bluuebunny/crossref_metadata_2025 huggingface dataset:
The reproductive ecology of the invasive Asian paddle crab, Charybdis japonica (Brachyura: Portunidae), in northeastern New Zealand
Authors: Wong Nicholas A. , Sewell Mary A.
Published: November 2015

The Asian paddle crab, Charybdis japonica, native to the northwest Pacific, is an invasive species that has established populations within northeastern New Zealand. Here, we provide a detailed examination of C. japonica's reproductive seasonality and gametogenesis, sizes at physiological maturity, and sex ratios outside its native range. Trapping in the Weiti River Estuary, Whangaparoa (36°38.4′S, 174°43.6′E) from February 2010 to May 2012 indicated a male‐biased population. Reproductive seasonality largely depended on female condition, since males contained ripe spermatozoa year‐round. Female gametogenesis began during late autumn, with oocyte development occurring throughout winter to early spring. Based on the presence of mature gametes during late winter and the appearance of gravid females in early November, mating began during early spring, with spawning in mid‐spring. Spawning coincided with a large drop in the gonad index, and occurred between sea surface temperatures of 17–22°C and 11.75–13.5 h day length. Females remained reproductive for up to 5 months of the year. Histological observation suggested that CW50 (the carapace width at which 50% of the population is mature) for females was 46.39 mm, while CW50 for males could not be determined due to a paucity of immature males. Histological analysis also suggested that females of C. japonica could produce store sperm and multiple broods annually.
Structural, Optical, and Piezoelectric Response of Lead‐Free Ba0.95Mg0.05Zr0.1Ti0.9O3 Nanocrystalline Powder
Authors: Bhimireddi Rajasekhar , Ponraj Bharathi , Varma Kalidindi B. R.
Published: November 2015

Nanocrystalline powders of Ba1−xMgxZr0.1Ti0.9O3 (x = 0.025–0.1) were synthesized via citrate assisted sol–gel method. Interestingly, the one with x = 0.05 in the system Ba1−xMgxZr0.1Ti0.9O3 exhibited fairly good piezoelectric response aside from the other physical properties. The phase and structural confirmation of synthesized powder was established by X‐ray powder diffraction (XRD) and Raman Spectroscopic techniques. Two distinct Raman bands i.e., 303 and 723 cm−1 characteristic of tetragonal phase were observed. Thermogravimetric analysis (TGA) was performed to evaluate the phase decomposition of the as‐synthesized Ba0.95Mg0.05Zr0.1Ti0.9O3 sample as a function of temperature. The average crystallite size associated with Ba0.95Mg0.05Zr0.1Ti0.9O3 was calculated using Scherrer formula based on the XRD data and was found to be 25 nm. However, Scanning and Transmission Electron Microscopy studies revealed the average crystallite size to be in the range of 30–40 nm, respectively. Kubelka–Munk function was employed to determine the optical band gap of these nanocrystallites. A piezoelectric response of 26 pm/V was observed for Ba0.95Mg0.05Zr0.1Ti0.9O3 nanocrystal by Piezoresponse Force Microscopy (PFM) technique. Photoluminescence (PL) study carried out on these nanocrystals exhibited a blue emission (470 nm) at room temperature.
The Role of Microstructure on Microwave Dielectric Properties of (Ba,Sr)TiO3 Ceramics
Authors: Song Zhe , Xu Qi , Zhang Shujun , Liu Hanxing , Luo Wei , Hao Hua , Cao Minghe , Yao Zhonghua , Hu Wei , Shi Yatong , Lanagan Michael T.
Published: November 2015

Microstructural effects on the microwave dielectric properties of (Ba0.4Sr0.6)TiO3 (BST) polycrystalline ceramics were investigated, focusing on the grain size. Sintering temperatures between 1350°C and 1500°C have a strong effect on the permittivity (880 < εr < 990), quality factor (570 GHz < Q×f < 1150 GHz), and temperature coefficient of resonant frequency (3920 ppm/°C < τf < 4560 ppm/°C) at microwave frequency (≈1.4 GHz). The tunable permittivity characteristics (measured at 10 kHz), were also found to be sensitive to the sintering process, demonstrating the possibility of tailoring material property by designed processing. In addition, the effect of the sintering process on grain structure was investigated by XRD calculation and Raman scattering characterization. Less confined phonons were believed to contribute to the enhanced microwave performance as an intrinsic effect (grain size effect), for samples with higher sintering temperature and longer dwell time. On the contrary, the macroscopic properties tend to saturate (or deteriorate), for samples at intensified sintering condition, being thought to be dominated by the extrinsic factors (such as the abundant defects in large grains), as confirmed by the SEM observations.
Governance Structure and Firm Performance in Private Family Firms
Authors: Che Limei , Langli John Christian
Published: November 2015

