bluuebunny/crossref_metadata_2025 huggingface dataset:
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
Authors: Ye Yuzhen , Tang Haixu
Published: August 2015

Motivation: Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture of microbial species) and other meta-omics approaches hold even greater promise for providing additional insights into functional and regulatory characteristics of the microbial communities. Current metatranscriptomics projects are often carried out without matched metagenomic datasets (of the same microbial communities). For the projects that produce both metatranscriptomic and metagenomic datasets, their analyses are often not integrated. Metagenome assemblies are far from perfect, partially explaining why metagenome assemblies are not used for the analysis of metatranscriptomic datasets.

Results: Here, we report a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k -mers ( k -mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We developed an application of this mapping algorithm: a reference-based approach to metatranscriptome assembly using graphs of metagenome assembly as the reference. Our results show that this new approach (called TAG) helps to assemble substantially more transcripts that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome.

Availability and implementation: TAG was implemented in C++ and has been tested extensively on the Linux platform. It is available for download as open source at http://omics.informatics.indiana.edu/TAG .

Contact:  yye@indiana.edu
Computing secure sets in graphs using answer set programming
Authors: Abseher Michael , Bliem Bernhard , Charwat Günther , Dusberger Frederico , Woltran Stefan
Published: September 2015

The notion of secure sets is a rather new concept in the area of graph theory. Applied to social network analysis, the goal is to identify groups of entities that can repel any attack or influence from the outside. In this article, we tackle this problem by utilizing Answer Set Programming (ASP). It is known that verifying whether a set is secure in a graph is already co-NP-hard. Therefore, the problem of enumerating all secure sets is challenging for ASP and its systems. In particular, encodings for this problem seem to require disjunction and also recursive aggregates. Here, we provide such encodings and analyse their performance using the Clingo system. Furthermore, we study several problem variants, including multiple secure or insecure sets, and weighted graphs.
Super-resolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes
Authors: Prakash Kirti , Fournier David , Redl Stefan , Best Gerrit , Borsos Máté , Ketting René , Tachibana-Konwalski KiKuë , Cremer Christoph , Birk Udo
Published: September 2015

During meiosis, homologous chromosomes associate to form a unique structure called synaptonemal complex (SC) whose disruption leads to infertility. Information about the epigenetic features of chromatin within this structure at the level of super-resolution microscopy is largely lacking. We combined single molecule localization microscopy with quantitative analytical methods to describe the epigenetic landscape of meiotic chromosomes at the pachytene stage in mouse oocytes. DNA is found to be non-randomly distributed along the length of the SC in condensed clusters. Periodic clusters of repressive chromatin (trimethylation of histone H3 at lysine 27, H3K27me3) are found at 500 nm intervals along the SC, while one of the ends of SC displays a large and dense cluster of centromeric histone mark (trimethylation of histone H3 at lysine 9, H3K9me3). Chromatin associated with active transcription (trimethylation of histone H3 at lysine 4, H3K4me3) is arranged in a radial hair-like loop pattern emerging laterally from the SC. These loops seem to be punctuated with small clusters of H3K4me3 mark with an average spread larger than their spacing. Our findings indicate that the nanoscale structure of the pachytene chromosomes is constrained by periodic patterns of chromatin marks, whose function in recombination and higher-order genome organisation is yet to be elucidated.
Genome scaffolding with PE-contaminated mate-pair libraries
Authors: Sahlin Kristoffer , Chikhi Rayan , Arvestad Lars
Published: August 2015

Scaffolding is often an essential step in a genome assembly process, in which contigs are ordered and oriented using read pairs from a combination of paired-ends libraries and longer-range mate-pair libraries. Although a simple idea, scaffolding is unfortunately hard to get right in practice. One source of problem is so-called PE-contamination in mate-pair libraries, in which a non-negligible fraction of the read pairs get the wrong orientation and a much smaller insert size than what is expected. This contamination has been discussed in previous work on integrated scaffolders in end-to-end assemblers such as Allpaths-LG and MaSuRCA but the methods relies on the fact that the orientation is observable,e.g.,by finding the junction adapter sequence in the reads. This is not always the case, making orientation and insert size of a read pair stochastic. Furthermore, work on modeling PE-contamination has so far been disregarded in stand-alone scaffolders and the effect that PE-contamination has on scaffolding quality has not been examined before.

We have addressed PE-contamination in an update of our scaffolder BESST. We formulate the problem as an Integer Linear Program (ILP) and use characteristics of the problem, such as contig lengths and insert size, to efficiently solve the ILP using a linear amount (with respect to the number of contigs) of Linear Programs. Our results show significant improvement over both integrated and standalone scaffolders. The impact of modeling PE-contamination is quantified by comparison with the previous BESST model. We also show how other scaffolders are vulnerable to PE-contaminated libraries, resulting in increased number of misassemblies, more conservative scaffolding, and inflated assembly sizes.

