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opencc-zeroJul 2020View details →

Data from: Mining the stable quantitative trait loci for agronomic traits in wheat (Triticum aestivum L.) based on an introgression line population

Background: Human demand for wheat will continue to increase together with the continuous global population growth. Agronomic traits in wheat are susceptible to environmental conditions. Therefore, in breeding practice, priority is given to QTLs of agronomic traits that can be stably detected across multiple environments and over many years. Results: In this study, QTL analysis was conducted for eight agronomic traits using an introgression line population across eight environments (drought stressed and well-watered) for five years. In total, 44 additive QTLs for the above agronomic traits were detected on 15 chromosomes. Among these, qPH-6A, qHD-1A, qSL-2A, qHD-2D and qSL-6A were detected across seven, six, five, five and four environments, respectively. The means in the phenotypic variation explained by these five QTLs were 12.26%, 9.51%, 7.77%, 7.23%, and 8.49%, respectively. Conclusions: We identified five stable QTLs, which includes qPH-6A, qHD-1A, qSL-2A, qHD-2D and qSL-6A. They play a critical role in wheat agronomic traits. One of the dwarf genes Rht14, Rht16, Rht18 and Rht25 on chromosome 6A might be the candidate gene for qPH-6A. The qHD-1A and qHD-2D were novel stable QTLs for heading date and they differed from known vernalization genes, photoperiod genes and earliness per se genes.

opencc-zeroOct 2019View details →

Data from: Using text-mined trait data to test for cooperate-and-radiate co-evolution between ants and plants

Mutualisms may be "key innovations" that spur lineage diversification by augmenting niche breadth, geographic range, or population size, thereby increasing speciation rates or decreasing extinction rates. Whether mutualism accelerates diversification in both interacting lineages is an open question. Research suggests that plants that attract ant mutualists have higher diversification rates than non-ant associated lineages. We ask whether the reciprocal is true: does the interaction between ants and plants also accelerate diversification in ants, i.e. do ants and plants cooperate-and-radiate? We used a novel text-mining approach to determine which ant species associate with plants in defensive or seed dispersal mutualisms. We investigated patterns of lineage diversification across a recent ant phylogeny using BiSSE, BAMM, and HiSSE models. Ants that associate mutualistically with plants had elevated diversification rates compared to non-mutualistic ants in the BiSSE model, with a similar trend in BAMM, suggesting ants and plants cooperate-and-radiate. However, the best-fitting model was a HiSSE model with a hidden state, meaning that diversification models that do no account for unmeasured traits are inappropriate to assess the relationship between mutualism and ant diversification. Against a backdrop of diversification rate heterogeneity, the best-fitting HiSSE model found that mutualism actually decreases diversification: mutualism evolved much more frequently in rapidly diversifying ant lineages, but then subsequently slowed diversification. Thus, it appears that ant lineages first radiated, then cooperated with plants.

opencc-by-4.0Oct 2020View details →

Mining data

Contains information about 13 Gold mining companies. Data were generated in 2017.

opennotspecifiedNov 2020View details →

FIGURE 1 in Ontogeny of an arlequin: morphological and colour pattern changes from juvenile to adult in Gnathophyllum elegans (Risso, 1816) (Decapoda: Palaemonidae), traced through citizen science and social media data mining

FIGURE 1. Morphological and colour pattern changes from juvenile to adult in Gnathophyllum elegans (Risso, 1816). A–C. Specimens from Capo Noli (Italy, Mediterranean Sea) (~44.199232N, 8.420455E), 15–16 m, on anthropogenic debris laying on a detritic bottom, 5–13.IX.2020. A. Photo by Walter Bassi. B–C. Photos by Alessandro Raho. D. Specimen from La Laja beach, Gran Canaria (Spain, Atlantic Ocean) (~28.060335N, -15.418428E), 1 m, amidst algae in a tide pool, 29.VIII.2017. Photo by Alberto Navarro. E. Specimen from Bat Galim reef, Haifa (Israel, Mediterranean Sea) (~32.833317N, 34.97431E), 2 m, under a rock on a rocky bottom, ~2017. Photo by Sarah Ohayon. F. Specimen from Capo Caccia, Sardinia (Italy, Mediterranean Sea) (~40.565506N, 8.165579E), 5 m, detritic bottom with rocks, 28.VIII.2015. Photo by Marco Colombo.

