Model documentation, chapter 4

The modeling groups are listed along with a brief description of the respective models

Manual for proposing a part of the list of available names (LAN) in zoology

Article 79 of the Fourth Edition of the International Code of Zoological Nomenclature (henceforth Code) describes an official List of Available Names in Zoology (henceforth LAN), consisting of a series of “Parts” (of defined taxonomic and temporal scope), compiled by relevant experts. The LAN represents a comprehensive inventory of names available under the Code. The aim of this manual is to define a procedure for implementing Article 79, with format suggestions for zoologists aiming to create a Part of the LAN for family-group, genus-group, or species-group names in zoological nomenclature. Because the LAN may serve as an important basis for retrospective content in ZooBank, the structure outlined here is designed to allow easy importation to ZooBank.Peer Reviewe

Community next steps for making globally unique identifiers work for biocollections data

Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided

Domain Adapted Deep-Learning for Improved Ultrasonic Crack Characterization Using Limited Experimental Data

Deep learning is an effective method for ultrasonic crack characterization due to its high level of automation and accuracy. Simulating the training set has been shown to be an effective method of circumventing the lack of experimental data common to nondestructive evaluation (NDE) applications. However, a simulation can neither be completely accurate nor capture all variability present in the real inspection. This means that the experimental and simulated data will be from different (but related) distributions, leading to inaccuracy when a deep learning algorithm trained on simulated data is applied to experimental measurements. This article aims to tackle this problem through the use of domain adaptation (DA). A convolutional neural network (CNN) is used to predict the depth of surface-breaking defects, with in-line pipe inspection as the targeted application. Three DA methods across varying sizes of experimental training data are compared to two non-DA methods as a baseline. The performance of the methods tested is evaluated by sizing 15 experimental notches of length (1–5 mm) and inclined at angles of up to 20° from the vertical. Experimental training sets are formed with between 1 and 15 notches. Of the DA methods investigated, an adversarial approach is found to be the most effective way to use the limited experimental training data. With this method, and only three notches, the resulting network gives a root-mean-square error (RMSE) in sizing of 0.5 ± 0.037 mm, whereas with only experimental data the RMSE is 1.5 ± 0.13 mm and with only simulated data it is 0.64 ± 0.044 mm

Taxonomy Based on Science is Necessary for Global Conservation

Taxonomy is a scientific discipline that has provided the universal naming and classification system of biodiversity for centuries and continues effectively to accommodate new knowledge. A recent publication by Garnett and Christidis (Garnett ST, Christidis L. Taxonomy anarchy hampers conservation. Nature. 2017; 546(7656):25±27. https://doi.org/10.1038/546025a) expressed concerns regarding the difficulty that taxonomic changes represent for conservation efforts and proposed the establishment of a system to govern taxonomic changes. Their proposal to restrict the freedom of taxonomic action through governing subcommittees that would review taxonomic papers for compliance and their assertion that the scientific community\u27s failure to govern taxonomy threatens the effectiveness of global efforts to halt biodiversity loss, damages the credibility of science, and is expensive to society are flawed in many respects. They also assert that the lack of governance of taxonomy damages conservation efforts, harms the credibility of science, and is costly to society. Despite its fairly recent release, Garnett and Christidis\u27 proposition has already been rejected by a number of colleagues. Herein, we contribute to the conversation between taxonomists and conservation biologists aiming to clarify some misunderstandings and issues in the proposition by Garnett and Christidis. Placing governance over the science of taxonomy blurs the distinction between taxonomy and nomenclature. Garnett and Christidis’s proposal is far-reaching but represents a narrow perspective of taxonomy, as utilized by conservation, and reflects an increasingly broad misunderstanding throughout biology of the scientific basis of taxonomy, formalized nomenclature, and the relationship between them. This trend may have resulted from the attenuation of instruction in taxonomic principles and, in particular, nomenclature at many universities, in part because of a shift in research priorities away from taxonomy. Garnett and Christidis assert that an “assumption that species are fixed entities underpins every international agreement on biodiversity conservation.” This assumption demonstrates a fundamental misunderstanding of taxonomy and the evolving view of what species represent. The essential features of science include documenting natural patterns and processes, developing and testing hypotheses, and refining existing ideas and descriptions of nature based on new data and insights. Taxonomy, the science of recognizing and delimiting species, adheres to these fundamental principles. Discoveries of new organisms together with advances in methodology continue unabated, leading to a constant reevaluation of the boundaries between taxonomic entities. Species (and higher taxa) comprise related organisms that may be clustered together differently depending on which sets of criteria are emphasized. Hey et al. acknowledge “the inherent ambiguity of species in nature” but point out that “species-related research and conservation efforts can proceed without suffering from, and without fear of, the ambiguity of species.” Through taxonomic research, our understanding of biodiversity and classifications of living organisms will continue to progress. Any system that restricts such progress runs counter to basic scientific principles, which rely on peer review and subsequent acceptance or rejection by the community, rather than third-party regulation. Thiele and Yeates cautioned that such a system “could lead to authoritarianism and a stifling of innovative taxonomic viewpoints. No other hypothesis-driven field of science would accept such a straitjacket”. Taxonomy and associated nomenclature are not without problems. Even with a common set of facts, alternative interpretations of how to classify organisms can lead to differing classifications. However, the science of taxonomy is increasingly rigorous, which can improve the foundation for targeted legislative action regarding species. Taxonomic instability does not affect all taxonomic groups equally. Garnett and Christidis provide examples from mammals and birds, which collectively represent a small fraction

