cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9902447
title: Metadata record for: The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system

description: This dataset contains key characteristics about the data described in the Data Descriptor The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format3. machine readable metadata file in ISA-Tab format (zipped folder)<br><br>Versioning Note:A revised version was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.
DOI: 10.6084/m9.figshare.9902567.v1
title: Breakthrough Therapy Designations Press Release and News Items

description: Data extracted from press releases and news articles announcing breakthrough therapy designations. Contains a nearly-complete list of Breakthrough Therapy Designations as of July 31, 2018.
DOI: 10.6084/m9.figshare.9902447.v1
title: Metadata record for: The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system

description: This dataset contains key characteristics about the data described in the Data Descriptor The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format3. machine readable metadata file in ISA-Tab format (zipped folder)<br><br>Versioning Note:A revised version was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.
DOI: 10.6084/m9.figshare.9902378
title: Data associated with manuscript

description: Files 1-6 are used for Price equation inputs. Each matrix is a bee group year combination. File 7 contains the data output from the Price equation when baseline selection was restricted to a single site for each matrix. These data are paired with parameters used to evaluate patterns in the Price equation terms (manuscript figure 3a,c). In File 8 we remove the baseline restriction and evaluate all pairwise comparisons within files 1-6 (manuscript figure 3b). These data were used as support for our focus on the nu' term. File 9 contains data from which we evaluated patterns of wild bee and honey bee abundance and plant diversity (Table S6). In file 10 we provide the data used to evaluate the benefits of plant richness for bee visitation (manuscript figures 2,S1,S2).
DOI: 10.6084/m9.figshare.9902369
title: Defect-induced electronic states amplify the cellular toxicity of ZnO nanoparticles

description: Zinc oxide nanoparticles (ZnO NPs) are used in numerous applications, including sunscreens, cosmetics, textiles, and electrical devices. Increased consumer and occupational exposure to ZnO NPs potentially poses a risk for toxicity. While many studies have examined the toxicity of ZnO NPs, little is known regarding the toxicological impact of inherent defects arising from batch-to-batch variations. It was hypothesized that the presence of varying chemical defects in ZnO NPs will contribute to cellular toxicity in rat aortic endothelial cells (RAECs). Pristine and defected ZnO NPs (oxidized, reduced, and annealed) were prepared and assessed three major cellular outcomes; cytotoxicity/apoptosis, reactive oxygen species production and oxidative stress, and endoplasmic reticulum (ER) stress. ZnO NPs chemical defects were confirmed by X-ray photoelectron spectroscopy and photoluminescence. Increased toxicity was observed in defected ZnO NPs compared to the pristine NPs as measured by cell viability, ER stress, and glutathione redox potential. It was determined that ZnO NPs induced ER stress through the PERK pathway. Taken together, these results demonstrate a previously unrecognized contribution of chemical defects to the toxicity of ZnO NPs, which should be considered in the risk assessment of engineered nanomaterials.
DOI: 10.6084/m9.figshare.9902369.v1
title: Defect-induced electronic states amplify the cellular toxicity of ZnO nanoparticles

description: Zinc oxide nanoparticles (ZnO NPs) are used in numerous applications, including sunscreens, cosmetics, textiles, and electrical devices. Increased consumer and occupational exposure to ZnO NPs potentially poses a risk for toxicity. While many studies have examined the toxicity of ZnO NPs, little is known regarding the toxicological impact of inherent defects arising from batch-to-batch variations. It was hypothesized that the presence of varying chemical defects in ZnO NPs will contribute to cellular toxicity in rat aortic endothelial cells (RAECs). Pristine and defected ZnO NPs (oxidized, reduced, and annealed) were prepared and assessed three major cellular outcomes; cytotoxicity/apoptosis, reactive oxygen species production and oxidative stress, and endoplasmic reticulum (ER) stress. ZnO NPs chemical defects were confirmed by X-ray photoelectron spectroscopy and photoluminescence. Increased toxicity was observed in defected ZnO NPs compared to the pristine NPs as measured by cell viability, ER stress, and glutathione redox potential. It was determined that ZnO NPs induced ER stress through the PERK pathway. Taken together, these results demonstrate a previously unrecognized contribution of chemical defects to the toxicity of ZnO NPs, which should be considered in the risk assessment of engineered nanomaterials.
DOI: 10.6084/m9.figshare.9902180
title: Data set for Gurukartick study 2016