Although a large proportion of firms are family owned and most family firms are private, our understanding of private family firms is limited. Using confidential information on family relationships between board members, CEOs, and shareholders, this is the first study to provide large‐scale evidence on the association between governance structure and firm performance in family‐controlled private firms. Our sample is unique as it covers almost all private limited liability firms in Norway, spans 11 years, traces firm ownership to ultimate owners, and identifies family relationship using data on kinship, marriage, and adoption. The results show a U‐shaped relationship between family ownership and firm performance. Higher ownership of the second largest owner, higher percentage of family members on the board, stronger family power, and smaller boards are associated with higher firm performance. In addition, the positive association between the ownership of the second largest owner and firm performance also occurs when the second largest owner is a member of the controlling family, but the association is stronger when the second largest owner is a non‐family member. We further test the relative importance of these test variables and find that ownership structure is more associated with firm performance than board structure.
Genome‐wide study on intramuscular fat in Italian Large White pig breed using the PorcineSNP60 BeadChip
Authors: Davoli R. , Luise D. , Mingazzini V. , Zambonelli P. , Braglia S. , Serra A. , Russo V.
Published: November 2015

Genome‐wide association study results are presented for intramuscular fat in Italian Large White pig breed. A total of 886 individuals were genotyped with PorcineSNP60 BeadChip. After quality control performed with plink software and in R environment, 49 208 markers remained for the association analysis. The genome‐wide association studies was conducted using linear mixed model implemented in GenABEL. We detected seven new SNPs of genes till now not found associated to intramuscular fat (IMF). Three markers map in a wide intergenic region rich of QTL linked to fat traits, one map 388 kb upstream the gene SDK1, one map inside PPP3CA gene, one inside SCPEP1 gene and the last is not mapped in the porcine genome yet. Associations here presented indicate a moderate effect of these genes on IMF. In particular, PPP3CA, that is involved in the oxidative metabolism of skeletal muscle, could be considerated as an interesting candidate gene for IMF content in pigs. However, further studies are needed to clarify the role of these genes on the physiological processes involved in IMF regulation. These results may be useful to control this trait that is important in terms of nutritional, technological and organoleptic characteristics of fresh meat and processed products.
Restoring the youth of aged red blood cells and extending their lifespan in circulation by remodelling membrane sialic acid
Authors: Huang Yao‐Xiong , Tuo Wei‐Wei , Wang Di , Kang Li‐Li , Chen Xing‐Yao , Luo Man
Published: November 2015

Membrane sialic acid (SA) plays an important role in the survival of red blood cells (RBCs), the age‐related reduction in SA content negatively impacts both the structure and function of these cells. We have therefore suggested that remodelling the SA in the membrane of aged cells would help recover cellular functions characteristic of young RBCs. We developed an effective method for the re‐sialylation of aged RBCs by which the cells were incubated with SA in the presence of cytidine triphosphate (CTP) and α‐2,3‐sialytransferase. We found that RBCs could be re‐sialylated if they had available SA‐binding groups and after the re‐sialylation, aged RBCs could restore their membrane SA to the level in young RBCs. Once the membrane SA was restored, the aged RBCs showed recovery of their biophysical and biochemical properties to similar levels as in young RBCs. Their life span in circulation was also extended to twofold. Our findings indicate that remodelling membrane SA not only helps restore the youth of aged RBCs, but also helps recover injured RBCs.
Resistance of cotton genotypes with different leaf colour and trichome density to Bemisia tabaci biotype B
Authors: do Prado J. C. , Peñaflor M. F. G. V. , Cia E. , Vieira S. S. , Silva K. I. , Carlini‐Garcia L. A. , Lourenção A. L.
Published: November 2015

The silverleaf whitefly (SLW), Bemisia tabaci biotype B, is considered one of the most serious pests in cotton worldwide. Its control is based on the use of pesticides, which are well‐known for their harmful effects on non‐target organisms and the environment. Here, we examined resistance of several cotton genotypes in terms of antixenosis and antibiosis against SLW. We also investigated the mechanisms of cotton genotypes involved in antixenosis against SLW by correlating with leaf trichome density and leaf colour parameters. In choice tests, we selected resistant cotton genotypes, Gossypium hirsutum palmeri, Aubum 56‐7, G. hirsutum morrilli, Mocó, Nu‐16 (B2 B3 B6)‐ 78/658, Paymaster 53‐816 and ‘IAC 23’, based on SLW oviposition and host preference. No‐choice tests with these genotypes confirmed antixenosis effect on SLW; however, no antibiosis resistance was detected in terms of developmental period and adult emergence rate. We found SLW oviposition preference was positively correlated with trichome density in the abaxial leaf surface, while adult host preference was mostly explained by high levels of green intensity of adaxial surface. Nevertheless, both SLW oviposition and host preference were negatively correlated with the lightness level of adaxial leaf surface. Probably, the underlying mechanism of cotton resistance is based on more than just these two parameters, but our study will contribute to selecting resistant cotton genotypes and helps to understand the mechanisms involved in cotton resistance against SLW. To our best knowledge, this is the first work showing that cotton leaf colour parameters are related to resistance against SLW.
Antipredator responses in Tetranychus urticae differ with predator specialization
Authors: Jacobsen S. K. , Alexakis I. , Sigsgaard L.
Published: November 2015

