cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12851976.v1
title: Incomplete removal of ribosomal RNA can affect chromatin RNA-seq data analysis

description: Incomplete removal of ribosomal RNA can affect chromatin RNA-seq data analysis
DOI: 10.6084/m9.figshare.12851976
title: Incomplete removal of ribosomal RNA can affect chromatin RNA-seq data analysis

description: Incomplete removal of ribosomal RNA can affect chromatin RNA-seq data analysis
DOI: 10.6084/m9.figshare.12851973
title: RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcription <i>in cis</i>

description: Transcription elongation is a highly regulated process affected by many proteins, RNAs and the underlying DNA. Here we show that the nascent RNA can interfere with transcription in human cells, extending our previous findings from bacteria and yeast. We identified a variety of Pol II-binding aptamers (RAPs), prominent in repeat elements such as ACRO1 satellites, LINE1 retrotransposons and CA simple repeats, and also in several protein-coding genes. ACRO1 repeat, when translated <i>in silico</i>, exhibits ~50% identity with the Pol II CTD sequence. Taken together with a recent proposal that proteins in general tend to interact with RNAs similar to their cognate mRNAs, this suggests a mechanism for RAP binding. Using a reporter construct, we show that ACRO1 potently inhibits Pol II elongation <i>in cis</i>. We propose a novel mode of transcriptional regulation in humans, in which the nascent RNA binds Pol II to silence its own expression.
DOI: 10.6084/m9.figshare.12851973.v1
title: RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcription <i>in cis</i>

description: Transcription elongation is a highly regulated process affected by many proteins, RNAs and the underlying DNA. Here we show that the nascent RNA can interfere with transcription in human cells, extending our previous findings from bacteria and yeast. We identified a variety of Pol II-binding aptamers (RAPs), prominent in repeat elements such as ACRO1 satellites, LINE1 retrotransposons and CA simple repeats, and also in several protein-coding genes. ACRO1 repeat, when translated <i>in silico</i>, exhibits ~50% identity with the Pol II CTD sequence. Taken together with a recent proposal that proteins in general tend to interact with RNAs similar to their cognate mRNAs, this suggests a mechanism for RAP binding. Using a reporter construct, we show that ACRO1 potently inhibits Pol II elongation <i>in cis</i>. We propose a novel mode of transcriptional regulation in humans, in which the nascent RNA binds Pol II to silence its own expression.
DOI: 10.5281/zenodo.4744575
title: Alaus oculatus SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744574
title: Alaus oculatus SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744401
title: Data from the publication "Identification of dominant hydrological mechanisms using Bayesian inference, multiple statistical hypothesis testing and flexible models, WRR, doi: 10.1029/2020WR028338"

description: Data: Identification of dominant hydrological mechanisms using Bayesian inference, multiple statistical hypothesis testing and flexible models, WRR, doi: 10.1029/2020WR028338 Cristina Prieto; Dmitri Kavetski; Nataliya Le Vine; Cesar Alvarez; Raul Medina !===== ! Purpose: These folders provide data from the publication Prieto et al 2021 ! Prieto C, Kavetski D, Le Vine N, Alvarez C, and Medina R (2021). Identification of dominant hydrological mechanisms using Bayesian inference, multiple statistical hypothesis testing and flexible models, Water Resources Research, doi: 10.1029/2020WR028338 !===== 1. Folder "obs": a) file "c8z1_data_obs.txt": observed hydrological data for the Leizaran catchment b) file "leizaran_mecha_identification.csv": number of bootstraps where a mecha is identified as dominant for the different time periods and significance levels 2. Folder "synthetic": a) folder "reliability_and_power__low_error_med_error_high_error": txt files with the following info: (i) reliability, (ii) power, (iii) true positives, (iv) false positives, and (v) false negatives; for different significance levels, error levels and processes, and across all error levels. Processes are abbreviated as follows: a1 = unsaturated zone, a2 = saturated zone, esoil = evaporation, interf = interflow, perc = percolation, rr = surface runoff, and rout = routing. E.g. file "alpha_r_p_tp_fp_fn_low_error_a1.txt" contains the following information for the lowest error, for the processes in the unsaturated zone: first column = significance level, alpha; second column = reliability, r; third column = power, p; fourth column = number of true positives, tp (out of 50); fifth column = number of false positives, fp (out of 50); sixth column = number of false negatives, fn (out of 50)
DOI: 10.5281/zenodo.4744400
title: Data from the publication "Identification of dominant hydrological mechanisms using Bayesian inference, multiple statistical hypothesis testing and flexible models, WRR, doi: 10.1029/2020WR028338"