opencc-by-4.0Sep 2020View details →

Empirical data for project: Mining user reviews of COVID contact-tracing apps

Empirical data for project: Mining user reviews of COVID contact-tracing apps

opencc-zeroJan 2021View details →

Data from: Changes in soil microbial communities in post mine ecological restoration: implications for monitoring using high throughput DNA sequencing

The ecological restoration of ecosystem services and biodiversity is a key intervention used to reverse the impacts of anthropogenic activities such as mining. Assessment of the performance of restoration against completion criteria relies on biodiversity monitoring. However, monitoring usually overlooks soil microbial communities (SMC), despite increased awareness of their pivotal role in many ecological functions. Recent advances in cost, scalability and technology has led to DNA sequencing being considered as a cost-effective biological monitoring tool, particularly for otherwise difficult to survey groups such as microbes. However, such approaches for monitoring complex restoration sites such as post-mined landscapes have not yet been tested. Here we examine bacterial and fungal communities across chronosequences of mine site restoration at three locations in Western Australia to determine if there are consistent changes in SMC diversity, community composition and functional capacity. Although we detected directional changes in community composition indicative of microbial recovery, these were inconsistent between locations and microbial taxa (bacteria or fungi). Assessing functional diversity provided greater understanding of changes in site conditions and microbial recovery than could be determined through assessment of community composition alone. These results demonstrate that high-throughput amplicon sequencing of environmental DNA (eDNA) is an effective approach for monitoring the complex changes in SMC following restoration. Future monitoring of mine site restoration using eDNA should consider archiving samples to provide improved understanding of changes in communities over time. Expansion to include other biological groups (e.g. soil fauna) and substrates would also provide a more holistic understanding of biodiversity recovery.

Data from: Mining for NRPS and PKS genes revealed a high diversity in the Sphagnum bog metagenome

Sphagnum bog ecosystems are among the oldest vegetation forms harboring a specific microbial community and are known to produce an exceptionally wide variety of bioactive substances. Although the Sphagnum metagenome shows a rich secondary metabolism, the genes have not yet been explored. To analyze nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), the diversity of NRPS and PKS genes in Sphagnum-associated metagenomes was investigated by in silico data mining and sequence-based screening (PCR amplification of 9,500 fosmid clones). The in silico Illumina-based metagenomic approach resulted in the identification of 279 NRPSs and 346 PKSs, as well as 40 PKS-NRPS hybrid gene sequences. The occurrence of NRPS sequences was strongly dominated by the members of the Protebacteria phylum, especially by species of the Burkholderia genus, while PKS sequences were mainly affiliated with Actinobacteria. Thirteen novel NRPS-related sequences were identified by PCR amplification screening, displaying amino acid identities of 48% to 91% to annotated sequences of members of the phyla Proteobacteria, Actinobacteria, and Cyanobacteria. Some of the identified metagenomic clones showed the closest similarity to peptide synthases from Burkholderia or Lysobacter, which are emerging bacterial sources of as-yet-undescribed bioactive metabolites. This report highlights the role of the extreme natural ecosystems as a promising source for detection of secondary compounds and enzymes, serving as a source for biotechnological applications.

