bluuebunny/crossref_metadata_2025_split huggingface dataset:
Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems
Authors: Evans Darren M. , Kitson James J. N. , Lunt David H. , Straw Nigel A. , Pocock Michael J. O. 
Published: March 2016

Summary

Significant advances in both mathematical and molecular approaches in ecology offer unprecedented opportunities to describe and understand ecosystem functioning. Ecological networks describe interactions between species, the underlying structure of communities and the function and stability of ecosystems. They provide the ability to assess the robustness of complex ecological communities to species loss, as well as a novel way of guiding restoration. However, empirically quantifying the interactions between entire communities remains a significant challenge.

Concomitantly, advances in DNA sequencing technologies are resolving previously intractable questions in functional and taxonomic biodiversity and provide enormous potential to determine hitherto difficult to observe species interactions. Combining DNA metabarcoding approaches with ecological network analysis presents important new opportunities for understanding large‐scale ecological and evolutionary processes, as well as providing powerful tools for building ecosystems that are resilient to environmental change.

We propose a novel ‘nested tagging’ metabarcoding approach for the rapid construction of large, phylogenetically structured species‐interaction networks. Taking tree–insect–parasitoid ecological networks as an illustration, we show how measures of network robustness, constructed using DNA metabarcoding, can be used to determine the consequences of tree species loss within forests, and forest habitat loss within wider landscapes. By determining which species and habitats are important to network integrity, we propose new directions for forest management.

Merging metabarcoding with ecological network analysis provides a revolutionary opportunity to construct some of the largest, phylogenetically structured species‐interaction networks to date, providing new ways to: (i) monitor biodiversity and ecosystem functioning; (ii) assess the robustness of interacting communities to species loss; and (iii) build ecosystems that are more resilient to environmental change.

A lay summary is available for this article.
Nutrient utilization traits vary systematically with intraspecific cell size plasticity
Authors: Malerba Martino E. , Heimann Kirsten , Connolly Sean R. 
Published: March 2016

Summary

Trait‐based approaches are increasingly used to help understanding community structure and ecosystem functioning. A large proportion of trait‐based studies define a species by its mean trait values and assume intraspecific trait variability to be negligible compared to interspecific differences. However, this assumption is rarely tested.

Phenotypic cell size plasticity can be particularly important in phytoplankton species, which are known for their rapid changes in cell size in response to variations in environmental conditions. While phytoplankton traits show clear systematic trends with mean cell size across species, how size‐related plasticity influences the dynamics of a species remains unknown.

In this study, we evaluate the effects of cell size plasticity on the nitrogen (N) utilization traits of the green alga Desmodesmus armatus (Chlorophyta), reared in different inorganic nitrogen sources (nitrate, ammonium or both) and nutrient histories (N‐replete and N‐deplete).

Results show that traits for per‐cell ammonium uptake, maximum cell growth rate and minimum N‐quota change substantially within the study species, depending on mean cell size and nutrient history. In contrast, per‐cell nitrate uptake was independent of cell size. These results indicate that representing phytoplankton species only by their mean trait values could underestimate the physiological performance of a species by as much as one order of magnitude.

This study highlights the extent to which explicit incorporation of within‐species trait variability can enhance our understanding of how species performance changes along environmental gradients.

A lay summary is available for this article.
How persistent are the impacts of logging roads on Central African forest vegetation?
Authors: Kleinschroth Fritz , Healey John R. , Sist Plinio , Mortier Frédéric , Gourlet‐Fleury Sylvie 
Published: March 2016

Summary

Logging roads can trigger tropical forest degradation by reducing the integrity of the ecosystem and providing access for encroachment. Therefore, road management is crucial in reconciling selective logging and biodiversity conservation. Most logging roads are abandoned after timber harvesting; however, little is known about their long‐term impacts on forest vegetation and accessibility, especially in Central Africa.

In 11 logging concessions in the Congo Basin, we field‐sampled a chronosequence of roads that, judging from satellite images, had been abandoned between 1985 and 2015. We assessed recovery of timber resources, tree diversity and above‐ground biomass in three zones: the road track, the road edge (where forest had been cleared during road construction) and the adjacent logged forest.

The density of commercial timber species <15 cm d.b.h. was almost three times higher in the road track (321 individuals ha−1) and edge (267) than in the logged adjacent forest (97). Over time, tree species diversity converged to a comparable level between roads and adjacent forests, along with an increase in canopy closure.

The average width of forest clearing for road construction was 20 m, covering a total 0·76% of the forest area inside concessions. After 15 years following abandonment, road tracks had recovered 24 Mg ha−1 of above‐ground woody biomass, which was 6% of that in the adjacent forest, while road edges had accumulated 167 Mg ha−1 (42%). Ten years after abandonment, roads were no longer penetrable by poachers on motorcycles. An exotic herb species was fully replaced by dominant Marantaceae that have even higher abundance in the adjacent forest.

