bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative visual ecology of cephalopods from different habitats
Authors: Chung Wen-Sung , Marshall N. Justin
Published: September 2016

Previous investigations of vision and visual pigment evolution in aquatic predators have focused on fish and crustaceans, generally ignoring the cephalopods. Since the first cephalopod opsin was sequenced in late 1980s, we now have data on over 50 cephalopod opsins, prompting this functional and phylogenetic examination. Much of this data does not specifically examine the visual pigment spectral absorbance position (λmax) relative to environment or lifestyle, and cephalopod opsin functional adaptation and visual ecology remain largely unknown. Here we introduce a new protocol for photoreceptor microspectrophotometry (MSP) that overcomes the difficulty of bleaching the bistable visual pigment and that reveals eight coastal coleoid cephalopods to be monochromatic withλmaxvarying from 484 to 505 nm. A combination of current MSP results, theλmaxvalues previously characterized using cephalopod retinal extracts (467–500 nm) and the corresponding opsin phylogenetic tree were used for systematic comparisons with an end goal of examining the adaptations of coleoid visual pigments to different light environments. Spectral tuning shifts are described in response to different modes of life and light conditions. A new spectral tuning model suggests that nine amino acid substitution sites may determine the direction and the magnitude of spectral shifts.
Spatially cascading effect of perturbations in experimental meta-ecosystems
Authors: Harvey Eric , Gounand Isabelle , Ganesanandamoorthy Pravin , Altermatt Florian
Published: September 2016

Ecosystems are linked to neighbouring ecosystems not only by dispersal, but also by the movement of subsidy. Such subsidy couplings between ecosystems have important landscape-scale implications because perturbations in one ecosystem may affect community structure and functioning in neighbouring ecosystems via increased/decreased subsidies. Here, we combine a general theoretical approach based on harvesting theory and a two-patch protist meta-ecosystem experiment to test the effect of regional perturbations on local community dynamics. We first characterized the relationship between the perturbation regime and local population demography on detritus production using a mathematical model. We then experimentally simulated a perturbation gradient affecting connected ecosystems simultaneously, thus altering cross-ecosystem subsidy exchanges. We demonstrate that the perturbation regime can interact with local population dynamics to trigger unexpected temporal variations in subsidy pulses from one ecosystem to another. High perturbation intensity initially led to the highest level of subsidy flows; however, the level of perturbation interacted with population dynamics to generate a crash in subsidy exchange over time. Both theoretical and experimental results show that a perturbation regime interacting with local community dynamics can induce a collapse in population levels for recipient ecosystems. These results call for integrative management of human-altered landscapes that takes into account regional dynamics of both species and resource flows.
SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences
Authors: Edgar Robert C.
Published: September 2016

Metagenomics experiments often characterize microbial communities by sequencing the ribosomal 16S and ITS regions. Taxonomy prediction is a fundamental step in such studies. The SINTAX algorithm predicts taxonomy by usingk-mer similarity to identify the top hit in a reference database and provides bootstrap confidence for all ranks in the prediction. SINTAX achieves comparable or better accuracy to the RDP Naive Bayesian Classifier with a simpler algorithm that does not require training. Most tested methods are shown to have high rates of over-classification errors where novel taxa are incorrectly predicted to have known names.
DNA Fountain enables a robust and efficient storage architecture
Authors: Erlich Yaniv , Zielinski Dina
Published: September 2016

DNA is an attractive medium to store digital information. Here, we report a storage strategy, called DNA Fountain, that is highly robust and approaches the information capacity per nucleotide. Using our approach, we stored a full computer operating system, movie, and other files with a total of 2.14 × 106bytes in DNA oligos and perfectly retrieved the information from a sequencing coverage equivalent of a single tile of Illumina sequencing. We also tested a process that can allow 2.18 × 1015retrievals using the original DNA sample and were able to perfectly decode the data. Finally, we explored the limit of our architecture in terms of bytes per molecules and obtained a perfect retrieval from a density of 215Petabyte/gram of DNA, orders of magnitudes higher than previous techniques.
Comparing Individual-Based Approaches to Modelling the Self-Organization of Multicellular Tissues
Authors: Osborne James M. , Fletcher Alexander G. , Pitt-Francis Joseph M. , Maini Philip K. , Gavaghan David J.
Published: September 2016

The coordinated behaviour of populations of cells plays a central role in tissue growth and renewal. Cells react to their microenvironment by modulating processes such as movement, growth and proliferation, and signalling. Alongside experimental studies, computational models offer a useful means by which to investigate these processes. To this end a variety of cell-based modelling approaches have been developed, ranging from lattice-based cellular automata to lattice-free models that treat cells as point-like particles or extended shapes. It is difficult to accurately compare between different modelling approaches, since one cannot distinguish between differences in behaviour due to the underlying model assumptions and those due to differences in the numerical implementation of the model. Here, we exploit the availability of an implementation of five popular cell-based modelling approaches within a consistent computational framework, Chaste (http://www.cs.ox.ac.uk/chaste). This framework allows one to easily change constitutive assumptions within these models. In each case we provide full details of all technical aspects of our model implementations. We compare model implementations using four case studies, chosen to reflect the key cellular processes of proliferation, adhesion, and short-and long-range signalling. These case studies demonstrate the applicability of each model and provide a guide for model usage.

