cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4234751
title: RAIN v1

description: <b>RAIN: RNA–protein Association and Interaction Networks</b><br>RAIN integrates non-coding RNA (ncRNA) and protein interaction networks in an easily accessible web interface. It contains three types of ncRNA associations: microRNA-target, ncRNA-protein and ncRNA-ncRNA interactions and combines them with protein-protein interaction available in the STRING database. ncRNA associations cover four model organisms and are extracted from experimental data, automatic literature mining and curated examples. For miRNAs, we further include precomputed target predictions.
DOI: 10.6084/m9.figshare.4234745
title: Supplementary Material for: Chromosome 1p31.1p31.3 Deletion in a Patient with Craniosynostosis, Central Nervous System and Renal Malformation: Case Report and Review of the Literature

description: Interstitial deletions in the short arm of chromosome 1 are infrequent. We report a female with a 1p31.1p31.3 deletion and cloverleaf skull, who presented with renal and central nervous system malformations, cleft palate, severe ocular anomalies, and cutis laxa, in addition to the previously described clinical data present in other cases with deletions encompassing this region, such as developmental delay, seizures, round face with a prominent nose, micro/retrognathia, half-opened mouth, short neck, hand/foot malformations, hernia, congenital heart malformations, and abnormal external genitalia. The deletion spanned ∼18.6 Mb and included a total of 68 OMIM protein coding genes. We have reviewed 17 cases previously described in the literature and in DECIPHER involving the chromosomal region 1p31.1p31.3. Only 3 of these affect the whole region, 9 are partial deletions of this region, and 5 are much smaller deletions. Taking into account the MORBID ID and the haploinsufficiency score of the genes, we go on to propose which genes may explain particular clinical features observed in the patient. <i>IL23R </i>may be responsible for the craniosynostosis,<i> FOXD2</i> for the renal anomalies, <i>LHX8 </i>for closure defects of the palate, and <i>ST6GALNAC3</i> for skin anomalies. In summary, we have identified a chromosome 1p31.1p31.3 deletion in a patient with an atypical presentation of craniosynostosis amongst other more typical features observed in individuals with similar deletions.
DOI: 10.6084/m9.figshare.4234751.v1
title: RAIN v1

description: <b>RAIN: RNA–protein Association and Interaction Networks</b><br>RAIN integrates non-coding RNA (ncRNA) and protein interaction networks in an easily accessible web interface. It contains three types of ncRNA associations: microRNA-target, ncRNA-protein and ncRNA-ncRNA interactions and combines them with protein-protein interaction available in the STRING database. ncRNA associations cover four model organisms and are extracted from experimental data, automatic literature mining and curated examples. For miRNAs, we further include precomputed target predictions.
DOI: 10.6084/m9.figshare.4234745.v1
title: Supplementary Material for: Chromosome 1p31.1p31.3 Deletion in a Patient with Craniosynostosis, Central Nervous System and Renal Malformation: Case Report and Review of the Literature

description: Interstitial deletions in the short arm of chromosome 1 are infrequent. We report a female with a 1p31.1p31.3 deletion and cloverleaf skull, who presented with renal and central nervous system malformations, cleft palate, severe ocular anomalies, and cutis laxa, in addition to the previously described clinical data present in other cases with deletions encompassing this region, such as developmental delay, seizures, round face with a prominent nose, micro/retrognathia, half-opened mouth, short neck, hand/foot malformations, hernia, congenital heart malformations, and abnormal external genitalia. The deletion spanned ∼18.6 Mb and included a total of 68 OMIM protein coding genes. We have reviewed 17 cases previously described in the literature and in DECIPHER involving the chromosomal region 1p31.1p31.3. Only 3 of these affect the whole region, 9 are partial deletions of this region, and 5 are much smaller deletions. Taking into account the MORBID ID and the haploinsufficiency score of the genes, we go on to propose which genes may explain particular clinical features observed in the patient. <i>IL23R </i>may be responsible for the craniosynostosis,<i> FOXD2</i> for the renal anomalies, <i>LHX8 </i>for closure defects of the palate, and <i>ST6GALNAC3</i> for skin anomalies. In summary, we have identified a chromosome 1p31.1p31.3 deletion in a patient with an atypical presentation of craniosynostosis amongst other more typical features observed in individuals with similar deletions.
DOI: 10.6084/m9.figshare.4234739
title: Durso & Mullin 2016 Heterodon nasicus stable isotope diet code

