cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1378818.v1
title: Tree retention practices in boreal forests: what kind of future landscapes are we creating?

description: Tree retention practices promoting biodiversity may reshape future boreal forest production landscapes. Using the Heureka system, scenarios of 0%, 5%, and 20% retained patches at the stand level were projected over 200 years in a 533 ha boreal landscape. Visualizations of future forest states at a landscape scale and a more detailed scale were made based on the projections. The no retention results in no forest &gt;120 years old, and no large trees (diameter at breast height &gt;40 cm for conifers and &gt;35 cm for broadleaved trees) 100 years from now. With retention levels of 5% and 20%, the area of old forest will comprise 7% and 19% of the total area, respectively. The average number of large trees per ha will be 4 and 13, respectively. Deadwood volumes will be 2.5 times higher at 5% retention and 4 times higher at 20% retention compared to no retention. Landscape visualizations indicate that retention patches covering 5% will marginally modify the visual impression, compared to clear-cuts, while 20% cover will create a much more varied landscape. We conclude that the retention approach is essential for restoring natural conditions. Landscape transformation will be slow and depend on starting conditions and retention levels.
DOI: 10.6084/m9.figshare.1378817
title: Late Permian to Early Triassic crustal evolution of the Kontum massif, central Vietnam: zircon U–Pb ages and geochemical and Nd–Hf isotopic composition of the Hai Van granitoid complex

description: The Hai Van granitoid complex constitutes an important part of the Indosinian batholith of the northern Kontum massif in central Vietnam. The Kontum massif is a key region for understanding the palaeo-Tethyan accretionary history and the crustal evolution of the Indochina terrane. In this study, zircon U–Pb ages and geochemical data on the Hai Van complex are reported to shed more light on these geological processes. Zircon U–Pb isotopic analyses of six representative samples by the LA-ICP-MS technique show that granitoids from this complex crystallized between 242 and 224 Ma, indicating a prolonged period of magmatism in a late orogenic stage. Rocks from the Hai Van complex have S-type geochemical characteristics with high SiO<sub>2</sub>, Na<sub>2</sub>O + K<sub>2</sub>O, and Zr contents as well as typical S-type minerals such as cordierite and muscovite. Trace elements of the samples are depleted in Ba, Nb, P, Sr, and Ti and enriched in Rb, K, Th, U, and Pb. Negative Eu-anomalies indicate feldspar fractionation during magma crystallization. The Hai Van granitoids exhibit Nd–Hf isotopic features similar to Proterozoic rocks exposed in South China, with low initial ɛ<sub>Hf</sub> and initial ɛ<sub>Nd</sub> values and two-stage Hf model ages of 1.9–1.7 Ga. It is suggested that during the palaeo-Tethyan orogeny, central Vietnam experienced strong early Mesozoic magmatism that originated from partial melting of crustal material similar in composition to the basement of the South China block.
DOI: 10.6084/m9.figshare.1378817.v1
title: Late Permian to Early Triassic crustal evolution of the Kontum massif, central Vietnam: zircon U–Pb ages and geochemical and Nd–Hf isotopic composition of the Hai Van granitoid complex

description: The Hai Van granitoid complex constitutes an important part of the Indosinian batholith of the northern Kontum massif in central Vietnam. The Kontum massif is a key region for understanding the palaeo-Tethyan accretionary history and the crustal evolution of the Indochina terrane. In this study, zircon U–Pb ages and geochemical data on the Hai Van complex are reported to shed more light on these geological processes. Zircon U–Pb isotopic analyses of six representative samples by the LA-ICP-MS technique show that granitoids from this complex crystallized between 242 and 224 Ma, indicating a prolonged period of magmatism in a late orogenic stage. Rocks from the Hai Van complex have S-type geochemical characteristics with high SiO<sub>2</sub>, Na<sub>2</sub>O + K<sub>2</sub>O, and Zr contents as well as typical S-type minerals such as cordierite and muscovite. Trace elements of the samples are depleted in Ba, Nb, P, Sr, and Ti and enriched in Rb, K, Th, U, and Pb. Negative Eu-anomalies indicate feldspar fractionation during magma crystallization. The Hai Van granitoids exhibit Nd–Hf isotopic features similar to Proterozoic rocks exposed in South China, with low initial ɛ<sub>Hf</sub> and initial ɛ<sub>Nd</sub> values and two-stage Hf model ages of 1.9–1.7 Ga. It is suggested that during the palaeo-Tethyan orogeny, central Vietnam experienced strong early Mesozoic magmatism that originated from partial melting of crustal material similar in composition to the basement of the South China block.
DOI: 10.6084/m9.figshare.1378804
title: Small and efficient basis sets for the evaluation of accurate interaction-induced linear and non-linear electric properties in model hydrogen-bonded complexes

