cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16640209.v3
title: Supplementary data to publication "Untargeted metabolomics reveals metabolic stress alleviation by prepartum exercise in transition dairy cows"

description: Prepartum exercise is one of the methods of optimizing perinatal management practices to improve health. However, mechanism of prepartum exercise regulates on metabolism are rarely been described. The objective of this study was to investigate metabolic changes in transition cows with exercise. 24 Holstein transition dairy cows were assigned to exercise (n = 12) and control group (n = 12) on approximately d 21 prepartum, plasma was collected during -21, -7, 0, +7, and +30 d relative to calving. The researchers assisted the exercise group cows to walk for a targeted 45 min at 3.25 km/h, 2 times/d. Plasma non-esterified fatty acid (NEFA), β-hydroxybutyric acid (BHBA), glucose, and triglycerides were evaluated, and metabolic profile was analyzed using ultra-high-performance liquid chromatography time-of-flight mass spectrometry. The results demonstrated that concentrations NEFA at -7 d, glucose at 0d, and BHBA at +7d relative to calving were obviously reduced in exercise cows. Untargeted metabolomics analyses showed that cows had experienced severe metabolic stress during calving, including increased fatty acid and glucose metabolism, and reduced bile acid and tryptophan metabolism. Four key metabolites were identified in cows with exercise during metabolic stress: gentisic acid, kynurenine, homovanillic acid, and cis-9-palmitoleic acids. Correlation and pathway analysis indicated that exercise had down-regulation of NEFA and BHBA production and maintained glucose levels through tryptophan-kynurenine metabolism, improving postpartum health.
DOI: 10.6084/m9.figshare.17059700
title: Evolution of fertilization-related genes provides insights into reproductive health in natural ascrotal mammals

description: Cryptorchidism is the failure of one or both testes to descend into the bottom of the scrotum. This common congenital malformation in humans and domestic animals is the best characterized risk factor for abnormal sperm functions and infertility. However, current treatment approaches for cryptorchidism do not ensure paternity in all cases. Some lineages of mammals (such as elephants and cetaceans) have natural ascrotal testes (i.e., undescended or incompletely descended testes) and normal sperm motility and fertility, providing an opportunity to understand the genetic basis of cryptorchidism.We uploaded 264 protein-coding sequences (CDSs) from four fertilization-related gene sets, (1) capacitation/decapacitation, (2) sperm motility, (3) sperm competition/fertilization, and (4) acrosomal reaction and zona reaction, in 49 representative taxa covering 20 major mammalian orders. In this study, we showed that genes associated with sperm motility and competition/fertility in ascrotal mammals experienced frequent, strong selective pressure. The fixation of specific amino acids and positive selection in ascrotal mammals could affect the physicochemical properties and functions of fertilization-related proteins. In a comparison between mammals with undescended testes and incompletely descended testes, discrepancies in genes showing evidence for adaptive evolution and in functional enrichment suggested that multiple molecular mechanisms contribute to the maintenance of fertility in the challenging testicular environment.
DOI: 10.6084/m9.figshare.17059700.v1
title: Evolution of fertilization-related genes provides insights into reproductive health in natural ascrotal mammals

description: Cryptorchidism is the failure of one or both testes to descend into the bottom of the scrotum. This common congenital malformation in humans and domestic animals is the best characterized risk factor for abnormal sperm functions and infertility. However, current treatment approaches for cryptorchidism do not ensure paternity in all cases. Some lineages of mammals (such as elephants and cetaceans) have natural ascrotal testes (i.e., undescended or incompletely descended testes) and normal sperm motility and fertility, providing an opportunity to understand the genetic basis of cryptorchidism.We uploaded 264 protein-coding sequences (CDSs) from four fertilization-related gene sets, (1) capacitation/decapacitation, (2) sperm motility, (3) sperm competition/fertilization, and (4) acrosomal reaction and zona reaction, in 49 representative taxa covering 20 major mammalian orders. In this study, we showed that genes associated with sperm motility and competition/fertility in ascrotal mammals experienced frequent, strong selective pressure. The fixation of specific amino acids and positive selection in ascrotal mammals could affect the physicochemical properties and functions of fertilization-related proteins. In a comparison between mammals with undescended testes and incompletely descended testes, discrepancies in genes showing evidence for adaptive evolution and in functional enrichment suggested that multiple molecular mechanisms contribute to the maintenance of fertility in the challenging testicular environment.
DOI: 10.4121/16635193
title: Video recording associated with the publication: The long-term reliability of pre-charged CMUTs for the powering of deep implanted devices

