cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3543293.v1
title: A tale of two paralogs: human Transformer2 proteins with differential RNA-binding affinities

description: The Transformer2 (Tra2) proteins in humans are homologues of the <i>Drosophila</i> Tra2 protein. One of the two RNA-binding paralogs, Tra2β, has been very well-studied over the past decade, but not much is known about Tra2α. It was very recently shown that the two proteins demonstrate the phenomenon of paralog compensation. Here, we provide a structural basis for this genetic backup circuit, using molecular modelling and dynamics studies. We show that the two proteins display similar binding specificities, but differential affinities to a short GAA-rich RNA stretch. Starting from the 6-nucleotide RNA in the solution structure, close to 4000 virtual mutations were modelled on RNA and the domain–RNA interactions were studied after energy minimisation to convergence. Separately, another known 13-nucleotide stretch was docked and the domain–RNA interactions were observed through a 100-ns dynamics trajectory. We have also demonstrated the ‘compensatory’ mechanism at the level of domains in one of the domain repeat-containing RNA-binding proteins.
DOI: 10.6084/m9.figshare.3543251
title: The effect of treeline proximity on predation pressure: an experiment with artificial nests along elevational gradients in the European Alps

description: <b>Capsule:</b> Predation rates of artificial nests along elevational gradients were higher closer to the treeline in the European Alps. <b>Aims:</b> Alpine grassland birds tend to show an avoidance of mature trees, possibly due to an edge effect, such as higher predation pressure close to the treeline. This study aimed to estimate potential predation pressure in relation to the distance from the treeline and other environmental variables by using artificial nests positioned along elevational transects in the Italian Alps. <b>Methods:</b> A total of 119 artificial nests were positioned and monitored during the breeding season. For each nest, habitat data at small and large scales were collected. Daily nest survival was estimated using MARK. <b>Results:</b> The most informative model included date, distance from the treeline and a micro-habitat structure variable. In particular, the model showed a positive relationship between nest survival and the distance from the treeline. <b>Conclusions:</b> This study suggests that if treelines advance due to climate change, the functional habitat loss may be greater than physical habitat loss, since the optimal breeding area would be further away from the forest edge. The conservation of high-elevation grasslands in relation to environmental changes may therefore be addressed through management strategies to maintain open habitats.
DOI: 10.6084/m9.figshare.3543251.v1
title: The effect of treeline proximity on predation pressure: an experiment with artificial nests along elevational gradients in the European Alps

description: <b>Capsule:</b> Predation rates of artificial nests along elevational gradients were higher closer to the treeline in the European Alps. <b>Aims:</b> Alpine grassland birds tend to show an avoidance of mature trees, possibly due to an edge effect, such as higher predation pressure close to the treeline. This study aimed to estimate potential predation pressure in relation to the distance from the treeline and other environmental variables by using artificial nests positioned along elevational transects in the Italian Alps. <b>Methods:</b> A total of 119 artificial nests were positioned and monitored during the breeding season. For each nest, habitat data at small and large scales were collected. Daily nest survival was estimated using MARK. <b>Results:</b> The most informative model included date, distance from the treeline and a micro-habitat structure variable. In particular, the model showed a positive relationship between nest survival and the distance from the treeline. <b>Conclusions:</b> This study suggests that if treelines advance due to climate change, the functional habitat loss may be greater than physical habitat loss, since the optimal breeding area would be further away from the forest edge. The conservation of high-elevation grasslands in relation to environmental changes may therefore be addressed through management strategies to maintain open habitats.
DOI: 10.6084/m9.figshare.3543248
title: Co-producing energy futures: impacts of participatory modelling

description: This transdisciplinary research case study sought to disrupt the usual ways public participation shapes future energy systems. An interdisciplinary group of academics and a self-assembling public of a North English town co-produced ‘bottom-up’ visions for a future local energy system by emphasizing local values, aspirations and desires around energy futures. The effects of participatory modelling are considered as part of a community visioning process on participants’ social learning and social capital. This paper examines both the within-process dynamics related to models and the impact of the outside process, political use of the models by the participants. Both a numerical model (to explore local electricity generation and demand) and a physical scale model of the town were developed to explore various aspects of participants’ visions. The case study shows that collaborative visioning of local energy systems can enhance social learning and social capital of communities. However, the effect of participatory modelling on these benefits is less clear. Tensions arise between ‘inspiring’ and ‘empowering’ role of visions. It is argued that the situatedness of the visioning processes needs to be recognized and integrated within broader aspects of governance and power relations.
DOI: 10.6084/m9.figshare.3543248.v1
title: Co-producing energy futures: impacts of participatory modelling

