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29,145 results for “Association”
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism
<ul> <li>Eight versions of COBRA-compliant SBML files are available for each Recon 2M.1 and Recon 2M.2 depending on the use of: MNXref versus BiGG IDs; Entrez gene IDs (GPR associations) versus Ensembl transcript IDs versus RefSeq transcript IDs versus UCSC transcript IDs (TPR associations for the last three database IDs).</li> <li>892 personal GEMs (only T-GEMs) built with Recon 2.2</li> <li>1,784 personal GEMs (both P-GEMs and T-GEMs) built with Recon 2M.1</li> <li>892 personal GEMs (only T-GEMs) built with Recon 2M.2</li> </ul> <p> </p> <p><strong>Publication</strong></p> <p>Jae Yong Ryu<sup>1</sup>, Hyun Uk Kim<sup>1</sup> & Sang Yup Lee<sup>*</sup>. Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism., <em>Proc. Natl. Acad. Sci. U.S.A.</em>, 2017, http://www.pnas.org/content/early/2017/10/23/1713050114</p> <p> </p>
Global scale leaf broadband optical properties derived from CliMA Land and associated CESM simulations
<p>Leaf level broadband reflectance and transmittance computed from leaf traits.</p> <ul> <li>clm_refl_tran_1m_weighted.nc: monthly data (144*96 pixels)</li> <li>surfdata_CMIP6_fluspect_v3.nc: surface data to run CESM (144*96 pixels)</li> </ul> <p>Global scale simulation results</p> <ul> <li>research_data_coupled_future_v2.nc: CESM coupled future simulations</li> <li>research_data_coupled_history_v2.nc: CESM coupled historical simulations</li> <li>research_data_uncoupled_history_v2.nc: CESM uncoupled future simulations</li> <li>research_data_uncoupled_ssp_v2.nc: CESM uncoupled SSP245 and SSP585 simulations</li> </ul> <p>Code changes</p> <ul> <li>SurfaceAlbedoMod.F90: modified CLM module</li> <li>Julia-and-Python-Code.tar.gz: code used for processing the data and plot the figures</li> </ul>
Type-II kinase inhibitors that target Parkinson's Disease-associated LRRK2
<p>This dataset includes all of the tabular data used in the tables and figures in the article. Additionally, we provide a table with key resources for data aquisition.</p> <p>Aberrant increases in kinase activity of leucine-rich repeat kinase 2 (LRRK2) are associated with Parkinson’s disease (PD). Numerous LRRK2-selective type-I kinase inhibitors have been developed and some have entered clinical trials. In this study, we present the first LRRK2-selective type-II kinase inhibitors. Targeting the inactive conformation of LRRK2 is functionally distinct from targeting the active-like conformation using type-I inhibitors. We designed these inhibitors using a combinatorial chemistry approach fusing selective LRRK2 type-I and promiscuous type-II inhibitors by iterative cycles of synthesis supported by structural biology and activity testing. Our current lead structures are selective and potent LRRK2 inhibitors. Through cellular assays, cryo-electron microscopy structural analysis, and in vitro motility assays, we show that our inhibitors stabilize the open, inactive kinase conformation. These new conformation-specific compounds will be invaluable as tools to study LRRK2’s function and regulation, and expand the potential therapeutic options for PD.</p>
Putative mutations associated with tetracycline resistance detected in Treponema spp.- an analysis of 4,355 Spirochaetales genomes
<p>Supplementary Table 1–4, , as well as multiple sequence alignment files for 16S rRNA, rpsC, and rpsJ loci, have been deposited.</p> <p>Additionally, the archive contains a <code>scripts.txt</code> file that includes all custom Bash scripts used for:</p> <ul> <li> <p>rRNA gene detection and quantification using <em>Barrnap</em></p> </li> <li> <p>Genome quality assessment using <em>CheckM</em></p> </li> <li> <p>Gene-by-gene schema creation, allele calling, and cgMLST extraction using <em>chewBBACA</em></p> </li> <li> <p>GFF merging and wide-format transformation for summarizing rRNA copy number per genome</p> </li> </ul> <p>These materials are provided to ensure reproducibility of the analyses and to support further investigations into antimicrobial resistance in <em>Spirochaetales</em>.</p>
Growth traits of a tropical timber species at Southeast Asia, Shorea macrophylla, and scripts for genome wide association study and genomic prediction
