bluuebunny/crossref_metadata_2025 huggingface dataset:
KRAS Mutation Is a Significant Prognostic Factor in Early-stage Lung Adenocarcinoma
Authors: Kadota Kyuichi , Sima Camelia S. , Arcila Maria E. , Hedvat Cyrus , Kris Mark G. , Jones David R. , Adusumilli Prasad S. , Travis William D.
Published: October 2016

The potential clinical impact of KRAS and epidermal growth factor receptor (EGFR) mutations has been investigated in lung adenocarcinomas; however, their prognostic value remains controversial. In our study, we sought to investigate the prognostic significance of driver mutations using a large cohort of early-stage lung adenocarcinomas. We reviewed patients with pathologic early-stage, lymph node–negative, solitary lung adenocarcinoma who had undergone surgical resection (1995 to 2005; stage I/II=463/19). Tumors were classified according to the IASLC/ATS/ERS classification and genotyped by Sequenom MassARRAY system and polymerase chain reaction–based assays. In stage I disease, the Kaplan-Meier method and cumulative incidence of recurrence analyses were used to estimate the probability of overall survival (OS) and recurrence, respectively. Of all, 129 (27%) patients had mutations in KRAS, 86 (18%) in EGFR, 8 (2%) in BRAF, 8 (2%) in PIK3CA, 4 (1%) in NRAS, and 1 (0.2%) in AKT1. EGFR L858R mutation correlated with lepidic predominant histology (P=0.006), whereas exon 19 deletion correlated with acinar predominant histology (P<0.001). EGFR mutations were not detected in invasive mucinous adenocarcinomas (P=0.033). The 5-year OS of patients with KRAS-mutant tumors was significantly worse (n=124; 5-year OS, 63%) than those with KRAS wild-type (n=339; 77%; P<0.001). In solid predominant tumors, KRAS mutations correlated with worse OS (P=0.008) and increased risk of recurrence (P=0.005). On multivariate analysis, KRAS mutation was an independent prognosticator of OS in all patients (hazard ratio, 1.87; P<0.001) and recurrence in solid predominant tumors (hazard ratio, 4.73; P=0.012). In patients with resected stage I lung adenocarcinomas, KRAS mutation was an independent prognostic factor for OS and recurrence, especially in solid predominant tumors.
A Prospective Study of Renal Transplant Recipients: A Fall in Insulin Secretion Underpins Dysglycemia After Renal Transplantation
Authors: Langsford David , Obeyesekere Varuni , Vogrin Sara , Teng Jessie , MacIsaac Richard J. , Ward Glenn , Alford Frank , Dwyer Karen M.
Published: October 2016

Background

Dysglycemia (encompassing impaired glucose tolerance and diabetes mellitus) arising after renal transplantation is common and confers a significant cardiovascular mortality risk. Nonetheless, the pathophysiology of posttransplant dysglycemia is not well described. The aim of this study was to prospectively and comprehensively assess glucose handling in renal transplant recipients from before to 12 months after transplantation to determine the underpinning pathophysiology.

Materials and Methods

Intravenous and oral glucose tolerance testing was conducted before and at 3 and 12 months posttransplantation. An intravenous glucose tolerance test was also performed on day 7 posttransplantation. We followed up 16 transplant recipients for 3 months and 14 recipients for 12 months. Insulin secretion, resistance and a disposition index (DI (IV)), a measure of β cell responsiveness in the context of prevailing insulin resistance, were also determined.

Results

At 12 months, 50% of renal transplant recipients had dysglycemia. Dysglycemia was associated with a dramatic fall in DI (IV) and this loss in β cell function was evident as early as 3 months posttransplantation (23.5 pretransplant; 6.4 at 3 months and 12.2 at 12 months posttransplant). Differences in the β cell response to oral glucose challenge were evident pretransplant in those destined to develop dysglycemia posttransplant (2-hour blood glucose level 5.6 mmol/L versus 6.8 mmol/L; P < 0.01).

Conclusions

Dysglycemia after renal transplantation is common, and the loss of insulin secretion is a major contributor. Subclinical differences in glucose handling are evident pretransplant in those destined to develop dysglycemia potentially heralding a susceptible β cell which under the stressors associated with transplantation fails.
Rapid Floral and Pitcher Scent Diversification in Carnivorous Pitcher Plants (Sarraceniaceae)
Authors: Ho Winnie W. , Nathan Kutz J. , Ng Julienne , Riffell Jeffrey A.
Published: October 2016

