cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5503720
title: Finding the Number of Normal Groups in Model-Based Clustering via Constrained Likelihoods

description: Deciding the number of clusters <i>k</i> is one of the most difficult problems in cluster analysis. For this purpose, complexity-penalized likelihood approaches have been introduced in model-based clustering, such as the well known BIC and ICL criteria. However, the classification/mixture likelihoods considered in these approaches are unbounded without any constraint on the cluster scatter matrices. Constraints also prevent traditional EM and CEM algorithms from being trapped in (spurious) local maxima. Controlling the maximal ratio between the eigenvalues of the scatter matrices to be smaller than a fixed constant <i>c</i> ≥ 1 is a sensible idea for setting such constraints. A new penalized likelihood criterion which takes into account the higher model complexity that a higher value of <i>c</i> entails, is proposed. Based on this criterion, a novel and fully automated procedure, leading to a small ranked list of optimal (<i>k, c</i>) couples is provided. A new plot called “car-bike” which provides a concise summary of the solutions is introduced. The performance of the procedure is assessed both in empirical examples and through a simulation study as a function of cluster overlap. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.5504086.v9
title: Robust_TIE_Solver.m

description: This function is utilized to robustly solve the transport-of-intensity equation (TIE) for retrieving the pseudo-phase of samples.
DOI: 10.6084/m9.figshare.5503816.v3
title: Appendix-1 and subject programs

description: This folder contains Appendix-1 and the source code of the subject programs we used in the experiments.
DOI: 10.6084/m9.figshare.5503720.v1
title: Finding the Number of Normal Groups in Model-Based Clustering via Constrained Likelihoods

description: Deciding the number of clusters <i>k</i> is one of the most difficult problems in cluster analysis. For this purpose, complexity-penalized likelihood approaches have been introduced in model-based clustering, such as the well known BIC and ICL criteria. However, the classification/mixture likelihoods considered in these approaches are unbounded without any constraint on the cluster scatter matrices. Constraints also prevent traditional EM and CEM algorithms from being trapped in (spurious) local maxima. Controlling the maximal ratio between the eigenvalues of the scatter matrices to be smaller than a fixed constant <i>c</i> ≥ 1 is a sensible idea for setting such constraints. A new penalized likelihood criterion which takes into account the higher model complexity that a higher value of <i>c</i> entails, is proposed. Based on this criterion, a novel and fully automated procedure, leading to a small ranked list of optimal (<i>k, c</i>) couples is provided. A new plot called “car-bike” which provides a concise summary of the solutions is introduced. The performance of the procedure is assessed both in empirical examples and through a simulation study as a function of cluster overlap. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.5503816.v4
title: Appendix-1 and subject programs

description: This folder contains Appendix-1 and the source code of the subject programs we used in the experiments.
DOI: 10.6084/m9.figshare.5503678
title: Petrology and isotopic evolution of granulites from central Madurai Block (southern India): reference to Ediacaran crustal evolution

description: The Madurai Block, constituting part of the southern granulite terrain in southern India, has contributed significantly towards understanding the UHT (ultrahigh-temperature) granulites that serve as a window into the mid-lower continental crust. The dominant rock types are charnockites, sapphirine-bearing granulites, garnet cordierite gneisses, and quartzites. Significant textural relations reveal multiphase reactions responsible for the formation of diverse mineral parageneses during prolonged metamorphic history of the area. Prograde reaction is evident from the textural relationship where biotite/sillimanite relics are seen as inclusion in garnet/orthopyroxene, suggesting dehydration reactions. The symplectitic assemblages that formed during isothermal decompression involve a series of cordierite-forming reactions, followed by retrogression and cooling. Variety of mineral assemblages present in the rocks of this area offer a wide spectrum of <i>P</i>–<i>T</i> sensors that provide details on the physical conditions of metamorphism. For the rigorous interpretation of the <i>P</i>–<i>T</i> path in the Perumalmalai area, quantitative phase diagrams (<i>P</i>–<i>T</i> pseudosections) have been constructed and contoured for the compositional as well as modal isopleths of involved mineral phases. The rocks of Perumalmalai area document a clockwise decompression <i>P</i>–<i>T</i> trajectory, consistent with crustal thickening followed by extensional collapse. SHRIMP U–Pb ages from zircon associated with sapphirine-bearing granulite facies rocks of Perumalmalai area suggest a widespread Ediacaran tectonothermal event. The occurrence of Ediacaran UHT metamorphism followed by isothermal decompression in the Madurai Block is consistent with the timing and physical conditions associated with the formation of East African Orogen during the amalgamation of Gondwana.
DOI: 10.6084/m9.figshare.5502199
title: Global_North_Atlantic_Alaska_synthesis_record.txt

