cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5883/ds-cerurafr
title: Integrative taxonomic revision of the Cerurina-Afrocerura genus-pair (Lepidoptera, Noctuoidea, Notodontidae, Cerurinae)

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.6084/m9.figshare.23803057.v1
title: Additional file 3 of Novel covalent CDK7 inhibitor potently induces apoptosis in acute myeloid leukemia and synergizes with Venetoclax

description: Additional file 3: Supplementary Table 3.
DOI: 10.6084/m9.figshare.23803054
title: Additional file 2 of Novel covalent CDK7 inhibitor potently induces apoptosis in acute myeloid leukemia and synergizes with Venetoclax

description: Additional file 2: Supplementary Table 2.
DOI: 10.6084/m9.figshare.13317130.v2
title: Chaperone-mediated autophagy controls the turnover of E3 ubiquitin ligase MARCHF5 and regulates mitochondrial dynamics

description: As a highly dynamic organelle, mitochondria undergo constant fission and fusion to change their morphology and function, coping with various stress conditions. Loss of the balance between fission and fusion leads to impaired mitochondria function, which plays a critical role in the pathogenesis of Parkinson disease (PD). Yet the mechanisms behind mitochondria dynamics regulation remain to be fully illustrated. Chaperone-mediated autophagy (CMA) is a lysosome-dependent process that selectively degrades proteins to maintain cellular proteostasis. In this study, we demonstrated that MARCHF5, an E3 ubiquitin ligase required for mitochondria fission, is a CMA substrate. MARCHF5 interacted with key CMA regulators and was degraded by lysosomes. Severe oxidative stress compromised CMA activity and stabilized MARCHF5, which facilitated DNM1L translocation and led to excessive fission. Increase of CMA activity promoted MARCHF5 turnover, attenuated DNM1L translocation, and reduced mitochondria fragmentation, which alleviated mitochondrial dysfunction under oxidative stress. Furthermore, we showed that conditional expression of LAMP2A, the key CMA regulator, in dopaminergic (DA) neurons helped maintain mitochondria morphology and protected DA neuronal viability in a rodent PD model. Our work uncovers a critical role of CMA in maintaining proper mitochondria dynamics, and loss of this regulatory control may occur in PD and underlie its pathogenic process. <b>Abbreviations:</b> CMA: chaperone-mediated autophagy; DA: dopaminergic; DNM1L: dynamin 1 like; FCCP: carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone; HSPA8: heat shock protein family A (Hsp70) member 8; LAMP2A: lysosomal associated membrane protein 2A; MARCHF5: membrane-associated ring-CH-type finger 5; MMP: mitochondria membrane potential; OCR: oxygen consumption rate; 6-OHDA: 6-hydroxydopamine; PD: Parkinson disease; SNc: substantia nigra pars compacta; TEM: transmission electron microscopy; TH: tyrosine hydroxylase; TMRE: tetramethylrhodamine ethyl ester perchlorate; WT: wild type.
DOI: 10.6084/m9.figshare.23803054.v1
title: Additional file 2 of Novel covalent CDK7 inhibitor potently induces apoptosis in acute myeloid leukemia and synergizes with Venetoclax

description: Additional file 2: Supplementary Table 2.
DOI: 10.6084/m9.figshare.13317112
title: Additional file 1 of Characterization of the virulence of Pseudomonas aeruginosa strains causing ventilator-associated pneumonia

description: Additional file 1. Supplementary material
DOI: 10.5883/ds-willszn
title: Pronounced seasonal turnover and intraspecific variation in leaf traits have a limited impact on host choice in leaf-chewing insects on six Salicaceae hosts

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.6084/m9.figshare.13317130
title: Chaperone-mediated autophagy controls the turnover of E3 ubiquitin ligase MARCHF5 and regulates mitochondrial dynamics

