cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14401601.v1
title: <i>WDR45</i>, one gene associated with multiple neurodevelopmental disorders

description: The <i>WDR45</i> gene is localized on the X-chromosome and variants in this gene are linked to six different neurodegenerative disorders, i.e., ß-propeller protein associated neurodegeneration, Rett-like syndrome, intellectual disability, and epileptic encephalopathies including developmental and epileptic encephalopathy, early-onset epileptic encephalopathy and West syndrome and potentially also specific malignancies. WDR45/WIPI4 is a WD-repeat β-propeller protein that belongs to the WIPI (WD repeat domain, phosphoinositide interacting) family. The precise cellular function of WDR45 is still largely unknown, but deletions or conventional variants in <i>WDR45</i> can lead to macroautophagy/autophagy defects, malfunctioning mitochondria, endoplasmic reticulum stress and unbalanced iron homeostasis, suggesting that this protein functions in one or more pathways regulating directly or indirectly those processes. As a result, the underlying cause of the WDR45-associated disorders remains unknown. In this review, we summarize the current knowledge about the cellular and physiological functions of WDR45 and highlight how genetic variants in its encoding gene may contribute to the pathophysiology of the associated diseases. In particular, we connect clinical manifestations of the disorders with their potential cellular origin of malfunctioning and critically discuss whether it is possible that one of the most prominent shared features, i.e., brain iron accumulation, is the primary cause for those disorders. <b>Abbreviations:</b> ATG/Atg: autophagy related; BPAN: ß-propeller protein associated neurodegeneration; CNS: central nervous system; DEE: developmental and epileptic encephalopathy; EEG: electroencephalograph; ENO2/neuron-specific enolase, enolase 2; EOEE: early-onset epileptic encephalopathy; ER: endoplasmic reticulum; ID: intellectual disability; IDR: intrinsically disordered region; MRI: magnetic resonance imaging; NBIA: neurodegeneration with brain iron accumulation; NCOA4: nuclear receptor coactivator 4; PtdIns3P: phosphatidylinositol-3-phosphate; RLS: Rett-like syndrome; WDR45: WD repeat domain 45; WIPI: WD repeat domain, phosphoinositide interacting
DOI: 10.6084/m9.figshare.16912048
title: SHISA5/SCOTIN restrains spontaneous autophagy induction by blocking contact between the ERES and phagophores

description: The phagophore expands into autophagosomes in close proximity to endoplasmic reticulum (ER) exit sites (ERESs). Here, we propose that a single-pass ER transmembrane protein, SHISA5/SCOTIN, acts as an autophagy suppressor under basal condition by blocking the contact between the phagophore and ERES. HeLa cells lacking SHISA5 displayed higher levels of macroautophagy/autophagy. The enhanced autophagy in <i>SHISA5</i> KO cells requires class III phosphatidylinositol 3-kinase complex I (PtdIns3K-C1) activity and functional assembly of ERES, but not ULK1 activity. A proximity ligation assay (PLA) of SEC16A (Sec16 homolog A, endoplasmic reticulum export factor)-WIPI2 (WD repeat domain, phosphoinositide interacting 2) and SEC31A (Sec31 homolog A, COPII coat complex component)-MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3 beta) demonstrated that contact between the ERES and phagophore increased in <i>SHISA5</i> KO cells, and the cytosolic domain of SHISA5 was sufficient to rescue this phenotype. Close proximity between ERES and phagophore in <i>SHISA5</i> KO cells was also visualized by performing an ultrastructure correlative image analysis of SEC31A associated with LC3-positive membranes. Furthermore, we observed that SHISA5 was located near ERES under basal conditions, but displaced away from ERES under autophagy-inducing conditions. These data suggest that SHISA5 functions to block spontaneous contact between ERES and phagophore, and the blockage effect of SHISA5 should be relieved for the proper induction of autophagy. ATG2: autophagy related 2; BECN1: beclin 1; COPII: coat protein II; DMSO: dimethyl sulfoxide; EBSS: Earle’s balanced salt solution; EGFP: enhanced green fluorescent protein; ER: endoplasmic reticulum; ERES: ER exit site(s); GFP: green fluorescent protein; H89: H-89 dihydrochloride hydrate; LAMP1: lysosomal-associated membrane protein 1; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTORC1: mechanistic target of rapamycin kinase complex 1; NS5A: nonstructural protein 5A; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PLA: proximity ligation assay; PtdIns3P: phosphatidylionositol-3-phosphate; RB1CC1/FIP200: RB1 inducible coiled-coil 1; RFP: red fluorescent protein; RPS6KB1/S6K: ribosomal protein S6 kinase B1; SBP: streptavidin binding protein; SEC16A: SEC16 homolog A, endoplasmic reticulum export factor; SEC31A: SEC31 homolog A, COPII coat complex component; siRNA: small interfering RNA; Str: streptavidin; ULK1: unc-51-like autophagy activating kinase 1; VSVG: vesicular stomatitis virus glycoprotein; WIPI2: WD repeat domain, phosphoinositide interacting 2; WT: wild type
DOI: 10.6084/m9.figshare.16912048.v1
title: SHISA5/SCOTIN restrains spontaneous autophagy induction by blocking contact between the ERES and phagophores