The behavioural response of Tetranychus urticae to chemical cues from specialist predatory mites, Phytoseiulus persimilis, or generalist predatory bugs, Orius majusculus, on either bean or strawberry was studied in experimental arenas. Predators were placed on the leaf disc for 24 h and removed before T. urticae females were introduced. After 24 h, prey fecundity (number of eggs laid) and dispersal (number of prey drowned in the water barrier) were assessed. Chemical cues from the specialist predator resulted in reduced prey fecundity, significantly different from the generalist predator and control treatments. No interaction effect was found between plant species and prey fecundity, while significantly more eggs were laid on bean than on strawberry. Predator cues irrespective of predator specialization resulted in more prey dispersal than in the control. Findings emphasize the importance of specialization in the predator species complex for the degree and type of antipredator responses and resulting biological control.
Does individual variation in metabolic phenotype predict fish behaviour and performance?
Authors: Metcalfe N. B. , Van Leeuwen T. E. , Killen S. S.
Published: November 2015

There is increasing interest in documenting and explaining the existence of marked intraspecific variation in metabolic rate in animals, with fishes providing some of the best‐studied examples. After accounting for variation due to other factors, there can typically be a two to three‐fold variation among individual fishes for both standard and maximum metabolic rate (SMR and MMR). This variation is reasonably consistent over time (provided that conditions remain stable), and its underlying causes may be influenced by both genes and developmental conditions. In this paper, current knowledge of the extent and causes of individual variation in SMR, MMR and aerobic scope (AS), collectively its metabolic phenotype, is reviewed and potential links among metabolism, behaviour and performance are described. Intraspecific variation in metabolism has been found to be related to other traits: fishes with a relatively high SMR tend to be more dominant and grow faster in high food environments, but may lose their advantage and are more prone to risk‐taking when conditions deteriorate. In contrast to the wide body of research examining links between SMR and behavioural traits, very little work has been directed towards understanding the ecological consequences of individual variation in MMR and AS. Although AS can differ among populations of the same species in response to performance demands, virtually nothing is known about the effects of AS on individual behaviours such as those associated with foraging or predator avoidance. Further, while factors such as food availability, temperature, hypoxia and the fish's social environment are known to alter resting and MMRs in fishes, there is a paucity of studies examining how these effects vary among individuals, and how this variation relates to behaviour. Given the observed links between metabolism and measures of performance, understanding the metabolic responses of individuals to changing environments will be a key area for future research because the environment will have a strong influence on which animals survive predation, become dominant and ultimately have the highest reproductive success. Although current evidence suggests that variation in SMR may be maintained within populations via context‐dependent fitness benefits, it is suggested that a more integrative approach is now required to fully understand how the environment can modulate individual performance via effects on metabolic phenotypes encompassing SMR, MMR and AS.
More Facts about Prices: France Before and During the Great Recession
Authors: BERARDI NICOLETTA , GAUTIER ERWAN , BIHAN HERVÉ LE
Published: November 2015

Using microprice data, we document new facts on price rigidity in France: (i) each month 20.1% of prices are changed, which compares to 24.1% in the United States—excluding sales, however, the fraction of prices modified each month is about the same in France and in the United States (around 17%); (ii) the distribution of price changes is quite dispersed; (iii) the frequencies of price increases and decreases contribute a lot to inflation variations, and price increases are more frequent in January (even when sales are excluded); (iv) sales contribute significantly to the volatility of inflation but play a minor role in the transmission of macroeconomic fluctuations to prices; and (v) during the Great Recession patterns of price adjustment were only slightly modified.
Strategic Interactions and Portfolio Choice in Money Management: Theory and Evidence
Authors: PEDRAZA ALVARO
Published: November 2015

I study portfolio choice of strategic fund managers in the presence of a peer‐based underperformance penalty. While the penalty generates herding behavior, correlated trading among managers is exacerbated when a strategic setting is considered. The equilibrium portfolios are driven by the least restricted manager, who may vary according to the realization of returns. I compare model predictions to evidence from the Colombian pension fund management industry, where six asset managers are in charge of portfolio allocation for the mandatory contributions of the working population. These managers are subject to a peer‐based underperformance penalty, which is known as the minimum return guarantee (MRG). I study trading behavior by managers before and after a change in the strictness of the MRG in June 2007. The evidence suggests that a tighter MRG results in more trading in the direction of peers, a behavior that is more pronounced for underperforming managers. I show that these findings are consistent with the qualitative and quantitative predictions of the theoretical model.
The efficacy and safety of combined microneedle fractional radiofrequency and sublative fractional radiofrequency for acne scars in Asian skin
Authors: Park Jae Yang , Lee Eo Gin , Yoon Moon Soo , Lee Hee Jung
Published: November 2015

Background

Microneedle fractional radiofrequency has been reported to be effective for improving wrinkles, enlarged pores and various scars. Sublative fractional radiofrequency has been shown to induce both fractional ablation of epidermis and upper dermal remodelling, which had rejuvenation effects in photoaged skin. Both modalities may have the potential synergy to improve acne scars.

