cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7065973
title: Experimental Datasets and Processing Codes for the Semantic PHD Filter

description: The water bottle detection dataset and measurement model dataset for the paper titled "The Semantic PHD Filter for Multi-class Target Tracking: From Theory to Practice" by Jun Chen, Zhanteng Xie and Philip Dames, and the paper titled "Experimental Datasets and Processing Codes for the Semantic PHD Filter" by Zhanteng Xie, Jun Chen and Philip Dames <strong>1. Detection dataset: </strong> Size: <br> Total: 4870 images<br> Training: 4000 images<br> Validation: 870 images Bottle Classes: Aquafina, Deer, Kirkland, Nestle Format: PASCAL VOC, Darknet Folder Structure:<br> - Annotations: containing the xml label files in PASCAL VOC format<br> - ImageSets: containing the training index files <br> - JPEGImages: containing the image data in jpg format<br> - Labels: containing the txt label files in Darknet format <strong>2. Measurement model dataset:</strong> Format: ROSBAG Duration: 19:59s (1199s) Topics:<br> /darknet_ros/detection_image 3543 msgs : sensor_msgs/Image<br> /map 1 msg : nav_msgs/OccupancyGrid<br> /sphd_measurements 3585 msgs : sphd_msgs/SPHDMeasurements<br> /tf 142727 msgs : tf2_msgs/TFMessage<br> /tf_static 1 msg : tf2_msgs/TFMessage Message Types:<br> nav_msgs/OccupancyGrid<br> sensor_msgs/Image<br> sphd_msgs/SPHDMeasurements<br> tf2_msgs/TFMessage <strong>3. Processing codes:</strong> Detection processing:<br> Zenodo: https://doi.org/10.5281/zenodo.7066045<br> GitHub: https://github.com/TempleRAIL/yolov3_bottle_detector<br> <br> Measurement model processing:<br> Zenodo: https://doi.org/10.5281/zenodo.7066050<br> GitHub: https://github.com/TempleRAIL/sphd_sensor_models
DOI: 10.14459/2022mp1686728
title: Changing Flows Balance Nutrient Absorption and Bacterial Growth along the Gut

description: Data and code related to article "Changing Flows Balance Nutrient Absorption and Bacterial Growth along the Gut"
DOI: 10.5281/zenodo.6846992
title: TrypTag: plate R4220 (replicate dated 20180417)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate R4220, replicate dated 20180417.
DOI: 10.5281/zenodo.6846993
title: TrypTag: plate R4220 (replicate dated 20180417)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate R4220, replicate dated 20180417.
DOI: 10.5281/zenodo.7071451
title: TrypTag: plate R4220 (replicate dated 20180417)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate R4220, replicate dated 20180417.
DOI: 10.5281/zenodo.6846870
title: TrypTag: plate R4216 (replicate dated 20180417)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate R4216, replicate dated 20180417.
DOI: 10.5281/zenodo.6846871
title: TrypTag: plate R4216 (replicate dated 20180417)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate R4216, replicate dated 20180417.
DOI: 10.5281/zenodo.7071448
title: TrypTag: plate R4216 (replicate dated 20180417)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate R4216, replicate dated 20180417.
DOI: 10.5281/zenodo.6846772
title: TrypTag: plate R4214 (replicate dated 20180320)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate R4214, replicate dated 20180320.
DOI: 10.5281/zenodo.6846773
title: TrypTag: plate R4214 (replicate dated 20180320)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate R4214, replicate dated 20180320.
DOI: 10.5281/zenodo.7071441
title: TrypTag: plate R4214 (replicate dated 20180320)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate R4214, replicate dated 20180320.
DOI: 10.5281/zenodo.6845308
title: TrypTag: plate L9106 (replicate dated 20171117)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate L9106, replicate dated 20171117.
DOI: 10.5281/zenodo.6845309
title: TrypTag: plate L9106 (replicate dated 20171117)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate L9106, replicate dated 20171117.
DOI: 10.5281/zenodo.7071356
title: TrypTag: plate L9106 (replicate dated 20171117)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate L9106, replicate dated 20171117.
DOI: 10.5281/zenodo.6843821
title: TrypTag: plate L9017 (replicate dated 20170727)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate L9017, replicate dated 20170727.
DOI: 10.5281/zenodo.6843822
title: TrypTag: plate L9017 (replicate dated 20170727)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate L9017, replicate dated 20170727.
DOI: 10.5281/zenodo.7071351
title: TrypTag: plate L9017 (replicate dated 20170727)

description: TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen <i>Trypanosoma brucei</i> by endogenous tagging with mNeonGreen (mNG). Raw microscopy data and per-cell line localisation annotation for plate L9017, replicate dated 20170727.
DOI: 10.5281/zenodo.7071706
title: SciExpeM - 10.5281/zenodo.7071706

