bluuebunny/crossref_metadata_2025 huggingface dataset:
Doctoral dissertations in Chinese Interpreting Studies: A scientometric survey using topic modeling
Authors: Xu Ziyun
Published: January 2018

Despite being a relatively new discipline, Chinese Interpreting Studies (CIS) has witnessed tremendous growth in the number of publications and diversity of topics investigated over the past two decades. The number of doctoral dissertations produced has also increased rapidly since the late 1990s. As CIS continues to mature, it is important to evaluate its dominant topics, trends and institutions, as well as the career development of PhD graduates in the subject. In addition to traditional scientometric techniques, this study’s empirical objectivity is heightened by its use of Probabilistic Topic Modeling (PTM), which uses Latent Dirichlet Allocation (LDA) to analyze the topics covered in a near-exhaustive corpus of CIS dissertations. The analysis reveals that the topics of allocation of cognitive resources, deverbalization, and modeling the interpreting process attracted most attention from doctoral researchers. Additional analyses were used to track the research productivity of institutions and the career trajectories of PhD holders: one school was found to stand out, accounting for more than half of the total dissertations produced, and a PhD in CIS was found to be a highly useful asset for new professional interpreters.
Agriculture-independent, sustainable, fail-safe and efficient food production by autotrophic single-cell protein
Authors: Bogdahn Ingvar
Published: January 2018

Food production with plants consumes large amounts of water, occupies large areas of land and cannot guarantee food security beyond the 21st century. Industrial agriculture in particular, is destructive to the environment, fosters climate change in profound ways, deteriorates public health and causes high ”hidden costs”. Single-cell protein (SCP) represents an alternative with minimal carbon-, water- and land footprints. However, when grown on biowastes of industrial agriculture, heterotrophic SCP does not truly improve sustainability or food security.

This hypothesis paper proposes autotrophic SCP bioprocess designs which enable sustainable, fail-safe and efficient production of edible biomass from CO2 and N2 or NH3. They can be driven by H2, CO or HCOOH from several sustainable sources. Besides H2O-electrolysis and syngas, surprisingly fossil fuel may provide an effectively carbon-negative and cheap supply of H2 through the decomposition of CH4 or oil. Most promising bioprocess designs consist of 2-stages. In the first stage, homoacetogenic bacteria fix CO2 up to 10 more efficiently than plants, and secrete it as acetate. In the second stage, selected microbes grow on the acetate and thereby form edible biomass. Bacteria have unique features including N2-fixation, H2S tolerance and O2-tolerant hydrogenases for fast light-independent growth. Eukaryotic microalgae are already approved as food and exhibit oxygenic photosynthesis which partly replaces solar-panels, seawater desalination and H2O-electrolyzers. Photoheterotrophic growth on acetate decouples these benefits from inefficient endogenous CO2 fixation. Slow gas mass-transfer, poor light distribution and expensive cell harvest are major challenges arising from the cultivation in liquid media. To cope with this, microbes grow as hydrated biofilms that are exposed directly to substrate gases, and that can be dry-harvested. Two suitable bioreactors are presented and adaptations for 2-stage designs are proposed. Since provision with substrates is expensive, two strategies are proposed for the safe extraction of substrates from food-grade as well as non-food- grade biowastes via partial anaerobic digestion. Additionally, alkalic pH and hydroxides formed at the cathode during electrolysis may be used to precipitate CO2 from the air as carbonates. In two use cases, 2-stage designs with solar-powered H2-generation from seawater were estimated to exceed productivity of wheat 20-200 fold, for moderate and arid climates respectively. Preliminary cost estimates and data about direct and indirect subsidies of industrial agriculture lead to the hypothesis that autotrophic SCP likely outperforms industrial agriculture not only in ecological but also in economical aspects.
Combining environmental suitability and population abundances to evaluate the invasive potential of the tunicate Ciona intestinalis along the temperate South American coast
Authors: Januario Stella , Estay Sergio A , Labra Fabio A , Lima Mauricio
Published: January 2018

