cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7567792
title: A Combined Deep Learning System for Automatic Detection of "Bovine" Aortic Arch on Computed Tomography Scans

description: A Combined Deep Learning System for Automatic Detection of “Bovine” Aortic Arch on Computed Tomography Scans <em>Appl. Sci.</em> <strong>2022</strong>, <em>12</em>(4), 2056; https://doi.org/10.3390/app12042056 Abstract The “bovine” aortic arch is an anatomic variant consisting in a common origin of the innominate and left carotid artery (CILCA), associated with a greater risk of thoracic aortic diseases (aneurysms and dissections), stroke, and complications after endovascular procedures. CILCA can be detected by visual assessment of computed tomography (CT) chest scans, but it is rarely reported. We developed a deep learning (DL) segmentation-plus-classification system to automatically detect CILCA based on 302 CT studies acquired at 2 centers. One model (3D U-Net) was trained from scratch (supervised by manual segmentation), validated, and tested for the automatic segmentation of the aortic arch and supra-aortic vessels. Three DL architectures (ResNet50, DenseNet-201, and SqueezeNet), pre-trained over millions of common images, were trained, validated, and tested for the automatic classification of CILCA versus non-CILCA, supervised by radiologist’s classification. The 3D U-Net-plus-DenseNet-201 was found to be the best system (Dice index 0.912); its classification performance obtained from internal, independent testing on 126 patients gave a receiver operating characteristic area under the curve of 87.0%, sensitivity 66.7%, specificity 90.5%, positive predictive value 87.5%, negative predictive value 73.1%, positive likelihood ratio 7.0, and negative likelihood ratio 0.4. In conclusion, a combined DL system applied to chest CT scans was developed and proven to be an effective tool to detect individuals with “bovine” aortic arch with a low rate of false-positive findings.
DOI: 10.5281/zenodo.7567791
title: A Combined Deep Learning System for Automatic Detection of "Bovine" Aortic Arch on Computed Tomography Scans

description: A Combined Deep Learning System for Automatic Detection of “Bovine” Aortic Arch on Computed Tomography Scans <em>Appl. Sci.</em> <strong>2022</strong>, <em>12</em>(4), 2056; https://doi.org/10.3390/app12042056 Abstract The “bovine” aortic arch is an anatomic variant consisting in a common origin of the innominate and left carotid artery (CILCA), associated with a greater risk of thoracic aortic diseases (aneurysms and dissections), stroke, and complications after endovascular procedures. CILCA can be detected by visual assessment of computed tomography (CT) chest scans, but it is rarely reported. We developed a deep learning (DL) segmentation-plus-classification system to automatically detect CILCA based on 302 CT studies acquired at 2 centers. One model (3D U-Net) was trained from scratch (supervised by manual segmentation), validated, and tested for the automatic segmentation of the aortic arch and supra-aortic vessels. Three DL architectures (ResNet50, DenseNet-201, and SqueezeNet), pre-trained over millions of common images, were trained, validated, and tested for the automatic classification of CILCA versus non-CILCA, supervised by radiologist’s classification. The 3D U-Net-plus-DenseNet-201 was found to be the best system (Dice index 0.912); its classification performance obtained from internal, independent testing on 126 patients gave a receiver operating characteristic area under the curve of 87.0%, sensitivity 66.7%, specificity 90.5%, positive predictive value 87.5%, negative predictive value 73.1%, positive likelihood ratio 7.0, and negative likelihood ratio 0.4. In conclusion, a combined DL system applied to chest CT scans was developed and proven to be an effective tool to detect individuals with “bovine” aortic arch with a low rate of false-positive findings.
DOI: 10.4119/unibi/2968403
title: Supplementary material for "Voy a tocarte toa: Preferences for sexist music and sexist attitudes predict unwanted sexual attention"
DOI: 10.6084/m9.figshare.21952967
title: Gut microbiota of Mink in Europe

description: One of the threats that the critically endangered European mink (<em>Mustela lutreola</em>) faces throughout its relict range, including the occidental population, is the impact of the American mink (<em>Mustela vison</em>) invasion in its natural habitat. We aimed to explore the differences in microbiota and genetic diversity between European and American mink to test phylosymbiosis theory. We investigated the gut microbiota composition of European and American mink in controlled environments (captive breeding compounds and fur farms respectively) to account for the impact of the environment on gut bacterial composition. We compared them to the gut microbiota of both mink species in the natural environment across habitats. Our exploratory results showed differences between free-ranging and captive individuals, with more extreme changes in American mink compared to European mink. However, feral American mink from a long-established population exhibited gut bacterial composition closer to the free-ranging native species compared to more recently established feral populations. This result could be explained by dietary shifts in the area sampled based on prey availability through different landscape, but also to a lesser extent due to greater genetic differentiation. This exploratory work contributes to the scarce literature currently available on the dynamics between gut microbiota and mammal invasion.
DOI: 10.6084/m9.figshare.21952967.v1
title: Gut microbiota of Mink in Europe

