bluuebunny/crossref_metadata_2025 huggingface dataset:
A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing
Authors: Smets Wenke , Leff Jonathan W , Bradford Mark A , McCulley Rebecca L , Lebeer Sarah , Fierer Noah
Published: January 2018

Many recent studies rely on 16S rRNA-based sequencing approaches to analyze bacterial or archaeal communities found in soil and other environmental samples. While this approach is valuable for determining the relative abundances of different microbial taxa found in a given sample, it does not provide information on how the total abundances of targeted microbes differ across samples. Here we demonstrate how the simple addition of an internal standard at the DNA extraction step allows for the quantitative comparison of taxon abundances across samples. The reliability of this method was assessed in two ways. First, we spiked a dilution series of two different soils with internal standards to ascertain whether we could accurately quantify differences in cell abundances. We tested two different internal standards, adding DNA from Aliivibrio fischeri or Thermus thermophilus, bacterial taxa unlikely to be found in soil. Both standards allowed us to accurately quantify microbial abundances in soil as there was a strong positive correlation between total 16S rRNA gene estimations based on the recovery of sequences from these internal standards and the different starting amounts of soil extracted. We then tested whether we could use this approach to quantify differences in microbial abundances across a wide range of soil types. Microbial biomass of these samples was determined with standard methods: phospholipid fatty acid (PLFA) analysis and substrate induced respiration (SIR) analysis. The taxon abundances estimated with the internal standard sequencing approach were significantly correlated with the independent biomass measurements, and were in fact better correlated to SIR and PLFA estimates than either of these two biomass measurements were correlated with one another. Together, these results demonstrate that adding a DNA internal standard to soil or other environmental samples prior to DNA extraction is an effective method for comparing absolute bacterial cell abundances across samples. Given the ease of adding DNA internal standards to soil samples prior to high-throughput marker gene sequencing, absolute abundances and community composition can now be determined simultaneously and routinely.
An early origin and diversification of macrophagous metriorhynchid crocodylomorphs, with evidence for multiple instances of parallel evolution
Authors: Young Mark T , Steel Lorna , Foffa Davide , Brusatte Stephen L , Kitson James J N , Gillett Conrad P D T , Bell Mark A , Allain Ronan , Lepage Yves
Published: January 2018

Metriorhynchids were a widely distributed group of marine crocodylomorphs that thrived during the Middle Jurassic–Early Cretaceous. Within this group there is a subclade, Geosaurini, that evolved craniodential characteristics indicative of macrophagy (feeding on large-bodied prey items). When this subclade evolved and began to diversify into the myriad of morphologically distinct lineages is still unclear. Previous phylogenetic analyses suggest this clade evolved during the Late Jurassic, and rapidly diversified into numerous different ecomorphotypes. It was hypothesized that this was in response to the absence of small and medium-sized pliosaurs after the Middle-Late Jurassic Boundary. However, re-examination of poorly preserved fossils from the Callovian of England and France casts doubt on this. Based on our comparative study of these fossils, and new phylogenetic analyses, we conclude that Geosaurini had evolved and diversified by the mid Callovian. Although comparatively rare in the Middle Jurassic, at least four morphofunctionally distinct lineages of macrophages had evolved. Moreover, based on maximum likelihood modelling analyses, numerous macrophagy-linked characters (e.g. contiguous tooth serrations, low tooth count) evolved independently in these different lineages. Thus, the characteristics that previously suggested a Late Jurassic origin of Geosaurini was due to long-branch attraction and incomplete sampling. That these different macrophagous lineages evolved distinct morphofunctional complexes and began niche partitioning early in their evolution, suggests that their diversification was driven by foraging specialisation. We hypothesise that this may be a common driver of rapid diversification in marine tetrapod evolution.
The phylogenetic implications of re-describing the English crocodyliform specimens referred to Pholidosaurus
Authors: Smith Thomas J , Young Mark T
Published: January 2018

Pholidosauridae was a clade of longirostrine crocodyliforms that radiated across Europe, Asia, Africa and the Americas between the Middle Jurassic to Late Cretaceous. The type genus of this clade, Pholidosaurus, is poorly understood and even the number of valid species referable is uncertain. There is considerable instability in this part of the crocodyliform tree, as previous phylogenetic analyses do not agree upon whether Pholidosauridae is monophyletic or not. Preliminary results based on a first-hand re-scoring of the type specimen of Pholidosaurus purbeckensis for different phylogenetic analyses (both in preparation modifications of published datasets) unfortunately does not resolve this issue. When P. purbeckensis is treated as separate OTU, a monophyletic Pholidosaurus is not recovered. The first matrix finds P. purbeckensis and P. schaumbergensis to be distantly related (i.e. a polyphyletic Pholidosaurus), whereas in the second matrix both Pholidosaurus species form a polytomy with Dyrosauridae and a large clade constituting most of Pholidosauridae (in this matrix the inclusion of P. purbeckensis greatly decreases the level of resolution). The on-going in-depth re-description and re-scoring of English Pholidosaurus specimens will help determine whether the genus is monophyletic. This further descriptive work will provide a platform from which the internal relationships of the Pholidosauridae can be investigated.
New specimen and revision of the late Jurassic teleosaurid 'Steneosaurus’ megarhinus
Authors: Foffa Davide , Young Mark T , Brusatte Stephen L , Steel Lorna
Published: January 2018

