cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24138909
title: Supplementary Material for: Macula-off retinal detachment with refractory macular hole previously closed with autologous platelet rich plasma: a case report

description: PURPOSE: To report a case of a refractory full thickness macular hole (FTMH) complicated with recurrent retinal detachment (RD) previously treated with an autologous platelet rich plasma (aPRP) plug. CASE PRESENTATION: A 65-years old male patient presented to our department with a FTMH, retinal detachment (RD) and a giant retinal break. Preoperative best corrected visual acuity (BCVA) was 1.40 logMAR (20/500). A 25-G pars plana vitrectomy (PPV) was performed, with peripheral retinal-breaks laser barrage, peeling of the internal limiting membrane (ILM), and silicon oil injection. One month later, spectral domain optical coherence tomography (SD-OCT) showed the persistence of the FTMH with a diameter of 712 µm. Therefore, the patient underwent silicon oil removal and autologous platelet-rich plasma (aPRP) injection with good anatomical outcome and improvement of BCVA to 0.6 log-MAR (20/80). Two months later a recurrence of macula-off RD was detected, but SD-OCT showed that the aPRP plug was still in place and kept the two margins of the macular hole together. The patient underwent a further PPV with silicon oil injection and subsequent silicon oil removal with no postoperative complications. Two months later, the retina remained attached, SD-OCT confirmed FTMH closure and BCVA was 0.52 logMAR (20/63). CONCLUSION: This case report aims to underline the remarkable efficacy of aPRP in promoting FTMH closure, which was maintained despite subsequent recurrence of macula-off RD.
DOI: 10.6084/m9.figshare.24203799
title: Dataset for the article named Material-Agnostic Machine Learning Approach Enables High Relative Density in Powder Bed Fusion Products

description: Data for training and testing a model to predict relative density (porosity) in powder bed fusion.
DOI: 10.6084/m9.figshare.6142940
title: Data from: Humans strategically shift decision bias by flexibly adjusting sensory evidence accumulation in visual cortex

description: This is the data from: Niels A. Kloosterman, Jan Willem de Gee, Markus Werkle-Bergner, Ulman Lindenberger, Douglas D. Garrett, Johannes Jacobus Fahrenfort 2018. Humans strategically shift decision bias by flexibly adjusting sensory evidence accumulation in visual cortex.<br>The analysis code for these data can be found here: https://github.com/nkloost1/critEEG
DOI: 10.6084/m9.figshare.24433561
title: Ecosocial proposals mapping

description: Overview of mapping of ecosocial policies in Excel spreadsheet.Sheet 'Mapping' shows data.Sheet 'Variables explanation' includes descriptions of all variables<br>
DOI: 10.6084/m9.figshare.24433561.v1
title: Ecosocial proposals mapping

description: Overview of mapping of ecosocial policies in Excel spreadsheet.Sheet 'Mapping' shows data.Sheet 'Variables explanation' includes descriptions of all variables<br>
DOI: 10.5067/measures/minds/data203
title: TROPOMI/S5P NO2 Tropospheric, Stratospheric and Total Columns MINDS 1-Orbit L2 Swath 5.5 km x 3.5 km V1.1
DOI: 10.5281/zenodo.7250504
title: Data and Code for the Manuscript: Aquatic insects balance growth with future supply of algal food resources

description: Some consumers depend on the contemporaneous growth of the resources they feed on. For example, <em>Tanytarsus gracilentus</em> midges feed on algae, and because midge generation time is much longer than that of algae, midges benefit not just from the standing stock but also from the growth of algae. This implies that an intermediate consumption rate maximizes midge somatic growth: low consumption rates constrain midge growth, whereas high consumption rates reduce algae and future food abundance. In an experiment, we manipulated midge presence and initial algal abundance. We found that midges could suppress algal growth, as measured by changes in algal primary production (GPP). We also found a positive relationship between GPP and midge growth. We then fit a consumer-resource model to the experimental data, which showed the expected hump-shaped relationship between midge consumption rates and their somatic growth. In the model, projected midge growth rates were only positively associated with GPP when midge consumption was below the value that optimized midge growth. Therefore, the observed relationship between instantaneous primary production and midge growth seen in the experiment suggests that midges did not overexploit algae. This work highlights the challenges faced by consumers that depend on contemporaneously growing resources.
DOI: 10.5281/zenodo.8113105
title: High resolution LiDAR dataset acquired using UAV (unmanned aerial vehicle) over two vineyards and two years located in 'Tomiño', Pontevedra, Spain.

