cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh355275.07fu
title: SH355275.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh355276.07fu
title: SH355276.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1720024.08fu
title: SH1720024.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.24396/ordar-142
title: weather station GISFI Homecourt 2016

description: Weather data of 2016 with absence of measurement: 2016-05-02 15:59; 2016-05-25 09:59; 2016-07-10 from 04:59 to 08:59; 2016-07-11 from 01:59 to 07:59; 2016-09-01 08:59; 2016-09-11 from 01:59 to 09:59; from 2016-09-11 21:59 to 2016-09-12 11:59; 2016-09-12 from 19:59 to 21:59
DOI: 10.6084/m9.figshare.12782726
title: Additional file 7 of Comparative transcriptome analyses define genes and gene modules differing between two Populus genotypes with contrasting stem growth rates

description: Additional file 7: Data S4. Summary of differential expressed genes between Neva and I-214 at different growth stages.
DOI: 10.6084/m9.figshare.12782729.v1
title: Additional file 8 of Comparative transcriptome analyses define genes and gene modules differing between two Populus genotypes with contrasting stem growth rates

description: Additional file 8: Data S5. Gene Ontology annotation and enrichment analysis of differential expressed genes between Neva and I-214 at different growth stages.
DOI: 10.6084/m9.figshare.12782732.v1
title: Additional file 9 of Comparative transcriptome analyses define genes and gene modules differing between two Populus genotypes with contrasting stem growth rates

description: Additional file 9: Data S6. Summary of differentially expressed transcription factors at different growth stages.
DOI: 10.6084/m9.figshare.12782930
title: Data File2.csv

description: The results of ICP algorithm and our proposed algorithm are compared
DOI: 10.6084/m9.figshare.7015595.v1
title: MOESM8 of The genome-wide transcriptional regulatory landscape of ecdysone in the silkworm

description: Additional file 8. The list of EcR peaks containing EcRE motif.
DOI: 10.6084/m9.figshare.22220182.v1
title: Late Eocene slab retreat, extension, and mantle upwelling inferred from mantle signatures in potassium-rich magmatism in NE Iran

description: There is considerable debate regarding the petrogenesis of K-rich magma, which are believed to occur in subduction settings. The districts of the potassic rocks in the rear-arc of the Cenozoic Iran have not been thoroughly investigated. In this study, we investigate Late Eocene K-rich rocks of the Roshtkhar area of NE Iran. We employ whole-rock geochemistry, Sr-Nd-Hf-isotopes and zircon U-Pb age data of intrusive rocks to identify the mantle signature, evaluate the timing of emplacement, and determine the geodynamic setting. The Roshtkhar intrusive rocks (RIR) encompass a narrow compositional spectrum from syenite to monzonite, belonging to K-rich series, and are enriched in light rare earth elements and large ion lithophile elements such as Cs, Rb, Ba, Th, and U, with positive K, Pb, and Sr anomalies. U-Pb LA-ICP-MS dating of zircon from two samples yielded ages of ca. 38 Ma. Epsilon Hf values for investigated Eocene zircons display variable range from +0.3 to +6.5. The RIR show relatively homogeneous initial epsilon Nd values ranging from +0.64 to −1.31 and modest variation in initial <sup>87</sup>Sr/<sup>86</sup>Sr from 0.7048 to 0.7052. The data show mantle contribution with small involvement of Cadomian upper crustal material up to 12% and an approximately 3% of contribution fluid derived from subducted sediment into the mantle source. The lack of rocks that are purely derived from the lower crust in the study area further argues against the partial melting of lower crust that delaminated into the mantle. We suggest slab retreat, extension, and mantle upwelling as the main mechanism for the generation of the primitive melts of RIR. Accordingly, decompression melting of metasomatized lithospheric mantle (e.g. phlogopite, apatite, and/or pargasite-bearing lherzolite) would be a plausible mechanism for the forming of K-rich basic melt in the mantle source.
DOI: 10.6084/m9.figshare.12782930.v1
title: Data File2.csv

description: The results of ICP algorithm and our proposed algorithm are compared
DOI: 10.6084/m9.figshare.12782933
title: Data File1.csv

description: Calculate the Straightness error and Angle error of X-axis
DOI: 10.6084/m9.figshare.12782933.v1
title: Data File1.csv

description: Calculate the Straightness error and Angle error of X-axis
DOI: 10.6084/m9.figshare.21171490.v1
title: Additional file 2 of A robust and transformation-free joint model with matching and regularization for metagenomic trajectory and disease onset