description: This dataset contains the video recordings associated with the publication. In the video, one CMUT element is exernally biased with a DC bias source, which is swept between 0 and 130 V and vice-versa. It can be seen that CMUTs go into collapse when the external DC bias voltage is higher than the collapse voltage (multiple rings of interference pattern appears at CMUTs cells, indicating a larger deflection profile). It can also be seen that not all the CMUT cells go into collapse and out-of-collapse at the same time.
DOI: 10.4121/16635193.v1
title: Video recording associated with the publication: The long-term reliability of pre-charged CMUTs for the powering of deep implanted devices

description: This dataset contains the video recordings associated with the publication. In the video, one CMUT element is exernally biased with a DC bias source, which is swept between 0 and 130 V and vice-versa. It can be seen that CMUTs go into collapse when the external DC bias voltage is higher than the collapse voltage (multiple rings of interference pattern appears at CMUTs cells, indicating a larger deflection profile). It can also be seen that not all the CMUT cells go into collapse and out-of-collapse at the same time.
DOI: 10.5281/zenodo.5644790
title: Dataset for Label-free Surface Enhanced Raman Scattering (SERS) on Centrifugal Silver Plasmonic Paper (CSPP): a novel methodology for unprocessed biofluids sampling and analysis.

description: This dataset contains all the spectra used in "Label-free Surface Enhanced Raman Scattering (SERS) on Centrifugal Silver Plasmonic Paper (CSPP): a novel methodology for unprocessed biofluids sampling and analysis". Data are available in 2 different formats: - a compressed archive ("Spectra.zip") with 5 folders ("Figure 1-5”) containing all the *.txt files used to generate the 5 figures in the original paper (1 file = 1 spectrum). - 5 single CSV files (“Figure-X_all-spectra-and-metadata.csv”) with all the spectra and metadata relative to a specific figure. The data are structured as follow, with each row being 1 spectrum, followed by metadata.
DOI: 10.5281/zenodo.5644789
title: Dataset for Label-free Surface Enhanced Raman Scattering (SERS) on Centrifugal Silver Plasmonic Paper (CSPP): a novel methodology for unprocessed biofluids sampling and analysis.

description: This dataset contains all the spectra used in "Label-free Surface Enhanced Raman Scattering (SERS) on Centrifugal Silver Plasmonic Paper (CSPP): a novel methodology for unprocessed biofluids sampling and analysis". Data are available in 2 different formats: - a compressed archive ("Spectra.zip") with 5 folders ("Figure 1-5”) containing all the *.txt files used to generate the 5 figures in the original paper (1 file = 1 spectrum). - 5 single CSV files (“Figure-X_all-spectra-and-metadata.csv”) with all the spectra and metadata relative to a specific figure. The data are structured as follow, with each row being 1 spectrum, followed by metadata.
DOI: 10.25403/upresearchdata.13793714
title: Horn measurements of sable antelope (Hippotragus niger) and their value in age determination

description: Horn measurements of sable antelope of known age were recorded during immobilisation for management purposes. Growth check counts were done from photograph records of mature females. Raw data was analysed to determine value in age determination
DOI: 10.5517/ccdc.csd.cc28c4f7
title: CCDC 2096078: Experimental Crystal Structure Determination

description: Related Article: Xinyi Wan, Shan Wang, Chengjun Wu, Jianbo Gan, Cunde Wang|2021|Org.Lett.|23|8799|doi:10.1021/acs.orglett.1c03301
DOI: 10.5517/ccdc.csd.cc28m547
title: CCDC 2103788: Experimental Crystal Structure Determination

description: Related Article: Teng Xue, Roger E. Cramer, David A. Vicic|2021|Organometallics|40|3585|doi:10.1021/acs.organomet.1c00469
DOI: 10.5517/ccdc.csd.cc28nln6
title: CCDC 2105168: Experimental Crystal Structure Determination

description: Related Article: Xian Shu, Guangzheng Wei, Yuben Qiao, Kexin Zhang, Jun Zhang, Guomin Ai, Man-cheng Tang, Yonghui Zhang, Shu-Shan Gao|2021|Org.Lett.|23|8947|doi:10.1021/acs.orglett.1c03432
DOI: 10.6084/m9.figshare.17059730.v1
title: The Cyprinidae Uniprot FASTA database version of 18.11.2020

description: The Cyprinidae UniProt FASTA database (realize 18.11.2020) was included 211 reviewed (swiss-prot) and 365,594 unreviewed entries.<br>
DOI: 10.6084/m9.figshare.17059730
title: The Cyprinidae Uniprot FASTA database version of 18.11.2020

