cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5349943
title: S. cerevisiae fragment datasets

description: Results data of two-round SECRiFY screens of human (HEK293) cDNA fragments in S. cerevisiae (3 replicate screens). Sequencing data was mapped on the human GRCh38 transcriptome assembled using known transcripts from protein-coding genes only.<br>"Sc_resultstable_all.txt" = all in-frame fragments detected in either the unsorted baseline library (merged for 3 replicates), or in all 3 sorted replicate samples. <br>"Sc_resultstable_enriched.txt" = those with log_FC &gt; 1 in all three replicates (11625)<br>"Sc_resultstable_depleted.txt" = those with log_FC &lt; -1 in all three replicates (136531)<br><br>For each fragment, the following information is provided:<br><br># Ensembl_geneID --&gt; Ensembl gene ID<br># Ensembl_txID --&gt; Ensembl transcript ID<br># tx_start --&gt; Transcript start position on human genome GRCh38<br># tx_end --&gt; Transcript end position on human genome GRCh38<br># chr --&gt; chromosome #<br># gene_symbol --&gt; official gene symbol<br># frag_start --&gt; fragment start position on the transcript, 0-based <br># frag_stop --&gt; fragment end position on the transcript, 0-based<br># cDNA --&gt; DNA sequence of the fragment<br># protein --&gt; translated AA sequence of the fragment in frame 1<br># IND_count --&gt; raw count value in the baseline (unsorted) library (merged for 3 replicates), NAs replaced by 0.001<br># SORT(1)_count --&gt; raw count value in the sorted sample replicate (1), NAs replaced by 0.001<br># IND_FPTM --&gt; normalized FPTM value in the baseline (unsorted) library <br># SORT(1)_FPTM --&gt; normalized FPTM value in the sorted sample replicate (1)<br># logFC_(1) --&gt; log2(SORT(1)_FPTM/IND_FPTM)<br>
DOI: 10.6084/m9.figshare.5349937
title: Untitled Item

description: Whole genome sequencing of C. albicans ATCC10231.
DOI: 10.6084/m9.figshare.5349955.v1
title: P. pastoris fragment datasets

description: Human fragments sequenced in all 3 replicates after SECRiFY secretability screening in <i>P. pastoris,</i> either detected in the input library or in all 3 replicates after sorting<i> </i>(Pp_resultstable_all.txt). The subsets of concordantly enriched and depleted fragments can be found in resp. Pp_resultstable_enriched.txt and Pp_resultstable_depleted.txt.<i><br></i>
DOI: 10.6084/m9.figshare.5349904
title: Duck ancestral state

description: The supplementary datasets of paper <strong>"</strong>Genomics analyses of wild × domestic segregation population to reveal selected genes associated with body size and plumage color of ducks<strong>".</strong>
DOI: 10.6084/m9.figshare.5349943.v1
title: S. cerevisiae fragment datasets

description: Human fragments sequenced after SECRiFY secretability screening in <i>S. cerevisiae</i>, specifically all those either detected in the input library, or in all 3 replicates after sorting (Sc_Resultstable_all.txt). Concordantly enriched/depleted fragments can be found in resp. Sc_resultstable_enriched.txt and Sc_resultstable_depleted.txt.<br>
DOI: 10.6084/m9.figshare.5349904.v1
title: Duck ancestral state

description: The supplementary datasets of paper <strong>"</strong>Genomics analyses of wild × domestic segregation population to reveal selected genes associated with body size and plumage color of ducks<strong>".</strong>
DOI: 10.6084/m9.figshare.5349943.v3
title: S. cerevisiae fragment datasets

