cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17126924.v1
title: Elephant microbiome code_final_Keady et al 2021

description: Analysis of elephant microbiome structure<br>
DOI: 10.5281/zenodo.5760175
title: New crater clusters on Mars

description: Crater cluster data set used in the submitted paper
DOI: 10.6084/m9.figshare.17126999
title: IMLS Pilot Study_Project code and files

description: R code, taxonomy table, meta data, DNA sequences, tree, feature table
DOI: 10.6084/m9.figshare.17126999.v1
title: IMLS Pilot Study_Project code and files

description: R code, taxonomy table, meta data, DNA sequences, tree, feature table
DOI: 10.5281/zenodo.5760191
title: Dataset for training and testing the SCFNN model

description: train_test_data.tar.gz contains the DFT calculation results of water cubic box under various strength of external electric field. This dataset is used to train and test the SCFNN model. HirshfeldMullikenCharges.tar.gz contains the DFT calculation results of Hirshfeld and Mulliken charges for the same water box. This dataset is used to train the 4G-HDNN model.
DOI: 10.5281/zenodo.5521327
title: Dataset for training and testing the SCFNN model

description: train_test_data.tar.gz contains the DFT calculation results of water cubic box under various strength of external electric field. This dataset is used to train and test the SCFNN model. HirshfeldMullikenCharges.tar.gz contains the DFT calculation results of Hirshfeld and Mulliken charges for the same water box. This dataset is used to train the 4G-HDNN model.
DOI: 10.3886/e119467v1-103360
title: Data and Code for: The Times They Are A-Changing: Experimenting With Dynamic Adverse Selection

description: This is data and analysis code for our paper at AEJ:Microeconomics. In the paper we examine a common-value dynamic matching environment where adverse selection accrues slowly over time. Theoretical best responses are therefore time varying, and where the prior experimental literature suggests that sequential environments might lead to greater understanding of adverse selection in this dynamic setting. However, while a sophisticated minority in our experiment do condition on time and are close to a best response, the majority use a stationary response, even after extended experience. In an environment with persistent uncertainty, our results indicate that sequentiality is insufficient for the large majority of participants to recognize the effects of adverse selection.<br>
description: Study invitations were sent randomly to students that had signed-up to participate in experiments.<br>
description: <br>Undergraduate students at the University of Pittsburgh<br>.
DOI: 10.6084/m9.figshare.17127401
title: Radiomics Assessment of the Tumor Immune Microenvironment to Predict Outcomes in Breast Cancer

description: Background: The immune microenvironment of tumors provides information on prognosis and prediction. A prior validation of the immunoscore for breast cancer (ISBC) was made on the basis of a systematic assessment of immune landscapes extrapolated from a large number of neoplastic transcripts. Our goal was to develop a non-invasive radiomics-based ISBC predictive factor. Methods: Immunocell fractions of 22 different categories were evaluated using CIBERSORT on the basis of a large, open breast cancer cohort derived from comprehensive information on gene expression. The ISBC was constructed using the LASSO Cox regression model derived from the Immunocell type scores, with 479 quantified features in the intratumoral and peritumoral regions as observed from DCEMRI. A radiomics signature [radiomics ImmunoScore (RIS)] was developed for the prediction of ISBC using a random forest machine-learning algorithm, and we further evaluated its relationship with prognosis. Results: An ISBC consisting of seven different immune cells was established through the use of a LASSO model. Multivariate analyses showed that the ISBC was an independent risk factor in prognosis (HR=2.42, with a 95% CI of 1.49–3.93; P&lt;0.01). A radiomic signature of 21 features of the ISBC was then exploited and validated (the areas under the curve [AUC] were 0.899 and 0.815). We uncovered statistical associations between the RIS signature with progression-free and overall survival rates (both P&lt;0.05). Conclusions: The RIS is a valuable instrument with which to assess the immunoscore, and offers important implications for the prognosis of breast cancer.
DOI: 10.6084/m9.figshare.17127401.v1
title: Radiomics Assessment of the Tumor Immune Microenvironment to Predict Outcomes in Breast Cancer