Authors’ contributions

JO and AF conceived of the study, designed the study, coordinated the study, carried out the computational modelling and drafted the manuscript. JP contributed to the computational modelling and helped draft the manuscript. PM and DG conceived of the study, designed the study and helped draft the manuscript. All authors gave final approval for publication.
Distant regulatory effects of genetic variation in multiple human tissues
Authors: Jo Brian , He Yuan , Strober Benjamin J. , Parsana Princy , Aguet François , Brown Andrew A. , Castel Stephane E. , Gamazon Eric R. , Gewirtz Ariel , Gliner Genna , Han Buhm , He Amy Z. , Kang Eun Yong , McDowell Ian C. , Li Xiao , Mohammadi Pejman , Peterson Christine B. , Quon Gerald , Saha Ashis , Segrè Ayellet V. , Sul Jae Hoon , Sullivan Timothy J. , Ardlie Kristin G. , Brown Christopher D. , Conrad Donald F. , Cox Nancy J. , Dermitzakis Emmanouil T. , Eskin Eleazar , Kellis Manolis , Lappalainen Tuuli , Sabatti Chiara ,   GTEx Consortium, Engelhardt Barbara E. , Battle Alexis
Published: September 2016

Understanding the genetics of gene regulation provides information on the cellular mechanisms through which genetic variation influences complex traits. Expression quantitative trait loci, or eQTLs, are enriched for polymorphisms that have been found to be associated with disease risk. While most analyses of human data has focused on regulation of expression by nearby variants (cis-eQTLs), distal or trans-eQTLs may have broader effects on the transcriptome and important phenotypic consequences, necessitating a comprehensive study of the effects of genetic variants on distal gene transcription levels. In this work, we identify trans-eQTLs in the Genotype Tissue Expression (GTEx) project data1, consisting of 449 individuals with RNA-sequencing data across 44 tissue types. We find 81 genes with a trans-eQTL in at least one tissue, and we demonstrate that trans-eQTLs are more likely than cis-eQTLs to have effects specific to a single tissue. We evaluate the genomic and functional properties of trans-eQTL variants, identifying strong enrichment in enhancer elements and Piwi-interacting RNA clusters. Finally, we describe three tissue-specific regulatory loci underlying relevant disease associations: 9q22 in thyroid that has a role in thyroid cancer, 5q31 in skeletal muscle, and a previously reported master regulator nearKLF14in adipose. These analyses provide a comprehensive characterization of trans-eQTLs across human tissues, which contribute to an improved understanding of the tissue-specific cellular mechanisms of regulatory genetic variation.
Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+T cell fate bifurcation
Authors: Lönnberg Tapio , Svensson Valentine , James Kylie R , Fernandez-Ruiz Daniel , Sebina Ismail , Montandon Ruddy , Soon Megan S. F. , Fogg Lily G , Stubbington Michael J. T. , Otzen Bagger Frederik , Zwiessele Max , Lawrence Neil , Souza-Fonseca-Guimaraes Fernando , Heath William R. , Billker Oliver , Stegle Oliver , Haque Ashraful , Teichmann Sarah A.
Published: September 2016

Differentiation of naïve CD4+T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to multiple levels of heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissectionin vivo. By using single-cell RNA transcriptomics and computational modelling of temporal mixtures, we reconstructed the developmental trajectories of Th1 and Tfh cell populations duringPlasmodiuminfection in mice at single-cell resolution. These cell fates emerged from a common, highly proliferative and metabolically active precursor. Moreover, by tracking clonality from T cell receptor sequences, we infer that ancestors derived from the same naïve CD4+T cell can concurrently populate both Th1 and Tfh subsets. We further found that precursor T cells were coached towards a Th1 but not a Tfh fate by monocytes/macrophages. The integrated genomic and computational approach we describe is applicable for analysis of any cellular system characterized by differentiation towards multiple fates.

One Sentence Summary

Using single-cell RNA sequencing and a novel unsupervised computational approach, we resolve the developmental trajectories of two CD4+T cell fatesin vivo, and show that uncommitted T cells are externally influenced towards one fate by inflammatory monocytes.
Women on the board of directors and corporate tax aggressiveness in Australia
Authors: Richardson Grant , Taylor Grantley , Lanis Roman
Published: September 2016

Purpose

This paper aims to investigate the impact of women on the board of directors on corporate tax avoidance in Australia.

