cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10616879
title: E3SM simulations of Hurricane Irene (Delaware River basin subset)

description: This repository consists of the E3SM simulation outputs of Hurricane Irene (subsetted within Delaware River basin) associated with the manuscript: "Simulation of Compound Flooding using River-Ocean Two-way Coupled E3SM Ensemble on Variable-resolution Meshes". Below are the descriptions for each file:

EAM_ensemble.nc - 25 EAM ensemble simulations.MOSART_1way_baseline.nc - 25 MOSART ensemble simulations for Experiment 1way_baselineMOSART_1way_datm_GSWP.nc - MOSART simulation for Experiment 1way_datm using GSWP forcingMOSART_1way_datm_JRA.nc - MOSART simulation for Experiment 1way_datm using JRA forcingMOSART_1way_r0125.nc - 25 MOSART ensemble simulations for Experiment 1way_r0125MOSART_2way.nc - 25 MOSART ensemble simulations for Experiment 2wayMOSART_1way_SSH.nc - 25 MOSART ensemble simulations for Experiment 1way_SSHMOSART_1way_MSL.nc - 25 MOSART ensemble simulations for Experiment 1way_MSLMPASO_subset_1way_ens001.nc ~ MPASO_subset_1way_ens025.nc - 25 MPAS-O ensemble simulations for Experiment 1way_baselineMPASO_subset_2way_ens001.nc ~ MPASO_subset_2way_ens001.nc - 25 MPAS-O ensemble simulations for Experiment 2way
DOI: 10.5281/zenodo.10902264
title: ODP site 811 SSTs
DOI: 10.5281/zenodo.3710499
title: Darwin's naturalization conundrum can be explained by spatial scale: R replication code

description: 1) Code for extracting climatic data:<br> 1_extract_env.R<br> 2_extract_env_county.R<br> 3_relatePlotCounty.R 2) Code for generating composite phylogenies:<br> 1_making_sunplin_trees.R 3) Code for relatedness analyses:<br> DNH_calculations_PHY_obs.cluster.R<br> DNH_calculations_PHY_random.cluster.R<br> DNH_calculations_TAX.cluster_obs.R<br> DNH_calculations_TAX.cluster_random.R
DOI: 10.5281/zenodo.7647319
title: Laser cooling a membrane-in-the-middle system close to the quantum ground state from room temperature

description: This dataset contains processed data corresponding to the figures in the main text of our paper "Laser cooling a membrane-in-the-middle system close to the quantum ground state from room temperature" The dataset consists of 10 .csv files and a jupyter notebook for generating the figures in the main text.
DOI: 10.5281/zenodo.7970944
title: Protein kinase inhibitors

description: The deposition contains data sets of human and mouse protein kinase inhibitors with reliable activity measurements and corresponding compounds classified as inactive that were assembled from public repositories. The human protein kinase inhibitors have recently been analyzed in detail [Xerxa et al., Data-Driven Global Assessment of Protein Kinase Inhibitors with Emphasis on Covalent Compounds. <em>J Med Chem</em>, 2023, in press, https://doi.org/10.1021/acs.jmedchem.3c00621].
DOI: 10.6084/m9.figshare.23703069
title: Notch filter designs: NF-72, NF-102 and TNF-74

description: This dataset contains json-files describing three different notch filter designs — NF-72, NF-102, TNF-74 and their targets. <br> This data is referenced in our companion paper "Advanced algorithms for monochromatic monitoring of complex optical coatings"
DOI: 10.6084/m9.figshare.24465772
title: Supplementary Material for: Venous thrombosis in a pseudohypoparathyroidism patient with a novel GNAS frameshift mutation and complete resolution of vascular calcifications with acetazolamide treatment

