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Data from: RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays
Hybridization with introduced rainbow trout threatens most native westslope cutthroat trout populations. Understanding the genetic effects of hybridization and introgression requires a large set of high-throughput, diagnostic genetic markers to inform conservation and management. Recently, we identified several thousand candidate single nucleotide polymorphism (SNP) markers based on RAD sequencing of 11 westslope cutthroat trout and 13 rainbow trout individuals. Here we used flanking sequence for 56 of these candidate SNP markers to design high-throughput genotyping assays. We validated the assays on a total of 92 individuals from 22 populations and seven hatchery strains. Forty-six assays (82%) amplified consistently and allowed easy identification of westslope cutthroat and rainbow trout alleles as well as heterozygote controls. The 46 SNPs will provide high power for early detection of population admixture and improved identification of hybrid and non-hybridized individuals. This technique shows promise as a very low-cost, reliable, and relatively rapid method for developing and testing SNP markers for non-model organisms with limited genomic resources.
Data from: Morphological and molecular diagnostic species characters of Staurozoa (Cnidaria) collected on the coast of Helgoland (German Bight, North Sea)
Scientific knowledge and records on staurozoans are limited probably because of their inconspicuous life habit and the small number of specialists for this taxon. To increase the awareness for Staurozoa, we identified morphological and molecular features of the three staurozoan species Haliclystus tenuis Kishinouye, 1910, Haliclystus auricula Clark, 1863, and Craterolophus convolvulus (Johnston, 1835) collected on the coast of the island Helgoland to evaluate their suitability as diagnostic characters. Useful macromorphological diagnostic features were the patterns of white spots of nematocysts and internal arm structures, whereas tentacle and gonad follicle numbers showed high intraspecific variations. Morphometric measurements on photographs of living specimens provided reliable data for interspecific comparisons. Comprehensive nematocyst analyses revealed interspecific shape differences of isorhizas and three types of rhopaloids, indicating that the staurozoan cnidome is more diverse than previously assumed. However, the taxonomic value of nematocyst analyses in Staurozoa remains unclear because comprehensive data is still lacking for most species. Comparative molecular genetic sequence analyses of mitochondrial 16S and COI and nuclear 18S ribosomal DNA identified the three species and confirmed their morphological identification. In comparison to published data, our analyses indicate similarities between H. auricula and Haliclystus antarcticus Pfeffer, 1889. Proteomic fingerprinting by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) differentiated all three species, suggesting that this technique could provide an alternative rapid identification method for staurozoans.
Data from: "Diagnostic SNPs for inferring population structure in American mink (Neovison vison) identified through RAD sequencing" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014
The article documents the public availability of RAD sequencing data and generated SNPs for the American mink (Neovison vison). 224,095 polymorphic loci were identified from 14 mink from which primers were designed for a subset of 380 SNPs. The panel was tested on 211 mink. Fisher's F-statistics (Fis, FIT and FST) as well as observed (HO), expected (HE) and unbiased expected (uHE) heterozygosity was calculated for the SNPs and 194 SNPs was validated as being useful for population genetic studies.
Data from: Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone
Studies of hybridization and introgression and, in particular, the identification of admixed individuals in natural populations benefit from the use of diagnostic genetic markers that reliably differentiate pure species from each other and their hybrid forms. Such diagnostic markers are often infrequent in the genomes of closely related species, and genomewide data facilitate their discovery. We used whole-genome data from Illumina HiSeqS2000 sequencing of two recently diverged (600,000 years) and hybridizing, avian, sister species, the Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) Sparrow, to develop a suite of diagnostic markers for high-resolution identification of pure and admixed individuals. We compared the microsatellite repeat regions identified in the genomes of the two species and selected a subset of 37 loci that differed between the species in repeat number. We screened these loci on 12 pure individuals of each species and report on the 34 that successfully amplified. From these, we developed a panel of the 12 most diagnostic loci, which we evaluated on 96 individuals, including individuals from both allopatric populations and sympatric individuals from the hybrid zone. Using simulations, we evaluated the power of the marker panel for accurate assignments of individuals to their appropriate pure species and hybrid genotypic classes (F1, F2, and backcrosses). The markers proved highly informative for species discrimination and had high accuracy for classifying admixed individuals into their genotypic classes. These markers will aid future investigations of introgressive hybridization in this system and aid conservation efforts aimed at monitoring and preserving pure species. Our approach is transferable to other study systems consisting of closely related and incipient species.
