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opencc-by-4.0Dec 2020View details →

Characterization of intrauterine growth, proliferation and biomechanical properties of the murine larynx

Raw data for all variables  in study

opencc-zeroDec 2017View details →

Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation

Body size plays a key role in the ecology and evolution of all organisms. Therefore, quantifying the sources of morphological (co)variation, dependent and independent of body size, is of key importance when trying to understand and predict responses to selection. We combine structural equation modeling with quantitative genetics analyses to study morphological (co)variation in a meta-population of house sparrows (Passer domesticus). As expected, we found evidence of a latent variable 'body size', causing genetic and environmental covariation between morphological traits. Estimates of conditional evolvability show that allometric relationships constrain the independent evolution of house sparrow morphology. We also found spatial differences in general body size and its allometric relationships. On islands where birds are more dispersive and mobile, individuals were smaller and had proportionally longer wings for their body size. While in islands where sparrows are more sedentary and nest in dense colonies, individuals were larger and had proportionally longer tarsi for their body size. We corroborated these results using simulations and show that our analyses produce unbiased allometric slope estimates. This study highlights that in the short term allometric relationships may constrain phenotypic evolution, but that in the long term selection pressures can also shape allometric relationships.

opencc-byJan 2021View details →

Following up the Kepler field: Masses of Targets for transit timing and atmospheric characterization

These are posterior samples from TTV models presented in "Following up the Kepler field: Masses of Targets for transit timing and atmospheric characterization" by D. Jontof-Hutter, D., A. Wolfgang A., E. B. Ford, J. J. Liassauer, D. C. Fabrycky and J. F. Rowe.

opencc-by-2.0Jan 2021View details →

Staphylococcus aureus isolated from ruminants with mastitis in northern Greece dairy herds: genetic relatedness and phenotypic and genotypic characterization

Figure S1: Dendrogram of SmaI PFGE pulsotypes (P) and characteristics of the 162 S. aureus isolates.

opencc-by-4.0Jan 2021View details →

Characterizing Technical Debt and Antipatterns in AI-Based Systems: A Systematic Mapping Study

All artifacts related to a systematic mapping study on technical debt and antipatterns in AI-based systems; the data consists of an Excel file (00-all-data.xlsx) which includes a tab for all important constructs plus a separate CSV file per construct: <ul> <li>List of primary studies (01-primary-studies.csv)</li> <li>Established types of technical debt (02-established-td-types.csv)</li> <li>New types of technical debt (03-new-td-types.csv)</li> <li>Affected software quality attributes (04-affected-qas.csv)</li> <li>Identified antipatterns (05-antipatterns.csv)</li> <li>Reported solutions to address technical debt or antipatterns (06-solutions.csv)</li> </ul>

opencc-by-4.0Jan 2021View details →

Characterizing Highly Cited Papers in Mass Cytometry through H-Classics: WoS dataset and citation report

Dataset and citation report extracted from Web of Science (WoS) used to characterize highly cited papers in mass cytometry research field from 2010 to 2019.

opencc-by-4.0Jan 2021View details →

Characterization of the microbiome and immune response in corals with chronic Montipora white syndrome.

Complete code and data files for the Motipora White Syndrome paper. Run in Qiime2 2020.11, mostly on the command line.

Data from: Genomics meets applied ecology: characterizing habitat quality for sloths in a tropical agroecosystem

Understanding how habitat quality in heterogeneous landscapes governs the distribution and fitness of individuals is a fundamental aspect of ecology. While mean individual fitness is generally considered a key to assessing habitat quality, a comprehensive understanding of habitat quality in heterogeneous landscapes requires estimates of dispersal rates among habitat types. The increasing accessibility of genomic approaches, combined with field-based demographic methods, provides novel opportunities for incorporating dispersal estimation into assessments of habitat quality. In this study, we integrated genomic kinship approaches with field-based estimates of fitness components and Approximate Bayesian Computation (ABC) procedures to estimate habitat-specific dispersal rates and characterize habitat quality in two-toed sloths (Choloepus hoffmanni) occurring in a Costa Rican agricultural ecosystem. Field-based observations indicated that birth and survival rates were similar in a sparsely-shaded cacao farm and adjacent cattle pasture-forest mosaic. Sloth density was threefold higher in pasture compared to cacao, whereas home range size and overlap were greater in cacao compared to pasture. Dispersal rates were similar between the two habitats, as estimated using ABC procedures applied to the spatial distribution of pairs of related individuals identified using 3,431 SNP and 11 microsatellite locus genotypes. Our results indicate that crops produced under a sparse overstory can, in some cases, constitute lower quality habitat than pasture-forest mosaics for sloths, perhaps because of differences in food resources or predator communities. Finally, our study demonstrates that integrating field-based demographic approaches with genomic methods can provide a powerful means for characterizing habitat quality for animal populations occurring in heterogeneous landscapes.

