bluuebunny/crossref_metadata_2025 huggingface dataset:
A global analysis of traits predicting species sensitivity to habitat fragmentation
Authors: Keinath Douglas A. , Doak Daniel F. , Hodges Karen E. , Prugh Laura R. , Fagan William , Sekercioglu Cagan H. , Buchart Stuart H. M. , Kauffman Matthew
Published: September 2016

Aim

Elucidating patterns in species responses to habitat fragmentation is an important focus of ecology and conservation, but studies are often geographically restricted, taxonomically narrow or use indirect measures of species vulnerability. We investigated predictors of species presence after fragmentation using data from studies around the world that included all four terrestrial vertebrate classes, thus allowing direct inter‐taxonomic comparison.

Location

World‐wide.

Methods

We used generalized linear mixed‐effect models in an information theoretic framework to assess the factors that explained species presence in remnant habitat patches (3342 patches; 1559 species, mostly birds; and 65,695 records of patch‐specific presence–absence). We developed a novel metric of fragmentation sensitivity, defined as the maximum rate of change in probability of presence with changing patch size (‘Peak Change’), to distinguish between general rarity on the landscape and sensitivity to fragmentation per se.

Results

Size of remnant habitat patches was the most important driver of species presence. Across all classes, habitat specialists, carnivores and larger species had a lower probability of presence, and those effects were substantially modified by interactions. Sensitivity to fragmentation (measured by Peak Change) was influenced primarily by habitat type and specialization, but also by fecundity, life span and body mass. Reptiles were more sensitive than other classes. Grassland species had a lower probability of presence, though sample size was relatively small, but forest and shrubland species were more sensitive.

Main conclusions

Habitat relationships were more important than life‐history characteristics in predicting the effects of fragmentation. Habitat specialization increased sensitivity to fragmentation and interacted with class and habitat type; forest specialists and habitat‐specific reptiles were particularly sensitive to fragmentation. Our results suggest that when conservationists are faced with disturbances that could fragment habitat they should pay particular attention to specialists, particularly reptiles. Further, our results highlight that the probability of presence in fragmented landscapes and true sensitivity to fragmentation are predicted by different factors.
DNA damage inhibits lateral root formation by up‐regulating cytokinin biosynthesis genes in Arabidopsis thaliana
Authors: Davis La Ode Muhammad Muchdar , Ogita Nobuo , Inagaki Soichi , Takahashi Naoki , Umeda Masaaki
Published: September 2016

Lateral roots (LRs) are an important organ for water and nutrient uptake from soil. Thus, control of LR formation is crucial in the adaptation of plant growth to environmental conditions. However, the underlying mechanism controlling LR formation in response to external factors has remained largely unknown. Here, we found that LR formation was inhibited by DNA damage. Treatment with zeocin, which causes DNA double‐strand breaks, up‐regulated several DNA repair genes in the LR primordium (LRP) through the signaling pathway mediated by the transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1). Cell division was severely inhibited in the LRP of zeocin‐treated sog1‐1 mutant, which in turn inhibited LR formation. This result suggests that SOG1‐mediated maintenance of genome integrity is crucial for proper cell division during LRP development. Furthermore, zeocin induced several cytokinin biosynthesis genes in a SOG1‐dependent manner, thereby activating cytokinin signaling in the LRP. LR formation was less inhibited by zeocin in mutants defective in cytokinin biosynthesis or signaling, suggesting that elevated cytokinin signaling is crucial for the inhibition of LR formation in response to DNA damage. We conclude that SOG1 regulates DNA repair and cytokinin signaling separately and plays a key role in controlling LR formation under genotoxic stress.
Post‐instrumentation pain after the use of either Mtwo or the SAF system: a randomized controlled clinical trial
Authors: Saumya‐Rajesh P. , Krithikadatta J. , Velmurugan N. , Sooriaprakas C.
Published: September 2016

Aim

This randomized controlled trial compared the incidence of post‐instrumentation pain associated with Mtwo rotary NiTi files and the self‐adjusting file system following canal shaping and cleaning.

Methodology

Following sample size estimation, a total of 130 patients were randomized into two groups based on selection criteria [group Mtwo and group SAF (self‐adjusting file)]. Root canal treatment was carried out in two appointments. The teeth were endodontically treated with the appropriate allotted systems following the similar clinical parameters. Patients were asked to rate the intensity of pre‐instrumentation and post‐instrumentation pain (at 2, 4, 6, 8, 24, 48 h) using the VAS score. The Kruskal–Wallis test was carried out for the overall comparisons of the two systems. The Friedman test was used to compare between time‐points with each system. Subgroup analyses for independent variables (gender, pulp status and diagnosis) used the Mann–Whitney test and Wilcoxon signed ranks test (P < 0.05).

Results

No significant difference was found between the two groups with respect to post‐instrumentation pain. Teeth with pulpal necrosis had significant pain at 8 h compared with teeth with vital pulps (P = 0.04). Teeth with vital pulps in the SAF group had significantly less post‐instrumentation pain compared with those in the Mtwo group at 6 h (P = 0.042). Patients who had teeth with nonvital pulps in the SAF group experienced more post‐instrumentation pain at 8 h (P = 0.017) and 24 h (P = 0.005).

