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opencc-by-4.0May 2020View details →

Statistical model training data for "Continuous Structural Parameterization: A proposed method for representing different model parameterizations within one structure demonstrated for atmospheric convection"

Gzipped CSV files containing convection scheme inputs and outputs used for training. Column format of each file: THETA_IN_1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,Q_IN_1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,DTHETA_1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,DQ_1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28 where THETA_IN are input values of potential temperature [K], Q_IN are input values of specific humidity [kg/kg], DTHETA are changes in potential temperature due to convection [K], DQ are changes in specific humidity due to convection [kg/kg]. Key: "llcs" are simulations with Lambert-Lewis. "gr" are simulations with Gregory-Rowntree. "4xco2" have 4 x pre-industrial atmospheric carbon dioxide concentration. (Others have 1 x pre-industrial atmospheric carbon dioxide concentration.) "rh0.7" and "rh0.9" have LLCS RHCRIT set to 70% and 90% respectively. All are 30 day simulations either for January "jan" or July "jul".

FIGURE 8 in A proposal for a new generic structure of the killifish family Aphaniidae, with the description of Aphaniops teimorii (Teleostei: Cyprinodontiformes)

FIGURE 8. Aphanius fasciatus, from the top: FSJF 4038, female, 35 mm SL; Croatia: Pag; FSJF 3012, male, 35 mm SL; Tunisia: Qued Zahzah.

FIGURE 6 in A proposal for a new generic structure of the killifish family Aphaniidae, with the description of Aphaniops teimorii (Teleostei: Cyprinodontiformes)

FIGURE 6. Aphaniops teimorii, left, from the top: ZFMK-ICH 122627, male, holotype, 33 mm SL; FSJF 4100, male, paratype, 39 m SL; Iran: Govdar River; right, from the top: not preserved, female, ~35 mm SL; Iran: Govdar River; not preserved, male, ~30 mm SL; Iran: Minhab River.

FIGURE 3 in A proposal for a new generic structure of the killifish family Aphaniidae, with the description of Aphaniops teimorii (Teleostei: Cyprinodontiformes)

FIGURE 3. Left column from the top, females: Anatolichthys anatoliae, FSJF 2485, 43 mm SL, Turkey: Lake Meyil; A. irregularis, FFR 08654, female, paratype, 52 mm SL, Turkey: Kaklık; A. villwocki, not preserved, same data as FSJF 2626, 35 mm SL, Turkey: Emirdağ; A. danfordii, FSJF 2601, 43 mm SL; Turkey: Soysallı; A. fontinalis, FSJF 3456, 32 mm SL, Yarışlı; right column from the top, males: Anatolichthys anatoliae, FSJF 2485, 40 mm SL, Turkey: Lake Meyil; A. irregularis, FFR 08653, male, holotype, 35 mm SL; Turkey: Kaklık; A. villwocki, not preserved, same data as FSJF 2626, 40 mm SL, Turkey: Emirdağ; A. danfordii, FSJF 2601, 38 mm SL; Turkey: Soysallı; A. fontinalis, FSJF 3456; 35 mm SL, Yarışlı.

FIGURE 2 in A proposal for a new generic structure of the killifish family Aphaniidae, with the description of Aphaniops teimorii (Teleostei: Cyprinodontiformes)

FIGURE 2. Anatolichthys splendens, from the top: ZMH 3506, 38 mm SL; ZMH 3505, lectotype, 31 mm SL; Turkey: Lake Gölcük.

FIGURE 11 in A proposal for a new generic structure of the killifish family Aphaniidae, with the description of Aphaniops teimorii (Teleostei: Cyprinodontiformes)

FIGURE 11. Left column from the top, females: Paraphanius mentoides, FSJF 2270, 60 mm SL; Turkey: Kırkgöz; P. striptus, FSJF 3495, 25 mm SL; Israel: Einot Timsach; P. similis, FSJF 3126, 31 mm SL; Turkey: Ereğli; right column from the top, males: P. mentoides, FSJF 2270, 58 mm SL; Turkey: Kırkgöz; P. striptus, FSJF 3495, 25 mm SL; Israel: Einot Timsach; P. similis, FSJF 3126, 28 mm SL; Turkey: Ereğli.