Prognathodes geminus, a new species of butterflyfish (Teleostei, Chaetodontidae) from Palau

A new species of the butterflyfish genus Prognathodes (Chaetodontidae) is described from two specimens collected at a depth of 116 m off Ngemelis Island, Palau. Prognathodes geminus sp. n. is similar to P. basabei Pyle & Kosaki, 2016 from the Hawaiian archipelago, and P. guezei (Maugé & Bauchot, 1976) from the western Indian Ocean, but differs from these species in the number of soft dorsal-fin rays, size of head, body width, and body depth. There are also subtle differences in life color, and substantial differences in the mtDNA cytochrome oxidase I sequence (d ≈ 0.08). Although genetic comparisons with P. guezei are unavailable, it is expected that the genetic divergence between P. guezei and P. geminus will be even greater than that between P. geminus and P. basabei. It is named for the strikingly similar color pattern it shares with P. basabei

Taxonomy Based on Science Is Necessary for Global Conservation [Formal comment]

Taxonomy is a scientific discipline that has provided the universal naming and classification system of biodiversity for centuries and continues effectively to accommodate new knowledge. A recent publication by Garnett and Christidis expressed concerns regarding the difficulty that taxonomic changes represent for conservation efforts and proposed the establishment of a system to govern taxonomic changes. Their proposal to “restrict the freedom of taxonomic action” through governing subcommittees that would “review taxonomic papers for compliance” and their assertion that “the scientific community\u27s failure to govern taxonomy threatens the effectiveness of global efforts to halt biodiversity loss, damages the credibility of science, and is expensive to society” are flawed in many respects. They also assert that the lack of governance of taxonomy damages conservation efforts, harms the credibility of science, and is costly to society. Despite its fairly recent release, Garnett and Christidis\u27 proposition has already been rejected by a number of colleagues. Herein, we contribute to the conversation between taxonomists and conservation biologists aiming to clarify some misunderstandings and issues in the proposition by Garnett and Christidis. Placing governance over the science of taxonomy blurs the distinction between taxonomy and nomenclature. Garnett and Christidis\u27s proposal is far-reaching but represents a narrow perspective of taxonomy, as utilized by conservation, and reflects an increasingly broad misunderstanding throughout biology of the scientific basis of taxonomy, formalized nomenclature, and the relationship between them. This trend may have resulted from the attenuation of instruction in taxonomic principles and, in particular, nomenclature at many universities, in part because of a shift in research priorities away from taxonomy

ZooKeys, unlocking Earth’s incredible biodiversity and building a sustainable bridge into the public domain: From “print-based” to “web-based” taxonomy, systematics, and natural history. ZooKeys Editorial Opening Paper

