cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11764116
title: Sgd1 is an MIF4G domain-containing cofactor of the RNA helicase Fal1 and associates with the 5’ domain of the 18S rRNA sequence

description: Assembly of eukaryotic ribosomal subunits is a complex and dynamic process involving the action of more than 200 <i>trans</i>-acting assembly factors. Although recent cryo-electron microscopy structures have provided information on architecture of several pre-ribosomal particles and the binding sites of many AFs, the RNA and protein interactions of many other AFs not captured in these snapshots still remain elusive. RNA helicases are key regulators of structural rearrangements within pre-ribosomal complexes and here we have analysed the eIF4A-like RNA helicase Fal1 and its putative cofactor Sgd1. Our data show that these proteins interact directly via the MIF4G domain of Sgd1 and that the MIF4G domain of Sgd1 stimulates the catalytic activity of Fal1 <i>in vitro</i>. The catalytic activity of Fal1, and the interaction between Fal1 and Sgd1, are required for efficient pre-rRNA processing at the A<sub>0</sub>, A<sub>1</sub> and A<sub>2</sub> sites. Furthermore, Sgd1 co-purifies the early small subunit biogenesis factors Lcp5 and Rok1, suggesting that the Fal1-Sgd1 complex likely functions within the SSU processome. <i>In vivo</i> crosslinking data reveal that Sgd1 binds to helix H12 of the 18S rRNA sequence and we further demonstrate that this interaction is formed by the C-terminal region of the protein, which is essential for its function in ribosome biogenesis.
DOI: 10.6084/m9.figshare.11764116.v1
title: Sgd1 is an MIF4G domain-containing cofactor of the RNA helicase Fal1 and associates with the 5’ domain of the 18S rRNA sequence

description: Assembly of eukaryotic ribosomal subunits is a complex and dynamic process involving the action of more than 200 <i>trans</i>-acting assembly factors. Although recent cryo-electron microscopy structures have provided information on architecture of several pre-ribosomal particles and the binding sites of many AFs, the RNA and protein interactions of many other AFs not captured in these snapshots still remain elusive. RNA helicases are key regulators of structural rearrangements within pre-ribosomal complexes and here we have analysed the eIF4A-like RNA helicase Fal1 and its putative cofactor Sgd1. Our data show that these proteins interact directly via the MIF4G domain of Sgd1 and that the MIF4G domain of Sgd1 stimulates the catalytic activity of Fal1 <i>in vitro</i>. The catalytic activity of Fal1, and the interaction between Fal1 and Sgd1, are required for efficient pre-rRNA processing at the A<sub>0</sub>, A<sub>1</sub> and A<sub>2</sub> sites. Furthermore, Sgd1 co-purifies the early small subunit biogenesis factors Lcp5 and Rok1, suggesting that the Fal1-Sgd1 complex likely functions within the SSU processome. <i>In vivo</i> crosslinking data reveal that Sgd1 binds to helix H12 of the 18S rRNA sequence and we further demonstrate that this interaction is formed by the C-terminal region of the protein, which is essential for its function in ribosome biogenesis.
DOI: 10.21954/ou.rd.11764062
title: 520,000 years of environmental change in West Africa: underpinning material

description: These files constitute the digital materials underpinning the thesis <em>520,000 years of environmental change in West Africa</em><br>Global temperatures are predicted to rise by 2-2.5°C by 2065, profoundly affecting the Earth's environment. The response of ecosystems to past climate fluctuations can inform on how systems will respond in the future. This thesis focuses on Quaternary environmental changes in West Africa, a region important because of its high ecological value and role in the global carbon cycle. In 2004, the International Continental Drilling Program recovered c. 291 m of sediments spanning the last c. 1 Myr from Lake Bosumtwi (Ghana). Pollen, charcoal and nitrogen isotopes (ᵟ<sup>15</sup>N) were analysed from the most recent c. 150m (c. 520 kyr). The latitudinal position and long duration of this core makes it unique for understanding West African monsoon dynamics and vegetation change. To aid characterisation of the Bosumtwi pollen succession, an atlas of present-day pollen was constructed for 364 pollen and spore taxa. The pollen record from Bosumtwi reveals dynamic vegetation change over the last c. 520 kyr, characterized by eleven biome shifts between savannah and forest. Savannah vegetation is dominated by Poaceae (&gt;55%) associated with Cyperaceae, Chenopodiaceae-Amaranthaceae and Caryophyllaceae. Forest vegetation is palynologically diverse, but broadly characterised by Moraceae, <i>Celtis, Uapaca, Macaranga</i> and <i>Trema</i>. Low ᵟ<sup>15</sup>N values correspond to forest expansion and these are driven by high lake levels. The timescale indicates that the six periods of forest expansion correspond to global interglacial periods. The record indicates that the wettest climate occurred during the Holocene, and the driest during Marine Isotope Stage 7. The vegetation and ᵟ<sup>15</sup>N records show a strong response to glacial-interglacial variability between 520- 320 kyr and 130- 0 kyr. Between 320- 130 kyr there is a weaker response to glacial-interglacial cycles probably related to high eccentricity during the peak of the 400-kyr component of eccentricity, with high eccentricity resulting in greater seasonality and ultimately drier conditions.<br><br>
DOI: 10.21954/ou.rd.11764062.v1
title: 520,000 years of environmental change in West Africa: underpinning material