The tunicate Ciona intestinalis is an opportunistic invader with high potential for causing economic losses in aquaculture centers. Recent phylogenetic and population genetic analysis support the existence of a genetic complex described as C. intestinalis with two main dominant species (sp A and B) occurring worldwide. In Chile, the species has been observed around 30o S of latitude, but no official reports exist for the presence of C. intestinalis in southern regions (above 40o S), where most of the mollusk aquaculture centers are located. Here, we used occurrences from multiple invaded regions and extensive field sampling to model and validate the environmental conditions that allow the species to persist and to find the geographic areas with the most suitable environmental conditions for the spread of C. intestinalis in the Chilean coast. By studying the potential expansion of C. intestinalis southward in the Chilean Coast, we aimed to provide valuable information that might help the development of control plans before the species becomes a significant problem, especially above 40o S. Our results highlight that, by using portions of the habitat that are apparently distinguishable, the species seem to be not only genetically distinct, but ecologically distinct as well. The two regional models fitted for sp A and for sp B showed disagreement on which sections of Chilean coastline are considered more suitable for these species. While the model for sp A identifies moderately to highly suitable areas between 30o and 40o S, the model for sp B classifies the areas around 45o S as the most appropriate. Data from field sampling show a positive linear relationship between density of C. intestinalis and the index of suitability for sp A in aquaculture centers. Understanding the relation of the distinct species with the surrounding environment provided valuable insights about probable routes of dispersion in Chile, especially into those areas considered suitable for aquaculture activities but where the species has not yet been recorded. We discuss the implications of our findings as a useful tool to anticipate the invasion of such harmful invasive species with regard to the most relevant environmental variables.
Quantitative microbial ecology through stable isotope probing
Authors: Hungate Bruce A , Mau Rebecca L , Schwartz Egbert , Caporaso J Gregory , Dijkstra Paul , van Gestel Natasja , Koch Benjamin J , Liu Cindy M , McHugh Theresa A , Marks Jane C , Morrissey Ember M , Price Lance B
Published: January 2018

Bacteria grow and transform elements at different rates, yet quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to Stable Isotope Probing (SIP) that enables determining the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon specific density curves are produced for labeled and non-labeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon’s density shift relative to that taxon’s density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative Stable Isotope Probing (qSIP). We demonstrate qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variation in 18O and 13C composition after exposure to 18O-H2O or 13C-glucose. Addition of glucose increased assimilation of 18O into DNA from 18O-H2O. However, the increase in 18O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because glucose addition indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.
Screening of cytoprotectors against methotrexate-induced cytogenotoxicity from bioactive phytochemicals, by umu test combined with micronucleus Assay
Authors: Gu Shaobin , Wu Ying , Yang Jianbo
Published: January 2018

To develop new cytoprotectors to reduce the risk of second cancers caused by methotrexate-induced cytogenotoxicity, cytoprotective effects of ten kinds of phytochemicals and their combinations were evaluated by umu test combined with micronucleus assay. It is demonstrated that allicin, proanthocyanidins, polyphenols, eleutherosides and isoflavones owned higher antimutagenic activities than other phytochemicals. At the highest dose tested, the MTX genetoxicity was inhibited by 34.03%~67.12%. Of all the bioactive phytochemical combinations, the combination of grape seed proanthocyanidins and eleutherosides from siberian ginseng as well as green tea polyphenols and eleutherosides showed stronger antimutagenic effects, the inhibition rate of methotrexate-induced genotoxicity separately reached 74.7 ± 6.5 % and 71.8 ± 4.7%. The Kunming mice treated by MTX along with bioactive phytochemicals combinations showed significant reduction in micronucleus induction and sperm abnormality rate compared to MTX treated control groups without cytoprotector candidates (p<0.01). Moreover, obvious increases in thymus and spleen indices were observed in cytoprotector candidates treated groups. The results indicated that bioactive phytochemicals combinations owned potentials to be used as new cytoprotectors, besides umu test was the same effective assay to evaluate antimutagenic potential of phytochemicals as Ames test.
Discrete time-cost tradeoff model for optimizing multi-mode construction project resource allocation
Authors: Nie Shuangshuang , Gao Jihong
Published: January 2018

The project scheduling and resource allocation problems have been studied using different optimization methods. The resource leveling problem was proposed to reduce the resource fluctuation and was always studied independently resource constraint problem. For example, resource-constrained project scheduling problem (RCPSP) was proposed to optimize scheduling under resource constraints. This research proposed a new model which integrates the resource leveling problem and resource-constrained time-cost tradeoff problem. The evolutionary multi-objective optimization technique, strength Pareto evolutionary approach II (SPEA II) was applied to calculate the Pareto front of time and cost. The resource leveling measured by the metric, resource release/re-hiring, was converted to resource cost. The analysis of the time complexity of the model showed that the runtime of the algorithm was polynomial times of the number of activities. The results of case testing showed that the model was reasonably accurate in comparison with a proposed baseline model.
Motif clustering with implications for transcription factor interactions
Authors: Grau Jan , Grosse Ivo , Posch Stefan , Keilwagen Jens
Published: January 2018

