cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1380304.v2
title: Spatio-temporal regulation of the human licensing factor Cdc6 in replication and mitosis

description: To maintain genome stability, the thousands of replication origins of mammalian genomes must only initiate replication once per cell cycle. This is achieved by a strict temporal separation of ongoing replication in S phase, and the formation of pre-replicative complexes in the preceding G1 phase, which "licenses" each origin competent for replication. The contribution of the loading factor Cdc6 to the timing of the licensing process remained however elusive due to seemingly contradictory findings concerning stabilization, degradation and nuclear export of Cdc6. Using fluorescently tagged Cdc6 (Cdc6-YFP) expressed in living cycling cells, we demonstrate here that Cdc6-YFP is stable and chromatin-associated during mitosis and G1 phase. It undergoes rapid proteasomal degradation during S phase initiation followed by active export to the cytosol during S and G2 phases. Biochemical fractionation abolishes this nuclear exclusion, causing aberrant chromatin association of Cdc6-YFP and, likely, endogenous Cdc6, too. In addition, we demonstrate association of Cdc6 with centrosomes in late G2 and during mitosis. These results show that multiple Cdc6-regulatory mechanisms coexist but are tightly controlled in a cell cycle-specific manner.
DOI: 10.6084/m9.figshare.1380112
title: Weaver Ant Nest Data

description: This dataset comprises of data associated with nests of the Asian weaver ant (<em>Oecophylla smaragdina</em>). It has details on the spatial location of weaver ant nests on different trees (in two different urban areas in India), along with information of nest characteristics, tree characteristics, and environmental variables.
DOI: 10.6084/m9.figshare.1380112.v1
title: Weaver Ant Nest Data

description: This dataset comprises of data associated with nests of the Asian weaver ant (<em>Oecophylla smaragdina</em>). It has details on the spatial location of weaver ant nests on different trees (in two different urban areas in India), along with information of nest characteristics, tree characteristics, and environmental variables.
DOI: 10.6084/m9.figshare.1380109
title: NG strains Genome Assembly

description: Assembly of NG strains: Ezewudo MN, Joseph SJ, Castillo-Ramirez S, Dean D, del Rio C, Didelot X, Dillon J, Selden RF, Shafer WM, Turingan RS, Unemo M, Read TD. (2015) Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance. PeerJ 3:e806
DOI: 10.6084/m9.figshare.1380304.v3
title: Spatio-temporal regulation of the human licensing factor Cdc6 in replication and mitosis

description: To maintain genome stability, the thousands of replication origins of mammalian genomes must only initiate replication once per cell cycle. This is achieved by a strict temporal separation of ongoing replication in S phase, and the formation of pre-replicative complexes in the preceding G1 phase, which "licenses" each origin competent for replication. The contribution of the loading factor Cdc6 to the timing of the licensing process remained however elusive due to seemingly contradictory findings concerning stabilization, degradation and nuclear export of Cdc6. Using fluorescently tagged Cdc6 (Cdc6-YFP) expressed in living cycling cells, we demonstrate here that Cdc6-YFP is stable and chromatin-associated during mitosis and G1 phase. It undergoes rapid proteasomal degradation during S phase initiation followed by active export to the cytosol during S and G2 phases. Biochemical fractionation abolishes this nuclear exclusion, causing aberrant chromatin association of Cdc6-YFP and, likely, endogenous Cdc6, too. In addition, we demonstrate association of Cdc6 with centrosomes in late G2 and during mitosis. These results show that multiple Cdc6-regulatory mechanisms coexist but are tightly controlled in a cell cycle-specific manner.
DOI: 10.6084/m9.figshare.1380085
title: Molluscan assemblages under the influence of peat-draining rivers off East Sumatra, Indonesia