description: Interaction-induced electric dipole moment, polarisability and first hyperpolarisability are investigated in model hydrogen-bonded clusters built of hydrogen fluoride molecules organised in three linear chains parallel to each other. The properties are evaluated within the finite field approach, using the second order Møller–Plesset method, and the LPol-<i>m</i> (<i>m</i> = ds, dl) and the optical rotation prediction (ORP) basis sets. These bases and correlation method are selected after a systematic basis set and correlation method convergence study carried out on the smallest of the complexes and taking properties obtained with Dunning's bases and the coupled cluster singles and doubles (CCSD) and the CCSD including connected triple corrections (CCSD(T)) methods as reference. Results are analysed in terms of many-body and cooperative effects.
DOI: 10.6084/m9.figshare.1378802
title: Towards a framework for agent-based image analysis of remote-sensing data

description: Object-based image analysis (OBIA) as a paradigm for analysing remotely sensed image data has in many cases led to spatially and thematically improved classification results in comparison to pixel-based approaches. Nevertheless, robust and transferable object-based solutions for automated image analysis capable of analysing sets of images or even large image archives without any human interaction are still rare. A major reason for this lack of robustness and transferability is the high complexity of image contents: Especially in very high resolution (VHR) remote-sensing data with varying imaging conditions or sensor characteristics, the variability of the objects’ properties in these varying images is hardly predictable. The work described in this article builds on so-called rule sets. While earlier work has demonstrated that OBIA rule sets bear a high potential of transferability, they need to be adapted manually, or classification results need to be adjusted manually in a post-processing step. In order to automate these adaptation and adjustment procedures, we investigate the coupling, extension and integration of OBIA with the agent-based paradigm, which is exhaustively investigated in software engineering. The aims of such integration are (a) autonomously adapting rule sets and (b) image objects that can adopt and adjust themselves according to different imaging conditions and sensor characteristics. This article focuses on self-adapting image objects and therefore introduces a framework for agent-based image analysis (ABIA).
DOI: 10.6084/m9.figshare.1378804.v2
title: Small and efficient basis sets for the evaluation of accurate interaction-induced linear and non-linear electric properties in model hydrogen-bonded complexes

description: Interaction-induced electric dipole moment, polarisability and first hyperpolarisability are investigated in model hydrogen-bonded clusters built of hydrogen fluoride molecules organised in three linear chains parallel to each other. The properties are evaluated within the finite field approach, using the second order Møller–Plesset method, and the LPol-<i>m</i> (<i>m</i> = ds, dl) and the optical rotation prediction (ORP) basis sets. These bases and correlation method are selected after a systematic basis set and correlation method convergence study carried out on the smallest of the complexes and taking properties obtained with Dunning's bases and the coupled cluster singles and doubles (CCSD) and the CCSD including connected triple corrections (CCSD(T)) methods as reference. Results are analysed in terms of many-body and cooperative effects.
DOI: 10.6084/m9.figshare.1378804.v1
title: Small and efficient basis sets for the evaluation of accurate interaction-induced linear and non-linear electric properties in model hydrogen-bonded complexes

description: Interaction-induced electric dipole moment, polarisability and first hyperpolarisability are investigated in model hydrogen-bonded clusters built of hydrogen fluoride molecules organised in three linear chains parallel to each other. The properties are evaluated within the finite field approach, using the second order Møller–Plesset method, and the LPol-<i>m</i> (<i>m</i> = ds, dl) and the optical rotation prediction (ORP) basis sets. These bases and correlation method are selected after a systematic basis set and correlation method convergence study carried out on the smallest of the complexes and taking properties obtained with Dunning's bases and the coupled cluster singles and doubles (CCSD) and the CCSD including connected triple corrections (CCSD(T)) methods as reference. Results are analysed in terms of many-body and cooperative effects.
DOI: 10.6084/m9.figshare.1378802.v1
title: Towards a framework for agent-based image analysis of remote-sensing data

