cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4518801
title: Experimental investigation of enzyme functional annotations reveals extensive annotation error

description: <strong>Only a small fraction of genes deposited to databases has been experimentally characterized. The majority of proteins have their function assigned automatically, which can result in erroneous annotations. The reliability of current annotations in public databases is largely unknown; experimental attempts to validate the accuracy of existing annotations are lacking. In this study we performed an overview of functional annotations to the BRENDA enzyme database. We first applied a high-throughput experimental platform to verify functional annotations to an enzyme class of S-2-hydroxyacid oxidases (EC 1.1.3.15). We chose 122 representative sequences of the class and screened them for their predicted function. Based on the experimental results, predicted domain architecture and similarity to previously characterized S-2-hydroxyacid oxidases, we inferred that at least 78% of sequences in the enzyme class are misannotated. We experimentally confirmed four alternative activities among the misannotated sequences and showed that misannotation in the enzyme class increased over time. Finally, we performed a computational analysis of annotations to all enzyme classes in BRENDA database, and showed that nearly 18% of all sequences are annotated to an enzyme class while sharing no similarity to experimentally characterised representatives. We showed that even well-studied enzyme classes of industrial relevance are affected by the problem of functional misannotation.</strong> <strong>This repository stores data files required to replicate the analysis.</strong>
description: {"references": ["https://doi.org/10.1101/2020.12.18.423474"]}
DOI: 10.5281/zenodo.4518800
title: Experimental investigation of enzyme functional annotations reveals extensive annotation error

description: <strong>Only a small fraction of genes deposited to databases has been experimentally characterized. The majority of proteins have their function assigned automatically, which can result in erroneous annotations. The reliability of current annotations in public databases is largely unknown; experimental attempts to validate the accuracy of existing annotations are lacking. In this study we performed an overview of functional annotations to the BRENDA enzyme database. We first applied a high-throughput experimental platform to verify functional annotations to an enzyme class of S-2-hydroxyacid oxidases (EC 1.1.3.15). We chose 122 representative sequences of the class and screened them for their predicted function. Based on the experimental results, predicted domain architecture and similarity to previously characterized S-2-hydroxyacid oxidases, we inferred that at least 78% of sequences in the enzyme class are misannotated. We experimentally confirmed four alternative activities among the misannotated sequences and showed that misannotation in the enzyme class increased over time. Finally, we performed a computational analysis of annotations to all enzyme classes in BRENDA database, and showed that nearly 18% of all sequences are annotated to an enzyme class while sharing no similarity to experimentally characterised representatives. We showed that even well-studied enzyme classes of industrial relevance are affected by the problem of functional misannotation.</strong> <strong>This repository stores data files required to replicate the analysis.</strong>
description: {"references": ["https://doi.org/10.1101/2020.12.18.423474"]}
DOI: 10.5281/zenodo.4529738
title: ARTIC pipeline validation datasets

description: ARTIC pipeline validation datasets
DOI: 10.5281/zenodo.4529737
title: ARTIC pipeline validation datasets

description: ARTIC pipeline validation datasets
DOI: 10.26302/sshade/experiment_sb_20210115_001
title: T-dependent optical constants of calcite and dolomite

description: Optical constants are obtained by reflectance measurements with polarized light in a temperature range of 10 K to 300 K
DOI: 10.23729/8232aec7-6c0d-47c0-a7e4-9c3f8442bb42
title: Gummern marble preview

description: Marble samples from OMYA mining operation in Gummern, Austria. Samples were imaged to see if we could show the contaminant minerals (quartz, calc-silicates, graphite) within the marble types at this scale. Preview of PAS-dataset: https://doi.org/10.23729/0a740162-93f2-4afb-a229-17b628941f2a
DOI: 10.5281/zenodo.4529814
title: Data set from Mazzaccaro D, Righini P, Zuccon G, Modafferi A, Malacrida G, Nano G. The reversed bell-bottom technique (ReBel-B) for the endovascular treatment of iliac artery aneurysms. Catheter Cardiovasc Interv. 2020 Oct 1;96(4):E479-E483. doi: 10.1002/ccd.29140. Epub 2020 Jul 18. PMID: 32681707.