description: This transdisciplinary research case study sought to disrupt the usual ways public participation shapes future energy systems. An interdisciplinary group of academics and a self-assembling public of a North English town co-produced ‘bottom-up’ visions for a future local energy system by emphasizing local values, aspirations and desires around energy futures. The effects of participatory modelling are considered as part of a community visioning process on participants’ social learning and social capital. This paper examines both the within-process dynamics related to models and the impact of the outside process, political use of the models by the participants. Both a numerical model (to explore local electricity generation and demand) and a physical scale model of the town were developed to explore various aspects of participants’ visions. The case study shows that collaborative visioning of local energy systems can enhance social learning and social capital of communities. However, the effect of participatory modelling on these benefits is less clear. Tensions arise between ‘inspiring’ and ‘empowering’ role of visions. It is argued that the situatedness of the visioning processes needs to be recognized and integrated within broader aspects of governance and power relations.
DOI: 10.6084/m9.figshare.3543245
title: The plant alkaloid chelerythrine binds to chromatin, alters H3K9Ac and modulates global gene expression

description: Chelerythrine (CHL), a plant alkaloid, possesses antimicrobial, anti-inflammatory, and antitumor properties. Although CHL influences several key signal transduction pathways, its ability to interact directly with nucleoprotein complex chromatin, in eukaryotic cells has so far not been looked into. Here we have demonstrated its association with hierarchically assembled chromatin components, viz. long chromatin, chromatosome, nucleosome, chromosomal DNA, and histone H3 and the consequent effect on chromatin structure. CHL was found to repress acetylation at H3K9. It is more target-specific in terms of gene expression alteration and less cytotoxic compared to its structural analog sanguinarine.
DOI: 10.6084/m9.figshare.3543245.v1
title: The plant alkaloid chelerythrine binds to chromatin, alters H3K9Ac and modulates global gene expression

description: Chelerythrine (CHL), a plant alkaloid, possesses antimicrobial, anti-inflammatory, and antitumor properties. Although CHL influences several key signal transduction pathways, its ability to interact directly with nucleoprotein complex chromatin, in eukaryotic cells has so far not been looked into. Here we have demonstrated its association with hierarchically assembled chromatin components, viz. long chromatin, chromatosome, nucleosome, chromosomal DNA, and histone H3 and the consequent effect on chromatin structure. CHL was found to repress acetylation at H3K9. It is more target-specific in terms of gene expression alteration and less cytotoxic compared to its structural analog sanguinarine.
DOI: 10.6084/m9.figshare.3543242
title: 2A4 binds soluble and insoluble light chain aggregates from AL amyloidosis patients and promotes clearance of amyloid deposits by phagocytosis<sup>†</sup>

description: Amyloid light chain (AL) amyloidosis is characterized by misfolded light chain (LC) (amyloid) deposition in various peripheral organs, leading to progressive dysfunction and death. There are no regulatory agency–approved treatments for AL amyloidosis, and none of the available standard of care approaches directly targets the LC protein that constitutes the amyloid. NEOD001, currently in late-stage clinical trials, is a conformation-specific, anti-LC antibody designed to specifically target misfolded LC aggregates and promote phagocytic clearance of AL amyloid deposits. The present study demonstrated that the monoclonal antibody 2A4, the murine form of NEOD001, binds to patient-derived soluble and insoluble LC aggregates and induces phagocytic clearance of AL amyloid <i>in vitro</i>. 2A4 specifically labeled all 21 fresh-frozen organ samples studied, which were derived from 10 patients representing both κ and λ LC amyloidosis subtypes. 2A4 immunoreactivity largely overlapped with thioflavin T–positive labeling, and 2A4 bound both soluble and insoluble LC aggregates extracted from patient tissue. Finally, 2A4 induced macrophage engagement and phagocytic clearance of AL amyloid deposits <i>in vitro</i>. These findings provide further evidence that 2A4/NEOD001 can effectively clear and remove human AL-amyloid from tissue and further support the rationale for the evaluation of NEOD001 in patients with AL amyloidosis.
DOI: 10.6084/m9.figshare.3543242.v1
title: 2A4 binds soluble and insoluble light chain aggregates from AL amyloidosis patients and promotes clearance of amyloid deposits by phagocytosis<sup>†</sup>