High-throughput data, for instance ChIP-seq data, measure binding of transcription factors (TFs) or other proteins to DNA and have become a widespread data source for de-novo motif discovery. Often, several ChIP-seq data sets study the same TF under different conditions resulting in several, potentially redundant motifs, which demands for identification and clustering of similar motifs. Here, we propose a refined measure of motif similarity based on the correlation between score profiles on de Bruijn sequences. We demonstrate the utility of the proposed measure in benchmark studies on artificial motifs and motifs discovered from ENCODE ChIP-seq data. We use this measure to cluster motifs discovered from 757 different ENCODE ChIP-seq data sets for 166 TFs and RNA-polymerase II and III. Based on this clustering, we derive a TF interaction network that reflects many known TF-TF interactions, but also reveals novel putative interaction partners.
From predicting to analyzing HIV-1 resistance to broadly neutralizing antibodies
Authors: Feldmann Anna , Pfeifer Nico
Published: January 2018

Treatment with broadly neutralizing antibodies (bNAbs) has recently proven effective against HIV-1 infections in humanized mice, non-human primates, and humans. For optimal treatment, susceptibility of the patient's viral strains to a particular bNAb has to be ensured. Since no computational approaches are so far available, susceptibility can only be tested in expensive and time-consuming neutralization experiments. Here, we present well-performing computational models (AUC up to 0.84) that can predict HIV-1 resistance to bNAbs given the envelope sequence of the virus. Having learnt important binding sites of the bNAbs from the envelope sequence, the models are also biologically meaningful and useful for epitope recognition. Additional to the prediction result, we provide a motif logo that displays the contribution of the pivotal residues of the test sequence to the prediction. As our prediction models are based on non-linear kernels, we introduce a new visualization technique to improve the model interpretability. Moreover, we confirmed previous experimental findings that there is a trend towards antibody resistance for the subtype B population of the virus. While previous experiments considered rather small and selected cohorts, we were able to show a similar trend for the global HIV-1 population comprising all major subtypes by predicting the neutralization sensitivity for around 36,000 HIV-1 sequences - a scale-up which is very difficult to achieve in an experimental setting.
A minimal model for explaining the higher ATP production in the Warburg effect
Authors: Schuster Stefan , Boley Daniel , Möller Philip , Kaleta Christoph
Published: January 2018

For producing ATP, tumor cells rely on glycolysis leading to lactate to about the same extent as on respiration. Thus, they use a higher fraction of glycolysis than the corresponding healthy cells. This is known as the Warburg effect (named after German biochemist Otto Warburg) and also applies to striated muscle cells, activated lymphocytes and microglia, endothelial cells and several other cell types. This effect is paradoxical at first sight because the ATP yield of glycolysis is much lower than that of respiration. Although a straightforward explanation is that glycolysis allows a higher ATP production rate, the question arises why the cell does not re-allocate protein to the high-yield pathway of respiration. We tackle this question by a minimal model only including three combined reactions. We consider the case where the cell can allocate protein on several enzymes in a varying distribution and model this by a linear programming problem in which not only the rates but also the maximal velocities are variable. Depending on side conditions and on protein costs, this leads to pure respiration, pure glycolysis, and respirofermentation as a mixed flux distribution.
Disorder affects judgements about a neighbourhood: Police presence does not
Authors: Hill Jessica M , Pollet Thomas V , Nettle Daniel
Published: January 2018

Many police forces operate a policy of high visibility in disordered neighbourhoods with high crime. However, little is known about whether increased police presence influences people’s beliefs about a neighbourhood’s social environment or their fear of crime. Three experimental studies compared people’s perceptions of social capital and fear of crime in disordered and ordered neighbourhoods, either with a police presence or no police presence. In all studies, neighbourhood disorder lowered perceptions of social capital, resulting in a higher fear of crime. Police presence or absence had no significant effect. The pervasive effects of disorder above other environmental cues are discussed.
Pharmacophagy in green lacewings (Neuroptera: Chrysopidae: Chrysopa spp.)?
Authors: Aldrich Jeffrey R , Chauhan Kamal , Zhang Qing-He
Published: January 2018