description: Background: The immune microenvironment of tumors provides information on prognosis and prediction. A prior validation of the immunoscore for breast cancer (ISBC) was made on the basis of a systematic assessment of immune landscapes extrapolated from a large number of neoplastic transcripts. Our goal was to develop a non-invasive radiomics-based ISBC predictive factor. Methods: Immunocell fractions of 22 different categories were evaluated using CIBERSORT on the basis of a large, open breast cancer cohort derived from comprehensive information on gene expression. The ISBC was constructed using the LASSO Cox regression model derived from the Immunocell type scores, with 479 quantified features in the intratumoral and peritumoral regions as observed from DCEMRI. A radiomics signature [radiomics ImmunoScore (RIS)] was developed for the prediction of ISBC using a random forest machine-learning algorithm, and we further evaluated its relationship with prognosis. Results: An ISBC consisting of seven different immune cells was established through the use of a LASSO model. Multivariate analyses showed that the ISBC was an independent risk factor in prognosis (HR=2.42, with a 95% CI of 1.49–3.93; P&lt;0.01). A radiomic signature of 21 features of the ISBC was then exploited and validated (the areas under the curve [AUC] were 0.899 and 0.815). We uncovered statistical associations between the RIS signature with progression-free and overall survival rates (both P&lt;0.05). Conclusions: The RIS is a valuable instrument with which to assess the immunoscore, and offers important implications for the prognosis of breast cancer.
DOI: 10.7931/ce1j-dm16
title: Stakeholder feedback on farm biodiversity tool
DOI: 10.3886/e120705v1-103380
title: Data and Code for: Emerging Markets at Risk

description: Policymakers would like to predict and mitigate the risks associated with the post-global financial crisis rise in corporate leverage in emerging markets. However, long-standing advanced-economy bankruptcy models fail to capture the idiosyncrasies that impact the solvency of emerging market firms. We study how a machine learning technique for variable selection, LASSO, can improve corporate distress risk models in emerging markets. Exploring the trade-off between model fit and predictive power, we find that larger models forecast distress with more accuracy during periods of economic stress (when global factors gain relevance), while more parsimonious specifications outperform during normal times<br>
DOI: 10.5281/zenodo.5760209
title: Data assimilation products by using multiple climate model simulations and different combinations of proxies

description: This dataset of the climate reconstruction by data assimilation using isotope ratios provides annual surface air temperature, precipitation amount, and other climate variables during 850–2000. Two isotopes-incorporated atmospheric general circulation models and 129 isotopic proxy data (65 corals, 43 ice cores, and 21 tree-ring cellulose) were used in this study. There are nine experiments using three type of simulations and three combinations of proxies. The associated publication: Shoji, S., Okazaki, A., & Yoshimura, K. (2020). Impact of proxies and prior estimates on data assimilation using isotope ratios for the climate reconstruction of the last millennium. (submitted to Earth and Space Science) [Data structure]<br> X(lon) x Y(lat) x Z(2) x Variables(8) x Year(1151)<br> Z(1): analyses<br> Z(2): priors
DOI: 10.5281/zenodo.4320463
title: Data assimilation products by using multiple climate model simulations and different combinations of proxies

description: This dataset of the climate reconstruction by data assimilation using isotope ratios provides annual surface air temperature, precipitation amount, and other climate variables during 850–2000. Two isotopes-incorporated atmospheric general circulation models and 129 isotopic proxy data (65 corals, 43 ice cores, and 21 tree-ring cellulose) were used in this study. There are nine experiments using three type of simulations and three combinations of proxies. The associated publication: Shoji, S., Okazaki, A., & Yoshimura, K. (2020). Impact of proxies and prior estimates on data assimilation using isotope ratios for the climate reconstruction of the last millennium. (submitted to Earth and Space Science) [Data structure]<br> X(lon) x Y(lat) x Z(2) x Variables(8) x Year(1151)<br> Z(1): analyses<br> Z(2): priors
DOI: 10.5281/zenodo.5760212
title: Properties of different biomass materials and their higher heating values (% Dry basis)

description: Properties of biomass materials and their higher heating values (% Dry basis) from literature. Aggregated for BSE 619: Mathematical Modeling for Engineers course for Fall 2021 semester at the University of Tennessee, Knoxville.
DOI: 10.5281/zenodo.5760211
title: Properties of different biomass materials and their higher heating values (% Dry basis)

description: Properties of biomass materials and their higher heating values (% Dry basis) from literature. Aggregated for BSE 619: Mathematical Modeling for Engineers course for Fall 2021 semester at the University of Tennessee, Knoxville.
DOI: 10.5281/zenodo.5760222
title: Proximate analysis parameters for residual biomass samples from Southeast USA.

