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423 results for “Haplotypes”
Fig. 3. Haplotype networks for A. oahuensis. Panels correspond with the 12S in Tuerkayana latens Ng and Hsi-Te Shih 2023, n. sp.
Fig. 3. Haplotype networks for A. oahuensis. Panels correspond with the 12S rDNA gene (Panel A), 16S rDNA gene (Panel B), COI (Panel C), and H3A (Panel D). Colors and locality IDs correspond with those used in all other Figures. Black circles represent unsampled (i.e., missing) haplotypes, with the size of circles proportional to the frequency at which each haplotype was recovered.
Fig. 2 Phylogenetic tree showing the relation between the Saudi Arabian haplotypes with 65 in Three species of Echinococcus granulosus sensu lato infect camels on the Arabian Peninsula
Fig. 2 Phylogenetic tree showing the relation between the Saudi Arabian haplotypes with 65 reference sequences. The Saudi Arabian haplotypes (H01-09) are in bold. The reference sequences along with their accession numbers and origin of isolate were included for each. T. solium was used as an outgroup taxon. The branch to outgroup was shortened by 0.2 substitutions per site
Fig. 3. Maximum Likelihood tree for the 35 haplotypes identified from 39 in Molecular confirmation of Hymenolepis hibernia in field mice (Apodemus sylvaticus) from St Kilda has potential to resolve a host-parasite relationship
Fig. 3. Maximum Likelihood tree for the 35 haplotypes identified from 39 mt-cox-1 sequences of Hymenolepis species. Of these, 19, 5, 2 and 8 haplotypes are identified in the Genbank database as H. diminuta, H. hibernia, H. microstoma and H. nana, respectively, and one haplotype (H-HA25) was identified here from the faeces of St Kilda mice 9 and X. Branches with bootstrap values (1000 replications) represented at the base of the nodes. The phylogeny is rooted with mt-cox-1 sequence of parasitic nematode H. contortus.
Fig. 3 Phylogenetic relationships among the 16 mtDNA haplotypes observed. a in Unveiling cryptic diversity among Müllerian co-mimics: insights from the Western Palaearctic Syntomis moths (Lepidoptera: Erebidae: Arctiinae)
Fig. 3 Phylogenetic relationships among the 16 mtDNA haplotypes observed. a Maximum likelihood tree retrieved by the analysis in IQTREE; support values at the relevant nodes are SH-aLRT support (%) and standard bootstrap support (%) based on 1000 replicates. b Maximum clade credibility tree recovered by the Bayesian analysis in BEAST, showing the divergence time from the most recent common
ACE gene haplotypes and social networks: Using a biocultural framework to investigate blood pressure variation in African Americans
<p>This dataset contains all processed data used in analyses reported in the manuscript, ACE gene haplotypes and social networks: Using a biocultural framework to investigate blood pressure variation in African Americans. This project is part of a larger study focused on investigating the role of stress, discrimination, genetic variants, and other sociocultural factors in hypertension in African Americans.</p> <p> </p> <p> </p> <p>Variable Names and Descriptions:</p> <p>HHID: Participant Identification number</p> <p>sbp-10: Average of two Systolic Blood Pressure readings without 10 point correction for blood pressure medication (mmHg)</p> <p>sbp: Average of two Systolic Blood Pressure readings with 10 point correction for blood pressure medication (mmHg)</p> <p>dbp-5: Average of two Diastolic Blood Pressure readings without 5 point correction for blood pressure medication (mmHg)</p> <p>dbp: Average of two Diastolic Blood Pressure readings with 5 point correction for blood pressure medication (mmHg)</p> <p>ACE.Genotype: ACE genotype (0= Deletion/Deletion, 1= Insertion/Deletion, 2= Insertion/Insertion)</p> <p>WNK1.Genotype: WNK1 Genotype (0= Deletion/Deletion, 1= Insertion/Deletion, 2= Insertion/Insertion)</p> <p>age: age (years)</p> <p>sex: sex (Male =1, Female = 2)</p> <p>bpmedtake: Whether the participant uses blood pressure medication</p> <p>bmi: Body Mass Index (calculated from height and weight)</p> <p>ALTER GENDER|Answer:Male|Value:0|Count: Number of male alters (social network members)</p> <p>Alter Gender Male: Percentage of alters that are male</p> <p>ALTER GENDER|Answer:Female|Value:1|Count: Number of female alters (social network members)</p> <p>Alter Gender Female: Percentage of alters that are female</p> <p>Closeness_Mean: Average closeness centrality of the network</p> <p>Between_Mean: Average between-ness centrality of the network</p> <p>percentage of family in structural percentage: Percentage of central network positions occupied by family members</p> <p>relationship max close family: The most close (centrally) network member is a family member</p> <p>Average distance: Average distance of individuals in a network</p> <p>Hap B: ACE gene haplotypes</p> <p> </p>
Figures 4–5. Mitochondrial D-loop 474 in Molecular confirmation of the occurrence of Anguilla interioris (Actinopterygii: Anguilliformes) in North Maluku of Indonesia and mitochondrial DNA haplotype diversity among existing specimens
Figures 4–5. Mitochondrial D-loop 474 bp sequence analyses. (4) Phylogenetic analysis based on maximum likelihood algorithm with the sample codes, GenBank accession numbers and sample sites shown. Bootstrap percentages are shown at the tree nodes. (5) Haplotype network with the haplotypes labelled as H1 to H9. The circle size is proportional to the number of samples, and different sample sites are represented by different colours. Small white circle represents median vector which is the hypothesized or missing haplotype. Each dash on the line symbolizes one mutational step.