opencc-by-4.0Jun 2021View details →

Characterizing high quality test methods, MSR'22

Replication Kit for "Characterizing high quality test methods" paper. Number of records: 15970; Number of columns: 50; Columns list: <ul> <li>Id;</li> <li>Project;</li> <li>Class;</li> <li>Method;</li> <li>Killed;</li> <li>Survived;</li> <li>TimedOut;</li> <li>Total;</li> <li>Score;</li> <li>WhileCount;</li> <li>ConditionCount;</li> <li>RedundantCount;</li> <li>AssertCount;</li> <li>IfCount;</li> <li>ExceptionCount;</li> <li>ForeachCount;</li> <li>PrintCount;</li> <li>SwitchCount;</li> <li>MysteryCount;</li> <li>ForCount;</li> <li>VerboseCount;</li> <li>ResourceOptimismCount;</li> <li>ThreadSleepCount;</li> <li>SensitiveCount;</li> <li>MagicNumberCount;</li> <li>Assertion Roulette;</li> <li>Mystery Guest;</li> <li>Sleepy Test;</li> <li>Unknown Test;</li> <li>Redundant Assertion;</li> <li>Dependent Test;</li> <li>Magic Number Test;</li> <li>Conditional Test Logic;</li> <li>EmptyTest;</li> <li>General Fixture;</li> <li>Sensitive Equality;</li> <li>Verbose Test;</li> <li>IgnoredTest;</li> <li>Resource Optimism;</li> <li>Duplicate Assert;</li> <li>Exception Catching Throwing;</li> <li>Print Statement;</li> <li>SLOC;</li> <li>Complexity;</li> <li>ModifyingCommits;</li> <li>Contributors;</li> <li>MaxExperienced;</li> <li>MinExperienced;</li> <li>MeanExperience;</li> <li>MedianExperience;</li> <li>StdevExperience</li> </ul> Format: CSV Attributes per category: Size & Complexity: number of lines of code, cyclomatic complexity, loop count and conditional count; Exception: exception count and resource optimism; Contributors: Developers' expertise and number of contributors; Changes: Number of modifications; Quality: Number of asserts, mystery guest count, magic number count, print count, sleep count, sensitive count Test Smells: Assertion Roulette, Mystery Guest, Sleepy Test, Unknown Test, Redundant Assertion, Dependent Test, Magic Number Test, Conditional Test Logic, EmptyTest, General Fixture, Sensitive Equality, Verbose Test, IgnoredTest, Resource Optimism, Duplicate Assert, Exception Catching Throwing, Print Statement;

opencc-zeroDec 2014View details →

Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

This paper reports on SNP discovery in the Atlantic mackerel transcriptome, using next generation sequencing technologies and applying developed methodology already proven successful for the European anchovy. A total of 9,966 high quality transcriptome contigs were assembled, from which 951 putative SNPs were discovered. In all, 479 putative SNPs and 1,624 simple sequence repeats (SSRs) suitable for genotyping were identified. A subset of 96 was selected for genotyping; from these, 80 SNPs were considered polymorphic and reliably scored after genotyping of 105 individuals from three locations in the Eastern Atlantic Ocean. These markers will be valuable for future studies on population genetic structure assessment and for product tracing.