description: Results data of two-round SECRiFY screens of human (HEK293) cDNA fragments in S. cerevisiae (3 replicate screens). Sequencing data was mapped on the human GRCh38 transcriptome assembled using known transcripts from protein-coding genes only.<br>"Sc_resultstable_all.txt" = all in-frame fragments detected in either the unsorted baseline library (merged for 3 replicates), or in all 3 sorted replicate samples. <br>"Sc_resultstable_enriched.txt" = those with log_FC &gt; 1 in all three replicates (11625)<br>"Sc_resultstable_depleted.txt" = those with log_FC &lt; -1 in all three replicates (136531)<br><br>For each fragment, the following information is provided:<br><br># Ensembl_geneID --&gt; Ensembl gene ID<br># Ensembl_txID --&gt; Ensembl transcript ID<br># tx_start --&gt; Transcript start position on human genome GRCh38<br># tx_end --&gt; Transcript end position on human genome GRCh38<br># chr --&gt; chromosome #<br># gene_symbol --&gt; official gene symbol<br># frag_start --&gt; fragment start position on the transcript, 0-based <br># frag_stop --&gt; fragment end position on the transcript, 0-based<br># cDNA --&gt; DNA sequence of the fragment<br># protein --&gt; translated AA sequence of the fragment in frame 1<br># IND_count --&gt; raw count value in the baseline (unsorted) library (merged for 3 replicates), NAs replaced by 0.001<br># SORT(1)_count --&gt; raw count value in the sorted sample replicate (1), NAs replaced by 0.001<br># IND_FPTM --&gt; normalized FPTM value in the baseline (unsorted) library <br># SORT(1)_FPTM --&gt; normalized FPTM value in the sorted sample replicate (1)<br># logFC_(1) --&gt; log2(SORT(1)_FPTM/IND_FPTM)<br>
DOI: 10.6084/m9.figshare.5349901.v1
title: Dataset for the article "A Metamorphic Testing Approach for Event Sequences"

description: Dataset for the article "A Metamorphic Testing Approach for Event Sequences"<br>
DOI: 10.6084/m9.figshare.5349886
title: S1_File.xlsx

description: Ecological data on percentage coverage of main functional groups of organisms colonising Boscombe Artificial Surf reef on the south coast of England 2009-2013. The data is published in association with article in PlosOne
DOI: 10.6084/m9.figshare.5349943.v2
title: S. cerevisiae fragment datasets

description: Human fragments sequenced after SECRiFY secretability screening in <i>S. cerevisiae</i>, specifically all those either detected in the input library, or in all 3 replicates after sorting (Sc_Resultstable_all.txt). Concordantly enriched/depleted fragments can be found in resp. Sc_resultstable_enriched.txt and Sc_resultstable_depleted.txt.<br>
DOI: 10.6084/m9.figshare.5349880
title: Data for paper "Both rare and common species support ecosystem services in scavenger communities", Global Ecology and Biogeography

description: Summarized data and main results of the manuscript "<b>Both rare and common species support ecosystem services in scavenger communities</b>" (Mateo-Tomás et al.) accepted for publication in <i>Global Ecology and Biogeography</i>.
DOI: 10.6084/m9.figshare.5349901.v3
title: Dataset

description: Dataset for the article "A Metamorphic Testing Approach for Event Sequences"<br>
DOI: 10.6084/m9.figshare.5349880.v1
title: Data for paper "Both rare and common species support ecosystem services in scavenger communities", Global Ecology and Biogeography

description: Summarized data and main results of the manuscript "<b>Both rare and common species support ecosystem services in scavenger communities</b>" (Mateo-Tomás et al.) accepted for publication in <i>Global Ecology and Biogeography</i>.
DOI: 10.6084/m9.figshare.5349901.v2
title: Dataset

description: Dataset for the article "A Metamorphic Testing Approach for Event Sequences"<br>
DOI: 10.6084/m9.figshare.5349232
title: Duck sample106 SNP variants

description: The supplementary datasets of paper <strong>"</strong>Genomics analyses of wild × domestic segregation population to reveal selected genes associated with body size and plumage color of ducks<strong>".</strong>
DOI: 10.6084/m9.figshare.5349229
title: PQR benchmark

description: Some pqr files for test<br>
DOI: 10.6084/m9.figshare.5349229.v1
title: PQR benchmark

