bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cityscape genetics: structural vs. functional connectivity of an urban lizard population
Authors: Beninde Joscha , Feldmeier Stephan , Werner Maike , Peroverde Daniel , Schulte Ulrich , Hochkirch Axel , Veith Michael 
Published: August 2016

AbstractFunctional connectivity is essential for the long‐term persistence of populations. However, many studies assess connectivity with a focus on structural connectivity only. Cityscapes, namely urban landscapes, are particularly dynamic and include numerous potential anthropogenic barriers to animal movements, such as roads, traffic or buildings. To assess and compare structural connectivity of habitats and functional connectivity of gene flow of an urban lizard, we here combined species distribution models (SDMs) with an individual‐based landscape genetic optimization procedure. The most important environmental factors of the SDMs are structural diversity and substrate type, with high and medium levels of structural diversity as well as open and rocky/gravel substrates contributing most to structural connectivity. By contrast, water cover was the best model of all environmental factors following landscape genetic optimization. The river is thus a major barrier to gene flow, while of the typical anthropogenic factors only buildings showed an effect. Nonetheless, using SDMs as a basis for landscape genetic optimization provided the highest ranked model for functional connectivity. Optimizing SDMs in this way can provide a sound basis for models of gene flow of the cityscape, and elsewhere, while presence‐only and presence–absence modelling approaches showed differences in performance. Additionally, interpretation of results based on SDM factor importance can be misleading, dictating more thorough analyses following optimization of SDMs. Such approaches can be adopted for management strategies, for example aiming to connect native common wall lizard populations or disconnect them from non‐native introduced populations, which are currently spreading in many cities in Central Europe.
Seascape genomics provides evidence for thermal adaptation and current‐mediated population structure in American lobster (Homarus americanus)
Authors: Benestan Laura , Quinn Brady K. , Maaroufi Halim , Laporte Martin , Clark Fraser K. , Greenwood Spencer J. , Rochette Rémy , Bernatchez Louis 
Published: August 2016

AbstractInvestigating how environmental features shape the genetic structure of populations is crucial for understanding how they are potentially adapted to their habitats, as well as for sound management. In this study, we assessed the relative importance of spatial distribution, ocean currents and sea surface temperature (SST) on patterns of putatively neutral and adaptive genetic variation among American lobster from 19 locations using population differentiation (PD) approaches combined with environmental association (EA) analyses. First, PD approaches (using bayescan, arlequin and outflank) found 28 outlier SNPs putatively under divergent selection and 9770 neutral SNPs in common. Redundancy analysis revealed that spatial distribution, ocean current‐mediated larval connectivity and SST explained 31.7% of the neutral genetic differentiation, with ocean currents driving the majority of this relationship (21.0%). After removing the influence of spatial distribution, no SST were significant for putatively neutral genetic variation whereas minimum annual SST still had a significant impact and explained 8.1% of the putatively adaptive genetic variation. Second, EA analyses (using Pearson correlation tests, bayescenv and lfmm) jointly identified seven SNPs as candidates for thermal adaptation. Covariation at these SNPs was assessed with a spatial multivariate analysis that highlighted a significant temperature association, after accounting for the influence of spatial distribution. Among the 505 candidate SNPs detected by at least one of the three approaches, we discovered three polymorphisms located in genes previously shown to play a role in thermal adaptation. Our results have implications for the management of the American lobster and provide a foundation on which to predict how this species will cope with climate change.
Evolution and function of eukaryotic‐like proteins from sponge symbionts
Authors: Reynolds David , Thomas Torsten 
Published: August 2016