description: This dataset features an extensive collection of LiDAR data from vineyards in northern Spain, targeting vineyards to address the growing demand for public UAV LiDAR datasets in Agricultural Sciences. The data was gathered using a DJI M300 multi-rotor platform equipped with a DJI Zenmuse L1 LiDAR sensor, conducting UAV flights at 20, 30, and 50 meters Above Ground Level (AGL) across two vineyards during 2021 and 2022. The dataset comprises ten high-density 3D LiDAR point clouds stored in .laz format with embedded RGB information in each point. This information is essential for studying vineyard morphology and development and plays a key role in refining vineyard management tactics. In addition, the dataset is valuable for agricultural robotics, providing detailed terrain and canopy data crucial for designing efficient flight paths and navigation algorithms. Finally, it serves as a true "ground truth" dataset to verify satellite-derived models, enabling the generation of high-precision digital elevation models (DEMs) and other derivatives.
DOI: 10.6084/m9.figshare.24307162
title: Input data: Can ∆<sup>14</sup>CO<sub>2</sub> observations help atmospheric inversions constrain the fossil CO2 emission budget of Europe?

description: Input data (true, prior, and prescribed fluxes and atmospheric ∆<sup>14</sup>C) generated for the manuscript: Can ∆<sup>14</sup>CO<sub>2</sub> observations help atmospheric inversions constrain the fossil CO2 emission budget of Europe? derived from: Basu, S., Lehman, S. J., Miller, J. B., Andrews, A. E., Sweeney, C., Gurney, K. R., Xu, X., Southon, J., and Tans, P. P.: Estimating US fossil fuel CO2 emissions from measurements of 14C in atmospheric CO2, Proceedings of the National Academy of Sciences, 117, 13 300–13 307, https://doi.org/10.1073/pnas.1919032117, 2020.
DOI: 10.17189/1519606
title: CASSINI S MIMI CHEMS SENSOR CALIBRATED DATA V1.0
DOI: 10.17632/3w3whp7r44.1
title: Gavrilov, Nieder_Distinct neural networks for the volitional control of vocal and manual actions in the monkey homologue of Broca's area.

description: data & code
DOI: 10.25452/figshare.plus.20338177
title: Dataset supporting "Functional antibodies exhibit light chain coherence"

description: The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies binding particular antigens. In most mammals, antibodies are composed of a heavy and a light chain which are sequentially generated by recombination of V, D (for heavy chains), J, and C gene segments. Each chain contains three complementarity-determining regions (CDR1-3), contributing to antigen specificity. Certain heavy and light chains are preferred for particular antigens. We considered pairs of B cells sharing the same heavy chain V gene and CDRH3 amino acid sequence and isolated from different donors, also known as public clonotypes. We show that for naive antibodies (not yet adapted to antigens), the probability that they use the same light chain V gene is ~10%, whereas for memory (functional) antibodies it is ~80%. This property of functional antibodies is a phenomenon we call <em>light chain coherence</em>. We also observe it when similar heavy chains recur <em>within</em> a donor. Thus, though naive antibodies appear to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.
DOI: 10.26180/22192846.v1
title: DIC Images and surface view photographs for 'The development of fault networks at the termination of continental transform faults when their connecting plate boundary is ‘misaligned’"

description: Supplementary material for the manuscript: <br> "The development of fault networks at the termination of continental transform faults when their connecting plate boundary is ‘misaligned’"
DOI: 10.26180/5f4d0cf8bb103
title: Survival & egg laying data for Zanco et al, 2021

description: Lifespan and egg laying data to accompany Zanco et al, 2020bioRxiv: https://doi.org/10.1101/2020.08.21.260489<br>updates:17th May 2021 - replaced files "rapamycin_eggs_eLife.xlsx" and "Yeast_extract_eggs_eLife.xlsx". This is to correct mislabelled treatments in both files.
DOI: 10.5281/zenodo.2543673
title: SLAFEEL: R scripts and reformatted data analyzed by Alamil et al. (2019)

description: SLAFEEL: Statistical Learning Approach For Estimating Epidemiological Links from deep sequencing data

This archive contains R scripts for running analyses proposed by Alamil et al. (2019; Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases), namely<br>
- functions.R that contains R functions required for computations,<br>
- influenza.R, ebola.R and potyvirus.R where the analyses are implemented for each case study, and<br>
- influenza-format-genomic-data.R giving an example of how to format data to be used in the statistical learning approach.

