cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14913725
title: Additional file 5 of HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

description: Additional file 5: Table S1–S24. HOME-BIO reports for bacteria identified with the Assembly de novo module in the twelve samples analyzed.
DOI: 10.6084/m9.figshare.14913719
title: Additional file 3 of HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

description: Additional file 3: Table S1–S24. HOME-BIO reports for viruses identified with the metagenomic module in the twelve samples analyzed.
DOI: 10.6084/m9.figshare.14913719.v1
title: Additional file 3 of HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

description: Additional file 3: Table S1–S24. HOME-BIO reports for viruses identified with the metagenomic module in the twelve samples analyzed.
DOI: 10.6084/m9.figshare.14913728
title: Additional file 6 of HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

description: Additional file 6: Table S1–S24. HOME-BIO reports for viruses identified with the Assembly de novo module in the twelve samples analyzed.
DOI: 10.6084/m9.figshare.14913728.v1
title: Additional file 6 of HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

description: Additional file 6: Table S1–S24. HOME-BIO reports for viruses identified with the Assembly de novo module in the twelve samples analyzed.
DOI: 10.6084/m9.figshare.14913725.v1
title: Additional file 5 of HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

description: Additional file 5: Table S1–S24. HOME-BIO reports for bacteria identified with the Assembly de novo module in the twelve samples analyzed.
DOI: 10.6084/m9.figshare.14913731.v1
title: Additional file 7 of HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

description: Additional file 7: Table S1–S24. HOME-BIO reports for protozoa identified with the Assembly de novo module in the twelve samples analyzed.
DOI: 10.6084/m9.figshare.14913722.v1
title: Additional file 4 of HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

description: Additional file 4: Table S1–S24. HOME-BIO reports for protozoa identified with the metagenomic module in the twelve samples analyzed.
DOI: 10.6084/m9.figshare.14913852
title: Additional file 8 of HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

description: Additional file 8: Table S1–S2. HOME-BIO reports for bacteria, viruses, and protozoa identified Can_Fam samples.
DOI: 10.6084/m9.figshare.13377615.v1
title: Beyond crystal mushes: evidence for uptake of high-T pyroxene antecrysts from mid- to upper crustal andesites into tephras from the Central Plateau, New Zealand

description: Pyroxene crystals from recent Central Plateau tephras are used to deduce their formation conditions through two-pyroxene thermobarometry. Crystals return pseudo-pressures and pseudo-temperatures that are artefacts of uptake of antecrysts formed at a range of crustal levels by isobaric cooling of previously intruded magmas. MELTS modelling of tephra glass compositions shows that pseudo-PT conditions are reproduced at oxygen fugacities above the nickel-nickel oxide buffer (NNO+1, NNO+2), mid- to upper crustal pressures (100–400 MPa), and temperatures between <i>c</i>. 900°C and &gt;1100°C. Modelled crystals from the deep crust (800 MPa) are restricted to clinopyroxenes. However, these display chemical equilibrium with shallow orthopyroxenes at higher pseudo-PT conditions than observed in Central Plateau pyroxenes. The data indicate uptake of high-temperature pyroxenes at mid- to shallow crustal levels into ascending andesitic melts and thus preclude the presence of long-lived crustal mush zones (&lt;1000°C) as a source for the crystal cargo of the Central Plateau tephras studied here. Further, the apparent absence of deep crustal pyroxene antecrysts does not preclude models of arc andesite genesis without a ‘deep crustal hot zone’ beneath the Central Plateau. Generation and ascent of primary andesites from a heterogeneous mantle wedge is therefore a possible scenario at the southern Hikurangi margin.
DOI: 10.6084/m9.figshare.14913731
title: Additional file 7 of HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

description: Additional file 7: Table S1–S24. HOME-BIO reports for protozoa identified with the Assembly de novo module in the twelve samples analyzed.
DOI: 10.6084/m9.figshare.14913852.v1
title: Additional file 8 of HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis

description: Additional file 8: Table S1–S2. HOME-BIO reports for bacteria, viruses, and protozoa identified Can_Fam samples.
DOI: 10.6084/m9.figshare.13377615
title: Beyond crystal mushes: evidence for uptake of high-T pyroxene antecrysts from mid- to upper crustal andesites into tephras from the Central Plateau, New Zealand