description: The Cyprinidae UniProt FASTA database (realize 18.11.2020) was included 211 reviewed (swiss-prot) and 365,594 unreviewed entries.<br>
DOI: 10.6084/m9.figshare.17059775.v1
title: The Cestoda UniProt database

description: The Cestoda UniProt database was contained 221,790 entries and included the following Cestoda species: <i>Anindobothrium anacolum</i>, <i>A. lisae</i>, <i>A. laciniatum</i>, <i>A. hobergi</i>, <i>Dibothriocephalus latus</i>,<i> Diphyllobothrium stemmacephalum</i>,<i> Echinococcus granulosus</i>,<i> E. multilocularis</i>,<i> Gangesia oligonchis</i>,<i> Hydatigena taeniaeformis</i>,<i> Hydatigera kamiyai</i>,<i> Hymenolepis diminuta</i>,<i> H. microstoma</i>,<i> Mesocestoides corti</i>,<i> Raillietina echinobothrida</i>,<i> Rhinebothrium reydai</i>,<i> Rodentolepis nana</i>,<i> Schistocephalus solidus</i>,<i> Sparganum proliferum</i>,<i> Spirometra erinaceieuropaei</i>,<i> Taenia asiatica</i>,<i> T. crassiceps</i>,<i> T. martis</i>,<i> T. multiceps</i>,<i> T. pisiformis</i>,<i> T. saginata</i>,<i> T. solium</i>,<i> T. twitchelli</i>,<i> Testudotaenia sp.,Tetrabothrius forsteri</i>, and<i> </i>unidentified pseudophyllidean.<br>
DOI: 10.6084/m9.figshare.17059775
title: The Cestoda UniProt database

description: The Cestoda UniProt database was contained 221,790 entries and included the following Cestoda species: <i>Anindobothrium anacolum</i>, <i>A. lisae</i>, <i>A. laciniatum</i>, <i>A. hobergi</i>, <i>Dibothriocephalus latus</i>,<i> Diphyllobothrium stemmacephalum</i>,<i> Echinococcus granulosus</i>,<i> E. multilocularis</i>,<i> Gangesia oligonchis</i>,<i> Hydatigena taeniaeformis</i>,<i> Hydatigera kamiyai</i>,<i> Hymenolepis diminuta</i>,<i> H. microstoma</i>,<i> Mesocestoides corti</i>,<i> Raillietina echinobothrida</i>,<i> Rhinebothrium reydai</i>,<i> Rodentolepis nana</i>,<i> Schistocephalus solidus</i>,<i> Sparganum proliferum</i>,<i> Spirometra erinaceieuropaei</i>,<i> Taenia asiatica</i>,<i> T. crassiceps</i>,<i> T. martis</i>,<i> T. multiceps</i>,<i> T. pisiformis</i>,<i> T. saginata</i>,<i> T. solium</i>,<i> T. twitchelli</i>,<i> Testudotaenia sp.,Tetrabothrius forsteri</i>, and<i> </i>unidentified pseudophyllidean.<br>
DOI: 10.6084/m9.figshare.17059784
title: Supplementary Material for: Maternal Intrapartum Antibiotic Treatment and Gut Microbiota Development in Healthy Term Infants

description: <b><i>Objective:</i></b> The aim of the study was to investigate the impact of intrapartum antibiotic treatment (IAT) on the compositional development of gut microbiota in healthy term infants. <b><i>Study Design:</i></b> A case-control study of 24 infants exposed to and 24 matched infants not exposed to IAT was conducted. All subjects were born by vaginal delivery at term and breastfed. None of the infants received antibiotics during the immediate neonatal period. Fecal samples were obtained at the ages of 1 and 6 months. The composition of the intestinal microbiota was assessed by 16S rRNA gene sequencing. <b><i>Results:</i></b> IAT was associated with reduced microbial richness but not diversity at 1 month of age. Furthermore, the relative abundances of Clostridiaceae and Erysipelotrichaceae were significantly altered in infants exposed to IAT as compared to nonexposed infants at 1 month of age. The observed deviations in gut microbiota composition between infants exposed and not exposed to IAT diminished by the age of 6 months. <b><i>Conclusions:</i></b> IAT is associated with short-term perturbations in the gut microbiota development in healthy term, vaginally delivered, breastfed infants. The composition of the gut microbiota is mostly restored by the age of 6 months.
DOI: 10.6084/m9.figshare.17059784.v1
title: Supplementary Material for: Maternal Intrapartum Antibiotic Treatment and Gut Microbiota Development in Healthy Term Infants