description: This three synthesis series was calculated and used in the study published by Linderholm et al. (2017). The methods used to select the series and caculate the records are available in the discussion paper.<br><br>Linderholm, H. W., Nicolle, M., Francus, P., Gajewski, K., Helama, S., Korhola, A., Solomina, O., Yu, Z., Zhang, P., D'Andrea, W. J., Debret, M., Divine, D., Gunnarson, B. E., Loader, N. J., Massei, N., Seftifgen, K., Thomas, E. K., and Werner, J.: Arctic hydroclimate variability during the last 2000 years – current understanding and research challenges, Clim. Past Discuss., https://doi.org/10.5194/cp-2017-34, in review, 2017. <br>
DOI: 10.6084/m9.figshare.5503678.v1
title: Petrology and isotopic evolution of granulites from central Madurai Block (southern India): reference to Ediacaran crustal evolution

description: The Madurai Block, constituting part of the southern granulite terrain in southern India, has contributed significantly towards understanding the UHT (ultrahigh-temperature) granulites that serve as a window into the mid-lower continental crust. The dominant rock types are charnockites, sapphirine-bearing granulites, garnet cordierite gneisses, and quartzites. Significant textural relations reveal multiphase reactions responsible for the formation of diverse mineral parageneses during prolonged metamorphic history of the area. Prograde reaction is evident from the textural relationship where biotite/sillimanite relics are seen as inclusion in garnet/orthopyroxene, suggesting dehydration reactions. The symplectitic assemblages that formed during isothermal decompression involve a series of cordierite-forming reactions, followed by retrogression and cooling. Variety of mineral assemblages present in the rocks of this area offer a wide spectrum of <i>P</i>–<i>T</i> sensors that provide details on the physical conditions of metamorphism. For the rigorous interpretation of the <i>P</i>–<i>T</i> path in the Perumalmalai area, quantitative phase diagrams (<i>P</i>–<i>T</i> pseudosections) have been constructed and contoured for the compositional as well as modal isopleths of involved mineral phases. The rocks of Perumalmalai area document a clockwise decompression <i>P</i>–<i>T</i> trajectory, consistent with crustal thickening followed by extensional collapse. SHRIMP U–Pb ages from zircon associated with sapphirine-bearing granulite facies rocks of Perumalmalai area suggest a widespread Ediacaran tectonothermal event. The occurrence of Ediacaran UHT metamorphism followed by isothermal decompression in the Madurai Block is consistent with the timing and physical conditions associated with the formation of East African Orogen during the amalgamation of Gondwana.
DOI: 10.6084/m9.figshare.5503816.v5
title: Appendix-1 and subject programs

description: This folder contains Appendix-1 and the source code of the subject programs we used in the experiments.
DOI: 10.6084/m9.figshare.5502199.v1
title: Global_North_Atlantic_Alaska_synthesis_record.txt

description: This three synthesis series was calculated and used in the study published by Linderholm et al. (2017). The methods used to select the series and caculate the records are available in the discussion paper.<br><br>Linderholm, H. W., Nicolle, M., Francus, P., Gajewski, K., Helama, S., Korhola, A., Solomina, O., Yu, Z., Zhang, P., D'Andrea, W. J., Debret, M., Divine, D., Gunnarson, B. E., Loader, N. J., Massei, N., Seftifgen, K., Thomas, E. K., and Werner, J.: Arctic hydroclimate variability during the last 2000 years – current understanding and research challenges, Clim. Past Discuss., https://doi.org/10.5194/cp-2017-34, in review, 2017. <br>
DOI: 10.6084/m9.figshare.5503816.v6
title: Appendix-1 and subject programs

description: This folder contains Appendix-1 and the source code of the subject programs we used in the experiments.
DOI: 10.6084/m9.figshare.5502025
title: Gait_Parameters

description: Gait parameters data extracted from experimental study: 'Gait parameters are differently affected by concurrent smartphone-based activities with scaled levels of cognitive effort'.Please refer to the readme.txt file for the additional information
DOI: 10.6084/m9.figshare.5503816.v8
title: Appendix-1 and subject programs

description: This folder contains Appendix-1 and the source code of the subject programs we used in the experiments.
DOI: 10.6084/m9.figshare.5502010
title: Supplementary information: A tangle of forms and phylogeny: extensive morphological homoplasy and molecular clock heterogeneity in Bonnetina and related tarantulas

