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opencc-by-4.0Dec 2019View details →

European Case Study SDM data

Baseline data and Impacts of Policy Cards for the for the System Dynamics Model of the European Case Study in Sim4Nexus.

opencc-zeroJun 2020View details →

Verifiability of genus-level classification under quantification and parsimony theories: a case study of follicucullid radiolarians

The classical taxonomy of fossil invertebrates is based on subjective judgments of morphology, which can cause confusion since there are no codified standards for the classification of genera. Here, we explore the validity of the genus taxonomy of 75 species and morphospecies of the Follicucullidae, a Late Paleozoic family of radiolarians, using a new method, <a name="_Hlk41571699">Hayashi's quantification theory II</a> (HQT-II), a general multivariate statistical method for categorical datasets relevant to discriminant analysis. We identify a scheme of ten genera rather than the currently accepted three genera (Follicucullus, Ishigaconus and Parafollicucullus). As HQT-II cannot incorporate stratigraphic data, a phylogenetic tree of Follicucullidae was reconstructed for 38 species using maximum parsimony. Six lineages emerged, roughly in concordance with the results of HQT-II. Combined with parsimony ancestral state reconstruction, the ancestral group of this family is Haplodiacanthus. Five other groups were discriminated, the Parafollicucullus, Curvalbaillella, Pseudoalbaillella, Longtanella, and Follicucullus–Cariver lineages. The morphological evolution of these lineages comprises a minimum essential list of eight states of four traits. <a name="_Hlk41488876">HQT-II is a novel discriminant analytical multivariate method that may be of value in other taxonomic problems of paleobiology.</a>

opencc-zeroDec 2019View details →

Data from: Identification of intraductal carcinoma of the prostate on tissue specimens using Raman micro-spectroscopy: A diagnostic accuracy case-control study with multicohort validation

Background Prostate cancer (PC) is the most frequently diagnosed cancer in North American men. Pathologists are in critical need of accurate biomarkers to characterize PC, particularly to confirm the presence of intraductal carcinoma of the prostate (IDC-P), an aggressive histopathological variant for which therapeutic options are now available. Our aim was to identify IDC-P with Raman micro-spectroscopy and machine learning technology following a protocol suitable for routine clinical histopathology laboratories. Methods and findings We used Raman micro-spectroscopy to differentiate IDC-P from PC, as well as PC and IDC-P from benign tissue on formalin-fixed paraffin-embedded first-line radical prostatectomy specimens (embedded in tissue microarrays, TMAs) from 483 patients treated in three Canadian institutions between 1993 and 2013. The main measures were the presence or absence of IDC-P and of PC, regardless of the clinical outcomes. Most of the 483 patients were pT2 stage (44–69%), and pT3a (22–49%) was more frequent than pT3b (9–12%). After approval of the construction of the TMAs by local ethics review board, the diagnostic accuracy study was approved by the Centre hospitalier de l'Université de Montréal (CHUM) ethics review board. Briefly, two consecutive sections of each TMA block were cut. The first section was transferred onto a glass slide to perform immunohistochemistry with H&E counterstaining for cell identification. The second section was placed on an aluminum slide, dewaxed, and then used to acquire an average of 7 Raman spectra per specimen (between 4 and 24 Raman spectra, 4 acquisitions / TMA core). Raman spectra of each cell type were then analyzed to retrieve tissue-specific molecular information and to generate classification models using machine learning technology. Models were trained and cross-validated using data from one institution. Accuracy, sensitivity and specificity were respectively of 87 ± 5%, 86 ± 6% and 89 ± 8% to differentiate PC from benign tissue, and of 95 ± 2%, 96 ± 4% and 94 ± 2% respectively to differentiate IDC-P from PC. The trained models were then tested on data from two independent institutions, reaching accuracies, sensitivities and specificities of 84 and 86%, 84 and 87%, and 81 and 82%, respectively to diagnose PC, and of 85 and 91%, 85 and 88%, and 86 and 93% respectively for the identification of IDC-P. IDC-P could further be differentiated from high-grade prostatic intraepithelial neoplasia (HGPIN), a pre-malignant intraductal proliferation which can be mistaken as IDC-P, with accuracies, sensitivities and specificities >95% in both training and testing cohorts. As we used stringent criteria to diagnose IDC-P, the main limitation of our study is the exclusion of borderline, difficult to classify lesions from our datasets. Conclusions In this study, we developed classification models for the analysis of Raman micro-spectroscopy data to differentiate IDC-P, PC and benign tissue, including HGPIN. Raman micro-spectroscopy could be a next-generation histopathological technique used to reinforce the identification of high-risk PC patients and lead to more precise diagnosis of IDC-P.

