bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring restoration options for habitats, species and ecosystem services in the European Union
Authors: Egoh Benis N. , Paracchini Maria L. , Zulian Grazia , Schägner Jan Philipp , Bidoglio Giovanni 
Published: March 2014

SummaryThe Convention on Biological Diversity (CBD) and the European Union have set a target of restoring 15% of degraded ecosystems by 2020 with the aim of conserving biodiversity and enhancing the supply of ecosystem services. This target must be implemented alongside other similar targets aimed at reducing the number of threatened habitat and species as assessed under the Birds and Habitats directives. However, there are several uncertainties associated with achieving these targets including the benefits of restoring biodiversity and ecosystem services, the contribution required from member states and the effect of different restoration scenarios on target achievement.In this study, we evaluate options that exist for meeting anEU‐wide 15% restoration target while conserving habitats and species and enhancing ecosystem services. We explored the effects of different restoration scenarios on the percentage of threatened habitat and species secured. Lastly, we explored the effects of including financial cost into the prioritization procedure.Focusing restoration efforts on habitats with inadequate conservation status in the reporting of the Habitats Directive provides the largest benefit for species and ecosystem services. If the restoration target is set at 10% for habitat and species with inadequate or most threatened conservation status, and at 2% for all ecosystem services, about 18% ofEUecosystems should be restored to meet these targets.When the target is set at 15% of habitat and species and 3% of all ecosystem services, results showed that France hosts the highest percentage of identified priority areas (13%) followed by Spain and Finland with about 11% and Sweden with 9%. However, these numbers change when financial cost is included alongside other criteria, with France containing 35% of all areas identified.Synthesis and applications. These results suggest that to achieve the greatest benefits, funding for restoration should be directed towards habitats with inadequate conservation status rather than to species. Countries with larger areas of threatened habitat and lower restoration costs may offer better opportunities to meet targets, but including cost at theEUlevel may result in unequal burden sharing among countries.
Optimal release strategies for cost‐effective reintroductions
Authors: Canessa Stefano , Hunter David , McFadden Michael , Marantelli Gerry , McCarthy Michael A. 
Published: March 2014

Summary

Ex situ programmes for endangered species commonly focus on two main objectives: insurance against immediate risk of extinction and reintroduction. Releases influence the size of captive and wild populations and may present managers with a trade‐off between the two objectives. This can be further complicated when considering the costs of the captive population and the possible release of different life stages.

We approached this decision problem by combining population models and decision‐analytic methods, using the reintroduction programme for the southern corroboree frog Pseudophryne corroboree in Australia as an example. We identified the optimal release rates of eggs and subadults which maximized the size of the captive and reintroduced populations while meeting constraints. We explored two scenarios: a long‐term programme for a stable age‐distributed captive population and a short‐term programme with non‐stable age distribution and limited budget. We accounted for uncertainty in the estimated vital rates and demographic stochasticity.

Assuming a stable age distribution, large proportions of individuals could be released without decreasing the captive population below its initial size. The optimal strategy was sensitive to the post‐release survival of both life stages, but subadult releases were generally most cost‐effective, producing a large wild population and requiring a cheaper captive population. Egg releases were optimal for high expected juvenile survival, whereas mixed releases of both life stages were never optimal.

In the short‐term realistic scenario, subadult releases also produced the largest wild population, but they required a large increase in the size and cost of the captive population that exceeded the available budget. Egg releases were cheaper but yielded smaller numbers in the wild, whereas joint releases of both life stages provided more wild individuals, meeting budget constraints without depleting the captive population.

Synthesis and applications. Optimal release strategies for endangered species reflect the trade‐offs between insurance and reintroduction objectives and depend on the vital rates of the released individuals. Although focusing on a single life stage may have practical advantages, mixed strategies can maximize cost‐effectiveness by combining the relative advantages of releasing early and late life stages.
Microbial community composition explains soil respiration responses to changing carbon inputs along anAndes‐to‐Amazon elevation gradient
Authors: Whitaker Jeanette , Ostle Nicholas , Nottingham Andrew T. , Ccahuana Adan , Salinas Norma , Bardgett Richard D. , Meir Patrick , McNamara Niall P. 
Published: March 2014

