cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5537239.v1
title: Lithium-induced gene expression alterations in two peripheral cell models of bipolar disorder

description: <b>Objectives:</b> The aim of our study was to investigate molecular mechanisms of lithium action by studying the gene expression profile of peripheral cell models generated from bipolar patients (BD) and healthy controls (HC). <b>Methods:</b> EBV-immortalised lymphoblastoid cells (LCLs) and fibroblast cells from BD and HC were incubated with either lithium chloride or plain medium for 3 weeks. We first conducted a microarray gene expression study. The most promising differentially regulated genes in terms of lithium-associated or disorder-associated pathways were then replicated by quantitative real-time PCR (qRT-PCR). <b>Results:</b> The pooled microarray analysis showed 459 genes to be differentially regulated in BD compared to HC and 58 due to lithium treatment in LCLs, and 295 genes to be differentially regulated in BD compared to HC and five due to lithium treatment in fibroblasts. After correction for multiple comparison, <i>EPHB1</i> disorder × treatment interactions remained significant in LCLs validated by qRT-PCR. In the control group, lithium influenced the expression of <i>ANP32E</i>, <i>PLEKHA2</i>, <i>KCNK1</i>, <i>PRKCH</i>, <i>ST3GAL6</i> and <i>AIF1</i>. In bipolar and control fibroblast cells lithium treatment decreased <i>FGF9</i> expression. <b>Conclusions:</b> The differentially regulated genes in our study add evidence for the relevance of inflammation, neuronal/glial development, phosphatidylinositol second-messenger pathway and ion channels in the mode of action of lithium.
DOI: 10.6084/m9.figshare.5537137
title: Antifilarial activity of caffeic acid phenethyl ester on <i>Brugia pahangi in vitro</i> and <i>in vivo</i>

description: Lymphatic filariasis (LF) is a vector borne disease caused by parasitic worms such as <i>Wuchereria bancrofti</i>, <i>Brugia malayi</i> and <i>B. timori</i>, which are transmitted by mosquitoes. Current therapeutics to treat LF are mainly microfilarcidal, and lack activity against adult worms. This set back, poses a challenge for the control and elimination of filariasis. Thus, in this study the activities of caffeic acid phenethyl ester (CAPE) against the filarial worm <i>B. pahangi</i> and its bacterial endosymbiont, <i>Wolbachia</i> were evaluated. Different concentrations (2, 5, 10, 15, 20 μg/ml) of CAPE were used to assess its effects on motility, viability and microfilarial (mf) production of <i>B. pahangi in vitro</i>. Anti-<i>Wolbachial</i> activity of CAPE was measured in worms by quantification of <i>Wolbachial wsp</i> gene copy number using real-time polymerase chain reaction. Our findings show that CAPE was found to significantly reduce adult worm motility, viability, and mf release both <i>in vitro</i> and <i>in vivo</i>. 20 μg/ml of CAPE halts the release of mf <i>in vitro</i> by day 6 of post treatment. Also, the number of adult worms recovered <i>in vivo</i> were reduced significantly during and after treatment with 50 mg/kg of CAPE relative to control drugs, diethylcarbamazine and doxycycline. Real time PCR based on the <i>Wolbachia fts</i>Z gene revealed a significant reduction in <i>Wolbachia</i> copy number upon treatment. Anti-<i>Wolbachia</i> and antifilarial properties of CAPE require further investigation as an alternative strategy to treat LF.
DOI: 10.6084/m9.figshare.5537137.v1
title: Antifilarial activity of caffeic acid phenethyl ester on <i>Brugia pahangi in vitro</i> and <i>in vivo</i>