description: Cong, Tanh Le; Bedjanian, Emma; Dagaut, Philippe - Combustion Science And Technology, 2010, (182), 333-349
DOI: 10.5281/zenodo.7071705
title: SciExpeM - 10.5281/zenodo.7071706

description: Cong, Tanh Le; Bedjanian, Emma; Dagaut, Philippe - Combustion Science And Technology, 2010, (182), 333-349
DOI: 10.5281/zenodo.7071688
title: Diet-induced obesity and NASH impair disease recovery in SARS-CoV-2-infected golden hamsters

description: Obese patients with nonalcoholic steatohepatitis (NASH) are prone to severe forms of COVID-19. There is an urgent need for new treatments that lower the severity of COVID-19 in this vulnerable population. To better replicate the human context, we set up a diet-induced model of obesity associated with dyslipidemia and NASH in the golden hamster (known to be a relevant preclinical model of COVID-19). A 20-week, free-choice diet induces obesity, dyslipidemia and NASH (liver inflammation and fibrosis) in golden hamsters. Obese NASH hamsters have higher blood and pulmonary levels of inflammatory cytokines. In the early stages of a SARS-CoV-2 infection, the lung viral load and inflammation levels were similar in lean hamsters and obese NASH hamsters. However, obese NASH hamsters showed worse recovery (i.e. less resolution of lung inflammation 10 days post-infection (dpi), and lower body weight recovery on dpi 25). Obese NASH hamsters also exhibited higher levels of pulmonary fibrosis on dpi 25. Unlike lean animals, obese NASH hamsters infected with SARS-CoV-2 presented long-lasting dyslipidemia and systemic inflammation. Relative to lean controls, obese NASH hamsters had lower serum levels of angiotensin-converting enzyme 2 activity and higher serum levels of angiotensin II - a component known to favor inflammation and fibrosis. Even though the SARS-CoV-2 infection resulted in early weight loss and incomplete body weight recovery, obese NASH hamsters showed sustained liver steatosis, inflammation, hepatocyte ballooning, and marked liver fibrosis on dpi 25.<strong> </strong>We conclude that diet-induced obesity and NASH impair disease recovery in SARS-CoV-2-infected hamsters. This model might be of value in characterizing the pathophysiologic mechanisms of COVID-19 and in evaluating the efficacy of treatments for the severe forms of COVID-19 observed in obese patients with NASH.
DOI: 10.5281/zenodo.7071687
title: Diet-induced obesity and NASH impair disease recovery in SARS-CoV-2-infected golden hamsters

description: Obese patients with nonalcoholic steatohepatitis (NASH) are prone to severe forms of COVID-19. There is an urgent need for new treatments that lower the severity of COVID-19 in this vulnerable population. To better replicate the human context, we set up a diet-induced model of obesity associated with dyslipidemia and NASH in the golden hamster (known to be a relevant preclinical model of COVID-19). A 20-week, free-choice diet induces obesity, dyslipidemia and NASH (liver inflammation and fibrosis) in golden hamsters. Obese NASH hamsters have higher blood and pulmonary levels of inflammatory cytokines. In the early stages of a SARS-CoV-2 infection, the lung viral load and inflammation levels were similar in lean hamsters and obese NASH hamsters. However, obese NASH hamsters showed worse recovery (i.e. less resolution of lung inflammation 10 days post-infection (dpi), and lower body weight recovery on dpi 25). Obese NASH hamsters also exhibited higher levels of pulmonary fibrosis on dpi 25. Unlike lean animals, obese NASH hamsters infected with SARS-CoV-2 presented long-lasting dyslipidemia and systemic inflammation. Relative to lean controls, obese NASH hamsters had lower serum levels of angiotensin-converting enzyme 2 activity and higher serum levels of angiotensin II - a component known to favor inflammation and fibrosis. Even though the SARS-CoV-2 infection resulted in early weight loss and incomplete body weight recovery, obese NASH hamsters showed sustained liver steatosis, inflammation, hepatocyte ballooning, and marked liver fibrosis on dpi 25.<strong> </strong>We conclude that diet-induced obesity and NASH impair disease recovery in SARS-CoV-2-infected hamsters. This model might be of value in characterizing the pathophysiologic mechanisms of COVID-19 and in evaluating the efficacy of treatments for the severe forms of COVID-19 observed in obese patients with NASH.
DOI: 10.48366/r216423
title: Efficient Transformer Models

description: A summary of architectures that make improvements around computational and memory efficiency of the original Transformer architecture. This is taken from the paper Efficient Transformers: A Survey, published in ACM Computing Surveys. In time-complexity, N refers to the sequence length, B is the local window or block size, $$N_g$$ denotes global model memory length, and $$N_c$$ refers to convolutionally-compressed sequence lengths respectively. The taxonomy of algorithms that improve the general efficiency of the Transformer architecture are presented in https://orkg.org/paper/R211075/R211081.
DOI: 10.48420/21071017.v1
title: MIRRAX: A Reconfigurable Robot for Limited Access Environments - Experimental Dataset