Objective

To evaluate the efficacy and safety of combined microneedle and sublative fractional radiofrequency for acne scars in Asian skin.

Methods

Twenty subjects comprised 11 males and 9 females (mean age 23.65 ± 2.94, skin phototype III–IV) with moderate to severe acne scars. The subjects received three consecutive combined microneedle and sublative fractional radiofrequency at 4‐week intervals over 12 weeks. Both blinded dermatologists and subjects assessed the clinical improvement based on the standardized photography and questionnaires, respectively. The quartile grading scale was utilized and defined as follows: grade 1, 0–25% improvement; grade 2, 26–50% improvement; grade 3, 51–75% improvement and grade 4, 76–100% improvement.

Results

All 20 subjects were assessed to have grade 2 or more clinical improvement by physicians; four (20%) had grade 4, 10 (50%) had grade 3, and six (30%) had grade 2 improvement. The subjects' grading also showed a good concordance as indicated by Kappa index of 0.695. The mean duration of post‐therapy crusting was 5.2 days and post‐therapy erythema lasted 2.5 days.

Conclusion

Combined microneedle and sublative fractional radiofrequency can have a positive therapeutic effect with no serious complications and may provide a new therapeutic approach on acne scars in Asians.
Rapid Detection of Watermelon Viruses by Reverse Transcription Loop‐Mediated Isothermal Amplification
Authors: Zhao Lei , Liu Yang , Wu Yunfeng , Hao Xingan
Published: November 2015

In this study, a stable, sensitive and specific one‐step reverse transcription loop‐mediated isothermal amplification (RT‐LAMP) assay was developed to detect three watermelon viruses. The RT‐LAMP primers were designed based on the coat protein gene sequences of the watermelon mosaic virus (WMV) and the squash mosaic virus (SqMV), as well as the cylindrical inclusion protein gene sequence of the zucchini yellow mosaic virus (ZYMV). Results could be obtained within an hour at temperatures of 60–61°C. The sensitivity of the RT‐LAMP assay was 10–100 times higher than that of the conventional RT‐PCR method. In addition, RT‐LAMP does not require specialized equipment and can be performed under general experimental conditions. This report is the first to use RT‐LAMP for WMV, SqMV and ZYMV detection. The proposed RT‐LAMP method has great potential for applications in watermelon virus detection, identification and control strategies.
Bible Beliefs, Conservative Religious Identity, and Same‐Sex Marriage Support: Examining Main and Moderating Effects
Authors: Perry Samuel L.
Published: November 2015

Research finds that Americans who espouse theologically conservative beliefs about the Bible generally oppose same‐sex marriage. Studies exploring this link, however, have been limited in that their operationalization of fundamentalist belief has been problematically conceptualized and they have potentially confounded the effect of conservative religious identity. The current study asks: (1) How do distinct beliefs about the nature and authority of the Bible influence same‐sex marriage support? (2) Do these beliefs influence same‐sex marriage support independently of conservative religious identity? (3) To what extent do Bible beliefs and conservative religious identity moderate one another's effects? And (4) to what extent are these factors moderated by religious tradition and frequency of Bible reading? Analyses of 2006 Portraits of American Life Study data reveal that while identifying as religiously conservative is the strongest predictor of opposition to same‐sex marriage, believing in inerrancy and creationism remain strong predictors in full models. I also find moderating effects between belief in creationism, inerrancy, inspiration; religious‐conservative identity; and religious tradition. Findings clarify how theological beliefs and religious identity shape support for same‐sex marriage across religious traditions.
Inequality and the Altruistic Life: A Study of the Priestly Vocation Rate
Authors: Fishman Robert M. , Gervasoni Carlos , Stater Keely Jones
Published: November 2015

This article takes the rate of new incorporations into the Catholic priesthood within national societies as a social fact revealing underlying societal tendencies of broad theoretical relevance extending well beyond the study of religion. Our emphasis lies on the impact of income inequality on the prevalence of altruistic life options. We examine cross‐national and time‐series variation in the priestly vocation rate as the empirical foundation to theorize social dynamics underpinning a life option that entails the renunciation of opportunities for individual material advantage alongside the commitment to serve a broader community. The article elaborates why we view the vocation rate as resting on a combination of piety and altruistic dispositions, and provides a theoretical rationale for expecting inequality to diminish this—and other—altruistic life options. We also examine the impact of other variables that have been theorized to influence the prevalence of Catholic clerical vocations and elaborate the broader theoretical relevance of our empirical findings.
Breeding Restrictions Decrease the Prevalence of Myxomatous Mitral Valve Disease in Cavalier King Charles Spaniels over an 8‐ to 10‐Year Period
Authors: Birkegård A.C. , Reimann M.J. , Martinussen T. , Häggström J. , Pedersen H.D. , Olsen L.H.
Published: November 2015

Background

Cavalier King Charles Spaniels (CKCS) are predisposed to myxomatous mitral valve disease (MMVD). Studies have indicated a strong genetic background.

