cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21603033.v8
title: Inhibition of mitochondrial complex III or dihydroorotate dehydrogenase (DHODH) triggers formation of poly(A)<sup>+</sup> RNA foci adjacent to nuclear speckles following activation of ATM (ataxia telangiectasia mutated)

description: Intracellular and intercellular signalling networks play an essential role in optimizing cellular homoeostasis and are thought to be partly reflected in nuclear mRNA dynamics. However, the regulation of nuclear mRNA dynamics by intracellular and intercellular signals remains largely unexplored, and research tools are lacking. Through an original screening based on the mRNA metabolic mechanism, we discovered that eight well-known inhibitors cause significant nuclear poly(A)<sup>+</sup> RNA accumulation. Among these inhibitors, we discovered a new mRNA metabolic response in which the addition of antimycin A, an inhibitor of mitochondrial respiratory-chain complex III (complex III), resulted in a marked accumulation of poly(A)<sup>+</sup> RNA near the nuclear speckles. Furthermore, dihydroorotate dehydrogenase (DHODH) inhibitors, a rate-limiting enzyme in the intracellular <i>de novo</i> pyrimidine synthesis reaction that specifically exchanges electrons with complex III, also caused a remarkable accumulation of nuclear poly(A)<sup>+</sup> RNA adjacent to the nuclear speckles, which was abolished by extracellular uridine supply, indicating that the depletion of intracellular pyrimidine affects poly(A)<sup>+</sup> RNA metabolism. Further analysis revealed that ataxia telangiectasia mutated (ATM), a serine and threonine kinase and a master regulator of DNA double-strand break (DSB) and nucleolar stress, is required for this poly(A)<sup>+</sup> RNA nuclear accumulation phenomenon. This study reports new insights into novel aspects of nuclear poly(A)<sup>+</sup> RNA metabolism, especially the relationship between mitochondrial respiratory-chain functions, pyrimidine metabolism, and nuclear RNA metabolism.
DOI: 10.5281/zenodo.10850503
title: HOT Primary Production and Flow Cytometry v2022

description: This dataset consists of measurements of photosynthetic primary production, chlorophyll a and phaeopigment concentrations, and flow cytometry-based determinations of the abundances of heterotrophic bacteria and the picophytoplankton - Prochlorococcus, Synechococcus and small eukaryotic phytoplankton. All samples were collected through the Hawaii Ocean Time-series (HOT) program, which began in 1988 with ~monthly cruises to Station ALOHA (A Long-term Oligotrophic Habitat Assessment; 22° 10 N, 158° 00 W). Photosynthetic production of organic matter was measured by the 14C tracer method. Details on the methods employed over the years are detailed in Karl et al., Progress in Oceanography (https://doi.org/10.1016/j.pocean.2021.102563). Flow cytometry-based determinations of microbial abundances were made using an EPICS 753 flow cytometer on HOT 22-173 (December 1980 – September 2005) and a B/D Influx flow cytometer beginning with HOT 174 . Details on the flow cytometry methods are provided at (https://hahana.soest.hawaii.edu/hot/methods/bact.html). Samples for chlorophyll a and phaeopigments were collected onto Whatman GF/F filters and extracted with 100% acetone and measured on a Turner Designs Model 10-AU fluorometer based on standard techniques described in Strickland and Parsons, 1972. Method details available at (https://hahana.soest.hawaii.edu/hot/methods/chl.html). Time is in a separate column from date. Dates and times are in local time (HST).
DOI: 10.5281/zenodo.10850504
title: HOT Primary Production and Flow Cytometry v2022

description: This dataset consists of measurements of photosynthetic primary production, chlorophyll a and phaeopigment concentrations, and flow cytometry-based determinations of the abundances of heterotrophic bacteria and the picophytoplankton - Prochlorococcus, Synechococcus and small eukaryotic phytoplankton. All samples were collected through the Hawaii Ocean Time-series (HOT) program, which began in 1988 with ~monthly cruises to Station ALOHA (A Long-term Oligotrophic Habitat Assessment; 22° 10 N, 158° 00 W). Photosynthetic production of organic matter was measured by the 14C tracer method. Details on the methods employed over the years are detailed in Karl et al., Progress in Oceanography (https://doi.org/10.1016/j.pocean.2021.102563). Flow cytometry-based determinations of microbial abundances were made using an EPICS 753 flow cytometer on HOT 22-173 (December 1980 – September 2005) and a B/D Influx flow cytometer beginning with HOT 174 . Details on the flow cytometry methods are provided at (https://hahana.soest.hawaii.edu/hot/methods/bact.html). Samples for chlorophyll a and phaeopigments were collected onto Whatman GF/F filters and extracted with 100% acetone and measured on a Turner Designs Model 10-AU fluorometer based on standard techniques described in Strickland and Parsons, 1972. Method details available at (https://hahana.soest.hawaii.edu/hot/methods/chl.html). Time is in a separate column from date. Dates and times are in local time (HST).
DOI: 10.6084/m9.figshare.21665289.v6
title: Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics

description: Endothelial cells (ECs) comprise the lumenal lining of all blood vessels and are critical for the functioning of the cardiovascular system. Their phenotypes can be modulated by alternative splicing of RNA to produce distinct protein isoforms. To characterize the RNA and protein isoform landscape within ECs, we applied a long read proteogenomics approach to analyse human umbilical vein endothelial cells (HUVECs). Transcripts delineated from PacBio sequencing serve as the basis for a sample-specific protein database used for downstream mass-spectrometry (MS) analysis to infer protein isoform expression. We detected 53,863 transcript isoforms from 10,426 genes, with 22,195 of those transcripts being novel. Furthermore, the predominant isoform in HUVECs does not correspond with the accepted “reference isoform” 25% of the time, with vascular pathway-related genes among this group. We found 2,597 protein isoforms supported through unique peptides, with an additional 2,280 isoforms nominated upon incorporation of long-read transcript evidence. We characterized a novel alternative acceptor for endothelial-related gene CDH5, suggesting potential changes in its associated signalling pathways. Finally, we identified novel protein isoforms arising from a diversity of RNA splicing mechanisms supported by uniquely mapped novel peptides. Our results represent a high-resolution atlas of known and novel isoforms of potential relevance to endothelial phenotypes and function.
DOI: 10.6084/m9.figshare.21603033.v9
title: Inhibition of mitochondrial complex III or dihydroorotate dehydrogenase (DHODH) triggers formation of poly(A)<sup>+</sup> RNA foci adjacent to nuclear speckles following activation of ATM (ataxia telangiectasia mutated)

description: Intracellular and intercellular signalling networks play an essential role in optimizing cellular homoeostasis and are thought to be partly reflected in nuclear mRNA dynamics. However, the regulation of nuclear mRNA dynamics by intracellular and intercellular signals remains largely unexplored, and research tools are lacking. Through an original screening based on the mRNA metabolic mechanism, we discovered that eight well-known inhibitors cause significant nuclear poly(A)<sup>+</sup> RNA accumulation. Among these inhibitors, we discovered a new mRNA metabolic response in which the addition of antimycin A, an inhibitor of mitochondrial respiratory-chain complex III (complex III), resulted in a marked accumulation of poly(A)<sup>+</sup> RNA near the nuclear speckles. Furthermore, dihydroorotate dehydrogenase (DHODH) inhibitors, a rate-limiting enzyme in the intracellular <i>de novo</i> pyrimidine synthesis reaction that specifically exchanges electrons with complex III, also caused a remarkable accumulation of nuclear poly(A)<sup>+</sup> RNA adjacent to the nuclear speckles, which was abolished by extracellular uridine supply, indicating that the depletion of intracellular pyrimidine affects poly(A)<sup>+</sup> RNA metabolism. Further analysis revealed that ataxia telangiectasia mutated (ATM), a serine and threonine kinase and a master regulator of DNA double-strand break (DSB) and nucleolar stress, is required for this poly(A)<sup>+</sup> RNA nuclear accumulation phenomenon. This study reports new insights into novel aspects of nuclear poly(A)<sup>+</sup> RNA metabolism, especially the relationship between mitochondrial respiratory-chain functions, pyrimidine metabolism, and nuclear RNA metabolism.
DOI: 10.5281/zenodo.10850494
title: Datos "Estudio biográfico-narrativo de experiencias universitarias en la madurez"
DOI: 10.5281/zenodo.10850495
title: Datos "Estudio biográfico-narrativo de experiencias universitarias en la madurez"
DOI: 10.5281/zenodo.10850527
title: Particle Flux HOT v2022

description: “Particle flux was measured at a standard reference depth of 150 m using multiple cylindrical particle interceptor traps deployed on a free-floating array for approximately 60 h during each cruise. Sediment trap design and collection methods are described in Winn et al. (1991). Samples were analyzed for particulate C, N, P & Si. Typically six traps are analyzed for PC and PN, three for PP, and another three traps for PSi.”  Time is in a separate column from date. Dates and times are in local time (HST).

