cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23898073
title: Nitrate leaching and its susceptibility in response to elevated nitrogen deposition in Japanese forests

description: Understanding the variability in nitrogen (N) leaching from forested ecosystems and its susceptibility to elevated atmospheric N deposition is essential for assessing the impact of atmospheric N deposition on forested ecosystems. This study explored the site variability in nitrate (NO<sub>3</sub><sup>−</sup>) leaching from forested areas and its susceptibility to elevated atmospheric N deposition from five sites in broadleaved forests grown on Andosols and Cambisols from northern to southern Japan. Site variability of NO<sub>3</sub><sup>−</sup> leaching and its possible contributing factors, including soil parent material and net nitrification rate, were evaluated using a generalized linear model with Akaike’s Information Criterion used for model selection. Three-year experimental N fertilization (50 kg N ha<sup>−1</sup> yr<sup>−1</sup> as ammonium nitrate) experiments were conducted at each site to evaluate the susceptibility of NO<sub>3</sub><sup>−</sup> leaching to elevated atmospheric N deposition. Soil solution NO<sub>3</sub><sup>−</sup> concentration below the rooting zone (50 cm below the ground surface) was variable among the five sites and was the highest in Shibecha, one of the Andosols sites in northern Japan where soil net nitrification tended to be higher than elsewhere. In model selection for NO<sub>3</sub><sup>−</sup> leaching, the soil parent material was not selected but soil net nitrification was selected, indicating that soil net nitrification could explain the variability of NO<sub>3</sub><sup>−</sup> leaching. A significant increase in NO<sub>3</sub><sup>–</sup> leaching after the 3-year N fertilization experiment was observed at the site with the highest levels of NO<sub>3</sub><sup>–</sup> leaching (Shibecha), indicating that the susceptibility of NO<sub>3</sub><sup>–</sup> leaching is high in locations where N leaching was originally high.
DOI: 10.6084/m9.figshare.23898073.v1
title: Nitrate leaching and its susceptibility in response to elevated nitrogen deposition in Japanese forests

description: Understanding the variability in nitrogen (N) leaching from forested ecosystems and its susceptibility to elevated atmospheric N deposition is essential for assessing the impact of atmospheric N deposition on forested ecosystems. This study explored the site variability in nitrate (NO<sub>3</sub><sup>−</sup>) leaching from forested areas and its susceptibility to elevated atmospheric N deposition from five sites in broadleaved forests grown on Andosols and Cambisols from northern to southern Japan. Site variability of NO<sub>3</sub><sup>−</sup> leaching and its possible contributing factors, including soil parent material and net nitrification rate, were evaluated using a generalized linear model with Akaike’s Information Criterion used for model selection. Three-year experimental N fertilization (50 kg N ha<sup>−1</sup> yr<sup>−1</sup> as ammonium nitrate) experiments were conducted at each site to evaluate the susceptibility of NO<sub>3</sub><sup>−</sup> leaching to elevated atmospheric N deposition. Soil solution NO<sub>3</sub><sup>−</sup> concentration below the rooting zone (50 cm below the ground surface) was variable among the five sites and was the highest in Shibecha, one of the Andosols sites in northern Japan where soil net nitrification tended to be higher than elsewhere. In model selection for NO<sub>3</sub><sup>−</sup> leaching, the soil parent material was not selected but soil net nitrification was selected, indicating that soil net nitrification could explain the variability of NO<sub>3</sub><sup>−</sup> leaching. A significant increase in NO<sub>3</sub><sup>–</sup> leaching after the 3-year N fertilization experiment was observed at the site with the highest levels of NO<sub>3</sub><sup>–</sup> leaching (Shibecha), indicating that the susceptibility of NO<sub>3</sub><sup>–</sup> leaching is high in locations where N leaching was originally high.
DOI: 10.6084/m9.figshare.23983929.v1
title: Dynamics of litterfall production in a forest damaged by oak wilt disease: a case study in a warm-temperate secondary forest

