cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9164315
title: Circadian oscillations persist in low malignancy breast cancer cells

description: Epidemiological studies have shown that humans with altered circadian rhythms have higher cancer incidence, with breast cancer being one of the most cited examples. To uncover how circadian disruptions may be correlated with breast cancer and its development, prior studies have assessed the expression of <i>BMAL1</i> and <i>PER2</i> core clock genes via RT-qPCR and western blot analyses. These and our own low-resolution data show that <i>BMAL1</i> and <i>PER2</i> expression are suppressed and arrhythmic. We hypothesized that oscillations persist in breast cancer cells, but due to limitations of protocols utilized, cannot be observed. This is especially true where dynamic changes may be subtle. In the present work, we generated luciferase reporter cell lines representing high- and low-grade breast cancers to assess circadian rhythms. We tracked signals for <i>BMAL1</i> and <i>PER2</i> to determine whether and to what extent oscillations exist and provide initial correlations of circadian rhythm alterations with breast cancer aggression. In contrast to previous studies, where no oscillations were apparent in any breast cancer cell line, our luminometry data reveal that circadian oscillations of <i>BMAL1</i> and <i>PER2</i> in fact exist in the low-grade, luminal A MCF7 cells but are not present in high-grade, basal MDA-MB-231 cells. To our knowledge, this is the first evidence of core circadian clock oscillations in breast cancer cells. This work also suggests that circadian rhythms are further disrupted in more aggressive/high tumor grades of breast cancer, and that use of real time luminometry to study additional representatives of breast and other cancer subtypes is merited.
DOI: 10.6084/m9.figshare.9164315.v4
title: Circadian oscillations persist in low malignancy breast cancer cells

description: Epidemiological studies have shown that humans with altered circadian rhythms have higher cancer incidence, with breast cancer being one of the most cited examples. To uncover how circadian disruptions may be correlated with breast cancer and its development, prior studies have assessed the expression of <i>BMAL1</i> and <i>PER2</i> core clock genes via RT-qPCR and western blot analyses. These and our own low-resolution data show that <i>BMAL1</i> and <i>PER2</i> expression are suppressed and arrhythmic. We hypothesized that oscillations persist in breast cancer cells, but due to limitations of protocols utilized, cannot be observed. This is especially true where dynamic changes may be subtle. In the present work, we generated luciferase reporter cell lines representing high- and low-grade breast cancers to assess circadian rhythms. We tracked signals for <i>BMAL1</i> and <i>PER2</i> to determine whether and to what extent oscillations exist and provide initial correlations of circadian rhythm alterations with breast cancer aggression. In contrast to previous studies, where no oscillations were apparent in any breast cancer cell line, our luminometry data reveal that circadian oscillations of <i>BMAL1</i> and <i>PER2</i> in fact exist in the low-grade, luminal A MCF7 cells but are not present in high-grade, basal MDA-MB-231 cells. To our knowledge, this is the first evidence of core circadian clock oscillations in breast cancer cells. This work also suggests that circadian rhythms are further disrupted in more aggressive/high tumor grades of breast cancer, and that use of real time luminometry to study additional representatives of breast and other cancer subtypes is merited.
DOI: 10.6084/m9.figshare.9164315.v3
title: Circadian oscillations persist in low malignancy breast cancer cells

description: Epidemiological studies have shown that humans with altered circadian rhythms have higher cancer incidence, with breast cancer being one of the most cited examples. To uncover how circadian disruptions may be correlated with breast cancer and its development, prior studies have assessed the expression of <i>BMAL1</i> and <i>PER2</i> core clock genes via RT-qPCR and western blot analyses. These and our own low-resolution data show that <i>BMAL1</i> and <i>PER2</i> expression are suppressed and arrhythmic. We hypothesized that oscillations persist in breast cancer cells, but due to limitations of protocols utilized, cannot be observed. This is especially true where dynamic changes may be subtle. In the present work, we generated luciferase reporter cell lines representing high- and low-grade breast cancers to assess circadian rhythms. We tracked signals for <i>BMAL1</i> and <i>PER2</i> to determine whether and to what extent oscillations exist and provide initial correlations of circadian rhythm alterations with breast cancer aggression. In contrast to previous studies, where no oscillations were apparent in any breast cancer cell line, our luminometry data reveal that circadian oscillations of <i>BMAL1</i> and <i>PER2</i> in fact exist in the low-grade, luminal A MCF7 cells but are not present in high-grade, basal MDA-MB-231 cells. To our knowledge, this is the first evidence of core circadian clock oscillations in breast cancer cells. This work also suggests that circadian rhythms are further disrupted in more aggressive/high tumor grades of breast cancer, and that use of real time luminometry to study additional representatives of breast and other cancer subtypes is merited.
DOI: 10.5066/p9bz0lck
title: Tidal Wetland Elevation Projections for Five San Francisco Bay Delta Regions Using WARMER-2, 2000-2100