The model is implemented in BESST. Source code and usage instructions are found athttps://github.com/ksahlin/BESST. BESST can also be downloaded using PyPI.
The mysterious orphans ofMycoplasmataceae
Authors: Tatarinova Tatiana V. , Lysnyansky Inna , Nikolsky Yuri V. , Bolshoy Alexander
Published: August 2015

Background

The length of a protein sequence is largely determined by its function, i.e. each functional group is associated with an optimal size. However, comparative genomics revealed that proteins’ length may be affected by additional factors. In 2002 it was shown that in bacteriumEscherichia coliand the archaeonArchaeoglobus fulgidus,protein sequences with no homologs are, on average, shorter than those with homologs [1]. Most experts now agree that the length distributions are distinctly different between protein sequences with and without homologs in bacterial and archaeal genomes. In this study, we examine this postulate by a comprehensive analysis of all annotated prokaryotic genomes and focusing on certain exceptions.

Results

We compared lengths’ distributions of “having homologs proteins” (HHPs) and “non-having homologs proteins” (orphans or ORFans) in all currently annotated completely sequenced prokaryotic genomes. As expected, the HHPs and ORFans have strikingly different length distributions in almost all genomes. As previously established, the HHPs, indeed, are, on average, longer than the ORFans, and the length distributions for the ORFans have a relatively narrow peak, in contrast to the HHPs, whose lengths spread over a wider range of values. However, about thirty genomes do not obey these rules. Practically all genomes ofMycoplasmaandUreaplasmahave atypical ORFans distributions, with the mean lengths of ORFan larger than the mean lengths of HHPs. These genera constitute over 80% of atypical genomes.

Conclusions

We confirmed on a ubiquitous set of genomes the previous observation that HHPs and ORFans have different gene length distributions. We also showed thatMycoplasmataceaegenomes have very distinctive distributions of ORFans lengths. We offer several possible biological explanations of this phenomenon.
Phylogenetic community structure metrics and null models: a review with new methods and software
Authors: Miller Eliot T. , Farine Damien R. , Trisos Christopher H.
Published: August 2015

Competitive exclusion and habitat filtering are believed to have an important influence on the assembly of ecological communities, but ecologists and evolutionary biologists have not reached a consensus on how to quantify patterns that would reveal the action of these processes. No fewer than 22 phylogenetic community structure metrics and nine null models can be combined, providing 198 approaches to test for such patterns. Choosing statistically appropriate approaches is currently a daunting task. First, given random community assembly, we assessed similarities among metrics and among null models in their behavior across communities varying in species richness. Second, we developed spatially explicit, individual-based simulations where communities were assembled either at random, by competitive exclusion or by habitat filtering. Third, we quantified the performance (type I and II error rates) of all 198 approaches against each of the three assembly processes. Many metrics and null models are functionally equivalent, more than halving the number of unique approaches. Moreover, an even smaller subset of metric and null model combinations is suitable for testing community assembly patterns. Metrics like mean pairwise phylogenetic distance and phylogenetic diversity were better able to detect simulated community assembly patterns than metrics like phylogenetic abundance evenness. A null model that simulates regional dispersal pressure on the community of interest outperformed all others. We introduce a flexible new R package,metricTester, to facilitate robust analyses of method performance. The package is programmed in parallel to readily accommodate integration of new row-wise matrix calculations (metrics) and matrix-wise randomizations (null models) to generate expectations and quantify error rates of proposed methods.
Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation
Authors: Love Michael I , Hogenesch John B , Irizarry Rafael A
Published: August 2015

RNA-seq technology is widely used in biomedical and basic science research. These studies rely on complex computational methods that quantify expression levels for observed transcripts. We find that current computational methods can lead to hundreds of false positive results related to alternative isoform usage. This flaw in the current methodology stems from a lack of modeling sample-specific bias that leads to drops in coverage and is related to sequence features like fragment GC content and GC stretches. By incorporating features that explain this bias into transcript expression models, we greatly increase the specificity of transcript expression estimates, with more than a four-fold reduction in the number of false positives for reported changes in expression. We introduce alpine, a method for estimation of bias-corrected transcript abundance. The method is available as a Bioconductor package that includes data visualization tools useful for bias discovery.
The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression
Authors: Senbabaoglu Yasin , Winer Andrew G , Gejman Ron S , Liu Ming , Luna Augustin , Ostrovnaya Irina , Weinhold Nils , Lee William , Kaffenberger Samuel D , Chen Ying Bei , Voss Martin H , Coleman Jonathan A , Russo Paul , Reuter Victor E , Chan Timothy A , Cheng Emily H , Scheinberg David A , Li Ming O , Hsieh James J , Sander Chris , Hakimi Ari
Published: September 2015