description: One of the threats that the critically endangered European mink (<em>Mustela lutreola</em>) faces throughout its relict range, including the occidental population, is the impact of the American mink (<em>Mustela vison</em>) invasion in its natural habitat. We aimed to explore the differences in microbiota and genetic diversity between European and American mink to test phylosymbiosis theory. We investigated the gut microbiota composition of European and American mink in controlled environments (captive breeding compounds and fur farms respectively) to account for the impact of the environment on gut bacterial composition. We compared them to the gut microbiota of both mink species in the natural environment across habitats. Our exploratory results showed differences between free-ranging and captive individuals, with more extreme changes in American mink compared to European mink. However, feral American mink from a long-established population exhibited gut bacterial composition closer to the free-ranging native species compared to more recently established feral populations. This result could be explained by dietary shifts in the area sampled based on prey availability through different landscape, but also to a lesser extent due to greater genetic differentiation. This exploratory work contributes to the scarce literature currently available on the dynamics between gut microbiota and mammal invasion.
DOI: 10.5281/zenodo.7567790
title: LOCATION DOMESTIC ARCHITECTURE AUGUSTA EMERITA (MERIDA, SPAIN)

description: This dataset is based on houses from the Roman colony of <em>Augusta Emerita </em>(ca. B.C 25- A.D. 382)<sup> <sup>[1]</sup></sup>. These dates are not chosen randomly: 25 B.C. saw the foundation <em>ex nihilo </em>of the settlement, according to Cass. Dio., <em>Hist</em>. 53.26.1<sup><sup>[2]</sup></sup>, and A.D. 382, the last time a name of a <em>vicarius</em> is attested in the epigraphy<sup><sup>[3]</sup></sup>. The remains from <em>Augusta Emerita </em>are particularity well suited to GIS analysis of this type because the site was occupied for more than two thousand years and was never abandoned, while also being occupied by several cultures over that time. [1] All documentation based on La arquitectura doméstica de Augusta Emerita (2015 Phd) https://dehesa.unex.es/handle/10662/2670# [2] The Duoviri's first couple is evidenced ca.20 B.C. from the fragment of the Fasti duovirales: A. Stylow and A. Ventura, “Los hallazgos epigráficos”, in R. Ayerbe, T. Barrientos and F. Palma (edd.), <em>El foro de Augusta Emerita. </em><em>Génesis y evolución de sus recintos monumentales</em> (Mérida 2009) 453-523. [3] L. Hidalgo and G. Méndez, “Octavius Clarus, un nuevo Vicarius Hispaniarum en Augusta Emerita”, <em>Mérida. Excavaciones Arqueológicas </em>8 (2005) 547-64.
description: ETRS89 Zone 29 N UTM
DOI: 10.5281/zenodo.7567789
title: LOCATION DOMESTIC ARCHITECTURE AUGUSTA EMERITA (MERIDA, SPAIN)

description: This dataset is based on houses from the Roman colony of <em>Augusta Emerita </em>(ca. B.C 25- A.D. 382)<sup> <sup>[1]</sup></sup>. These dates are not chosen randomly: 25 B.C. saw the foundation <em>ex nihilo </em>of the settlement, according to Cass. Dio., <em>Hist</em>. 53.26.1<sup><sup>[2]</sup></sup>, and A.D. 382, the last time a name of a <em>vicarius</em> is attested in the epigraphy<sup><sup>[3]</sup></sup>. The remains from <em>Augusta Emerita </em>are particularity well suited to GIS analysis of this type because the site was occupied for more than two thousand years and was never abandoned, while also being occupied by several cultures over that time. [1] All documentation based on La arquitectura doméstica de Augusta Emerita (2015 Phd) https://dehesa.unex.es/handle/10662/2670# [2] The Duoviri's first couple is evidenced ca.20 B.C. from the fragment of the Fasti duovirales: A. Stylow and A. Ventura, “Los hallazgos epigráficos”, in R. Ayerbe, T. Barrientos and F. Palma (edd.), <em>El foro de Augusta Emerita. </em><em>Génesis y evolución de sus recintos monumentales</em> (Mérida 2009) 453-523. [3] L. Hidalgo and G. Méndez, “Octavius Clarus, un nuevo Vicarius Hispaniarum en Augusta Emerita”, <em>Mérida. Excavaciones Arqueológicas </em>8 (2005) 547-64.
description: ETRS89 Zone 29 N UTM
DOI: 10.6084/m9.figshare.21776924
title: Supplementary Material for: Clinical efficacy and safety of nivolumab in malignant non-pleural mesothelioma: A multicenter, open-label, single-arm, Japanese phase II trial (VIOLA) protocol