description: Projections of marsh elevation change with WARMER-2 across five regions of the San Francisco Bay Delta (Cache Yolo, South Delta, North Delta, Central Delta, and Suisun). The model was run across a range of initial elevations for each region and for scenarios of sea-level rise (30, 61, 91, 122, 152, 183, 305 cm by 2100), sediment availability (historic, constant, declining, and increase), and with and without a temporally dynamic tidal range. Results from the Delta Simulation Model 2 hydrodynamic model were used to calculate rates of tide range increase with sea-level rise. WARMER-2 was calibrated using soil cores from Callaway et al 2012 (Rush Ranch and Browns Island cores), and a soil core from Miners Slough. References: Callaway, J.C., Borgnis, E.L., Turner, R.E. and Milan, C.S., 2012. Carbon sequestration and sediment accretion in San Francisco Bay tidal wetlands. Estuaries and Coasts, 35(5), pp.1163-1181.
DOI: 10.6084/m9.figshare.23192822
title: Shal (a-1)

description: Shal ewes ovary tissue
DOI: 10.6084/m9.figshare.23192822.v1
title: Shal (a-1)

description: Shal ewes ovary tissue
DOI: 10.5066/p9xg4ksk
title: Nocturnal Incubation Recess and Flushing Behavior by Duck Hens Nesting in Grizzly Island Wildlife Area 2015-2018

description: This dataset describes nocturnal incubation recess behavior for mallard and gadwall hens nesting in Grizzly Island Wildlife Area in breeding seasons 2015-2018. It includes the frequency, start time and duration of recesses, and details a method for determining whether a recess was initiated in response to a predator at the nest using nest temperature data. These data support the following publication: Croston, R.L., Peterson, S.E., Hartman, C.A., Herzog, M.P., Feldheim, C.L., Casazza, M.L., Ackerman, J.T., 2021. Nocturnal incubation recess and flushing behavior by duck hens. Ecology and Evolution
DOI: 10.6084/m9.figshare.22814129
title: Dataset

description: data collected by google form questionnaire
DOI: 10.6084/m9.figshare.22814129.v2
title: Dataset

description: data collected by google form questionnaire
DOI: 10.5066/p98rj12i
title: Trap records used to analyze trends in mammalian predator control trapping events intended to protect ground-nesting, endangered birds at Haleakal? National Park, Hawai'i (2000 - 2014)

description: Predation and habitat degradation by non-native species are principal terrestrial threats to the federally endangered Hawaiian Petrel ('ua'u, Pterodroma sandwichensis) and Hawaiian Goose (nene, Branta sandvicensis) within Haleakala National Park (HALE), Maui, Hawai'i. Since 1981, HALE has maintained a network of live-traps to control invasive mammalian predators and protect these endangered birds. To continue evaluations of trapping efficiency in HALE, we analyzed 2000 - 2014 trap events. Trap events were divided up into six event types classified into three event categories: no event, other event [bait lost, or trap triggered], or predator event [rat, cat, or mongoose caught]. Event type analysis was divided up for temporal and spatial analysis. Temporal variables included month, year, 'Ua'u Season (off-season, pre-laying, incubation, or nestling), and Trapline (15 different traplines throughout HALE). Temporal variables were also compared to climate variables (Longman et al. 2015) and moon phase. Spatial variables included the number of 'Ua'u burrows around the trap, the distance to roads, trails, fences and other structures, elevation, slope, and vegetation class and cover (derived from HALE unpublished data and LANDFIRE [Landfire, 2010]). These data support the following publication: Kelsey, E.C., Adams, J., Czapanskiy, M.F., Felis, J.J., Yee, J.L., Kaholoaa R.L., and Natividad Bailey, C., 2019, Trends in mammalian predator control trapping events intended to protect ground-nesting, endangered birds at Haleakala National Park, Hawai'i: 2000-14: U.S. Geological Survey Open-File Report 2019-1122, 27 p., https://doi.org/10.3133/ofr20191122. References: Landfire, 2010, Existing Vegetation Type Layer, Existing Vegetation Cover Layer, Elevation Layer, Slope Layer, LANDFIRE 1.3.0, U.S. Department of the Interior, Geological Survey. Accessed 24 October 2016 at http://landfire.cr.usgs.gov/viewer/. Longman, R. J., T. W. Giambelluca, M. A. Nullet and L. L. Loope. 2015. Climatology of Haleakala.
DOI: 10.5281/zenodo.7711520
title: Climate co-benefits of tiger conservation