Green lacewings (Neuroptera: Chrysopidae) are voracious predators of aphids and other small, soft-bodied insects and mites. Earlier, we identified the first lacewing pheromone from field-collected males of the goldeneyed lacewing, Chrysopa oculata Say; (1R,2S,5R,8R)-iridodial is released from thousands of microscopic dermal glands on the abdominal sterna of males, along with comparable amounts of nonanal, nonanol and nonanoic acid. Iridodial-baited traps attract C. oculata and other Chrysopa spp. males into traps, while females come to the vicinity of, but do not usually enter baited traps. Despite their healthy appearance, normal fertility and usual amounts of C9 compounds, laboratory-reared C. oculata males do not produce iridodial. However, we observed that goldeneyed lacewing males caught alive in iridodial-baited traps sometimes try to eat the lure, and in Asia Chrysopa spp. males reportedly eat the native plant, Actinidia polygama (Siebold & Zucc.) Maxim. (Actinidiaceae) to obtain the iridoid, neomatatabiol. These observations prompted us to investigate why laboratory-reared Chrysopa green lacewings do not produce iridodial. Lacewing adult males fed various monoterpenes reduced carbonyls to alcohols and saturated double bonds, but did not convert these compounds to iridodial. Males fed the bicyclic iridoid aphid pheromone component, (4aS,7S,7aR)-nepetalactone, converted ~75% to dihydronepetalactone, but did not produce iridodial; however, wild C. oculata males collected in May often contained traces of dihydronepetalactone. On the other hand, adult males fed the second common aphid pheromone component, (1R,4aS,7S,7aR)-nepetalactol, converted this compound to iridodial. In California the peak late-season attraction of green lacewings to nepetalactol (the lactone is unattractive) occurs at least a month earlier than the peak in aphid oviparae (the pheromone producing morph of aphids), consistent with the hypothesis that Chrysopa males feed on oviparae to obtain nepetalactol as a precursor to iridodial. Adult males from laboratory-reared C. oculata larvae fed nepetalactol failed to produce iridodial, and wild C. oculata males collected early in the spring produce less iridodial than males collected later in the season. Therefore, we further hypothesize that Asian Chrysopa eat A. polygama to obtain iridoid precursors in order to make their pheromone, and that other iridoid-producing plants elsewhere in the world must be similarly usurped by male Chrysopa species to sequester pheromone precursors. Whether or not sequestration of iridodial precursors from oviparae and/or iridoid-containing plants is truly the explanation for lack of pheromone in laboratory-reared Chrysopa awaits further research .
A survey on tourist attitudes towards invertebrate conservation through entotourism activities in Sabah, Borneo of Malaysia
Authors: Ak Matusin Ak Mohd Rafiq , Saikim Fiffy Hanisdah , Mohd Suki Norazah , M. Dawood Mahadi Menakbar
Published: January 2018

The Tabin Wildlife Reserve (TWR), Lahad Datu, Sabah is a popular tourist spot in Malaysia. It is the largest wildlife reserve in Sabah, mainly focusing on endangered mammals and birds. Thus, in this research, it is proposed to include invertebrates’ information in the current ecotourism activities in TWR. Implicitly, it could increase a sustainable invertebrate conservation. Invertebrates possess many benefits to humankind, namely waste recycling whereby, they cycle minerals and organic minerals for plants and animals. Thus, this investigation aimed to study the tourists’ perception on including invertebrate information in the current TWR ecotourism activity. Hence, to collect data from tourists, pre-visit and post-visit questionnaire surveys were adopted as the methodological approach during preliminary entotourism activities. Two different conceptual framework sets (pre-visit and post-visit) were posited in this investigation. The collected data were analysed via Statistical Package for Social Sciences (SPSS) and Analysis of Moment Structure (AMOS) software program by adopting Structural Equation Modelling (SEM). SEM analyses revealed that both pre-visit and post-visit surveys have significant variance towards Ecotourism. This implied a good potential in including invertebrates in ecotourism activities especially in Sabah. The findings of this study are important to contribute to the literature of invertebrate conservation awareness in Sabah, since very limited researches were conducted specifically on entotourism field.
Generation of high order geometry representations in octree meshes
Authors: Klimach Harald G , Zudrop Jens , Roller Sabine P
Published: January 2018

We propose a robust method to convert triangulated surface data into polynomial volume data. Such polynomial representations are required for high-order partial differential solvers, as low-order surface representations would diminish the accuracy of their solution. Our proposed method deploys a first order spatial bisection algorithm to find robustly an approximation of given geometries. The resulting voxelization is then used to generate Legendre polynomials of arbitrary degree. By embedding the locally defined polynomials in cubical elements of a coarser mesh, this method can reliably approximate even complex structures, like porous media. It thereby is possible to provide appropriate material definitions for high order discontinuous Galerkin schemes. We describe the method to construct the polynomial and how it fits into the overall mesh generation. Our discussion includes numerical properties of the method and we show some results from applying it to various geometries. We have implemented the described method in our mesh generator Seeder, which is publically available under a permissive open-source license.
First records on habitat use of semi-feral cattle in southern forests: topography reveals more than vegetation
Authors: Seoane Nicolás
Published: January 2018