Design/methodology/approach

The authors use multivariate regression analysis to test the association between the presence of female directors on the board and tax aggressiveness. They also test for self-selection bias in the regression model by using the two-stage Heckman procedure.

Findings

This paper finds that relative to there being one female board member, high (i.e. greater than one member) female presence on the board of directors reduces the likelihood of tax aggressiveness. The results are robust after controlling for self-selection bias and using several alternative measures of tax aggressiveness.

Research limitations/implications

This study extends the extant literature on corporate governance and tax aggressiveness. This study is subject to several caveats. First, the sample is restricted to publicly listed Australian firms. Second, this study only examines the issue of women on the board of directors and tax aggressiveness in the context of Australia.

Practical implications

This research is timely, as there has been increased pressure by government bodies in Australia and globally to develop policies to increase female representation on the board of directors.

Originality/value

This study is the first to provide empirical evidence concerning the association between the presence of women on the board of directors and tax aggressiveness.
Victoria’s banning notice provisions: parliamentary, procedural and individual vulnerabilities
Authors: Farmer Clare
Published: September 2016

Purpose

Alcohol-related disorder in Australia’s night-time economy has precipitated an expanding regulatory and legislative framework. A key feature is the growth of police-imposed discretionary justice, one example of which are Victoria’s banning provisions. Banning notices are imposed on-the-spot, may be issued pre-emptively, but permit no right of independent appeal. However, there has been little analysis of the enactment, implementation or use of police-imposed banning provisions. The paper aims to discuss these issues.

Design/methodology/approach

This paper draws upon a detailed examination of the record of parliamentary debate of the banning notice legislation to document how the provisions, and their embedded procedural vulnerabilities, were legitimised. In addition, an analysis of Victoria Police data informs consideration of the ongoing scrutiny of the police power to ban.

Findings

The absolute discretion afforded to police officers, and a lack of effective oversight, has created the potential for the disproportionate and discriminatory implementation of Victoria’s banning notice powers. The findings highlight procedural vulnerabilities within the provisions, and concern regarding the particular risk of banning notices for vulnerable recipients.

Research limitations/implications

The nature of Victoria’s banning provisions created the circumstances for their inequitable imposition, but public scrutiny of their use and effect is limited. Omissions and deficiencies in the published data restricts meaningful analysis of how banning works in practice.

Originality/value

The research underpinning this paper was the first detailed examination of the implementation and ongoing scrutiny of Victoria’s banning notice provisions. The findings presented in this paper highlight key procedural vulnerabilities resulting from the passage of the legislation and the absence of effective oversight.
Ameliorating vulnerability arising from involvement with criminal courts
Authors: Henning Terese
Published: September 2016

Purpose

The purpose of this paper is to provide an overview of major mechanisms instituted in Australia to ameliorate the experience of vulnerability arising as a corollary of involvement in Australian criminal courts as defendants, victims or witnesses of crime or family members/friends of such people.

Design/methodology/approach

The paper begins by providing an overview of two major categories of vulnerability within the criminal justice system – generally experienced vulnerability arising as a corollary of involvement in Australian criminal courts and attribute-based vulnerability. It focusses on the former locating it within a human rights framework. It then outlines dominant responses to this form of vulnerability. Finally it considers the potential for the Court Network program to achieve a more integrated approach to ameliorating this form of vulnerability.

Findings

The paper takes the view that major responses to systemic vulnerability in the criminal justice system fall short of adequately managing this form of vulnerability. It suggests that the Court Network model has the potential to address some lacunae in other responses and importantly to provide a gateway to them.

Originality/value

It explores an aspect of vulnerability that is now infrequently addressed and considers one option to supply lacunae in other major responses that has not yet been brought into the scholarly discussion in any significant way.
Document phenomenology: a framework for holistic analysis
Authors: Gorichanaz Tim , Latham Kiersten F.
Published: September 2016

Purpose

The purpose of this paper is to advance document ontology and epistemology by proposing a framework for analysing documents from multiple perspectives of research and practice.

Design/methodology/approach

Understanding is positioned as an epistemic aim of documents, which can be approached through phenomenology.

Findings

A phenomenological framework for document analysis is articulated. Key concepts in this framework are include intrinsic information, extrinsic information, abtrinsic information, and adtrinsic information. Information and meaning are distinguished. Finally, documents are positioned as part of a structural framework, which includes individual documents, parts of documents (docemes and docs), and systems of documents.

Research limitations/implications

Scholarship is extended with an eye toward holism; still, it is possible that important aspects of documents are overlooked. This framework serves as a stepping-stone along the continual refinement of methods for understanding documents.

Practical implications

Both scholars and practitioners can consider documents through this framework. This will lead to further co-understanding and collaboration, as well as better education and a deeper understanding of all manner of document experiences.