Infiltrating T cells in the tumor microenvironment have crucial roles in the competing processes of pro-tumor and anti-tumor immune response. However, the infiltration level of distinct T cell subsets and the signals that draw them into a tumor, such as the expression of antigen presenting machinery (APM) genes, remain poorly characterized across human cancers. Here, we define a novel mRNA-based T cell infiltration score (TIS) and profile infiltration levels in 19 tumor types. We find that clear cell renal cell carcinoma (ccRCC) is the highest for TIS and among the highest for the correlation between TIS and APM expression, despite a modest mutation burden. This finding is contrary to the expectation that immune infiltration and mutation burden are linked. To further characterize the immune infiltration in ccRCC, we use RNA-seq data to computationally infer the infiltration levels of 24 immune cell types in a discovery cohort of 415 ccRCC patients and validate our findings in an independent cohort of 101 ccRCC patients. We find three clusters of tumors that are primarily separated by levels of T cell infiltration and APM gene expression. In ccRCC, the levels of Th17 cells and the ratio of CD8+ T/Treg levels are associated with improved survival whereas the levels of Th2 cells and Tregs are associated with negative clinical outcome. Our analysis illustrates the utility of computational immune cell decomposition for solid tumors, and the potential of this method to guide clinical decision-making.
Preferring green and rejecting “unethical” hotels
Authors: Tilikidou Irene , Delistavrou Antonia
Published: September 2015

Purpose

– The purpose of this paper is to examine simultaneously all types of ethical tourism and investigate some of the factors able to affect it; and to explore the number and the size of green hotels’ customers segments.

Design/methodology/approach

– A survey in the urban area Thessaloniki, Greece. Probability, large enough household sample. “Intentions to visit a green hotel”, “Boycotting” and “Discursive Activities” towards unethical hotels were investigated. External (EC)/Internal controls (IC) and past experience served as potential antecedents of behavioural intentions.

Findings

– Intentions to visit a green hotel were found to correlate strongly both with other people’s impact (EC) and with respondents’ perceptions about their own means (IC); intentions are moderately influenced by previous experience. Clustering indicated that the “Willing” segment (26.6 per cent) gathered consumers, who obtained higher scores than their counterparts in the other two segments, namely “Hesitant” (40.4 per cent) and “Reluctant” (33 per cent).

Research limitations/implications

– Incomplete demographical analysis, limited geographical area, social desirability. Future research might consider the employment of Theory of Planned Behaviour.

Practical implications

– Communication strategy of green hotels should utilize important people’s suggestions. Targets should be persuaded that green hotels are neither more expensive nor more difficult to find. Travel searching engines should include the green key attribute. Need to create and promote the image of an ethical hotel being a concept beyond a green hotel.

Originality/value

– All types of ethical tourism simultaneously examined. EC/IC provided significant evidence of impact on intentions. Cluster analysis of the ethical tourism market.
Strategic framework showcasing Greece in the Chinese tourism market
Authors: Kapiki Soultana Tania , Fu Jing , Mou Lei
Published: September 2015

Purpose

– The purpose of this paper is to take a holistic view of the body of knowledge of the second wave of Chinese outbound tourists so as to develop a strategic framework towards positioning Greece in the China outbound tourism market.

Design/methodology/approach

– The survey adopted a perspective from knowledge management, investigating a deeper understanding of the knowledge about, from and for the Chinese tourists, and Greece was taken as a case study. An online survey with quantitative aspects was conducted from October 2013 to January 2014.

Findings

– The knowledge about the Chinese tourists depicts a young, well-educated segment with a predominance of female and western China residents. The knowledge from the Chinese tourists reveals that they prefer: visiting islands and heritage sites; safety while travelling; a faster visa process; a direct flight between China and Greece; and making a trip combined with other Schengen countries. The knowledge for the Chinese tourists indicates that purchasing tourism products/services online provides better price, is enjoyable, convenient and time-saving; and the top five digital platforms often used are Ctrip, Qunar, QQ, Weibo and WeChat, which could be effective tools for the promotion of Greek tourism in China.

Originality/value

– This research offers a first step to investigate the knowledge of Chinese tourists for the destination of Greece. The findings help to propose a strategic knowledge framework for the Greek tourism authorities so that Greece can become a more active player in the Chinese outbound tourism market.
The growth-profitability nexus among Swedish SMEs
Authors: Yazdanfar Darush , Öhman Peter
Published: September 2015

Purpose

– The purpose of this paper is to examine the growth-profitability nexus among small- and medium-sized enterprises (SMEs).

Design/methodology/approach

– The data comprise 106,884 observations covering 26,721 Swedish SMEs in six industry sectors over the 2008-2011 period. The data were analysed using several statistical techniques, including two-stage least squares regression, fixed-effects and random regressions, and bootstrapped quantile regression.

Findings

– Consistent with the hypotheses derived from the resource-based approach, the results indicate that current profitability significantly and positively affects firm growth. The firm-level control variable size significantly and positively affects firm growth, though firm age significantly and negatively affects growth. Firm industry affiliation also affects firm growth.

