cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8247761
title: Group A <i>Streptococcus</i> modulates RAB1- and PIK3C3 complex-dependent autophagy

description: Autophagy selectively targets invading bacteria to defend cells, whereas bacterial pathogens counteract autophagy to survive in cells. The initiation of canonical autophagy involves the PIK3C3 complex, but autophagy targeting Group A <i>Streptococcus</i> (GAS) is PIK3C3-independent. We report that GAS infection elicits both PIK3C3-dependent and -independent autophagy, and that the GAS effector NAD-glycohydrolase (Nga) selectively modulates PIK3C3-dependent autophagy. GAS regulates starvation-induced (canonical) PIK3C3-dependent autophagy by secreting streptolysin O and Nga, and Nga also suppresses PIK3C3-dependent GAS-targeting-autophagosome formation during early infection and facilitates intracellular proliferation. This Nga-sensitive autophagosome formation involves the ATG14-containing PIK3C3 complex and RAB1 GTPase, which are both dispensable for Nga-insensitive RAB9A/RAB17-positive autophagosome formation. Furthermore, although MTOR inhibition and subsequent activation of ULK1, BECN1, and ATG14 occur during GAS infection, ATG14 recruitment to GAS is impaired, suggesting that Nga inhibits the recruitment of ATG14-containing PIK3C3 complexes to autophagosome-formation sites. Our findings reveal not only a previously unrecognized GAS-host interaction that modulates canonical autophagy, but also the existence of multiple autophagy pathways, using distinct regulators, targeting bacterial infection. <b>Abbreviations</b>: ATG5: autophagy related 5; ATG14: autophagy related 14; ATG16L1: autophagy related 16 like 1; BECN1: beclin 1; CALCOCO2: calcium binding and coiled-coil domain 2; GAS: group A <i>streptococcus</i>; GcAV: GAS-containing autophagosome-like vacuole; LAMP1: lysosomal associated membrane protein 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTORC1: mechanistic target of rapamycin kinase complex 1; Nga: NAD-glycohydrolase; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; PtdIns3P: phosphatidylinositol-3-phosphate; PtdIns4P: phosphatidylinositol-4-phosphate; RAB: RAB, member RAS oncogene GTPases; RAB1A: RAB1A, member RAS oncogene family; RAB11A: RAB11A, member RAS oncogene family; RAB17: RAB17, member RAS oncogene family; RAB24: RAB24, member RAS oncogene family; RPS6KB1: ribosomal protein S6 kinase B1; SLO: streptolysin O; SQSTM1: sequestosome 1; ULK1: unc-51 like autophagy activating kinase 1; WIPI2: WD repeat domain, phosphoinositide interacting 2
DOI: 10.6084/m9.figshare.8247761.v1
title: Group A <i>Streptococcus</i> modulates RAB1- and PIK3C3 complex-dependent autophagy

description: Autophagy selectively targets invading bacteria to defend cells, whereas bacterial pathogens counteract autophagy to survive in cells. The initiation of canonical autophagy involves the PIK3C3 complex, but autophagy targeting Group A <i>Streptococcus</i> (GAS) is PIK3C3-independent. We report that GAS infection elicits both PIK3C3-dependent and -independent autophagy, and that the GAS effector NAD-glycohydrolase (Nga) selectively modulates PIK3C3-dependent autophagy. GAS regulates starvation-induced (canonical) PIK3C3-dependent autophagy by secreting streptolysin O and Nga, and Nga also suppresses PIK3C3-dependent GAS-targeting-autophagosome formation during early infection and facilitates intracellular proliferation. This Nga-sensitive autophagosome formation involves the ATG14-containing PIK3C3 complex and RAB1 GTPase, which are both dispensable for Nga-insensitive RAB9A/RAB17-positive autophagosome formation. Furthermore, although MTOR inhibition and subsequent activation of ULK1, BECN1, and ATG14 occur during GAS infection, ATG14 recruitment to GAS is impaired, suggesting that Nga inhibits the recruitment of ATG14-containing PIK3C3 complexes to autophagosome-formation sites. Our findings reveal not only a previously unrecognized GAS-host interaction that modulates canonical autophagy, but also the existence of multiple autophagy pathways, using distinct regulators, targeting bacterial infection. <b>Abbreviations</b>: ATG5: autophagy related 5; ATG14: autophagy related 14; ATG16L1: autophagy related 16 like 1; BECN1: beclin 1; CALCOCO2: calcium binding and coiled-coil domain 2; GAS: group A <i>streptococcus</i>; GcAV: GAS-containing autophagosome-like vacuole; LAMP1: lysosomal associated membrane protein 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTORC1: mechanistic target of rapamycin kinase complex 1; Nga: NAD-glycohydrolase; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; PtdIns3P: phosphatidylinositol-3-phosphate; PtdIns4P: phosphatidylinositol-4-phosphate; RAB: RAB, member RAS oncogene GTPases; RAB1A: RAB1A, member RAS oncogene family; RAB11A: RAB11A, member RAS oncogene family; RAB17: RAB17, member RAS oncogene family; RAB24: RAB24, member RAS oncogene family; RPS6KB1: ribosomal protein S6 kinase B1; SLO: streptolysin O; SQSTM1: sequestosome 1; ULK1: unc-51 like autophagy activating kinase 1; WIPI2: WD repeat domain, phosphoinositide interacting 2
DOI: 10.6084/m9.figshare.8247749
title: Figure