description: Quantification of litterfall production is crucial for evaluating net primary productivity and nutrient cycling in forest ecosystems. High mortality among trees in the family Fagaceae due to Japanese oak wilt disease (JOW) might affect litterfall production in secondary forests; however, few studies have quantified these effects. We investigated litterfall production and forest structure in warm-temperate secondary forests in the Kaisho Forest over 6 and 12 years, respectively, and compared the dynamics among different phases of a JOW outbreak to assess the impacts of JOW on litterfall production. We found that total annual litterfall and leaf fall showed little change in peak to post-JOW periods and that changes in basal area were unrelated to total litterfall and leaf fall. The observed fluctuation in BA in the Kaisho Forest may not have been large enough to clearly reveal the effect of JOW during these periods. Canopy gaps formed by JOW may enhance the recruitment and growth rates of sub-canopy and understory trees. Our results may only be applicable to warm secondary forests where evergreen trees are replacing deciduous trees. Additional information on litterfall production in JOW-disturbed secondary forests is needed.
DOI: 10.6084/m9.figshare.24187918
title: Importance of large-diameter conifer snags for saproxylic beetle (Cerambycidae) assemblages in old-growth remnants in Japan

description: Conversion of old-growth forests to managed forests reduces the amount and variety of dead wood, particularly large snags (standing dead trees) are disappeared. Therefore, organisms that rely on large snags are considered to be severely affected by forest practices that convert old-growth forests to managed forests. We examined the effect of snag characteristics (diameter, bark cover, and decay gradient) on longicorn beetle (Cerambycidae) assemblages to search for species that prefer large-diameter snags in two old-growth remnants in a cool-temperate mixed forest and a sub-boreal conifer forest in Hokkaido, Japan. We collected beetles using window traps attached to conifer snags belonging to genus <i>Abies</i> and <i>Picea</i> and evaluated how snag characteristics affected beetles that feed on conifers with considering spatial autocorrelation. Species richness and total abundance were not associated with any of the snag characteristics. However, permutation tests in redundancy analysis revealed that snag diameter and bark cover affected species composition in the mixed forest, while only snag diameter had a significant effect in the conifer forest. Two (<i>Macroleptura regalis</i> and <i>Prionus insularis insularis</i>) and one (<i>Sachalinobia koltzei</i>) species preferred large-diameter snags in the mixed forest and the conifer forest, respectively. These species should be used as conservation targets to reduce the impacts of forest practices on saproxylic beetles. In contrast, one species (<i>Molorchus minor fuscus</i>) preferred small-diameter snags in the conifer forest. To conserve species that rely on large snags, we should maintain large snags in harvesting operations and retain large living trees for the future recruitment of large snags.
DOI: 10.6084/m9.figshare.24314517.v1
title: Haplotype-resolved <i>de novo</i> genome assemblies of four coniferous tree species

description: Coniferous trees in gymnosperm are an important source of wood production. Because of their long lifecycle, the breeding programs of coniferous tree are time- and labor-consuming. Genomics could accelerate the selection of superior trees or clones in the breeding programs; however, the genomes of coniferous trees are generally giant in size and exhibit high heterozygosity. Therefore, the generation of long contiguous genome assemblies of coniferous species has been difficult. In this study, we employed high-fidelity (HiFi) long-read sequencing technology to sequence and assemble the genomes of four coniferous tree species, <i>Larix kaempferi</i>, <i>Chamaecyparis obtusa</i>, <i>Cryptomeria japonica</i>, and <i>Cunninghamia lanceolata</i>. Genome assemblies of the four species totaled 13.5 Gb (<i>L. kaempferi</i>), 8.5 Gb (<i>C. obtusa</i>), 9.2 Gb (<i>C. japonica</i>), and 11.7 Gb (<i>C. lanceolata</i>), which covered 99.6% of the estimated genome sizes on average. The contig N50 value, which indicates assembly contiguity, ranged from 1.2 Mb in <i>C. obtusa</i> to 16.0 Mb in <i>L. kaempferi</i>, and the assembled sequences contained, on average, 89.2% of the single-copy orthologs conserved in embryophytes. Assembled sequences representing alternative haplotypes covered 70.3–95.1% of the genomes, suggesting that the four coniferous tree genomes exhibit high heterozygosity levels. The genome sequence information obtained in this study represents a milestone in tree genetics and genomics, and will facilitate gene discovery, allele mining, phylogenetics, and evolutionary studies in coniferous trees, and accelerate forest tree breeding programs.
DOI: 10.6084/m9.figshare.24304451
title: Aquatic hyphomycete assemblages of <i>Abies sachalinensis</i> leaf litter immersed in a stream in Hokkaido, Japan

