cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12851525.v1
title: RanBP1 controls the Ran pathway in mammalian cells through regulation of mitotic RCC1 dynamics

description: The Ran GTPase plays critical roles in multiple cellular processes including interphase nucleocytoplasmic transport and mitotic spindle assembly. During mitosis in mammalian cells, GTP-bound Ran (Ran-GTP) is concentrated near mitotic chromatin while GDP-bound Ran (Ran-GDP) is more abundant distal to chromosomes. This pattern spatially controls spindle formation because Ran-GTP locally releases spindle assembly factors (SAFs), such as Hepatoma Up-Regulated Protein (HURP), from inhibitory interactions near chromosomes. Regulator of Chromatin Condensation 1 (RCC1) is Ran’s chromatin-bound exchange factor, and RanBP1 is a conserved Ran-GTP-binding protein that has been implicated as a mitotic regulator of RCC1 in embryonic systems. Here, we show that RanBP1 controls mitotic RCC1 dynamics in human somatic tissue culture cells. In addition, we observed the re-localization of HURP in metaphase cells after RanBP1 degradation, consistent with the idea that altered RCC1 dynamics functionally modulate SAF activities. Together, our findings reveal an important mitotic role for RanBP1 in human somatic cells, controlling the spatial distribution and magnitude of mitotic Ran-GTP production and thereby ensuring the accurate execution of Ran-dependent mitotic events. AID: Auxin-induced degron; FLIP: Fluorescence loss in photobleaching; FRAP: Fluorescence recovery after photobleaching; GDP: guanosine diphosphate; GTP: guanosine triphosphate; HURP: Hepatoma Up-Regulated Protein; NE: nuclear envelope; NEBD: Nuclear Envelope Breakdown; RanBP1: Ran-binding protein 1; RanGAP1: Ran GTPase-Activating Protein 1; RCC1: Regulator of Chromatin Condensation 1; RRR complex: RCC1/Ran/RanBP1 heterotrimeric complex; SAF: Spindle Assembly Factor; TIR1: Transport Inhibitor Response 1 protein; XEE: Xenopus egg extract.
DOI: 10.6084/m9.figshare.14109842
title: Crossmodal Correspondence Between Auditory Timbre and Visual Shape: Semantic Task ANOVAs, Tables, and Figures

description: This document contains supplementary data for the project entitled "Crossmodal Correspondence Between Auditory Timbre and Visual Shape". This data is from the Semantic Differential task used to assess participants' perceived meaning of stimuli. Twelve 4x6 ANOVAs (4 base stimuli x 6 transformations per stimuli) are presented, one sound ANOVA and one shape ANOVA for each of the 6 rating scales. Additionally, 12 interactions tables and 12 corresponding figures are presented. Six of these tables/figures show the interaction between base shape and transformation on each scale while the other 6 show the interaction between base sound and transformation on each scale. Finally, brief descriptions of the pattern of results are included.
DOI: 10.6084/m9.figshare.14109842.v5
title: Crossmodal Correspondence Between Auditory Timbre and Visual Shape: Semantic Task ANOVAs, Tables, and Figures

description: This document contains supplementary data for the project entitled "Crossmodal Correspondence Between Auditory Timbre and Visual Shape". This data is from the Semantic Differential task used to assess participants' perceived meaning of stimuli. Twelve 4x6 ANOVAs (4 base stimuli x 6 transformations per stimuli) are presented, one sound ANOVA and one shape ANOVA for each of the 6 rating scales. Additionally, 12 interactions tables and 12 corresponding figures are presented. Six of these tables/figures show the interaction between base shape and transformation on each scale while the other 6 show the interaction between base sound and transformation on each scale. Finally, brief descriptions of the pattern of results are included.
DOI: 10.6084/m9.figshare.14109842.v4
title: Crossmodal Correspondence Between Auditory Timbre and Visual Shape: Semantic Task ANOVAs, Tables, and Figures

description: This document contains supplementary data for the project entitled "Crossmodal Correspondence Between Auditory Timbre and Visual Shape". This data is from the Semantic Differential task used to assess participants' perceived meaning of stimuli. Twelve 4x6 ANOVAs (4 base stimuli x 6 transformations per stimuli) are presented, one sound ANOVA and one shape ANOVA for each of the 6 rating scales. Additionally, 12 interactions tables and 12 corresponding figures are presented. Six of these tables/figures show the interaction between base shape and transformation on each scale while the other 6 show the interaction between base sound and transformation on each scale. Finally, brief descriptions of the pattern of results are included.
DOI: 10.6084/m9.figshare.11413395.v1
title: Scaling Spatial Pattern Metrics: Data and Downscaling Code