Data from: Mining from transcriptomes: 315 single-copy orthologous genes concatenated for the phylogenetic analyses of Orchidaceae

Phylogenetic relationships are hotspots for orchid studies with controversial standpoints. Traditionally, the phylogenies of orchids are based on morphology and subjective factors. Although more reliable than classic phylogenic analyses, the current methods are based on a few gene markers and PCR amplification, which are labor intensive and cannot identify the placement of some species with degenerated plastid genomes. Therefore, a more efficient, labor-saving and reliable method is needed for phylogenic analysis. Here, we present a method of orchid phylogeny construction using transcriptomes. Ten representative species covering five subfamilies of Orchidaceae were selected, and 315 single-copy orthologous genes extracted from the transcriptomes of these organisms were applied to reconstruct a more robust phylogeny of orchids. This approach provided a rapid and reliable method of phylogeny construction for Orchidaceae, one of the most diversified family of angiosperms. We also showed the rigorous systematic position of holomycotrophic species, which has previously been difficult to determine because of the degenerated plastid genome. We concluded that the method presented in this study is more efficient and reliable than methods based on a few gene markers for phylogenic analyses, especially for the holomycotrophic species or those whose DNA sequences have been difficult to amplify. Meanwhile, a total of 315 single-copy orthologous genes of orchids are offered and more informative loci could be used in the future orchid phylogenetic studies.

opencc-zeroDec 2016View details →

Data from: Acoustic monitoring of coastal dolphins and their response to naval mine neutralization exercises

To investigate the potential impacts of naval mine neutralization exercises (MINEX) on odontocete cetaceans, a long-term passive acoustic monitoring study was conducted at a US Navy training range near Virginia Beach, USA. Bottom-moored acoustic recorders were deployed in 2012–2016 near the epicentre of MINEX training activity and were refurbished every 2–4 months. Recordings were analysed for the daily presence/absence of dolphins, and dolphin acoustic activity was quantified in detail for the hours and days before and after 31 MINEX training events. Dolphins occurred in the area year-round, but there was clear seasonal variability, with lower presence during winter months. Dolphins exhibited a behavioural response to underwater detonations. Dolphin acoustic activity near the training location was lower during the hours and days following detonations, suggesting that animals left the area and/or reduced their signalling. Concurrent acoustic monitoring farther away from the training area suggested that the radius of response was between 3 and 6 km. A generalized additive model indicated that the predictors that explained the greatest amount of deviance in the data were the day relative to the training event, the hour of the day and circumstances specific to each training event.

Data from: Effects of mountaintop removal mining and valley filling on the occupancy and abundance of stream salamanders

Human-induced land-use changes are among the primary causes of ecosystem degradation and biodiversity loss. Across central Appalachia (USA), mountaintop removal mining and valley filling (MTR/VF) is the prevailing form of land-use change and represents a stressor to stream ecosystems. Salamanders are the dominant vertebrate in Appalachian headwater streams. Thus, we addressed the question: Is salamander occupancy and conditional abundance reduced in streams impacted by MTR/VF? We conducted repeated counts of adult and larval salamanders within 10-m reaches in 11 valley-filled streams and 12 reference streams in south-eastern Kentucky. Relationships between occupancy, conditional abundance, and site type (MTR/VF vs. reference) were modelled using the hurdle model (Ecology, 94, 2013 and 1472), where occupancy is modelled separately from abundance while accounting for differences in per-individual detection probabilities among groups. We found mean occupancy probabilities were >0·85 for all groups in reference reaches, whereas mean occupancy probabilities were relatively lower in MTR/VF reaches (ranging from 0·23 to 0·66). Posterior means of the difference in occupancy between site types were negative across all groups, although MTR/VF stream reaches were at least 95% less likely to be occupied by spring salamander Gyrinophilus porphyriticus, adult southern two-lined salamander Eurycea cirrigera and larval dusky salamanders Desmognathus compared to reference reaches. Posterior means of the difference in conditional abundance between MTR/VF and reference stream reaches were negative across all groups; 95% credible interval for difference in conditional abundance covered zero for only one species (red salamander Pseudotriton ruber). After adjusting for goodness-of-fit, point estimates of differences in occupancy and conditional abundance still remained below zero for most species. Additionally, MTR/VF reaches had higher ion concentrations, total organic carbon and specific conductance compared to reference reaches. Synthesis and applications. Our study concludes that mountaintop removal mining and valley filling (MTR/VF) reduces salamander occupancy and conditional abundance. Although the potential mechanisms responsible for reduction are numerous, our findings suggest a change in the current regulatory framework is needed to offset the impacts of MTR/VF on stream ecosystems and biota. Reclamation techniques that enhance conditions for vegetative succession within catchments may improve habitat on reclaimed surface mines.