Synthesis and applications. Our evidence of vegetation recovery suggests that logging roads are mostly transient elements in the forest landscapes. However, given the slow recovery of biomass on abandoned road tracks, we advocate both reducing the width of forest clearing for road construction and reopening old logging roads for future harvests, rather than building new roads in intact forests. Road edges seem suitable for post‐logging silviculture which needs to be assisted by removing dominant herbs during the early years after abandonment while the road track is still accessible.
Heterotrophic Proteobacteria in the vicinity of diffuse hydrothermal venting
Authors: Meier Dimitri V. , Bach Wolfgang , Girguis Peter R. , Gruber‐Vodicka Harald R. , Reeves Eoghan P. , Richter Michael , Vidoudez Charles , Amann Rudolf , Meyerdierks Anke 
Published: March 2016

SummaryDeep‐sea hydrothermal vents are highly dynamic habitats characterized by steep temperature and chemical gradients. The oxidation of reduced compounds dissolved in the venting fluids fuels primary production providing the basis for extensive life. Until recently studies of microbial vent communities have focused primarily on chemolithoautotrophic organisms. In our study, we targeted the change of microbial community compositions along mixing gradients, focusing on distribution and capabilities of heterotrophic microorganisms. Samples were retrieved from different venting areas within the Menez Gwen hydrothermal field, taken along mixing gradients, including diffuse fluid discharge points, their immediate surroundings and the buoyant parts of hydrothermal plumes. High throughput 16S rRNA gene amplicon sequencing, fluorescence in situ hybridization, and targeted metagenome analysis were combined with geochemical analyses. Close to diffuse venting orifices dominated by chemolithoautotrophic Epsilonproteobacteria, in areas where environmental conditions still supported chemolithoautotrophic processes, we detected microbial communities enriched for versatile heterotrophic Alpha‐ and Gammaproteobacteria. The potential for alkane degradation could be shown for several genera and yet uncultured clades. We propose that hotspots of chemolithoautotrophic life support a ‘belt’ of heterotrophic bacteria significantly different from the dominating oligotrophic microbiota of the deep sea.
‘A Reformer's Wife ought to be an Heroine’: Gender, Family and English Radicals Imprisoned under the Suspension of Habeas Corpus Act of 1817
Authors: NAVICKAS KATRINA 
Published: March 2016

AbstractIn 1817, the British government reacted to the rise of popular agitation for parliamentary reform by passing the Suspension of Habeas Corpus Act and arresting the leaders of the new working‐class radical societies. The imprisonment of these men was a severe blow to the democratic movement. Despite the recent revival of scholarly interest in early nineteenth‐century popular politics, historians have treated the events of 1817 as a brief interlude before the better‐known Peterloo Massacre of 1819. This article argues that the development of the post‐war democratic movement cannot be understood without examining the impact of the imprisonments on the radical leaders and their families. It analyses a previously unstudied series of letters confiscated from the radical prisoners and kept in the Home Office files. The correspondence demonstrates the essential role of letter‐writing within radical culture, and how radical thought and self‐expression were mediated through the pressures of both government surveillance and financial difficulty. This article secondly offers new evidence about the gender politics of radicalism in this period. It shows how women's experience of separation from their husbands, and male attitudes towards their role in 1817–18 crucially shaped the emergence of female radicalism in public for the first time in 1819.
Organic‐ and Animal Welfare‐labelled Eggs: Competing for the Same Consumers?
Authors: Gerini Francesca , Alfnes Frode , Schjøll Alexander 
Published: March 2016

AbstractTo understand the market for sustainable foods, it is important to allow for heterogeneous preferences. However, most studies of consumer preferences for sustainable foods only investigate average consumer preferences. They do not take into account that some consumer segments attempt to purchase as much sustainable food as possible, others are almost indifferent to the notion of sustainable food, and still others consider sustainable food a complete hoax. The aim of this study is to explore the preferences for various types of premium eggs across three consumer segments. We conduct a choice experiment including 900 Norwegian consumers and perform a behavioural segmentation based on the frequency of organic food purchase. We find that the segment purchasing the most organic food is, as expected, willing to pay a significant premium for organic eggs over eggs displaying only enhanced animal welfare. However, most consumers, who only occasionally purchase organic products, are unwilling to pay more for organic eggs than for enhanced animal welfare eggs, suggesting diminishing marginal utility for additional attributes. We find that a third consumer segment attempts to avoid organic eggs, even when they cost the same as other eggs. Our findings suggest that organic products will be unsuccessful in acquiring a larger share of the market as long as most consumers are unwilling to pay a premium for organic products with all their cost increasing sustainable attributes over products that have only a single sustainable attribute, in our case enhanced animal welfare.
Curriculum Mapping: A Before‐and‐After Look at Faculty Perceptions of Their Courses and the Mapping Process
Authors: Joyner (Melito) Helen S. 
Published: March 2016