description: These files constitute the digital materials underpinning the thesis <em>520,000 years of environmental change in West Africa</em><br>Global temperatures are predicted to rise by 2-2.5°C by 2065, profoundly affecting the Earth's environment. The response of ecosystems to past climate fluctuations can inform on how systems will respond in the future. This thesis focuses on Quaternary environmental changes in West Africa, a region important because of its high ecological value and role in the global carbon cycle. In 2004, the International Continental Drilling Program recovered c. 291 m of sediments spanning the last c. 1 Myr from Lake Bosumtwi (Ghana). Pollen, charcoal and nitrogen isotopes (ᵟ<sup>15</sup>N) were analysed from the most recent c. 150m (c. 520 kyr). The latitudinal position and long duration of this core makes it unique for understanding West African monsoon dynamics and vegetation change. To aid characterisation of the Bosumtwi pollen succession, an atlas of present-day pollen was constructed for 364 pollen and spore taxa. The pollen record from Bosumtwi reveals dynamic vegetation change over the last c. 520 kyr, characterized by eleven biome shifts between savannah and forest. Savannah vegetation is dominated by Poaceae (&gt;55%) associated with Cyperaceae, Chenopodiaceae-Amaranthaceae and Caryophyllaceae. Forest vegetation is palynologically diverse, but broadly characterised by Moraceae, <i>Celtis, Uapaca, Macaranga</i> and <i>Trema</i>. Low ᵟ<sup>15</sup>N values correspond to forest expansion and these are driven by high lake levels. The timescale indicates that the six periods of forest expansion correspond to global interglacial periods. The record indicates that the wettest climate occurred during the Holocene, and the driest during Marine Isotope Stage 7. The vegetation and ᵟ<sup>15</sup>N records show a strong response to glacial-interglacial variability between 520- 320 kyr and 130- 0 kyr. Between 320- 130 kyr there is a weaker response to glacial-interglacial cycles probably related to high eccentricity during the peak of the 400-kyr component of eccentricity, with high eccentricity resulting in greater seasonality and ultimately drier conditions.<br><br>
DOI: 10.6084/m9.figshare.11764047
title: Supplementary Figure 11

description: XRD of HER catalysts<br>
DOI: 10.6084/m9.figshare.11764047.v1
title: Supplementary Figure 11

description: XRD of HER catalysts<br>
DOI: 10.6084/m9.figshare.11764026
title: Supplementary Figure 6

description: OER data of NiFe using NiFe catalysts<br>
DOI: 10.6084/m9.figshare.11764026.v1
title: Supplementary Figure 6

description: OER data of NiFe using NiFe catalysts<br>
DOI: 10.6084/m9.figshare.11764008
title: Supplementary Figure 2

description: 1H NMR for TMA ionomers<br>
DOI: 10.6084/m9.figshare.11764014
title: Three-dimensional analysis of chloroplast protrusion formed under osmotic stress by polyethylene glycol in rice leaves