description: Amyloid light chain (AL) amyloidosis is characterized by misfolded light chain (LC) (amyloid) deposition in various peripheral organs, leading to progressive dysfunction and death. There are no regulatory agency–approved treatments for AL amyloidosis, and none of the available standard of care approaches directly targets the LC protein that constitutes the amyloid. NEOD001, currently in late-stage clinical trials, is a conformation-specific, anti-LC antibody designed to specifically target misfolded LC aggregates and promote phagocytic clearance of AL amyloid deposits. The present study demonstrated that the monoclonal antibody 2A4, the murine form of NEOD001, binds to patient-derived soluble and insoluble LC aggregates and induces phagocytic clearance of AL amyloid <i>in vitro</i>. 2A4 specifically labeled all 21 fresh-frozen organ samples studied, which were derived from 10 patients representing both κ and λ LC amyloidosis subtypes. 2A4 immunoreactivity largely overlapped with thioflavin T–positive labeling, and 2A4 bound both soluble and insoluble LC aggregates extracted from patient tissue. Finally, 2A4 induced macrophage engagement and phagocytic clearance of AL amyloid deposits <i>in vitro</i>. These findings provide further evidence that 2A4/NEOD001 can effectively clear and remove human AL-amyloid from tissue and further support the rationale for the evaluation of NEOD001 in patients with AL amyloidosis.
DOI: 10.6084/m9.figshare.3543206
title: Supplementary Material for: Quantification of Gait Abnormalities in Healthy-Looking Multiple Sclerosis Patients (with Expanded Disability Status Scale 0-1.5)

description: <strong><em>Background:</em></strong> Gait impairment is a common symptom in multiple sclerosis (MS) patients, but there is a lack of evidence about gait performance in the group of MS patients with no apparent disability. The aim of our study was to evaluate gait characteristics in MS patients with no apparent impairment of walking and with an Expanded Disability Status Scale (EDSS 0-1.5), and to determine whether any abnormalities are detectable by common clinical tests. <b><i>Methods:</i></b> This was an observational study of 64 MS patients with an EDSS 0-1.5 and 47 age- and sex-matched healthy controls. We measured their performance in the timed 25-foot walk test (T25FWT) and the 2-minute walk test (2MWT). The spatiotemporal parameters of gait were measured using a GAITRite instrument. <b><i>Results:</i></b> MS patients with no apparent disability (EDSS 0-1.5) performed worse in T25FWT and 2MWT than normal controls. During the self-selected walking speed test on GAITRite, MS patients had a prolonged double support phase, and during the fast walking speed test, they had lower cadence and decreased step length.
DOI: 10.6084/m9.figshare.3543206.v1
title: Supplementary Material for: Quantification of Gait Abnormalities in Healthy-Looking Multiple Sclerosis Patients (with Expanded Disability Status Scale 0-1.5)

description: <strong><em>Background:</em></strong> Gait impairment is a common symptom in multiple sclerosis (MS) patients, but there is a lack of evidence about gait performance in the group of MS patients with no apparent disability. The aim of our study was to evaluate gait characteristics in MS patients with no apparent impairment of walking and with an Expanded Disability Status Scale (EDSS 0-1.5), and to determine whether any abnormalities are detectable by common clinical tests. <b><i>Methods:</i></b> This was an observational study of 64 MS patients with an EDSS 0-1.5 and 47 age- and sex-matched healthy controls. We measured their performance in the timed 25-foot walk test (T25FWT) and the 2-minute walk test (2MWT). The spatiotemporal parameters of gait were measured using a GAITRite instrument. <b><i>Results:</i></b> MS patients with no apparent disability (EDSS 0-1.5) performed worse in T25FWT and 2MWT than normal controls. During the self-selected walking speed test on GAITRite, MS patients had a prolonged double support phase, and during the fast walking speed test, they had lower cadence and decreased step length.
DOI: 10.6084/m9.figshare.3543194
title: Supplementary Material for: Hanging Maneuver for Stomach Traction in Laparoscopic Distal Pancreatic Resections: An Original Technique Applied in 218 Patients