Research limitations/implications

– Since SME performance is commonly equated with access to knowledge, consultancy services or business training programmes sponsored by governmental organizations can help SMEs improve their management skills and thereby their performance. Moreover, adopting advanced financial management practices can improve the use of financial resources, leading to higher profitability and thereby sustainable growth. This implies that managers should change their strategy from “growth now, profitability later” to “profitable growth now”.

Originality/value

– Unlike most previous studies, this study employs several multivariate methods to analyse a comprehensive, cross-sectoral sample comprising non-financial, independent, and active SMEs in several industries. This study focuses explicitly on SMEs, which play a fundamental role in the Swedish economy.
Intraday analysis of currency ETFs
Authors: Ivanov Stoyu I.
Published: September 2015

Purpose

– The purpose of this paper is to find if erosion of value exists in grantor trust structured exchange traded funds. The author examines the performance of six currency exchange traded funds’ tracking errors and pricing deviations on intradaily-one-minute interval basis. All of these exchange traded funds are grantor trusts. The author also studies which metric is of more importance to investors in these exchange traded funds by examining how these performance metrics are related to the exchange traded funds’ arbitrage mechanism.

Design/methodology/approach

– The Australian Dollar ETF (FXA) is designed to be 100 times the US Dollar (USD) value of the Australian Dollar, the British Pound ETF (FXB) is designed to be 100 times the USD value of the British Pound, the Canadian Dollar ETF (FXC) is designed to be 100 times the USD value of the Canadian Dollar, the Euro ETF (FXE) is designed to be 100 times the USD value of the Euro, the Swiss Franc ETF (FXF) is designed to be 100 times the USD value of the Swiss Franc and the Japanese Yen ETF (FXY) is designed to be 10,000 times the USD value of the Japanese Yen. The author uses these proportions to estimate pricing deviations. The author uses a moving average model based on an Elton et al. (2002) to estimate if tracking error or pricing deviation are more relevant in ETF arbitrage and thus to investors.

Findings

– The author documents that the average intradaily tracking errors for the six currency ETFs are relatively small and stable. The tracking errors are highest for the FXF, 0.000311 percent and smallest for FXB, −0.000014 percent. FXB is the only ETF with a negative tracking error. All six ETFs average intradaily pricing deviations are negative with the exception of the FXA pricing deviation which is a positive $0.17; the rest of the ETFs pricing deviations are −0.3778 for FXB, −0.3231 for FXC, −0.2697 for FXC, −0.2697 for FXE, −0.6484 for FXF and −0.9273 for FXY. All exhibit skewness, kurtosis, very high levels of positive autocorrelation and negative trends, which suggests erosion of value. The author also found that these exchange traded funds’ arbitrage mechanism is more closely related to the exchange traded funds’ pricing deviation than tracking error.

Research limitations/implications

– The paper uses high-frequency one-minute interval data in the analysis of pricing deviation which might be artificially deflating standard errors and thus inflating the t-test significance values.

Originality/value

– The paper is relevant to ETF investors and contributes to the continuing search in the finance literature of better ETF performance metric.
The relationship between recognised intangible assets and voluntary intellectual capital disclosure
Authors: Schiemann Frank , Richter Kai , Günther Thomas
Published: September 2015

Purpose

– The capitalisation of intangible investments is discussed controversially in the financial accounting literature. International accounting standards are concerned with this issue and generally demand more intellectual capital to be recognised on the face of the balance sheet. If investors and analysts already gather monetary information about intangible assets from the financial report and find such information useful, then the necessity to complement such information with voluntary intellectual capital disclosure will diminish. Accordingly, there should be an association between recognised intangible assets and voluntary intellectual capital disclosure. The paper aims to discuss these issues.

Design/methodology/approach

– The authors analyse the voluntary disclosure of 264 investor conference and roadshow presentations of German DAX 30 firms in the year 2001, 2003, 2005, and 2007. The authors apply regression models to analyse the association between recognition of intangible assets and voluntary intellectual capital disclosure and control for other determinants of voluntary disclosure.

Findings

– The authors find that the magnitude of recognised intangible assets is significantly and negatively associated with the quantity and quality of voluntary intellectual capital disclosure. The authors show that this association is mainly driven by goodwill accounting. In more detailed analyses we find different directions (positive, negative and insignificant) of this relationship for different categories of intellectual capital.

Research limitations/implications

– Future studies on voluntary intellectual capital disclosure need to consider recognised intangible assets as a determinant to avoid omitted variable problems.

Practical implications

– The authors provide descriptive evidence about voluntary intellectual capital disclosure practice of Germany’s largest firms.