description: The phagophore expands into autophagosomes in close proximity to endoplasmic reticulum (ER) exit sites (ERESs). Here, we propose that a single-pass ER transmembrane protein, SHISA5/SCOTIN, acts as an autophagy suppressor under basal condition by blocking the contact between the phagophore and ERES. HeLa cells lacking SHISA5 displayed higher levels of macroautophagy/autophagy. The enhanced autophagy in <i>SHISA5</i> KO cells requires class III phosphatidylinositol 3-kinase complex I (PtdIns3K-C1) activity and functional assembly of ERES, but not ULK1 activity. A proximity ligation assay (PLA) of SEC16A (Sec16 homolog A, endoplasmic reticulum export factor)-WIPI2 (WD repeat domain, phosphoinositide interacting 2) and SEC31A (Sec31 homolog A, COPII coat complex component)-MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3 beta) demonstrated that contact between the ERES and phagophore increased in <i>SHISA5</i> KO cells, and the cytosolic domain of SHISA5 was sufficient to rescue this phenotype. Close proximity between ERES and phagophore in <i>SHISA5</i> KO cells was also visualized by performing an ultrastructure correlative image analysis of SEC31A associated with LC3-positive membranes. Furthermore, we observed that SHISA5 was located near ERES under basal conditions, but displaced away from ERES under autophagy-inducing conditions. These data suggest that SHISA5 functions to block spontaneous contact between ERES and phagophore, and the blockage effect of SHISA5 should be relieved for the proper induction of autophagy. ATG2: autophagy related 2; BECN1: beclin 1; COPII: coat protein II; DMSO: dimethyl sulfoxide; EBSS: Earle’s balanced salt solution; EGFP: enhanced green fluorescent protein; ER: endoplasmic reticulum; ERES: ER exit site(s); GFP: green fluorescent protein; H89: H-89 dihydrochloride hydrate; LAMP1: lysosomal-associated membrane protein 1; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTORC1: mechanistic target of rapamycin kinase complex 1; NS5A: nonstructural protein 5A; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PLA: proximity ligation assay; PtdIns3P: phosphatidylionositol-3-phosphate; RB1CC1/FIP200: RB1 inducible coiled-coil 1; RFP: red fluorescent protein; RPS6KB1/S6K: ribosomal protein S6 kinase B1; SBP: streptavidin binding protein; SEC16A: SEC16 homolog A, endoplasmic reticulum export factor; SEC31A: SEC31 homolog A, COPII coat complex component; siRNA: small interfering RNA; Str: streptavidin; ULK1: unc-51-like autophagy activating kinase 1; VSVG: vesicular stomatitis virus glycoprotein; WIPI2: WD repeat domain, phosphoinositide interacting 2; WT: wild type
DOI: 10.58120/upstate.23660583
title: JBC 2024 - LECT2 Flow Shear