description: The central Indo-west Pacific biodiversity hotspot is of outstanding biological interest in terms of both taxonomy and ecology. However, the molluscan fauna of the region is poorly known. Here we present death assemblages of the subtidal (1–56 m) waters off Eastern Sumatra, Indonesia. Molluscan shells were sampled from a variety of settings from estuaries to coral reef-related carbonate environments. A total of 5064 shells was counted and 197 species were identified. Four shelly death assemblages which are defined by characteristic taxa are found in specific environments. A deposit-feeding community with low diversity and low abundances was recorded in settings with high amounts of terrigenous mud. Greater abundances and higher diversity were found farther offshore, especially in carbonate sediments in the vicinity of offshore islands where pteriomorphian bivalves are characteristic taxa. Protobranch bivalves, especially a species of <i>Nuculana</i>, appear to be best adapted to the organic-rich but food-limited, muddy substrate of the proximal marine environment influenced by peat-draining rivers. Thus, in addition to dominating deep-sea molluscan assemblages, some protobranch bivalves appear to be specialists in exploiting refractory organic materials of shelf environments.
DOI: 10.6084/m9.figshare.1380109.v1
title: NG strains Genome Assembly

description: Assembly of NG strains: Ezewudo MN, Joseph SJ, Castillo-Ramirez S, Dean D, del Rio C, Didelot X, Dillon J, Selden RF, Shafer WM, Turingan RS, Unemo M, Read TD. (2015) Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance. PeerJ 3:e806
DOI: 10.6084/m9.figshare.1380013
title: Comparison of Single-Arm vs. Randomized Phase II Clinical Trials: A Bayesian Approach

description: Single-arm studies are typically used in phase II of clinical trials, whose main objective is to determine whether a new treatment warrants further testing in a randomized phase III trial. The introduction of randomization in phase II, to avoid the limits of studies based on historical controls, is a critical issue widely debated in the recent literature. We use a Bayesian approach to compare single-arm and randomized studies, based on a binary response variable, in terms of their abilities of reaching the correct decision about the new treatment, both when it performs better than the standard one and when it is less effective. We evaluate how the historical control rate, the total sample size, and the elicitation of the prior distributions affect the decision about which study performs better.
DOI: 10.6084/m9.figshare.1380001
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1380085.v1
title: Molluscan assemblages under the influence of peat-draining rivers off East Sumatra, Indonesia

description: The central Indo-west Pacific biodiversity hotspot is of outstanding biological interest in terms of both taxonomy and ecology. However, the molluscan fauna of the region is poorly known. Here we present death assemblages of the subtidal (1–56 m) waters off Eastern Sumatra, Indonesia. Molluscan shells were sampled from a variety of settings from estuaries to coral reef-related carbonate environments. A total of 5064 shells was counted and 197 species were identified. Four shelly death assemblages which are defined by characteristic taxa are found in specific environments. A deposit-feeding community with low diversity and low abundances was recorded in settings with high amounts of terrigenous mud. Greater abundances and higher diversity were found farther offshore, especially in carbonate sediments in the vicinity of offshore islands where pteriomorphian bivalves are characteristic taxa. Protobranch bivalves, especially a species of <i>Nuculana</i>, appear to be best adapted to the organic-rich but food-limited, muddy substrate of the proximal marine environment influenced by peat-draining rivers. Thus, in addition to dominating deep-sea molluscan assemblages, some protobranch bivalves appear to be specialists in exploiting refractory organic materials of shelf environments.
DOI: 10.6084/m9.figshare.1380001.v1
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1380013.v1
title: Comparison of Single-Arm vs. Randomized Phase II Clinical Trials: A Bayesian Approach

description: Single-arm studies are typically used in phase II of clinical trials, whose main objective is to determine whether a new treatment warrants further testing in a randomized phase III trial. The introduction of randomization in phase II, to avoid the limits of studies based on historical controls, is a critical issue widely debated in the recent literature. We use a Bayesian approach to compare single-arm and randomized studies, based on a binary response variable, in terms of their abilities of reaching the correct decision about the new treatment, both when it performs better than the standard one and when it is less effective. We evaluate how the historical control rate, the total sample size, and the elicitation of the prior distributions affect the decision about which study performs better.
DOI: 10.6084/m9.figshare.1379989
title: Ethyl mercury induces Ca<sup>2+</sup> uptake through the P2×7 receptor in a mouse cerebellar microglia cell line