Conclusion

The incidence of post‐instrumentation pain at different time intervals in patients undergoing root canal treatment was similar for both the self‐adjusting file and Mtwo file systems.
Tecnología, deslocalización y tareas definitorias de las ocupaciones en el Reino Unido
Authors: AKÇOMAK Semih , KOK Suzanne , ROJAS‐ROMAGOSA Hugo
Published: September 2016

Los autores analizan los cambios de las tareas definitorias (margen intensivo) y de los niveles de empleo (margen extensivo) de las ocupaciones en el Reino Unido de 1997 a 2006 con datos de la Encuesta nacional sobre calificaciones (Skills Survey). Encuentran que las tareas definitorias de las ocupaciones cambiaron significativamente, y que la magnitud del cambio fue similar a la encontrada en el margen extensivo. Según sus resultados econométricos, este cambio de las tareas definitorias puede explicarse por los avances tecnológicos, pero no por la deslocalización.
Prevalence of systemic anticancer therapy for patients within the last 30 days of life: experience in a private hospital oncology group
Authors: Wein L. , Rowe C. , Brady B. , Handolias D. , Lipton L. , Pook D. , Stanley R. , Haines I.
Published: September 2016

Background

In recent years, there has been a significant increase in the number of cancer treatments that have become available. However, it has remained difficult to choose the most appropriate time to cease active therapy in individual patients.

Aims

To determine the proportion of patients being treated with palliative intent who received systemic anticancer treatment in the last 30 days of life.

Methods

This is a retrospective cohort study conducted within the Melbourne Oncology Group at Cabrini Hospital. Patients managed with palliative intent who died between 1 January 2014 and 30 June 2014 were included. Outcomes measured were the percentage of patients who received systemic anticancer treatment in the last 30 days of life, palliative care referral status, Emergency Department presentations, hospital admissions and place of death.

Results

A total of 80 patients was included in the study. Of these patients, 21 (26%) received systemic anticancer treatment in the last 30 days of life. There was no statistically significant difference between patients who received treatment in the last month of life and those who did not in terms of the number of patients who were referred to palliative care, presented to an Emergency Department, were admitted to hospital or died in an acute ward.

Conclusion

Although over a quarter of patients dying from advanced cancer received anticancer treatment in the last month of life, these patients did not present acutely to hospital more often and had the same extent of palliative care team involvement.
Entering the field in qualitative field research: a rite of passage into a complex practice world
Authors: Chughtai Hameed , Myers Michael D.
Published: September 2016

The concept of ‘the field’ is significant in ethnographic research as well as qualitative research methods more generally. However, how a field researcher enters the field is usually taken for granted after gaining access to the field. We suggest that entrance is a distinct phase of fieldwork that differs from negotiating access. Entrance is not a trivial event; rather, it is a rite of passage into a complex practice world and marks a critical field moment. Drawing on our ethnography and insights from hermeneutics and anthropology, we show that a practical understanding of the field represents a fusion of horizons where a fieldworker is thrown. The concept of thrownness highlights the fact that the fieldworkers' own historicity and prejudices affect their entrance into the field; hence, entrance into the field orientates an ethnographer in the field and influences the entire period of fieldwork that follows. Our theorizing is intended as a contribution towards advancing the discussion of qualitative research methods.
The Desire for Sovereignty – An Explanation of EU Attitudes in the Arab World
Authors: Isani Mujtaba , Schlipphak Bernd
Published: September 2016

A growing body of survey research shows that the European Union (EU) has a relatively benign image around the world, except among Arab populations. What informs Arab citizens' sceptical attitudes toward the European Union (EU)? Combining literature on Arab public opinion and perceptions of the EU, we argue that Arab citizens' feelings about the EU are influenced most prominently by their desire for sovereignty. Moreover, traditional utilitarian and cue‐taking mechanisms should also impact Arab EU attitudes. We empirically test our argument using data from the third wave of the Arab Barometer (AB). Our findings confirm that Arab citizens' EU views seem to be informed by their desire for sovereignty, as well as economic considerations and trust in domestic elites. Having provided evidence on Arab opinions about the EU, we discuss relevant theoretical and methodological directions for future research.
Patient‐reported outcomes and aesthetic evaluation of root coverage procedures: a 12‐month follow‐up of a randomized controlled clinical trial
Authors: Stefanini Martina , Jepsen Karin , de Sanctis Massimo , Baldini Nicola , Greven Björn , Heinz Bernd , Wennström Jan , Cassel Björn , Vignoletti Fabio , Sanz Mariano , Jepsen Søren , Zucchelli Giovanni
Published: September 2016

Aim

To assess patient‐reported outcome measures (PROMs), aesthetics and stability of root coverage procedures from a previous 6‐month RCT after 1 year.

Material & Methods

Forty‐five patients (90 recessions) had received a coronally advanced flap (CAF = control) only or a xenogeneic collagen matrix in addition (CAF + CMX = test). Visual analogue scales (VAS) and questionnaires were used for PROMs and the root coverage aesthetic score (RES) for professional aesthetic evaluations.

