bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatio‐temporal variation in density and size structure of the endangered sea cucumber Isostichopus fuscus in Huatulco National Park, Mexico
Authors: Glockner‐Fagetti Andrea , Benítez‐Villalobos Francisco 
Published: September 2016

AbstractThe brown sea cucumber Isostichopus fuscus (Ludwig, 1875) has been subjected to strong fishing pressure and is currently considered an endangered species by the IUCN Red List of Threatened Species. Spatial and temporal variations in density were analysed and population parameters of I. fuscus were estimated in three localities of the Southern Mexican Pacific. Density was estimated using circular transects covering a 300 m2 area in each locality. Body length and weight were also measured. The mean density was 0.018 ± 0.013 individuals·m−2, and was statistically significantly lower during summer. The mean length and weight were 22.4 ± 3.8 cm and 396 ± 130 g, respectively, and statistically significant differences were found among localities. The weight–length relationship was W = 0.28·L1.32 and the mean relative condition index (Kn) = 1.04 ± 0.31. The von Bertalanffy growth equation was Lt = 38.7·(1–exp(−0.4·t)). The lowest values of length, weight and age were found at Dos Hermanas, suggesting that this locality could be favorable for the settlement of larvae and recruitment and growth of juveniles. The present study is the second to estimate densities of I. fuscus and the first one to publish data on size structure and growth for the population at Bahias de Huatulco. The densities were so low in the three sampled localities that none of them would be able to support a fishery, even under a sustainable management scheme. The information collected in the present study could be helpful for management programs of the Huatulco National Park, as all the data used for these currently come mainly from the populations of I. fuscus in the Gulf of California.
Global population genetic dynamics of a highly migratory, apex predator shark
Authors: Bernard Andrea M. , Feldheim Kevin A. , Heithaus Michael R. , Wintner Sabine P. , Wetherbee Bradley M. , Shivji Mahmood S. 
Published: September 2016

AbstractKnowledge of genetic connectivity dynamics in the world's large‐bodied, highly migratory, apex predator sharks across their global ranges is limited. One such species, the tiger shark (Galeocerdo cuvier), occurs worldwide in warm temperate and tropical waters, uses remarkably diverse habitats (nearshore to pelagic) and possesses a generalist diet that can structure marine ecosystems through top‐down processes. We investigated the phylogeography and the global population structure of this exploited, phylogenetically enigmatic shark by using 10 nuclear microsatellites (n = 380) and sequences from the mitochondrial control region (CR, n = 340) and cytochrome oxidase I gene (n = 100). All three marker classes showed the genetic differentiation between tiger sharks from the western Atlantic and Indo‐Pacific ocean basins (microsatellite FST > 0.129; CR ΦST > 0.497), the presence of North vs. southwestern Atlantic differentiation and the isolation of tiger sharks sampled from Hawaii from other surveyed locations. Furthermore, mitochondrial DNA revealed high levels of intraocean basin matrilineal population structure, suggesting female philopatry and sex‐biased gene flow. Coalescent‐ and genetic distance‐based estimates of divergence from CR sequences were largely congruent (dcorr = 0.0015–0.0050), indicating a separation of Indo‐Pacific and western Atlantic tiger sharks <1 million years ago. Mitochondrial haplotype relationships suggested that the western South Atlantic Ocean was likely a historical connection for interocean basin linkages via the dispersal around South Africa. Together, the results reveal unexpectedly high levels of population structure in a highly migratory, behaviourally generalist, cosmopolitan ocean predator, calling for management and conservation on smaller‐than‐anticipated spatial scales.
Causes and consequences of large clonal assemblies in a poplar hybrid zone
Authors: Macaya‐Sanz David , Heuertz Myriam , Lindtke Dorothea , Vendramin Giovanni G. , Lexer Christian , González‐Martínez Santiago C. 
Published: September 2016

