cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6455105
title: A Cretaceous sporomorph palynozonation and the palaeobiogeography of northern Egypt

description: The multiple biozonal nomenclatures given for the same time segment at different locations in northern Egypt are problematic, as such multiplicity is highly confusing and considerably limits the correlative value of these nomenclatures within the Egyptian territory, in the Elaterates phytogeoprovince and in the Tethyan Realm. Thirty-one wells are selected and used in this work to establish a standard and unified, semi-formal, generalised Egyptian sporomorph palynozonation scheme for northern Egypt. Marker taxa are carefully picked and tracked from the different previously established palynostratigraphies, and they are methodically re-used in the present unified framework on a regular basis, where their first down-hole appearance [last appearance datum (LAD)] palynoevents are utilised to erect a regional palynostratigraphical scheme. Ten sporomorph interval zones (IZ) and two subzones are reconstructed, established and palynologically specified from all of the studied wells. The authors surveyed the palynofloral assemblages characterising different areas of the world in order to derive meaningful palaeobiogeographical implications. Connecting these databases furnishes a comprehensive palynostratigraphical framework for inter-continental correlations with the Egyptian assemblages. In addition, such correlations confirm the dating acquired from the recovered palynological markers and assemblages presented in the current review. Comparisons of coeval assemblages confirm that the extensions and boundary limits of the palaeoprovinces of the recorded sporomorphs exhibited a gradual change and that their areal extent evolved with time. Due to the wide geographical occurrences of the recorded marker taxa during the pre-Albian stages of North and West Africa, western Atlantic and east South America, the proposed sporomorph zones can be confidently applied in these areas. During the Albian–Cenomanian such correlations can be applied only between North and West Africa and east South America.
DOI: 10.6084/m9.figshare.6455105.v1
title: A Cretaceous sporomorph palynozonation and the palaeobiogeography of northern Egypt

description: The multiple biozonal nomenclatures given for the same time segment at different locations in northern Egypt are problematic, as such multiplicity is highly confusing and considerably limits the correlative value of these nomenclatures within the Egyptian territory, in the Elaterates phytogeoprovince and in the Tethyan Realm. Thirty-one wells are selected and used in this work to establish a standard and unified, semi-formal, generalised Egyptian sporomorph palynozonation scheme for northern Egypt. Marker taxa are carefully picked and tracked from the different previously established palynostratigraphies, and they are methodically re-used in the present unified framework on a regular basis, where their first down-hole appearance [last appearance datum (LAD)] palynoevents are utilised to erect a regional palynostratigraphical scheme. Ten sporomorph interval zones (IZ) and two subzones are reconstructed, established and palynologically specified from all of the studied wells. The authors surveyed the palynofloral assemblages characterising different areas of the world in order to derive meaningful palaeobiogeographical implications. Connecting these databases furnishes a comprehensive palynostratigraphical framework for inter-continental correlations with the Egyptian assemblages. In addition, such correlations confirm the dating acquired from the recovered palynological markers and assemblages presented in the current review. Comparisons of coeval assemblages confirm that the extensions and boundary limits of the palaeoprovinces of the recorded sporomorphs exhibited a gradual change and that their areal extent evolved with time. Due to the wide geographical occurrences of the recorded marker taxa during the pre-Albian stages of North and West Africa, western Atlantic and east South America, the proposed sporomorph zones can be confidently applied in these areas. During the Albian–Cenomanian such correlations can be applied only between North and West Africa and east South America.
DOI: 10.6084/m9.figshare.6455102
title: Pollen-vegetation relationship in surface sediments, Coringa mangrove ecosystem, India: palaeoecological applications