description: Pyroxene crystals from recent Central Plateau tephras are used to deduce their formation conditions through two-pyroxene thermobarometry. Crystals return pseudo-pressures and pseudo-temperatures that are artefacts of uptake of antecrysts formed at a range of crustal levels by isobaric cooling of previously intruded magmas. MELTS modelling of tephra glass compositions shows that pseudo-PT conditions are reproduced at oxygen fugacities above the nickel-nickel oxide buffer (NNO+1, NNO+2), mid- to upper crustal pressures (100–400 MPa), and temperatures between <i>c</i>. 900°C and &gt;1100°C. Modelled crystals from the deep crust (800 MPa) are restricted to clinopyroxenes. However, these display chemical equilibrium with shallow orthopyroxenes at higher pseudo-PT conditions than observed in Central Plateau pyroxenes. The data indicate uptake of high-temperature pyroxenes at mid- to shallow crustal levels into ascending andesitic melts and thus preclude the presence of long-lived crustal mush zones (&lt;1000°C) as a source for the crystal cargo of the Central Plateau tephras studied here. Further, the apparent absence of deep crustal pyroxene antecrysts does not preclude models of arc andesite genesis without a ‘deep crustal hot zone’ beneath the Central Plateau. Generation and ascent of primary andesites from a heterogeneous mantle wedge is therefore a possible scenario at the southern Hikurangi margin.
DOI: 10.6084/m9.figshare.12003987.v1
title: Auckland Volcanic Field magmatism, volcanism, and hazard: a review

description: Auckland Volcanic Field (AVF) is a basaltic intraplate volcanic field in North Island, New Zealand, upon which &gt;1.6 million people live. Seismic velocity tomography and geochemistry suggest a primary mantle source region at a depth of 70–90 km. Geochemical analysis indicates a range of magma compositions, and that melts ascend with little crustal interaction. Eruptions generally began with a phreatomagmatic phase forming maar and tuff rings with tephra fall, base surges, and ballistic projectiles as the main hazards. Subsequent magmatic phases formed scoria cones, and sometimes produced lava flows. Ages of 47 of the 53 volcanic centres reveal that the AVF first erupted ∼193 ka, and last erupted ∼500 yrs. BP. These geochronological constraints indicate repose periods ≤0.1–13 kyr, which have decreased since ∼60 ka. From known geological and exposure information, and using an interdisciplinary approach, eight future eruption scenarios have been developed for planning processes. Outstanding questions for the AVF concern the cause of mantle melting, the structure of the underlying lithosphere, magma ascent rates, controls on repose periods and eruptive volumes. Answering these questions may improve our understanding of warning periods, monitoring strategies, spatiotemporal risk profiles, and socio-economic impacts of volcanism on New Zealand’s largest city.
DOI: 10.6084/m9.figshare.12003987
title: Auckland Volcanic Field magmatism, volcanism, and hazard: a review

description: Auckland Volcanic Field (AVF) is a basaltic intraplate volcanic field in North Island, New Zealand, upon which &gt;1.6 million people live. Seismic velocity tomography and geochemistry suggest a primary mantle source region at a depth of 70–90 km. Geochemical analysis indicates a range of magma compositions, and that melts ascend with little crustal interaction. Eruptions generally began with a phreatomagmatic phase forming maar and tuff rings with tephra fall, base surges, and ballistic projectiles as the main hazards. Subsequent magmatic phases formed scoria cones, and sometimes produced lava flows. Ages of 47 of the 53 volcanic centres reveal that the AVF first erupted ∼193 ka, and last erupted ∼500 yrs. BP. These geochronological constraints indicate repose periods ≤0.1–13 kyr, which have decreased since ∼60 ka. From known geological and exposure information, and using an interdisciplinary approach, eight future eruption scenarios have been developed for planning processes. Outstanding questions for the AVF concern the cause of mantle melting, the structure of the underlying lithosphere, magma ascent rates, controls on repose periods and eruptive volumes. Answering these questions may improve our understanding of warning periods, monitoring strategies, spatiotemporal risk profiles, and socio-economic impacts of volcanism on New Zealand’s largest city.
DOI: 10.6084/m9.figshare.14913858
title: A chromosome-level genome of cotton bollworm