description: Figure of Result Analysis
DOI: 10.6084/m9.figshare.8247752
title: Ranked models describing variability in density (D), baseline detection (p0), and space use (σ) of the red-backed salamander as a function of site, season and time for population in James River Park, Richmond, VA. from Unexpected spatial population ecology of a widespread terrestrial salamander near its southern range edge

description: Complete list of the 325 ranked models
DOI: 10.6084/m9.figshare.8247752.v1
title: Ranked models describing variability in density (D), baseline detection (p0), and space use (σ) of the red-backed salamander as a function of site, season and time for population in James River Park, Richmond, VA. from Unexpected spatial population ecology of a widespread terrestrial salamander near its southern range edge

description: Complete list of the 325 ranked models
DOI: 10.6084/m9.figshare.8247749.v1
title: Figure

description: Figure of Result Analysis
DOI: 10.6084/m9.figshare.8247737
title: List of Table

description: List of Table
DOI: 10.6084/m9.figshare.8247737.v1
title: List of Table

description: List of Table
DOI: 10.6084/m9.figshare.12547337
title: Poland - COVID-19

description: Results of a survey conducted on a representative sample of 1001 Poles using the CAWI technique. The study was conducted in the middle of April 2020 - at the time of the strictest restrictions in Poland related to the pandemic were in force.
DOI: 10.6084/m9.figshare.12547337.v3
title: Poland - COVID-19

description: Results of a survey conducted on a representative sample of 1001 Poles using the CAWI technique. The study was conducted in the middle of April 2020 - at the time of the strictest restrictions in Poland related to the pandemic were in force.
DOI: 10.6084/m9.figshare.12547337.v2
title: Poland - COVID-19

description: Results of a survey conducted on a representative sample of 1001 Poles using the CAWI technique. The study was conducted in the middle of April 2020 - at the time of the strictest restrictions in Poland related to the pandemic were in force.
DOI: 10.6084/m9.figshare.8247647
title: Effect of land consolidation on soil microbial diversity

description: 10 samples from the land consolidation, others not.
DOI: 10.6084/m9.figshare.8247647.v1
title: Effect of land consolidation on soil microbial diversity

description: 10 samples from the land consolidation, others not.
DOI: 10.6084/m9.figshare.8247551
title: Differences in exploitation and interference ability between two dominant ants: the invasive Argentine ant (<i>Linepithema humile</i>) and <i>Tapinoma magnum</i>

description: The Argentine ant is a highly invasive species that can cause significant ecosystem alterations. Its spread in the invaded areas is usually associated with the displacement of native ant species by means of strong interference competition mechanisms. According to recent studies, <i>Tapinoma nigerrimum</i> s.l., a native Mediterranean ant, can potentially limit the expansion of the Argentine ant. The aim of the present study is to determine the ethological features that discriminate against the ability of <i>L. humile</i> and <i>T. magnum</i> (<i>nigerrimum</i> complex) to exploit a trophic resource both in the presence and in the absence of the competitor. We conducted behavioural assays on experimental colonies using foraging arenas in a laboratory experiment. <i>Linepithema humile</i> colonies showed the ethological profile typical of the species, as they carried out more intense recruitment, initially concentrated on the whole foraging site rather than on the bait. <i>Linepithema humile</i> workers were more aggressive and fought cooperatively during inter-specific interactions. <i>Tapinoma magnum</i> colonies apparently showed a more food-oriented profile as they were faster in the search for food and concentrated the recruitment on it rather than on the whole foraging site. <i>Tapinoma magnum</i> workers tried to avert the competitor using threat postures rather than physical aggression. <i>Tapinoma magnum</i> colonies were systematically excluded by <i>L. humile</i> colonies from the trophic resource and underwent a visible reduction in surface activity. These results suggest that <i>L. humile</i> used a different and more effective interference competition strategy compared to <i>T. magnum</i>.
DOI: 10.6084/m9.figshare.8247539
title: A different methylation profile of circadian genes promoter in breast cancer patients according to clinicopathological features

