cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7910/dvn/v1rjpf/sbnfmn
title: snk20151003_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3898485
title: Transcriptome - Parvularia atlantis (Nuclearia sp. ATCC 50694)

description: Reads are deposited in NCBI: https://www.ncbi.nlm.nih.gov/sra/?term=SRS725006<br><br>- Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br>- clean.fasta: Assembly cleaned from cross-contamination of other species multiplexed (Corallochytrium limacisporum Hawaii, Pirum gemmata and Abeoforma whisleri) after applying CroCo V0.1.1 (Simion et al. in prep). It may contain bacterial contamination.<br><br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015) <em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em> <strong><em>Current Biology </em></strong>25(18):2404-10.<br>www.multicellgenome.com
DOI: 10.6084/m9.figshare.3898485.v1
title: Nuclearia sp. ATCC 50694 - Transcriptome

description: - Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015) <em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em> <strong><em>Current Biology </em></strong>25(18):2404-10.
DOI: 10.7910/dvn/v1rjpf/re9fpp
title: snk20161202_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3897444
title: Pan Traps In Grassland and Woodlot Habitats/Sites at York Univesity

description: Hypothesis:If bright coloured pan traps are used, then there would be an increase in abundance of captured insects. This is because insects are only capable of seeing the environment in ultraviolet (UV) spectrum. Since, light colours, like yellow and white, can reflect more UV light; insects are therefore more attracted to light colours.Prediction 1: Dark coloured pan traps attract the least amount of insectsPrediction 2: Placing pan traps about one meter apart from one another, would attract more insects.Metadata:The purpose of this experiment, done on September 28, 2016, at 2:30 p.m., was to determine which colour and arrangement of pan traps would attract the most insects. The data was collected by placing coloured solo bowls filled with soapy water in different habitat types at the beginning of lab,approximately 3:00 p.m. . These bowls were placed in a particular sequence: yellow, white, blue and were spaced approximately one meter apart. Nine of these bowls were placed in the grassland habitat and nine of them were placed in the woodlot habitat. At approximately 4:15 p.m., we returned to these habitats and recorded the data, which can be seen in the excel file above. The Variables:Site: Also known as habitat which in this case were both grassland and woodlot.Colour of Pan Trap: We were provided with three different colours of the bowls which were blue, white and yellow. The three kinds of bowls were placed in a distinct sequence: yellow, white and blue. Abundance: This was calculated by counting the number of flies that were in each coloured bowl. As one can see from the data, that in both habitats or sites, yellow and white bowls collected more insects than the blue bowls.RTU: This stands for recognizable taxonomic units. This is calculated by analyzing the species of the insects. As one can see from the data that the yellow and white bowls had more or the same number of RTUs in the blue bowl. In the grassland habitat, there were mostly Diptera flies, specifically flesh flies,which were found mainly in the yellow and white bowls. In the woodlot habitat, there was mainly no insect found in the blue bowls. White bowls mostly consisted of Diptera, specifically houseflys. The yellow bowls were where one mostly found an unknown particular species of flies. <br><br>
DOI: 10.6084/m9.figshare.3897444.v1
title: Pan Traps In Grassland and Woodlot Habitats/Sites at York Univesity

description: Hypothesis:If bright coloured pan traps are used, then there would be an increase in abundance of captured insects. This is because insects are only capable of seeing the environment in ultraviolet (UV) spectrum. Since, light colours, like yellow and white, can reflect more UV light; insects are therefore more attracted to light colours.Prediction 1: Dark coloured pan traps attract the least amount of insectsPrediction 2: Placing pan traps about one meter apart from one another, would attract more insects.Metadata:The purpose of this experiment, done on September 28, 2016, at 2:30 p.m., was to determine which colour and arrangement of pan traps would attract the most insects. The data was collected by placing coloured solo bowls filled with soapy water in different habitat types at the beginning of lab,approximately 3:00 p.m. . These bowls were placed in a particular sequence: yellow, white, blue and were spaced approximately one meter apart. Nine of these bowls were placed in the grassland habitat and nine of them were placed in the woodlot habitat. At approximately 4:15 p.m., we returned to these habitats and recorded the data, which can be seen in the excel file above. The Variables:Site: Also known as habitat which in this case were both grassland and woodlot.Colour of Pan Trap: We were provided with three different colours of the bowls which were blue, white and yellow. The three kinds of bowls were placed in a distinct sequence: yellow, white and blue. Abundance: This was calculated by counting the number of flies that were in each coloured bowl. As one can see from the data, that in both habitats or sites, yellow and white bowls collected more insects than the blue bowls.RTU: This stands for recognizable taxonomic units. This is calculated by analyzing the species of the insects. As one can see from the data that the yellow and white bowls had more or the same number of RTUs in the blue bowl. In the grassland habitat, there were mostly Diptera flies, specifically flesh flies,which were found mainly in the yellow and white bowls. In the woodlot habitat, there was mainly no insect found in the blue bowls. White bowls mostly consisted of Diptera, specifically houseflys. The yellow bowls were where one mostly found an unknown particular species of flies. <br><br>
DOI: 10.7910/dvn/v1rjpf/ilnbhe
title: snk20150503_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/pqyfmb
title: snk20161115_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/9asz6d
title: snk20160329_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3895752
title: Transcriptome - Abeoforma whisleri