description: These Figshare files consist of raw/unprocessed images in various formats, processed data and statistical analysis (Graphpad Prism), high resolution versions of some images in the paper, and MATLAB scripts used to analyze/process the microfluidic data.Figure2.zip-Raw light microcsope images of microfluidic aggregates in Zeiss .czi format<br>Figure3.zip-GraphPad Prism files containing processed data derived from images in Figure 2, and statistical analysis<br>Figure4.zip-Raw light microscope images of microfluidic aggregates from seeding experiments, in Zeiss .czi format<br>Figure6.zip-Raw EM images of negatively-stained samples in Gatan .dm3 format-Raw cryo-EM image of frozen vitrified sample in .mrc format-2D average of fibrils-Power spectrum calculated from 2D average<br>Figure7.zip-GraphPad Prism file containing processed data derived from images in Figure 4, and statistical analysis<br>FigureS3.zip-Raw light microscope images of microfluidic aggregates in Zeiss .czi format, from another biological repeat<br>FiguresS5-S11.zip-Raw light microscope images of microfluidic aggregates in Zeiss .czi format-GraphPad Prism files containing processed data derived from above images, and statistical analysis<br>FigureS12.zip-Raw light microscope images of microfluidic aggregates in Zeiss .czi format, testing dependence of aggregation on protein concentration-Graphpad Prism file containing processed data derived from above images, and statistical analysis<br>FigureS14.zip:-Raw light microscope images of microfluidic aggregates from additional biological repeats of seeding experiments, in Zeiss .czi format-GraphPad Prism files containing processed data derived from above images, and statistical analysis<br>ProcessChannelsV6.zip-MATLAB scripts for calculating areas and intensities of aggregates in microfluidic channels
DOI: 10.58120/upstate.23660583.v1
title: JBC 2024 - LECT2 Flow Shear

description: These Figshare files consist of raw/unprocessed images in various formats, processed data and statistical analysis (Graphpad Prism), high resolution versions of some images in the paper, and MATLAB scripts used to analyze/process the microfluidic data.Figure2.zip-Raw light microcsope images of microfluidic aggregates in Zeiss .czi format<br>Figure3.zip-GraphPad Prism files containing processed data derived from images in Figure 2, and statistical analysis<br>Figure4.zip-Raw light microscope images of microfluidic aggregates from seeding experiments, in Zeiss .czi format<br>Figure6.zip-Raw EM images of negatively-stained samples in Gatan .dm3 format-Raw cryo-EM image of frozen vitrified sample in .mrc format-2D average of fibrils-Power spectrum calculated from 2D average<br>Figure7.zip-GraphPad Prism file containing processed data derived from images in Figure 4, and statistical analysis<br>FigureS3.zip-Raw light microscope images of microfluidic aggregates in Zeiss .czi format, from another biological repeat<br>FiguresS5-S11.zip-Raw light microscope images of microfluidic aggregates in Zeiss .czi format-GraphPad Prism files containing processed data derived from above images, and statistical analysis<br>FigureS12.zip-Raw light microscope images of microfluidic aggregates in Zeiss .czi format, testing dependence of aggregation on protein concentration-Graphpad Prism file containing processed data derived from above images, and statistical analysis<br>FigureS14.zip:-Raw light microscope images of microfluidic aggregates from additional biological repeats of seeding experiments, in Zeiss .czi format-GraphPad Prism files containing processed data derived from above images, and statistical analysis<br>ProcessChannelsV6.zip-MATLAB scripts for calculating areas and intensities of aggregates in microfluidic channels
DOI: 10.21942/uva.24745611
title: WIRES - Enhanced sampling strategies for the molecular simulation of DNA

description: Molecular dynamics (MD) simulations can provide detailed insights into molecular systems, including DNA, at high resolution in space and time. With current computer architectures, time scales of tens of microseconds are feasible with the current all-atom force fields. However, these timescales are insufficiently long to accurately characterize conformational transitions in DNA and compare calculations to experimental data. This review discusses the advantages and drawbacks of two simulation approaches to overcome the timescale issue. One approach is based on adding biasing potentials to the system to drive transitions. Umbrella sampling, steered MD, and metadynamics are examples of these methods. A key challenge of such methods is the necessity of selecting one or a few efficient coordinates, commonly referred to as collective variables (CVs), along which to apply the biasing potential. The novel path-metadynamics methodology addresses this issue by finding the optimal route(s) between states in a multi-dimensional collective variable space. Another strategy is path sampling, which focuses MD simulations on the transitions. The assumption is that even though transitions between states are rare, they are usually fast. Stopping the simulations as soon as they reach a stable state can significantly increase simulation efficiency. We introduce these methods on the two-dimensional Müller-Brown potential. Applications to DNA are featured for two different processes: the Watson-Crick-Franklin to Hoogsteen transition in adenine-thymine base pairs and the binding of a DNA-binding protein domain to DNA.
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DOI: 10.21942/uva.24745611.v3
title: WIRES - Enhanced sampling strategies for the molecular simulation of DNA

