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FIGURE S3 in Morphological and molecular data on helminths of Didelphis virginiana and Philander vossi (Mammalia: Didelphidae) from the Yucatán Peninsula, southeast Mexico
FIGURE S3. Maximum-likelihood (ML) phylogenetic tree of Oligacanthorhynchidae inferred with 28S rRNA sequence data using the GTR + G model (ln likelihood -6392.437537). GenBank accession numbers precede species name, followed by host name. Bootstrap support values for ML are provided at the nodes. The new sequences of the present study are in bold.
Fault-Tolerant Computing with Single Qudit Encoding in a Molecular Spin. Open data set
<div> <p>Data supporting the original figures 2, 3 and 4 (ESI) of the related manuscript.</p> </div>
Coronavirus Data Base (CoDaB-19): Banco de alvos moleculares contra o coronavírus da síndrome respiratória aguda grave 2 (SARS-CoV-2)
Open the record for dataset details and reuse information.
Data from: Genome-wide Polygenic Risk Scores Predict Risk of Glioma and Molecular Subtypes
<div> <div> <div> <p><strong>Background</strong>: Polygenic risk scores (PRS) aggregate the contribution of many risk variants to provide a personalized genetic susceptibility profile. Since sample sizes of glioma genome-wide association studies (GWAS) remain modest, there is a need to efficiently capture genetic risk using available data.</p> <p><strong>Methods</strong>: We applied a method based on continuous shrinkage priors (PRS-CS) to model the joint effects of over 1 million common variants on disease risk and compared this to an approach (PRS-CT) that only selects a limited set of independent variants that reach genome-wide significance (P<5×10-8). PRS models were trained using GWAS stratified by histological (10,346 cases, 14,687 controls) and molecular subtype (2,632 cases, 2,445 controls), and validated in two independent cohorts.</p> <p><strong>Results</strong>: PRS-CS was generally more predictive than PRS-CT with a median increase in explained variance (R2) of 24% (interquartile range=11-30%) across glioma subtypes. Improvements were pronounced for glioblastoma (GBM), with PRS-CS yielding larger odds ratios (OR) per standard deviation (OR=1.93, P=2.0×10-54 vs. OR=1.83, P=9.4×10-50) and higher explained variance (R2=2.82% vs. R2=2.56%). Individuals in the 80th percentile of the PRS- CS distribution had significantly higher risk of GBM (0.107%) at age 60 compared to those with average PRS (0.046%, P=2.4×10-12). Lifetime absolute risk reached 1.18% for glioma and 0.76% for IDH wildtype tumors for individuals in the 95th PRS percentile. PRS-CS augmented the classification of IDH mutation status in cases when added to demographic factors (AUC=0.839 vs. AUC=0.895, P=6.8×10-9).</p> <p><strong>Conclusions</strong>: Genome-wide PRS has potential to enhance the detection of high-risk individuals and help distinguish between prognostic glioma subtypes.</p> <p><strong>Citation</strong>: Nakase T, Guerra GA, Ostrom QT, et al. Genome-wide Polygenic Risk Scores Predict Risk of Glioma and Molecular Subtypes. <em>Neuro-Oncology</em>. Published online June 25, 2024:noae112. doi:10.1093/neuonc/noae112</p> </div> </div> </div>
Supplementary Data for "Molecular Docking, ADMET, Synthesis and Evaluation of New Indomethacin Hydrazide Derivatives as Antibacterial Agents"
<p>This supplementary data file contains additional information supporting the findings presented in the research article "<strong>Molecular Docking, ADMET, Synthesis and Evaluation of New Indomethacin Hydrazide Derivatives as Antibacterial Agents</strong>". The data includes:</p> <ul> <li>Infrared (IR) spectra of the synthesized compounds</li> <li>Proton nuclear magnetic resonance (H NMR) spectra of the synthesized compounds</li> <li>Minimum inhibitory concentration (MIC) and zone of inhibition (ZOI) data for the synthesized compounds against tested microorganisms</li> </ul>
FIGURE 2. Molecular phylogeny estimated using IQTREE2 in A cautionary note on synonymization based on mitochondrial data in Orthoptera: a comment of Hochkirch et al. 2023
FIGURE 2. Molecular phylogeny estimated using IQTREE2 (Minh et al. 2020) and the complete mitochondrial genome showing the paraphyly of the species within the genus Omocestus and Gomphocerrippus. Node supports are ultra-fast bootstrap supports. The code to the right of the species name indicates SRA accession number. All data are from Hawlitschek et al. 2022 except Omocestus haemorrhoidalis accession SRR21022974. Abbreviation: O. = Omocestus, P. = Pseudochorthippus and G. = Gomphocerrippus.