This archive also contains the reformatted data analyzed by Alamil et al. (2019). The datasets that are provided concern swine influenza virus (reformatted from Murcia et al., 2012), Ebola virus (reformatted from Gire et al., 2014) and a wild salsify potyvirus. Two rds files are provided for swine influenza, the first one for the naive chain, the second one for the vaccinated chain. Ebola rds files are compressed into the archive ebolaRDS.zip. rds files can be loaded in the R statistical software with the command "readRDS(filename)", which returns a list. The list contains a "readme" item describing the contents of the list, as well as a "host.table" item providing metadata about host units and a "set.of.sequences" item providing sequencing data formatted in numeric matrices.

Murcia PR, Hughes J, Battista P, Lloyd L, Baillie GJ, Ramirez-Gonzalez RH, et al. Evolution of an Eurasian avian-like influenza virus in naive and vaccinated pigs. PLoS Pathogens. 2012;8(5):e1002730.

Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014;345:1369–1372

 

Funded by the ANR - Project name: SMITID (2016-2020) - Grant number: ANR-16-CE35-0006
description: {"references": ["Alamil M, Hughes J., Berthier K, Desbiez C, Th\u00e9baud G Soubeyrand S (2018) Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases. Technical Report, BioSP, INRA, Avignon.", "Murcia PR, Hughes J, Battista P, Lloyd L, Baillie GJ, Ramirez-Gonzalez RH, et al. Evolution of an Eurasian avian-like influenza virus in naive and vaccinated pigs. PLoS Pathogens. 2012;8(5):e1002730.", "Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014;345:1369\u20131372"]}
DOI: 10.5281/zenodo.5230306
title: One shot generalization in humans revealed through a drawing task - Dataset

description: Dataset for: One shot generalization in humans revealed through a drawing task. Henning Tiedemann, Yaniv Morgenstern, Filipp Schmidt, Roland W Fleming. bioRxiv 2021.05.31.446461; doi: https://doi.org/10.1101/2021.05.31.446461
DOI: 10.5281/zenodo.7081664
title: Dataset 2 for the reproduction of figures used in "High-resolution, basin-scale simulations reveal the impact of intermediate zonal jets on the Atlantic oxygen minimum zones""

description: This is the second dataset with data necessary for the reproduction of the figures used in the manuscript.
DOI: 10.5281/zenodo.7229219
title: Datasets for "High-resolution, basin-scale simulations reveal the impact of intermediate zonal jets on the Atlantic oxygen minimum zones".

description: This repository contains the 7-year averaged files from runs TATL10 and TATL3 used in the manuscript "High-resolution, basin-scale simulations reveal the impact of intermediate zonal jets on the Atlantic oxygen minimum zones". Additional files include the CARS oxygen climatology and the CMEMS model output used in the study.
DOI: 10.5281/zenodo.8047592
title: Dataset Non-shared coding of observed and executed actions prevails in macaque ventral premotor mirror neurons

description: This dataset is related to "Non-shared coding of observed and executed actions prevails in macaque ventral premotor mirror neurons".
DOI: 10.5281/zenodo.8193532
title: Dataset underlying the paper Generating variability from motor primitives during infant locomotor development

description: EMG data after basic preprocessing Each file is a matrix of M colomns and S*T raws with : M = number of muscles (from m1 to m10: right Rectus Femoris, left Rectus Femoris, right Tibialis Anterior, left Tibialis Anterior, right Biceps Femoris, left Biceps Femoris, right Soleus, left Soleus, right Gluteus Medius, left Gluteus Medius). S = number of steps (specific to each file) T = number of time points per step (always equals to 200) File names are ordered as follows: inputMat_S{subjectnumber}_C{conditionnumber}_a{agenumber}_200bins_10muscles subject number car take values between 1 and 18 condition number can take the following values: 1 for stepping on a treadmill, 2 for stepping overground, 4 for kicking and 5 for walking age number can take the following values: 1 for around birth, 2 for around three months, 4 for around walking onset
DOI: 10.5281/zenodo.8273007
title: Observation of an isotope effect in state-selective mutual neutralization of lithium with hydrogen