description: As a highly dynamic organelle, mitochondria undergo constant fission and fusion to change their morphology and function, coping with various stress conditions. Loss of the balance between fission and fusion leads to impaired mitochondria function, which plays a critical role in the pathogenesis of Parkinson disease (PD). Yet the mechanisms behind mitochondria dynamics regulation remain to be fully illustrated. Chaperone-mediated autophagy (CMA) is a lysosome-dependent process that selectively degrades proteins to maintain cellular proteostasis. In this study, we demonstrated that MARCHF5, an E3 ubiquitin ligase required for mitochondria fission, is a CMA substrate. MARCHF5 interacted with key CMA regulators and was degraded by lysosomes. Severe oxidative stress compromised CMA activity and stabilized MARCHF5, which facilitated DNM1L translocation and led to excessive fission. Increase of CMA activity promoted MARCHF5 turnover, attenuated DNM1L translocation, and reduced mitochondria fragmentation, which alleviated mitochondrial dysfunction under oxidative stress. Furthermore, we showed that conditional expression of LAMP2A, the key CMA regulator, in dopaminergic (DA) neurons helped maintain mitochondria morphology and protected DA neuronal viability in a rodent PD model. Our work uncovers a critical role of CMA in maintaining proper mitochondria dynamics, and loss of this regulatory control may occur in PD and underlie its pathogenic process. <b>Abbreviations:</b> CMA: chaperone-mediated autophagy; DA: dopaminergic; DNM1L: dynamin 1 like; FCCP: carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone; HSPA8: heat shock protein family A (Hsp70) member 8; LAMP2A: lysosomal associated membrane protein 2A; MARCHF5: membrane-associated ring-CH-type finger 5; MMP: mitochondria membrane potential; OCR: oxygen consumption rate; 6-OHDA: 6-hydroxydopamine; PD: Parkinson disease; SNc: substantia nigra pars compacta; TEM: transmission electron microscopy; TH: tyrosine hydroxylase; TMRE: tetramethylrhodamine ethyl ester perchlorate; WT: wild type.
DOI: 10.6084/m9.figshare.13317100.v1
title: Additional file 3 of Whole blood co-expression modules associate with metabolic traits and type 2 diabetes: an IMI-DIRECT study

description: Additional file 3. Supplementary Tables. This file contains Tables. S1 – S14.
DOI: 10.5883/bold:aac4784
title: Overview of Barcode Index Number - BOLD:AAC4784

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.6084/m9.figshare.25213766.v1
title: KD calculation from graphpad

description: Calculation of KD for guanine, acyclovir, and valacyclovir.
DOI: 10.6084/m9.figshare.25213766
title: KD calculation from graphpad

description: Calculation of KD for guanine, acyclovir, and valacyclovir.
DOI: 10.5883/bold:aag2100
title: Overview of Barcode Index Number - BOLD:AAG2100

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.6084/m9.figshare.14890051.v1
title: Alcohol Consumption and Age-related Macular Degeneration: A Systematic Review and Dose–response Meta-analysis

description: <b>Purpose</b>: To perform a systematic review on the association between alcohol consumption and risk of age-related macular degeneration (AMD) using a meta-analytical approach. <b>Method</b>: Systematic literature research was conducted according to the Preferred Reporting Items for Systematic Review and Meta-Analyses guidelines. Both categorical and dose–response meta-analysis was performed separately for early and late AMD. A fixed-effect model was used to calculate pooled effect estimates with 95% confidence interval (CI). <b>Result</b>: Seven studies were included in the analysis with 4,566 and 440 cases of early and late AMD, respectively. Compared to the nondrinkers or occasional drinkers, the pooled effect estimates for early AMD with moderate (1.19, 95% CI [1.03–1.37]) and heavy (1.24, [1.10–1.39]) alcohol consumption, but not light (0.95, [0.90–1.06]) alcohol consumption, were statistically significant. However, the pooled effect estimates for late AMD with light (1.03, [0.79–1.33]), moderate (1.13, [0.83–1.55]), and heavy (0.98, [0.63–1.53]) alcohol consumption were found to be insignificant. A linear dose–response relationship was established (<i>P</i> &lt; .05) between alcohol consumption and risk of early AMD, and the pooled effect estimate for an increase in alcohol consumption of 10 g/day was 1.14 (1.08–1.21). <b>Conclusion</b>: Moderate and heavy alcohol consumption could increase the risk of early AMD, but not late AMD, with a linear dose–response relationship.
DOI: 10.6084/m9.figshare.13317130.v1
title: Chaperone-mediated autophagy controls the turnover of E3 ubiquitin ligase MARCHF5 and regulates mitochondrial dynamics