<p><em><span>Shorea macrophylla</span></em><span> is a commercially important tropical tree species grown for timber and oil. It is amenable to plantation forestry due to its fast initial growth. Genomic selection (GS) has been used in tree breeding studies to shorten long breeding cycles but has not previously been applied to <em>S. macrophylla</em>. To build genomic prediction models for GS, leaves and growth trait data were collected from a half-sib progeny population of <em>S. macrophylla</em> in Sari Bumi Kusuma forest concession, central Kalimantan, Indonesia. 18037 SNP markers were identified in two ddRAD-seq libraries. Genomic prediction models based on these SNPs were then generated for breast height and total height in the 7th year from planting (D7 and H7). These traits were chosen because of their relatively high narrow-sense genomic heritability and because seven years was considered long enough to assess initial growth. Genomic prediction models were built using 12 methods with the full set of identified SNPs and subsets of 48, 96, and 192 SNPs selected based on the results of a genome-wide association study (GWAS). The GBLUP and RKHS methods gave the highest predictive ability (PA) for D7 and H7 and showed that D7 has an additive genetic architecture while H7 has an epistatic genetic architecture. LightGBM and CNN1D also achieved high PA for D7 with 48 and 96 selected SNPs, and for H7 with 96 and 192 selected SNPs, showing that gradient boosting decision trees and deep learning can be useful in genomic prediction. For almost all methods and both traits, PA was higher when SNPs were selected based on their GWAS P-values than when using the full set of SNPs. These results suggest that GS with GWAS-based SNP selection could be used in <em>S. macrophylla </em>breeding to improve initial growth and reduce genotyping costs for next generation seedlings.</span></p>
Climate-associated variation in the drivers of benthic macroinvertebrate species-area relationships across shallow freshwater lakes
<p><span>The island species-area relationship (ISAR) describes how species richness increases with increasing area of a given island or island-like habitat, such as freshwater lakes. </span><span>While the ISAR is one of the most common phenomena observed in ecology, there is variation in both the form of the relationship and its underlying mechanisms.</span></p> <p><span>We compiled a global dataset of benthic macroinvertebrates from 524 shallow freshwater lakes, ranging from 1 to 293300 ha in area. We used individual-based rarefaction to determine the degree to which ISAR was influenced by mechanisms other than passive sampling (larger islands passively sample more individuals from the regional pool and, therefore, have more species than smaller islands), which would bias results away from expected relationships between rarefied species richness (and other measures that capture relative abundances) and lake area. We also examined how climate may alter the shape of the ISARs. </span></p> <p><span>We found that both rarefied species richness (the number of species standardized by area or number of individuals) and a measure of evenness emphasizing common species exhibit non-significant relationships with lake area, suggesting that the expected ISARs in these lakes most likely result from passive sampling. </span><span>While there was considerable variation among ISARs across the investigated lakes, we found an overall positive rarefied ISAR for lakes in warm (i.e., tropical/subtropical) regions (n = 195), and in contrast, an overall negative rarefied ISAR in cool (i.e., north temperate) lakes (n = 329). This suggested that mechanisms beyond passive sampling (e.g., colonization-extinction dynamics and/or heterogeneity) were more likely to operate in warm lakes. One possible reason for this difference is that the area-dependent intensity of fish predation, which can lead to flatter ISARs, is weaker in warmer relative to cooler lakes.</span></p> <p><span>Our study illustrates the importance of understanding both the pattern and potential processes underlying the ISARs of freshwater lakes in different climatic regions. Further, it provides a baseline for understanding how further changes to the ecosystem (i.e., in lake area or climate) might influence biodiversity patterns. </span></p>
Observational Bias and Young Massive Cluster Characterisation II. Can Gaia accurately observe young clusters and associations?