Plant volatiles play vital roles in signaling with their insect associates. Empirical studies show that both pollinators and herbivores exert strong selective pressures on plant phenotypes. While studies often evoke the assumption that volatiles from floral and vegetative tissues are distinct due to strong pollinator-mediated selection operating on the flowers or selection from herbivores acting on the leaves, explicit tests of these assumptions are often lacking. In this study, we examined the evolution of floral and vegetative volatiles in the North American (NA) pitcher plants (Sarraceniaceae). In these taxa, insects are attracted for both pollination and prey capture, providing an ideal opportunity to understand the evolution of scent compounds across different plant organs. We collected a comprehensive dataset of floral and vegetative volatiles from across the NA Sarraceniaceae. We used multivariate analysis methods to examine whether volatile profiles are distinct between plant tissues, and investigated rates of scent evolution in these unique taxa. Our major findings revealed that (i) flowers and pitchers produced highly distinct scent profiles, consistent with the hypothesis that volatiles alleviate trade-offs due to incidental pollinator consumption; (ii) across species, floral scent separated into distinct regions of scent space, while pitchers showed little evidence of clustering – this may be due to convergence on a generalist strategy for insect capture; and (iii) rates of scent evolution depended on tissue type, suggesting that pollinators and herbivores differentially influence the evolution of chemical traits. We emphasize the need for additional functional studies to further distinguish between volatile functions.
A roadmap for a quantitative ecosystem-based environmental impact assessment
Authors: Coston-Guarini J. , Guarini J-M , Edmunds J. , Hinz Shawn , Wilson Jeff , Chauvaud L.
Published: October 2016

A new roadmap for quantitative methodologies of Environmental Impact Assessment (EIA) is proposed, using an ecosystem-based approach. EIA recommendations are currently based on case-by-case rankings, distant from statistical methodologies, and based on ecological ideas that lack proof of generality or predictive capacities. These qualitative approaches ignore process dynamics, scales of variations and interdependencies and are unable to address societal demands to link socio-economic and ecological processes (e.g.population dynamics). We propose to re-focus EIA around the systemic formulation of interactions between organisms (organized in populations and communities) and their environments but inserted within a strict statistical framework. A systemic formulation allows scenarios to be built that simulate impacts on chosen receptors. To illustrate the approach, we design a minimum ecosystem model that demonstrates non-trivial effects and complex responses to environmental changes. We suggest further that an Ecosystem-Based EIA - in which the socio-economic system is an evolving driver of the ecological one - is more promising than a socio-economic-ecological system where all variables are treated as equal. This refocuses the debate on cause-and-effect, processes, identification of essential portable variables, and a potential for quantitative comparisons between projects, which is important in cumulative effects determinations.
De novo assembly of viral quasispecies using overlap graphs
Authors: Baaijens Jasmijn A. , Zine El Aabidine Amal , Rivals Eric , Schönhuth Alexander
Published: October 2016

A viral quasispecies, the ensemble of viral strains populating an infected person, can be highly diverse. For optimal assessment of virulence, pathogenesis and therapy selection, determining the haplotypes of the individual strains can play a key role. As many viruses are subject to high mutation and recombination rates, high-quality reference genomes are often not available at the time of a new disease outbreak. We present SAVAGE, a computational tool for reconstructing individual haplotypes of intrahost virus strains without the need for a high-quality reference genome. SAVAGE makes use of either FM-index based data structures or ad-hoc consensus reference sequence for constructing overlap graphs from patient sample data. In this overlap graph, nodes represent reads and/or contigs, while edges reflect that two reads/contigs, based on sound statistical considerations, represent identical haplotypic sequence. Following an iterative scheme, a new overlap assembly algorithm that is based on the enumeration of statistically well-calibrated groups of reads/contigs then efficiently reconstructs the individual haplotypes from this overlap graph. In benchmark experiments on simulated and on real deep coverage data, SAV-AGE drastically outperforms generic de novo assemblers as well as the only specialized de novo viral quasispecies assembler available so far. When run on ad-hoc consensus reference sequence, SAVAGE performs very favorably in comparison with state-of-the-art reference genome guided tools. We also apply SAVAGE on two deep coverage samples of patients infected by the Zika and the hepatitis C virus, respectively, which sheds light on the genetic structures of the respective viral quasispecies.
Analysis of noise mechanisms in cell size control
Authors: Modi Saurabh , Vargas-Garcia Cesar A. , Ghusinga Khem Raj , Singh Abhyudai
Published: October 2016