While the presence of cattle in forests is quite common, how they use this habitat is often overlooked. When this is examined, most studies focus on measurements of the vegetation variables influencing habitat selection. This current report provides a suitable model to study habitat use by livestock in forested areas by means of GPS tracking on selected individuals. The model was applied to data from semi-feral cattle in order to obtain the first description of their habitat use in southern forests. Furthermore, the model accounted for individual variability, and hinted at population patterns of habitat use. The positions of 15 individual cows with GPS collars were recorded covering twelve months in a Nothofagus (southern beech) forest in Patagonia (Argentina). By projecting these GPS location data into a geographical information system (GIS), a resource selection probability function (RSPF) that considers topographic and vegetation variables was built. The habitat selection by semi-feral cattle in southern beech forests showed a large interindividual variability, but also some similar characteristics which enable a proper description of habitat-use patterns. It was found that habitat selection by cattle was mainly affected by topographic variables such as altitude and the combination of slope and aspect. In both cases the variables were selected below average relative to availability, suggesting a preferred habitat range. Livestock also tended to avoid areas of closed shrublands and showed a slight preference for meadows. Cattle give significant importance to topographic variables to define their habitat selection in this type of mountainous forests. This might be because of an ecological adaptation to the major features of these types of forests due to ferality. Furthermore, these results are the basis for management applications such as predictive maps of use by semi-feral livestock in forested landscapes.
Tolerance-based interaction: A new model targeting opinion formation and diffusion in social networks
Authors: Topirceanu Alexandru , Udrescu Mihai , Vladutiu Mircea , Marculescu Radu
Published: January 2018

One of the main motivations behind social network analysis is the quest for understanding opinion formation and diffusion. Previous models have limitations, as they typically assume opinion interaction mechanisms based on thresholds which are either fixed or evolve according to a random process that is external to the social agent. Indeed, our empirical analysis on large real-world datasets such as Twitter, Meme Tracker, and Yelp, uncovers previously unaccounted for dynamic phenomena at population-level, namely the existence of distinct opinion formation phases and social balancing. We also reveal that a phase transition from an erratic behavior to social balancing can be triggered by network topology and by the ratio of opinion sources. Consequently, in order to build a model that properly accounts for these phenomena, we propose a new (individual-level) opinion interaction model based on tolerance. As opposed to the existing opinion interaction models, the new tolerance model assumes that individual's inner willingness to accept new opinions evolves over time according to basic human traits. Finally, by employing discrete event simulation on diverse social network topologies, we validate our opinion interaction model and show that, although the network size and opinion source ratio are important, the phase transition to social balancing is mainly fostered by the democratic structure of the small-world topology.
Reverse transcriptase-related enzymes are associated with horizontal chromosome transfer in an asexual pathogen
Authors: Huang Xiaoqiu , Das Anindya , Sahu Binod B , Srivastava Subodh K , Leandro Leonor F , O'Donnell Kerry , Bhattacharyya Madan K
Published: January 2018

Supernumerary chromosomes have been shown to transfer horizontally from one isolate to another. However, the mechanism by which horizontal chromosome transfer (HCT) occurs is unknown. In this study, we compared the genomes of 11 isolates comprising six Fusarium species that cause soybean sudden death syndrome (SDS) or bean root rot (BRR), and detected numerous instances of HCT in supernumerary chromosomes. We also identified a statistically significant number (21 standard deviations above the mean) of single nucleotide polymorphisms (SNPs) in the supernumerary chromosomes between isolates of the asexual pathogen F. virguliforme. Supernumerary chromosomes carried reverse transcriptase-related genes (RVT); the presence of long RVT open reading frames (ORFs) in the supernumerary chromosome was correlated with the presence of two or more chromosome copies with a significant number of SNPs between them. Our results suggest that supernumerary chromosomes transfer horizontally via an RNA intermediate. Understanding the mechanism by which HCT occurs will have a profound impact on understanding evolution and applying biotechnology as well as accepting HCT as a natural source of genetic variation.
Multidimensional biases, gaps and uncertainties in global plant occurrence information
Authors: Meyer Carsten , Weigelt Patrick , Kreft Holger
Published: January 2018

