bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternative eyrie use in peregrine falcons: is it a female choice?
Authors: Zuberogoitia I. , Zabala J. , Martínez J. E. , Olsen J. 
Published: February 2015

AbstractAll animals face the decision of where to breed, a decision that exerts a strong impact on fitness. We examined changes in choice of nest site in peregrine falcons (Falco peregrinus) over a 17‐year period in northern Spain. Falcons had a mean of 3.1 eyries per territory, each location used for a mean of 3.0 consecutive years. Surprisingly, change in eyrie location was not predicted by breeding productivity. However, breeding success decreased with the number of consecutive years that eyries were reused. Ectoparasitic infestation was not a significant predictor in the models. The number of fledglings in the previous season was the main factor explaining the eyrie‐switching decision, with successful pairs being more prone to move. Newly established females showed a higher tendency to switch (59%) than older territorial females (38%) but males did not exhibit the same tendency. High rainfall in April had a negative effect on productivity. In the case of females, changing the eyrie from one season to the next had a positive effect on productivity. In the case of models run with males as a random factor, rainfall in April and eyrie shelter reached significance. So, contrary to the ‘win–stay, lose–switch’ rule and in direct contrast with general literature, peregrines changed eyries after successfully raising large broods and eyrie switching increased the breeding success of females but not of males.
Evidence for alternative male morphs in a Tanganyikan cichlid fish
Authors: Hellmann J. K. , O'Connor C. M. , Ligocki I. Y. , Farmer T. M. , Arnold T. J. , Reddon A. R. , Garvy K. A. , Marsh‐Rollo S. E. , Balshine S. , Hamilton I. M. 
Published: February 2015

AbstractTeleost fish show tremendous variation in breeding systems. In particular, indeterminate growth and external fertilization create great disparities in reproductive success among males, which drive the evolution of male reproductive polymorphisms. Here, we present evidence for alternative male reproductive tactics in Neolamprologus modestus, a substrate‐spawning African cichlid fish. We observed two types of males in our study site: (1) males that guarded large territories comprised of smaller subterritories of several females and (2) males that did not hold territories and were vigorously attacked by the guarding males upon intrusion into the guarding male's territory. We hypothesized that these intruder males constitute an alternative male phenotype. To test this hypothesis, we collected both territorial males and these intruder males to determine if there were differences in overall body size, gonad size, age or hormone profiles between the two male phenotypes that would be consistent with alternative reproductive tactics in this species. We also collected guarded offspring from territorial male and female pairs to determine if there was any extra‐pair paternity in N. modestus that could indicate the possibility of alternative reproductive tactics. We found that intruder males were significantly smaller in body size and had significantly larger testes in absolute and relative mass compared with territorial paired males. While we assigned no paternity to any collected intruder males, we found that extra‐pair paternity occurred in eight of the 12 collected broods and accounted for c. 27% of all offspring across all broods. Finally, the two sets of males did not differ significantly in age or in circulating androgen levels, suggesting that individuals may not change morphs within their lifetime, but instead may adopt distinct life history strategies. Collectively, we provide strong evidence that intruder N. modestus males represent an alternative small‐bodied male morph that may practice alternative reproductive tactics.
Triple therapy with boceprevir or telaprevir in a European cohort of cirrhotic HIV/HCV genotype 1‐coinfected patients
Authors: Miailhes Patrick , Gilbert Camille , Lacombe Karine , Arends Joop E. , Puoti Massimo , Rockstroh Jürgen K. , Sogni Philippe , Fontaine Hélène , Rosenthal Eric , Winnock Maria , Loko Marc‐Arthur , Wittkop Linda , Dabis François , Salmon Dominique ,   the ESCMID European Study Group on Viral Hepatitis
Published: February 2015

