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8,038 results for “validation.”
Data from: Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels
Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different to ensure sequencing, replication, and oligonucleotide synthesis errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against substitution errors during sequencing and extant tag sets contain too few tag sequences. We developed an open-source software package to validate sequence tags for conformance to two distance metrics and design sequence tags robust to indel and substitution errors. We use this software package to evaluate several commercial and non-commercial sequence tag sets, design several large sets (maxcount=7,198) of edit metric sequence tags having different lengths and degrees of error correction, and integrate a subset of these edit metric tags to polymerase chain reaction (PCR) primers and sequencing adapters. We validate a subset of these edit metric tagged PCR primers and sequencing adapters by sequencing on several platforms and subsequent comparison to commercially available alternatives. We find that several commonly used sets of sequence tags or design methodologies used to produce sequence tags do not meet the minimum expectations of their underlying distance metric, and we find that PCR primers and sequencing adapters incorporating edit metric sequence tags designed by our software package perform as well as their commercial counterparts. We suggest that researchers evaluate sequence tags prior to use or evaluate tags that they have been using. The sequence tag sets we design improve on extant sets because they are large, valid across the set, and robust to the suite of substitution, insertion, and deletion errors affecting massively parallel sequencing workflows on all currently used platforms.
Data from: Validation of perfusion quantification with 3D gradient echo dynamic contrast-enhanced magnetic resonance imaging using a blood pool contrast agent in skeletal swine muscle
The purpose of our study was to validate perfusion quantification in a low-perfused tissue by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) with shared k-space sampling using a blood pool contrast agent. Perfusion measurements were performed in a total of seven female pigs. An ultrasonic Doppler probe was attached to the right femoral artery to determine total flow in the hind leg musculature. The femoral artery was catheterized for continuous local administration of adenosine to increase blood flow up to four times the baseline level. Three different stable perfusion levels were induced. The MR protocol included a 3D gradient-echo sequence with a temporal resolution of approximately 1.5 seconds. Before each dynamic sequence, static MR images were acquired with flip angles of 5°, 10°, 20°, and 30°. Both static and dynamic images were used to generate relaxation rate and baseline magnetization maps with a flip angle method. 0.1 mL/kg body weight of blood pool contrast medium was injected via a central venous catheter at a flow rate of 5 mL/s. The right hind leg was segmented in 3D into medial, cranial, lateral, and pelvic thigh muscles, lower leg, bones, skin, and fat. The arterial input function (AIF) was measured in the aorta. Perfusion of the different anatomic regions was calculated using a one- and a two-compartment model with delay- and dispersion-corrected AIFs. The F-test for model comparison was used to decide whether to use the results of the one- or two-compartment model fit. Total flow was calculated by integrating volume-weighted perfusion values over the whole measured region. The resulting values of delay, dispersion, blood volume, mean transit time, and flow were all in physiologically and physically reasonable ranges. In 107 of 160 ROIs, the blood signal was separated, using a two-compartment model, into a capillary and an arteriolar signal contribution, decided by the F-test. Overall flow in hind leg muscles, as measured by the ultrasound probe, highly correlated with total flow determined by MRI, R = 0.89 and P = 10−7. Linear regression yielded a slope of 1.2 and a y-axis intercept of 259 mL/min. The mean total volume of the investigated muscle tissue corresponds to an offset perfusion of 4.7mL/(min ⋅ 100cm3). The DCE-MRI technique presented here uses a blood pool contrast medium in combination with a two-compartment tracer kinetic model and allows absolute quantification of low-perfused non-cerebral organs such as muscles.
Data from: Identification and validation of single nucleotide polymorphisms as tools to detect hybridization and population structure in freshwater stingrays
Single nucleotide polymorphism (SNP) markers were identified and validated for two stingrays species, Potamotrygon motoro and Potamotrygon falkneri, using double digest restriction-site associated DNA (ddRAD) reads using 454-Roche technology. A total of 226 774 reads (65.5 Mb) were obtained (mean read length 289 ± 183 bp) detecting a total of 5399 contigs (mean contig length: 396 ± 91 bp). Mining this data set, a panel of 143 in silico SNPs was selected. Eighty-two of these SNPs were successfully validated and 61 were polymorphic: 14 in P. falkneri, 21 in P. motoro, 3 in both species and 26 fixed for alternative variants in both species, thus being useful for population analyses and hybrid detection.