Data from: How do patients and health workers interact around malaria rapid diagnostic testing, and how are the tests experienced by patients in practice? A qualitative study in western Uganda
Background: Successful scale-up in the use of malaria rapid diagnostic tests (RDTs) requires that patients accept testing and treatment based on RDT results and that healthcare providers treat according to test results. Patient-provider communication is a key component of quality care, and leads to improved patient satisfaction, higher adherence to treatment and better health outcomes. Voiced or perceived patient expectations are also known to influence treatment decision-making among healthcare providers. While there has been a growth in literature on provider practices around rapid testing for malaria, there has been little analysis of inter-personal communication around the testing process. We investigated how healthcare providers and patients interact and engage throughout the diagnostic and treatment process, and how the testing service is experienced by patients in practice. Methods: This research was conducted alongside a larger study which explored determinants of provider treatment decision-making following negative RDT results in a rural district (Kibaale) in mid-western Uganda, ten months after RDT introduction. Fifty-five patients presenting with fever were observed during routine outpatient visits at 12 low-level public health facilities. Observation captured communication practices relating to test purpose, results, diagnosis and treatment. All observed patients or caregivers were immediately followed up with in-depth interview. Analysis followed the 'framework' approach. A summative approach was also used to analyse observation data. Results: Providers failed to consistently communicate the reasons for carrying out the test, and particularly to RDT-negative patients, a diagnostic outcome or the meaning of test results, also leading to confusion over what the test can detect. Patients appeared to value testing, but were frustrated by the lack of communication on outcomes. RDT-negative patients were dissatisfied by the absence of information on an alternative diagnosis and expressed uncertainty around adequacy of proposed treatment. Conclusions: Poor provider communication practices around the testing process, as well as limited inter-personal exchange between providers and patients, impacted on patients' perceptions of their proposed treatment. Patients have a right to health information and may be more likely to accept and adhere to treatment when they understand their diagnosis and treatment rationale in relation to their perceived health needs and visit expectations.
Data from: Diagnostic accuracy of presepsin in predicting bacteremia in elderly patients admitted to the emergency department: prospective study in Japan
<p class="CxSpFirst"><span><b>Objective</b></span></p> <p class="CxSpMiddle"><span><a name="_Hlk1399924">Early detection of bacteremia in the elderly is needed in the emergency department (ED). </a></span></p> <p class="CxSpMiddle"><span><a name="_Hlk11878757"><b>Design, Setting, and Participants</b></a></span></p> <p class="CxSpMiddle"><span>Prospective study in Japan, single center trial in patients who satisfied the sepsis criteria was conducted between September 2014 and March 2016. Forty-six elderly patients aged ≥70 years were included.</span></p> <p class="CxSpMiddle"><span><b>Interventions</b></span></p> <p class="CxSpMiddle"><span>Blood sampling to evaluate C-reactive protein (CRP), procalcitonin (PCT) and presepsin plasma levels; two sets of blood sampling for bacterial cultures; and evaluations of the Sequential Organ Failure Assessment (SOFA) and Acute Physiology and Chronic Health Evaluation (APACHE II) scores were performed upon arrival at the ED. The results were compared between patients with bacteremia and those without bacteremia.</span></p> <p class="CxSpMiddle"><span><a name="_Hlk11878769"><b>Main Outcome Measure</b></a></span></p> <p class="CxSpMiddle"><span>The accuracy of detecting bacteremia</span></p> <p class="CxSpMiddle"><span><b>Results</b></span></p> <p class="CxSpMiddle"><span>The presepsin value was significantly higher in the bacteremia group than in the non-bacteremia group (866.6 ± 184.6 pg/mL vs. 639.9 ± 137.1 pg/mL, p = 0.03). The PCT and CRP did not significantly differ between the groups. The area under the receiver-operating-characteristic curve (AUC) values were not significantly different among presepsin (0.69), PCT (0.61), and CRP (0.53). Multivariate analysis showed that presepsin was independently associated with bacteremia (odds ratio, 8.84; 95% confidence interval, 0.95–81.79; p = 0.02).</span></p> <p class="CxSpMiddle"><span><b>Conclusion<a name="_Hlk1399945"></a></b></span></p> <p class="CxSpMiddle"><span>Presepsin could be a good biomarker to predict bacteremia in elderly patients with sepsis criteria admitted to the ED.</span></p>
Data from: Diagnostic gene expression biomarkers of coral thermal stress
Gene expression biomarkers can enable rapid assessment of physiological conditions in situ, providing a valuable tool for reef managers interested in linking organism physiology with large-scale climatic conditions. Here, we assessed the ability of quantitative PCR (qPCR) based gene expression biomarkers to evaluate (1) the immediate cellular stress response (CSR) of Porites astreoides to incremental thermal stress and (2) the magnitude of CSR and cellular homeostasis response (CHR) during a natural bleaching event. Expression levels largely scaled with treatment temperature, with the strongest responses occurring in heat shock proteins. This is the first demonstration of a "tiered" CSR in a coral, where the magnitude of expression change is proportional to stress intensity. Analysis of a natural bleaching event revealed no signature of an acute CSR in normal or bleached corals, indicating that the bleaching stressor(s) had abated by the day of sampling. Another long-term stress CHR-based indicator assay was significantly elevated in bleached corals; though assay values overall were low, suggesting good prospects for recovery. This study represents the first step in linking variation in gene expression biomarkers to stress tolerance and bleaching thresholds in situ by quantifying the severity of ongoing thermal stress and its accumulated long-term impacts.