description: Supplementary information of paper: A tangle of forms and phylogeny: extensive morphological homoplasy and molecular clock heterogeneity in <i>Bonnetina</i> and related tarantulas<b></b>
DOI: 10.6084/m9.figshare.5502025.v1
title: Gait_Parameters

description: Gait parameters data extracted from experimental study: 'Gait parameters are differently affected by concurrent smartphone-based activities with scaled levels of cognitive effort'.Please refer to the readme.txt file for the additional information
DOI: 10.6084/m9.figshare.5503816.v7
title: Appendix-1 and subject programs

description: This folder contains Appendix-1 and the source code of the subject programs we used in the experiments.
DOI: 10.6084/m9.figshare.5502088.v1
title: Supplemental Material 3_Custom Transcriptome Reference

description: Contains the full list of putative ncRNA and coding transcripts in a multifasta format. Must be compiled in to the appropriate reference using the particular mapper of interest (RSEM, Kallisto, Salmon)
DOI: 10.6084/m9.figshare.5502010.v2
title: Supplementary information: A tangle of forms and phylogeny: extensive morphological homoplasy and molecular clock heterogeneity in Bonnetina and related tarantulas

description: Supplementary information of paper: A tangle of forms and phylogeny: extensive morphological homoplasy and molecular clock heterogeneity in <i>Bonnetina</i> and related tarantulas<b></b>
DOI: 10.6084/m9.figshare.5501854
title: Potential carbon stock in the Kruger National Park, South Africa

description: Global concern about climate change motivates for increasing interests in revising the management plan of natural ecosystems to include carbon sequestration services. Such revision must be informed of knowledge of carbon storage capacity of these ecosystems and the underlying factors. Here, the aim is twofold: to quantify the carbon stock that could be expected from the diversity of trees (~500 species) in the Kruger National Park (KNP; ~2 million ha) if all individual trees recorded in 110 plots of 50 m × 50 m grow to their maximal potential; and to test the predictive power of several potential correlates of the physiology of carbon storage. The results indicated the KNP is a potential reservoir of ~2 × 10<sup>8</sup> tonnes of carbon with a total mean density (above + below-ground carbon) of ~105 tonnes ha<sup>−1</sup>, a carbon density comparable with that of many other natural systems. Carbon storage in the KNP did not correlate with phylogeny and species abundance, but did so with phenology and wood density. However, only 4% of the variation in carbon storage was explained, indicating that key determinants of carbon storage are missing in this analysis. Although this study suffered a number of limitations that are presented, the expectation from this study is that it would raise increased interests into the potential of carbon stocked in the KNP in South Africa as one of the key diverse services this park provides beyond biodiversity conservation.
DOI: 10.6084/m9.figshare.5502010.v1
title: Supplementary information: A tangle of forms and phylogeny: extensive morphological homoplasy and molecular clock heterogeneity in Bonnetina and related tarantulas

description: Supplementary information of paper: A tangle of forms and phylogeny: extensive morphological homoplasy and molecular clock heterogeneity in <i>Bonnetina</i> and related tarantulas<b></b>
DOI: 10.6084/m9.figshare.5501854.v1
title: Potential carbon stock in the Kruger National Park, South Africa

description: Global concern about climate change motivates for increasing interests in revising the management plan of natural ecosystems to include carbon sequestration services. Such revision must be informed of knowledge of carbon storage capacity of these ecosystems and the underlying factors. Here, the aim is twofold: to quantify the carbon stock that could be expected from the diversity of trees (~500 species) in the Kruger National Park (KNP; ~2 million ha) if all individual trees recorded in 110 plots of 50 m × 50 m grow to their maximal potential; and to test the predictive power of several potential correlates of the physiology of carbon storage. The results indicated the KNP is a potential reservoir of ~2 × 10<sup>8</sup> tonnes of carbon with a total mean density (above + below-ground carbon) of ~105 tonnes ha<sup>−1</sup>, a carbon density comparable with that of many other natural systems. Carbon storage in the KNP did not correlate with phylogeny and species abundance, but did so with phenology and wood density. However, only 4% of the variation in carbon storage was explained, indicating that key determinants of carbon storage are missing in this analysis. Although this study suffered a number of limitations that are presented, the expectation from this study is that it would raise increased interests into the potential of carbon stocked in the KNP in South Africa as one of the key diverse services this park provides beyond biodiversity conservation.
DOI: 10.6084/m9.figshare.5501773
title: Vitamin D supplementation and non-alcoholic fatty liver disease: A critical and systematic review of clinical trials