description: Introduction Pseudohypoparathyroidism type IA (PHP1A) is characterized by end-organ resistance to multiple hormones and Albright’s hereditary osteodystrophy (AHO). PHP1A is caused by inactivating mutations of the GNAS gene encoding the α-subunit of the stimulatory G protein (Gsα). In line with the underlying genetic defect, impaired inhibition of platelet aggregation has been demonstrated in some patients. However, no PHP1A case with thrombotic events has been described. Also, PHP1A cases typically have subcutaneous ossifications, but soft tissue calcifications are another common finding. Treatment options for those and other non-hormonal features of PHP1A are limited. Case Presentation A female patient presented with short stature, fatigue, and exercise-induced carpopedal spasms at age 117/12 years. Diagnosis of PHP1A was made based on hypocalcemia, hyperphosphatemia, elevated serum PTH, and AHO features, including short stature and brachydactyly. A novel frameshift variant was detected in the last exon of GNAS (c.1065_1068delGCGT, p.R356Tfs*47), showing complete loss of baseline and receptor-stimulated activity in transfected cells. The patient developed venous thrombosis and vascular and subcutaneous calcifications on both forearms after venous puncture on the right and extravasation of calcium gluconate during treatment on the left. The thrombosis and calcifications completely resolved following treatment with low molecular weight heparin and acetazolamide for 5 and 8 months, respectively. Conclusions This case represents the first PHP1A patient displaying thrombosis and the first successful use of acetazolamide for PHP1A-associated soft tissue calcifications, thus providing new insights into the treatment of non-endocrinological features in this disease.
DOI: 10.6084/m9.figshare.24547312
title: Supplementary Material for: Sensitivity and Accuracy of Doppler Ultrasound compared to CT Angiography for the Diagnosis of Carotid Webs: Systematic Review

description: Introduction: Carotid webs (CaW) are increasingly recognized as a cause of cryptogenic acute ischemic stroke (AIS). Due to the risk of recurrent ischemic stroke associated with CaW, it is important to identify them. Although several studies report digital subtraction angiography (DSA) and computerized tomography angiography (CTA) to be better at diagnosing CaW than Doppler ultrasound (DUS), it remains to be defined which is the best radiological method to diagnose CaW. Our aim was to evaluate sensitivity and accuracy of DUS compared to CTA for CaW diagnosis. Methods: We searched PUBMED and EMBASE databases from inception through August 2022. We included studies with patients with CaW diagnosed by DUS and/or CTA, in which both methods were used in each patient. Demographic characteristics, diagnostic reports of each method and histology reports were collected. Descriptive analysis and sensitivity and accuracy estimates were made to evaluate DUS compared to CTA. Results: We included 27 articles in the systematic review (121 patients with CaW). DUS identified 94 patients with CaW and CTA 116 patients. DUS missed diagnosis in 22.3% (27 patients) and CTA did not identified CaW detected by DUS in 4.13% (5 patients). Accuracy rate between DUS and CTA was 73.6% (95% CI 64.8 to 81.2%). Sensitivity of DUS to diagnose CaW compared to CTA was 76.7% (95% CI 68.0 to 84.1%). Most common misdiagnosis with DUS were normal exam (44.4%), atherosclerosis (22.2%) and dissection (22.2%). Conclusion: The sensitivity and accuracy of DUS to diagnosis of CaW were moderate. It might detect CaW in some cases in which it was not identified by CTA. Increase recognition of CaW and specific ultrasound protocols may enhance diagnosis of CaW by DUS.
DOI: 10.6084/m9.figshare.24803196.v4
title: BSDA_Speckle decorrelation OD=0.35&0.5 pH2&pH8

description: BSDA_Speckle decorrelation datasets. Speckle decorrelation curves of five bacteria under different conditions. OD=0.35&0.5 pH2&pH8. The bacteria are: L. acidophilus, L. gasseri, L. casei Shirota, L. plantarum, and 37 5AS.
DOI: 10.6084/m9.figshare.24884580
title: Supplementary Material for: Analysis of Immune-Related Adverse Events of Atezolizumab and Bevacizumab in Patients with Hepatocellular Carcinoma: A Multicenter Cohort Study