At the single-cell level, noise features in multiple ways through the inherent stochasticity of biomolecular processes, random partitioning of resources at division, and fluctuations in cellular growth rates. How these diverse noise mechanisms combine to drive variations in cell size within an isoclonal population is not well understood. To address this problem, we systematically investigate the contributions of different noise sources in well-known paradigms of cell-size control, such as the adder (division occurs after adding a fixed size from birth) and the sizer (division occurs upon reaching a size threshold). Analysis reveals that variance in cell size is most sensitive to errors in partitioning of volume among daughter cells, and not surprisingly, this process is well regulated among microbes. Moreover, depending on the dominant noise mechanism, different size control strategies (or a combination of them) provide efficient buffering of intercellular size variations. We further explore mixer models of size control, where a timer phase precedes/follows an adder, as has been proposed inCaulobacter crescentus. While mixing a timer with an adder can sometimes attenuate size variations, it invariably leads to higher-order moments growing unboundedly over time. This results in the cell size following a power-law distribution with an exponent that is inversely dependent on the noise in the timer phase. Consistent with theory, we find evidence of power-law statistics in the tail ofC. crescentuscell-size distribution, but there is a huge discrepancy in the power-law exponent as estimated from data and theory. However, the discrepancy is removed after data reveals that the size added by individual newborns from birth to division itself exhibits power-law statistics. Taken together, this study provides key insights into the role of noise mechanisms in size homeostasis, and suggests an inextricable link between timer-based models of size control and heavy-tailed cell size distributions.
Functional analysis of a biosynthetic cluster essential for production of 4-formylaminooxyvinylglycine, a germination-arrest factor fromPseudomonas fluorescensWH6
Authors: Okrent Rachel A. , Trippe Kristin M. , Maselko Maciej , Manning Viola
Published: October 2016

Rhizosphere-associatedPseudomonas fluorescensWH6 produces the germination-arrest factor, 4-formylaminooxyvinylglycine (FVG). FVG has previously been shown to both arrest the germination of weedy grasses and to inhibit the growth of the bacterial plant pathogenErwinia amylovora.Very little is known about the mechanism by which FVG is produced. Although a previous study identified a region of the genome that may be involved in FVG biosynthesis, it has not yet been determined which genes within that region are sufficient and necessary for FVG production. In the current study, we explored the role of each of the putative genes encoded in that region by constructing deletion mutations. Mutant strains were assayed for their ability to produce FVG with a combination of biological assays and thin-layer chromatographic analyses. This work defined the core FVG biosynthetic gene cluster and revealed several interesting characteristics of FVG production. We determined that FVG biosynthesis requires two small open reading frames of less than 150 nucleotides and that multiple transporters have overlapping but distinct functionality. In addition, two genes in the center of the biosynthetic gene cluster are not required for FVG production, suggesting that additional products may be produced from the cluster. Transcriptional analysis indicated that at least three active promoters play a role in the expression of genes within this cluster. The results of this study enrich our knowledge regarding the diversity of mechanisms by which bacteria produce non-proteinogenic amino acids like vinylglycines.
Focal cortical seizures start as standing waves and propagate respecting homotopic connectivity
Authors: Rossi L Federico , Wykes Robert C , Kullmann Dimitri M , Carandini Matteo
Published: October 2016

Focal epilepsy involves excessive cortical activity that propagates both locally and distally. Does this propagation follow the same routes as normal cortical activity? We pharmacologically induced focal seizures in primary visual cortex (V1) of awake mice, and compared their propagation to the retinotopic organization of V1 and higher visual areas. We used simultaneous local field potential recordings and widefield imaging of a genetically encoded calcium indicator to measure prolonged seizures (ictal events) and brief interictal events. Both types of event are orders of magnitude larger than normal visual responses, and both start as standing waves: synchronous elevated activity in the V1 focus and in homotopic locations in higher areas, i.e. locations with matching retinotopic preference. Following this common beginning, however, seizures persist and propagate both locally and into homotopic distal regions, and eventually invade all of visual cortex and beyond. We conclude that seizure initiation resembles the initiation of interictal events, and seizure propagation respects the connectivity underlying normal visual processing.
Rethinking Skinner’s model: strategic trade-offs in products and services
Authors: Sarmiento Roberto , Thurer Matthias , Whelan Garvan
Published: October 2016

Purpose

The purpose of this paper is to further clarify the link between the theoretical and practical/real-life implications of a seminal topic in the strategic operations management field: Wickham Skinner’s strategic trade-offs model. This will help researchers, practitioners and students to realize the “everyday life” consequences of this highly influential model.

Design/methodology/approach

A theoretical analysis is made of previous research dealing with the strategic trade-offs model. Building on these investigations, a Popperian approach is used to logically develop the model, and the authors demonstrate how it can be empirically tested.

Findings

Previous investigations on Skinner’s model mainly focus on trade-offs between competitive capabilities (e.g. cost, quality, delivery) at the firm level. This paper demonstrates that the implications of this model necessarily should include consideration of the strategic trade-offs between the competitive characteristics of products/services that practitioners, students and the general public can observe.

Originality/value

While previous investigations have provided necessary clarifications, no paper has addressed the issue of the existence of strategic trade-offs between the competitive characteristics of products/services. This paper offers guidelines for researchers and practitioners on the way that the strategic trade-offs model can be conceptualized, understood and tested.
Enhancing learning effectiveness by adopting a knowledge-based usability guidelines
Authors: Chin Sylvia Ping-Ping , Tsui Eric , Lee Chien-Sing
Published: October 2016

Purpose

– Guidelines for the design of knowledge-based e-learning usability systems are absent from the current recognized set of usability design heuristics and from an established evaluation methodology of e-learning system developments. Such systems can help Web designers and instructional designers design for different user needs and decide which properties are of a higher priority, thus meriting more design and development efforts. The authors aim to help students develop higher-order thinking skills, such as application, evaluation and syntheses of knowledge.