description: Object-based image analysis (OBIA) as a paradigm for analysing remotely sensed image data has in many cases led to spatially and thematically improved classification results in comparison to pixel-based approaches. Nevertheless, robust and transferable object-based solutions for automated image analysis capable of analysing sets of images or even large image archives without any human interaction are still rare. A major reason for this lack of robustness and transferability is the high complexity of image contents: Especially in very high resolution (VHR) remote-sensing data with varying imaging conditions or sensor characteristics, the variability of the objects’ properties in these varying images is hardly predictable. The work described in this article builds on so-called rule sets. While earlier work has demonstrated that OBIA rule sets bear a high potential of transferability, they need to be adapted manually, or classification results need to be adjusted manually in a post-processing step. In order to automate these adaptation and adjustment procedures, we investigate the coupling, extension and integration of OBIA with the agent-based paradigm, which is exhaustively investigated in software engineering. The aims of such integration are (a) autonomously adapting rule sets and (b) image objects that can adopt and adjust themselves according to different imaging conditions and sensor characteristics. This article focuses on self-adapting image objects and therefore introduces a framework for agent-based image analysis (ABIA).
DOI: 10.6084/m9.figshare.1378802.v2
title: Towards a framework for agent-based image analysis of remote-sensing data

description: Object-based image analysis (OBIA) as a paradigm for analysing remotely sensed image data has in many cases led to spatially and thematically improved classification results in comparison to pixel-based approaches. Nevertheless, robust and transferable object-based solutions for automated image analysis capable of analysing sets of images or even large image archives without any human interaction are still rare. A major reason for this lack of robustness and transferability is the high complexity of image contents: Especially in very high resolution (VHR) remote-sensing data with varying imaging conditions or sensor characteristics, the variability of the objects’ properties in these varying images is hardly predictable. The work described in this article builds on so-called rule sets. While earlier work has demonstrated that OBIA rule sets bear a high potential of transferability, they need to be adapted manually, or classification results need to be adjusted manually in a post-processing step. In order to automate these adaptation and adjustment procedures, we investigate the coupling, extension and integration of OBIA with the agent-based paradigm, which is exhaustively investigated in software engineering. The aims of such integration are (a) autonomously adapting rule sets and (b) image objects that can adopt and adjust themselves according to different imaging conditions and sensor characteristics. This article focuses on self-adapting image objects and therefore introduces a framework for agent-based image analysis (ABIA).
DOI: 10.6084/m9.figshare.1378802.v4
title: Towards a framework for agent-based image analysis of remote-sensing data

description: Object-based image analysis (OBIA) as a paradigm for analysing remotely sensed image data has in many cases led to spatially and thematically improved classification results in comparison to pixel-based approaches. Nevertheless, robust and transferable object-based solutions for automated image analysis capable of analysing sets of images or even large image archives without any human interaction are still rare. A major reason for this lack of robustness and transferability is the high complexity of image contents: Especially in very high resolution (VHR) remote-sensing data with varying imaging conditions or sensor characteristics, the variability of the objects’ properties in these varying images is hardly predictable. The work described in this article builds on so-called rule sets. While earlier work has demonstrated that OBIA rule sets bear a high potential of transferability, they need to be adapted manually, or classification results need to be adjusted manually in a post-processing step. In order to automate these adaptation and adjustment procedures, we investigate the coupling, extension and integration of OBIA with the agent-based paradigm, which is exhaustively investigated in software engineering. The aims of such integration are (a) autonomously adapting rule sets and (b) image objects that can adopt and adjust themselves according to different imaging conditions and sensor characteristics. This article focuses on self-adapting image objects and therefore introduces a framework for agent-based image analysis (ABIA).
DOI: 10.6084/m9.figshare.1378802.v3
title: Towards a framework for agent-based image analysis of remote-sensing data