description: Many observations are reported that organic mercury compounds are involved in increasing intracellular Ca<sup>2+</sup> levels. However, the issue of which substances on the cell membrane participate in the Ca<sup>2+</sup> uptake that is induced by ethyl mercury is unclear. The findings of this study suggest that the P2X receptor participates in this process. The uptake of Ca<sup>2+</sup> by C8-B4 cells was induced in the presence of ethyl mercury. Ca channels in the cell membrane were not affected in this process. In contrast, pretreatment with suramin, an antagonist of the P2X receptor, inhibited the Ca<sup>2+</sup> uptake induced by ethyl mercury, and also brilliant blue G, a nonselective antagonist of P2×4, P2×5, and P2×7 receptors. In addition, A438079 and A740003, selective antagonists of P2×7 receptor, reduced Ca<sup>2+</sup> uptake, while 5-BDBD, a selective antagonist of P2×4 receptor, did not. Furthermore, the mRNAs of both the P2×4 and P2×7 receptors were expressed in the presence of ethyl mercury, but the P2×5 receptor mRNA was not. These findings suggest that ethyl mercury may induce Ca<sup>2+</sup> uptake through the P2×7 receptor of the cell membrane.
DOI: 10.6084/m9.figshare.1380085.v3
title: Molluscan assemblages under the influence of peat-draining rivers off East Sumatra, Indonesia

description: The central Indo-west Pacific biodiversity hotspot is of outstanding biological interest in terms of both taxonomy and ecology. However, the molluscan fauna of the region is poorly known. Here we present death assemblages of the subtidal (1–56 m) waters off Eastern Sumatra, Indonesia. Molluscan shells were sampled from a variety of settings from estuaries to coral reef-related carbonate environments. A total of 5064 shells was counted and 197 species were identified. Four shelly death assemblages which are defined by characteristic taxa are found in specific environments. A deposit-feeding community with low diversity and low abundances was recorded in settings with high amounts of terrigenous mud. Greater abundances and higher diversity were found farther offshore, especially in carbonate sediments in the vicinity of offshore islands where pteriomorphian bivalves are characteristic taxa. Protobranch bivalves, especially a species of <i>Nuculana</i>, appear to be best adapted to the organic-rich but food-limited, muddy substrate of the proximal marine environment influenced by peat-draining rivers. Thus, in addition to dominating deep-sea molluscan assemblages, some protobranch bivalves appear to be specialists in exploiting refractory organic materials of shelf environments.
DOI: 10.6084/m9.figshare.1380085.v2
title: Molluscan assemblages under the influence of peat-draining rivers off East Sumatra, Indonesia

description: The central Indo-west Pacific biodiversity hotspot is of outstanding biological interest in terms of both taxonomy and ecology. However, the molluscan fauna of the region is poorly known. Here we present death assemblages of the subtidal (1–56 m) waters off Eastern Sumatra, Indonesia. Molluscan shells were sampled from a variety of settings from estuaries to coral reef-related carbonate environments. A total of 5064 shells was counted and 197 species were identified. Four shelly death assemblages which are defined by characteristic taxa are found in specific environments. A deposit-feeding community with low diversity and low abundances was recorded in settings with high amounts of terrigenous mud. Greater abundances and higher diversity were found farther offshore, especially in carbonate sediments in the vicinity of offshore islands where pteriomorphian bivalves are characteristic taxa. Protobranch bivalves, especially a species of <i>Nuculana</i>, appear to be best adapted to the organic-rich but food-limited, muddy substrate of the proximal marine environment influenced by peat-draining rivers. Thus, in addition to dominating deep-sea molluscan assemblages, some protobranch bivalves appear to be specialists in exploiting refractory organic materials of shelf environments.
DOI: 10.6084/m9.figshare.1379989.v2
title: Ethyl mercury induces Ca<sup>2+</sup> uptake through the P2×7 receptor in a mouse cerebellar microglia cell line