description: As a highly dynamic organelle, mitochondria undergo constant fission and fusion to change their morphology and function, coping with various stress conditions. Loss of the balance between fission and fusion leads to impaired mitochondria function, which plays a critical role in the pathogenesis of Parkinson disease (PD). Yet the mechanisms behind mitochondria dynamics regulation remain to be fully illustrated. Chaperone-mediated autophagy (CMA) is a lysosome-dependent process that selectively degrades proteins to maintain cellular proteostasis. In this study, we demonstrated that MARCHF5, an E3 ubiquitin ligase required for mitochondria fission, is a CMA substrate. MARCHF5 interacted with key CMA regulators and was degraded by lysosomes. Severe oxidative stress compromised CMA activity and stabilized MARCHF5, which facilitated DNM1L translocation and led to excessive fission. Increase of CMA activity promoted MARCHF5 turnover, attenuated DNM1L translocation, and reduced mitochondria fragmentation, which alleviated mitochondrial dysfunction under oxidative stress. Furthermore, we showed that conditional expression of LAMP2A, the key CMA regulator, in dopaminergic (DA) neurons helped maintain mitochondria morphology and protected DA neuronal viability in a rodent PD model. Our work uncovers a critical role of CMA in maintaining proper mitochondria dynamics, and loss of this regulatory control may occur in PD and underlie its pathogenic process. <b>Abbreviations:</b> CMA: chaperone-mediated autophagy; DA: dopaminergic; DNM1L: dynamin 1 like; FCCP: carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone; HSPA8: heat shock protein family A (Hsp70) member 8; LAMP2A: lysosomal associated membrane protein 2A; MARCHF5: membrane-associated ring-CH-type finger 5; MMP: mitochondria membrane potential; OCR: oxygen consumption rate; 6-OHDA: 6-hydroxydopamine; PD: Parkinson disease; SNc: substantia nigra pars compacta; TEM: transmission electron microscopy; TH: tyrosine hydroxylase; TMRE: tetramethylrhodamine ethyl ester perchlorate; WT: wild type.
DOI: 10.6084/m9.figshare.12788767.v1
title: Additional file 3 of Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields

description: Additional file 3. Pearson correlation analysis (P ≥ 0.05) among functional traits regarding P. notoginseng yields.
DOI: 10.5281/zenodo.10076627
title: Models and analyses of simulated datasets described in "Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN"

description: This repository contains data to inspect and reproduce results described in our tomoDRGN manuscript (https://doi.org/10.1101/2023.05.31.542975). Specifically, this repository contains requisite data and scripts to simulate the datasets used, and the model configurations, weights, logs, and outputs used in our analyses of simulated datasets.
DOI: 10.5281/zenodo.10076628
title: Models and analyses of simulated datasets described in "Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN"

description: This repository contains data to inspect and reproduce results described in our tomoDRGN manuscript (https://doi.org/10.1101/2023.05.31.542975). Specifically, this repository contains requisite data and scripts to simulate the datasets used, and the model configurations, weights, logs, and outputs used in our analyses of simulated datasets.
DOI: 10.6084/m9.figshare.23803051
title: Additional file 1 of Novel covalent CDK7 inhibitor potently induces apoptosis in acute myeloid leukemia and synergizes with Venetoclax

description: Additional file 1: Supplementary Table 1.
DOI: 10.6084/m9.figshare.14361812
title: Additional file 2 of Immunological significance of prognostic alternative splicing signature in hepatocellular carcinoma

description: Additional file 2: Table S1. Univariate Cox regression analysis between AS events and survial. Table S2. Formula prognostic signature of HCC. Table S3. The list of splicing factor (SF) genes. Table S4. Results of correlation between AS events and SFs.
DOI: 10.6084/m9.figshare.12788764.v1
title: Additional file 2 of Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields

description: Additional file 2. Abundance of the metagenomic microbial function profiling (KEGG orthology function category).
DOI: 10.25549/hhrohp-ouc113170524
title: Mandeep Dhaliwal, interview, New York, NY, USA, 2022

description: Mandeep Dhaliwal, New York, New York, USA, 2022 September 29, oral history interview by Lillie Guo, Los Angeles, California, USA. The inteview was conducted over the Internet (Zoom) as part of the Health and Human Rights Oral History Project.Dr. Mandeep Dhaliwal is the Director of the United Nations Development Program's HIV, Health and Development Group. A physician and lawyer, Dr. Dhaliwal has over 20 years of experience working on HIV, health, human rights and evidence-based policy and programming in low-and middle-income countries. She joined UNDP in 2008 as the Cluster Leader: Human Rights, Gender and Sexual Diversities in the HIV/AIDS Group. She was also the architect and lead for the Global Commission on HIV and the Law which UNDP convened on behalf of the Joint UN Program on HIV/AIDS. In her oral history, Dr. Dhaliwal discusses major inflection points in the global HIV response, beginning with her early interventions representing sex workers in India, to her work with the Lawyer’s Collective where she pioneered work on HIV and the law. Dr. Dhaliwal later went on to serve as a senior adviser to the Dutch Royal Tropical Institute’s Special Program on HIV/AIDS and as the lead on HIV care and treatment at the International HIV/AIDS Alliance. She shares critical reflections on centering the voices and experiences of those living with HIV, as well as community engagement and civil society activism.
DOI: 10.5281/zenodo.10652110
title: Colombian Cutín (Pristimantis) frog coloration