Teleosaurids were a successful group of semi-aquatic crocodylomorphs that were an abundant part of coastal marine/lagoonal faunas during the Jurassic. Their fossil record suggests that the group declined in diversity and abundance during the Late Jurassic. 'Steneosaurus’ megarhinus (Hulke, 1871) from the Kimmeridge Clay Formation is a little known gracile longirostrine species of teleosaurid from the Late Jurassic (late Kimmeridgian). The holotype, an incomplete snout NHMUK PV OR43086, was firstly described by Hulke in 1871. Since then only one other specimen, an almost complete skull from the slightly older Aulacostephanus eudoxus Sub-Boreal ammonite Zone of “La Crouzette”, Francoulès (Quercy, France), has been referred to this species. Here, we describe, DORCM G.5067i-v, the anterior rostrum of a teleosaurid from the same horizon and locality as the holotype. We demonstrate that DORCM G.5067i-v is referable to Steneosaurus’ megarhinus based on a unique combination of characters, which include: strongly ventrally deflected anterior margin of the premaxilla; five premaxillary alveoli, the caudal-most being considerably reduced in size; anterodorsally oriented external nares; conical teeth bearing carinae which are only visible on the apical third of the crown. Importantly, the tooth count, shape of external nares and strong premaxillary deflection distinguish Steneosaurus’ megarhinus from all other Middle and Late Jurassic longirostrine teleosaurids. Some of these characteristics resemble those seen in pholidosaurids, suggesting some convergence between these clades.
The development of Negative Self-Beliefs Inventory (NSBI): Cultural adaptation and psychometric validation
Authors: Tang Xiaoqing , Duan Wenjie , Wang Ying , Guo Pengfei
Published: January 2018

Social anxiety is an emotional disorder common to various populations around the world. The newly developed Self-Beliefs Related to Social Anxiety Scale (SBSA) aims to assess three kinds of self-beliefs through 15 items that include self-related cognitive factors that evidently result in social anxiety. This study explored the psychometric characteristics of SBSA among 978 Chinese. An eight-item Negative Self-beliefs Inventory (NSBI) was developed through qualitative and quantitative analyses. Exploratory factor analysis, confirmatory factor analysis, and multi-group confirmatory factor analysis suggested that NSBI contained clear, meaningful, stable, and invariant three-factor structure consistent with the original SBSA. Further analyses showed that the three subscales and the entire scale exhibited high internal consistency (0.779–0.837), good criterion validity, and good convergent and divergent validity (i.e., negative associations with flourishing and positive associations with anxiety, depression, and stress). These findings indicated that NSBI is reliable and valid for measuring negative self-beliefs in the Chinese population. Higher total score of NSBI indicates the more serious negative self-beliefs. Limitations of the present study and implications for research and practice were also discussed. Further studies are needed to evaluate the predictive ability, incremental validity, and potential role of NSBI in clinical and large-scale populations.
Screening for Alternaria brassicicola resistance in the Brassicaceae: Bio-assay optimization and confocal microscopy insights into the infection process
Authors: Nowakowska Marzena , Wrzesińska Małgorzata , Kamiński Piotr , Nowicki Marcin , Lichocka Małgorzata , Tartanus Michał , Kozik Elżbieta U
Published: January 2018

Heavy losses incited yearly by Alternaria brassicicola on the vegetable Brassicaceae – have prompted our search for sources of genetic resistance against the pathogen and the resultant disease, dark leaf spot. We optimized several parameters to test the performance of the plants under controlled conditions to this disease, including leaf age and position, inoculum concentration, and incubation temperature. Using these optimized conditions, we screened a collection of 38 Brassicaceae cultigens with two methods (detached leaf and seedlings). Our results show, that either method can be used for the A. brassicicola resistance breeding, while the plant’s genotype was crucial in determining its response to the pathogen. The laboartory bio-assays for A. brassicicola resistance were run under more stringent conditions than the field tests, and resulted in identification of two interspecific hybrids that might be used in breeding programs. Confocal microscopy analyses of the leaf samples provided data into the pathogen mode of infection: Direct epidermal infection or stomatal attack were related to plants’ resistance against A. brassicicola among the cultigens tested. Further, the actin network of the host cells reorganized around the papillas deposited under the pathogen’s appressorium.
An important plesiosaur discovery from the Oxford Clay: how cooperation between science and industry is benefitting palaeontology
Authors: Harrington Carl , Graham Mark R , Nicklin Cliff , Wildman Mark , Tranter Shona , Moore-Fay Scott , Wills Simon , Middleton Heather , Benson Roger BJ , Ketchum Hilary
Published: January 2018