description: Many observations are reported that organic mercury compounds are involved in increasing intracellular Ca<sup>2+</sup> levels. However, the issue of which substances on the cell membrane participate in the Ca<sup>2+</sup> uptake that is induced by ethyl mercury is unclear. The findings of this study suggest that the P2X receptor participates in this process. The uptake of Ca<sup>2+</sup> by C8-B4 cells was induced in the presence of ethyl mercury. Ca channels in the cell membrane were not affected in this process. In contrast, pretreatment with suramin, an antagonist of the P2X receptor, inhibited the Ca<sup>2+</sup> uptake induced by ethyl mercury, and also brilliant blue G, a nonselective antagonist of P2×4, P2×5, and P2×7 receptors. In addition, A438079 and A740003, selective antagonists of P2×7 receptor, reduced Ca<sup>2+</sup> uptake, while 5-BDBD, a selective antagonist of P2×4 receptor, did not. Furthermore, the mRNAs of both the P2×4 and P2×7 receptors were expressed in the presence of ethyl mercury, but the P2×5 receptor mRNA was not. These findings suggest that ethyl mercury may induce Ca<sup>2+</sup> uptake through the P2×7 receptor of the cell membrane.
DOI: 10.6084/m9.figshare.1379976
title: 0-back/1-back fMRI study

description: Dataset of data output from the PsychoPy task used in the fMRI study. There are 2 files for each subject because each performed 2 functional runs of the task.
DOI: 10.6084/m9.figshare.1379982
title: Image database

description: Images, Maps, GIS images
DOI: 10.6084/m9.figshare.1379989.v1
title: Ethyl mercury induces Ca<sup>2+</sup> uptake through the P2×7 receptor in a mouse cerebellar microglia cell line

description: Many observations are reported that organic mercury compounds are involved in increasing intracellular Ca<sup>2+</sup> levels. However, the issue of which substances on the cell membrane participate in the Ca<sup>2+</sup> uptake that is induced by ethyl mercury is unclear. The findings of this study suggest that the P2X receptor participates in this process. The uptake of Ca<sup>2+</sup> by C8-B4 cells was induced in the presence of ethyl mercury. Ca channels in the cell membrane were not affected in this process. In contrast, pretreatment with suramin, an antagonist of the P2X receptor, inhibited the Ca<sup>2+</sup> uptake induced by ethyl mercury, and also brilliant blue G, a nonselective antagonist of P2×4, P2×5, and P2×7 receptors. In addition, A438079 and A740003, selective antagonists of P2×7 receptor, reduced Ca<sup>2+</sup> uptake, while 5-BDBD, a selective antagonist of P2×4 receptor, did not. Furthermore, the mRNAs of both the P2×4 and P2×7 receptors were expressed in the presence of ethyl mercury, but the P2×5 receptor mRNA was not. These findings suggest that ethyl mercury may induce Ca<sup>2+</sup> uptake through the P2×7 receptor of the cell membrane.
DOI: 10.6084/m9.figshare.1379976.v1
title: 0-back/1-back fMRI study

description: Dataset of data output from the PsychoPy task used in the fMRI study. There are 2 files for each subject because each performed 2 functional runs of the task.
DOI: 10.6084/m9.figshare.1379935
title: 0-back/1-back behavioral study

description: Dataset of data output from the PsychoPy task used for our behavioral study.
DOI: 10.6084/m9.figshare.1379935.v1
title: 0-back/1-back behavioral study

description: Dataset of data output from the PsychoPy task used for our behavioral study.
DOI: 10.6084/m9.figshare.1379982.v1
title: Images

description: Images, Maps, GIS images
DOI: 10.6084/m9.figshare.1379982.v3
title: Image database

description: Images, Maps, GIS images
DOI: 10.6084/m9.figshare.1379982.v2
title: Images

description: Images, Maps, GIS images
DOI: 10.6084/m9.figshare.1379899
title: Interactive streamgraph visualization of measles cases over the 20th Century