description: The QRule_NeutralModels.zip dataset contains 37,620 binary rasters generated from the software QRule (https://www.umces.edu/qrule). Each raster (landscape) is a 512x512 raster. Each landscape was generated using one of 19 proportion values (P), where P ranges [5,95] in increments of 5. Each landscape was generated using one of 20 H values, where H ranges [0,95] in increments of 5. There are 380 unique P-H combinations, and we generated 99 repetitions of each for a total of 37,620 landscapes.<br>computeDownscaledMetrics.m is Matlab code for fitting scaling functions, downscaling those functions to predict values at 30 m resolution, and comparing predicted values to true values computed directly from the neutral model landscapes. The NeutralModels.xlsx contains a set of sample data for running the Matlab code.
DOI: 10.6084/m9.figshare.11413395
title: Scaling Spatial Pattern Metrics: Data and Downscaling Code

description: The QRule_NeutralModels.zip dataset contains 37,620 binary rasters generated from the software QRule (https://www.umces.edu/qrule). Each raster (landscape) is a 512x512 raster. Each landscape was generated using one of 19 proportion values (P), where P ranges [5,95] in increments of 5. Each landscape was generated using one of 20 H values, where H ranges [0,95] in increments of 5. There are 380 unique P-H combinations, and we generated 99 repetitions of each for a total of 37,620 landscapes.<br>computeDownscaledMetrics.m is Matlab code for fitting scaling functions, downscaling those functions to predict values at 30 m resolution, and comparing predicted values to true values computed directly from the neutral model landscapes. The NeutralModels.xlsx contains a set of sample data for running the Matlab code.
DOI: 10.25919/0crn-s711
title: Parkes observations for project P1054 semester 2021APRS_12

description: With this proposal we ask time for a timing follow-up campaign of the first 5 mllisecond pulsars discovered in the TRAPUM (TRAnsients and PUlsars with Meerkat) survey. The sources have been detected in targeted observations of Fermi unidentified point sources. At least two of the new pulsars belong to binary systems and an initial orbital period of 8.5 hrs has already been estimated for the brightest source. Timing observations have an essential role in exploiting the full potential of any pulsar discovery, allowing the precise measurement of rotational, astrometric and orbital parameters which, in turn, give us powerful tools to improve our understanding of the physics in extreme environments as well as of the population of neutron stars as a whole. The UWL receiver of the Parkes telescope is a sensitive, versatile instrument that will allow us to successfully time these new sources, in the bright-end of TRAPUM discoveries. The UWL has also the unique advantage of allowing detailed studies of the eclipses of the so-called 'spider' pulsars, the vast majority of which have an associated Fermi counterpart.
DOI: 10.6084/m9.figshare.12851567.v2
title: TRIM71 binds to IMP1 and is capable of positive and negative regulation of target RNAs

description: TRIM71 is an important RNA-binding protein in development and disease, yet its direct targets have not been investigated globally. Here we describe a number of disease and developmentally-relevant TRIM71 RNA targets such as the <i>MBNL</i> family, <i>LIN28B, MDM2</i>, and <i>TCF7L2</i>. We describe a new role for TRIM71 as capable of positive or negative RNA regulation depending on the RNA target. We found that TRIM71 co-precipitated with IMP1 which could explain its multiple mechanisms of RNA regulation, as IMP1 is typically thought to stabilize RNAs. Deletion of the NHL domain of TRIM71 impacted its ability to bind to RNA and RNAs bound by congenital hydrocephalus-associated point mutations in the RNA-binding NHL domain of TRIM71 clustered closely with RNAs bound by the NHL deletion mutant. Our work expands the possible mechanisms by which TRIM71 may regulate RNAs and elucidates further potential RNA targets.
DOI: 10.6084/m9.figshare.16640113
title: K.O. Maeno et al., 2021

description: Density-dependent mating behaviors reduce male mating harassment in locusts
DOI: 10.6084/m9.figshare.16640113.v1
title: K.O. Maeno et al., 2021

description: Density-dependent mating behaviors reduce male mating harassment in locusts
DOI: 10.5281/zenodo.5563130
title: Parastichopus regalis decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5563129
title: Parastichopus regalis decontaminated FSCR

description: .
DOI: 10.6084/m9.figshare.12851486
title: Thrombospondin-1 counteracts the p97 inhibitor CB-5083 in colon carcinoma cells