description: This excel file has anonymized data and codebook
DOI: 10.6084/m9.figshare.9902186
title: Sediment Deficit for Coastal Louisiana 2006 to 2016

description: These data come from the interpolation of Coastwide Reference Monitoring System accretion rates, bulk density, and organic fraction for marsh sediments along the Louisiana coast. These data show the volume and mass deficit from 2006 to 2016 for the coast and associated hydrologic basins.<br>
DOI: 10.6084/m9.figshare.9902378.v1
title: Data associated with manuscript

description: Data associated with manuscript by Bloom et al. titled "A novel application of the Price equation reveals that landscape diversity promotes the response of bees to regionally rare plant species."
DOI: 10.6084/m9.figshare.9902168
title: Supplementary Material for: The Interstitial Lung Disease-Gender-Age-Physiology Index Can Predict the Prognosis in Surgically Resected Patients with Interstitial Lung Disease and Concomitant Lung Cancer

description: <b><i>Background:</i></b> The interstitial lung disease-gender-age-physiology (ILD-GAP) index and staging system have been reported as a clinical prognostic factor for ILD, including all ILD subtypes. <b><i>Objectives:</i></b> The purpose of this study was to clarify the association of various prognostic indices, including the ILD-GAP index, with the prognosis, the incidence of acute exacerbations of ILD (ILD-AE), and the use of long-term oxygen therapy (LTOT) after surgery in surgically resected patients with ILD and concomitant lung cancer, to provide additional information when considering whether it is safe to perform surgery. <b><i>Methods:</i></b> The medical records of patients with ILD and concomitant lung cancer who had undergone surgery at Shinshu University Hospital between August 2001 and September 2016 were retrospectively analyzed. <b><i>Results:</i></b> There were significant differences in survival between the ILD-GAP index: 0–1 and ≥4 groups (<i>p</i> = 0.0001) and between the ILD-GAP index: 2–3 and ≥4 groups (<i>p</i> = 0.0236). A higher ILD-GAP index was independently associated with the risk of death (hazard ratio [HR] 1.32030; <i>p</i> = 0.0059). A higher body mass index (BMI) and a higher serum C-reactive protein (CRP) level were independently associated with the incidence of ILD-AE (HR 1.28336; <i>p</i> = 0.0206 and HR 26.3943; <i>p</i> = 0.0165, respectively). A higher severity of ILD on chest high-resolution computed tomography (HRCT) was independently associated with the use of LTOT (HR 2.78670; <i>p</i> = 0.0313). <b><i>Conclusions:</i></b> The ILD-GAP index can predict the prognosis in surgically resected patients with ILD and concomitant lung cancer. The BMI and serum CRP levels were independent determinants that predicted the incidence of ILD-AE. The severity of ILD on chest HRCT was an independent determinant that predicted the use of LTOT.
DOI: 10.6084/m9.figshare.9902159
title: Supplementary Material for: High Diagnostic Accuracy of Transbronchial Cryobiopsy in Fibrotic Interstitial Lung Diseases Compared to Final Explant Diagnosis

description: <b><i>Background:</i></b> A diagnostic lung biopsy may be required in some cases of fibrotic interstitial lung diseases (ILD). Transbronchial cryobiopsy has been suggested as a possible alternative to surgical lung biopsy. However, previous estimates of its diagnostic yield were not validated compared to the definitive diagnosis in explanted lungs. <b><i>Objectives:</i></b> We aimed to assess the diagnostic accuracy of cryobiopsy in fibrotic ILD patients who subsequently had lung transplantation. <b><i>Methods:</i></b> All 197 patients who underwent lung transplantation at our Center due to fibrotic ILD from January 2010 to May 2018, were screened for the presence of a pre-transplant cryobiopsy. Fourteen patients who underwent cryobiopsy before transplantation were identified. Two expert lung pathologists blinded<i></i>to the explant diagnoses, independently examined these cryobiopsy specimens to decide if they match guideline criteria for usual interstitial pneumonia (UIP) pattern or an alternative diagnosis. The primary measure was the diagnostic accuracy of cryobiopsy to detect or refute a UIP pattern, as compared to the final explant diagnosis. <b><i>Results:</i></b> Median time between cryobiopsy and transplantation was 1.4 years. All 14 cryobiopsy samples contained adequate alveolar tissue. The explant diagnosis of 13/14 patients was UIP. The two pathologists correctly diagnosed or refuted UIP in the cryobiopsy specimen in 12/14 cases (85.7%) and 11/14 cases (78.6%), respectively. The level of diagnostic agreement between pathologists was good (kappa 0.59, <i>p</i> = 0.016). <b><i>Conclusions:</i></b> Compared to the final explant diagnosis, transbronchial cryobiopsy had high diagnostic accuracy and good inter-observer agreement for UIP pattern. These findings support a potential diagnostic role for cryobiopsy in experienced centers.
DOI: 10.6084/m9.figshare.9902186.v1
title: Sediment Deficit for Coastal Louisiana 2006 to 2016