description: Data: Identification of dominant hydrological mechanisms using Bayesian inference, multiple statistical hypothesis testing and flexible models, WRR, doi: 10.1029/2020WR028338 Cristina Prieto; Dmitri Kavetski; Nataliya Le Vine; Cesar Alvarez; Raul Medina !===== ! Purpose: These folders provide data from the publication Prieto et al 2021 ! Prieto C, Kavetski D, Le Vine N, Alvarez C, and Medina R (2021). Identification of dominant hydrological mechanisms using Bayesian inference, multiple statistical hypothesis testing and flexible models, Water Resources Research, doi: 10.1029/2020WR028338 !===== 1. Folder "obs": a) file "c8z1_data_obs.txt": observed hydrological data for the Leizaran catchment b) file "leizaran_mecha_identification.csv": number of bootstraps where a mecha is identified as dominant for the different time periods and significance levels 2. Folder "synthetic": a) folder "reliability_and_power__low_error_med_error_high_error": txt files with the following info: (i) reliability, (ii) power, (iii) true positives, (iv) false positives, and (v) false negatives; for different significance levels, error levels and processes, and across all error levels. Processes are abbreviated as follows: a1 = unsaturated zone, a2 = saturated zone, esoil = evaporation, interf = interflow, perc = percolation, rr = surface runoff, and rout = routing. E.g. file "alpha_r_p_tp_fp_fn_low_error_a1.txt" contains the following information for the lowest error, for the processes in the unsaturated zone: first column = significance level, alpha; second column = reliability, r; third column = power, p; fourth column = number of true positives, tp (out of 50); fifth column = number of false positives, fp (out of 50); sixth column = number of false negatives, fn (out of 50)
DOI: 10.6084/m9.figshare.9901298.v1
title: LRRK2 binds to the Rab32 subfamily in a GTP-dependent manner <i>via</i> its armadillo domain

description: LRRK2 is a multi-domain Ser/Thr kinase that is associated with inherited and sporadic cases of Parkinson’s disease. Many mutations linked to disease are associated within a central ROC-COR regulatory region and the subsequent kinase domain, leading to enhanced catalytic activity. The N-terminus of human LRRK2 consists of armadillo repeat motifs (ARMs) followed by ankyrin repeats (ANKs). Recently, Rab GTPases have emerged as key players in LRRK2 function, both as substrates of the kinase, and as regulators of the catalytic activity. Rabs recruit effector proteins <i>via</i> their GTP-dependent switch 1 and 2 regions to distinct sub-cellular compartments to regulate membrane trafficking. LRRK2 phosphorylates Rab8, Rab10 and Rab12 in switch 2, and this activity is regulated <i>via</i> interactions with Rab29. Furthermore, the related Rab32-subfamily GTPases, Rab32 and Rab38, have also been shown to interact with LRRK2. Here, we have mapped the interactions of the Rab32-subfamily to the ARM domain of LRRK2. The complexes are dependent on the GTP state of the Rabs <i>in vitro</i>, implying that LRRK2 may be an effector of the Rab32-subfamily of small GTPases. X-ray crystal structures of the Rab32-family GTPases and subsequent mutational studies reveal that a positively charged residue in switch 1 is critical for binding of Rab32/38 to LRRK2. Homology modelling and mutational analyses of the ARM domain point to a patch of negatively charged residues that contribute to complex formation. These structural and biochemical studies provide a framework for understanding the molecular basis for Rab regulation of LRRK2 and its role in Parkinson’s disease.
DOI: 10.6084/m9.figshare.9901298
title: LRRK2 binds to the Rab32 subfamily in a GTP-dependent manner <i>via</i> its armadillo domain