description: Lymphatic filariasis (LF) is a vector borne disease caused by parasitic worms such as <i>Wuchereria bancrofti</i>, <i>Brugia malayi</i> and <i>B. timori</i>, which are transmitted by mosquitoes. Current therapeutics to treat LF are mainly microfilarcidal, and lack activity against adult worms. This set back, poses a challenge for the control and elimination of filariasis. Thus, in this study the activities of caffeic acid phenethyl ester (CAPE) against the filarial worm <i>B. pahangi</i> and its bacterial endosymbiont, <i>Wolbachia</i> were evaluated. Different concentrations (2, 5, 10, 15, 20 μg/ml) of CAPE were used to assess its effects on motility, viability and microfilarial (mf) production of <i>B. pahangi in vitro</i>. Anti-<i>Wolbachial</i> activity of CAPE was measured in worms by quantification of <i>Wolbachial wsp</i> gene copy number using real-time polymerase chain reaction. Our findings show that CAPE was found to significantly reduce adult worm motility, viability, and mf release both <i>in vitro</i> and <i>in vivo</i>. 20 μg/ml of CAPE halts the release of mf <i>in vitro</i> by day 6 of post treatment. Also, the number of adult worms recovered <i>in vivo</i> were reduced significantly during and after treatment with 50 mg/kg of CAPE relative to control drugs, diethylcarbamazine and doxycycline. Real time PCR based on the <i>Wolbachia fts</i>Z gene revealed a significant reduction in <i>Wolbachia</i> copy number upon treatment. Anti-<i>Wolbachia</i> and antifilarial properties of CAPE require further investigation as an alternative strategy to treat LF.
DOI: 10.6084/m9.figshare.5537080
title: OC trios

description: Ocular coloboma.
DOI: 10.6084/m9.figshare.5537080.v1
title: OC trios

description: Ocular coloboma.
DOI: 10.25405/data.ncl.12886832
title: Chlorination effects on DNA based characterization of water microbiomes and implications for the interpretation of data from disinfected systems

description: The data set is the detailed OTU table for all the samples used in this study. The samples include, i) commercially bought bottled water from Tanzania, Malaysia, Thailand and Nepal, ii) Tap water from UK and iii) lake water before and after chlorine treatment.
DOI: 10.25405/data.ncl.12886832.v1
title: Chlorination effects on DNA based characterization of water microbiomes and implications for the interpretation of data from disinfected systems

description: The data set is the detailed OTU table for all the samples used in this study. The samples include, i) commercially bought bottled water from Tanzania, Malaysia, Thailand and Nepal, ii) Tap water from UK and iii) lake water before and after chlorine treatment.
DOI: 10.6084/m9.figshare.5536744
title: Variant Site Strain Typer (VaST): Efficient strain typing using a minimal number of variant genomic sites

description: This repository contains the matrices used to build the minimum spanning sets for <i>Yersenia pestis, Bacillus anthracis, </i><i>Escherichia</i><i> coli, Burkholderia pseudomallei, and Francisella tularensis. </i>The target sites identified for resolving each strain complex is also provided in the haplotype files. The loci used for the truncated, experimentally-validated panel are also listed. <br>
DOI: 10.6084/m9.figshare.5536744.v1
title: Variant Site Strain Typer (VaST): Efficient strain typing using a minimal number of variant genomic sites

description: This repository contains the matrices used to build the minimum spanning sets for <i>Yersenia pestis, Bacillus anthracis, </i><i>Escherichia</i><i> coli, Burkholderia pseudomallei, and Francisella tularensis. </i>The target sites identified for resolving each strain complex is also provided in the haplotype files. The loci used for the truncated, experimentally-validated panel are also listed. <br>
DOI: 10.6084/m9.figshare.5536744.v3
title: Variant Site Strain Typer (VaST): Efficient strain typing using a minimal number of variant genomic sites

description: This repository contains the matrices used to build the minimum spanning sets for <i>Yersenia pestis, Bacillus anthracis, </i><i>Escherichia</i><i> coli, Burkholderia pseudomallei, and Francisella tularensis. </i>The target sites identified for resolving each strain complex is also provided in the haplotype files. The loci used for the truncated, experimentally-validated panel are also listed. <br>
DOI: 10.6084/m9.figshare.5536654
title: Identifying witness accounts from social media using imagery