description: <strong><em>Background:</em></strong> Stomach traction done to expose the pancreas is still a problem in laparoscopic left pancreatic resections. We developed a simple hanging maneuver to retract the stomach rapidly and effectively. <b><i>Methods:</i></b> After dividing the gastrocolic ligament, the stomach was encircled with a tape, turned along its horizontal axis and pulled with an epigastric trocar, which was later removed. This technique was used in all patients who underwent laparoscopic left pancreatic resections including 165 distal pancreatectomies (DP), 35 central pancreatectomies (CP) and 18 enucleations (En). Demographics, surgical and postoperative outcome data were recorded. <b><i>Results:</i></b> There were no mortalities. The mean operative time for DP, CP and En were 174, 191 and 104 min, respectively. The transfusion (0-4%) and conversion (0-3%) rates were low for all procedures. Morbidity was mainly represented by pancreatic fistula and grades (B + C) for DP, CP and En were observed in 26, 22 and 17%, respectively. No complication related to hanging of the stomach, like gastric perforation, was observed. Re-intervention and the mean hospital stay for DP, CP and En were observed in 5, 11 and 0% and were 16, 22 and 12, respectively. The readmission rate was low (0-9%). <b><i>Conclusions:</i></b> Hanging maneuver of the stomach is a simple procedure to rapidly, safely and effectively retract the stomach during left laparoscopic pancreatic resections.
DOI: 10.6084/m9.figshare.3543194.v1
title: Supplementary Material for: Hanging Maneuver for Stomach Traction in Laparoscopic Distal Pancreatic Resections: An Original Technique Applied in 218 Patients

description: <strong><em>Background:</em></strong> Stomach traction done to expose the pancreas is still a problem in laparoscopic left pancreatic resections. We developed a simple hanging maneuver to retract the stomach rapidly and effectively. <b><i>Methods:</i></b> After dividing the gastrocolic ligament, the stomach was encircled with a tape, turned along its horizontal axis and pulled with an epigastric trocar, which was later removed. This technique was used in all patients who underwent laparoscopic left pancreatic resections including 165 distal pancreatectomies (DP), 35 central pancreatectomies (CP) and 18 enucleations (En). Demographics, surgical and postoperative outcome data were recorded. <b><i>Results:</i></b> There were no mortalities. The mean operative time for DP, CP and En were 174, 191 and 104 min, respectively. The transfusion (0-4%) and conversion (0-3%) rates were low for all procedures. Morbidity was mainly represented by pancreatic fistula and grades (B + C) for DP, CP and En were observed in 26, 22 and 17%, respectively. No complication related to hanging of the stomach, like gastric perforation, was observed. Re-intervention and the mean hospital stay for DP, CP and En were observed in 5, 11 and 0% and were 16, 22 and 12, respectively. The readmission rate was low (0-9%). <b><i>Conclusions:</i></b> Hanging maneuver of the stomach is a simple procedure to rapidly, safely and effectively retract the stomach during left laparoscopic pancreatic resections.
DOI: 10.6084/m9.figshare.3533456
title: Transfer of selected <i>Ahnfeltiopsis</i> (Phyllophoraceae, Rhodophyta) species to the genus <i>Besa</i> and description of <i>Schottera koreana</i> sp. nov.

description: We investigated species in the family Phyllophoraceae from Korea using nuclear large-subunit ribosomal RNA, mitochondrial COI and plastid <i>rbc</i>L sequences and morphological examination. To understand the taxonomic relationships of Korean <i>Ahnfeltiopsis</i>, we also analysed topotype materials of <i>A. leptophylla</i> and <i>Besa papillaeformis</i> from California. Both individual and combined datasets revealed that Korean <i>Ahnfeltiopsis</i> (except <i>A. flabelliformis</i>) consistently formed a clade with Californian <i>A. leptophylla</i> and <i>Besa papillaeformis</i> with strong support, and this <i>Besa</i> clade was distinct from other genera or genetic groups in the Phyllophoraceae. The form and development of reproductive structures in topotype material of <i>B. papillaeformis</i> as well as those of the four <i>Ahnfeltiopsis</i> species supported the molecular phylogeny and underlined the distinctiveness of the <i>Besa</i> clade. We therefore propose to transfer four <i>Ahnfeltiopsis</i> species to the genus <i>Besa</i> as <i>Besa catenata, B. divaricata, B. leptophylla</i> and <i>B. paradoxa</i>. The concept of the genus <i>Besa</i> is extended to species having a heteromorphic life history and conspicuous erect gametophytes. On the basis of our molecular phylogeny, we restore <i>A. flabelliformis</i> to the genus <i>Gymnogongrus</i>. We describe a new member of the Phyllophoraceae, <i>Schottera koreana</i> sp. nov., a deep-water species occurring along western and southern coastlines of Korea.
DOI: 10.6084/m9.figshare.3533456.v1
title: Transfer of selected <i>Ahnfeltiopsis</i> (Phyllophoraceae, Rhodophyta) species to the genus <i>Besa</i> and description of <i>Schottera koreana</i> sp. nov.