description: - Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br>- clean.fasta: Assembly cleaned from cross-contamination of other species multiplexed (Corallochytrium limacisporum Hawaii, Pirum gemmata and Parvularia atlantis [Nuclearia sp ATCC 50694]) after applying CroCo V0.1.1 (Simion et al. in prep).<br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015) <em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em> <strong><em>Current Biology </em></strong>25(18):2404-10.<br>www.multicellgenome.com
DOI: 10.7910/dvn/v1rjpf/guiak8
title: snk20160620_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/skjkpr
title: snk20150406_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3895752.v1
title: Abeoforma whisleri's transcriptome

description: - Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015) <em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em> <strong><em>Current Biology </em></strong>25(18):2404-10.
DOI: 10.7910/dvn/v1rjpf/pkv5hx
title: snk20160920_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3892506
title: Pasoh tree H.xlsx

description: This file contains data on tree height and diameter for 1161 individual trees the 50 ha Pasoh plot in Malaysia (http://www.teamnetwork.org/site/pasoh-forest-reserve). Tree height was measured using a vertex device.The data was collected in August 2015.
DOI: 10.7910/dvn/v1rjpf/fg8iir
title: snk20160306_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3895752.v2
title: Transcriptome - Abeoforma whisleri's

description: - Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015) <em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em> <strong><em>Current Biology </em></strong>25(18):2404-10.<br>www.multicellgenome.com
DOI: 10.7910/dvn/v1rjpf/atz6hl
title: snk20170304_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3887301
title: Disulfide High Mobility Group Box-1 Causes Bladder Pain through Bladder Toll-Like Receptor 4

description: Intravesical partially oxidized form of high mobility group box-1 (disulfide HMGB1) causes abdominal mechanical hypersensitivity, an indicator of bladder pain, through bladder toll like receptor 4 (TLR4). This is an important development in our understanding of mechanisms mediating bladder pain and the role of HMGB1 in bladder pain and inflammation.
DOI: 10.7910/dvn/v1rjpf/ixl1yi
title: snk20170107_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3895752.v3
title: Transcriptome - Abeoforma whisleri's

description: - Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015) <em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em> <strong><em>Current Biology </em></strong>25(18):2404-10.<br>www.multicellgenome.com
DOI: 10.6084/m9.figshare.3887301.v1
title: Disulfide High Mobility Group Box-1 Causes Bladder Pain through Bladder Toll-Like Receptor 4

description: Intravesical partially oxidized form of high mobility group box-1 (disulfide HMGB1) causes abdominal mechanical hypersensitivity, an indicator of bladder pain, through bladder toll like receptor 4 (TLR4). This is an important development in our understanding of mechanisms mediating bladder pain and the role of HMGB1 in bladder pain and inflammation.
DOI: 10.7910/dvn/v1rjpf/eqqsep
title: snk20170618_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3878223
title: Financial innovation in the Canadian Press: actors and reporting verbs

description: This corpus helped to investigate the business sections of seven Canadian newspapers over a period spanning from 2001 to 2008 in English and in French. The newspapers are: <i>The National Post</i>, <i>The Globe and Mail</i>, <i>The Toronto Star</i>, <i>The Gazette</i>, <i>La Presse</i>, <i>Le Devoir</i> and <i>Le Droit</i>. The focus was on the sources whose speech was selected and reported by journalists in direct or indirect style when covering new subprime-driven financial derivative instruments, namely collateralized debt obligations (CDOs) and credit default swaps (CDS). With the use of the monolingual concordancer WordSmith 6.0, we looked at the following keywords:<i> </i><i>collateralized, backed, CDO, CDS</i> and their French equivalents. The results were treated in 2 Excel files. In particular, we identified the different voices/actors who used the financial innovation terms. These voices could be the journalists or different institutional actors such as central banks or Canadian banks. When reported speech was used, we also identified reporting verbs.<br>
DOI: 10.7910/dvn/v1rjpf/nc2wpm
title: snk20170214_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3878196
title: Capillary electrophoresis/immunosubtraction as a better alternative to immunofixation for detecting and immunotyping serum monoclonal proteins in patients with immunoglobulin light chain (AL) amyloidosis