Originality/value

– The paper provides primary evidence on the association between recognised intangible assets and voluntary intellectual capital disclosure.
Semantic web, ubiquitous computing, or internet of things? A macro-analysis of scholarly publications
Authors: Olson Nasrine , Nolin Jan Michael , Nelhans Gustaf
Published: September 2015

Purpose

– The purpose of this paper is to investigate concepts that are used in depicting future visions of society, as afforded by technology, to map the extent of their use, examine the level of their dominance in different research areas and geographic boundaries, identify potential overlaps, analyse their longitudinal growth, and examine whether any of the identified concepts has assumed an overarching position.

Design/methodology/approach

– In total, 14 concepts, each of which is used to depict visions of future information infrastructures, were identified. More than 20,000 scholarly documents related to 11 of these concepts (those with 20 or more documents) are analysed by various qualitative/quantitative methods.

Findings

– The concepts most referred to aresemantic webandubiquitous computing(all years), andinternet of things(Year 2013). Publications on some newer concepts (e.g.digital living,real world internet) are minimal. There are variations in the extent of use and preferred concepts based on geographic and disciplinary boundaries. The overlap in the use of these terms is minimal and none of these terms has assumed an overarching umbrella position.

Research limitations/implications

– This study is limited to scholarly publications; it would be relevant to also study the pattern of usage in governmental communications and policy documents.

Social implications

– By mapping multiplicity of concepts and the dispersion of discussions, the authors highlight the need for, and facilitate, a broader discussion of related social and societal implications.

Originality/value

– This paper is the first to present a collective of these related concepts and map the pattern of their occurrence and growth.
Stranger in a strange land; enabling information resilience in resettlement landscapes
Authors: Lloyd Annemaree
Published: September 2015

Purpose

– The purpose of this paper is to introduce and explore the concept of information resilience.

Design/methodology/approach

– The concept of information resilience emerges from a qualitative study that explored the health information experience and information practices of resettling refugees. Semi-structured face-to-face interviews were employed and the data collected were analysed using an grounded theory approach.

Findings

– The present study describes information resilience as an outcome of information literacy practice. As an emerging concept information resilience has the potential to focus research attention towards the critical role that information and information practices such as information literacy have in supporting people whose knowledge bases, social networks and information landscapes have become disrupted during transition.

Practical implications

– Public libraries role in support the development of information resilience is considered.

Social implications

– The paper draws from a study of the health information experiences of refugees during resettlement (Lloyd, 2014). The concept of information resilience emerges as an outcome of information literacy practice, for people whose knowledge base has become disrupted; and, who because of this disruption, must engage with new information environments and construct new information landscapes to rebuild social capital and bridge the transition into a new community.

Originality/value

– Introduces the concept of information resilience as a focal point for investigating transition from an information studies perspective.
Design and implementation of a capacity development program – experience with combating money laundering and financing of terrorism in Mongolia
Authors: Png Cheong-Ann , DeFeo Michael , Hicks Tristram
Published: September 2015

Purpose

– This paper aims to share experience in the design and implementation of a two-year capacity development program for combating money laundering and financing of terrorism in Mongolia.

Design/methodology/approach

– The paper reflects the experience of the authors in the design and implementation of the program with inputs from their counterparts in Mongolia.

Findings

– The program outcomes and the level of collaboration are generally positive, and the authorities and the Asian Development Bank agreed on a two-year extension of the program to further the progress made.

Originality/value

– The authors hope to share key reflections from the program for the purpose of other similar programs or studies in the field of combating money laundering and financing of terrorism.
New therapies for controlling atopic itch
Authors: Furue Masutaka , Kadono Takafumi
Published: September 2015

Chronic itch in atopic dermatitis markedly diminishes the quality of life of affected individuals. Sleep disturbance and impaired productivity in work due to chronic itch impose a socioeconomic burden. Conventional therapies for atopic dermatitis are capable of reducing atopic itch. However, the majority of patients are not satisfied with the antipruritic capacity of conventional treatments. In this review, we summarize recent progress in itch signaling in the skin, dorsal root ganglion and spinal cord. New therapies for controlling atopic itch are also discussed.
Effects of management on aquatic tree‐hole communities in temperate forests are mediated by detritus amount and water chemistry
Authors: Gossner Martin M. , Lade Peggy , Rohland Anja , Sichardt Nora , Kahl Tiemo , Bauhus Jürgen , Weisser Wolfgang W. , Petermann Jana S.
Published: September 2015

Arthropod communities in water‐filled tree holes may be sensitive to impacts of forest management, for example via changes in environmental conditions such as resource input.

We hypothesized that increasing forest management intensity (ForMI) negatively affects arthropod abundance and richness and shifts community composition and trophic structure of tree hole communities. We predicted that this shift is caused by reduced habitat and resource availability at the forest stand scale as well as reduced tree hole size, detritus amount and changed water chemistry at the tree holes scale.

We mapped 910 water‐filled tree holes in two regions in Germany and studied 199 tree hole inhabiting arthropod communities.