Design/methodology/approach

– The authors applied Merrill
'
s first principles of instruction and usability properties as pedagogical and usability design guidelines, knowledge management (KM) and hierarchical task analysis as methodological knowledge bases. The authors proposed a KM e-learning usability framework which frames our mapping of Web usability attributes to e-learning usability properties. The authors aim to investigate whether adopting Merrill
'
s first principles of instruction and usability properties as knowledge-based guidelines/design factors would help learners develop higher-order thinking skills and whether this design would result in positive technology acceptance. The authors also developed a method matrix to map the selected methods of cognitive engineering to its potential uses in the KM e-learning usability framework of this paper and mapped e-learning usability tools with components in the KM e-learning usability system.

Findings

– Findings indicated that our design effectively helped learners to demonstrate higher-order thinking skills and positive technology acceptance, promising indications toward the design and development of knowledge-based usability frameworks and systems.

Research/limitations/implications

– The sample size of this paper is small. Hence, conclusions are not generalizable at this moment.

Originality/Value

– The authors’ contributions are twofold: First, the authors proposed a KM e-learning usability framework, which frames the mapping of KM processes to e-learning principles and usability properties. Second, the authors proposed a method matrix which maps the selected methods of cognitive engineering to its potential uses in their KM e-learning usability framework. Based on these mappings and focusing on the usability properties navigation and learning support, the authors used ICT/Web2.0 tools to present/visualize information more clearly and more sensibly/manageably to students, to help trigger new knowledge and develop higher-order thinking skills, such as application, evaluation and syntheses of knowledge and articulate information from different perspectives throughout the KM life cycle.
Organizational performance through the donation and collection of interorganizational knowledge
Authors: Nodari Felipe , Oliveira Mirian , Maçada Antonio Carlos Gastaud
Published: October 2016

Purpose

– This paper aims to provide empirical evidence to support the relationship between interorganizational knowledge sharing, absorptive capacity and organizational performance, and proposes that interorganizational knowledge sharing is composed of two processes: knowledge donation and collection.

Design/methodology/approach

– A quantitative methodology is adopted to examine the proposed relationship between interorganizational knowledge sharing, absorptive capacity and organizational performance. The study uses survey data from 269 companies in Brazil. Structural equation modeling is applied to test the stated hypotheses and the model.

Findings

– The empirical findings indicate that interorganizational knowledge sharing is composed of the donation and collection of knowledge. Interorganizational knowledge collection is found to have a positive effect on interorganizational knowledge donation, while collection is found to have a positive effect, mediated by absorptive capacity, on organizational performance.

Research limitations/implications

– One limitation of this research was the predominant participation of smaller companies. Another is that the data were only collected from Brazilian companies. Moreover, an instrument to measure these constructs was proposed and validated to enable future research to be conducted into the process of interorganizational knowledge sharing and its components: knowledge donation and knowledge collection.

Practical implications

– Managers can enhance organizational performance by developing both the donation and collection of knowledge. Knowledge donation is particularly important because, in addition to its impact on absorptive capacity and organizational performance, it contributes to the development of knowledge collection, which is also indirectly related to performance.

Originality value

– The donation and collection of knowledge were validated as components of the interorganizational knowledge-sharing process, and the relationship between these processes and organizational performance is mediated by the absorptive capacity of the organization.
Prioritizing lean practices for implementation in IT support services
Authors: Kundu Goutam Kumar , Manohar Murali
Published: October 2016

Purpose

– The purpose of this study is to capture the perception of the IT support service practitioners regarding the applicability of the lean practices and prioritize them after analyzing the gaps with respect to current usage and importance from practitioners’ perspective.

Design/methodology/approach

– It involved development of an instrument to capture the perceptions of the IT support service practitioners. The data collected was quantitatively analyzed by using statistical techniques and it involved testing of the hypotheses.

Findings

– The study conducted a gap analysis on the perceived current usage of the lean practices versus the perceived ideal usages of the lean practices from practitioners’ perspective. The gap analysis report revealed that gaps of all practices are not same from the practitioners’ viewpoint. This gap analysis was useful for prioritizing of the practices and resource allocation.