description: <b><i>Objective:</i></b> The aim of the study was to investigate the impact of intrapartum antibiotic treatment (IAT) on the compositional development of gut microbiota in healthy term infants. <b><i>Study Design:</i></b> A case-control study of 24 infants exposed to and 24 matched infants not exposed to IAT was conducted. All subjects were born by vaginal delivery at term and breastfed. None of the infants received antibiotics during the immediate neonatal period. Fecal samples were obtained at the ages of 1 and 6 months. The composition of the intestinal microbiota was assessed by 16S rRNA gene sequencing. <b><i>Results:</i></b> IAT was associated with reduced microbial richness but not diversity at 1 month of age. Furthermore, the relative abundances of Clostridiaceae and Erysipelotrichaceae were significantly altered in infants exposed to IAT as compared to nonexposed infants at 1 month of age. The observed deviations in gut microbiota composition between infants exposed and not exposed to IAT diminished by the age of 6 months. <b><i>Conclusions:</i></b> IAT is associated with short-term perturbations in the gut microbiota development in healthy term, vaginally delivered, breastfed infants. The composition of the gut microbiota is mostly restored by the age of 6 months.
DOI: 10.5281/zenodo.5717756
title: msd-errors - Data for the LLZO figure

description: Data for the figure showing the diffusion and Arrhenius plots for a short simulation of LLZO. <br><br>Created using showyourwork from this GitHub repo.
DOI: 10.6084/m9.figshare.14779377
title: Simultaneous Inference for Empirical Best Predictors With a Poverty Study in Small Areas

description: Today, generalized linear mixed models (GLMM) are broadly used in many fields. However, the development of tools for performing simultaneous inference has been largely neglected in this domain. A framework for joint inference is indispensable to carry out statistically valid multiple comparisons of parameters of interest between all or several clusters. We therefore develop simultaneous confidence intervals and multiple testing procedures for empirical best predictors under GLMM. In addition, we implement our methodology to study widely employed examples of mixed models, that is, the unit-level binomial, the area-level Poisson-gamma and the area-level Poisson-lognormal mixed models. The asymptotic results are accompanied by extensive simulations. A case study on predicting poverty rates illustrates applicability and advantages of our simultaneous inference tools.
DOI: 10.6084/m9.figshare.14779377.v2
title: Simultaneous Inference for Empirical Best Predictors With a Poverty Study in Small Areas

description: Today, generalized linear mixed models (GLMM) are broadly used in many fields. However, the development of tools for performing simultaneous inference has been largely neglected in this domain. A framework for joint inference is indispensable to carry out statistically valid multiple comparisons of parameters of interest between all or several clusters. We therefore develop simultaneous confidence intervals and multiple testing procedures for empirical best predictors under GLMM. In addition, we implement our methodology to study widely employed examples of mixed models, that is, the unit-level binomial, the area-level Poisson-gamma and the area-level Poisson-lognormal mixed models. The asymptotic results are accompanied by extensive simulations. A case study on predicting poverty rates illustrates applicability and advantages of our simultaneous inference tools.
DOI: 10.6084/m9.figshare.14779377.v1
title: Simultaneous Inference for Empirical Best Predictors with a Poverty Study in Small Areas

description: Today, generalized linear mixed models are broadly used in many fields. However, the development of tools for performing simultaneous inference has been largely neglected in this domain. A framework for joint inference is indispensable to carry out statistically valid multiple comparisons of parameters of interest between all or several clusters. We therefore develop simultaneous confidence intervals and multiple testing procedures for empirical best predictors under generalized linear mixed models. In addition, we implement our methodology to study widely employed examples of mixed models, that is, the unit-level binomial, the area-level Poisson-gamma and the area-level Poisson-lognormal mixed models. The asymptotic results are accompanied by extensive simulations. A case study on predicting poverty rates illustrates applicability and advantages of our simultaneous inference tools.
DOI: 10.5281/zenodo.5706440
title: Data and code for the publication "Tracking microplastics across the streambed interface: Using laser-induced fluorescence to quantitatively analyze microplastic transport in an experimental flume"

description: This archive contains datasets and codes that were used in the publication "Tracking microplastics across the streambed interface: Using laser-induced fluorescence to quantitatively analyse microplastic transport in an experimental flume".
description: Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 391977956 – SFB 1357.
DOI: 10.5281/zenodo.5706439
title: Data and code for the publication "Tracking microplastics across the streambed interface: Using laser-induced fluorescence to quantitatively analyze microplastic transport in an experimental flume"