description: Pollen in the surface sediment collected in a transect from sea to land in the Coringa mangrove wetland was analysed to determine the spatial and quantitative composition of the pollen record for palaeoecological interpretation. Autochthonous pollen preservation of the existing mangrove species was predominant in the sediments and serves as a potential indicator of coastal wetlands. The low quantity of allochthonous and parautochthonous pollen in the sediment reflects the regional plant community. Statistical analysis of the palynological data shows a high association between pollen from <i>Avicennia marina</i> and <i>Clerodendrum inerme</i> and their vegetation. <i>Aegiceras corniculatum</i>, <i>Sonneratia</i>, <i>Ceriops decandra</i>, <i>Xylocarpus mekongenesis</i>, <i>Cocos nucifera</i>, <i>Azadirachta indica</i>, <i>Syzygium</i>, Chenopodiaceae, Poaceae and Cyperaceae show overrepresentation. Ordination techniques for individual species using fidelity and dispersibility indices and regression analyses suggest four different floristic groups, of (i) high dispersibility-moderate fidelity taxa; (ii) high dispersibility-low fidelity taxa; (iii) moderate dispersibility-low fidelity taxa; and (iv) low dispersibility-high fidelity taxa. Species with high fidelity and moderate-low dispersibility indices could be used to identify the vegetation types in sedimentary sequences. The presence of discriminatory taxa (<i>Avicennia marina</i>, <i>Sonneratia</i> sp.), even in small quantities, helps in accurate identification of the local vegetation. Results indicate that while mangrove pollen is transported over short distances, non-mangrove pollen and spores are transported from longer distances. Thus, the status of mangrove and non-mangrove pollen in the sediments provides a clue to the (palaeo)coastal ecology and the (palaeo)climatic conditions.
DOI: 10.6084/m9.figshare.6455102.v2
title: Pollen-vegetation relationship in surface sediments, Coringa mangrove ecosystem, India: palaeoecological applications

description: Pollen in the surface sediment collected in a transect from sea to land in the Coringa mangrove wetland was analysed to determine the spatial and quantitative composition of the pollen record for palaeoecological interpretation. Autochthonous pollen preservation of the existing mangrove species was predominant in the sediments and serves as a potential indicator of coastal wetlands. The low quantity of allochthonous and parautochthonous pollen in the sediment reflects the regional plant community. Statistical analysis of the palynological data shows a high association between pollen from <i>Avicennia marina</i> and <i>Clerodendrum inerme</i> and their vegetation. <i>Aegiceras corniculatum</i>, <i>Sonneratia</i>, <i>Ceriops decandra</i>, <i>Xylocarpus mekongenesis</i>, <i>Cocos nucifera</i>, <i>Azadirachta indica</i>, <i>Syzygium</i>, Chenopodiaceae, Poaceae and Cyperaceae show overrepresentation. Ordination techniques for individual species using fidelity and dispersibility indices and regression analyses suggest four different floristic groups, of (i) high dispersibility-moderate fidelity taxa; (ii) high dispersibility-low fidelity taxa; (iii) moderate dispersibility-low fidelity taxa; and (iv) low dispersibility-high fidelity taxa. Species with high fidelity and moderate-low dispersibility indices could be used to identify the vegetation types in sedimentary sequences. The presence of discriminatory taxa (<i>Avicennia marina</i>, <i>Sonneratia</i> sp.), even in small quantities, helps in accurate identification of the local vegetation. Results indicate that while mangrove pollen is transported over short distances, non-mangrove pollen and spores are transported from longer distances. Thus, the status of mangrove and non-mangrove pollen in the sediments provides a clue to the (palaeo)coastal ecology and the (palaeo)climatic conditions.
DOI: 10.6084/m9.figshare.6455102.v1
title: Pollen-vegetation relationship in surface sediments, Coringa mangrove ecosystem, India: palaeoecological applications