AbstractBackground & AimsThe efficacy and safety of triple therapy combining boceprevir (BOC) or telaprevir (TVR) with pegylated interferon‐alfa and ribavirin (PegIFN/RBV) has rarely been investigated in human immunodeficiency virus/hepatitis C virus (HIV/HCV) genotype 1‐coinfected patients with cirrhosis.MethodsWe conducted a European (France, Italy, Germany, Netherlands) multicentre study of triple therapy in cirrhotic HIV/HCV GT1‐coinfected patients.ResultsFifty‐nine patients (47 TVR, 12 BOC) were studied. Median CD4 cell count was 457 (293–578)/mm3, and HIV viral load was <50 copies/ml in 93% of patients. The HCV genotype was GT1a (78%) or GT1b (13%). Previous PegIFN/RBV therapy had resulted in non‐response (73%) or relapse (12%), and 15% of patients were treatment‐naïve. The sustained virological response rate at week 12 (SVR12) was 53% overall (57% with TVR, 36% with BOC). A baseline HCV‐RNA level <800 000 IU/ml tended to be associated with SVR12 (65 vs 42%, P = 0.11). In multivariate analysis, a virological response at week 4 after BOC or TVR initiation was significantly associated with SVR12 (P = 0.040). Early discontinuation of triple therapy was frequent (n = 26, 44%), because of non‐response/breakthrough (65%) or adverse events (AEs) (35%). Three patients died. Severe anaemia (<9 g/dl) occurred in 14 patients (25%), leading to RBV dose reduction (22%), erythropoietin use (56%) or blood transfusion (14%). In multivariate analysis, lack of RBV dose reduction was significantly associated with severe AEs (P = 0.006).ConclusionsMore than half of HIV/HCV GT1‐coinfected patients with cirrhosis achieved a SVR12. To avoid unnecessary adverse effects, therapy should be discontinued if no response is obtained at week 4.
The role of climate adaptation in colonization success in Arabidopsis thaliana
Authors: Hamilton Jill A. , Okada Miki , Korves Tonia , Schmitt Johanna 
Published: February 2015

AbstractUnderstanding the genetic mechanisms that contribute to range expansion and colonization success within novel environments is important for both invasion biology and predicting species‐level responses to changing environments. If populations are adapted to local climates across a species' native range, then climate matching may predict which genotypes will successfully establish in novel environments. We examine evidence for climate adaptation and its role in colonization of novel environments in the model species, Arabidopsis thaliana. We review phenotypic and genomic evidence for climate adaptation within the native range and describe new analyses of fitness data from European accessions introduced to Rhode Island, USA, in spring and fall plantings. Accessions from climates similar to the Rhode Island site had higher fitness indicating a potential role for climate pre‐adaptation in colonization success. A genomewide association study (GWAS), and genotypic mean correlations of fitness across plantings suggest the genetic basis of fitness in Rhode Island differs between spring and autumn cohorts, and from previous fitness measurements in European field sites. In general, these observations suggest a scenario of conditional neutrality for loci contributing to colonization success, although there was evidence of a fitness trade‐off between fall plantings in Norwich, UK, and Rhode Island. GWAS suggested that antagonistic pleiotropy at a few specific loci may contribute to this trade‐off, but this conclusion depended upon the accessions included in the analysis. Increased genomic information and phenotypic information make A. thaliana a model system to test for the genetic basis of colonization success in novel environments.
The relative power of genome scans to detect local adaptation depends on sampling design and statistical method
Authors: Lotterhos Katie E. , Whitlock Michael C. 
Published: February 2015

AbstractAlthough genome scans have become a popular approach towards understanding the genetic basis of local adaptation, the field still does not have a firm grasp on how sampling design and demographic history affect the performance of genome scans on complex landscapes. To explore these issues, we compared 20 different sampling designs in equilibrium (i.e. island model and isolation by distance) and nonequilibrium (i.e. range expansion from one or two refugia) demographic histories in spatially heterogeneous environments. We simulated spatially complex landscapes, which allowed us to exploit local maxima and minima in the environment in ‘pair’ and ‘transect’ sampling strategies. We compared FST outlier and genetic–environment association (GEA) methods for each of two approaches that control for population structure: with a covariance matrix or with latent factors. We show that while the relative power of two methods in the same category (FST or GEA) depended largely on the number of individuals sampled, overall GEA tests had higher power in the island model and FST had higher power under isolation by distance. In the refugia models, however, these methods varied in their power to detect local adaptation at weakly selected loci. At weakly selected loci, paired sampling designs had equal or higher power than transect or random designs to detect local adaptation. Our results can inform sampling designs for studies of local adaptation and have important implications for the interpretation of genome scans based on landscape data.
Hfq binds directly to the ribosome‐binding site of IS10 transposase mRNA to inhibit translation
Authors: Ellis Michael J. , Trussler Ryan S. , Haniford David B. 
Published: February 2015