description: Capillary electrophoresis/immunosubtraction (CE/IS) is a simple method for detecting and immunotyping serum or urine monoclonal proteins. To our knowledge, there are no previous reports of the use of CE/IS for characterizing patients with Immunoglobulin light chain (AL) amyloidosis, and there are no convincing data available to compare CE/IS with serum immunofixation electrophoresis (IFE) and free light chain (FLC) assay. The aim of this study was to evaluate the clinical utility of CE/IS in patients with AL amyloidosis as a diagnostic accuracy study. This study included 50 patients with AL amyloidosis (17 newly diagnosed and 33 undergoing treatment). Serum IFE identified monoclonal proteins in 15/50 (30%) of all cases and in 7/17 (41%) of newly diagnosed cases. CE/IS identified monoclonal proteins in 16/50 (32%) of all cases and in 7/17 (41%) of newly diagnosed cases. The FLC assay detected an abnormal ratio of kappa and lambda light chains in 26/50 (52%) of all cases and in 15/17 (88%) of newly diagnosed cases. IFE and CE/IS combined with FLC assay identified monoclonal proteins more sensitive than IFE alone and CE/IS alone, in newly diagnosed patients (<i>p</i> = 0.002 and 0.002, respectively) and in patients undergoing treatment (<i>p</i> = 0.031 and 0.016, respectively). CE/IS is an acceptable alternative to IFE.
DOI: 10.6084/m9.figshare.3878196.v1
title: Capillary electrophoresis/immunosubtraction as a better alternative to immunofixation for detecting and immunotyping serum monoclonal proteins in patients with immunoglobulin light chain (AL) amyloidosis

description: Capillary electrophoresis/immunosubtraction (CE/IS) is a simple method for detecting and immunotyping serum or urine monoclonal proteins. To our knowledge, there are no previous reports of the use of CE/IS for characterizing patients with Immunoglobulin light chain (AL) amyloidosis, and there are no convincing data available to compare CE/IS with serum immunofixation electrophoresis (IFE) and free light chain (FLC) assay. The aim of this study was to evaluate the clinical utility of CE/IS in patients with AL amyloidosis as a diagnostic accuracy study. This study included 50 patients with AL amyloidosis (17 newly diagnosed and 33 undergoing treatment). Serum IFE identified monoclonal proteins in 15/50 (30%) of all cases and in 7/17 (41%) of newly diagnosed cases. CE/IS identified monoclonal proteins in 16/50 (32%) of all cases and in 7/17 (41%) of newly diagnosed cases. The FLC assay detected an abnormal ratio of kappa and lambda light chains in 26/50 (52%) of all cases and in 15/17 (88%) of newly diagnosed cases. IFE and CE/IS combined with FLC assay identified monoclonal proteins more sensitive than IFE alone and CE/IS alone, in newly diagnosed patients (<i>p</i> = 0.002 and 0.002, respectively) and in patients undergoing treatment (<i>p</i> = 0.031 and 0.016, respectively). CE/IS is an acceptable alternative to IFE.
DOI: 10.7910/dvn/v1rjpf/mqmzsn
title: snk20170720_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3877944
title: Hancock, P.A., White, V.L., Ritchie, S.A.,Hoffmann, A.A. and Godfray, H.C.J. 2016 Predicting Wolbachia invasion dynamics in Aedes aegypti populations using models of density-dependent demographic traits. BMC Biology. Data from field-cage experiments: Abundance of juvenile mosquito life stages. Wolbachia infection rates in juvenile mosquito life stages. Water temperature in the field cage larval container habitat.

description: Data describing the population dynamics of juvenile mosquito life stages and Wolbachia bacteria in two field-cage Aedes aegypti mosquito populations. All larvae and pupae in the field cage were counted on the dates specified. Wolbachia frequency in the first instar larvae and pupae was monitored in individuals sampled at regular time points. Water temperature data is also provided.
DOI: 10.6084/m9.figshare.3878223.v1
title: Financial innovation in the Canadin Press: actors and reporting verbs

