Thinking small: Next-generation sensor networks close the size gap in vertebrate biologging.
Ontology highlight
ABSTRACT:
SUBMITTER: Ripperger SP
PROVIDER: S-EPMC7117662 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis from wild samples in five non-model animal species, based on next-generation sequencing transcriptome data. We introduce a pipe-line for cDNA assembly, read mapping, SNP/genotype calling, and data cleaning, with specific focus on the issue of hidden paralogy detection. In two species for which a reference genome is available, similar results were obtained whether the reference was used or not, demonstrating the robustness of our de novo inferences. The population genomic profile of a hare, a turtle, an oyster, a tunicate, and a termite were found to be intermediate between those of human and Drosophila, indicating that the discordant genomic diversity patterns that have been reported between these two species do not reflect a generalized vertebrate versus invertebrate gap. The genomic average diversity was generally higher in invertebrates than in vertebrates (with the notable exception of termite), in agreement with the notion that population size tends to be larger in the former than in the latter. The non-synonymous to synonymous ratio, however, did not differ significantly between vertebrates and invertebrates, even though it was negatively correlated with genetic diversity within each of the two groups. This study opens promising perspective regarding genome-wide population analyses of non-model organisms and the influence of population size on non-synonymous versus synonymous diversity.
| S-EPMC3623758 | biostudies-literature
Project description:This in situ study investigated whether there is a relationship between gap size and wall lesion development in dentin next to 2 composite materials, and whether a clinically relevant threshold for the gap size could be established. For 21 days, 14 volunteers wore a modified occlusal splint containing human dentin samples with 5 different interfaces: 4 gaps of 50 µm, 100 µm, 200 µm, or 400 µm and 1 non-bonded interface without a gap. Eight times a day, the splint with samples was dipped in a 20% sucrose solution for 10 minutes. Before and after caries development, specimens were imaged with transversal wavelength-independent microradiography (T-WIM), and lesion depth (LD) and mineral loss (ML) were calculated at the 5 different interfaces. After correction for the confounder location (more mesial or distal), a paired t test clustered within volunteers was performed for comparison of gap widths. Results showed no trend for a relationship between the corrected lesion depth and the gap size. None of the differences in lesion depth for the different gap sizes was statistically significant. Also, the composite material (AP-X or Filtek Supreme) gave no statistically significant differences in lesion depth and mineral loss. A minimum gap size could not be established, although, in a non-bonded interface without a measurable gap, wall lesion development was never observed.
| S-EPMC4107545 | biostudies-literature
Project description:BackgroundAedes aegypti mosquito-borne viruses including Zika (ZIKV), dengue (DENV), yellow fever (YFV), and chikungunya (CHIKV) have emerged and re-emerged globally, resulting in an elevated burden of human disease. Aedes aegypti is found worldwide in tropical, sub-tropical, and temperate areas. The characterization of mosquito blood meals is essential to understand the transmission dynamics of mosquito-vectored pathogens.Methodology/principal findingsHere, we report Ae. aegypti and Culex quinquefasciatus host feeding patterns and arbovirus transmission in Northern Mexico using a metabarcoding-like approach with next-generation deep sequencing technology. A total of 145 Ae. aegypti yielded a blood meal analysis result with 107 (73.8%) for a single vertebrate species and 38 (26.2%) for two or more. Among the single host blood meals for Ae. aegypti, 28.0% were from humans, 54.2% from dogs, 16.8% from cats, and 1.0% from tortoises. Among those with more than one species present, 65.9% were from humans and dogs. For Cx. quinquefasciatus, 388 individuals yielded information with 326 (84%) being from a single host and 63 (16.2%) being from two or more hosts. Of the single species blood meals, 77.9% were from dogs, 6.1% from chickens, 3.1% from house sparrows, 2.4% from humans, while the remaining 10.5% derived from other 12 host species. Among those which had fed on more than one species, 11% were from dogs and humans, and 89% of other host species combinations. Forage ratio analysis revealed dog as the most over-utilized host by Ae. aegypti (= 4.3) and Cx. quinquefasciatus (= 5.6) and the human blood index at 39% and 4%, respectively. A total of 2,941 host-seeking female Ae. aegypti and 3,536 Cx. quinquefasciatus mosquitoes were collected in the surveyed area. Of these, 118 Ae. aegypti pools and 37 Cx. quinquefasciatus pools were screened for seven arboviruses (ZIKV, DENV 1-4, CHIKV, and West Nile virus (WNV)) using qRT-PCR and none were positive (point prevalence = 0%). The 95%-exact upper limit confidence interval was 0.07% and 0.17% for Ae. aegypti and Cx. quinquefasciatus, respectively.Conclusions/significanceThe low human blood feeding rate in Ae. aegypti, high rate of feeding on mammals by Cx. quinquefasciatus, and the potential risk to transmission dynamics of arboviruses in highly urbanized areas of Northern Mexico is discussed.
| S-EPMC7806141 | biostudies-literature
Project description:In recent years, next generation sequencing (NGS) has gradually replaced microarray as the major platform in measuring gene expressions. Compared to microarray, NGS has many advantages, such as less noise and higher throughput. However, the discreteness of NGS data also challenges the existing statistical methodology. In particular, there still lacks an appropriate statistical method for reconstructing gene regulatory networks using NGS data in the literature. The existing local Poisson graphical model method is not consistent and can only infer certain local structures of the network. In this article, we propose a random effect model-based transformation to continuize NGS data and then we transform the continuized data to Gaussian via a semiparametric transformation and apply an equivalent partial correlation selection method to reconstruct gene regulatory networks. The proposed method is consistent. The numerical results indicate that the proposed method can lead to much more accurate inference of gene regulatory networks than the local Poisson graphical model and other existing methods. The proposed data-continuized transformation fills the theoretical gap for how to transform discrete data to continuous data and facilitates NGS data analysis. The proposed data-continuized transformation also makes it feasible to integrate different types of data, such as microarray and RNA-seq data, in reconstruction of gene regulatory networks.