description: Pristimantis is the most species-rich genus in all vertebrates (Waddell, Emily H., et al., 2018), containing 614 species. Though very species rich the genus is concentrated in the neotropics and often occupy similar niches, additionally, species often use flash marks to identify each other (Rojas, Bibiana, J. P. Lawrence, and Roberto Márquez., 2023). This dataset contains data on the body colouration (dorsal, and flash marking) of 56 species found in Columbia.  The data set will allow users to make pilot investigations patterns in special distributions, phylogenetic, evolutionary and more withing the highly speciated genera of Pristimantis. The dataset is specified for Colombia due to the high variation of habitats, and biodiversity, additionally, of the 224 species 1/4th of the species where used due to the large sample size and limited time. Species names whose phenotype has not yet been recorded are in the dataset to allow for future additions. Though a major limitation this dataset can be used as a pilot dataset which can expanded upon in the future. Lastly, references can be found on the dataset.
DOI: 10.5281/zenodo.10652111
title: Colombian Cutín (Pristimantis) frog coloration

description: Pristimantis is the most species-rich genus in all vertebrates (Waddell, Emily H., et al., 2018), containing 614 species. Though very species rich the genus is concentrated in the neotropics and often occupy similar niches, additionally, species often use flash marks to identify each other (Rojas, Bibiana, J. P. Lawrence, and Roberto Márquez., 2023). This dataset contains data on the body colouration (dorsal, and flash marking) of 56 species found in Columbia.  The data set will allow users to make pilot investigations patterns in special distributions, phylogenetic, evolutionary and more withing the highly speciated genera of Pristimantis. The dataset is specified for Colombia due to the high variation of habitats, and biodiversity, additionally, of the 224 species 1/4th of the species where used due to the large sample size and limited time. Species names whose phenotype has not yet been recorded are in the dataset to allow for future additions. Though a major limitation this dataset can be used as a pilot dataset which can expanded upon in the future. Lastly, references can be found on the dataset.
DOI: 10.5281/zenodo.10649725
title: Maximum length of teleosts

description: Studies have shown a decline in average body size for many species of fish in recent years. We rely upon many species for food and other consumables. Reduced sizes lead to reduced fishing yields. It is important to identify the cause of this trend. Could it be linked to increasing ocean temperatures or loss of habitiat?

Literature search protocol

Used Google Scholar and Scopus

Search terms - MAXIMUM LENGTH OR BODY SIZE OR BODY MASS, AND TELEOSTS AND LOCATION OR GEOGRAPHIC                      - Sorted most recently published, then most cited.

Metadata Infraclass - taxonomic rank between order and phylum Scientific Name - binomial/latin name Commom Name - Accepted common nameYear observed - Year the data was collected Min/Max longitude - geographic co-ordinatesMin/Max Latitude - geographic co-ordinates Maximum length - Length from mouth to caudal fin in centimetres 

References

Coulson, Peter., Wakefield, Corey., 2022. Reproduction, sexually dimorphic growth, exceptional longevity and low natural mortality of the knifejaw, Oplegnathus woodwardi, from temperate waters in the south-eastern Indian Ocean., Fisheries Research 256

Goodman, M.C., S.M. Hannah, and B.I. Ruttenberg. 2019. The relationship between geographic range extent, sea surface temperature and adult traits in coastal temperate fishes. Journal of Biogeography 46: 1438–1450.