The Peterborough Member of the Oxford Clay Formation is renowned for its abundant and well preserved marine reptile fossils. In recent years, however, the primary source of these fossils, the brick making industry, has gone into serious decline – so much so that there is only one remaining working quarry in the Lower Oxford Clay and, with the future of UK brick manufacturing unclear, the importance of this quarry to vertebrate palaeontology should not be underestimated. The Oxford Clay Working Group (OCWG) was set up in 2011, in collaboration with the quarry owners, to collect, protect and document vertebrate fossils from this very important resource. Despite collecting unassociated fossils, particularly teeth and isolated bones, efforts to secure articulated or disarticulated skeletons have been hampered by modern quarrying techniques and a change of practice in excavating to the most productive levels. Here we report on a newly recovered, partially articulated plesiosaur skeleton representing a fully mature individual, which was saved because of the combined efforts of the OCWG in conjunction with both the quarry owners and employees. The specimen, which has been safely conserved and secured by the group, will be deposited into an accredited institution and so made available for scientific study and, perhaps, public display. It is planned that the skull block is CT scanned which may not only provide hitherto unknown data relative to Plesiosauroidea but may help, together with other skeletal elements, to solve anatomical and taxonomic problems within Cryptoclididae and, perhaps, Elasmosauridae.
The set of \((N/2^i)\)-distance graphs of \(C_N\) and its application to efficient information broadcast among \(N\) nodes over \(K_N\)
Authors: Pabico Jaderick P
Published: January 2018

The set \(S\) of \(\left(\frac{N}{2^i}\right)\)-distance graphs of order \(N\) cycle graphs \(\mathbb{C}_N\) is defined here as \[S = \left\{ s_i= \bigcup_1^{\frac{N}{2^i}} \mathbb{C}_{2^i} \quad\Bigg\vert\quad i=1,2, \dots, \log N\right\},\] where w.o.l.o.g. \(N=2^k\), \(\forall k=2, 3, \dots\), and \(\log\) is base two. The utility of the computation of \(S\) is demonstrated by a \(\mathcal{O}(|S| = \log N)\)-step implementation of various information broadcasts and their corresponding duals (i.e., reduction) among \(N\) completely-connected nodes \(\mathbb{K}_N\) exchanging messages under a realistic \((1, 1, 2)\) communication model (i.e., concurrent one in-port and one out-port over a duplex connection). Information broadcast over \(\mathbb{K}_N\) under \((1,1,2)\) is currently implemented with \(\mathcal{O}(N)\) steps using a series of \(N\) circular 1-shift operations (or one circular \(N\)--shift). Algorithmically, the \(i\)th element \(s_i\in S\) partially coincides with the \(i\)th dimension of a \(\mathbb{K}_N\)-embedded \((\log N)\)-cube.
Sonification of reference markers for auditory graphs: Effects on non-visual point estimation tasks
Authors: Metatla Oussama , Bryan-Kinns Nick , Stockman Tony , Martin Fiore
Published: January 2018

Research has suggested that adding contextual information such as reference markers to data sonification can improve interaction with auditory graphs. This paper presents results of an experiment that contributes to quantifying and analysing the extent of such benefits for an integral part of interpreting graphed data: point estimation tasks. We examine three pitch-based sonification mappings; pitch-only, one-reference, and multiple-references that we designed to provide information about distance from an origin and assess their effects on users' performances when completing point estimation tasks. Results showed that the addition of reference tones increases users accuracy with a trade-off for task completion times, and that the multiple-references mapping is particularly effective when dealing with points that are positioned at the midrange of a given axis.
Scanning electron microscope analysis of enamel microstructure in a Polycotylid (Plesiosauria) from the Pierre Shale Group, South Dakota, U.S.A.
Authors: Testin Jason J
Published: January 2018

The teeth of polycotylid plesiosaurs are generally simple, cone shaped, non-serrated and only slightly recurved without distinct carinae. The surface of crowns are characterized by a series of vertical enamel wrinkles that are more highly developed on the lingual surface of the crown, and decrease in width and number toward the apex. Some of the most promising research related to fossil dentition, involves the analysis of surface and internal dental microstructure. This study, is an attempt to examine and describe polycotylid dental microstructure. It gives an overview of polycotylid plesiosaur enamel and dentine microstructures using a scanning electron microscope. Enamel type and structures vary, based on its position on the surface of the crown, and its perceived strength requirements. The dentition layer is “honeycombed” with tubular structure, possibly to provide nourishment to fast growing crowns. The study of crown microstructures may lead to a better understanding of polycotylid niche preference in the late Cretaceous oceans.
Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area
Authors: Harris Stephen E , Munshi-South Jason , Obergfell Craig , O'Neill Rachel
Published: January 2018

