bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanical vulnerability explains size‐dependent mortality of reef corals
Authors: Madin Joshua S. , Baird Andrew H. , Dornelas Maria , Connolly Sean R. 
Published: June 2014

AbstractUnderstanding life history and demographic variation among species within communities is a central ecological goal. Mortality schedules are especially important in ecosystems where disturbance plays a major role in structuring communities, such as coral reefs. Here, we test whether a trait‐based, mechanistic model of mechanical vulnerability in corals can explain mortality schedules. Specifically, we ask whether species that become increasingly vulnerable to hydrodynamic dislodgment as they grow have bathtub‐shaped mortality curves, whereas species that remain mechanically stable have decreasing mortality rates with size, as predicted by classical life history theory for reef corals. We find that size‐dependent mortality is highly consistent between species with the same growth form and that the shape of size‐dependent mortality for each growth form can be explained by mechanical vulnerability. Our findings highlight the feasibility of predicting assemblage‐scale mortality patterns on coral reefs with trait‐based approaches.
A bioenergetic framework for the temperature dependence of trophic interactions
Authors: Gilbert Benjamin , Tunney Tyler D. , McCann Kevin S. , DeLong John P. , Vasseur David A. , Savage Van , Shurin Jonathan B. , Dell Anthony I. , Barton Brandon T. , Harley Christopher D.G. , Kharouba Heather M. , Kratina Pavel , Blanchard Julia L. , Clements Christopher , Winder Monika , Greig Hamish S. , O'Connor Mary I. 
Published: June 2014

AbstractChanging temperature can substantially shift ecological communities by altering the strength and stability of trophic interactions. Because many ecological rates are constrained by temperature, new approaches are required to understand how simultaneous changes in multiple rates alter the relative performance of species and their trophic interactions. We develop an energetic approach to identify the relationship between biomass fluxes and standing biomass across trophic levels. Our approach links ecological rates and trophic dynamics to measure temperature‐dependent changes to the strength of trophic interactions and determine how these changes alter food web stability. It accomplishes this by using biomass as a common energetic currency and isolating three temperature‐dependent processes that are common to all consumer–resource interactions: biomass accumulation of the resource, resource consumption and consumer mortality. Using this framework, we clarify when and how temperature alters consumer to resource biomass ratios, equilibrium resilience, consumer variability, extinction risk and transient vs. equilibrium dynamics. Finally, we characterise key asymmetries in species responses to temperature that produce these distinct dynamic behaviours and identify when they are likely to emerge. Overall, our framework provides a mechanistic and more unified understanding of the temperature dependence of trophic dynamics in terms of ecological rates, biomass ratios and stability.
Identification and characterization of a prophenoloxidase‐1 (PPO1) cDNA in the cabbage butterfly Pieris rapae L.
Authors: Lu Yan‐Li , Li Bin , Gong Wei , Gao Li , Zhang Xin , Xue Chao‐Bin 
Published: June 2014

AbstractPhenoloxidase (PO) is a melanin‐synthesizing enzyme widely distributed in animals, plants and microorganisms. It plays an important role in insect immune response. Here we report the cloning of a prophenoloxidase (PPO) cDNA from Pieris rapae, prophenoloxidase‐1 (PrPPO1). The full‐length cDNA consisted of 3338 bp, containing an open reading frame of 2049 bp encoding 682 amino acid (aa) residues. Two putative copper‐binding sites, a proteolytic activation site, three conserved hemocyanin domains and a thiolester motif, but no signal sequence, were found in the deduced aa sequence. A BLASTp search and neighbor‐joining analysis showed the deduced aa sequence had high identity to the published sequence of PPO1 from other lepidopteran insects, ranging from 71.31 to 73.15%. The results of real‐time polymerase chain reaction (PCR) showed that the highest expression of PrPPO1 was in the 4th instar larvae and the highest density of oenocytoids was observed in the 4th instar larvae also. PrPPO1 transcripts in the 4th instar larvae were significantly decreased at 6 h and 12 h with Beauveria bassiana infection; however, they were sharply increased at 72 h. PrPPO1 transcriptional level in the 5th instar larvae showed no significant changes compared with the control at 4 h with quercetin injection; however it was significantly increased at 12 h. The expression level of PrPPO1 was mainly related to the treatment time of the quercetin, but not the dose.
Examining common assumptions about recruitment: a meta‐analysis of recruitment dynamics for worldwide marine fisheries
Authors: Szuwalski Cody S , Vert‐Pre Katyana A , Punt André E , Branch Trevor A , Hilborn Ray 
Published: June 2014

