cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6652328
title: Phenological responses to small-scale spatial variation in snowmelt timing reveal compensatory and conservative strategies in subarctic-alpine plants

description: <b><i>Background</i></b>: In tundra ecosystems, the adjustment of phenological events, such as bud burst, to snowmelt timing is crucial to the climatic adaptation of plants. Natural small-scale variations in microclimate potentially enable plant populations to persist in a changing climate. <b><i>Aims</i></b>: To assess how plant phenology responds to natural differences in snowmelt timing. <b><i>Methods</i></b>: We observed the timing of eight vegetative and reproductive phenophases in seven dwarf-shrub species in relation to differences in snowmelt timing on a small spatial scale in an alpine environment in subarctic Finland. <b><i>Results</i></b>: Some species and phenophases showed accelerated development with later snowmelt, thus providing full or partial compensation for the shorter snow-free period. Full compensation resulted in synchronous occurrence of phenophases across the snowmelt gradient. In other species, there was no acceleration of development. The timing of phenophases varied between two consecutive years and two opposing mountain slope aspects. <b><i>Conclusions</i></b>: The results have shown three distinct patterns in the timing of phenophases in relation to snowmelt and suggest alternative strategies for adaptation to snowmelt timing. These strategies potentially apply to other species and tundra ecosystems and provide a framework, enabling one to compare and generalise phenological responses to snowmelt timing under different future climate scenarios.
DOI: 10.6084/m9.figshare.6652328.v1
title: Phenological responses to small-scale spatial variation in snowmelt timing reveal compensatory and conservative strategies in subarctic-alpine plants

description: <b><i>Background</i></b>: In tundra ecosystems, the adjustment of phenological events, such as bud burst, to snowmelt timing is crucial to the climatic adaptation of plants. Natural small-scale variations in microclimate potentially enable plant populations to persist in a changing climate. <b><i>Aims</i></b>: To assess how plant phenology responds to natural differences in snowmelt timing. <b><i>Methods</i></b>: We observed the timing of eight vegetative and reproductive phenophases in seven dwarf-shrub species in relation to differences in snowmelt timing on a small spatial scale in an alpine environment in subarctic Finland. <b><i>Results</i></b>: Some species and phenophases showed accelerated development with later snowmelt, thus providing full or partial compensation for the shorter snow-free period. Full compensation resulted in synchronous occurrence of phenophases across the snowmelt gradient. In other species, there was no acceleration of development. The timing of phenophases varied between two consecutive years and two opposing mountain slope aspects. <b><i>Conclusions</i></b>: The results have shown three distinct patterns in the timing of phenophases in relation to snowmelt and suggest alternative strategies for adaptation to snowmelt timing. These strategies potentially apply to other species and tundra ecosystems and provide a framework, enabling one to compare and generalise phenological responses to snowmelt timing under different future climate scenarios.
DOI: 10.6084/m9.figshare.6652325
title: Supplementary Material for: Gα<sub>i</sub> Proteins are Indispensable for Hearing