AbstractThe increased interest in program‐ and university‐level assessment over the past few decades has led to increased faculty involvement in developing program learning outcomes and performing program assessment activities. Depending on the level of support and encouragement faculty receive from administration and other entities, they may support or resist these activities. Faculty resistance may stem from fear of losing control of their course content, discouragement over previous failed assessment attempts, or confusion from inconsistent leadership. The School of Food Science, a joint program between the Washington State University and the University of Idaho, recently completed a curriculum mapping and assessment exercise that was conducted entirely by faculty. Faculty members teaching undergraduate courses were surveyed about their opinions of the mapping and assessment process both before and after the process was conducted. The goal of the surveys was to evaluate faculty opinion of these processes and how that opinion changed after completing the processes. Faculty members were generally supportive of the mapping and assessment processes, and willing to participate, and this opinion did not change after the processes were complete. The results of the mapping and assessment activities surprised most of the faculty, and they stated that they had ideas to address the issues found during the exercises. Overall, these results are encouraging in terms of faculty support of the mapping and assessment processes. Provided that administrative support of these processes continues and there is consistent leadership, faculty should continue to be supportive of program level assessment.
Ancestry Estimation in Forensic Anthropology: Geometric Morphometric versus Standard and Nonstandard Interlandmark Distances
Authors: Katherine Spradley M. , Jantz Richard L. 
Published: March 2016

AbstractStandard cranial measurements are commonly used for ancestry estimation; however, 3D digitizers have made cranial landmark data collection and geometric morphometric (GM) analyses more popular within forensic anthropology. Yet there has been little focus on which data type works best. The goal of the present research is to test the discrimination ability of standard and nonstandard craniometric measurements and data derived from GM analysis. A total of 31 cranial landmarks were used to generate 465 interlandmark distances, including a subset of 20 commonly used measurements, and to generate principal component scores from procrustes coordinates. All were subjected to discriminant function analysis to ascertain which type of data performed best for ancestry estimation of American Black and White and Hispanic males and females. The nonstandard interlandmark distances generated the highest classification rates for females (90.5%) and males (88.2%). Using nonstandard interlandmark distances over more commonly used measurements leads to better ancestry estimates for our current population structure.
Left Diaphragm Laceration Due to Cardiopulmonary Resuscitation
Authors: Dupont Vincent , Rougé‐Maillart Clotilde , Gaudin Arnaud , Jeanneteau Audrey , Jousset Nathalie , Malbranque Stéphane 
Published: March 2016

AbstractExternal cardiac massage is the essential life‐saving gesture for the management of any cardiac arrest. Since the 1960s, many recommendations have been published to improve the effectiveness of chest compressions alongside the development of automated systems intended to maximize the chances of survival. The use of these manual and/or instrumental techniques can cause secondary injuries, of which rib fractures are the most commonly observed by forensic pathologists. However, a comprehensive review of the literature seldom highlights reports of injuries to the abdomen, even less so to the diaphragm. In this observation, an iatrogenic left diaphragmatic laceration for the first time is described, as a result of manual and instrumental cardiopulmonary resuscitation, in a victim from an intrathoracic wound caused by a bladed weapon.
Evaluation of Virulence Factors and Antifungal Susceptibility in Yeast Isolates from Postmortem Specimens
Authors: Yagmur Gulhan , Sav Hafize , Ziyade Nihan , Elgormus Neval , Sen Sumeyye , Akkoyun Bilgi Esma , Atan Yusuf , Buyuk Yalcin , Kiraz Nuri 
Published: March 2016

AbstractInvasive fungal infections are a leading cause of morbidity and mortality in immunocompromised patients, especially in cases requiring a prolonged stay in the intensive care unit. A total of 99 yeast strains were isolated from 42 postmortem cases. In this study, virulence factors and antifungal susceptibility of these species were evaluated. The isolates were identified as Candida albicans (54), C. tropicalis (15), C. glabrata (12), C. parapsilosis (6), C. lipolytica (3), C. utilis (3), C. krusei (2), C. kefyr (1), and Cryptococcus neoformans (3). The most commonly isolated species was C. albicans, and no resistant species were determined. Despite the equal number of specimens, no secretion of significant virulence factors was associated with the postmortem specimen in the Candida species. Postmortem fungal investigations in forensic autopsies are useful in explaining cause of death in such cases, also may lead to protocols for the treatment of fungal infections and contribute to fungal pathogenesis and epidemiological data.
Cinnamomum camphora Seed Kernel Oil Ameliorates Oxidative Stress and Inflammation in Diet‐Induced Obese Rats
Authors: Fu Jing , Zeng Cheng , Zeng Zheling , Wang Baogui , Gong Deming 
Published: March 2016