description: Proximate analysis parameters for residual biomass samples for 142 samples collected from different logging mills in the Southeast USA for a USDA-AFRI research study (Grant.gov grant#: 12688125).
DOI: 10.5281/zenodo.5760221
title: Proximate analysis parameters for residual biomass samples from Southeast USA.

description: Proximate analysis parameters for residual biomass samples for 142 samples collected from different logging mills in the Southeast USA for a USDA-AFRI research study (Grant.gov grant#: 12688125).
DOI: 10.25345/c5cz8m
title: MassIVE MSV000088518 - Glycomic analysis reveals a conserved response to bacterial sepsis induced by different bacterial pathogens
title: Sepsis is an extreme inflammatory response to infection that occurs in the bloodstream and causes damage throughout the body. Glycosylation is known to play a role in immunity and inflammation, but the role of glycans in sepsis is not well defined. Herein, we profiled the serum glycomes of experimental mouse sepsis models to identify changes induced by 4 different clinical bacterial pathogens (Gram-positive: Streptococcus pneumoniae, Staphylococcus aureus, Gram-negative: Escherichia coli and Salmonella Typhimurium) using our lectin microarray technology. We observed global shifts in the blood sera glycome that were conserved across all four species, regardless of whether they were Gram positive or negative. Bisecting GlcNAc was decreased upon sepsis and a strong increase in core 1/3 O-glycans was observed. Lectin blot analysis revealed a high molecular weight protein induced in sepsis by all four bacteria as the major cause of the core 1/3 O-glycan shift. Mass spectrometry analysis of this band identified the proteins inter-alpha-trypsin inhibitor heavy chains (ITIHs) and fibronectin, both of which are associated with human sepsis. Shifts in the glycosylation of these proteins were observed. Overall, our work points towards a common mechanism for bacterially-induced sepsis, marked by conserved changes in the glycome.
DOI: 10.6084/m9.figshare.17127650
title: rRNA probes

description: 160 DNA probes for rRNA depletion
DOI: 10.6084/m9.figshare.12851087
title: Risk of major adverse cardiovascular events of <i>CYP2C19</i> loss-of-function genotype guided prasugrel/ticagrelor vs clopidogrel therapy for acute coronary syndrome patients undergoing percutaneous coronary intervention: a meta-analysis

description: The most effective antiplatelet treatments for acute coronary syndrome (ACS) patients carrying <i>CYP2C19</i> loss-of-function (LoF) alleles undergoing percutaneous coronary intervention (PCI) is still debating and conflicting. It was aimed to compare the efficacy and safety endpoints for these patients treated with alternative P2Y12 receptor blockers (e.g. prasugrel or ticagrelor) against clopidogrel. Literature was searched in PubMed, Cochrane library, Synapse and 1000 Genomes databases following PRISMA guidelines for identifying relevant studies. Aggregated risk was estimated by RevMan software using either fixed/random-effects models where <i>P</i> values&lt;0.05 (two-sided) were considered statistically significant. Nine studies comprising 16,132 ACS patients undergoing PCI were included in this analysis in which 2,746 and 2,640 patients were in the <i>CYP2C19</i> LoF clopidogrel and alternatives treatment group, respectively. It was demonstrated that patients treated with prasugrel or ticagrelor significantly reduced the risk of MACEs (RR 0.58; 95% CI 0.45–0.76; <i>P</i>&lt;0.0001) as compared to patients with clopidogrel where both groups carrying <i>CYP2C19</i> LoF alleles. Subgroup analysis showed that prasugrel or ticagrelor significantly reduced the risk of cardiovascular death (RR 0.44; 95% CI: 0.25–0.74; <i>P</i>=0.002) and MI (RR 0.60; 95% CI: 0.44–0.81; <i>P</i>=0.0008) while other clinical outcomes were not found statistically significant between these two groups; stroke (RR 0.77; 95% CI: 0.43–1.38; <i>P</i> =0.39), stent thrombosis (RR 0.67; 95% CI: 0.38–1.18; <i>P</i> =0.17), unstable angina (RR 0.55; 95% CI: 0.13–2.33; <i>P</i> =0.42), revascularisation (RR 0.79; 95% CI: 0.28–2.24; <i>P</i>=0.66). Bleeding events were not found significantly different between these groups (RR 1.06; 95% CI: 0.88–1.28; <i>P</i>=0.55). Considering efficacy and safety, alternative antiplatelets (e.g. prasugrel or ticagrelor) may be regarded as better treatment option as compared to clopidogrel for ACS patients undergoing PCI.
DOI: 10.6084/m9.figshare.12851087.v1
title: Risk of major adverse cardiovascular events of <i>CYP2C19</i> loss-of-function genotype guided prasugrel/ticagrelor vs clopidogrel therapy for acute coronary syndrome patients undergoing percutaneous coronary intervention: a meta-analysis