AbstractSponges (Porifera) are ancient metazoans that harbour diverse microorganisms, whose symbiotic interactions are essential for the host's health and function. Although symbiosis between bacteria and sponges are ubiquitous, the molecular mechanisms that control these associations are largely unknown. Recent (meta‐) genomic analyses discovered an abundance of genes encoding for eukaryotic‐like proteins (ELPs) in bacterial symbionts from different sponge species. ELPs belonging to the ankyrin repeat (AR) class from a bacterial symbiont of the sponge Cymbastela concentrica were subsequently found to modulate amoebal phagocytosis. This might be a molecular mechanism, by which symbionts can control their interaction with the sponge. In this study, we investigated the evolution and function of ELPs from other classes and from symbionts found in other sponges to better understand the importance of ELPs for bacteria–eukaryote interactions. Phylogenetic analyses showed that all of the nine ELPs investigated were most closely related to proteins found either in eukaryotes or in bacteria that can live in association with eukaryotes. ELPs were then recombinantly expressed in Escherichia coli and exposed to the amoeba Acanthamoeba castellanii, which is functionally analogous to phagocytic cells in sponges. Phagocytosis assays with E. coli containing three ELP classes (AR, TPR‐SEL1 and NHL) showed a significantly higher percentage of amoeba containing bacteria and average number of intracellular bacteria per amoeba when compared to negative controls. The result that various classes of ELPs found in symbionts of different sponges can modulate phagocytosis indicates that they have a broader function in mediating bacteria–sponge interactions.
Hidden histories of gene flow in highland birds revealed with genomic markers
Authors: Zarza Eugenia , Faircloth Brant C. , Tsai Whitney L.E. , Bryson Robert W. , Klicka John , McCormack John E. 
Published: August 2016

AbstractGenomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species‐rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well‐studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these ‘hidden histories’ using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation‐with‐bouts‐of‐gene‐flow will turn out to be a common mode of speciation.
Evolutionary processes and cellular functions underlying divergence in Alexandrium minutum
Authors: Le Gac Mickael , Metegnier Gabriel , Chomérat Nicolas , Malestroit Pascale , Quéré Julien , Bouchez Olivier , Siano Raffaele , Destombe Christophe , Guillou Laure , Chapelle Annie 
Published: August 2016

AbstractUnderstanding divergence in the highly dispersive and seemingly homogeneous pelagic environment for organisms living as free drifters in the water column remains a challenge. Here, we analysed the transcriptome‐wide mRNA sequences, as well as the morphology of 18 strains of Alexandrium minutum, a dinoflagellate responsible for harmful algal blooms worldwide, to investigate the functional bases of a divergence event. Analysis of the joint site frequency spectrum (JSFS) pointed towards an ancestral divergence in complete isolations followed by a secondary contact resulting in gene flow between the two diverging groups, but heterogeneous across sites. The sites displaying fixed SNPs were associated with a highly restricted gene flow and a strong overrepresentation of nonsynonymous polymorphism, suggesting the importance of selective pressures as drivers of the divergence. The most divergent transcripts were homologs to genes involved in calcium/potassium fluxes across the membrane, calcium transduction signal and saxitoxin production. The implication of these results in terms of ecological divergence and build‐up of reproductive isolation is discussed. Dinoflagellates are especially difficult to study in the field at the ecological level due to their small size and the dynamic nature of their natural environment, but also at the genomic level due to their huge and complex genome and the absence of closely related model organism. This study illustrates the possibility to identify the traits of primary importance in ecology and evolution starting from high‐throughput sequencing data, even for such organisms.
Systems proteomic analysis reveals that clusterin and tissue inhibitor of metalloproteinases 3 increase in leptomeningeal arteries affected by cerebral amyloid angiopathy
Authors: Manousopoulou A. , Gatherer M. , Smith C. , Nicoll J. A. R. , Woelk C. H. , Johnson M. , Kalaria R. , Attems J. , Garbis S. D. , Carare R. O. 
Published: August 2016