description: Background: Despite the emergence of atezolizumab and bevacizumab (A+B) as standard first-line systemic therapy for unresectable hepatocellular carcinoma (HCC), a comprehensive understanding of the clinical significance of immune-related adverse events (irAEs) remains limited. We aimed to assess the impact of irAEs on patients with HCC undergoing A+B treatment.
Methods: This multicentre retrospective study included consecutive patients with HCC who were treated with the A+B regimen from September 2020 to December 2022. Patients were categorised into three groups based on the severity of irAEs, ranging from those without any experience of irAEs to those with severe irAEs, classified as grade 3 or higher.
Results: This study included 150 patients with HCC, with a mean age of 63.3 years. Among them, 93.3% of patients were classified as Barcelona Clinic Liver Cancer stage C, 52.0% had portal vein tumour thrombosis (PVTT), and 60.7% extrahepatic spread. Patients were classified as follows: Group 1 (n = 84) had no irAEs, Group 2 (n = 37) had mild irAEs (grade 1–2), and Group 3 (n = 29) had severe irAEs (grade ≥ 3). The median overall survival (OS), progression-free survival (PFS), and time-to-treatment discontinuation (TTD) were 13.6, 5.7, and 3.6 months, respectively. Group 2 demonstrated significantly superior OS compared to Group 1 (9.5 months) and Group 3 (5.6 months), with a median OS of 23.0 months (p &lt; 0.001). Furthermore, Group 2 demonstrated significantly better outcomes in terms of PFS and TTD compared to both Group 1 and Group 3 (p &lt; 0.001 for both). Multivariate analysis identified mild irAEs (hazard ratio [HR], 0.353; p = 0.010), ALBI grade 1 (HR, 0.389; p = 0.006), Child-Pugh class A (HR, 0.338; p = 0.002), and the absence of PVTT (HR, 0.556; p = 0.043) as independent predictors of better OS.
Conclusions: Our study highlights the significant impact of irAE severity on the outcomes of patients with HCC receiving A+B. Notably, the occurrence of mild irAEs was independently associated with favourable survival, suggesting their potential role as surrogate indicators of HCC prognosis.
DOI: 10.6084/m9.figshare.24916191
title: Supplementary Material for: Management of Chronic Obstructive Pulmonary Disease: constraints in the patient pathway and mitigation strategies

description: Introduction: Respiratory diseases, ranking third in Portugal, contribute significantly to illness and mortality. Chronic Obstructive Pulmonary Disease (COPD) is the third leading cause of death globally. Identifying high-risk individuals and implementing early treatment is crucial due to the variability of COPD symptoms and exacerbations. This study aims to identify effective strategies for preventing exacerbations and complications.
Methods: A Delphi involving 15 experts was performed. Experts included physicians, nurses, health managers, policymakers, public health experts, and patient organizations. Consensus was achieved at 73.3% for each strategy using a scale ranging from "Agree" to "Disagree." Three rounds were conducted to address six questions related to early diagnosis and patient follow-up. Challenges faced by the Portuguese Health System in managing COPD, obstacles in COPD exacerbation diagnose and management, and effective strategies to overcome barriers were identified in the first round. The second and third rounds involved analyzing the gathered information and voting on each indicator to achieve consensus. Indicators were categorized into constraints and barriers, and strategies for reducing COPD exacerbations and disease burden.
Results: Out of a total of 134 valid indicators generated, 108 achieved consensus. Among the indicators agreed upon by experts, 18 pertained to barriers, challenges, and constraints, while 90 focused on action strategies for COPD. Among the strategies formulated, 25 consensus indicators target prevention strategies, 24 consensus indicators aim to enhance COPD referrals, and 41 consensus indicators focus on mitigating COPD exacerbations and reducing the overall disease burden. 
Discussion/Conclusion: This study emphasizes the need for integrated investment in respiratory healthcare and recognition of the impact of COPD on patients, healthcare systems, and economies. Prevention and appropriate treatment of exacerbations are crucial for effective COPD management and reducing associated morbidity and mortality. Experts highlight the importance of improving coordination between different levels of care, integrating information systems, and decentralizing hospital responsibilities. The COVID-19 pandemic has further emphasized the importance of individual and collective respiratory health, necessitating investment in health promotion and COPD awareness.
DOI: 10.6084/m9.figshare.25045715
title: Supplementary Material for: Genome-wide analysis of DNA methylation in pseudomyxoma peritonei originated from appendiceal neoplasms

description: Introduction:
Pseudomyxoma peritonei (PMP) is a disease characterized by progressive accumulation of intraperitoneal mucinous ascites produced by neoplasms in the abdominal cavity. Since the prognosis of patients with PMP remain unsatisfactory, the development of effective therapeutic drug(s) is a matter of pressing concern. Genetic analyses of PMP have clarified the frequent activation of GNAS and/or KRAS. However, the involvement of global epigenetic alterations in PMPs has not been reported.

Methods:
To clarify the genetic background of the 15 PMP tumors, we performed genetic analysis using AmpliSeq Cancer HotSpot Panel v2. We further investigated global DNA methylation in the 15 tumors and eight non-cancerous colonic epithelial cells using Methylation EPIC array BeadChip (Infinium 850k) containing a total of 865,918 probes. 