 https://hahana.soest.hawaii.edu/hot/methods/pflux.html
DOI: 10.5281/zenodo.10850528
title: Particle Flux HOT v2022

description: “Particle flux was measured at a standard reference depth of 150 m using multiple cylindrical particle interceptor traps deployed on a free-floating array for approximately 60 h during each cruise. Sediment trap design and collection methods are described in Winn et al. (1991). Samples were analyzed for particulate C, N, P & Si. Typically six traps are analyzed for PC and PN, three for PP, and another three traps for PSi.”  Time is in a separate column from date. Dates and times are in local time (HST).

 https://hahana.soest.hawaii.edu/hot/methods/pflux.html
DOI: 10.5281/zenodo.10850538
title: Zooplankton Community Structure HOT v2022

description: “Large zooplankton and micronekton play important roles in the export of organic material from surface waters in the open ocean. Global Ocean Flux planning models suggest that the relationship between primary production and passive particulate export flux is strongly influenced by size structure of the zooplankton community (e.g., Paffenhöffer & Knowles, 1979; Small et al., 1987; Frost, 1984). Active vertical migrations also have important implications for the transport and transformation of surface-derived organic particulates to dissolved inorganic constituents at depth (Longhurst & Harrison, 1988; Longhurst et al., 1990; Al-Mutairi & Landry, 2001; Hannides et al., 2008). The zooplankton component of the time-series sampling effort allows such processes to be considered in the interpretation of seasonal and interannual variations in measured flux and the elemental mass balance (e.g., carbon and nitrogen sources and sinks) of the euphotic zone. At Station ALOHA, 6 net tows are scheduled per cruise. Three midnight (2200 - 0200) and 3 mid-day (1000 - 1400) oblique tows are done using a 1-m2 net (3-m length) with 202-µm mesh Nitex netting. The net is towed obliquely at approximately 1 knot, from the surface to approximately 175 m and then back to the surface. Towing time is approximately 20-30 minutes. The tows are subsequently size-fractioned and analyzed for mesozooplankton wet and dry weight and C and N biomass.” Rows with no depth value have been removed. Time is in local time (HST).

https://hahana.soest.hawaii.edu/hot/methods/plankton.html
DOI: 10.5281/zenodo.10850539
title: Zooplankton Community Structure HOT v2022

description: “Large zooplankton and micronekton play important roles in the export of organic material from surface waters in the open ocean. Global Ocean Flux planning models suggest that the relationship between primary production and passive particulate export flux is strongly influenced by size structure of the zooplankton community (e.g., Paffenhöffer & Knowles, 1979; Small et al., 1987; Frost, 1984). Active vertical migrations also have important implications for the transport and transformation of surface-derived organic particulates to dissolved inorganic constituents at depth (Longhurst & Harrison, 1988; Longhurst et al., 1990; Al-Mutairi & Landry, 2001; Hannides et al., 2008). The zooplankton component of the time-series sampling effort allows such processes to be considered in the interpretation of seasonal and interannual variations in measured flux and the elemental mass balance (e.g., carbon and nitrogen sources and sinks) of the euphotic zone. At Station ALOHA, 6 net tows are scheduled per cruise. Three midnight (2200 - 0200) and 3 mid-day (1000 - 1400) oblique tows are done using a 1-m2 net (3-m length) with 202-µm mesh Nitex netting. The net is towed obliquely at approximately 1 knot, from the surface to approximately 175 m and then back to the surface. Towing time is approximately 20-30 minutes. The tows are subsequently size-fractioned and analyzed for mesozooplankton wet and dry weight and C and N biomass.” Rows with no depth value have been removed. Time is in local time (HST).

https://hahana.soest.hawaii.edu/hot/methods/plankton.html
DOI: 10.5281/zenodo.10850553
title: CTD Hydrography HOT v2022

description: “The majority of our sampling effort, approximately 60-72 h per standard HOT cruise, is spent at Station ALOHA. High vertical resolution environmental data are collected with a Sea-Bird CTD having external temperature (T), conductivity (C), dissolved oxygen (DO) and fluorescence (F) sensors and an internal pressure (P) sensor. A Sea-Bird 24-place carousel and an aluminum rosette that is capable of supporting 24 12-L PVC bottles are used to obtain water samples from desired depths. The CTD and rosette are deployed on a 3-conductor cable allowing for real-time display of data and for tripping the bottles at specific depths of interest. The CTD system takes 24 samples s-1 and the raw data are stored both on the computer and, for redundancy, on VHS-format video tapes. In February 2006, before cruise 178, we replaced our 24 aging 12-L PVC rosette bottles with new 12-L bottles fabricated at the University of Hawaii Engineering Support Facility, using plans and specifications from John Bullister (PMEL).” Time is in GMT.  

