cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21208196
title: Nest architecture influences host use by avian brood parasites and is shaped by coevolutionary dynamics

description: Brood (social) parasites and their hosts exhibit a wide range of adaptations and counter-adaptations as part of their ongoing coevolutionary arms races. Obligate avian brood parasites are expected to use potential host species with more easily accessible nests, whilst potential hosts are expected to evade parasitism by building more concealed nests that are also difficult for parasites to enter and lay eggs in. We used phylogenetically-informed comparative analyses, a global database of the world’s brood parasites, their host species, and the design of avian host and non-host nests (~6200 species) to examine first, whether parasites preferentially target host species that build open nests and, second, whether host species targeted by specialist parasites are more likely to build enclosed nests. We found that species building more accessible nests are more likely to serve as hosts, while host species with some of the more inaccessible nests are targeted by more specialist brood parasites. Furthermore, evolutionary-transition analyses demonstrate that host species building enclosed nests frequently evolve to become non-hosts. We conclude that nest architecture and the accessibility of nests for parasitism represent a critical stage of the ongoing coevolutionary arms race between avian brood parasites and their hosts.
DOI: 10.6084/m9.figshare.21208196.v2
title: Nest architecture influences host use by avian brood parasites and is shaped by coevolutionary dynamics

description: Brood (social) parasites and their hosts exhibit a wide range of adaptations and counter-adaptations as part of their ongoing coevolutionary arms races. Obligate avian brood parasites are expected to use potential host species with more easily accessible nests, whilst potential hosts are expected to evade parasitism by building more concealed nests that are also difficult for parasites to enter and lay eggs in. We used phylogenetically-informed comparative analyses, a global database of the world’s brood parasites, their host species, and the design of avian host and non-host nests (~6200 species) to examine first, whether parasites preferentially target host species that build open nests and, second, whether host species targeted by specialist parasites are more likely to build enclosed nests. We found that species building more accessible nests are more likely to serve as hosts, while host species with some of the more inaccessible nests are targeted by more specialist brood parasites. Furthermore, evolutionary-transition analyses demonstrate that host species building enclosed nests frequently evolve to become non-hosts. We conclude that nest architecture and the accessibility of nests for parasitism represent a critical stage of the ongoing coevolutionary arms race between avian brood parasites and their hosts.
DOI: 10.6084/m9.figshare.21208196.v1
title: Nest architecture influences host use by avian brood parasites and is shaped by coevolutionary dynamics

description: Brood (social) parasites and their hosts exhibit a wide range of adaptations and counter-adaptations as part of their ongoing coevolutionary arms races. Obligate avian brood parasites are expected to use potential host species with more easily accessible nests, whilst potential hosts are expected to evade parasitism by building more concealed nests that are also difficult for parasites to enter and lay eggs in. We used phylogenetically informed comparative analyses and a global database of the world’s brood parasites, their host species, and the design of avian host and non-host nests (~6200 species) to examine first, whether parasites preferentially target host species building open nests and, second, whether host species targeted by specialist parasites build enclosed nests. As predicted, the nests of host species tend to be more accessible to brood parasites than the nests of non-host species, and host species targeted by specialist brood parasites build more concealed nests than host species targeted by more generalist brood parasites. Furthermore, evolutionary transition analyses demonstrate that host species building closed nests evolve to either remain nesting in closed structures and become non-hosts or evolve to build open nests and remain hosts. We conclude that nest architecture, and the accessibility of nests for parasitism, represent a critical and previously under-appreciated stage of the ongoing coevolutionary arms race between avian brood parasites and their hosts.
DOI: 10.21223/yy7kc9
title: Dataset for: Study on Vitamin C Concentrations in Potato Clones at Different Post-Harvest Storage Durations - Ayacucho