Results:
This is the first report of comprehensive DNA methylation profiles of PMPs in the world. We clarified that the 15 PMPs could be classified into at least two epigenotypes, unique methylation epigenotype (UME) and normal-like methylation epigenotype (NLME), and that genes associated with neuronal development and synaptic signaling may be involved in the development of PMPs. In addition, we identified a set of hypermethylation marker genes such as HOXD1 and TSPYL5 in the 15 PMPs.

Conclusions:
These findings may help the understanding of the molecular mechanism(s) of PMP and contribute to the development of therapeutic strategies for this life-threatening disease.
DOI: 10.6084/m9.figshare.25283269
title: Supplementary Material for: α1-antichymotrypsin complex (SERPINA3) is an independent predictor of all-cause but not cardiovascular mortality in patients hospitalized for chest pain of suspected coronary origin.

description: Introduction: 
SERPINA3 is an acute phase protein triggered by inflammation. It is upregulated after an acute myocardial infarction (AMI). Data on its long-term prognostic value in MI patients are scarce. We aimed to assess the utility of SERPINA3 as a prognostic marker in patients hospitalized for chest pain of suspected coronary origin.
Methods: 
A total of 871 consecutive patients, 386 diagnosed with AMI, were included. Stepwise Cox regression models, applying continuous loge-transformed values, were fitted for the biomarker with all-cause mortality and cardiac death within 2-years or all-cause mortality within median 7 years as dependent variables. An analysis of MI and stroke, and combined endpoints, respectively, was added. The hazard ratio (HR) (95% CI) was assessed in a univariate and multivariable model.
Results: 
Plasma samples from 847 patients were available. By 2 years follow-up, 138 (15.8%) patients had died, of which 86 were cardiac deaths. The univariate analysis showed a significant association between SERPINA3 and all-cause mortality [HR 1.41 (95% 1.19-1.68), p&lt;0.001], but not for cardiac death. Associations after adjustment were non-significant. 
By 7 years follow-up, 332 (38.1%) patients had died. SERPINA3 was independently associated with all-cause mortality from the third year onwards. The HR was 1.14 (95% CI, 1.02-1.28), p=0.022. Similar results applied to combined endpoints, but not for MI and stroke, respectively. The prognostic value of SERPINA3 was limited to non-AMI patients. No independent associations were noted among AMI patients.
Conclusions: 
SERPINA3 predicts long-term all-cause mortality, but failed to predict outcome in AMI patients.
DOI: 10.6084/m9.figshare.25471156.v1
title: Dataset of minimal clinically important difference in physical activity in patients with stroke.

description: dataset related to the study (10.12688/f1000research.149214.1)
DOI: 10.6084/m9.figshare.25669749
title: SWAMPY (Dunedin) magnetometer data for September 2017

description: Format is a Matlab datafile (.mat)The 9 columns of data are: UT (yr, mth, dy, hr, mn, s), X, Y, ZSampling interval is 0.9771 s, magnetic fields are in nT
DOI: 10.12751/g-node.3lvs3q
title: GluA1-KO LFP data

description: Raw data of GluA1-WT and -KO mice used for LFP analysis
description: IsSupplementTo: Strahnen, D., Kapanaiah, S. K. T., Bygrave, A. M. & Kaetzel, D. Lack of redundancy between electrophysiological measures of longrange neuronal communication. bioRxiv 2020.07.16.207001 (2020) doi:10.1101/2020.07.16.207001 [Preprint]. (https://doi.org/10.1101/2020.07.16.207001)
DOI: 10.13020/5xq3-wb66
title: Phenology data for watermilfoil taxa Myriophyllum spicatum, M. sibiricum, and M. spicatum x M. sibiricum in Minnesota, USA, 2017 - 2018 Glisson, Wesley J; Larkin, Daniel J (2021)