description: Molecular dynamics (MD) simulations can provide detailed insights into molecular systems, including DNA, at high resolution in space and time. With current computer architectures, time scales of tens of microseconds are feasible with the current all-atom force fields. However, these timescales are insufficiently long to accurately characterize conformational transitions in DNA and compare calculations to experimental data. This review discusses the advantages and drawbacks of two simulation approaches to overcome the timescale issue. One approach is based on adding biasing potentials to the system to drive transitions. Umbrella sampling, steered MD, and metadynamics are examples of these methods. A key challenge of such methods is the necessity of selecting one or a few efficient coordinates, commonly referred to as collective variables (CVs), along which to apply the biasing potential. The novel path-metadynamics methodology addresses this issue by finding the optimal route(s) between states in a multi-dimensional collective variable space. Another strategy is path sampling, which focuses MD simulations on the transitions. The assumption is that even though transitions between states are rare, they are usually fast. Stopping the simulations as soon as they reach a stable state can significantly increase simulation efficiency. We introduce these methods on the two-dimensional Müller-Brown potential. Applications to DNA are featured for two different processes: the Watson-Crick-Franklin to Hoogsteen transition in adenine-thymine base pairs and the binding of a DNA-binding protein domain to DNA.
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DOI: 10.21942/uva.24745611.v2
title: WIRES - Enhanced sampling strategies for the molecular simulation of DNA

description: Molecular dynamics (MD) simulations can provide detailed insights into molecular systems, including DNA, at high resolution in space and time. With current computer architectures, time scales of tens of microseconds are feasible with the current all-atom force fields. However, these timescales are insufficiently long to accurately characterize conformational transitions in DNA and compare calculations to experimental data. This review discusses the advantages and drawbacks of two simulation approaches to overcome the timescale issue. One approach is based on adding biasing potentials to the system to drive transitions. Umbrella sampling, steered MD, and metadynamics are examples of these methods. A key challenge of such methods is the necessity of selecting one or a few efficient coordinates, commonly referred to as collective variables (CVs), along which to apply the biasing potential. The novel path-metadynamics methodology addresses this issue by finding the optimal route(s) between states in a multi-dimensional collective variable space. Another strategy is path sampling, which focuses MD simulations on the transitions. The assumption is that even though transitions between states are rare, they are usually fast. Stopping the simulations as soon as they reach a stable state can significantly increase simulation efficiency. We introduce these methods on the two-dimensional Müller-Brown potential. Applications to DNA are featured for two different processes: the Watson-Crick-Franklin to Hoogsteen transition in adenine-thymine base pairs and the binding of a DNA-binding protein domain to DNA.
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DOI: 10.17909/628w-9m17
title: Data from paper
DOI: 10.17909/g5zr-se07
title: Data from paper
DOI: 10.5281/zenodo.10849483
title: Table S1: Average photosynthetic photon flux densities (PPFD) used as six lighting treatments in the trial. The lights were on for a photoperiod of 16 h, and the respective daily light integral (DLI) provided by the light-emitting diode (LED) lights, sunlight, and the sum of LED + sunlight were calculated for all treatments and each cultivar.
DOI: 10.5281/zenodo.10849484
title: Table S1: Average photosynthetic photon flux densities (PPFD) used as six lighting treatments in the trial. The lights were on for a photoperiod of 16 h, and the respective daily light integral (DLI) provided by the light-emitting diode (LED) lights, sunlight, and the sum of LED + sunlight were calculated for all treatments and each cultivar.
DOI: 10.5281/zenodo.10849449
title: PCPI-S and PCPI-C French version Switzerland