description: This study aimed to assess the changes in Vitamin C concentrations at different post-harvest storage durations, including T0 (immediately after harvest), T1 (6 weeks after harvest), T2 (12 weeks after harvest), and T3 (18 weeks after harvest). We evaluated a total of eleven clones, utilizing a randomized complete block design (RCBD) with three replications. These clones were sourced from planting activities in Ayacucho."
DOI: 10.6084/m9.figshare.24236926
title: 20231004_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.6084/m9.figshare.24236926.v1
title: 20231004_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.25326/522
title: LIAISE_ELS-PLANS_UKMO_LAI_01DAY_L1

description: Leaf Area Index (LAI) measured at Els Plans on three occasions during the LIAISE long observation period (LOP) between July 2021 and April 2022. Measurements were made a 10 locations around the Els Plans sites. Measurements were made during the summer IOP on 18 July 2021, during the winter on 18 January 2022 and during the spring IOP on 7 April 2022.
DOI: 10.25345/c5x921v68
title: MassIVE MSV000093019 - Characterization of a glutamate racemase from an uncultivated bacterium
title: Project description: In this study, we have characterized with distinct biochemical assays the activity of a predicted glutamate racemase from an uncultivated bacterium (Candidatus Saccharimonas aalborgenesis), classified taxonomically within the Candidate Phyla Radiation (CPR). This racemase was produced in a Salmonella auxotrophic mutant defective in its endogenous glutamate racemase. Despite the low identity of the predicated racemase from this uncultivated bacterium compared to that of Salmonella (MurI), ~32.0%, it exhibited high specificity for glutamate as substrate in in vitro racemization assays among the rest of canonical amino acids. Moreover, the expression of this novel racemase complemented the D-Glu auxotrophy of the host bacterium used as chassis (Salmonella). Besides these physiological analyses, the study also characterized the composition and structure of the peptidoglycan produced by bacteria expressing each of the two glutamate racemases, exogenous and endogenous. Data processing protocol: Three biological replicates of two Salmonella strains expressing either the predicted glutamate racemase from the uncultivated bacterium Candidatus Saccharimonas aalborgenesis (Delta-murI-CPR, R1-R3) or the endogenous glutamate racemase (MurI) (Delta-murI-SAL, R1-R3) were grown in the nutrient rich medium LB to reach the exponential phase. At this time, bacteria were collected by centrifugation, washed and lysed by boiling in a 4% SDS-containing buffer. From this material, peptidoglycan was purified by standard protocol. Briefly, after high-speed centrifugation, the pellet containing peptidoglycan as the only SDS-insoluble material was subjected to successive enzymatic treatments with alpha-amylase, pronase (as protease) and, muramidase to cleave the glycan chains and to yield individual uncross-linked and cross-linked muropeptides. The muropeptide mixtures were analysed by LC-MS/MS to obtain a list of parental masses representing the complexity of the sample, i.e. the diversity of co-existing muropeptide classes. The parental masses were assigned as "muropeptides" when a mass of 204.3, corresponding to the N-acetyl-glucosamine molecule, was detected in the fragmentation spectra. The complete lists of parental masses were examined using FreeStyle (Thermo) software and compared among samples (biological replicas and control-problem pairs) by statistical parameters using XCMS software.
DOI: 10.6073/pasta/74ac4c8d78f89935e4a77a8f310c9ac4
title: Density of Seagrass in Virginia Coastal Bays, 2007-2021

description: This dataset contains measurements of seagrass shoot density in restored Z. marina meadows in the Virginia coastal bays. Measurements were made annually in June-July at plots in Hog Island Bay and South Bay, VA. GPS locations of sampling plots are available in the companion data set VCR11180.
DOI: 10.6084/m9.figshare.22811384
title: Guppy and M. picta repeats_annotation