description: Object-based image analysis (OBIA) as a paradigm for analysing remotely sensed image data has in many cases led to spatially and thematically improved classification results in comparison to pixel-based approaches. Nevertheless, robust and transferable object-based solutions for automated image analysis capable of analysing sets of images or even large image archives without any human interaction are still rare. A major reason for this lack of robustness and transferability is the high complexity of image contents: Especially in very high resolution (VHR) remote-sensing data with varying imaging conditions or sensor characteristics, the variability of the objects’ properties in these varying images is hardly predictable. The work described in this article builds on so-called rule sets. While earlier work has demonstrated that OBIA rule sets bear a high potential of transferability, they need to be adapted manually, or classification results need to be adjusted manually in a post-processing step. In order to automate these adaptation and adjustment procedures, we investigate the coupling, extension and integration of OBIA with the agent-based paradigm, which is exhaustively investigated in software engineering. The aims of such integration are (a) autonomously adapting rule sets and (b) image objects that can adopt and adjust themselves according to different imaging conditions and sensor characteristics. This article focuses on self-adapting image objects and therefore introduces a framework for agent-based image analysis (ABIA).
DOI: 10.6084/m9.figshare.1378789
title: Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function

description: A growing number of gene-centric studies have highlighted the emerging significance of lncRNAs in cancer. However, these studies primarily focus on a single cancer type. Therefore, we conducted a pan-cancer analysis of lncRNAs comparing tumor and matched normal expression levels using RNA-Seq data from ∼ 3,000 patients in 8 solid tumor types. While the majority of differentially expressed lncRNAs display tissue-specific expression we discovered 229 lncRNAs with outlier or differential expression across multiple cancers, which we refer to as 'onco-lncRNAs'. Due to their consistent altered expression, we hypothesize that these onco-lncRNAs may have conserved oncogenic and tumor suppressive functions across cancers. To address this, we associated the onco-lncRNAs in biological processes based on their co-expressed protein coding genes. To validate our predictions, we experimentally confirmed cell growth dependence of 2 novel oncogenic lncRNAs, <i>onco-lncRNA-3</i> and <i>onco-lncRNA-12</i>, and a previously identified lncRNA <i>CCAT1</i>. Overall, we discovered lncRNAs that may have broad oncogenic and tumor suppressor roles that could significantly advance our understanding of cancer lncRNA biology.
DOI: 10.6084/m9.figshare.1378786
title: <i>Symbiodinium tridacnidorum</i> sp. nov., a dinoflagellate common to Indo-Pacific giant clams, and a revised morphological description of <i>Symbiodinium microadriaticum</i> Freudenthal, emended Trench & Blank

description: ABSTRACTThe dinoflagellate genus <i>Symbiodinium</i> contains numerous genetically distinct lineages that appear ‘morphologically cryptic’. However, detailed morphological assessments of plate formulae visible in the motile phase (mastigote) of two distantly related <i>Symbiodinium</i> spp., representing Clades ‘A’ and ‘E’, were recently shown to be different. While there are several formally described species in Clade A, genetic evidence indicates that many more remain uncharacterized. We focused on closely related phylogenetic lineages within this group to examine whether differences in morphology can be used together with genetic and ecological evidence to describe new species. We found fixed differences in nuclear (internal transcribed spacer (ITS) and large subunit rDNA), chloroplast (cp23S) and mitochondrial (cob) gene sequences from cultured and field-collected samples of <i>Symbiodinium microadriaticum</i> (<i>sensu</i> Trench & Blank, 1987) and <i>Symbiodinium</i> sp. associated predominantly with giant clams and Pacific <i>Cassiopea</i> jellyfish (comprising members of the ITS2 <i>A3</i> lineage, <i>sensu</i> LaJeunesse 2001). Amphiesmal plate tabulations were formulated for the strain of <i>S. microadriaticum</i> (CCMP2464) used by Trench & Blank (1987) in their emended description, and two strains of type <i>A3</i> (CCMP832 and rt-272) cultured from Indo-Pacific giant clams in the subfamily Tridacninae. The Kofoidian plate formula for type <i>A3</i> consists of the small plate (x), the elongated amphiesmal vesicle (EAV), 5′, 6a, 8′′, 9–11s, a 2-row cingulum, 7′′′ and 3′′′′ (and occasionally 2′′′′), and is different from <i>S. microadriaticum</i>, which has a plate formula of x, EAV, 4′, 5a, 8′′, 9–13s, a 2-row cingulum, 6′′′ and 2′′′′. Based on morphological and genetic comparisons, we recognized <i>Symbiodinium tridacnidorum</i> sp. nov., a new Indo-Pacific species. The plate arrangement exhibited by <i>S. microadriaticum</i> appears to be more similar to the distantly related <i>S. natans</i> (also in Clade A). When the tabulations for all three Clade A species are compared with <i>S. voratum</i> (Clade E), the amount of morphological differentiation between species does not correspond to their degree of genetic divergence.
DOI: 10.6084/m9.figshare.1378789.v1
title: Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function