Originality/value

This paper fills a need for a common way to conceptualise documents that respects the numerous ways in which documents exist and are used and examined. Such coherence is vital for the advancement of document scholarship and is the promotion of document literacy in society, which is becoming increasingly important.
Outsourcing trust to the information infrastructure in schools
Authors: Sundin Olof , Carlsson Hanna
Published: September 2016

Purpose

This paper investigates the experiences of school teachers of supporting pupils and their apprehensions of how pupils search and assess information when search engines have become a technology of literacy in schools. By situating technologies of literacy as sociomaterial the purpose of this paper is to analyse and discuss these experiences and understandings in order to challenge dominant views of search in information literacy research.

Design/methodology/approach

Six focus group interviews with in total 39 teachers working at four different elementary and secondary schools were conducted in the autumn of 2014. Analysis was done using a sociomaterial perspective, which provides tools for understanding how pupils and teachers interact with and are demanded to translate their interest to technologies of literacy, in this case search engines, such as Google.

Findings

The teachers expressed difficulties of conceptualizing search as something they could teach. When they did, search was most often identified as a practical skill. A critical perspective on search, recognizing the role of Google as a dominant part of the information infrastructure and a co-constructor of what there is to know was largely lacking. As a consequence of this neglected responsibility of teaching search, critical assessment of online information was conflated with Google’s relevance ranking.

Originality/value

The study develops a critical understanding of the role of searching and search engines as technologies of literacy in relation to critical assessment in schools. This is of value for information literacy training.
Gender discrimination and firms’ profit: evidence from Brazil
Authors: Liu Wenjun , Nomura Tomokazu , Nishijima Shoji
Published: September 2016

Purpose

This paper investigates discrimination against women within the Brazilian labour market using firm-level data from the World Bank Investment Climate Survey. The purpose of this paper is to determine whether the female employees in the Brazilian labour market are paid less than their productivity warrants due to the existence of discrimination.

Design/methodology/approach

Based on employer discrimination model proposed by Becker (1971) that considered the proportion of female employees as a proxy for the extent of discrimination, the authors estimate the profit function using OLS analysis, and regress it on the proportion of female employees and other firm characteristics. To address the endogeneity problem caused by unobservable productivity shocks, the authors employed the methods proposed by Olley and Pakes (1996) and Levinsohn and Petrin (2003), respectively.

Findings

The results indicate that the proportion of female employees has positive effect on firms’ profit in 2002, but has no effect in 2007. This finding gives evidence of the existence of discrimination against female employees within the Brazilian labour market in the early 2000s, while the gender discrimination was reduced overtime.

Originality/value

This paper’s main contribution is to provide an approach that differs from that of previous research to determine whether discrimination exists within the Brazilian labour market. This paper also provides policy insights for Brazilian labour market.
Global trajectories, dynamics, and tendencies of business software piracy
Authors: Andrés Antonio Rodríguez , Asongu Simplice
Published: September 2016

Purpose

The purpose of this paper is to examine global trajectories, dynamics, and tendencies of software piracy to ease the benchmarking of current efforts toward harmonizing the standards and enforcements of intellectual property rights (henceforth IPRs) protection worldwide.

Design/methodology/approach

For that purpose, the authors estimate dynamic panel data models for 99 countries over the period 1994-2010.

Findings

The main finding suggest that, a genuine timeframe for standardizing IPRs laws in the fight against software piracy is most feasible within a horizon of 4.3-10.4 years. In other words, full (100 percent) convergence within the specified timeframe will mean the enforcements of IPRs regimes without distinction of nationality or locality within identified fundamental characteristics of software piracy. The absence of convergence (in absolute and conditional terms) for the World panel indicates that, blanket policies may not be effective unless they are contingent on the prevailing trajectories, dynamics and tendencies of software piracy. Policy implications and caveats are also discussed.

Originality/value

It is the first attempt to empirically assess the convergence of IPRs systems across countries.
Do trade reforms affect changes in patterns of comparative advantage?
Authors: Choi Namsuk
Published: September 2016

Purpose

The purpose of this paper is to examine the effects of foreign trade liberalization and trade reforms on the process of structural upgrading, and explore the extent to which they provide impetus for exports.

Design/methodology/approach

This paper accounts for trade liberalization dates, cumulative years in open regime, and the density of 1,006 products in the patterns of comparative advantage for 132 countries from 1975 to 2000. The effects of trade liberalizations and trade reforms in open regime on future export performance are estimated by using various empirical strategies.

Findings

This paper finds that the speed of moving from simple poor-country goods to rich-country goods in export depends not only on having a route to nearby goods of increasingly higher value, but also on the increase in the cumulative years in open regime. In particular, a 1 percent change in the relatedness across products with trade reform in open regime increases the probability of exporting a new product by 2.0 percent more.