Results

VAS scores (patient satisfaction) amounted to 8.58 ± 1.86 (test) versus 8.38 ± 2.46 (control). Six patients preferred CAF + CMX concerning surgical procedure and aesthetics, six preferred CAF and 29 were equally satisfied. RES was 7.85 ± 2.42 for the test group versus 7.34 ± 2.90 for the controls. Root coverage (RC) was 76.28% for test and 75.05% for control defects. The mean increase in keratinized tissue width was higher in test (from 1.97 to 3.02 mm) than in controls (from 2.00 to 2.64 mm) (p = 0.0413). Likewise, test sites showed more gain in gingival thickness (0.52 mm) than control sites (0.27 mm) (p = 0.0023). Compared to 6 months, clinical outcomes were stable.

Conclusions

Results for PROMs, RES and RC did not significantly differ between treatment groups. Thickness and width of keratinized tissue were enhanced following CAF + CMX compared to CAF alone.
A model for perception‐based identification of sensitive skin
Authors: Richters R.J.H. , Uzunbajakava N.E. , Hendriks J.C.M. , Bikker J.‐W. , van Erp P.E.J. , van de Kerkhof P.C.M.
Published: September 2016

Background

With high prevalence of sensitive skin (SS), lack of strong evidence on pathomechanisms, consensus on associated symptoms, proof of existence of ‘general’ SS and tools to recruit subjects, this topic attracts increasing attention of research.

Objective

To create a model for selecting subjects in studies on SS by identifying a complete set of self‐reported SS characteristics and factors discriminatively describing it.

Methods

A survey (n = 3058) was conducted, comprising questions regarding socio‐demographics, atopy, skin characteristics, personal care, degree of self‐assessed SS and subjective and objective reactions to endogenous and exogenous factors. Exploratory factor analysis on 481 questionnaires was performed to identify underlying dimensions and multivariate logistic regression to find contributing variables to the likelihood of reporting SS.

Results

The prevalence of SS was found to be 41%, and 56% of SS subjects reports a concomitant atopic condition. The most discriminative were the eliciting factors toiletries and emotions, and not specific skin symptoms in general.

Conclusion

Triggers of different origins seem to elicit SS, it is not defined by concomitant skin diseases only, suggesting existence of ‘general’ SS. A multifactorial questionnaire could be a better diagnostic than a one‐dimensional provocative test.
The Energy Structure of the Canadian Economy
Authors: Kennedy Christopher A. , Bachmann Christian
Published: September 2016

We developed a model of a national economy in which the phenomena of supply, demand, economic growth, and international trade are represented in terms of energy flows. In examining the structure of the economy, we distinguish between the energy embodied in capital assets used in the production and distribution of energy and that embodied in capital assets and goods that consume energy. Sources used to quantify the energy flows include: end‐use energy data by economic sector; International Energy Agency–style national energy balances, and national input‐output tables. As an example, the Canadian economy for 2008 produced 16.97 exajoules (EJ) of energy, which after net export of 6.16 EJ and other adjustments left a total primary energy consumption of 10.61 EJ. The energy supply and distribution sectors used close to 32% (3.36 EJ) of total primary consumption. Analysis of primary energy consumption shows that 25.14% was embodied in household consumption, 22.85% was consumed directly by households, 7.88% was embodied in government services, and 34.07% was embodied in exports. Of significance to economic growth, 7.14% was embodied in capital in energy demanding sectors, 1.25% in energy consuming personal assets, and 1.52% in supply sector capital. The energy return on energy investment was relatively constant, averaging 5.14 between 1990 and 2008. Capital investments required to decouple the Canadian economy from its dependence on fossil fuels are discerned.
Additive Technology: Update on Current Materials and Applications in Dentistry
Authors: Barazanchi Abdullah , Li Kai Chun , Al‐Amleh Basil , Lyons Karl , Waddell J. Neil
Published: September 2016

Additive manufacturing or 3D printing is becoming an alternative to subtractive manufacturing or milling in the area of computer‐aided manufacturing. Research on material for use in additive manufacturing is ongoing, and a wide variety of materials are being used or developed for use in dentistry. Some materials, however, such as cobalt chromium, still lack sufficient research to allow definite conclusions about the suitability of their use in clinical dental practice. Despite this, due to the wide variety of machines that use additive manufacturing, there is much more flexibility in the build material and geometry when building structures compared with subtractive manufacturing. Overall additive manufacturing produces little material waste and is energy efficient when compared to subtractive manufacturing, due to passivity and the additive layering nature of the build process. Such features make the technique suitable to be used with fabricating structures out of hard to handle materials such as cobalt chromium. The main limitations of this technology include the appearance of steps due to layering of material and difficulty in fabricating certain material generally used in dentistry for use in 3D printing such as ceramics. The current pace of technological development, however, promises exciting possibilities.
Labov, vernacularity and sociolinguistic change
Authors: Coupland Nikolas
Published: September 2016