AbstractAssumptions about the future productivity of a stock are necessary to calculate sustainable catches in fisheries management. Fisheries scientists often assume the number of young fish entering a population (recruitment) is related to the biomass of spawning adults and that recruitment dynamics do not change over time. Thus, managers often use a target biomass based on spawning biomass as the basis for calculating sustainable catches. However, we show recruitment and spawning biomass are not positively related over the observed range of stock sizes for 61% of 224 stocks in the RAM Legacy Stock Assessment Database. Furthermore, 85% of stocks for which spawning biomass may not drive recruitment dynamics over the observed ranges exhibit shifts in average recruitment, which is often used in proxies for target biomasses. Our results suggest that the environment more strongly influences recruitment than spawning biomass over the observed stock sizes for many stocks. Management often endeavours to maintain stock sizes within the observed ranges, so methods for setting management targets that include changes within an ecosystem may better define the status of some stocks, particularly as climate changes.
Plastic, viscoplastic and creep fracture problems with the boundary element method
Authors: Pineda‐León E. , Rodríguez‐Castellanos A. , Basaldúa‐Sánchez J. E. , Flores‐Méndez E. , Aliabadi M. H. 
Published: June 2014

ABSTRACTThe present paper shows the applicability of the dual boundary element method to analyse plastic, viscoplastic and creep behaviours in fracture mechanics problems. Several models with a crack, including a square plate, a holed plate and a notched plate, are analysed. Special attention is taken when the discretization of the domain is performed. In fact, for the plasticity and viscoplasticity cases, only the region susceptible to yielding was discretized, whereas the creep case required the discretization of the whole domain. The proposed formulation is presented as an alternative technique to study these kinds of nonlinear problems. Results from the present formulation are compared to those of the well‐established finite element technique, and they are in good agreement. Important fracture mechanic parameters like KI, KII, J‐integrals and C‐integrals are also included. In general, the results, for the plastic, viscoplastic and creep cases, exhibit that the highest stress concentrations are in the vicinity of the crack tip and they decrease as the distance from the crack tip is increased.
Patterns of lake occupancy by fish indicate different adaptations to life in a harsh Arctic environment
Authors: Haynes Trevor B. , Rosenberger Amanda E. , Lindberg Mark S. , Whitman Matthew , Schmutz Joel A. 
Published: June 2014

Summary

For six fish species sampled from 86 lakes on the Arctic Coastal Plain, Alaska, we examined whether lake occupancy was related to variables representing lake size, colonisation potential and/or the presence of overwintering habitat.

We found the relative importance of each factor for a given species could be related to its ecology and adult size. The three large‐bodied migratory species, least cisco (Coregonus sardinella), broad whitefish (Coregonus nasus) and arctic grayling (Thymallus arcticus), were influenced by factors associated with the likelihood of fish recolonising lakes, including whether the lakes had a stream connection. Of the large‐bodied species, least cisco had the highest likelihood of occupancy (0.52 ± 0.05) and models provided evidence that least cisco exhibit both migratory and resident forms.

Models for small‐bodied fish differed among species, indicating different niches. Ninespine stickleback (Pungitius pungitius) were the most widespread and ubiquitous of the species captured (occupancy probability = 0.97 ± 0.01); they were captured in lakes that freeze to the bottom, suggesting that they disperse widely and rapidly after the spring freshet, including colonisation of sink habitats. Alaska blackfish (Dallia pectoralis) had a lower occupancy (occupancy probability = 0.76 ± 0.05) with a distribution that reflected tolerance to harsh conditions. Slimy sculpin (Cottus cognatus) had an occupancy probability of 0.23 ± 0.06, with a distribution indicating its marine origin.