Data from: Diagnostic pathways and direct medical costs incurred by new adult pulmonary tuberculosis patients prior to anti-tuberculosis treatment – Tamil Nadu, India
Background: Tuberculosis (TB) patients face substantial delays prior to treatment initiation, and out of pocket (OOP) expenditures often surpass the economic productivity of the household. We evaluated the pre-diagnostic cost and health seeking behaviour of new adult pulmonary TB patients registered at Primary Health Centres (PHCs) in Vellore district, Tamil Nadu, India. Methods: This descriptive study, part of a randomised controlled trial conducted in three rural Tuberculosis Units from Dec 2012 to Dec 2015, collected data on number of health facilities, dates of visits prior to the initiation of anti-tuberculosis treatment, and direct OOP medical costs associated with TB diagnosis. Logistic regression analysis examined the factors associated with delays in treatment initiation and OOP expenditures. Results: Of 880 TB patients interviewed, 34.7% presented to public health facilities and 65% patients sought private health facilities as their first point of care. The average monthly individual income was $77.79 (SD 57.14). About 69% incurred some pre-treatment costs at an average of $39.74. Overall, patients experienced a median of 6 days (3-11 IQR) of time to treatment initiation and 21 days (10-30 IQR) of health systems delay. Age ≤ 40 years (aOR: 1.73; CI: 1.22 - 2.44), diabetes (aOR: 1.63; CI: 1.08 - 2.44) and first visit to a private health facility (aOR: 17.2; CI: 11.1 - 26.4) were associated with higher direct OOP medical costs, while age ≤ 40 years (aOR: 0.64; CI: 0.48 - 0.85) and first visit to private health facility (aOR: 1.79, CI: 1.34 - 2.39) were associated with health systems delay. Conclusion: The majority of rural TB patients registering at PHCs visited private health facilities first and incurred substantial direct OOP medical costs and delays prior to diagnosis and anti-tuberculosis treatment initiation. This study highlights the need for PHCs to be made as the preferred choice for first point of contact, to combat TB more efficiently.
FIGURE 6. Proleptonchus japonicus n in Three new and a known species of the genus Proleptonchus Lordello, 1955 (Nematoda: Leptonchidae) with a diagnostic compendium of the genus
FIGURE 6. Proleptonchus japonicus n. sp. A. Entire female. B. Anterior region. C. Anterior end showing amphid. D. Pharyngeal region. E. Pharyngeal bulb. F. Female genital system. G. Vulval region. H. Female posterior region.
FIGURE 8 in Postembryonic development of the dorsal chaetotaxy in Seira dowlingi (Collembola, Entomobryidae); with an analysis of the diagnostic and phylogenetic significance of primary chaetotaxy in Seira
FIGURE 8. Synthesis of adult chaetotaxy for abdominal segment IV in Seira sp. described in this study; symbols as in Fig. 1; Most microchaetae around botriothrica T2 and T4, including D1p and T3, are fan-shaped.