description: Some pqr files for test<br>
DOI: 10.6084/m9.figshare.5349232.v1
title: Untitled Item

description: aaaaaaaaaaaaAaaa
DOI: 10.6084/m9.figshare.5349106
title: Maternal polycyclic aromatic hydrocarbon (PAH) transfer and effects on offspring of copepods exposed to dispersed oil with and without oil droplets

description: Copepods of the genus <i>Calanus</i> have the potential for accumulating lipophilic oil components due to their high lipid content and found to filter and ingest oil droplets during exposure. As female copepods produce eggs at the expense of lipid storage, there is a concern for transfer of lipophilic contaminants to offspring. To assess the potential for maternal transfer of oil components, ovigerous female copepods (<i>Calanus finmarchicus</i>) were exposed to filtered and unfiltered oil dispersions for 4 days, collected and eggs maintained in clean seawater and hatching and gene expression examined in hatched nauplii. Oil droplet exposure contributed to polycyclic aromatic hydrocarbon (PAH) uptake in dispersion-treated adult copepods, as displayed through PAH body residue analyses and fluorescence microscopy. Applying the latter methodology, transfer of heavy PAH from copepod mothers to offspring were detected Subtle effects were observed in offspring as evidenced by a temporal reduction in hatching success appear to be occurring only when mothers were exposed to the unfiltered oil dispersions. Offspring reared in clean water through to late naupliar stages were collected for RNA extraction and preparation of libraries for high-throughput transcriptome sequencing. Differentially expressed genes were identified through pairwise comparisons between treatments. Among these, several expressed genes have known roles in responses to chemical stress including xenobiotic metabolism enzymes, antioxidants, chaperones, and components of the inflammatory response. While gene expression results suggest a transgenerational activation of stress responses, the increase in relatively small number of differentially expressed genes suggests a minor long-term effect on offspring following maternal exposure.
DOI: 10.6084/m9.figshare.5349103
title: Mortality and transcriptional effects of inorganic mercury in the marine copepod <i>Calanus finmarchicus</i>

description: Inorganic mercury (Hg) is highly toxic to organisms including crustaceans and displays multiple toxic modes of action (MoA). The main aim of this investigation was to assess the acute and sublethal toxicity mediated by mercury chloride (HgCl<sub>2</sub>) in the marine copepod <i>Calanus finmarchicus</i>. A combination of short-term static studies to determine acute toxicity and a transcriptional investigation to characterize the sublethal MoA of HgCl<sub>2</sub> were conducted with an in-house continuous culture of <i>C. finmarchicus</i>. Transcriptional changes were determined by a custom 6.6 k <i>C. finmarchicus</i> Agilent oligonucleotide microarray and quantitative RT-PCR analysis. Data demonstrate that HgCl<sub>2</sub> produced a concentration- and time-dependent reduction in survival (NOEC<sub>48 h</sub> = 6.9 μg/L [Hg<sup>2+</sup>] and LC<sub>50</sub> of 279, 73, 48, and 34 µg/L [Hg<sup>2+</sup>] after 24, 48, 72, and 96 h, respectively) and that exposure to sublethal concentrations of HgCl<sub>2</sub> (5 μg/L [Hg2<sup>+</sup>]) induced differential expression of 98 features (probes) on the microarray. Gene ontology (GO) and toxicological pathway analyses suggested that the main MOA were (1) uncoupling of mitochondrial oxidative phosphorylation (OXPHOS) and ATP production, (2) oxidative stress and macromolecular damage, (3) inactivation of cellular enzymes, (4) induction of cellular apoptosis and autophagocytosis, (5) over-excitation of glutamate receptors (neurotoxicity), (6) disruption of calcium homeostasis and signaling, and (7) modulation of nuclear receptor activity involved in vitamin D receptor signaling. Quantitative RT-PCR analysis verified that oligoarray performed reliably in terms of specificity and response, thus demonstrating that Hg<sup>2+</sup> exerts multiple potential MoA in <i>C. finmarchicus</i>.
DOI: 10.6084/m9.figshare.5349106.v1
title: Maternal polycyclic aromatic hydrocarbon (PAH) transfer and effects on offspring of copepods exposed to dispersed oil with and without oil droplets