AimsAmyloid beta (Aβ) accumulation in the walls of leptomeningeal arteries as cerebral amyloid angiopathy (CAA) is a major feature of Alzheimer's disease. In this study, we used global quantitative proteomic analysis to examine the hypothesis that the leptomeningeal arteries derived from patients with CAA have a distinct endophenotypic profile compared to those from young and elderly controls.MethodsFreshly dissected leptomeningeal arteries from the Newcastle Brain Tissue Resource and Edinburgh Sudden Death Brain Bank from seven elderly (82.9 ± 7.5 years) females with severe capillary and arterial CAA, as well as seven elderly (88.3 ± 8.6 years) and five young (45.4 ± 3.9 years) females without CAA were used in this study. Arteries from four patients with CAA, two young and two elderly controls were individually analysed using quantitative proteomics. Key proteomic findings were then validated using immunohistochemistry.ResultsBioinformatics interpretation of the results showed a significant enrichment of the immune response/classical complement and extracellular matrix remodelling pathways (P < 0.05) in arteries affected by CAA vs. those from young and elderly controls. Clusterin (apolipoprotein J) and tissue inhibitor of metalloproteinases‐3 (TIMP3), validated using immunohistochemistry, were shown to co‐localize with Aβ and to be up‐regulated in leptomeningeal arteries from CAA patients compared to young and elderly controls.ConclusionsGlobal proteomic profiling of brain leptomeningeal arteries revealed that clusterin and TIMP3 increase in leptomeningeal arteries affected by CAA. We propose that clusterin and TIMP3 could facilitate perivascular clearance and may serve as novel candidate therapeutic targets for CAA.
Topical tocopherol for treatment of reticular oral lichen planus: a randomized, double‐blind, crossover study
Authors: Bacci C , Vanzo V , Frigo AC , Stellini E , Sbricoli L , Valente M 
Published: August 2016

ObjectiveThis randomized, double‐blind, placebo‐controlled crossover study assessed the efficacy of topical tocopherol acetate compared with placebo in easing oral discomfort in patients with reticular oral lichen planus (ROLP).Materials and MethodsThirty‐four patients with clinically diagnosed and histologically confirmed ROLP were randomly assigned to two groups, which received first one of two treatments (treatment 1 or 2) for a month, then the other (treatment 2 or 1) for another month, with a two‐week washout between them. One treatment contained tocopherol acetate and the other only liquid paraffin. The primary outcome was less discomfort, measured on a visual analog scale (VAS). Secondary outcomes were as follows: length of striae measured and photographed at each follow‐up; surface area of lesions; and a modified Thongprasom score.ResultsNo statistically significant differences emerged between the two treatments (1 vs 2) in terms of VAS scores (P > 0.05; 0.8624) or length of striae (P = 0.0883). Significant differences were seen for surface area of lesions (P < 0.05, P = 0.0045) and modified Thongprasom scores (P = 0.0052).ConclusionThe two treatments differed only in terms of the surface area of the lesions and Thongprasom scores, not in VAS scores for discomfort or the length of patients’ striae. Topical tocopherol proved effective in the treatment of ROLP.
The agreement between oscillometric and intra‐arterial technique for blood pressure monitoring in the lower extremities for infants and toddlers undergoing aortic coarctation repair
Authors: Peng Zhe‐Zhe , Zhang Ma‐Zhong , Sun Ying , Bai Jie , Gu Hong‐Bin , Liu Pei‐Pei , Li Min , Cai Mei‐Hua 
Published: August 2016

