cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2064942.v3
title: Archaeal metadata with OTU assignments, taxonomy, and environmental classification

description: Archaeal metadata with OTU assignments, taxonomy, and environmental classification
DOI: 10.6084/m9.figshare.2064882
title: ASH.pdf

description: ASH paper presentation<br>
DOI: 10.6084/m9.figshare.2064885
title: Results of simulation study

description: Results of simulation study on smoothing algorithms on the performance of parallel analysis in factor analysis of ordered categorical items<br>
DOI: 10.6084/m9.figshare.2064924.v1
title: all_archaea.filter.unique.precluster.an.rarefaction.gz

description: Archaeal rarefaction data at unique, 0.03, 0.05, 0.10, and 0.20
DOI: 10.6084/m9.figshare.2064885.v1
title: Results of simulation study

description: Results of simulation study on smoothing algorithms on the performance of parallel analysis in factor analysis of ordered categorical items<br>
DOI: 10.6084/m9.figshare.2064927.v2
title: bacteria.v123.metadata.gz

description: Bacterial metadata with OTU assignments, taxonomy, and environmental classification
DOI: 10.6084/m9.figshare.2064924.v2
title: Archaeal rarefaction data at unique, 0.03, 0.05, 0.10, and 0.20

description: Archaeal rarefaction data at unique, 0.03, 0.05, 0.10, and 0.20
DOI: 10.6084/m9.figshare.2064882.v3
title: ASH.pdf

description: ASH paper presentation<br>
DOI: 10.6084/m9.figshare.2064927.v3
title: Bacterial metadata with OTU assignments, taxonomy, and environmental classification

description: Bacterial metadata with OTU assignments, taxonomy, and environmental classification
DOI: 10.6084/m9.figshare.2064882.v2
title: ASH.pdf

description: ASH paper presentation<br>
DOI: 10.6084/m9.figshare.2064828
title: Exact Optimal Confidence Intervals for Hypergeometric Parameters

description: For a hypergeometric distribution, denoted by Hyper(M,N,n), where <i>N</i> is the population size, <i>M</i> is the number of population units with some attribute, and <i>n</i> is the given sample size, there are two parametric cases: (i) <i>N</i> is unknown and <i>M</i> is given; (ii) <i>M</i> is unknown and <i>N</i> is given. For each case, we first show that the minimum coverage probability of commonly used approximate intervals is much smaller than the nominal level for any <i>n</i>, then we provide exact smallest lower and upper one-sided confidence intervals and an exact admissible two-sided confidence interval, a complete set of solutions, for each parameter. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2064828.v1
title: Exact Optimal Confidence Intervals for Hypergeometric Parameters

description: For a hypergeometric distribution, denoted by Hyper(M,N,n), where <i>N</i> is the population size, <i>M</i> is the number of population units with some attribute, and <i>n</i> is the given sample size, there are two parametric cases: (i) <i>N</i> is unknown and <i>M</i> is given; (ii) <i>M</i> is unknown and <i>N</i> is given. For each case, we first show that the minimum coverage probability of commonly used approximate intervals is much smaller than the nominal level for any <i>n</i>, then we provide exact smallest lower and upper one-sided confidence intervals and an exact admissible two-sided confidence interval, a complete set of solutions, for each parameter. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2064864.v2
title: ANALYZING PULSE POSITION MODULATION TIME HOPPING UWB IN IEEE UWB CHANNEL, multipath channel, GESJ: Computer Science and Telecommunications journal

description: Ultra-wideband (UWB) employs very narrow band pulses of nano-seconds duration to provide high data rate communications. Pulses spread the energy over a wide frequency because of that it is called ultra-wideband. Ultra wideband (UWB) technology, useful for both communication and sensing applications, uses the radio spectrum differently than the vast majority of radio communication technologies. In this paper, we will discuss the UWB pulse position multiple access modulation schemes using rake configurations with help of MATLAB simulations.
DOI: 10.6084/m9.figshare.2064684
title: BCL10 is recruited to sites of DNA damage to facilitate DNA double-strand break repair

