cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5125141.v1
title: Supplementary Material for: Comparison of Immunosuppressive and Cytotoxic Cells in Angiosarcoma: Development of a Possible Supportive Therapy for Angiosarcoma

description: An imbalance of immunosuppressive and cytotoxic cells plays an important role in inhibiting the anti-tumor immune response of the tumor-bearing host. The purpose of this study was to elucidate the involvement of immunosuppressive cells, such as regulatory T cells and CD163+ M2 macrophages as well as cytotoxic cells, such as granulysin-bearing cells and TIA-1+ cells in cutaneous angiosarcoma (AS) by immunohistochemical staining. In addition we evaluated the potencies of bisphosphonate, which was previously reported to suppress the expression of matrix metalloproteinase 9 (MMP-9), as a supportive therapy for AS together with docetaxel in 6 cases of cutaneous AS. These findings suggest that a high number of immunosuppressive cells might be related to the prognosis of AS, and that a combination of docetaxel with bisphosphonate risedronate sodium might be effective for MMP-9-expressing AS.
DOI: 10.6084/m9.figshare.12871460.v1
title: Supplementary Material for: Glycosylation of Anti-Thyroglobulin IgG1 and IgG4 Subclasses in Thyroid Diseases

description: <b><i>Objective:</i></b> Thyroglobulin antibodies (TgAb), principally comprising immunoglobulin G (IgG), are frequently found in healthy individuals. Previously, we showed that the glycosylation levels of TgAb IgG differed across various thyroid diseases, suggesting an important role of glycosylation on antibodies in the pathogenesis of thyroid diseases. Since IgG1 and IgG4 are the primary TgAb IgG subclasses, this study aimed to investigate the glycosylation of TgAb IgG1 and IgG4 subclasses in thyroid diseases. <b><i>Methods:</i></b> TgAb IgG was purified by affinity chromatography from the serum of patients with Hashimoto’s thyroiditis (HT) (<i>n</i> = 16), Graves’ disease (GD) (<i>n</i> = 8), papillary thyroid carcinoma (PTC) (<i>n</i> = 6), and PTC with histological lymphocytic thyroiditis (PTC-T) (<i>n</i> = 9) as well as healthy donors (<i>n</i> = 10). TgAb IgG1 and IgG4 concentrations were determined by enzyme-linked immunosorbent assay, and a lectin microassay was used to assess TgAb IgG1 and IgG4 glycosylation. <b><i>Results:</i></b> Significantly elevated mannose, sialic acid, and galactose levels on TgAb IgG1 were found in HT and PTC patients compared to GD patients and healthy controls (all <i>p</i> &lt; 0.05). The mannose, sialic acid, and core fucose levels on TgAb IgG1 in PTC-T patients were higher than in healthy controls (all <i>p</i> &lt; 0.05). Additionally, TgAb IgG1 from PTC-T patients exhibited lower sialylation than that from patients with PTC and higher fucosylation than that from patients with HT (both <i>p</i> &lt; 0.05). However, TgAb IgG4 glycosylation did not differ among the five groups (<i>p</i> &lt; 0.05). <b><i>Conclusion:</i></b> Our study describes different distributions of TgAb IgG1 glycosylation in various thyroid diseases. The aberrantly increased glycosylation levels of TgAb IgG1 observed in HT, PTC, and PTC-T might be indicative of immune disorders and participate in the pathogenesis of these diseases.
DOI: 10.6084/m9.figshare.13942967.v1
title: Supplementary Material for: Which Staging System Is More Suitable for Gastric Neuroendocrine Cancer and Mixed Adenoneuroendocrine Carcinomas? A Multicenter Cohort Study

description: <b><i>Purpose:</i></b> To evaluate whether the European Neuroendocrine Tumor Society (ENETS) system or the 8th American Joint Committee on Cancer (AJCC) staging manual are suitable for gastric neuroendocrine carcinomas and/or mixed adenoneuroendocrine carcinomas (G-NECs/MANECs). <b><i>Methods:</i></b> Patients in a multicentric series with G-NEC/MANEC who underwent curative-intent surgical resection for a primary tumor were included. An optimal staging system was proposed base on analysis of the T and N status and validated by the SEER database. <b><i>Results:</i></b> Compared with the ENETS system, the survival curves of the T category and N category in the 8th AJCC system were better separated and distributed in a more balanced way, but the survival curves of T2 vs. T3, N0 vs. N1, and N3a vs. N3b overlapped. For the T category, the 8th AJCC T category was modified by combining T2 and T3, which was consistent with the T category in the 6th AJCC manual for GC. For the N category, the optimal cut-off values of metastatic lymph nodes using X-tile were also similar to those of the N category in the 6th AJCC system. The Kaplan-Meier plots of the 6th AJCC system showed statistically significant differences between individual substages. Compared with the other 2 classifications, the 6th AJCC system also showed superior prognostic stratification. Similar results were obtained in both multicentric and SEER validation sets. <b><i>Conclusions:</i></b> Compared to the 8th AJCC and ENETS systems, the 6th AJCC staging system for GC is more suitable for G-NEC/MANEC and can be adopted in clinical practice.
DOI: 10.6084/m9.figshare.3515423.v1
title: Appendix B. Geochemical data from the north- and mid-basin cores.