description: Copepods of the genus <i>Calanus</i> have the potential for accumulating lipophilic oil components due to their high lipid content and found to filter and ingest oil droplets during exposure. As female copepods produce eggs at the expense of lipid storage, there is a concern for transfer of lipophilic contaminants to offspring. To assess the potential for maternal transfer of oil components, ovigerous female copepods (<i>Calanus finmarchicus</i>) were exposed to filtered and unfiltered oil dispersions for 4 days, collected and eggs maintained in clean seawater and hatching and gene expression examined in hatched nauplii. Oil droplet exposure contributed to polycyclic aromatic hydrocarbon (PAH) uptake in dispersion-treated adult copepods, as displayed through PAH body residue analyses and fluorescence microscopy. Applying the latter methodology, transfer of heavy PAH from copepod mothers to offspring were detected Subtle effects were observed in offspring as evidenced by a temporal reduction in hatching success appear to be occurring only when mothers were exposed to the unfiltered oil dispersions. Offspring reared in clean water through to late naupliar stages were collected for RNA extraction and preparation of libraries for high-throughput transcriptome sequencing. Differentially expressed genes were identified through pairwise comparisons between treatments. Among these, several expressed genes have known roles in responses to chemical stress including xenobiotic metabolism enzymes, antioxidants, chaperones, and components of the inflammatory response. While gene expression results suggest a transgenerational activation of stress responses, the increase in relatively small number of differentially expressed genes suggests a minor long-term effect on offspring following maternal exposure.
DOI: 10.6084/m9.figshare.5349232.v2
title: Duck sample106 SNP

description: The supplementary databases of paper <b>"The evolutionary route from mallards to Pekin ducks".</b>
DOI: 10.6084/m9.figshare.5349103.v1
title: Mortality and transcriptional effects of inorganic mercury in the marine copepod <i>Calanus finmarchicus</i>

description: Inorganic mercury (Hg) is highly toxic to organisms including crustaceans and displays multiple toxic modes of action (MoA). The main aim of this investigation was to assess the acute and sublethal toxicity mediated by mercury chloride (HgCl<sub>2</sub>) in the marine copepod <i>Calanus finmarchicus</i>. A combination of short-term static studies to determine acute toxicity and a transcriptional investigation to characterize the sublethal MoA of HgCl<sub>2</sub> were conducted with an in-house continuous culture of <i>C. finmarchicus</i>. Transcriptional changes were determined by a custom 6.6 k <i>C. finmarchicus</i> Agilent oligonucleotide microarray and quantitative RT-PCR analysis. Data demonstrate that HgCl<sub>2</sub> produced a concentration- and time-dependent reduction in survival (NOEC<sub>48 h</sub> = 6.9 μg/L [Hg<sup>2+</sup>] and LC<sub>50</sub> of 279, 73, 48, and 34 µg/L [Hg<sup>2+</sup>] after 24, 48, 72, and 96 h, respectively) and that exposure to sublethal concentrations of HgCl<sub>2</sub> (5 μg/L [Hg2<sup>+</sup>]) induced differential expression of 98 features (probes) on the microarray. Gene ontology (GO) and toxicological pathway analyses suggested that the main MOA were (1) uncoupling of mitochondrial oxidative phosphorylation (OXPHOS) and ATP production, (2) oxidative stress and macromolecular damage, (3) inactivation of cellular enzymes, (4) induction of cellular apoptosis and autophagocytosis, (5) over-excitation of glutamate receptors (neurotoxicity), (6) disruption of calcium homeostasis and signaling, and (7) modulation of nuclear receptor activity involved in vitamin D receptor signaling. Quantitative RT-PCR analysis verified that oligoarray performed reliably in terms of specificity and response, thus demonstrating that Hg<sup>2+</sup> exerts multiple potential MoA in <i>C. finmarchicus</i>.
DOI: 10.6084/m9.figshare.5349145.v1
title: The phylogenetic tree and sequence alignment of EF-Tu in prokaryotes.