description: Recent studies have found BCL10 can localize to the nucleus and that this is linked to tumor aggression and poorer prognosis. These studies suggest that BCL10 localization plays a novel role in the nucleus that may contribute to cellular transformation and carcinogenesis. In this study, we show that BCL10 functions as part of the DNA damage response (DDR). We found that BCL10 facilitates the rapid recruitment of RPA, BRCA1 and RAD51 to sites of DNA damage. Furthermore, we also found that ATM phosphorylates BCL10 in response to DNA damage. Functionally, BCL10 promoted DNA double-strand breaks repair, enhancing cell survival after DNA damage. Taken together our results suggest a novel role for BCL10 in the repair of DNA lesions.
DOI: 10.6084/m9.figshare.2064684.v1
title: BCL10 is recruited to sites of DNA damage to facilitate DNA double-strand break repair

description: Recent studies have found BCL10 can localize to the nucleus and that this is linked to tumor aggression and poorer prognosis. These studies suggest that BCL10 localization plays a novel role in the nucleus that may contribute to cellular transformation and carcinogenesis. In this study, we show that BCL10 functions as part of the DNA damage response (DDR). We found that BCL10 facilitates the rapid recruitment of RPA, BRCA1 and RAD51 to sites of DNA damage. Furthermore, we also found that ATM phosphorylates BCL10 in response to DNA damage. Functionally, BCL10 promoted DNA double-strand breaks repair, enhancing cell survival after DNA damage. Taken together our results suggest a novel role for BCL10 in the repair of DNA lesions.
DOI: 10.6084/m9.figshare.2064693
title: Tetraploidization or autophagy: The ultimate fate of senescent human endometrial stem cells under ATM or p53 inhibition

description: Previously we demonstrated that endometrium-derived human mesenchymal stem cells (hMESCs) via activation of the ATM/p53/p21/Rb pathway enter the premature senescence in response to oxidative stress. Down regulation effects of the key components of this signaling pathway, particularly ATM and p53, on a fate of stressed hMESCs have not yet been investigated. In the present study by using the specific inhibitors Ku55933 and Pifithrin-α, we confirmed implication of both ATM and p53 in H<sub>2</sub>O<sub>2</sub>-induced senescence of hMESCs. ATM or p53 down regulation was shown to modulate differently the cellular fate of H<sub>2</sub>O<sub>2</sub>-treated hMESCs. ATM inhibition allowed H<sub>2</sub>O<sub>2</sub>-stimulated hMESCs to escape the permanent cell cycle arrest due to loss of the functional ATM/p53/p21/Rb pathway, and induced bypass of mitosis and re-entry into S phase, resulting in tetraploid cells. On the contrary, suppression of the p53 transcriptional activity caused a pronounced cell death of H<sub>2</sub>O<sub>2</sub>-treated hMESCs via autophagy induction. The obtained data clearly demonstrate that down regulation of ATM or p53 shifts senescence of human endometrial stem cells toward tetraploidization or autophagy.
DOI: 10.6084/m9.figshare.2064693.v1
title: Tetraploidization or autophagy: The ultimate fate of senescent human endometrial stem cells under ATM or p53 inhibition

description: ABSTRACTPreviously we demonstrated that endometrium-derived human mesenchymal stem cells (hMESCs) via activation of the ATM/p53/p21/Rb pathway enter the premature senescence in response to oxidative stress. Down regulation effects of the key components of this signaling pathway, particularly ATM and p53, on a fate of stressed hMESCs have not yet been investigated. In the present study by using the specific inhibitors Ku55933 and Pifithrin-α, we confirmed implication of both ATM and p53 in H<sub>2</sub>O<sub>2</sub>-induced senescence of hMESCs. ATM or p53 down regulation was shown to modulate differently the cellular fate of H<sub>2</sub>O<sub>2</sub>-treated hMESCs. ATM inhibition allowed H<sub>2</sub>O<sub>2</sub>-stimulated hMESCs to escape the permanent cell cycle arrest due to loss of the functional ATM/p53/p21/Rb pathway, and induced bypass of mitosis and re-entry into S phase, resulting in tetraploid cells. On the contrary, suppression of the p53 transcriptional activity caused a pronounced cell death of H<sub>2</sub>O<sub>2</sub>-treated hMESCs via autophagy induction. The obtained data clearly demonstrate that down regulation of ATM or p53 shifts senescence of human endometrial stem cells toward tetraploidization or autophagy.
DOI: 10.5281/zenodo.4013873
title: Parametrization of lakes water dynamics in the ISBA-CTRIP land surface system (SURFEX v8.1)

description: Supplement for the scientific paper CTRIP_MLake submitted in GMD
DOI: 10.6084/m9.figshare.2064669
title: Direct interactions with both p27 and Cdk2 regulate Spy1-mediated proliferation <i>in vivo</i> and <i>in vitro</i>