description: ROS Bag files of experiments conducted in support of the IEEE TRO paper "MIRRAX: A Reconfigurable Robot for Limited Access Environments"
DOI: 10.48420/21071017
title: MIRRAX: A Reconfigurable Robot for Limited Access Environments - Experimental Dataset

description: ROS Bag files of experiments conducted in support of the IEEE TRO paper "MIRRAX: A Reconfigurable Robot for Limited Access Environments"
DOI: 10.17632/px3mmn6kg8.1
title: Soccer fan rivalry between two Mexican teams

description: Soccer is the most popular sport in Mexico, with over 55% of the population stating they are followers of one of the many first or second division teams, but even in this soccer-loving country, the city of Guadalajara stands out. Well-known players of the Mexican national team, such as Javier “Chicharito” Hernández, Rafa Márquez, and Andrés Guardado are products of the farm systems of the two current local teams: Guadalajara and Atlas. Though both teams have a similar history, they are far apart in terms of successes. Guadalajara can boast 11 championships in those 100 years, while Atlas has only one, and that was obtained over 70 years ago. Logic would say that Guadalajara would have many more fans than Atlas does, yet the city is almost evenly divided between the two. An online survey was conducted and respondents were 370 cases, 51.2% followers of Guadalajara and 48.8% of Club Atlas. The analysis shows significant statistical differences between motivations of fans of one team compared to the other.
DOI: 10.17632/px3mmn6kg8.2
title: Soccer fan rivalry between two Mexican teams

description: Soccer is the most popular sport in Mexico, with over 55% of the population stating they are followers of one of the many first or second division teams, but even in this soccer-loving country, the city of Guadalajara stands out. Well-known players of the Mexican national team, such as Javier “Chicharito” Hernández, Rafa Márquez, and Andrés Guardado are products of the farm systems of the two current local teams: Guadalajara and Atlas.
Though both teams have a similar history, they are far apart in terms of successes. Guadalajara can boast 11 championships in those 100 years, while Atlas has only one, and that was obtained over 70 years ago.
Logic would say that Guadalajara would have many more fans than Atlas does, yet the city is almost evenly divided between the two. An online survey was conducted and respondents were 370 cases, 51.2% followers of Guadalajara and 48.8% of Club Atlas. The analysis shows significant statistical differences between motivations of fans of one team compared to the other.
DOI: 10.17632/bv6fzsbct8.1
title: Supplementary Table 1: Patterns of Use of Reflectance Confocal Microscopy at a Tertiary Referral Dermatology Clinic

description: Supplementary Table 1
Clinical tracking of diagnostic lesions imaged with RCM: The lesions included in the primary three clinical concern categories (suspected diseases) for which RCM imaging was performed. We show the clinical concern of the lesion, the RCM impression, management decision, and the pathology result of the lesion if and when it is biopsied. Lesions were considered benign if biopsy proven or continued follow-up, and malignant only if biopsy proven. Indeterminate lesions did not have any RCM features diagnostic of a benign or malignant process and therefore were classified as intermediate. The positive predictive value for melanoma was 47%, between 50-79% for BCC (due to empirically treated lesions), and between 31-69% for SCC (due to empirically treated lesions). The negative predictive value is 97% for melanoma, 80-88% for BCC (due to empirically treated lesions), and 83% for SCC.
DOI: 10.17632/66ynzwm63d.1
title: AtBPM1 regulates DDR complex activity and RdDM mediated DNA methylation via a cullin 3 independent mechanism

description: AtBPM1 regulates DDR complex activity and RdDM mediated DNA methylation via a cullin 3 independent mechanism

Mateja Jagić1§, Tamara Vuk1§, Andreja Škiljaica1, Lucija Markulin1, Vedrana Vičić Bočkor1, Mirta Tokić1, Karlo Miškec1, Genadij Razdorov2, Siniša Habazin2 Marko Šoštar3, Igor Weber3, Nataša Bauer1, Dunja Leljak Levanić1*

1Division of Molecular Biology, Department of Biology, Faculty of Science, University of 11 Zagreb, Zagreb, Croatia
2Genos Glycoscience Research Laboratory, Zagreb, Croatia
3Division of Molecular Biology,Institute Ruđer Bošković, Zagreb, Croatia