description: Previous observational studies have found a relationship between vitamin D deficiency and non-alcoholic fatty liver disease (NAFLD). However, this type of study could not show the causal relationship between these two conditions. Therefore, we systematically and critically reviewed the available clinical trials to elucidate such relationship. We searched databases such as Medline, Scopus and Cochrane to identify the clinical trials that assessed the effects of vitamin D supplementation in adults with NAFLD. The outcome variables of interest were indicators of hepatic steatosis, liver enzymes, insulin resistance, inflammation and oxidative stress. A total of 6 studies were included in the qualitative analysis. Only in two studies the grade of hepatic steatosis decreased significantly after vitamin D supplementation. The changes in insulin resistance parameters were reported significant only in one. Of the 3 included studies that measured biomarkers of inflammation and oxidative stress, one revealed a significant decrease in these biomarkers after vitamin D supplementation. Findings from current review study provided new insight into the factors that could affect the therapeutic role of vitamin D in NAFLD. Factors such as gender differences, baseline serum status of vitamin D, co-supplementation with calcium and gene polymorphism should be considered when designing future clinical trials.
DOI: 10.25345/c52f44
title: MassIVE MSV000086050 - Lamellodysidea herbacea GUM007 (sponge) extract
title: GUM007 whole-sponge tissue was pulverized and extracted with 3 x 20-ml MeOH for 30 to 60 min on a benchtop nutator. The combined extracts were dried in vacuo. Approx. 100 mg MeOH extract and 40 mL RNALater (used to store the sponge tissue) were loaded onto 1g C18 solid-phase extraction columns (Canadian Life Science) and fractionated from 5% - 100% MeCN. Three standards, dysinosin A, dysinosin B, and dysinosin C, kindly provided by Ron Quinn from Griffith University, were prepared as 0.1 mg/ml solutions in MeOH and analyzed with the GUM007 MeCN fractions using the Agilent 6530 Accurate-Mass Q-TOF MS with a Phenomenex Kinetex 5 uM C18(2) 100-A, 150 by 4.6 mm column (0 to 3 min 5% MeCN isocratic, 3 - 23 min, 5 - 100% MeCN, 23 to 26 min 100% MeCN isocratic at 0.7 ml/min). The dysinosin standards revealed a characteristic loss of sulfate, which led to the discovery of the desoxydysinosins, present in the 15% and 20% MeCN fractions.
DOI: 10.6084/m9.figshare.5501716
title: CNN trained in Mathematica to distinguish between clubmosses and spikemosses

description: CNN trained in Mathematica to distinguish between clubmosses and spikemosses
DOI: 10.6084/m9.figshare.5501695
title: Data Eucalyptus-Becerra et al.xlsx

description: Data of the field study
DOI: 10.6084/m9.figshare.5501638
title: Floristic and climatic reconstructions of two Lower Cretaceous successions from Peru

description: Climate during the Early Cretaceous in tropical South America has often been reconstructed as arid. However, some areas seem to have been humid. We reconstructed the floristic composition of two tropical stratigraphic successions in Peru using quantitative palynology (rarefied species richness and abundance), and used the abundance of aridity vs. humidity indicator species to infer the predominant climate conditions of this region. The Berriasian to Hauterivian La Merced succession was dominated by fern spores and was predominantly humid. The Albian Aguas Frias succession yielded rich palynofloras, with 127 species, and also indicates predominantly humid conditions. These results support the hypothesis that the west margin of South America was humid during the Early Cretaceous, thus improving the tropical climate reconstructions during the Cretaceous severe global warming episodes.
DOI: 10.6084/m9.figshare.5501773.v1
title: Vitamin D Supplementation and Non-alcoholic fatty liver disease: A Critical and Systematic Review of Clinical Trials