description: Families of cyclin-like proteins have emerged that bind and activate cyclin dependent kinases (Cdk)s, directing the phosphorylation of noncanonical Cdk substrates. One of these proteins, Spy1, has demonstrated the unique ability to directly bind and activate both Cdk1 and Cdk2, as well as binding and promoting the degradation of at least one Cdk inhibitor, p27<sup>Kip1</sup>. Spy1 accelerates somatic cell growth and proliferation and is implicated in a number of human cancers including the breast, brain and liver. Herein we isolate key residues mediating the direct interaction with p27. We use mutants of Spy1 to determine the physiological role of direct interactions with distinct binding partners Cdk2 and p27. We demonstrate that disrupting the direct interaction with either Spy1 binding partner decreased endogenous activity of Cdk2, as well as Spy1-mediated proliferation. However, only the direct interaction with p27 was essential for Spy1-mediated effects on p27 stability. <i>In vivo</i> neither mutation completely prevented tumorigenesis, although each mutation slowed the rate of Spy1-mediated tumorigenesis and decreased overall tumor volumes. This work supports the conclusion that direct interaction with both p27 and Cdk2 contribute to Spy1-mediated effects on cell growth. It is important to elucidate the dynamics of these interactions and to consider these data when assessing functional outcomes.
DOI: 10.6084/m9.figshare.2064669.v2
title: Direct interactions with both p27 and Cdk2 regulate Spy1-mediated proliferation <i>in vivo</i> and <i>in vitro</i>

description: Families of cyclin-like proteins have emerged that bind and activate cyclin dependent kinases (Cdk)s, directing the phosphorylation of noncanonical Cdk substrates. One of these proteins, Spy1, has demonstrated the unique ability to directly bind and activate both Cdk1 and Cdk2, as well as binding and promoting the degradation of at least one Cdk inhibitor, p27<sup>Kip1</sup>. Spy1 accelerates somatic cell growth and proliferation and is implicated in a number of human cancers including the breast, brain and liver. Herein we isolate key residues mediating the direct interaction with p27. We use mutants of Spy1 to determine the physiological role of direct interactions with distinct binding partners Cdk2 and p27. We demonstrate that disrupting the direct interaction with either Spy1 binding partner decreased endogenous activity of Cdk2, as well as Spy1-mediated proliferation. However, only the direct interaction with p27 was essential for Spy1-mediated effects on p27 stability. <i>In vivo</i> neither mutation completely prevented tumorigenesis, although each mutation slowed the rate of Spy1-mediated tumorigenesis and decreased overall tumor volumes. This work supports the conclusion that direct interaction with both p27 and Cdk2 contribute to Spy1-mediated effects on cell growth. It is important to elucidate the dynamics of these interactions and to consider these data when assessing functional outcomes.
DOI: 10.6084/m9.figshare.2064693.v3
title: Tetraploidization or autophagy: The ultimate fate of senescent human endometrial stem cells under ATM or p53 inhibition

description: Previously we demonstrated that endometrium-derived human mesenchymal stem cells (hMESCs) via activation of the ATM/p53/p21/Rb pathway enter the premature senescence in response to oxidative stress. Down regulation effects of the key components of this signaling pathway, particularly ATM and p53, on a fate of stressed hMESCs have not yet been investigated. In the present study by using the specific inhibitors Ku55933 and Pifithrin-α, we confirmed implication of both ATM and p53 in H<sub>2</sub>O<sub>2</sub>-induced senescence of hMESCs. ATM or p53 down regulation was shown to modulate differently the cellular fate of H<sub>2</sub>O<sub>2</sub>-treated hMESCs. ATM inhibition allowed H<sub>2</sub>O<sub>2</sub>-stimulated hMESCs to escape the permanent cell cycle arrest due to loss of the functional ATM/p53/p21/Rb pathway, and induced bypass of mitosis and re-entry into S phase, resulting in tetraploid cells. On the contrary, suppression of the p53 transcriptional activity caused a pronounced cell death of H<sub>2</sub>O<sub>2</sub>-treated hMESCs via autophagy induction. The obtained data clearly demonstrate that down regulation of ATM or p53 shifts senescence of human endometrial stem cells toward tetraploidization or autophagy.
DOI: 10.6084/m9.figshare.2064669.v1
title: Direct interactions with both p27 and Cdk2 regulate Spy1-mediated proliferation <i>in vivo</i> and <i>in vitro</i>