description: Data set from the article Mazzaccaro D, Righini P, Zuccon G, Modafferi A, Malacrida G, Nano G. The reversed bell-bottom technique (ReBel-B) for the endovascular treatment of iliac artery aneurysms. Catheter Cardiovasc Interv. 2020 Oct 1;96(4):E479-E483. doi: 10.1002/ccd.29140. Epub 2020 Jul 18. PMID: 32681707. <strong>Abstract</strong> <strong>Objective: </strong>To describe the results of the reversed bell-bottom (ReBel-B) technique for the endovascular treatment of iliac aneurysms (IA) involving the origin of hypogastric artery (HA). <strong>Methods: </strong>The ReBel-B technique is a strategy for the occlusion of HA in selected patients presenting with IA, in whom the HA cannot be spared or safely occluded with coils or vascular plugs. When employing this technique, an iliac flared ("bell-bottom") extension is deployed in a reverse fashion, through a contralateral crossover femoral access that allows the occlusion of the HA at its origin, by exploiting the flared "bell" part of the reversed endograft. A second limb is then deployed to complete the implant, from the common iliac to the external iliac artery, inside the previous graft. Data of all consecutive patients treated with this technique in our experience were then retrospectively reviewed, and outcomes analyzed. <strong>Results: </strong>The ReBel-B technique was employed in total of six patients who came in an emergent setting for the rupture of a common IA, from January 2014 to December 2018. Endovascular exclusion was performed using a ReBel-B graft plus iliac leg in five out of six cases. In the remaining case, a bifurcated aortic endograft was used to complete the aneurysm exclusion. Technical success was 100%. No complications occurred. <strong>Conclusions: </strong>In selected cases, the ReBel-B technique can be used for the complete exclusion of IA preventing type II endoleak from the HA, when the embolization with coils or plug or the preservation of the HA is anatomically unfeasible.
DOI: 10.5281/zenodo.4529813
title: Data set from Mazzaccaro D, Righini P, Zuccon G, Modafferi A, Malacrida G, Nano G. The reversed bell-bottom technique (ReBel-B) for the endovascular treatment of iliac artery aneurysms. Catheter Cardiovasc Interv. 2020 Oct 1;96(4):E479-E483. doi: 10.1002/ccd.29140. Epub 2020 Jul 18. PMID: 32681707.

description: Data set from the article Mazzaccaro D, Righini P, Zuccon G, Modafferi A, Malacrida G, Nano G. The reversed bell-bottom technique (ReBel-B) for the endovascular treatment of iliac artery aneurysms. Catheter Cardiovasc Interv. 2020 Oct 1;96(4):E479-E483. doi: 10.1002/ccd.29140. Epub 2020 Jul 18. PMID: 32681707. <strong>Abstract</strong> <strong>Objective: </strong>To describe the results of the reversed bell-bottom (ReBel-B) technique for the endovascular treatment of iliac aneurysms (IA) involving the origin of hypogastric artery (HA). <strong>Methods: </strong>The ReBel-B technique is a strategy for the occlusion of HA in selected patients presenting with IA, in whom the HA cannot be spared or safely occluded with coils or vascular plugs. When employing this technique, an iliac flared ("bell-bottom") extension is deployed in a reverse fashion, through a contralateral crossover femoral access that allows the occlusion of the HA at its origin, by exploiting the flared "bell" part of the reversed endograft. A second limb is then deployed to complete the implant, from the common iliac to the external iliac artery, inside the previous graft. Data of all consecutive patients treated with this technique in our experience were then retrospectively reviewed, and outcomes analyzed. <strong>Results: </strong>The ReBel-B technique was employed in total of six patients who came in an emergent setting for the rupture of a common IA, from January 2014 to December 2018. Endovascular exclusion was performed using a ReBel-B graft plus iliac leg in five out of six cases. In the remaining case, a bifurcated aortic endograft was used to complete the aneurysm exclusion. Technical success was 100%. No complications occurred. <strong>Conclusions: </strong>In selected cases, the ReBel-B technique can be used for the complete exclusion of IA preventing type II endoleak from the HA, when the embolization with coils or plug or the preservation of the HA is anatomically unfeasible.
DOI: 10.5281/zenodo.4512571
title: Banding Patches Dataset

description: The<strong> Banded Patches Dataset.zip</strong> file features: The Dataset features 169,501 patches of size 235x235. These patches were used to train a CNN classier which can be further used to obtain Deep Banding Index for a Banded Image. The zip features training, validation, and testing dataset, each such folder further contains banded and nonbanded patches.
description: {"references": ["A. Kapoor, J. Sapra and Z. Wang, \"Capturing banding in images: database construction and objective assessment,\" IEEE International Conference on Acoustics, Speech and Signal Processing, Jun. 2021."]}
DOI: 10.5281/zenodo.4512570
title: Banding Patches Dataset