<p>Field-of-View for synthetic Gaia observations of clusters Orion-type-3, Orion-type-5.5 and Wd2-type presented in Buckner et al. (2023).</p><p>Files contain both simulation and field stars along the Line-of-Sight (l = 270^o, b = 0^o) for the clusters when placed at 500pc, 2500pc and 4300pc distances.</p><p>The original simulation files are included for reference.</p><p>Included README files provide more detailed descriptions of the files.</p>
Data from: The genetic basis of traits associated with the evolution of serpentine endemism in monkeyflowers
<p>The floras on chemically and physically challenging soils, such as gypsum, shale, and serpentine, are characterized by narrowly endemic species. The evolution of edaphic endemics may be facilitated or constrained by genetic correlations among traits contributing to adaptation and reproductive isolation across soil boundaries. The yellow monkeyflowers in the <em>Mimulus guttatus</em> species complex are an ideal system in which to examine these evolutionary patterns. To determine the genetic basis of adaptive and prezygotic isolating traits, we performed genetic mapping experiments with F2 hybrids derived from a cross between a serpentine endemic, <em>M. nudatus</em>, and its close relative <em>M. guttatus</em>. Few large effect and many small effect QTL contribute to interspecific divergence in life history, floral and leaf traits, and a history of directional selection contributed to trait divergence. Loci contributing to adaptive traits and prezygotic reproductive isolation overlap, and their allelic effects are largely in the direction of species divergence. These loci contain promising candidate genes regulating flowering time and plant organ size. Together our results suggest that genetic correlations among traits can facilitate the evolution of adaptation and speciation and may be a common feature of the genetic architecture of divergence between edaphic endemics and their widespread relatives.</p>
FIGURE 3 in A.J. BRUCE (2013) Onycocaris maui sp. nov., a new pontoniine sponge associate (Crustacea: Decapoda: Palaemonidae) from the Hawai'ian Islands. Zootaxa, 3691 (3), 377-388.
FIGURE 3. Onycocaris maui sp. nov., post-ovigerous female paratype, Maui, QM W29192. A, rostrum, lateral. B, same, dorsal. C, carapace and anterior appendages. D, same, dorsal. E, eye. F, sixth abdominal segment, dorsal. G, telson. H, same, posterior spines. I, uropod. J, same, exopod, distolateral angle.
FIGURE 6 in A.J. BRUCE (2013) Onycocaris maui sp. nov., a new pontoniine sponge associate (Crustacea: Decapoda: Palaemonidae) from the Hawai'ian Islands. Zootaxa, 3691 (3), 377-388.
FIGURE 6. Onycocaris maui sp. nov., post-ovigerous female paratype, Maui, QM W29192. A, major second pereiopod, lateral. B, same, dactyl. C, same, fixed finger. D, minor second pereiopod, E, same, fingers. F, same, fixed finger, lateral. G, same, distal finger.
