cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10265626
title: Dataset for first resonant PXCT experiments at the SWING beamline at Synchrotron Soleil

description: This dataset was acquired at the SWING beamline at the French synchrotron SOLEIL. The ptychographic scans consisted of 205 diffraction patterns from a field of view of 14x12 µm² with an exposure time of 100 ms per point. The ptychographic reconstruction was carried out using the PtychoShelves Matlab software package [1], involving 200 iterations of the difference map (DM) algorithm, followed by 100 iterations of the maximum likelihood (ML) algorithm.

The dataset consists of the ptychographic reconstructions of two ptychographic tomography scans at energies 8383 eV and 8337 eV, the angle files, and the corresponding tomograms as slices.

Niwire_3D_8383 - ptychographic reconstructions of the 200 projections at 3838 eV

Niwire_3D_8337 - ptychographic reconstructions of the 210 projections at 8337 eV (10 duplicate angles)

Niwire8383_TIFF_delta_FBP_ram-lak_freqscl_1.00 - tomographic reconstruction (with PtychoShelves [2]) of the Niwire measured at 8383 eV

Niwire8337_TIFF_delta_FBP_ram-lak_freqscl_1.00 - tomographic reconstruction (with PtychoShelves [2]) of the Niwire measured at 8337 eV

angles_Niwire8383 - the angles of the tomographic scan at 8383 eV

angles_Niwire8383 - the angles of the tomographic scan at 8337 eV

 

[1] Wakonig, K., Stadler, H.-C., Odstrčil, M., Tsai, E. H. R., Diaz, A., Holler, M., Usov, I., Raabe, J., Menzel, A. & Guizar-Sicairos, M. (2020). PtychoShelves, a versatile high-level framework for high-performance analysis of ptychographic data. J. Appl. Cryst. 53, 574-586.

[2] Michal Odstrčil, Mirko Holler, Jörg Raabe, and Manuel Guizar-Sicairos, "Alignment methods for nanotomography with deep subpixel accuracy," Opt. Express 27, 36637-36652 (2019)
DOI: 10.6084/m9.figshare.9614102.v3
title: RETRACTED ARTICLE: Long noncoding RNA H19 regulates HIF-1α/AXL signaling through inhibiting miR-20b-5p in endometrial cancer

description: We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: He Zhu, Yue-Mei Jin, Xue-Man Lyu, Li-Mei Fan & Fei Wu (2019) Long noncoding RNA H19 regulates HIF-1α/AXL signaling through inhibiting miR-20b-5p in endometrial cancer, Cell Cycle, 18:19, 2454-2464, DOI: 10.1080/15384101.2019.1648958 Since publication, the authors have found significant errors in the statistical analysis of the research reported in this article. As this error directly impacts the accuracy of the results and conclusions, the authors alerted the issue to the Editor and Publisher and all have agreed to retract the article to ensure the integrity of the scholarly record. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.6084/m9.figshare.20098763.v1
title: Additional file 1 of A comparison of three bone graft struts for interbody fusion using a posterior approach for lower lumbar spinal tuberculosis in adults: a midterm follow-up study

description: Additional file 1. The datasets used and analyzed in this study.
DOI: 10.6084/m9.figshare.24299040
title: CD70-induced differentiation of proinflammatory Th1/17/22/GM lymphocytes associated with disease progression and immune reconstitution during HIV infection

