Coefficient shifts in geographical ecology: an empirical evaluation of spatial and non-spatial regression

Copyright © 2009 The Authors. Copyright © ECOGRAPHY 2009.A major focus of geographical ecology and macro ecology is to understand the causes of spatially structured ecological patterns. However, achieving this understanding can be complicated when using multiple regressions, because the relative importance of explanatory variables, as measured by regression coefficients, can shift depending on whether spatially explicit or non-spatial modelling is used. However, the extent to which coefficients may shift and why shifts occur are unclear. Here, we analyze the relationship between environmental predictors and the geographical distribution of species richness, body size, range size and abundance in 97 multi-factorial data sets. Our goal was to compare standardized partial regression coefficients of non-spatial ordinary least squares regressions (i.e. models fitted using ordinary least squares without taking autocorrelation into account; “OLS models” hereafter) and eight spatial methods to evaluate the frequency of coefficient shifts and identify characteristics of data that might predict when shifts are likely. We generated three metrics of coefficient shifts and eight characteristics of the data sets as predictors of shifts. Typical of ecological data, spatial autocorrelation in the residuals of OLS models was found in most data sets. The spatial models varied in the extent to which they minimized residual spatial autocorrelation. Patterns of coefficient shifts also varied among methods and datasets, although the magnitudes of shifts tended to be small in all cases. We were unable to identify strong predictors of shifts, including the levels of autocorrelation in either explanatory variables or model residuals. Thus, changes in coefficients between spatial and non-spatial methods depend on the method used and are largely idiosyncratic, making it difficult to predict when or why shifts occur. We conclude that the ecological importance of regression coefficients cannot be evaluated with confidence irrespective of whether spatially explicit modelling is used or not. Researchers may have little choice but to be more explicit about the uncertainty of models and more cautious in their interpretation

An extensive reef system at the Amazon River mouth

Large rivers create major gaps in reef distribution along tropical shelves. The Amazon River represents 20% of the global riverine discharge to the ocean, generating up to a 1.3 x 10(6)-km(2) plume, and extensive muddy bottoms in the equatorial margin of South America. As a result, a wide area of the tropical North Atlantic is heavily affected in terms of salinity, pH, light penetration, and sedimentation. Such unfavorable conditions were thought to imprint a major gap in Western Atlantic reefs. We present an extensive carbonate system off the Amazon mouth, underneath the river plume. Significant carbonate sedimentation occurred during lowstand sea level, and still occurs in the outer shelf, resulting in complex hard-bottom topography. A permanent near-bottom wedge of ocean water, together with the seasonal nature of the plume's eastward retroflection, conditions the existence of this extensive (similar to 9500 km(2)) hard-bottom mosaic. The Amazon reefs transition from accretive to erosional structures and encompass extensive rhodolith beds. Carbonate structures function as a connectivity corridor for wide depth-ranging reef-associated species, being heavily colonized by large sponges and other structure-forming filter feeders that dwell under low light and high levels of particulates. The oxycline between the plume and subplume is associated with chemoautotrophic and anaerobic microbial metabolisms. The system described here provides several insights about the responses of tropical reefs to suboptimal and marginal reef-building conditions, which are accelerating worldwide due to global changes.Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)Coordenadoria de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERS)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)BrasoilMCTIBrazilian NavyU.S. NSFGordon and Betty Moore Foundation (GBMF)Univ Fed Rio de Janeiro UFRJ, Inst Biol, BR-21941599 Rio De Janeiro, RJ, BrazilUniv Fed Rio de Janeiro, COPPE, Inst Alberto Luiz Coimbra Posgrad & Pesquisa Engn, Lab Sistemas Avancados Gestao Prod, BR-21941972 Rio de Janeiro, RJ, BrazilInst Pesquisas Jardim Bot Rio de Janeiro, BR-22460030 Rio De Janeiro, RJ, BrazilUniv Sao Paulo, Inst Oceanog, BR-05508120 Sao Paulo, SP, BrazilUniv Fed Espirito Santo, Dept Oceanog, BR-29199970 Vitoria, ES, BrazilUniv Estadual Norte Fluminense, Lab Ciencias Ambientais, Ctr Biociencias & Biotecnol, BR-28013602 Campos Dos Goytacazes, RJ, BrazilUniv Fed Fluminense, Inst Geociencias, BR-24210346 Niteroi, RJ, BrazilUniv Fed Fluminense, Inst Biol, BR-24210130 Niteroi, RJ, BrazilUniv Fed Rio de Janeiro, Museo Nacl, BR-20940040 Rio De Janeiro, RJ, BrazilFed Univ Para, Inst Estudos Costeiros, BR-68600000 Braganca, PA, BrazilUniv Fed Sao Paulo, Dept Ciencias Mar, BR-11070100 Santos, SP, BrazilUniv Fed Pernambuco, Dept Oceanog, BR-50670901 Recife, PE, BrazilUniv Georgia, Dept Marine Sci, Athens, GA 30602 USAUniv Fed Paraiba, BR-58297000 Rio Tinto, PB, BrazilUniv Estadual Santa Cruz, Dept Ciencias Biol, BR-45650000 Ilheus, BA, BrazilUniv Fed Sao Paulo, Dept Ciencias Mar, BR-11070100 Santos, SP, BrazilU.S. NSF: OCE-0934095GBMF: 2293GBMF: 2928Web of Scienc

Rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART): Study protocol for a randomized controlled trial

Background: Acute respiratory distress syndrome (ARDS) is associated with high in-hospital mortality. Alveolar recruitment followed by ventilation at optimal titrated PEEP may reduce ventilator-induced lung injury and improve oxygenation in patients with ARDS, but the effects on mortality and other clinical outcomes remain unknown. This article reports the rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART). Methods/Design: ART is a pragmatic, multicenter, randomized (concealed), controlled trial, which aims to determine if maximum stepwise alveolar recruitment associated with PEEP titration is able to increase 28-day survival in patients with ARDS compared to conventional treatment (ARDSNet strategy). We will enroll adult patients with ARDS of less than 72 h duration. The intervention group will receive an alveolar recruitment maneuver, with stepwise increases of PEEP achieving 45 cmH(2)O and peak pressure of 60 cmH2O, followed by ventilation with optimal PEEP titrated according to the static compliance of the respiratory system. In the control group, mechanical ventilation will follow a conventional protocol (ARDSNet). In both groups, we will use controlled volume mode with low tidal volumes (4 to 6 mL/kg of predicted body weight) and targeting plateau pressure <= 30 cmH2O. The primary outcome is 28-day survival, and the secondary outcomes are: length of ICU stay; length of hospital stay; pneumothorax requiring chest tube during first 7 days; barotrauma during first 7 days; mechanical ventilation-free days from days 1 to 28; ICU, in-hospital, and 6-month survival. ART is an event-guided trial planned to last until 520 events (deaths within 28 days) are observed. These events allow detection of a hazard ratio of 0.75, with 90% power and two-tailed type I error of 5%. All analysis will follow the intention-to-treat principle. Discussion: If the ART strategy with maximum recruitment and PEEP titration improves 28-day survival, this will represent a notable advance to the care of ARDS patients. Conversely, if the ART strategy is similar or inferior to the current evidence-based strategy (ARDSNet), this should also change current practice as many institutions routinely employ recruitment maneuvers and set PEEP levels according to some titration method.Hospital do Coracao (HCor) as part of the Program 'Hospitais de Excelencia a Servico do SUS (PROADI-SUS)'Brazilian Ministry of Healt

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Phylogenetic classification of the world's tropical forests

Knowledge about the biogeographic affinities of the world’s tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world’s tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: (i) Indo-Pacific, (ii) Subtropical, (iii) African, (iv) American, and (v) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northern-hemisphere forests.</p

Estrutura hierárquica na resposta das distribuições geográficas de plantas do Cerrado s mudanças climáticas