Despite some well‐known problems in its early formulation, Labov's concept of ‘the vernacular’ has enduring relevance in sociolinguistics. This is even more the case if we recast it more abstractly – as ‘vernacularity’, ideologically contrasted with ‘standardness’. Following Labov, class‐associated vernacular practices have been a major empirical focus of the discipline; they have also locked in the discipline's political consciousness. The paper traces some different ways in which sociolinguistics has positioned itself in relation to vernacularity. Taking the U.K. as a case in point, the paper then asks how large‐scale changes in social class experience may be shifting the bases on which we have defined and researched vernacular language. It considers vernacularisation as a sociolinguistic change running counter to the better‐established process of linguistic standardisation.
Labov in anthropology
Authors: Gal Susan
Published: September 2016

Early sociolinguistics was determinedly multidisciplinary and Labov's work was eagerly read by anthropologists. Nevertheless, the ethnographic and interpretivist commitments of anthropology contrasted with Labov's correlational method and positivist philosophical assumptions. This paper discusses three debates between those two broad methodological/philosophical traditions and traces their outcomes: on the nature of linguistic heterogeneity; the (re)production of social inequality; and the significance of linguistic style. I argue that the debates were productive. Although anthropologists often forcefully critiqued Labov's methods and conceptual proposals, dialogue with Labov's research has had positive effects: current work bears the marks of these engagements.
Afterword: Where are we now?
Authors: Labov William
Published: September 2016

Labov recapitulates his view of linguistics when he entered the field in 1961, and what he hoped to achieve. He acknowledges Meyerhoff's stress on the convergence of methods and Coupland's view of the vernacular as an ‘overdetermined’ concept which is simultaneously undervalued. The value of new methods for the study of variation has been tested by their application to other cultures (Gal), to African American Vernacular English (Rickford), and to indigenous and endangered languages (Stanford). Thomas indicates how the Atlas of North American English builds on traditional methods of American dialect geography. Johnstone's account of Labov's approach to narrative links sociolinguistic work to broader areas in the humanities. Cornips and Gregersen see Labov's contribution to general linguistic theory as a joint enterprise in which intuitions and observations form a harmonious database.
Overweight, obesity and foot posture in children: A cross‐sectional study
Authors: Gijon‐Nogueron Gabriel , Montes‐Alguacil Jesus , Martinez‐Nova Alfonso , Alfageme‐Garcia Pilar , Cervera‐Marin Jose A , Morales‐Asencio Jose M
Published: September 2016

Aim

The aim of this study is to examine the relationship between obesity and foot posture in children.

Methods

This cross‐sectional study is based on a sample population of 1798 schoolchildren (873 boys and 925 girls) aged between 6 and 12 years. The height and weight of each subject was measured and the body mass index (BMI) was calculated. Foot posture was described by means of the foot posture index (FPI). The differences among various foot postures in relation to BMI, for the total sample, were tested using the Games‐Howell test. In addition, cross tabulation for different gender groups and BMI categories was applied and tested using χ2.

Results

The mean BMI was 18.94 (standard deviation (SD) 3.65 kg/m2) in the boys and 18.90 (SD 3.64 kg/m2) in the girls, and the FPI was 3.97 (SD 2.98) in the boys and 3.68 (SD 2.86) in the girls. The FPI results show that among the boys aged 6 years, the right foot was more pronated than among the girls (FPI 4.8–4.1, P = 0.034), while among the boys aged 7 years, this was true for the left foot (4.4–3.7, P = 0.049). For the other ages, there were no significant differences in the FPI between the sexes. There were no significant differences between the value, or categories, of BMI and the FPI in the different age groups.

Conclusion

In children aged between 6 and 12 years, body mass does not appear to have an important bearing on static foot posture. Furthermore, the variables gender and age are of scant importance in determining foot posture in children.
No detectable resistance to tenofovir disoproxil fumarate in HBeAg+ and HBeAg− patients with chronic hepatitis B after 8 years of treatment
Authors: Liu Y. , Corsa A. C. , Buti M. , Cathcart A. L. , Flaherty J. F. , Miller M. D. , Kitrinos K. M. , Marcellin P. , Gane E. J.
Published: September 2016