description: This archive contains datasets and codes that were used in the publication "Tracking microplastics across the streambed interface: Using laser-induced fluorescence to quantitatively analyse microplastic transport in an experimental flume".
description: Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project Number 391977956 – SFB 1357.
DOI: 10.6084/m9.figshare.16816099
title: Hadal aragonite records venting of stagnant paleoseawater in the hydrated forearc mantle

description: This repository includes dataset used in the following article:Oyanagi, R., Okamoto, A., Satish-Kumar, M., Minami, M., Harigane, Y., Michibayashi, K. (2021) Hadal aragonite records venting of stagnant paleoseawater in the hydrated forearc mantle, <i>Communications Earth & Environment</i>. <br><br>Contents<b>thermoLT600bat.dat</b> : Thermodynamic dataset for Geochemist's Workbench.<br><br><b>result_ReactionPathModeling(FigureS5).xlsx</b> : Summary of the reaction path calculation used in Supplementary Figure 5.<br><br><b>X-ray CT data.zip</b> : X-ray CT data of serpentinized peridotite in DICOM format. These data are used in Figure 2d in the paper.<br><b>X-rayCT_movie.avi</b> : Field of view is 3 mm diameter. Dark gray part is serpentine. Light gray part is aragonite. Their intermediate is olivine. White part is spinel and magnetite.<br><b>Supplementary_Table_1.xlsx: </b> <b> </b>Microsoft Excel spreadsheet of the supplementary table 1.<br><br><b>Supplementary_Table_2.xlsx: </b> <b> </b>Microsoft Excel spreadsheet of the supplementary table 2.<br><br><b>Supplementary_Table_3.xlsx: </b> <b> </b>Microsoft Excel spreadsheet of the supplementary table 3.<br>
DOI: 10.5281/zenodo.5717791
title: msd-errors - Data for variance and covariance figure

description: Data for a figure that presents the variance and covariance for a true random walk. There is a comparison shown between the numerical result from 1024 unique random walks and the analysis, by kinisi, of the same 1024 random walks.<br><br>Created using showyourwork from this GitHub repo.
DOI: 10.34740/kaggle/dsv/2838697
title: AutoXGB
DOI: 10.6084/m9.figshare.16834825.v1
title: Metadata on the oxidative stress related RNA-seq samples in the dataset used for the meta-analysis (OS dataset)

description: Information on oxidative stress related RNA-seq samples used for meta-analysis is organized as the dataset called OS dataset. It includes information on pairs of oxidative stress and normal state samples.
DOI: 10.5281/zenodo.5717733
title: Geomorphic dating of across-fault gully incision reveals time-invariant late Quaternary slip-rates at the eastern termination of the Altyn Tagh Fault

description: Interpretation of fault slip-rates inferred from tectonically offset fluvial landforms is often limited by uncertainties associated with difficulties to explicitly date fluvial incision across the fault. Here, we employed morphology-based modeling to ameliorate this universal dating limitation for gullies that were differentially offset in a sinistral sense across the Altyn Tagh Fault near its eastern termination at ~97°E. Using a stream-power erosion model with locally calibrated coefficients we calculated across-fault gully incision ages that decrease with offset magnitude, are up to threefold younger than the age of the terrace they incised and all-together point towards time-invariant sinistral slip. Luminescence dating of offset alluvial terraces at the same site suggests constant sinistral slip at 0.5±0.1 mm/yr since 52±4 ka. Our results are consistent with northeastward expansion of the Tibetan Plateau into stable parts of central Asia through an episodic, “stepwise” process punctuated by prolonged geologic time intervals of constant deformation rates.
DOI: 10.5281/zenodo.5717732
title: Geomorphic dating of across-fault gully incision reveals time-invariant late Quaternary slip-rates at the eastern termination of the Altyn Tagh Fault

description: Interpretation of fault slip-rates inferred from tectonically offset fluvial landforms is often limited by uncertainties associated with difficulties to explicitly date fluvial incision across the fault. Here, we employed morphology-based modeling to ameliorate this universal dating limitation for gullies that were differentially offset in a sinistral sense across the Altyn Tagh Fault near its eastern termination at ~97°E. Using a stream-power erosion model with locally calibrated coefficients we calculated across-fault gully incision ages that decrease with offset magnitude, are up to threefold younger than the age of the terrace they incised and all-together point towards time-invariant sinistral slip. Luminescence dating of offset alluvial terraces at the same site suggests constant sinistral slip at 0.5±0.1 mm/yr since 52±4 ka. Our results are consistent with northeastward expansion of the Tibetan Plateau into stable parts of central Asia through an episodic, “stepwise” process punctuated by prolonged geologic time intervals of constant deformation rates.