description: <b><i>Background/Aims:</i></b> From invertebrates to mammals, Gα<sub>i</sub> proteins act together with their common binding partner Gpsm2 to govern cell polarization and planar organization in virtually any polarized cell. Recently, we demonstrated that Gα<sub>i3</sub>-deficiency in pre-hearing murine cochleae pointed to a role of Gα<sub>i3</sub> for asymmetric migration of the kinocilium as well as the orientation and shape of the stereociliary (“hair”) bundle, a requirement for the progression of mature hearing. We found that the lack of Gα<sub>i3</sub> impairs stereociliary elongation and hair bundle shape in high-frequency cochlear regions, linked to elevated hearing thresholds for high-frequency sound. How these morphological defects translate into hearing phenotypes is not clear. <b><i>Methods:</i></b> Here, we studied global and conditional <i>Gnai3</i> and <i>Gnai2</i> mouse mutants deficient for either one or both Gα<sub>i</sub> proteins. Comparative analyses of global versus Foxg1-driven conditional mutants that mainly delete in the inner ear and telencephalon in combination with functional tests were applied to dissect essential and redundant functions of different Gα<sub>i</sub> isoforms and to assign specific defects to outer or inner hair cells, the auditory nerve, satellite cells or central auditory neurons. <b><i>Results:</i></b> Here we report that lack of Gα<sub>i3</sub> but not of the ubiquitously expressed Gα<sub>i2</sub> elevates hearing threshold, accompanied by impaired hair bundle elongation and shape in high-frequency cochlear regions. During the crucial reprogramming of the immature inner hair cell (IHC) synapse into a functional sensory synapse of the mature IHC deficiency for Gα<sub>i2</sub> or Gα<sub>i3</sub> had no impact. In contrast, double-deficiency for Gα<sub>i2</sub> and Gα<sub>i3</sub> isoforms results in abnormalities along the entire tonotopic axis including profound deafness associated with stereocilia defects. In these mice, postnatal IHC synapse maturation is also impaired. In addition, the analysis of conditional versus global Gα<sub>i3</sub>-deficient mice revealed that the amplitude of ABR wave IV was disproportionally elevated in comparison to ABR wave I indicating that Gα<sub>i3</sub> is selectively involved in generation of neural gain during auditory processing. <b><i>Conclusion:</i></b> We propose a so far unrecognized complexity of isoform-specific and overlapping Gα<sub>i</sub> protein functions particular during final differentiation processes.
DOI: 10.6084/m9.figshare.6652325.v1
title: Supplementary Material for: Gα<sub>i</sub> Proteins are Indispensable for Hearing

description: <b><i>Background/Aims:</i></b> From invertebrates to mammals, Gα<sub>i</sub> proteins act together with their common binding partner Gpsm2 to govern cell polarization and planar organization in virtually any polarized cell. Recently, we demonstrated that Gα<sub>i3</sub>-deficiency in pre-hearing murine cochleae pointed to a role of Gα<sub>i3</sub> for asymmetric migration of the kinocilium as well as the orientation and shape of the stereociliary (“hair”) bundle, a requirement for the progression of mature hearing. We found that the lack of Gα<sub>i3</sub> impairs stereociliary elongation and hair bundle shape in high-frequency cochlear regions, linked to elevated hearing thresholds for high-frequency sound. How these morphological defects translate into hearing phenotypes is not clear. <b><i>Methods:</i></b> Here, we studied global and conditional <i>Gnai3</i> and <i>Gnai2</i> mouse mutants deficient for either one or both Gα<sub>i</sub> proteins. Comparative analyses of global versus Foxg1-driven conditional mutants that mainly delete in the inner ear and telencephalon in combination with functional tests were applied to dissect essential and redundant functions of different Gα<sub>i</sub> isoforms and to assign specific defects to outer or inner hair cells, the auditory nerve, satellite cells or central auditory neurons. <b><i>Results:</i></b> Here we report that lack of Gα<sub>i3</sub> but not of the ubiquitously expressed Gα<sub>i2</sub> elevates hearing threshold, accompanied by impaired hair bundle elongation and shape in high-frequency cochlear regions. During the crucial reprogramming of the immature inner hair cell (IHC) synapse into a functional sensory synapse of the mature IHC deficiency for Gα<sub>i2</sub> or Gα<sub>i3</sub> had no impact. In contrast, double-deficiency for Gα<sub>i2</sub> and Gα<sub>i3</sub> isoforms results in abnormalities along the entire tonotopic axis including profound deafness associated with stereocilia defects. In these mice, postnatal IHC synapse maturation is also impaired. In addition, the analysis of conditional versus global Gα<sub>i3</sub>-deficient mice revealed that the amplitude of ABR wave IV was disproportionally elevated in comparison to ABR wave I indicating that Gα<sub>i3</sub> is selectively involved in generation of neural gain during auditory processing. <b><i>Conclusion:</i></b> We propose a so far unrecognized complexity of isoform-specific and overlapping Gα<sub>i</sub> protein functions particular during final differentiation processes.
DOI: 10.6084/m9.figshare.6652319
title: Plot data from the paper "A modern analogue of the Pleistocene steppe-tundra ecosystem in southern Siberia" (Chytry et al.)