description: These three .R scripts generate all the data and figures used in our paper:<br><br>http://www.sciencedirect.com/science/article/pii/S094420061630068X<br><br>hognose_diet.R is the primary data analysis with the mixing models and most of the figures<br>hog mcp graphs.R is the code for generating Figure 1<br>appendix2_vary_TEF.R is the code for generating the results found in Appendix 2
DOI: 10.6084/m9.figshare.4234739.v2
title: Durso & Mullin 2016 Heterodon nasicus stable isotope diet code

description: These three .R scripts generate all the data and figures used in our paper:<br><br>http://www.sciencedirect.com/science/article/pii/S094420061630068X<br><br>hognose_diet.R is the primary data analysis with the mixing models and most of the figures<br>hog mcp graphs.R is the code for generating Figure 1<br>appendix2_vary_TEF.R is the code for generating the results found in Appendix 2
DOI: 10.6084/m9.figshare.4234727
title: Durso & Mullin 2016 Heterodon nasicus stable isotope diet data

description: We collected data on stable isotope signatures of carbon and nitrogen from scale tissue, red blood cells, and blood plasma to assess the diet of wild plains hog-nosed snakes (<em>Heterodon nasicus</em>) in Illinois, as well as their prey.<br>r.iso.cast_manuallymodified.csv contains a manual modification that I made to the data during coding, which I couldn't figure out how to do in R. I'm sure it's possible, but it was much faster just to do it this way.<br><br>The code at:<br>https://dx.doi.org/10.6084/m9.figshare.4234739<br>contains steps to import and use both data files.<br>See our paper for more details:<br><br>http://dx.doi.org/10.1016/j.zool.2016.07.004
DOI: 10.6084/m9.figshare.4234727.v1
title: Durso & Mullin 2016 Heterodon nasicus stable isotope diet data

description: We collected data on stable isotope signatures of carbon and nitrogen from scale tissue, red blood cells, and blood plasma to assess the diet of wild plains hog-nosed snakes (<em>Heterodon nasicus</em>) in Illinois, as well as their prey.<br>r.iso.cast_manuallymodified.csv contains a manual modification that I made to the data during coding, which I couldn't figure out how to do in R. I'm sure it's possible, but it was much faster just to do it this way.<br><br>The code at:<br>https://dx.doi.org/10.6084/m9.figshare.4234739<br>contains steps to import and use both data files.<br>See our paper for more details:<br><br>http://dx.doi.org/10.1016/j.zool.2016.07.004
DOI: 10.6084/m9.figshare.4234688
title: Evaluating alternative mowing regimes for conservation management of Central European mesic hay meadows: A field experiment

description: Conservation status of hay meadows highly depends on their management. The main goal of this study was to assess the efficiency of different mowing regimes in maintenance of plant species richness and diversity of mesic hay meadows. The field experiment was carried out on a species rich, mesic hay meadow in Western Hungary. We evaluated the effects of four alternative types of management on the plant community after 7 years of continuous treatment: (1) mowing twice a year, typical traditional management, (2) mowing once a year in May, most practised currently by local farmers, (3) mowing once a year in September, often proposed for conservation management and (4) abandonment of mowing. Traditional mowing resulted in significantly higher number and higher diversity of vascular plant species than other mowing regimes. Mowing twice a year was the only efficient way to control the spread of the invasive <i>Solidago gigantea,</i> and mowing in September was more successful in it than mowing in May. We conclude that the traditional mowing regime is the most suitable to maintain botanical diversity of mesic hay meadows; however, other regimes should also be considered if certain priority species are targeted by conservation.
DOI: 10.6084/m9.figshare.4234688.v1
title: Evaluating alternative mowing regimes for conservation management of Central European mesic hay meadows: A field experiment

description: Conservation status of hay meadows highly depends on their management. The main goal of this study was to assess the efficiency of different mowing regimes in maintenance of plant species richness and diversity of mesic hay meadows. The field experiment was carried out on a species rich, mesic hay meadow in Western Hungary. We evaluated the effects of four alternative types of management on the plant community after 7 years of continuous treatment: (1) mowing twice a year, typical traditional management, (2) mowing once a year in May, most practised currently by local farmers, (3) mowing once a year in September, often proposed for conservation management and (4) abandonment of mowing. Traditional mowing resulted in significantly higher number and higher diversity of vascular plant species than other mowing regimes. Mowing twice a year was the only efficient way to control the spread of the invasive <i>Solidago gigantea,</i> and mowing in September was more successful in it than mowing in May. We conclude that the traditional mowing regime is the most suitable to maintain botanical diversity of mesic hay meadows; however, other regimes should also be considered if certain priority species are targeted by conservation.
DOI: 10.6084/m9.figshare.4234634
title: PtGrey-vs-Flash4.zip