Figure 1 in Molecular confirmation of the occurrence of Anguilla interioris (Actinopterygii: Anguilliformes) in North Maluku of Indonesia and mitochondrial DNA haplotype diversity among existing specimens
Figure 1. Sampling locations of Anguilla interioris in North Maluku of East Indonesia. Sampling locations are shown in red (circle: COI, triangle: D-loop). Locations of Bougainville of Papua New Guinea, Papua New Guinea mainland, Negros Oriental and Sibutad of Philippines, and Ambon and Bengkulu of Indonesia, which were used in molecular phylogenetic and haplotype network analyses, are shown in purple (circle: COI, triangle: D-loop). Specimen records are shown in square with growth stages; L [larval (leptocephalus); Kuroki et al. 2006, Wouthuyzen et al. 2009, Aoyama et al. 2018], J [juvenile (glass eel); Sugeha et al. 2008, Fahmi et al. 2012, Wibowo et al. 2021] and A (adult; Watanabe et al. 2004, Fahmi et al. 2012, Wibowo et al. 2021, this study). Base maps were downloaded from http://viewer. nationalmap.gov/viewer (USGS 2022) and from the OpenStreetMap at https://www.openstreetmap.org.
Figure 1 in Haplotype diversity of brown trout Salmo trutta (L.) in the broader Iron Gate area
Figure 1. Sampling sites on the streams Brnjica (1), Dobrinjska reka (2), Kožica (3), Mala Boljetinska reka (4), Zlatica (5), Porečka reka (6), Rečka reka (7), Vratna (8), and Zamna (9) in the broader Iron Gate area with the position in the Balkan region given in small figure in lower left.
Figure 2 in Haplotype diversity of brown trout Salmo trutta (L.) in the broader Iron Gate area
Figure 2. Relationships between CR haplotypes of brown trout populations in the broader Iron Gate area constructed using maximum likelihood (A) and maximum parsimony (B) methods (numbers at particular branches represent bootstrap probabilities; bootstrap values under 40% are not represented).
Figure 1. A in Increased haplotype diversity of Emys orbicularis (Linnaeus, 1758) (Reptilia: Emydidae) in northern Iran
Figure 1. A) Map of Eurasia and the samples used for this study. Shaded area at lower right indicates the study area and the colors of the occurrence points correspond to the lineage numbers in the phylogenetic tree. B) Map of Iran, Armenia and Azerbaijan and samples for lineage VII. Red circles indicate samples from Genbank (Fitz et al., 2009), red stars are our new samples.
Figure 2 in Increased haplotype diversity of Emys orbicularis (Linnaeus, 1758) (Reptilia: Emydidae) in northern Iran
Figure 2. Bayesian inference tree (MrBayes) based on the cytochrome b gene fragment. Colors of the branches correspond to the lineage colors in Figure 1. Posterior probabilities and divergence time estimation (n parentheses) are next to the nodes.
Fig. 2. Statistical parsimony cladogram network representing relationships among the 45 haplotypes for a 615 in Genetic diversity of Halyomorpha halys (Hemiptera, Pentatomidae) in Korea and comparison with COI sequence datasets from East Asia, Europe, and North America
Fig. 2. Statistical parsimony cladogram network representing relationships among the 45 haplotypes for a 615 bp fragment of the COI gene of Halyomorpha halys. Each circle is labeled with haplotype number, and the size of each circle is proportional to the frequency of each haplotype [H3 (n = 353); H1 (n = 285); H22 (n = 43); H8 (n = 34); H33 (n = 23); H2 (n = 16); H32 (n = 8); H7, H9–H13, and H43 (n = 3); H6, H14, H34, H39, and H40 (n = 2); H4–H5, H12, H15–H21, H23, H30–H31, H35–H38, H41, H42, and H44–H51 (n = 1)]. Differing colors indicate countries in which samples were collected.