https://www.soest.hawaii.edu/HOT_WOCE/intro.html
DOI: 10.5281/zenodo.10850554
title: CTD Hydrography HOT v2022

description: “The majority of our sampling effort, approximately 60-72 h per standard HOT cruise, is spent at Station ALOHA. High vertical resolution environmental data are collected with a Sea-Bird CTD having external temperature (T), conductivity (C), dissolved oxygen (DO) and fluorescence (F) sensors and an internal pressure (P) sensor. A Sea-Bird 24-place carousel and an aluminum rosette that is capable of supporting 24 12-L PVC bottles are used to obtain water samples from desired depths. The CTD and rosette are deployed on a 3-conductor cable allowing for real-time display of data and for tripping the bottles at specific depths of interest. The CTD system takes 24 samples s-1 and the raw data are stored both on the computer and, for redundancy, on VHS-format video tapes. In February 2006, before cruise 178, we replaced our 24 aging 12-L PVC rosette bottles with new 12-L bottles fabricated at the University of Hawaii Engineering Support Facility, using plans and specifications from John Bullister (PMEL).” Time is in GMT.  

https://www.soest.hawaii.edu/HOT_WOCE/intro.html
DOI: 10.15472/zmhyff
title: Estimación del contenido de carbono en biomasa aérea del Bosque Las Mercedes y zonas anexas

description: El objetivo de esta investigación fue la de evaluar el contenido de carbono almacenado en los componentes de biomasa aérea, necromasa y suelo en el Bosque Las Mercedes, en las áreas del bosque, áreas con procesos de restauración de mas de 5 años y de menos de dos años. Para esto, en cada área se establecieron cinco parcelas circulares de 30m de diámetro en las cuales se midieron todos los árboles con más de 10cm de DAP, en subparcelas de 6m de diámetro se midieron todos los latizales y arbustales de menos de 10 cm de DAP y en subparcelas de 1m2 se colectaron todas las herbáceas para determinar su biomasa en laboratorio. Esta investigación se desarrollará en el marco del Proyecto 7679 del Jardín Botánico de Bogotá, aportando al desarrollo de procesos de investigación en restauración ecológica de los efectos de los disturbios naturales y antrópicos sobre la composición estructura y función de los ecosistemas. Contribuye al cumplimiento de las metas de investigaciones para analizar dinámicas, mecanismos y procesos ecológicos a nivel de ecosistemas y paisaje de la Línea de Investigación en Restauración Ecológica de la Subdirección Científica del JBB.
description: El conjunto de datos cuenta con 838 registros tomados en 40 eventos de muestreo durante abril y junio de 2023 en el Bosque las Mercedes.
DOI: 10.6084/m9.figshare.25433098
title: Tolerance breadths, niche breadths, and latitude: implications for climate change in tropical organisms: Supplementary Data

description: <b>Aim: </b>Tropical species may be more vulnerable to global warming. One potential explanation is the seasonality hypothesis, the idea that a species' exposure to a narrow range of climatic temperatures over the year (low seasonality) limits the evolution of physiological tolerances to a narrower range of temperatures. Low temperature variability in the tropics may explain a higher frequency of climate-related local extinctions, but it is unclear whether this is due to narrow physiological tolerances to temperature extremes. The seasonality hypothesis predicts a strong, positive relationship between species’ climatic niche breadths and their physiological tolerance breadths. It also assumes that both niche breadths and tolerance breadths should be positively related to latitude. Here, we test these ideas using physiological, climatic, and phylogenetic data for 386 species spanning amphibians, squamates, birds, and mammals.<b>Methods: </b>We used phylogenetic comparative methods to test relationships among species' tolerance breadths, niche breadths, and latitude.<b>Results:</b> We found that the relationship between niche breadths (maximum minus minimum annual temperatures) and tolerance breadths (upper minus lower thermal tolerances) differed strongly among clades. In birds and mammals, these relationships were weak and non-significant. Niche breadths were significantly and positively related to tolerance breadths in amphibians and squamates, but niche breadths explained only 6% of the variation in tolerance breadths among squamates compared to 29% in amphibians. Niche breadths were more strongly related to latitude than tolerance breadths. Latitude was significantly related to tolerance breadths in amphibians and squamates, but the relationship was weak among squamates and not significant in birds and mammals.<b>Main Conclusions:</b> These results provide evidence against the seasonality hypothesis and the idea that narrower physiological tolerance breadths in the tropics explain why narrower climatic temperature niche breadths predict climate-driven extinctions. Overall, our results suggest that physiological tolerance breadths may not predict species' vulnerability to warming.
DOI: 10.6084/m9.figshare.25433098.v1
title: Tolerance breadths, niche breadths, and latitude: implications for climate change in tropical organisms: Supplementary Data