FIGURE 1. Molecular phylogeny estimated using IQTREE2 in A cautionary note on synonymization based on mitochondrial data in Orthoptera: a comment of Hochkirch et al. 2023
FIGURE 1. Molecular phylogeny estimated using IQTREE2 (Minh et al. 2020) and ITS2 loci. Colours represent species according to Supplementary Table 1 of Hochkirch et al. 2023. Dotted lines indicate species not supported by the phylogenetic estima.
Molecular dynamics simulation trajectory data for "Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function"
<p>Trajectories and input files corresponding to entries in Supplementary Table S1.</p>
FIGURE 6 in Morphology and molecular data reveal the presence of two new species under Rhamdia quelen (Quoy & Gaimard, 1824) (Siluriformes: Heptapteridae) species complex
FIGURE 6. LineAr regression PloTs of The mAin morPhologiCAl meAsuremenTs ThAT diAgnose The Two new sPeCies of Rhamdia in souThern CDSEB region. Blue CirCle: Rhamdia Aff. quelen; red CirCle: Rhamdia gabrielae; green TriAngle: Rhamdia eurycephala. DAshed lines rePresenT 95% ConfidenCe inTervAl.
FIGURE 3 in Morphology and molecular data reveal the presence of two new species under Rhamdia quelen (Quoy & Gaimard, 1824) (Siluriformes: Heptapteridae) species complex
FIGURE 3. MismATCh disTribuTion for: (A) CoAsTAl PlAin GrouP (Rhamdia aff. quelen), (B) MAquiné-MAmPiTubA GrouP (Rhamdia gabrielae), And (C) TubArão GrouP (Rhamdia eurycephala). Coloured line is observed dATA And grAy line is exPeCTed dATA.
FIGURE 9 in Morphology and molecular data reveal the presence of two new species under Rhamdia quelen (Quoy & Gaimard, 1824) (Siluriformes: Heptapteridae) species complex
FIGURE 9. Rhamdia eurycephala (UFRGS 19908), holoTyPe, 246.6 mm SL. In dorsAl, lATerAl, And venTrAl views.
FIGURE 2 in Morphology and molecular data reveal the presence of two new species under Rhamdia quelen (Quoy & Gaimard, 1824) (Siluriformes: Heptapteridae) species complex
FIGURE 2. HAPloTyPe neTwork using MediAn-Joining for Rhamdia sAmPles for miToChondriAl dATA (mTDNA) And nuCleAr dATA (nDNA). EACh CirCle rePresenTs A single hAPloTyPe And iTs size is ProPorTionAl To iTs frequenCy. DifferenT Colours rePresenT differenT PoPulATions. CoAsTAl PlAin GrouP (Rhamdia Aff. quelen) rePresenTed in blues And grAy, TubArão GrouP (Rhamdia eurycephala) rePresenTed in green, And MAquiné-MAmPiTubA GrouP (Rhamdia gabrielae) rePresenTed in hoT Colours. '
FIGURE 8 in Morphology and molecular data reveal the presence of two new species under Rhamdia quelen (Quoy & Gaimard, 1824) (Siluriformes: Heptapteridae) species complex
FIGURE 8. HoloTyPe of Rhamdia gabrielae (UFRGS 20010), holoTyPe, 194 mm SL. In dorsAl, lATerAl, And venTrAl views.
FIGURE 5 in Morphology and molecular data reveal the presence of two new species under Rhamdia quelen (Quoy & Gaimard, 1824) (Siluriformes: Heptapteridae) species complex
FIGURE 5. SPeCies Tree wiTh sTrongesT suPPorT ACCording To BAyesiAn PosTerior ProbAbiliTies ProduCed in BeAsT. Numbers on The ToP rePresenT PosTerior ProbAbiliTies And number on The boTTom of Are The divergenCe dATes of The resPeCTive node. The Colourful brAnChes indiCATe The grouPs reCovered in Previous AnAlyses. (A) CoAsTAl PlAin GrouP, (B) MAquiné-MAmPiTubA GrouP (Rhamdia gabrielae) And (C) TubArão GrouP (Rhamdia eurycephala).