description: The most effective antiplatelet treatments for acute coronary syndrome (ACS) patients carrying <i>CYP2C19</i> loss-of-function (LoF) alleles undergoing percutaneous coronary intervention (PCI) is still debating and conflicting. It was aimed to compare the efficacy and safety endpoints for these patients treated with alternative P2Y12 receptor blockers (e.g. prasugrel or ticagrelor) against clopidogrel. Literature was searched in PubMed, Cochrane library, Synapse and 1000 Genomes databases following PRISMA guidelines for identifying relevant studies. Aggregated risk was estimated by RevMan software using either fixed/random-effects models where <i>P</i> values&lt;0.05 (two-sided) were considered statistically significant. Nine studies comprising 16,132 ACS patients undergoing PCI were included in this analysis in which 2,746 and 2,640 patients were in the <i>CYP2C19</i> LoF clopidogrel and alternatives treatment group, respectively. It was demonstrated that patients treated with prasugrel or ticagrelor significantly reduced the risk of MACEs (RR 0.58; 95% CI 0.45–0.76; <i>P</i>&lt;0.0001) as compared to patients with clopidogrel where both groups carrying <i>CYP2C19</i> LoF alleles. Subgroup analysis showed that prasugrel or ticagrelor significantly reduced the risk of cardiovascular death (RR 0.44; 95% CI: 0.25–0.74; <i>P</i>=0.002) and MI (RR 0.60; 95% CI: 0.44–0.81; <i>P</i>=0.0008) while other clinical outcomes were not found statistically significant between these two groups; stroke (RR 0.77; 95% CI: 0.43–1.38; <i>P</i> =0.39), stent thrombosis (RR 0.67; 95% CI: 0.38–1.18; <i>P</i> =0.17), unstable angina (RR 0.55; 95% CI: 0.13–2.33; <i>P</i> =0.42), revascularisation (RR 0.79; 95% CI: 0.28–2.24; <i>P</i>=0.66). Bleeding events were not found significantly different between these groups (RR 1.06; 95% CI: 0.88–1.28; <i>P</i>=0.55). Considering efficacy and safety, alternative antiplatelets (e.g. prasugrel or ticagrelor) may be regarded as better treatment option as compared to clopidogrel for ACS patients undergoing PCI.
DOI: 10.6084/m9.figshare.12851084.v1
title: Relation between mutations in the 5′ UTR of ANKRD26 gene and inherited thrombocytopenia with predisposition to myeloid malignancies. An Egyptian study

description: Inherited thrombocytopenias are a heterogeneous group of diseases characterized by a reduced number of platelets and a bleeding tendency that ranges from very mild to life threatening especially in surgery. Mutations in the 5′ untranslated region (UTR) of Ankirin repeat domain 26 (ANKRD26) are responsible for autosomal-dominant form of thrombocytopenia, that is known as ANKRD26-related thrombocytopenia (ANKRD26 RT), characterized by a moderate thrombocytopenia with mild propensity to bleeding and predisposition to hematological malignancies including AML and MDS. We included 90 unrelated patients with inherited thrombocytopenia. In addition, we investigated 45 patients with ITP. Peripheral blood and bone marrow samples were collected and examined and molecular detection of mutations in the 5︡ UTR of ANKRD26 gene was performed for all the patients. Also, screening of the mutation and development of myeloid malignancies in the extended series of the affected subjects was done. ANKRD26 mutations were identified in 10% of the patients with inherited thrombocytopenia. The most common types were c.128 G &gt; A and c.127A&gt;T, while no mutations were found in the ITP group. In those affected, the median number of platelets was 69 x10<sup>9</sup>/L (43–106) with normal MPV in most of the patients (9.4–11.6). There was a statistically significant increase in the unexpected high frequency of myeloid malignancies in the extended series of the mutated subjects compared with the ITP group-extended series (<i>P</i>
DOI: 10.6084/m9.figshare.14701665
title: Statins potentiate the antibacterial effect of platelets on <i>Staphylococcus aureus</i>