Data from: Recovery of a mining-damaged stream ecosystem

This paper presents a 30+ year record of changes in benthic macroinvertebrate communities and fish populations associated with improving water quality in mining-influenced streams. Panther Creek, a tributary to the Salmon River in central Idaho, USA suffered intensive damage from mining and milling operations at the Blackbird Mine that released copper (Cu), arsenic (As), and cobalt (Co) into tributaries. From the 1960s through the 1980s, no fish and few aquatic invertebrates could be found in 40 km of mine-affected reaches of Panther Creek downstream of the metals contaminated tributaries, Blackbird and Big Deer Creeks. Efforts to restore water quality began in 1995, and by 2002 Cu levels had been reduced by about 90%, with incremental declines since. Rainbow Trout (Oncorhynchus mykiss) were early colonizers, quickly expanding their range as areas became habitable when Cu concentrations dropped below about 3X the U.S. Environmental Protection Agency's biotic ligand model (BLM) based chronic aquatic life criterion. Anadromous Chinook Salmon (O. tshawytscha) and steelhead (O. mykiss) have also reoccupied Panther Creek. Full recovery of salmonid populations occurred within about 12-years after the onset of restoration efforts and about 4-years after the Cu chronic criteria had mostly been met, with recovery interpreted as similarity in densities, biomass, year class strength, and condition factors between reference sites and mining-influenced sites. Shorthead Sculpin (Cottus confusus) were slower than salmonids to disperse and colonize. While benthic macroinvertebrate biomass has increased, species richness has plateaued at about 70 to 90% of reference despite the Cu criterion having been met for several years. Different invertebrate taxa had distinctly different recovery trajectories. Among the slowest taxa to recover were Ephemerella, Cinygmula and Rhithrogena mayflies, Enchytraeidae oligochaetes, and Heterlimnius aquatic beetles. Potential reasons for the failure of some invertebrate taxa to recover include competition, and high sensitivity to Co and Cu.

opencc-zeroMay 2020View details →

Data from: Co-introduction of native mycorrhizal fungi and plant seeds accelerates restoration of post-mining landscapes

1. Grasslands are among the most threatened terrestrial biomes, and habitat conservation alone will be insufficient to meet biodiversity goals. While restoration of indigenous grasslands is a priority, conflict with economic objectives means that incorporation of alternative habitats is necessary to offset grassland loss. With up to 800,000 km² of land affected by mining globally, there is an opportunity to create additional grassland habitat in post-mining landscapes. 2. We aimed to assess whether co-introduction of native arbuscular mycorrhizal (AM) fungi and plants is an efficient means of initializing species rich vegetation recovery in barren post-mining landscapes. We established an experiment in three post-mining areas in Estonia, where we seeded plots with native plant seeds and inoculated them with trap cultured native AM fungi from a similar habitat. We measured the abundance and composition of soil AM fungal and aboveground plant communities in two consecutive years using relevés, high-throughput sequencing and fatty acid profiling. 3. Our results demonstrate that co-introduction of native plants and AM fungi is an effective way to establish species rich vegetation in post-mining areas. Co-introduction of symbiotic partners resulted in higher richness, diversity and abundance of plants and AM fungi than when either partner was introduced individually. However, the plant and AM fungal communities in sown and inoculated plots were not distinct from those in uninoculated treatments; they rather formed a subset of all taxa present on the sites but exhibited higher diversity than uninoculated plots. 4. Synthesis and applications: This study shows that managing the below-ground microbiome is an essential part of vegetation restoration. The availability of symbiotic partners can be considered a key aspect determining the diversity of restored vegetation. Targeted inoculations with native and habitat-specific AM fungi could therefore increase restoration success.28-Apr-2020

opencc-zeroDec 2013View details →

Data from: Restoration as mitigation: analysis of stream mitigation for coal mining impacts in southern Appalachia

