bluuebunny/crossref_metadata_2025 huggingface dataset:
Avoiding accuracy-limiting pitfalls in the study of protein-ligand interactions with isothermal titration calorimetry
Authors: Boyce Sarah E. , Tellinghuisen Joel , Chodera John D.
Published: August 2015

Isothermal titration calorimetry (ITC) can yield precise (3%) estimates of the thermodynamic parameters describing biomolecular association (affinity, enthalpy, and entropy), making it an indispensable tool for biochemistry and drug discovery. Surprisingly, interlaboratory comparisons suggest that errors of ∽ 20% are common and widely underreported. Here, we show how to reduce precision- and accuracy-limiting errors while obtaining good estimates and minimizing material and time consumed by an experiment. We provide a simple spreadsheet that allows practitioners to identify precision-limiting operations during protocol design, track precision during the experiment, and propagate error to yield realistic final uncertainties.
Species Tree Estimation from Genome-wide Data with Guenomu
Authors: Oliveira Martins Leonardo de , Posada David
Published: August 2015

The history of particular genes and that of the species that carry them can be different due to different reasons. In particular, gene trees and species trees can truly differ due to well-known evolutionary processes like gene duplication and loss, lateral gene transfer or incomplete lineage sorting. Different species tree reconstruction methods have been developed to take this incongruence into account, which can be divided grossly into supertree and supermatrix approaches. Here, we introduce a new Bayesian hierarchical model that we have recently developed and implemented in the program Guenomu, that considers multiple sources of gene tree/species tree disagreement. Guenomu takes as input the posterior distributions of unrooted gene tree topologies for multiple gene families, in order to estimate the posterior distribution of rooted species tree topologies.
D3M: Detection of differential distributions of methylation levels
Authors: Matsui Yusuke , Mizuta Masahiro , Miyano Satoru , Shimamura Teppei
Published: August 2015

Motivation:DNA methylation is an important epigenetic modification related to a variety of diseases including cancers. We focus on the methylation data from Illumina’s Infinium HumanMethylation450 BeadChip. One of the key issues of methylation analysis is to detect the differential methylation sites between case and control groups. Previous approaches describe data with simple summary statistics and kernel function, and then use statistical tests to determine the difference. However, a summary statistics-based approach cannot capture complicated underlying structure, and a kernel functions-based approach lacks interpretability of results.

Results:We propose a novel method D3M, for detection of differential distribution of methylation, based on distribution-valued data. Our method can detect high-order moments, such as shapes of underlying distributions in methylation profiles, based on the Wasserstein metric. We test the significance of the difference between case and control groups and provide an interpretable summary of the results. The simulation results show that the proposed method achieves promising accuracy and shows favorable results compared with previous methods. Glioblastoma multiforme and lower grade glioma data from The Cancer Genome Atlas show that our method supports recent biological advances and suggests new insights.

Availability:R implemented code is freely available from

https://github.com/ymatts/D3M/

https://cran.r-project.org/package=D3M.

Contact:ymatsui@med.nagoya-u.ac.jp
Genomic DNA transposition induced by human PGBD5
Authors: Henssen Anton G. , Henaff Elizabeth , Jiang Eileen , Eisenberg Amy R. , Carson Julianne R. , Villasante Camila M. , Ray Mondira , Still Eric , Burns Melissa , Gandara Jorge , Feschotte Cedric , Mason Christopher E. , Kentsis Alex
Published: August 2015

Transposons are mobile genetic elements that are found in nearly all organisms, including humans. Mobilization of DNA transposons by transposase enzymes can cause genomic rearrangements, but our knowledge of human genes derived from transposases is limited. Here, we find that the protein encoded by humanPGBD5, the most evolutionarily conserved transposable element-derived gene in chordates, can induce stereotypical cut-and-paste DNA transposition in human cells. Genomic integration activity of PGBD5 requires distinct aspartic acid residues in its transposase domain, and specific DNA sequences with inverted terminal repeats with similarity topiggyBactransposons. DNA transposition catalyzed by PGBD5 in human cells occurs genome-wide, with precise transposon excision and preference for insertion at TTAA sites. The apparent conservation of DNA transposition activity by PGBD5 raises the possibility that genomic remodeling may contribute to its biological function.
The impact of partitioning on phylogenomic accuracy
Authors: Darriba Diego , Posada David
Published: August 2015