description: The<strong> Banded Patches Dataset.zip</strong> file features: The Dataset features 169,501 patches of size 235x235. These patches were used to train a CNN classier which can be further used to obtain Deep Banding Index for a Banded Image. The zip features training, validation, and testing dataset, each such folder further contains banded and nonbanded patches.
description: {"references": ["A. Kapoor, J. Sapra and Z. Wang, \"Capturing banding in images: database construction and objective assessment,\" IEEE International Conference on Acoustics, Speech and Signal Processing, Jun. 2021."]}
DOI: 10.5281/zenodo.4513740
title: HD Images Dataset with Banded and NonBanded region Information

description: HD_images_dataset_size_1920x1080.zip features Original Images and a Quantized version of these Images along with XML files which carry labeled information about the presence of banded and non-banded regions in the Quantized Images.
description: {"references": ["A. Kapoor, J. Sapra and Z. Wang, \"Capturing banding in images: database construction and objective assessment,\" IEEE International Conference on Acoustics, Speech and Signal Processing, Jun. 2021."]}
DOI: 10.5281/zenodo.4513739
title: HD Images Dataset with Banded and NonBanded region Information

description: HD_images_dataset_size_1920x1080.zip features Original Images and a Quantized version of these Images along with XML files which carry labeled information about the presence of banded and non-banded regions in the Quantized Images.
description: {"references": ["A. Kapoor, J. Sapra and Z. Wang, \"Capturing banding in images: database construction and objective assessment,\" IEEE International Conference on Acoustics, Speech and Signal Processing, Jun. 2021."]}
DOI: 10.5281/zenodo.4529840
title: Data set from Dozio E, Vettoretti S, Caldiroli L, Nerini-Molteni S, Tacchini L, Ambrogi F, Messa P, Corsi Romanelli MM. Advanced Glycation End Products (AGE) and Soluble Forms of AGE Receptor: Emerging Role as Mortality Risk Factors in CKD. Biomedicines. 2020 Dec 21;8(12):638. doi: 10.3390/biomedicines8120638. PMID: 33371369; PMCID: PMC7767383.

description: Data set from the article Dozio E, Vettoretti S, Caldiroli L, Nerini-Molteni S, Tacchini L, Ambrogi F, Messa P, Corsi Romanelli MM. Advanced Glycation End Products (AGE) and Soluble Forms of AGE Receptor: Emerging Role as Mortality Risk Factors in CKD. Biomedicines. 2020 Dec 21;8(12):638. doi: 10.3390/biomedicines8120638. PMID: 33371369; PMCID: PMC7767383. This is the abstract: Advanced glycation end-products (AGE) can promote chronic kidney disease (CKD) progression and CKD-related morbidities. The soluble receptor for AGE (sRAGE) is a potential biomarker of inflammation and oxidative stress. Here, we explored the role of AGE, glycated albumin, sRAGE and its different forms, cRAGE and esRAGE, as prognostic factors for mortality in 111 advanced CKD patients. The median follow-up time was 39 months. AGE were quantified by fluorescence, sRAGE and its forms by ELISA. Malnutrition was screened by the Malnutrition Inflammation Score (MIS). The Cox proportional hazards regression model was used to assess the association of variables with all-cause mortality. Mean levels of sRAGE, esRAGE and cRAGE were 2318 ± 1224, 649 ± 454 and 1669 ± 901 pg/mL. The mean value of cRAGE/esRAGE was 2.82 ± 0.96. AGE were 3026 ± 766 AU and MIS 6.0 ± 4.7. eGFR correlated negatively with AGE, sRAGE, esRAGE and cRAGE, but not with cRAGE/esRAGE. Twenty-eight patients died. No difference was observed between diabetic and non-diabetic patients. Starting dialysis was not associated with enhanced risk of death. AGE, esRAGE and cRAGE/esRAGE were independently associated with all-cause mortality. AGE, esRAGE and cRAGE/esRAGE may help to stratify overall mortality risk. Implementing the clinical evaluation of CKD patients by quantifying these biomarkers can help to improve patient outcomes.
DOI: 10.5281/zenodo.4529839
title: Data set from Dozio E, Vettoretti S, Caldiroli L, Nerini-Molteni S, Tacchini L, Ambrogi F, Messa P, Corsi Romanelli MM. Advanced Glycation End Products (AGE) and Soluble Forms of AGE Receptor: Emerging Role as Mortality Risk Factors in CKD. Biomedicines. 2020 Dec 21;8(12):638. doi: 10.3390/biomedicines8120638. PMID: 33371369; PMCID: PMC7767383.