description: Geochemical data from the north- and mid-basin cores.
DOI: 10.6084/m9.figshare.25672755.v2
title: data_COMMSENV-23-2057A.xlsx

description: Data related to the publication:NAME OF JOURNAL: Communications Earth & Environment<br>TITLE OF MANUSCRIPT: Underestimation of carbon dioxide emissions from organic-rich agricultural soilsMANUSCRIPT NUMBER: COMMSENV-23-2057A<br>CORRESPONDING AUTHORS NAME: Lars ElsgaardAUTHOR NAMES: Zhi Liang, Cecilie Hermansen, Peter L. Weber, Charles Pesch, Mogens H. Greve, Lis W. de Jonge, Maarit Mäenpää, Jens Leifeld & Lars ElsgaardPlease note that data given in the shared file is on the original scale wheras reported means in the paper are results extracted from the statistical models after back-transforming from the log or square root scale, using the <i>emmeans</i> function (i.e., <i>emmeans</i> (model, ~OC content, type=”response”)).<br>
DOI: 10.6084/m9.figshare.6743498.v1
title: datasets

description: Spectral dataset for grapevine varietal classification. Python source code for model training is also included.
DOI: 10.6084/m9.figshare.19499138.v1
title: patches and local annotations, slide 193, zoom 248x248 um2

description: patches and local annotations: data for slide with ID of the last 3 characters of the file name: local annotations in csv format and a folder with patches at zoom level indicated at the 6th character of the file name
DOI: 10.6084/m9.figshare.28823159.v1
title: CODERData2.1.0

description: Cancer Organoid Data
DOI: 10.6084/m9.figshare.3563052.v1
title: Appendix A. Details on preliminary experiments, size and biomass of taxa used in the experiments, and information on the interaction calculations.

description: Details on preliminary experiments, size and biomass of taxa used in the experiments, and information on the interaction calculations.
DOI: 10.26187/5bb6c6fd42dbd
title: Boron nitride nanomaterials (nanotubes, nanowires and nanosheets)
DOI: 10.6084/m9.figshare.15059670.v1
title: Supplementary Material for: The Association between Glomerular Diameter and Secondary Focal Segmental Glomerulosclerosis in Chronic Kidney Disease

description: <b><i>Introduction:</i></b> When nephron loss occurs, the glomerular filtration rate (GFR) is suggested to be maintained by glomerular hypertrophy, but excessive hypertrophy can rather lead to the formation of focal segmental glomerulosclerosis (FSGS), thereby causing progressive kidney damage. However, it is not clear how much glomerular hypertrophy leads to the formation of FSGS. We examined the association between glomerular diameter and FSGS lesions in chronic kidney disease (CKD) patients. <b><i>Methods:</i></b> We recruited 77 patients who underwent renal biopsy during 2016–2017; however, those identified with primary FSGS and glomerulonephritis with active glomerular lesion were excluded. We evaluated the maximal glomerular diameter (Max GD), an indicator of glomerular size, in each renal biopsy specimen and examined its association with FSGS lesion. <b><i>Results:</i></b> The median age, blood pressure, and estimated GFR of the patients were 53 years, 122/70 mm Hg, and 65 mL/min/1.73 m<sup>2</sup>, respectively. The optimal cutoff threshold of Max GD for predicting the presence of FSGS lesions, assessed by receiver operating characteristic curve analysis, was determined to be at 224 μm (area under the curve, 0.81; sensitivity, 81%; specificity, 72%). Multivariate logistic regression analyses demonstrated that Max GD ≥224 μm was significantly associated with the presence of FSGS lesions, independent of other confounding factors (odds ratio, 11.70; 95% confidence interval, 1.93–70.84). <b><i>Discussion/Conclusion:</i></b> Glomerular hypertrophy (Max GD ≥224 μm) has been associated with FSGS lesions in CKD patients and may reflect the limits of the compensatory process.
DOI: 10.6084/m9.figshare.19738822.v1
title: Supplementary Material for: Nerve-Sparing Laparoscopic Cystoprostatectomy Based on Inferior Hypogastric Plexus Dissection: Our Initial Experience

