cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1575699.v1
title: COI-based barcoding of Chinese vipers (Reptilia: Squamata: Viperidae)

description: DNA barcoding seeks to assemble a standardized reference library for rapid and unambiguous identification of species, and can be used to screen for potentially cryptic species. The 5′ region of cytochrome oxidase subunit I (COI), which is a mitochondrial DNA (mtDNA) gene fragment, has been proposed as a universal marker for this purpose among animals. However, DNA barcoding of reptiles is still supported only by few datasets compared with other groups. We investigated theutilization of COI to discriminate 34 putative species of vipers, representing almost 92% of the recorded species in China.
Based on a total of 241 sequences, our results indicated that the average degree of intraspecific variability (0.0198) tends to be one-sixth the average of interspecific divergence (0.0931), but no barcoding gap was detected between them. The threshold method, BLOG analyses and tree-based methods all can identify species with a high success rate. These results consistently suggested the usefulness and reliability of the DNA barcoding approach in Chinese vipers.
DOI: 10.6084/m9.figshare.1577588
title: Supplemental data

description: The supplemental data for the following article:
Zhao, Y., Wang, S., Yang, J., Zhang, Z., Liu, Y., Input-Output Analysis of Carbon Emissions Embodied in China-Japan Trade. Appl. Econ. DOI:10.1080/00036846.2015.1102845.
The file includes data of figures below:
Figure 1. CO2 emissions embodied in China–Japan trade, 1995–2009 (Mt).
Figure 2. The sector structure of CO2 emissions embodied in exports (CEE) from China to Japan with the CET definition, 1995–2009.
Figure 3. The sector structure of CO2 emissions embodied in imports (CEI) from Japan to China with the CET definition, 1995–2009.
Figure 4. The sector structure of CO2 emissions embodied in exports (CEE) from China to Japan with the CIT definition, 1995–2009.
Figure 5. The sector structure of CO2 emissions embodied in imports (CEI) from Japan to China with the CIT definition, 1995–2009.
<em>Notes</em>:
1. CEE, CO2 emissions embodied in exports; CEI, CO2 emissions embodied in imports. At the sector level, embodied CO2 emissions can be defined as either the CO2 emissions embodied in trade products of each sector (CET) or the CO2 emissions of each sector induced by total trade products (CIT).
2. The legends of figures contained in this file are colorful for the convenience of examination.
DOI: 10.6084/m9.figshare.1577588.v1
title: Supplemental data

description: The supplemental data for the following article:
Zhao, Y., Wang, S., Yang, J., Zhang, Z., Liu, Y., Input-Output Analysis of Carbon Emissions Embodied in China-Japan Trade. Appl. Econ. DOI:10.1080/00036846.2015.1102845.
The file includes data of figures below:
Figure 1. CO2 emissions embodied in China–Japan trade, 1995–2009 (Mt).
Figure 2. The sector structure of CO2 emissions embodied in exports (CEE) from China to Japan with the CET definition, 1995–2009.
Figure 3. The sector structure of CO2 emissions embodied in imports (CEI) from Japan to China with the CET definition, 1995–2009.
Figure 4. The sector structure of CO2 emissions embodied in exports (CEE) from China to Japan with the CIT definition, 1995–2009.
Figure 5. The sector structure of CO2 emissions embodied in imports (CEI) from Japan to China with the CIT definition, 1995–2009.
<em>Notes</em>:
1. CEE, CO2 emissions embodied in exports; CEI, CO2 emissions embodied in imports. At the sector level, embodied CO2 emissions can be defined as either the CO2 emissions embodied in trade products of each sector (CET) or the CO2 emissions of each sector induced by total trade products (CIT).
2. The legends of figures contained in this file are colorful for the convenience of examination.
DOI: 10.6084/m9.figshare.1582707
title: Whole genome analyses reveal no pathogenetic single nucleotide or structural differences between monozygotic twins discordant for amyotrophic lateral sclerosis

description: The contribution of genetic and environmental factors to the pathogenesis of sporadic amyotrophic lateral sclerosis (ALS) remains unclear. To investigate the genetic component of the disease, we performed whole genome sequencing on ALS discordant monozygotic twins. Illumina whole genome sequencing on white blood cell DNA of five ALS-discordant monozygotic twin pairs (10 samples in total) yielded ∼30x coverage per individual. All single nucleotide variants, indels, and structural variants (copy number variants, inversions and translocations) were called and evaluated for functional consequence, evolutionary conservation, population frequency and overlap with known ALS associated variants and genes. Results showed that no validated discordant coding or regulatory single nucleotide variants or indels were found, and nor were any genome-wide discordant structural variants detected. Concordant variants of particular interest were: 1) two rare, highly-conserved heterozygous non-synonymous variants in <i>SYT9</i> and <i>EWSR1,</i> genes previously associated with ALS (out of 2044 rare heterozygous variants detected); 2) three rare homozygous missense variants; and 3) three novel copy number deletions that overlapped genes. In conclusion, no convincing coding or regulatory nucleotide or genome-wide structural differences were found between ALS discordant monozygotic twins. The results suggest that more work is needed to elucidate possible environmental, epigenetic, oligogenic and somatic genetic factors that could underlie susceptibility to sporadic ALS.
DOI: 10.6084/m9.figshare.1582707.v1
title: Whole genome analyses reveal no pathogenetic single nucleotide or structural differences between monozygotic twins discordant for amyotrophic lateral sclerosis

