A weight of evidence approach for selecting exposure biomarkers for biomonitoring

Context: It is known that there are usually several biomarkers and/or medium combinations that can be applied to answer a specific exposure question. To help determine an appropriate combination for the specific question, we have developed a weight-of-evidence Framework that provides a relative appropriateness score for competing combinations.

Methods: The Framework is based on an expert assessor’s evaluation of the relevance and suitability of the biomarker and medium for the question based on a set of criteria. We provide a computer based modeling tool to guide the researcher through the process.

Results: We present an example with six biomarkers of benzene exposure in one matrix; the six are either the most commonly used biomarkers and/or have recent widespread usage. The example clearly demonstrates the usefulness of the Framework for scoring the choices, as well as the transparency of the method that provides the basis for discussion.

Conclusions: The Framework provides for the first time a method to transparently document the rationale behind selecting, from among a set of alternatives, the most scientifically supportable exposure biomarker to address a specific biomonitoring question, thus providing a reproducible account of expert opinions on the suitability of a biomarker.     

The Weight of Evidence Does Not Support the Listing of Styrene as “Reasonably Anticipated to be a Human Carcinogen” in NTP's Twelfth Report on Carcinogens

Styrene was listed as “reasonably anticipated to be a human carcinogen” in the twelfth edition of the National Toxicology Program's Report on Carcinogens based on what we contend are erroneous findings of limited evidence of carcinogenicity in humans, sufficient evidence of carcinogenicity in experimental animals, and supporting mechanistic data. The epidemiology studies show no consistent increased incidence of, or mortality from, any type of cancer. In animal studies, increased incidence rates of mostly benign tumors have been observed only in certain strains of one species (mice) and at one tissue site (lung). The lack of concordance of tumor incidence and tumor type among animals (even within the same species) and humans indicates that there has been no particular cancer consistently observed among all available studies. The only plausible mechanism for styrene-induced carcinogenesis—a non-genotoxic mode of action that is specific to the mouse lung—is not relevant to humans. As a whole, the evidence does not support the characterization of styrene as “reasonably anticipated to be a human carcinogen,” and styrene should not be listed in the Report on Carcinogens.     

Biochemical evidence accumulates across neurons to drive a network-level eruption

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Restoration Ecology's silver jubilee: innovation,debate, and creating a future for restoration ecology

At a time when the science and practice of restoration ecology is adapting to ongoing environmental and social change, innovations in both methods and concepts are essential. Encouraging innovation means allowing open debate about alternative approaches that may add to the toolbox available for restoration. Such approaches are usually being examined as additions to, rather than substitutes for, traditional restoration practices. Recent debate has focused on the scope and intent of restoration as defined in documents such as the Society for Ecological Restoration Standards. There is a mismatch between the default aim in the standards of full restoration to a native reference system and the goals of international restoration efforts that have a broader and more functional focus. The next generation of restoration scientists and practitioners will need to navigate these issues to ensure that restoration remains effective and relevant. This will require, amongst other things, ongoing learning, sharing information and insights, humility, objectivity, continuous examination of assumptions, and questioning current practices and perspectives.     

Pterosaur dietary hypotheses: a review of ideas and approaches

Pterosaurs are an extinct group of Mesozoic flying reptiles, whose fossil record extends from approximately 210 to 66 million years ago. They were integral components of continental and marginal marine ecosystems, yet their diets remain poorly constrained. Numerous dietary hypotheses have been proposed for different pterosaur groups, including insectivory, piscivory, carnivory, durophagy, herbivory/frugivory, filter‐feeding and generalism. These hypotheses, and subsequent interpretations of pterosaur diet, are supported by qualitative (content fossils, associations, ichnology, comparative anatomy) and/or quantitative (functional morphology, stable isotope analysis) evidence. Pterosaur dietary interpretations are scattered throughout the literature with little attention paid to the supporting evidence. Reaching a robustly supported consensus on pterosaur diets is important for understanding their dietary evolution, and their roles in Mesozoic ecosystems. A comprehensive examination of the pterosaur literature identified 314 dietary interpretations (dietary statement plus supporting evidence) from 126 published studies. Multiple alternative diets have been hypothesised for most principal taxonomic pterosaur groups. Some groups exhibit a high degree of consensus, supported by multiple lines of evidence, while others exhibit less consensus. Qualitative evidence supports 87.3% of dietary interpretations, with comparative anatomy most common (62.1% of total). More speciose groups of pterosaur tend to have a greater range of hypothesised diets. Consideration of dietary interpretations within alternative phylogenetic contexts reveals high levels of consensus between equivalent monofenestratan groups, and lower levels of consensus between equivalent non‐monofenestratan groups. Evaluating the possible non‐biological controls on apparent patterns of dietary diversity reveals that numbers of dietary interpretations through time exhibit no correlation with patterns of publication (number of peer‐reviewed publications through time). 73.8% of dietary interpretations were published in the 21st century. Overall, consensus interpretations of pterosaur diets are better accounted for by non‐biological signals, such as the impact of the respective quality of the fossil record of different pterosaur groups on research levels. That many interpretations are based on qualitative, often untestable lines of evidence adds significant noise to the data. More experiment‐led pterosaur dietary research, with greater consideration of pterosaurs as organisms with independent evolutionary histories, will lead to more robust conclusions drawn from repeatable results. This will allow greater understanding of pterosaur dietary diversity, disparity and evolution and facilitate reconstructions of Mesozoic ecosystems.     