Based on these patterns, we propose an overall model of primary controls on the distribution of fish on the Arctic Coastal Plain of Alaska. Harsh conditions, including lake freezing, limit occupancy in winter through extinction events while lake occupancy in spring and summer is driven by directional migration (large‐bodied species) and undirected dispersal (small‐bodied species).
Soil phosphorus constrains biodiversity across European grasslands
Authors: Ceulemans Tobias , Stevens Carly J. , Duchateau Luc , Jacquemyn Hans , Gowing David J. G. , Merckx Roel , Wallace Hilary , van Rooijen Nils , Goethem Thomas , Bobbink Roland , Dorland Edu , Gaudnik Cassandre , Alard Didier , Corcket Emmanuel , Muller Serge , Dise Nancy B. , Dupré Cecilia , Diekmann Martin , Honnay Olivier 
Published: June 2014

AbstractNutrient pollution presents a serious threat to biodiversity conservation. In terrestrial ecosystems, the deleterious effects of nitrogen pollution are increasingly understood and several mitigating environmental policies have been developed. Compared to nitrogen, the effects of increased phosphorus have received far less attention, although some studies have indicated that phosphorus pollution may be detrimental for biodiversity as well. On the basis of a dataset covering 501 grassland plots throughout Europe, we demonstrate that, independent of the level of atmospheric nitrogen deposition and soil acidity, plant species richness was consistently negatively related to soil phosphorus. We also identified thresholds in soil phosphorus above which biodiversity appears to remain at a constant low level. Our results indicate that nutrient management policies biased toward reducing nitrogen pollution will fail to preserve biodiversity. As soil phosphorus is known to be extremely persistent and we found no evidence for a critical threshold below which no environmental harm is expected, we suggest that agro‐environmental schemes should include grasslands that are permanently free from phosphorus fertilization.
The economics and greenhouse gas balance of land conversion to Jatropha: the case of Tanzania
Authors: Achten Wouter M. J. , Dillen Koen , Trabucco Antonio , Verbist Bruno , Messemaker Lode , Muys Bart , Mathijs Erik 
Published: June 2014

AbstractDue to higher oil prices, abundance of labor and suitable land and its stable political climate, Tanzania attracted many investments in Jatropha. Although several studies on Jatropha's economic potential are available, its true economics are still uncertain. This paper aims to add to the growing body of knowledge on the socio‐economic performance of the Jatropha system by (i) studying the economic potential (net present value – NPV) of the current most prevailing Jatropha system for Tanzanian farmers and its regional differences, by (ii) making a greenhouse gas (GHG) balance and its economic value of the Jatropha activities on regional level, and by (iii) calculating break‐even thresholds for yield and seed price. Therefore, regional yield modeling, regional life‐cycle assessment, and NPV calculations based on Monte Carlo simulations, each with its set of assumptions, are combined. This study shows positive economic potential of Jatropha cultivation in most of the Tanzanian regions. However, the results also show that 13 of 20 Tanzanian regions will not attain a net positive GHG balance within 10 years. This indicates that the environmental impacts might be more restrictive for Jatropha's sustainability potential in Tanzania than the socio‐economic potential. These results are based on the combination of three models, which consists of strong interdisciplinary modeling work. However, this modeling also contains simplifications (e.g., no opportunity cost for ‘marginal’ land) and uncertainties (e.g., using globally modeled potential yield estimations), which have to be considered in the interpretation of the results.
Groundwater App to Determine Flow Direction and Gradient
Authors: Morrison Derek , Munster Clyde 
Published: June 2014

AbstractA computational program, called the groundwater flow calculator, was created to quickly and easily determine the hydraulic gradient and direction of groundwater flow. The groundwater flow calculator automates the hand‐drawn process by Ralph Heath in the U.S. Geological Survey (USGS) Water Supply Paper 2220. In addition, a mobile app was developed to allow this procedure to run on a smart phone for use in the field.
Similar bleeding phenotype in young children with haemophilia A or B: a cohort study
Authors: Clausen N. , Petrini P. , Claeyssens‐Donadel S. , Gouw S. C. , Liesner R. ,   PedNet and Research of Determinants of Inhibitor development (RODIN) Study Group
Published: June 2014