description: <b><i>Introduction:</i></b> The aim of this study was to implement our technique for the initial dissection of the inferior hypogastric plexus and protection of the autonomic nerve supply to the corpora cavernosa in laparoscopic radical cystoprostatectomy with an orthotopic ileal neobladder and report the initial outcomes. <b><i>Methods:</i></b> Eleven normally potent patients with preoperative cT2N0 bladder cancer who underwent bilateral nerve-sparing laparoscopic cystoprostatectomy performed by the same surgeon were selected from May 2018 to September 2020. In this procedure, the anterior part of the inferior hypogastric plexus was dissected first between the prehypogastric nerve fascia and rectal proper fascia medial to the distal ureter. Then the Denonvilliers’ fascia and the nerves around the prostate were preserved according to current intrafascial principles. The preliminary operative, oncologic, and functional results are presented. <b><i>Results:</i></b> The median follow-up duration was 18 months. We observed early and late complications in 5 patients, but none exceeded grade III. Of the 11 patients, ten gained daytime continence (90.9%), and 8 (72.7%) showed nocturnal continence at the last follow-up. Regarding postoperative potency, 10 of the 11 patients (90.9%) remained potent with or without oral medications, excluding one who had partial tumescence but did not follow our recommendations regarding medication use. No local recurrence or positive surgical margins were noted. <b><i>Conclusion:</i></b> In addition to emphasizing our cavernosal nerve-sparing procedure, this report on the precise dissection and protection of the inferior hypogastric plexus could be of clinical significance, providing potentially ideal short-term functional results.
DOI: 10.6084/m9.figshare.24129069.v1
title: Replication Data for: The Reality of the Good Faith Exception

description: Dataset associated with The Reality of the Good Faith Exception. The document is an excel spreadsheet containing a comprehensive set of coded Fourth Amendment cases from July 2021, July 2018, and July 2015.
DOI: 10.6084/m9.figshare.7513814.v1
title: Biochemical identification of pathogenic bacteria isolates of ornamental fish in the state of Amazon

description: Ornamental fish in the Amazon are largely exported to the major centers of distribution and sale of ornamental fish in the world, located in the USA, Japan and Germany and at least eight species stand out as major. These species are collected in the medium and upper Rio Negro, in the municipality of Barcelos, in the state of Amazonas, which accounts for about 70% of exports of ornamental fish from Brazil and generating annual revenues of more than 6 million dollars. Because of the intense ornamental fish trade in the region, importers of fish from the Amazon have questioned the sanity of these animals about microorganisms, especially bacteria and viruses that cause disease in these animals. Bacterial and viral diseases can occur in all species of fish maintained under conditions of exploitation causing significant economic losses. Our goal was to verify the occurrence of potentially pathogenic bacteria in ornamental fishes exported from the state of Amazonas. Biochemical characterization of bacterial isolates from five species of ornamental fish allowed the identification of genus (Staphylococcus,Nocardia, Acinetobacter andLactococcus), with important bacterial species causing mortalities in marine and freshwater fish. While Amazon has great biodiversity, there are few studies to investigate this complexity, mainly related to the presence of pathogens causing bacterial diseases on ornamental fish. The results demonstrate the occurrence of pathogenical bacteria or with pathogenic potential in different species of ornamental fish traded from the state of Amazonas.
DOI: 10.6084/m9.figshare.8067743.v1
title: 1G4.tar.gz

description: MD simulations of the 1G4 TCR.<br>
DOI: 10.6084/m9.figshare.28513607.v1
title: Supplementary Material for: Heterogeneity in the study of peppermint in aromatherapy on cognition and attention: A critical scoping review

