cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23098475.v1
title: Supplementary Material for: Multimodal integrative genomics and pathology analyses in neoadjuvant nivolumab treatment for intermediate and locally-advanced HCC

description: Introduction: Immunotherapy has resulted in pathologic responses in hepatocellular carcinoma (HCC) but the benefits and molecular mechanisms of neoadjuvant immune checkpoint blockade are largely unknown. Methods: In this study, we evaluated the efficacy and safety of pre-operative nivolumab (anti-PD1) in patients with intermediate and locally-advanced HCC and determined the molecular markers for predicting treatment response. Results: Between July 2020 and November 2021, 20 treatment-naïve HCC patients with intermediate and locally advanced tumors received preoperative nivolumab at 3 mg/kg for 3 cycles prior to surgical resection. Nineteen patients underwent surgical resection on-trial. Seven (36.8%) of the 19 patients had major pathologic tumor necrosis (≥60%) in the post-nivolumab resection specimens, with 3 having almost complete (&gt;90%) tumor necrosis. The tumor necrosis was hemorrhagic and often accompanied with increased or dense immune cell infiltrate at the border of the tumors. None of the patients developed major adverse reactions contradicting hepatectomy. RNA-sequencing analysis on both pre-nivolumab tumor biopsies and post- nivolumab resected specimens showed, in cases with major pathologic necrosis, the proportion of CD8 T cells in the HCC tissues predominantly increased after treatment. Moreover, to investigate non-invasive biomarker for nivolumab response, we evaluated the copy number variation (CNV) using target-panel sequencing on plasma cell-free DNA of the patients and derived a CNV-based anti-PD1 score. The score correlated with the extent of tumor necrosis and was validated in a Korean patient cohort with anti-PD1 treatment. Conclusion: Neoadjuvant nivolumab demonstrated promising clinical activity in intermediate and locally-advanced HCC patients. We also identified useful non-invasive biomarker predicting responsiveness.
DOI: 10.6084/m9.figshare.3438878.v2
title: CRP_all raw data_final.xlsx

description: This data correspond to a manuscript of Plos One (ID : PONE-D-16-16329). We introduced a cardiac rehabilitation program that utilizes only a smartphone, with no external devices. As an efficient guide for cardiac rehabilitation exercise, we developed an application to automatically indicate the exercise intensity by comparing the estimated heart rate with the target heart rate zone. To evaluate HR estimation from our developed application during exercise, we used a modified version of the Bruce protocol, which consists of 5 min of walking for a warm-up, 10 min of jogging, 5 min of rest, and additional 10 min of jogging, and 5 min of waling for cool-down, all on a treadmill. The data are from 32 subjects for motion artifact analysis plus 4 subjects for maximum exercise testing.<sub> </sub><br><br>
DOI: 10.6084/m9.figshare.21113851.v1
title: Data of Optimizing the quality of epitaxial Y3Fe5O12 thin films via a two-step post-annealing process

description: Data of Optimizing the quality of epitaxial Y3Fe5O12 thin films via a two-step post-annealing process
DOI: 10.6084/m9.figshare.28078976.v1
title: data.zip

description: experimental data
DOI: 10.6084/m9.figshare.28436603.v1
title: Narrative-Driven Learning: Teaching Finite State Machines Through Storytelling

description: Teaching embedding systems demands a thorough understanding of computation models, with Finite State Machines (FSM) serving as one of the frameworks for developing the intricate behaviors of these systems. This study investigates the effectiveness of teaching Finite State Machines through storytelling using a controlled experiment with two groups: a Control Group (CG) taught traditionally and a Storytelling Group (SG) taught using a narrative-driven video. Data from pre-tests and post-tests and feedback questionnaires reveal that while storytelling did not significantly improve post-test scores, it enhanced application skills in the SG group. Storytelling helped students better connect FSM concepts to real-life scenarios like traffic lights and vending machines, while CG responses remained more abstract. Additionally, SG participants rated the video highly for attention and clarity, though some preferred more direct explanations. These findings suggest storytelling supports conceptual understanding and engagement, offering a complementary approach to teaching FSMs.<br>
DOI: 10.17632/s9xydt6rfj
title: Summarized RNA-seq data

description: Our research hypothesizes that Notch1 plays a critical role in regulating macrophage polarization and inflammatory pathways in the CLP-induced sepsis model. This transcriptomic dataset is derived from peritoneal macrophages of wild-type (WT) mice and macrophage-specific Notch1 conditional knockout (Notch1 CKO) mice under septic conditions, revealing the regulatory mechanisms of Notch1 in macrophage function.