Originality/value

A contribution of this paper is that it measures the extent to which trade reform in open regime affects the evolution of comparative advantage, even after taking account of the role of relatedness of exported products as in the Hausmann and Klinger (2006, 2007). In this paper, empirical findings of a comprehensive product level cross-country time-series data analysis may contribute to generalize the role of trade reform on structural upgrading not only for a pro-competitive export country like Korea but also for a typical developing country.
Underutilisation of self-service libraries in Chinese cities
Authors: Zhou Lihong , Song Yaqian , Zhou Tong
Published: September 2016

Purpose

Self-service libraries (SSLs) have been regarded as an effective approach to provide convenient book services to the enormously large populations of China’s cities. These SSLs are in fact automatic book service machines, which provide a combination of services, including reading card issuing, book lending and returning, and book reservations and collection. However, despite acclaimed success, SSL services are not well received by patrons and are underutilised. The purpose of this paper is to identify and understand the causes of the underutilisation of SSL services in Chinese cities.

Design/methodology/approach

This study adopted an inductive approach and a case study research design. The SSL services in Wuhan, the capital city of Hubei Province, were adopted as the case study, in which 20 public librarians, SSL workers and managers, and library patrons were approached and interviewed using semi-structured question scripts. The interview data were analysed using a thematic analysis approach.

Findings

The analysis pointed to 13 causes in three main themes: management problems, service limitations, and the implicit role of government. Further conceptualisation of the findings revealed that the underutilisation of SSL services has resulted from the absence of a patron-centric perspective and the negligence of patrons’ needs and requirements. Therefore, to increase the popularity and usage of SSLs, it is necessary to develop patron-centric management mechanisms through which patrons’ needs and requirements can be effectively understood and responded to.

Originality/value

This study aims to develop specific suggestions to improve the usage of SSLs. Furthermore, although this study focuses on SSL development in China, this research can provide useful suggestions and implications that can be shared across international borders.
E-books in the mobile age: advocacy and acceptance in India
Authors: Ghosh Maitrayee
Published: September 2016

Purpose

This paper aims to understand e-books’ popularity in India and the potential of mobile devices to reach huge number of readers because of content absorption through mobile phones and iPods.

Design/methodology/approach

To accomplish the goal of this study, the author used a mixed method of study: an analysis of the academic literature, data collection through personal interaction, questionnaire survey and library website to understand users’ perceptions on potential of mobile devices on access to content, and appraised on mobile-friendly services in libraries and strategies for promoting mobile content and best practices.

Findings

The mobile age has brought tremendous scope for reading on low-cost mobile devices that are within the reach of almost every Indian and has incorporated optimism in a highly populated country like India. The technology and expertise for digitisation in India correlate with not only digital-savvy but also multimedia- and animation-skilled workforce, which altogether developed an ecosystem favourable for e-book production.

Originality/value

The literature on e-books in India is scanty, although there are a handful of case studies on academic libraries conducted by librarians but no systematic large-scale research on initiatives, advocacy programs and promotional processes to improve the overall scenario; this paper is an attempt to fill the gap.
Universities as multinational enterprises? The multinational university analyzed through the eclectic paradigm
Authors: Guimon Jose
Published: September 2016

Purpose

The aim of this paper is to examine the emergence of multinational universities through the lens of Dunning’s eclectic paradigm.

Design/methodology/approach

An analytical framework combining the eclectic paradigm with the three missions of universities is proposed to explore the motives behind the cross-border activity of universities.

Findings

Although the analogy between a university and a multinational enterprise is flawed, this paper shows how the eclectic paradigm can still serve the purpose of better understanding why universities locate fully pledged campuses or research departments in foreign locations. A set of implications for universities and host countries are also discussed.

Originality/value

The internationalization of universities has been widely analyzed in the higher education literature, but few attempts have been made to draw connections with international business research. The originality of this paper lies in addressing this cross-disciplinary gap.
Network analyses reveal intra‐ and interspecific differences in behaviour when passing a complex migration obstacle
Authors: Kirk Mark A. , Caudill Christopher C.
Published: September 2016

Network theory offers new perspective on movement data by evaluating the relationships between animal movements (links) and detection locations (nodes) in spatially complex systems, including human‐altered landscapes.

We applied network analyses to intra‐ and interspecific movement patterns in the migration behaviour and dam passage success of two anadromous fish species, Pacific lamprey Entosphenus tridentatus Gairdner and Chinook salmon Oncorhynchus tshawytscha Walbaum, when moving through a large multifishway hydroelectric project (Bonneville Dam, USA).

Network analyses revealed greater variation in movement for Pacific lamprey compared with Chinook salmon. Salmon that passed the dam had networks consisting of more direct passage routes with fewer overall movements compared with lamprey that passed the dam. Lamprey that did not pass the dam exhibited a wide range of behaviours, from approaching only one fishway site to testing all possible passage routes. Accounting for the time spent in the network improved the ability to detect biological differences in network structure for lamprey that did and did not pass the dam.

The movement patterns likely resulted from different behavioural responses to complex environmental and internal factors affecting a philopatric species (Chinook salmon) vs. a non‐philopatric species (Pacific lamprey) when moving through an engineered environment designed primarily for salmon.