description: The dataset was produced using RepeatModeler2 (Flynn et al. 2020) to generate an initial comprehensive set of candidate TE families in the male reference genome assembly (Fraser et al. 2020). RepeatMasker (Smit et al. http:// repeatmasker.org) was used to make a library of consensus sequences from the RepeatModeler2 analysis plus Teleostei repeats from Repbase (https://www.girinst.org/repbase/). A filtered list of candidates was created and manually annotated following the procedures and criteria described by Goubert et al. (2022). RepeatMasker was then run again to find and annotate repeat copies throughout the male reference genome. 2. There are two files with results from the guppy, , as follows. GUPPY_consensus_library.fa (consensus TE library from RepeatModeler) guppy_ref.align_with_div.noCpG.size.out (RepeatMasker result) 3. Micropoecilia picta: 6 files from the RepeatModeler and RepeatMasker analyses of the M. picta assembly. Files from the RepeatModeler and RepeatMasker analyses of the M. picta assembly For the whole genome picta_assembly.unmasked.out picta_assembly.unmasked.out.gff For just chromosome 12, the sex chromosome LG12_picta.fa.out LG12_picta.fa.out.gff The consensus sequences produced by RepeatModeler consensi_picta.fa.classified consensi.fa References Flynn, J. M., R. Hubley, C. Goubert, J. Rosen, A. G. Clark et al., 2020 RepeatModeler2: automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences of the United States of America 117: 9451-9457. doi: 10.1073/pnas.1921046117 Fraser, B. A., J. R. Whiting, J. R. Paris, C. J. Weadick, P. J. Parsons et al., 2020 Improved reference genome uncovers novel sex-linked regions in the guppy (Poecilia reticulata). Genome Biology and Evolution 12: 1789–1805. doi: 10.1093/gbe/evaa187 Goubert, C., R. J. Craig, A. F. Bilat, V. Peona, A. A. Vogan et al., 2022 A beginner's guide to manual curation of transposable elements. Mob DNA 13: 7. doi: 10.1186/s13100-021-00259-7 Smit, A., R. Hubley and P. Green, 2013-2015 RepeatMasker Open-4.0<br>1. There are two files with results from the guppy, as follows.GUPPY_consensus_library.fa (consensus TE library from RepeatModeler)guppy_ref.align_with_div.noCpG.size.out (RepeatMasker result)<br>2. <i>Micropoecilia picta</i>: 6 files from the RepeatModeler and RepeatMasker analyses of the M. picta assembly.<br>Files from the RepeatModeler and RepeatMasker analyses of the M. picta assemblyFor the whole genomepicta_assembly.unmasked.outpicta_assembly.unmasked.out.gff<br>For just chromosome 12, the sex chromosomeLG12_picta.fa.outLG12_picta.fa.out.gff<br>The consensus sequences produced by RepeatModelerconsensi_picta.fa.classifiedconsensi.fa<br>
DOI: 10.6084/m9.figshare.22811384.v4
title: Guppy and M. picta repeats_annotation