Objective

The aim of this study was to evaluate the effect of a breeding scheme involving auscultation and echocardiography.

Animals

In the Danish Kennel Club mandatory breeding scheme, 997 purebredCKCSwere examined during the period 2002–2011. Each dog was evaluated 1–4 times with a total of 1,380 examinations.

Methods

Auscultation and echocardiography were performed to evaluate mitral regurgitation murmur severity and degree of mitral valve prolapse (MVP). The odds of having mitral regurgitation murmur orMVP> grade 1 in 2010–2011 compared to 2002–2003 were estimated using logistic regression analysis including age and sex as covariates. Odds were estimated for dogs that were products of the breeding scheme (defined as dogs with both parents approved by the breeding scheme before breeding) and non‐products of the breeding scheme (defined as dogs with at least 1 parent with unknown cardiac status).

Results

In 2010–2011, the odds of having mitral regurgitation murmur were 0.27 if dogs were a product of the breeding scheme compared with dogs in 2002–2003, reflecting a 73% decreased risk (P < .0001). If non‐products of the breeding scheme examined in 2010–2011 were compared with dogs in 2002–2003, no difference in odds was found (P = .49).

Conclusion and Clinical Importance

A mandatory breeding scheme based on auscultation and echocardiography findings significantly decreased the prevalence ofMMVDover the 8‐ to 10‐year period. Such a breeding scheme therefore is recommended forCKCS.
Governance of Defense and Policymaking in Chile
Authors: Solar Carlos
Published: November 2015

As Latin American countries work toward leaving military regimes well behind, the current governing of defense in the hands of civilians unveils a series of challenges for democratically elected leaders. This article analyzes the case study of Chile's contemporary defense sector and its policymaking after three decades of evolving civil–military relations. The research focuses particularly on the Estrategia Nacional de Seguridad y Defensa (ENSYD), a government‐led policy program launched in 2013 that failed to achieve its goals and faced extensive opposition, for example, in its human security approach to understanding security threats. The article explores and builds on civil–military relations literature and suggests the governance of defense as a concept to study further the constant governing processes by which institutions assume different beliefs and interests in relation to how policies are planned and executed.
Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes
Authors: Saenz‐Agudelo Pablo , Dibattista Joseph D. , Piatek Marek J. , Gaither Michelle R. , Harrison Hugo B. , Nanninga Gerrit B. , Berumen Michael L.
Published: November 2015

Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographical features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two‐band anemonefish Amphiprion bicinctus across its entire geographical range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the southern coast of Oman. Both the Red Sea and the Arabian Sea are complex and environmentally heterogeneous marine systems that provide an ideal scenario to address these questions. Our findings confirm the presence of two genetic clusters previously reported for A. bicinctus in the Red Sea. Genetic structure analyses suggest a complex seascape configuration, with evidence of both isolation by distance (IBD) and isolation by environment (IBE). In addition to IBD and IBE, genetic structure among sites was best explained when two barriers to gene flow were also accounted for. One of these coincides with a strong oligotrophic–eutrophic gradient at around 16–20˚N in the Red Sea. The other agrees with a historical bathymetric barrier at the straight of Bab al Mandab. Finally, these data support the presence of interspecific hybrids at an intermediate suture zone at Socotra and indicate complex patterns of genomic admixture in the Gulf of Aden with evidence of introgression between species. Our findings highlight the power of recent genomic approaches to resolve subtle patterns of gene flow in marine seascapes.
The role of parasite‐driven selection in shaping landscape genomic structure in red grouse (Lagopus lagopus scotica)
Authors: Wenzel Marius A. , Douglas Alex , James Marianne C. , Redpath Steve M. , Piertney Stuart B.
Published: November 2015

Landscape genomics promises to provide novel insights into how neutral and adaptive processes shape genome‐wide variation within and among populations. However, there has been little emphasis on examining whether individual‐based phenotype–genotype relationships derived from approaches such as genome‐wide association (GWAS) manifest themselves as a population‐level signature of selection in a landscape context. The two may prove irreconcilable as individual‐level patterns become diluted by high levels of gene flow and complex phenotypic or environmental heterogeneity. We illustrate this issue with a case study that examines the role of the highly prevalent gastrointestinal nematode Trichostrongylus tenuis in shaping genomic signatures of selection in red grouse (Lagopus lagopus scotica). Individual‐level GWAS involving 384 SNPs has previously identified five SNPs that explain variation in T. tenuis burden. Here, we examine whether these same SNPs display population‐level relationships between T. tenuis burden and genetic structure across a small‐scale landscape of 21 sites with heterogeneous parasite pressure. Moreover, we identify adaptive SNPs showing signatures of directional selection using outlier analysis and relate population‐ and individual‐level patterns of multilocus neutral and adaptive genetic structure to T. tenuis burden. The five candidate SNPs for parasite‐driven selection were neither associated with T. tenuis burden on a population level, nor under directional selection. Similarly, there was no evidence of parasite‐driven selection in SNPs identified as candidates for directional selection. We discuss these results in the context of red grouse ecology and highlight the broader consequences for the utility of landscape genomics approaches for identifying signatures of selection.
The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens
Authors: Wilson Benjamin A. , Garud Nandita R. , Feder Alison F. , Assaf Zoe J. , Pennings Pleuni S.
Published: November 2015

Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance.
The rate of adaptive evolution in animal mitochondria
Authors: James Jennifer E. , Piganeau Gwenael , Eyre‐Walker Adam
Published: November 2015

We have investigated whether there is adaptive evolution in mitochondrial DNA, using an extensive data set containing over 500 animal species from a wide range of taxonomic groups. We apply a variety of McDonald–Kreitman style methods to the data. We find that the evolution of mitochondrial DNA is dominated by slightly deleterious mutations, a finding which is supported by a number of previous studies. However, when we control for the presence of deleterious mutations using a new method, we find that mitochondria undergo a significant amount of adaptive evolution, with an estimated 26% (95% confidence intervals: 5.7–45%) of nonsynonymous substitutions fixed by adaptive evolution. We further find some weak evidence that the rate of adaptive evolution is correlated to synonymous diversity. We interpret this as evidence that at least some adaptive evolution is limited by the supply of mutations.
Inferring speciation history in the Andes with reduced‐representation sequence data: an example in the bay‐backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.)
Authors: Winger Benjamin M. , Hosner Peter A. , Bravo Gustavo A. , Cuervo Andrés M. , Aristizábal Natalia , Cueto Luis E. , Bates John M.
Published: November 2015

In the Andes, humid‐forest organisms frequently exhibit pronounced genetic structure and geographic variation in phenotype, often coincident with physical barriers to dispersal. However, phylogenetic relationships of clades have often been difficult to resolve due to short internodes. Consequently, even in taxa with well‐defined genetic structure, the temporal and geographic sequences of dispersal and vicariance events that led to this differentiation have remained opaque, hindering efforts to test the association between diversification and earth history and to understand the assembly of species‐rich communities on Andean slopes. Here, we use mitochondrial DNA and thousands of short‐read sequences generated with genotyping by sequencing (GBS) to examine the geographic history of speciation in a lineage of passerine birds found in the humid forest of the Andes, the ‘bay‐backed’ antpitta complex (Grallaria hypoleuca s. l). Mitochondrial DNA genealogies documented genetic structure among clade but were poorly resolved at nodes relevant for biogeographic inference. By contrast, relationships inferred from GBS loci were highly resolved and suggested a biogeographic history in which the ancestor originated in the northern Andes and dispersed south. Our results are consistent with a scenario of vicariant speciation wherein the range of a widespread ancestor was fragmented as a result of geologic or climatic change, rather than a stepping‐stone series of dispersal events across pre‐existing barriers. However, our study also highlights challenges of distinguishing dispersal‐mediated speciation from static vicariance. Our results further demonstrate the substantial evolutionary timescale over which the diverse biota of the Andes was assembled.
Natural killer cell‐mediated damage of clinical isolates of mucormycetes
Authors: Schmidt Stanislaw , Schneider Andreas , Demir Asuman , Lass‐Flörl Cornelia , Lehrnbecher Thomas
Published: November 2015

Haematopoietic stem cell transplant (HSCT) recipients are at high risk for mucormycosis, which has a mortality of up to 90%. The adoptive transfer of Natural killer (NK) cells is a promising therapeutic option in order to improve the reconstitution of host immunity after HSCT and to directly combat the fungal pathogen. As a number of fungal pathogens have developed strategies to evade the innate immune system, we investigated the interaction of human NK cells with various clinical isolates of different species of mucormycetes. Our results show that human IL‐2 prestimulated NK cells damaged all mucormycetes tested. The extent of the damage depended, at least in part, on the growth curve characteristics of the individual fungal isolate. All isolates decreased the secretion of interferon‐γ by NK cells to a similar extent. Our data suggest that NK cells damage a wide spectrum of mucormycetes, but that the antifungal effect is higher if NK cells are administered at an early time point of infection.
Applicability of digital analysis and imaging technology in neuropathology assessment
Authors: Dunn William D. , Gearing Marla , Park Yuna , Zhang Lifan , Hanfelt John , Glass Jonathan D. , Gutman David A.
Published: November 2015