description: This data contain the minimal annotation for datasets described in the publication:<br>Identifying witness accounts from social media using imagery, (2017). ISPRS International Journal of Geo-Information.<br>
DOI: 10.6084/m9.figshare.5536744.v2
title: Variant Site Strain Typer (VaST): Efficient strain typing using a minimal number of variant genomic sites

description: This repository contains the matrices used to build the minimum spanning sets for <i>Yersenia pestis, Bacillus anthracis, </i><i>Escherichia</i><i> coli, Burkholderia pseudomallei, and Francisella tularensis. </i>The target sites identified for resolving each strain complex is also provided in the haplotype files. The loci used for the truncated, experimentally-validated panel are also listed. <br>
DOI: 10.6084/m9.figshare.5536654.v1
title: Identifying witness accounts from social media using imagery

description: This data contain the minimal annotation for datasets described in the publication:<br>Identifying witness accounts from social media using imagery, (2017). ISPRS International Journal of Geo-Information.<br>
DOI: 10.17608/k6.auckland.5536492
title: University of Auckland’s approach to DMPs: design thinking (activity sheet)

description: Short activity delivered within the Australian National Data Service's pre-conference workshop - <i>DMPs: current thinking, future directions</i>, 17th October, as part of eResearch Australasia 2017<br><br>Accompanying presentation: 10.17608/k6.auckland.5536486
DOI: 10.17608/k6.auckland.5536492.v1
title: University of Auckland’s approach to DMPs: design thinking (activity sheet)

description: Short activity delivered within the Australian National Data Service's pre-conference workshop - <i>DMPs: current thinking, future directions</i>, 17th October, as part of eResearch Australasia 2017<br><br>Accompanying presentation: 10.17608/k6.auckland.5536486
DOI: 10.6084/m9.figshare.5536459
title: idigbio_rodents.sqlite

description: An SQLite database file created from data downloaded from http://portal.idigbio.org/. This file is for use in the Introduction to Structured Query Language (SQL) and R Lessons in the Data Carpentry for Natural History Collections material.<br> <br> Dataset description: "common rodents in the continental United States from major institutions that publish extended information about their specimens"
DOI: 10.25377/sussex.5536444
title: Data for research article: "Domestic horses (Equus caballus) prefer to approach humans displaying a submissive body posture rather than a dominant body posture"

description: Raw data for article appearing in the journal Animal Cognition. Tables show subjects' responses to human postures (sheet one for choice data, sheet two for latency data).<br><b>Abstract from article</b>Signals of dominance and submissiveness are central to conspecific communication in many species. For domestic animals, sensitivities to these signals in humans may also be beneficial. We presented domestic horses with a free choice between two unfamiliar humans, one adopting a submissive and the other a dominant body posture, with vocal and facial cues absent. Horses had previously been given food rewards by both human demonstrators, adopting neutral postures, to encourage approach behaviour. Across four counterbalanced test trials, horses showed a significant preference for approaching the submissive posture in both the first trial and across subsequent trials, and no individual subject showed an overall preference for dominant postures. There was no significant difference in latency to approach the two postures. This study provides novel evidence that domestic horses may spontaneously discriminate between, and attribute communicative significance to, human body postures of dominance; and further, that familiarity with the signaller is not a requirement for this response. These findings raise interesting questions about the plasticity of social signal perception across the species barrier.
DOI: 10.6084/m9.figshare.5536459.v1
title: idigbio_rodents.sqlite

description: An SQLite database file created from data downloaded from http://portal.idigbio.org/. This file is for use in the Introduction to Structured Query Language (SQL) Lesson in the Data Carpentry for Natural History Collections material.<br> <br> Dataset description: "common rodents in the continental United States from major institutions that publish extended information about their specimens"
DOI: 10.6084/m9.figshare.5536459.v3
title: idigbio_rodents.sqlite

