cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7964102.v1
title: <i>In vivo</i> transcriptomes of <i>Streptococcus suis</i> reveal genes required for niche-specific adaptation and pathogenesis

description: <i>Streptococcus suis</i> is a Gram-positive bacterium and a zoonotic pathogen residing in the nasopharynx or the gastrointestinal tract of pigs with a potential of causing life-threatening invasive disease. It is endemic in the porcine production industry worldwide, and it is also an emerging human pathogen. After invasion, the pathogen adapts to cause bacteremia and disseminates to different organs including the brain. To gain insights in this process, we infected piglets with a highly virulent strain of <i>S. suis</i>, and bacterial transcriptomes were obtained from blood and different organs (brain, joints, and heart) when animals had severe clinical symptoms of infection. Microarrays were used to determine the genome-wide transcriptional profile at different infection sites and during growth in standard growth medium <i>in vitro</i>. We observed differential expression of around 30% of the Open Reading Frames (ORFs) and infection-site specific patterns of gene expression. Genes with major changes in expression were involved in transcriptional regulation, metabolism, nutrient acquisition, stress defenses, and virulence, amongst others, and results were confirmed for a subset of selected genes using RT-qPCR. Mutants were generated in two selected genes, and the encoded proteins, i.e., NADH oxidase and MetQ, were shown to be important virulence factors in coinfection experiments and <i>in vitro</i> assays. The knowledge derived from this study regarding <i>S. suis</i> gene expression <i>in vivo</i> and identification of virulence factors is important for the development of novel diagnostic and therapeutic strategies to control <i>S. suis</i> disease.
DOI: 10.6084/m9.figshare.7964075
title: Electroantennogram Literature

description: Literature relating to Electroantennography collected in late 2018 using Scopus and Google Scholar for the PhD of Isobel Roberts - including search terms; EAG, GC-EAD, electroantennogram, electroantennograph, antenna(e), insect response, plant-insect interaction(s), ant, and insect(s). A total of 365 papers were returned with the search, with a final total of 362 full text documents with details pertinent to the research being included within this table. Articles ranged in date from 1971 to 2018.
DOI: 10.6084/m9.figshare.7963991
title: The Structures and Developents of Plant

description: These course materials constituting the combination of some references that could be coming from any sources and could be also used openly by people outside there in order to make a deliverable and better sciences information.<br><br>Created by <b>Ahmad Taufiq</b><br>
DOI: 10.6084/m9.figshare.7964087.v1
title: FAK signaling pathway.pptx

description: Focal adhesion kinase (FAK) is a critical factor to modulate the cell motility.
DOI: 10.6084/m9.figshare.7964075.v2
title: Electroantennogram Literature

description: Literature relating to Electroantennography collected in late 2018 using Scopus and Google Scholar for the PhD of Isobel Roberts - including search terms; EAG, GC-EAD, electroantennogram, electroantennograph, antenna(e), insect response, plant-insect interaction(s), ant, and insect(s). A total of 365 papers were returned with the search, with a final total of 362 full text documents with details pertinent to the research being included within this table. Articles ranged in date from 1971 to 2018.
DOI: 10.6084/m9.figshare.7964075.v1
title: Electroantennogram Literature

description: Literature relating to Electroantennography collected in late 2018 using Scopus and Google Scholar for the PhD of Isobel Roberts - including search terms; EAG, GC-EAD, electroantennogram, electroantennograph, antenna(e), insect response, plant-insect interaction(s), ant, and insect(s). A total of 365 papers were returned with the search, with a final total of 363 full text documents with details pertinent to the research being included within this table. Articles ranged from in date from 1971 to 2018.
DOI: 10.6084/m9.figshare.7963889
title: Additional file 2: of Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces

description: Dataset S1. Amplicon Sequence Variant (ASV) table generated from 16S rRNA gene and fungal ITS region iTag sequencing. (XLSX 182 kb)
DOI: 10.6084/m9.figshare.7963889.v1
title: Additional file 2: of Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces

description: Dataset S1. Amplicon Sequence Variant (ASV) table generated from 16S rRNA gene and fungal ITS region iTag sequencing. (XLSX 182 kb)
DOI: 10.6084/m9.figshare.7963868
title: MUTIT1.eps

description: Using entropy evaluation method on selecting of stop andsignal control at intersections
DOI: 10.6084/m9.figshare.7963871
title: New U–Pb zircon ages and a revised integrated age model for the late Miocene northern Taranaki coastal section, New Zealand