description: <b>Aim: </b>Tropical species may be more vulnerable to global warming. One potential explanation is the seasonality hypothesis, the idea that a species' exposure to a narrow range of climatic temperatures over the year (low seasonality) limits the evolution of physiological tolerances to a narrower range of temperatures. Low temperature variability in the tropics may explain a higher frequency of climate-related local extinctions, but it is unclear whether this is due to narrow physiological tolerances to temperature extremes. The seasonality hypothesis predicts a strong, positive relationship between species’ climatic niche breadths and their physiological tolerance breadths. It also assumes that both niche breadths and tolerance breadths should be positively related to latitude. Here, we test these ideas using physiological, climatic, and phylogenetic data for 386 species spanning amphibians, squamates, birds, and mammals.<b>Methods: </b>We used phylogenetic comparative methods to test relationships among species' tolerance breadths, niche breadths, and latitude.<b>Results:</b> We found that the relationship between niche breadths (maximum minus minimum annual temperatures) and tolerance breadths (upper minus lower thermal tolerances) differed strongly among clades. In birds and mammals, these relationships were weak and non-significant. Niche breadths were significantly and positively related to tolerance breadths in amphibians and squamates, but niche breadths explained only 6% of the variation in tolerance breadths among squamates compared to 29% in amphibians. Niche breadths were more strongly related to latitude than tolerance breadths. Latitude was significantly related to tolerance breadths in amphibians and squamates, but the relationship was weak among squamates and not significant in birds and mammals.<b>Main Conclusions:</b> These results provide evidence against the seasonality hypothesis and the idea that narrower physiological tolerance breadths in the tropics explain why narrower climatic temperature niche breadths predict climate-driven extinctions. Overall, our results suggest that physiological tolerance breadths may not predict species' vulnerability to warming.
DOI: 10.6084/m9.figshare.24953490
title: Terahertz time-domain of the samples.csv

description: Terahertz time-domain data of the samples.
DOI: 10.6084/m9.figshare.24953493
title: Frequency-domain data of the samples.csv

description: Frequency-domain data of the samples
DOI: 10.6084/m9.figshare.24953493.v1
title: Frequency-domain data of the samples.csv

description: Frequency-domain data of the samples
DOI: 10.6084/m9.figshare.24953502
title: Absorption coefficient for samples with different TFe contents.csv

description: Absorption coefficient for samples with different TFe contents
DOI: 10.6084/m9.figshare.24953502.v1
title: Absorption coefficient for samples with different TFe contents.csv

description: Absorption coefficient for samples with different TFe contents
DOI: 10.6084/m9.figshare.24953505
title: Refractive index data for samples with different TFe contents.csv

description: Refractive index data for samples with different TFe contents
DOI: 10.6084/m9.figshare.24953505.v1
title: Refractive index data for samples with different TFe contents.csv

description: Refractive index data for samples with different TFe contents
DOI: 10.6084/m9.figshare.24953508
title: FIG2.csv

description: TFe elemental content of protolith samples at different
depths. Absorption coefficients at different frequencies versus depth. Refractive index versus depth at different frequencies.
DOI: 10.6084/m9.figshare.24953508.v1
title: FIG2.csv

description: TFe elemental content of protolith samples at different
depths. Absorption coefficients at different frequencies versus depth. Refractive index versus depth at different frequencies.
DOI: 10.6084/m9.figshare.24953511
title: FIG3.csv

description: TFe content vs absorption coefficient of 1.32 THz
TFe content vs refractive index of 0.12 THz
DOI: 10.6084/m9.figshare.24953511.v1
title: FIG3.csv

description: TFe content vs absorption coefficient of 1.32 THz
TFe content vs refractive index of 0.12 THz
DOI: 10.6084/m9.figshare.24953523.v1
title: Correlation analysis（A.ys）.tex

description: The correlation matrix between terahertz spectral absorption
coefficients and the content of each element in the protoliths.