description: Additional file 2: Supplementary Table S1. The list of OTUs detected by JMR, JMR-NC, LMM-N, individually, as shown in Figure 7.
DOI: 10.6084/m9.figshare.12258707.v3
title: Identifying Heterogeneous Effect Using Latent Supervised Clustering With Adaptive Fusion

description: Precision medicine is an important area of research with the goal of identifying the optimal treatment for each individual patient. In the literature, various methods are proposed to divide the population into subgroups according to the heterogeneous effects of individuals. In this article, a new exploratory machine learning tool, named latent supervised clustering, is proposed to identify the heterogeneous subpopulations. In particular, we formulate the problem as a regression problem with subject specific coefficients, and use adaptive fusion to cluster the coefficients into subpopulations. This method has two main advantages. First, it relies on little prior knowledge and weak parametric assumptions on the underlying subpopulation structure. Second, it makes use of the outcome-predictor relationship, and hence can have competitive estimation and prediction accuracy. To estimate the parameters, we design a highly efficient accelerated proximal gradient algorithm which guarantees convergence at a competitive rate. Numerical studies show that the proposed method has competitive estimation and prediction accuracy, and can also produce interpretable clustering results for the underlying heterogeneous effect. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.21171545
title: Additional file 2 of ANGPTL3 is involved in kidney injury in high-fat diet-fed mice by suppressing ACTN4 expression

description: Additional file 2.
DOI: 10.6084/m9.figshare.12258707.v1
title: Identifying Heterogeneous Effect using Latent Supervised Clustering with Adaptive Fusion

description: Precision medicine is an important area of research with the goal of identifying the optimal treatment for each individual patient. In the literature, various methods are proposed to divide the population into subgroups according to the heterogeneous effects of individuals. In this paper, a new exploratory machine learning tool, named latent supervised clustering, is proposed to identify the heterogeneous subpopulations. In particular, we formulate the problem as a regression problem with subject specific coefficients, and use adaptive fusion to cluster the coefficients into subpopulations. This method has two main advantages. First, it relies on little prior knowledge and weak parametric assumptions on the underlying subpopulation structure. Second, it makes use of the outcome-predictor relationship, and hence can have competitive estimation and prediction accuracy. To estimate the parameters, we design a highly efficient accelerated proximal gradient algorithm which guarantees convergence at a competitive rate. Numerical studies show that the proposed method has competitive estimation and prediction accuracy, and can also produce interpretable clustering results for the underlying heterogeneous effect.
DOI: 10.6084/m9.figshare.12258707.v2
title: Identifying Heterogeneous Effect Using Latent Supervised Clustering With Adaptive Fusion

description: Precision medicine is an important area of research with the goal of identifying the optimal treatment for each individual patient. In the literature, various methods are proposed to divide the population into subgroups according to the heterogeneous effects of individuals. In this article, a new exploratory machine learning tool, named latent supervised clustering, is proposed to identify the heterogeneous subpopulations. In particular, we formulate the problem as a regression problem with subject specific coefficients, and use adaptive fusion to cluster the coefficients into subpopulations. This method has two main advantages. First, it relies on little prior knowledge and weak parametric assumptions on the underlying subpopulation structure. Second, it makes use of the outcome-predictor relationship, and hence can have competitive estimation and prediction accuracy. To estimate the parameters, we design a highly efficient accelerated proximal gradient algorithm which guarantees convergence at a competitive rate. Numerical studies show that the proposed method has competitive estimation and prediction accuracy, and can also produce interpretable clustering results for the underlying heterogeneous effect. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.22220182
title: Late Eocene slab retreat, extension, and mantle upwelling inferred from mantle signatures in potassium-rich magmatism in NE Iran

description: There is considerable debate regarding the petrogenesis of K-rich magma, which are believed to occur in subduction settings. The districts of the potassic rocks in the rear-arc of the Cenozoic Iran have not been thoroughly investigated. In this study, we investigate Late Eocene K-rich rocks of the Roshtkhar area of NE Iran. We employ whole-rock geochemistry, Sr-Nd-Hf-isotopes and zircon U-Pb age data of intrusive rocks to identify the mantle signature, evaluate the timing of emplacement, and determine the geodynamic setting. The Roshtkhar intrusive rocks (RIR) encompass a narrow compositional spectrum from syenite to monzonite, belonging to K-rich series, and are enriched in light rare earth elements and large ion lithophile elements such as Cs, Rb, Ba, Th, and U, with positive K, Pb, and Sr anomalies. U-Pb LA-ICP-MS dating of zircon from two samples yielded ages of ca. 38 Ma. Epsilon Hf values for investigated Eocene zircons display a variable range from +0.3 to +6.5. The RIR show relatively homogeneous initial epsilon Nd values ranging from +0.64 to −1.31 and modest variation in initial <sup>87</sup>Sr/<sup>86</sup>Sr from 0.7048 to 0.7052. The data show mantle contribution with small involvement of Cadomian upper crustal material of up to 12% and an approximately 3% contribution fluid derived from subducted sediment into the mantle source. The lack of rocks that are purely derived from the lower crust in the study area further argues against the partial melting of lower crust that delaminated into the mantle. We suggest slab retreat, extension, and mantle upwelling as the main mechanisms for the generation of the primitive melts of RIR. Accordingly, decompression melting of metasomatized lithospheric mantle (e.g. phlogopite, apatite, and/or pargasite-bearing lherzolite) would be a plausible mechanism for the forming of K-rich basic melt in the mantle source.
DOI: 10.6084/m9.figshare.21696159.v1
title: Dynamics of heavy metals in the fine sediments from a subtropical forest headwater stream during a rainy season