PHYLOGENY OF AULACOSEIRA (BACILLARIOPHYTA) BASED ON MOLECULES AND MORPHOLOGY1

The phylogeny of 67 populations representing 45 species of Aulacoseira Thwaites was estimated by maximum parsimony methods using a combination of nucleotide sequence data and qualitative and quantitative morphological characteristics of the silica cell wall gathered primarily from original observation by LM and SEM. A new type of character using continuous quantitative variables that describe the ontogenetic‐allometric trajectories of cell wall characteristics over the life cycle (size range) of diatoms is introduced. In addition to the 45 Aulacoseira species, the phylogeny also incorporated one Miosira Krammer, Lange‐Bertalot, and Schiller species and two outgroup species (Melosira varians Agardh and Stephanopyxis nipponica Gran & Yendo). Fifteen species, represented by 24 populations, also contained molecular data from the nuclear genome (18S rDNA), and 11 of these species (18 populations) contained data from the chloroplast genome (rbcL) as well, which were sequenced or downloaded from GenBank. The phylogeny of Aulacoseira is composed of five major clades: 1) an A. crenulata (Ehrenburg) Thwaites and A. italica (Ehrenburg) Simonsen clade, which is the most basal; 2) an A. granulata (Ehrenburg) Simonsen complex clade; 3) an A. ambigua (Grunow) Simonsen clade; 4) an A. subarctica (O. Müller) Haworth and A. distans (Ehrenburg) Simonsen clade; and 5) an A. islandica (O. Müller) Simonsen clade that also contained endemic species from Lake Baikal, Siberia and many extinct Aulacoseira taxa. Monophyly of Aulacoseira can only be achieved if Miosira is no longer given separate generic status.     

关于北京猿人用火的证据:研究历史、争议与新进展

周口店第1地点古人类用火证据是该遗址一系列重大科学发现中的一项重要内容,在很长时期内,作为同类遗存中最早的记录及其分析论证结果被国际学术界广泛接受。但随着少数西方学者的质疑和挑战,从上世纪八十年代中期开始在这一问题上出现争议,其后开展的埋藏学和地球化学分析又得出进一步否定的结论。但周口店遗址的洞穴地层十分复杂,目前残存的堆积与古人类生存时期的状态有重大差别,与当初大规模发掘时见证的遗物遗迹的分布与埋藏状况也有很大不同,在剖面表层做局部有限的采样分析并不足以推翻以前的系统性研究结论,何况很多否定性的意见源自学术理论思潮的转变和缺乏具体分析的常规性推理。从以前的发掘记录和各种分析结果看,周口店遗址埋藏着丰富的古人类用火证据,这些证据不是孤立的,是可以相互验证和支持的。2009年以来在遗址开展的新的发掘与研究获得重要进展,揭示出具有结构的火塘、烧骨、石灰化的灰岩块等原地用火产生的遗物与遗迹,对相关材料的现代科技分析进一步确定这些遗存的人类用火性质。这样,遗址上文化层的用火证据变得明确无误,相关争议终可尘埃落定。对于下部地层中的用火证据,尚需做同样的发掘、分析和研究工作。     

Evaluating the efficacy of continuous quantitative characters for reconstructing the phylogeny of a morphologically homogeneous spider taxon (Araneae, Mygalomorphae, Antrodiaetidae, Antrodiaetus)

The use of continuous quantitative characters for phylogenetic analyses has long been contentious in the systematics literature. Recent studies argue for and against their use, but there have been relatively few attempts to evaluate whether these characters provide an accurate estimate of phylogeny, despite the fact that a number of methods have been developed to analyze these types of data for phylogenetic inference. A tree topology will be produced for a given methodology and set of characters, but little can be concluded with regards to the accuracy of phylogenetic signal without an independent evaluation of those characters. We assess the performance of continuous quantitative characters for the mygalomorph spider genus Antrodiaetus, a group that is morphologically homogeneous and one for which few discrete (morphological) characters have been observed. Phylogenetic signal contained in continuous quantitative characters is compared to an independently derived phylogeny inferred on the basis of multiple nuclear and mitochondrial gene loci. Tree topology randomizations, regression techniques, and topological tests all demonstrate that continuous quantitative characters in Antrodiaetus conflict with the phylogenetic signal contained in the gene trees. Our results show that the use of continuous quantitative characters for phylogenetic reconstruction may be inappropriate for reconstructing Antrodiaetus phylogeny and indicate that due caution should be exercised before employing this character type in the absence of other independently derived sources of characters.