description: Pollen in the surface sediment collected in a transect from sea to land in the Coringa mangrove wetland was analysed to determine the spatial and quantitative composition of the pollen record for palaeoecological interpretation. Autochthonous pollen preservation of the existing mangrove species was predominant in the sediments and serves as a potential indicator of coastal wetlands. The low quantity of allochthonous and parautochthonous pollen in the sediment reflects the regional plant community. Statistical analysis of the palynological data shows a high association between pollen from <i>Avicennia marina</i> and <i>Clerodendrum inerme</i> and their vegetation. <i>Aegiceras corniculatum</i>, <i>Sonneratia</i>, <i>Ceriops decandra</i>, <i>Xylocarpus mekongenesis</i>, <i>Cocos nucifera</i>, <i>Azadirachta indica</i>, <i>Syzygium</i>, Chenopodiaceae, Poaceae and Cyperaceae show overrepresentation. Ordination techniques for individual species using fidelity and dispersibility indices and regression analyses suggest four different floristic groups, of (i) high dispersibility-moderate fidelity taxa; (ii) high dispersibility-low fidelity taxa; (iii) moderate dispersibility-low fidelity taxa; and (iv) low dispersibility-high fidelity taxa. Species with high fidelity and moderate-low dispersibility indices could be used to identify the vegetation types in sedimentary sequences. The presence of discriminatory taxa (<i>Avicennia marina</i>, <i>Sonneratia</i> sp.), even in small quantities, helps in accurate identification of the local vegetation. Results indicate that while mangrove pollen is transported over short distances, non-mangrove pollen and spores are transported from longer distances. Thus, the status of mangrove and non-mangrove pollen in the sediments provides a clue to the (palaeo)coastal ecology and the (palaeo)climatic conditions.
DOI: 10.6084/m9.figshare.6455096
title: Gene Ontology Enrichment - unfiltered

description: Gene Ontology Enrichment results based on differentially expressed gene lists.<br>see README.md for more details.
DOI: 10.6084/m9.figshare.6455024
title: LIHC transcriptome Stages Analysis - supplementary information

description: Sarathi, A and Palaniappan A. Novel significant stage-specific differentially expressed genes in liver hepatocellular carcinoma.<i> </i>(2018) <i>https://www.biorxiv.org/content/early/2018/06/08/342204</i> <br>Supplementary Information.
DOI: 10.6084/m9.figshare.6455024.v1
title: LIHC transcriptome Stages Analysis - supplementary information

description: Sarathi, A and Palaniappan A. Novel significant stage-specific differentially expressed genes in liver hepatocellular carcinoma.<i> </i>(2018) <i>https://www.biorxiv.org/content/early/2018/06/08/342204</i> <br>Supplementary Information.
DOI: 10.6084/m9.figshare.6455021
title: Raw Kymographs - Optical DNA Mapping

description: Supporting data for publication "The Resistomes of Six Carbapenem-Resistant Pathogens – A Critical Genotype-Phenotype Analysis."<br><br>Data provided as raw Kymographs (TIFF) from Optical DNA mapping experiments. File name indicates plasmid followed by molecule number within ().<strong><br></strong><strong></strong>
DOI: 10.6084/m9.figshare.6455021.v1
title: Raw Kymographs - Optical DNA Mapping

description: Supporting data for publication "The Resistomes of Six Carbapenem-Resistant Pathogens – A Critical Genotype-Phenotype Analysis."<br><br>Data provided as raw Kymographs (TIFF) from Optical DNA mapping experiments. File name indicates plasmid followed by molecule number within ().<strong><br></strong><strong></strong>
DOI: 10.6084/m9.figshare.6454973.v1
title: SNU, SNU MELANOMA, and Reddit dataset + Quiz

description: <b>1. SNU_thumbnail100.zip</b>SNU Dataset2201 images; thumbnail<br>Red rectangle - diagnosed by biopsyBlack rectangle - diagnosed by clinical impression<br><b>2. SNU_melanoma_thumbnail100.zip</b>SNU MELANOMA Dataset151 images; thumbnail<br><b>3. Reddit_thumbnail100.zip</b>Reddit Dataset222 images; thumbnailreddit.ods - download URLs of the images<br><b>4. quiz.zip</b>SNU Dataset; Quiz for AI and Dermatologist240 images; SNU datasetQUIZ.pdfANSWER.xlsxdoctor.xlsxdoctor_AI.xlsxpublic.xlsxpublic_AI.xlsx<br><br><b># Edinburgh dataset</b>Edinburgh dermofit image library is a commercial library.; https://licensing.edinburgh-innovations.ed.ac.uk/i/software/dermofit-image-library.html<br>
DOI: 10.6084/m9.figshare.6454973.v3
title: SNU, SNU MELANOMA, and Reddit dataset + Quiz