description: This is a set of images comparing the performance of the a Point Grey Research Chameleon3 CM3-U3-31S4M versus a Hamamatsu Flash4.0 camera. Images of a Molecular Probes FluoCells #2 slide were captured with different exposure times. Images were captured with a 10x / 0.45 and 20x / 0.75 objective, and with either the same exposure time on each camera, or with a 3.5x longer exposure on the Point Grey camera to compensate for the different pixel size of the two cameras. The 3.5x longer exposure ensures that the same number of photons per pixel are recorded by the two cameras. Finally, a 10 ms and 1 s dark image taken with the Point Grey camera are included.
DOI: 10.6084/m9.figshare.4234634.v1
title: PtGrey-vs-Flash4.zip

description: This is a set of images comparing the performance of the a Point Grey Research Chameleon3 CM3-U3-31S4M versus a Hamamatsu Flash4.0 camera. Images of a Molecular Probes FluoCells #2 slide were captured with different exposure times. Images were captured with a 10x / 0.45 and 20x / 0.75 objective, and with either the same exposure time on each camera, or with a 3.5x longer exposure on the Point Grey camera to compensate for the different pixel size of the two cameras. The 3.5x longer exposure ensures that the same number of photons per pixel are recorded by the two cameras. Finally, a 10 ms and 1 s dark image taken with the Point Grey camera are included.
DOI: 10.6084/m9.figshare.4234634.v2
title: PtGrey-vs-Flash4.zip

description: This is a set of images comparing the performance of the a Point Grey Research Chameleon3 CM3-U3-31S4M versus a Hamamatsu Flash4.0 camera. Images of a Molecular Probes FluoCells #2 slide were captured with different exposure times. Images were captured with a 10x / 0.45 and 20x / 0.75 objective, and with either the same exposure time on each camera, or with a 3.5x longer exposure on the Point Grey camera to compensate for the different pixel size of the two cameras. The 3.5x longer exposure ensures that the same number of photons per pixel are recorded by the two cameras. Finally, a 10 ms and 1 s dark image taken with the Point Grey camera are included.
DOI: 10.6084/m9.figshare.4234280
title: ebola.spillover.intensity.final

description: R workspace (set of data), raster datasets, and code used to generate spatiotemporal triggers of Ebola across Africa and figures in the article.<br>
DOI: 10.6084/m9.figshare.4234280.v1
title: ebola.spillover.intensity.final.Rmd

description: R workspace (set of data) and code used to generate spatiotemporal triggers of Ebola across Africa.<br>
DOI: 10.6084/m9.figshare.4234280.v2
title: ebola.spillover.intensity.final.Rmd

description: R workspace (set of data) and code used to generate spatiotemporal triggers of Ebola across Africa.<br>
DOI: 10.6084/m9.figshare.4234280.v3
title: ebola.spillover.intensity.final

description: R workspace (set of data) and code used to generate spatiotemporal triggers of Ebola across Africa.<br>
DOI: 10.6084/m9.figshare.4234250
title: Ubiquitination of ERMES components by the E3 ligase Rsp5 is involved in mitophagy

description: Mitochondria are dynamic organelles that undergo permanent fission and fusion events. These processes play an essential role in maintaining normal cellular function. In the yeast <i>Saccharomyces cerevisiae</i>, the endoplasmic reticulum-mitochondrial encounter structure (ERMES) is a marker of sites of mitochondrial division, but it is also involved in a plethora of other mitochondrial functions. However, it remains unclear how these different functions are regulated. We show here that Mdm34 and Mdm12, 2 components of ERMES, are ubiquitinated by the E3 ligase Rsp5. This ubiquitination is not involved in mitochondrial dynamics or in the distribution and turnover of ERMES. Nevertheless, the ubiquitination of Mdm34 and Mdm12 was required for efficient mitophagy. We thus report here the first identification of ubiquitinated substrates participating in yeast mitophagy.
DOI: 10.6084/m9.figshare.4234250.v1
title: Ubiquitination of ERMES components by the E3 ligase Rsp5 is involved in mitophagy