A major hurdle in the long‐term treatment of chronic hepatitis B (CHB) patients is to maintain viral suppression in the absence of drug resistance. To date, no evidence of resistance to tenofovir disoproxil fumarate (TDF) has been observed. A cumulative evaluation of CHB patients who qualified for resistance surveillance over 8 years of TDF treatment was conducted. Patients in studies GS‐US‐174‐0102 (HBeAg−) and GS‐US‐174‐0103 (HBeAg+) were randomized 2:1 to receive TDF or adefovir dipivoxil (ADV) for 48 weeks followed by open‐label TDF through year 8. Population sequencing of HBV pol/RT was attempted for all TDF‐treated patients at baseline and, annually if viremic, at discontinuation, or with addition of emtricitabine. Overall, 88/641 (13.7%) patients qualified for sequence analysis at one or more time points. The percentage of patients qualifying for sequence analysis declined over time, from 9 to 11% in years 1‐2 to <4% over years 3‐8. Forty‐one episodes of virologic breakthrough (VB) occurred throughout the study, with most (n=29, 70%) associated with nonadherence to study medication. Fifty‐nine per cent of VB patients with an opportunity to resuppress HBV achieved HBV DNA resuppression. A minority of patients who qualified for sequencing had polymorphic (41/165, 24.8%) or conserved (17/165, 10.3%) site changes in pol/RT, with six patients developing lamivudine and/or ADV resistance‐associated mutations. No accumulation of conserved site changes was detected. The long‐term treatment of CHB with TDF monotherapy maintains effective suppression of HBV DNA through 8 years, with no evidence of TDF resistance or accumulation of conserved site changes.
Formulation of an Alternative Culture Medium for Arthrospira maxima (Spirulina) Based on “Tequesquite,” a Traditional Mineral Resource
Authors: Martínez‐Jerónimo Fernando , Flores‐Hernández Dante Ivo , Galindez‐Mayer Juvencio
Published: September 2016

Culture media formulation for Arthrospira maxima (formerly designated as Spirulina maxima) production is a constraining factor. Use of synthetic media could be expensive because most of the commercial strains require salinity conditions higher than 20 g/L. In this study, a traditional, pre‐Hispanic mineral resource, known as “tequesquite,” was used as the base for the formulation of an alternative and low‐cost culture medium. Tequesquite is available from outcrop areas located in the basin of the former Lake Texcoco, where A. maxima thrived in pre‐Hispanic times. The effect on the biomass production of different tequesquite‐based formulations, varying N, P, and , was tested and compared with results obtained with Zarrouk's medium (ZM). Growth of biomass in some alternative formulations showed no significant differences compared with ZM. Production in a bubble‐column photobioreactor of the alternative medium reached a maximum of X = 2570.4 mg/L dry weight, compared with X = 2931.4 mg/L dry weight obtained with ZM. The proposed tequesquite‐medium formulation has equivalent N and P concentrations as ZM, but only 50% of NaHCO3, thus reducing the medium's cost. In addition, it avoids the use of seawater or NaCl to provide the salinity condition required for the adequate growth of Arthrospira.
Buzz off! An evaluation of ultrasonic acoustic vibration for the disruption of marine micro-organisms on sensor-housing materials
Authors: McQuillan J.S. , Hopper D.J. , Magiopoulos I. , Arundell M. , Brown R. , Shorter S. , Mowlem M.C. , Pascal R.W. , Connelly D.
Published: September 2016

Biofouling is a process of ecological succession which begins with the attachment and colonization of micro-organisms to a submerged surface. For marine sensors and their housings, biofouling can be one of the principle limitations to long-term deployment and reliability. Conventional antibiofouling strategies using biocides can be hazardous to the environment, and therefore alternative chemical-free methods are preferred. In this study, custom-made testing assemblies were used to evaluate ultrasonic vibration as an antibiofouling process for marine sensor-housing materials over a 28-day time course. Microbial biofouling was measured based on (i) surface coverage, using fluorescence microscopy and (ii) bacterial 16S rDNA gene copies, using Quantitative polymerase chain reaction (PCR). Ultrasonic vibrations (20 KHz, 200 ms pulses at 2-s intervals; total power 16·08 W) significantly reduced the surface coverage on two plastics, poly(methyl methacrylate) and polyvinyl chloride (PVC) for up to 28 days. Bacterial gene copy number was similarly reduced, but the results were only statistically significant for PVC, which displayed the greatest overall resistance to biofouling, regardless of whether ultrasonic vibration was applied. Copper sheet, which has intrinsic biocidal properties was resistant to biofouling during the early stages of the experiment, but inhibited measurements made by PCR and generated inconsistent results later on.

Significance and Impact of the Study

In this study, ultrasonic acoustic vibration is presented as a chemical-free, ecologically friendly alternative to conventional methods for the perturbation of microbial attachment to submerged surfaces. The results indicate the potential of an ultrasonic antibiofouling method for the disruption of microbial biofilms on marine sensor housings, which is typically a principle limiting factor in their long-term operation in the oceans. With increasing deployment of scientific apparatus in aquatic environments, including further offshore and for longer duration, the identification and evaluation of novel antifouling strategies that do not employ hazardous chemicals are widely sought.
Assessment of the distribution of sponge chips in the sediment of East Pacific Ocean reefs
Authors: Carballo Jose Luis , Ovalle‐Beltrán Humberto , Yáñez Benjamin , Bautista‐Guerrero Eric , Nava‐Bravo Héctor
Published: September 2016