description: New LA–ICP–MS U–Pb zircon ages of tuffs, from the northern Taranaki coastal section constrain depositional ages of the Mount Messenger Formation to 9.69 ± 0.12 and 9.43 ± 0.17 Ma at the Mohakatino and Tongaporutu rivers, respectively, and the Urenui Formation near Waiau Stream to 8.45 ± 0.10 Ma. Our preferred new radiometric–biostratigraphic age model comprises lower and upper intervals characterised by relatively low and high un-decompacted sedimentation rates of 102 ± 96 m/Ma (MSWD = 6.0) and 1358 ± 144 m/Ma (MSWD = 1.32), respectively. The poor linear fit to the lower interval could indicate either variable sedimentation rates, or an unconformity (0.7 ± 0.2 Ma) in the upper Mohakatino Formation or at the base of the Mount Messenger Formation. The 1569 m-thick upper interval between Mohakatino River and Waiau Stream was deposited in 1.16 ± 0.01 Ma between 9.67 + 0.07/−0.05 and 8.52 + 0.06/−0.07 Ma. Predicted ages for intra-Tongaporutuan bioevents (e.g. base Tukemokihi Coiling Zone) do not overlap their assigned ages, highlighting the importance of propagating uncertainties into bioevent absolute ages and opportunities for future improvements to the age model, namely using high-precision geochronology to acquire ages for additional tuffs and improve precision of existing ages.
DOI: 10.6084/m9.figshare.7963871.v1
title: New U–Pb zircon ages and a revised integrated age model for the late Miocene northern Taranaki coastal section, New Zealand

description: New LA–ICP–MS U–Pb zircon ages of tuffs, from the northern Taranaki coastal section constrain depositional ages of the Mount Messenger Formation to 9.69 ± 0.12 and 9.43 ± 0.17 Ma at the Mohakatino and Tongaporutu rivers, respectively, and the Urenui Formation near Waiau Stream to 8.45 ± 0.10 Ma. Our preferred new radiometric–biostratigraphic age model comprises lower and upper intervals characterised by relatively low and high un-decompacted sedimentation rates of 102 ± 96 m/Ma (MSWD = 6.0) and 1358 ± 144 m/Ma (MSWD = 1.32), respectively. The poor linear fit to the lower interval could indicate either variable sedimentation rates, or an unconformity (0.7 ± 0.2 Ma) in the upper Mohakatino Formation or at the base of the Mount Messenger Formation. The 1569 m-thick upper interval between Mohakatino River and Waiau Stream was deposited in 1.16 ± 0.01 Ma between 9.67 + 0.07/−0.05 and 8.52 + 0.06/−0.07 Ma. Predicted ages for intra-Tongaporutuan bioevents (e.g. base Tukemokihi Coiling Zone) do not overlap their assigned ages, highlighting the importance of propagating uncertainties into bioevent absolute ages and opportunities for future improvements to the age model, namely using high-precision geochronology to acquire ages for additional tuffs and improve precision of existing ages.
DOI: 10.6084/m9.figshare.7963868.v1
title: MUTIT1.eps

description: Using entropy evaluation method on selecting of stop andsignal control at intersections
DOI: 10.6084/m9.figshare.7963820
title: The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data

description: Tea is a globally consumed non-alcohol beverage with great economic importance. Lacking of the reference genome has largely hampered the utilization of the precious tea plant genetic resources towards breeding. To address this, we generated a high-quality reference genome of tea plant using Illumina and PacBio sequencing technology that totally produced 2,124 Gb (~700-fold coverage) short and 125 Gb (~41-fold) long read data, respectively. We employed a hybrid strategy to assemble the genome that has been publicly released. We here described the data framework used to generate, annotate and validate the genome assembly. Besides, we re-predicted the protein-coding genes and annotated their putative functions using more complete omics datasets and improved training models. We reassessed the assembly and annotation quality using the latest version of BUSCO. These data can be used to develop new methodologies/tools for better assembly of complex genomes, aid in finding of novel genes, variations and evolutionary clues associated with tea quality, and thus help to breed new varieties with high yields and quality in the future.
DOI: 10.6084/m9.figshare.7963823
title: Osteopathy Clinical Teaching Questionnaire - Self-efficacy data

description: Clinical educator self-efficacy and its relationship to student evaluations of teaching
DOI: 10.6084/m9.figshare.7963814
title: Interactive community responses to disturbance in streams: disturbance history moderates the influence of disturbance types

description: Data for Eveleens, McIntosh and Warburton 2019 "Interactive community responses to disturbance in streams: disturbance history moderates the influence of disturbance types" testing the relationship between disturbance history and type on aquatic invertebrate community composition using an in-stream channel experiment. This dataset includes invertebrate abundance data for both the communities within the experimental channels and the drift of invertebrates out of channels, measured during disturbance treatments. For this experiment, disturbance treatments included three disturbance types (flooding, drying and a control) applied to individual channels nested within two levels of disturbance history ('stable' and 'frequently disturbed' streams). Full details can be found at http://dx.doi.org/10.1111/oik.05868
DOI: 10.6084/m9.figshare.7963793
title: CCDB_3716.jpg