description: <b>1. SNU_thumbnail100.zip</b>SNU Dataset2201 images; thumbnail<br>Red rectangle - diagnosed by biopsyBlack rectangle - diagnosed by clinical impression<br><b>2. SNU_melanoma_thumbnail100.zip</b>SNU MELANOMA Dataset151 images; thumbnail<br><b>3. SNU_melanoma_Breslow.zip</b>SNU Dataset49 images; thumbnailSNU_melanoma_Breslow.xlsx : 1) Breslow thickness 2) invasive vs in situ 3) Age/Sex<br><br><b>4. quiz.zip</b>SNU Dataset; Quiz for AI and Dermatologist240 images; SNU datasetQUIZ.pdfANSWER.xlsxdoctor.xlsxdoctor_AI.xlsxpublic.xlsxpublic_AI.xlsx<br><b>5. quiz2201.zip</b>SNU Dataset; Quiz for AI and Dermatologist2201 images; thumbnail (1.jpg ~ 36.jpg)quiz2201.xlsxquiz2201_AI.xlsx<br>answer.ods<br><br><b># Edinburgh dataset</b>Edinburgh dermofit image library is a commercial library.; https://licensing.edinburgh-innovations.ed.ac.uk/i/software/dermofit-image-library.html<br>
DOI: 10.6084/m9.figshare.6454973.v6
title: SNU and SNU MELANOMA dataset + Quiz

description: <b>1. SNU_thumbnail100.zip</b>SNU Dataset2201 images; thumbnail<br>Red rectangle - diagnosed by biopsyBlack rectangle - diagnosed by clinical impression<br><b>2. SNU_melanoma_thumbnail100.zip</b>SNU MELANOMA Dataset151 images; thumbnail<br><b>3. SNU_melanoma_Breslow.zip</b>SNU Dataset49 images; thumbnailSNU_melanoma_Breslow.xlsx : 1) Breslow thickness 2) invasive vs in situ 3) Age/Sex<br><br><b>4. quiz.zip</b>SNU Dataset; Quiz for AI and Dermatologist240 images; SNU datasetQUIZ.pdfANSWER.xlsxdoctor.xlsxdoctor_AI.xlsxpublic.xlsxpublic_AI.xlsx<br><b>5. quiz2201.zip</b>SNU Dataset; Quiz for AI and Dermatologist2201 images; thumbnail (1.jpg ~ 36.jpg)quiz2201.xlsxquiz2201_AI.xlsx<br>answer.ods<br><b>6. Raw output - Miss rate</b>We calculated miss rate (1-sensitivity) from the raw outputs of CNN with the whole SNU dataset (2201 images).<br>The X-axis is raw_output and Y-axis is miss rate, and the graph is close to a straight line.We used miss rate instead of raw output. Thus, we make it possible to follow up the obtained value even if the algorithm will be changed.<br><b>7. disease code_with_ICD10</b>The name of 174 training classes with ICD-10We tested with 134 disorders (Table 3 of the paper).<br><br><b># Edinburgh dataset</b>Edinburgh dermofit image library is a commercial library.; https://licensing.edinburgh-innovations.ed.ac.uk/i/software/dermofit-image-library.html<br>
DOI: 10.6084/m9.figshare.6454973.v9
title: SNU dataset + Quiz