Plants are a hyperdiverse clade that plays a key role in maintaining ecological and evolutionary processes as well as human livelihoods. Glaring biases, gaps, and uncertainties in plant occurrence information remain a central problem in ecology and conservation, but these limitations have never been assessed globally. In this synthesis, we propose a conceptual framework for analyzing information biases, gaps and uncertainties along taxonomic, geographical, and temporal dimensions and apply it to all c. 370,000 species of land plants. To this end, we integrated 120 million point-occurrence records with independent databases on plant taxonomy, distributions, and conservation status. We find that different data limitations are prevalent in each dimension. Different information metrics are largely uncorrelated, and filtering out specific limitations would usually lead to extreme trade-offs for other information metrics. In light of these multidimensional data limitations, we critically discuss prospects for global plant ecological and biogeographical research, monitoring and conservation, and outline critical next steps towards more effective information usage and mobilization. We provide an empirical baseline for evaluating and improving global floristic knowledge and our conceptual framework can be applied to the study of other hyperdiverse clades.
Insights into iguanodontian dental architecture from an Early Cretaceous Chinese basal hadrosauriform maxilla (Ornithischia: Iguanodontia)
Authors: Pittman Michael , Xu Xing , Ali Jason R , Pei Rui , Ma Waisum , Meng Jin , Bi Shundong
Published: January 2018

Basal hadrosauriform iguanodontian dinosaurs have been invaluable towards understanding the evolution of the complex and highly efficient advanced hadrosauriform tooth battery dental system. Here we report a new basal hadrosauriform maxilla specimen - IVPP V22529 - from the Dashuiguo Formation of Maortu, Nei Mongol, China that preserves a corrugated middle ventrolateral margin that differs from the straight and undulating ventral margins found in most iguandontian and non-iguanodontian dinosaurs. The uniqueness of this ventrolateral margin relates to a new dental structure - cementum ‘jackets’ that wrap about the labial sides of the teeth. To our knowledge this is the first time that cementum has been described migrated onto the tooth crowns of iguandontians (and other dinosaurs), but this trait is common amongst mammals. This dental morphology - seen in a similar form in the basal hadrosauriform Equijubus – therefore broadens our knowledge of iguanodontian maxillary anatomy and shows that the basal hadrosauriform dental system was more morphologically complex than previously thought. IVPP V22529 resembles maxillae specimens of Probactrosaurus gobiensis, a contemporaneous taxon known from the same locality in North China, in sharing an inferred subtriangular shape, a relatively flat lateral surface bearing a low row of foramina as well as similar-looking teeth. However, the presence of a unique corrugated middle ventrolateral margin in IVPP V22529, a low row of foramina on its lateral surface that also open anteriorly and increase in size posteriorly as well as a prominent medial shelf suggests that this specimen does not belong to P. gobiensis. However, these differences could conceivably be related to ontogenetic and sexual variation, which have not been fully documented in P. gobiensis. More detailed comparisons of IVPP V22529 and Probactrosaurus are also hampered by the missing posterior portion of IVPP V22529 as well as the missing anterior ramii in Probactrosaurus maxillae specimens. It is clear though that IVPP V22529 is different from the more advanced Northern Chinese hadrosauriforms Bactrosaurus and Gilmoreosaurus. The latter lack well-developed maxillary grooves on their medial shelves, unlike IVPP V22529, but all three taxa possess less-developed ones on the medial surfaces of the anteromedial processes of the anterior ramii. Different to IVPP V22529, Gilmoreosaurus also has foramina that are more highly-positioned on the lateral surface of its maxilla as well as a row of larger and more circular ‘special’ foramina on its medial surface. Thus, at this time, IVPP V22529 is identified as a basal hadrosauriform and not as a new genus or as a new species of Probactrosaurus.
Reliability and validity of neurobehavioral function on the Psychology Experimental Building Language test battery in young-adults
Authors: Piper Brian J , Mueller Shane T , Geerken Alexander R , Dixon Kyle L , Kroliczak Gregory , Olsen Reid HJ , Miller Jeremy K
Published: January 2018

Background. The Psychology Experiment Building Language (PEBL) software consists of over one-hundred computerized tests based on classic cognitive neuropsychology and behavioral neurology measures. Although the PEBL tests are becoming more widely utilized, there is currently very limited information about the psychometric properties of these measures. Methods. Study I examined inter-relationships among ten PEBL tests including indices of motor-function (Pursuit Rotor and Dexterity), attention (Test of Attentional Vigilance and Time-Wall), working memory (Digit Span Forward), and executive-function (PEBL Trail Making Test, Berg/Wisconsin Card Sorting Test, Iowa Gambling Test, and Mental Rotation) in a normative sample (N = 189, ages 18-22). Study II evaluated test-retest reliability with a two-week interest interval between administrations in a separate sample (N = 79, ages 18-22). Results. Moderate intra-test, but low inter-test, correlations were observed and ceiling/floor effects were uncommon. Sex differences were identified on the Pursuit Rotor (Cohen’s d = 0.89) and Mental Rotation (d = 0.31) tests. The correlation between the test and retest was high for tests of motor learning (Pursuit Rotor time on target r = .86) and attention (Test of Attentional Vigilance response time r = .79), intermediate for memory (digit span r = .63) but lower for the executive function indices (Wisconsin/Berg Card Sorting Test perseverative errors = .45, Tower of London moves = .15). Significant practice effects were identified on several indices of executive function. Conclusions. These results are broadly supportive of the reliability and validity of individual PEBL tests in this sample. These findings indicate that the freely downloadable, open-source, PEBL battery http://pebl.sourceforge.net is a versatile research tool to study individual differences in neurocognitive performance.
Spintharus flavidus in the Caribbean – a 30 million year biogeographical history and radiation of a ‘widespread species’
Authors: Dziki Austin , Binford Greta , Coddington Jonathan A , Agnarsson Ingi
Published: January 2018