description: An SQLite database file created from data downloaded from http://portal.idigbio.org/. This file is for use in the Introduction to Structured Query Language (SQL) and R Lessons in the Data Carpentry for Natural History Collections material.<br> <br> Dataset description: "common rodents in the continental United States from major institutions that publish extended information about their specimens"
DOI: 10.6084/m9.figshare.5535769
title: Angeles_Cover_Data

description: Core Spatial Data examining % Herbaceous cover throughout ANF<br>
DOI: 10.6084/m9.figshare.5535769.v1
title: Angeles_Cover_Data

description: Core Spatial Data examining % Herbaceous cover throughout ANF<br>
DOI: 10.6084/m9.figshare.5535727
title: specimens.csv

description: The Data Carpentry for Natural History Collections Lessons use data downloaded from iDigBio (http://portal.idigbio.org).<br><br>This specimens.csv file is a subset of just the specimen data (not locality or taxon names) from the idigbio_rodents.csv dataset is just over 10k records and contains data from natural history collections specimen records representing 5 genera from 4 major US collections, limited to US records. All records are from the Order Rodentia. All the data are mapped to the biodiversity data standard Darwin Core (http://rs.tdwg.org/dwc/terms/).
DOI: 10.6084/m9.figshare.5535733
title: species.csv

description: A comma-separated text file created from data downloaded from http://portal.idigbio.org/. This file is for use in the Data Carpentry for Natural History Collections Lessons.<br> <br>The entire dataset (idigbio_rodents.csv) is just over 10k records and contains data from natural history collections specimen records representing 5 genera from 4 major US collections, limited to US records. All records are from the Order Rodentia. All the data are mapped to the biodiversity data standard Darwin Core (http://rs.tdwg.org/dwc/terms/).<br><br>This species.csv file contains just the taxon names applied to these 10k records.<br>
DOI: 10.6084/m9.figshare.5535730
title: localities.csv

description: The Data Carpentry for Natural History Collections Lessons use data from iDigBio (http://portal.idigbio.org).<br><br>The localities.csv dataset is a subset of only the locality data extracted from the idigbio_rodents.csv file which contains just over 10k records. The idigbio_rodents.csv contains data from natural history collections specimen records representing 5 genera from 4 major US collections, limited to US records. All records are from the Order Rodentia. All the data are mapped to the biodiversity data standard Darwin Core (http://rs.tdwg.org/dwc/terms/). <br><br><br>
DOI: 10.6084/m9.figshare.5535727.v1
title: specimens.csv

description: The Data Carpentry for Natural History Collections Lessons use data downloaded from iDigBio (http://portal.idigbio.org).<br><br>This specimens.csv file is a subset of just the specimen data (not locality or taxon names) from the idigbio_rodents.csv dataset is just over 10k records and contains data from natural history collections specimen records representing 5 genera from 4 major US collections, limited to US records. All records are from the Order Rodentia. All the data are mapped to the biodiversity data standard Darwin Core (http://rs.tdwg.org/dwc/terms/).
DOI: 10.6084/m9.figshare.5535724
title: idigbio_rodents.csv

description: The Data Carpentry for Natural History Collections Lessons use data downloaded from iDigBio (http://portal.idigbio.org).<br><br>The idigbio_rodents.csv dataset is just over 10k records and contains data from natural history collections specimen records representing 5 genera from 4 major US collections, limited to US records. All records are from the Order Rodentia. All the data are mapped to the biodiversity data standard Darwin Core (http://rs.tdwg.org/dwc/terms/).
DOI: 10.6084/m9.figshare.5535652
title: pruned-6-gene_dataset.nex

description: This is the "pruned" six-gene dataset ("pruned" from Schoch et al. 2009, with Laboulbeniomycetes sequences added) used for Maximum Likelihood inference.
DOI: 10.6084/m9.figshare.5535655
title: pruned-6-gene_phylogeny_ML.result

description: This is the resulting pruned-6-gene_phylogeny_ML.result file from the Maximum Likelihood analysis of the pruned six-gene dataset.
DOI: 10.6084/m9.figshare.5535652.v1
title: pruned-6-gene_dataset.nex

