, PostGIS and PostgreSQL). According to the Analytical Hierarchy Process (AHP), they were integrated with their percentage weights on liveability deriving from stakeholders interviews. Then, to investigate the liveability levels of local population, main statistics of liveability values were calculated per census section. Results include overall liveability indices at a local scale, and key statistics of liveability related to resident population. The work highlights the effectiveness of LISAM to assess local liveability and to deliver important information for policy-makers. LISAM approach opens the opportunity to integrate also ecosystem and urban disservices together with ES and US in liveability assessment to consider also the factors generated by landscape components that reduce the overall level of place liveability.
WebWorldWind, achievements and future of the ESA-NASA partnership
Authors: Voumard Yann , Sacramento Paulo , Marchetti Pier Giorgio , Hogan Patrick
Published: January 2018

Web World Wind is a 3D virtual globe API for HTML5 and JavaScript developed by NASA with support of the European Space Agency (ESA) and other partners. In this paper, the results of the first year for the on-going collaboration between ESA and NASA on Web World Wind development are presented, highlighting concrete examples built with the newly introduced features and putting them in relation to possible research and education use cases. Finally, the next steps and roadmap are briefly introduced.
WebWorldWind, achievements and future of the ESA-NASA partnership
Authors: Voumard Yann , Sacramento Paulo , Marchetti Pier Giorgio , Hogan Patrick
Published: January 2018

Web World Wind is a 3D virtual globe API for HTML5 and JavaScript developed by NASA with support of the European Space Agency (ESA) and other partners. In this paper, Web World Wind is compared to other virtual globe technologies and the results of the first year for the on-going collaboration between ESA and NASA on Web World Wind development are presented. Concrete examples built with the newly introduced features are highlighted and put in relation to possible research and education use cases. Finally, the next steps and roadmap are briefly introduced.
A geoprocessing modelling interoperable framework for AgriGIS using open data and open standards
Authors: Santos Roberto , Huynh Dai , Anand Suchith , Ray Rumiana , Mayes Sean , Leibovici Didier
Published: January 2018

We retrace the construction of AgriGIS framework between multiple disciplines around a common objective of facilitating research on model simulations for sustainable food security. The geospatial media enabling multidisciplinary research in crop modelling but also supporting new types of hypothesis and analysis, is described with interoperability principles and seamless access and sharing for data, metadata and processing models. Designing the platform achieving this main objective generated a transdisciplinary vision of modelling and forecasting for sustainable agriculture.
NASA World Wind: virtual globe for an open smart city
Authors: Brovelli Maria A , Kilsedar Candan E , Hogan Patrick J , Prestifilippo Gabriele , Zamboni Giorgo
Published: January 2018

In this article, firstly the open source framework NASA World Wind is introduced. NASA World Wind comes mainly with two versions. The Java version is well established in the market and has many customers. On the other hand the new version, which is the Web version, Web World Wind, is still at the dawn of development cycle, with many features implemented and already used in several applications, with a great future ahead. Following the introduction of NASA World Wind, the features available in the Web World Wind are listed and a short comparison with Cesium library is provided. Additionally, an application developed in the smart cities context with Web World Wind is described.
Directional and balancing selection on proprotein convertase subtilisin/kexin type 6 (PCSK6)
Authors: Kuderer Sonja , Fieder Martin , Kirchengast Sylvia
Published: January 2018