description: In North America, the hybrid aquatic plant Myriophyllum spicatum × Myriophyllum sibiricum (hybrid watermilfoil, HWM) is a cross between non-native invasive Eurasian watermilfoil (M. spicatum, EWM) and native northern watermilfoil (M. sibiricum, NWM). We compared HWM to its parental taxa, EWM and NWM, by examining the amount and timing of: 1) flowering, 2) surface cover, and 3) biomass (using stem counts as a proxy). We conducted repeat surveys of Myriophyllum beds at eight lakes (2–3 lakes/taxon) in the Minneapolis-St. Paul Metropolitan area (Minnesota, USA) between June 2017 and November 2018. To sample biomass without destroying plants, we developed a novel sampling device that uses underwater video to measure Myriophyllum stems; we validated the utility of this device by comparing Myriophyllum stem counts and biomass collected from the same locations. The data from these studies are provided and documented here.
description: The files include data collected at each Myriophyllum sampling location over the course of the study, including data collected at the water's surface (Myriophyllum flower heads, Myriophyllum surface cover, and water chemistry) and data collected with the underwater video sampling device (Myriophyllum stem counts and vertical stem cover). Surface data include a single row for each site (i.e., point location) on each lake for each sampling event. The underwater stem data includes multiple rows for for each site on each lake for each sampling event; these rows correspond to four video subsamples collected at each site, and subsequent 0.5-m depth intervals at which Myriophyllum stems were assessed for each subsample. Additionally, there is a data file that includes biomass measurements that correspond to stem counts from video subsamples. Data across files can be linked via "siteID".
DOI: 10.15156/bio/786334
title: UNITE QIIME release for Fungi

description: Three sets of QIIME files are released, corresponding to the SHs resulting from clustering at the 97% and 99% threshold levels. The third set of files is the result of a dynamic use of clustering thresholds, such that some SHs are delimited at the 97% level, some at the 97.5% level, some at the 98% level, and so on; these choices were made manually by experts of those particular lineages of fungi. The syntax is the same throughout the three sets of files.
description: Three sets of QIIME files are released, corresponding to the SHs resulting from clustering at the 97% and 99% threshold levels. The third set of files is the result of a dynamic use of clustering thresholds, such that some SHs are delimited at the 97% level, some at the 97.5% level, some at the 98% level, and so on; these choices were made manually by experts of those particular lineages of fungi. The syntax is the same throughout the three sets of files. Includes singletons set as RefS (in dynamic files).
DOI: 10.23729/11673bf8-3094-4a11-9b8c-604bef025f76
title: Thermal disorder prevents the suppression of ultra-fast photochemistry in the strong light-matter coupling regime

description: This dataset contains experimental and simulation data for the article "Thermal disorder prevents the suppression of ultra-fast photochemistry in the strong light-matter coupling regime".
DOI: 10.34740/kaggle/dsv/3364939
title: Alzheimer MRI Preprocessed Dataset
DOI: 10.5066/f7gh9h6f
title: Round goby eDNA survey, evaluation, and laboratory data in Lakes Michigan and Huron 2016-2017

description: Data included are from a series of field sample collections from Lakes Michigan and Huron, and laboratory mesocosms targeting the round goby fish (Neogobius melanostomus). The round goby is a benthic fish that has heavily invaded four of the five Laurentian Great Lakes. Because it inhabits a variety of substrates, including coastal breakwaters, traditional methods (e.g., trawling, trapping) are inadequate to quantify overall population size. Environmental DNA (eDNA) may be a viable option for improving detection and quantification of the species. Field data include number of round goby caught and associated ambient conditions of the aquatic matrix (temperature, pH, turbidity, conductivity, dissolved oxygen). Mesocosm data include information about mesocosm test (DNA shedding, decay), information about the individual fish used (length, weight), ambient conditions of the aqueous matrix (pH, turbidity). Data from laboratory testing of both field and mesocosm water include results from quantitative polymerase chain reaction (qPCR) method for detection of round goby-specific DNA (DNA quality, quantity). Data are being used to correlate round goby individuals with eDNA present in the water and to calculate rates of DNA shedding by the round goby and rates of DNA decay
DOI: 10.5281/zenodo.10781807
title: A fully hybrid integrated erbium-based laser

description: Data and scripts used to produce the figures in Y. Liu et al., "A fully hybrid integrated erbium-based laser" (doi:0.1038/s41566-024-01454-7)

Codes have been tested with Matlab 2020b version.
DOI: 10.5281/zenodo.10795940
title: Generative convective parametrization of a dry atmospheric boundary layer

description: The repository contains simulation snapshots of a dry convective boundary layer (CBL). The snapshots comprise horizontal snapshots of vertical velocity (w) and buoyancy (b) field at three heights, namely z/h(t) = 0.2, 0.5, 1.0. Further, the Python scripts for the Generative Adversarial Network (GAN) are also provided, as well as the DNS renormalization procedure.