description: The data files found here contain the data as obtained and displayed in : "Observation of an isotope effect in state-selective mutual neutralization of lithium with hydrogen" published in Physical Review A (2023).  Each file contains an explanatory header. Header lines start with #.
DOI: 10.6084/m9.figshare.19826221
title: Supplementary Material for: Insulin-like growth factor-1 promotes human uterine leiomyoma cells proliferation via PI3K/AKT/mTOR pathway

description: The present research aims to evaluate the expression of insulin-like growth factor-1 (IGF-1) in uterine leiomyoma, and explore its relationship with the occurrence and development of uterine leiomyoma and potential signal pathways. QRT-PCR and enzyme linked immunosorbent assay (ELISA) were used for estimating the levels of IGF-1 in human uterine leiomyoma compared to myometrium. The expression of cell proliferation and PI3K/AKT/mTOR signaling pathway related proteins in uterine leiomyoma cells were evaluated by Western blot. Cell viability analysis was performed by CCK-8 assay. Lentivirus infection was used for IGF-1 overexpression and knockdown in uterine leiomyoma cells. IGF-1 expression level was elevated in human uterine leiomyomas compared to myometrium. IGF-1 promoted the cell viability of human uterine leiomyoma cells. Overexpression of IGF-1 induced the expression of pro-proliferation markers including c-Myc, PCNA and cyclin D1 in uterine leiomyoma cells. IGF-1 elevated the phosphorylation levels of PI3K, AKT and mTOR, thus modifying PI3K/AKT/mTOR signaling in uterine leiomyoma cells. IGF-1 promotes human uterine leiomyoma cells proliferation via PI3K/AKT/mTOR pathway.
DOI: 10.6084/m9.figshare.21673160
title: Supplementary Material for: Association of Dietary Patterns with Parkinson’s Disease: A Cross-Sectional Study Based on the United States National Health and Nutritional Examination Survey Database

description: <b><i>Introduction:</i></b> Although studies have explored some dietary patterns for Parkinson’s disease (PD), more other dietary patterns and food item under the dietary pattern are needed to investigate. This study aimed to identify more categories of dietary patterns for PD and further explore the association of single food item with PD. <b><i>Methods:</i></b> The 2015–2018 US National Health and Nutritional Examination Survey (NHANES) database was used for data extraction. The data on demographics and nutrient intake were collected. Dietary patterns were derived from food categories by factor analysis. The association between dietary patterns or single food item and PD was explored using logistic regression analysis in the overall and only in secure PD cases, and results were expressed as odds ratio (OR) with 95% confidence intervals (CIs). Sensitivity analysis was performed by excluding participants using unsecure PD medication. <b><i>Results:</i></b> Among 5,824 participants aged over 50 years, 91 were diagnosed as PD. Factor analysis identified 5 major dietary pattern factors. We observed that the increased adherence to Mediterranean diet (MeDi) was associated with the reduced odds of PD (OR = 0.78, 95% CI: 0.65–0.93). The higher adherence to Western pattern was associated with the increased odds of PD (OR = 2.19, 95% CI: 1.16–4.14). In addition, high intake of sweets under Western pattern was found to be associated with the higher odds of PD (OR = 2.01, 95% CI: 1.08–3.71). <b><i>Conclusions:</i></b> The odds of PD decreased by higher MeDi adherence and increased by higher Western pattern adherence, especially sweets intake in this pattern, suggesting population ≥50 years should adhere to MeDi pattern and decrease the adherence to Western pattern, reducing the intake of sweets.
DOI: 10.6084/m9.figshare.21737303
title: Continuous odor profile monitoring to study olfactory navigation in small animals

description: Dataset for analysis and demo code for publication: "Continuous odor profile monitoring to study olfactory navigation in small animals" Chen et al. 2022
DOI: 10.6084/m9.figshare.21989792
title: Supplementary Material for: Infants with Congenital Adrenal Hyperplasia Exhibit Thalamic Discrepancies in Early Brain Structure