The selective pressures challenging the human population leave genetic signatures. This study was designed to detect positive and balancing selection on the proprotein convertase subtilisin/kexin type 6 (PCSK6) gene by four different approaches (FDIST, BayeScan, EHH, iHS). The outlier programs FDIST and BayeScan found 27 overlapping single nucleotide polymorphisms (SNPs) under selection, of which twelve are under strong positive directional selection and 15 under balancing selection. In the EHH analysis, all SNPs detected under positive selection show a slow decay of the derived extended haplotype. The integrated haplotype scores (iHS) for eight loci under positive selection were found to be larger than one. Based on these results, we provide a short overview of PCSK6-related mechanisms potentially associated with the detected positive or balancing selection patterns. Positive selection possibly reflects the key role of PCSK6 in tumorigenesis, in nociception, in rheumatoid arthritis and osteoarthritis, in the cardiovascular circulatory as well as in blood pressure regulation. Balancing selection acting on the PCSK6 locus might be explained by its involvement in vertebral left-right asymmetry and therefore in human handedness. Whereas until now the exact nature of the selective pressures acting on PCSK6 remained incompletely understood, the results of this study provide for the first time insights into the enzyme’s evolutionary significance owing to its functional manifoldness.
Who’s your mama? Riverine hybridisation of threatened freshwater Trout Cod and Murray Cod
Authors: Couch Alan J , Unmack Peter J , Dyer Fiona J , Lintermans Mark
Published: January 2018

Rates of hybridization and introgression are increasing dramatically worldwide because of translocations, restocking of organisms and habitat modifications (Allendorf et al., 2001) thus determining whether hybridization is beneficial or detrimental for the species involved is commensurately important for conservation. Restocking programs are sometimes criticized because of the genetic consequences of hatchery-bred fish breeding with wild populations. These concerns are important to conservation restocking programs, including Percichthyidae. Two of the better known Australian Percichthyidae are the Murray Cod (Maccullochella peelii) and Trout Cod (Maccullochella macquariensis) which were formerly widespread over the Murray Darling Basin. In much of the Murrumbidgee River Trout Cod and Murray Cod were sympatric until the late 1970s when Trout Cod were extirpated. Here we use genetic SNP data to examine hybridization and introgression between Murray Cod and Trout Cod in the upper Murrumbidgee River and consider implications for restocking programs. For the first time we have confirmed restocked riverine Trout Cod as reproducing in the wild. We detected hybrid Trout Cod-Murray Cod in the Upper Murrumbidgee, recording the first hybrid larvae in the wild. Although hybrid larvae, juveniles and adults have been recorded in hatcheries and impoundments, and hybrid adults have been recorded in rivers previously (Douglas, Gooley & Ingram, 1994a; Douglas et al., 1995) , this is the first time fertile F1 have been recorded in the wild. The F1 backcrosses with Murray cod have also been found to be fertile. All backcrosses noted were with pure Murray Cod. Such introgression has not been recorded previously in these two species, and the imbalance in hybridization direction may have important implications for restocking programs.
Biofeedback based on mobile accelerometry to improve running in space – ideas and first results
Authors: Daumer Martin , Müller Karl , Mercader Alexandra , Lederer Christian
Published: January 2018

Background – actibelt technology – a 3D accelerometer in a belt buckle and a package of algorithms, mainly used in international multi centre clinical trials – has also been evaluated for various applications in space, moon and mars in a series of studies and projects since roughly 10 years (2 parabola flight campaigns by ESA, 1 parabola flight campaign by NASA, mars 500).

Aim – To develop a training feedback application which compares the similarity of running parameters under artificial gravity conditions with natural running on earth.

Methods - We use an actibelt BLU2, a version of the actibelt with bluetooth transmission capability, an android tablet with internet access and R packages to visualize and quantify acceleration patterns. Data, including video documentation in some cases, was collected from various runners (marathon, mountain runs, B2run) and various running styles. Written informed consent was obtained.

Results: We have developed an application running on an android tablet. It displays an overview of the projections of the accelerometry pattern of the individual steps in the sagittal plane as well as a summary measure for the mean area per step. There are clear differences between extremes of running style (heel strike overstriding vs. forefoot) both in the area and the shape of the curve.