Data from: PrimerMiner: an R package for development and in silico validation of DNA metabarcoding primers
1. DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing a standardized gene marker region. Its success is often limited due to variable binding sites that introduce amplification biases. Thus the development of optimized primers for communities or taxa under study in a certain geographic region and/or ecosystems is of critical importance. However, no tool for obtaining and processing of reference sequence data in bulk that can serve as a backbone for primer design is currently available. 2. We developed the R package PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units (OTUs) to reduce biases introduced by the different number of available sequences per species. Additionally, PrimerMiner offers functionalities to evaluate primers in silico, which are in our opinion more realistic then the strategy employed in another available software for that purpose, ecoPCR. 3. We used PrimerMiner to download cytochrome c oxidase subunit I (COI) sequences for 15 important freshwater invertebrate groups, relevant for ecosystem assessment. By processing COI markers from both databases, we were able to increase the amount of reference data 249-fold on average, compared to using complete mitochondrial genomes alone. Furthermore, we visualized the generated OTU sequence alignments and describe how to evaluate primers in silico using PrimerMiner. 4. With PrimerMiner we provide a useful tool to obtain relevant sequence data for targeted primer development and evaluation. The OTU based reference alignments generated with PrimerMiner can be used for manual primer design, or processed with bioinformatic tools for primer development.
Data from: Numerical simulations of targeted delivery of magnetic drug aerosols in the human upper and central respiratory system: a validation study
In the present study, we investigate the concept of the targeted delivery of pharmaceutical drug aerosols in an anatomically realistic geometry of the human upper and central respiratory system. The geometry considered extends from the mouth inlet to the 8th generation of the bronchial bifurcations and is identical to the phantom model used in the experimental studies of [Banko {em et al.} (2015), Exp. Fluids, {bf 56} (117):1-12]. In our computer simulations, we combine the transitional Reynolds-Averaged Navier-Stokes (RANS) and the wall-resolved Large Eddy Simulation (LES) methods for the air phase with the Lagrangian approach for the particulate (aerosol) phase. We validated simulations against recently obtained magnetic resonance velocimetry (MRV) measurements of [Banko {em et al.} (2015), Exp. Fluids, {bf 56} (117):1-12] that provide full a 3D mean velocity field for steady inspiratory conditions. Both approaches produced good agreement with experiments, and the transitional RANS approach is selected for the multi-phase simulations of aerosols transport, because of significantly lower computational costs. The local and total deposition efficiency are calculated for different classes of pharmaceutical particles (in the $0.1mu$m$le d_{rm p} le 10mu$m range) without and with a paramagnetic core (the shell-core particles). For the latter, an external magnetic field is imposed. The source of the imposed magnetic field was placed in the proximity of the first bronchial bifurcation. We demonstrated that both total- and local-depositions of aerosols at targeted locations can be significantly increased by an applied magnetization force. This finding confirms the possible potential for further advancement of the magnetic drug targeting (MDT) technique for more efficient treatments for respiratory diseases.
FIGURES 12 in Xantholinus dvoraki Coiffait, 1956, the only valid species of the subgenus Meneidophallus Bordoni, 1999, with remarkably variable internal sac of aedeagus (Coleoptera, Staphylinidae)
FIGURES 12. Xantholinus dvoraki Coiffait (1 – Turkey, Abant Dagh; 2 – Russia, Rostovna Donu).
FIGURE 6 in Macrodon atricauda (Günther, 1880) (Perciformes: Sciaenidae), a valid species from the southwestern Atlantic, with comments on its conservation
FIGURE 6. Number of times the largest front canine is contained in eye horizontal diameter.