description: Immune overactivation is a hallmark of chronic HIV infection, which is critical to HIV pathogenesis and disease progression. The imbalance of helper T cell (Th) differentiation and subsequent cytokine dysregulation are generally considered to be the major drivers of excessive activation and inflammatory disorders in HIV infection. However, the accurate factors driving HIV-associated Th changes remained to be established. CD70, which was a costimulatory molecule, was found to increase on CD4<sup>+</sup> T cells during HIV infection. Overexpression of CD70 on CD4<sup>+</sup> T cells was recently reported to associate with highly pathogenic proinflammatory Th1/Th17 polarization in multiple sclerosis. Thus, the role of CD70 in the imbalance of Th polarization and immune overactivation during HIV infection needs to be investigated. Here, we found that the elevated frequency of CD70 <sup>+ </sup>CD4<sup>+</sup> T cells was negatively correlated with CD4 count and positively associated with immune activation in treatment-naïve people living with HIV (PLWH). More importantly, CD70 expression defined a population of proinflammatory Th1/17/22/GM subsets in PLWH. Blocking CD70 decreased the mRNA expression of subset-specific markers during Th1/17/22/GM polarization. Furthermore, we demonstrated that CD70 influenced the differentiation of these Th cells through STAT pathway. Finally, it was revealed that patients with a high baseline level of CD70 on CD4<sup>+</sup> T cells exhibited a greater risk of poor immune reconstitution after antiretroviral therapy (ART) than those with low CD70. In general, our data highlighted the role of CD70 in Th1/17/22/GM differentiation during HIV infection and provided evidence for CD70 as a potential biomarker for predicting immune recovery.
DOI: 10.6084/m9.figshare.24299040.v2
title: CD70-induced differentiation of proinflammatory Th1/17/22/GM lymphocytes associated with disease progression and immune reconstitution during HIV infection

description: Immune overactivation is a hallmark of chronic HIV infection, which is critical to HIV pathogenesis and disease progression. The imbalance of helper T cell (Th) differentiation and subsequent cytokine dysregulation are generally considered to be the major drivers of excessive activation and inflammatory disorders in HIV infection. However, the accurate factors driving HIV-associated Th changes remained to be established. CD70, which was a costimulatory molecule, was found to increase on CD4<sup>+</sup> T cells during HIV infection. Overexpression of CD70 on CD4<sup>+</sup> T cells was recently reported to associate with highly pathogenic proinflammatory Th1/Th17 polarization in multiple sclerosis. Thus, the role of CD70 in the imbalance of Th polarization and immune overactivation during HIV infection needs to be investigated. Here, we found that the elevated frequency of CD70 <sup>+ </sup>CD4<sup>+</sup> T cells was negatively correlated with CD4 count and positively associated with immune activation in treatment-naïve people living with HIV (PLWH). More importantly, CD70 expression defined a population of proinflammatory Th1/17/22/GM subsets in PLWH. Blocking CD70 decreased the mRNA expression of subset-specific markers during Th1/17/22/GM polarization. Furthermore, we demonstrated that CD70 influenced the differentiation of these Th cells through STAT pathway. Finally, it was revealed that patients with a high baseline level of CD70 on CD4<sup>+</sup> T cells exhibited a greater risk of poor immune reconstitution after antiretroviral therapy (ART) than those with low CD70. In general, our data highlighted the role of CD70 in Th1/17/22/GM differentiation during HIV infection and provided evidence for CD70 as a potential biomarker for predicting immune recovery.
DOI: 10.6084/m9.figshare.9619055
title: Optimal Designs for the Two-Dimensional Interference Model

description: Recently, there have been some major advances in the theory of optimal designs for interference models when the block is arranged in one-dimensional layout. Relatively speaking, the study for two-dimensional interference model is quite limited partly due to technical difficulties. This article tries to fill this gap. Specifically, we set the tone by characterizing all possible universally optimal designs simultaneously through one linear equations system (LES) with respect to the proportions of block arrays. However, such a LES is not readily solvable due to the extremely large number of block arrays. This computational issue could be resolved by identifying a small subset of block arrays with the theoretical guarantee that any optimal design is supported by this subset. The nature of two-dimensional layout of the block has made this task very technically challenging, and we have theoretically derived such subset for any size of the treatment array and any number of treatments under comparison. This facilitates the development of the algorithm for deriving either approximate or exact designs. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.9619055.v2
title: Optimal Designs for the Two-Dimensional Interference Model