Discussion/Conclusion: We speculate that online-biofeedback of the acceleration patterns and extracted parameters could advise astronauts during their treadmill training how to best adapt their running style as to optimally avoid loss of bone mineral density. As with running on earth also footwear – with or without heel cushioning, minimal footwear, barefoot – may play an important role.
Minimum soil nutrient guidelines for turfgrass developed from Mehlich 3 soil test results
Authors: Woods Micah S , Stowell Larry J , Gelernter Wendy D
Published: January 2018

Conventional soil nutrient guidelines are higher than needed to produce high quality turfgrass. Although there have been repeated calls for more turfgrass soil calibration research, it is not practical to conduct conventional soil test calibrations for this global crop. Turfgrass comprises more than 10 common species and hundreds of cultivars, grown in a multitude of soils and climates. We took an indirect approach to identify universally applicable guidelines by studying a large sample of 16,163 Mehlich 3 soil test results collected from good-performing turf. We modeled a subset (n = 3,683) of those results, specifically from soils with low nutrient holding capacity, as 2 parameter log-logistic distributions. We take these continuous probability distributions to be representative of soils in which good-performing turf is being produced. The minimum levels for sustainable nutrition (MLSN) guidelines were selected as the value \(x\) at which the probability of a random sample \(X\) drawn from the distribution being less than or equal to \(x\) is \( 0.1\). That is, we identified the level \(x\) where \(P (X ≤ x) = 0.1\). We propose the MLSN guidelines as minimum levels for all turfgrass sites, with fertilizer recommendations suggested as the quantity sufficient to prevent each element from dropping below the MLSN guideline. The MLSN guidelines from the Mehlich 3 data used in this paper are, for K, P, Ca, Mg, and S respectively, 37, 21, 348, 47, and 7 mg kg-1.
Visual analogies in anatomic and clinical pathology
Authors: Kipersztok Lisa , Masukume Gwinyai , Lakhtakia Ritu , Cohen Michael B
Published: January 2018

Visual medical analogies have been utilized by multiple medical disciplines for decades. Despite misgivings that some might have about such analogies, they act as excellent learning aids and will undoubtedly remain useful for decades to come. The microscope from about the seventeenth century onwards revolutionized medicine and cellular biology. In this article, we specifically consider in a pictorial essay culinary medical analogies as they pertain to the microscopic world, a gap in the literature on visual medical analogies.
Structure prediction of ordered domains of Huntingtin
Authors: Brandi Valentina , Polticelli Fabio
Published: January 2018

An abnormal polyglutamine (polyQ) expansion in the N-terminal fragment of the Huntingtin (Htt) protein leads to the devastating neurodegenerative disorder Huntington’s disease (HD). Htt is ubiquitous both at the tissue and subcellular levels and is fundamental for the survival and functioning of the brain neurons that predominantly degenerate in HD. In the hope of finding a cure for HD, there has been intense research aimed at understanding the molecular mechanisms underlying the deleterious effects of the presence of the abnormal polyQ expansion in Htt (Saudou and Humbert, 2016). It is a protein of 3144 amino acids and its high molecular weight prevents crystals production and X-ray diffraction studies to determine its three-dimensional structure. Further, Htt doesn’t display significant sequence similarity with other proteins of known structure, making difficult the study of its structure-function relationships (Zuccato et al., 2010). Therefore the main motivation of this study was that of obtaining structural information on Htt using ab initio/threading protein structure prediction techniques, information which could provide new insight into its functions and the mechanisms through which the mutation leads to the neurodegeneration. Ordered and disordered regions of Htt were predicted using Foldindex (Prilusky et al., 2005), GlobPlot (Linding et al., 2003), Predict Protein (Yachdav et al., 2014), Anchor (Dosztányi et al., 2009), InterPro (Mitchell et al., 2014), Smart (Letunic et al., 2014), HMMER (Finn et al., 2011), Espritz (Potenza et al., 2014) and MobiDB (Walsh et al., 2012). Structure prediction was performed through the use of I-TASSER (Roy et al., 2010), Rosetta (Kaufmann et al., 2010) and Robetta (Kim et al., 2004). The Dali server (Holm and Rosenström, 2010) has been used to infer structural similarities and hypothesize a possible function for each Htt domain. Using a consensus between different order/disorder prediction methods, Htt sequence has been divided in five regions predicted to form ordered domains (Hunt1-5). Then a structure prediction was performed for each ordered domain, obtaining the structural models depicted in Figure 1. Four out of five models are characterized by a prevalence of α-helical structure, in agreement with the predicted presence in Htt of Heat repeats. A structural homolog has been identified for each model of Htt ordered domains. Interestingly, Hunt1, 2 and 5 models display structural similarity with the subunit A of protein Phosphatase 2, the most important serin/threonine phosphatase involved in many essential aspects of cellular function (Xu et al., 2006). Hunt3 model displays structural similarity with the karyopherin Kap121p while Hunt4 model with poly U polymerase Cid1. To our knowledge, this work represents the first attempt to predict the structural and functional features of all Htt domains and the results obtained may represent a starting point for future experimental studies.
Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses
Authors: Lin Mei Fang , Chou Wen Hwa , Kitahara Marcelo V , Chen Chao Lun Allen , Miller David John , Foret Sylvain
Published: January 2018