AbstractAsexual reproduction is a common and fundamental mode of reproduction in plants. Although persistence in adverse conditions underlies most known cases of clonal dominance, proximal genetic drivers remain unclear, in particular for populations dominated by a few large clones. In this study, we studied a clonal population of the riparian treePopulus albain the Douro river basin (northwestern Iberian Peninsula) where it hybridizes withPopulus tremula, a species that grows in highly contrasted ecological conditions. We used 73 nuclear microsatellites to test whether genomic background (species ancestry) is a relevant cause of clonal success, and to assess the evolutionary consequences of clonal dominance by a few genets. Additional genotyping‐by‐sequencing data were produced to estimate the age of the largest clones. We found that a few ancient (over a few thousand years old) and widespread genets dominate the population, both in terms of clone size and number of sexual offspring produced. Interestingly, large clones possessed two genomic regions introgressed fromP. tremula, which may have favoured their spread under stressful environmental conditions. At the population level, the spread of large genets was accompanied by an overall ancient (>0.1 Myr) but soft decline of effective population size. Despite this decrease, and the high clonality and dominance of sexual reproduction by large clones, the Douro hybrid zone still displays considerable genetic diversity and low inbreeding. This suggests that even in extreme cases as in the Douro, asexual and sexual dominance of a few large, geographically extended individuals does not threaten population survival.
Interactions between parental traits, environmental harshness and growth rate in determining telomere length in wild juvenile salmon
Authors: McLennan D. , Armstrong J. D. , Stewart D. C. , Mckelvey S. , Boner W. , Monaghan P. , Metcalfe N. B. 
Published: September 2016

AbstractA larger body size confers many benefits, such as increased reproductive success, ability to evade predators and increased competitive ability and social status. However, individuals rarely maximize their growth rates, suggesting that this carries costs. One such cost could be faster attrition of the telomeres that cap the ends of eukaryotic chromosomes and play an important role in chromosome protection. A relatively short telomere length is indicative of poor biological state, including poorer tissue and organ performance, reduced potential longevity and increased disease susceptibility. Telomere loss during growth may also be accelerated by environmental factors, but these have rarely been subjected to experimental manipulation in the natural environment. Using a wild system involving experimental manipulations of juvenile Atlantic salmon Salmo salar in Scottish streams, we found that telomere length in juvenile fish was influenced by parental traits and by direct environmental effects. We found that faster‐growing fish had shorter telomeres and there was a greater cost (in terms of reduced telomere length) if the growth occurred in a harsher environment. We also found a positive association between offspring telomere length and the growth history of their fathers (but not mothers), represented by the number of years fathers had spent at sea. This suggests that there may be long‐term consequences of growth conditions and parental life history for individual longevity.
Genomic divergence and lack of introgressive hybridization between two 13‐year periodical cicadas support life cycle switching in the face of climate change
Authors: Koyama Takuya , Ito Hiromu , Fujisawa Tomochika , Ikeda Hiroshi , Kakishima Satoshi , Cooley John R. , Simon Chris , Yoshimura Jin , Sota Teiji 
Published: September 2016

AbstractLife history evolution spurred by post‐Pleistocene climatic change is hypothesized to be responsible for the present diversity in periodical cicadas (Magicicada), but the mechanism of life cycle change has been controversial. To understand the divergence process of 13‐year and 17‐year cicada life cycles, we studied genetic relationships between two synchronously emerging, parapatric 13‐year periodical cicada species in the Decim group, Magicicada tredecim and M. neotredecim. The latter was hypothesized to be of hybrid origin or to have switched from a 17‐year cycle via developmental plasticity. Phylogenetic analysis using restriction‐site‐associated DNA sequences for all Decim species and broods revealed that the 13‐year M. tredecim lineage is genomically distinct from 17‐year Magicicada septendecim but that 13‐year M. neotredecim is not. We detected no significant introgression between M. tredecim and M. neotredecim/M. septendecim thus refuting the hypothesis that M. neotredecim are products of hybridization between M. tredecim and M. septendecim. Further, we found that introgressive hybridization is very rare or absent in the contact zone between the two 13‐year species evidenced by segregation patterns in single nucleotide polymorphisms, mitochondrial lineage identity and head width and abdominal sternite colour phenotypes. Our study demonstrates that the two 13‐year Decim species are of independent origin and nearly completely reproductively isolated. Combining our data with increasing observations of occasional life cycle change in part of a cohort (e.g. 4‐year acceleration of emergence in 17‐year species), we suggest a pivotal role for developmental plasticity in Magicicada life cycle evolution.
Duopolistic Price Competition with Captives
Authors: Babutsidze Zakaria 
Published: September 2016