description: We <i>de novo</i> assembled a high-quality, chromosome-level reference genome (contig N50 equals to 7.34 Mb) of <i>H. a. armigera</i>, using PacBio long-reads. Creating and utilizing a genetic map, 99.13% sequences were assigned into 31 chromosomes (Z-chromosome + 30 autosomes).
DOI: 10.6084/m9.figshare.14913396.v1
title: Additional file 1 of An engineered genetic circuit for lactose intolerance alleviation

description: Additional file 1 Table S1 to S9. Detailed data of results. Table S1: Detailed sequences of all the parts of our designed circuits; Table S2: Raw data for the fluorescence measurement of the protein & promoter; Table S3: Raw data for the fluorescence measurement of the protein & protein interaction of CIII & CII; Table S4: Parameters for tri-stable circuit modelling; Table S5: The variation of pH, β-galactosidase activity and l-lactate dehydrogenase activity in in vitro experiment to confirm the functionality of the circuit; Table S6: The variation of pH of the mice colon in the in vivo experiment to confirm the functionality of the circuit; Table S7: The variation of the β-galactosidase of the mice feces in the in vivo experiment to confirm the functionality of the circuit. Table S8: The experiment design and fecal sample collection of the 21-days in vivo experiment to detect the variation of mice gut microbiota; Table S9: The mean abundance of ASVs in the network and their taxonomic annotations.
DOI: 10.6084/m9.figshare.14913323.v1
title: Additional file 3 of Influenza in Malaysian adult patients hospitalized with community-acquired pneumonia, acute exacerbation of chronic obstructive pulmonary disease or asthma: a multicenter, active surveillance study

description: Additional file 3. List of influenza sequences used in analysis.
DOI: 10.6084/m9.figshare.14913194.v1
title: Additional file 1 of Community engagement and involvement in Ghana: conversations with community stakeholders to inform surgical research

description: Additional file 1: Appendix 1 and 2. Patient conversation templates.
DOI: 10.6084/m9.figshare.14913530
title: Additional file 24 of Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

description: Additional file 24. maxmiss.7.maf0.01.vcf VCF file with SNP calls.
DOI: 10.6084/m9.figshare.14914278.v1
title: diracfdm.rar from Semiclassical approach for excitonic spectrum of Coulomb coupling between two Dirac particles

description: The properties of the energy spectrum of excitons in monolayer transition metal dichalcogenides are investigated using a multiband model. In the multiband model, we use the excitonic Hamiltonian in the product base of the Dirac single-particle states at the conduction and valence band edges. Following the separation of variables, we decouple the corresponding energy eigenvalue system of the first-order ODE radial equations rigorously and solve the resulting second-order ODE self-consistently, using the finite difference method, thus we determine the energy eigenvalues of the discrete excitonic spectrum and the corresponding wave functions. We also developed a WKB approach to solve the same spectral problem in semiclassical approximation for the resulting ODE. We compare the results for the energy spectrum and the corresponding eigen-function forms for WS<sub>2</sub> and WSe<sub>2</sub> obtained by means of both methods. We also compare our results for the energy spectrum with other theoretical works for excitons, and with available experimental data.
DOI: 10.6084/m9.figshare.13887152.v1
title: Calcareous nannofossil biostratigraphy of the Late Cretaceous‒early Paleocene interval in the Zagros basin (southeastern Tethys), Iran