Fig. 7 in Species Composition And Distribution Of The Dominant Flyingfishes (Exocoetidae) Associated With The Kuroshio Current, South China Sea
Fig. 7. Monthly median (square dot) with 25 th and 75th quartiles (vertical line) for (a) flyingfishes catch proportion (proportion of catch, adjusted by number of trips in the month, to the overall catches of the sampling year), (b) SST (°C), (c) tide level (cm), and (d) tidal range (cm). Tidal range in the plot is the difference of tide level within one hour. Dashed lines indicate roughly the area with high catch
Fig. 5 in Species Composition And Distribution Of The Dominant Flyingfishes (Exocoetidae) Associated With The Kuroshio Current, South China Sea
Fig. 5. Monthly flyingfish densities by (a) vertical catch layer (upper: Fig. 4. Flyingfish compositions of the six dominant species by 0–1.2 m, middle: 1.2–2.4 m, and bottom: 2.4–3.6 m), and (b) mesh sampling area, collected by in-port sampling and at-sea survey size of net (5.6 cm, 4 cm, and 2.8 cm for large, medium, and small
Raw dataset and additional data for article "Nonmotor symptoms associated with progressive loss of dopaminergic neurons in a mouse model of Parkinson's disease"
<p>Dataset from the project investigating the presence of nonmotor symptoms of Parkinson's disease in a mouse model of progressive loss of dopaminergic neurons (namely,TIF-IADATCreERT2 strain). Mice were tested for executive and cognitive functions (males: Operant Sensation Seeking test, OSS; females: Probabilistic Reversal Learning Task in Intellicages), olfactory acuity (males: buried food test), saccharin preference (males and females), and motor performance (males and females: test using CatWalk apparatus).</p><p>The dataset includes files used to perform statistical analyses but their names may vary from the ones used in the scripts. For the purpose of recreating our analyses, please refer to the GitHub page, where both scripts and input data file names (in 'Raw data files' section) are compliant: https://github.com/annaradli/tif-pd-behavior.</p><p><strong>Description of files:</strong></p><p><i>Raw data files:</i></p><ul><li>animals_info.csv - animals data: genotype, sex, age, Intellicage tag identifier</li><li>catwalk_run_statistics_all_females.csv - data recorded in CatWalk apparatus for females</li><li>catwalk_run_statistics_all_males.csv - data recorded in CatWalk apparatus for males</li><li>females_weight_raw_data_revised.csv - females' body weight (revised for containing Polish words)</li><li>intellicage_raw_data.csv - data recorded in IntelliCage exported to .csv format</li><li>intellicage_raw_data_R.RData - data recorded in IntelliCage in .RData format</li><li>males_weight_raw_data.csv - males' body weight</li><li>olfactory_time_digging_raw_data.csv - time to start digging at the right place in the buried food test</li><li>olfactory_time_retrieve_raw_data.csv- time to retrieve cracker in the buried food test</li><li>oss_raw_data.csv - data recorded in the OSS test</li><li>saccharin_preference_males_raw_data.csv - saccharin preference test results for males</li><li>snvta_cells_count.csv - number of TH+ cells in SN and VTA in male mice (3+3) 14 weeks after tamoxifen treatment</li></ul><p><i>Additional data files:</i></p><ul><li>all_anova.xlsx - summary of two-way ANOVAs of all behavioral tests and weight measurements for males and females</li><li>catwalk_complete.xlsx - CatWalk complete dataset with datapoints</li><li>catwalk_correlation_between_paws.xlsx - correlation coefficients of CatWalk parameters between the left and right paws</li><li>catwalk_reduced.xlsx - CatWalk parameters used in linear regression model reduction of data</li><li>intelli.xlsx - IntelliCage data summarized in bins</li><li>oss.xlsx - operant sensation-seeking data</li></ul><p>v2 contains the corrected 'animals_info.csv' file without an unnecessary column.</p><p>v3 has a revised version of file containing females' weight measurements and also added a file with midbrain cell counts</p><p>v4 has a whole section of 'Additional data files' added</p>
Figs. 152–155. 152 in Reclassification of the North Temperate Taxa Associated with Staphylinus Sensu Lato, Including Comments on Relevant Subtribes of Staphylinini (Coleoptera: Staphylinidae)
Figs. 152–155. 152. Agelosus carinatus, underside of head, showing abbreviated infraorbital ridge (arrow). 153. Agelosus carinatus, last segment of labial palpus. 154. Tasgius melanarius, mesosternal intercoxal process. 155. Tasgius ater, pronotal hypomeron and prosternum.
