cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6585188.v2
title: Patient reported experiences of using community rehabilitation and/or support services whilst living with a long-term neurological condition: a qualitative systematic review and meta-aggregation

description: <b>Objectives:</b> The objective of this study is to identify patient reported experiences of using community rehabilitation and/or support services whilst living with a long-term neurological condition, and perceptions of their impact on quality of life. <b>Methods</b>: Nine electronic databases were searched for peer-reviewed qualitative studies from 2005 to 2016, which met the inclusion criteria. Critical appraisal, data extraction, and quality assessment of 37 included papers were performed by three reviewers. One hundred and one findings were extracted. Meta-aggregation was used to synthesize findings. <b>Findings:</b> Seven ‘synthesized findings’ [SF] were produced: Interactions with some professionals provide active participation, choice, confidence and autonomy [SF1]; Interactions with some professionals are disempowering and depersonalized [SF2]; Effective communication, specialist knowledge and an individualized approach to information provision is needed [SF3]; Indicators of success vary and may not be clear [SF4]; Informal support from family/friends is valued [SF5]; Opportunities for peer support/social interaction is valued [SF6]; Coordination required to ensure continuity during transition to community [SF7]. <b>Conclusion:</b> Patient reported experiences identified common factors associated with process quality (respect, choice, autonomy, information provision, communication) and activities of patient centered care (personalized care, shared decision-making, self-management support) despite heterogeneity of neurological conditions, service configurations, and geographical location. These factors impact quality of life.Implications for RehabilitationPatient reported experiences provide useful information about courtesy, respect, choice, autonomy, information provision, and communication.Outcomes of self-efficacy and self-management are important for people with stable and progressive long-term neurological conditions.Interactions with individual professionals influence engagement, self-efficacy, and self-management for people with long-term neurological conditions.Training for health and social care professionals should develop the advanced communication skills and behavior required to facilitate self-efficacy and self-management. Patient reported experiences provide useful information about courtesy, respect, choice, autonomy, information provision, and communication. Outcomes of self-efficacy and self-management are important for people with stable and progressive long-term neurological conditions. Interactions with individual professionals influence engagement, self-efficacy, and self-management for people with long-term neurological conditions. Training for health and social care professionals should develop the advanced communication skills and behavior required to facilitate self-efficacy and self-management.
DOI: 10.6084/m9.figshare.6585188.v1
title: Patient reported experiences of using community rehabilitation and/or support services whilst living with a long-term neurological condition: a qualitative systematic review and meta-aggregation

description: <b>Objectives:</b> The objective of this study is to identify patient reported experiences of using community rehabilitation and/or support services whilst living with a long-term neurological condition, and perceptions of their impact on quality of life. <b>Methods</b>: Nine electronic databases were searched for peer-reviewed qualitative studies from 2005 to 2016, which met the inclusion criteria. Critical appraisal, data extraction, and quality assessment of 37 included papers were performed by three reviewers. One hundred and one findings were extracted. Meta-aggregation was used to synthesize findings. <b>Findings:</b> Seven ‘synthesized findings’ [SF] were produced: Interactions with some professionals provide active participation, choice, confidence and autonomy [SF1]; Interactions with some professionals are disempowering and depersonalized [SF2]; Effective communication, specialist knowledge and an individualized approach to information provision is needed [SF3]; Indicators of success vary and may not be clear [SF4]; Informal support from family/friends is valued [SF5]; Opportunities for peer support/social interaction is valued [SF6]; Coordination required to ensure continuity during transition to community [SF7]. <b>Conclusion:</b> Patient reported experiences identified common factors associated with process quality (respect, choice, autonomy, information provision, communication) and activities of patient centered care (personalized care, shared decision-making, self-management support) despite heterogeneity of neurological conditions, service configurations, and geographical location. These factors impact quality of life.Implications for RehabilitationPatient reported experiences provide useful information about courtesy, respect, choice, autonomy, information provision, and communication.Outcomes of self-efficacy and self-management are important for people with stable and progressive long-term neurological conditions.Interactions with individual professionals influence engagement, self-efficacy, and self-management for people with long-term neurological conditions.Training for health and social care professionals should develop the advanced communication skills and behavior required to facilitate self-efficacy and self-management. Patient reported experiences provide useful information about courtesy, respect, choice, autonomy, information provision, and communication. Outcomes of self-efficacy and self-management are important for people with stable and progressive long-term neurological conditions. Interactions with individual professionals influence engagement, self-efficacy, and self-management for people with long-term neurological conditions. Training for health and social care professionals should develop the advanced communication skills and behavior required to facilitate self-efficacy and self-management.
DOI: 10.6084/m9.figshare.6584984
title: Gale Crater Stereo CTX DTMs + Orthoimages