James Wilder Orr (2021) "Three New Small Snailfishes of the Genus Careproctus (Teleostei: Cottiformes: Liparidae) from the Aleutian Islands, Alaska," Ichthyology & Herpetology, 109(2), 456-466,

Lavin, C.P., Gordó-Vilaseca, C., Costello, M.J. et al. Warm and cold temperatures limit the maximum body length of teleost fishes across a latitudinal gradient in Norwegian waters. Environ Biol Fish 105

Price, Samantha et al. (2022). FishShapes v1: functionally relevant measurements of teleost shape and size on three dimensions

RM Foster, A-R Childs, BQ Mann & WM Potts (2022) Age and growth of the Cape knifejaw Oplegnathus conwayi, an endemic South African teleost, African Zoology, 57:1, 1-11

Yoshihiro Fujiwara et al. (2022). Detection of the Largest Deep-Sea-Endemic Teleost Fish at Depths of Over 2,000 m Through a Combination of eDNA Metabarcoding and Baited Camera Observations. Deep sea environments and ecology. Volume 9
DOI: 10.5281/zenodo.10649726
title: Maximum length of teleosts

description: Studies have shown a decline in average body size for many species of fish in recent years. We rely upon many species for food and other consumables. Reduced sizes lead to reduced fishing yields. It is important to identify the cause of this trend. Could it be linked to increasing ocean temperatures or loss of habitiat?

Literature search protocol

Used Google Scholar and Scopus

Search terms - MAXIMUM LENGTH OR BODY SIZE OR BODY MASS, AND TELEOSTS AND LOCATION OR GEOGRAPHIC                      - Sorted most recently published, then most cited.

Metadata Infraclass - taxonomic rank between order and phylum Scientific Name - binomial/latin name Commom Name - Accepted common nameYear observed - Year the data was collected Min/Max longitude - geographic co-ordinatesMin/Max Latitude - geographic co-ordinates Maximum length - Length from mouth to caudal fin in centimetres 

References

Coulson, Peter., Wakefield, Corey., 2022. Reproduction, sexually dimorphic growth, exceptional longevity and low natural mortality of the knifejaw, Oplegnathus woodwardi, from temperate waters in the south-eastern Indian Ocean., Fisheries Research 256

Goodman, M.C., S.M. Hannah, and B.I. Ruttenberg. 2019. The relationship between geographic range extent, sea surface temperature and adult traits in coastal temperate fishes. Journal of Biogeography 46: 1438–1450.

James Wilder Orr (2021) "Three New Small Snailfishes of the Genus Careproctus (Teleostei: Cottiformes: Liparidae) from the Aleutian Islands, Alaska," Ichthyology & Herpetology, 109(2), 456-466,

Lavin, C.P., Gordó-Vilaseca, C., Costello, M.J. et al. Warm and cold temperatures limit the maximum body length of teleost fishes across a latitudinal gradient in Norwegian waters. Environ Biol Fish 105

Price, Samantha et al. (2022). FishShapes v1: functionally relevant measurements of teleost shape and size on three dimensions

RM Foster, A-R Childs, BQ Mann & WM Potts (2022) Age and growth of the Cape knifejaw Oplegnathus conwayi, an endemic South African teleost, African Zoology, 57:1, 1-11

Yoshihiro Fujiwara et al. (2022). Detection of the Largest Deep-Sea-Endemic Teleost Fish at Depths of Over 2,000 m Through a Combination of eDNA Metabarcoding and Baited Camera Observations. Deep sea environments and ecology. Volume 9
DOI: 10.5281/zenodo.10093309
title: Models and analyses of experimental datasets described in "Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN"

description: This repository contains data to inspect and reproduce results described in our tomoDRGN manuscript (https://doi.org/10.1101/2023.05.31.542975). Specifically, this repository contains input STA data (excluding particle stacks which have been deposited as EMPIAR-11843), and the model configurations, weights, logs, and outputs used in our analyses of experimental datasets.
DOI: 10.5281/zenodo.10093310
title: Models and analyses of experimental datasets described in "Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN"

description: This repository contains data to inspect and reproduce results described in our tomoDRGN manuscript (https://doi.org/10.1101/2023.05.31.542975). Specifically, this repository contains input STA data (excluding particle stacks which have been deposited as EMPIAR-11843), and the model configurations, weights, logs, and outputs used in our analyses of experimental datasets.
DOI: 10.5281/zenodo.10648305
title: Zoe Wright Silver Birch Dataset

description: email: zwright475@gmail.com

 

 Please see the README file for the additional information on the dataset.
DOI: 10.5281/zenodo.10648306
title: Zoe Wright Silver Birch Dataset

description: email: zwright475@gmail.com

 

 Please see the README file for the additional information on the dataset.
DOI: 10.6084/m9.figshare.23803051.v1
title: Additional file 1 of Novel covalent CDK7 inhibitor potently induces apoptosis in acute myeloid leukemia and synergizes with Venetoclax

description: Additional file 1: Supplementary Table 1.