Fig. 18 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 18. Phylogeny of the family Clevelandellidae Kidder, 1938 based on 18S rRNA gene sequences. Bootstrap values for maximum likelihood analyses performed in IQTrees and PhyML as well as posterior probabilities for Bayesian interference performed in MrBayes and Phycas were mapped onto the best scoring IQTree. Dashes indicate statistical support below 50%. Sequences obtained in this study are in bold face. Members of each morphospecies are marked by the same color, as shown in Fig. 17. For specimen codes and further details, see Table 6. The scale bar denotes six substitutions per one thousand nucleotide positions.

Fig. 14. Paraclevelandia brevis Kidder, 1937. Thai I in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 14. Paraclevelandia brevis Kidder, 1937. Thai I specimens (A–C, F–G) isolated from Panesthia angustipennis angustipennis (Illiger, 1801) and Vietnamese specimens (D–E) isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 from life (A–C) and after protargol impregnation (D–G). A. Ventral overview, showing the general body organization. Arrows mark the proximal end of the peristomial opening, black arrowheads denote the proximal end of the adoral zone of membranelles, white arrowheads denote the karyophore attached to the anterior body pole. B–C. Ciliary pattern of ventral and dorsal sides. Asterisks mark the position of the ciliary whorl (posterior suture). D–G. Ventral views of specimens with well-preserved body shape. Scale bars = 20 μm.

Fig. 13. Paraclevelandia brevis Kidder, 1937. Thai I in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 13. Paraclevelandia brevis Kidder, 1937. Thai I specimens isolated from Panesthia angustipennis angustipennis (Illiger, 1801) after protargol impregnation. A–J. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. Scale bar = 20 μm.

Fig. 4 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 4. Clevelandella hastula (Kidder, 1937). Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 from life (A) and after protargol impregnation (B–N). A. Ventral view of a representative specimen, length 90 μm. B–K. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. L. Semi-schematic diagram, showing the general body organization. M–N. Ciliary pattern of ventral and dorsal sides. Arrow marks the right suture and black arrowheads denote the position of the ciliary whorl (posterior suture). Scale bars = 30 μm.

Fig. 2 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 2. Clevelandella constricta (Kidder, 1937). Thai I specimens isolated from Panesthia angustipennis angustipennis (Illiger, 1801) after protargol impregnation. A–J. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. Scale bar = 50 μm.

Fig. 7 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 7. Clevelandella panesthiae (Kidder, 1937). Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 after protargol impregnation. A–D. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. Scale bar = 50 μm.

Fig. 17 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 17. Phylogeny of the order Clevelandellida de Puytorac & Grain, 1976 based on 18S rRNA gene sequences. Some metopids were used as outgroup. Bootstrap values for maximum likelihood analyses performed in IQTrees and PhyML as well as posterior probabilities for Bayesian interference performed in MrBayes and Phycas were mapped onto the best scoring IQTree. Dashes indicate statistical support below 50%, asterisks denote mismatch with the topology shown. Sequences obtained in this study are in bold face. Members of each morphospecies are marked by the same color, following the code in the inset. For specimen codes and further details, see Table 6. The scale bar denotes three substitutions per one hundred nucleotide positions.