description: The dataset was produced using RepeatModeler2 (Flynn et al. 2020) to generate an initial comprehensive set of candidate TE families in the male reference genome assembly (Fraser et al. 2020). RepeatMasker (Smit et al. http:// repeatmasker.org) was used to make a library of consensus sequences from the RepeatModeler2 analysis plus Teleostei repeats from Repbase (https://www.girinst.org/repbase/). A filtered list of candidates was created and manually annotated following the procedures and criteria described by Goubert et al. (2022). RepeatMasker was then run again to find and annotate repeat copies throughout the male reference genome. 2. There are two files with results from the guppy, , as follows. GUPPY_consensus_library.fa (consensus TE library from RepeatModeler) guppy_ref.align_with_div.noCpG.size.out (RepeatMasker result) 3. Micropoecilia picta: 6 files from the RepeatModeler and RepeatMasker analyses of the M. picta assembly. Files from the RepeatModeler and RepeatMasker analyses of the M. picta assembly For the whole genome picta_assembly.unmasked.out picta_assembly.unmasked.out.gff For just chromosome 12, the sex chromosome LG12_picta.fa.out LG12_picta.fa.out.gff The consensus sequences produced by RepeatModeler consensi_picta.fa.classified consensi.fa References Flynn, J. M., R. Hubley, C. Goubert, J. Rosen, A. G. Clark et al., 2020 RepeatModeler2: automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences of the United States of America 117: 9451-9457. doi: 10.1073/pnas.1921046117 Fraser, B. A., J. R. Whiting, J. R. Paris, C. J. Weadick, P. J. Parsons et al., 2020 Improved reference genome uncovers novel sex-linked regions in the guppy (Poecilia reticulata). Genome Biology and Evolution 12: 1789–1805. doi: 10.1093/gbe/evaa187 Goubert, C., R. J. Craig, A. F. Bilat, V. Peona, A. A. Vogan et al., 2022 A beginner's guide to manual curation of transposable elements. Mob DNA 13: 7. doi: 10.1186/s13100-021-00259-7 Smit, A., R. Hubley and P. Green, 2013-2015 RepeatMasker Open-4.0<br>1. There are two files with results from the guppy, as follows.GUPPY_consensus_library.fa (consensus TE library from RepeatModeler)guppy_ref.align_with_div.noCpG.size.out (RepeatMasker result)<br>2. <i>Micropoecilia picta</i>: 6 files from the RepeatModeler and RepeatMasker analyses of the M. picta assembly.<br>Files from the RepeatModeler and RepeatMasker analyses of the M. picta assemblyFor the whole genomepicta_assembly.unmasked.outpicta_assembly.unmasked.out.gff<br>For just chromosome 12, the sex chromosomeLG12_picta.fa.outLG12_picta.fa.out.gff<br>The consensus sequences produced by RepeatModelerconsensi_picta.fa.classifiedconsensi.fa<br>
DOI: 10.21223/ghffwr
title: Dataset for: Assessment of Adg x Tbr Potato Clones in Huancayo, Junin

description: An evaluation of yield components was conducted for 27 clones in the La Victoria area of Huancayo, Junin, in 2004, using a Completely Randomized Block Design (DBCA) with 3 replications. The evaluated clones belong to the Solanum tuberosum x S. andigenum.
DOI: 10.5281/zenodo.8403540
title: test data

description: test data
DOI: 10.5281/zenodo.8403539
title: test data

description: test data
DOI: 10.5517/ccdc.csd.cc2f0yt7
title: CCDC 2235249: Experimental Crystal Structure Determination

description: Related Article: Wenjie Lan, Xuan Yu, Mengzhu Li, Rongchao Lei, Zhaohai Qin, Bin Fu|2023|Org.Biomol.Chem.|21|7535|doi:10.1039/D3OB01140B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f58hd
title: CCDC 2239393: Experimental Crystal Structure Determination

description: Related Article: Mitchell T. Howell, Peter Kei, Maksim V. Anokhin, Yaroslav Losovyj, Frank R. Fronczek, Evgueni E. Nesterov|2023|Polym.Chem.|14|4319|doi:10.1039/D3PY00580A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f94jf
title: CCDC 2243114: Experimental Crystal Structure Determination

description: Related Article: Reyilan Maituoheti, Ruxianguli Rouzimaimaiti, Dan Tang, Jiangyu Zhao, Haji Akber Aisa|2023|Phytochemistry|215|113839|doi:10.1016/j.phytochem.2023.113839
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fwssx
title: CCDC 2261040: Experimental Crystal Structure Determination

description: Related Article: Yongbo Fan, Shengting Xu, Xinxin Cai, Zhijing Hou, Tianxiang Chen, Guozhang Fu, Zhongzhi Zhu, Xiuwen Chen|2023|Org.Biomol.Chem.|21|7593|doi:10.1039/D3OB01271A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2g3zl5
title: CCDC 2267947: Experimental Crystal Structure Determination