description: LRRK2 is a multi-domain Ser/Thr kinase that is associated with inherited and sporadic cases of Parkinson’s disease. Many mutations linked to disease are associated within a central ROC-COR regulatory region and the subsequent kinase domain, leading to enhanced catalytic activity. The N-terminus of human LRRK2 consists of armadillo repeat motifs (ARMs) followed by ankyrin repeats (ANKs). Recently, Rab GTPases have emerged as key players in LRRK2 function, both as substrates of the kinase, and as regulators of the catalytic activity. Rabs recruit effector proteins <i>via</i> their GTP-dependent switch 1 and 2 regions to distinct sub-cellular compartments to regulate membrane trafficking. LRRK2 phosphorylates Rab8, Rab10 and Rab12 in switch 2, and this activity is regulated <i>via</i> interactions with Rab29. Furthermore, the related Rab32-subfamily GTPases, Rab32 and Rab38, have also been shown to interact with LRRK2. Here, we have mapped the interactions of the Rab32-subfamily to the ARM domain of LRRK2. The complexes are dependent on the GTP state of the Rabs <i>in vitro</i>, implying that LRRK2 may be an effector of the Rab32-subfamily of small GTPases. X-ray crystal structures of the Rab32-family GTPases and subsequent mutational studies reveal that a positively charged residue in switch 1 is critical for binding of Rab32/38 to LRRK2. Homology modelling and mutational analyses of the ARM domain point to a patch of negatively charged residues that contribute to complex formation. These structural and biochemical studies provide a framework for understanding the molecular basis for Rab regulation of LRRK2 and its role in Parkinson’s disease.
DOI: 10.6084/m9.figshare.9734774
title: RhoG and Cdc42 can contribute to Rac-dependent lamellipodia formation through WAVE regulatory complex-binding

description: Cell migration frequently involves the formation of lamellipodial protrusions, the initiation of which requires Rac GTPases signalling to heteropentameric WAVE regulatory complex (WRC). While Rac-related RhoG and Cdc42 can potently stimulate lamellipodium formation, so far presumed to occur by upstream signalling to Rac activation, we show here that the latter can be bypassed by RhoG and Cdc42 given that WRC has been artificially activated. This evidence arises from generation of B16-F1 cells simultaneously lacking both Rac GTPases and WRC, followed by reconstitution of lamellipodia formation with specific Rho-GTPase and differentially active WRC variant combinations. We conclude that formation of canonical lamellipodia requires WRC activation through Rac, but can possibly be tuned, in addition, by WRC interactions with RhoG and Cdc42.
DOI: 10.6084/m9.figshare.9734774.v1
title: RhoG and Cdc42 can contribute to Rac-dependent lamellipodia formation through WAVE regulatory complex-binding

description: Cell migration frequently involves the formation of lamellipodial protrusions, the initiation of which requires Rac GTPases signalling to heteropentameric WAVE regulatory complex (WRC). While Rac-related RhoG and Cdc42 can potently stimulate lamellipodium formation, so far presumed to occur by upstream signalling to Rac activation, we show here that the latter can be bypassed by RhoG and Cdc42 given that WRC has been artificially activated. This evidence arises from generation of B16-F1 cells simultaneously lacking both Rac GTPases and WRC, followed by reconstitution of lamellipodia formation with specific Rho-GTPase and differentially active WRC variant combinations. We conclude that formation of canonical lamellipodia requires WRC activation through Rac, but can possibly be tuned, in addition, by WRC interactions with RhoG and Cdc42.
DOI: 10.6084/m9.figshare.12851964.v1
title: Genetic deletion of the Rho GEF <i>Net1</i> impairs mouse macrophage motility and actin cytoskeletal organization

description: Macrophages are innate immune cells that constantly patrol an organism to fulfill protective and homeostatic roles. Previous studies have shown that Rho GTPase activity is required for macrophage mobility, yet the roles of upstream regulatory proteins controlling Rho GTPase function in these cells are not well defined. Previously we have shown that the RhoA GEF Net1 is required for human breast cancer cell motility and extracellular matrix invasion. To assess the role of Net1 in macrophage motility, we isolated bone marrow macrophage (BMM) precursors from wild type and <i>Net1</i> knockout mice. Loss of <i>Net1</i> did not affect the ability of BMM precursors to differentiate into mature macrophages <i>in vitro</i>, as measured by CD68 and F4/80 staining. However, <i>Net1</i> deletion significantly reduced RhoA activation, F-actin accumulation, adhesion, and motility in these cells. Nevertheless, similar to <i>RhoA/RhoB</i> double knockout macrophages, <i>Net1</i> deletion did not impair macrophage recruitment to the peritoneum in a mouse model of sterile inflammation. These data demonstrate that Net1 is an important regulator of RhoA signaling and motility in mouse macrophages <i>in vitro</i>, but that its function may be dispensable for macrophage recruitment to inflammatory sites <i>in vivo</i>.
DOI: 10.6084/m9.figshare.12851964
title: Genetic deletion of the Rho GEF <i>Net1</i> impairs mouse macrophage motility and actin cytoskeletal organization