* Correspondence:
Dunja Leljak Levanić
dunja@zg.biol.pmf.hr

§ Both authors contributed equally to this work

Abstract

The best-known function of MATH-BTB proteins, including those from Arabidopsis (the BPM proteins) is their role as substrate-specific adaptors of CUL3-based E3 ligases in the ubiquitin proteasome pathway. In this process, BTB domain enables assembly with the CUL3, while less conserved MATH domain serves as an adaptor and binds substrates destined for degradation via 26S proteasome. Here, we report a new CUL3 independent role of AtBPM1 in RNA directed DNA methylation (RdDM). Proved by different interaction assays, nuclear fraction of BPM1 interacted with DMS3 and RDM1 proteins, the components of the chromatin remodeling DDR complex that is involved in positioning of RdDM methylation machinery. BTB domain itself had a strong interaction affnity for RDM1, while MATH domain itself, despite detected interactions with both partners, was not essential for the interactions, both suggesting that DMS3 and RDM1 are not substrates for proteasomal degradation. Moreover, in transgenic line lacking a functional CUL3-based E3 ligase complex, DMS3 remained ubiquitinated and the levels of DMS3 did not differ between BPM1-overexpresing plants and wild type. Finally, increased CHH methylation status of the two RdDM controled genes, FWA and CLM41 in BPM1-overexpressing plants confirmed that BPM1 does not participate in DMS3 and RDM1 degradation, instead it is involved in recruitment of the RdDM to specific chromatin positions destined for de novo DNA methylation.
DOI: 10.17632/66ynzwm63d.2
title: BPM1 regulates  RdDM-mediated DNA methylation via a cullin 3 independent mechanism

description: AtBPM1 regulates DDR complex activity and RdDM mediated DNA methylation via a cullin 3 independent mechanism

Mateja Jagić1§, Tamara Vuk1§, Andreja Škiljaica1, Lucija Markulin1, Vedrana Vičić Bočkor1, Mirta Tokić1, Karlo Miškec1, Genadij Razdorov2, Siniša Habazin2 Marko Šoštar3, Igor Weber3, Nataša Bauer1, Dunja Leljak Levanić1*

1Division of Molecular Biology, Department of Biology, Faculty of Science, University of 11 Zagreb, Zagreb, Croatia
2Genos Glycoscience Research Laboratory, Zagreb, Croatia
3Division of Molecular Biology,Institute Ruđer Bošković, Zagreb, Croatia

* Correspondence:
Dunja Leljak Levanić
dunja@zg.biol.pmf.hr

§ Both authors contributed equally to this work

Abstract

The best-known function of MATH-BTB proteins, including those from Arabidopsis (the BPM proteins) is their role as substrate-specific adaptors of CUL3-based E3 ligases in the ubiquitin proteasome pathway. In this process, BTB domain enables assembly with the CUL3, while less conserved MATH domain serves as an adaptor and binds substrates destined for degradation via 26S proteasome. Here, we report a new CUL3 independent role of AtBPM1 in RNA directed DNA methylation (RdDM). Proved by different interaction assays, nuclear fraction of BPM1 interacted with DMS3 and RDM1 proteins, the components of the chromatin remodeling DDR complex that is involved in positioning of RdDM methylation machinery. BTB domain itself had a strong interaction affnity for RDM1, while MATH domain itself, despite detected interactions with both partners, was not essential for the interactions, both suggesting that DMS3 and RDM1 are not substrates for proteasomal degradation. Moreover, in transgenic line lacking a functional CUL3-based E3 ligase complex, DMS3 remained ubiquitinated and the levels of DMS3 did not differ between BPM1-overexpresing plants and wild type. Finally, increased CHH methylation status of the two RdDM controled genes, FWA and CLM41 in BPM1-overexpressing plants confirmed that BPM1 does not participate in DMS3 and RDM1 degradation, instead it is involved in recruitment of the RdDM to specific chromatin positions destined for de novo DNA methylation.
DOI: 10.17632/nnrkbt5zdm.1
title: Digital Economy, COVID-19 and Employment - Data and Commands

description: The compressed file contains the data and commands for the paper titled "Digital Economy, COVID-19 and Employment." The data file named SampleData.dta contains the data set. The command file named Command.do contains all the execution commands. Please note that the commands interact with the data set.
DOI: 10.5519/qd.7624flvw
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.17632/dvvk2gxtwv.1
title: Climate-growth relationships of Daniellia oliveri (Rolfe) Hutch. & Dalziel in the Sudanian zone of Mali, West Africa.

description: These data related to the MS are the raw data.  The data is composed of the annual radial growth of the species of Daniellia oliveri collecte in the Sudanian zone of Mali. The cumulative growth diameter calculated from the annual radial growth. the annual precipitation from 1920 to 2020, the mean annual temperature from 1950 to 2020. There are also the data related to the chronologies (Standard chronology and residual chronology) developed from the species of Daniellia oliveri. The results show that the rainfall are the main factor influencing the tree growth in our study area while the temperature  has influence on the growth of the species of Daniellia oliveri.  The species of Daniellia oliveri can be use for dendroclimatology studies.