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar ‘urban adapter’. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.
Corals of the genus Porites are a locally abundant component of the epibiont community on mangrove prop roots at Calabash Caye, Turneffe Atoll, Belize
Authors: Bengtsson Zachary A , Kuhn Kirsten M , Battaglino Anya T , Li Allen S , Talbot Matthew N , Wafapoor Marzie , Atta Calder J , Kowalski Michael B , Margolis Sarah P , Rar Ekaterina A , Burmester Elizabeth M , Lesneski Kathryn C , Scavo Karina , Kaufman Les , Stewart Nathan L , Finnerty John R
Published: January 2018

Mangrove prop roots support diverse epibiont communities, but they are generally regarded as inhospitable for corals. However, recent reports have documented corals thriving on mangrove roots in the U.S. Virgin Islands and Cuba, and it has been proposed that mangroves may provide a refuge from environmental conditions that trigger coral mortality on nearby reefs. It also raises interesting questions about the potential evolutionary significance of coral populations in mangrove forest. We investigated diverse mangrove habitats for the presence of corals at Calabash Caye, Belize, part of a recently designated marine reserve on Turneffe Atoll. Here we present data on the distribution, size and morphology of 127 colonies of branching Porites found in a survey of 1858 meters of mangrove prop roots fringing three qualitatively distinct bodies of water: a high-flow channel, a moderate-flow creek, and a low-flow mangrove pond. The distribution of Porites was highly clumped, with 108 colonies occurring in a 178-meter stretch of shoreline along the high flow channel. Colony morphology varied widely, from bushy colonies with more than 40 branch tips per 1000 cm3 of ecological volume, to spindly colonies with fewer than 10 branch tips per 1000 cm3, to new recruits that have not yet developed distinct branches. Comparisons of the same coral-bearing roots in 2013 and 2014 revealed that colonies can experience substantial growth in a year’s time. We also document a much more diverse coral fauna living in the mangroves at Crooked Creek, a high flow environment on the western edge of Turneffe Atoll. The data described here contribute to an emerging picture of mangroves as potentially important habitat for corals, while suggesting that different types of mangrove habitat vary in their suitability for different species of coral. Future studies are needed to identify the critical environmental features of mangrove habitats that support coral, to further characterize those corals that can utilize mangrove habitat, and to investigate potential connectivity between coral populations in mangroves and nearby reef habitats.
Structure and stability of recombinant bovine odorant-binding protein: III. Peculiarities of the wild type bOBP unfolding in crowded milieu
Authors: Stepanenko Olga V , Roginskii Denis O , Stepanenko Olesya V , Kuznetsova Irina M , Uversky Vladimir N , Turoverov Konstantin K
Published: January 2018

Contrarily to the majority of the members of the lipocalin family, which are stable monomers with the specific OBP fold (a β-barrel consisting of a 8-stranded anti-parallel β-sheet followed by a short α-helical segment, a ninth β-strand, and a disordered C-terminal tail) and a conserved disulfide bond, bovine odorant-binding protein (bOBP) does not have such a disulfide bond and forms a domain-swapped dimer that involves crossing the α-helical region from each monomer over the β-barrel of the other monomer. Furthermore, although natural bOBP isolated from bovine tissues exists as a stable domain-swapped dimer, recombinant bOBP has decreased dimerization potential and therefore exists as a mixture of monomeric and dimeric variants. In this article, we investigated the effect model crowding agents of similar chemical nature but different molecular mass on conformational stability of the recombinant bOBP. These experiments were conducted in order shed light on the potential influence of model crowded environment on the unfolding-refolding equilibrium. To this end, we looked at the influence of PEG-600, PEG-4000, and PEG-12000 in concentrations of 80, 150, and 300 mg/mL on the equilibrium unfolding and refolding transitions induced in the recombinant bOBP by guanidine hydrochloride.
De novo clustering methods out-perform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
Authors: Westcott Sarah L , Schloss Patrick
Published: January 2018

Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is the most rigorous. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the ability of the method to properly represent the distances between the sequences is more important. Methods. Our analysis implemented five de novo clustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and the open and closed-reference methods. Using two previously published datasets we used the Matthew’s Correlation Coefficient (MCC) to assess the stability and quality of OTU assignments. Results. The stability of OTU assignments did not reflect the quality of the assignments. Depending on the dataset being analyzed, the average linkage and the distance and abundance-based greedy clustering methods generated more robust OTUs than the open and closed-reference methods. We also demonstrated that for the greedy algorithms VSEARCH produced assignments that were comparable to those produced by USEARCH making VSEARCH a viable free and open source alternative to USEARCH. Further interrogation of the reference-based methods indicated that when USEARCH is used to identify the closest reference, the OTU assignments were sensitive to the order of the reference sequences because the reference sequences can be identical over the region being considered. More troubling was the observation that while both USEARCH and VSEARCH have a high level of sensitivity to detect reference sequences, the specificity of those matches was poor relative to the true best match. Discussion. Our analysis calls into question the quality and stability of OTU assignments generated by the open and closed-reference methods as implemented in current version of QIIME. This study demonstrates that de novo methods are the most rigorous and that the quality of clustering assignments needs to be assessed for multiple methods to identify the optimal clustering method for a particular dataset.
Implications of an educed circadian rhythm of implicit racial preference for online data collection
Authors: Schofield Timothy P
Published: January 2018

Time-of-day effects in human psychological functioning have been known of since the 1800s. However, outside of those specifically focused on the quantification of circadian rhythms, they have largely been neglected. Recent moves toward online data collection now mean that psychological investigations take place around the clock, but researchers have not started to take account of the effect of circadian cycles. The presence of circadian rhythms in most psychological processes are argued to be ‘unknown’, and one such unknown process – implicit racial preferences – are investigated using open data from Project Implicit. Despite their having been no prior speculation that implicit preferences should show time-of-day effects, analysis of over 1.1 million cases via cosinor regression indicates that they do. Given the unknown status of circadian rhythms in most psychological processes, the importance of giving time-of-day the time of day in the era of online data collection is advocated.
The first Mares Conference on Marine Ecosystems Health and Conservation 2014: key messages and outcomes
Authors: Deprez Tim , Vincx Magda , Canario Adelino V.M. , Erzini Karim , Brownlie Katherine
Published: January 2018

The first Mares Conference on Marine Ecosystems Health and Conservation was a successful event organized by the MARES doctoral programme bringing together over 150 researchers in Olhão, Portugal from November 17th to 21st 2014. The conference was opened by Prof. Dr. Hans-Otto Pörtner, whose keynote address focused on a sectoral analysis by the Intergovernmental Panel on Climate Change Fifth Assessment Report (IPCC AR5) on the impacts of climate change on the world’s oceans. The first session on “Future oceans” was opened with a talk by Dr. Frank Melzner highlighting the problems calcifying invertebrates face in the warmer, more acidic and hypoxic waters. Other presenters dealt with changing global diversity patterns, ocean acidification, and the loss the genetic diversity. The second session on “Natural resources” was opened by Dr. Rainer Froese, who focused on whether or not the oceans can feed humanity. This talk introduced other contributions in the session, dealing with fisheries issues and Marine Protected Areas, as well as problems with proper identifications of species used for economic purposes. “Biodiversity effects” was the scope of the third session opened by a talk on oxygenation and marine biodiversity challenges in the 21st Century by Prof. Lisa Levin. Rapid ocean deoxygenation is a process which is currently less investigated but which has considerable effects on body size, taxonomic composition, habitat heterogeneity, and nutrient cycling. The following presentations focused on other factors having a strong effect on marine biodiversity, ranging from the harvesting of algae to the fragmentation of ecosystems. The fourth session addressed “Biological invasions”. Dr. Gregory Ruiz discussed biological invasions in North American marine ecosystems and the need for constant monitoring, and the use of a dynamic and multi-vector approach. Problems with invasive species in European waters were addressed with examples from the Baltic Sea, the North Sea, and the Mediterranean Sea. The fifth session on “Ocean Noise” was opened by Prof. Peter Tyack with a talk on the effects of anthropogenic sound on marine mammals. Although ocean noise issues are often linked to marine mammals, the effects of sound related to marine constructions on fish behaviour, nicely illustrated that ocean noise is a factor with a much broader impact than expected. The last session of the first Mares Conference dealt with “Habitat loss”. Dr. Michael Beck focused on this topic with his talk on ‘Building Coastal Resilience for Climate Adaptation and Risk Reduction’. Talks in the session ranged from the use of telemetry as a tool to monitor species in changed habitats, to cases dealing with sea level rise related problems in for example salt-marshes. The first Mares Conference offered a broad range of oral and poster presentations, as well as digital presentations. The poster and digital object presentations included over 100 contributions.
Data reuse and scholarly reward: understanding practice and building infrastructure
Authors: Vision Todd J , Piwowar Heather A
Published: January 2018