AbstractCinnamomum camphora seed kernel oil (CCSKO) was found to reduce body fat deposition and improve blood lipid in both healthy and obese rats. The study was aimed to investigate the antioxidative stress and anti‐inflammatory effects of CCSKO in high‐fat‐diet‐induced obese rats. The obese rats were treated with CCSKO, lard, and soybean oil, respectively, for 12 wk. The level of total antioxidant capacity (T‐AOC), activities of superoxide dismutase (SOD), glutathione peroxidase, and catalase, and levels of malondialdehyde (MDA), tumor necrosis factor (TNF)‐α, peroxisome proliferator‐activated receptor (PPAR)‐γ, interleukin (IL)‐6, and P65 were compared among CCSKO, lard, and soybean oil groups. Our results showed that the level of T‐AOC and activities of SOD and catalase were significantly increased and the level of MDA was significantly decreased in CCSKO group. In addition, CCSKO treatment reduced the activities of serum glutamic oxaloacetic transaminase and glutamate‐pyruvate transaminase, and levels of serum TNF‐α, IL‐6, and P65 through raising the level of PPAR‐γ. In conclusion, CCSKO has, for the first time, been found to ameliorate oxidative stress and inflammation in high‐fat‐diet‐induced obese rats.
Development of a universal double‐digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa
Authors: Burford Reiskind M. O. , Coyle K. , Daniels H. V. , Labadie P. , Reiskind M. H. , Roberts N. B. , Roberts R. B. , Schaff J. , Vargo E. L. 
Published: March 2016

AbstractThe generation of genome‐scale data is critical for a wide range of questions in basic biology using model organisms, but also in questions of applied biology in nonmodel organisms (agriculture, natural resources, conservation and public health biology). Using a genome‐scale approach on a diverse group of nonmodel organisms and with the goal of lowering costs of the method, we modified a multiplexed, high‐throughput genomic scan technique utilizing two restriction enzymes. We analysed several pairs of restriction enzymes and completed double‐digestion RAD sequencing libraries for nine different species and five genera of insects and fish. We found one particular enzyme pair produced consistently higher number of sequence‐able fragments across all nine species. Building libraries off this enzyme pair, we found a range of usable SNPs between 4000 and 37 000 SNPS per species and we found a greater number of usable SNPs using reference genomes than de novo pipelines in STACKS. We also found fewer reads in the Read 2 fragments from the paired‐end Illumina Hiseq run. Overall, the results of this study provide empirical evidence of the utility of this method for producing consistent data for diverse nonmodel species and suggest specific considerations for sequencing analysis strategies.
Zero expiratory pressure and low oxygen concentration promote heterogeneity of regional ventilation and lung densities
Authors: Borges J. B. , Porra L. , Pellegrini M. , Tannoia A. , Derosa S. , Larsson A. , Bayat S. , Perchiazzi G. , Hedenstierna G. 
Published: March 2016

BackgroundIt is not well known what is the main mechanism causing lung heterogeneity in healthy lungs under mechanical ventilation. We aimed to investigate the mechanisms causing heterogeneity of regional ventilation and parenchymal densities in healthy lungs under anesthesia and mechanical ventilation.MethodsIn a small animal model, synchrotron imaging was used to measure lung aeration and regional‐specific ventilation (sV̇). Heterogeneity of ventilation was calculated as the coefficient of variation in sV̇ (CVsV̇). The coefficient of variation in lung densities (CVD) was calculated for all lung tissue, and within hyperinflated, normally and poorly aerated areas. Three conditions were studied: zero end‐expiratory pressure (ZEEP) and FIO2 0.21; ZEEP and FIO2 1.0; PEEP 12 cmH2O and FIO21.0 (Open Lung‐PEEP = OLP).ResultsThe mean tissue density at OLP was lower than ZEEP‐1.0 and ZEEP‐0.21. There were larger subregions with low sV̇ and poor aeration at ZEEP‐0.21 than at OLP: 12.9 ± 9.0 vs. 0.6 ± 0.4% in the non‐dependent level, and 17.5 ± 8.2 vs. 0.4 ± 0.1% in the dependent one (P = 0.041). The CVsV̇ of the total imaged lung at PEEP 12 cmH2O was significantly lower than on ZEEP, regardless of FIO2, indicating more heterogeneity of ventilation during ZEEP (0.23 ± 0.03 vs. 0.54 ± 0.37, P = 0.049). CVD changed over the different mechanical ventilation settings (P = 0.011); predominantly, CVD increased during ZEEP. The spatial distribution of the CVD calculated for the poorly aerated density category changed with the mechanical ventilation settings, increasing in the dependent level during ZEEP.ConclusionZEEP together with low FIO2 promoted heterogeneity of ventilation and lung tissue densities, fostering a greater amount of airway closure and ventilation inhomogeneities in poorly aerated regions.