description: Recently, there have been some major advances in the theory of optimal designs for interference models when the block is arranged in one-dimensional layout. Relatively speaking, the study for two-dimensional interference model is quite limited partly due to technical difficulties. This article tries to fill this gap. Specifically, we set the tone by characterizing all possible universally optimal designs simultaneously through one linear equations system (LES) with respect to the proportions of block arrays. However, such a LES is not readily solvable due to the extremely large number of block arrays. This computational issue could be resolved by identifying a small subset of block arrays with the theoretical guarantee that any optimal design is supported by this subset. The nature of two-dimensional layout of the block has made this task very technically challenging, and we have theoretically derived such subset for any size of the treatment array and any number of treatments under comparison. This facilitates the development of the algorithm for deriving either approximate or exact designs. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.21677687
title: Version 2 of the global ocean diazotroph database

description: This is a second version of marine diazotroph database, including nitrogen fixation rates, cell-count-based abundance and <i>nifH</i>-based abundance.Updated file (20240109) has modified some errors in data.
DOI: 10.24403/jp.1355594
title: Kritische Revision der "Thlaspi"-Arten Europas, Afrikas und Vorderasiens. Spezieller Teil : X. Atropatenia / Friedrich Karl Meyer
DOI: 10.6084/m9.figshare.11192039
title: Effects of Temperature on Bacterial Biodiversity and Qualities of Fermented Yucha Products

description: Yucha is a home-made, fermented fish product in South China. The quality of yucha can vary depending on environmental factors. In order to determine the effects of temperature on bacterial biodiversity and quality of fermented yucha products, in the present study, yucha was fermented at 15°C, 20°C, 25°C, and 30°C. Bacterial cells in all yucha samples grew from 3.7 log CFU/g at the onset of the fermentation and reached growth over 7.0 log CFU/g within 1 week. <i>Lactobacillus plantarum</i> was predominated in the 20°C and 25°C fermented yucha products, while <i>Lactobacillus sakei</i> and <i>Lactobacillus brevis</i> were the most abundant in the yucha products fermented at 15°C and 30°C, respectively. Predominant bacterial species are presumed to be potential starters to drive yucha fermentation. Evaluation of yucha qualities demonstrated that lower biogenic amine contents, better texture properties, and more desirable volatile compounds were identified in yucha products fermented at 20°C. Therefore, this temperature is recommended for industrial yucha processing in the future.
DOI: 10.6084/m9.figshare.11192039.v1
title: Effects of Temperature on Bacterial Biodiversity and Qualities of Fermented Yucha Products

description: Yucha is a home-made, fermented fish product in South China. The quality of yucha can vary depending on environmental factors. In order to determine the effects of temperature on bacterial biodiversity and quality of fermented yucha products, in the present study, yucha was fermented at 15°C, 20°C, 25°C, and 30°C. Bacterial cells in all yucha samples grew from 3.7 log CFU/g at the onset of the fermentation and reached growth over 7.0 log CFU/g within 1 week. <i>Lactobacillus plantarum</i> was predominated in the 20°C and 25°C fermented yucha products, while <i>Lactobacillus sakei</i> and <i>Lactobacillus brevis</i> were the most abundant in the yucha products fermented at 15°C and 30°C, respectively. Predominant bacterial species are presumed to be potential starters to drive yucha fermentation. Evaluation of yucha qualities demonstrated that lower biogenic amine contents, better texture properties, and more desirable volatile compounds were identified in yucha products fermented at 20°C. Therefore, this temperature is recommended for industrial yucha processing in the future.
DOI: 10.6084/m9.figshare.8046371
title: Flow Cross K-function: a bivariate flow analytical method

description: Spatial flow data represent meaningful interaction activities between pairs of corresponding locations, such as daily commuting, animal migration, and merchandise shipping. Despite recent advances in flow data analytics, there is a lack of literature on detecting bivariate or multivariate spatial flow patterns. In this paper we introduce a new spatial statistical method called Flow Cross K-function, which combines the Cross K-function that detects marked point patterns and the Flow K-function that detects univariate flow clustering patterns. Flow Cross K-function specifically assesses spatial dependence of two types of flow events, in other words, whether one type of flows is spatially associated with the other, and if so, whether this is according to a clustering or dispersion trend. Both a global version and a local version of Flow Cross K-function are developed. The former measures the overall bivariate flow patterns in the study area, while the latter can identify anomalies at local scales that may not follow the global trend. We test our method with carefully designed synthetic data that simulate the extreme situations. We exemplify the usefulness of this method with an empirical study that examines the distributions of taxi trip flows in New York City.
DOI: 10.6084/m9.figshare.8046371.v2
title: Flow Cross K-function: a bivariate flow analytical method