Alzheimer's disease (AD) is a progressive neurological disorder that affects more than 30 million people worldwide. While various dementia‐related losses in cognitive functioning are its hallmark clinical symptoms, ultimate diagnosis is based on manual neuropathological assessments using various schemas, including Braak staging, CERAD (Consortium to Establish a Registry for Alzheimer's Disease) and Thal phase scoring. Since these scoring systems are based on subjective assessment, there is inevitably some degree of variation between readers, which could affect ultimate neuropathology diagnosis. Here, we report a pilot study investigating the applicability of computer‐driven image analysis for characterizing neuropathological features, as well as its potential to supplement or even replace manually derived ratings commonly performed in medical settings. In this work, we quantitatively measured amyloid beta (Aβ) plaque in various brain regions from 34 patients using a robust digital quantification algorithm. We next verified these digitally derived measures to the manually derived pathology ratings using correlation and ordinal logistic regression methods, while also investigating the association with other AD‐related neuropathology scoring schema commonly used at autopsy, such as Braak and CERAD. In addition to successfully verifying our digital measurements of Aβ plaques with respective categorical measurements, we found significant correlations with most AD‐related scoring schemas. Our results demonstrate the potential for digital analysis to be adapted to more complex staining procedures commonly used in neuropathological diagnosis. As the efficiency of scanning and digital analysis of histology images increases, we believe that the basis of our semi‐automatic approach may better standardize quantification of neuropathological changes and AD diagnosis, ultimately leading to a more comprehensive understanding of neurological disorders and more efficient patient care.
The tomato mutant ars1 (altered response to salt stress 1) identifies an R1‐type MYB transcription factor involved in stomatal closure under salt acclimation
Authors: Campos Juan F. , Cara Beatriz , Pérez‐Martín Fernando , Pineda Benito , Egea Isabel , Flores Francisco B. , Fernandez‐Garcia Nieves , Capel Juan , Moreno Vicente , Angosto Trinidad , Lozano Rafael , Bolarin Maria C.
Published: November 2015

A screening under salt stress conditions of a T‐DNA mutant collection of tomato (Solanum lycopersicum L.) led to the identification of the altered response to salt stress 1 (ars1) mutant, which showed a salt‐sensitive phenotype. Genetic analysis of the ars1 mutation revealed that a single T‐DNA insertion in the ARS1 gene was responsible of the mutant phenotype. ARS1 coded for an R1‐MYB type transcription factor and its expression was induced by salinity in leaves. The mutant reduced fruit yield under salt acclimation while in the absence of stress the disruption of ARS1 did not affect this agronomic trait. The stomatal behaviour of ars1 mutant leaves induced higher Na+ accumulation via the transpiration stream, as the decreases of stomatal conductance and transpiration rate induced by salt stress were markedly lower in the mutant plants. Moreover, the mutation affected stomatal closure in a response mediated by abscisic acid (ABA). The characterization of tomato transgenic lines silencing and overexpressing ARS1 corroborates the role of the gene in regulating the water loss via transpiration under salinity. Together, our results show that ARS1 tomato gene contributes to reduce transpirational water loss under salt stress. Finally, this gene could be interesting for tomato molecular breeding, because its manipulation could lead to improved stress tolerance without yield penalty under optimal culture conditions.
Incidence, risk factors, and outcomes of opportunistic infections in pediatric renal transplant recipients
Authors: Jordan Cameron L. , Taber David J. , Kyle Maggee O. , Connelly James , Pilch Nicole W. , Fleming James , Meadows Holly B. , Bratton Charles F. , Nadig Satish N. , McGillicuddy John W. , Chavin Kenneth D. , Baliga Prabhakar K. , Shatat Ibrahim F. , Twombley Katherine
Published: November 2015

OIs present significant risks to patients following solid organ transplantation. The purpose of this study was to identify risk factors for the development of OIs after kidney transplantation in pediatric patients and to evaluate the impact of OIs on outcomes in this patient population. A single‐center retrospective longitudinal cohort analysis including pediatric patients 21 yr of age or younger transplanted from July 1999 to June 2013 at an academic medical center was conducted. Patients were excluded if they received multi‐organ transplant. A total of 175 patients were included in the study. Patients who developed OIs were more likely to be female and younger at the time of transplant. A six‐factor risk model for OI development was developed. Death, disease recurrence, and PTLD development were similar between groups but trended toward increased incidence in the OI group. Incidence of rejection was significantly higher in the OI group (p = 0.04). Patients who developed OIs had several important risk factors, including younger age, EBV‐negative serostatus, CMV donor (+)/recipient (−), biopsy‐proven acute rejection, ANC <1000, MMF dose >500 mg/m2, and any infection. Incidence of rejection was higher in the OI group, but rate of graft loss was not statistically different.
Asymmetric Linkages between BRICS Stock Returns and Country Risk Ratings: Evidence from Dynamic Panel Threshold Models
Authors: Mensi Walid , Hammoudeh Shawkat , Yoon Seong‐Min , Nguyen Duc Khuong
Published: November 2015

This study investigates the asymmetric linkages between the five BRICS (Brazil, Russia, India, China and South Africa) countries’ stock markets and three country risk ratings (financial, economic and political risk) in the presence of major global economic and financial factors. Using the dynamic panel threshold models, we find evidence of asymmetry in most cases. However, the significance and the signs of the effects of these risk ratings on the BRICS market returns differ across the lower and upper regimes. Furthermore, improvements in the global stock, West Texas Intermediate (WTI) and gold markets enhance the BRICS stock market performance. Increases in implied volatility indices lead to drops in the BRICS markets.
Spillovers from Foreign Exporters
Authors: Bohnstedt Anna
Published: November 2015