description: We investigated species in the family Phyllophoraceae from Korea using nuclear large-subunit ribosomal RNA, mitochondrial COI and plastid <i>rbc</i>L sequences and morphological examination. To understand the taxonomic relationships of Korean <i>Ahnfeltiopsis</i>, we also analysed topotype materials of <i>A. leptophylla</i> and <i>Besa papillaeformis</i> from California. Both individual and combined datasets revealed that Korean <i>Ahnfeltiopsis</i> (except <i>A. flabelliformis</i>) consistently formed a clade with Californian <i>A. leptophylla</i> and <i>Besa papillaeformis</i> with strong support, and this <i>Besa</i> clade was distinct from other genera or genetic groups in the Phyllophoraceae. The form and development of reproductive structures in topotype material of <i>B. papillaeformis</i> as well as those of the four <i>Ahnfeltiopsis</i> species supported the molecular phylogeny and underlined the distinctiveness of the <i>Besa</i> clade. We therefore propose to transfer four <i>Ahnfeltiopsis</i> species to the genus <i>Besa</i> as <i>Besa catenata, B. divaricata, B. leptophylla</i> and <i>B. paradoxa</i>. The concept of the genus <i>Besa</i> is extended to species having a heteromorphic life history and conspicuous erect gametophytes. On the basis of our molecular phylogeny, we restore <i>A. flabelliformis</i> to the genus <i>Gymnogongrus</i>. We describe a new member of the Phyllophoraceae, <i>Schottera koreana</i> sp. nov., a deep-water species occurring along western and southern coastlines of Korea.
DOI: 10.6084/m9.figshare.3532568
title: Nothing to see, I just can't find delete

description: yh9g<br>
DOI: 10.6084/m9.figshare.3532568.v1
title: Data and Results

description: G-zipped tar file containing two folders, data and results, as part of the R pipeline available on GitHub.<br><br>Data contains all downloaded trees from TreeBase and literature trees, see metadata.csv files for links to original datasources.<br><br>Results contains simulated trees for multiple analyses, simulated clades, raw PDF figures.<br>
DOI: 10.6084/m9.figshare.3532568.v3
title: Nothing to see, I just can't find delete

description: yh9g<br>
DOI: 10.6084/m9.figshare.3532568.v2
title: Data and Results

description: G-zipped tar file containing two folders, data and results, as part of the R pipeline available on GitHub.<br><br>Data contains all downloaded trees from TreeBase and literature trees, see metadata.csv files for links to original datasources.<br><br>Results contains simulated trees for multiple analyses, simulated clades, raw PDF figures.<br>
DOI: 10.6084/m9.figshare.3532265
title: Full Archive

description: Full Archive
DOI: 10.6084/m9.figshare.3532265.v1
title: Full Archive

description: Full Archive
DOI: 10.6084/m9.figshare.3532259
title: Appendix A. Pairwise comparisons between population projection matrix (PPM) elements for which the sensitivity of one element was consistently greater than or equal to that of the other.

description: Pairwise comparisons between population projection matrix (PPM) elements for which the sensitivity of one element was consistently greater than or equal to that of the other.
DOI: 10.6084/m9.figshare.3532259.v1
title: Appendix A. Pairwise comparisons between population projection matrix (PPM) elements for which the sensitivity of one element was consistently greater than or equal to that of the other.

description: Pairwise comparisons between population projection matrix (PPM) elements for which the sensitivity of one element was consistently greater than or equal to that of the other.
DOI: 10.6084/m9.figshare.3532256
title: Appendix B. Pairwise comparisons between PPM elements for which the elasticity of one element was consistently greater than or equal to that of the other.

description: Pairwise comparisons between PPM elements for which the elasticity of one element was consistently greater than or equal to that of the other.