description: Spatial flow data represent meaningful interaction activities between pairs of corresponding locations, such as daily commuting, animal migration, and merchandise shipping. Despite recent advances in flow data analytics, there is a lack of literature on detecting bivariate or multivariate spatial flow patterns. In this paper we introduce a new spatial statistical method called Flow Cross K-function, which combines the Cross K-function that detects marked point patterns and the Flow K-function that detects univariate flow clustering patterns. Flow Cross K-function specifically assesses spatial dependence of two types of flow events, in other words, whether one type of flows is spatially associated with the other, and if so, whether this is according to a clustering or dispersion trend. Both a global version and a local version of Flow Cross K-function are developed. The former measures the overall bivariate flow patterns in the study area, while the latter can identify anomalies at local scales that may not follow the global trend. We test our method with carefully designed synthetic data that simulate the extreme situations. We exemplify the usefulness of this method with an empirical study that examines the distributions of taxi trip flows in New York City.
DOI: 10.6084/m9.figshare.8046371.v1
title: Flow Cross K-function: a bivariate flow analytical method

description: Spatial flow data represent meaningful interaction activities between pairs of corresponding locations, such as daily commuting, animal migration, and merchandise shipping. Despite recent advances in flow data analytics, there is a lack of literature on detecting bivariate or multivariate spatial flow patterns. In this paper we introduce a new spatial statistical method called Flow Cross K-function, which combines the Cross K-function that detects marked point patterns and the Flow K-function that detects univariate flow clustering patterns. Flow Cross K-function specifically assesses spatial dependence of two types of flow events, in other words, whether one type of flows is spatially associated with the other, and if so, whether this is according to a clustering or dispersion trend. Both a global version and a local version of Flow Cross K-function are developed. The former measures the overall bivariate flow patterns in the study area, while the latter can identify anomalies at local scales that may not follow the global trend. We test our method with carefully designed synthetic data that simulate the extreme situations. We exemplify the usefulness of this method with an empirical study that examines the distributions of taxi trip flows in New York City.
DOI: 10.6084/m9.figshare.22721263.v1
title: Additional file 1 of Automated recognition and analysis of body bending behavior in C. elegans

description: Additional file 1. Specific experimental data of Caenorhabditis elegans behavioral phenotypes database and ‘escape response’ database.
DOI: 10.6084/m9.figshare.22721263
title: Additional file 1 of Automated recognition and analysis of body bending behavior in C. elegans

description: Additional file 1. Specific experimental data of Caenorhabditis elegans behavioral phenotypes database and ‘escape response’ database.
DOI: 10.6084/m9.figshare.19572594.v1
title: Additional file 3 of Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer

description: Additional file 3: Supplementary Table S2. Matrix of identified phophoproteins in EESCC and EDAC.
DOI: 10.6084/m9.figshare.14338010
title: miR-128 participates in the pathogenesis of chronic constipation by regulating the p38α/M-CSF inflammatory signaling pathway

description: Supplementary Table 1. PCR Primer<br>Supplementary Table 2. Antibody Information<br>
DOI: 10.34740/kaggle/dsv/7616513
title: OnlineFree
DOI: 10.6084/m9.figshare.14329436.v1
title: Additional file 5 of High-dose rapamycin exerts a temporary impact on T. reesei RUT-C30 through gene trFKBP12

description: Additional file 5: Table S2. Transcriptional level of DEGs related to transporters in T. reesei RUT-C30.
DOI: 10.34740/kaggle/dsv/7616511
title: AutoXGB
DOI: 10.6084/m9.figshare.20099664.v1
title: Additional file 4 of Gene expression variation explains maize seed germination heterosis

description: Additional file 4: Table S3. Distribution of DEGs into different categories of GO in Maize (Zea mays L.).
DOI: 10.6084/m9.figshare.20099664
title: Additional file 4 of Gene expression variation explains maize seed germination heterosis