The data demonstrate significant gene expression differences between the two groups of macrophages, showing that Notch1 CKO markedly alters the transcriptomic profile of macrophages, particularly in pathways associated with M1 polarization and inflammation. Specifically, the expression of inflammatory cytokines (e.g., IL-1β, TNF-α) is significantly reduced in Notch1 CKO macrophages, accompanied by the suppression of key signaling pathways such as β-Catenin and NF-κB. These findings highlight the role of Notch1 in promoting M1 polarization and inflammatory responses. Additionally, increased expression of genes associated with an anti-inflammatory phenotype was observed following Notch1 deletion, indicating its pivotal role in maintaining the balance of macrophage polarization.

The data were obtained using transcriptomic sequencing. Peritoneal macrophages were isolated from septic mice subjected to CLP, and RNA was extracted for high-throughput sequencing. The mice included two genotypes (WT and Notch1 CKO) and were sampled at the same time point post-CLP induction. Sequencing data underwent quality control, mapping to the mouse reference genome, differential gene expression analysis, and pathway enrichment using tools such as DESeq2 and GSEA.

These data underscore the critical role of Notch1 in regulating the transcriptional programs of macrophages in a sepsis model and reveal its molecular mechanisms in promoting M1 polarization through the β-Catenin and NF-κB signaling pathways. The findings provide valuable insights into the potential of targeting Notch1 as a therapeutic strategy for sepsis and other inflammation-related diseases. Researchers can utilize this dataset to investigate gene regulatory networks in macrophages and Notch1-dependent inflammatory mechanisms, as well as validate or compare findings in studies of immune and inflammatory diseases. The data are organized in a standardized format to facilitate reproducibility and further analysis.
DOI: 10.6084/m9.figshare.22128377.v1
title: Supplementary Material for: Visual Cue to Reduce False No-Show Registration in Riyadh Primary Healthcare: A Randomized Controlled Trial

description: <b><i>Introduction:</i></b> Preliminary field visits to the Saudi Ministry of Health’s primary healthcare centers (PHCs) confirmed a proportion of prior reported no-show appointments to be false due to staff registering patient arrivals inappropriately. We sought to investigate whether visual cue reminders would prime the staff to register patients properly. <b><i>Methods:</i></b> A randomized controlled trial was conducted in 2019 involving 35 PHCs in Riyadh, Saudi Arabia. Visual posters were installed in the intervention PHCs wherever patient arrivals were registered. The primary outcome was patient no-show appointments. Staff who registered appointment arrivals were observed and interviewed. Multilevel logistic regression analyzed the change in no-shows across an intervention group and a control group. <b><i>Results:</i></b> The intervention group had lower odds ratio (OR) of no-shows than the control group, although not significantly (OR 0.81, 95% confidence interval [CI] = 0.50–1.31). The period during Ramadan saw fewer no-shows than pre-Ramadan (OR 1.60, 95% CI = 1.55–1.66). Compared to family medicine appointments, no-shows were higher for the smoking cessation clinic (OR 3.95, 95% CI = 3.43–4.54), dental appointments (OR 2.14, 95% CI = 1.97–2.32), and vaccine appointments (OR 1.31, 95% CI = 1.27–1.35). Qualitative analysis shows that PHCs’ appointment processing was arbitrary without a unified structure. <b><i>Conclusion:</i></b> The reduction in no-show rates using visual cues was not significant. However, certain confounders, if not addressed prior to intervention implementation, can lead to cognitive overload and burnout, inviting unwanted behavior. Further implications are discussed.
DOI: 10.6084/m9.figshare.24587406.v2
title: (DFT )Files.zip

description: <b>DFT Summary for Hydrodehalogenation Project</b>
DOI: 10.6084/m9.figshare.5124757.v1
title: Supplementary Material for: Sleep-Disordered Breathing and Periodic Limb Movements in Narcolepsy with Cataplexy: A Systematic Analysis of 35 Consecutive Patients