description: This repository contains the dataset and code used in the publication 'Climate Co-benefits of Tiger Conservation' published in Nature Ecology and Evolution (https://www.nature.com/articles/s41559-023-02069-x). Our study provides the first detailed appraisal of an enhanced tiger conservation policy in India and its benefits to forest protection. We demonstrate how biodiversity conservation initiatives could translate to ecosystem services, specifically additional carbon storage, and present empirical evidence at a broad geographical scale to align biodiversity conservation and climate mitigation goals. Our results suggest that there exist additional opportunities for funding the protection and restoration of species habitats through carbon offsets and valuation of ecosystem services.
DOI: 10.5281/zenodo.7711519
title: Climate co-benefits of tiger conservation

description: This repository contains the dataset and code used in the publication 'Climate Co-benefits of Tiger Conservation' published in Nature Ecology and Evolution (https://www.nature.com/articles/s41559-023-02069-x). Our study provides the first detailed appraisal of an enhanced tiger conservation policy in India and its benefits to forest protection. We demonstrate how biodiversity conservation initiatives could translate to ecosystem services, specifically additional carbon storage, and present empirical evidence at a broad geographical scale to align biodiversity conservation and climate mitigation goals. Our results suggest that there exist additional opportunities for funding the protection and restoration of species habitats through carbon offsets and valuation of ecosystem services.
DOI: 10.18434/mds2-3026
title: Measuring the permittivity tensor of anisotropic DyScO3 to 110 GHz
DOI: 10.22002/p0shh-48m13
title: Dataset: C. albicans UME7 deletion does not have major impacts on white opaque switching, filamentation, or virulence

description: raw data for white opaque switching
DOI: 10.5281/zenodo.7963452
title: IFEED: Interactive Facial Expression and Emotion Detection Dataset

description: Interactive Facial Expression and Emotion Detection (IFEED) is an annotated dataset that can be used to train, validate, and test Deep Learning models for facial expression and emotion recognition. It contains pre-filtered and analysed images of the interactions between the six main characters of the Friends television series, obtained from the video recordings of the Multimodal EmotionLines Dataset (MELD). The images were obtained by decomposing the videos into multiple frames and extracting the facial expression of the correctly identified characters. A team composed of 14 researchers manually verified and annotated the processed data into several classes: Angry, Sad, Happy, Fearful, Disgusted, Surprised and Neutral. IFEED can be valuable for the development of intelligent facial expression recognition solutions and emotion detection software, enabling binary or multi-class classification, or even anomaly detection or clustering tasks. The images with ambiguous or very subtle facial expressions can be repurposed for adversarial learning. The dataset can be combined with additional data recordings to create more complete and extensive datasets and improve the generalization of robust deep learning models.
description: This work was done and funded under project For-Pharmacy (P2020-COMPETE-FEDER nr 070053). This work has also received funding from UIDB/00760/2020.
DOI: 10.5281/zenodo.7971730
title: IFEED: Interactive Facial Expression and Emotion Detection Dataset