description: Primary data from 182 plots of 10 m x 10 m sampled in 12 habitat types of the steppe-tundra landscape in the SE Russian Altai Mountains in summers of 2005, 2006 and 2011. The dataset contains species composition of vascular plants, bryophytes, lichens and snails, and environmental data from the same plots including measurements of primary aboveground productivity, nutrient contents in the aboveground biomass and soil chemistry.<br>Sampling methods are described in the paper Chytrý et al.: A modern analogue of the Pleistocene steppe-tundra ecosystem in southern Siberia.<br>The dataset is provided in two files, one in the XLSX format for Excel 2013, another in tab-delimited table in the TXT format.<br>Plant species data were originally recorded with covers on the nine-degree Braun-Blanquet scale, which has been transformed to percentages as follows: 1, 2, 3, 4, 8, 18, 38, 63, 88. Other values can occur in case when original records of the same species in different layers were merged for the analyses. Snail data indicate species presence (1) or absence (0). NA means absence of measurement in the plot.<br><br>
DOI: 10.6084/m9.figshare.6652319.v2
title: Plot data from the paper "A modern analogue of the Pleistocene steppe-tundra ecosystem in southern Siberia" (Chytry et al.)

description: Primary data from 182 plots of 10 m x 10 m sampled in 12 habitat types of the steppe-tundra landscape in the SE Russian Altai Mountains in summers of 2005, 2006 and 2011. The dataset contains species composition of vascular plants, bryophytes, lichens and snails, and environmental data from the same plots including measurements of primary aboveground productivity, nutrient contents in the aboveground biomass and soil chemistry.<br>Sampling methods are described in the paper Chytrý et al.: A modern analogue of the Pleistocene steppe-tundra ecosystem in southern Siberia.<br>The dataset is provided in two files, one in the XLSX format for Excel 2013, another in tab-delimited table in the TXT format.<br>Plant species data were originally recorded with covers on the nine-degree Braun-Blanquet scale, which has been transformed to percentages as follows: 1, 2, 3, 4, 8, 18, 38, 63, 88. Other values can occur in case when original records of the same species in different layers were merged for the analyses. Snail data indicate species presence (1) or absence (0). NA means absence of measurement in the plot.<br><br>
DOI: 10.6084/m9.figshare.6652319.v1
title: Plot data from the paper "A modern analogue of the Pleistocene steppe-tundra ecosystem in southern Siberia" (Chytrý et al.)

description: Primary data from 182 plots of 10 m x 10 m sampled in 12 habitat types of the steppe-tundra landscape in the SE Russian Altai Mountains in summers of 2005, 2006 and 2011. The dataset contains species composition of vascular plants, bryophytes, lichens and snails, and environmental data from the same plots including measurements of primary aboveground productivity, nutrient contents in the aboveground biomass and soil chemistry.<br>Sampling methods are described in the paper Chytrý et al.: A modern analogue of the Pleistocene steppe-tundra ecosystem in southern Siberia.<br>The dataset is provided in two files, one in the XLSX format for Excel 2013, another in tab-delimited table in the TXT format.<br>Plant species data were originally recorded with covers on the nine-degree Braun-Blanquet scale, which has been transformed to percentages as follows: 1, 2, 3, 4, 8, 18, 38, 63, 88. Other values can occur in case when original records of the same species in different layers were merged for the analyses. Snail data indicate species presence (1) or absence (0). NA means absence of measurement in the plot.<br><br>
DOI: 10.6084/m9.figshare.6652310
title: Supplementary Material for: <b><i>Uncaria rhynchophylla</i></b> Ameliorates Parkinson’s Disease by Inhibiting HSP90 Expression: Insights from Quantitative Proteomics