description: Data set from the article Dozio E, Vettoretti S, Caldiroli L, Nerini-Molteni S, Tacchini L, Ambrogi F, Messa P, Corsi Romanelli MM. Advanced Glycation End Products (AGE) and Soluble Forms of AGE Receptor: Emerging Role as Mortality Risk Factors in CKD. Biomedicines. 2020 Dec 21;8(12):638. doi: 10.3390/biomedicines8120638. PMID: 33371369; PMCID: PMC7767383. This is the abstract: Advanced glycation end-products (AGE) can promote chronic kidney disease (CKD) progression and CKD-related morbidities. The soluble receptor for AGE (sRAGE) is a potential biomarker of inflammation and oxidative stress. Here, we explored the role of AGE, glycated albumin, sRAGE and its different forms, cRAGE and esRAGE, as prognostic factors for mortality in 111 advanced CKD patients. The median follow-up time was 39 months. AGE were quantified by fluorescence, sRAGE and its forms by ELISA. Malnutrition was screened by the Malnutrition Inflammation Score (MIS). The Cox proportional hazards regression model was used to assess the association of variables with all-cause mortality. Mean levels of sRAGE, esRAGE and cRAGE were 2318 ± 1224, 649 ± 454 and 1669 ± 901 pg/mL. The mean value of cRAGE/esRAGE was 2.82 ± 0.96. AGE were 3026 ± 766 AU and MIS 6.0 ± 4.7. eGFR correlated negatively with AGE, sRAGE, esRAGE and cRAGE, but not with cRAGE/esRAGE. Twenty-eight patients died. No difference was observed between diabetic and non-diabetic patients. Starting dialysis was not associated with enhanced risk of death. AGE, esRAGE and cRAGE/esRAGE were independently associated with all-cause mortality. AGE, esRAGE and cRAGE/esRAGE may help to stratify overall mortality risk. Implementing the clinical evaluation of CKD patients by quantifying these biomarkers can help to improve patient outcomes.
DOI: 10.17632/vxg4bgc96t.1
title: Numerical verification of Littlewood's bounds for |L(1,χ)|, data

description: Max and min values for |L(1,χ)|, χ Dirichlet character mod q, q prime. Example of the results used in the paper with primes primes in [19000,20000], 30011, 83089, 991027, (minL attained here) 4305479 (maxL attained here). These values can be reproduced using the attached CodeOcean Capsule for this work. Whole sets of values for every odd prime up to 10^7 are at the following page:https://www.math.unipd.it/~languasc/Littlewood_ineq.html (see the Numerical results paragraph). Journal of Number Theory Volume 223, June 2021, Pages 12-34, https://doi.org/10.1016/j.jnt.2020.12.017
DOI: 10.17632/xx6f327rb5.4
title: C-test Meta-analysis

description: This dataset contains all of the spreadsheets, code, and files that we used to complete our meta-analysis of correlation coefficients reported in C-test studies (published in English). Files can also be found on my personal website (https://rb.gy/z7nov3).
DOI: 10.17632/sj4sthhryn.2
title: Experimental dataset on water levels in the study of multi-layer shock flood wave over bumpy downstream

description: Experimental dataset of free surface water level: In this file, all water level data associated with 6 different dam break scenarios were extracted from high-quality experimental video images. The dataset are collected, classified and presented a total of 6 tables in 3 categories based on the radiuses of downstream semi-circular obstacles; 0, 4.5 and 7.5 cm. Initial upstream sediment depths were 3 and 7.5 cm and the upstream reservoir was initially occupied by 10 to 25% sedimentation (in respect to 30 cm height of the upstream reservoir). Tables 1 and 2, present the free surface water level data at 20 different locations along the flume and 15 snap times after the dam break, while initial upstream sediment depths were 3 and 7.5 cm, respectively and the radius of downstream semi-circular obstacle was 4.5 cm. Tables 3 and 4, provide the free surface water level data at all abovementioned sections and snap times while initial upstream sediment depths were 3 and 7.5 cm, respectively and the radius of downstream semi-circular obstacle was 7.5 cm. Tables 5 and 6, present the free surface water level data at all abovementioned sections and snap times while initial upstream sediment depths were 3 and 7.5 cm, respectively and there were no obstacles in the dam downstream. The unit that has been used to measure data is centimeter and the abbreviations including O_r and S_d are the radiuses of downstream semi-circular obstacles and upstream initial sediment depth, respectively. Time also refer to the time snaps after sudden removal of the gate using second as a unit of measurement. It should be noted that the vertical column on the left of the tables indicates the distances of different locations in centimeter from the beginning point of the laboratory flume. So, L column indicates all 20 distinct locations along the flume and their distances from the reservoir beginning in centimeter as a unit of measurement. Affiliations 1st Author: Foad Vosoughi, Research Associate, Department of Civil and Environmental Engineering, Shiraz University, Shiraz, Iran. foad.vosooghi@gmail.com 2nd Author: Gholamreza Rakhshandehroo, Professor, Department of Civil and Environmental Engineering, Shiraz University, Shiraz, Iran. 3rd Author: Mohammad Reza Nikoo, Associate Professor, Department of Civil and Environmental Engineering, Shiraz University, Shiraz, Iran.
DOI: 10.17632/64sy6w5vkz.2
title: Experimental dataset on water levels in the study of flash flood wave without sediment (clear water) over bumpy downstream