description: The phylogeny of EF-Tu in prokaryotes constructed based on protein sequence alignment. The alignment was performed with MAFFT v7.043b. The phylogenetic tree was generated using RAxML with PROTCATJTT as the substitution model and 100 bootstrap replicates.
DOI: 10.6084/m9.figshare.5349082
title: Data for Smith et al. Nature Communications

description: Data that corresponds to recently accepted manuscript, Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought. Nature Communications (2017-2018).A. Peyton Smith<sup>1</sup><sup>*</sup>, Ben Bond-Lamberty<sup>2</sup>, Brian W. Benscoter<sup>3</sup>, Malak M. Tfaily<sup>4</sup>, C. Ross Hinkle<sup>5</sup>, Chongxuan Liu<sup>1,6</sup>, and Vanessa L. Bailey<sup>1*</sup> <sup>1</sup>Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA<sup>2</sup>Joint Global Change Research Institute, Pacific Northwest National Laboratory, 5825 University Research Court, Suite 3500, College Park, MD 20740 USA<sup>3</sup>Florida Atlantic University, Department of Biological Sciences, 3200 College Avenue, Davie, FL 33314 USA<sup>4</sup>Environmental Molecular Sciences Laboratory,<sup> </sup>Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA<sup>5</sup>University of Central Florida, Ecosystem Processes and Services Laboratory, 4110 Libra Drive, Orlando, FL 3216-2368 USA<sup>6</sup>Southern University of Science and Technology, Shenzhen, 518055 China*Correspondence and requests for materials should be addressed to A. Peyton Smith (apeyton.smith@gmail.com) and Vanessa Bailey (vanessa.bailey@pnnl.gov). <b> </b>
DOI: 10.6084/m9.figshare.5349145.v2
title: The phylogenetic tree and protein sequence alignment of EF-Tu in prokaryotes.

description: The phylogeny of EF-Tu in prokaryotes constructed based on protein sequence alignment. The alignment was performed with MAFFT v7.043b. The phylogenetic tree was generated using RAxML with PROTCATJTT as the substitution model and 100 bootstrap replicates.
DOI: 10.6084/m9.figshare.5349145
title: The phylogenetic tree and sequence alignment of EF-Tu in prokaryotes.

description: The phylogeny of EF-Tu in prokaryotes constructed based on protein sequence alignment. The alignment was performed with MAFFT v7.043b. The phylogenetic tree was generated using RAxML v8.2.4 with PROTCATJTT as the substitution model and 100 bootstrap replicates.
DOI: 10.6084/m9.figshare.5349082.v1
title: Data for Smith et al. Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought. Nature Communications (2017-2018).

description: Data that corresponds to recently accepted manuscript, Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought. Nature Communications (2017-2018).A. Peyton Smith<sup>1</sup><sup>*</sup>, Ben Bond-Lamberty<sup>2</sup>, Brian W. Benscoter<sup>3</sup>, Malak M. Tfaily<sup>4</sup>, C. Ross Hinkle<sup>5</sup>, Chongxuan Liu<sup>1,6</sup>, and Vanessa L. Bailey<sup>1*</sup> <sup>1</sup>Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA<sup>2</sup>Joint Global Change Research Institute, Pacific Northwest National Laboratory, 5825 University Research Court, Suite 3500, College Park, MD 20740 USA<sup>3</sup>Florida Atlantic University, Department of Biological Sciences, 3200 College Avenue, Davie, FL 33314 USA<sup>4</sup>Environmental Molecular Sciences Laboratory,<sup> </sup>Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA<sup>5</sup>University of Central Florida, Ecosystem Processes and Services Laboratory, 4110 Libra Drive, Orlando, FL 3216-2368 USA<sup>6</sup>Southern University of Science and Technology, Shenzhen, 518055 China*Correspondence and requests for materials should be addressed to A. Peyton Smith (apeyton.smith@gmail.com) and Vanessa Bailey (vanessa.bailey@pnnl.gov). <b> </b>
DOI: 10.6084/m9.figshare.5349082.v2
title: Data for Smith et al. Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought. Nature Communications (2017-2018).