Originality/value

– This study was conducted in a relatively new domain, where mature empirically based studies are scarce. This study set out to determine the practitioners’ perception of the applicability of lean practices in IT support service organizations. It provides a sound basis for further research on lean implementation in IT support service area.
Efficacy and safety of ixekizumab treatment for Japanese patients with moderate to severe plaque psoriasis, erythrodermic psoriasis and generalized pustular psoriasis: Results from a 52‐week, open‐label, phase 3 study (UNCOVER‐J)
Authors: Saeki Hidehisa , Nakagawa Hidemi , Nakajo Ko , Ishii Taeko , Morisaki Yoji , Aoki Takehiro , Cameron Gregory S. , Osuntokun Olawale O. ,   the Japanese Ixekizumab Study Group
Published: October 2016

Psoriasis, a chronic, immune‐mediated skin disease characterized by red, scaly plaques, affects approximately 0.3% of the population in Japan. The aim of this open‐label study was to evaluate the long‐term efficacy and safety of ixekizumab, a humanized, anti‐interleukin‐17A monoclonal antibody, in Japanese patients with plaque psoriasis (n = 78, including 11 psoriatic arthritis), erythrodermic psoriasis (n = 8) and generalized pustular psoriasis (n = 5). Ixekizumab was administrated s.c. at baseline (week 0, 160 mg), from weeks 2 to 12 (80 mg every 2 weeks), and from weeks 16 to 52 (80 mg every 4 weeks). At week 52, 92.3% of patients with plaque psoriasis achieved Psoriasis Area and Severity Index (PASI) 75, 80.8% achieved PASI 90, 48.7% achieved PASI 100, and 52.6% had remission of plaques (by static Physician Global Assessment, sPGA [0]). Difficult to treat areas of psoriasis (nail or scalp) also responded to ixekizumab. All patients with psoriatic arthritis who were assessed (5/5) achieved an American College of Rheumatology 20 response. Most patients with erythrodermic psoriasis or generalized pustular psoriasis responded to ixekizumab and the clinical outcome was maintained over 52 weeks (75% and 60% of patients achieved sPGA [0, 1] at week 52, respectively). Mostly mild or moderate treatment‐emergent adverse events were reported by 79 of 91 patients; the most common were nasopharyngitis, eczema, seborrheic dermatitis, urticaria and injection site reactions. In conclusion, 52‐week ixekizumab treatment was efficacious and well tolerated in Japanese patients with plaque psoriasis. Efficacy was also observed in patients with erythrodermic psoriasis, generalized pustular psoriasis and psoriatic arthritis.
Metabolic rates, and not hormone levels, are a likely mediator of between‐individual differences in behaviour: a meta‐analysis
Authors: Holtmann Benedikt , Lagisz Malgorzata , Nakagawa Shinichi
Published: October 2016

Consistent individual differences in hormone levels and metabolic rates have been proposed to be potential state variables underlying consistent individual differences in behaviour (i.e. animal personality). However, it remains unclear whether either one alone or both of these potential state variables could be an underlying driver of animal personality.

We address this question using meta‐analyses of published data from bird species. We hypothesized that state variables that mediate individual differences in behaviour would display similar or higher repeatability estimates than behavioural traits. To test this hypothesis, we quantified repeatability estimates of hormone levels, metabolic rates and behavioural traits.

We found moderate to high mean repeatability estimates for both metabolic rates and behavioural traits, but low repeatability estimates for hormone levels. These findings indicate that metabolic rates likely represent an important mechanism for generating adaptive personality differences in behaviour.

We also show that: (i) for hormones and behaviour, repeatability decreased with increasing interval time between two measurements; (ii) males and females differed in repeatability for behavioural traits; (iii) stress‐induced hormone levels were more repeatable than baseline levels.

Future studies are now required to determine the direction of the association between metabolic rates and behavioural traits. At the same time, these studies should try to investigate which of the proposed mechanisms is responsible for the relationship between state variable and state‐dependent behaviour.

In addition, we encourage researchers to report the coefficient of variation for between‐individual variance (CVB) along with repeatability estimates because these two indices carry different information. We discuss how CVB may better facilitate future comparative studies, including meta‐analyses.

A lay summary is available for this article.
Aphid as a network creator for the plant‐associated arthropod community and its consequence for plant reproductive success
Authors: Ando Yoshino , Utsumi Shunsuke , Ohgushi Takayuki
Published: October 2016

Ecological communities consist of antagonistic and mutualistic interactions that can vary in their strength. Indirect effects act among species within or across trophic levels through multiple pathways in an interaction network. Although there are many studies showing indirect effects in ecological communities, we know little about how indirect effects impact the wider community by linking other direct and indirect interactions.

Herbivore‐induced indirect effects are ubiquitous and powerful forces in structuring ecological communities. In a plant‐associated network, aphids have the potential to connect multiple interactions through ant‐ and plant‐mediated indirect effects on co‐occurring and/or temporally separated species.

We examined how aphids affect the interaction network on tall goldenrod, Solidago altissima, based on data of arthropod species on it with and without the aphid, Uroleucon nigrotuberculatum, using structural equation modelling (SEM) analysis.