description: <b>1. SNU_thumbnail100.zip</b>SNU Dataset2201 images; thumbnail<br>Red rectangle - diagnosed by biopsyBlack rectangle - diagnosed by clinical impression<br><b>2. quiz.zip</b><br>SNU Dataset; Quiz for AI and Dermatologist240 images; SNU datasetQUIZ.pdfANSWER.xlsxdoctor.xlsxdoctor_AI.xlsxpublic.xlsxpublic_AI.xlsx<br><b>3. quiz2201.zip</b>SNU Dataset; Quiz for AI and Dermatologist2201 images; thumbnail (1.jpg ~ 36.jpg)quiz2201.xlsxquiz2201_AI.xlsx<br>answer.ods<br><b>4. disease code_with_ICD10</b>174 disease classes for the model training<br><br><b>5. SUPPLEMENTARY dataset</b>Validation dataset that used to draw Figure S1151 images; thumbnailBreslow thickness<br><br><b># Edinburgh dataset</b>Edinburgh dermofit image library is a commercial library.; https://licensing.edinburgh-innovations.ed.ac.uk/i/software/dermofit-image-library.html<br>
DOI: 10.6084/m9.figshare.6454877
title: Supplementary Material for: Tenacity of Collateral Perfusion in Proximal Cerebral Arterial Occlusions 6–12 h after Onset

description: <b><i>Background:</i></b> Clinical trials have shown that benefits of endovascular recanalization (EVT) for acute ischemic stroke patients with sizable penumbral tissues seems plausible even beyond 6 h after their last seen normal (LSN). Persistency of ischemic penumbra remains unclear in delayed periods. <b><i>Methods:</i></b> From a prospective stroke registry database, we identified 111 acute ischemic stroke patients who had internal carotid artery or middle cerebral artery occlusion with baseline National Institutes of Health Stroke Scale scores ≥6 points and arrived 6–12 h after LSN. Baseline information and functional outcomes were prospectively collected as a clinical registry. Attending physicians made treatment decisions for EVT based on the current guidelines and institutional protocols. MR image parameters, including the volume of diffusion-restricted lesions and mapping of the ­hypoperfused area, were quantified using automated commercial software. Binary logistic regression analysis models, with modified Rankin Scale (mRS) scores of 0–1 at 3 months after stroke included as a dependent variable, were constructed. <b><i>Results:</i></b> Between 6 and 12 h after onset, 58% had a mismatch ratio of ≥1.8 at baseline and 42% had favorable imaging profiles as determined by DEFUSE 2 study. After 9 h, there was a mismatch ratio of ≥1.8 in 47 and 38% favorable profiles. EVT was performed in 54% of cases. A 3-month mRS score of 0–1 was found in 19% (25% in EVT and 12% in medical treatment groups) of cases. EVT was associated with an increased OR of having a mRS score of 0–1 at 3 months after stroke (adjusted OR 7.59 [95% CI 1.28–61.60]). <b><i>Conclusions:</i></b> Penumbral tissues were persistent in a substantial proportion of anterior circulation occlusion cases 6–12 h after LSN. EVT at 6–12 h in a predominantly Asian cohort resulted in better outcomes.
DOI: 10.6084/m9.figshare.6454877.v1
title: Supplementary Material for: Tenacity of Collateral Perfusion in Proximal Cerebral Arterial Occlusions 6–12 h after Onset

description: <b><i>Background:</i></b> Clinical trials have shown that benefits of endovascular recanalization (EVT) for acute ischemic stroke patients with sizable penumbral tissues seems plausible even beyond 6 h after their last seen normal (LSN). Persistency of ischemic penumbra remains unclear in delayed periods. <b><i>Methods:</i></b> From a prospective stroke registry database, we identified 111 acute ischemic stroke patients who had internal carotid artery or middle cerebral artery occlusion with baseline National Institutes of Health Stroke Scale scores ≥6 points and arrived 6–12 h after LSN. Baseline information and functional outcomes were prospectively collected as a clinical registry. Attending physicians made treatment decisions for EVT based on the current guidelines and institutional protocols. MR image parameters, including the volume of diffusion-restricted lesions and mapping of the ­hypoperfused area, were quantified using automated commercial software. Binary logistic regression analysis models, with modified Rankin Scale (mRS) scores of 0–1 at 3 months after stroke included as a dependent variable, were constructed. <b><i>Results:</i></b> Between 6 and 12 h after onset, 58% had a mismatch ratio of ≥1.8 at baseline and 42% had favorable imaging profiles as determined by DEFUSE 2 study. After 9 h, there was a mismatch ratio of ≥1.8 in 47 and 38% favorable profiles. EVT was performed in 54% of cases. A 3-month mRS score of 0–1 was found in 19% (25% in EVT and 12% in medical treatment groups) of cases. EVT was associated with an increased OR of having a mRS score of 0–1 at 3 months after stroke (adjusted OR 7.59 [95% CI 1.28–61.60]). <b><i>Conclusions:</i></b> Penumbral tissues were persistent in a substantial proportion of anterior circulation occlusion cases 6–12 h after LSN. EVT at 6–12 h in a predominantly Asian cohort resulted in better outcomes.
DOI: 10.6084/m9.figshare.6453902.v2
title: Schematic representation of the parameters for the power simulation using powsim