This is the publisher's version, also available electronically from http://zookeys.pensoft.net/articles.php?id=1929.Publishing taxonomic and systematics studies in the digital era faces major challenges and requires new approaches, many of which are currently stimulating spirited discussions amongst taxonomists and systematists. New amendments to the International Code of Zoological Nomenclature are expected to regulate electronic publishing of new taxa and create a standard form for their registration (ZooBank). Responding to a perceived need, this editorial announces establishment of ZooKeys – a new online and print journal in zoological taxonomy and systematics, which aims to quickly respond and adapt to the newest developments in taxonomic publishing. Open Access is accepted as mandatory for ZooKeys. Th e rationale for and concept of ZooKeys is discussed in detail

Co-ordinated Airborne Studies in the Tropics (CAST)

This is the author accepted manuscript. The final version is available from the American Meteorological Society via http://dx.doi.org/10.1175/BAMS-D-14-00290.1The Co-ordinated Airborne Studies in the Tropics (CAST) project is studying the chemical composition of the atmosphere in the Tropical Warm Pool region to improve understanding of trace gas transport in convection. The main field activities of the CAST (Co-ordinated Airborne Studies in the Tropics) campaign took place in the West Pacific in January/February 2014. The field campaign was based in Guam (13.5°N, 144.8°E) using the UK FAAM BAe-146 atmospheric research aircraft and was coordinated with the ATTREX project with the unmanned Global Hawk and the CONTRAST campaign with the Gulfstream V aircraft. Together, the three aircraft were able to make detailed measurements of atmospheric structure and composition from the ocean surface to 20 km. These measurements are providing new information about the processes influencing halogen and ozone levels in the tropical West Pacific as well as the importance of trace gas transport in convection for the upper troposphere and stratosphere. The FAAM aircraft made a total of 25 flights between 1°S-14°N and 130°-155°E. It was used to sample at altitudes below 8 km with much of the time spent in the marine boundary layer. It measured a range of chemical species, and sampled extensively within the region of main inflow into the strong West Pacific convection. The CAST team also made ground-based measurements of a number of species (including daily ozonesondes) at the Atmospheric Radiation Measurement program site on Manus Island, Papua New Guinea (2.1°S, 147.4°E). This article presents an overview of the CAST project focussing on the design and operation of the West Pacific experiment. It additionally discusses some new developments in CAST, including flights of new instruments on the Global Hawk in February/March 2015.CAST is funded by NERC and STFC, with grant NE/ I030054/1 (lead award), NE/J006262/1, NE/J006238/1, NE/J006181/1, NE/J006211/1, NE/J006061/1, NE/J006157/1, NE/J006203/1, NE/J00619X/1, and NE/J006173/1. N. R. P. Harris was supported by a NERC Advanced Research Fellowship (NE/G014655/1). P. I. Palmer acknowledges his Royal Society Wolfson Research Merit Award. The BAe-146-301 Atmospheric Research Aircraft is flown by Directflight Ltd and managed by the Facility for Airborne Atmospheric Measurements, which is a joint entity of the Natural Environment Research Council and the Met Office. The authors thank the staff at FAAM, Directflight and Avalon Aero who worked so hard toward the success of the aircraft deployment in Guam, especially for their untiring efforts when spending an unforeseen 9 days in Chuuk. We thank the local staff at Chuuk and Palau, as well as the authorities in the Federated States of Micronesia for their help in facilitating our research flights. Special thanks go to the personnel associated with the ARM facility at Manus, Papua New Guinea without whose help the ground-based measurements would not have been possible. Thanks to the British Atmospheric Data Centre (BADC) for hosting our data and the NCAS Atmospheric Measurement Facility for providing the radiosonde and ground-based ozone equipment. Chlorophyll-a data used in Figure 1 were extracted using the Giovanni online data system, maintained by the NASA GES DISC. We also acknowledge the MODIS mission scientists and associated NASA personnel for the production of this data set. Finally we thank many individual associated with the ATTREX and CONTRAST campaigns for their help in the logistical planning, and we would like to single out Jim Bresch for his excellent and freely provided meteorological advice