opencc-zeroAug 2020View details →

Data from: Agroforestry coffee soils increase the insect-suppressive potential offered by entomopathogenic fungi over full-sun soils: a case proposing a "bait-survival technique"

Entomopathogenic fungi are important natural enemies of insects. However, there is little information on the insect-suppressive potential of these fungi and possible effects of farming management on this. Meanwhile, changes in natural landscapes due to agricultural intensification have caused considerable biodiversity loss and consequent decay of ecosystem services. However, the adoption of practices such as agroforestry in agroecosystems can foster abiotic and biotic conditions that conserve biodiversity, consequently restoring the provision of ecosystems services. Here, we assessed the effect of management systems (agroforestry or full-sun) on the pest-suppressive potential of entomopathogenic fungi in Brazilian coffee plantations. We used the insect-bait method coupled with survival analyses to assess the speed of kill by entomopathogenic fungi and their presence in soil samples from both farming systems. We found that insects exposed to agroforestry soils died more quickly than insects exposed to full-sun soils. Of the fungi isolated from the insect-baits, Metarhizium was found most frequently, followed by Beauveria. Meanwhile, Fusarium was frequently isolated as primary or secondary infections. We propose that the differential survival of insects is indicative of a greater suppressive potential by entomopathogenic fungi in agroforestry, and that this could be promoted by the diversified landscape, microclimatic stability and reduced soil disturbance in agroforestry systems. Furthermore, our results provide a useful demonstration of the potential use of the insect bait method to investigate pest suppressive potential through insect-bait mortality, and we term this the "bait survival technique".

opencc-by-4.0Oct 2020View details →

Dataset for "Sorption, anomalous water transport and dynamic porosity in cement paste: A spatially localised 1H NMR relaxation study and a proposed mechanism"

This record is the dataset for Figures 4, 5, 6, 7, 8 and 9 in the journal article "Sorption, anomalous water transport and dynamic porosity in cement paste: A spatially localised 1H NMR relaxation study and a proposed mechanism" published in Cement and Concrete Research, Volume 133, July 2020, 106045, https://doi.org/10.1016/j.cemconres.2020.106045. Abstract: The link between anomalous water sorption and dynamic porosity in cement pastes is explored using spatially resolved GARField1H nuclear magnetic resonance (NMR) relaxation analysis. A model is developed in which the effective capillary diffusion coefficient is dependent on the instantaneous pore size distribution. This and earlier data show changes in pore size distribution resultant from changes in saturation that do not occur instantaneously with changes in degree of saturation. Therefore, it is assumed that the pore size distribution is always relaxing exponentially towards a (saturation dependent) equilibrium. It follows that the diffusivity is sample history (i.e. time) dependent as well as saturation dependent. This is sufficient to explain anomalies in rapid capillary water sorption. The same concepts are applied to slow drying. In this case, porosity changes occur on a timescale much shorter than drying so the system is always in dynamic equilibrium and anomalies are therefore not seen.

opencc-by-4.0Nov 2020View details →

A process proposal on how to move from data requirements to semantic data in the context of the MDA

This work proposes a process for the identification of the requirements associated with the data, along with and a set of transformations in Model Driven Architecture (MDA) context, in order to obtain a semantically annotated dataset, as a result of the unification and alignment of the data in the context of its initial domain. Our proposal identifies four phases (from CIM to code), in which is describe the artifacts and transformations required to progress to the next phase:  a target domain model is first obtained from the data requirements, after which the ontological schema and the ontology is generated from the previous model. A domain-specific language (DSL), also proposed in this work, is then used to obtain the semantic data model (the DSL code), which generates the final semantic dataset. We have validated the proposal by studying two cases: one with data from the public transport domain and the other with data concerning those affected by the COVID-19 pandemic.