Several strategies have been proposed to assign substitution models in phylogenomic datasets, or partitioning. The accuracy of these methods, and most importantly, their impact on phylogenetic estimation has not been thoroughly assessed using computer simulations. We simulated multiple partitioning scenarios to benchmark twoa prioripartitioning schemes (one model for the whole alignment, one model for each data block), and two statistical approaches (hierarchical clustering and greedy) implemented in PartitionFinder and in our new program, PartitionTest. Most methods were able to identify optimal partitioning schemes closely related to the true one. Greedy algorithms identified the true partitioning scheme more frequently than the clustering algorithms, but selected slightly less accurate partitioning schemes and tended to underestimate the number of partitions. PartitionTest was several times faster than PartitionFinder, with equal or better accuracy. Importantly, maximum likelihood phylogenetic inference was very robust to the partitioning scheme. Best-fit partitioning schemes resulted in optimal phylogenetic performance, without appreciable differences compared to the use of the true partitioning scheme. However, accurate trees were also obtained by a “simple” strategy consisting of assigning independent GTR+G models to each data block. On the contrary, leaving the data unpartitioned always diminished the quality of the trees inferred, to a greater or lesser extent depending on the simulated scenario. The analysis of empirical data confirmed these trends, although suggesting a stronger influence of the partitioning scheme. Overall, our results suggests that statistical partitioning, but also thea prioriassignment of independent GTR+G models, maximize phylogenomic performance.
Trait Evolution on Phylogenetic Networks
Authors: Jhwueng Dwueng-Chwuan , O’Meara Brian C.
Published: August 2015

Species may evolve on a reticulate network due to hybridization or other gene flow rather than on a strictly bifurcating tree, but comparative methods to deal with trait evolution on a network are lacking. We create such a method, which uses a Brownian motion model. Our method seeks to separately or jointly detect a bias in trait value coming from hybridization (β) and a burst of variation at the time of hybridization (vH) associated with the hybridization event, as well as traditional Brownian motion parameters of ancestral state (μ) and rate of evolution (σ2) of Brownian motion, as well as measurement error of the tips (SE). We test the method with extensive simulations. We also apply the model to two empirical examples, cichlid body size andNicotianadrought tolerance, and find substantial measurement error and a hint that hybrids have greater drought tolerance in the latter case. The new methods are available in CRAN R packageBMhyd.
Disentangling sources of selection on exonic transcriptional enhancers
Authors: Agoglia Rachel M. , Fraser Hunter B.
Published: August 2015

In addition to coding for proteins, exons can also impact transcription by encoding regulatory elements such as enhancers. It has been debated whether such features confer heightened selective constraint, or evolve neutrally. We have addressed this question by developing a new approach to disentangle the sources of selection acting on exonic enhancers, in which we model the evolutionary rates of every possible substitution as a function of their effects on both protein sequence and enhancer activity. In three exonic enhancers, we found no significant association between evolutionary rates and effects on enhancer activity. This suggests that despite having biochemical activity, these exonic enhancers have no detectable selective constraint, and thus are unlikely to play a major role in protein evolution.
Australian government budget balance numbers
Authors: Wines Graeme , Scarborough Helen
Published: August 2015

Purpose

– The purpose of this paper is to analyse the nature and comparability of budget balance (surplus/deficit) numbers headlined by the Australian Commonwealth Government and the governments of the six Australian States and the two Australian Territories. It does this in the context of the transition to Australian accounting standard AASB 1049 Whole of Government and General Government Sector Financial Reporting.

Design/methodology/approach

– A case study research method is adopted, based on a content/documentary analysis of the headline budget balance numbers in the general government sector budget statements of each of the nine governments for the eight financial years from 2004-2005 to 2011-2012.

Findings

– Findings indicate some variation in the measurement bases adopted and a number of departures from the measurement bases prescribed in the reporting frameworks, including AASB 1049. Findings also reveal that none of the nine governments have headlined a full accrual based budget balance number since the implementation of AASB 1049 in 2008.

Research limitations/implications

– While the study focuses on the Australian general government sector environment, it has significant implications in highlighting the ambiguity in the government budget balance numbers presented and the monitoring and information asymmetry problems that can arise. Research findings have wider relevance internationally in highlighting issues arising with the public sector adoption of accrual accounting.

Practical implications

– The paper highlights the manner in which governments have been selective in the manner in which they present important budget aggregates. This has important practical and social implications, as the budget balance number is one of the most important measures used to evaluate a government’s fiscal management and responsibility.

Originality/value

– The paper represents the first detailed examination of aspects of the effect of the transition to AASB 1049.
The effect of financial crisis on auditor conservatism: US evidence
Authors: Beams Joseph , Yan Yun-Chia
Published: August 2015

Purpose

– This paper aims to examine the effect that the recent financial crisis had on auditor conservatism in the form of increased going-concern opinions.

Design/methodology/approach

– This study uses a sample of US’ distressed firms from 2005 to 2011 to test the change in going-concern opinions issued. This paper uses a logistic regression model to control for other predictors of going-concern opinions to determine when the financial crisis led to an increase in auditor conservatism.