description: Headwater streams, as the capillaries of rivers, largely control the functional integrity of the entire river network. Headwater stream sediments, especially fine sediments, are essential ecosystem components and dominant reservoirs for heavy metals, with these reservoirs significantly affecting their cycling in streams. However, the dynamics of heavy metals in headwater stream sediments are not well assessed in the literature. Here, we assessed the temporal and spatial storage dynamics of several common heavy metals (i.e., Mn, Zn, Cu, Cr, Cd, and Pb) in the fine sediments from a typical subtropical forest headwater stream during the rainy season of 2021 (Mar–Aug). We found that (1) the mean storage of fine sediment of heavy metals was ordered Mn (21.57 g m<sup>−2</sup>) &gt; Pb (2.53 g m<sup>−2</sup>) &gt; Zn (2.27 g m<sup>−2</sup>) &gt; Cr (0.66 g m<sup>−2</sup>) &gt; Cu (0.12 g m<sup>−2</sup>) &gt; Cd (0.006 g m<sup>−2</sup>); (2) their storage had a transient increase during the rainy season, followed by a decrease, but storage of both Zn and Cr was unevenly distributed from stream source to mouth; and (3) the key factors controlling heavy metal storage were water alkalinity, temperature, and pH, as well as monthly precipitation. These findings suggest that forest headwater streams can store heavy metals, but the amounts vary across temporal and spatial scales. Our results help us better understand the role of headwater streams in storing and transferring materials in forest ecosystems.
DOI: 10.6084/m9.figshare.22220643.v2
title: Cross-species infection potential of avian influenza H13 viruses isolated from wild aquatic birds to poultry and mammals

description: Wild aquatic birds are the primary hosts of H13 avian influenza viruses (AIVs). Herein, we performed a genetic analysis of two H13 AIVs isolated from wild birds in China and evaluated their infection potential in poultry to further explore the potential for transmission from wild aquatic birds to poultry. Our results showed that the two strains belong to different groups, one strain (A/mallard/Dalian/DZ-137/2013; abbreviated as DZ137) belongs to Group I, whereas the other strain (A/Eurasian Curlew/Liaoning/ZH-385/2014; abbreviated as ZH385) belongs to Group III. In vitro experiments showed that both DZ137 and ZH385 can replicate efficiently in chicken embryo fibroblast cells. We found that these H13 AIVs can also efficiently replicate in mammalian cell lines, including human embryonic kidney cells and Madin-Darby canine kidney cells. In vivo experiments showed that DZ137 and ZH385 can infect 1-day-old specific pathogen-free (SPF) chickens, and that ZH385 has a higher replication ability in chickens than DZ137. Notably, only ZH385 can replicate efficiently in 10-day-old SPF chickens. However, neither DZ137 nor ZH385 can replicate well in turkeys and quails. Both DZ137 and ZH385 can replicate in 3-week-old mice. Serological surveillance of poultry showed a 4.6%-10.4% (15/328-34/328) antibody-positive rate against H13 AIVs in farm chickens. Our findings indicate that H13 AIVs have the replication ability in chickens and mice and may have a risk of crossing the host barrier from wild aquatic birds to poultry or mammals in the future.
DOI: 10.6084/m9.figshare.13297066
title: Additional file 1 of Immunological classification of gliomas based on immunogenomic profiling

description: Additional file 1: Table S1. A summary of five glioma datasets used in this study.
DOI: 10.6084/m9.figshare.21696159
title: Dynamics of heavy metals in the fine sediments from a subtropical forest headwater stream during a rainy season