description: Introduction
Aromatherapy has not accrued enough evidence to be integrated into standardized clinical medicine. If high-quality evidence supports the effects of aromatherapy, it will be handled as a parallel option to standardized medical treatment. The aromatherapeutic impact of peppermint (Mentha × piperita L.) essential oil has been researched to a certain extent, such as on pain, anxiety, fatigue, or depression. Considering the rising expenditure on dementia care, the potential effects of peppermint on cognition have become increasingly significant. Therefore, we performed a systematic review of the studies on the impact of peppermint on cognition and attention. 
Methods
We focused on human research, and the effects of peppermint scents were required to be inhaled. According to the inclusion criteria, searching from PubMed, Scopus, and Gale Academic OneFile, we identified a total of 115 studies. Finally, eight references were selected for review. The risk of bias was analyzed according to the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) criteria. 
Results
Each reviewed reference had its own strength in investigating the effects of peppermint scent. However, as most studies have noted, the impact of peppermint should be assessed from multiple perspectives, including psychological, physiological, neurological, and pharmacological factors. The risk of bias was not found to be severe (high risk of bias rate: 35.7 ± 3.4%), our critical review elucidated the heterogeneity of the reviewed studies.
Conclusion
In summary, drawing a definitive conclusion at this stage is premature. Therefore, more carefully designed studies are needed to confirm this hypothesis.
DOI: 10.26181/5d19ae385c38b
title: Quantitative flow-ecology relationships using distributed lag nonlinear models - Large floods in the Murray River could have delayed effects on aquatic macroinvertebrates lasting more than three decades

description: The data sets and R code used for analyzing the long-term delayed effects of flows on macroinvertebrate richness and abundance on the Murray River, Australia.<br>
DOI: 10.6084/m9.figshare.22581715.v1
title: Other infrastructure stocks 1978-2020

description: 43,473 records are weight in total and by 3 types of materials embodied in other infrastructure (street lamps and telecommunications) in 337 cities from 1978 to 2020
DOI: 10.6084/m9.figshare.24152160.v1
title: Balancing non-CO2 GHG emissions and soil carbon sequestration in U.S. rice paddies: implications for natural climate solutions

description: The U.S. rice paddy systems play an increasingly vital role in ensuring food security, which also contribute massive anthropogenic non-CO<sub>2</sub> (CH<sub>4</sub> and N<sub>2</sub>O) greenhouse gas (GHG) emissions with expanding cultivation area. However, the magnitude and spatiotemporal variations of net GHG balance, i.e., trade-offs between SOC (Soil Organic Carbon) sequestration and non-CO<sub>2</sub> GHG emissions, in paddy soils and the drivers of their changes, have not yet been rigorously assessed. Integrating an improved agricultural ecosystem model with a meta-analysis of multiple field studies (a total of 322 site-year data representing 43 locations for U.S. rice paddies and 3402 site-year data representing 1113 locations for global rice paddies), here we found that U.S. rice paddy was a rapidly growing net GHG emission source, increased 138% from 3.73 ± 1.16 Tg CO<sub>2</sub>eq yr<sup>-1</sup> in the 1960s to 8.88 ± 2.65 Tg CO<sub>2</sub>eq yr<sup>-1</sup> in the 2010s. CH<sub>4</sub> emission made the most significant contribution (10.12 ± 2.28 Tg CO<sub>2</sub>eq yr<sup>-1</sup>) to this increase in net GHG emissions in the 2010s, but increasing N<sub>2</sub>O emissions, accounting for ~2.4% (0.21 ± 0.03 Tg CO<sub>2</sub>eq yr<sup>-1</sup>), cannot be ignored. SOC sequestration could offset about 14.0% (1.45 ± 0.46 Tg CO<sub>2</sub>eq yr<sup>-1</sup>) of the climate-warming effects of soil non-CO<sub>2</sub> GHG emissions in the 2010s. The intensification of land use/cover area, atmospheric CO<sub>2</sub>,synthetic N fertilizer usage and the application of manure were the dominant factors that induced net GHG emissions aggravation in rice paddies. Climate change was also critical in aggravating ~21% of soil N<sub>2</sub>O emission and ~10% of soil CO<sub>2</sub> release in the 2010s. However, adopting no/reduced tillage resulted in a substantial decrease of ~10 % in net soil GHG emissions, and non-continuous irrigation exhibited the potential to mitigate around 39% of soil non-CO<sub>2</sub> GHG emissions. Overall, the cost of this net GHG emissions for achieving increased U.S. rice yield markedly declined from 1960 to 2018, resulting in 0.84 ± 0.18 kg CO<sub>2</sub>eq ha<sup>-1</sup> of net soil GHGs on average for each kilogram of grain produced in the 2010s. There would be a great potential to reduce emissions intensity in the mid-South U.S., especially the Mississippi Delta region, through optimization of the synthetic N fertilizer and manure ratio, reduction of tillage practices, and implementation of non-continuous irrigation. Our findings underscore the importance of net CO<sub>2</sub> GHG mitigation in U.S. rice paddies for achieving net zero-emission and climate-friendly rice production.Unit: CH4 (g C/m2); N2O (g N/m2); CO2 (g C/m2)
DOI: 10.6084/m9.figshare.28845968.v1
title: Pintanel_etal_2025-Ecology OPEN Research section