description: Previous observational studies have found a relationship between vitamin D deficiency and non-alcoholic fatty liver disease (NAFLD). However, this type of study could not show the causal relationship between these two conditions. Therefore, we systematically and critically reviewed the available clinical trials to elucidate such relationship. We searched databases such as Medline, Scopus and Cochrane to identify the clinical trials that assessed the effects of vitamin D supplementation in adults with NAFLD. The outcome variables of interest were indicators of hepatic steatosis, liver enzymes, insulin resistance, inflammation and oxidative stress. A total of 6 studies were included in the qualitative analysis. Only in two studies the grade of hepatic steatosis decreased significantly after vitamin D supplementation. The changes in insulin resistance parameters were reported significant only in one. Of the 3 included studies that measured biomarkers of inflammation and oxidative stress, one revealed a significant decrease in these biomarkers after vitamin D supplementation. Findings from current review study provided new insight into the factors that could affect the therapeutic role of vitamin D in NAFLD. Factors such as gender differences, baseline serum status of vitamin D, co-supplementation with calcium and gene polymorphism should be considered when designing future clinical trials.
DOI: 10.6084/m9.figshare.5501695.v1
title: Data Eucalyptus-Becerra et al.xlsx

description: Data of the field study
DOI: 10.6084/m9.figshare.5501716.v2
title: CNN trained in Mathematica to distinguish between clubmosses and spikemosses

description: CNN trained in Mathematica to distinguish between clubmosses and spikemosses
DOI: 10.6084/m9.figshare.5501632
title: Sequencing native transaminase KpTam III.1b

description: Sequencing of P. pastoris native transaminase KpTam III.1b was performed using these primers:-TAm4_Mid_Fwd-TAm4_Mid_Rev-NESPTA4FWD-NESPTA4REV
DOI: 10.6084/m9.figshare.5501635
title: Sequencing native transaminase KpTam III.2a

description: Sequencing of P. pastoris native transaminase KpTam III.2a was performed using these primers:-TAm2_Mid_Fwd-TAm2_Mid_Rev-NESPTA2FWD-NESPTA2REV<br>
DOI: 10.6084/m9.figshare.5501626
title: Sequencing TK151-TAmCV2025

description: Sequencing of the double construct TK-TAm was performed using these primers:-5AOX1JH-JH3AOX1-TK151_Mid_FWR<br>-TK151_Mid_REV
DOI: 10.6084/m9.figshare.5501629
title: Sequencing native transaminase KpTam III.1a

description: Sequencing of P. pastoris native transaminase KpTam III.1a was performed using these primers:-TAm1_Mid_Fwd-TAm1_Mid_Rev-NESPTA1FWD-NESPTA1REV<br>
DOI: 10.6084/m9.figshare.5501632.v1
title: Sequencing native transaminase KpTam III.1b

description: Sequencing of P. pastoris native transaminase KpTam III.1b was performed using these primers:-TAm4_Mid_Fwd-TAm4_Mid_Rev-NESPTA4FWD-NESPTA4REV
DOI: 10.6084/m9.figshare.5501635.v1
title: Sequencing native transaminase KpTam III.2a

description: Sequencing of P. pastoris native transaminase KpTam III.2a was performed using these primers:-TAm2_Mid_Fwd-TAm2_Mid_Rev-NESPTA2FWD-NESPTA2REV<br>
DOI: 10.6084/m9.figshare.5501629.v1
title: Sequencing native transaminase KpTam III.1a

description: Sequencing of P. pastoris native transaminase KpTam III.1a was performed using these primers:-TAm1_Mid_Fwd-TAm1_Mid_Rev-NESPTA1FWD-NESPTA1REV<br>
DOI: 10.6084/m9.figshare.5501626.v1
title: Sequencing TK151-TAmCV2025

description: Sequencing of the double construct TK-TAm was performed using these primers:-5AOX1JH-JH3AOX1-TK151_Mid_FWR<br>-TK151_Mid_REV
DOI: 10.6084/m9.figshare.5501596
title: Putative 'radula' in Halkieria evangelista

description: High-resolution photographs of Halkieria evangelista from the Sirius Passet. Specimen SMX26926 is tentatively interpreted as possessing a radula by Conway Morris & Peel (1995).<br>Photographs taken under dark field photography with different angles of illumination. The first image combines two images lit under opposite illumination directions using GIMP's grain extract mode to emphasize relief.
DOI: 10.6084/m9.figshare.5501614
title: Sequencing CV2025 transaminase

description: Sequencing of CV2025 transaminase was performed using these primers:-CV2025.opt.Mid_Rev-JH3AOX1<br>-5AOX1JH<br>
DOI: 10.6084/m9.figshare.5501596.v1
title: Putative 'radula' in Halkieria evangelista

description: High-resolution photographs of Halkieria evangelista from the Sirius Passet. Specimen SMX26926 is tentatively interpreted as possessing a radula by Conway Morris & Peel (1995).<br>Photographs taken under dark field photography with different angles of illumination. The first image combines two images lit under opposite illumination directions using GIMP's grain extract mode to emphasize relief.