We found that increasing ForMI indeed significantly reduced arthropod abundance and richness in water‐filled tree holes. The most important indirect effects of management intensity on tree hole community structure were the reduced amounts of detritus for the tree hole inhabiting organisms and changed water chemistry at the tree hole scale, both of which seem to act as a habitat filter. Although habitat availability at the forest stand scale decreased with increasing management intensity, this unexpectedly increased local arthropod abundance in individual tree holes. However, regional species richness in tree holes significantly decreased with increasing management intensity, most likely due to decreased habitat diversity. We did not find that the management‐driven increase in plant diversity at the forest stand scale affected communities of individual tree holes, for example via resource availability for adults.

Our results suggest that management of temperate forests has to target a number of factors at different scales to conserve diverse arthropod communities in water‐filled tree holes.
Cold‐seeking behaviour mitigates reproductive losses from fungal infection in Drosophila
Authors: Hunt Vicky L. , Zhong Weihao , McClure Colin D. , Mlynski David T. , Duxbury Elizabeth M.L. , Keith Charnley A. , Priest Nicholas K.
Published: September 2015

Animals must tailor their life‐history strategies to suit the prevailing conditions and respond to hazards in the environment. Animals with lethal infections are faced with a difficult choice: to allocate more resources to reproduction and suffer higher mortality or to reduce reproduction with the expectation of enhanced immunity and late‐age reproduction. However, the strategies employed to mediate shifts in life‐history traits are largely unknown.

Here, we investigate the temperature preference of the fruit fly, Drosophila melanogaster, during infection with the fungal pathogen, Metarhizium robertsii, and the consequence of temperature preference on life‐history traits.

We have measured the temperature preference of fruit flies under different pathogen conditions. We conducted multiple fitness assays of the host and the pathogen under different thermal conditions. From these data, we estimated standard measures of fitness and used age‐specific methodologies to test for the fitness trade‐offs that are thought to underlie differences in life‐history strategy.

We found that fungus‐infected fruit flies seek out cooler temperatures, which facilitates an adaptive shift in their life‐history strategy. The colder temperatures preferred by infected animals were detrimental to the pathogen because it increased resistance to infection. But, it did not provide net benefits that were specific to infected animals, as cooler temperatures increased lifetime reproductive success and survival whether or not the animals were infected. Instead, we find that cold‐seeking benefits infected animals by increasing their late‐age reproductive output, at a cost to their early‐age reproductive output. In contrast, naive control flies prefer warmer temperatures that optimize early‐age reproductive, at a cost to reproductive output at late ages.

These findings show that infected animals exhibit fundamentally different reproductive strategies than their healthy counterparts. Temperature preference can facilitate shifts in strategy, but not without inevitable trade‐offs.
Contrasting the roles of section length and instream habitat enhancement for river restoration success: a field study of 20 European restoration projects
Authors: Hering Daniel , Aroviita Jukka , Baattrup‐Pedersen Annette , Brabec Karel , Buijse Tom , Ecke Frauke , Friberg Nikolai , Gielczewski Marek , Januschke Kathrin , Köhler Jan , Kupilas Benjamin , Lorenz Armin W. , Muhar Susanne , Paillex Amael , Poppe Michaela , Schmidt Torsten , Schmutz Stefan , Vermaat Jan , Verdonschot Piet F. M. , Verdonschot Ralf C. M. , Wolter Christian , Kail Jochem
Published: September 2015

Restoration of river hydromorphology often has limited detected effects on river biota. One frequently discussed reason is that the restored river length is insufficient to allow populations to develop and give the room for geomorphological processes to occur.

We investigated ten pairs of restored river sections of which one was a large project involving a long, intensively restored river section and one represented a smaller restoration effort. The restoration effect was quantified by comparing each restored river section to an upstream non‐restored section. We sampled the following response variables: habitat composition in the river and its floodplain, three aquatic organism groups (aquatic macrophytes, benthic invertebrates and fish), two floodplain‐inhabiting organism groups (floodplain vegetation, ground beetles), as well as food web composition and land–water interactions reflected by stable isotopes.

For each response variable, we compared the difference in dissimilarity of the restored and nearby non‐restored section between the larger and the smaller restoration projects. In a second step, we regrouped the pairs and compared restored sections with large changes in substrate composition to those with small changes.

When comparing all restored to all non‐restored sections, ground beetles were most strongly responding to restoration, followed by fish, floodplain vegetation, benthic invertebrates and aquatic macrophytes. Aquatic habitats and stable isotope signatures responded less strongly.

When grouping the restored sections by project size, there was no difference in the response to restoration between the projects targeting long and short river sections with regard to any of the measured response variables except nitrogen isotopic composition. In contrast, when grouping the restored sections by substrate composition, the responses of fish, benthic invertebrates, aquatic macrophytes, floodplain vegetation and nitrogen isotopic composition were greater in sections with larger changes in substrate composition as compared to those with smaller changes.