description: Data that corresponds to recently accepted manuscript, Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought. Nature Communications (2017-2018).A. Peyton Smith<sup>1</sup><sup>*</sup>, Ben Bond-Lamberty<sup>2</sup>, Brian W. Benscoter<sup>3</sup>, Malak M. Tfaily<sup>4</sup>, C. Ross Hinkle<sup>5</sup>, Chongxuan Liu<sup>1,6</sup>, and Vanessa L. Bailey<sup>1*</sup> <sup>1</sup>Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA<sup>2</sup>Joint Global Change Research Institute, Pacific Northwest National Laboratory, 5825 University Research Court, Suite 3500, College Park, MD 20740 USA<sup>3</sup>Florida Atlantic University, Department of Biological Sciences, 3200 College Avenue, Davie, FL 33314 USA<sup>4</sup>Environmental Molecular Sciences Laboratory,<sup> </sup>Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA<sup>5</sup>University of Central Florida, Ecosystem Processes and Services Laboratory, 4110 Libra Drive, Orlando, FL 3216-2368 USA<sup>6</sup>Southern University of Science and Technology, Shenzhen, 518055 China*Correspondence and requests for materials should be addressed to A. Peyton Smith (apeyton.smith@gmail.com) and Vanessa Bailey (vanessa.bailey@pnnl.gov). <b> </b>
DOI: 10.6084/m9.figshare.5348155
title: Optimized microhydrated carbonate clusters, at the MP2/6-311++G** level of theory

description: These are structures of carbonate ion clusters CO3(-2)(H2O)n for n=0 to 9, optimized at the MP2/6-311++G** level of theory.
DOI: 10.6084/m9.figshare.5346748
title: Petdogstress.xlsx

description: Parents ratings (1= observed behaviour; 0 = not observed behaviour) of dogs behaviours with their child in the past month.
DOI: 10.6084/m9.figshare.5348155.v1
title: Optimized microhydrated carbonate clusters, at the MP2/6-311++G** level of theory

description: These are structures of carbonate ion clusters CO3(-2)(H2O)n for n=0 to 9, optimized at the MP2/6-311++G** level of theory.
DOI: 10.6084/m9.figshare.5346715
title: Raw Data_Philippine Bats

description: Raw data of the on-going review paper on Philippine bat research
DOI: 10.6084/m9.figshare.5346748.v1
title: Petdogstress.xlsx

description: Parents ratings (1= observed behaviour; 0 = not observed behaviour) of dogs behaviours with their child in the past month.
DOI: 10.6084/m9.figshare.5346715.v1
title: Raw Data_Philippine Bats

description: Raw data of the on-going review paper on Philippine bat research
DOI: 10.6084/m9.figshare.5346571
title: COMP 111 Syllabus: History of Computing at Loyola University Chicago

description: The social and organizational history of humanity is intricately entangled with the history of technology in general and the technology of information in particular. Advances in this area have often been closely involved in social and political transformations. While the contemporary period is often referred to by such names as the Computing and Information Age, this is the culmination of a series of historical transformations that have been centuries in the making. This course will provide a venue for students to learn about history through the evolution of number systems and arithmetic, calculating and computing machines, and advanced communication technology via the Internet. Students who take this course will attain a degree of technological literacy while studying core historical concepts. Students who complete this course will learn the key vocabulary of the computing discipline, which is playing a significant role in modern human thought and new media communications. The History of Computing will be organized around the historical perspective. The relationships between social organization, intellectual climate, and technology will be examined and stressed.