The Caribbean island biota is characterized by high levels of endemism, the result of an interplay between colonization opportunities on islands and effective oceanic barriers among them. A relatively small percentage of the biota is represented by ‘widespread species’, presumably taxa for which oceanic barriers are ineffective. Few studies have explored in detail the genetic structure of widespread Caribbean taxa. The cobweb spider Spintharus flavidus Hentz, 1850 (Theridiidae) is one of two described Spintharus species and is unique in being widely distributed from northern N. America to Brazil and throughout the Caribbean. As a taxonomic hypothesis, Spintharus “flavidus” predicts maintenance of gene flow among Caribbean islands, a prediction that seems contradicted by known S. flavidus biology, which suggests limited dispersal ability. As part of an extensive survey of Caribbean arachnids (project CarBio), we conducted the first molecular phylogenetic analysis of S. flavidus with the primary goal of testing the ‘widespread species’ hypothesis. Our results, while limited to three molecular loci, reject the hypothesis of a single widespread species. Instead this lineage seems to represent a radiation with at least 16 species in the Caribbean region. Nearly all are short range endemics with several distinct mainland groups and others being single island endemics. While limited taxon sampling, with a single specimen from S. America, constrains what we can infer about the biogeographical history of the lineage, clear patterns still emerge. Consistent with limited overwater dispersal, we find evidence for a single colonization of the Caribbean about 30 million years ago, coinciding with the timing of the GAARLandia landbridge hypothesis. In sum, S. “flavidus” is not a single species capable of frequent overwater dispersal, but rather a 30 my old radiation of single island endemics that provides preliminary support for a complex and contested geological hypothesis.
A hidden scale dependency in conserving working woodlands
Authors: Lazarus Eli , Schaible David
Published: January 2018

Because plans for large-scale landscape preservation in the US do not rely exclusively on lands held in trust, conservation programs have a vested interest in forest stewardship by private landowners. Selective harvests for commercial sale are often highlighted as a financial incentive for owners of non-industrial "family forests" to sustainably maintain the working character of their acreage rather than subdivide it or convert it for development. However, the business costs inherent in even a small-scale commercial timber harvest typically mean that forest parcels smaller than approximately 80 acres are too small to support a financial return. Statistics for private forest ownership in the U.S. suggest this minimum scale makes commercial harvest incentives effectively inaccessible to more than 90% of forest owners. Rural landscape conservation and commercial timber harvests depend on the same economies of scale to be viable. Designs for regional-scale forest conservation need to account for non-industrial but nonetheless commercial economies of scale that set an inherent limit on financial incentives intended to foster stewardship activity among family-forest landowners.
The Cardiac Electrophysiology Web Lab
Authors: Cooper Jonathan , Scharm Martin , Mirams Gary R
Published: January 2018

Computational modelling of cardiac cellular electrophysiology has a long history, with many models now available for different species, cell types, and experimental preparations. This success brings with it a challenge: how do we assess and compare the underlying hypotheses and emergent behaviours, in order to choose a model as a suitable basis for a new study, or characterize how a particular model behaves in different scenarios? We have created an online resource for the characterization and comparison of electrophysiological cell models under a wide range of experimental scenarios. The details of the mathematical model (quantitative assumptions and hypotheses formulated as ordinary differential equations) are separated from the experimental protocol being simulated. Each model and protocol is then encoded in computer-readable formats. A simulation tool runs virtual experiments on models, and a website – https://chaste.cs.ox.ac.uk/FunctionalCuration – provides a friendly interface, allowing users to store and compare results. The system currently contains a sample of 36 models and 23 protocols, including current-voltage curve generation, action potential properties under steady pacing at different rates, restitution properties, block of particular channels, and hypo-/hyper-kalaemia. This resource is publicly available, open source, and free; and we invite the community to use it and become involved in future developments. Those interested in comparing competing hypotheses using models can make a more informed decision; those developing new models can upload them for easy evaluation under the existing protocols, and even add their own protocols.
Whale shark regional research collaboration between Utila, Honduras and Isla Mujeres, México.
Authors: Galvan Beatriz Eugenia , Fox Steve , de la Parra Rafael
Published: January 2018