Recently introduced funding agency policies seek to increase the availability of data from individual published studies for reuse by the research community at large. The success of such policies can be measured both by data input (“is useful data being made available?”) and research output (“are these data being reused by others?”). A key determinant of data input is the extent to which data producers receive adequate professional credit for making data available. One of us (HP) previously reported a large citation difference for published microarray studies with and without data available in a public repository. Analysis of a much larger sample, with more covariates, provides a more reliable estimate of this citation boost, as well as additional insights into patterns of reuse and how the availability of data affects publication impact. A more recent study tracking the reuse of 100 datasets from each of ten different primary data repositories reveals large variation in patterns of reuse and citation. Our findings (a) illuminate ways in which the reuses of archived data tend to differ in purpose from that of the original producers; (b) inform data archiving policy, such as how long data embargoes need to be in order to protect the proprietary interests of producers; (c) and allow us to answer the vexing question of what the return on investment is for data archiving. In conducting these studies, we have become aware of gaps in data citation practice and infrastructure that limit the extent to which researchers receive credit for their contributions. We describe early efforts to bake good data citation and usage tracking into cyberinfrastructure as part of DataONE, the Data Observation Network for Earth. Finally, we introduce total-impact, a tool that allows researchers to track the diverse impacts of all their research outputs, including data, and empowers them to be recognized for their scholarly work on their own terms.

Software and Data Availability:

Research software and data: https://github.com/hpiwowar (CCZero for data where possible, MIT for code);

Dryad: new BSD license: http://code.google.com/p/dryad;

DataONE: Apache license: http://www.dataone.org/developer-resources;

total-impact: MIT license: https://github.com/total-impact.

This is an abstract that was submitted to the iEvoBio 2012 conference, held on July 10-11, 2012, in Ottawa, Canada.
Myiarchus flycatchers are the primary seed dispersers of Bursera longipes in a Mexican dry forest: An overlooked coevolutionary process?
Authors: Almazán-Núñez R. Carlos , Eguiarte Luis E. , Arizmendi María del Coro , Corcuera Pablo
Published: January 2018

We evaluated the seed dispersal of Bursera longipes by birds along a successional gradient of tropical dry forest (TDF) in southwestern Mexico. B. longipes is an endemic tree to the TDF in the Balsas basin. The relative abundance of frugivorous birds, their frequency of visits to B. longipes and the number of removed fruits were recorded at three study sites with different stages of forest succession (early, intermediate and mature) characterized by distinct floristic and structural elements. Flycatchers of the Myiarchus and Tyrannus genera removed the majority of fruits at each site. Overall, visits to B. longipes were less frequent at the early successional site. Birds that function as legitimate dispersers by consuming whole seeds and regurgitating or defecating intact seeds in the process also remove the pseudoaril from seeds, thereby facilitating the germination process. The highest germination percentages were recorded for seeds that passed through the digestive tract of two migratory flycatchers: M. cinerascens and M. nutingii. Perch plants, mainly composed of legumes (e.g., Eysenhardtia polystachya, Acacia cochliacantha, Calliandra eryophylla, Mimosa polyantha), serve also as nurse plants since the number of young individuals recruited from B. longipes was higher under these than expected by chance. This study shows that Myiarchus flycatchers are the most efficient seed dispersers of B. longipes across all successional stages. This suggests a close mutualistic relationship derived from adaptive processes and local specializations throughout the distribution of both taxa, as supported by the geographic mosaic theory of coevolution.
May arsenic pollution contribute to limiting Artemia franciscana invasion in southern Spain?
Authors: Sánchez Marta I , Petit Cathleen , Martínez-Haro Mónica , Taggart Mark A , Green Andy J
Published: January 2018

Limited information exists regarding complex interactions between biological invasions, pollution, and climate change. Most studies indicate that pollution tends to favor invasive species. Here, we provide evidence that arsenic (As) pollution may contribute to limit the invasion of the exotic brine shrimp Artemia franciscana. We tested As toxicity in natural populations of Artemia parthenogenetica (native) and A. franciscana from high and low As contaminated environments in southern Spain, under current temperature conditions and as per a future climate scenario (i.e., an increase of 4ºC). Acute toxicity was estimated on the basis of the median lethal concentration (at 24h), and chronic toxicity (at 26 days) was evaluated by measuring Artemia survival and growth under sublethal exposures. At 25ºC native A. parthenogenetica from the highly polluted Odiel and Tinto estuary was much more resistant to acute As stress (LC50-24h, 24.67 mg L-1) than A. franciscana (15.78 mg L-1) and A. parthenogenetica populations from unpolluted sites (12.04 mg L-1) - suggesting that local adaptation to polluted conditions may occur. At 29ºC, resistance of A. parthenogenetica from Odiel decreased significantly, and there were no statistical differences in sensitivity between the three species/populations, suggesting that climate change may enhance the probability of invasion. Resistance increased with developmental stage from nauplii to adults, and was extremely high in cysts which still hatched at As concentrations of up to 6400mg L-1. Under sublethal chronic exposure A. franciscana performed better (survival and growth) than A. parthenogenetica, and both species experienced a faster growth when exposed, compared with unexposed (control) individuals, probably due to the hormesis. We discuss the ecological implications of our results.
Software development: do good manners matter?
Authors: Destefanis Giuseppe , Ortu Marco , Counsell Steve , Marchesi Michele , Tonelli Roberto
Published: January 2018

