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  • Authors: Wang, Xiaozhu; Jaraquemada-Peláez, María De Guadalupe; Rodríguez-Rodríguez, Cristina; Cao, Yang; +7 Authors

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures. Related Article: Xiaozhu Wang, María de Guadalupe Jaraquemada-Peláez, Cristina Rodríguez-Rodríguez, Yang Cao, Christian Buchwalder, Neha Choudhary, Una Jermilova, Caterina F. Ramogida, Katayoun Saatchi, Urs O. Häfeli, BrianO. P|2018|J.Am.Chem.Soc.|140|15487|doi:10.1021/jacs.8b09964

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  • Authors: Garai, Sumanta; Leo, Luciana M.; Szczesniak, Anna-Maria; Hurst, Dow P.; +14 Authors

    Related Article: Sumanta Garai, Luciana M. Leo, Anna-Maria Szczesniak, Dow P. Hurst, Peter C. Schaffer, Ayat Zagzoog, Tallan Black, Jeffrey R. Deschamps, Elke Miess, Stefan Schulz, David R. Janero, Alex Straiker, Roger G. Pertwee, Mary E. Abood, Melanie E. M. Kelly, Patricia H. Reggio, Robert B. Laprairie, Ganesh A. Thakur|2021|J.Med.Chem.|64|8104|doi:10.1021/acs.jmedchem.1c00040

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Rashid, Asim J.; Yan, Chen; Mercaldo, Valentina; Hsiang, Hwa-Lin; +9 Authors

    Collections of cells called engrams are thought to represent memories. Although there has been progress in identifying and manipulating single engrams, little is known about how multiple engrams interact to influence memory. In lateral amygdala (LA), neurons with increased excitability during training outcompete their neighbors for allocation to an engram. We examined whether competition based on neuronal excitability also governs the interaction between engrams. Mice received two distinct fear conditioning events separated by different intervals. LA neuron excitability was optogenetically manipulated and revealed a transient competitive process that integrates memories for events occurring closely in time (coallocating overlapping populations of neurons to both engrams) and separates memories for events occurring at distal times (disallocating nonoverlapping populations to each engram). Rashid et al Science 2016- Data for Figs 1-4, S1-S9Excel file with all data presented in manuscript (each sheet corresponds to specific figures as indicated).Rashid et al Science 2016.xlsx

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    Dataset . 2016
    Data sources: B2FIND
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      Dataset . 2016
      Data sources: B2FIND
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  • Authors: McKinnie, Shaun M. K.; Wang, Wang; Fischer, Conrad; McDonald, Tyler; +5 Authors

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures. Related Article: Shaun M. K. McKinnie, Wang Wang, Conrad Fischer, Tyler McDonald, Kevin R. Kalin, Xavier Iturrioz, Catherine Llorens-Cortes, Gavin Y. Oudit, and John C. Vederas|2017|J.Med.Chem.|60|6408|doi:10.1021/acs.jmedchem.7b00723

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  • Authors: Choudhary, Neha; Jaraquemada-Peláez, Marı́a de Guadalupe; Zarschler, Kristof; Wang, Xiaozhu; +4 Authors

    Related Article: Neha Choudhary, Marı́a de Guadalupe Jaraquemada-Peláez, Kristof Zarschler, Xiaozhu Wang, Valery Radchenko, Manja Kubeil, Holger Stephan, Chris Orvig|2020|Inorg.Chem.|59|5728|doi:10.1021/acs.inorgchem.0c00509

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    Authors: Bernhardt, Boris C.; Fadaie, Fatemeh; Liu, Min; Caldairou, Benoit; +6 Authors

    OBJECTIVE. To assess whether HS severity is mirrored at the level of large-scale networks. METHODS. We studied preoperative high-resolution anatomical and diffusion-weighted MRI of 44 TLE patients with histopathological diagnosis of HS (n=25; TLE-HS) and isolated gliosis (n=19; TLE-G), and 25 healthy controls. Hippocampal measurements included surface-based subfield mapping of atrophy and T2 hyperintensity indexing cell loss and gliosis, respectively. Whole-brain connectomes were generated via diffusion tractography and examined using graph theory along with a novel network control theory paradigm which simulates functional dynamics from structural network data. RESULTS. Compared to controls, we observed markedly increased path length and decreased clustering in TLE-HS compared to controls, indicating lower global and local network efficiency, while TLE-G showed only subtle alterations. Similarly, network controllability was lower in TLE-HS only, suggesting limited range of functional dynamics. Hippocampal imaging markers were positively associated with macroscale network alterations, particularly in ipsilateral CA1-3. Systematic assessment across several networks revealed maximal changes in the hippocampal circuity. Findings were consistent when correcting for cortical thickness, suggesting independence from grey matter atrophy. CONCLUSIONS. Severe HS is associated with marked remodeling of connectome topology and structurally-governed functional dynamics in TLE, as opposed to isolated gliosis which has negligible effects. Cell loss, particularly in CA1-3, may exert a cascading effect on brain-wide connectomes, underlining coupled disease processes across multiple scales. Data_phen_conn_dryadPhenotypic information and mean connectome feature data for Bernhardt et al. (2019) Temporal lobe epilepsy: hippocampal pathology modulates white matter connectome topology and controllability. Neurology