Compensatory mitigation is commonly used to replace aquatic natural resources being lost or degraded but little is known about the success of stream mitigation. This article presents a synthesis of information about 434 stream mitigation projects from 117 permits for surface mining in Appalachia. Data from annual monitoring reports indicate that the ratio of lengths of stream impacted to lengths of stream mitigation projects were < 1 for many projects, and most mitigation was implemented on perennial streams while most impacts were to ephemeral and intermittent streams. Regulatory requirements for assessing project outcome were minimal; visual assessments were the most common and 97% of the projects reported suboptimal or marginal habitat even after 5 years of monitoring. Less than a third of the projects provided biotic or chemical data; most of these were impaired with biotic indices below state standards and stream conductivity exceeding federal water quality criteria. Levels of selenium known to impair aquatic life were reported in 7 of the 11 projects that provided Se data. Overall, the data show that mitigation efforts being implemented in southern Appalachia for coal mining are not meeting the objectives of the Clean Water Act to replace lost or degraded streams ecosystems and their functions.

opencc-zeroDec 2012View details →

Data from: Cross-ontology multi-level association rule mining in the Gene Ontology

The Gene Ontology (GO) has become the internationally accepted standard for representing function, process, and location aspects of gene products. The wealth of GO annotation data provides a valuable source of implicit knowledge of relationships among these aspects. We describe a new method for association rule mining to discover implicit co-occurrence relationships across the GO sub-ontologies at multiple levels of abstraction. Prior work on association rule mining in the GO has concentrated on mining knowledge at a single level of abstraction and/or between terms from the same sub-ontology. We have developed a bottom-up generalization procedure called Cross-ontology Data Mining-Level by Level (COLL) that takes into account the structure and semantics of the GO, generates generalized transactions from annotation data and mines interesting multi-level cross-ontology association rules. We applied our method on publicly available chicken and mouse GO annotation datasets and mined 5368 and 3959 multi-level cross ontology rules from the two datasets respectively. We show that our approach discovers more and higher quality association rules from the GO as evaluated by biologists in comparison to previously published methods. Biologically interesting rules discovered by our method reveal unknown and surprising knowledge about co-occurring GO terms.

opencc-zeroDec 2015View details →

Data from: A molecular phylogeny and revised higher-level classification for the leaf-mining moth family Gracillariidae and its implications for larval host-use evolution

Gracillariidae are one of the most diverse families of internally feeding insects, and many species are economically important. Study of this family has been hampered by lack of a robust and comprehensive phylogeny. In the present paper, we sequenced up to 22 genes in 96 gracillariid species, representing all previously recognized subfamilies and genus groups, plus 20 outgroups representing other families and superfamilies. Following objective identification and removal of two rogue taxa, two datasets were constructed: dataset 1, which included 12 loci totalling 9927 bp for 94 taxa, and dataset 2, which supplemented dataset 1 with 10 additional loci for 10 taxa, for a total of 22 loci and 16 167 bp. Maximum likelihood analyses strongly supported the monophyly of Gracillariidae and most previously recognized subfamilies and genus groups. On this basis, we propose a new classification consisting of eight subfamilies, four of which are newly recognized or resurrected: Acrocercopinae Kawahara & Ohshima subfam. n.; Gracillariinae Stainton; Lithocolletinae Stainton; Marmarinae Kawahara & Ohshima subfam. n.; Oecophyllembiinae Réal & Balachowsky; Parornichinae Kawahara & Ohshima subfam. n.; Ornixolinae Kuznetzov & Baryshnikova stat. rev.; and Phyllocnistinae Zeller. The subfamily Gracillariinae is restricted to the monophyletic group comprising Gracillaria Haworth and closely related genera. We also formally transfer Acrocercops scriptulata Meyrick to Ornixolinae and use the name Diphtheroptila Vári, creating Diphtheroptila scriptulata comb. n. An exploratory mapping of larval host-use traits on the phylogeny shows strong conservation of modes of leaf mining but much higher lability of associations with host plant orders and families, suggesting that host shifts could play a significant role in gracillariid diversification.