Fig. 2. Minimum spanning network for haemosporidian mitochondrial DNA cytochrome b haplotypes identified from blood samples collected from Emperor Geese inhabiting the YukonKuskokwim Delta, Alaska during 2006–2016 in Negligible evidence for detrimental effects of Leucocytozoon infections among Emperor Geese (Anser canagicus) breeding on the Yukon-Kuskokwim Delta, Alaska
Fig. 2. Minimum spanning network for haemosporidian mitochondrial DNA cytochrome b haplotypes identified from blood samples collected from Emperor Geese inhabiting the YukonKuskokwim Delta, Alaska during 2006–2016. Circles are drawn proportional to the frequency at which haplotypes were detected. Shading represented the assignment of representative sequences for haplotypes to L. simondi clade A (teal), L. simondi clade B (orange), or other Leucocytozoon (grey) in phylogenetic analyses (see Results and Fig. 5). Lines are drawn proportional to genetic distance and are labeled per the number of mutations represented (except single nucleotide polymorphisms which are unlabeled). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in A single Haemoproteus plataleae haplotype is widespread in white ibis (Eudocimus albus) from urban and rural sites in southern Florida
Fig. 2. Typical Haemoproteus plataleae stages from three infected white ibis (Eudocimus alba) from South Florida. All ibis were genetically confirmed to be infected with the EUDRUB01 lineage. A-E, an ibis from Juno Beach urban park; F, an ibis from Indian Creek urban park; and G-L, an ibis from the Solid Waste site. The latter bird had rare round forms (K-L), which were absent from other H. plataleae-infected ibis. Younger stages (C, H, I) had a an evident 'cleft' between the gametocyote and erythrocyte nucleus.
Fig. 3 in A single Haemoproteus plataleae haplotype is widespread in white ibis (Eudocimus albus) from urban and rural sites in southern Florida
Fig. 3. Phylogenetic relationship of Haemoproteus plataleae from white ibis (Eudocimus albus) with other Haemoproteus spp.
Fig. 1 in A single Haemoproteus plataleae haplotype is widespread in white ibis (Eudocimus albus) from urban and rural sites in southern Florida
Fig. 1. Box plots of parasitemia values of Haemoproteus plataleae in white ibis (Eudocimus albus) sampled from South Florida from 2010 to 2022 by year (A.), season (B.), and age (C. and D.). C. shows all ibis with general adult vs. juvenile age class designations and D. shows data for the subset of ibis that were aged to specific year for juveniles (1, 2, or 3 yrs old). Years 2015 and 2017 were significantly different from each other, but both were similar to other years. For remaining figures, factors that are differently colored are significantly different from each other. Note that the x-axis maximum varies between plots.
Fig. 5. Haplotypes from female S in Syngamus trachea in free-ranging white stork (Ciconia ciconia) nestlings in Switzerland
Fig. 5. Haplotypes from female S. trachea nematodes collected from five different white stork nestlings (WS1-5).
Detection of novel P. falciparum haplotypes under treatment pressure in pediatric severe malaria
<p>The dataset contains Amplicon sequencing data targeting three <em>Plasmodium falciparum</em> polymorphic markers—<em>cpmp</em>, <em>cpp</em>, and <em>ama1</em>. These markers were analyzed to investigate the association between parasite clearance rate and the multiplicity of infection in Beninese children undergoing treatment for severe malaria.</p>
Fig. 3. Haplotype network for E in Prevalence, molecular characterisation and phylogenetic analyses of hydatid cysts and cysticercus tenuicollis isolates and first report of E. canadensis (G6/G7) in wild boars in Bingol province, Türkiye
Fig. 3. Haplotype network for E. canadensis (G6/G7) using cox1 gene (616 bp) sequences of different countries. The E. canadensis (G6/G7) isolate obtained in this investigation (Hap_01) and the sequences identified as G7 in the Genbank database were utilized. Circle size relative to haplotype data set frequency. Each hatch mark is representative of one nucleotide change. Haplotypes formed by the isolates obtained in this study are marked with an asterisk.
Fig. 2. Haplotype network constructed using cox1 in Prevalence, molecular characterisation and phylogenetic analyses of hydatid cysts and cysticercus tenuicollis isolates and first report of E. canadensis (G6/G7) in wild boars in Bingol province, Türkiye
Fig. 2. Haplotype network constructed using cox1 (744 bp) gene sequences of T. hydatigena. Seven haplotypes formed by the T. hydatigena isolates obtained in this study: (Hap 1-Hap 7). Circle size relative to haplotype data set frequency. Each hatch mark is representative of one nucleotide change. Haplotypes formed by the isolates obtained in this study are marked with an asterisk.
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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.