description: The contribution of genetic and environmental factors to the pathogenesis of sporadic amyotrophic lateral sclerosis (ALS) remains unclear. To investigate the genetic component of the disease, we performed whole genome sequencing on ALS discordant monozygotic twins. Illumina whole genome sequencing on white blood cell DNA of five ALS-discordant monozygotic twin pairs (10 samples in total) yielded ∼30x coverage per individual. All single nucleotide variants, indels, and structural variants (copy number variants, inversions and translocations) were called and evaluated for functional consequence, evolutionary conservation, population frequency and overlap with known ALS associated variants and genes. Results showed that no validated discordant coding or regulatory single nucleotide variants or indels were found, and nor were any genome-wide discordant structural variants detected. Concordant variants of particular interest were: 1) two rare, highly-conserved heterozygous non-synonymous variants in <i>SYT9</i> and <i>EWSR1,</i> genes previously associated with ALS (out of 2044 rare heterozygous variants detected); 2) three rare homozygous missense variants; and 3) three novel copy number deletions that overlapped genes. In conclusion, no convincing coding or regulatory nucleotide or genome-wide structural differences were found between ALS discordant monozygotic twins. The results suggest that more work is needed to elucidate possible environmental, epigenetic, oligogenic and somatic genetic factors that could underlie susceptibility to sporadic ALS.
DOI: 10.6084/m9.figshare.1582729
title: How Many Communities Are There?

description: Stochastic blockmodels and variants thereof are among the most widely used approaches to community detection for social networks and relational data. A stochastic blockmodel partitions the nodes of a network into disjoint sets, called communities. The approach is inherently related to clustering with mixture models; and raises a similar model selection problem for the number of communities. The Bayesian information criterion (BIC) is a popular solution, however, for stochastic blockmodels, the conditional independence assumption given the communities of the endpoints among different edges is usually violated in practice. In this regard, we propose composite likelihood BIC (CL-BIC) to select the number of communities, and we show it is robust against possible misspecifications in the underlying stochastic blockmodel assumptions. We derive the requisite methodology and illustrate the approach using both simulated and real data. Supplementary materials containing the relevant computer code are available online.
DOI: 10.6084/m9.figshare.1582729.v1
title: How Many Communities Are There?

description: Stochastic blockmodels and variants thereof are among the most widely used approaches to community detection for social networks and relational data. A stochastic blockmodel partitions the nodes of a network into disjoint sets, called communities. The approach is inherently related to clustering with mixture models; and raises a similar model selection problem for the number of communities. The Bayesian information criterion (BIC) is a popular solution, however, for stochastic blockmodels, the conditional independence assumption given the communities of the endpoints among different edges is usually violated in practice. In this regard, we propose composite likelihood BIC (CL-BIC) to select the number of communities, and we show it is robust against possible misspecifications in the underlying stochastic blockmodel assumptions. We derive the requisite methodology and illustrate the approach using both simulated and real data. Supplementary materials containing the relevant computer code are available online.
DOI: 10.6084/m9.figshare.1583393
title: A Multi-State Model for Designing Clinical Trials for Testing Overall Survival Allowing for Crossover after Progression

description: In designing a clinical trial for comparing two or more treatments with respect to overall survival (OS), a proportional hazards assumption is commonly made. However, in many cancer clinical trials, patients pass through various disease states prior to death and because of this may receive treatments other than originally assigned. For example, patients may crossover from the control treatment to the experimental treatment at progression. Even without crossover, the survival pattern after progression may be very different than the pattern prior to progression. The proportional hazards assumption will not hold in these situations and the design power calculated on this assumption will not be correct. In this article, we describe a simple and intuitive multi-state model allowing for progression, death before progression, post-progression survival, and crossover after progression and apply this model to the design of clinical trials for comparing the OS of two treatments. For given values of the parameters of the multi-state model, we simulate the required number of deaths to achieve a specified power and the distribution of time required to achieve the requisite number of deaths. The results may be quite different from those derived using the usual PH assumption. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1583393.v1
title: A Multi-state Model for Designing Clinical Trials for Testing Overall Survival Allowing for Crossover after Progression