description: Mitochondria are dynamic organelles that undergo permanent fission and fusion events. These processes play an essential role in maintaining normal cellular function. In the yeast <i>Saccharomyces cerevisiae</i>, the endoplasmic reticulum-mitochondrial encounter structure (ERMES) is a marker of sites of mitochondrial division, but it is also involved in a plethora of other mitochondrial functions. However, it remains unclear how these different functions are regulated. We show here that Mdm34 and Mdm12, 2 components of ERMES, are ubiquitinated by the E3 ligase Rsp5. This ubiquitination is not involved in mitochondrial dynamics or in the distribution and turnover of ERMES. Nevertheless, the ubiquitination of Mdm34 and Mdm12 was required for efficient mitophagy. We thus report here the first identification of ubiquitinated substrates participating in yeast mitophagy.
DOI: 10.6084/m9.figshare.4234211
title: University of Otago Open Access Publishing Survey Dataset

description: Dataset from the University of Otago survey of staff attitudes towards and publishing practices in open access.<br>CSV format, comma-delimited, Unicode (UTF-8)<br>Notes:* The full set of questions are availble in various formats in the Figshare collection for this project.* The data in this file has been modified for public release to remove any potentially identifying information. Certain responses have been redacted and the [removed] inserted to indicate modification to preserve anonymity.* Top row = question number* Second row = question text* Column A is a unique ResponseID generated by the software used (Qualtrics)* Responses in this dataset are provided as text not codes* Questions with multiple possible answers are presented as separate columns with the top row indicating this: Q10_1, Q10_2, ... Q10_9, Q10_OTHER_TEXT, etc.* Send questions to copyright@otago.ac.nz
DOI: 10.6084/m9.figshare.4234199.v1
title: Design for sequential follow-up experiments in computer emulations

description: Sequential experiments composed of initial experiments and follow-up experiments are widely adopted for economical computer emulations. Many kinds of Latin hypercubes with good space-filling properties have been constructed for designing the initial computer experiments. However, few works based on Latin hypercubes have focused on the design of the follow-up experiments. Although some constructions of nested Latin hypercube designs can be adapted to sequential designs, the size of the follow-up experiments needs to be a multiple of that of the initial experiments. In this paper, a general method for constructing sequential designs of flexible size is proposed, which allows the combined designs to have good one-dimensional space-filling properties. Moreover, the sampling properties and central limit theorems are derived for these designs. Several improvements of these designs are made to achieve better space-filling properties. Some simulations are carried out to verify the theoretical results.
DOI: 10.6084/m9.figshare.4234187
title: Ubiquitin-coated nanodiamonds bind to autophagy receptors for entry into the selective autophagy pathway

description: Selective macroautophagy/autophagy plays a pivotal role in the processing of foreign pathogens and cellular components to maintain homeostasis in human cells. To date, numerous studies have demonstrated the uptake of nanoparticles by cells, but their intracellular processing through selective autophagy remains unclear. Here we show that carbon-based nanodiamonds (NDs) coated with ubiquitin (Ub) bind to autophagy receptors (SQSTM1 [sequestosome 1], OPTN [optineurin], and CALCOCO2/NDP52 [calcium binding and coiled-coil domain 2]) and are then linked to MAP1LC3/LC3 (microtubule-associated protein 1 light chain 3) for entry into the selective autophagy pathway. NDs are ultimately delivered to lysosomes. Ectopically expressed SQSTM1-green fluorescence protein (GFP) could bind to the Ub-coated NDs. By contrast, the Ub-associated domain mutant of SQSTM1 (ΔUBA)-GFP did not bind to the Ub-coated NDs. Chloroquine, an autophagy inhibitor, prevented the ND-containing autophagosomes from fusing with lysosomes. Furthermore, autophagy receptors OPTN and CALCOCO2/NDP52, involved in the processing of bacteria, were found to be involved in the selective autophagy of NDs. However, ND particles located in the lysosomes of cells did not induce mitotic blockage, senescence, or cell death. Single ND clusters in the lysosomes of cells were observed in the xenografted human lung tumors of nude mice. This study demonstrated for the first time that Ub-coated nanoparticles bind to autophagy receptors for entry into the selective autophagy pathway, facilitating their delivery to lysosomes.
DOI: 10.6084/m9.figshare.4234187.v1
title: Ubiquitin-coated nanodiamonds bind to autophagy receptors for entry into the selective autophagy pathway