Data from: De novo transcriptome characterization of a sterilizing trematode parasite (Microphallus sp.) from two species of New Zealand snails

Snail-borne trematodes represent a large, diverse, and evolutionarily, ecologically, and medically important group of parasites, often imposing strong selection on their hosts and causing host morbidity and mortality. Even so, there are very few genomic and transcriptomic resources available for this important animal group. We help to fill this gap by providing transcriptome resources from trematode metacercariae infecting two congeneric snail species, Potamopyrgus antipodarum and P. estuarinus. This genus of New Zealand snails has gained prominence in large part through the development of P. antipodarum and its sterilizing trematode parasite Microphallus livelyi into a textbook model for host-parasite coevolutionary interactions in nature. By contrast, the interactions between Microphallus trematodes and P. estuarinus, an estuary-inhabiting species closely related to the freshwater P. antipodarum, are relatively unstudied. Here, we provide the first annotated transcriptome assemblies from Microphallus isolated from P. antipodarum and P. estuarinus. We also use these transcriptomes to produce genomic resources that will be broadly useful to those interested in host-parasite coevolution, local adaption, and molecular evolution and phylogenetics of this and other snail-trematode systems. Analyses of the two Microphallus transcriptomes revealed that the two trematode types are more genetically differentiated from one another than are M. livelyi infecting different populations of P. antipodarum, suggesting that the Microphallus infecting P. estuarinus represent a distinct lineage. We also provide a promising set of candidate genes likely involved in parasitic infection and response to salinity stress.

opencc-zeroApr 2020View details →

Data from: Characterization of gut microbiota composition in hemodialysis patients with normal weight obesity

Background: Normal weight obesity (NWO), defined by a normal body mass index (BMI) but increased body fat percentage (BF%), is associated with an increased risk of cardiovascular disease and mortality. NWO is characterized by inflammation and muscle wasting in chronic kidney disease (CKD), but the underlying mechanisms remain largely unknown. Gut microbiota has been implicated in the regulation of host metabolism and may play important roles in the development of NWO in CKD. Methods: In this case-control study, we examined the gut microbial diversity and taxonomy in 96 hemodialysis patients with normal weight (BMI <25 kg/m2 and BF% ≤25% for men or ≤35% for women, n = 32), NWO (BMI <25 kg/m2 and BF% >25% for men or >35% for women, n = 32), and overweight/obesity (BMI ≥25 kg/m2, n = 32), matched for age, gender, and diabetes. BF% was measured using bioimpedance spectroscopy device. Gut microbiota was determined by 16S rRNA sequencing. Results: We found that α-diversity was significantly different among the 3 adiposity phenotypes, with NWO being the least diverse. α-diversity was positively correlated with BMI, subjective global assessment score, and physical activity, but negatively correlated with interleukin-6 and tumor necrosis factor-α. Patients with or without NWO were distinguished with respect to principal coordinate analysis of β-diversity. Notably, the relative abundance of butyrate-producing bacteria, such as Faecalibacterium prausnitzii and Coprococcus, was markedly reduced in patients with NWO. Conclusion: Our findings support associations between gut dysbiosis and a proinflammatory and catabolic state in hemodialysis patients with NWO.

Data from: Genomic characterization of the evolutionary potential of the sea urchin Strongylocentrotus droebachiensis facing ocean acidification

Ocean acidification (OA) is increasing due to anthropogenic CO2 emissions and poses a threat to marine species and communities worldwide. To better project the effects of acidification on organisms' health and persistence, an understanding is needed of the 1) mechanisms underlying developmental and physiological tolerance and 2) potential populations have for rapid evolutionary adaptation. This is especially challenging in nonmodel species where targeted assays of metabolism and stress physiology may not be available or economical for large-scale assessments of genetic constraints. We used mRNA sequencing and a quantitative genetics breeding design to study mechanisms underlying genetic variability and tolerance to decreased seawater pH (-0.4 pH units) in larvae of the sea urchin Strongylocentrotus droebachiensis. We used a gene ontology-based approach to integrate expression profiles into indirect measures of cellular and biochemical traits underlying variation in larval performance (i.e., growth rates). Molecular responses to OA were complex, involving changes to several functions such as growth rates, cell division, metabolism, and immune activities. Surprisingly, the magnitude of pH effects on molecular traits tended to be small relative to variation attributable to segregating functional genetic variation in this species. We discuss how the application of transcriptomics and quantitative genetics approaches across diverse species can enrich our understanding of the biological impacts of climate change.