A successful software project is the result of a complex process involving, above all, people. Developers are the key factors for the success of a software development process, not merely as executors of tasks, but as protagonists and core of the whole development process. This paper investigates social aspects among developers working on software projects developed with the support of Agile tools. We studied 22 open source software projects developed using the Agile board of the JIRA repository. All comments committed by developers involved in the projects were analyzed and we explored whether the politeness of comments affected the number of developers involved and the time required to fix any given issue. Our results showed that the level of politeness in the communication process among developers does have an effect on the time required to fix issues and, in the majority of the analysed projects, it had a positive correlation with attractiveness of the project to both active and potential developers. The more polite developers were, the less time it took to fix an issue. In the majority of the analysed cases, the more developers wanted to be part of a project, the more they were willing to continue working on the project over time.
How are functionally similar code clones different?
Authors: Wagner Stefan , Abdulkhaleq Asim , Bogicevic Ivan , Ostberg Jan-Peter , Ramadani Jasmin
Published: January 2018

Background. Today, redundancy in source code, so-called “clones”, caused by copy&paste can be found reliably using clone detection tools. Redundancy can arise also independently, however, caused not by copy&paste. At present, it is not clear how only functionally similar clones (FSC) differ from clones created by copy&paste. Our aim is to understand and categorise the differences in FSCs that distinguish them from copy&paste clones in a way that helps clone detection research. Methods. We conducted an experiment using known functionally similar programs in Java and C from coding contests. We analysed syntactic similarity with traditional detection tools and explored whether concolic clone detection can go beyond syntax. We ran all tools on 2,800 programs and manually categorised the differences in a random sample of 70 program pairs. Results. We found no FSCs where complete files were syntactically similar. We could detect a syntactic similarity in a part of the files in < 16 % of the program pairs. Concolic detection found 1 of the FSCs. The differences between program pairs were in the categories algorithm, data structure, OO design, I/O and libraries. We selected 58 pairs for an openly accessible benchmark representing these categories. Discussion. The majority of differences between functionally similar clones are beyond the capabilities of current clone detection approaches. Yet, our benchmark can help to drive further clone detection research.
The effect of agmatine on trichothecene type B and zearalenone production in Fusarium graminearum, F. culmorum and F. poae
Authors: Pasquali Matias , Cocco Emmanuelle , Guignard Cedric , Hoffmann Lucien
Published: January 2018

Agmatine and other putrescines are known strong inducers of deoxynivalenol (DON) production in Fusarium graminearum. Other important cereal species produce DON and/or other trichothecene type B toxins (3 acetylated DON, 15 Acetylated DON, Fusarenon-X, Nivalenol) such as F. culmorum and F. poae. In order to verify if the mechanism of regulation of trichothecenes type B induction by agmatine is shared by different species of Fusarium, we tested the hypothesis on 19 strains belonging to 3 Fusarium species (F. graminearum, F. culmorum, F. poae) with diverse genetic chemotypes (3ADON, 15ADON, NIV) by measuring trichothecene B toxins such as DON, NIV, Fusarenon-X, 3ADON and 15ADON. Moreover we also tested whether other toxins like zearalenone were also boosted by agmatine. The trichothecene type B boosting effect was observed in the majority of strains used (13 over 19) in all the three species. Representative strains from all the three genetic chemotypes were able to boost toxin production after agmatine treatment. We identified strains not responding to the agmatine stimulus which may contribute to deciphering the regulatory mechanisms that link toxin production to agmatine (and more in general polyamines).
Textual analysis or natural language parsing? A software engineering perspective
Authors: Panichella Sebastiano
Published: January 2018

The problem of designing effective methodology to summarize, and analyze the amount of textual information produced by developers remains particularly challenging especially when the goal is to help developers in making better development/maintenance decisions. Moreover, contrasting results might be obtained depending on the communication channel being mined and the technique adopted for its analysis. In our work we investigate the usage of Natural Language Parsing (NLP) and Textual Analysis (TA) techniques to automatically classify development content. Results of our study highlight the superiority of NLP techniques over the traditional TA techniques when used to analyze the textual data produced in software development. We also show the benefits of NLP when used to enhance software engineering recommenders.
The impact of induced anxiety on affective response inhibition
Authors: Aylward Jessica , Valton Vincent , Mkrtchian Anahit , Lally Níall , Limbachya Tarun , Robinson Oliver J
Published: January 2018