SummaryThe bleeding phenotype has been suggested to differ between haemophilia A and B. More knowledge on the bleeding phenotype at initiation of treatment is important to optimize patient care. The aim of this study was to investigate the severity of the bleeding phenotype and the variation in bleeding in children with severe or moderate haemophilia A and B. Consecutive, previously untreated patients with severe or moderate haemophilia A and B (factor VIII or IX activity <0.01 or 0.01–0.05 IU mL−1 respectively) born between January 1st 2000 and January 1st 2010 were included. Primary outcome was severity of bleeding tendency. Secondary outcome was variation in bleeding pattern. A total of 582 patients with severe haemophilia A and 76 with severe haemophilia B did not differ in age at first exposure to clotting factor (0.81 vs. 0.88 years, P = 0.20), age at first bleed (0.82 vs. 0.88 years, P = 0.36), and age at first joint bleed (1.18 vs. 1.20 years, P = 0.59). Patients with moderate haemophilia were older compared to patients with severe haemophilia. In patients with moderate haemophilia there were no clear differences between haemophilia A and B. Severity and variation in bleeding phenotype are similar during the early stage of treatment in patients with severe and moderate haemophilia A and B respectively. The findings imply that children with haemophilia B should be observed and treated as vigilantly as those with haemophilia A.
Risk assessment for coronary heart disease in patients with haemophilia: a single centre study in the United States
Authors: Sait A. S. , Kuo A. , Bettencourt R. , Bergstrom J. , Allison M. , von Drygalski A. 
Published: June 2014

SummaryIn haemophilia, coronary heart disease (CHD) occurs at a similar frequency as in the general population, but the contributing risk factors in haemophilia are incompletely understood. To investigate risk factors and 10‐year CHD risk in a single centre cohort of patients with haemophilia (PWH) ≥20 years old (n = 89). We retrospectively applied the modified Framingham National Cholesterol Education Program/Adult Treatment Panel (NCEP/ATP) III risk prediction equation. Three risk levels were defined: <10% (low), 10–20% (intermediate) and >20% (high). Results were compared to the National Health and Nutrition Examination Survey (NHANES). Mean age in both cohorts was similar. Compared to NHANES, systolic blood pressures were significantly higher in PWH, but current smoking and cholesterol were lower. CHD risk differed significantly between PWH and NHANES (P = 0.005) with a higher proportion of PWH classified at low risk (77.5% vs. 61.0%). The proportion of low risk patients was also significantly higher for severe haemophilia patients compared to non‐severe haemophilia patients (88.6% vs. 66.7%, P = 0.02). Among PWH, and compared to PWH who were hepatitis C (HepC) negative, HepC positive patients had significantly lower cholesterol, LDL and triglycerides. The CHD risk of HepC positive patients differed significantly from NHANES (P = 0.03) with a lower proportion of HepC positives being classified as high risk (5.7% vs. 17.3%). Favourable CHD risk classification in PWH may be influenced by low cholesterol associated with HepC infection. Estimates of CHD risk in PWH by composite scoring may not be accurate and will require studies correlating risk factors with incident CHD.
Headaches, Quality of Life, and Academic Performance in Schoolchildren and Adolescents
Authors: Rocha‐Filho Pedro A.S. , Santos Patricia V. 
Published: June 2014

BackgroundJust a few studies to date have focused on headaches, quality of life, and academic performance in children.ObjectiveDetermine the effect of headaches on the life of schoolchildren and the association between headaches and academic performance.MethodsWe conducted a cross‐sectional study. One hundred and ninety‐five students from an elementary school were randomly selected out of 355 students aged from 10 to 15 years old. Semi‐structured interview, the Pediatric Quality of Life Inventory Version 4.0, the Children's Depression Inventory, and the State‐Trait Anxiety Inventory were used. The variables relating to academic performance were obtained by consulting the academic records.ResultsPrevalence of headaches: headache: 97.3% (179/184); migraine: 51% (94/184); tension‐type headache: 33% (61/184); primary stabbing headache: 7.6% (14/184); unclassified headaches: 5.4% (10/184). Migraine (relative risk: 3.11; 95% confidence interval: 1.54‐6.30) and more severe headaches (relative risk: 7.93; 95% confidence interval: 2.65‐23.7) were associated with lower quality of life (P < .01; multivariate logistic regression). More severe headaches were associated with lower grades in school (P < .01; multiple linear regression). Variables relating to headaches were not associated with “failing the school year” (P > .05; chi‐square test and Fisher's exact test).ConclusionHeadaches were found to be associated with lower quality of life and poor academic performance.
Do serrated neoplasms of the small intestine represent a distinct entity? Pathological findings and molecular alterations in a series of 13 cases
Authors: Rosty Christophe , Campbell Catherine , Clendenning Mark , Bettington Mark , Buchanan Daniel D , Brown Ian S 
Published: June 2014