description: <b><i>Background/Aims:</i></b> <i>Uncaria rhynchophylla</i>, known as “Gou-teng”, is a traditional Chinese medicine (TCM) used to extinguish wind, clear heat, arrest convulsions, and pacify the liver. Although <i>U. rhynchophylla</i> has a long history of being often used to treat central nervous system (CNS) diseases, its efficacy and potential mechanism are still uncertain. This study investigated neuroprotective effect and the underlying mechanism of <i>U. rhynchophylla</i> extract (URE) in MPP<sup>+</sup>-induced SH-SY5Y cells and MPTP-induced mice. <b><i>Methods:</i></b> MPP<sup>+</sup>-induced SH-SY5Y cells and MPTP-induced mice were used to established Parkinson’s disease (PD) models. Quantitative proteomics and bioinformatics were used to uncover proteomics changes of URE. Western blotting was used to validate main differentially expressed proteins and test HSP90 client proteins (apoptosis-related, autophagy-related, MAPKs, PI3K, and AKT proteins). Flow cytometry and JC-1 staining assay were further used to confirm the effect of URE on MPP<sup>+</sup>-induced apoptosis in SH-SY5Y cells. Gait analysis was used to detect the behavioral changes in MPTP-induced mice. The levels of dopamine (DA) and their metabolites were examined in striatum (STR) by HPLC-EC. The positive expression of tyrosine hydroxylase (TH) was detected by immunohischemical staining and Western blotting. <b><i>Results:</i></b> URE dose-dependently increased the cell viability in MPP<sup>+</sup>-induced SH-SY5Y cells. Quantitative proteomics and bioinformatics results confirmed that HSP90 was an important differentially expressed protein of URE. URE inhibited the expression of HSP90, which further reversed MPP<sup>+</sup>-induced cell apoptosis and autophagy by increasing the expressions of Bcl-2, Cyclin D1, p-ERK, p-PI3K p85, PI3K p110α, p-AKT, and LC3-I and decreasing cleaved caspase 3, Bax, p-JNK, p-p38, and LC3-II. URE also markedly decreased the apoptotic ratio and elevated mitochondrial transmembrane potential (DΨ<sub>m</sub>). Furthermore, URE treatment ameliorated behavioral impairments, increased the contents of DA and its metabolites and elevated the positive expressions of TH in SN and STR as well as the TH protein. <b><i>Conclusions:</i></b> URE possessed the neuroprotective effect <i>in vivo</i> and <i>in vitro</i>, regulated MAPK and PI3K-AKT signal pathways, and inhibited the expression of HSP90. <i>U. rhynchophylla</i> has potentials as therapeutic agent in PD treatment.
DOI: 10.6084/m9.figshare.6652295
title: The Agreement’s impact on political cooperation

description: This article aims to examine the impact of the Agreement on political cooperation. It examines party political cooperation in Northern Ireland and also bilateral British–Irish intergovernmental cooperation. In the first section, the Agreement’s consociational system and its criticisms are outlined. In the second section, the effect of the Agreement on cooperation between the Northern Ireland political parties is assessed. In the third section, the impact on British–Irish East–West cooperation is assessed along with the effects of Brexit.
DOI: 10.6084/m9.figshare.6652295.v1
title: The Agreement’s impact on political cooperation

description: This article aims to examine the impact of the Agreement on political cooperation. It examines party political cooperation in Northern Ireland and also bilateral British–Irish intergovernmental cooperation. In the first section, the Agreement’s consociational system and its criticisms are outlined. In the second section, the effect of the Agreement on cooperation between the Northern Ireland political parties is assessed. In the third section, the impact on British–Irish East–West cooperation is assessed along with the effects of Brexit.
DOI: 10.6084/m9.figshare.6652292
title: Worker mobility under attack? Explaining labour market chauvinism in the EU

description: The aim of this paper is to investigate citizen views on the free movement of workers within the European Union (EU). We are interested in how situational and relational factors affect labour market chauvinist attitudes. Drawing on the threat theory, we advance new hypotheses on the role of intertemporal relative deprivation in amplifying chauvinist inclinations. From the intergroup contact theory and transnational approaches, we borrow insights on the role played by cross-border experiences and inclusion in discursive and associational networks in containing chauvinism. The analysis uses the original ‘Reconciling Economic and Social Europe’ (REScEU) survey conducted in six EU countries (i.e., France, Germany, Italy, Poland, Spain and Sweden) in the fall of 2016. The article shows that – though rooted in class and status positions – chauvinist attitudes are clearly sensitive to contingent situations and lifeworld experiences.
DOI: 10.6084/m9.figshare.6652292.v1
title: Worker mobility under attack? Explaining labour market chauvinism in the EU