description: Single image through a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease
DOI: 10.6084/m9.figshare.7963793.v1
title: CCDB_3716.jpg

description: Single image through a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease
DOI: 10.6084/m9.figshare.7963769
title: Functions of waterfowl nests as habitat in medicinal leech (Hirudo verbana) populations to inhabit and to deposit cocoon: A sample of periodic ecological relationships

description: This data was related to a study entitled "Functions of waterfowl nests as habitat in medicinal leech (<i>Hirudo verbana</i>) populations to inhabit and to deposit cocoon: A sample of periodic ecological relationships"
DOI: 10.6084/m9.figshare.12877267.v1
title: Additional file 5 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file 5:Annotation results. This table holds the most-likely annotation of 2,551 unigenes based on searches against several databases. Source of the EST and number of independent sequences from various stages is indicated as are the unigene sequence match to the preliminary Pt genome 454 reads, the prediction by GeneMark and the closest homolog found among the predicted Pgt proteins. GO-annotations are also given according to cellular location, function or process, as well as EC and KEGG annotations (as produced by annot8r). (XLS 1 MB)
DOI: 10.6084/m9.figshare.12877267
title: Additional file 5 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file 5:Annotation results. This table holds the most-likely annotation of 2,551 unigenes based on searches against several databases. Source of the EST and number of independent sequences from various stages is indicated as are the unigene sequence match to the preliminary Pt genome 454 reads, the prediction by GeneMark and the closest homolog found among the predicted Pgt proteins. GO-annotations are also given according to cellular location, function or process, as well as EC and KEGG annotations (as produced by annot8r). (XLS 1 MB)
DOI: 10.6084/m9.figshare.12877270
title: Additional file 6 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file 6:Pt unigene sequences matching U. maydis ESTs. The file shows possible homologs between the two species and their representation over the various cDNA libraries (life cycle stages). (XLS 3 MB)
DOI: 10.6084/m9.figshare.12877270.v1
title: Additional file 6 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file 6:Pt unigene sequences matching U. maydis ESTs. The file shows possible homologs between the two species and their representation over the various cDNA libraries (life cycle stages). (XLS 3 MB)
DOI: 10.6084/m9.figshare.7963757
title: Leech heartbeat circuit synapse data

description: Data used for spike-trigered averaging to estimate synaptic conductances between premotor inhibitory interneurons and motor neurons. Can be used with HN-HE-synapses-STA software published on Github (see link below).<br>
DOI: 10.6084/m9.figshare.12877273
title: Additional file 7 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file 7:Pt non-redundant unigene sequences specific for and shared between spore stages as presented in the Venn diagram (supporting Figure 3) with annotation results. (XLS 197 KB)
DOI: 10.6084/m9.figshare.12877279
title: Additional file 9 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file 9:Pt unigenes were compared to sets of known or predicted (small) secreted proteins (SSPs). This file reveals families of likely paralogous proteins and their matches to orthologous and homeologous predicted SSPs in various in rust fungi and U. maydis. It includes representation of ESTs over the sampled stages. (XLS 929 KB)
DOI: 10.6084/m9.figshare.12877282.v12
title: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
DOI: 10.6084/m9.figshare.12877276.v1
title: Additional file 8 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file 8:Pt unigenes whose EST counts in the various spore stages correlate with EST counts of U. maydis homologs in equivalent cell types/spore stages. (XLS 46 KB)
DOI: 10.6084/m9.figshare.12877279.v1
title: Additional file 9 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file 9:Pt unigenes were compared to sets of known or predicted (small) secreted proteins (SSPs). This file reveals families of likely paralogous proteins and their matches to orthologous and homeologous predicted SSPs in various in rust fungi and U. maydis. It includes representation of ESTs over the sampled stages. (XLS 929 KB)
DOI: 10.6084/m9.figshare.12877276
title: Additional file 8 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file 8:Pt unigenes whose EST counts in the various spore stages correlate with EST counts of U. maydis homologs in equivalent cell types/spore stages. (XLS 46 KB)
DOI: 10.6084/m9.figshare.12877282.v11
title: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
DOI: 10.6084/m9.figshare.12877282.v14
title: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
DOI: 10.6084/m9.figshare.7963733
title: Leech heartbeat motor neuron inputs from 6 different animals

