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Regulatory single nucleotide polymorphisms (rSNPs) in human genomes are thought to be responsible for phenotypic differences, including susceptibility to diseases and treatment outcomes, even they do not change any gene product. However, a genome-wide search for rSNPs has not been properly addressed so far. In this work, a computational method for rSNP identification is proposed. As background SNPs far outnumber rSNPs, an ensemble method is applied to handle imbalanced data, which firstly converts an unbalanced dataset into several balanced ones and then models for every balanced dataset. Two major types of features are extracted, that are sequence based features and allele-specific based features. Then random forest is applied to build the recognition model for each balanced dataset. Finally, ensemble strategies are adopted to combine the result of each model together. We have tested our method on a set of experimentally verified rSNPs, and leave-one-out cross-validation results showed that our method can achieve accuracy with sensitivity of 73.8%, specificity of 71.8% and the area under ROC curve (AUC) is 0.756. In addition, our method is threshold free and doesn’t rely on data of regulatory elements, thus it will have better adaptability when facing different data scenarios. The original data and the source matlab codes involved are available at https://sourceforge.net/projects/rsnpdect/.
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Microclimatic conditions influence fungal growth, yet accurate descriptions of the relationships between the occurrence of fungi and microclimate (especially temperature) are lacking for dead wood in natural conditions. Here, we studied the occurrence of fungal fruit bodies on 2 m long segments of both standing and lying trunks of Norway spruce (Picea abies). The fungal assemblages were associated with properties of the segments related to the progression in wood decay, causes of tree death, and temperature and moisture conditions. Fluctuations in the temperature of wood decreased with increasing water content, and both water content and temperature stability increased with diameter and with the progression in wood decay. Red-listed species differed in their relations to both wood and microclimate parameters, which highlights the importance of the simultaneous presence of various wood types for the occurrence of rare and threatened species.
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The flora in China is highly endemic. Decisions about conservation and management of biodiversity based on hotspots and conservation gaps of endemic seed plant species diversity in China are essential. In this paper, based on a species distribution data set with 12,824 Chinese endemic plants, we measured Chinese endemic seed plant diversity using five indices: endemic species richness (ER), weighted endemism (WE), phylogenetic diversity (PD), phylogenetic endemism (PE), and biogeographically weighted evolutionary distinctiveness (BED). Five percent of China's total land area with the highest biodiversity was used to identify hotspots for each index. In total, 19 hotspots covering 7.96% of China's total land area were identified. Most hotspots are located in mountainous areas, mainly in the Qinling Mountains and further south or in the Hengduan Mountains and to the east in China. Nine hotspots are identified with all five indices. These hotspots include the Hengduan Mountains, the Xishuangbanna Region, the Qinling Mountains, southwest Chongqing, and five mountainous areas (located in east Chongqing and west Hubei; in east Yunnan and west Guangxi; in north Guangxi, southeast Guizhou and southwest Hunan; in north Guangdong and south Hunan; and in southeast Tibet, respectively). Furthermore, we detected conservation gaps for hotspots of Chinese endemic seed flora by overlaying national nature reserves with the identified hotspots, and we designated priority conservation gaps for hotspots by overlaying global biodiversity hotspots with conservation gaps for hotspots. Most hotspots for Chinese endemic seed plant species are badly protected. Only 26.48% of the hotspot areas of Chinese endemic seed plant species were covered by nature reserves. We suggest that it is essential to pay more attention to herbaceous plants in biodiversity conservation, and to promote a network function of nature reserves within these hotspots in China.
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We present an efficient, automated workflow for validating model chemistries in computational quantum chemistry by integrating several open-source web and semantic technologies within a discipline-specific context. We combine a range of open-source functionalities to (i) canonicalize the outputs of standard, popular computational chemistry software; (ii) store and index data within a central networked repository; (iii) query the data against a range of relevant properties; and (iv) compute robust statistical measures of model accuracy. Our workflow is tested by committing data from 10,304 ab initio potential energy surface calculations to a central repository and subsequently applying nested queries and analytics. Specifically, we investigate the performance of 44 different model chemistries (coupled with polarized, double-zeta basis sets) at reproducing CCSD(T)/CBS(D,T) potential energy surfaces of eight different Lewis acid/base pairs, whose dative bonds are known to be challenging to model for many electronic structure theories.