AimsTo characterize pathological, immunohistochemical and molecular features of small intestinal serrated neoplasms.Methods and resultsWe report 13 serrated neoplasms located predominantly in the duodenum (median age, 71 years; male to female ratio, 7:6). The serrated adenomas demonstrated prominent serration, ectopic crypt formations and cytological features reminiscent of colorectal traditional serrated adenomas. Almost half the serrated adenomas demonstrated high‐grade dysplasia or were associated with an adenocarcinoma. Immunohistochemical and molecular analysis showed an intestinal (CDX2‐positive) phenotype in all tumours, abnormal β‐catenin staining in three cases (23%), abnormal p53 expression in four cases (31%), focal loss of MGMT expression in one case (8%), KRAS mutation in five cases (38%) and CpG island methylator phenotype in six cases (50%). A diffuse pattern of Ki67 expression was present in eight adenomas (62%) and was associated with high‐grade dysplasia (P = 0.02). No BRAFV600E mutation or loss of MLH1 expression was observed.ConclusionsTo our knowledge, this is the first series reporting serrated adenoma in the small intestine, a rare subtype of adenomas resembling traditional serrated adenoma with aggressive morphological features. The absence of the BRAFV600E mutation does not support a role for the serrated neoplasia pathway in the development of these lesions, as in colorectal serrated polyps.
Efficacy of lead‐in silibinin and subsequent triple therapy in difficult‐to‐treat HIV/hepatitis C virus‐coinfected patients
Authors: Braun DL , Rauch A , Durisch N , Eberhard N , Anagnostopoulos A , Ledergerber B , Metzner KJ , Böni J , Weber R , Fehr J 
Published: June 2014

ObjectivesThe efficacy of current hepatitis C virus (HCV) triple therapy, including a protease inhibitor, is limited in HIV/HCV‐coinfected patients with advanced liver fibrosis and nonresponse to previous peginterferon‐ribavirin. These patients have a low chance (only 30%) of achieving a sustained virological response (SVR) during triple therapy and cannot wait for next‐generation anti‐HCV drugs. In a pilot study, we investigated the efficacy of a lead‐in therapy with silibinin before triple therapy in difficult‐to‐treat patients.MethodsInclusion criteria were HIV/HCV coinfection with advanced liver fibrosis and documented failure of previous peginterferon‐ribavirin treatment. Intervention was lead‐in therapy with intravenous silibinin 20 mg/kg/day for 14 days. Subsequently, peginterferon‐ribavirin combined with telaprevir was initiated for 12 weeks, followed by peginterferon‐ribavirin dual therapy until week 48 after initiation of triple therapy. The outcome measurements were HCV RNA after silibinin lead‐in, at weeks 2, 4 and 12 of triple therapy, and SVR at week 24 after the end of treatment.ResultsWe examined six HIV/HCV‐coinfected patients (four infected with genotype 1a). All had fibrosis grade METAVIR ≥F3 and were on fully suppressive antiretroviral therapy. Mean HCV RNA decline after silibinin therapy was 2.6 log10 IU/mL (range 2–3 log10 IU/mL). Five of the six patients were virologically suppressed at weeks 2 and 4, and all six at week 12 of triple therapy. One experienced a viral breakthrough thereafter. Four of five patients (80%) showed an SVR 24. One patient had an SVR 12 but has not yet reached week 24.ConclusionsA lead‐in with silibinin before triple therapy is highly effective and increases the probability of HCV treatment success in difficult‐to‐treat HIV/HCV‐coinfected patients with advanced liver fibrosis and previous failure of peginterferon‐ribavirin.