Figs. 156–159. 156 in Reclassification of the North Temperate Taxa Associated with Staphylinus Sensu Lato, Including Comments on Relevant Subtribes of Staphylinini (Coleoptera: Staphylinidae)
Figs. 156–159. 156. Tasgius melanarius, mentum and submentum. 157. Tasgius melanarius, prosternum. 158. Tasgius melanarius, metasternum, showing anterior metasternal projection. 159. Platydracus stercorarius, pronotum.
Figs. 146–151. 146 in Reclassification of the North Temperate Taxa Associated with Staphylinus Sensu Lato, Including Comments on Relevant Subtribes of Staphylinini (Coleoptera: Staphylinidae)
Figs. 146–151. 146. Protogoerius brullei, underside of head, showing gula. 147. Protogoerius brullei, left mandible, dorsal view. 148. Protogoerius brullei, maxillary (left) and labial palpus (right). 149. Ocypus tenebricosus, maxilla, showing setae on palpifer. 150. Ocypus tenebricosus, maxillary palpus. 151. Ocypus tenebricosus, labial palpus.
Figs. 142–145. 142. Dinothenarus fossor, mesosternum. 143 in Reclassification of the North Temperate Taxa Associated with Staphylinus Sensu Lato, Including Comments on Relevant Subtribes of Staphylinini (Coleoptera: Staphylinidae)
Figs. 142–145. 142. Dinothenarus fossor, mesosternum. 143. Miobdelus sp., left mandibular prostheca, ventral view. 144. Miobdelus sp., maxillary palpus. 145. Miobdelus sp., labial palpus.
Figs. 129–135. 129 in Reclassification of the North Temperate Taxa Associated with Staphylinus Sensu Lato, Including Comments on Relevant Subtribes of Staphylinini (Coleoptera: Staphylinidae)
Figs. 129–135. 129. Protogoerius brullei, last segment of maxillary palpus. 130. Ocypus picipennis picipennis, hind tibia with spines (arrow) on dorsolateral face. 131. Ocypus mus, last segment of labial palpus. 132. Ocypus weisei, last segment of labial palpus. 133. Ocypus olens, last segment of labial palpus. 134. Platydracus stercorarius, last segment of maxillary palpus. 135. Platydracus stercorarius, last segment of labial palpus.
Figs. 123–128. 123 in Reclassification of the North Temperate Taxa Associated with Staphylinus Sensu Lato, Including Comments on Relevant Subtribes of Staphylinini (Coleoptera: Staphylinidae)
Figs. 123–128. 123. Abemus chloropterus, labium and mentum. 124. Abemus chloropterus, left mandible, dorsal view. 125. Miobdelus sp., posterolateral portion of head, showing pitlike depressions. 126. Miobdelus sp., first three visible abdominal tergites, showing bisinuate posterior basal line. 127. Ocypus picipennis picipennis, left mandible, ventral view. 128. Ocypus picipennis picipennis, right mandible, ventral view.
Figs. 111–116. 111 in Reclassification of the North Temperate Taxa Associated with Staphylinus Sensu Lato, Including Comments on Relevant Subtribes of Staphylinini (Coleoptera: Staphylinidae)
Figs. 111–116. 111. Dinothenarus pubescens, pronotum showing both marginal lines of pronotal hypomeron, and two lateral macrosetae, lateral view. 112. Staphylinus erythropterus, pronotum showing both marginal lines of pronotal hypomeron, and two lateral macrosetae, lateral view. 113. Ocypus ophthalmicus ophthalmicus, pronotum showing both marginal lines of pronotal hypomeron, and two lateral macrosetae, ventrolateral view. 114. Ocypus nitens semialatus, pronotum showing both marginal lines of pronotal hypomeron, and two lateral macrosetae, lateral view. 115. Physetops sp., dorsal face of neck, with dorsal portion of nuchal ridge missing. 116. Ontholestes cingulatus, dorsal face of neck, with nuchal ridge.
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.