SummaryTheAndes are predicted to warm by 3–5 °C this century with the potential to alter the processes regulating carbon (C) cycling in these tropical forest soils. This rapid warming is expected to stimulate soil microbial respiration and change plant species distributions, thereby affecting the quantity and quality ofCinputs to the soil and influencing the quantity of soil‐derivedCO2released to the atmosphere.We studied tropical lowland, premontane and montane forest soils taken from along a 3200‐m elevation gradient located in south‐eastAndeanPeru. We determined how soil microbial communities and abiotic soil properties differed with elevation. We then examined how these differences in microbial composition and soil abiotic properties affected soilC‐cycling processes, by amending soils withCsubstrates varying in complexity and measuring soil heterotrophic respiration (RH).Our results show that there were consistent patterns of change in soil biotic and abiotic properties with elevation. Microbial biomass and the abundance of fungi relative to bacteria increased significantly with elevation, and these differences in microbial community composition were strongly correlated with greater soilCcontent andC:N(nitrogen) ratios. We also found thatRHincreased with addedCsubstrate quality and quantity and was positively related to microbial biomass and fungal abundance.Statistical modelling revealed thatRHresponses to changingCinputs were best predicted by soil pHand microbial community composition, with the abundance of fungi relative to bacteria, and abundance of gram‐positive relative to gram‐negative bacteria explaining much of the model variance.Synthesis. Our results show that the relative abundance of microbial functional groups is an important determinant ofRHresponses to changingCinputs along an extensive tropical elevation gradient inAndeanPeru. Although we do not make an experimental test of the effects of climate change on soil, these results challenge the assumption that different soil microbial communities will be ‘functionally equivalent’ as climate change progresses, and they emphasize the need for better ecological metrics of soil microbial communities to help predictCcycle responses to climate change in tropical biomes.
Physician Practice Participation in Accountable Care Organizations: The Emergence of the Unicorn
Authors: Shortell Stephen M. , McClellan Sean R. , Ramsay Patricia P. , Casalino Lawrence P. , Ryan Andrew M. , Copeland Kennon R. 
Published: March 2014

ObjectiveTo provide the first nationally based information on physician practice involvement in ACOs.Data Sources/Study SettingPrimary data from the third National Survey of Physician Organizations (January 2012–May 2013).Study DesignWe conducted a 40‐minute phone survey in a sample of physician practices. A nationally representative sample of practices was surveyed in order to provide estimates of organizational characteristics, care management processes, ACO participation, and related variables for four major chronic illnesses.Data Collection/Extraction MethodsWe evaluated the associations between ACO participation, organizational characteristics, and a 25‐point index of patient‐centered medical home processes.Principal FindingsWe found that 23.7 percent of physician practices (n = 280) reported joining an ACO; 15.7 percent (n = 186) were planning to become involved within the next 12 months and 60.6 percent (n = 717) reported no involvement and no plans to become involved. Larger practices, those receiving patients from an IPA and/or PHO, those that were physician‐owned versus hospital/health system‐owned, those located in New England, and those with greater patient‐centered medical home (PCMH) care management processes were more likely to have joined an ACO.ConclusionsPhysician practices that are currently participating in ACOs appear to be relatively large, or to be members of an IPA or PHO, are less likely to be hospital‐owned and are more likely to use more care management processes than nonparticipating practices.
Incident User Cohorts for Assessing Medication Cost‐Offsets
Authors: Stuart Bruce , Loh F. Ellen , Roberto Pamela , Miller Laura 
Published: March 2014

ObjectiveTo develop and test incident drug user designs for assessing cost savings from statin use in diabetics.Data SourceRandom 5 percent sample of Medicare beneficiaries, 2006–2008.Study DesignSeven‐step incident user design to assess impact of statin initiation on subsequent Medicare spending: (1) unadjusted pre/post initiation test; (2) unadjusted difference‐in‐difference (DID) with comparison series; (3) adjusted DID; (4) propensity score (PS)‐matched DID with static and dynamic baseline covariates; (5) PS‐matched DID by drug adherence strata; (6) PS‐matched DID for high adherers controlling for healthy adherer bias; and (7) replication for ACE‐inhibitor/ARB initiators.Data Collection/Extraction MethodsSubjects with prevalent diabetes and no statin use (January–June 2006) and statin initiation (July 2006–January 2008) compared to nonusers with a random “potential‐initiation” month. Monthly Medicare spending tracked 24 months pre‐ and post‐initiation.Principal FindingsStatistically significant savings in Medicare spending were observed beginning 7 months post‐initiation for statins and 13 months post‐initiation for ACEIs/ARBs. However, these savings were only observed for adherent patients in steps 5 and 6.ConclusionsDrug initiator designs are more robust to confounding than prevalent user designs in assessing cost‐offsets from drug use but still require other adjustments and sensitivity analysis to ensure proper inference.
Tissue storage and primer selection influence pyrosequencing‐based inferences of diversity and community composition of endolichenic and endophytic fungi
Authors: U'Ren Jana M. , Riddle Jakob M. , Monacell James T. , Carbone Ignazio , Miadlikowska Jolanta , Arnold A. Elizabeth 
Published: March 2014