description: These data come from the interpolation of Coastwide Reference Monitoring System accretion rates, bulk density, and organic fraction for marsh sediments along the Louisiana coast. These data show the volume and mass deficit from 2006 to 2016 for the coast and associated hydrologic basins.<br>
DOI: 10.6084/m9.figshare.9902180.v2
title: Data set for Gurukartick study 2016

description: This excel file has anonymized data and codebook
DOI: 10.6084/m9.figshare.9902150
title: Supplementary Material for: Clinical Characteristics and Outcomes of Community-Acquired versus Hospital-Acquired Acute Kidney Injury: A Meta-Analysis

description: <b><i>Background:</i></b> The different clinical characteristics of community-acquired acute kidney injury (CA-AKI) versus hospital-acquired AKI (HA-AKI) have remained inconclusive, and thus, a meta-analysis was conducted to summarize and quantify the clinical significance distinguishing the 2 types of AKI. <b><i>Methods:</i></b> We identified observational studies reporting the clinical characteristics and prognosis of HA-AKI and CA-AKI. ORs and mean differences (MDs) were extracted for each outcome and the results aggregated. The primary outcome was defined as the mortality rate; renal recovery, oliguria incidence, dialysis, intensive care unit (ICU) requirement, and length of hospital stay were secondary outcomes. <b><i>Results:</i></b> Fifteen eligible studies involving 46,157 patients (22,791 CA-AKI patients and 23,366 HA-AKI patients) were included. Mortality was significantly lower in CA-AKI than in HA-AKI patients, with an OR of 0.43 (95% CI 0.35–0.53). The incidence of oliguria and need for ICU were also lower in CA-AKI patients (OR 0.58, 95% CI 0.38–0.88; OR 0.24, 95% CI 0.14–0.40, respectively). CA-AKI patients had a shorter hospital stay (MD –9.42, 95% CI –13.73 to –5.12). The renal recovery rate and dialysis need between CA- and HA-AKI were similar (OR 1.27, 95% CI 0.53–3.02; OR 1.05, 95% CI 0.82–1.34, respectively). <b><i>Conclusions:</i></b> CA-AKI showed better clinical manifestations with a lower incidence of oliguria, reduced risk of ICU treatment, and shorter hospital stay. Mortality associated with CA-AKI was lower compared with HA-AKI, indicating a better prognosis. The rate of renal recovery and need for dialysis showed no significant difference between the 2 groups.
DOI: 10.6084/m9.figshare.9902150.v1
title: Supplementary Material for: Clinical Characteristics and Outcomes of Community-Acquired versus Hospital-Acquired Acute Kidney Injury: A Meta-Analysis

description: <b><i>Background:</i></b> The different clinical characteristics of community-acquired acute kidney injury (CA-AKI) versus hospital-acquired AKI (HA-AKI) have remained inconclusive, and thus, a meta-analysis was conducted to summarize and quantify the clinical significance distinguishing the 2 types of AKI. <b><i>Methods:</i></b> We identified observational studies reporting the clinical characteristics and prognosis of HA-AKI and CA-AKI. ORs and mean differences (MDs) were extracted for each outcome and the results aggregated. The primary outcome was defined as the mortality rate; renal recovery, oliguria incidence, dialysis, intensive care unit (ICU) requirement, and length of hospital stay were secondary outcomes. <b><i>Results:</i></b> Fifteen eligible studies involving 46,157 patients (22,791 CA-AKI patients and 23,366 HA-AKI patients) were included. Mortality was significantly lower in CA-AKI than in HA-AKI patients, with an OR of 0.43 (95% CI 0.35–0.53). The incidence of oliguria and need for ICU were also lower in CA-AKI patients (OR 0.58, 95% CI 0.38–0.88; OR 0.24, 95% CI 0.14–0.40, respectively). CA-AKI patients had a shorter hospital stay (MD –9.42, 95% CI –13.73 to –5.12). The renal recovery rate and dialysis need between CA- and HA-AKI were similar (OR 1.27, 95% CI 0.53–3.02; OR 1.05, 95% CI 0.82–1.34, respectively). <b><i>Conclusions:</i></b> CA-AKI showed better clinical manifestations with a lower incidence of oliguria, reduced risk of ICU treatment, and shorter hospital stay. Mortality associated with CA-AKI was lower compared with HA-AKI, indicating a better prognosis. The rate of renal recovery and need for dialysis showed no significant difference between the 2 groups.
DOI: 10.6084/m9.figshare.9902180.v1
title: Data set for Gurukartick study 2016