description: Calcareous nannofossil biostratigraphy reveals a continuous depositional record through the Upper Cretaceous‒Paleocene succession in the Zagros Basin; southwest Iran (southeastern part of the Neo-Tethys), especially through the Cretaceous‒Paleogene and the Danian‒Selandian boundaries. The upper part of the Gurpi Formation and the lower part of the Pabdeh Formation were investigated. Calcareous nannofossil assemblages from these formations are characterized by abundant, diverse and moderate- to well-preserved forms with Tethyan affinities. This study concentrates on two sections (the Gurpi and Kabir-Kuh sections) in the west and southwest of Iran in the Zagros Basin, which span biozones CC25c/UC20bTP to NP6/NTp10B in the Kabir-Kuh and CC25b/UC20aTP to NP5/NTp9 in the Gurpi section. Late Maastrichtian nannofossil abundance and diversity in the studied intervals is high with a sharp decrease slightly above the K/Pg boundary. The K/Pg boundary interval is marked by the FO of <i>Biantholithus sparsus</i>, an acme of the dinoflagellate cyst <i>Thoracosphaera operculata</i>, a notable decrease in Cretaceous calcareous nannofossil abundance and diversity, and the appearance of new Paleocene taxa. An increased abundance of <i>Thoracosphaera</i> is recorded similar to that in the El Kef (Global Stratotype Section and Point, GSSP, for the K/Pg boundary), Ellés (auxiliary section), Egypt, Atlantic Ocean and sections elsewhere in the world. Reworked Cretaceous calcareous nannofossils are recorded from the base of the Danian along with the new Paleocene species. The Danian‒Selandian boundary is marked by the appearance of <i>Lithoptychius ulii</i>, <i>Lithoptychius pileatus</i> and <i>Lithoptychius janii</i> at the base of NTp8C; this level is also marked by the second radiation of <i>Fasciculithus</i>. <i>Azam Mahanipour [a_mahanipour@uk.ac.ir], Department of Geology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran; Mohammad Parandavar [parandavar.m@gmail.com], Paleontological Research Department, Exploration Directorate of Oil and Gas, NIOC, Tehran; Mohamed Youssef [myousefgeology@gmail.com], Department of Geology, Faculty of Science, South Valley University, 83523 Qena, Egypt.</i>
DOI: 10.6084/m9.figshare.13887152
title: Calcareous nannofossil biostratigraphy of the Late Cretaceous‒early Paleocene interval in the Zagros basin (southeastern Tethys), Iran

description: Calcareous nannofossil biostratigraphy reveals a continuous depositional record through the Upper Cretaceous‒Paleocene succession in the Zagros Basin; southwest Iran (southeastern part of the Neo-Tethys), especially through the Cretaceous‒Paleogene and the Danian‒Selandian boundaries. The upper part of the Gurpi Formation and the lower part of the Pabdeh Formation were investigated. Calcareous nannofossil assemblages from these formations are characterized by abundant, diverse and moderate- to well-preserved forms with Tethyan affinities. This study concentrates on two sections (the Gurpi and Kabir-Kuh sections) in the west and southwest of Iran in the Zagros Basin, which span biozones CC25c/UC20bTP to NP6/NTp10B in the Kabir-Kuh and CC25b/UC20aTP to NP5/NTp9 in the Gurpi section. Late Maastrichtian nannofossil abundance and diversity in the studied intervals is high with a sharp decrease slightly above the K/Pg boundary. The K/Pg boundary interval is marked by the FO of <i>Biantholithus sparsus</i>, an acme of the dinoflagellate cyst <i>Thoracosphaera operculata</i>, a notable decrease in Cretaceous calcareous nannofossil abundance and diversity, and the appearance of new Paleocene taxa. An increased abundance of <i>Thoracosphaera</i> is recorded similar to that in the El Kef (Global Stratotype Section and Point, GSSP, for the K/Pg boundary), Ellés (auxiliary section), Egypt, Atlantic Ocean and sections elsewhere in the world. Reworked Cretaceous calcareous nannofossils are recorded from the base of the Danian along with the new Paleocene species. The Danian‒Selandian boundary is marked by the appearance of <i>Lithoptychius ulii</i>, <i>Lithoptychius pileatus</i> and <i>Lithoptychius janii</i> at the base of NTp8C; this level is also marked by the second radiation of <i>Fasciculithus</i>. <i>Azam Mahanipour [a_mahanipour@uk.ac.ir], Department of Geology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran; Mohammad Parandavar [parandavar.m@gmail.com], Paleontological Research Department, Exploration Directorate of Oil and Gas, NIOC, Tehran; Mohamed Youssef [myousefgeology@gmail.com], Department of Geology, Faculty of Science, South Valley University, 83523 Qena, Egypt.</i>
DOI: 10.6084/m9.figshare.7877999.v1
title: Priority effect between annual and perennial plants