description: Background: There is no authorized treatment for malignant non-pleural mesothelioma (MNPM) worldwide. In contrast to malignant pleural mesothelioma (MPM), MNPM has not been investigated, and no treatment has been established due to its rarity. Objectives: This multicenter, open-label, single-arm, Japanese phase II trial aims at evaluating the efficacy and safety of nivolumab, an immune checkpoint inhibitor, in advanced or metastatic MNPM treatment. Methods: This phase II trial commenced in October 2020. Twenty-three patients with advanced or metastatic MNPM who meet the inclusion and exclusion criteria were enrolled from five institutions within 2 years. Regardless of prior therapy, 240 mg of nivolumab will be administered intravenously to MNPM patients every 2 weeks to investigate its efficacy and safety until disease progression or unacceptable toxicities are detected, or the patient’s condition meets the withdrawal criteria. Results: The primary endpoint is the objective response rate by central assessment following the Response Evaluation Criteria in Solid Tumors version 1.1. The secondary endpoints include disease control rate, overall survival, progression-free survival, adverse events, and treatment-related adverse events. Conclusions: This is the first prospective investigator-initiated trial to evaluate the effect of nivolumab monotherapy for MNPM.
DOI: 10.5281/zenodo.7488941
title: Native and exotic plants play different roles in urban pollination networks across seasons

description: Datasets for 'Native and exotic plants play different roles in urban pollination networks across seasons' by Zaninotto et al. (2023) in Oecologia.
DOI: 10.5281/zenodo.7488942
title: Native and exotic plants play different roles in urban pollination networks across seasons

description: Datasets for 'Native and exotic plants play different roles in urban pollination networks across seasons' by Zaninotto et al. (2023) in Oecologia.
DOI: 10.5281/zenodo.7129527
title: Polarisation-independent ultrafast laser selective etching processing in fused silica

description: Data files for the manuscript: Polarisation-independent ultrafast laser selective etching processing in fused silica
DOI: 10.5281/zenodo.7129526
title: Polarisation-independent ultrafast laser selective etching processing in fused silica

description: Data files for the manuscript: Polarisation-independent ultrafast laser selective etching processing in fused silica
DOI: 10.5281/zenodo.7567845
title: A Wide-Proteome Analysis to Identify Molecular Pathways Involved in Kidney Response to High-Fat Diet in Mice

description: Dozio E, Maffioli E, Vianello E, Nonnis S, Grassi Scalvini F, Spatola L, Roccabianca P, Tedeschi G, Corsi Romanelli MM. A Wide-Proteome Analysis to Identify Molecular Pathways Involved in Kidney Response to High-Fat Diet in Mice. Int J Mol Sci. 2022 Mar 30;23(7):3809. doi: 10.3390/ijms23073809. PMID: 35409168; PMCID: PMC8999052. Abstract The etiopathogenesis of obesity-related chronic kidney disease (CKD) is still scarcely understood. To this aim, we assessed the effect of high-fat diet (HF) on molecular pathways leading to organ damage, steatosis, and fibrosis. Six-week-old male C57BL/6N mice were fed HF diet or normal chow for 20 weeks. Kidneys were collected for genomic, proteomic, histological studies, and lipid quantification. The main findings were as follows: (1) HF diet activated specific pathways leading to fibrosis and increased fatty acid metabolism; (2) HF diet promoted a metabolic shift of lipid metabolism from peroxisomes to mitochondria; (3) no signs of lipid accumulation and/or fibrosis were observed, histologically; (4) the early signs of kidney damage seemed to be related to changes in membrane protein expression; (5) the proto-oncogene MYC was one of the upstream transcriptional regulators of changes occurring in protein expression. These results demonstrated the potential usefulness of specific selected molecules as early markers of renal injury in HF, while histomorphological changes become visible later in obesity-related CDK. The integration of these information with data from biological fluids could help the identification of biomarkers useful for the early detection and prevention of tissue damage in clinical practice.
DOI: 10.5281/zenodo.7567844
title: A Wide-Proteome Analysis to Identify Molecular Pathways Involved in Kidney Response to High-Fat Diet in Mice