Sponges are one of the principal agents of bioerosion and sediment production in coral reefs. They generate small carbonate chips that can be found in the sediments, and we investigated whether these could provide a means for assessment of bioerosion applicable to reef monitoring. We tested this hypothesis on samples from 12 Mexican coral reefs distributed along the Pacific coast, where boring sponges were particularly abundant, and quantified the amount of chips in samples of superficial sediment in three grain‐size fractions: fine (<44 μm), medium (44–210 μm) and coarse (>210 μm). The grain‐size distribution varied among reefs, with the majority of the sediment of most reefs being composed of coarse sands, and the medium and fine fractions dominating only at La Entrega and Playa Blanca. All the reefs presented clear evidence of bioerosion by sponges, with the characteristic chips present in the sediment, although at most sites the percentage of chips was very low (from 1% to 3% of the total sediment). Only at La Entrega and Playa Blanca did they constitute a significant fraction of the total sediment (18% and 16%, respectively). While not statistically significant, there was an interesting trend between sponge chips versus sponge abundance that suggests that quantification of the chips in the sediment could be used as a proxy for sponge erosion of the entire community, which cannot be estimated in by laboratory experiments. However, while this methodology could provide an integrated approach to monitor sponge bioerosion, more studies are necessary due to the influence of environmental factors on the transport and deposition of these chips.
Ecological assessments of the coral reef communities in the Eastern Caribbean and the effects of herbivory in influencing coral juvenile density and algal cover
Authors: Williams Stacey M. , Sánchez‐Godínez Cristina , Newman Steven P. , Cortés Jorge
Published: September 2016

Caribbean reefs have been unevenly surveyed, with many areas lacking baseline data. In this study, the current status of Orbicella reefs, a structurally complex forereef habitat, was quantified in an understudied region, the Eastern Caribbean. During 2011 the same observers surveyed benthic assemblages, coral juvenile density, herbivorous fishes, and invertebrates at 30 Orbicella reefs in four Eastern Caribbean areas: Antigua, Barbados, St Lucia, and St Vincent and the Grenadines (hereafter St Vincent). Not all Orbicella forereefs were functionally the same in the Eastern Caribbean. Benthic communities and herbivorous fishes varied greatly among islands. Hard coral had the highest overall percent cover on most reefs in this study, with an average cover of 22%, and was greater than fleshy macroalgal cover at 83% of the sites. Overall, coral juvenile density was low but was positively associated with higher densities of Diadema antillarum, highlighting the importance of herbivory on the reefs. Nearshore coral reefs in Barbados were in a better state than other areas, exhibiting higher coral cover dominated by spawning corals, higher densities of coral juveniles exhibiting higher coral cover dominated by spawning corals, higher densities of coral juveniles and D. antillarum. Low biomass of herbivorous fishes at a majority of the coral reef sites is of major concern for the functioning of these reefs. Conservation of parrotfishes and other herbivores is necessary given the abundance of algae on most of these reefs and the beneficial effect of their presence on coral juveniles. This is the first comprehensive study that compares the state of Orbicella reefs in the Eastern Caribbean, providing valuable information that will be useful in creating realistic targets for future management and conservation.
Global variations in regolith properties on asteroid Vesta from Dawn's low‐altitude mapping orbit
Authors: Denevi Brett W. , Beck Andrew W. , Coman Ecaterina I. , Thomson Bradley J. , Ammannito Eleonora , Blewett David T. , Sunshine Jessica M. , De Sanctis Maria Cristina , Li Jian‐Yang , Marchi Simone , Mittlefehldt David W. , Petro Noah E. , Raymond Carol A. , Russell Christopher T.
Published: September 2016

We investigate the depth, variability, and history of regolith on asteroid Vesta using data from the Dawn spacecraft. High‐resolution (15–20 m pixel−1) Framing Camera images are used to assess the presence of morphologic indicators of a shallow regolith, including the presence of blocks in crater ejecta, spur‐and‐gully–type features in crater walls, and the retention of small (<300 m) impact craters. Such features reveal that the broad, regional heterogeneities observed on Vesta in terms of albedo and surface composition extend to the physical properties of the upper ~1 km of the surface. Regions of thin regolith are found within the Rheasilvia basin and at equatorial latitudes from ~0–90°E and ~260–360°E. Craters in these areas that appear to excavate material from beneath the regolith have more diogenitic (Rheasilvia, 0–90°E) and cumulate eucrite (260–360°E) compositions. A region of especially thick regolith, where depths generally exceed 1 km, is found from ~100–240°E and corresponds to heavily cratered, low‐albedo surface with a basaltic eucrite composition enriched in carbonaceous chondrite material. The presence of a thick regolith in this area supports the idea that this is an ancient terrain that has accumulated a larger component of exogenic debris. We find evidence for the gardening of crater ejecta toward more howarditic compositions, consistent with regolith mixing being the dominant form of “weathering” on Vesta.
High migration rates shape the postglacial history of amphi‐Atlantic bryophytes
Authors: Désamoré Aurélie , Patiño Jairo , Mardulyn Patrick , Mcdaniel Stuart F. , Zanatta Florian , Laenen Benjamin , Vanderpoorten Alain
Published: September 2016

Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi‐Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe. In contrast with this hypothesis, the best‐fit demographic model involved similar patterns of population size contractions, comparable levels of genetic diversity and balanced migration rates between European and North American populations. Our results thus suggest that bryophytes have experienced comparable demographic glacial histories on both sides of the Atlantic. Although a weak, but significant genetic structure was systematically recovered between European and North American populations, evidence for migration from and towards both continents suggests that amphi‐Atlantic bryophyte population may function as a metapopulation network. Reconstructing the biogeographic history of either North American or European bryophyte populations therefore requires a large, trans‐Atlantic geographic framework.
Population structure and gene flow in the global pest, Helicoverpa armigera
Authors: Anderson C. J. , Tay W. T. , McGaughran A. , Gordon K. , Walsh T. K.
Published: September 2016

Helicoverpa armigera is a major agricultural pest that is distributed across Europe, Asia, Africa and Australasia. This species is hypothesized to have spread to the Americas 1.5 million years ago, founding a population that is at present, a distinct species, Helicoverpa zea. In 2013, H. armigera was confirmed to have re‐entered South America via Brazil and subsequently spread. The source of the recent incursion is unknown and population structure in H. armigera is poorly resolved, but a basic understanding would highlight potential biosecurity failures and determine the recent evolutionary history of region‐specific lineages. Here, we integrate several end points derived from high‐throughput sequencing to assess gene flow in H. armigera and H. zea from populations across six continents. We first assemble mitochondrial genomes to demonstrate the phylogenetic relationship of H. armigera with other Heliothine species and the lack of distinction between populations. We subsequently use de novo genotyping‐by‐sequencing and whole‐genome sequences aligned to bacterial artificial chromosomes, to assess levels of admixture. Primarily, we find that Brazilian H. armigera are derived from diverse source populations, with strong signals of gene flow from European populations, as well as prevalent signals of Asian and African ancestry. We also demonstrate a potential field‐caught hybrid between H. armigera and H. zea, and are able to provide genomic support for the presence of the H. armigera conferta subspecies in Australasia. While structure among the bulk of populations remains unresolved, we present distinctions that are pertinent to future investigations as well as to the biosecurity threat posed by H. armigera.
Environment not dispersal limitation drives clonal composition of Arctic Daphnia in a recently deglaciated area
Authors: Haileselasie Tsegazeabe H. , Mergeay Joachim , Weider Lawrence J. , Sommaruga Ruben , Davidson Thomas A. , Meerhoff Mariana , Arndt Hartmut , Jürgens Klaus , Jeppesen Erik , De Meester Luc
Published: September 2016

One of the most prominent manifestations of the ongoing climate warming is the retreat of glaciers and ice sheets around the world. Retreating glaciers result in the formation of new ponds and lakes, which are available for colonization. The gradual appearance of these new habitat patches allows us to determine to what extent the composition of asexual Daphnia (water flea) populations is affected by environmental drivers vs. dispersal limitation. Here, we used a landscape genetics approach to assess the processes structuring the clonal composition of species in the D. pulex species complex that have colonized periglacial habitats created by ice‐sheet retreat in western Greenland. We analysed 61 populations from a young (<50 years) and an old cluster (>150 years) of lakes and ponds. We identified 42 asexual clones that varied widely in spatial distribution. Beta‐diversity was higher among older than among younger systems. Lineage sorting by the environment explained 14% of the variation in clonal composition whereas the pure effect of geographical distance was very small and statistically insignificant ( = 0.010, P = 0.085). Dispersal limitation did not seem important, even among young habitat patches. The observation of several tens of clones colonizing the area combined with environmentally driven clonal composition of populations illustrates that population assembly of asexual species in the Arctic is structured by environmental gradients reflecting differences in the ecology of clones.
Parapatric genetic introgression and phenotypic assimilation: testing conditions for introgression between Hercules beetles (Dynastes, Dynastinae)
Authors: Huang Jen‐Pan
Published: September 2016

The prevalence and consequences of genetic introgression between species have been intensively debated. I used Hercules beetles as examples to test for conditions that may be associated with the occurrence of introgression. RADseq data were used to reconstruct the species tree and history of introgression between Hercules beetles. Image data from museum specimens were used to investigate the phenotypic similarity of two adaptive traits between species from two distinct climatic realms (Nearctic vs. Neotropical). Genetic introgression was identified between Hercules beetles living in geographic proximity (parapatric). Phylogenetic relatedness and phenotypic similarity did not predict nor preclude genetic introgression between species. Phenotypic assimilation in body coloration was evident between distantly related Hercules beetles codistributed in Central America, where directional introgression was also statistically supported from the putative donor to receiver lineages. The number of introgressed loci was significantly higher between species with than without phenotypic similarity. I discuss the implications of recent studies on adaptive genetic introgression by providing supporting evidence from the Hercules beetle system.
Using long‐term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin‐treated mouse gut
Authors: Lescat Mathilde , Launay Adrien , Ghalayini Mohamed , Magnan Mélanie , Glodt Jérémy , Pintard Coralie , Dion Sara , Denamur Erick , Tenaillon Olivier
Published: September 2016