description: <b><i>Background:</i></b> Disturbed sleep is a core feature of narcolepsy with cataplexy (NC). Few studies have independently assessed sleep-disordered breathing (SDB) and periodic limb movements (PLMs) in non-homogeneous series of patients with and without cataplexy. We systematically assessed both SDB and PLMs in well-defined NC patients. <b><i>Methods:</i></b> We analyzed the clinical and polysomnographic features of 35 consecutive NC patients (mean age 40 ± 16 years, 51% males, 23/23 hypocretin-deficient) to assess the prevalence of SDB (apnea-hypopnea index &gt;5) and PLMs (periodic leg movements in sleep (PLMI) &gt;15) together with their impact on nocturnal sleep and daytime sleepiness using the multiple sleep latency test. <b><i>Results:</i></b> 11 (31%) and 14 (40%) patients had SDB and PLMs, respectively. SDB was associated with older age (49 ± 16 vs. 35 ± 13 years, p = 0.02), higher BMI (30 ± 5 vs. 27 ± 6, p = 0.05), and a trend towards higher PLMI (25 ± 20 vs. 12 ± 23, p = 0.052), whereas PLMs with older age (50 ± 16 vs. 33 ± 11 years, p = 0.002) and reduced and fragmented sleep (e.g. sleep efficiency of 82 ± 12% vs. 91 ± 6%, p = 0.015; sleep time of 353 ± 66 vs. 395 ± 28, p = 0.010). SDB and PLMs were also mutually associated (p = 0.007), but not correlated to daytime sleepiness. <b><i>Conclusions:</i></b> SDB and PLMs are highly prevalent and associated in NC. Nevertheless, SDB and PLMs are rarely severe, suggesting an overall limited effect on clinical manifestations.
DOI: 10.4225/49/595c4bb64c320
title: Canu (v1.5, f356c2c) + 5 x Pilon (v1.22) assemblies (hybrid Illumina and ONT)

description: Canu assemblies of 12 isolates of <i>Klebsiella pneumoniae</i>, generated with ONT reads, followed by five rounds of Pilon polishing using Illumina reads.
DOI: 10.6084/m9.figshare.7195436.v1
title: Intraplate extension of the Indochina plate deduced from 26 to 24 Ma A-type granites and tectonic implications

description: In recent years, abundant Cenozoic potassic magmatic rocks from eastern Tibet and the Indochina Block have been studied extensively; however, until now, knowledge of Cenozoic A-type granites from the interior of the Indochina Block has been limited. U–Pb zircon ages for six samples of the Salei granite pluton within the Indochina Block range from 26 to 24 Ma. <i>In situ</i> Lu–Hf and Sr–Nd isotope data indicate that the Salei pluton was sourced mostly from Mesoproterozoic basement rocks of the Indochina Block, mixed with a small volume of juvenile crust derived from the underplated mantle. Whole-rock major element geochemistry indicates that the six samples are peraluminous high-K calc-alkaline granites. The trace and rare earth element patterns are typical of within-plate A-type granites. In combination with previous research, the present results suggest that the late Oligocene Salei granite formed from the convective removal of thickened lower continental lithospheric mantle. Moreover, the presence of 26<b>–</b>24 Ma A-type granites in the Indochina Block indicates within-plate extension in the interior of the block during the late Oligocene.
DOI: 10.17632/n9snfr7m59
title: QuPWM: Feature Extraction Method for MEG Epileptic Spike Detection

description: The used data set are already quantized frames extracted using frame length = 100 sample and step=2 sample from three MEG session of two healthy patient (E001 and E002) and three MEG session of two epileptic patient (C001 and C002). These signal are licensed to National Neural Institute- King Fahad Medical City (NNI-KFMC), Riyadh, Saudi Arabia. This data was conducted in accordance with the approval of the Institutional Review Board at KFMC (IRB log number: 15-086, 2015). For more information, Please contact professor Saleh Alshebeili at : dsaleh@ksu.edu.sa
DOI: 10.6084/m9.figshare.3530696.v1
title: Appendix B. Indicator values for the nine significant species found in three multivariate regression tree (MRT) groups, and distribution maps of individuals of those species.

description: Indicator values for the nine significant species found in three multivariate regression tree (MRT) groups, and distribution maps of individuals of those species.
DOI: 10.6084/m9.figshare.4522928.v4
title: Dataset for BG-2016-559 (Tree growth and its climate signal along latitudinal and altitudinal gradients: comparison of tree rings between Finland and Tibetan Plateau)

description: This is a dataset for the paper bg-2016-559. It covers the underlying data and the main results of the figures in the paper titled "Tree growth and its climate signal along latitudinal and altitudinal gradients: comparison of tree rings between Finland and Tibetan Plateau".<br>p.s.: The sliding correlation analyses were conducted in R, and the scripts is also sharable upon request to Dr. Lixin Lyu at lixinlv@ibcas.ac.cn. <br>
DOI: 10.6084/m9.figshare.3563529.v1
title: Appendix B. Tables showing (1) Species status and dietary preferences of fishes in the study area of the Rio Grande, New Mexico, and (2) specimens sampled for C and N isotopic analysis, tabulated by species, location, and time.