description: These are the data files used to produce an interactive streamgraph visualization of the mean weekly number of measles cases over the 20th century in US states, highlighting the dramatic impact that introducung the measles vaccine had on the case rate from this dreadful disease.
DOI: 10.6084/m9.figshare.1379874
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1379877
title: Data from: Identifying effective actions to guide volunteer-based and nation-wide conservation efforts for a ground-nesting farmland bird

description: The two excel files contain the original data on nest survey information used for analyses and pixel level values presented in figure 4 of Santangeli et al. (2015). Each file contains a sheet with the data and a sheet with description of the data.
DOI: 10.6084/m9.figshare.1379874.v1
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1379877.v1
title: Data from: Identifying effective actions to guide volunteer-based and nation-wide conservation efforts for a ground-nesting farmland bird

description: The two excel files contain the original data on nest survey information used for analyses and pixel level values presented in figure 4 of Santangeli et al. (2015). Each file contains a sheet with the data and a sheet with description of the data.
DOI: 10.6084/m9.figshare.1379859
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1379846
title: University of Southampton APCs 2014-15 (Aug-June)

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Southampton during the period 1 August 2014 to 30 June 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/) and has been released with permission of the University of Southampton Library. <strong>UPDATE 05/08/2015</strong>: Data added for April-June 2015.
DOI: 10.6084/m9.figshare.1379832
title: Corpus of Soqotri Oral Literature

description: <em>The Corpus of Soqotri Oral Literature</em> is a unique source of grammatical, lexical and folkloristic data about the extremely archaic, yet heavily understudied, Modern South Arabian language Soqotri (island Soqotra, Gulf of Aden, Yemen).
DOI: 10.6084/m9.figshare.1379859.v1
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1379803
title: GigaDB schema update to accommodate the growing variety of data.

description: GigaScience (http://www.gigasciencejournal.com) is an online, open-access journal that includes, as part of its publishing activities, the database GigaDB (http://www.gigadb.org). GigaScience is co-published in collaboration between BGI and BioMed Central, to meet the needs of a new generation of biological and biomedical research as it enters the era of “big-data.” The journal’s scope covers studies from the entire spectrum of the life sciences that produce and use large-scale data as the center of their work. Data from these articles are hosted in GigaDB, from where they can be cited to provide a direct link between the study and the data supporting it, as well as access to relevant tools for reproducing or reusing these data. Due to the scope of GigaScience, GigaDB needs to host a wider variety of data type than most biological databases. In order to make this possible, we have created and launched a new version of GigaDB that now uses a fully extensible database schema capable of handling this variety of data types and standards. The schema has 3 main areas, centered around these tables: Dataset Sample Data/File These are roughly analogous to those used by other common systems for submitting /curating biological data, including the SRA (http://www.ebi.ac.uk/ena/submit/metadata-model), and the ISA infrastructure (http://isatab.sourceforge.net/format.html). The dataset part includes tables to store information about the overall study design, the authors and funding bodies. It also acts as a holder to link together all the samples and data associated with it, as well as providing links to external sources. The Sample area of the schema plays host to the sample metadata and sample relationships, including their relationship to particular data files. Here we present the schema, and in an poster we show how it is implemented for metadata capture in our Submission Wizard.
DOI: 10.6084/m9.figshare.1379832.v1
title: Corpus of Soqotri Oral Literature

description: <em>The Corpus of Soqotri Oral Literature</em> is a unique source of grammatical, lexical and folkloristic data about the extremely archaic, yet heavily understudied, Modern South Arabian language Soqotri (island Soqotra, Gulf of Aden, Yemen).
DOI: 10.6084/m9.figshare.1379846.v2
title: University of Southampton APCs 2014-15 (Aug-June)

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Southampton during the period 1 August 2014 to 30 June 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/) and has been released with permission of the University of Southampton Library. <strong>UPDATE 05/08/2015</strong>: Data added for April-June 2015.
DOI: 10.6084/m9.figshare.1379783
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1379784
title: Gaussian Job Archive for C6H6Br6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.