description: In designing a clinical trial for comparing two or more treatments with respect to overall survival (OS), a proportional hazards assumption is commonly made. However, in many cancer clinical trials, patients pass through various disease states prior to death and because of this may receive treatments other than originally assigned. For example, patients may crossover from the control treatment to the experimental treatment at progression. Even without crossover, the survival pattern after progression may be very different than the pattern prior to progression. The proportional hazards assumption will not hold in these situations and the design power calculated on this assumption will not be correct. In this paper we describe a simple and intuitive multi-state model allowing for progression, death before progression, post-progression survival and crossover after progression and apply this model to the design of clinical trials for comparing the OS of two treatments. For given values of the parameters of the multi-state model, we simulate the required number of deaths to achieve a specified power and the distribution of time required to achieve the requisite number of deaths. The results may be quite different from those derived using the usual PH assumption.
DOI: 10.6084/m9.figshare.1583393.v3
title: A Multi-State Model for Designing Clinical Trials for Testing Overall Survival Allowing for Crossover after Progression

description: In designing a clinical trial for comparing two or more treatments with respect to overall survival (OS), a proportional hazards assumption is commonly made. However, in many cancer clinical trials, patients pass through various disease states prior to death and because of this may receive treatments other than originally assigned. For example, patients may crossover from the control treatment to the experimental treatment at progression. Even without crossover, the survival pattern after progression may be very different than the pattern prior to progression. The proportional hazards assumption will not hold in these situations and the design power calculated on this assumption will not be correct. In this article, we describe a simple and intuitive multi-state model allowing for progression, death before progression, post-progression survival, and crossover after progression and apply this model to the design of clinical trials for comparing the OS of two treatments. For given values of the parameters of the multi-state model, we simulate the required number of deaths to achieve a specified power and the distribution of time required to achieve the requisite number of deaths. The results may be quite different from those derived using the usual PH assumption. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1583393.v2
title: A Multi-State Model for Designing Clinical Trials for Testing Overall Survival Allowing for Crossover after Progression

description: In designing a clinical trial for comparing two or more treatments with respect to overall survival (OS), a proportional hazards assumption is commonly made. However, in many cancer clinical trials, patients pass through various disease states prior to death and because of this may receive treatments other than originally assigned. For example, patients may crossover from the control treatment to the experimental treatment at progression. Even without crossover, the survival pattern after progression may be very different than the pattern prior to progression. The proportional hazards assumption will not hold in these situations and the design power calculated on this assumption will not be correct. In this article, we describe a simple and intuitive multi-state model allowing for progression, death before progression, post-progression survival, and crossover after progression and apply this model to the design of clinical trials for comparing the OS of two treatments. For given values of the parameters of the multi-state model, we simulate the required number of deaths to achieve a specified power and the distribution of time required to achieve the requisite number of deaths. The results may be quite different from those derived using the usual PH assumption. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1584565
title: A new polyketide, penicillolide from the marine-derived fungus <i>Penicillium sacculum</i>

description: A new polyketide, penicillolide (<b>1</b>) was isolated from the fermentation broth of the marine-derived fungus <i>Penicillium sacculum</i> GT-308. Compound <b>1</b> is a polyketide with a unique carbon skeleton. The structure of this compound was established via extensive spectroscopic analyses including 1D-, 2D-NMR, and HRESI-MS.
DOI: 10.6084/m9.figshare.1584565.v2
title: A new polyketide, penicillolide from the marine-derived fungus <i>Penicillium sacculum</i>

description: A new polyketide, penicillolide (<b>1</b>) was isolated from the fermentation broth of the marine-derived fungus <i>Penicillium sacculum</i> GT-308. Compound <b>1</b> is a polyketide with a unique carbon skeleton. The structure of this compound was established via extensive spectroscopic analyses including 1D-, 2D-NMR, and HRESI-MS.
DOI: 10.6084/m9.figshare.1585017
title: nmrlipids.blogspot.fi — on October 25th 2015

description: Snapshot of the blog nmrlipids.blogspot.fi on October 25th 2015.
 
The NMRlipids project is an open scientific collaboration to understand the atomistic resolution structures of lipid bilayers through classical molecular dynamics simulations. The project is progressed through the comments in the blog and using the GitHub organization (see links). The main results are also published in traditional peer reviewed scientific journals.
DOI: 10.6084/m9.figshare.1585017.v1
title: nmrlipids.blogspot.fi — on October 25th 2015

description: Snapshot of the blog nmrlipids.blogspot.fi on October 25th 2015.
 