description: Interactive Facial Expression and Emotion Detection (IFEED) is an annotated dataset that can be used to train, validate, and test Deep Learning models for facial expression and emotion recognition. It contains pre-filtered and analysed images of the interactions between the six main characters of the Friends television series, obtained from the video recordings of the Multimodal EmotionLines Dataset (MELD). The images were obtained by decomposing the videos into multiple frames and extracting the facial expression of the correctly identified characters. A team composed of 14 researchers manually verified and annotated the processed data into several classes: Angry, Sad, Happy, Fearful, Disgusted, Surprised and Neutral. IFEED can be valuable for the development of intelligent facial expression recognition solutions and emotion detection software, enabling binary or multi-class classification, or even anomaly detection or clustering tasks. The images with ambiguous or very subtle facial expressions can be repurposed for adversarial learning. The dataset can be combined with additional data recordings to create more complete and extensive datasets and improve the generalization of robust deep learning models.
description: This work was done and funded under project For-Pharmacy (P2020-COMPETE-FEDER nr 070053). This work has also received funding from UIDB/00760/2020.
DOI: 10.5281/zenodo.7963451
title: IFEED: Interactive Facial Expression and Emotion Detection Dataset

description: Interactive Facial Expression and Emotion Detection (IFEED) is an annotated dataset that can be used to train, validate, and test Deep Learning models for facial expression and emotion recognition. It contains pre-filtered and analysed images of the interactions between the six main characters of the Friends television series, obtained from the video recordings of the Multimodal EmotionLines Dataset (MELD). The images were obtained by decomposing the videos into multiple frames and extracting the facial expression of the correctly identified characters. A team composed of 14 researchers manually verified and annotated the processed data into several classes: Angry, Sad, Happy, Fearful, Disgusted, Surprised and Neutral. IFEED can be valuable for the development of intelligent facial expression recognition solutions and emotion detection software, enabling binary or multi-class classification, or even anomaly detection or clustering tasks. The images with ambiguous or very subtle facial expressions can be repurposed for adversarial learning. The dataset can be combined with additional data recordings to create more complete and extensive datasets and improve the generalization of robust deep learning models.
description: This work was done and funded under project For-Pharmacy (P2020-COMPETE-FEDER nr 070053). This work has also received funding from UIDB/00760/2020.
DOI: 10.6084/m9.figshare.13096416
title: RepoMan stimulates the chromosome-dependent pathway of microtubule assembly

description: RepoMan is a chromosome-associated scaffold protein that integrates signaling of multiple kinases and phosphatases to coordinate spindle-kinetochore interactions, chromosome (de)condensation and nuclear envelope (dis)assembly during mitosis. Another key mitotic event is the assembly of a microtubule-based spindle, which involves redundant pathways emanating from the centrosomes, microtubules and chromosomes. Here we describe a novel mitotic function of RepoMan in regulating chromosome-dependent microtubule assembly. At limiting concentrations of microtubule-destabilizing agents, RepoMan-depleted cells showed enhanced chromosome clustering. This clustering was completely dependent on the partial inhibition of microtubule growth originating from the chromosome-dependent pathway. We also demonstrated that RepoMan interacts with prime regulators of the chromosome-dependent spindle assembly such as NuSAP1, NuMA, and TPX2. In addition, RepoMan was required to enable or maintain phosphorylation of NuSAP1 at CDK sites, thereby enabling activation of NuSAP1 through dissociation of inhibitory importin β/7. Our data identify RepoMan as an enhancer of microtubule assembly at chromosomes.
DOI: 10.6084/m9.figshare.13096416.v1
title: RepoMan stimulates the chromosome-dependent pathway of microtubule assembly

description: RepoMan is a chromosome-associated scaffold protein that integrates signaling of multiple kinases and phosphatases to coordinate spindle-kinetochore interactions, chromosome (de)condensation and nuclear envelope (dis)assembly during mitosis. Another key mitotic event is the assembly of a microtubule-based spindle, which involves redundant pathways emanating from the centrosomes, microtubules and chromosomes. Here we describe a novel mitotic function of RepoMan in regulating chromosome-dependent microtubule assembly. At limiting concentrations of microtubule-destabilizing agents, RepoMan-depleted cells showed enhanced chromosome clustering. This clustering was completely dependent on the partial inhibition of microtubule growth originating from the chromosome-dependent pathway. We also demonstrated that RepoMan interacts with prime regulators of the chromosome-dependent spindle assembly such as NuSAP1, NuMA, and TPX2. In addition, RepoMan was required to enable or maintain phosphorylation of NuSAP1 at CDK sites, thereby enabling activation of NuSAP1 through dissociation of inhibitory importin β/7. Our data identify RepoMan as an enhancer of microtubule assembly at chromosomes.
DOI: 10.6084/m9.figshare.13174909
title: Intravital imaging reveals cell cycle-dependent myogenic cell migration during muscle regeneration