description: Macrophages are innate immune cells that constantly patrol an organism to fulfill protective and homeostatic roles. Previous studies have shown that Rho GTPase activity is required for macrophage mobility, yet the roles of upstream regulatory proteins controlling Rho GTPase function in these cells are not well defined. Previously we have shown that the RhoA GEF Net1 is required for human breast cancer cell motility and extracellular matrix invasion. To assess the role of Net1 in macrophage motility, we isolated bone marrow macrophage (BMM) precursors from wild type and <i>Net1</i> knockout mice. Loss of <i>Net1</i> did not affect the ability of BMM precursors to differentiate into mature macrophages <i>in vitro</i>, as measured by CD68 and F4/80 staining. However, <i>Net1</i> deletion significantly reduced RhoA activation, F-actin accumulation, adhesion, and motility in these cells. Nevertheless, similar to <i>RhoA/RhoB</i> double knockout macrophages, <i>Net1</i> deletion did not impair macrophage recruitment to the peritoneum in a mouse model of sterile inflammation. These data demonstrate that Net1 is an important regulator of RhoA signaling and motility in mouse macrophages <i>in vitro</i>, but that its function may be dispensable for macrophage recruitment to inflammatory sites <i>in vivo</i>.
DOI: 10.5281/zenodo.4744580
title: Ara chloropterus SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744579
title: Ara chloropterus SPAdes preassembly

description: .
DOI: 10.34740/kaggle/dsv/2214127
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.5281/zenodo.4744589
title: Chrysina resplendens SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744588
title: Chrysina resplendens SPAdes preassembly

description: .
DOI: 10.6084/m9.figshare.14561814
title: VAK list of journal titles v.2021.04.08

description: List of VAK journals (https://vak.minobrnauki.gov.ru/documents#tab=_tab:editions~) dated as of April 8, 2021<br>
DOI: 10.5281/zenodo.4744596
title: Curcuma longa SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744595
title: Curcuma longa SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744600
title: Vertical profiles of 3D cluster properties

description: These two files contain the properties of the 3D clusters used in the submission version of the Paper "Size-dependence of surface-rooted three-dimensional convective objects in continental shallow cumulus simulations". The paper was submitted to JAMES in May 2021. When unzipped, the data is stored in python panda dataframes in pkl files. Warning! Unzipping the files increases the data size by a factor of 20.
DOI: 10.6084/m9.figshare.14562171
title: FS_IQ_EQ_TL_PS

description: Dataset
DOI: 10.6084/m9.figshare.14562171.v1
title: FS_IQ_EQ_TL_PS

description: Dataset
DOI: 10.5281/zenodo.4744603
title: Eclectus roratus SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744602
title: Eclectus roratus SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4673838
title: Database Systematic Mapping of the Social Construction of Learning (2015-2020)

description: Database Systematic Mapping
DOI: 10.5281/zenodo.4673837
title: Database Systematic Mapping of the Social Construction of Learning (2015-2020)

description: Database Systematic Mapping
DOI: 10.5281/zenodo.4744627
title: Graphium colonna SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744626
title: Graphium colonna SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744525
title: Actenoides hombroni SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4744524
title: Actenoides hombroni SPAdes preassembly

description: .
DOI: 10.5281/zenodo.4743535
title: The association between dating apps and alcohol consumption in an Italian sample of active users, former users and non-users

description: Open-access dataset regarding the survey "The association between dating apps and alcohol consumption in an Italian sample of active users, former users and non-users", by L.Flesia, V.Fietta, C.Foresta and M.Monaro
DOI: 10.5281/zenodo.4743534
title: The association between dating apps and alcohol consumption in an Italian sample of active users, former users and non-users

description: Open-access dataset regarding the survey "The association between dating apps and alcohol consumption in an Italian sample of active users, former users and non-users", by L.Flesia, V.Fietta, C.Foresta and M.Monaro
DOI: 10.5281/zenodo.4743611
title: COVID-19 haze date sharing

description: COVID-19
DOI: 10.5281/zenodo.4743610
title: COVID-19 haze date sharing

description: COVID-19
DOI: 10.6084/m9.figshare.9907247.v1
title: Identification of genetic markers associated with milk production traits in Chinese Holstein cattle based on post genome-wide association studies