The presence of aphids greatly changed the strength of several species interactions throughout the season. In the early season, aphids had negative indirect effects on leafhoppers and moth caterpillars through ants. On the other hand, aphid‐induced leaf regrowth decreased scale insects but increased grasshoppers in the late season, when the aphid was no longer present. Moreover, the aphid‐generated interactions increased seed production of tall goldenrods, due to indirect pathways through the leaf regrowth.

The aphid thus played a critical role as a network creator in determining the interaction network by generating ant‐ and plant‐mediated indirect effects. In particular, the aphid‐induced leaf regrowth contributed to interaction diversity (i.e. total number of positive/negative interactions and link density per each species) by connecting arthropod species in the early and late seasons.

We disentangled the complexity of direct and indirect pathways generated by the aphid (i.e. keystone herbivore), which largely determines community structure of associated arthropods and plant reproductive success. Our study combining ant‐ and plant‐mediated indirect interactions mediated by the aphid provides a basis of better understanding of the underlying mechanisms of how the impact of the keystone herbivore can spread through plant‐based insect networks via direct and indirect pathways.

A lay summary is available for this article.
Linear reaction norms of thermal limits in Drosophila: predictable plasticity in cold but not in heat tolerance
Authors: Schou Mads Fristrup , Mouridsen Marie Brandt , Sørensen Jesper Givskov , Loeschcke Volker
Published: October 2016

Thermal limits of ectotherms have been studied extensively and are believed to be evolutionarily constrained, leaving ectotherms at risk under future climate change. Phenotypic plasticity may extend the thermal limits, but we lack detailed characterizations of thermal limit reaction norms as well as an understanding of the interspecific variation in these reaction norms.

Here, we investigated the interspecific variation in phenotypic plasticity of thermal limits in 13 Drosophila species. We obtained high‐resolution reaction norms for upper and lower thermal limits across the permissive developmental thermal range (12·5–30 °C). The estimated phenotypes were then associated (while accounting for phylogeny) with climatic parameters from the species’ distributional range.

All species showed linear reaction norms for cold tolerance (CTmin) and heat tolerance (CTmax) across developmental acclimation temperatures. We observed strong beneficial cold acclimation to lower temperatures in all species. Conversely, the heat acclimation response was non‐existent in some species, and decreasing or increasing with increasing developmental acclimation temperatures in other species. The degree of phenotypic plasticity of CTmin and CTmax was related neither to the basal thermal limits (trade‐off hypothesis) nor to climatic parameters connected to latitudinal distributions (latitudinal hypothesis).

A substantial and linear developmental plasticity of lower thermal limits is a general characteristic of Drosophila species, which allows for straightforward application in species distribution models. In general, upper thermal limits also show linear norms of reaction, but their adaptive significance is limited and highly variable among species, making general predictions across species rather impossible.

High‐resolution estimates of norms of reaction of thermal limits can considerably increase our understanding of the capacity of ectotherms to acclimate to different thermal environments. However, our understanding of the environmental drivers of the evolution of phenotypic plasticity and thus of the interspecific differences remains ambiguous, potentially constrained by limited microclimate information.

A lay summary is available for this article.
The specialization continuum in pollination systems: diversity of concepts and implications for ecology, evolution and conservation
Authors: Armbruster William Scott
Published: October 2016

Specialization in plant–pollinator relationships is a core concept in discussions of plant evolution and ecology; it is central to our thinking, not just about the ecology of plant–pollinator interactions and pollinator services, but also about reproductive isolation, speciation, extinction and assembly of communities. However, as reviewed here, the concept ‘plant–pollinator specialization’ has multiple definitions and uses, and these disparate uses have engendered confusion in the literature. Organizing these disparate uses into a comprehensive framework is an overdue task, prior efforts notwithstanding.

This contribution attempts to make clear the variation in meaning and usage of plant–pollinator specialization, including distinguishing between ecological specialization (interacting with few partners or resources), evolutionary specialization (genetic change associated with increased specialization) and phenotypic specialization (having specialized or derived phenotypic traits), with application of all three concepts to both plants and flower‐visiting animals. These variations in interpretation of specialization affect how we view evolutionary and biogeographical trends, as well as extinction risk.

In the light of this conceptual diversity, I evaluate the relationships between specialization and possible trends in floral evolution and rates of speciation and extinction. I also address several implications of specialization for community ecology and resilience of pollination services in the face of environmental disturbance.

Alay summaryis available for this article.
Integrating intraspecific variation in community ecology unifies theories on body size shifts along climatic gradients
Authors: Classen Alice , Steffan‐Dewenter Ingolf , Kindeketa William J. , Peters Marcell K.
Published: October 2016

Physiological and energetic mechanisms have been proposed to constrain body sizes of organisms along climatic gradients; however, these provide contrasting predictions. While Bergmann's rule predicts increases in body sizes in cooler climates resulting from physiological constraints, energy‐based community assembly rules suggest declines in the mean body size of species caused by increased extinction probabilities for large‐bodied species in low‐energy habitats.