description: One of the supposed mechanisms that may lead to breast cancer (BC) is an alteration of circadian gene expression and DNA methylation. We undertook an integrated approach to identify methylation pattern of core circadian promoter regions in BC patients with regard to clinical features. We performed a quantitative methylation-specific real-time PCR analysis of a promoter methylation profile in 107 breast tumor and matched non-tumor tissues. A panel of circadian genes <i>CLOCK, BMAL1, PERIOD (PER1, 2, 3), CRYPTOCHROME (CRY1, 2)</i> and <i>TIMELESS</i> as well as their association with clinicopathological characteristics were included in the analysis. Three out of the eight analyzed genes exhibited marked hypermethylation (<i>PER1, 2, 3</i>), whereas <i>CLOCK, BMAL1, CRY2</i> showed significantly lower promoter CpG methylation in the BC tissues when compared to the non-tumor tissues. Among variously methylated genes we found an association between the elevated methylation level of <i>PERs</i> promoter region and molecular subtypes, histological subtypes and tumor grading of BC. Methylation status may be associated with a gene expression level of circadian genes in BC patients. An aberrant methylation pattern in circadian genes in BC may provide information that could be used as novel biomarkers in clinics and molecular epidemiology as well as play an important role in BC etiology.
DOI: 10.6084/m9.figshare.8247551.v1
title: Differences in exploitation and interference ability between two dominant ants: the invasive Argentine ant (<i>Linepithema humile</i>) and <i>Tapinoma magnum</i>

description: The Argentine ant is a highly invasive species that can cause significant ecosystem alterations. Its spread in the invaded areas is usually associated with the displacement of native ant species by means of strong interference competition mechanisms. According to recent studies, <i>Tapinoma nigerrimum</i> s.l., a native Mediterranean ant, can potentially limit the expansion of the Argentine ant. The aim of the present study is to determine the ethological features that discriminate against the ability of <i>L. humile</i> and <i>T. magnum</i> (<i>nigerrimum</i> complex) to exploit a trophic resource both in the presence and in the absence of the competitor. We conducted behavioural assays on experimental colonies using foraging arenas in a laboratory experiment. <i>Linepithema humile</i> colonies showed the ethological profile typical of the species, as they carried out more intense recruitment, initially concentrated on the whole foraging site rather than on the bait. <i>Linepithema humile</i> workers were more aggressive and fought cooperatively during inter-specific interactions. <i>Tapinoma magnum</i> colonies apparently showed a more food-oriented profile as they were faster in the search for food and concentrated the recruitment on it rather than on the whole foraging site. <i>Tapinoma magnum</i> workers tried to avert the competitor using threat postures rather than physical aggression. <i>Tapinoma magnum</i> colonies were systematically excluded by <i>L. humile</i> colonies from the trophic resource and underwent a visible reduction in surface activity. These results suggest that <i>L. humile</i> used a different and more effective interference competition strategy compared to <i>T. magnum</i>.
DOI: 10.6084/m9.figshare.8247539.v1
title: A different methylation profile of circadian genes promoter in breast cancer patients according to clinicopathological features

description: One of the supposed mechanisms that may lead to breast cancer (BC) is an alteration of circadian gene expression and DNA methylation. We undertook an integrated approach to identify methylation pattern of core circadian promoter regions in BC patients with regard to clinical features. We performed a quantitative methylation-specific real-time PCR analysis of a promoter methylation profile in 107 breast tumor and matched non-tumor tissues. A panel of circadian genes <i>CLOCK, BMAL1, PERIOD (PER1, 2, 3), CRYPTOCHROME (CRY1, 2)</i> and <i>TIMELESS</i> as well as their association with clinicopathological characteristics were included in the analysis. Three out of the eight analyzed genes exhibited marked hypermethylation (<i>PER1, 2, 3</i>), whereas <i>CLOCK, BMAL1, CRY2</i> showed significantly lower promoter CpG methylation in the BC tissues when compared to the non-tumor tissues. Among variously methylated genes we found an association between the elevated methylation level of <i>PERs</i> promoter region and molecular subtypes, histological subtypes and tumor grading of BC. Methylation status may be associated with a gene expression level of circadian genes in BC patients. An aberrant methylation pattern in circadian genes in BC may provide information that could be used as novel biomarkers in clinics and molecular epidemiology as well as play an important role in BC etiology.
DOI: 10.6084/m9.figshare.8247527
title: Data and Code for "Limits on amplifiers of natural selection under death-Birth updating"