Synthesis and applications. The effects of hydromorphological restoration measures on aquatic and floodplain biota strongly depend on the creation of habitat for aquatic organisms, which were limited or not present prior to restoration. These positive effects on habitats are not necessarily related to the restored river length. Therefore, we recommend a focus on habitat enhancement in river restoration projects.
Conservation under uncertainty: optimal network protection strategies for worst‐case disturbance events
Authors: Acevedo Miguel A. , Sefair Jorge A. , Smith J. Cole , Reichert Brian , Fletcher Robert J.
Published: September 2015

Conservation goals are ideally set after a thorough understanding of potential threats; however, predicting future spatial patterns of threats, such as disturbance, remains challenging. Here, we develop a novel extension of network fortification–interdiction models (NFIM) that deals with uncertainty in future spatial patterns of disturbance by optimally selecting sites that will best mitigate a worst‐case scenario for a given magnitude of disturbance.

This approach uses information on between‐patch movement probabilities and patch‐specific survival, which can be estimated from mark–recapture data, to optimize life expectancy. Optimization occurs in three interrelated stages: protection, followed by disturbance and then assessment.

We applied the modelling approach to two mark–recapture data sets: roseate ternsSterna dougalliiin the north‐eastern United States and the Everglade snail kiteRostrhamus sociabilis plumbeusin Florida. We contrasted the results to a more conventional approach of protecting sites that maximize connectivity (by minimizing the distances among protected sites) and a bi‐objective model that maximizes connectivity and the number of individuals under protection.

Protecting sites that best mitigate future worst‐case disturbance scenarios consistently resulted in higher predicted life expectancies than protecting patches that minimize dispersal distance. Predicted life expectancy was similar betweenNFIMand the bi‐objective model for the small roseate tern network, yet theNFIMpredicted higher life expectancy than any of the scenarios in the bi‐objective model in the snail kite network.

Synthesis and applications. This application of interdiction models prescribed a combination of patches for protection that results in the least possible decrease in life expectancy. Our analyses of the snail kite and roseate tern networks suggest that managing to protect these prescribed patches by the network fortification ‐interdiction models (i.e. protecting against the worst‐case disturbance scenario) is more beneficial than managing patches that minimize dispersal distance or maximize the number of individuals under protection if the conservation goal is to ensure the long‐term persistence of a species.
Effects of minocycline on parameters of cardiovascular recovery after cardioplegic arrest in a rabbit Langendorff heart model
Authors: Salameh Aida , Halling Michelle , Seidel Thomas , Dhein Stefan
Published: September 2015

Pharmacological cardiac organ protection during cardiopulmonary bypass presents an opportunity for improvement. A number of different strategies have been established to minimize ischemia/reperfusion‐induced damage to the heart. Among these, cardioplegia with histidine‐tryptophan‐ketoglutarate solution and hypothermia are the most frequently used regimens. The antibiotic minocycline has been used in this context for neuroprotection. The aim of the current study was to evaluate whether the application of minocycline prior to cardioplegia exerts a protective effect on cardiac muscle. For this purpose, this study investigated six rabbit hearts with minocycline treatment (1 μmol/L) and six without in a Langendorff model of 90 min cold cardioplegic arrest using Custodiol followed by a 30 min recovery phase. Histological analysis of cardiac muscle revealed that markers of apoptosis, oxidative and nitrosative stress were significantly lower in the minocycline group, whereas adenosine triphosphate (ATP)‐ and malondialdehyde (MDA)‐levels and O2‐consumption were not affected by minocycline. Functionally, recovery of dP/dt (max) and dP/dt (min) was significantly faster in the minocycline group than in control. This leads to the conclusion that adding minocycline to the cardioplegic solution may improve left ventricular recovery after cardioplegic arrest involving reduced pro‐apoptotic effects.
Think Twice Before Going for Incentives: Social Norms and the Principal's Decision on Compensation Contracts
Authors: CARDINAELS EDDY , YIN HUAXIANG
Published: September 2015

Principals make decisions on various issues, ranging from contract design to control system implementation. Few studies examine the principal's active role in these decisions. We experimentally investigate this role by studying how a principal's choice of an incentive contract that may discourage misrepresentation, compared to a fixed‐salary contract, affects the honesty of his or her agents’ cost reporting. Results show that, besides an incentive effect and a principal trust effect, the active choice for incentives produces a negative “information leakage” effect. When principals use incentives, their choices not only incentivize truthful reporting and signal distrust, but they also leak important information about the social norm, namely, that other agents are likely to report dishonestly. Agents conform to this social norm by misrepresenting cost information more. Our results have important practical implications. Managers must recognize that their decisions can leak information to their agents, which may produce unanticipated consequences for the social norms of the organization.
Managing Soil Organic Carbon: A Farm Perspective
Authors: Ingram Julie , Mills Jane , Frelih‐Larsen Ana , Davis McKenna , Merante Paulo , Ringrose Sian , Molnar Andras , Sánchez Berta , Ghaley Bhim Bahadur , Karaczun Zbigniew
Published: September 2015