SummaryHfq is a critical component of post‐transcriptional regulatory networks in most bacteria. It usually functions as a chaperone for base‐pairing small RNAs, although non‐canonical regulatory roles are continually emerging. We have previously shown that Hfq represses IS10/Tn10 transposase expression through both antisense RNA‐dependent and independent mechanisms. In the current work, we set out to define the regulatory role of Hfq in the absence of the IS10 antisense RNA. We show here that an interaction between the distal surface of Hfq and the ribosome‐binding site of transposase mRNA (RNA‐IN) is required for repressing translation initiation. Additionally, this interaction was critical for the in vivo association of Hfq and RNA‐IN. Finally, we present evidence that the small RNA ChiX activates transposase expression by titrating Hfq away from RNA‐IN. The current results are considered in the broader context of Hfq biology and implications for Hfq titration by ChiX are discussed.
Mutability in Pseudomonas viridiflava as a programmed balance between antibiotic resistance and pathogenicity
Authors: Bartoli Claudia , Lamichhane Jay Ram , Berge Odile , Varvaro Leonardo , Morris Cindy E. 
Published: February 2015

SummaryMutable bacterial cells are defective in their DNA repair system and often have a phenotype different from that of their wild‐type counterparts. In human bacterial pathogens, the mutable and hypermutable phenotypes are often associated with general antibiotic resistance. Here, we quantified the occurrence of mutable cells in Pseudomonas viridiflava, a phytopathogenic bacterium in the P. syringae complex with a broad host range and capacity to live as a saprophyte. Two phenotypic variants (transparent and mucoid) were produced by this bacterium. The transparent variant had a mutator phenotype, showed general antibiotic resistance and could not induce disease on the plant species tested (bean). In contrast, the mucoid variant did not display mutability or resistance to antibiotics and was capable of inducing disease on bean. Both the transparent and mucoid variants were less fit when grown in vitro, whereas, in planta, both of the variants and wild‐types attained similar population densities. Given the importance of the methyl‐directed mismatch repair system (MMR) in the occurrence of mutable and hypermutable cells in human bacterial pathogens, we investigated whether mutations in mut genes were associated with mutator transparent cells in P. viridiflava. Our results showed no mutations in MMR genes in any of the P. viridiflava cells tested. Here, we report that a high mutation rate and antibiotic resistance are inversely correlated with pathogenicity in P. viridiflava, but are not associated with mutations in MMR. In addition, P. viridiflava variants differ from variants produced by other phytopathogenic bacteria in the absence of reversion to the wild‐type phenotype.
Comparing immunocompetent and immunodeficient mice as animal models for bone tissue engineering
Authors: Zhang Y , Li X , Chihara T , Mizoguchi T , Hori A , Udagawa N , Nakamura H , Hasegawa H , Taguchi A , Shinohara A , Kagami H 
Published: February 2015