description: Dozio E, Maffioli E, Vianello E, Nonnis S, Grassi Scalvini F, Spatola L, Roccabianca P, Tedeschi G, Corsi Romanelli MM. A Wide-Proteome Analysis to Identify Molecular Pathways Involved in Kidney Response to High-Fat Diet in Mice. Int J Mol Sci. 2022 Mar 30;23(7):3809. doi: 10.3390/ijms23073809. PMID: 35409168; PMCID: PMC8999052. Abstract The etiopathogenesis of obesity-related chronic kidney disease (CKD) is still scarcely understood. To this aim, we assessed the effect of high-fat diet (HF) on molecular pathways leading to organ damage, steatosis, and fibrosis. Six-week-old male C57BL/6N mice were fed HF diet or normal chow for 20 weeks. Kidneys were collected for genomic, proteomic, histological studies, and lipid quantification. The main findings were as follows: (1) HF diet activated specific pathways leading to fibrosis and increased fatty acid metabolism; (2) HF diet promoted a metabolic shift of lipid metabolism from peroxisomes to mitochondria; (3) no signs of lipid accumulation and/or fibrosis were observed, histologically; (4) the early signs of kidney damage seemed to be related to changes in membrane protein expression; (5) the proto-oncogene MYC was one of the upstream transcriptional regulators of changes occurring in protein expression. These results demonstrated the potential usefulness of specific selected molecules as early markers of renal injury in HF, while histomorphological changes become visible later in obesity-related CDK. The integration of these information with data from biological fluids could help the identification of biomarkers useful for the early detection and prevention of tissue damage in clinical practice.
DOI: 10.5281/zenodo.7567853
title: DATASET Sound production mechanism in triggerfish (Balistidae): a synapomorphy

description: Dataset corresponding to the article "Sound production mechanism in triggerfish (Balistidae): a synapomorphy". This dataset contains the sounds of three species of Balistidae : <em>Balistapus undulatus</em>, <em>Rhinecanthus aculeatus</em> and <em>Rhinecanthus rectangulus</em>. All the specimens are from Moorea Island (French Polynesia)<br> <em>B. undulatus</em> [standard length (SL) 10.59–15.35 cm]<br> <em>R. aculeatus</em> (SL: 12.7–17.4 cm) <br> <em>R. rectangulus</em> (SL: 8.1–15.3 cm) Specimens were recorded hand-held in a glass aquarium with a hydrophone HTI-96-MIN (sensitivity: −163.9dB V μPa−1; High Tech Inc., Long Beach, MS, USA) connected to a TASCAM DR-07 recorder (TEAC, Wiesbaden, Germany).<br> The sounds were digitized at 44.1 kHz (16-bit resolution).
description: {"references": ["\uf0fc\tRaick, X., Lecchini, D., Kever, L., Colleye, O., Bertucci, F., & Parmentier, E. (2018). Sound production mechanism in triggerfish (Balistidae): a synapomorphy. Journal of Experimental Biology 221: 168948 doi:10.1242/jeb.168948"]}
DOI: 10.5281/zenodo.7567852
title: DATASET Sound production mechanism in triggerfish (Balistidae): a synapomorphy

description: Dataset corresponding to the article "Sound production mechanism in triggerfish (Balistidae): a synapomorphy". This dataset contains the sounds of three species of Balistidae : <em>Balistapus undulatus</em>, <em>Rhinecanthus aculeatus</em> and <em>Rhinecanthus rectangulus</em>. All the specimens are from Moorea Island (French Polynesia)<br> <em>B. undulatus</em> [standard length (SL) 10.59–15.35 cm]<br> <em>R. aculeatus</em> (SL: 12.7–17.4 cm) <br> <em>R. rectangulus</em> (SL: 8.1–15.3 cm) Specimens were recorded hand-held in a glass aquarium with a hydrophone HTI-96-MIN (sensitivity: −163.9dB V μPa−1; High Tech Inc., Long Beach, MS, USA) connected to a TASCAM DR-07 recorder (TEAC, Wiesbaden, Germany).<br> The sounds were digitized at 44.1 kHz (16-bit resolution).
description: {"references": ["\uf0fc\tRaick, X., Lecchini, D., Kever, L., Colleye, O., Bertucci, F., & Parmentier, E. (2018). Sound production mechanism in triggerfish (Balistidae): a synapomorphy. Journal of Experimental Biology 221: 168948 doi:10.1242/jeb.168948"]}
DOI: 10.6084/m9.figshare.21750362.v1
title: Supplementary Material for: The different prognosis of hepatocellular carcinoma with previous tenofovir vs entecavir treatment for chronic hepatitis B virus: analysis based on 15 propensity score–matched studies