description: Introduction: Patients with classical congenital adrenal hyperplasia (CAH) have prenatal and postnatal hormonal imbalances. To characterize the ontogeny of reported brain and behavior changes in older children with CAH, we aimed to study brain structure in infants with CAH compared to healthy controls. Methods: We performed neuroimaging in 16 infants with classical CAH due to 21-hydroxylase deficiency [8 males, gestational age 38.2 ± 1.7 weeks, post-conceptional age (PCA) 42.2 ± 3.0 weeks] and 14 control infants (9 males, gestational age 38.5 ± 1.8 weeks, PCA 42.5 ± 2.4 weeks) utilizing 3-Tesla magnetic resonance imaging. Regional brain volumes were adjusted for PCA and sex, along with an additional adjustment for total brain volume (TBV), for group comparisons by regression analyses [mean, 95% confidence interval (CI)]. The degree to which each brain region was differentiated between CAH and control infants was examined by relaimpo analyses, adjusting for all other brain regions, PCA, and sex. Results: Infants with CAH had significantly smaller thalamic volumes [8606 mm3, 95% CI (8209, 9002)] compared to age-matched control infants [9215 mm3, 95% CI (8783, 9647); β = -609; p = 0.02], which remained smaller after further adjustment for TBV. Upon further adjustment for TBV, the temporal lobe was larger in infants with CAH [66817 mm3, CI (65957, 67677)] compared to controls [65616 mm3, CI (64680, 66551); β = 1202, p = 0.03]. The brain regions most differentiated between CAH vs controls were the thalamus (22%) and parietal lobe (10%). Conclusions: Infants with CAH exhibit smaller thalamic regions from early life, suggesting a prenatal influence on brain development in CAH. Thalamic emergence at 8-14 weeks makes the region particularly vulnerable to changes in the intrauterine environment, with potential implications for later maturing brain regions. These changes may take time to manifest, meriting longitudinal study through adolescence in CAH.
DOI: 10.6084/m9.figshare.22269742
title: Supplementary Material for: Immunomodulation Effect of Regional Citrate Anticoagulation in Acute Kidney Injury Requiring Renal Replacement Therapy

description: <b><i>Introduction:</i></b> Acute kidney injury (AKI) is a common syndrome in critically ill patients. Continuous renal replacement therapy (CRRT) is the standard treatment for patients with AKI. Research on the immunomodulating effects of regional citrate anticoagulation (RCA) remains limited in patients with AKI receiving CRRT. We aimed to evaluate the immunomodulating effects of RCA in patients with AKI receiving CRRT. <b><i>Methods:</i></b> A randomized controlled trial study on critically ill adult patients with AKI undergoing CRRT was undertaken. Participants were randomized into either a regional citrate group or control group (either heparin anticoagulant or normal saline). Measurements were taken at baseline, 6 and 24 h after commencing CRRT for CD11b expression, C3a, C5a, and plasminogen activator inhibitor-1 (PAI-1) levels. Clinical outcomes assessed were 28-day survival rate, length of ICU stay, renal support duration, and renal function at discharge. <b><i>Results:</i></b> Thirty patients were recruited and randomized into 2 groups of 15 subjects. Baseline demographic and clinical data were comparable between groups. In the citrate group, CD11b expression was significantly decreased at 24 h compared to the control group (1.84% [1.18–3.32] versus 4.92% [2.63–6.93], <i>p</i> &lt; 0.01). The complement level, including c3b and c5a, was stable during CRRT. Additionally, the PAI-1 levels were significantly decreased at 24 h compared to the control group (114 ng/mL [19–193] versus 359 ng/mL [264–491], <i>p</i> &lt; 0.01). No significant difference in survival rate was observed. <b><i>Conclusions:</i></b> RCA may have the potential to mitigate the inflammatory response by decreasing CD11b expression of neutrophil and improve fibrinolysis activity through a reduction of PAI-1 levels. Larger clinical trials are warranted to test this immunomodulation effect of RCA.
DOI: 10.6084/m9.figshare.24249424
title: Supplementary Material for: Cystoid macular edema following treatment with nanoparticle albumin-bound paclitaxel and atezolizumab for metastatic breast cancer

description: Cystoid macular edema (CME) is a rare side effect associated with chemotherapy. Although the development of CME has been reported to occur following treatment with taxane drugs, such as nanoparticle albumin-bound paclitaxel (Nab-PTX), the occurrence of CME with treatment with atezolizumab has not yet been reported. Here, we report the case of a 49-year-old woman who developed CME 19 months into chemotherapy with Nab-PTX and atezolizumab. Improvement was not acheieved with steroid injections into the Tenon’s sac, and Nab-PTX and atezolizumab treatments were ceased. One month later, there was subjective improvement in her symptoms. Although many reports have indicated that cessation of chemotherapy has successfully improved CME, a specific treatment for CME has not yet been established. Clinicians should be aware of the ophthalmologic side effects and offer immediate treatment if symptoms develop.