description: This is the "pruned" six-gene dataset ("pruned" from Schoch et al. 2009, with Laboulbeniomycetes sequences added) used for Maximum Likelihood inference.
DOI: 10.6084/m9.figshare.5535631
title: 6-gene_dataset.nex

description: This is the six-gene dataset used for ML inference.
DOI: 10.6084/m9.figshare.5535655.v1
title: pruned-6-gene_phylogeny_ML.result

description: This is the resulting pruned-6-gene_phylogeny_ML.result file from the Maximum Likelihood analysis of the pruned six-gene dataset.
DOI: 10.6084/m9.figshare.5534356
title: Fast and Reliable Structure-Oriented Video Noise Estimation

description: Noise can significantly impact the effectiveness of video processing algorithms. This paper proposes a fast white-noise variance estimation that is reliable even in images with large textured areas. This method finds intensity-homogeneous blocks first and then estimates the noise variance in these blocks, taking image structure into account. This paper proposes a new measure to determine homogeneous blocks and a new structure analyzer for rejecting blocks with structure. This analyzer is based on high-pass operators and special masks for corners to stabilize the homogeneity estimation. For typical video quality (PSNR of 20â€“40 dB), the proposed method outperforms other methods significantly and the worst-case estimation error is 3 dB, which is suitable for real applications such as video broadcasts. The method performs well both in highly noisy and good-quality images. It also works well in images including few uniform blocks.
DOI: 10.6084/m9.figshare.5535586
title: Create Molecular Dynamics starting configuration

description: Little script (relying on GROMACS) to create initial molecular dynamics (MD) boxes. The example attached is for a box of a fullerene derivative, PTEG-1, but the script can be adapted to anything else. See the "a_new_fullerene_box.sh" for some instructions. There is plenty of room for improving the script.<br>The MD files (i.e., single molecule coordinates and topology) for the fullerene derivative are from:<br><b>Enhancing doping efficiency by improving host-dopant miscibility for fullerene-based n-type thermoelectrics</b>L. Qiu, J. Liu, R. Alessandri, X. Qiu, M. Koopmans, R.W.A. Havenith, S.J. Marrink, R.C. Chiechi, L.J.A. Koster, J.C. Hummelen<i>Journal of Material Chemistry A</i>, 2017, DOI: 10.1039/C7TA06609K
DOI: 10.6084/m9.figshare.5535628
title: 6-gene_phylogeny_ML.result

description: Resulting 6-gene_phylogeny_ML.result file from the Maximum Likelihood analysis of the six-gene dataset.
DOI: 10.6084/m9.figshare.5534236
title: Engagement and outreach for data management: FORCE 2017 presentation

description: My presentation for FORCE 2017, presented on 25 October 2017.
DOI: 10.6084/m9.figshare.5534356.v1
title: Fast and Reliable Structure-Oriented Video Noise Estimation

description: Noise can significantly impact the effectiveness of video processing algorithms. This paper proposes a fast white-noise variance estimation that is reliable even in images with large textured areas. This method finds intensity-homogeneous blocks first and then estimates the noise variance in these blocks, taking image structure into account. This paper proposes a new measure to determine homogeneous blocks and a new structure analyzer for rejecting blocks with structure. This analyzer is based on high-pass operators and special masks for corners to stabilize the homogeneity estimation. For typical video quality (PSNR of 20â€“40 dB), the proposed method outperforms other methods significantly and the worst-case estimation error is 3 dB, which is suitable for real applications such as video broadcasts. The method performs well both in highly noisy and good-quality images. It also works well in images including few uniform blocks.
DOI: 10.6084/m9.figshare.5535586.v1
title: Create Molecular Dynamics starting configuration