description: Data and Code for "Limits on amplifiers of natural selection under death-Birth updating": Python script used to compute the data and Mathematica notebooks used to produce the plots.
DOI: 10.6084/m9.figshare.8247509
title: On the role of data balancing for Machine Learning-based Code Smell Detection

description: Code smells can compromise software quality in the long term by inducing technical debt.For this reason, in the last decade many approaches aimed at identifying these design flaws have been proposed.Most of them are based on heuristics in which a set of metrics (e.g., code metrics, process metrics) is used to detect smelly code components.However, these techniques suffer of subjective interpretation, low agreement between detectors, and threshold dependability.To overcome the limitations, previous work applied Machine Learning techniques that can learn from previous datasets without needing any threshold definition.However, more recent work has shown that Machine Learning is not always suitable for code smell detection due to the highly unbalanced nature of the problem.In this study we investigate several approaches able to mitigate data unbalancing issues to understand their impact on ML-based code smells detection algorithms.Our findings highlight a number of limitations and open issues with respect to the usage of data balancing for ML-based code smell detection.
DOI: 10.6084/m9.figshare.8247503
title: Assessing multiple mating and reproductive skew in three species of clinid fishes (Blenniiformes: Clinidae: Clinini), in reference to multiple mating in viviparous teleosts

description: This study investigated multiple mating in three species of intertidal klipfishes (family Clinidae): super klipfish <i>Clinus superciliosus</i>, bluntnose klipfish <i>Clinus cottoides</i>, and nosestripe klipfish <i>Muraenoclinus dorsalis</i>. These species display the rare reproductive mode of female vivipary with superfetation, a phenomenon where offspring at various stages of development are found within the female. Three or four microsatellite loci were used to genotype 25–30 adults of each species, as well as embryos of 131 <i>C. superciliosus</i> from six broods, 103 <i>C. cottoides</i> from six broods, and 63 <i>M. dorsalis</i> from five broods. The presence of multiple mating by females was assessed by maximum-likelihood sibship reconstruction implemented in the program COLONY, and the non-random distribution of reproductive success among individuals (reproductive skew) within broods was tested using the binomial skew index. Multiple mating by females was pervasive and observed in 83%, 100% and 80% of the broods of <i>C. superciliosus</i>, <i>C. cottoides</i> and <i>M. dorsalis</i>, respectively. The mean number of sires per brood was 4.3, 3.0 and 3.2, and, correspondingly, 5/5, 5/6 and 1/4 of multiply-sired broods showed significant reproductive skew in <i>C. superciliosus</i>, <i>C. cottoides</i> and <i>M. dorsalis</i>, respectively. The presence of pronounced reproductive skew may indicate post-copulatory processes taking place that bias paternity. We compared our results on multiple mating within the klipfish family, and with four other fish families that have vivipary with superfetation, and found the klipfish patterns were among those of live-bearing vertebrate groups with the highest average numbers of sires per brood.
DOI: 10.6084/m9.figshare.8247509.v2
title: On the role of data balancing for Machine Learning-based Code Smell Detection

description: Code smells can compromise software quality in the long term by inducing technical debt.For this reason, in the last decade many approaches aimed at identifying these design flaws have been proposed.Most of them are based on heuristics in which a set of metrics (e.g., code metrics, process metrics) is used to detect smelly code components.However, these techniques suffer of subjective interpretation, low agreement between detectors, and threshold dependability.To overcome the limitations, previous work applied Machine Learning techniques that can learn from previous datasets without needing any threshold definition.However, more recent work has shown that Machine Learning is not always suitable for code smell detection due to the highly unbalanced nature of the problem.In this study we investigate several approaches able to mitigate data unbalancing issues to understand their impact on ML-based code smells detection algorithms.Our findings highlight a number of limitations and open issues with respect to the usage of data balancing for ML-based code smell detection.
DOI: 10.6084/m9.figshare.8247509.v1
title: On the role of data balancing for Machine Learning-based Code Smell Detection