description: Chloroplast protrusions (CPs), large stromal areas lacking thylakoid membranes, are present before the formation of Rubisco-containing bodies (RCBs). RCBs are round bodies found within the cytoplasm and transported to the vacuole via the autophagy pathway. In the present study, we observed CPs and RCBs in rice mesophyll cells under polyethylene glycol-induced osmotic stress following 3D reconstruction of transmission electron microscopy images of serial sections. Osmotic stress induced the formation of CPs and RCBs whose features were similar to those observed under salt stress, suggesting that osmotic effect contributes to the formation of CPs and RCBs. The 3D image of CPs revealed that some CPs were formed far from the main chloroplast body, and one of the CP was in physical contact with a mitochondrion and a peroxisome, which were located far from the main chloroplast body. Thus, the CPs may aid the association with mitochondria and peroxisomes far from the main chloroplast body. Additionally, a CP with a connection to the main chloroplast body by a narrow structure was observed three-dimensionally. Since the volume of CPs was similar to that of RCBs, the CP with the narrow structure may be a precursor structure just before the release of an RCB into the cytoplasm. In the present study, the volumes of two CPs among 24 CPs were markedly larger than the volumes of other CPs and RCBs. Thus, the large body of the CP could be an unviable structure that fails to release RCBs.
DOI: 10.6084/m9.figshare.11764008.v1
title: Supplementary Figure 2

description: 1H NMR for TMA ionomers<br>
DOI: 10.6084/m9.figshare.11764014.v1
title: Three-dimensional analysis of chloroplast protrusion formed under osmotic stress by polyethylene glycol in rice leaves

description: Chloroplast protrusions (CPs), large stromal areas lacking thylakoid membranes, are present before the formation of Rubisco-containing bodies (RCBs). RCBs are round bodies found within the cytoplasm and transported to the vacuole via the autophagy pathway. In the present study, we observed CPs and RCBs in rice mesophyll cells under polyethylene glycol-induced osmotic stress following 3D reconstruction of transmission electron microscopy images of serial sections. Osmotic stress induced the formation of CPs and RCBs whose features were similar to those observed under salt stress, suggesting that osmotic effect contributes to the formation of CPs and RCBs. The 3D image of CPs revealed that some CPs were formed far from the main chloroplast body, and one of the CP was in physical contact with a mitochondrion and a peroxisome, which were located far from the main chloroplast body. Thus, the CPs may aid the association with mitochondria and peroxisomes far from the main chloroplast body. Additionally, a CP with a connection to the main chloroplast body by a narrow structure was observed three-dimensionally. Since the volume of CPs was similar to that of RCBs, the CP with the narrow structure may be a precursor structure just before the release of an RCB into the cytoplasm. In the present study, the volumes of two CPs among 24 CPs were markedly larger than the volumes of other CPs and RCBs. Thus, the large body of the CP could be an unviable structure that fails to release RCBs.
DOI: 10.6084/m9.figshare.11763996
title: Translation and adaptation of three English tinnitus patient-reported outcome measures to Spanish

description: <b>Objective:</b> The objective of this study was to improve the range of standardised tinnitus Spanish Patient-Reported Outcome Measures (PROMS) available by translating and ensuring cross-cultural adaptation of three English PROMs to Spanish. <b>Design:</b> The Tinnitus and Hearing Survey, Tinnitus Cognition Questionnaire, and Tinnitus Qualities Questionnaire were translated to Spanish using recently established good practice guidelines. <b>Study sample:</b> The translation process addressed 22 items included in six main steps specified in the guidelines. The translated PROMs were field tested on a sample of tinnitus patients who were recruited through convenience sampling using cognitive debriefing (<i>n</i> = 5) and pilot testing (<i>n</i> = 10) methods. <b>Results:</b> The translation process employed the required steps and provided specific details about the process and procedures. In addition, practical issues encountered while translating and adapting the questionnaires that may influence future translations were revealed. <b>Conclusions:</b> This is the first account of translating and adapting PROMs from one language to another using the good practice guidelines specific to hearing-related questionnaires. Following the rigorous procedures should ensure that the translated PROMs have linguistic and cultural equivalence to the original versions, although psychometric evaluation would remain necessary to confirm the functional equivalence.
DOI: 10.6084/m9.figshare.11763996.v1
title: Translation and adaptation of three English tinnitus patient-reported outcome measures to Spanish