description: Experimental dataset of free surface water level: In this file, all water level data associated with 3 different dam break scenarios were extracted from high-quality experimental video images. The dataset are collected, classified and presented a total of 3 tables in 3 categories based on the radiuses of downstream semi-circular obstacles; 0, 4.5 and 7.5 cm. Initial upstream sediment depth was 0 cm and the upstream reservoir was filled-up with clear water. Table 1, presents the free surface water level data at 20 different locations along the flume and 15 snap times after the dam break, while the radius of downstream semi-circular obstacle was 4.5 cm. Table 2, provides the free surface water level data at all abovementioned sections and snap times while the radius of downstream semi-circular obstacle was 7.5 cm. Table 3, presents the free surface water level data at all abovementioned sections and snap times while there were no obstacles in the dam downstream. The unit that has been used to measure data is centimeter and the abbreviation of O_r is the radiuses of downstream semi-circular obstacles. Time also refer to the time snaps after sudden removal of the gate using second as a unit of measurement. It should be noted that the vertical column on the left of the tables indicates the distances of different locations in centimeter from the beginning point of the laboratory flume. So, L column indicates all 20 distinct locations along the flume and their distances from the reservoir beginning in centimeter as a unit of measurement. Affiliations 1st Author: Foad Vosoughi, Research Associate, Department of Civil and Environmental Engineering, Shiraz University, Shiraz, Iran. foad.vosooghi@gmail.com 2nd Author: Gholamreza Rakhshandehroo, Professor, Department of Civil and Environmental Engineering, Shiraz University, Shiraz, Iran. 3rd Author: Mohammad Reza Nikoo, Associate Professor, Department of Civil and Environmental Engineering, Shiraz University, Shiraz, Iran.
DOI: 10.17632/mmp3dhv9fj.2
title: Experimental dataset on sediment depths in the study of multi-layer shock flood wave over bumpy downstream bed

description: Experimental dataset of sediment depth: In this file, all sediment depth data associated with 6 different dam break scenarios were extracted from high-quality experimental video images. The dataset are collected, classified and presented a total of 6 tables in 3 categories based on the radiuses of downstream semi-circular obstacles; 0, 4.5 and 7.5 cm. Initial upstream sediment depths were 3 and 7.5 cm and the upstream reservoir was initially occupied by 10 to 25% sedimentation (in respect to 30 cm height of the upstream reservoir). Tables 1 and 2, present the sediment depth data at 20 different locations along the flume and 15 snap times after the dam break, while initial upstream sediment depths were 3 and 7.5 cm, respectively and the radius of downstream semi-circular obstacle was 4.5 cm. Tables 3 and 4, provide the sediment depth data at all abovementioned sections and snap times while initial upstream sediment depths were 3 and 7.5 cm, respectively and the radius of downstream semi-circular obstacle was 7.5 cm. Tables 5 and 6, present the sediment depth data at all abovementioned sections and snap times while initial upstream sediment depths were 3 and 7.5 cm, respectively and there were no obstacles in the dam downstream. The unit that has been used to measure data is centimeter and the abbreviations including O_r and S_d are the radiuses of downstream semi-circular obstacles and upstream initial sediment depth, respectively. Time also refer to the time snaps after sudden removal of the gate using second as a unit of measurement. It should be noted that the vertical column on the left of the tables indicates the distances of different locations in centimeter from the beginning point of the laboratory flume. So, L column indicates all 20 distinct locations along the flume and their distances from the reservoir beginning in centimeter as a unit of measurement. Affiliations 1st Author: Foad Vosoughi, Research Associate, Department of Civil and Environmental Engineering, Shiraz University, Shiraz, Iran. foad.vosooghi@gmail.com 2nd Author: Gholamreza Rakhshandehroo, Professor, Department of Civil and Environmental Engineering, Shiraz University, Shiraz, Iran. 3rd Author: Mohammad Reza Nikoo, Associate Professor, Department of Civil and Environmental Engineering, Shiraz University, Shiraz, Iran.