ObjectivesTo understand the differences and similarities between immunocompetent and immunodeficient mice as ectopic transplantation animal models for bone tissue engineering.Materials and MethodsOsteogenic cells from mouse leg bones were cultured, seeded on β‐TCP granules, and transplanted onto the backs of either immunocompetent or immunodeficient nude mice. At 1, 2, 4, and 8 weeks postoperatively, samples were harvested and evaluated by hematoxylin–eosin staining, tartrate‐resistant acid phosphatase (TRAP) staining, and immunohistochemical staining and quantitative PCR.ResultsIn immunocompetent mice, inflammatory cell infiltration was evident at 1 week postoperatively and relatively higher expression of TNF‐α and IL‐4 was observed. In immunodeficient mice, new bone area and the number of TRAP‐positive cells were larger at 4 weeks than in immunocompetent mice. The volume of new bone area in immunodeficient mice was reduced by 8 weeks.ConclusionsBone regeneration was feasible in immunocompetent mice. However, some differences were observed between immunocompetent and immunodeficient mice in the bone regeneration process possibly due to different cytokine expression, which should be considered when utilizing in vivo animal models.
Real‐time visualization of melanin granules in normal human skin using combined multiphoton and reflectance confocal microscopy
Authors: Majdzadeh Ali , Lee Anthony M. D. , Wang Hequn , Lui Harvey , McLean David I. , Crawford Richard I. , Zloty David , Zeng Haishan 
Published: February 2015

SummaryBackgroundRecent advances in biomedical optics have enabled dermal and epidermal components to be visualized at subcellular resolution and assessed noninvasively. Multiphoton microscopy (MPM) and reflectance confocal microscopy (RCM) are noninvasive imaging modalities that have demonstrated promising results in imaging skin micromorphology, and which provide complementary information regarding skin components. This study assesses whether combined MPM/RCM can visualize intracellular and extracellular melanin granules in the epidermis and dermis of normal human skin.MethodsWe perform MPM and RCM imaging of in vivo and ex vivo skin in the infrared domain. The inherent three‐dimensional optical sectioning capability of MPM/RCM is used to image high‐contrast granular features across skin depths ranging from 50 to 90 μm. The optical images thus obtained were correlated with conventional histologic examination including melanin‐specific staining of ex vivo specimens.ResultsMPM revealed highly fluorescent granular structures below the dermal–epidermal junction (DEJ) region. Histochemical staining also demonstrated melanin‐containing granules that correlate well in size and location with the granular fluorescent structures observed in MPM. Furthermore, the MPM fluorescence excitation wavelength and RCM reflectance of cell culture‐derived melanin were equivalent to those of the granules.ConclusionThis study suggests that MPM can noninvasively visualize and quantify subepidermal melanin in situ.
Biocontrol traits of two Paenibacillus polymyxa strains SQR‐21 and WR‐2 in response to fusaric acid, a phytotoxin produced by Fusarium species
Authors: Raza W. , Yuan J. , Wu Y. C. , Rajer F. U. , Huang Q. , Qirong S. 
Published: February 2015

The aim of the present study was to investigate the effects of the phytotoxin fusaric acid (FA) on the biocontrol traits of two biocontrol strains Paenibacillus polymyxa WR‐2 and SQR‐21. The results showed that the growth of both WR‐2 and SQR‐21 decreased with increasing FA concentration, and at 70 and 80 μg mL−1 FA, respectively, the strains were unable to grow. The biocontrol traits of both strains were negatively affected by FA concentration higher than 2·5 μg mL−1. However, at 2·5 μg mL−1 FA, biofilm formation and root colonization were not affected and there was even a positive effect on the production of spores and hydrolytic enzymes (protease and β‐l,3‐glucanase). The production of fusaricidin‐type antifungal compounds was increased with an increase in FA concentration up to 50 and 60 μg mL−1 for WR‐2 and SQR‐21, respectively. The production of antifungal volatile organic compounds by WR‐2 and SQR‐21 was increased only at 2·5 μg mL−1 FA. The effect of FA on the overall metabolic activity of WR‐2 and SQR‐21 was also determined. This study will help to understand the response of P. polymyxa strains to FA and will help to improve their biocontrol efficiency.
Beyond Enforcement: Welcomeness, Local Law Enforcement, and Immigrants
Authors: Williams Linda M. 
Published: February 2015