Findings

– The authors find that auditors became more conservative in the form of issuing higher levels of going-concern opinions even after controlling for other predictors of going-concern opinions. This increased conservatism was present in both Big 4 and non-Big 4 accounting firms. The increased conservatism quickly returned to normal levels when the financial crisis eased.

Originality/value

– These findings add to the literature on the effects of environmental changes on audit opinions. Additionally, this study finds a difference in the timing of the reaction by large and small accounting firms, but, overall, it finds consistency in that both increased conservatism during the crisis and quickly returned to normal afterward.
Embodied prejudices: a study on diversity and practices
Authors: Figueiredo Marina Dantas de
Published: August 2015

Purpose

– The purpose of this paper is to analyze organizational diversity with a focus on the concept of socially sustained practices, grounding the analyses in a practice-based approach.

Design/methodology/approach

– Based on data from ethnographic research, the author seeks to explain how the body and embodied marks that indicate an unequal distribution of power in society interfere with access to knowledge and in the organization of work.

Findings

– Data analyses suggest that embodied prejudices affect the division of labor and access to knowledge in organizational settings, contributing to perpetuating cultural and historical structures of domination that spark conscious attempts to manage race and gender diversity.

Originality/value

– Little research has investigated diversity from a practice-based standpoint. The originality of this paper is in its adoption of a phenomenological perspective to explain the experience of diversity as an ongoing bodily and embodied process.
Understanding context in diversity management: a multi-level analysis
Authors: Pringle Judith K. , Ryan Irene
Published: August 2015

Purpose

– The purpose of this paper is to operationalize context in diversity management research.

Design/methodology/approach

– A case analysis provides an example of the influences of context at macro, meso and micro levels. Country context (macro) and professional and organization contexts (meso) are analysed in relation to the micro individual experiences of gender and indigeneity at work.

Findings

– Tensions and inconsistencies at macro and meso levels impact on diversity management at a micro level. The authors demonstrate how power and context are intertwined in the biopolitical positioning of subjects in terms of gender and indigeneity. The contested legacy of indigenous-colonial relations and societal gender dynamics are “played out” in a case from the accounting profession.

Research limitations/implications

– Within critical diversity studies context and power are linked in a reciprocal relationship; analysis of both is mandatory to strengthen theory and practice. The multi-level analytical framework provides a useful tool to understand advances and lack of progress for diversity groups within specific organizations.

Originality/value

– While many diversity scholars agree that the analysis of context is important, hitherto its application has been vague. The authors conduct a multi-level analysis of context, connecting the power dynamics between the levels. The authors draw out implications within one profession in a specific country socio-politics. Multi-level analyses of context and power have the potential to enhance the theory and practice of diversity management.
Urbanization, tourism revenue growth and regional non-equilibrium
Authors: Guo Yang , Chai Yi , Wang Shengyang
Published: August 2015

Purpose

– The purpose of this paper is to analyze regional correlation contributions of urbanization rate and tourism revenue, based on the dynamic panel data from 2000 to 2010 of 31 provinces in China.

Design/methodology/approach

– Based on the Modified Cobb-Douglas and fixed effect regression models, the study analyzes the dynamic panel data of 31 provinces in China from 2000 to 2010. The paper conducts tests on the correlation and the economic influence between urbanization rate and tourism revenue in different regions.

Findings

– The empirical results show that on the national scale, the urbanization rate has a positive contribution to the increase rate of tourism revenue with 3.1 percent. The influence of urbanization on tourism revenue in different regions has considerable non-equilibrium characteristics. In the central region, the correlation contributing potential is even stronger than in the eastern and western regions. Different regions have significant regional disparities in the tourism growth pattern.

Originality/value

– On the national scale, the urbanization rate has a positive correlation contribution to the development of tourism economics. Urbanization has made remarkable achievements, and has played an important role in propelling the development of tourism industry. In the process of deepening the urbanization trend, the urbanization rate has a positive contribution to the increase rate of tourism revenue with 3.1 percent.
Gatekeepers of sustainability information: exploring the roles of accountants
Authors: Schaltegger Stefan , Zvezdov Dimitar
Published: August 2015

Purpose

– This paper aims to, with the continuous take-up of sustainability issues by companies and with the growing experience companies gain in dealing with this topic, raise the question of whether accountants are involved in the corporate practice of managing sustainability information, and if yes, what their role is. The actual involvement of accountants in corporate environmental and sustainability management has merely been investigated to date.

Design/methodology/approach

– Based on 58 in-depth interviews with corporate practitioners, this paper, first, explores the roles in the sustainability accounting practice in companies which are considered to be leading in sustainability reporting in the UK and Germany. Second, the role of accountants is analysed from a power theory perspective.