Studying the effects of experimentally induced anxiety in healthy volunteers may increase our understanding of the mechanisms underpinning anxiety disorders. Prior work has shown that experimentally induced anxiety (via threat of unpredictable shock) improves accuracy at withholding a response on the Sustained Attention to Response Task (SART), and in separate studies improves accuracy to classify fearful faces, creating an affective bias. Integrating these findings, in this study participants (N=47) at a public science engagement event were recruited to explore the effects of experimentally induced anxiety on an affective version of the SART. On the basis of previous work, we hypothesised that we would see an increased accuracy at withholding a response to affectively congruent stimuli (i.e. increased accuracy at withholding a response to fearful “no-go” distractors) under threat of shock. Replicating previous findings, threat of shock slowed reaction time. However, contrary to predictions there was no evidence to suggest an interaction between induced anxiety and stimulus valence on accuracy. Indeed Bayesian analysis provided decisive evidence in favour of the null. We suggest that valence effects could emerge after processing durations longer than those allowed by the present task.
Genome-wide analyses reveal clustering in Cannabis cultivars: the ancient trilogy of a panacea
Authors: Henry Philippe
Published: January 2018

In the present research, I used an open access data set (Medicinal Genomics) consisting of nearly 200'000 genome-wide single nucleotide polymorphisms (SNPs) typed in 28 cannabis accessions to shed light on the plant's underlying genetic structure. Genome-wide loadings were used to sequentially cull less informative markers. The process involved reducing the number of SNPs to 100K, 10K, 1K, 100 until I identified a set of 42 highly informative SNPs that I present here. The two first principal components, encompass over 3/4 of the genetic variation present in the dataset (PCA1 = 48.6%, PCA2= 26.3%). This set of diagnostic SNPs is then used to identify clusters into which cannabis accession segregate. I identified three clear and consistent clusters; reflective of the ancient trilogy of the genus Cannabis.
SimpleDSFviewer: a tool to analyse and view differential scanning fluorimetry data for characterising protein thermal stability and interactions
Authors: Sun Changye , Li Yong , Yates Edwin A , Fernig David G
Published: January 2018

Differential scanning fluorimetry (DSF) is used widely as a thermal shift assay to study protein stability and protein-ligand interactions. The benefit of DSF is that it is simple, cheap and can generate melting curves in 96-well plates providing good throughput. However, data analysis remains a challenge, and requires different methods to optimise and analyse the collected raw data. Here, the program SimpleDSFviewer is introduced to help view and analyse DSF data in an efficient way and with a user-friendly interface. The data analysis, optimisation and view methods provided by the program are described, using sample melting curves of fibroblast growth factors.
Brain size varies with temperature in vertebrates
Authors: Gillooly James F
Published: January 2018

The tremendous variation in brain size among vertebrates has long been thought to be related to differences in species’ metabolic rates. Species with higher metabolic rates can supply more energy to support the relatively high cost of brain tissue. And yet, while body temperature is known to be a major determinant of metabolic rate, the possible effects of temperature on brain size have scarcely been explored. Thus, here I explore the effects of temperature on brain size among diverse vertebrates (fishes,amphibians, reptiles, birds and mammals). I find that, after controlling for body size,brain size increases exponentially with temperature in much the same way asmetabolic rate. These results suggest that temperature-dependent changes in aerobic capacity, which have long been known to affect physical performance, similarly affect brain size. The observed temperature-dependence of brain size may explain observed gradients in brain size among both ectotherms and endotherms across broad spatial and temporal scales.
Foraging potential of underground storage organ plants in the southern Cape, South Africa
Authors: Singels Elzanne , Potts Alastair J , Esler Karen J , Cowling Richard M , Marean Curtis W , De Vynck Jan C
Published: January 2018

Underground storage organs (USOs) serve as a staple source of carbohydrates for many hunter-gatherer societies and they feature prominently in discussions of diets of early modern humans. While the way of life of hunter-gatherers in South Africa’s Cape is no longer in existence, there is extensive ethnographic, historical and archaeological evidence of hunter-gatherers’ use of such plants as foodstuffs. This is to be expected, given that the Cape supports the largest concentration of plants with USOs globally. The southern Cape is the location of several Middle Stone Age sites that are highly significant to research on the origins of behaviourally modern humans, and this provided the context for our research. Here we evaluate the foraging potential of USOs by identifying how abundant edible biomass is in a coastal setting of the southern Cape, how easily it is gathered, and how nutritious it is. We staged a range of foraging events to provide an indication of the potential return rates for selected USOs when a forager is likely to be naïve about foraging for them. Nearly all of the sites sampled (83%) contained edible USOs, and the edible biomass can be highly concentrated in space. The edible USO biomass fell within the range of biomass observed in areas supporting extant hunter-gatherer communities. The six USO species we assessed for nutritional content contained between 40-228 calories/100 g. They also grow near the soil surface, mostly in sandy soils, and were gathered with minimal effort. Some 50% of the foraging events conducted yielded enough calories to meet the daily requirements of a hunter-gatherer of small stature within 2 hours. Thus, we demonstrate that USOs are a readily available source of carbohydrates in the southern Cape landscape and that they likely played a critical role in providing food for early humans.