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.
An agent-based model to assess the forest fires dynamic in the southern Swiss alpine region
Authors: Minelli Annalisa , Tonini Marj
Published: January 2018

Alpine fires are mainly slope-driven, spreading along the forested steep slopes. Fire ignitions are here highly clustered near anthropogenic infrastructures and this characteristic behavior also affects the definition of the wildland urban interface (WUI). This last is known as the area where houses and other human infrastructures meet or intermingle with wildland vegetation, rural zone or forest. The main objective of the present study is to create a simulation model to assess the forest fire dynamic in pilot area located in the in the southern Swiss alpine region. This allows to investigate, for example, the influence of the mobility of people on the fires occurrences by simulating the daily movement of each single active person; or to simulate the displacement of the firefighters over the territory in order to evaluate the efficiency of different fires fight strategies in time. In this preliminary study the core simulation model has been implemented in GAMA, an open source agent based simulation platform. A long term objective is to conduct a study at global scale, over a wider area (e.g. the entire Canton Ticino), to understand the evolution of the WUI in time, analysing the affecting factors like the population growth or of the urbanisation and land use management.
Deer herbivory reduces web-building spider abundance by simplifying forest vegetation structure
Authors: Roberson Elizabeth J , Chips Michael J , Carson Walter P , Rooney Thomas P
Published: January 2018

Indirect effects are a common feature of ecological systems, arising when one species affects interactions among two or more other species. We examined how browsing by white-tailed deer (Odocoileus virginianus) affected the abundance and composition of a web-building spider guild through their effects on the structure of the ground and shrub layers of northern hardwood forests. We examined paired plots consisting of deer-free and control plots in Pennsylvania and Wisconsin. We recorded the abundance of seven types of webs, each corresponding to a family of web-building spiders. We quantified vegetation structure and habitat suitability for the spiders by computing a web scaffold availability index (WSAI) at 0.5 m and 1.0 m above the ground. At Wisconsin sites, we recorded prey availability. Spider webs were twice as abundant in deer-free plots compared to control plots, while WSAI was 7-12 times greater in deer-free plots. Prey availability was also higher in deer-free plots. With the exception of funnel web-builders, all spider web types were significantly more abundant in deer-free plots. Both deer exclusion and the geographic region of plots were significant predictors of spider community structure. In closed canopy forests with high browsing pressure, the low density of tree saplings and shrubs provides few locations for web-building spiders to anchor webs. Recruitment of these spiders may become coupled with forest disturbance events that increase tree and shrub recruitment. By modifying habitat structure, deer indirectly modify arthropod food web interactions. As deer populations have increased in eastern North America over the past several decades, the effects of deer on web-building spiders may be widespread throughout the region.