Findings

– The main findings suggest that accountants are partially involved in sustainability accounting practice but mainly exert a gate-keeping role between sustainability managers and higher management. The findings raise questions of how to better involve accountants in earlier steps of the sustainability management accounting process.

Research limitations/implications

– The explorative research is based on interviews in European companies considered to be among the leaders in sustainability reporting.

Practical implications

– Empirically investigating the role of accountants can help improve sustainability accounting practice and education. Should it turn out that the accountants have no other option but to act as gatekeepers, accounting education will play a major role in overcoming this deficiency in the pursuit of improved sustainability knowledge and performance. If, on the other hand, it is the defensive stance of accountants and the fear of losing power in corporate structures which motivates them to act as gatekeepers, mechanisms to motivate them to cooperate should be researched.

Social implications

– The paper empirically investigates and discusses the accountant’s contribution to sustainability information management. This can help overcome organisational challenges impeding companies to successfully implement sustainability measures.

Originality/value

– The paper investigates and discusses the accountant’s contribution to sustainability information management. The empirical analysis is based on a framework to identify different roles in sustainability accounting. Two possible development paths for a stronger constructive involvement of accountants are identified – to improve sustainability education for accountants if lack of sustainability knowledge is a major obstacle, and/or to improve incentives and structures motivating accountants to contribute with their information management expertise on all steps of the sustainability accounting process.
The Strengthening Families Programme in Spain: a long-term evaluation
Authors: Orte Carmen , Ballester Lluís , March Martí X. , Amer Joan , Vives Marga , Pozo Rosario
Published: August 2015

Purpose

– The purpose of this paper is to first assess the long-term effects of the adaptation of the American Strengthening Families Programme in Spain (known as the Programa de Competencia Familiar, translated into English as the Family Competence Programme (FCP)). The second aim is to identify family typologies and family changes regarding family competence over time. The paper’s initial hypothesis is that families have different behaviours and take advantage of the FCP in different ways.

Design/methodology/approach

– Monitored applications of the FCP were conducted using a quasi-experimental design consisting of a control group and pre-test, post-test and two-year follow-up assessments. The sample was made up of 136 families who took part in the programme and another 18 who participated in the control groups. Validated instruments were applied to assess the methodological processes and the family assessments. A cluster analysis was undertaken to identify different family typologies and their evolution in relation to the FCP goals.

Findings

– The FCP shows effective and consistent results over time for families in a variety of difficult situations, with important result maintenance. The longitudinal analysis (i.e. the two-year follow-up) demonstrates that the majority of changes identified (using the factors under consideration) maintained their relevance for most of the families, producing positive change.

Originality/value

– There is little long-term evaluation or longitudinal analysis of family prevention programmes that are evidence-based and include cognitive-emotional content. This paper analyses the long-term evaluation of family prevention programmes and identifies the ways in which families change over time.
Collaborative consumption: business model opportunities and barriers for fashion libraries
Authors: Pedersen Esben Rahbek Gjerdrum , Netter Sarah
Published: August 2015

Purpose

– The purpose of this paper is to explore barriers and opportunities for business models based on the ideas of collaborative consumption within the fashion industry.

Design/methodology/approach

– The analysis is based on a multiple-case study of Scandinavian fashion libraries – a new, clothes-sharing concept that has emerged as a fashion niche within the last decade.

Findings

– It is concluded that fashion libraries offers interesting perspectives, e.g. by allowing people to experiment with styles without having to pay the full cost and becoming a meeting place for young designers and end consumers. However, at present fashion libraries remain a small-scale phenomenon with difficulties reaching the mainstream market, not least due to limited financial and human resources as well as conventional fashion consumption patterns.

Research limitations/implications

– The study is limited to the new phenomenon of fashion libraries and does not cover other types of collaborative consumption within the fashion industry (Swap-parties, etc.).

Originality/value

– The paper is one of the first attempts to examine new business models of collaborative consumption in general and the fashion library concept in particular. The study contributes to the discussions of whether and how fashion sharing and collaboration holds promise as a viable business model and as a means to promote sustainability.
Human body as fashion space: fashion accessories, design and woven fabrics
Authors: Ribeiro Liliana Simões , Miguel Rui Alberto Lopes , Pereira Maria Madalena Rocha , Lucas José Mendes , Trindade Isabel Maria Gonçalves
Published: August 2015

Purpose

– Considering that the human body is undeniable a fashion space, the purpose of this paper is to highlight the importance of design and material choice in the relationship between clothing and accessories, namely, bags, for the fashion consumer.