| S-EPMC6258556 | biostudies-literature
Project description:The unparalleled efficiency of next-generation sequencing (NGS) has prompted widespread adoption, but significant problems remain in the use of NGS data for whole genome assembly. We explore the advantages and disadvantages of chicken genome assemblies generated using a variety of sequencing and assembly methodologies. NGS assemblies are equivalent in some ways to a Sanger-based assembly yet deficient in others. Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references.
| S-EPMC3129681 | biostudies-literature
Project description:The IMES1 Implantable MyoElectric Sensor device is currently in human clinical trials led by the Alfred Mann Foundation. The IMES is implanted in a residual limb and is powered wirelessly using a magnetic field. EMG signals resulting from the amputee's voluntary movement are amplified and transmitted wirelessly by the IMES to an external controller which controls movement of an external motorized prosthesis. Development of the IMES technology is on-going, producing the next-generation IMES2. Among various improvements, a new feature of the IMES2 is a low-power polling mode. In this low-power mode, the IMES2 power consumption can be dramatically reduced when the limb is inactive through the use of a polled sampling. With the onset of EMG activity, the IMES2 system can switch to the normal higher sample rate to allow the acquisition of high-fidelity EMG data for prosthesis control.
| S-EPMC4654573 | biostudies-literature
Project description:NGPS is a method for de-novo, full-length protein sequencing in high throughput. The method is based on cleavage of the protein at semi-random sites by microwave-assisted acid hydrolysis (MAAH), enrichment of LC-MS/MS amenable peptides from the hydrolysate by solid-phase-extraction, LC-MS/MS analysis, de-novo long peptide tag sequencing of resulting peptides and assembly of peptide tags into consensus contigs.
2017-04-03 | PXD003804 | Pride
Project description:The alkali fullerides, A(3)C(60) (A = alkali metal) are molecular superconductors that undergo a transition to a magnetic Mott-insulating state at large lattice parameters. However, although the size and the symmetry of the superconducting gap, ?, are both crucial for the understanding of the pairing mechanism, they are currently unknown for superconducting fullerides close to the correlation-driven magnetic insulator. Here we report a comprehensive nuclear magnetic resonance (NMR) study of face-centred-cubic (f.c.c.) Cs(3)C(60) polymorph, which can be tuned continuously through the bandwidth-controlled Mott insulator-metal/superconductor transition by pressure. When superconductivity emerges from the insulating state at large interfullerene separations upon compression, we observe an isotropic (s-wave) ? with a large gap-to-superconducting transition temperature ratio, 2?0/k(B)T(c) = 5.3(2) [?0 = ?(0 K)]. 2?0/k(B)T(c) decreases continuously upon pressurization until it approaches a value of ~3.5, characteristic of weak-coupling BCS theory of superconductivity despite the dome-shaped dependence of Tc on interfullerene separation. The results indicate the importance of the electronic correlations for the pairing interaction as the metal/superconductor-insulator boundary is approached.
| S-EPMC3939459 | biostudies-literature
Project description:Despite the important discoveries reported by genome-wide association (GWA) studies, for most traits and diseases the prediction R-squared (R-sq.) achieved with genetic scores remains considerably lower than the trait heritability. Modern biobanks will soon deliver unprecedentedly large biomedical data sets: Will the advent of big data close the gap between the trait heritability and the proportion of variance that can be explained by a genomic predictor? We addressed this question using Bayesian methods and a data analysis approach that produces a surface response relating prediction R-sq. with sample size and model complexity (e.g., number of SNPs). We applied the methodology to data from the interim release of the UK Biobank. Focusing on human height as a model trait and using 80,000 records for model training, we achieved a prediction R-sq. in testing (n = 22,221) of 0.24 (95% C.I.: 0.23-0.25). Our estimates show that prediction R-sq. increases with sample size, reaching an estimated plateau at values that ranged from 0.1 to 0.37 for models using 500 and 50,000 (GWA-selected) SNPs, respectively. Soon much larger data sets will become available. Using the estimated surface response, we forecast that larger sample sizes will lead to further improvements in prediction R-sq. We conclude that big data will lead to a substantial reduction of the gap between trait heritability and the proportion of interindividual differences that can be explained with a genomic predictor. However, even with the power of big data, for complex traits we anticipate that the gap between prediction R-sq. and trait heritability will not be fully closed.
| S-EPMC5676235 | biostudies-literature
Project description:This data article contains information on a new intelligent bandwidth allocation model for future network (Smart Allocation). The included data describe the topology of the network testbed and the obtained results. Obtained data show the effectiveness of the proposed model in comparison with the MAM and RDM bandwidth allocation models. In relation to the performances evaluation, a variety of flows are used such as: voice over IP (VoIP), video, HTTP, and Internet Control Message Protocol (ICMP). The evaluation criteria are: VoIP latency and jitter, Peak Signal to Noise Ratio (PSNR) video, retransmission video, goodput, HTTP response page, and the Round-Trip Time (RTT) ICMP delay. The presented data are extracted based on simulation.
| S-EPMC6134167 | biostudies-literature