description: Platelets have largely demonstrated their implication in anti-infectious immunity. This effect is ensured by the secreted molecules stored mostly in platelet alpha granules. Previous studies have reported that <i>Staphylococcus aureus</i> showed sensitivity to this antibacterial effect of platelets. Statins, for their part, have shown a modulating effect on platelet activation. Furthermore, several studies have reported a protective effect of statins in staphylococcal endocarditis. The aim of this study was to investigate the influence of statins on the antibacterial effect of washed platelets. Blood samples were collected from healthy donors (n = 35). PRP was prepared according to the ISTH recommendation. Bacteria were incubated for four hours with untreated-washed platelets, or rather treated by statins and/or GPIIbIIIa antagonists. In order to evaluate the antibacterial effect, the platelet-bacteria mix was spread on the blood agar to count the number of colonies after 18 hours of incubation. Measurement of CD 41 and CD62P expression by flow cytometry was performed to evaluate the effect of statin on bacterial-induced platelet activation. Statins have shown a potentiation of the antibacterial effect of washed platelets (<i>p</i> p vs untreated washed platelets condition). This effect of statins was dose-dependent and was more significant at 20 μM. The addition of Fluvastatin to platelet-bacterial mix significantly increased the expression of platelet CD41 and CD62P (<i>p</i> p Staphylococcus aureus infective endocarditis. Further studies are therefore required to explain this effect at the molecular level and to assess its impact <i>in vivo</i>.
DOI: 10.6084/m9.figshare.14701665.v1
title: Statins potentiate the antibacterial effect of platelets on <i>Staphylococcus aureus</i>

description: Platelets have largely demonstrated their implication in anti-infectious immunity. This effect is ensured by the secreted molecules stored mostly in platelet alpha granules. Previous studies have reported that <i>Staphylococcus aureus</i> showed sensitivity to this antibacterial effect of platelets. Statins, for their part, have shown a modulating effect on platelet activation. Furthermore, several studies have reported a protective effect of statins in staphylococcal endocarditis. The aim of this study was to investigate the influence of statins on the antibacterial effect of washed platelets. Blood samples were collected from healthy donors (n = 35). PRP was prepared according to the ISTH recommendation. Bacteria were incubated for four hours with untreated-washed platelets, or rather treated by statins and/or GPIIbIIIa antagonists. In order to evaluate the antibacterial effect, the platelet-bacteria mix was spread on the blood agar to count the number of colonies after 18 hours of incubation. Measurement of CD 41 and CD62P expression by flow cytometry was performed to evaluate the effect of statin on bacterial-induced platelet activation. Statins have shown a potentiation of the antibacterial effect of washed platelets (<i>p</i> p vs untreated washed platelets condition). This effect of statins was dose-dependent and was more significant at 20 μM. The addition of Fluvastatin to platelet-bacterial mix significantly increased the expression of platelet CD41 and CD62P (<i>p</i> p Staphylococcus aureus infective endocarditis. Further studies are therefore required to explain this effect at the molecular level and to assess its impact <i>in vivo</i>.
DOI: 10.6084/m9.figshare.12851084
title: Relation between mutations in the 5′ UTR of ANKRD26 gene and inherited thrombocytopenia with predisposition to myeloid malignancies. An Egyptian study

description: Inherited thrombocytopenias are a heterogeneous group of diseases characterized by a reduced number of platelets and a bleeding tendency that ranges from very mild to life threatening especially in surgery. Mutations in the 5′ untranslated region (UTR) of Ankirin repeat domain 26 (ANKRD26) are responsible for autosomal-dominant form of thrombocytopenia, that is known as ANKRD26-related thrombocytopenia (ANKRD26 RT), characterized by a moderate thrombocytopenia with mild propensity to bleeding and predisposition to hematological malignancies including AML and MDS. We included 90 unrelated patients with inherited thrombocytopenia. In addition, we investigated 45 patients with ITP. Peripheral blood and bone marrow samples were collected and examined and molecular detection of mutations in the 5︡ UTR of ANKRD26 gene was performed for all the patients. Also, screening of the mutation and development of myeloid malignancies in the extended series of the affected subjects was done. ANKRD26 mutations were identified in 10% of the patients with inherited thrombocytopenia. The most common types were c.128 G &gt; A and c.127A&gt;T, while no mutations were found in the ITP group. In those affected, the median number of platelets was 69 x10<sup>9</sup>/L (43–106) with normal MPV in most of the patients (9.4–11.6). There was a statistically significant increase in the unexpected high frequency of myeloid malignancies in the extended series of the mutated subjects compared with the ITP group-extended series (<i>P</i>