description: Little script (relying on GROMACS) to create initial molecular dynamics (MD) boxes. The example attached is for a box of a fullerene derivative, PTEG-1, but the script can be adapted to anything else. See the "a_new_fullerene_box.sh" for some instructions. There is plenty of room for improving the script.<br>The MD files (i.e., single molecule coordinates and topology) for the fullerene derivative are from:<br><b>Enhancing doping efficiency by improving host-dopant miscibility for fullerene-based n-type thermoelectrics</b>L. Qiu, J. Liu, R. Alessandri, X. Qiu, M. Koopmans, R.W.A. Havenith, S.J. Marrink, R.C. Chiechi, L.J.A. Koster, J.C. Hummelen<i>Journal of Material Chemistry A</i>, 2017, DOI: 10.1039/C7TA06609K
DOI: 10.6084/m9.figshare.5535631.v2
title: 6-gene_dataset.nex

description: This is the six-gene dataset used for ML inference.
DOI: 10.6084/m9.figshare.5533918
title: Hurricane Katrina County Jobs Data 2004-2006

description: County level place of work employment data for 2004, 2005, 2006.
DOI: 10.6084/m9.figshare.5534218
title: Demo-DOD-HPCPortal_Gateways2017

description: Presentation on DOD HPC Portal for Gateways 2017
DOI: 10.6084/m9.figshare.5535628.v1
title: 6-gene_phylogeny_ML.result

description: Resulting 6-gene_phylogeny_ML.result file from the Maximum Likelihood analysis of the six-gene dataset.
DOI: 10.6084/m9.figshare.5534218.v1
title: Demo-DOD-HPCPortal_Gateways2017

description: Presentation on DOD HPC Portal for Gateways 2017
DOI: 10.6084/m9.figshare.5533918.v1
title: Hurricane Katrina County Jobs Data 2004-2006

description: County level place of work employment data for 2004, 2005, 2006.
DOI: 10.6084/m9.figshare.5533249
title: First far-infrared high-resolution analysis of the ν<sub>2</sub> and ν<sub>4</sub> bands of phosgene <sup>35</sup>Cl<sub>2</sub>CO and <sup>35</sup>Cl<sup>37</sup>ClCO

description: A Fourier transform spectrum of phosgene (Cl<sub>2</sub>CO) has been recorded in the 17.3-μm spectral region at a temperature of 180 K and at a resolution of 0.00102 cm<sup>−1</sup> using a Bruker IFS125HR spectrometer coupled to synchrotron radiation, leading to the observation of the ν<sub>2</sub> and ν<sub>4</sub> vibrational bands of the two isotopologues <sup>35</sup>Cl<sub>2</sub>CO and <sup>35</sup>Cl<sup>37</sup>ClCO. The corresponding upper-state ro-vibrational levels were fit using a Hamiltonian model accounting for the A-type Coriolis interaction linking the rotational levels of the 2<sup>1</sup> and 4<sup>1</sup> vibrational states. In this way, it was possible to reproduce the upper-state ro-vibrational levels to within the experimental uncertainty, i.e. ∼0.30 × 10<sup>−3</sup> cm<sup>−1</sup>. Very accurate rotational and centrifugal distortion and interaction constants were derived from the fit, together with the following band centres: ν<sub>0</sub>(ν<sub>2,</sub> <sup>35</sup>Cl<sub>2</sub>CO) = 572.526299(30) cm<sup>−1</sup>, ν<sub>0</sub>(ν<sub>4,</sub> <sup>35</sup>Cl<sub>2</sub>CO) = 582.089026(30) cm<sup>−1</sup>, ν<sub>0</sub>(ν<sub>2,</sub> <sup>35</sup>Cl<sup>37</sup>ClCO) = 568.951791(35) cm<sup>−1</sup> and ν<sub>0</sub>(ν<sub>4</sub>, <sup>35</sup>Cl<sup>37</sup>ClCO) = 581.758279(35) cm<sup>−1</sup>.
DOI: 10.6084/m9.figshare.5534236.v2
title: Engagement and outreach for data management: FORCE 2017 presentation

description: My presentation for FORCE 2017, presented on 25 October 2017.