description: p97 has recently emerged as a therapeutic target for cancer due to its essential functions in protein homeostasis. CB-5083 is a first-in-class, potent and selective ATP-competitive p97 inhibitor that induces proteotoxic stress in cancer cells. Potential mechanisms regulating the sensitivity of cells to p97 inhibition remain poorly studied. Here, we demonstrate that Thrombospondin-1 (THBS1) is a CB-5083-upregulated gene that helps confer resistance of HCT116 cells to CB-5083. Our immunoblotting and immunofluorescence data showed that CB-5083 significantly increases the steady-state abundance of THBS1. Blockade of THBS1 induction sensitized cells to CB-5083-mediated growth inhibition. Suppression of THBS1 caused an increase of CB-5083-induced sub-G1 population and caspase 3/7 activity suggesting that its function is linked to the survival of cancer cells in response to p97 inhibition. Altogether our data provide new evidence that THBS1 is important for the susceptibility of cells to p97 inhibition.
DOI: 10.6084/m9.figshare.12851486.v2
title: Thrombospondin-1 counteracts the p97 inhibitor CB-5083 in colon carcinoma cells

description: p97 has recently emerged as a therapeutic target for cancer due to its essential functions in protein homeostasis. CB-5083 is a first-in-class, potent and selective ATP-competitive p97 inhibitor that induces proteotoxic stress in cancer cells. Potential mechanisms regulating the sensitivity of cells to p97 inhibition remain poorly studied. Here, we demonstrate that Thrombospondin-1 (THBS1) is a CB-5083-upregulated gene that helps confer resistance of HCT116 cells to CB-5083. Our immunoblotting and immunofluorescence data showed that CB-5083 significantly increases the steady-state abundance of THBS1. Blockade of THBS1 induction sensitized cells to CB-5083-mediated growth inhibition. Suppression of THBS1 caused an increase of CB-5083-induced sub-G1 population and caspase 3/7 activity suggesting that its function is linked to the survival of cancer cells in response to p97 inhibition. Altogether our data provide new evidence that THBS1 is important for the susceptibility of cells to p97 inhibition.
DOI: 10.6084/m9.figshare.12851486.v1
title: Thrombospondin-1 counteracts the p97 inhibitor CB-5083 in colon carcinoma cells

description: p97 has recently emerged as a therapeutic target for cancer due to its essential functions in protein homeostasis. CB-5083 is a first-in-class, potent and selective ATP-competitive p97 inhibitor that induces proteotoxic stress in cancer cells. Potential mechanisms regulating the sensitivity of cells to p97 inhibition remain poorly studied. Here, we demonstrate that Thrombospondin-1 (THBS1) is a CB-5083-upregulated gene that helps confer resistance of HCT116 cells to CB-5083. Our immunoblotting and immunofluorescence data showed that CB-5083 significantly increases the steady-state abundance of THBS1. Blockade of THBS1 induction sensitized cells to CB-5083-mediated growth inhibition. Suppression of THBS1 caused an increase of CB-5083-induced sub-G1 population and caspase 3/7 activity suggesting that its function is linked to the survival of cancer cells in response to p97 inhibition. Altogether our data provide new evidence that THBS1 is important for the susceptibility of cells to p97 inhibition.
DOI: 10.5517/ccdc.csd.cc28xrsr
title: CCDC 2113015: Experimental Crystal Structure Determination

description: Related Article: J. G. Malecki|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc28xxz3
title: CCDC 2113176: Experimental Crystal Structure Determination

description: Related Article: J. G. Malecki|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc28y4x9
title: CCDC 2113391: Experimental Crystal Structure Determination

description: Related Article: Brian W. Skelton, Effendy, Allan H. White|2021|CSD Communication|||
DOI: 10.6084/m9.figshare.12851555
title: Dynamic pattern of histone H3 core acetylation in human early embryos

description: After fertilization, highly differentiated sperm and oocyte are reprogrammed to totipotent embryo, which subsequently cleavages and develops into an individual through spatial-temporal differentiation. Histone modifications play critical roles to coordinate with other reprogramming events in early stages of embryogenesis. However, most of studies focus on modifications at N-terminus of histones, those at nucleosome core were not well understood. Here, we characterize the three key acetylation events in the histone H3 core, H3K56/K64/K122ac, in early human embryos. The three residues localize at DNA entry-exit position of the nucleosome. Globally, H3K56ac, H3K64ac and H3K122ac were detectable throughout preimplantation stages, with H3K64ac levels being relatively stronger and H3K122ac levels being much weaker. Besides, H3K56ac level had a peak at two-cell stage. Moreover, we found that LINEs also peak at two-cell stage, and H3K56ac was enriched at young LINE-1 in human ESCs, supporting that H3K56ac is an important driving force for young LINE-1 activation in human preimplantation embryos. Our results suggest that acetylation in the nucleosome core of histone H3 is dynamic and various during preimplantation development, and may drive diverse chromatin remodeling events in this developmental window.
DOI: 10.6084/m9.figshare.12851555.v2
title: Dynamic pattern of histone H3 core acetylation in human early embryos