description: Aquatic hyphomycetes are key decomposers of plant-litter in freshwater environments. Previous studies have shown that conifer needles are colonized less frequently by aquatic hyphomycetes than broad-leaf species. Sakhalin fir (<i>Abies sachalinensis</i>) is the most common coniferous tree species planted for timber production in Hokkaido, Japan. Herein, we investigated aquatic hyphomycete assemblages involving Sakhalin fir needle litter and compared them with those of broad-leaf tree species, including Japanese oak (<i>Quercus crispula</i>) and Japanese linden (<i>Tilia japonica</i>), during immersion in a stream. Seventy percent of the total fungal species observed in fir needles were also observed in broad-leaf litter. However, the structure of the aquatic hyphomycete assemblages differed between the fir and two broad-leaf species, especially in the middle to late stages of the immersion period. The increase in species number and conidia number in fir needles was slower than that in oak leaves in the early stages of the immersion period. However, they continued to increase rapidly relative to the broad-leaf tree litter during the middle stages of the immersion period. These results suggest that fir needle litter was not difficult for aquatic hyphomycetes to colonize in the middle to late stages of the immersion period.
DOI: 10.6084/m9.figshare.24314517
title: Haplotype-resolved <i>de novo</i> genome assemblies of four coniferous tree species

description: Coniferous trees in gymnosperm are an important source of wood production. Because of their long lifecycle, the breeding programs of coniferous tree are time- and labor-consuming. Genomics could accelerate the selection of superior trees or clones in the breeding programs; however, the genomes of coniferous trees are generally giant in size and exhibit high heterozygosity. Therefore, the generation of long contiguous genome assemblies of coniferous species has been difficult. In this study, we employed high-fidelity (HiFi) long-read sequencing technology to sequence and assemble the genomes of four coniferous tree species, <i>Larix kaempferi</i>, <i>Chamaecyparis obtusa</i>, <i>Cryptomeria japonica</i>, and <i>Cunninghamia lanceolata</i>. Genome assemblies of the four species totaled 13.5 Gb (<i>L. kaempferi</i>), 8.5 Gb (<i>C. obtusa</i>), 9.2 Gb (<i>C. japonica</i>), and 11.7 Gb (<i>C. lanceolata</i>), which covered 99.6% of the estimated genome sizes on average. The contig N50 value, which indicates assembly contiguity, ranged from 1.2 Mb in <i>C. obtusa</i> to 16.0 Mb in <i>L. kaempferi</i>, and the assembled sequences contained, on average, 89.2% of the single-copy orthologs conserved in embryophytes. Assembled sequences representing alternative haplotypes covered 70.3–95.1% of the genomes, suggesting that the four coniferous tree genomes exhibit high heterozygosity levels. The genome sequence information obtained in this study represents a milestone in tree genetics and genomics, and will facilitate gene discovery, allele mining, phylogenetics, and evolutionary studies in coniferous trees, and accelerate forest tree breeding programs.
DOI: 10.6084/m9.figshare.24304451.v1
title: Aquatic hyphomycete assemblages of <i>Abies sachalinensis</i> leaf litter immersed in a stream in Hokkaido, Japan

description: Aquatic hyphomycetes are key decomposers of plant-litter in freshwater environments. Previous studies have shown that conifer needles are colonized less frequently by aquatic hyphomycetes than broad-leaf species. Sakhalin fir (<i>Abies sachalinensis</i>) is the most common coniferous tree species planted for timber production in Hokkaido, Japan. Herein, we investigated aquatic hyphomycete assemblages involving Sakhalin fir needle litter and compared them with those of broad-leaf tree species, including Japanese oak (<i>Quercus crispula</i>) and Japanese linden (<i>Tilia japonica</i>), during immersion in a stream. Seventy percent of the total fungal species observed in fir needles were also observed in broad-leaf litter. However, the structure of the aquatic hyphomycete assemblages differed between the fir and two broad-leaf species, especially in the middle to late stages of the immersion period. The increase in species number and conidia number in fir needles was slower than that in oak leaves in the early stages of the immersion period. However, they continued to increase rapidly relative to the broad-leaf tree litter during the middle stages of the immersion period. These results suggest that fir needle litter was not difficult for aquatic hyphomycetes to colonize in the middle to late stages of the immersion period.
DOI: 10.6084/m9.figshare.24187918.v1
title: Importance of large-diameter conifer snags for saproxylic beetle (Cerambycidae) assemblages in old-growth remnants in Japan