description: During muscle regeneration, extracellular signal-regulated kinase (ERK) promotes both proliferation and migration. However, the relationship between proliferation and migration is poorly understood in this context. To elucidate this complex relationship on a physiological level, we established an intravital imaging system for measuring ERK activity, migration speed, and cell-cycle phases in mouse muscle satellite cell-derived myogenic cells. We found that <i>in vivo</i>, ERK is maximally activated in myogenic cells two days after injury, and this is then followed by increases in cell number and motility. With limited effects of ERK activity on migration on an acute timescale, we hypothesized that ERK increases migration speed in the later phase by promoting cell-cycle progression. Our cell-cycle analysis further revealed that in myogenic cells, ERK activity is critical for G1/S transition, and cells migrate more rapidly in S/G2 phase 3 days after injury. Finally, migration speed of myogenic cells was suppressed after CDK1/2—but not CDK1—inhibitor treatment, demonstrating a critical role of CDK2 in myogenic cell migration. Overall, our study demonstrates that in myogenic cells, the ERK-CDK2 axis promotes not only G1/S transition but also migration, thus providing a novel mechanism for efficient muscle regeneration.
DOI: 10.6084/m9.figshare.13174909.v1
title: Intravital imaging reveals cell cycle-dependent myogenic cell migration during muscle regeneration

description: During muscle regeneration, extracellular signal-regulated kinase (ERK) promotes both proliferation and migration. However, the relationship between proliferation and migration is poorly understood in this context. To elucidate this complex relationship on a physiological level, we established an intravital imaging system for measuring ERK activity, migration speed, and cell-cycle phases in mouse muscle satellite cell-derived myogenic cells. We found that <i>in vivo</i>, ERK is maximally activated in myogenic cells two days after injury, and this is then followed by increases in cell number and motility. With limited effects of ERK activity on migration on an acute timescale, we hypothesized that ERK increases migration speed in the later phase by promoting cell-cycle progression. Our cell-cycle analysis further revealed that in myogenic cells, ERK activity is critical for G1/S transition, and cells migrate more rapidly in S/G2 phase 3 days after injury. Finally, migration speed of myogenic cells was suppressed after CDK1/2—but not CDK1—inhibitor treatment, demonstrating a critical role of CDK2 in myogenic cell migration. Overall, our study demonstrates that in myogenic cells, the ERK-CDK2 axis promotes not only G1/S transition but also migration, thus providing a novel mechanism for efficient muscle regeneration.
DOI: 10.6084/m9.figshare.13134837
title: RETRACTED ARTICLE: LncRNA GAS5/miR‑4465 axis regulates the malignant potential of nasopharyngeal carcinoma by targeting COX2

description: We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: Qiong Zhong, Zongqi Wang, Xiaohong Liao, Renrui Wu and Xiaoqing Guo. LncRNA GAS5/miR‑4465 axis regulates the malignant potential of nasopharyngeal carcinoma by targeting COX2. Cell Cycle. 2020;19(22):3004-3017. doi: 10.1080/15384101.2020.1816280 Since publication, concerns have been raised about the integrity of the data in the article. When approached for an explanation, the authors checked their data and confirmed there are fundamental errors present. Therefore, they have agreed to the retraction of this article. The authors apologise for this oversight. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
DOI: 10.6084/m9.figshare.13134837.v2
title: RETRACTED ARTICLE: LncRNA GAS5/miR‑4465 axis regulates the malignant potential of nasopharyngeal carcinoma by targeting COX2

description: We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: Qiong Zhong, Zongqi Wang, Xiaohong Liao, Renrui Wu and Xiaoqing Guo. LncRNA GAS5/miR‑4465 axis regulates the malignant potential of nasopharyngeal carcinoma by targeting COX2. Cell Cycle. 2020;19(22):3004-3017. doi: 10.1080/15384101.2020.1816280 Since publication, concerns have been raised about the integrity of the data in the article. When approached for an explanation, the authors checked their data and confirmed there are fundamental errors present. Therefore, they have agreed to the retraction of this article. The authors apologise for this oversight. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.