AbstractWe extend the Bertrand duopolistic competition to include captives. These are consumers that have no choice between the suppliers. Usual population of shoppers are modeled performing a sequential search in order to decide where to buy a homogenous good. These two simple departures from the original setup have sharp consequences. First, we find that duopolistic price competition is not robust to inclusion of captives. The equilibrium results starkly differ and the only possible equilibrium now includes duopolists charging monopolistic prices. Second, addition of sequential search introduces multiplicity of pure strategy Nash equilibria. In this setup, we observe perverse optimal response to competitor's price changes. Notably, we find that the firm might want to reduce the price in response to the competitor's price increase, which is at odds with the usual undercutting principle. Third, we investigate the behavior of equilibrium prices depending on the heterogeneity in consumer risk attitudes. We find that the higher consumer heterogeneity with respect to acceptance of risky gambles leads to higher prices in equilibrium.
Alterations of CorTFL1 and CorAP1 expression correlate with major evolutionary shifts of inflorescence architecture in Cornus (Cornaceae) – a proposed model for variation of closed inflorescence forms
Authors: Ma Qing , Liu Xiang , Franks Robert G. , Xiang Qiu‐Yun (Jenny) 
Published: September 2016

Summary

TFL1‐, AP1‐ and LFY‐like genes are known to be key regulators of inflorescence development. However, it remains to be tested whether the evolutionary modifications of inflorescence morphology result from shifts in their expression patterns.

We compared the spatiotemporal expression patterns of CorTFL1, CorAP1 and CorLFY in six closely related Cornus species that display four types of closed inflorescence morphology using quantitative real‐time polymerase chain reaction (qRT‐PCR) and RNA in situ hybridization. Character mapping on the phylogeny was conducted to identify evolutionary changes and to assess the correlation between changes in gene expression and inflorescence morphology.

Results demonstrated variation of gene expression patterns among species and a strong correlation between CorTFL1 expression and the branch index of the inflorescence type. Evolutionary changes in CorTFL1 and CorAP1 expression co‐occurred on the phylogeny with the morphological changes underpinning inflorescence divergence.

The study found a clear correlation between the expression patterns of CorTFL1 and CorAP1 and the inflorescence architecture in a natural system displaying closed inflorescences. The results suggest a role for the alteration in CorTFL1 and CorAP1 expression during the evolutionary modification of inflorescences in Cornus. We propose that a TFL1‐like and AP1‐like gene‐based model may explain variation of closed inflorescences in Cornus and other lineages.
Introduction
Authors: Balfour Danny L. , Newbold Stephanie P. 
Published: September 2016

Related Content: King (PAR November/December 2016)Related Content: Fiorino (PAR November/December 2016)Related Content: Knox (PAR November/December 2016)Related Content: Brook (PAR November/December 2016)Related Content: Ingrams (PAR November/December 2016)
The Effects of Urbanization on Insurance Consumption—The experience of China
Authors: Barrese James , Wang Ping , Zhang Ji 
Published: September 2016