We develop a general equilibrium model of international trade with heterogeneous firms that accounts for productivity spillovers transmitted by foreign exporters. Everything else equal, stronger spillovers increase welfare. We embed the model framework into a trade policy scenario where countries strategically set inter‐country variable trade costs for the trading partner. In the strategic Nash‐equilibrium policy, governments trade‐off welfare gains from protectionism and those that are due to spillovers from foreign exporters. The equilibrium degree of protectionism is decreasing in the strength of the spillover. Policy coordination induces welfare gains but these gains can be hump‐shaped in the spillover strength.
Overborrowing and Balance of Payments Imbalances in a Monetary Union
Authors: Sy Mouhamadou
Published: November 2015

The sources of the balance of payments imbalances in the Euro area can be characterized by a combination of four phenomena: (i) the credit imbalances between the core and the periphery of the Economic and Monetary Union (EMU) (ii) the credit misallocation between the tradable and the nontradable sectors in the periphery (iii) the rapid increase in the output and the price of nontradable goods in the periphery since the beginning of the EMU and (iv) the current account imbalances within the EMU. This paper explains all four of these stylized facts within a single model as a result of the interaction between the common monetary policy, inflation heterogeneity and a relaxation of the credit constraint in the nontradable sector of the periphery. When nontradable goods are used as collateral, an increase in their prices can initiate an overborrowing spiral and lead to a balance of payment imbalances. Furthermore, the model endogenizes differences in unit labor costs between the core and the periphery of the Euro area.
Correction of the HLA‐DQB1*04:01:01 sequence at position 79 in exon 1
Authors: Okudaira Y. , Hosomichi K. , Ozaki Y. , Shiina T. , Mitsunaga S.
Published: November 2015

The HLA‐DQB1*04:01:01 sequence is corrected at position 79 in exon 1 (G > A, Ala > Thr).
A genome‐scale metabolic network reconstruction of tomato (Solanum lycopersicum L.) and its application to photorespiratory metabolism
Authors: Yuan Huili , Cheung C.Y. Maurice , Poolman Mark G. , Hilbers Peter A. J. , van Riel Natal A. W.
Published: November 2015

Tomato (Solanum lycopersicum L.) has been studied extensively due to its high economic value in the market, and high content in health‐promoting antioxidant compounds. Tomato is also considered as an excellent model organism for studying the development and metabolism of fleshy fruits. However, the growth, yield and fruit quality of tomatoes can be affected by drought stress, a common abiotic stress for tomato. To investigate the potential metabolic response of tomato plants to drought, we reconstructed iHY3410, a genome‐scale metabolic model of tomato leaf, and used this metabolic network to simulate tomato leaf metabolism. The resulting model includes 3410 genes and 2143 biochemical and transport reactions distributed across five intracellular organelles including cytosol, plastid, mitochondrion, peroxisome and vacuole. The model successfully described the known metabolic behaviour of tomato leaf under heterotrophic and phototrophic conditions. The in silico investigation of the metabolic characteristics for photorespiration and other relevant metabolic processes under drought stress suggested that: (i) the flux distributions through the mevalonate (MVA) pathway under drought were distinct from that under normal conditions; and (ii) the changes in fluxes through core metabolic pathways with varying flux ratio of RubisCO carboxylase to oxygenase may contribute to the adaptive stress response of plants. In addition, we improved on previous studies of reaction essentiality analysis for leaf metabolism by including potential alternative routes for compensating reaction knockouts. Altogether, the genome‐scale model provides a sound framework for investigating tomato metabolism and gives valuable insights into the functional consequences of abiotic stresses.
Load-based Exergetic Assessment of an Offshore Thermal Power Plant in an Equatorial Environment
Authors: Adumene Sidum
Published: November 2015

The Load-based exergetic assessment of a thermal power plant for offshore utilization was carried out. The gas turbine systems were split into sub-systems and simplified into control volume to show inflow and outflow of exergy at different loading. The operating parameters of the plant were monitored for 12 months through human machine interface (HMI), and the data collected were used with thermodynamic relations to carry out the assessment.  MATLAB 7.3 ® Software was used to evaluate the various model equations and results tabulated. The results show that for every 1% drop in the operational load, the thermal efficiency and exergy efficiency drop by 0.17% and 0.25% respectively. It further shows that there is about 0.006% decrease in fuel consumption under the same conditions, and at 44% loading the system has the highest percentage of exergy loss of about 21.3%. This means that as the operational load decrease, the percentage exergy loss increase proportionally. Enormous exergy is lost in the exhaust system due to absence of heat recovery steam generator. The assessment established that the components of the power plant degrade in the quality of exergy and performance at different loading of the plant due to mechanical loss and irreversibility.