description: ABSTRACTA growing number of gene-centric studies have highlighted the emerging significance of lncRNAs in cancer. However, these studies primarily focus on a single cancer type. Therefore, we conducted a pan-cancer analysis of lncRNAs comparing tumor and matched normal expression levels using RNA-Seq data from ˜3000 patients in eight solid tumor types. While the majority of differentially expressed lncRNAs display tissue-specific expression we discovered 229 lncRNAs with outlier or differential expression across multiple cancers, which we refer to as ‘onco-lncRNAs’. Due to their consistent altered expression, we hypothesize that these onco-lncRNAs may have conserved oncogenic and tumor suppressive functions across cancers. To address this, we associated the onco-lncRNAs in biological processes based on their co-expressed protein coding genes. To validate our predictions, we experimentally confirmed cell growth dependence of two novel oncogenic lncRNAs, <i>onco-lncRNA-3</i> and <i>onco-lncRNA-12</i>, and a previously identified lncRNA <i>CCAT1</i>. Overall, we discovered lncRNAs that may have broad oncogenic and tumor suppressor roles that could significantly advance our understanding of cancer lncRNA biology.
DOI: 10.6084/m9.figshare.1378786.v1
title: <i>Symbiodinium tridacnidorum</i> sp. nov., a dinoflagellate common to Indo-Pacific giant clams, and a revised morphological description of <i>Symbiodinium microadriaticum</i> Freudenthal, emended Trench & Blank

description: ABSTRACTThe dinoflagellate genus <i>Symbiodinium</i> contains numerous genetically distinct lineages that appear ‘morphologically cryptic’. However, detailed morphological assessments of plate formulae visible in the motile phase (mastigote) of two distantly related <i>Symbiodinium</i> spp., representing Clades ‘A’ and ‘E’, were recently shown to be different. While there are several formally described species in Clade A, genetic evidence indicates that many more remain uncharacterized. We focused on closely related phylogenetic lineages within this group to examine whether differences in morphology can be used together with genetic and ecological evidence to describe new species. We found fixed differences in nuclear (internal transcribed spacer (ITS) and large subunit rDNA), chloroplast (cp23S) and mitochondrial (cob) gene sequences from cultured and field-collected samples of <i>Symbiodinium microadriaticum</i> (<i>sensu</i> Trench & Blank, 1987) and <i>Symbiodinium</i> sp. associated predominantly with giant clams and Pacific <i>Cassiopea</i> jellyfish (comprising members of the ITS2 <i>A3</i> lineage, <i>sensu</i> LaJeunesse 2001). Amphiesmal plate tabulations were formulated for the strain of <i>S. microadriaticum</i> (CCMP2464) used by Trench & Blank (1987) in their emended description, and two strains of type <i>A3</i> (CCMP832 and rt-272) cultured from Indo-Pacific giant clams in the subfamily Tridacninae. The Kofoidian plate formula for type <i>A3</i> consists of the small plate (x), the elongated amphiesmal vesicle (EAV), 5′, 6a, 8′′, 9–11s, a 2-row cingulum, 7′′′ and 3′′′′ (and occasionally 2′′′′), and is different from <i>S. microadriaticum</i>, which has a plate formula of x, EAV, 4′, 5a, 8′′, 9–13s, a 2-row cingulum, 6′′′ and 2′′′′. Based on morphological and genetic comparisons, we recognized <i>Symbiodinium tridacnidorum</i> sp. nov., a new Indo-Pacific species. The plate arrangement exhibited by <i>S. microadriaticum</i> appears to be more similar to the distantly related <i>S. natans</i> (also in Clade A). When the tabulations for all three Clade A species are compared with <i>S. voratum</i> (Clade E), the amount of morphological differentiation between species does not correspond to their degree of genetic divergence.