description: This excel file has anonymized data and codebook
DOI: 10.6084/m9.figshare.9902132
title: Supplementary Material for: Classification and Prognostic Stratification of Bronchopulmonary Neuroendocrine Neoplasms

description: The accuracy and reproducibility of the World Health Organization (WHO) 2015 classification of bronchopulmonary neuroendocrine neoplasms (BP-NENs) is disputed. The aim of this study is to classify and grade BP-NENs using the WHO 2019 classification of digestive system NENs (DiS-NEN-WHO 2019), and to analyze its accuracy and prognostic impact. Two BP-NEN cohorts from Japan and Germany, 393 tumors (88% surgically resected), were reviewed and the clinicopathological data of the resected tumors (<i>n</i> = 301) correlated to patients’ disease-free survival (DFS). The DiS-NEN-WHO 2019 stratified the 350 tumors into 91 (26%) neuroendocrine tumors (NET) G1, 52 (15%) NET G2, 15 (4%) NET G3, and 192 (55%) neuroendocrine carcinomas (NEC). NECs, but not NETs, were immunohistochemically characterized by abnormal p53 (100%) and retinoblastoma 1 (83%) expression. The Ki67 index, which was on average 4 times higher than mitotic count (<i>p</i> &lt; 0.0001), was prognostically more accurate than the mitotic count. NET G3 patients had a worse outcome than NET G1 (<i>p</i> &lt; 0.01) and NET G2 patients (<i>p</i> = 0.02), respectively. No prognostic difference was detected between NET G3 and NEC patients after 5 year DFS. It is concluded that stratifying BP-NEN patients according to the DiS-NEN-WHO 2019 classification results in 3 prognostically well-defined NET groups, if grading is solely based on Ki67 index. Mitotic count alone may underestimate malignant potential of NETs.
DOI: 10.6084/m9.figshare.9902117
title: Supplementary Material for: Assessment of Quality of Life in Postmenopausal Women with Early Breast Cancer Participating in the PACT Trial: The Impact of Additional Patient Information Material Packages and Patient Compliance

description: <b><i>Background:</i></b> Breast cancer patients’ self-understanding of their disease can impact their quality of life (QoL); the relationship between compliance and QoL is poorly understood. <b><i>Patients and Methods:</i></b> The Patient’s Anastrozole Compliance to Therapy (PACT) program, a prospective, randomized study, investigated the effect of additional patient information material (IM) packages on compliance with adjuvant aromatase inhibitor (AI) therapy in postmenopausal women with hormone receptor-positive early breast cancer. The QoL subanalysis presented here examined the impact of IM packages on QoL and the association between QoL and compliance. European Organization for Research and Treatment of Cancer (EORTC) QLQ-C30 and QLQ-BR23 questionnaires were completed at baseline, 12 and 24 months, or study termination to assess health-related QoL and disease-related symptoms. <b><i>Results:</i></b> Of the 4,844 patients randomized to standard therapy or standard therapy + IM packages (1:1), 4,253 were available for QoL analysis. No difference in QoL was observed between groups at baseline. IM packages did not have a statistically significant impact on patient QoL at the 12- or 24-month follow-up. Compliant patients experienced improvement in multiple items across the QLQ-C30 and QLQ-BR23 scales at 12 months. However, those results should be interpreted carefully due to limitations in the statistical analyses. <b><i>Conclusions:</i></b> Provision of IM packages did not influence patients’ QoL or satisfaction with care during AI therapy. Compliant patients appear to experience improved QoL compared to noncompliant patients, perhaps indicating a more self-empowered perception of their condition.
DOI: 10.6084/m9.figshare.9902132.v1
title: Supplementary Material for: Classification and Prognostic Stratification of Bronchopulmonary Neuroendocrine Neoplasms