description: <b>CTX Stereo Digital Terrain Models (DTMS) and Orthorectified Images</b> See Readme for full details.<br> These data products were produced by Peter Grindrod and Joel Davis at the Natural History Museum, London. They are shared here in an "as is" format. Please read the following information carefully. <b>Data Structure</b> The file "Index_ DTMs.xlsx" gives the image numbers and DTM filenames. <b>Data Sets</b> The exact products for each image pair include: - 20 m/px DTM - 20 m/px FOM (Figure of Merit - see below) - 6 m/px orthoimage Each image has been orthorectified using the relevant DTM. No data have been georeferenced to either another data set in this release, nor another Mars data set. Therefore care should be taken in the first instance in georeferencing as required. Although each DTM is tied to MOLA, there are likely to be some small elevation steps across DTM boundaries as a result of no bundle adjustment across DTMs. Finally, the quality of the DTMs is on the whole good, but noise levels vary – check the FOM and create a hillshade to ensure that each DTM is adequate for required use. <b>DTM Vertical Precision</b> The vertical precision of the DTMs can be estimated by using the method outlined in: - Kirk, R. L., E. Howington-Kraus, B. Redding, D. Galuszka, T. M. Hare, B. A. Archinal, L. A. Soderblom, and J. M. Barrett, (2003), High-resolution topomapping of candidate MER landing sites with Mars Orbiter Camera narrow-angle images, <i>J. Geophys. Res.</i>, 108(E12), 8088, doi:10.1029/2003JE002131. - Kirk, R. L., et al. (2008), Ultrahigh resolution topographic mapping of Mars with MRO HiRISE stereo images: Meter-scale slopes of candidate Phoenix landing sites, <i>J. Geophys. Res.</i>, 113, E00A24, doi:10.1029/2007JE003000. <b>File Format</b> Each file is available in geotiff format. <b>Credit</b> CTX images should be credited "Image: NASA/JPL-Caltech/MSSS” Derived DTMs should be credited as "DTM: NASA/JPL-Caltech/MSSS/NHM”, and as follows, if possible "The stereo DTM processing was carried out at the Natural History Museum, London" <b>Figure of Merit (FOM) explanation</b> If present, the FOM is a data product produced by the BAE Systems SOCET SET software, which is essentially a measure of the quality of the DTM. The numerical value of each pixel corresponds to either how the pixel was generated or the confidence in the value.<br>
DOI: 10.6084/m9.figshare.6582761
title: NYCIII medium for culturing anaerobic bacteria

description: Adjusted from https://www.atcc.org/~/media/FA8074C3B4B9450899EE2542D6AD7116.ashxUsed in http://www.reblab.org/ongoing-experiments-log/carbohydrate-active-enzymes-in-lactobacillus-crispatus-a-possible-link-between-the-pullulanase-gene-and-growth-on-glycogen/
DOI: 10.6084/m9.figshare.6582761.v1
title: NYCIII medium for culturing anaerobic bacteria

description: Adjusted from https://www.atcc.org/~/media/FA8074C3B4B9450899EE2542D6AD7116.ashxUsed in http://www.reblab.org/ongoing-experiments-log/carbohydrate-active-enzymes-in-lactobacillus-crispatus-a-possible-link-between-the-pullulanase-gene-and-growth-on-glycogen/
DOI: 10.6084/m9.figshare.6580871
title: Supplementary materials to 'The effect of dictionary omissions on phylogenies computationally inferred from lexical data' by Igor Yanovich.

description: File S1: R code for generating pseudo-datasets for studying dictionary omissionFile S2: Python 2.7 code preparing likelihood-adjusted data for BEASTFile S3: Recoded Lezgian NEXUS file with Lezgian data from Kassian (2015). The recoding was as described in Section 2.1.File S4: Posterior clade probabilities from a MrBayes analysis analogous to Fig. 5(a).Analyses reported in Fig. 5 were performed using BEAST, while those in Fig. 6 were done using MrBayes. Here, I provide a part of the log of a MrBayes analysis with mostly the same settings as the BEAST analysis reported in Fig. 5(a). (The two differ in using different wide priors on the speciation rate.) Comparison of the clade posteriors in File S4 (containing the output of MrBayes) shows that both software packages correctly sample from one and the same posterior, as expected. Furthermore, the tree height is almost exactly the same (BEAST: [0.1191, 0.1332] 95% HPDI, MrBayes: [0.1196, 0.1333] 95% HPDI), though the inferred speciation rates differ (BEAST: [6.8348, 18.204] 95% HPDI, MrBayes: [3.9682, 10.5462] 95% HPDI). The difference in the speciation rate goes in the direction we expect, given the influence of the prior (the exponential(1) prior in the MrBayes analysis depresses that rate compared to the uniform prior in the BEAST analysis).<br>
DOI: 10.6084/m9.figshare.6580871.v1
title: Supplementary materials to 'The effect of dictionary omissions on phylogenies computationally inferred from lexical data' by Igor Yanovich.