description: Selective macroautophagy/autophagy plays a pivotal role in the processing of foreign pathogens and cellular components to maintain homeostasis in human cells. To date, numerous studies have demonstrated the uptake of nanoparticles by cells, but their intracellular processing through selective autophagy remains unclear. Here we show that carbon-based nanodiamonds (NDs) coated with ubiquitin (Ub) bind to autophagy receptors (SQSTM1 [sequestosome 1], OPTN [optineurin], and CALCOCO2/NDP52 [calcium binding and coiled-coil domain 2]) and are then linked to MAP1LC3/LC3 (microtubule-associated protein 1 light chain 3) for entry into the selective autophagy pathway. NDs are ultimately delivered to lysosomes. Ectopically expressed SQSTM1-green fluorescence protein (GFP) could bind to the Ub-coated NDs. By contrast, the Ub-associated domain mutant of SQSTM1 (ΔUBA)-GFP did not bind to the Ub-coated NDs. Chloroquine, an autophagy inhibitor, prevented the ND-containing autophagosomes from fusing with lysosomes. Furthermore, autophagy receptors OPTN and CALCOCO2/NDP52, involved in the processing of bacteria, were found to be involved in the selective autophagy of NDs. However, ND particles located in the lysosomes of cells did not induce mitotic blockage, senescence, or cell death. Single ND clusters in the lysosomes of cells were observed in the xenografted human lung tumors of nude mice. This study demonstrated for the first time that Ub-coated nanoparticles bind to autophagy receptors for entry into the selective autophagy pathway, facilitating their delivery to lysosomes.
DOI: 10.6084/m9.figshare.4234181
title: HSF1 stress response pathway regulates autophagy receptor SQSTM1/p62-associated proteostasis

description: Proteostasis is important for protecting cells from harmful proteins and is mainly controlled by the HSF1 (heat shock transcription factor 1) stress response pathway. This pathway facilitates protein refolding by molecular chaperones; however, it is unclear whether it functions in autophagy or inclusion formation. The autophagy receptor SQSTM1/p62 is involved in selective autophagic clearance and inclusion formation by harmful proteins, and its phosphorylation at S349, S403, and S407 is required for binding to substrates. Here, we demonstrate that casein kinase 1 phosphorylates the SQSTM1 S349 residue when harmful proteins accumulate. Investigation of upstream factors showed that both SQSTM1 S349 and SQSTM1 S403 residues were phosphorylated in an HSF1 dependent manner. Inhibition of SQSTM1 phosphorylation suppressed inclusion formation by ubiquitinated proteins and prevented colocalization of SQSTM1 with aggregation-prone proteins. Moreover, HSF1 inhibition impaired aggregate-induced autophagosome formation and elimination of protein aggregates. Our findings indicate that HSF1 triggers SQSTM1-mediated proteostasis.
DOI: 10.6084/m9.figshare.4234181.v1
title: HSF1 stress response pathway regulates autophagy receptor SQSTM1/p62-associated proteostasis

description: Proteostasis is important for protecting cells from harmful proteins and is mainly controlled by the HSF1 (heat shock transcription factor 1) stress response pathway. This pathway facilitates protein refolding by molecular chaperones; however, it is unclear whether it functions in autophagy or inclusion formation. The autophagy receptor SQSTM1/p62 is involved in selective autophagic clearance and inclusion formation by harmful proteins, and its phosphorylation at S349, S403, and S407 is required for binding to substrates. Here, we demonstrate that casein kinase 1 phosphorylates the SQSTM1 S349 residue when harmful proteins accumulate. Investigation of upstream factors showed that both SQSTM1 S349 and SQSTM1 S403 residues were phosphorylated in an HSF1 dependent manner. Inhibition of SQSTM1 phosphorylation suppressed inclusion formation by ubiquitinated proteins and prevented colocalization of SQSTM1 with aggregation-prone proteins. Moreover, HSF1 inhibition impaired aggregate-induced autophagosome formation and elimination of protein aggregates. Our findings indicate that HSF1 triggers SQSTM1-mediated proteostasis.