Synthesis and applications. Our case study highlights the potential for network analyses to link questions of basic movement ecology with monitoring of movement and behaviour in human‐altered landscapes. Network analyses can thus serve as a valuable tool for describing movement and behaviour in the face of environmental change and assessing the effectiveness of mitigation efforts at spatially complex obstacles to animal movement.
Community management indicators can conflate divergent phenomena: two challenges and a decomposition‐based solution
Authors: Adams Georgina L. , Jennings Simon , Reuman Daniel C.
Published: September 2016

Community indicators are used to assess the state of ecological communities and to guide management. They are usually calculated from monitoring data, often collected annually. Since any given community indicator provides a univariate summary of complex multivariate phenomena, different changes in the community may lead to the same response in the indicator. Sampling variation can also mask ecologically important trends.

This study addresses these challenges for community indicators, with a focus on the large fish indicator (LFI), internationally used to report status of marine fish communities. The LFI expresses ‘large’ fish biomass as a proportion of total fish biomass and is calculated from species–size–abundance data collected on trawl surveys. We develop new methods to decompose the contributions of species, sampling locations and season to trends over time in the LFI, and highlight consequences for assessment and management.

Our results showed that both species and locations made divergent contributions to overall trends in the LFI indicator, with contributions differing by several orders of magnitude and in sign. Only small proportions of species and locations drove overall LFI trends, and their contributions changed with season (spring and autumn surveys). To assess significance of component trends, a resampling method was developed. Our method can be generalized and applied to many other community indicators based on survey data.

Synthesis and applications. Our new method for decomposing community indicators and generating confidence intervals makes it possible to extract much more information on what drives a ‘headline’ indicator, providing a solution to challenges arising from multiple possible interpretations of changes in the indicator and from sampling variation. Analysis of the effects of indicator components on headline indicator values is recommended, because the results allow assessors and managers to identify and interpret how divergent factors (e.g. species, sampling locations and seasons) contribute to the headline indicator value.
How will predicted land‐use change affect waterfowl spring stopover ecology? Inferences from an individual‐based model
Authors: Beatty William S. , Kesler Dylan C. , Webb Elisabeth B. , Naylor Luke W. , Raedeke Andrew H. , Humburg Dale D. , Coluccy John M. , Soulliere Gregory J.
Published: September 2016

Habitat loss, habitat fragmentation, overexploitation and climate change pose familiar and new challenges to conserving natural populations throughout the world. One approach conservation planners may use to evaluate the effects of these challenges on wildlife populations is scenario planning.

We developed an individual‐based model to evaluate the effects of future land use and land cover changes on spring‐migrating dabbling ducks in North America. We assessed the effects of three Intergovernmental Panel on Climate Change emission scenarios (A1B, A2 and B1) on dabbling duck stopover duration, movement distances and mortality. We specifically focused on migration stopover duration because previous research has demonstrated that individuals arriving earlier on the nesting grounds exhibit increased reproductive fitness.

Compared to present conditions, all three scenarios increased stopover duration and movement distances of agent ducks.

Although all three scenarios presented migrating ducks with increased amounts of wetland habitat, scenarios also contained substantially less cropland, which decreased overall carrying capacity of the study area.

Synthesis and applications. Land‐use change may increase waterfowl spring migration stopover duration in the midcontinent region of North America due to reduced landscape energetic carrying capacity. Climate change will alter spatial patterns of crop distributions with corn and rice production areas shifting to different regions. Thus, conservation planners will have to address population‐level energetic implications of shifting agricultural food resources and increased uncertainty in yearly precipitation patterns within the next 50 years.
Successful conservative treatment of cervical pregnancy with uterine artery embolization followed by curettage: a report of 19 cases
Authors: Hu J , Tao X , Yin L , Shi Y
Published: September 2016

Objective

The purpose of this retrospective study was to evaluate the safety and efficacy of uterine artery embolization (UAE) followed by curettage for conservative management of cervical pregnancy.

Design

Retrospective review.

Setting

Peking University First Hospital.

Sample

Patients with cervical pregnancy diagnosed by trans‐vaginal ultrasound at Peking University First Hospital between January 2003 and December 2014.

Methods

We retrospectively reviewed the clinical background and outcomes of patients with cervical pregnancy who underwent UAE followed by curettage for prevention of massive vaginal bleeding and removal of gestational tissue from the cervix. We also reviewed the literature on the role of UAE in the treatment of cervical pregnancy.

Main outcome measures

Clinical assessments included gestational age, gravidity, endocervical canal mass, serum beta‐human chorionic gonadotrophin (β‐HCG) level, blood loss, hospitalisation stay and expenses, time of resumption of menstruation and subsequent pregnancy outcomes.