Design/methodology/approach

– Initially the paper provides a historical framing of the use of materials in bags and its relation with clothing. Then, are described the characteristics of materials and how the human body relates to them, specifically how the sense of touch plays a decisive role in materials choice. Thus a natural fiber-based fabric as wool fabric is presented as a choice for some brands in the development of fashion accessories.

Findings

– It was found that there are an immense variety of materials that can be used in bags creation, and the use of them has changed over the years, influenced by social and economic conditions, fashion trends, and by technology evolutions in the production of fibers and composites. Taking in consideration that there is a long history of use of woven fabrics with natural fibers and a growing demand for sustainable and organic products, the use of wool natural fabrics in the production of bags were presented as a following road to the fashion industry.

Originality/value

– Since the relationship between materials used in apparel and fashion accessories is an area barely documented, this paper contributes to underline the possibility to exceed conventional design barriers and develop innovative and creative wool products pleasant for the human body as a fashion space.
The development of an apparel industry business model for Canada
Authors: Campaniaris Constantine , Murray Richard , Hayes Steven , Jeffrey Michael
Published: August 2015

Purpose

– Earlier attempts to develop a strategy for the apparel industry in Canada to counter the adverse effects of trade liberalisation on Canadian apparel suppliers have been based on the concept of clustering. However, despite the support from government-supported industry bodies, clustering has not been forthcoming and this situation has created a pressing need for the development of an alternative to the clustering strategy. A study by the Canadian Apparel Human Resources Council offered up several different strategies including clustering, that the Canadian apparel industry might pursue, but these have not been taken up. Evidence gained from government reports on the industry and its performance, industry case studies, an experience survey and questionnaire reported earlier, leads to a radically different alternative with a more direct relationship between Canadian apparel suppliers and retailer. The purpose of this paper is to report and construct an evidence-based collaborative strategy together with its accompanying apparel industry business model.

Design/methodology/approach

– The evidence gained from case studies of Canadian apparel businesses, a secondary data search, an experience survey and an online questionnaire has been followed and combined with retailer requirements from apparel suppliers.

Findings

– The information gained from apparel industry representatives, government sources and industry reports has enabled step-by-step construction of an evidence-based business model centred on the formation of collaborative partnerships between apparel suppliers and retailers.

Originality/value

– The model reflects the fact that Canadian apparel retailers have taken the leading role in the supplier/retailer relationship and shows how Canadian apparel suppliers might better position themselves to combat competition from offshore suppliers through the formation of closer links with retail partners. It points not only to a requirement for Canadian apparel suppliers to become integrated into their retail partner’s retail management systems and technology, but also demonstrates the need for the formation of strong alliances through collaborative partnerships between supplier and retailer to address the needs of the apparel market.
Clients’ means of influence on mortgage valuation in Nigeria
Authors: Nwuba Chukwuma C. , Egwuatu Uche S. , Salawu Babatunde M.
Published: August 2015

Purpose

– The purpose of this paper is to investigate client influence on mortgage valuation in Nigeria to establish and rank the means of influence clients employ, and the impact of firm characteristics on client influence.

Design/methodology/approach

– A combination of cross-sectional survey and focus groups research designs was adopted. Questionnaire structured on five-point Likert format was used to collect data from a sample of valuation firms in five Nigerian cities. Descriptive statistics,χ2, and moderated hierarchical linear model were used for data analysis.

Findings

– Clients’ means of influence on valuation are more of subtle approach than threat or coercion. The most prevalent means are respectively, plea for assistance, promise of continued retainership on banks’ valuer panels, and disclosing the loan amount. Client influence differs across cities; firm characteristics have no influence on client pressure.

Practical implications

– The research provides basis for valuation bodies to review practice rules and standards and seek for legislation for valuer independence. It can serve as material for teaching and training in professional ethics.

Social implications

– Biased valuations jeopardises credit risk mitigation process with potential for destabilising banks, finance sector, and consequences for the economy.

Originality/value

– The study provides empirical evidence of the nature of client influence across several major Nigerian cities. In contrast to existing Nigerian studies that focus on single cities, the study covers several cities. It therefore provides a broad basis for problem-solving and decision-making.
Examining the perception of tenants in sustainable office buildings
Authors: Jailani Junaidah , Reed Richard , James Kimberley
Published: August 2015

Purpose

– The purpose of this paper is to address two major challenges faced by sustainable building owners: first, address the gap between an occupant’s expectations of sustainable building outcomes and what the building actually provides and second, overcome the lack of user knowledge about sustainability design and operation for a particular with regards to performance.

Design/methodology/approach

– This study used a focus group approach to investigate the gap between: user expectations and sustainable building performance. The study surveyed occupants of sustainable office buildings in Melbourne, Australia.