Fig. 9 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 9. Clevelandella parapanesthiae (Kidder, 1937). Thai I specimens isolated from Panesthia angustipennis angustipennis (Illiger, 1801) from life (A) and after protargol impregnation (B–N). A. Ventral view of a representative specimen, length 90 μm. B–K. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. L. Semi-schematic diagram, showing the general body organization. M–N. Ciliary pattern of ventral and dorsal sides. Arrow marks the right suture, black arrowheads indicate the position of the ciliary whorl (posterior suture). Scale bars = 30 μm.

Fig. 12. Paraclevelandia brevis Kidder, 1937 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 12. Paraclevelandia brevis Kidder, 1937. Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 from life (A) and after protargol impregnation (B–N). A. Ventral view of a representative specimen, length 50 μm. B–K. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. L. Semi-schematic diagram, showing the general body organization. M–N. Ciliary pattern of ventral and dorsal sides. Arrow marks the right suture, black arrowheads indicate the position of the ciliary whorl (posterior suture). Scale bars = 20 μm.

Fig. 6 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 6. Clevelandella panesthiae (Kidder, 1937). Thai I specimens isolated from Panesthia angustipennis angustipennis (Illiger, 1801) from life (A) and after protargol impregnation (B–N). A. Ventral view of a representative specimen, length 105 μm. B–K. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. L. Semi-schematic diagram, showing the general body organization. M–N. Ciliary pattern of ventral and dorsal sides. Arrow marks the right suture, black arrowheads denote the position of the ciliary whorl (posterior suture). Scale bars = 50 μm.

Fig. 8 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 8. Clevelandella panesthiae (Kidder, 1937). Vietnamese specimens (A, E–G) isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 and Thai I specimens (B–D) isolated from Panesthia angustipennis angustipennis (Illiger, 1801) from life (A, E–G) and after protargol impregnation (B–D). A–D. Ventral view of specimens with well-preserved body shape. Arrow marks the proximal end of the peristomial opening, black arrowheads denote the proximal end of the adoral zone of membranelles, white arrowheads mark the karyophore fibers attaching to the left and right body margins. E. Ventral view, showing the general body organization. F–G. Ciliary pattern of ventral and dorsal sides. Asterisks mark the position of the ciliary whorl (posterior suture), white double arrowhead denotes the right suture. Scale bars = 50 μm.

Fig. 16 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 16. Ordination analyses of 94 specimens of six clevelandellid morphospecies based on morphometric data (A) and cell shape information (B). A. Multidimensional scaling of the Gower's similarity matrix. B. Principal component analysis of the Fourier coefficients. Eigenvalues of the first two ordination axes are λ1= 0.723 and λ2= 0.135, explaining 85.8% of the total variation. The morphometric and geometrical data delimit the clevelandellid morphospecies consistently and unambiguously, i.e., each clevelandellid morphospecies forms a homogeneous cluster that is well isolated from all other morphospecies analyzed. Members of each morphospecies are highlighted by the same color as in Fig. 15.

Fig. 15 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)

Fig. 15. Cluster analyses of 94 specimens of six clevelandellid morphospecies based on morphometric data (A) and the cell shape information (B). A. Weighted average linkage clustering method in a combination with Gower's similarity index. B. Ward's D2 clustering method in a combination with the Manhattan city block distance. The morphometric and geometrical data delimit the clevelandellid morphospecies consistently and unambiguously, i.e., each clevelandellid morphospecies forms a homogeneous cluster that is well isolated from all other morphospecies analyzed. Since both techniques are phenetic, their results refer only to the similarity of the analyzed morphospecies in phenotypic space and not to their relatedness. Members of each morphospecies are highlighted by the same color.