description: Tables showing (1) Species status and dietary preferences of fishes in the study area of the Rio Grande, New Mexico, and (2) specimens sampled for C and N isotopic analysis, tabulated by species, location, and time.
DOI: 10.6084/m9.figshare.24018321.v1
title: Nelson et al LogiMML microscopy images

description: Microscopy images from the manuscript:Logic-based mechanistic machine learning on high-content images reveals how drugs differentially regulate cardiac fibroblasts | bioRxiv
DOI: 10.6084/m9.figshare.5831931.v1
title: SCRstatistics.R

description: A .R open source script that allows to extract descriptive statistics from the database multisensory_emotions_R.rda
DOI: 10.6084/m9.figshare.9735800.v1
title: Wave fetch GIS layers for Chile at 100m scale

description: This data layer gives values of summed wave fetch in 32 angular sectors around focal cells, using a model modified from that given in Burrows et al (2012 - see reference). Wave fetch is the distance to the nearest land in a defined direction. The model performs a three-scale search for land around each cell in the model, sparsely (every 10km) up to 200km, every 1km up to 20km away, and every 100m up to 1km distant.<br>Values represent the summed number of grid cells to the nearest land across all 32 11.5° sectors. The file is a GeoTIFF using the WGS84 projection.
DOI: 10.6084/m9.figshare.11813601.v1
title: Production of ancient dissolved organic carbon in Arctic Ocean sediment: A pathway of carbon cycling in the extreme environment

description: Concentration and carbon isotope values of sediment TOC, hydrocarbon and porewater DOC
DOI: 10.6084/m9.figshare.19422233.v1
title: Data of two observed flow patterns over a physical model

description: The dataset containing the orthoimages of two observed flow patterns from point sources over a physical model located in Hohai University. DEMs with multiple resolutions used in the reference are also contained. Specially, the sinks in the DEM are not removed. <br> Citation: Wu, P., Liu, J., Han, X., Feng, M., Fei, J., & Shen, X. (2022). An improved triangular form-based multiple flow direction algorithm for determining the nonuniform flow domain over grid networks. Water Resources Research,<br> 58, e2021WR031706. <br>
DOI: 10.6084/m9.figshare.25604109.v1
title: Code

description: Code
DOI: 10.6084/m9.figshare.19336733.v1
title: Supplementary Material for: A Comparative Study of Patient-Derived Tumor Models of Pancreatic Ductal Adenocarcinoma Involving Orthotopic Implantation

description: <b><i>Background:</i></b> Pancreatic ductal adenocarcinoma (PDA) is associated with very poor prognoses. Therefore, new therapies and preclinical models are urgently needed. In the present study, we sought to develop more realistic experimental models for use in PDA research. <b><i>Methods:</i></b> We developed patient-derived xenografts (PDXs), established PDX-derived cell lines (PDCLs), and generated cell line-derived xenografts (CDXs), which we integrated to create 13 matched “trios” – i.e., patient-derived tumor models of PDA. We then compared and contrasted histological and molecular alterations between these three model systems. <b><i>Results:</i></b> Orthotopic implantation (OI) of the PDCLs resulted in tumorigenesis and metastases to the liver and peritoneum. Morphological comparisons of OI-CDXs and OI-PDXs with passaged tumors revealed that the histopathological features of the original tumor were maintained in both models. Molecular alterations in PDX tumors (including those to <i>KRAS</i>, <i>TP53</i>, <i>SMAD4</i>, and <i>CDKN2A</i>) were similar to those in the respective PDCLs and CDX tumors. When gene expression levels in the PDCLs, ectopic tumors, and OI tumors were compared, the distant metastasis-promoting gene <i>CXCR4</i> was specifically upregulated in OI tumors, whose immunohistochemical profiles suggested epithelial-mesenchymal transition and adeno-squamous trans-differentiation. <b><i>Conclusion:</i></b> These patient-derived tumor models provide useful tools for monitoring responses to antineoplastic agents and for studying PDA biology.
DOI: 10.6084/m9.figshare.23909046.v1
title: 8,496 MAGs of saliva samples

description: We obtained a total of 8,496 genomic bins from the salivary samples.
DOI: 10.17632/tzc88kcnwv
title: Intangible benefits of nature-based solutions for wastewater treatment

description: This dataset is part of a research project on the eco-cultural wastewater treatment technologies in New Zealand. The research hypothesis posits that eco-cultural wastewater treatment systems, which integrate environmental, social and cultural dimensions, provide significant intangible benefits that are often overlooked in traditional economic evaluations. This study aims to quantify these benefits within the framework of total economic valuation framework. Data were sourced from the Ecosystem Services Valuation Database (ESVD) and relevant literature on NBS for wastewater treatment. 