O clima pode ser considerado um fator extremamente importante na distribuição da vegetação e suas caracterí­sticas em um contexto global. Os modelos de distribuição geográfica potencial ("spatial distribution model") são importantes ferramentas para predizer mudanças induzidas pelo clima na distribuição das espécies. Em geral, estudos sobre as consequências das mudanças climáticas na redistribuição dos biomas englobam apenas sua distribuição geográfica ou analisam as espécies individualmente. O objetivo principal deste trabalho é avaliar se existe uma estrutura hierárquica no deslocamento das distribuições futuras do bioma Cerrado, das regiões fitoecológicas e das espécies de plantas do bioma, sob o efeito de mudanças climáticas. Este estudo demonstrou que não existe estrutura hierárquica na resposta da distribuição vegetacional frente  s previsões de mudanças climáticas para o ano de 2080 no Cerrado brasileiro. Em geral, nas três escalas estudadas, as distribuições deslocam-se para o sudeste do Brasil, de modo que essa região passa a ter um ganho de diversidade local enquanto o restante do Cerrado será afetado com o empobrecimento de sua diversidade. Este estudo aponta ainda, que num futuro próximo, as espécies do Cerrado serão afetadas com a perda de habitat

Estrutura hierárquica na resposta das distribuições geográficas de plantas do Cerrado s mudanças climáticas

O clima pode ser considerado um fator extremamente importante na distribuição da vegetação e suas caracterí­sticas em um contexto global. Os modelos de distribuição geográfica potencial ("spatial distribution model") são importantes ferramentas para predizer mudanças induzidas pelo clima na distribuição das espécies. Em geral, estudos sobre as consequências das mudanças climáticas na redistribuição dos biomas englobam apenas sua distribuição geográfica ou analisam as espécies individualmente. O objetivo principal deste trabalho é avaliar se existe uma estrutura hierárquica no deslocamento das distribuições futuras do bioma Cerrado, das regiões fitoecológicas e das espécies de plantas do bioma, sob o efeito de mudanças climáticas. Este estudo demonstrou que não existe estrutura hierárquica na resposta da distribuição vegetacional frente  s previsões de mudanças climáticas para o ano de 2080 no Cerrado brasileiro. Em geral, nas três escalas estudadas, as distribuições deslocam-se para o sudeste do Brasil, de modo que essa região passa a ter um ganho de diversidade local enquanto o restante do Cerrado será afetado com o empobrecimento de sua diversidade. Este estudo aponta ainda, que num futuro próximo, as espécies do Cerrado serão afetadas com a perda de habitat

The Adaptor Protein Myd88 Is a Key Signaling Molecule in the Pathogenesis of Irinotecan-Induced Intestinal Mucositis.

Intestinal mucositis is a common side effect of irinotecan-based anticancer regimens. Mucositis causes cell damage, bacterial/endotoxin translocation and production of cytokines including IL-1 and IL-18. These molecules and toll-like receptors (TLRs) activate a common signaling pathway that involves the Myeloid Differentiation adaptor protein, MyD88, whose role in intestinal mucositis is unknown. Then, we evaluated the involvement of TLRs and MyD88 in the pathogenesis of irinotecan-induced intestinal mucositis. MyD88-, TLR2- or TLR9-knockout mice and C57BL/6 (WT) mice were given either saline or irinotecan (75 mg/kg, i.p. for 4 days). On day 7, animal survival, diarrhea and bacteremia were assessed, and following euthanasia, samples of the ileum were obtained for morphometric analysis, myeloperoxidase (MPO) assay and measurement of pro-inflammatory markers. Irinotecan reduced the animal survival (50%) and induced a pronounced diarrhea, increased bacteremia, neutrophil accumulation in the intestinal tissue, intestinal damage and more than twofold increased expression of MyD88 (200%), TLR9 (400%), TRAF6 (236%), IL-1β (405%), IL-18 (365%), COX-2 (2,777%) and NF-κB (245%) in the WT animals when compared with saline-injected group (P<0.05). Genetic deletion of MyD88, TLR2 or TLR9 effectively controlled the signs of intestinal injury when compared with irinotecan-administered WT controls (P<0.05). In contrast to the MyD88-/- and TLR2-/- mice, the irinotecan-injected TLR9-/- mice showed a reduced survival, a marked diarrhea and an enhanced expression of IL-18 versus irinotecan-injected WT controls. Additionally, the expression of MyD88 was reduced in the TLR2-/- or TLR9-/- mice. This study shows a critical role of the MyD88-mediated TLR2 and TLR9 signaling in the pathogenesis of irinotecan-induced intestinal mucositis