opencc-zeroMar 2020View details →

Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient Neotropical mountains

Mountains are among the most biodiverse areas on the globe. In young mountain ranges, exceptional plant species-richness is often associated to recent and rapid radiations linked to the mountain uplift itself. In ancient mountains, however, orogeny vastly precedes the evolution of vascular plants, so species-richness has been explained by species accumulation during long periods of low extinction rates. Here we evaluate these assumptions by analyzing plant diversification dynamicsin thecampo rupestre, an ecosystem associated to pre-Cambrian mountaintops and highlands of eastern South America, areas where plant species-richness and endemism are among the highest in the world. Analyses of 15 angiosperm clades show that radiations of endemics present fastest rates of diversification during the climatically unstable period of the last 5 million years. However, results from ancestral range estimations using different models disagree on the age of the earliest in situspeciation events and point to a complex floristic assembly. There is a general trend for higher diversification rates associated to these areas, but endemism may also increase or reduce extinction rates, depending on the group. Montane habitats, no matter their geological age, may lead to boosts in speciation rates by accelerating population isolation in archipelago-like systems, circumstances that can also result in higher extinction rates and fast species turnover, misleading age estimates of endemic lineages.

opencc-zeroDec 2009View details →

Data from: Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha

Molecular population genetics of non-model organisms has been dominated by the use of microsatellite loci over the last two decades. The availability of extensive genomic resources for many species is contributing to a transition to the use of single nucleotide polymorphisms (SNPs) for the study of many natural populations. Here we describe the discovery of a large number of SNPs in Chinook salmon, one of the world's most important fishery species, through large-scale Sanger sequencing of expressed sequence tag (EST) regions. More than 3MB of sequence was collected in a survey of variation in more than 131KB of unique genic regions, from more than 225 separate ESTs, in a diverse ascertainment panel of 24 salmon. This survey yielded 117 TaqMan (5' nuclease) assays, almost all from separate EST regions, which were validated in population samples from 5 major stocks of salmon from the three largest basins on the Pacific coast of the coterminous United States: the Sacramento, Klamath and Columbia Rivers. The proportion of these loci that was variable in each of these stocks ranged from 86.3 to 90.6% and the mean minor allele frequency ranged from 0.194 to 0.236. There was substantial differentiation between populations with these markers, with a mean FST estimate of 0.107, and values for individual loci ranging from 0 to 0.592. This substantial polymorphism and population-specific differentiation indicates that these markers will be broadly useful, including for both pedigree reconstruction and genetic stock identification applications.

Data from: Discovery and characterization of single nucleotide polymorphisms in two anadromous alosine fishes of conservation concern

Freshwater habitat alteration and marine fisheries can affect anadromous fish species, and populations fluctuating in size elicit conservation concern and coordinated management. We describe the development and characterization of two sets of 96 single nucleotide polymorphism (SNP) assays for two species of anadromous alosine fishes, alewife and blueback herring (collectively known as river herring), that are native to the Atlantic coast of North America. We used data from high-throughput DNA sequencing to discover SNPs and then developed molecular genetic assays for genotyping sets of 96 individual loci in each species. The two sets of assays were validated with multiple populations that encompass both the geographic range and the known regional genetic stocks of both species. The SNP panels developed herein accurately resolved the genetic stock structure for alewife and blueback herring that was previously identified using microsatellites and assigned individuals to regional stock of origin with high accuracy. These genetic markers, which generate data that are easily shared and combined, will greatly facilitate ongoing conservation and management of river herring including genetic assignment of marine caught individuals to stock of origin.

opencc-zeroJan 2020View details →

Data from: The fire ant social supergene is characterized by extensive gene and transposable element copy number variation

In the fire ant Solenopsis invicta, a supergene composed of ~600 genes and having two variants, SB and Sb, regulates colony social form. In single queen colonies all individuals carry only the SB allele, while in multiple queen colonies, some individuals carry the Sb allele. In this study we characterized genes with copy number variation between SB and Sb-carrying individuals. We showed extensive acquisition of gene duplicates in Sb genome, with some likely involved in polygyne-related phenotypes. We found 260 genes with differences in copy number between SB and Sb, of which 239 are in greater copy number in Sb. We observed TE accumulation on Sb, likely due to the accumulation of repetitive elements on the non-recombining chromosome. We found a weak correlation between TE copy number and differential expression, suggesting some TEs may still be proliferating in Sb, however many of the duplicated TEs were already silenced. Among the 115 non-TE genes with higher copy in Sb, enzymes responsible for cuticular hydrocarbon synthesis were highly represented. These include a desaturase and an elongase; both potentially responsible for differential queen odor and likely beneficial for polygyne ants. These genes seem to have translocated into the supergene from other chromosomes and proliferated by multiple duplication events. While the presence of transposable elements (TEs) in supergenes is well documented, little is known about duplication of non-TE genes and their possible adaptive role. Overall, our results suggest that gene duplications may be an important factor leading to monogyne and polygyne ant societies.