The database contains detailed information about various studies evaluating the intangible benefits of Nature-Based Solutions (NBS) for wastewater treatment. It includes data from the Ecosystem Services Valuation Database (ESVD) and other relevant studies, focusing on non-market valuation estimates. Key Columns in the Database:
-Study ID: Unique identifier for each study.
-OB: Additional identifier or grouping code.
-ESVD2.0_Biome: Biome or ecosystem type (e.g., Coastal systems, Marine).
-ES_Text: Ecosystem service described in text (e.g., water filtration).
-ES: Ecosystem service category (e.g., Waste treatment).
-Value Groups: Grouping of value types (e.g., Waste treatment and processing) based on the total economic valuation framework
-Countries: Country where the study was conducted.
-Site Area Unit: Unit of the site area (e.g., hectare).
-Site Area: Size of the study area.
-Valuation Methods: Methods used for valuation (e.g., Contingent Valuation (CE)).
-Value Year: Year the value was estimated.
-Original Value: Original estimated value.
-NZD: Converted value in 2023 New Zealand Dollars (NZD).
-Title: Title of the study.

Key Findings: 
1. Diversity of Ecosystem Services: The studies cover a wide range of ecosystem services, including water filtration, habitat for species, recreational opportunities, and storm protection. This demonstrates the multifaceted benefits of NBS beyond traditional wastewater treatment.
2. Valuation Methods: Common methods used include Contingent Valuation (CE) and other non-market valuation approaches. These methods help quantify benefits that are not typically traded in markets, such as cultural and recreational values.
3. Geographical Spread: The studies span various countries, indicating a global interest in NBS and their benefits. However, a significant portion of the data pertains to specific regions like Saint Martin, which may influence the generalizability of the findings.
4. Economic Valuation: The values of intangible benefits are converted to 2023 NZD for consistency. This allows for easier comparison across studies and helps in understanding the economic significance of these benefits in a current context.
DOI: 10.60893/figshare.pof.27883365.v1
title: Supplementary Material

description: Supplementary Material
DOI: 10.6084/m9.figshare.26488528.v1
title: Smart building awareness dataset

description: Dataset for Enabling Factors for Smart Building Diffusion in Nigeria: Insights from Industry Experts. Research.
DOI: 10.6084/m9.figshare.28380467.v1
title: Evaluation of Conformance Criteria for Preference Indication in Collaborative Flight Prioritization in Air Traffic Flow Management - Resources

description: The resources created, including the datasets, the data created during the experiments, the visualizations, and experimental insights for the master's thesis with the title:<b>Evaluation of Conformance </b><b>Criteria for Preference </b><b>Indication in Collaborative </b><b>Flight Prioritization in Air </b><b>Traffic Flow Management</b>
DOI: 10.17632/cytx9tt93b
title: Condensate liquid viscosity data-bank for modelling and optimizing gas-condensate reservoirs below the saturation pressure. 

description: The gas-condensate liquid viscosity is recorded as a function of Pressure, Temperature and Solution gas to oil ratio (GOR) or normally presented as Rs using constant volume depletion experiment. All three aforementioned parameters of pressure, temperature and GOR strongly define the true characteristics of gas-condensate reservoir fluid below the saturation pressure, hence condensate liquid viscosity. 

The units for each factor are as follow:
The pressure recorded in Pounds per square inch absolute (psia), Temperature recorded in degree Fahrenheit (F), solution gas to oil ratio corrected from Standing correlation and recorded in standard cubic foot per stock tank barrel (scf/STB) and condensate liquid viscosity is measured and recorded in centipoise (cp). 

The data can be used in modelling condensate liquid viscosity as a predominant factor in modelling and simulation of gas-condensate reservoirs below the saturation pressure. This also helps better performance modelling of such reservoirs and increase production efficiency.