description: Families of cyclin-like proteins have emerged that bind and activate cyclin dependent kinases (Cdk)s, directing the phosphorylation of noncanonical Cdk substrates. One of these proteins, Spy1, has demonstrated the unique ability to directly bind and activate both Cdk1 and Cdk2, as well as binding and promoting the degradation of at least one Cdk inhibitor, p27<sup>Kip1</sup>. Spy1 accelerates somatic cell growth and proliferation and is implicated in a number of human cancers including the breast, brain and liver. Herein we isolate key residues mediating the direct interaction with p27. We use mutants of Spy1 to determine the physiological role of direct interactions with distinct binding partners Cdk2 and p27. We demonstrate that disrupting the direct interaction with either Spy1 binding partner decreased endogenous activity of Cdk2, as well as Spy1-mediated proliferation. However, only the direct interaction with p27 was essential for Spy1-mediated effects on p27 stability. <i>In vivo</i> neither mutation completely prevented tumorigenesis, although each mutation slowed the rate of Spy1-mediated tumorigenesis and decreased overall tumor volumes. This work supports the conclusion that direct interaction with both p27 and Cdk2 contribute to Spy1-mediated effects on cell growth. It is important to elucidate the dynamics of these interactions and to consider these data when assessing functional outcomes.
DOI: 10.5281/zenodo.4013872
title: Parametrization of lakes water dynamics in the ISBA-CTRIP land surface system (SURFEX v8.1)

description: Supplement for the scientific paper CTRIP_MLake submitted in GMD
DOI: 10.6084/m9.figshare.2064693.v2
title: Tetraploidization or autophagy: The ultimate fate of senescent human endometrial stem cells under ATM or p53 inhibition

description: Previously we demonstrated that endometrium-derived human mesenchymal stem cells (hMESCs) via activation of the ATM/p53/p21/Rb pathway enter the premature senescence in response to oxidative stress. Down regulation effects of the key components of this signaling pathway, particularly ATM and p53, on a fate of stressed hMESCs have not yet been investigated. In the present study by using the specific inhibitors Ku55933 and Pifithrin-α, we confirmed implication of both ATM and p53 in H<sub>2</sub>O<sub>2</sub>-induced senescence of hMESCs. ATM or p53 down regulation was shown to modulate differently the cellular fate of H<sub>2</sub>O<sub>2</sub>-treated hMESCs. ATM inhibition allowed H<sub>2</sub>O<sub>2</sub>-stimulated hMESCs to escape the permanent cell cycle arrest due to loss of the functional ATM/p53/p21/Rb pathway, and induced bypass of mitosis and re-entry into S phase, resulting in tetraploid cells. On the contrary, suppression of the p53 transcriptional activity caused a pronounced cell death of H<sub>2</sub>O<sub>2</sub>-treated hMESCs via autophagy induction. The obtained data clearly demonstrate that down regulation of ATM or p53 shifts senescence of human endometrial stem cells toward tetraploidization or autophagy.
DOI: 10.6084/m9.figshare.2064531
title: Assessing the phylogenetic dimension of Australian <i>Acacia</i> species introduced outside their native ranges

description: AbstractBiological invasion is a long process that starts with humans introducing intentionally (most of the time) species into a new environment to benefit from the ecosystem services that these species provide. Increasing evidence suggests that species providing ecosystem services might be phylogenetically closer than expected, but only a few studies actually demonstrate this. Also, recent studies indicate that naturalized and invasive species are two functionally distinct groups, but evidence that they are also two phylogenetically distinct groups is mixed. Using the set of Australian <i>Acacia</i> species known to have been introduced intentionally by humans to several parts of the world for the ecosystem services they provide, we first tested whether there is a phylogenetic pattern in the subset of introduced species. We found that species moved beyond Australia are phylogenetically more closely related than expected at random, suggesting that the ecosystem services that guide human-mediated introduction of these species into new areas (e.g. famine food, medicines, fuel, fodder, ornament) may be shared between closely related species. We also found that naturalized non-invasive and naturalized invasive species are closely related and both are not a phylogenetically random subset of introduced species based on mean phylogenetic distance, suggesting that naturalization and invasion processes may be phylogenetically mediated. Collectively, our study indicates that phylogeny might play different roles at different stages of the biological invasion process.
DOI: 10.6084/m9.figshare.2064516
title: Modern surface pollen assemblages from the Middle and High Atlas, Morocco: insights into pollen representation and transport