AbstractNext‐generation sequencing technologies have provided unprecedented insights into fungal diversity and ecology. However, intrinsic biases and insufficient quality control in next‐generation methods can lead to difficult‐to‐detect errors in estimating fungal community richness, distributions and composition. The aim of this study was to examine how tissue storage prior to DNA extraction, primer design and various quality‐control approaches commonly used in 454 amplicon pyrosequencing might influence ecological inferences in studies of endophytic and endolichenic fungi. We first contrast 454 data sets generated contemporaneously from subsets of the same plant and lichen tissues that were stored in CTAB buffer, dried in silica gel or freshly frozen prior to DNA extraction. We show that storage in silica gel markedly limits the recovery of sequence data and yields a small fraction of the diversity observed by the other two methods. Using lichen mycobiont sequences as internal positive controls, we next show that despite careful filtering of raw reads and utilization of current best‐practice OTU clustering methods, homopolymer errors in sequences representing rare taxa artificially increased estimates of richness c. 15‐fold in a model data set. Third, we show that inferences regarding endolichenic diversity can be improved using a novel primer that reduces amplification of the mycobiont. Together, our results provide a rationale for selecting tissue treatment regimes prior to DNA extraction, demonstrate the efficacy of reducing mycobiont amplification in studies of the fungal microbiomes of lichen thalli and highlight the difficulties in differentiating true information about fungal biodiversity from methodological artefacts.
Understanding co‐occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)
Authors: Pollock Laura J. , Tingley Reid , Morris William K. , Golding Nick , O'Hara Robert B. , Parris Kirsten M. , Vesk Peter A. , McCarthy Michael A. 
Published: March 2014

Summary

A primary goal of ecology is to understand the fundamental processes underlying the geographic distributions of species. Two major strands of ecology – habitat modelling and community ecology – approach this problem differently. Habitat modellers often use species distribution models (SDMs) to quantify the relationship between species’ and their environments without considering potential biotic interactions. Community ecologists, on the other hand, tend to focus on biotic interactions and, in observational studies, use co‐occurrence patterns to identify ecological processes. Here, we describe a joint species distribution model (JSDM) that integrates these distinct observational approaches by incorporating species co‐occurrence data into a SDM.

JSDMs estimate distributions of multiple species simultaneously and allow decomposition of species co‐occurrence patterns into components describing shared environmental responses and residual patterns of co‐occurrence. We provide a general description of the model, a tutorial and code for fitting the model in R. We demonstrate this modelling approach using two case studies: frogs and eucalypt trees in Victoria, Australia.

Overall, shared environmental correlations were stronger than residual correlations for both frogs and eucalypts, but there were cases of strong residual correlation. Frog species generally had positive residual correlations, possibly due to the fact these species occurred in similar habitats that were not fully described by the environmental variables included in the JSDM. Eucalypt species that interbreed had similar environmental responses but had negative residual co‐occurrence. One explanation is that interbreeding species may not form stable assemblages despite having similar environmental affinities.

Environmental and residual correlations estimated from JSDMs can help indicate whether co‐occurrence is driven by shared environmental responses or other ecological or evolutionary process (e.g. biotic interactions), or if important predictor variables are missing. JSDMs take into account the fact that distributions of species might be related to each other and thus overcome a major limitation of modelling species distributions independently.
treeNODF: nestedness to phylogenetic, functional and other tree‐based diversity metrics
Authors: Melo Adriano S. , Cianciaruso Marcus V. , Almeida‐Neto Mário 
Published: March 2014

Summary

Available measures of nestedness consider descriptor variables (e.g. species) as equally associated, ignoring evolutionary or ecological dissimilarities. Here, we introduce treeNODF, a new class of nestedness that takes into account the resemblance of descriptor variables.

The method is an extension of the NODF index and can be applied to systems in which the resemblance of descriptor variables is described by a tree‐like object. Computation of treeNODF is similar to NODF, but uses branch lengths instead of the sum of species occurrences. In this way, we can calculate a phyloNODF for metacommunities if a phylogeny is used to account for differences in phylogenetic diversity (PD) and traitNODF if a functional dendrogram constructed from species ecological traits is used to account for the functional diversity (FD) of communities. Similar to NODF, treeNODF can also be used to assess nestedness among species. In this case, envNODF uses a dendrogram describing the resemblance among the environmental conditions of different sites, to test whether rare species occur in a subset of the environmental conditions in the habitats occupied by frequent species.

treeNODF is a composite metric that can be additively partitioned into compositional (S.fraction) and tree‐topology (topoNODF = treeNODF – S.fraction) components of the descriptor variables. Tests of treeNODF and its components can be carried out using null models and, if a hypothetical factor is used to order metacommunity data, permutation tests. We show that treeNODF is robust for matrix size and fill, as well as for tree topology.