description: After fertilization, highly differentiated sperm and oocyte are reprogrammed to totipotent embryo, which subsequently cleavages and develops into an individual through spatial-temporal differentiation. Histone modifications play critical roles to coordinate with other reprogramming events in early stages of embryogenesis. However, most of studies focus on modifications at N-terminus of histones, those at nucleosome core were not well understood. Here, we characterize the three key acetylation events in the histone H3 core, H3K56/K64/K122ac, in early human embryos. The three residues localize at DNA entry-exit position of the nucleosome. Globally, H3K56ac, H3K64ac and H3K122ac were detectable throughout preimplantation stages, with H3K64ac levels being relatively stronger and H3K122ac levels being much weaker. Besides, H3K56ac level had a peak at two-cell stage. Moreover, we found that LINEs also peak at two-cell stage, and H3K56ac was enriched at young LINE-1 in human ESCs, supporting that H3K56ac is an important driving force for young LINE-1 activation in human preimplantation embryos. Our results suggest that acetylation in the nucleosome core of histone H3 is dynamic and various during preimplantation development, and may drive diverse chromatin remodeling events in this developmental window.
DOI: 10.6084/m9.figshare.12851555.v1
title: Dynamic pattern of histone H3 core acetylation in human early embryos

description: After fertilization, highly differentiated sperm and oocyte are reprogrammed to totipotent embryo, which subsequently cleavages and develops into an individual through spatial-temporal differentiation. Histone modifications play critical roles to coordinate with other reprogramming events in early stages of embryogenesis. However, most of studies focus on modifications at N-terminus of histones, those at nucleosome core were not well understood. Here, we characterize the three key acetylation events in the histone H3 core, H3K56/K64/K122ac, in early human embryos. The three residues localize at DNA entry-exit position of the nucleosome. Globally, H3K56ac, H3K64ac and H3K122ac were detectable throughout preimplantation stages, with H3K64ac levels being relatively stronger and H3K122ac levels being much weaker. Besides, H3K56ac level had a peak at two-cell stage. Moreover, we found that LINEs also peak at two-cell stage, and H3K56ac was enriched at young LINE-1 in human ESCs, supporting that H3K56ac is an important driving force for young LINE-1 activation in human preimplantation embryos. Our results suggest that acetylation in the nucleosome core of histone H3 is dynamic and various during preimplantation development, and may drive diverse chromatin remodeling events in this developmental window.
DOI: 10.17632/vhswhkdjkn.1
title: Data for: Low-temperature preparation achieving 10.95 %-efficiency of hole-free and carbon-based all-inorganic CsPbI3 perovskite solar cells

description: I-V for the solar cell with the best performance
DOI: 10.17632/m4knvrw7jf.1
title: Metagenomic dataset of Wedge-tailed shearwater (Ardenna pacifica)

description: A cutaneous tissue sample was collected from Wedge-tailed shearwater originating from Lord Howe Island, New South Wales (ID:15-1526, year of sampling: 2015, GPS location: 32.53° S, 159.08° E). The sample was collected with the permission of the Lord Howe Island Board (permit no. LHIB 02/14) under the approval of the University of Tasmania and Charles Sturt University Animal Ethics Committees (permit no. A0010874, A0011586, and 09/046). The genomic DNA was isolated according to our previously established protocol (Sarker et al., 2017) using the Qiagen Blood and Tissue mini kit (Qiagen, Germany). The extracted DNA has been stored at -20 °C at Charles Sturt University. The library preparation and sequencing was performed as previously described (Sarker et al., 2017) and cite SW1 paper. Sequencing data used in this study were analysed according to the previously established pipeline (Sarker et al., 2017; Sarker et al., 2019a; Sarker et al., 2019b) cite SW1 paper using Geneious (version 10.2.2, Biomatters, New Zealand) and CLC Genomics Workbench (version 9.5.4). Briefly, a total of 15.36 million reads with a read length of 150 bp was used to obtain the complete mitogenome of A. pacifica.
DOI: 10.17632/t78p5tgvrc.1
title: Metagenomic dataset of flesh-footed shearwater (Ardenna carneipes)