description: The accuracy and reproducibility of the World Health Organization (WHO) 2015 classification of bronchopulmonary neuroendocrine neoplasms (BP-NENs) is disputed. The aim of this study is to classify and grade BP-NENs using the WHO 2019 classification of digestive system NENs (DiS-NEN-WHO 2019), and to analyze its accuracy and prognostic impact. Two BP-NEN cohorts from Japan and Germany, 393 tumors (88% surgically resected), were reviewed and the clinicopathological data of the resected tumors (<i>n</i> = 301) correlated to patients’ disease-free survival (DFS). The DiS-NEN-WHO 2019 stratified the 350 tumors into 91 (26%) neuroendocrine tumors (NET) G1, 52 (15%) NET G2, 15 (4%) NET G3, and 192 (55%) neuroendocrine carcinomas (NEC). NECs, but not NETs, were immunohistochemically characterized by abnormal p53 (100%) and retinoblastoma 1 (83%) expression. The Ki67 index, which was on average 4 times higher than mitotic count (<i>p</i> &lt; 0.0001), was prognostically more accurate than the mitotic count. NET G3 patients had a worse outcome than NET G1 (<i>p</i> &lt; 0.01) and NET G2 patients (<i>p</i> = 0.02), respectively. No prognostic difference was detected between NET G3 and NEC patients after 5 year DFS. It is concluded that stratifying BP-NEN patients according to the DiS-NEN-WHO 2019 classification results in 3 prognostically well-defined NET groups, if grading is solely based on Ki67 index. Mitotic count alone may underestimate malignant potential of NETs.
DOI: 10.6084/m9.figshare.9902081
title: Supplementary Material for: Long-Term Outcome of Treatment for Persistent Depressive Disorder: A Naturalistic Follow-Up Study

description: Medicine
DOI: 10.6084/m9.figshare.9902117.v1
title: Supplementary Material for: Assessment of Quality of Life in Postmenopausal Women with Early Breast Cancer Participating in the PACT Trial: The Impact of Additional Patient Information Material Packages and Patient Compliance

description: <b><i>Background:</i></b> Breast cancer patients’ self-understanding of their disease can impact their quality of life (QoL); the relationship between compliance and QoL is poorly understood. <b><i>Patients and Methods:</i></b> The Patient’s Anastrozole Compliance to Therapy (PACT) program, a prospective, randomized study, investigated the effect of additional patient information material (IM) packages on compliance with adjuvant aromatase inhibitor (AI) therapy in postmenopausal women with hormone receptor-positive early breast cancer. The QoL subanalysis presented here examined the impact of IM packages on QoL and the association between QoL and compliance. European Organization for Research and Treatment of Cancer (EORTC) QLQ-C30 and QLQ-BR23 questionnaires were completed at baseline, 12 and 24 months, or study termination to assess health-related QoL and disease-related symptoms. <b><i>Results:</i></b> Of the 4,844 patients randomized to standard therapy or standard therapy + IM packages (1:1), 4,253 were available for QoL analysis. No difference in QoL was observed between groups at baseline. IM packages did not have a statistically significant impact on patient QoL at the 12- or 24-month follow-up. Compliant patients experienced improvement in multiple items across the QLQ-C30 and QLQ-BR23 scales at 12 months. However, those results should be interpreted carefully due to limitations in the statistical analyses. <b><i>Conclusions:</i></b> Provision of IM packages did not influence patients’ QoL or satisfaction with care during AI therapy. Compliant patients appear to experience improved QoL compared to noncompliant patients, perhaps indicating a more self-empowered perception of their condition.
DOI: 10.6084/m9.figshare.9902081.v1
title: Supplementary Material for: Long-Term Outcome of Treatment for Persistent Depressive Disorder: A Naturalistic Follow-Up Study

description: Medicine
DOI: 10.6084/m9.figshare.9901838
title: Metadata record for: Linkage Disequilibrium Maps for European and African Populations Constructed from Whole Genome Sequence Data

description: This dataset contains key characteristics about the data described in the Data Descriptor Linkage Disequilibrium Maps for European and African Populations Constructed from Whole Genome Sequence Data. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9901838.v2
title: Metadata record for: Linkage Disequilibrium Maps for European and African Populations Constructed from Whole Genome Sequence Data

description: This dataset contains key characteristics about the data described in the Data Descriptor Linkage Disequilibrium Maps for European and African Populations Constructed from Whole Genome Sequence Data. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>