SummaryObjectiveAnesthetic management for patients undergoing surgical repair of aortic coarctation (CoA) should include constant blood pressure monitoring of the right upper extremity and a lower extremity. The delayed or absent pulse in the lower limbs often leads to unsuccessful arterial cannulation in infants and the oscillometric technique used for blood pressure measurement. The aim of this study was to evaluate the agreement between the oscillometric method and intra‐arterial technique for blood pressure monitoring in the lower limbs of infants undergoing CoA.MethodsA total of 45 infants diagnosed with isolated CoA were initially enrolled in this study and five were excluded because of cannulation failure. Thus, 40 patients had their blood pressure measured simultaneously by both oscillometric technique on the thigh and femoral artery catheterization. After induction and intubation, five pairs of blood pressure readings from each patient were collected in an interval of 3 min. Statistical analysis was accomplished by revised Bland–Altman analysis.ResultsThere was a strong correlation between oscillometric and invasive blood pressure measurements [systolic blood pressure (SBP) r = 0.771, diastolic blood pressure (DBP) r = 0.704 and mean artery pressure (MAP) r = 0.850]. The mean difference and 95% limits of agreement (95% LOA) between oscillometric and femoral artery blood pressure readings was 3.830 mmHg (−19.297, 26.957) for SBP, −8.725 mmHg (−26.236, 8.786) for DBP, and −3.235 mmHg (−18.842, 12.372) for MAP. There were only one pair of MAP (1/40) and two pairs of SBP readings (2/40) out of range (95% LOA), and all of paired DBP readings were within 95% LOA.ConclusionThere was a good agreement between oscillometric and invasive blood pressure measurements of lower extremities in infants with isolated CoA statistically. However, the oscillometry‐measured SBP showed a tendency to overestimate the intra‐arterial blood pressure reference, while oscillometry‐measured DBP underestimated its reference. MAP measurement provided the most accurate and reliable results in this study.
Gastric ultrasound as a preoperative bedside test for residual gastric contents volume in children
Authors: Schmitz Achim , Schmidt Alexander R. , Buehler Philipp K. , Schraner Thomas , Frühauf Melanie , Weiss Markus , Klaghofer Richard , Kellenberger Christian J. 
Published: August 2016

SummaryBackgroundEmergency situations and conditions with impaired gastric emptying enhance the risk of perioperative pulmonary aspiration due to increased residual gastric contents volume (GCV). Gastric ultrasonographic (US) measurement of the gastric antral cross‐sectional area (CSA) has been proposed to estimate preanesthetic GCV. However, only few healthy children and fasted pediatric patients have been investigated so far, predicting GCV with considerable imprecision. This study aimed to compare GCV assessed by US in different patient positions for measuring CSA, using magnetic resonance imaging (MRI) as reference, and to evaluate its potential as diagnostic test.MethodsHealthy volunteer children were examined in a crossover design on 2 days. After baseline examination, they received a light breakfast, followed by 7 ml·kg−1 clear fluid after 2 or 4 h. Gastric emptying was examined with MRI over 4 or 6 h, respectively. US was performed immediately after MRI in right lateral decubital (RLD) and supine with upper body elevated (SUBE) positions. Correlation coefficients (Pearson R; 95%CI) between CSA and body weight corrected GCV (GCVw) as determined by MRI volumetry were calculated. Data are presented as median (range).ResultsEighteen children aged 9.8 (6.8–12.2) years had 72 US examinations completed. CSA was 401 (101–1311) mm2 and 271 (118–582) mm2, and R between CSA and GCVw was 0.76 (0.76–1) and 0.57 (0.41–0.88) for the RLD and SUBE positions, respectively. The corresponding GCVw was 2.1 (0.1–13.8) ml·kg−1. A linear regression model from RLD was similar to one previously derived. Bland–Altman analysis and ROC plots are presented.ConclusionCSA correlated with GCVw in healthy children over a wide range of gastric filling, with the RLD position clearly superior to the SUBE position, confirming a previously derived formula. Although direct calculation of GCVw is imprecise, this technique has the potential to become a diagnostic risk assessment test.
Balance in children with acute lymphoblastic leukemia
Authors: Varedi Mitra , McKenna Raymond , Lamberg Eric M 
Published: August 2016