Although microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole‐genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, and epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long‐term adaptation of an E. coli natural isolate, the streptomycin‐resistant strain 536, in the digestive tract of streptomycin‐treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro, and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on D‐galactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the nonrandom associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that ‘evolve and sequence’ approach coupled with an analysis of convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment.
Invasion history and demographic processes associated with rapid morphological changes in the Red‐whiskered bulbul established on tropical islands
Authors: Le Gros Ariane , Clergeau Philippe , Zuccon Dario , Cornette Raphaël , Mathys Blake , Samadi Sarah
Published: September 2016

The Red‐whiskered bulbul is a very successful invasive bird species. Morphological differences have been reported among individuals inhabiting the humid and dry coasts of Reunion Island, in a 30‐year‐old population. This suggests a capacity for rapid local adaptation which could explain the general invasive success of this species. However, the origin and invasion history of this population is unknown. It is therefore not possible to establish with certainty the cause of these morphological differences. Here, we investigated the invasion history of populations of Red‐whiskered bulbul established on Reunion Island, Mauritius and Oahu (three geographically similar tropical islands) to assess the link between invasion history and morphological changes in these populations. We first assessed the source(s) of the invasive populations. We then compared the morphology of the individuals between the invasive and native populations and between the dry and humid coasts of invaded islands. Finally, we inferred the invasion history of the invasive populations to investigate the role of neutral processes (e.g. founder effect and drift) on morphology. We found that the invasive populations have a similar origin and that the morphology of the individuals in these populations has diverged in a similar way from the native range, suggesting a convergent adaptation to tropical islands. Like on Reunion, we found differences in morphology between the dry and humid coasts on Mauritius. These morphological differences can be explained by invasion history on Reunion but not on Mauritius. Both neutral evolution and adaptation thus shape the morphology of invasive Red‐whiskered bulbuls.
Distinguishing contemporary hybridization from past introgression with postgenomic ancestry‐informative SNPs in strongly differentiated Ciona species
Authors: Bouchemousse Sarah , Liautard‐Haag Cathy , Bierne Nicolas , Viard Frédérique
Published: September 2016

Biological introductions bring into contact species that can still hybridize. The evolutionary outcomes of such secondary contacts may be diverse (e.g. adaptive introgression from or into the introduced species) but are not yet well examined in the wild. The recent secondary contact between the non‐native sea squirt Ciona robusta (formerly known as C. intestinalis type A) and its native congener C. intestinalis (formerly known as C. intestinalis type B), in the Western English Channel, provides an excellent case study to examine. To examine contemporary hybridization between the two species, we developed a panel of 310 ancestry‐informative SNPs from a population transcriptomic study. Hybridization rates were examined on 449 individuals sampled in eight sites from the sympatric range and five sites from allopatric ranges. The results clearly showed an almost complete absence of contemporary hybridization between the two species in syntopic localities, with only one‐first‐generation hybrid and no other genotype compatible with recent backcrosses. Despite the almost lack of contemporary hybridization, shared polymorphisms were observed in sympatric and allopatric populations of both species. Furthermore, one allopatric population from SE Pacific exhibited a higher rate of shared polymorphisms compared to all other C. robusta populations. Altogether, these results indicate that the observed level of shared polymorphism is more probably the outcome of ancient gene flow spread afterwards at a worldwide scale. They also emphasize efficient reproductive barriers preventing hybridization between introduced and native species, which suggests hybridization should not impede too much the expansion and the establishment of the non‐native species in its introduction range.
Do metabolic derangements in end‐stage polycystic kidney disease differ versus other primary kidney diseases?
Authors: Jankowska Magdalena , Qureshi Abdul Rashid , Barany Peter , Heimburger Olof , Stenvinkel Peter , Lindholm Bengt
Published: September 2016

Aim

Autosomal dominant polycystic kidney disease (ADPKD), a systemic disorder caused by mutation in genes encoding polycystins, has been reported to lead to metabolic derangements including new‐onset diabetes mellitus after kidney transplantation. We analyzed markers of insulin resistance (IR), inflammation, nutritional status and insulin‐like growth factor‐1 (IGF‐1) in end‐stage renal disease (ESRD) patients with ADPKD and ESRD patients with other primary kidney diseases.

Methods

In a post hoc cross‐sectional analysis in 254 non‐diabetic CKD 5 patients starting on dialysis, glucose metabolism (insulin, IGF‐1, homeostasis model assessment of IR, HOMA‐IR), inflammation (high sensitivity C‐reactive protein, interleukin‐6, and tumour necrosis factor), nutritional status, and bone mineral density (BMD), were assessed. Survival was recorded for median time of 28 months (IQR 15–48 months).

Results

Neither indices of IR, nor IGF‐1, inflammatory status, nutritional status, or BMD were different in patients with ADPKD as compared to other aetiologies of ESRD. Kaplan–Meier curves showed better survival among the ADPKD group versus other aetiologies, even after an exclusion of diabetic patients.

Conclusions

The ESRD phenotype did not differ in ADPKD versus other primary kidney diseases in terms of markers of IR, inflammation, and nutritional status. This argues against the proposition that ADPKD patients are more prone to develop metabolic derangements beyond those generally observed in advanced CKD. However, additional studies are warranted to further elucidate systemic metabolic aspects of ADPKD.