Results

A total of 19 patients with cervical pregnancy treated with UAE followed by curettage were identified. Curettage was performed 24–72 hours after UAE in 16 patients, within 24 hours after UAE in three patients. None of the patients underwent a hysterectomy as a result of cervical pregnancy. Of the nine patients with available follow‐up information (median follow‐up time 59 months), eight resumed normal menstruation and one had a term pregnancy with a normal vaginal delivery. Quick regression of serum β‐HCG level, low blood loss and short hospital stay were observed.

Conclusion

UAE combined with curettage is a safe, effective and fertility‐sparing choice for treatment of patients with cervical pregnancy.

Tweetable abstract

A serial of 19 patients with cervical pregnancy treated with UAE followed by curettage showed a good prognosis.
Performance of prenatal screening using maternal serum and ultrasound markers for Down syndrome in Chinese women: a systematic review and meta‐analysis
Authors: Tu S , Rosenthal M , Wang D , Huang J , Chen Y
Published: September 2016

Background

Controversies about the performance of conventional prenatal screening using maternal serum and ultrasound markers (PSMSUM) in detecting Down syndrome (DS) have been raised as a result of a recently available noninvasive prenatal test based on cell‐free fetal DNA sequencing.

Objectives

To evaluate the screening performance of PSMSUM in detecting DS in Chinese women.

Search strategy

An exhaustive literature search of MEDLINE, Embase, the Cochrane Library, ISI Web of Science and China BioMedical Disc.

Selection criteria

Primary studies, published from January 2004 to November 2014, which examined the screening accuracy of PSMSUM in pregnant Chinese women, compared with a reference standard, either chromosomal verification or inspection of the newborn.

Data collection and analysis

Data were extracted as screening positive/negative results for Down and non‐Down syndrome pregnancies, allowing estimation of sensitivities and specificities. Risks of bias within and across studies were assessed. Screening accuracy measures were pooled using a bivariate random effects regression model.

Main results

Seventy‐eight studies, involving six categories of PSMSUM, were included. Second‐trimester double serum [pooled sensitivity (SEN) = 0.80, pooled specificity (SPE) = 0.95] and triple‐serum (pooled SEN = 0.79, pooled SPE = 0.96) screening were the predominant PSMSUM methods. The screening performances of these methods achieved the national standard but varied enormously across studies. First‐trimester combined screening (pooled SEN = 0.92, pooled SPE = 0.93) and second‐trimester quadruple serum screening (median SEN = 0.86, median SPE = 0.96) performed better, but were rarely used.

Author's conclusions

Second‐trimester maternal serum screening has the potential to achieve satisfactory screening performance in middle‐ and low‐income countries. The reported enormous range in screening performance of second‐trimester PSMSUM calls for urgent implementation of methods for performance optimization.

Tweetable abstract

Meta‐analysis results show good accuracy of maternal serum and ultrasound screening for trisomy 21 in Chinese women.
Socioeconomic Differences in Use of Low‐Value Cancer Screenings and Distributional Effects in Medicare
Authors: Xu Wendy Yi , Jung Jeah Kyoungrae
Published: September 2016

Objective

Consuming low‐value health care not only highlights inefficient resource use but also brings an important concern regarding the economics of disparities. We identify the relation of socioeconomic characteristics to the use of low‐value cancer screenings in Medicare fee‐for‐service (FFS) settings, and quantify the amount subsidized from nonusers and taxpayers to users of these screenings.

Data Sources

2007–2013 Medicare Current Beneficiary Survey, Medicare FFS claims, and the Area Health Resource Files.

Study Design

Our sample included enrollees in FFS Part B for the entire calendar year. We excluded beneficiaries with a claims‐documented or self‐reported history of targeted cancers, or those enrolled in Medicaid or Medicare Advantage plans. We identified use of low‐value Pap smears, mammograms, and prostate‐specific antigen tests based on established algorithms, and estimated a logistic model with year dummies separately for each test.

Data Collection/Extraction Methods

Secondary data analyses.

Principal Findings

We found a statistically significant positive association between privileged socioeconomic characteristics and use of low‐value screenings. Having higher income and supplemental private insurance strongly predicted more net subsidies from Medicare.

Conclusions

FFS enrollees who are better off in terms of sociodemographic characteristics receive greater subsidies from taxpayers for using low‐value cancer screenings.
Tyrosine decarboxylase activity of Enterococcus mundtii: new insights into phenotypic and genetic aspects
Authors: Gatto Veronica , Tabanelli Giulia , Montanari Chiara , Prodomi Valentina , Bargossi Eleonora , Torriani Sandra , Gardini Fausto
Published: September 2016