description: This corpus helped to investigate the business sections of seven Canadian newspapers over a period spanning from 2001 to 2008 in English and in French. The newspapers are: <i>The National Post</i>, <i>The Globe and Mail</i>, <i>The Toronto Star</i>, <i>The Gazette</i>, <i>La Presse</i>, <i>Le Devoir</i> and <i>Le Droit</i>. The focus was on the sources whose speech was selected and reported by journalists in direct or indirect style when covering new subprime-driven financial derivative instruments, namely collateralized debt obligations (CDOs) and credit default swaps (CDS). With the use of the monolingual concordancer WordSmith 6.0, we looked at the following keywords:<i> </i><i>collateralized, backed, CDO, CDS</i> and their French equivalents. The results were treated in an Excel file. In particular, we identified the different voices/actors who used the financial innovation terms. These voices could be the journalists or different institutional actors such as central banks or Canadian banks. When reported speech was used, we also identified reporting verbs.<br>
DOI: 10.7910/dvn/v1rjpf/tcznmy
title: snk20170822_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3877944.v1
title: Hancock, P.A., White, V.L., Ritchie, S.A.,Hoffmann, A.A. and Godfray, H.C.J. 2016 Predicting Wolbachia invasion dynamics in Aedes aegypti populations using models of density-dependent demographic traits. BMC Biology. Data from field-cage experiments: Abundance of juvenile mosquito life stages. Wolbachia infection rates in juvenile mosquito life stages. Water temperature in the field cage larval container habitat.

description: Data describing the population dynamics of juvenile mosquito life stages and Wolbachia bacteria in two field-cage Aedes aegypti mosquito populations. All larvae and pupae in the field cage were counted on the dates specified. Wolbachia frequency in the first instar larvae and pupae was monitored in individuals sampled at regular time points. Water temperature data is also provided.
DOI: 10.7910/dvn/v1rjpf/bzdjt5
title: snk20170623_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/mthhkz
title: snk20171216_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3872433
title: <i>In Silico</i> prediction of the molecular basis of ClTx and AaCTx interaction with matrix metalloproteinase-2 (MMP-2) to inhibit glioma cell invasion

description: Glioblastoma is the deadliest type of brain cancer. Treatment could target the Matrix metalloproteinase-2 (MMP-2), which is known to be involved in the invasion process of glioblastoma cells. But current available inhibitors are not selective to MMP-2 due to their interaction with the catalytic binding site, which is highly conserved in all MMPs structures. Interestingly, members of the chloride channel blocker scorpion toxins, such as chlorotoxin (ClTx) and AaCTx, inhibit glioblastoma cell invasion and show a promising therapeutic potential. Indeed, it has been shown that CITx inhibits selectively MMP-2 and was also able to cross the blood brain and tissue barriers. Although ClTx and AaCTx show high sequence similarity, AaCTx is ten times less active than ClTx. By using molecular modeling, molecular dynamics and MM-PB(GB)SA free energy estimation, we present the first computational study reporting the interaction mode of ClTx/AaCTx with MMP-2. We found that the two peptides probably act on an exosite of MMP-2 comprising mainly residues from the collagen binding domain, a feature that could be exploited to enhance the selectivity toward MMP-2. van der Waals and hydrophobic forces are the primary mediators of this interaction. The N- and C-termini of the two peptides harbor the key residues of the interaction spread across a conserved amino acid patch. In particular, F6 contributes mostly to the binding free energy in ClTx. We also suggest that the lack of the C-terminal arginine and the residues P10 and R24, might be responsible for altering the activity of AaCTx toward glioblastoma cells compared to ClTx.
DOI: 10.6084/m9.figshare.3872433.v1
title: <i>In Silico</i> prediction of the molecular basis of ClTx and AaCTx interaction with matrix metalloproteinase-2 (MMP-2) to inhibit glioma cell invasion

description: Glioblastoma is the deadliest type of brain cancer. Treatment could target the Matrix metalloproteinase-2 (MMP-2), which is known to be involved in the invasion process of glioblastoma cells. But current available inhibitors are not selective to MMP-2 due to their interaction with the catalytic binding site, which is highly conserved in all MMPs structures. Interestingly, members of the chloride channel blocker scorpion toxins, such as chlorotoxin (ClTx) and AaCTx, inhibit glioblastoma cell invasion and show a promising therapeutic potential. Indeed, it has been shown that CITx inhibits selectively MMP-2 and was also able to cross the blood brain and tissue barriers. Although ClTx and AaCTx show high sequence similarity, AaCTx is ten times less active than ClTx. By using molecular modeling, molecular dynamics and MM-PB(GB)SA free energy estimation, we present the first computational study reporting the interaction mode of ClTx/AaCTx with MMP-2. We found that the two peptides probably act on an exosite of MMP-2 comprising mainly residues from the collagen binding domain, a feature that could be exploited to enhance the selectivity toward MMP-2. van der Waals and hydrophobic forces are the primary mediators of this interaction. The N- and C-termini of the two peptides harbor the key residues of the interaction spread across a conserved amino acid patch. In particular, F6 contributes mostly to the binding free energy in ClTx. We also suggest that the lack of the C-terminal arginine and the residues P10 and R24, might be responsible for altering the activity of AaCTx toward glioblastoma cells compared to ClTx.
DOI: 10.7910/dvn/v1rjpf/m8qoos
title: snk20171120_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/44vnpt
title: snk20170814_03.txt.gz

description: :unav