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    Dataset . 2019
    Data sources: B2FIND
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    ZENODO; DRYAD; NARCIS
    Dataset . 2019
    License: CC 0
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      Dataset . 2019
      Data sources: B2FIND
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      ZENODO; DRYAD; NARCIS
      Dataset . 2019
      License: CC 0
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    Authors: Zhan, Shing Hei; Drori, Michal; Goldberg, Emma E.; Otto, Sarah P.; +1 Authors

    Premise of the study: Polyploidization is a common and recurring phenomenon in plants and is often thought to be a mechanism of "instant speciation." Whether polyploidization is associated with the formation of new species ("cladogenesis") or simply occurs over time within a lineage ("anagenesis") has never, however, been assessed systematically. Methods: Here, we tested this hypothesis using phylogenetic and karyotypic information from 235 plant genera (mostly angiosperms). We first constructed a large database of combined sequence and chromosome number data sets using an automated procedure. We then applied likelihood models (ClaSSE) that estimate the degree of synchronization between polyploidization and speciation events in maximum likelihood and Bayesian frameworks. Key results: Our maximum likelihood analysis indicated that 35 genera supported a model that includes cladogenetic transitions over a model with only anagenetic transitions, whereas three genera supported a model that incorporates anagenetic transitions over one with only cladogenetic transitions. Furthermore, the Bayesian analysis supported a preponderance of cladogenetic change in four genera but did not support a preponderance of anagenetic change in any genus. Conclusions: Overall, these phylogenetic analyses provide the first broad confirmation that polyploidization is temporally associated with speciation events, suggesting that it is indeed a major speciation mechanism in plants, at least in some genera. PloiDBPhylogenetic trees inferred using MrBayes, ploidy estimates using ChromEvol, and TPL-based genus species diversity estimates for 223 genera.ploidb_dryad.tar.gz

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    Dataset . 2016
    Data sources: B2FIND
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    Borealis
    Dataset . 2021
    Data sources: Datacite
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      Dataset . 2016
      Data sources: B2FIND
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      Borealis
      Dataset . 2021
      Data sources: Datacite
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  • Authors: Choudhary, Neha; Scheiber, Hayden; Zhang, Jiale; Patrick, Brian O.; +2 Authors

    Related Article: Neha Choudhary, Hayden Scheiber, Jiale Zhang, Brian O. Patrick, María de Guadalupe Jaraquemada-Peláez, Chris Orvig|2021|Inorg.Chem.|60|12855|doi:10.1021/acs.inorgchem.1c01175

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    Authors: Dinesh Kumar, Barupal; Sili, Fan; Benjamin, Wancewicz; Tomas, Cajka; +7 Authors

    Alzheimer's disease (AD) is a major public health priority with a large socioeconomic burden and complex etiology. The Alzheimer Disease Metabolomics Consortium (ADMC) and the Alzheimer Disease Neuroimaging Initiative (ADNI) aim to gain new biological insights in the disease etiology. We report here an untargeted lipidomics of serum specimens of 806 subjects within the ADNI1 cohort (188 AD, 392 mild cognitive impairment and 226 cognitively normal subjects) along with 83 quality control samples. Lipids were detected and measured using an ultra-high-performance liquid chromatography quadruple/time-of-flight mass spectrometry (UHPLC-QTOF MS) instrument operated in both negative and positive electrospray ionization modes. The dataset includes a total 513 unique lipid species out of which 341 are known lipids. For over 95% of the detected lipids, a relative standard deviation of better than 20% was achieved in the quality control samples, indicating high technical reproducibility. Association modeling of this dataset and available clinical, metabolomics and drug-use data will provide novel insights into the AD etiology. These datasets are available at the ADNI repository at http://adni.loni.usc.edu/.