We tested these contrasting hypotheses by quantifying trait distributions in bee communities along a 3·6‐km elevational gradient at Mt. Kilimanjaro. Traditionally, intra‐ and interspecific trait shifts along environmental gradients have been investigated in isolation. However, a surge of theoretical approaches and studies on plants demonstrated that the explicit integration of trait variation among and within species can be essential for identifying the mechanisms that shape traits and related ecosystem functions along environmental gradients. We therefore studied variation in body size and related morphological traits at both the intra‐ and interspecific level.

We found support for both physiological constraints and energy‐based community assembly rules as drivers of trait distribution in bee communities along elevational gradients, which, however, affected different levels of biotic organization, that is the population and community level. While the number of bee species with large body sizes declined with elevation, individuals within species became on average larger, resulting in contrasting trends in morphometric parameters at the community versus population level.

Furthermore, body size within bee communities became less variable at higher elevations, largely as a result of a non‐random, directive loss of species, but paralleled by a decline in intraspecific variance, suggesting intensified filtering effects with increasing elevation. Similar patterns were found for other functional traits related to the foraging ecology of bees (tongue length, relative forewing length).

We conclude that along climatic gradients both physiological and energetic constraints shape trait distributions of pollinators, but at different levels of biological organization.

A lay summary is available for this article.
Spatial behaviour of Rayleigh waves in layered half‐spaces under active surface sources
Authors: Chai Hua‐You , Li Tian‐Bin , Phoon Kok‐Kwang , Chen Elton J. , Zhang Dian‐Ji
Published: October 2016

In the free state, Rayleigh waves are assumed to travel in the form of planar wavefronts. Under such an assumption, the propagation behaviour of the modes of Rayleigh waves in layered half‐spaces is only frequency dependent. The frequency behaviour, which is often termed as dispersion, is determined by the shear wave velocity profile of layered soils within the depth related to wavelength (or frequency). According to this characteristic, the shear wave velocity profile can be back‐analysed from the dispersion. The technique is widely used in the surface wave testing. However, the wavefronts of Rayleigh waves activated by the surface sources are non‐planar. The geometric discrepancy could result in Rayleigh waves manifesting distance‐dependent behaviour, which is referred to as spatial behaviour in this paper. Conventional analysis ignoring this spatial behaviour could introduce unexpected errors. In order to take the effects of sources on the propagation behaviour into account, a new mathematical model is established for Rayleigh waves in layered elastic media under vertical disc‐like surface sources using the thin‐layer method. The spatial behaviour of the activated modes and the apparent phase velocity, which is the propagation velocity of Rayleigh waves superposed by the multiple modes, are then analysed. Aspects of the spatial behaviour investigated in this paper include the equilibrium path, the particle orbit, and the geometric attenuation of the activated Rayleigh waves. The results presented in this paper can provide some guidelines for developing new inverse mathematical models and algorithms.
Accounting for genetic differences among unknown parents in microevolutionary studies: how to include genetic groups in quantitative genetic animal models
Authors: Wolak Matthew E. , Reid Jane M.
Published: October 2016

Quantifying and predicting microevolutionary responses to environmental change requires unbiased estimation of quantitative genetic parameters in wild populations. ‘Animal models’, which utilize pedigree data to separate genetic and environmental effects on phenotypes, provide powerful means to estimate key parameters and have revolutionized quantitative genetic analyses of wild populations.

However, pedigrees collected in wild populations commonly contain many individuals with unknown parents. When unknown parents are non‐randomly associated with genetic values for focal traits, animal model parameter estimates can be severely biased. Yet, such bias has not previously been highlighted and statistical methods designed to minimize such biases have not been implemented in evolutionary ecology.

We first illustrate how the occurrence of non‐random unknown parents in population pedigrees can substantially bias animal model predictions of breeding values and estimates of additive genetic variance, and create spurious temporal trends in predicted breeding values in the absence of local selection. We then introduce ‘genetic group’ methods, which were developed in agricultural science, and explain how these methods can minimize bias in quantitative genetic parameter estimates stemming from genetic heterogeneity among individuals with unknown parents.

We summarize the conceptual foundations of genetic group animal models and provide extensive, step‐by‐step tutorials that demonstrate how to fit such models in a variety of software programs. Furthermore, we provide new functions in r that extend current software capabilities and provide a standardized approach across software programs to implement genetic group methods.

Beyond simply alleviating bias, genetic group animal models can directly estimate new parameters pertaining to key biological processes. We discuss one such example, where genetic group methods potentially allow the microevolutionary consequences of local selection to be distinguished from effects of immigration and resulting gene flow.