description: We think that the power simulation should reflect the measured data of each single-cell RNA-seq method; therefore, the user should enter each appropriate parameter for powsim. We empirically used a number of detected genes based on measured data (including Quartz-Seq2 data and reported single-cell RNA-seq data as the “ngenes parameter” in each powsimR simulation. We already showed that a number of detected genes greatly differed by method. For example, the detected gene count differed greatly between Quartz-Seq2 and Drop-seq (Quartz-Seq2: 6,322 ± 144 genes; Drop-seq: 2,574 genes). Moreover, the number of differentially expressed genes strongly depended on the number of detected genes. In particular, the DESetup object for the simulateDE function had an ngenes parameter in PowsimR. For each method, we indicated a mean number of detected genes for the ngenes parameter of the DESetup object. We had already mentioned this in Quartz-Seq2 paper (main text: lines 1,137–1,148). In Ziegenhain et al. (2017), the ngenes parameter might be fixed at the same number (i.e., 13,361 genes) for all methods. The parameter presumes that the gene-detection capability of each method is the same; however, in reality, the number of detected genes differs by method. The fixed number of ngenes parameter is very different from the measured single-cell RNA-sequencing data; therefore, we used the number of detected genes based on the measured data as the “ngenes parameter” and calculated the number of true positive differentially expressed genes. The parameter (based on measured data) makes power simulation more meaningful.
DOI: 10.6084/m9.figshare.6453893.v1
title: Data.xlsx

description: This file includes monthly or phenological-periodic mean values of litterfall, leaf area index, water-use efficiency, air temperature and soil water content in Southwest China rubber plantations at four stand ages and three planting densities.
DOI: 10.6084/m9.figshare.6453893.v2
title: Data.xlsx

description: This file includes monthly or phenological-periodic mean values of litterfall, leaf area index, water-use efficiency, air temperature and soil water content in Southwest China rubber plantations at four stand ages and three planting densities.
DOI: 10.6084/m9.figshare.6453893.v4
title: Data.xlsx

description: This file includes monthly or phenological-periodic mean values of litterfall, leaf area index, water-use efficiency, air temperature and soil water content in Southwest China rubber plantations at four stand ages and planting densities.
DOI: 10.6084/m9.figshare.6453893.v3
title: Data.xlsx

description: This file includes monthly or phenological-periodic mean values of litterfall, leaf area index, water-use efficiency, air temperature and soil water content in Southwest China rubber plantations at four stand ages and planting densities.
DOI: 10.6084/m9.figshare.6453872
title: Intuitive and efficient computer-aided music rearrangement with optimised processing of audio transitions

description: A promising approach to create new versions of existing music pieces automatically is to cut out and rearrange sections so that transitions are minimally perceptible and constraints regarding duration or structure are fulfilled. We evaluate previous work and improve on its limitations, particularly the disregard for loudness changes at cuts and the unintuitive control over the musical structure of the output. Our software provides a user-friendly interface, which we make more responsive by greatly accelerating the search for an optimal output track using the A* algorithm. Listening experiments demonstrate an improvement in perceived audio quality.