FIGURES 1–2. 1 in Postembryonic development of the dorsal chaetotaxy in Seira dowlingi (Collembola, Entomobryidae); with an analysis of the diagnostic and phylogenetic significance of primary chaetotaxy in Seira
FIGURES 1–2. 1, Synthesis of adult dorsal head chaetotaxy in Seira blanca, S. brasiliana, S. desapercibida, S. dowlingi and S. steinmetzi; 2, Seta types present in Seira.
FIGURE 84 in Postembryonic development of the dorsal chaetotaxy in Seira dowlingi (Collembola, Entomobryidae); with an analysis of the diagnostic and phylogenetic significance of primary chaetotaxy in Seira
FIGURE 84. Dorsal chaetotaxy of fourth abdominal segment in Seira annulicornis, redrawn from Szeptycki (1979).
FIGURES 5–7 in Postembryonic development of the dorsal chaetotaxy in Seira dowlingi (Collembola, Entomobryidae); with an analysis of the diagnostic and phylogenetic significance of primary chaetotaxy in Seira
FIGURES 5–7. Synthesis of adult chaetotaxy for abdominal segments 1–3 in Seira sp., described in this study; symbols as in Fig. 1; 5, Abdomen I; 6, Abdomen II, most microchaetae around botriothrica m2 and a5, including m3ea, are fanshaped; 7, Abdomen, III double-headed arrow points to alternate insertion of m4, most microchaetae around botriothrica m2, a5 and m5 are fan-shaped.
FIGURES 80–83 in Postembryonic development of the dorsal chaetotaxy in Seira dowlingi (Collembola, Entomobryidae); with an analysis of the diagnostic and phylogenetic significance of primary chaetotaxy in Seira
FIGURES 80–83. Dorsal chaetotaxy of fourth abdominal segment; 80, Seira blanca; 81, S. steinmetzi; 82, S. desapercibida; 83, S. brasiliana.
FIGURES 27–30 in Postembryonic development of the dorsal chaetotaxy in Seira dowlingi (Collembola, Entomobryidae); with an analysis of the diagnostic and phylogenetic significance of primary chaetotaxy in Seira
FIGURES 27–30. Adult dorsal head chaetotaxy; 27, Seira dowlingi; 28, S. desapercibida; 29, S. brasiliana; 30, S. blanca.
FIGURES 3–4 in Postembryonic development of the dorsal chaetotaxy in Seira dowlingi (Collembola, Entomobryidae); with an analysis of the diagnostic and phylogenetic significance of primary chaetotaxy in Seira
FIGURES 3–4. Synthesis of adult thorax chaetotaxy in Seira sp. described in this study; symbols as in Fig. 1; 3, Mesothorax; 4, Metathorax, double-headed arrows point to alternate insertions of a6 and m6p.
FIGURES 28–31. Superior volsella and digitus. 28 in Evaluation of diagnostic characters of the Tanytarsus chinyensis group (Diptera: Chironomidae), with description of a new species from Lapland
FIGURES 28–31. Superior volsella and digitus. 28: Tanytarsus chinyensis, 29: T. cretensis (according to Reiss 1987), 30: T. heusdensis, 31: T. palettaris.
FIGURES 19–27. Hypopygial volsellae. 19–21 in Evaluation of diagnostic characters of the Tanytarsus chinyensis group (Diptera: Chironomidae), with description of a new species from Lapland
FIGURES 19–27. Hypopygial volsellae. 19–21: superior volsella and digitus, 22–24: median volsella and inner margin of coxite, 25–27: inferior volsella. 19, 22, 25: Tanytarsus brundini; 20, 23, 26: T. curticornis; 21, 24, 27: T. salmelai sp. n.
FIGURES 5–18 in Evaluation of diagnostic characters of the Tanytarsus chinyensis group (Diptera: Chironomidae), with description of a new species from Lapland
FIGURES 5–18. Variability in hypopygial anal point. 5–9: Tanytarsus brundini, 10–14: T. curticornis, 15–18: T. salmelai sp. n.
FIGURE 1 in Diagnostic clarification, new morphological data and phylogenetic placement of Amphisbaena arenaria Vanzolini, 1991 (Amphisbaenia, Amphisbaenidae)
FIGURE 1. Phylogenetic relationships within Amphisbaena, showing the placement of A. arenaria (red branch); scale bar represents estimated substitutions per site. Insert map depicts the known records (green dots) and type locality (red dot) of A. arenaria; yellow line represents the borders of Raso da Catarina Ecological Station. Photo by J. Rodrigues.
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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.