FIGURE 5 in Redescription of larva of the South African endemic dobsonfly genus Chloroniella Esben-Petersen, 1924 (Megaloptera, Corydalidae), with a proposed terminology for Corydalidae larval sclerites

FIGURE 5. Setae of abdominal terga of late-instar larva of Chloroniella peringueyi Esben-Petersen, 1924 (Megaloptera: Corydalinae). A) Dorsal surface of an abdominal tergite with three distinct types of setae; B) Long, slender, smooth, erect and tapering macrosetae, with inconspicuous openings; C) Small, smooth, decumbent and rounded microsetae, with inconspicuous opening; D–E) Medial, smooth, erect and tubular macrosetae, with widened and upper portion and open tip.

FIGURE 1 in Redescription of larva of the South African endemic dobsonfly genus Chloroniella Esben-Petersen, 1924 (Megaloptera, Corydalidae), with a proposed terminology for Corydalidae larval sclerites

FIGURE 1. Late-instar larva of Chloroniella peringueyi Esben-Petersen, 1924 (Megaloptera: Corydalinae). A) habitus dorsal; B) habitus ventral.

FIGURE 4 in Redescription of larva of the South African endemic dobsonfly genus Chloroniella Esben-Petersen, 1924 (Megaloptera, Corydalidae), with a proposed terminology for Corydalidae larval sclerites

FIGURE 4. Thorax of late-instar larva of Chloroniella peringueyi Esben-Petersen, 1924 (Megaloptera: Corydalinae). A) dorsal view; B) ventral view; C) lateral view. Abbreviations: DM, dorsal medial sclerite; Cv, cervical sclerite; LPa, lateral posterior anterior sclerite; LPm, lateral posterior medial sclerite; LPp, lateral posterior posterior sclerite; sp, spiracle; VM, ventral medial sclerite; VP, ventral posterior sclerite.

FIGURE 7 in Redescription of larva of the South African endemic dobsonfly genus Chloroniella Esben-Petersen, 1924 (Megaloptera, Corydalidae), with a proposed terminology for Corydalidae larval sclerites

FIGURE 7. Abdominal detail of late-instar larva of Chloroniella peringueyi Esben-Petersen, 1924 (Megaloptera: Corydalinae). A–B) Seventh abdominal segment, ventral view; C–D) Abdominal apex, dorsal view; E–F) Abdominal apex, ventral view. VM, ventral medial sclerite.

FIGURE 3 in Redescription of larva of the South African endemic dobsonfly genus Chloroniella Esben-Petersen, 1924 (Megaloptera, Corydalidae), with a proposed terminology for Corydalidae larval sclerites

FIGURE 3. Mouthparts of late-instar larva of Chloroniella peringueyi Esben-Petersen, 1924 (Megaloptera: Corydalinae). A) labrum and clypeus, dorsal view; B) right mandible, dorsal view; C) labium, ventral view; D) maxilla, ventral view. Abbreviations: atcly, anteclypeus; a tooth, apical tooth; crd, cardo; ga, galea; lbp, labial palp; lbr, labrum; lig, ligula; mt, mentum; mtpls, mental plates; mxp, maxillar palp; pmt, prementum; ptcly, postclypeus; p teeth, preapical teeth; smt, submentum; smpro, submental projection; sti, stipes.

FIGURE 6 in Redescription of larva of the South African endemic dobsonfly genus Chloroniella Esben-Petersen, 1924 (Megaloptera, Corydalidae), with a proposed terminology for Corydalidae larval sclerites

FIGURE 6. Abdominal lateral filament of late-instar larva of Chloroniella peringueyi Esben-Petersen, 1924 (Megaloptera: Corydalinae). A–B) Lateral view; (C) Detail of the small macrosetae and microsetae on ventral surface; D) Detail of the long macrosetae of dorsal surface with substrate.

FIGURE 2 in Redescription of larva of the South African endemic dobsonfly genus Chloroniella Esben-Petersen, 1924 (Megaloptera, Corydalidae), with a proposed terminology for Corydalidae larval sclerites

FIGURE 2. Head of late-instar larva of Chloroniella peringueyi Esben-Petersen, 1924 (Megaloptera: Corydalinae). A–B) dorsal view; C–D) ventral view. Abbreviations: ant, antenna; atg, anterior tentorial grooves; cri, nearly circular ridge delimiting neck region; cs, coronal suture; fs, frontal suture; ge, gena; gu, gula; pgscl, postgular sclerite; ptg, posterior tentorial grooves; sen, sensorium; smt, submentum; sri, secondary parietal ridge; ste, stemmata.