description: Conversion of old-growth forests to managed forests reduces the amount and variety of dead wood, particularly large snags (standing dead trees) are disappeared. Therefore, organisms that rely on large snags are considered to be severely affected by forest practices that convert old-growth forests to managed forests. We examined the effect of snag characteristics (diameter, bark cover, and decay gradient) on longicorn beetle (Cerambycidae) assemblages to search for species that prefer large-diameter snags in two old-growth remnants in a cool-temperate mixed forest and a sub-boreal conifer forest in Hokkaido, Japan. We collected beetles using window traps attached to conifer snags belonging to genus <i>Abies</i> and <i>Picea</i> and evaluated how snag characteristics affected beetles that feed on conifers with considering spatial autocorrelation. Species richness and total abundance were not associated with any of the snag characteristics. However, permutation tests in redundancy analysis revealed that snag diameter and bark cover affected species composition in the mixed forest, while only snag diameter had a significant effect in the conifer forest. Two (<i>Macroleptura regalis</i> and <i>Prionus insularis insularis</i>) and one (<i>Sachalinobia koltzei</i>) species preferred large-diameter snags in the mixed forest and the conifer forest, respectively. These species should be used as conservation targets to reduce the impacts of forest practices on saproxylic beetles. In contrast, one species (<i>Molorchus minor fuscus</i>) preferred small-diameter snags in the conifer forest. To conserve species that rely on large snags, we should maintain large snags in harvesting operations and retain large living trees for the future recruitment of large snags.
DOI: 10.5066/p9qa831i
title: Water level, water temperature, and specific conductance data collected during natural gradient tests in observation wells set in the upper transmissive zone of the Ogallala Aquifer, North East 2nd Street Superfund Site, Happy, Texas, 2023

description: Water level, water temperature, and specific conductance data were collected during natural gradient tests on six observation wells screened in the upper transmissive zone of the Ogallala aquifer at the North East 2nd Street Superfund site in Happy, Texas, from November 6-13, 2023. Tests involved gravity draining 100-160 gallons of a low-concentration salt-spiked solution with an associated specific conductance of less than 8,000 microsiemens per centimeter (µs/cm) into the wells, measuring water level responses, and recording continuous downhole water temperature and water conductivity (specific conductance). Gravity drainage of the salt-spiked solution into each well took approximately 1 hour at average rates of 2.4 to 5.2 gallons per minute. Depth profiles of water temperature and specific conductance were collected under ambient conditions (prior to draining the salt-spiked solution into each well). Another depth profile was collected after the salt-spiked solution was added to each well (to identify vertical changes in the water column of the well and the degree of vertical mixing of the spiked water). The single well natural gradient tests allow for the analysis of hydraulic responses of the aquifer during gravity drainage and assessment of ambient flow through the well after the emplacement of the salt-spiked solution and subsequent flushing out of the solution back to ambient conditions. Monitoring at each well continued for at least 24 hours after gravity-drainage of the salt-spiked solution into each well was completed to ascertain whether background conditions were achieved. This data release contains information on the well construction of the six wells tested in 2023 for natural gradient tests, the volume and concentration of the dilute salt spike used, profiles of specific conductance and water temperature of the wells pre- and post-spiked, water levels, and continuous monitoring of specific conductance and water temperature.
DOI: 10.34740/kaggle/dsv/7828896
title: BBC News
DOI: 10.25919/vet9-7b25
title: Parkes observations for project P1219 semester 2023OCTS_25

description: The magnetic field potentially regulates the process of star formation and the evolution of molecular clouds. It is inherently difficult to measure interstellar magnetic field strengths, with the measurement of Zeeman splitting a unique method to estimate the magnetic field strength along the line of sight directly. Despite the detection of Zeeman splitting in other mediums, there are as yet no Zeeman detections against compact background sources in quiescent molecular clouds or the cold neutral medium. Pulsars with extremely small solid angles and relatively high transverse velocities are ideal background sources to study the magnetic field in molecular clouds, providing a distinct signal to measure splitting against. There are four pulsars with OH absorption detections, namely PSR B1849+00, B1641-45, B1718-35, and B1749-28. We propose to utilize these four pulsars to explore the properties of the magnetic field and its variations within molecular clouds through both the Zeeman splitting of OH absorption and rotation measure estimations, between epochs. If a detection is confirmed, it will open a new window on the hard-to-measure magnetic fields in molecular clouds, independent of interpretation, thus shedding light on the physics of star formation and the interstellar medium.
DOI: 10.25919/g7vh-w352
title: Parkes observations for project P268 semester 2007OCTS_01