Farming practices that lead to declining returns and inputs of carbon to soils pose a threat to key soil functions. The EU FP7 interdisciplinary project SmartSOIL is using scientific testing and modeling to identify management practices that can optimise soil carbon storage and crop productivity. A consultation with advisors and policymakers in six European case study regions seeks to identify barriers to, and incentives for, uptake of such practices. Results from preliminary interviews are reported. Overall advisor and farmer awareness of management practices specifically directed towards soil carbon is low. Most production‐related decisions are taken in the short term, but managing soil carbon needs a long‐term approach. Key barriers to uptake of practices include: perceived scientific uncertainty about the efficacy of practices; lack of real life ‘best practice’ examples to show farmers; difficulty in demonstrating the positive effects of soil carbon management practices and economic benefits over a long time scale; and advisors being unable to provide suitable advice due to inadequate information or training. Most farmers are unconvinced of the economic benefits of practices for managing soil carbon. Incentives are therefore needed, either as subsidies or as evidence of the cost effectiveness of practices. All new measures and advice should be integrated into existing programmes to avoid a fragmented policy approach.
The effect of genetic structure on molecular dating and tests for temporal signal
Authors: Murray Gemma G. R. , Wang Fang , Harrison Ewan M. , Paterson Gavin K. , Mather Alison E. , Harris Simon R. , Holmes Mark A. , Rambaut Andrew , Welch John J.
Published: September 2015

‘Dated‐tip’ methods of molecular dating use DNA sequences sampled at different times, to estimate the age of their most recent common ancestor. Several tests of ‘temporal signal’ are available to determine whether data sets are suitable for such analysis. However, it remains unclear whether these tests are reliable.

We investigate the performance of several tests of temporal signal, including some recently suggested modifications. We use simulated data (where the true evolutionary history is known), and whole genomes of methicillin‐resistant Staphylococcus aureus (to show how particular problems arise with real‐world data sets).

We show that all of the standard tests of temporal signal are seriously misleading for data where temporal and genetic structures are confounded (i.e. where closely related sequences are more likely to have been sampled at similar times). This is not an artefact of genetic structure or tree shape per se, and can arise even when sequences have measurably evolved during the sampling period. More positively, we show that a ‘clustered permutation’ approach introduced by Duchêne et al. (Molecular Biology and Evolution, 32, 2015, 1895) can successfully correct for this artefact in all cases and introduce techniques for implementing this method with real data sets.

The confounding of temporal and genetic structures may be difficult to avoid in practice, particularly for outbreaks of infectious disease, or when using ancient DNA. Therefore, we recommend the use of ‘clustered permutation’ for all analyses. The failure of the standard tests may explain why different methods of dating pathogen origins have reached such wildly different conclusions.
Converging Patterns of Alcohol Use and Related Outcomes Among Females and Males in the United States, 2002 to 2012
Authors: White Aaron , Castle I‐Jen P. , Chen Chiung M. , Shirley Mariela , Roach Deidra , Hingson Ralph
Published: September 2015

Background

Females in the United States consume less alcohol and cause and experience fewer alcohol‐related harms than males. However, recent research suggests such gaps might be narrowing. The purpose of this study was to explore changes in alcohol use and associated outcomes among females and males in the United States between 2002 and 2012.

Methods

Data from the National Survey on Drug Use and Health were used to assess the prevalence and trends for females and males aged 12+ in lifetime abstinence, age of onset, current drinking, binge drinking, drinking and driving, reaching DSM‐IV criteria for an alcohol use disorder, combining alcohol with other drugs such as marijuana, and other variables. Of particular interest was whether differences between females and males narrowed during the decade under study.

Results

Differences in the drinking patterns of females and males aged 12+ narrowed between 2002 and 2012 for current drinking, number of drinking days per month, past year DSM‐IV alcohol abuse, and past‐year driving under the influence of alcohol. In addition, convergence was noted in 1 or more age subgroups for the prevalence of binge drinking and DSM‐IV alcohol dependence and mean age at drinking onset. Divergence in drinking habits did not occur for any measure in any age subgroups with the exception of a greater increase in the prevalence of combining alcohol with marijuana among young adult male drinkers than female drinkers aged 18 to 25.

Conclusions

Between 2002 and 2012, differences in alcohol consumption and related outcomes narrowed for females and males. Reasons for converging patterns of alcohol use are unclear and do not appear to be easily explainable by recent trends in employment status, pregnancy status, or marital status. More research is needed to identify the psychosocial and environmental contributors to these changes and to assess implications for prevention and treatment efforts.