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    Europe PubMed Central
    Article . 2018
    Data sources: PubMed Central
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      Europe PubMed Central
      Article . 2018
      Data sources: PubMed Central
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  • Authors: Chitnis, Saurabh S.; Sparkes, Hazel A.; Annibale, Vincent T.; Pridmore, Natalie E.; +2 Authors

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures. Related Article: Saurabh S. Chitnis, Hazel A. Sparkes, Vincent T. Annibale, Natalie E. Pridmore, Alex M. Oliver, Ian Manners|2017|Angew.Chem.,Int.Ed.|56|9536|doi:10.1002/anie.201704991

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289 Research products
  • Authors: Wang, Xiaozhu; Jaraquemada-Peláez, María De Guadalupe; Rodríguez-Rodríguez, Cristina; Cao, Yang; +7 Authors

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures. Related Article: Xiaozhu Wang, María de Guadalupe Jaraquemada-Peláez, Cristina Rodríguez-Rodríguez, Yang Cao, Christian Buchwalder, Neha Choudhary, Una Jermilova, Caterina F. Ramogida, Katayoun Saatchi, Urs O. Häfeli, BrianO. P|2018|J.Am.Chem.Soc.|140|15487|doi:10.1021/jacs.8b09964

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  • Authors: Garai, Sumanta; Leo, Luciana M.; Szczesniak, Anna-Maria; Hurst, Dow P.; +14 Authors

    Related Article: Sumanta Garai, Luciana M. Leo, Anna-Maria Szczesniak, Dow P. Hurst, Peter C. Schaffer, Ayat Zagzoog, Tallan Black, Jeffrey R. Deschamps, Elke Miess, Stefan Schulz, David R. Janero, Alex Straiker, Roger G. Pertwee, Mary E. Abood, Melanie E. M. Kelly, Patricia H. Reggio, Robert B. Laprairie, Ganesh A. Thakur|2021|J.Med.Chem.|64|8104|doi:10.1021/acs.jmedchem.1c00040

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    Authors: Rashid, Asim J.; Yan, Chen; Mercaldo, Valentina; Hsiang, Hwa-Lin; +9 Authors

    Collections of cells called engrams are thought to represent memories. Although there has been progress in identifying and manipulating single engrams, little is known about how multiple engrams interact to influence memory. In lateral amygdala (LA), neurons with increased excitability during training outcompete their neighbors for allocation to an engram. We examined whether competition based on neuronal excitability also governs the interaction between engrams. Mice received two distinct fear conditioning events separated by different intervals. LA neuron excitability was optogenetically manipulated and revealed a transient competitive process that integrates memories for events occurring closely in time (coallocating overlapping populations of neurons to both engrams) and separates memories for events occurring at distal times (disallocating nonoverlapping populations to each engram). Rashid et al Science 2016- Data for Figs 1-4, S1-S9Excel file with all data presented in manuscript (each sheet corresponds to specific figures as indicated).Rashid et al Science 2016.xlsx

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    DANS-EASY
    Dataset . 2016
    Data sources: B2FIND
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      DANS-EASY
      Dataset . 2016
      Data sources: B2FIND
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  • Authors: McKinnie, Shaun M. K.; Wang, Wang; Fischer, Conrad; McDonald, Tyler; +5 Authors

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures. Related Article: Shaun M. K. McKinnie, Wang Wang, Conrad Fischer, Tyler McDonald, Kevin R. Kalin, Xavier Iturrioz, Catherine Llorens-Cortes, Gavin Y. Oudit, and John C. Vederas|2017|J.Med.Chem.|60|6408|doi:10.1021/acs.jmedchem.7b00723

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  • Authors: Choudhary, Neha; Jaraquemada-Peláez, Marı́a de Guadalupe; Zarschler, Kristof; Wang, Xiaozhu; +4 Authors

    Related Article: Neha Choudhary, Marı́a de Guadalupe Jaraquemada-Peláez, Kristof Zarschler, Xiaozhu Wang, Valery Radchenko, Manja Kubeil, Holger Stephan, Chris Orvig|2020|Inorg.Chem.|59|5728|doi:10.1021/acs.inorgchem.0c00509

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    Authors: Bernhardt, Boris C.; Fadaie, Fatemeh; Liu, Min; Caldairou, Benoit; +6 Authors

    OBJECTIVE. To assess whether HS severity is mirrored at the level of large-scale networks. METHODS. We studied preoperative high-resolution anatomical and diffusion-weighted MRI of 44 TLE patients with histopathological diagnosis of HS (n=25; TLE-HS) and isolated gliosis (n=19; TLE-G), and 25 healthy controls. Hippocampal measurements included surface-based subfield