openafl-3.0Jul 2015View details →

International Journal of Hidden Data Mining and Scientific Knowledge Discovery

Welcome to the first issue of the International Journal of Hidden Data Mining and Scientific Knowledge Discovery: http://scholarpage.org/journal We decided to use the following acronym HDSKD for the journal. Hidden data represents data or information that is more or less hidden, unseen or encrypted so that it becomes difficult to extract it. Scientific knowledge represents every information that comes by a scientific way, such as theories, experimental observations or scientific evidences of some phenomenon. The last term in the journal title, namely "Discovery" has a great importance, since it means that we are looking for scientific information particularly and hidden data in general. Authors are encouraged to submit their latest research results to the HDSKD journal Hence, we are proud to announce the opening of our first journal issue in hidden data mining and scientific knowledge discovery (a peer reviewed journal) and encourage authors to submit their latest research results to HDSKD. The criteria of selection are based on the review decision, which will lead to the acceptance or reject of the paper. The readers’ comments are also welcome and everyone is invited to read or download the papers for a scientific or academic purposes. The journal is a non-profit academic source of knowledge and does not permit any commercial use of the articles. The Editorial Board

FIGURES 59–65 in Four new leaf-mining Acalyptris species from Guatemala and Belize, with new data on bionomics of Stigmella pruinosa (Lepidoptera: Nepticulidae)

FIGURES 59–65. Collecting localities in Guatemala, Belize and Honduras, and key habitats in Guatemala. 59, map of major collecting localities (courtesy of T. Patterson, USA); 60, 61, mixed montane and cloud forests, highlands of Guatemala, Quetzaltenango, with Quercus feeding Stigmella species occurring (see Stonis et al., 2013a); 62, moist montane forest, Panajachel (new Stigmella species described in Stonis et al., 2013a); 63, tropical premontane forest on south western slopes of the Sierra Madre, NE of Retalhuleu; 64, 65, lowland evergreen broadleaf tropical forests, Petén Dept.

FIGURES 55–58. Stigmella pruinosa Puplesis & Robinson. 55 in Four new leaf-mining Acalyptris species from Guatemala and Belize, with new data on bionomics of Stigmella pruinosa (Lepidoptera: Nepticulidae)

FIGURES 55–58. Stigmella pruinosa Puplesis & Robinson. 55, male genitalia, capsule, genitalia slide no. RA494. Scale 100 µm; 56, same, aedeagus. Scale 100 µm; 57, general view with aedeagus inside capsule, genitalia slide no. RA493. Scale 100 µm; 58, female genitalia, genitalia slide no. RA477. Scale 250 µm.

FIGURES 42–47 in Four new leaf-mining Acalyptris species from Guatemala and Belize, with new data on bionomics of Stigmella pruinosa (Lepidoptera: Nepticulidae)

FIGURES 42–47. Acalyptris statuarius Diškus & Stonis, sp. nov., male genitalia. 42, capsule, holotype, genitalia slide no. AD520. Scale 100 µm; 43, valva, paratype, genitalia slide no. AD519. Scale 100 µm; 44, aedeagus, holotype, genitalia slide no. AD520. Scale 100 µm; 45, general view of genitalia with aedeagus inside capsule, paratype, genitalia slide no. AD519. Scale 125 µm; 46, juxta, ventral view, holotype, genitalia slide no. AD520. Scale 50 µm; 47, same, dorsal view. Scale 75 µm.

FIGURES 48–54. Stigmella pruinosa Puplesis & Robinson. 48 in Four new leaf-mining Acalyptris species from Guatemala and Belize, with new data on bionomics of Stigmella pruinosa (Lepidoptera: Nepticulidae)

FIGURES 48–54. Stigmella pruinosa Puplesis & Robinson. 48, currently known distribution; 49, habitat, lowland secondary evergreen broadleaf tropical forest near El Remate, Petén Region; 50, 51, host-plant (Guazuma ulmifolia Lam., Malvaceae); 52, leaf-mine; 53, cocoon. Scale 1 mm. 54, female adult, Petén Dept., Guatemala. Scale 1 mm.