description: Source of sampling and extraction of DNA

A cutaneous tissue sample was collected from Flesh-footed Shearwater originating from Lord Howe Island, New South Wales, located approximately 500 km off the east coast of Australia during April 2015 (sample ID15-1527, GPS location: 32.53° S, 159.08° E). The sample was collected with the permission of the Lord Howe Island Board (permit no. LHIB 02/14) under the approval of the University of Tasmania and Charles Sturt University Animal Ethics Committees (permit no. A0010874, A0011586, and 09/046). The genomic DNA was isolated according to our previously established protocol (Sarker et al., 2017) using the Qiagen Blood and Tissue mini kit (Qiagen, Germany). The extracted DNA has been stored at -20 °C for further testing at Charles Sturt University. 

Sequencing, assembly and annotation of complete mitogenome of A. carneipes 
The library preparation and sequencing was performed as previously described (Sarker et al., 2017). Briefly, the paired-end library with an insert size of 150 bp was prepared using the Illumina paired-end sample preparation kit (Illumina, San Diego, CA) according to the manufacturer's instructions. Sequencing of the pooled DNA-library was performed on a HiSeq4000 sequencing platform (Illumina) according to the manufacturer’s instructions by Novogene, China. Sequencing data used in this study were analysed according to the previously established pipeline (Sarker et al., 2017; Sarker et al., 2019a; Sarker et al., 2019b) using Geneious (version 10.2.2, Biomatters, New Zealand) and CLC Genomics Workbench (version 9.5.4). Briefly, a total of 14.42 million reads with a read length of 150 bp was used to obtain the complete mitochondrial genome of A. carneipes.
DOI: 10.3886/e140701v3-98600
title: 2021 COVID-19 Vaccine Attitudes among People Experiencing Homelessness in Los Angeles, CA

description: This is a limited dataset from a pilot mobile survey of attitudes and behaviors surrounding COVID-19, including vaccine attitudes, among people experiencing homelessness in Los Angeles, CA. The dataset includes basic demographic data (including age, race, sex, and housing status), COVID-19 protective behaviors, COVID-19 threat perception, trusted news sources, COVID-19 vaccination status and attitudes, and depression status (as measured by PHQ-4). Baseline demographic data was collected in November 2020 - January 2021. Data for variables relating to COVID-19 and depression status was collected February 2021, which was the 3rd wave of monthly data collection from this survey.
description: Convenience sample of individuals flagged as homeless in the records of Venice Family Clinic, a Federally Qualified Health Center in West Los Angeles, CA.
description: People experiencing homelessness &gt;=18 years old in Los Angeles, CA.
description: web-based survey; Data was collected through mobile survey answered directly by respondents (people experiencing homelessness in Los Angeles, CA)
DOI: 10.5281/zenodo.5563139
title: Water Cluster Electron Density Database

description: This database contains electron densities represented in the def2-universal-JFIT atom centered basis for select members of the Database of Water Cluster Minima from Rakshit and co-workers. All densities are projected from the one particle reduced density matrix with the total number of electrons constrained to the correct number. See attached description for details.
DOI: 10.5281/zenodo.5563138
title: Water Cluster Electron Density Database

description: This database contains electron densities represented in the def2-universal-JFIT atom centered basis for select members of the Database of Water Cluster Minima from Rakshit and co-workers. All densities are projected from the one particle reduced density matrix with the total number of electrons constrained to the correct number. See attached description for details.
DOI: 10.6084/m9.figshare.16786528
title: Isolation of Rhodococcus equi from the gastrointestinal contents of earthworms (family Megascolecidae)

description: <i>Rhodococcus equi </i>is Gram-positive, soil-dwelling pathogenic bacteria that cause pulmonary and extra pulmonary pyogranulomatous infections in various animal species and humans. This study showed that <i>R. equi</i> could multiply in the gastrointestinal contents of earthworms, suggesting that they act as an amplifier of <i>R. equi</i> in soil environments and as a source, reservoir, or both of the infection.
DOI: 10.6084/m9.figshare.16786504
title: Data for "Maternal high-fat diet in mice induces cerebrovascular, microglial and long-term behavioural alterations in offspring"

description: Clariom<sup>TM</sup>S microarray data obtained for normal and high fat diet. See file "Info Samples.xlsx" for details. <br>To be published in the Communications Biology journal.