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The intercontinental distribution of living freshwater osteoglossiform fishes (Osteoglossomorpha, Teleostei) was hypothesized to predominantly represent the vicariant result of the fragmentation of Gondwana based on physiological and phylogenetic evidence. The fossil record, however, challenges this hypothesis by making transoceanic dispersal plausible because it provides post-fragmentation minimum ages of intercontinental clades and it includes several marine forms. The aim of this study was to test whether the divergence of Osteoglossiformes was compatible with the breakup of Gondwana using newly reconstructed time-calibrated phylogenetic trees based on a large dataset combining extant and fossil taxa and molecular and morphological characters. Bayesian tip-dating and node-dating approaches with different Teleostei age calibrations were employed. The results of the divergence tests are largely dependent on the a priori calibrated age of crown-group Teleostei, with two of the three specific vicariance hypotheses tested in this study not being rejected only when the age of the Teleostei was constrained to be as old as the early Permian. Molecules consistently push the age of crown-group Teleostei back to the Paleozoic, while the fossil record, which is considered informative, does not support such an ancient origin. Reconciling molecular and paleontological estimates of the age of crown-group Teleostei is central to determining the role of Gondwanan breakup in the intercontinental distribution of freshwater teleosts, including Osteoglossiformes.
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The Groupe Européen de Recherches Gazières (GERG) 2008 multi-parameter equation of state (EOS) is considered the reference model for the prediction of natural gas mixture properties. However, the limited quality of thermodynamic property data available for many key binary mixtures at the time of its development constrained both its range of validity and achievable uncertainty. The data situation for the binary system (CH4+C4H10) in particular was identified previously as limiting the ability of the GERG-EOS to describe rich natural gases at low temperatures. Recently, new vapour-liquid equilibrium (VLE) and liquid mixture heat capacity data measured at low temperatures and high pressures have been published that significantly improve the data situation for this crucial binary, allowing erroneous literature data to be identified and the predictive behaviour of the GERG-EOS when extrapolated to be tested. The 10 basis functions in the generalised departure function used by the GERG-EOS for several binaries including (CH4+C4H10) were examined to eliminate the term causing a divergence between measured and predicted liquid mixture isobaric heat capacities at T<150K. With a simplified nine-term departure function, the maximum relative deviation between the measured and predicted heat capacities was reduced from nearly (110 to 7) %. The interaction parameters in the GERG equation were also re-determined by including, for the first time for this binary, reliable low temperature VLE data together with most of the other high temperature data used in the original development of the model. The new interaction parameters for (CH4+C4H10) reduced the relative deviation of bubble point pressures measured and calculated at T=244K from (9 to 1.4) %, without affecting the accuracy of property predictions at higher temperatures.
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Nassariidae are a group of scavenging, predominantly marine, snails that are diversified on soft bottoms as well as on rocky shores, and are the subject of numerous research papers in ecology, ecotoxicology or paleontology. A weak and/or apparently continuous variation in shell characters has resulted in an intimidating taxonomy, with complex synonymy lists. Over 1320 extant nominal species have been described, of which 442 are currently regarded as valid. Above species level, the state of the art is equally hazy, with four subfamilies and twelve genera currently accepted, and many other names in the graveyard of synonymy. A molecular analysis based on three mitochondrial (COI, 16S, 12S) and two nuclear (28S, H3) markers was conducted. Our dataset includes 218 putative nassariid species, comprising 9 of the 12 valid genera, and 25 nominal genera represented by their type species. The monophyly of the Nassariidae as classically construed is not confirmed. Species of Antillophos, Engoniophos, Phos, Nassaria, Tomlinia and Anentome (formerly considered Buccinidae) are included inside the Nassariidae clade. Within the Nassariinae, the tree unexpectedly demonstrates that species from the Atlantic and the Indo-Pacific form different clades which represent several independent diversification events. Through an integrative approach, the reconstruction of ancestral states was addressed for eight characters supposedly informative for taxonomy. Using numerous fossil calibration points, Nassariidae appear to have originated 120 MYA ago in Atlantic temperate waters during the Lower Cretaceous. Our results have a profound impact on nassariid taxonomy, especially with regard to the validity of subfamily- and genus-level names.