description: Background: This meta-analysis of high-quality PSM studies was designed to provide robust estimates for comparative HCC prognosis between groups receiving tenofovir or entecavir. Methods: PubMed, Embase, Cochrane Library and Web of Science were searched from inception to July 10, 2022 for relevant studies that comparing the different prognosis of HCC between TDF and ETV. Results: A total of 15 PSM studies were identified, with 24035 sample sizes in tenofovir group and 61410 sample sizes in entecavir group respectively. Pooled data indicated that, compared with entecavir, patients receiving tenofovir experienced significantly lower overall death or liver transplantation, with a pooled OR of 0.55 (95% CI 0.45 ‒ 0.68). Subgroup analysis by population also found similar results with pooled ORs of 0.52 (95% CI 0.38 ‒ 0.70) in entire cohort and 0.62 (95% CI 0.50 ‒ 0.77) in PSM cohort. Conclusions: Our analysis indicated that there was clinically meaningful difference in prognosis of HCC between patients who received entecavir and patients who received tenofovir. Tenofovir treatment may be one of independent favorable factors of prognosis for HCC patients with CHBV.
DOI: 10.6084/m9.figshare.21750362
title: Supplementary Material for: The different prognosis of hepatocellular carcinoma with previous tenofovir vs entecavir treatment for chronic hepatitis B virus: analysis based on 15 propensity score–matched studies

description: Background: This meta-analysis of high-quality PSM studies was designed to provide robust estimates for comparative HCC prognosis between groups receiving tenofovir or entecavir. Methods: PubMed, Embase, Cochrane Library and Web of Science were searched from inception to July 10, 2022 for relevant studies that comparing the different prognosis of HCC between TDF and ETV. Results: A total of 15 PSM studies were identified, with 24035 sample sizes in tenofovir group and 61410 sample sizes in entecavir group respectively. Pooled data indicated that, compared with entecavir, patients receiving tenofovir experienced significantly lower overall death or liver transplantation, with a pooled OR of 0.55 (95% CI 0.45 ‒ 0.68). Subgroup analysis by population also found similar results with pooled ORs of 0.52 (95% CI 0.38 ‒ 0.70) in entire cohort and 0.62 (95% CI 0.50 ‒ 0.77) in PSM cohort. Conclusions: Our analysis indicated that there was clinically meaningful difference in prognosis of HCC between patients who received entecavir and patients who received tenofovir. Tenofovir treatment may be one of independent favorable factors of prognosis for HCC patients with CHBV.
DOI: 10.6084/m9.figshare.21781541
title: Supplementary Material for: Serum sclerostin levels and mortality in hemodialysis patients: An 8-year prospective study

description: Introduction: Sclerostin is an osteocyte-derived inhibitor of bone formation and is increased in kidney failure. Sclerostin might be involved in the pathogenesis of vascular calcification, but few studies have examined the association between sclerostin and mortality in hemodialysis patients. Methods: We analyzed a prospective cohort of 654 patients undergoing maintenance hemodialysis. The primary exposure variable was the baseline serum sclerostin level measured at study enrollment. The primary outcome was 8-year all-cause mortality. Mortality risk was assessed using Cox regression models adjusted for potential confounders. Results: During a median follow-up of 7.6 years (IQR, 4.1-8.0 years), 229 of the 654 participants died. In univariate analysis, serum sclerostin levels were not associated with mortality (HR per doubling, 0.94; 95% CI, 0.76-1.17). This result was unchanged after adjustment for age, sex, dialysis vintage, diabetes, prior cardiovascular disease, and, body mass index (HR per doubling, 0.92; 95% CI, 0.72-1.17). Similar results were obtained for cardiovascular mortality. Conclusion: Serum sclerostin levels were not associated with mortality in maintenance hemodialysis patients. Further research is required to determine the role of sclerostin in vascular calcification and cardiovascular disease in kidney failure.