opencc-by-nc-4.0Mar 2021View details →

Figure 1 in First characterization of a taxonomically well-resolved trophic network composed by host plants and gall midges (Diptera: Cecidomyiidae) in the Neotropical region

Figure 1. Bipartite network of host plants and gall midge species at the Restinga of Barra de Maricá (Maricá, RJ, Brazil). Lower bars represent host plant species and upper bars represent gall-midge species; grey bars represent interactions. Bar thickness is proportional to the number of interactions of each species. ble interactions. The observed connectance (C = 0.028) decades), which enhances the sampling of rarer interacwas lower than expected from null model values (Null tions, and consequently increases the specialization of C = 0.032 ± 0.001, p <0.001). Similarly, the observed num- the network. However, this fact reinforces the relevance ber of links per species (L = 0.608) also was lower than of the observed patterns, because even with such a long expected by chance (Null L = 0.710 ± 0.020, p <0.001). sampling, only species-specific plant-galling interactions The observed modularity for plant-galling network was were registered. very high (M = 0.958), but did not differ from null model The structure of the network formed by the gall midgvalues (Null M = 0.959 ± 0.001, p> 0.05). Robustness ob- es and their host plants proved to be highly specialized. served was relatively low (R = 1.343), but was higher than The connectance observed in the present study (2.8%) expected by chance (Null R = 1.334 ± 0.232, p <0.001). was low as compared to other plant-phytophagous networks (review in Araújo et al., 2015). However, comparing with other networks of galling arthropods, the val- DISCUSSION ue observed here was higher than observed by Araújo

opencc-by-4.0Jan 2017View details →

Chemical characterization of atmospheric ions at the High-Alpine station Jungfraujoch (Switzerland)

The ion composition at high-altitude (3454 m a.s.l.) was measured with an Atmospheric Pressure interface Time of Flight mass spectrometer (APi-TOF) during a period of nine months, from August 2013 to April 2014. The negative mass spectra were dominated by the ions of sulfuric, nitric, malonic and methanesulfonic acid (MSA) as well as SO5- . The most prominent positive ion peaks were from amines. The other cations were mainly organic compounds clustered with a nitrogen-containing ion, which could be either NH4+ or an aminium. Occasionally the positive spectra were characterized by groups of compounds each differing by a methylene group. In the negative spectrum, sulfuric acid was always observed during clear sky conditions following the diurnal cycle of sun irradiation. On many occasions we also saw a high signal of sulfuric acid during night time when clusters up to the tetramer were observed. A plausible reason for these events could be evaporation from particles at low relative humidity. A remarkably strong correlation between the signals of SO5- and CH3SO3- was observed for the full measurement period. The presence of these two ions during both the day and the night suggests a non-photochemical channel of formation which is possibly linked to halogen chemistry. Halogenated species, especially Br– and IO3- , were frequently observed in air masses that originated mainly from the Atlantic Ocean and occasionally from continental areas based on back trajectory analyses. We found I2O5 clustered with an ion, a species that was proposed from laboratory and modelling studies. All halogenated ions exhibited an unexpected diurnal behaviour with low values during day time. New particle formation (NPF) events were observed and characterized by 1) highly oxygenated molecules (HOMs) and low sulfuric acid or 2) ammonia-sulfuric acid clusters. We present characteristic spectra for each of these two event types based on 26 nucleation episodes. The mass spectrum of the ammonia-sulfuric acid nucleation event compares very well with laboratory measurements reported from the CLOUD chamber. A source receptor analysis indicates that new particle formation events at the Jungfraujoch take place within a restricted period of time of 24-48 hours after air masses have had contact with boundary layer. This time frame appears to be crucial to reach an optimal oxidation state and concentration of organic molecules necessary to facilitate nucleation.