opencc-by-4.0Jun 2020View details →

Strong Scaling Tools 1 Al-Zn-Mg-Cu case study

All data, results, and scripts from Al-Zn-Mg-Cu high-throughput case study. *.zip are the specimen-specific PARAPROBE results and POS rawdata. *.pdf are the PDF reports that were created with the automation of paraprobe-autoreporter. src.zip contains the source code of the paraprobe-autoreporter Python classes with which the results were computed. This source code is meant as a documentation of the results only! Instead, all users should always use the latest versions of the PARAPROBE tools from the GitLab repository https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe https://paraprobe-toolbox.readthedocs.org

opencc-zeroAug 2020View details →

First use of acoustic calls to distinguish cryptic fish species: Dascyllus aruanus complex as a case study

From a practical point of view, the determination of species in the wild is based on their phenotypes. Consequently, many species remain unknown because they are visually indistinguishable from described species. Although molecular methods and advances in bioacoustical analysis have been extensively used to uncover cryptic species, the combination of both methodologies is still rare and concerns only some terrestrial taxa such as insects, bats, frogs and birds. In this study, we aim to determine whether the sounds produced by different populations of fish can also be a tool to distinguish and identify cryptic species. The humbug damselfish complex, Dascyllus aruanus, is widely distributed across the Indo-Pacific Ocean and, since 2019, is thought to be composed of at least two species with Dascyllus aruanus in the Pacific Ocean and Dascyllus abudafur in the Indian Ocean. Recordings were made over a large geographical area with populations from Madagascar (Indian Ocean), Taiwan (Pacific Ocean) and French Polynesia (Society Islands). Two kinds of sounds were used for analysis: sounds associated with conspecific chases, and sounds produced during the "signal jump" of courtship behaviour. The sounds associated with signal jumps differ geographically. Acoustic feature differences between Taiwan and Madagascar align with the existence of genetic differences confirming specific status and supporting for the first time that sounds can help to discriminate cryptic species in Teleosts. However, differences in both acoustic features and genetic data can also be found between Taiwan and French Polynesia suggesting two clearly distinct populations. Using the same reasoning, we propose to resurrect the epithet "emamo" (Lesson 1830) for the Society Island humbug damselfish. Interestingly, sounds associated to conspecific chases are more variable than sounds related to signal jumps, suggesting that there are more constraints on sounds related to courtship since they would serve as indicators for species identity and contribute to premating isolation.

opencc-zeroAug 2020View details →

Towards an understanding of cosmopolitanism in deep time: a case study of ammonoids from the middle Permian to the Middle Triassic

Cosmopolitanism occurred recurrently during the geological past, especially after mass extinctions, but the underlying mechanisms remain poorly known. Three theoretical models, not mutually exclusive, can lead to cosmopolitanism: (1) selective extinction in endemic taxa, (2) endemic taxa becoming cosmopolitan after the extinction and (3) an increase in the number of newly originated cosmopolitan taxa after extinction. We analyzed an updated occurrence dataset including 831 middle Permian to Middle Triassic ammonoid genera and used two network methods to distinguish major episodes of ammonoid cosmopolitanism during this time interval. Then, we tested the three proposed models in these case studies. Our results confirm that at least two remarkable cosmopolitanism events after the Permian–Triassic and late Smithian (Early Triassic) extinctions, respectively. Partitioned analyses of survivors and newcomers revealed that the immediate cosmopolitanism event (Griesbachian) after the Permian–Triassic event can be attributed to endemic genera becoming cosmopolitan (Model 2) and an increase in the number of newly originated cosmopolitan genera after the extinction (Model 3). Late Smithian cosmopolitanism is caused by selective extinction in endemic taxa (Model 1) and an increase in the number of newly originated cosmopolitan genera (Model 3). We found that the survivors of Permian–Triassic mass extinction did not show a wider geographic range, suggesting that this mass extinction is nonselective among the biogeographic range, while late Smithian survivors exhibit a wide geographic range, indicating selective survivorship among cosmopolitan genera. These successive cosmopolitanism events during severe extinctions are associated with marked environmental upheavals such as rapid climate changes and oceanic anoxic events, suggesting that environmental fluctuations play a significant role in cosmopolitanism.