description: <b>Objective:</b> The objective of this study was to improve the range of standardised tinnitus Spanish Patient-Reported Outcome Measures (PROMS) available by translating and ensuring cross-cultural adaptation of three English PROMs to Spanish. <b>Design:</b> The Tinnitus and Hearing Survey, Tinnitus Cognition Questionnaire, and Tinnitus Qualities Questionnaire were translated to Spanish using recently established good practice guidelines. <b>Study sample:</b> The translation process addressed 22 items included in six main steps specified in the guidelines. The translated PROMs were field tested on a sample of tinnitus patients who were recruited through convenience sampling using cognitive debriefing (<i>n</i> = 5) and pilot testing (<i>n</i> = 10) methods. <b>Results:</b> The translation process employed the required steps and provided specific details about the process and procedures. In addition, practical issues encountered while translating and adapting the questionnaires that may influence future translations were revealed. <b>Conclusions:</b> This is the first account of translating and adapting PROMs from one language to another using the good practice guidelines specific to hearing-related questionnaires. Following the rigorous procedures should ensure that the translated PROMs have linguistic and cultural equivalence to the original versions, although psychometric evaluation would remain necessary to confirm the functional equivalence.
DOI: 10.6084/m9.figshare.11763975
title: Working_data_PCV_Baseline.dta

description: Population-based incidence and serotype distribution of invasive pneumococcal disease prior to introduction of conjugate pneumococcal vaccine in Bangladesh
DOI: 10.6084/m9.figshare.11763858
title: Figure 2 raw data

description: Raw fluorescence intensities and stochastic simulation outputs for data presented in Figure 2.<br><b>Figure 2.</b> Positive feedback of Rab5 activation depends on GEF recruitment. (A) Illustration of protein interactions responsible for collective Rab5 switching. Positive feedback originates from a direct interaction between Rabex5:Rabaptin5 and Rab5:GTP. (B) Fluorescence intensity traces obtained from experiments depicted in A. Solid lines are mean normalized intensities, shaded areas are SD (Rabex5:Rabaptin5, ΔRabex5:Rabaptin5 N = 4; ΔRabex5, Rabex5:ΔRBDRabaptin5 N = 3). (C) Stochastic model simulations with and without Rabex5:Rabaptin5:Rab5:GTP complex formation (k5, k6 = 0) for 200 Rabex5:Rabaptin5 particles. Average curves from 50 individual runs are depicted in bold with 10 random traces per condition. The effective simulation time was scaled to align with experimental results. (D) Kinetic traces of CF488A-Rab5 and Rabex5:sCy5-Rabaptin5 activation. Solid line is mean normalized fluorescence intensity, shaded area is SD (N = 5). Inset: Ti for CF488A-Rab5 (blue) and Rabex5:sCy5-Rabaptin5 (orange). (E) Stochastic model simulations for Rab5 and Rabex5:Rabaptin5 membrane binding for 200 Rabex5:Rabaptin5 particles. Shown are curves from 50 independent runs, the mean line is depicted bold with 10 random traces per condition. (F) Schematic of the reconstitution experiment with pre-activated SLB-immobilized Rab5Q80L-His10:GTP. (G) Collective switching is faster with pre-activated Rab5. Left: Rab5 switching time courses in presence of 500 nM Rab5Q80L-His10 with increasing DOGS-NTA lipid concentration in the SLB. Solid line is mean normalized fluorescence intensity over time, shaded area is SD (N = 3). Right: corresponding time delays Ti and relative maximum rates kmax.<br>
DOI: 10.6084/m9.figshare.11763858.v1
title: Figure 2 raw data

description: Raw fluorescence intensities and stochastic simulation outputs for data presented in Figure 2.<br><b>Figure 2.</b> Positive feedback of Rab5 activation depends on GEF recruitment. (A) Illustration of protein interactions responsible for collective Rab5 switching. Positive feedback originates from a direct interaction between Rabex5:Rabaptin5 and Rab5:GTP. (B) Fluorescence intensity traces obtained from experiments depicted in A. Solid lines are mean normalized intensities, shaded areas are SD (Rabex5:Rabaptin5, ΔRabex5:Rabaptin5 N = 4; ΔRabex5, Rabex5:ΔRBDRabaptin5 N = 3). (C) Stochastic model simulations with and without Rabex5:Rabaptin5:Rab5:GTP complex formation (k5, k6 = 0) for 200 Rabex5:Rabaptin5 particles. Average curves from 50 individual runs are depicted in bold with 10 random traces per condition. The effective simulation time was scaled to align with experimental results. (D) Kinetic traces of CF488A-Rab5 and Rabex5:sCy5-Rabaptin5 activation. Solid line is mean normalized fluorescence intensity, shaded area is SD (N = 5). Inset: Ti for CF488A-Rab5 (blue) and Rabex5:sCy5-Rabaptin5 (orange). (E) Stochastic model simulations for Rab5 and Rabex5:Rabaptin5 membrane binding for 200 Rabex5:Rabaptin5 particles. Shown are curves from 50 independent runs, the mean line is depicted bold with 10 random traces per condition. (F) Schematic of the reconstitution experiment with pre-activated SLB-immobilized Rab5Q80L-His10:GTP. (G) Collective switching is faster with pre-activated Rab5. Left: Rab5 switching time courses in presence of 500 nM Rab5Q80L-His10 with increasing DOGS-NTA lipid concentration in the SLB. Solid line is mean normalized fluorescence intensity over time, shaded area is SD (N = 3). Right: corresponding time delays Ti and relative maximum rates kmax.<br>
DOI: 10.6084/m9.figshare.11763636
title: Visual question answering