Findings

– There is no significant relationship between users’ expectations and users’ experience of sustainable building performance and users’ knowledge about sustainability and the building they were worked in.

Research limitations/implications

– The research was limited to sustainable office buildings. New office buildings seeking to incorporate sustainability which need to focus on the needs of tenants in order to maximise value.

Practical implications

– There is an urgent need to ensure sustainable office buildings meet the needs of present and future occupiers without compromising short and long-term occupier satisfaction levels with regards to sustainability and operation of the building.

Social implications

– Increasing the level of sustainability in office buildings has been a major trend over the past decade however the tenants need to be consulted in the post-occupancy phase.

Originality/value

– Little attention has been given in the property management literature to sustainable office buildings and value drivers. This is an original and innovative study, partly due to the recent developments in sustainable buildings.
Spatial scale and movement behaviour traits control the impacts of habitat fragmentation on individual fitness
Authors: Cattarino Lorenzo , McAlpine Clive A. , Rhodes Jonathan R.
Published: August 2015

Habitat fragmentation, that is the breaking apart of habitat, can occur at multiple spatial scales at the same time, as a result of different land uses. Individuals of most species spend different amounts of times moving in different modes, during which they cover different distances and experience different fitness impacts. The scale at which fragmentation occurs interacts with the distance that individuals move in a particular mode to affect an individual's ability to find habitat. However, there is little knowledge of the fitness consequences of different scales of fragmentation for individuals with different traits of movement behaviour. This is critical to understand the mechanisms of persistence of different species in fragmented landscapes.

The aim of this study was to quantify the impacts of habitat fragmentation at different scales on the fitness components (reproduction and survival) of individuals with different traits of movement behaviour.

We developed a demographic model of individuals that adopt short and tortuous movements within foraging areas (foraging mode) and long and straight movements between foraging areas (searching mode). We considered individuals that adopt different movement modes with varying frequencies, inherently move different searching distances and experience different risks of mortality during searching. We then applied the model within a spatially explicit simulation framework where we varied simultaneously the degree of fragmentation within (fine scale) and between foraging areas (coarse scale).

Fine‐scale fragmentation had a greater impact on reproduction and survival than coarse‐scale fragmentation, for those individuals with a low searching propensity. The impact of fine‐scale fragmentation on reproduction and survival interacted with the impact of coarse‐scale fragmentation on reproduction and survival, to affect the fitness of individuals with a high searching propensity, large inherent searching distances and high searching mortality rates. Habitat selection strongly mitigated the impact of the scale at which fragmentation occurred on individual fitness.

Our findings suggest that the land use to target with conservation actions to reduce fragmentation, such as financial schemes that promote re‐vegetation or retention of standing vegetation, depends on the scale at which fragmentation occurs and the movement behaviour traits of the species of conservation concern.
Lotic cyprinid communities can be structured as nest webs and predicted by the stress‐gradient hypothesis
Authors: Peoples Brandon K. , Blanc Lori A. , Frimpong Emmanuel A.
Published: August 2015

Little is known about how positive biotic interactions structure animal communities. Nest association is a common reproductive facilitation in which associate species spawn in nests constructed by host species. Nest‐associative behaviour is nearly obligate for some species, but facultative for others; this can complicate interaction network topology.

Nest web diagrams can be used to depict interactions in nesting‐structured communities and generate predictions about those interactions, but have thus far only been applied to cavity‐nesting vertebrate communities. Likewise, the stress‐gradient hypothesis (SGH) predicts that prevalent biotic interactions shift from competition to facilitation as abiotic and biotic stress increase; this model has been hardly applied to animal communities. Here, both of these models were applied to nest‐associative fish communities and extended in novel ways to broaden their applicability.

A nest web was constructed using spawning observations over 3 years in several streams in south‐western Virginia, USA. Structural equation modelling (SEM) was then implemented through an information‐theoretic framework to identify the most plausible nest web topology in stream fish communities at 45 sites in the New River basin of the central Appalachian Mountains, USA. To test the SGH, the per‐nest reproductive success of ‘strong’ (nearly obligate) nest associates was used to represent interaction importance. Eigenvectors were extracted from a principal coordinate analysis (PCoA) of proportional species abundances to represent community structure. Both of these metrics were regressed on physical stress, a combination of catchment‐scale agricultural land use and stream size (representing spatiotemporal habitat variability).

Seventy‐one per cent of SEM model evidence supported a parsimonious interaction topology in which strong associates rely on a single host (Nocomis), but not other species. PCoA identified a gradient of community structure dominated by Nocomis and associates, to communities dominated by other reproductive groups. Both metrics of interaction importance responded positively to physical stress.