description: Headwater streams, as the capillaries of rivers, largely control the functional integrity of the entire river network. Headwater stream sediments, especially fine sediments, are essential ecosystem components and dominant reservoirs for heavy metals, with these reservoirs significantly affecting their cycling in streams. However, the dynamics of heavy metals in headwater stream sediments are not well assessed in the literature. Here, we assessed the temporal and spatial storage dynamics of several common heavy metals (i.e., Mn, Zn, Cu, Cr, Cd, and Pb) in the fine sediments from a typical subtropical forest headwater stream during the rainy season of 2021 (Mar–Aug). We found that (1) the mean storage of fine sediment of heavy metals was ordered Mn (21.57 g m<sup>−2</sup>) &gt; Pb (2.53 g m<sup>−2</sup>) &gt; Zn (2.27 g m<sup>−2</sup>) &gt; Cr (0.66 g m<sup>−2</sup>) &gt; Cu (0.12 g m<sup>−2</sup>) &gt; Cd (0.006 g m<sup>−2</sup>); (2) their storage had a transient increase during the rainy season, followed by a decrease, but storage of both Zn and Cr was unevenly distributed from stream source to mouth; and (3) the key factors controlling heavy metal storage were water alkalinity, temperature, and pH, as well as monthly precipitation. These findings suggest that forest headwater streams can store heavy metals, but the amounts vary across temporal and spatial scales. Our results help us better understand the role of headwater streams in storing and transferring materials in forest ecosystems.
DOI: 10.6084/m9.figshare.13296970.v1
title: Additional file 3 of miR-31-5p regulates cold acclimation of the wood-boring beetle Monochamus alternatus via ascaroside signaling

description: Additional file 3: Dataset S1. Differently expressed transcripts (DETs) after low temperature acclimation. Dataset S2. KEGG enrichment of DETs after low temperature acclimation (P &lt; 0.05). Dataset S3. Differently expressed transcripts after feeding asc-C9. Dataset S4. Enriched genes in metabolic process by GO analysis. Dataset S5. The enrichment GO terms of differently expressed transcripts (DETs) after feeding asc-C9. Dataset S6. The programs used in bioinformatic analysis in this study. Dataset S7. Primers used in this study. Dataset S8. The nucleotide sequences used in this study.
DOI: 10.6084/m9.figshare.13297108.v1
title: Additional file 10 of Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

description: Additional file 10: Table S7. List of the primer information for the validation of CNVs by PCR and qPCR.
DOI: 10.6084/m9.figshare.13297108
title: Additional file 10 of Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

description: Additional file 10: Table S7. List of the primer information for the validation of CNVs by PCR and qPCR.
DOI: 10.6084/m9.figshare.13297123.v1
title: Additional file 5 of Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

description: Additional file 5: Table S3. List of CNVRs and genes overlapping with CNVRs identified in this study.
DOI: 10.6084/m9.figshare.13297111
title: Additional file 1 of Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

description: Additional file 1: Table S1. Summary of mapping statistics for 85 goat samples and nine high-depth resequenced goats included in this study.
DOI: 10.6084/m9.figshare.13297129.v1
title: Additional file 7 of Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

description: Additional file 7: Table S5. List of highly differentiated CNVs between BI and domestic goats and between TC and lowland goats.
DOI: 10.6084/m9.figshare.13296970
title: Additional file 3 of miR-31-5p regulates cold acclimation of the wood-boring beetle Monochamus alternatus via ascaroside signaling

description: Additional file 3: Dataset S1. Differently expressed transcripts (DETs) after low temperature acclimation. Dataset S2. KEGG enrichment of DETs after low temperature acclimation (P &lt; 0.05). Dataset S3. Differently expressed transcripts after feeding asc-C9. Dataset S4. Enriched genes in metabolic process by GO analysis. Dataset S5. The enrichment GO terms of differently expressed transcripts (DETs) after feeding asc-C9. Dataset S6. The programs used in bioinformatic analysis in this study. Dataset S7. Primers used in this study. Dataset S8. The nucleotide sequences used in this study.
DOI: 10.6084/m9.figshare.13297066.v1
title: Additional file 1 of Immunological classification of gliomas based on immunogenomic profiling

description: Additional file 1: Table S1. A summary of five glioma datasets used in this study.
DOI: 10.6084/m9.figshare.13297125
title: Additional file 6 of Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region

description: Additional file 6: Table S5. List of genes experiencing fast evolution (FEGs).
DOI: 10.6084/m9.figshare.13297125.v1
title: Additional file 6 of Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region

description: Additional file 6: Table S5. List of genes experiencing fast evolution (FEGs).
DOI: 10.6084/m9.figshare.13297131
title: Additional file 8 of Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region

description: Additional file 8: Table S7. Results from enrichment analysis of convergent and parallel genes based on dataset 1.