description: Matlab Codes for the paper ‘priority effects between annual and perennial plants’. These files include the models from the main text and the appendix. I recommend downloading all the files into the same directory before running them because the scripts are using functions which are located in different files. <br>please read the file 'matlab codes for the paper' for brief description of the codes
DOI: 10.6084/m9.figshare.14914278
title: diracfdm.rar from Semiclassical approach for excitonic spectrum of Coulomb coupling between two Dirac particles

description: The properties of the energy spectrum of excitons in monolayer transition metal dichalcogenides are investigated using a multiband model. In the multiband model, we use the excitonic Hamiltonian in the product base of the Dirac single-particle states at the conduction and valence band edges. Following the separation of variables, we decouple the corresponding energy eigenvalue system of the first-order ODE radial equations rigorously and solve the resulting second-order ODE self-consistently, using the finite difference method, thus we determine the energy eigenvalues of the discrete excitonic spectrum and the corresponding wave functions. We also developed a WKB approach to solve the same spectral problem in semiclassical approximation for the resulting ODE. We compare the results for the energy spectrum and the corresponding eigen-function forms for WS<sub>2</sub> and WSe<sub>2</sub> obtained by means of both methods. We also compare our results for the energy spectrum with other theoretical works for excitons, and with available experimental data.
DOI: 10.6084/m9.figshare.7877999
title: Alternative stable states driven by a life-history tradeoff

description: Matlab Codes for the paper ‘Alternative stable states driven by a life-history tradeoff’. These files include the models from the main text and the appendix. I recommend downloading all the files into the same directory before running them because the scripts are using functions which are located in different files. <br>please read the file 'matlab codes for the paper' for brief description of the codes
DOI: 10.6084/m9.figshare.7877999.v3
title: Alternative stable states driven by a life-history tradeoff

description: Matlab Codes for the paper ‘Alternative stable states driven by a life-history tradeoff’. These files include the models from the main text and the appendix. I recommend downloading all the files into the same directory before running them because the scripts are using functions which are located in different files. <br>please read the file 'matlab codes for the paper' for brief description of the codes
DOI: 10.6084/m9.figshare.7877999.v2
title: Alternative stable states driven by a life-history tradeoff

description: Matlab Codes for the paper ‘Alternative stable states driven by a life-history tradeoff’. These files include the models from the main text and the appendix. I recommend downloading all the files into the same directory before running them because the scripts are using functions which are located in different files. <br>please read the file 'matlab codes for the paper' for brief description of the codes
DOI: 10.6084/m9.figshare.8135366.v2
title: The effects of ecological selection on species diversity and trait distribution: predictions and an empirical test

description: Codes and data for the theoretical model presented in the manuscript "The effects of ecological selection on species diversity and trait distribution: predictions and an empirical test". For running the simulation, I recommend downloading all Matlab codes to the same directory. 1. Species_pool_main_simulation - this script includes the main simulation (producing Fig 3 in the main text). It can also produce some of the results present in the appendix. The file is based on the function “community_attributes_all_time”. 2. community_attributes_all_time – this function that calculate community attributes (species diversity, functional diversity). 3. Drift mesocosm – this script is a specific parameterization of the model for the mesocosm experiment. 4. Speciesl_pool_transient,species_pool_alternative_function, species_pool_SD_traits,species_pool_uniform - these scripts are used for investigating the model (their results are presented in the appendix only)<br>
DOI: 10.6084/m9.figshare.8135366
title: The effects of ecological selection on species diversity and trait distribution: predictions and an empirical test

description: Codes and data for the theoretical model presented in the manuscript "The effects of ecological selection on species diversity and trait distribution: predictions and an empirical test". For running the simulation, I recommend downloading all Matlab codes to the same directory. 1. Species_pool_main_simulation - this script includes the main simulation (producing Fig 3 in the main text). It can also produce some of the results present in the appendix. The file is based on the function “community_attributes_all_time”. 2. community_attributes_all_time – this function that calculate community attributes (species diversity, functional diversity). 3. Drift mesocosm – this script is a specific parameterization of the model for the mesocosm experiment. 4. Speciesl_pool_transient,species_pool_alternative_function, species_pool_SD_traits,species_pool_uniform - these scripts are used for investigating the model (their results are presented in the appendix only)<br>