AbstractCross‐country studies of insurance find little support for a hypothesized urbanization–insurance consumption link. Unlike the literature, we argue and find that the relationship is positive. Our study refines the literature relating economic development and financial service activities. The empirical evidence in the existing literature is based on cross‐country samples that are criticized as unrepresentative because they are disproportionately composed of highly developed economies and consequently have limited range in the variables considered; this limits confidence in the resulting evidence. The current study overcomes these empirical difficulties by focusing on one large country with a unique recent development pattern. Like the existing studies, we find a positive insurance–economic development link. In contrast to cross‐country studies, we find that insurance consumption is influenced by urbanization and that the country's World Trade Organization entry had a differential impact on its insurance markets.
Indian Country Poverty: Place‐Based Poverty on American Indian Territories, 2006–10
Authors: Whitney Mauer K. 
Published: September 2016

AbstractThis article examines place‐based poverty in Indian Country, emphasizing that reservation characteristics are influenced by the system of federal Indian policy that affects American Indian self‐determination and antipoverty strategies within reservation boundaries. Using data from the American Community Survey five‐year file, 2006–10, I model poverty rates using multivariate, nested regression along key dimensions associated with American Indian antipoverty strategies and place‐based poverty. The results indicate that rates of female‐headed households and opportunity structures, such as lack of work, contribute to higher rates of reservation poverty while gaming acts as a slight buffer against poverty. Surprisingly, natural‐resource‐related occupations, thought to be associated with expropriation of tribal resources, was not associated with higher poverty, while self‐governance compacts, acting as a proxy for tribal autonomy, had no significant impact on poverty rates. As tribal governments seek to address poverty through strategies enabled by self‐determination policies, there is a critical need for more comprehensive and reliable data to understand how and whether tribal governments can effectively adapt federal policies to specific reservation conditions.
Quantitative assessment of biliary stent artifacts on MR images: Potential implications for target delineation in radiotherapy
Authors: Gurney‐Champion Oliver J. , Bruins Slot Thijs , Lens Eelco , van der Horst Astrid , Klaassen Remy , van Laarhoven Hanneke W. M. , van Tienhoven Geertjan , van Hooft Jeanin E. , Nederveen Aart J. , Bel Arjan 
Published: September 2016

PurposeBiliary stents may cause susceptibility artifacts, gradient‐induced artifacts, and radio frequency (RF) induced artifacts on magnetic resonance images, which can hinder accurate target volume delineation in radiotherapy. In this study, the authors investigated and quantified the magnitude of these artifacts for stents of different materials.MethodsEight biliary stents made of nitinol, platinum‐cored nitinol, stainless steel, or polyethylene from seven vendors, with different lengths (57–98 mm) and diameters (3.0–11.7 mm), were placed in a phantom. To quantify the susceptibility artifacts sequence‐independently, ΔB0‐maps and T2∗‐maps were acquired at 1.5 and 3 T. To study the effect of the gradient‐induced artifacts at 3 T, signal decay in images obtained with maximum readout gradient‐induced artifacts was compared to signal decay in reference scans. To quantify the RF induced artifacts at 3 T, B1‐maps were acquired. Finally, ΔB0‐maps and T2∗‐maps were acquired at 3 T of two pancreatic cancer patients who had received platinum‐cored nitinol biliary stents.ResultsOutside the stent, susceptibility artifacts dominated the other artifacts. The stainless steel stent produced the largest susceptibility artifacts. The other stents caused decreased T2∗ up to 5.1 mm (1.5 T) and 8.5 mm (3 T) from the edge of the stent. For sequences with a higher bandwidth per voxel (1.5 T: BWvox > 275 Hz/voxel; 3 T: BWvox > 500 Hz/voxel), the B0‐related susceptibility artifacts were negligible (<0.2 voxels). The polyethylene stent showed no artifacts. In vivo, the changes in B0 and T2∗ induced by the stent were larger than typical variations in B0 and T2∗ induced by anatomy when the stent was at an angle of 30° with the main magnetic field.ConclusionsSusceptibility artifacts were dominating over the other artifacts. The magnitudes of the susceptibility artifacts were determined sequence‐independently. This method allows to include additional safety margins that ensure target irradiation.
Technical Note: Calibrating radiochromic film in beams of uncertain quality
Authors: Peet Samuel C. , Wilks Rachael , Kairn Tanya , Trapp Jamie V. , Crowe Scott B. 
Published: September 2016