This study demonstrates that nest webs can be useful in a variety of systems and that SEM can be a quantitative extension of this framework. Likewise, the SGH can be used to understand positive interactions in animal communities and can be extended to predict proportional representation of facilitating and beneficiary species in communities.
Edge effects and geometric constraints: a landscape‐level empirical test
Authors: Ribeiro Suzy E. , Prevedello Jayme A. , Delciellos Ana Cláudia , Vieira Marcus Vinícius
Published: August 2015

Edge effects are pervasive in landscapes yet their causal mechanisms are still poorly understood. Traditionally, edge effects have been attributed to differences in habitat quality along the edge–interior gradient of habitat patches, under the assumption that no edge effects would occur if habitat quality was uniform. This assumption was questioned recently after the recognition that geometric constraints tend to reduce population abundances near the edges of habitat patches, the so‐called geometric edge effect (GEE).

Here, we present the first empirical, landscape‐level evaluation of the importance of theGEEin shaping abundance patterns in fragmented landscapes.

Using a data set on the distribution of small mammals across 18 forest fragments, we assessed whether the incorporation of theGEEinto the analysis changes the interpretation of edge effects and the degree to which predictions based on theGEEmatch observed responses. Quantitative predictions were generated for each fragment using simulations that took into account home range, density and matrix use for each species.

The incorporation of theGEEinto the analysis changed substantially the interpretation of overall observed edge responses at the landscape scale. Observed abundances alone would lead to the conclusion that the small mammals as a group have no consistent preference for forest edges or interiors and that the black‐eared opossumDidelphis aurita(a numerically dominant species in the community) has on average a preference for forest interiors. In contrast, incorporation of theGEEsuggested that the small mammal community as a whole has a preference for forest edges, whereasD. auritahas no preference for forest edges or interiors. Unexplained variance in edge responses was reduced by the incorporation ofGEE, but remained large, varying greatly on a fragment‐by‐fragment basis.

This study demonstrates how to model and incorporate theGEEin analyses of edge effects and that this incorporation is necessary to properly interpret edge effects in landscapes. It also suggests that geometric constraints alone are unlikely to explain the variability in edge responses of a same species among different areas, highlighting the need to incorporate other ecological factors into explanatory models of edge effects.
Alternative reproductive tactics in female striped mice: heavier females are more likely to breed solitarily than communally
Authors: Hill Davina L. , Pillay Neville , Schradin Carsten
Published: August 2015

Alternative reproductive tactics (ARTs) are discrete reproductive phenotypes governed by decision rules called strategies. ARTs are fixed for life in species with alternative strategies, while tactic expression is plastic in species with a single strategy. ARTs have been investigated in males of many species, but few studies have tested whether the same theoretical framework applies in females.

Female striped mice (Rhabdomys pumilio) employ three ARTs: communal breeders give birth in a nest shared with female kin and a breeding male and show allo‐parental care; returners give birth away from the shared nest and later return to it; and solitary breeders give birth away from the shared nest and do not return to the group.

Here, studying free‐living female striped mice over six breeding seasons, we tested whether ARTs arise from alternative strategies or a single strategy.

We also asked to what extent stochastic extrinsic factors explain whether individuals become solitary rather than group living.

Females switched tactics, consistent with a single strategy, so we tested whether this represented a mixed or conditional single strategy. Only the latter predicts differences between ARTs in traits indicating competitive ability, such as body mass or age, before individuals adopt a tactic. We weighed females at conception when they were still group living to eliminate potential confounding effects of gestation and subsequent social tactic (solitary versus group living) on body mass.

Females that went on to use a solitary ART were heavier than those that became communal breeders and returners, in support of a conditional strategy.

Solitary breeders also arose through extrinsic factors (mortality of all adult female group members). They weighed less than females that became solitary while relatives were alive, but did not differ in body mass from communal breeders and returners.

We conclude that ART theory applies to both sexes, with female striped mice following a conditional single strategy. Future studies should consider the possibility that phenotypes that superficially resemble evolved tactics might also arise through non‐adaptive extrinsic causes.
Separate effects of moisture content and water activity on the hyphal extension of Penicillium rubens on porous media
Authors: van Laarhoven Karel A. , Huinink Hendrik P. , Segers Frank J. J. , Dijksterhuis Jan , Adan Olaf C. G.
Published: August 2015