description: Code smells can compromise software quality in the long term by inducing technical debt.For this reason, in the last decade many approaches aimed at identifying these design flaws have been proposed.Most of them are based on heuristics in which a set of metrics (e.g., code metrics, process metrics) is used to detect smelly code components.However, these techniques suffer of subjective interpretation, low agreement between detectors, and threshold dependability.To overcome the limitations, previous work applied Machine Learning techniques that can learn from previous datasets without needing any threshold definition.However, more recent work has shown that Machine Learning is not always suitable for code smell detection due to the highly unbalanced nature of the problem.In this study we investigate several approaches able to mitigate data unbalancing issues to understand their impact on ML-based code smells detection algorithms.Our findings highlight a number of limitations and open issues with respect to the usage of data balancing for ML-based code smell detection.
DOI: 10.6084/m9.figshare.8247503.v2
title: Assessing multiple mating and reproductive skew in three species of clinid fishes (Blenniiformes: Clinidae: Clinini), in reference to multiple mating in viviparous teleosts

description: This study investigated multiple mating in three species of intertidal klipfishes (family Clinidae): super klipfish <i>Clinus superciliosus</i>, bluntnose klipfish <i>Clinus cottoides</i>, and nosestripe klipfish <i>Muraenoclinus dorsalis</i>. These species display the rare reproductive mode of female vivipary with superfetation, a phenomenon where offspring at various stages of development are found within the female. Three or four microsatellite loci were used to genotype 25–30 adults of each species, as well as embryos of 131 <i>C. superciliosus</i> from six broods, 103 <i>C. cottoides</i> from six broods, and 63 <i>M. dorsalis</i> from five broods. The presence of multiple mating by females was assessed by maximum-likelihood sibship reconstruction implemented in the program COLONY, and the non-random distribution of reproductive success among individuals (reproductive skew) within broods was tested using the binomial skew index. Multiple mating by females was pervasive and observed in 83%, 100% and 80% of the broods of <i>C. superciliosus</i>, <i>C. cottoides</i> and <i>M. dorsalis</i>, respectively. The mean number of sires per brood was 4.3, 3.0 and 3.2, and, correspondingly, 5/5, 5/6 and 1/4 of multiply-sired broods showed significant reproductive skew in <i>C. superciliosus</i>, <i>C. cottoides</i> and <i>M. dorsalis</i>, respectively. The presence of pronounced reproductive skew may indicate post-copulatory processes taking place that bias paternity. We compared our results on multiple mating within the klipfish family, and with four other fish families that have vivipary with superfetation, and found the klipfish patterns were among those of live-bearing vertebrate groups with the highest average numbers of sires per brood.
DOI: 10.6084/m9.figshare.8247494
title: TreeBASEdmp-2019-06-10

description: TreeBASE (http://www.treebase.org) schema and data ingestible by PostgreSQL
DOI: 10.6084/m9.figshare.8247491
title: The results of alternative splicing model

description: alternative 3′ splice site
DOI: 10.6084/m9.figshare.8247494.v1
title: TreeBASEdmp-2019-06-10

description: TreeBASE (http://www.treebase.org) schema and data ingestible by PostgreSQL
DOI: 10.6084/m9.figshare.8247488
title: The results of alternative splicing model

description: alternative 5′ splice site
DOI: 10.6084/m9.figshare.8247485
title: The results of alternative splicing model

description: alternative first exon
DOI: 10.6084/m9.figshare.8247491.v1
title: The results of alternative splicing model

description: alternative 3′ splice site
DOI: 10.6084/m9.figshare.8247479
title: The results of alternative splicing model

description: mutually exclusive exon
DOI: 10.6084/m9.figshare.8247482
title: The results of alternative splicing model

description: alternative last exon
DOI: 10.6084/m9.figshare.8247488.v1
title: The results of alternative splicing model

description: alternative 5′ splice site
DOI: 10.6084/m9.figshare.8247476
title: The results of alternative splicing model

description: retained intron
DOI: 10.6084/m9.figshare.8247479.v1
title: The results of alternative splicing model

description: mutually exclusive exon
DOI: 10.6084/m9.figshare.8247482.v1
title: The results of alternative splicing model

description: alternative last exon
DOI: 10.6084/m9.figshare.8247485.v1
title: The results of alternative splicing model

description: alternative first exon
DOI: 10.6084/m9.figshare.8247473
title: The results of alternative splicing model

description: The isoforms of transcripts with alternative splicing