AbstractStudies of local law enforcement actions toward immigrants show that while some cities engage in enforcement, many others do not. The extent and determinants of enforcement have been assessed, but these studies have not evaluated the full range of practices, including welcoming practices, toward immigrants. This article introduces the concept of “welcomeness,” develops a framework for measuring it, and, using a nationwide survey of local police departments, examines how widely departments are welcoming (or unwelcoming) to immigrants. The data show that many police departments have consciously and deliberately developed practices intended to foster positive relationships between the police and immigrants and to encourage immigrants to call the police for assistance.Practitioner PointsWelcomeness encompasses a range of practices toward immigrants that are often intentionally created, thoughtfully implemented, and found in a variety of communities.The dimensions of welcomeness provide a framework for police departments to assess their practices and provide a model for police departments that want to engage positively with immigrants.Welcoming practices may improve interactions between police officers and immigrants and may improve immigrants’ perceptions of local law enforcement.Welcoming police departments often have a deeper commitment to community policing.
Psychometric evaluation of the Swedish language Person‐centred Climate Questionnaire – family version
Authors: Lindahl Jeanette , Elmqvist Carina , Thulesius Hans , Edvardsson David 
Published: February 2015

BackgroundIn a holistic view of care, the family is important for the patient as well as for the staff and integration of family members in health care is a growing trend. Yet, family participation in the care is sparsely investigated and valid assessment instruments are needed.SettingData were collected from 200 family members participating in an intervention study at an emergency department (ED) in Sweden.MethodThe Person‐centred Climate Questionnaire – Family (PCQ‐F) is a measure for how family members perceive the psychosocial climate. PCQ‐F is a self‐report instrument that contains 17 items assessing safety, everydayness and hospitality – three subscale dimensions that mirror the Swedish patient version of the questionnaire, the PCQ‐P.AimThe aim of this study was to evaluate the psychometric properties of the Swedish version of the PCQ‐F in an ED context.ResultsThe psychometric properties of the PCQ‐F were evaluated using statistical estimates of validity and reliability and showed high content validity and internal consistency. Cronbach's Alpha was >0.7 and item–total correlations were >0.3 and <0.7.ConclusionIn terms of psychometrics, the findings in this study indicate that the PCQ‐F can be used with satisfactory validity and reliability to explore to what degree family members perceive ED settings as being person‐centred, safe, welcoming and hospitable within an everyday and decorated physical environment. As the PCQ already exists in a valid and reliable patient (PCQ‐P) and staff (PCQ‐S) version, this new family member version is a significant addition to the literature as it enables further comparative studies of how diverse care settings are perceived by different stakeholders.
Factors associated with low physical activity in patients with chronic obstructive pulmonary disease: a cross‐sectional study
Authors: Tödt Kristina , Skargren Elisabeth , Jakobsson Per , Theander Kersti , Unosson Mitra 
Published: February 2015

ObjectivesLow physical activity (PA) in chronic obstructive pulmonary disease (COPD) is associated with poor prognosis. In addition, physical activity seems to be low early in the disease. The aim of this study was to describe the level of PA in patients with stable COPD and to explore factors associated with low PA, with a focus on fatigue, symptom burden and body compositionMethodsIn a cross‐sectional study, 101 patients (52 women) with COPD were classified having low, moderate or high PA according to the International Physical Activity Questionnaire – Short. Fatigue, dyspnoea, depression and anxiety, symptom burden, body composition, physical capacity (lung function, exercise capacity, muscle strength), exacerbation rate and systemic inflammation were assessed. A multiple logistic regression was used to identify independent associations with low PA.ResultsMean age was 68 (±7) years, and mean percentage of predicted forced expiratory volume in 1 second was 50 (±16.5). Forty‐two patients reported a low PA level, while 34 moderate and 25 reported high levels. Factors independently associated with low PA, presented as odds ratio (95% confidence interval), were severe fatigue 5.87 (1.23–28.12), exercise capacity 0.99 (0.99–1.0) and the number of pack‐years 1.04 (1.01–1.07). No relationship was found between depression, anxiety, body composition, exacerbation rate or systemic inflammation and PA.ConclusionsSevere fatigue, worse exercise capacity and a higher amount of smoking were independently associated with low PA. Promoting physical activity is important in all patients with COPD. Our result suggests that patients with severe fatigue might need specific strategies to prevent physical inactivity.