FIGURE 5 in Macrodon atricauda (Günther, 1880) (Perciformes: Sciaenidae), a valid species from the southwestern Atlantic, with comments on its conservation
FIGURE 5. Occurrence areas: Yellow, M. ancylodon; Green, M. atricauda.
FIGURE 4 in Macrodon atricauda (Günther, 1880) (Perciformes: Sciaenidae), a valid species from the southwestern Atlantic, with comments on its conservation
FIGURE 4. Same-size specimens of M. atricauda (A) and M. ancylodon (B), showing the front canines.
FIGURE 3 in Macrodon atricauda (Günther, 1880) (Perciformes: Sciaenidae), a valid species from the southwestern Atlantic, with comments on its conservation
FIGURE 3. Same-size specimens of M. atricauda (A) and M. ancylodon (B).
FIGURE 2. M. atricauda, 309 in Macrodon atricauda (Günther, 1880) (Perciformes: Sciaenidae), a valid species from the southwestern Atlantic, with comments on its conservation
FIGURE 2. M. atricauda, 309 mm SL, recently collected from Guarujá, São Paulo.
FIGURE 38 in Revision of Hista Oiticica (Lepidoptera: Castniidae) and discussion on the validity of its subspecies
FIGURE 38. Distribution of Hista fabricii (Swainson, 1823) and variation of wing color in females.
FIGURES 67–68 in Revision of Hista Oiticica (Lepidoptera: Castniidae) and discussion on the validity of its subspecies
FIGURES 67–68. Wing venation of H. hegemon (Kollar, 1839). 67. Forewing. 68. Hindwing. Scales 1 cm.
FIGURE 4 in The validity of Hexacharis Kieffer with taxonomic notes on Anacharitinae genera (Hymenoptera: Cynipoidea: Figitidae)
FIGURE 4. Variability in the sculpture of mesopleuron Hexacharis flavipes (a–d).
FIGURE 6. Himantolophus pseudalbinares AIM 6850, 98.9 in A new species of deep-sea anglerfish, genus Himantolophus (Lophiiformes: Himantolophidae) from the Western South Pacific, with comments on the validity of H. pseudalbinares
FIGURE 6. Himantolophus pseudalbinares AIM 6850, 98.9 mm SL. Drawing: M. Freeborn.
FIGURE 5. Himantolophus albinares NMNZ P.033996, 80 in A new species of deep-sea anglerfish, genus Himantolophus (Lophiiformes: Himantolophidae) from the Western South Pacific, with comments on the validity of H. pseudalbinares
FIGURE 5. Himantolophus albinares NMNZ P.033996, 80 mm SL. Drawing: M. Freeborn.
FIGURE 4. Himantolophus albinares NMNZ P.031256, 148 in A new species of deep-sea anglerfish, genus Himantolophus (Lophiiformes: Himantolophidae) from the Western South Pacific, with comments on the validity of H. pseudalbinares
FIGURE 4. Himantolophus albinares NMNZ P.031256, 148 mm SL. Photo: C. Roberts/C. Struthers Te Papa.
FIGURE 2. Himantolophus litoceras. Holotype NMNZ P.042004, 276 in A new species of deep-sea anglerfish, genus Himantolophus (Lophiiformes: Himantolophidae) from the Western South Pacific, with comments on the validity of H. pseudalbinares
FIGURE 2. Himantolophus litoceras. Holotype NMNZ P.042004, 276 mm SL. Drawing: M. Freeborn.
FIGURE 2. Acrossota amboinensis, n in Pinnuleless polyps: a new genus and new species of IndoPacific Clavulariidae and validation of the soft coral genus Acrossota and the family Acrossotidae (Coelenterata: Octocorallia)
FIGURE 2. Acrossota amboinensis, n. comb., holotype: A,B, closeups of main portions of colony.
FIGURE 8 in Pinnuleless polyps: a new genus and new species of IndoPacific Clavulariidae and validation of the soft coral genus Acrossota and the family Acrossotidae (Coelenterata: Octocorallia)
FIGURE 8. Acrossota cf. amboinensis n. comb.: A, NTM C15379 in life; B, NTM C13626 in life.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.