We highlight some remaining limitations of genetic group models and discuss opportunities for further development and application in evolutionary ecology. We suggest that genetic group methods should no longer be overlooked by evolutionary ecologists, but should become standard components of the toolkit for animal model analyses of wild population data sets.
Shading impacts by coastal infrastructure on biological communities from subtropical rocky shores
Authors: Pardal‐Souza André Luiz , Dias Gustavo Muniz , Jenkins Stuart Rees , Ciotti Áurea Maria , Christofoletti Ronaldo Adriano
Published: October 2016

Artificial shading has been highlighted as an important human disturbance, affecting both productivity and community organization. However, studies of shading have been poorly explored from an environmental impact perspective.

We compared community structure on subtropical rocky shores in areas shaded by human constructions with those in unshaded areas. We then implemented a manipulative field experiment to determine the effects of shading on the macrobenthic community, biofilm biomass and larval recruitment.

Shading consistently affected the biological community of rocky shores. The biomass and cover of macroalgae and the size of most sedentary grazers were smaller in shaded habitat. In the infralittoral fringe, we recorded a shift in dominance from macroalgae in unshaded habitats to invertebrate filter feeders in shaded ones. In a similar way, the community from the mesolittoral was also affected by shading but not at all locations.

Experimental manipulation of shading led to a total loss of macroalgae from the infralittoral fringe and no community replacement over a period of 220 days. In the mesolittoral, oysters became more abundant in shaded conditions, while barnacles decreased in abundance. Larval recruitment was also affected, with oysters and barnacles recruiting more in shaded habitats.

Synthesis and applications. We demonstrate a clear impact of shading by artificial human‐made structures on patterns and processes regulating biodiversity on rocky shores and thus consequences for coastal ecosystem functioning. We argue that shading by artificial coastal structures, such as those proposed in the port expansion in our study site in south‐eastern Brazil, is potentially underestimated. Our work emphasizes the importance of careful evaluations of artificial structures in order to promote sustainable coastal development. As a result, we do not recommend the proposed expansion by suspended structures of the port of São Sebastião, as the consequent shading will negatively affect the biodiversity and ecosystem functioning of the Araçá Bay and surrounding areas.
Photoprotective and antioxidant responses to light spectrum and intensity variations in the coastal diatom Skeletonema marinoi
Authors: Smerilli Arianna , Orefice Ida , Corato Federico , Gavalás Olea Antonio , Ruban Alexander V. , Brunet Christophe
Published: October 2016

Photosynthesis is known to produce reactive oxygen species together with the transformation of light into biochemical energy. To fill the gap of the knowledge on the protective antioxidant network of microalgae, a series of experiments to explore the role of spectral composition and intensity of light in the modulation of the photodefence mechanisms developed by the coastal diatom Skeletonema marinoi were performed. The modulation of the total phenolic content, ascorbic acid and the enzymes glutathione reductase, catalase, ascorbate peroxidase and superoxide dismutase together with xanthophyll cycle and non‐photochemical quenching in response to variations in the light environment were analysed. Most of the enzymes' activity was promptly affected by the red light. Yet, the monochromatic high intensity blue light enhanced the synthesis of total phenolic content and ascorbic acid in parallel to the xanthophyll cycle activity. This study reveals the dual effects of spectral composition and intensity of light on the modulation of photoprotective mechanisms. Diatoms developed a complementary and/or alternative tuning processes to cope with the variable light environment they experience in the water column. They also provided valuable insights into light manipulation regimes for diatom cultivation that will help to maximize production of bioactive molecules.
The extracellular matrix of the oleolytic biofilms of Marinobacter hydrocarbonoclasticus comprises cytoplasmic proteins and T2SS effectors that promote growth on hydrocarbons and lipids
Authors: Ennouri Habiba , d'Abzac Paul , Hakil Florence , Branchu Priscilla , Naïtali Murielle , Lomenech Anne‐Marie , Oueslati Ridha , Desbrières Jacques , Sivadon Pierre , Grimaud Régis
Published: October 2016

The assimilation of the nearly water insoluble substrates hydrocarbons and lipids by bacteria entails specific adaptations such as the formation of oleolytic biofilms. The present article reports that the extracellular matrix of an oleolytic biofilm formed by Marinobacter hydrocarbonoclasticus at n‐hexadecane–water interfaces is largely composed of proteins typically cytoplasmic such as translation factors and chaperones, and a lesser amount of proteins of unknown function that are predicted extra‐cytoplasmic. Matrix proteins appear to form a structured film on hydrophobic interfaces and were found mandatory for the development of biofilms on lipids, alkanes and polystyrene. Exo‐proteins secreted through the type‐2 secretion system (T2SS) were shown to be essential for the formation of oleolytic biofilms on both alkanes and triglycerides. The T2SS effector involved in biofilm formation on triglycerides was identified as a lipase. In the case of biofilm formation on n‐hexadecane, the T2SS effector is likely involved in the mass transfer, capture or transport of alkanes. We propose that M. hydrocarbonoclasticus uses cytoplasmic proteins released by cell lysis to form a proteinaceous matrix and dedicated proteins secreted through the T2SS to act specifically in the assimilation pathways of hydrophobic substrates.