Few information is available about the tyraminogenic potential of the species Enterococcus mundtii. In this study, two plant‐derived strains of E. mundtii were selected and investigated to better understand the phenotypic behaviour and the genetic mechanisms involved in tyramine accumulation. Both the strains accumulated tyramine from the beginning of exponential phase of growth, independently on the addition of tyrosine to the medium. The strains accumulated also 2‐phenylethylamine, although with lower efficiency and in greater extent when tyrosine was not added. Accordingly, the tyrosine decarboxylase (tyrDC) gene expression level increased during the exponential phase with tyrosine added, while it remained constant and high without precursor. The genetic organization as well as sequence identity levels of tyrDC and tyrosine permease (tyrP) genes indicated a correlation with those of phylogenetically closer enterococcal species, such as E. faecium, E. hirae and E. durans; however, the gene Na+/H+ antiporter (nhaC) that usually follow tyrP is missing. In addition, BLAST analysis revealed the presence of additional genes encoding for decarboxylase and permease in the genome of several E. mundtii strains. It is speculated the occurrence of a duplication event and the acquisition of different specificity for these enzymes that deserves further investigations.
The Relationship Between Airway Antioxidant Levels, Alcohol Use Disorders, and Cigarette Smoking
Authors: Burnham Ellen L. , McNally Alicia , Gaydos Jeanette , Brown Lou Ann S.
Published: September 2016

Background

Alcohol use disorders (AUDs) and cigarette smoking are associated with pulmonary oxidative stress, likely related to antioxidant depletion. Pulmonary oxidative stress may adversely affect innate immunity, leading to increased pneumonia susceptibility and severity, including development of the acute respiratory distress syndrome. In people with AUDs, most of whom smoke, antioxidant therapy can potentially restore immune cell function and attenuate pneumonia development. Challenges to human investigations of antioxidant therapies include an inability to identify pulmonary oxidative stress noninvasively and the optimal route to deliver pulmonary antioxidants. We sought to determine whether bronchoalveolar lavage (BAL) measures of thiol antioxidants from a 50‐ml upper airway aliquot approximated those in the alveolar space and to determine whether AUDs and/or smoking affected these relationships.

Methods

Healthy human subjects with and without AUDs, including smokers and nonsmokers, underwent BAL. Samples obtained after the first 50‐ml normal saline aliquot were analyzed as representing bronchial airways; subsequent 50‐ml aliquots were analyzed as representative of the alveolar space. Reduced and oxidized (GSSG) glutathione, cysteine (Cys), and its oxidized species, cystine, along with mixed disulfides (MDs) were quantified using high‐performance liquid chromatography. The percent of total thiols present in their oxidized forms, and thiol redox potentials, were calculated.

Results

Positive correlations between upper and lower BAL fluid thiol species were observed that were most robust for GSSG (ρ = 0.85), Cys (ρ = 0.83), and MDs (ρ = 0.69), but poor for thiol redox potential measures. In contrast to nonsmokers (either with or without AUDs), in subjects with AUDs who smoked, upper BAL fluid %GSSG, Cys, and MD measures were relatively increased compared to lower.

Conclusions

A small volume BAL procedure may be suitable to assess intrapulmonary oxidative stress related to thiol depletion. Factors including AUDs and smoking may disproportionately increase upper airways oxidative stress that could be relevant for therapeutic interventions.
Density‐dependent reproduction and pollen limitation in an invasive milkweed, Calotropis procera (Ait.) R. Br. (Apocynaceae)
Authors: Menge Enock O. , Greenfield Michele Lisa , McConchie Cameron A. , Bellairs Sean M. , Lawes Michael J.
Published: September 2016

Calotropis procera (Ait.) R.Br. (Apocynaceae), an invasive woody milkweed, has expanded its range in northern Australia affecting rangeland and pastoral productivity. While self‐compatibility should enhance the species range expansion, spread of C. procera is limited by the availability of larger wasp and bee species that are able to vector its solid pollinia. Pollination efficiency is thus likely dependent on both pollinator abundance and plant density. Calotropis procera flowers year round in Australia but fruiting is limited to the warm months of the year when pollinators are most abundant, indicating that seasonal regulation of reproduction may be due to pollinator limitation. We examine the propositions that C. procera reproduction is regulated by the interaction between plant population density and pollinator pressure and that low pollinator pressure causes low per capita plant fecundity. All pollinators belonged to Order Hymenoptera and pollinator composition was similar at six of the seven sites. Fruit production per plant (fecundity) was lower above and below intermediate densities (350–550 plants ha−1) of flowering plants with evidence of a weak Allee effect at lower plant density. Pollinator visitation rates per plant were low at high and low plant densities, and greatest at intermediate densities, while pollen supplementation experiments showed that C. procera is pollen limited (Pollen Limitation Indexfruit = 0.9) even at intermediate densities. Pollen limitation caused by low pollinator pressure at low plant densities and pollinator satiation at high plant densities may account for these fruit production trends. Management should be conducted in the colder months when pollinator pressure is low and plants are not reproducing. In addition, where stand eradication cannot be achieved in one attempt, management should reduce flowering plants to below intermediate densities where the fecundity per plant is low.