description: Pulsar multibeam survey
DOI: 10.25919/b0vp-ej55
title: Parkes observations for project PX500 semester 2023OCTS_13

description: This proposal relates to time purchased by the Chinese Academy of Sciences for Parkes follow-up confirmation and timing of FAST discoveries. As the observing time has been purchased this proposal (and the related PX501) does not require TAC grading. The primary reason for submitting a proposal is to ensure an outreach statement and that the proposal is entered into OPAL for the data archive to access. The Chinese team have two time requests. The time scheduled for the first, relating to this proposal, will be allocated in blocks of 24 hours and the data will become available in the data archive with an 18 month embargo period. The second type of time will be scheduled in shorter blocks and the data archived with a 10 year embargo.
DOI: 10.25919/dqkb-ak26
title: Parkes observations for project P268 semester 2010OCTS_01

description: Pulsar multibeam survey
DOI: 10.25919/zbd5-sk43
title: Parkes observations for project P268 semester 2008APRS_02

description: Pulsar multibeam survey
DOI: 10.25919/gx0r-hw82
title: Parkes observations for project P1219 semester 2023OCTS_26

description: The magnetic field potentially regulates the process of star formation and the evolution of molecular clouds. It is inherently difficult to measure interstellar magnetic field strengths, with the measurement of Zeeman splitting a unique method to estimate the magnetic field strength along the line of sight directly. Despite the detection of Zeeman splitting in other mediums, there are as yet no Zeeman detections against compact background sources in quiescent molecular clouds or the cold neutral medium. Pulsars with extremely small solid angles and relatively high transverse velocities are ideal background sources to study the magnetic field in molecular clouds, providing a distinct signal to measure splitting against. There are four pulsars with OH absorption detections, namely PSR B1849+00, B1641-45, B1718-35, and B1749-28. We propose to utilize these four pulsars to explore the properties of the magnetic field and its variations within molecular clouds through both the Zeeman splitting of OH absorption and rotation measure estimations, between epochs. If a detection is confirmed, it will open a new window on the hard-to-measure magnetic fields in molecular clouds, independent of interpretation, thus shedding light on the physics of star formation and the interstellar medium.
DOI: 10.6084/m9.figshare.25395748
title: <b>SUD raw data 2024.03.12</b>

description: The transient receptor potential melastatin 7 channel (TRPM7) is a non-selected cation channel highly expressed in some human cancer tissues. TRPM7 is involved in the proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) of cancer cells. Modulation of TRPM7 could be a promising therapeutic strategy for treating cancer, however, efficient and selective pharmacological TRPM7 modulators are lacking. In this study we investigated N- [ 4- (4, 6- dimethyl- 2- pyrimidinyloxy) - 3- methylphenyl] -N' - [ 2 -(dimethylamino)] benzoylurea (SUD), a newly synthesized benzoylurea derivative, for its effects on cancer cell migration and EMT and on functional expression of TRPM7. Our previous studies showed that SUD induces cell cycle arrest and apoptosis of MCF-7 and BGC-823 cells (human breast cancer and gastric cancer cell lines, respectively). Here we show that SUD significantly decreased the migration of both types of cancer cells. Moreover, SUD decreased vimentin expression and increased E-cadherin expression in both cell types, indicating that EMT is also decreased by SUD. Importantly, SUD potetnly reduced the TRPM7 current in a concentration-dependent manner. Additionally, SUD also decreased TRPM7 expression through the PI3K/Akt signaling pathway. Finally, molecular docking simulations were used to investigate potential SUD binding site on TRPM7. In summary, our research demonstrated that SUD is an effective TRPM7 inhibitor and a potential agent to suppress the metastasis of breast and gastric cancer by inhibiting TRPM7 expression and function.
DOI: 10.17606/xx8m-xg27
title: Pointer to replication dataset for: Attitudes and beliefs of academic librarians in Germany and the USA