description: Person-centred care is associated with improved clinical outcomes, patient satisfaction, work environment factors and economic outcomes. Although measures could improve understanding of the benefits of person-centred practice and support its implementation, few validated instruments are available to date. Limtations of available instrument include the lack of clarification of theory-based concepts, scales that do not refer to an existing theoretical framework and that do not assess all aspects of person-centred care. Existing scales are mainly developed in English and used in English healthcare systems and may not be adapted to healthcare contexts in other countries. Prof. McCormack and Prof. McCance developed and tested the Person-centred Practice Inventory-Staff (PCPI-S) and the Person-centred Practice Inventory-Care (PCPI-C) based on the Person-centred Practice Framework (PCPF) to measure professionals' and patients' perception of person-centred practice.

The PCPI-S and the PCPI-S were translated in French and psychometrically tested in the French-speaking part of Switzerland.
DOI: 10.5281/zenodo.10849450
title: PCPI-S and PCPI-C French version Switzerland

description: Person-centred care is associated with improved clinical outcomes, patient satisfaction, work environment factors and economic outcomes. Although measures could improve understanding of the benefits of person-centred practice and support its implementation, few validated instruments are available to date. Limtations of available instrument include the lack of clarification of theory-based concepts, scales that do not refer to an existing theoretical framework and that do not assess all aspects of person-centred care. Existing scales are mainly developed in English and used in English healthcare systems and may not be adapted to healthcare contexts in other countries. Prof. McCormack and Prof. McCance developed and tested the Person-centred Practice Inventory-Staff (PCPI-S) and the Person-centred Practice Inventory-Care (PCPI-C) based on the Person-centred Practice Framework (PCPF) to measure professionals' and patients' perception of person-centred practice.

The PCPI-S and the PCPI-S were translated in French and psychometrically tested in the French-speaking part of Switzerland.
DOI: 10.6084/m9.figshare.25451785
title: 20240322_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.6084/m9.figshare.25451785.v1
title: 20240322_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.6084/m9.figshare.17111542
title: Development of epithelial-mesenchymal transition-related lncRNA signature for predicting survival and immune microenvironment in pancreatic cancerwithexperiment validation

description: Long non-coding RNAs (LncRNAs) have crucial function in epithelial–mesenchymal transition (EMT) in pancreatic cancer. It is necessary to comprehensively analyze the potential role of EMT-related lncRNA in pancreatic cancer. In the present study, genomic data of pancreatic cancer from the TCGA database were downloaded and we found 368 EMT-related lncRNAs. According to the expression characteristics of prognostic-related lncRNAs, all samples could be divided into two clusters with different clinical outcomes and different tumor microenvironments. Moreover, an eleven EMT-related lncRNAs signature was established and verified. Patients with pancreatic cancer in the high-risk group had a shorter overall survival than those in the low-risk group and the signature could act as an independent prognostic factor. Further analysis suggested that the EMT-related lncRNAs might affect the prognosis of patients through immune mechanisms. All findings indicated that the signature and eleven lncRNAs might serve as potential prognostic biomarkers and therapeutic targets in the treatment of pancreatic cancer.
DOI: 10.6084/m9.figshare.17111542.v1
title: Development of epithelial-mesenchymal transition-related lncRNA signature for predicting survival and immune microenvironment in pancreatic cancerwithexperiment validation

description: Long non-coding RNAs (LncRNAs) have crucial function in epithelial–mesenchymal transition (EMT) in pancreatic cancer. It is necessary to comprehensively analyze the potential role of EMT-related lncRNA in pancreatic cancer. In the present study, genomic data of pancreatic cancer from the TCGA database were downloaded and we found 368 EMT-related lncRNAs. According to the expression characteristics of prognostic-related lncRNAs, all samples could be divided into two clusters with different clinical outcomes and different tumor microenvironments. Moreover, an eleven EMT-related lncRNAs signature was established and verified. Patients with pancreatic cancer in the high-risk group had a shorter overall survival than those in the low-risk group and the signature could act as an independent prognostic factor. Further analysis suggested that the EMT-related lncRNAs might affect the prognosis of patients through immune mechanisms. All findings indicated that the signature and eleven lncRNAs might serve as potential prognostic biomarkers and therapeutic targets in the treatment of pancreatic cancer.