PurposeThe dose‐response of radiochromic film has been shown to be dependent on the quality of the incident radiation, particularly at low energies. Difficulty therefore arises when a calibration is required for radiation of uncertain energy. This study investigates the ability of a recently published calibration method [see M. Tamponi et al., “A new form of the calibration curve in radiochromic dosimetry. Properties and results,” Med. Phys. 43, 4435–4446 (2016)] to reduce the energy‐dependence of radiochromic film. This allows for corrections to be applied that may improve the accuracy and precision of measurements taken in beams of uncertain energy or where the beam quality is known but calibration doses cannot be delivered.MethodsGafchromic EBT3 film was irradiated with a range of superficial, orthovoltage, and high‐energy photon beams. Calibrations were then applied using a typical net optical density approach and compared with the Tamponi et al. method that instead defines the response as a ratio of two net optical densities. To quantify the energy dependence, the response at each beam quality and dose was then normalized to the response at a preselected reference quality. This resulted in a relative measure that could be used to correct the calibration curve at the reference beam quality to any other quality of interest.ResultsThe Tamponi et al. calibration method resulted in substantially less energy dependence compared to the standard net optical density approach, without compromising the calibration fit. The maximum deviation from the reference beam calibration curve was 7% across the range of energies and doses analyzed, reducing to <3% for doses greater than 200 cGy. However, the ability of the calibration curve to fit the data deteriorated as the curve was refitted with measurements at higher doses than those originally studied.ConclusionsThe Tamponi et al. calibration method, based on the ratio of two net optical densities, considerably reduces the energy dependence of Gafchromic EBT3 film. Manipulating the calibration data in the fashion presented in this study allows for a readily available calibration curve to be corrected to represent calibration curves at different energies. This may be useful when a calibration is desired for a beam where the delivery of a set of calibration doses is problematic, such as with out‐of‐field measurements, radioactive sources, and imaging applications.
Draft Genome Sequence of Klebsiella pneumoniae Strain AS Isolated from Zhejiang Provincial Hospital of TCM, China
Authors: Yang Xue-Jing , Wang Sai , Cao Jun-Min , Hou Jia-Hui 
Published: September 2016

ABSTRACT

Klebsiella pneumoniae
is a Gram-negative, nonmotile, encapsulated, lactose-fermenting, facultative anaerobic, rod-shaped bacterium. Here we present draft genome assemblies of
Klebsiella pneumoniae
AS, which was isolated in China. The genomic information will provide a better understanding of the physiology, adaptation, and evolution of
K. pneumoniae
.
Draft Genome Sequence of a Cardiobacterium hominis Strain Isolated from Blood Cultures of a Patient with Infective Endocarditis
Authors: Tagini Florian , Pillonel Trestan , Asner Sandra , Prod'hom Guy , Greub Gilbert 
Published: September 2016

ABSTRACT

Cardiobacterium hominis
is a well-known commensal bacterium of the oral cavity and an agent of infective endocarditis in humans. Here, we provide a draft genome sequence of a pathogenic strain isolated from blood cultures of a patient with infectious endocarditis.
Draft Genome Sequences of Histamine- and Non-Histamine-Producing
Photobacterium
Strains
Authors: Bjornsdottir-Butler Kristin , Sanchez Leon Maria , Dunlap Paul V. , Benner Ronald A. 
Published: September 2016

ABSTRACT

Histamine-producing bacteria (HPBs) have recently been identified from the marine environment. The identification and characterization of HPBs is important to developing effective mitigation strategies for scombrotoxin fish poisoning. We report here the draft genomes of seven histamine-producing and two non-histamine-producing marine
Photobacterium
strains.