The NMRlipids project is an open scientific collaboration to understand the atomistic resolution structures of lipid bilayers through classical molecular dynamics simulations. The project is progressed through the comments in the blog and using the GitHub organization (see links). The main results are also published in traditional peer reviewed scientific journals.
DOI: 10.6084/m9.figshare.1585064
title: Identification of ALK5 inhibitor via structure-based virtual screening and ADMET prediction

description: TGF-β plays a critical role in the initiation and progression of fibrosis in various organ systems such as kidney, heart, lung and liver. TGF-β and its receptors (ALK5 and TβR II) are able to control the cellular growth and promote several biological responses. To date, many pharmaceutical companies have employed virtual screening to identify potent inhibitors against ALK5. Nevertheless, none of these studies had involved the <i>in silico</i> ADMET evaluation and Raccoon filtering. In our experiment, all 57423 molecules were downloaded from TCM database and were filtered and converted to PDBQT formats by Raccoon software. Then 24 189 structures were run through AutoDock Vina in PyRx 0.8, 164 molecules were selected and further evaluated by ADMET Predictor 6.5, and 56 structures were selected and docked by Glide 6.2. Finally, the top 10 hits were identified as promising oral ALK5 inhibitors according to their Glide scores. The Glide scores of the best two compounds, 40686 and 33534, were −10.75 and −10.30 kcal/mol, respectively. This research provides a set of combined and detailed virtual screening protocol and is helpful for explaining the mechanism of receptor–ligand interactions.
DOI: 10.6084/m9.figshare.1585064.v1
title: Identification of ALK5 inhibitor via structure-based virtual screening and ADMET prediction

description: TGF-β plays a critical role in the initiation and progression of fibrosis in various organ systems such as kidney, heart, lung and liver. TGF-β and its receptors (ALK5 and TβR II) are able to control the cellular growth and promote several biological responses. To date, many pharmaceutical companies have employed virtual screening to identify potent inhibitors against ALK5. Nevertheless, none of these studies had involved the <i>in silico</i> ADMET evaluation and Raccoon filtering. In our experiment, all 57423 molecules were downloaded from TCM database and were filtered and converted to PDBQT formats by Raccoon software. Then 24 189 structures were run through AutoDock Vina in PyRx 0.8, 164 molecules were selected and further evaluated by ADMET Predictor 6.5, and 56 structures were selected and docked by Glide 6.2. Finally, the top 10 hits were identified as promising oral ALK5 inhibitors according to their Glide scores. The Glide scores of the best two compounds, 40686 and 33534, were −10.75 and −10.30 kcal/mol, respectively. This research provides a set of combined and detailed virtual screening protocol and is helpful for explaining the mechanism of receptor–ligand interactions.
DOI: 10.6084/m9.figshare.1585895
title: Linking Microbial Community Structure to S, N and Fe Biogeochemical Cycling in the Hot Springs at the Tengchong Geothermal Fields, Southwest China

description: Sediment and water samples collected from one acidic and three alkaline high temperature hot springs at the Tengchong terrestrial geothermal field, Southwest China, were examined using mineralogical, geochemical, and molecular biological techniques. The mineralogical and geochemical analyses suggested that these hot springs contained relatively high concentrations of S, Fe and N chemical species. Specifically, the acidic water was rich in Fe<sup>2+</sup>, SO<sub>4</sub><sup>2−</sup> and NH<sub>4</sub><sup>+</sup>, while the alkaline waters were high in NO<sub>3</sub><sup>−</sup>, H<sub>2</sub>S and S<sub>2</sub>O<sub>3</sub><sup>−</sup>. Analyses of 16S rRNA gene sequences showed their bacterial communities were dominated by phyla <i>Aquificae, Cyanobacteria, Deinococci-Thermus, Firmicutes, Proteobacteria</i>, and <i>Thermodesulfobacteria</i>, while the archaeal clone libraries were dominated by orders <i>Desulfurococcales, Sulfolobales</i>, and <i>Thermoproteales</i>. Potential S-, N- and Fe-metabolizing prokaryotes were present at a relatively high proportion, but with large differences in the diversity and metabolic functions of each sample. These findings provide implications for uncovering microbial functions in elemental biogeochemical cycles within the Tengchong geothermal environments: <i>i).</i> the distinct differences in abundance and diversity of microbial communities in geothermal sediments were related to different <i>in situ</i> physicochemical conditions; <i>ii).</i> the S-, N- and Fe-related prokaryotes would take advantage of the strong chemical disequilibria in the hot springs; and <i>iii).</i> in return, their metabolic activities could promote the transformation of the S, Fe and N chemical species, thereby forming the basis of biogeochemical cycles in the terrestrial geothermal environments.