FIGURE 8 in Redescription of larva of the South African endemic dobsonfly genus Chloroniella Esben-Petersen, 1924 (Megaloptera, Corydalidae), with a proposed terminology for Corydalidae larval sclerites

FIGURE 8. Distribution of Chloroniella peringueyi Esben-Petersen, 1924 (Megaloptera: Corydalinae). A) African Continent, overview; B) South Africa; C) Western Cape. This map was made with data from Esben-Petersen (1924), Barnard (1931), Penny (1993), Mansell (2003), and this study.

opencc-zeroFeb 2020View details →

Data from: Using parsimony-guided tree proposals to accelerate convergence in Bayesian phylogenetic inference

Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topologies. MCMC algorithms using such moves tend to get trapped in tree space, making them slow in finding the globally most probable trees (known as `convergence') and in estimating the correct proportions of the different types of them (known as `mixing'). Here, we introduce a new class of moves, which propose trees based on their parsimony scores. The proposal distribution derived from the parsimony scores is a quickly computable albeit rough approximation of the conditional posterior distribution over candidate trees. We demonstrate with simulations that parsimony-guided moves correctly sample the uniform distribution of topologies from the prior. We then evaluate their performance against standard moves using six challenging empirical datasets, for which we were able to obtain accurate reference estimates of the posterior using long MCMC runs, a mix of topology proposals, and Metropolis coupling. On these datasets, ranging in size from 357 to 934 taxa and from 1,740 to 5,681 sites, we find that single chains using parsimony-guided moves usually converge an order of magnitude faster than chains using standard moves. They also exhibit better mixing, that is, they cover the most probable trees more quickly. Our results show that tree moves based on quick and dirty estimates of the posterior probability can significantly outperform standard moves. Future research will have to show to what extent the performance of such moves can be improved further by finding better ways of approximating the posterior probability, taking the trade-off between accuracy and speed into account.

opencc-zeroDec 2017View details →

Data from: Assessment of mesophotic coral ecosystem connectivity for proposed expansion of a marine sanctuary in the northwest Gulf of Mexico: population genetics

While there are several areas containing shallow coral habitats in the Gulf of Mexico (GOM), the availability of suitable reef habitat at mesophotic depths (~30–150 m) along the continental shelf margin suggests the potential for ecologically connected coral populations across hundreds of kilometers in the northwest (NW) GOM. The NW GOM includes a relatively high proportion of mesophotic habitats, including salt diapirs in Flower Garden Banks National Marine Sanctuary (FGBNMS), Bright Bank, and McGrail Bank, the latter two being Habitat Areas of Particular Concern (HAPCs). In response to a proposed expansion plan for the sanctuary boundaries to include additional mesophotic banks in the NW GOM, we investigated the genetic connectivity of the depth-generalist coral Montastraea cavernosa, a ubiquitous member of scleractinian communities throughout the Tropical Western Atlantic. Montastraea cavernosa populations in the NW GOM demonstrated strong connectivity with relatively high levels of gene flow and no significant genetic differentiation occurring over banks up to 120 km apart. Historical migration models based on genetic data predicted panmixia of M. cavernosa across the NW GOM. The comparisons between genetic and biophysical models (see Garavelli et al., 2018; associate manuscript) highlight not only the importance of incorporating multiple assessments of connectivity into management schemes, but also the potentially stochastic nature of oceanographic patterns in the NW GOM and their effect on migration estimates among coral habitats. These trends indicate that M. cavernosa populations have remained well-connected in the NW GOM and that coral populations on each bank have likely been receiving larval recruitment through time. Thus, M. cavernosa populations should be managed as a combined unit within the NW GOM, which supports the proposal to expand the NMS boundaries to include mesophotic habitats beyond West and East FGB.