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The phase diagrams of NdBr3–MBr (M=Li…Cs) pseudobinary systems measured by different authors show discrepancies. Therefore in the present work mentioned systems have been re-examined and the compatibility of their phase diagrams have been evaluated. The dependences of mixing enthalpies on NdBr3 mole fraction, heat capacities of M3NdBr6 intermediate compounds (M=Li…Cs) formed in the investigated systems and evaluated phase diagrams have been used for optimization of coupled phase diagrams. The experimental data have been used to predict of an unknown thermodynamic properties of M2NdBr5 and MNd2Br7 (M=Li…Cs) intermediate compounds. The Associate Model of the liquid phase has been applied and the dependence of mixing entropy on NdBr3 mole fraction for the set of the phase diagrams have been found. The amount of the main associate {3M++NdBr63−} in each system has been estimated.
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The neogastropod family Fasciolariidae Gray, 1853 – tulips, horse-conchs, spindles, etc., comprises important representatives of tropical and subtropical molluscan assemblages, with over 500 species in the subfamilies Fasciolariinae Gray, 1853, Fusininae Wrigley, 1927 and Peristerniinae Tryon, 1880. Fasciolariids have had a rather complicated taxonomical history, with several genus names for a long time used as waste baskets to group many unrelated species; based on shell characters, recent taxonomic revisions have, however, began to set some order in its taxonomy. The present work is the first molecular approach to the phylogeny of Fasciolariidae based on a multigene dataset, which provides support for fasciolariids, an old group with a fossil record dating back to the Cretaceous. Molecular markers used were the mitochondrial genes 16S rRNA and cytochrome c oxidase subunit I, and the nuclear genes 18S rRNA, 28S rRNA and histone H3, sequenced for up to 116 ingroup taxa and 17 outgroups. Phylogenetic analyses revealed monophyly of Dolicholatirus Bellardi, 1884 and Teralatirus Coomans, 1965, however it was not possible to discern if the group is the sister clade to the remaining fasciolariids; the latter, on the other hand, proved monophyletic and contained highly supported groups. A first split grouped fusinines and Pseudolatirus Bellardi, 1884; a second split grouped the peristerniine genera Peristernia Mörch, 1852 and Fusolatirus Kuroda and Habe, 1971, while the last group comprised fasciolariines and the remaining peristerniines. None of these clades correspond to the present-day accepted circumscription of the three recognized subfamilies.
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Allatostatin-type A (AST-A), kisspeptin (KISS) and galanin (GAL) G-protein coupled receptor (GPCR) systems share a common ancestral origin in arthropods and the vertebrates where they regulate metabolism and reproduction. The molluscs are the second most diverse phylum in the animal kingdom, they occupy an important phylogenetic position, and their genome is more similar to deuterostomes than the arthropods and nematodes and thus they are good models for studies of gene family evolution and function. This mini-review intends to extend the current knowledge about AST-A, KISS and GAL GPCR system evolution and their putative function in the mollusc mantle. Comparative evolutionary analysis of the target GPCR systems was established by identifying homologues in genomes and tissue transcriptome datasets available for molluscs and comparing them to those of other metazoan systems. Studies in arthropods have revealed the existence of the AST-A system but the loss of homologues of the KISS and GAL systems. Homologues of the insect AST-AR and vertebrate KISSR genes were found in molluscs but putative GALR genes were absent. Receptor gene number suggested that members of this family have suffered lineage specific evolution during the molluscan radiation. In molluscs, orthologues of the insect AST-A peptides were not identified but buccalin peptides that are structurally related were identified and are putative receptor agonists. The identification of AST-AR and KISSR genes in molluscs strengthens the hypotheses that in metazoans members of the AST-AR subfamily share evolutionary proximity with KISSRs. The variable number of receptors and large repertoire of buccalin peptides may be indicative of the functional diversity of the AST-AR/KISSR systems in molluscs. The identification of AST-A and KISS receptors and ligands in the mantle transcriptome indicates that in molluscs they may have acquired a novel function and may play a role in shell development or sensory detection in the mantle.
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