description: Thirty-three modern surface samples were collected in the environmentally and climatologically contrasting regions of the Middle and High Atlas Mountains, Morocco. Samples representing forest and steppe montane environments (1935–2760 m above sea level) are clustered around study sites at Lake Tislit (High Atlas, semi-arid oro-Mediterranean bioclime) and Lake Sidi Ali and Michliffen (Middle Atlas, sub-humid montane Mediterranean bioclime). Good discrimination between regional pollen spectra is evident, with Middle Atlas samples reflecting higher arboreal cover (<i>Cedrus</i> and evergreen <i>Quercus</i>) and High Atlas samples with high abundances of non-arboreal taxa, including <i>Artemisia</i> and Fabaceae. These four taxa (<i>Cedrus</i>, evergreen <i>Quercus, Artemisia</i> and Fabaceae) are furthermore shown to be reliable indicators of local source vegetation within a 100 m<sup>2</sup> quadrat, taking into account threshold abundances of 7%, 20%, 4% and 10%, respectively. Deciduous <i>Quercus, Olea</i> and <i>Phillyrea</i> show long-distance pollen dispersal across both regions, contributing to non-trivial arboreal pollen (AP) values of up to 35% (typically 20–30%) in the High Atlas spectra. In the Middle Atlas, AP values of 40 to 50% occur in open sampling locations and &gt; 60% under forest canopy cover. These insights should be taken into account when interpreting ancient pollen spectra from regional lakes and bogs for palaeoenvironmental reconstruction.
DOI: 10.6084/m9.figshare.2064531.v1
title: Assessing the phylogenetic dimension of Australian <i>Acacia</i> species introduced outside their native ranges

description: AbstractBiological invasion is a long process that starts with humans introducing intentionally (most of the time) species into a new environment to benefit from the ecosystem services that these species provide. Increasing evidence suggests that species providing ecosystem services might be phylogenetically closer than expected, but only a few studies actually demonstrate this. Also, recent studies indicate that naturalized and invasive species are two functionally distinct groups, but evidence that they are also two phylogenetically distinct groups is mixed. Using the set of Australian <i>Acacia</i> species known to have been introduced intentionally by humans to several parts of the world for the ecosystem services they provide, we first tested whether there is a phylogenetic pattern in the subset of introduced species. We found that species moved beyond Australia are phylogenetically more closely related than expected at random, suggesting that the ecosystem services that guide human-mediated introduction of these species into new areas (e.g. famine food, medicines, fuel, fodder, ornament) may be shared between closely related species. We also found that naturalized non-invasive and naturalized invasive species are closely related and both are not a phylogenetically random subset of introduced species based on mean phylogenetic distance, suggesting that naturalization and invasion processes may be phylogenetically mediated. Collectively, our study indicates that phylogeny might play different roles at different stages of the biological invasion process.
DOI: 10.6084/m9.figshare.2064516.v1
title: Modern surface pollen assemblages from the Middle and High Atlas, Morocco: insights into pollen representation and transport

description: Thirty-three modern surface samples were collected in the environmentally and climatologically contrasting regions of the Middle and High Atlas Mountains, Morocco. Samples representing forest and steppe montane environments (1935–2760 m above sea level) are clustered around study sites at Lake Tislit (High Atlas, semi-arid oro-Mediterranean bioclime) and Lake Sidi Ali and Michliffen (Middle Atlas, sub-humid montane Mediterranean bioclime). Good discrimination between regional pollen spectra is evident, with Middle Atlas samples reflecting higher arboreal cover (<i>Cedrus</i> and evergreen <i>Quercus</i>) and High Atlas samples with high abundances of non-arboreal taxa, including <i>Artemisia</i> and Fabaceae. These four taxa (<i>Cedrus</i>, evergreen <i>Quercus, Artemisia</i> and Fabaceae) are furthermore shown to be reliable indicators of local source vegetation within a 100 m<sup>2</sup> quadrat, taking into account threshold abundances of 7%, 20%, 4% and 10%, respectively. Deciduous <i>Quercus, Olea</i> and <i>Phillyrea</i> show long-distance pollen dispersal across both regions, contributing to non-trivial arboreal pollen (AP) values of up to 35% (typically 20–30%) in the High Atlas spectra. In the Middle Atlas, AP values of 40 to 50% occur in open sampling locations and &gt; 60% under forest canopy cover. These insights should be taken into account when interpreting ancient pollen spectra from regional lakes and bogs for palaeoenvironmental reconstruction.