Finally, we illustrate the use of treeNODF by analysing data on Caribbean bats using phyloNODF, traitNODF and envNODF, as well as their composition and tree‐topology components.
Staging bipolar disorder: clinical, biochemical, and functional correlates
Authors: Grande I. , Magalhães P. V. , Chendo I. , Stertz L. , Panizutti B. , Colpo G. D. , Rosa A. R. , Gama C. S. , Kapczinski F. , Vieta E. 
Published: March 2014

ObjectiveThere are several models of staging in bipolar disorder (BD), but none has been validated. The aims of this study were to empirically investigate clinical variables that may be useful to classify patients in clusters according to stage and study the association with biomarkers as biological validators.MethodThis was a historical cohort study. Patients (n = 115) diagnosed with BD and not in an acute episode and first‐degree relatives of patients diagnosed with BD (n = 25) were recruited. Sociodemographic, clinical, and functional data were collected. Serum cytokines, brain‐derived neurotrophic factor, and biomarkers of lipid and protein oxidation were assessed. Cluster analysis was carried out to build a model of staging, and logistic regression was conducted to study associations between the model and biomarkers.ResultsCluster analysis divided the sample into two equitable groups, denominated early and late stage, with empirical cutoffs for the Functioning Assessment Short Test score, number of episodes, age at onset of the disorder, and time elapsed since first episode. In the logistic regression, IL‐6 was associated with late stage (P = 0.029).ConclusionThis study supports that clinical, functional, and biochemical variables may help to define a classification of staging in BD.
Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test
Authors: Banks Michael A. , Jacobson David P. , Meusnier Isabelle , Greig Carolyn A. , Rashbrook Vanessa K. , Ardren William R. , Smith Christian T. , Bernier‐Latmani Jeremiah , Van Sickle John , O'Malley Kathleen G. 
Published: March 2014

SummaryThe application of DNA‐based markers toward the task of discriminating among alternate salmon runs has evolved in accordance with ongoing genomic developments and increasingly has enabled resolution of which genetic markers associate with important life‐history differences. Accurate and efficient identification of the most likely origin for salmon encountered during ocean fisheries, or at salvage from fresh water diversion and monitoring facilities, has far‐reaching consequences for improving measures for management, restoration and conservation. Near‐real‐time provision of high‐resolution identity information enables prompt response to changes in encounter rates. We thus continue to develop new tools to provide the greatest statistical power for run identification. As a proof of concept for genetic identification improvements, we conducted simulation and blind tests for 623 known‐origin Chinook salmon (Oncorhynchus tshawytscha) to compare and contrast the accuracy of different population sampling baselines and microsatellite loci panels. This test included 35 microsatellite loci (1266 alleles), some known to be associated with specific coding regions of functional significance, such as the circadian rhythm cryptochrome genes, and others not known to be associated with any functional importance. The identification of fall run with unprecedented accuracy was demonstrated. Overall, the top performing panel and baseline (HMSC21) were predicted to have a success rate of 98%, but the blind‐test success rate was 84%. Findings for bias or non‐bias are discussed to target primary areas for further research and resolution.
KIT and melanoma predisposition in pigs: sequence variants and association analysis
Authors: Fernández‐Rodríguez A. , Estellé J. , Blin A. , Muñoz M. , Créchet F. , Demenais F. , Vincent‐Naulleau S. , Bourneuf E. 
Published: March 2014

SummaryKIT mutations have been detected in different cancer subtypes, including melanoma. The gene also has been extensively studied in farm animals for its prominent role in coat color. The present work aimed at detecting KIT variants in a porcine model of cutaneous melanoma, the melanoblastoma‐bearing Libechov Minipig (MeLiM). By sequencing exons and intron borders, 36 SNPs and one indel were identified. Of 10 coding SNPs, three were non‐synonymous mutations, likely to affect the protein conformation. A promising variant, located in exon 19 (p.Val870Ala), was genotyped in a MeLiM × Duroc cross, and an association analysis was conducted on several melanoma‐related traits. This variant showed a significant association with melanoma development, tumor ulceration and cutaneous invasion. In conclusion, although the KIT gene would not be a major causal gene for melanoma development in pig, its genetic variation could be influencing this trait.