AbstractBackgroundTreatment for acute lymphoblastic leukemia (ALL) can affect balance via different mechanisms, including sensory and motor peripheral neuropathy, cognitive impairment, and reduced muscle strength and flexibility. To provide an overview of what is currently known about the effects of cancer treatment on balance in pediatric ALL patients and survivors, and of the predictors of poor balance, a review of the literature was conducted.MethodsFive databases were searched for English‐language original research articles on balance during or after treatment for pediatric ALL.ResultsFrom a total of nine studies, six identified significant balance problems in children with ALL during or after treatment. The percentage of patients or survivors with impaired balance varied between 27% and 69% during treatment, 7% and 65% a few years after completion of treatment, and 14% and 17% many years after the completion of treatment. Factors associated with impaired balance were higher body mass index; higher intrathecal methotrexate dose; cranial radiation; knee extensor weakness; and impaired cognition.ConclusionAlthough heterogeneity between the studies regarding patient age; age at diagnosis; time since completion of treatment; and methods of quantifying balance make it difficult to reach a single conclusion, the evidence suggests that survivors may experience short‐ and/or long‐term balance difficulties. While there is a need for additional studies to better understand the effects of impaired balance in survivors, clinicians treating both child and adult survivors of ALL need to be aware of these potential risks.
Reproductive biology of a hummingbird‐pollinated Billbergia: light influence on pollinator behaviour and specificity in a Brazilian semi‐deciduous forest
Authors: Pansarin E. R. , de Pedro S. R. M. 
Published: August 2016

Abstract

Ornithophily has evolved in parallel several times during evolution of angiosperms. Bird pollination is reported for 65 families, including Bromeliaceae. One of the most diverse bromeliad is Billbergia, which comprises species pollinated mainly by hummingbirds.

Based on investigations on flowering phenology, morpho‐anatomy, volume and concentration of nectar, pollinators and breeding system, this paper explores the reproductive biology and pollinator specificity of B. distachia in a mesophytic semi‐deciduous forest of southeastern Brazil.

The results have show that B. distachia is pollinated by a single species of hermit hummingbird, Phaethornis eurynome, which search for nectar produced by a septal nectary, where the secretory tissue is located above the placenta. The species is self‐incompatible. The combination of pollinator specificity, due to long corolla tubes that exclude visitation of short‐billed hummingbirds, complete self‐incompatibility and non‐territorial behaviour of pollinators, it is very important to reduce pollen loss and increase gene flow within population.

Our results indicate that studies on pollination biology and reproduction are essential to understand the evolutionary history of pollination systems of plants since, at least in Billbergia, variation in the pollinator spectrum has been recorded for different habitats among Brazilian forests. Furthermore, according to our data, foraging of Phaethornis on flowers is independent of air temperature and humidity, while the main factor influencing hummingbird visitation is daylight. Considering current knowledge on climatic parameters influencing hummingbird foraging, pollination and reproductive biology of Neotropical flora and environment of the hermit hummingbird in tropical forests, new insights on plant–pollinator interaction are provided.
Towards a Natural History of Foodgetting
Authors: Friedmann Harriet 
Published: August 2016

AbstractLike all species, humans change our environments to get food.Foodgetting is the dimension of human history that links us directly and indirectly with all other beings. Inescapably and at once both historical and natural, human foodgetting can be understood both as natural history and as historical nature. It implicates our species being in the evolving web of life. In its complex embodied, encultured and social relations, human nature evolves. To embrace that recognition requires thorough revision of inherited ideas. I draw on specific contributions among many thinkers engaged in this project by following a foodgetting thread through several literatures: (1) approaches to reconnecting natural with social sciences of human nature; (2) a “deep history” (Shryock and Smail 2011) of agriculture, which connects prehistory to written history, by Mazoyer and Roudart (1997, 2006), and its limits; (3) ecological resilience theory, and its model of panarchy, which resonates with emergence, dissolution, and reconstellation of food regimes and food regime transitions. This sets the stage for (4) clarifying different paths taken by food regime analysts, including my differences with co‐founder Philip McMichael. (5) I conclude by suggesting an approach to intentional change of human institutions centred on emergence, and (6) an example of emerging ways of organising territory centred on foodgetting.