description: Data from 6 leeches: 5_19A 5_19B 5_20B 5_22B 5_26A 5_27B<br>Described in:<br>Norris BJ, Weaver AL, Wenning A, García PS, Calabrese RL (2007a).<br> A central pattern generator producing alternative outputs: pattern, strength, and dynamics of premotor synaptic input to leech heart motor neurons. J Neurophysiol, 98(5):2992 3005. doi: 10.1152/jn.00877.2007. URL http://dx.doi.org/10.1152/jn.00877.2007.<br><br>Norris BJ, Weaver AL, Wenning A, García PS, Calabrese RL neurons (2007b). A central pattern generator producing alternative outputs: phase relations of leech heart motor neurons with respect to premotor synaptic input. J Neurophysiol, 98(5):2983 2991. doi: 10.1152/jn.00407.2007. URL http://dx.doi.org/10.1152/jn.00407.2007.<br><br>Wright TM, Calabrese RL (2011b). Patterns of presynaptic activity and synaptic strength interact http://dx.doi.<br> to produce motor output. J Neurosci, 31(48):17555 17571. doi: 10.1523/JNEUROSCI.4723-11.2011. URL http://dx.doi.10.1523/JNEUROSCI.4723-11.2011. <br>Can be used by software HE-Model published on Github (see reference link below)<br>
DOI: 10.6084/m9.figshare.12877273.v1
title: Additional file 7 of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file 7:Pt non-redundant unigene sequences specific for and shared between spore stages as presented in the Venn diagram (supporting Figure 3) with annotation results. (XLS 197 KB)
DOI: 10.6084/m9.figshare.12877282.v10
title: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
DOI: 10.6084/m9.figshare.7963742
title: Proteins_individual_exosomes

description: Protein abundance on individual exosomes of each sample.
DOI: 10.6084/m9.figshare.7963769.v1
title: Preference of endangered medicinal leech, Hirudo verbana populations to live and lay cocoon in the waterfowl nests

description: This data was related to a study entitled "Preference of endangered medicinal leech, Hirudo verbana populations to live and lay cocoon in the waterfowl nests"
DOI: 10.6084/m9.figshare.12877282
title: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
DOI: 10.6084/m9.figshare.12877282.v13
title: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

description: Additional file of Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
DOI: 10.6084/m9.figshare.7963769.v3
title: Preference of endangered medicinal leech, Hirudo verbana populations to live and lay cocoon in the waterfowl nests

description: This data was related to a study entitled "Preference of endangered medicinal leech, Hirudo verbana populations to live and lay cocoon in the waterfowl nests"
DOI: 10.6084/m9.figshare.7963733.v2
title: Leech heartbeat motor neuron inputs from 6 different animals

description: Data from 6 leeches: 5_19A 5_19B 5_20B 5_22B 5_26A 5_27B<br>Described in:<br>Norris BJ, Weaver AL, Wenning A, García PS, Calabrese RL (2007a).<br> A central pattern generator producing alternative outputs: pattern, strength, and dynamics of premotor synaptic input to leech heart motor neurons. J Neurophysiol, 98(5):2992 3005. doi: 10.1152/jn.00877.2007. URL http://dx.doi.org/10.1152/jn.00877.2007.<br><br>Norris BJ, Weaver AL, Wenning A, García PS, Calabrese RL neurons (2007b). A central pattern generator producing alternative outputs: phase relations of leech heart motor neurons with respect to premotor synaptic input. J Neurophysiol, 98(5):2983 2991. doi: 10.1152/jn.00407.2007. URL http://dx.doi.org/10.1152/jn.00407.2007.<br><br>Wright TM, Calabrese RL (2011b). Patterns of presynaptic activity and synaptic strength interact http://dx.doi.<br> to produce motor output. J Neurosci, 31(48):17555 17571. doi: 10.1523/JNEUROSCI.4723-11.2011. URL http://dx.doi.10.1523/JNEUROSCI.4723-11.2011. <br>Can be used by software HE-Model published on Github (see reference link below)<br>
DOI: 10.6084/m9.figshare.7963712
title: A mitogenomic phylogeny of chitons (Mollusca: Polyplacophora)

description: Alignments and trees<br>
DOI: 10.6084/m9.figshare.7963712.v1
title: A mitogenomic phylogeny of chitons (Mollusca: Polyplacophora)

description: Alignments and trees<br>
DOI: 10.6084/m9.figshare.7963688
title: Supplementary Movie 1, 2, and 3.

description: Supplementary Movie 1: Shows assembly formation occurring live.<br>Supplementary Movie 2 and 3: Show snapshots of the assemblies under CryoEM.
DOI: 10.6084/m9.figshare.7963664
title: Cochlonema

description: This is the raw image for Fig. 1E<br>
DOI: 10.6084/m9.figshare.7963643
title: Accompanying Raw Data for the Paper: Adaptive smartphone-based sensor fusion for estimating competitive rowing kinematic metrics

description: Kinematic data collected via both a smartphone and differential GPS system on two rowed boats for several trials at different target stroke rates. See the included README for details as well as the related paper and software.<br>Preprint: https://doi.org/10.31224/osf.io/nykuh<br>Paper source: https://gitlab.com/mechmotum/row_filter_paper<br><br>Software: https://gitlab.com/mechmotum/row_filter<br>