description: Discovering how species’ thermal limits evolve and vary spatially is crucial for predicting their vulnerability to ongoing environmental warming. Current evidence indicates that heat tolerance is less spatially variable than cold tolerance among species, presenting a major concern for organismal vulnerability in a rapidly warming world. This asymmetry in thermal limits has been supported by large-scale geographic studies, across latitudinal and elevational gradients (known as Brett´s heat invariant rule). Yet, how critical limits vary across finer spatial scales (e.g., across microenvironments) is less understood. Here, we show that minimum temperatures are more variable than maximum temperatures at large geographic scales (across latitude/elevation), but are less variable at local scales (within sites), guiding spatial asymmetries in thermal tolerances. Using thermal tolerance measurements from amphibians, insects, and reptiles, we confirm the invariance of heat tolerance at large spatial scales and also find more variable heat than cold tolerances at local scales (an inverted Brett’s heat invariant rule at fine spatial scales). Our results suggest that regional or global-level studies will likely obscure fine-scale structuring in thermal habitats and corresponding local heat tolerance adaptation patterns. We emphasize that inferences based on broadscale geographic patterns obscure fine-scale variation in thermal physiology. For instance, a genetic basis for fine-scale variation in thermal physiology may reshuffle spatial and phylogenetic patterns of vulnerability.
DOI: 10.6084/m9.figshare.22305904.v1
title: ls_repo_VSe2.zip

description: A Quantum Monte Carlo study of the structural, energetic, and magnetic properties of two-dimensional (2D) H and T phase VSe2: Line-search data and analysis <br> Published in Journal of Physical Chemistry Letters (2023) <br> https://arxiv.org/abs/2301.11404 <br> <br> Authors: Daniel Wines, Juha Tiihonen, Kayahan Saritas, Jaron T. Krogel and Can Ataca <br> Author of the data repository: Juha Tiihonen <br> This small data repository contains data and scripts to reproduce geometry relaxation of two-dimensional VSe2 in H and T phases using a line-search tool. The repository has three directories with the following contents: <br> src/ source code for the line-search tool, referred here as the software ls_data/ production data of the line-search iteration and analysis postproc/ postprocessing scripts and figures
DOI: 10.6084/m9.figshare.26124754.v1
title: Supplementary Material for: Cognitive benefits of folic acid, docosahexaenoic acid and a combination of both nutrients in mild cognitive impairment; possible alterations though mitochondrial function and DNA damage

description: Introduction: It is uncertain whether folic acid (FA) combined with docosahexaenoic acid (DHA) could improve cognitive performance. This study evaluated the effects of a 12-month FA and DHA supplementation, in combination or alone, on cognitive function, DNA oxidative damage, and mitochondrial function in participants with mild cognitive impairment (MCI).
Methods: This randomized, double-blind, placebo-controlled trial recruited MCI participants aged 60 years and older. Two hundred and eighty participants were randomly divided in equal proportion into four groups: FA+DHA (FA 800μg/d + DHA 800mg/d), FA (800μg/d), DHA (800mg/d), and placebo groups daily orally for 12 months. The primary outcome was cognitive function evaluated by the Wechsler Adult Intelligence Scale-Revised (WAIS-RC). Cognitive tests and blood mechanism-related biomarkers were determined at baseline and 12 months.
Results: During the 12-month follow, scores of full intelligence quotient (FIQ) (βDHA: 1.302, 95%CI: 0.615, 1.990, p &lt; 0.001; βFA: 1.992, 95%CI: 1.304, 2.679, p &lt; 0.001; βFA+DHA: 2.777, 95%CI: 2.090, 3.465, p &lt; 0.001), verbal intelligence quotient, and some subtests of the WAIS-RC were significantly improved in FA+DHA and single intervention groups compared to the placebo group. Moreover, the FA and DHA intervention combination was superior to either intervention alone (p &lt; 0.001). Meanwhile, FA, DHA and their combined use significantly decreased 8-OHdG level and increased mitochondrial DNA copy number compared to the placebo (p &lt; 0.05).
Conclusions: Supplementation of FA and DHA, alone or combined, for 12 months can improve cognitive function in MCI participants, possibly through mitigating DNA oxidative damage and enhancing mitochondrial function. Combined supplementation may provide more cognitive benefit than supplementation alone.
Trial registration: Chinese Clinical Trial Registry, ChiCTR2000034351. Registered 3 July 2020 - Retrospectively registered, https://www.chictr.org.cn/showproj.html?proj=53345