Background. Utila, Bay Islands, Honduras, is one of the few locations in the Western Hemisphere where whale sharks can be spotted year-round, while off the northeastern Yucatan Peninsula, Mexico, they aggregate during summertime in large numbers of up to several hundred. When our research on these sharks began, we hypothesized they migrate south to north from Honduras, then to Belize and finally to Mexico. Methods. From 2007-2013, we documented the presence of whale sharks in both locations using visual tags and photo-identification, to establish the connections between the sites. The international whale shark library ECOCEAN was an important tool for this research. Results. Our research collaboration began on 2007, we have registered and photographed 59 “encounters”, from these, 9 were “Belizeans” and 8 become new Honduran recruits. While 5 more remain as unassigned since positive individual identification has not been possible yet. From our database and ECOCEAN compare, we know that we share several individuals in between the two locations, and some even visit Belize. Conclusion. At least some individuals of the western Atlantic population travel between Honduras and Mexico, and some hang around Belize in between as well.We conclude that whale sharks wander in the Caribbean, the Gulf of México and the open Atlantic Ocean, and aggregate when food blooms are available.
Restored eelgrass (Zostera marina L.) as a refuge for epifaunal biodiversity in mid-Western Atlantic coastal bays
Authors: Lefcheck Jonathan , Marion Scott R , Orth Robert J
Published: January 2018

As nearshore ecosystems are increasingly degraded by human activities, active restoration is a critical strategy in ensuring the continued provision of goods and services by coastal habitats. After being absent for nearly six decades, over 1800 ha of the foundational species eelgrass (Zostera marina L.) has been successfully reestablished in the coastal bays of the mid-western Atlantic, USA, but nothing is known about the recovery of associated animal communities in this region. Here, we determine the patterns and drivers of functional recovery in epifaunal invertebrates associated with the restored eelgrass habitat from 2001-2013. After less than a decade, the invertebrate community in the restored bed was richer, more even, and exhibited greater variation in functional traits than a nearby reference bed. Analysis of a suite of environmental and physical variables using random forests revealed these differences were primarily due to the increasing area and density of eelgrass directly attributable to ongoing restoration efforts. Based on analysis of functional traits, we propose that the rapid life histories of constituent organisms may have played a key role in their successful recovery. We also speculate that diverse epifaunal communities may have contributed to the restoration success through a predefined mutualism with eelgrass. Given that restored eelgrass now make up 32% of total seagrass cover in the mid-Atlantic coastal bays, this restoration may conserve regional biodiversity by providing new and pristine habitat, particularly given the general decline of existing eelgrass in this region.
Invited presentations, junior research groups and research highlights at GCB 2015
Authors: Mosig Axel , Rahnenführer Jörg , Eisenacher Martin , Rahmann Sven
Published: January 2018

There are several types of presentations at the German Conference on Bioinformatics (GCB): original research (proceedings track), highlights, posters, and, for the first time in 2015, junior research group presentations.

This document collects the abstracts of invited presentations, of the junior research groups and of research highlights from the past year that were presented at GCB 2015. The program committee accepted 8 out of 10 submitted highlight abstracts and 6 out of 8 submitted junior research group presentations.

As junior research group presentations are new to the conference, we would especially invite feedback about this new track, in addition to other feedback you may have about the conference.
Estimating and comparing microbial diversity in the presence of sequencing errors
Authors: Chiu Chun-Huo , Chao Anne
Published: January 2018

Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here for the first time a nonparametric estimator of the true singleton count to replace the spurious singleton count. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons. To quantify microbial diversity, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures’ emphasis on rare or common species, include taxa richness (q=0), Shannon diversity (q=1), and Simpson diversity (q=2). Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach based on standardizing sample size or sample completeness via seamless rarefaction and extrapolation sampling curves of Hill numbers. (2) An asymptotic approach based on a continuous diversity (Hill number) profile which depicts the estimated asymptotes of diversities as a function of order q. Replacing the spurious singleton count by our estimated count, we can greatly remove the positive biases associated with diversity estimates due to spurious singletons in the two approaches and make fair comparison across microbial communities, as illustrated in applying our method to analyze sequencing data from viral metagenomes.