description: Related Article: Matteo L. Zaffalon, Ye Wu, Francesca Cova, Luca Gironi, Xiaoming Li, Valerio Pinchetti, Yang Liu, Muhammad Imran, Alessia Cemmi, Ilaria Di Sarcina, Liberato Manna, Haibo Zeng, Sergio Brovelli|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2g40vh
title: CCDC 2267986: Experimental Crystal Structure Determination

description: Related Article: Tunde Blessed Shonde, Biwu Ma|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d53tj
title: CCDC 2209457: Experimental Crystal Structure Determination

description: Related Article: Zhang Chuanbao|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fwtcj
title: CCDC 2261058: Experimental Crystal Structure Determination

description: Related Article: SUSHANTA PARIDA|2023|CSD Communication|||
description: Related Article: Sushanta Kumar Parida, Saurav Joshi, Sandip Murarka|2023|Org.Biomol.Chem.|21|5784|doi:10.1039/D3OB00899A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2g4c99
title: CCDC 2268310: Experimental Crystal Structure Determination

description: Related Article: Joel Mague, L. El Ghayati|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2g4jrx
title: CCDC 2268479: Experimental Crystal Structure Determination

description: Related Article: Jan L. Wikaira, Mark M. Turnbbull|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2g4k28
title: CCDC 2268489: Experimental Crystal Structure Determination

description: Related Article: Robert McKeown,  Mark M. Turnbull|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.21223/wqdob2/3scjw5
title: 01_Fieldbook_PTYL200408_AYMARA_Guano.txt

description: :unav
DOI: 10.21223/wqdob2/uj1iw4
title: 04_Fieldbook_TPHEN200408_AYMARA_Guano.txt

description: :unav
DOI: 10.21223/wqdob2/4deniv
title: TPHEN200408_AYMARA_Guano.xls

description: :unav
DOI: 10.21223/wqdob2/tojoq0
title: 03_Fieldbook_TVIT200408_AYMARA_Guano.txt

description: :unav
DOI: 10.21223/wqdob2/zbmftf
title: TMIN200408_AYMARA_Guano.xls

description: :unav
DOI: 10.21223/wqdob2/e41t4w
title: 02_Fieldbook_TMIN200408_AYMARA_Guano.txt

description: :unav
DOI: 10.21223/wqdob2/wwbpe3
title: 05_Material_list.txt

description: :unav
DOI: 10.21223/wqdob2/bmfbx4
title: PTYL200408_AYMARA_Guano.xls

description: :unav
DOI: 10.21223/wqdob2/enz1wk
title: TVIT200408_AYMARA_Guano.xls

description: :unav
DOI: 10.21223/wqdob2/q9v705
title: 06_Datadictionary.txt

description: :unav
DOI: 10.21223/wqdob2
title: Dataset for: Field Evaluation and Nutritional Analysis of native potato in the Aymara - Huancavelica

description: Field Evaluation of 20 Native Potato Varieties Conducted under a Factorial Design with 4 Treatments: Chicken Manure, Control, Guano Island, and Sheep Manure. The Experiment Included 3 Replications in the Aymara Zone of Huancavelica. Additionally, Micronutrient Concentrations, Vitamin C, and Polyphenols were determined.
DOI: 10.6084/m9.figshare.24204747
title: Raw data all figures

description: Raw data to all figures in the manuscript
DOI: 10.6084/m9.figshare.24204747.v1
title: Raw data all figures

description: Raw data to all figures in the manuscript
DOI: 10.5281/zenodo.8400618
title: Dataset for the Rab-1A and Rab-1B antibody screening study

description: This project contains the underlying data included in a study which characterized twelve commercially-available antibodies for the two Rab1 isoforms, Rab-1A and Rab-1B. Seven antibodies were intended to target Rab-1A and five antibodies intended to target Rab-1B. The study is also available on Zenodo (https://doi.org/10.5281/zenodo.8356353).