description: This are the image features extracted from Inception v3 network to be included for solving the VQA problem.
DOI: 10.6084/m9.figshare.11763636.v1
title: Visual question answering

description: This are the image features extracted from Inception v3 network to be included for solving the VQA problem.
DOI: 10.6084/m9.figshare.11763591
title: Non-coding RNAs as cell wall regulators in <i>Saccharomyces cerevisiae</i>

description: The cell wall of <i>Saccharomyces cerevisiae</i> is an extracellular organelle crucial for preserving its cellular integrity and detecting environmental cues. The cell wall is composed of mannoproteins attached to a polysaccharide network and is continuously remodelled as cells undergo cell division, mating, gametogenesis or adapt to stressors. This makes yeast an excellent model to study the regulation of genes important for cell wall formation and maintenance. Given that certain yeast strains are pathogenic, a better understanding of their life cycle is of clinical relevance. This is why transcriptional regulatory mechanisms governing genes involved in cell wall biogenesis or maintenance have been the focus of numerous studies. However, little is known about the roles of long non-coding RNAs (lncRNAs), a class of transcripts that are thought to possess little or no protein coding potential, in controlling the expression of cell wall-related genes. This review outlines currently known mechanisms of lncRNA-mediated regulation of gene expression in <i>S. cerevisiae</i> and describes examples of lncRNA-regulated genes encoding cell wall proteins. We suggest that the association of currently annotated lncRNAs with the coding sequences and/or promoters of cell wall-related genes highlights a potential role for lncRNAs as important regulators of the yeast cell wall structure.
DOI: 10.6084/m9.figshare.11763609
title: Chlorophyll <i>a</i> relationships with nutrients and temperature, and predictions for lakes across perialpine and Balkan mountain regions

description: Model-derived relationships between chlorophyll <i>a</i> (Chl-<i>a</i>) and nutrients and temperature have fundamental implications for understanding complex interactions among water quality measures used for lake classification, yet accuracy comparisons of different approaches are scarce. Here, we (1) compared Chl<i>-a</i> model performances across linear and nonlinear statistical approaches; (2) evaluated single and combined effects of nutrients, depth, and temperature as lake surface water temperature (LSWT) or altitude on Chl<i>-a</i>; and (3) investigated the reliability of the best water quality model across 13 lakes from perialpine and central Balkan mountain regions. Chl<i>-a</i> was modelled using in situ water quality data from 157 European lakes; elevation data and LSWT in situ data were complemented by remote sensing measurements. Nonlinear approaches performed better, implying complex relationships between Chl<i>-a</i> and the explanatory variables. Boosted regression trees, as the best performing approach, accommodated interactions among predictor variables. Chl<i>-a</i>–nutrient relationships were characterized by sigmoidal curves, with total phosphorus having the largest explanatory power for our study region. In comparison with LSWT, utilization of altitude, the often-used temperature surrogate, led to different influence directions but similar predictive performances. These results support utilizing altitude in models for Chl<i>-a</i> predictions. Compared to Chl<i>-a</i> observations, Chl<i>-a</i> predictions of the best performing approach for mountain lakes (oligotrophic–eutrophic) led to minor differences in trophic state categorizations. Our findings suggest that both models with LSWT and altitude are appropriate for water quality predictions of lakes in mountain regions and emphasize the importance of incorporating interactions among variables when facing lake management challenges.