To prevent indoor fungal growth, understanding the moisture relations of fungi is a key element. Indoor moisture is quantified by the relative humidity (RH). RH controls the water activity of the indoor materials that fungi grow on, a well‐studied parameter known to limit fungal growth. RH, however, also controls the amount of water present in these materials, the moisture content. The significance of the moisture content of these materials to indoor fungal growth is currently overlooked. In the work reported here, growth experiments with the indoor fungus Penicillium rubens on gypsum substrates were performed to test whether the moisture content influences growth on porous materials. Second, we report the development of a video microscopy method that for the first time quantified hyphal growth on a porous material. It is found that a higher moisture content leads to earlier colonization and higher hyphal extension rates. This is a fundamental step in unravelling the effect of RH on indoor fungal growth. The real‐time monitoring of colonization of gypsum provides a new view of growth on indoor surfaces.
Dissatisfied Citizens: An Asset to or a Liability on the Democratic Functioning of Society?
Authors: Abdelzadeh Ali , Özdemir Metin , Van Zalk Maarten
Published: August 2015

Past research has shown that, although a majority of citizens in democracies support the idea of democracy as a form of governance, some tend to be distrustful of democratic institutions and express dissatisfaction with the way democracy works. It is argued in this article that to better understand the role of various groups of dissatisfied citizens in the democratic functioning of a society, one should examine their democratic characteristics. Based on youth's dissatisfaction with the performance of political institutions and the principles of democracy, four distinct groups of citizens are identified. These groups are then compared in terms of their political engagement, knowledge and interest, values and attitudes, and disposition to break the law. The results showed that youths with high levels of principle‐ and performance‐driven dissatisfaction were less likely to participate in politics, less knowledgeable and interested in political issues, and more likely to break the law, even if people got hurt compared with other groups. In contrast, youths who were only dissatisfied with the performance of democratic institutions were more likely to participate in politics, and had higher tolerance towards immigrants, and political interest and knowledge. They were also more likely, peacefully and without harming other people, to break the law to change society. Overall, by examining distinct groups of dissatisfied citizens and their democratic characteristics, this study contributes to the general debate on the role of dissatisfied citizens in democracies.
Frames of Public Reactions in Crisis
Authors: Nilsson Sofia , Alvinius Aida , Enander Ann
Published: August 2015

The aim of this study was to identify and analyze the ways in which images and reactions of the public are described and framed in media articles and reports. Reporting from six major events affecting the Swedish public was studied using a thematic method of analysis. The results show three dynamic interrelated processes at work simultaneously in framing the public: identification, characterization and evaluation. A significant contribution of this study is the emphasis on how this often subtle and implicit framing influences the portrayal of human reactions, thus possibly influencing the expectations and evaluations of both the public in general and crisis managers in particular.
Benchmarking Outpatient Rehabilitation Clinics Using Functional Status Outcomes
Authors: Gozalo Pedro L. , Resnik Linda J. , Silver Benjamin
Published: August 2015

Objective

To utilize functional status (FS) outcomes to benchmark outpatient therapy clinics.

Data Sources

Outpatient therapy data from clinics using Focus on Therapeutic Outcomes (FOTO) assessments.

Study Design

Retrospective analysis of 538 clinics, involving 2,040 therapists and 90,392 patients admitted July 2006–June 2008. FS at discharge was modeled using hierarchical regression methods with patients nested within therapists within clinics. Separate models were estimated for all patients, for those with lumbar, and for those with shoulder impairments. All models risk‐adjusted for intake FS, age, gender, onset, surgery count, functional comorbidity index, fear‐avoidance level, and payer type. Inverse probability weighting adjusted for censoring.

Data Collection Methods

Functional status was captured using computer adaptive testing at intake and at discharge.

Principal Findings

Clinic and therapist effects explained 11.6 percent of variation in FS. Clinics ranked in the lowest quartile had significantly different outcomes than those in the highest quartile (p < .01). Clinics ranked similarly in lumbar and shoulder impairments (correlation = 0.54), but some clinics ranked in the highest quintile for one condition and in the lowest for the other.

Conclusions

Benchmarking models based on validated FS measures clearly separated high‐quality from low‐quality clinics, and they could be used to inform value‐based‐payment policies.
Decomposition Rate and Pattern in Hanging Pigs
Authors: Lynch‐Aird Jeanne , Moffatt Colin , Simmons Tal
Published: August 2015

Accurate prediction of the postmortem interval requires an understanding of the decomposition process and the factors acting upon it. A controlled experiment, over 60 days at an outdoor site in the northwest of England, used 20 freshly killed pigs (Sus scrofa) as human analogues to study decomposition rate and pattern. Ten pigs were hung off the ground and ten placed on the surface. Observed differences in the decomposition pattern required a new decomposition scoring scale to be produced for the hanging pigs to enable comparisons with the surface pigs. The difference in the rate of decomposition between hanging and surface pigs was statistically significant (p = 0.001). Hanging pigs reached advanced decomposition stages sooner, but lagged behind during the early stages. This delay is believed to result from lower variety and quantity of insects, due to restricted beetle access to the aerial carcass, and/or writhing maggots falling from the carcass.