description: Additional file 4: Table S3. Distribution of DEGs into different categories of GO in Maize (Zea mays L.).
DOI: 10.6084/m9.figshare.20099670
title: Additional file 6 of Gene expression variation explains maize seed germination heterosis

description: Additional file 6: Table S5. The sequence of primers used for RT-qPCR.
DOI: 10.6084/m9.figshare.20099661.v1
title: Additional file 3 of Gene expression variation explains maize seed germination heterosis

description: Additional file 3: Table S2. The ASE genes and the allelic ratio with statistic test in F1.
DOI: 10.6084/m9.figshare.20099670.v1
title: Additional file 6 of Gene expression variation explains maize seed germination heterosis

description: Additional file 6: Table S5. The sequence of primers used for RT-qPCR.
DOI: 10.6084/m9.figshare.20099667.v1
title: Additional file 5 of Gene expression variation explains maize seed germination heterosis

description: Additional file 5: Table S4. The 9 most enriched KEGG pathway terms in Maize (Zea mays L.).
DOI: 10.6084/m9.figshare.9614102.v2
title: RETRACTED ARTICLE: Long noncoding RNA H19 regulates HIF-1α/AXL signaling through inhibiting miR-20b-5p in endometrial cancer

description: We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: He Zhu, Yue-Mei Jin, Xue-Man Lyu, Li-Mei Fan & Fei Wu (2019) Long noncoding RNA H19 regulates HIF-1α/AXL signaling through inhibiting miR-20b-5p in endometrial cancer, Cell Cycle, 18:19, 2454-2464, DOI: 10.1080/15384101.2019.1648958 Since publication, the authors have found significant errors in the statistical analysis of the research reported in this article. As this error directly impacts the accuracy of the results and conclusions, the authors alerted the issue to the Editor and Publisher and all have agreed to retract the article to ensure the integrity of the scholarly record. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.6084/m9.figshare.22721338
title: Additional file 4 of Circular RNA EPHA3 suppresses progression and metastasis in prostate cancer through the miR-513a-3p/BMP2 axis

description: Additional file 4: The 58 differentially expressed genes (DEGs) were screened and regulated in both PC-3 and DU145 cells after transfected circEPHA3 lentivirus.
DOI: 10.5281/zenodo.15210120
title: Data for "Resolving Inhomogeneous Cloud Microphysics Through Cloud-Top Observations of Blue Corona Discharges"

description: Data related to the paper "Resolving Inhomogeneous Cloud Microphysics Through Cloud-Top Observations of Blue Corona Discharges"

diffusion coefficient D profiles, [alititude (km), D(m^2/s)]

collision rate Nu profiles, [altitude (km), Nu(s^-1)]

obs_model data, [time(ms), flux(\mu W/m^2)]
DOI: 10.5281/zenodo.15210121
title: Data for "Resolving Inhomogeneous Cloud Microphysics Through Cloud-Top Observations of Blue Corona Discharges"

description: Data related to the paper "Resolving Inhomogeneous Cloud Microphysics Through Cloud-Top Observations of Blue Corona Discharges"

diffusion coefficient D profiles, [alititude (km), D(m^2/s)]

collision rate Nu profiles, [altitude (km), Nu(s^-1)]

obs_model data, [time(ms), flux(\mu W/m^2)]
DOI: 10.15468/dl.ng4yhp
title: Occurrence Download

description: A dataset containing 320 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Belgica antarctica Jacobs, 1900"
 ]
}

 The dataset includes 320 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0105754-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10521686
title: Glioblastoma cells increase expression of notch signaling and synaptic genes within infiltrated brain tissue
DOI: 10.5281/zenodo.10521687
title: Glioblastoma cells increase expression of notch signaling and synaptic genes within infiltrated brain tissue
DOI: 10.15468/dl.ppv6fv
title: Occurrence Download

description: A dataset containing 4369 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (Africa, Antarctica, Asia, Oceania, Europe, North America, South America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (January, February, March, April, May, June, July, August, September, October, November, December)",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera onca (Linnaeus, 1758)",
 "Year 2000-2024"
 ]
}

 The dataset includes 4369 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0105756-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.