FIGURE 7 in Morphology and molecular data reveal the presence of two new species under Rhamdia quelen (Quoy & Gaimard, 1824) (Siluriformes: Heptapteridae) species complex
FIGURE 7. SCATTer PloT of Combined sAmPles of Rhamdia gabrielae (red), Rhamdia eurycephala (green) And Rhamdia Aff. quelen (blue) on The seCond And Third PrinCiPAl ComPonenT Axis.
FIGURE 10 in Morphology and molecular data reveal the presence of two new species under Rhamdia quelen (Quoy & Gaimard, 1824) (Siluriformes: Heptapteridae) species complex
FIGURE 10. VAriATion in seA level for The lAsT 2 MA shown ACCording To Miller et al. (2011). The red lines rePresenT The PoinTs of divergenCe beTween The lines of RhAmdiA, A) FirsT divergenCe And B) seCond divergenCe
FIGURE 4 in Morphology and molecular data reveal the presence of two new species under Rhamdia quelen (Quoy & Gaimard, 1824) (Siluriformes: Heptapteridae) species complex
FIGURE 4. Gene Tree for All DNA dATA seT ProduCed by BAyesiAn AnAlysis in MrBAyes. VAlues on nodes rePresenT BAyesiAn PosTerior ProbAbiliTies: (A) CoAsTAl PlAin GrouP (Rhamdia Aff. quelen), (B) MAquiné-MAmPiTubA GrouP (Rhamdia gabrielae) And (C) TubArão GrouP (Rhamdia eurycephala). TB (green)—rio TubArão; ARA (OrAnge)—uPPer rio ArArAnguá; MP (Pink)— rio MAmPiTubA; TF (red)—rio Três ForquilhAs; MAQ (yellow)—rio MAquiné; TR (dArk blue)—TrAmAndAí lAgoons; ARAB (lighT blue)—lower rio ArArAnguá; CM (grey)—lAgunA dos PATos.
FIGURE 1 in Morphology and molecular data reveal the presence of two new species under Rhamdia quelen (Quoy & Gaimard, 1824) (Siluriformes: Heptapteridae) species complex
FIGURE 1. STudy AreA: 1) rio MAquiné; 2) rio Três ForquilhAs; 3) rio MAmPiTubA; 4) rio ArArAnguá, And 5) rio TubArão. The hydrogrAPhiC bAsins Are surrounded by Coloured lines. Rivers 1–4 form PArT of The TrAmAndAí-MAmPiTubA eCoregion. Red doTs rePresenT ColleCTion loCAliTies of Rhamdia sPeCimens used in geneTiC AnAlyses.
Supplementary material 3 from: Bragança PHN, Amorim PF, Costa WJEM (2018) Pantanodontidae (Teleostei, Cyprinodontiformes), the sister group to all other cyprinodontoid killifishes as inferred by molecular data. Zoosystematics and Evolution 94(1): 137-145. https://doi.org/10.3897/zse.94.22173
Maximum Likelihood (A) and Bayesian Inference (B) analysis including the 16S gene. : Explanation note: Maximum Likelihood (A) and Bayesian Inference (B) analysis including segments of the nuclear genes ENC1, GLYT, MYH6, SH3PX3, RAG1, the mitochondrial genes 16S and first and second codon position of the COI. In ML, bootstrap values under 50 are not represented, and posterior probability values under 0.5 are not represented in BI.
Supplementary material 5 from: Bragança PHN, Amorim PF, Costa WJEM (2018) Pantanodontidae (Teleostei, Cyprinodontiformes), the sister group to all other cyprinodontoid killifishes as inferred by molecular data. Zoosystematics and Evolution 94(1): 137-145. https://doi.org/10.3897/zse.94.22173
Bayesian Inference tree : Explanation note: Bayesian inference tree comprising segments of the nuclear genes ENC1, GLYT, MYH6, SH3PX3, RAG1 and first and second codon position of the mitochondrial gene COI (5,083 bp). Numbers on each node are posterior probablity values; values under 50 are not present in the tree.
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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.