description: With the rapid development of dairy industry, the breeding process of dairy cows has been accelerated. In previous genome-wide association studies (GWAS), a large number of genetic markers have been reported which may contribute to the selection of Holstein populations with superior milk-producing traits, but they remain to be further verified before practical application. In this study, 90 single nucleotide polymorphisms (SNPs) were selected, which were reported to be significantly associated with five milk production traits, including 305-day milk yield (305MY), 305-day milk fat percent (305FC), 305-day milk protein percent (305PC), 305-day milk fat yield (305FY) and 305-day milk protein yield (305PY). Effective 305-day data and fresh DNA samples were obtained from 295 healthy cows with gestational age of 1–4. Matrix-assisted laser desorption/ionization—time of flight (MALDI-TOF) was used to perform precise genotyping of these loci, followed by site association and haplotype analysis. Results showed that 36 out of 90 loci were supported to be used as genetic markers. In particular, several novel and effective haplotypes were also presented. Overall, our results verified tens of useful markers and provided a basis for further development of breeding strategies.
DOI: 10.6084/m9.figshare.9907247
title: Identification of genetic markers associated with milk production traits in Chinese Holstein cattle based on post genome-wide association studies

description: With the rapid development of dairy industry, the breeding process of dairy cows has been accelerated. In previous genome-wide association studies (GWAS), a large number of genetic markers have been reported which may contribute to the selection of Holstein populations with superior milk-producing traits, but they remain to be further verified before practical application. In this study, 90 single nucleotide polymorphisms (SNPs) were selected, which were reported to be significantly associated with five milk production traits, including 305-day milk yield (305MY), 305-day milk fat percent (305FC), 305-day milk protein percent (305PC), 305-day milk fat yield (305FY) and 305-day milk protein yield (305PY). Effective 305-day data and fresh DNA samples were obtained from 295 healthy cows with gestational age of 1–4. Matrix-assisted laser desorption/ionization—time of flight (MALDI-TOF) was used to perform precise genotyping of these loci, followed by site association and haplotype analysis. Results showed that 36 out of 90 loci were supported to be used as genetic markers. In particular, several novel and effective haplotypes were also presented. Overall, our results verified tens of useful markers and provided a basis for further development of breeding strategies.
DOI: 10.5281/zenodo.4744632
title: Database Mediation and learning online (2015-2020)

description: This database contains information related to the systematic mapping of the 2015-2020 period on Mediation and online learning.
DOI: 10.5281/zenodo.4744631
title: Database Mediation and learning online (2015-2020)

description: This database contains information related to the systematic mapping of the 2015-2020 period on Mediation and online learning.
DOI: 10.6084/m9.figshare.13811888
title: A phase 1b clinical trial optimizing regulatory T cell depletion in combination with platinum-based chemotherapy in thoracic cancers

description: <b>Background</b>: Single-agent cyclophosphamide can deplete regulatory T-cells (Treg). We aimed to determine optimal dosing and scheduling of oral cyclophosphamide, alongside pemetrexed-based chemotherapy, to deplete Treg in mesothelioma or non-small-cell lung cancer patients. <b>Methods</b>: 31 Patients received pemetrexed ± cisplatin or carboplatin on day 1 of a 21-day cycle (maximum 6 cycles). From cycle two, patients received cyclophosphamide, 50 mg/day, with intrapatient escalation to maximum 100/150 mg/day alternately. Immunological changes were examined by flow cytometry. Primary endpoint was Treg proportion of CD4<sup>+</sup> T-cells, with doses tailored to target Treg nadir &lt;4%. <b>Results</b>: Reduction in Treg proportion was observed on day 8 of all cycles, and was not augmented by cyclophosphamide. Few patients achieved the &lt;4% Treg target. Treg proliferation reached nadir one week after chemotherapy, and peaked on day 1 of the subsequent cycle. Efficacy parameters were similar to chemotherapy alone. Seventeen percent of patients ceased cyclophosphamide due to toxicity. <b>Conclusions</b>: Specific Treg depletion to the degree seen with single-agent cyclophosphamide was not observed during pemetrexed-based chemotherapy. This study highlights the poor evidence basis for use of cyclophosphamide as an immunotherapeutic in combination with chemotherapy, and the importance of detailed flow cytometry studies. <b>Trial registration</b>: Clinical trial registration: www.anzctr.org.au identifier is ACTRN12609000260224.