description: The aim of this paper is to investigate citizen views on the free movement of workers within the European Union (EU). We are interested in how situational and relational factors affect labour market chauvinist attitudes. Drawing on the threat theory, we advance new hypotheses on the role of intertemporal relative deprivation in amplifying chauvinist inclinations. From the intergroup contact theory and transnational approaches, we borrow insights on the role played by cross-border experiences and inclusion in discursive and associational networks in containing chauvinism. The analysis uses the original ‘Reconciling Economic and Social Europe’ (REScEU) survey conducted in six EU countries (i.e., France, Germany, Italy, Poland, Spain and Sweden) in the fall of 2016. The article shows that – though rooted in class and status positions – chauvinist attitudes are clearly sensitive to contingent situations and lifeworld experiences.
DOI: 10.6084/m9.figshare.6652289
title: The bifurcated stem loop 4 (SL4) is crucial for efficient packaging of mouse mammary tumor virus (MMTV) genomic RNA

description: Packaging the mouse mammary tumor virus (MMTV) genomic RNA (gRNA) requires the entire 5ʹ untranslated region (UTR) in conjunction with the first 120 nucleotides of the <i>gag</i> gene. This region includes several palindromic (pal) sequence(s) and stable stem loops (SLs). Among these, stem loop 4 (SL4) adopts a bifurcated structure consisting of three stems, two apical loops, and an internal loop. Pal II, located in one of the apical loops, mediates gRNA dimerization, a process intricately linked to packaging. We thus hypothesized that the bifurcated SL4 structure could constitute the major gRNA packaging determinant. To test this hypothesis, the two apical loops and the flanking sequences forming the bifurcated SL4 were individually mutated. These mutations all had deleterious effects on gRNA packaging and propagation. Next, single and compensatory mutants were designed to destabilize then recreate the bifurcated SL4 structure. A structure-function analysis using bioinformatics predictions and RNA chemical probing revealed that mutations that led to the loss of the SL4 bifurcated structure abrogated RNA packaging and propagation, while compensatory mutations that recreated the native SL4 structure restored RNA packaging and propagation to wild type levels. Altogether, our results demonstrate that SL4 constitutes the principal packaging determinant of MMTV gRNA. Our findings further suggest that SL4 acts as a structural switch that can not only differentiate between RNA for translation <i>versus</i> packaging/dimerization, but its location also allows differentiation between spliced and unspliced RNAs during gRNA encapsidation.
DOI: 10.6084/m9.figshare.6652289.v2
title: The bifurcated stem loop 4 (SL4) is crucial for efficient packaging of mouse mammary tumor virus (MMTV) genomic RNA

description: Packaging the mouse mammary tumor virus (MMTV) genomic RNA (gRNA) requires the entire 5ʹ untranslated region (UTR) in conjunction with the first 120 nucleotides of the <i>gag</i> gene. This region includes several palindromic (pal) sequence(s) and stable stem loops (SLs). Among these, stem loop 4 (SL4) adopts a bifurcated structure consisting of three stems, two apical loops, and an internal loop. Pal II, located in one of the apical loops, mediates gRNA dimerization, a process intricately linked to packaging. We thus hypothesized that the bifurcated SL4 structure could constitute the major gRNA packaging determinant. To test this hypothesis, the two apical loops and the flanking sequences forming the bifurcated SL4 were individually mutated. These mutations all had deleterious effects on gRNA packaging and propagation. Next, single and compensatory mutants were designed to destabilize then recreate the bifurcated SL4 structure. A structure-function analysis using bioinformatics predictions and RNA chemical probing revealed that mutations that led to the loss of the SL4 bifurcated structure abrogated RNA packaging and propagation, while compensatory mutations that recreated the native SL4 structure restored RNA packaging and propagation to wild type levels. Altogether, our results demonstrate that SL4 constitutes the principal packaging determinant of MMTV gRNA. Our findings further suggest that SL4 acts as a structural switch that can not only differentiate between RNA for translation <i>versus</i> packaging/dimerization, but its location also allows differentiation between spliced and unspliced RNAs during gRNA encapsidation.
DOI: 10.6084/m9.figshare.6652283
title: Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea

description: #miRCc Version 1.0 (June 2018)#This program develops algorithms for predicting microRNA-like RNAs in the model mushroom <i>Coprinopsis cinerea</i><br>Please read carefully the README.txt file before running the programs.<br>The algorithms are implemented in Perl. Please make sure that Perl (https://www.perl.org/) is properly installed on your computer.<br>All source codes are included in this fileset. You can modify some of the codes to suit the purpose of your study.<br>