description: File S1: R code for generating pseudo-datasets for studying dictionary omissionFile S2: Python 2.7 code preparing likelihood-adjusted data for BEASTFile S3: Recoded Lezgian NEXUS file with Lezgian data from Kassian (2015). The recoding was as described in Section 2.1.File S4: Posterior clade probabilities from a MrBayes analysis analogous to Fig. 5(a).Analyses reported in Fig. 5 were performed using BEAST, while those in Fig. 6 were done using MrBayes. Here, I provide a part of the log of a MrBayes analysis with mostly the same settings as the BEAST analysis reported in Fig. 5(a). (The two differ in using different wide priors on the speciation rate.) Comparison of the clade posteriors in File S4 (containing the output of MrBayes) shows that both software packages correctly sample from one and the same posterior, as expected. Furthermore, the tree height is almost exactly the same (BEAST: [0.1191, 0.1332] 95% HPDI, MrBayes: [0.1196, 0.1333] 95% HPDI), though the inferred speciation rates differ (BEAST: [6.8348, 18.204] 95% HPDI, MrBayes: [3.9682, 10.5462] 95% HPDI). The difference in the speciation rate goes in the direction we expect, given the influence of the prior (the exponential(1) prior in the MrBayes analysis depresses that rate compared to the uniform prior in the BEAST analysis).<br>
DOI: 10.6084/m9.figshare.6580427
title: Protocol and data for dbCAN analysis of Lactobacillus crispatus strains

description: Protocol and data for dbCAN analysis of <i>Lactobacillus crispatus</i> strains. Belonging to http://www.reblab.org/ongoing-experiments-log/carbohydrate-active-enzymes-in-lactobacillus-crispatus-a-possible-link-between-the-pullulanase-gene-and-growth-on-glycogen/
DOI: 10.6084/m9.figshare.6580382
title: Appendices to 'Using ancestral state reconstruction methods for onomasiological reconstruction in multilingual word lists'.

description: The appendices contain a list of all age constraints for Indo-European that were used in our phylogenetic reconstruction study (Appendix A) as well as a detailed, qualitative analysis of all differences between the automatic and the gold standard assessments in IElex (Appendix B1) and BCD (Appendix B2). <br>Current efforts in computational historical linguistics are predominantly concerned with phylogenetic inference. Methods for ancestral state reconstruction have only been applied sporadically. In contrast to phylogenetic algorithms, automatic reconstruction methods presuppose phylogenetic information in order to explain what has evolved when and where. Here we report a pilot study exploring how well automatic methods for ancestral state reconstruction perform in the task of onomasiological reconstruction in multilingual word lists, where algorithms are used to infer how the words evolved along a given phylogeny, and reconstruct which cognate classes were used to express a given meaning in the ancestral languages. Comparing three different methods, Maximum Parsimony, Minimal Lateral Networks, and Maximum Likelihood on three different test sets (Indo-European, Austronesian, Chinese) using binary and multi-state coding of the data as well as single and sampled phylogenies, we find that Maximum Likelihood largely outperforms the other methods. At the same time, however, the general performance was disappointingly low, ranging between 0.66 (Chinese) and 0.79 (Austronesian) for the F-Scores. A closer linguistic evaluation of the reconstructions proposed by the best method and the reconstructions given in the gold standards revealed that the majority of the cases where the algorithms failed can be attributed to problems of independent semantic shift (homoplasy), to morphological processes in lexical change, and to wrong reconstructions in the independently created test sets that we employed.
DOI: 10.6084/m9.figshare.6580382.v1
title: Appendices to 'Using ancestral state reconstruction methods for onomasiological reconstruction in multilingual word lists'.

description: The appendices contain a list of all age constraints for Indo-European that were used in our phylogenetic reconstruction study (Appendix A) as well as a detailed, qualitative analysis of all differences between the automatic and the gold standard assessments in IElex (Appendix B1) and BCD (Appendix B2). <br>Current efforts in computational historical linguistics are predominantly concerned with phylogenetic inference. Methods for ancestral state reconstruction have only been applied sporadically. In contrast to phylogenetic algorithms, automatic reconstruction methods presuppose phylogenetic information in order to explain what has evolved when and where. Here we report a pilot study exploring how well automatic methods for ancestral state reconstruction perform in the task of onomasiological reconstruction in multilingual word lists, where algorithms are used to infer how the words evolved along a given phylogeny, and reconstruct which cognate classes were used to express a given meaning in the ancestral languages. Comparing three different methods, Maximum Parsimony, Minimal Lateral Networks, and Maximum Likelihood on three different test sets (Indo-European, Austronesian, Chinese) using binary and multi-state coding of the data as well as single and sampled phylogenies, we find that Maximum Likelihood largely outperforms the other methods. At the same time, however, the general performance was disappointingly low, ranging between 0.66 (Chinese) and 0.79 (Austronesian) for the F-Scores. A closer linguistic evaluation of the reconstructions proposed by the best method and the reconstructions given in the gold standards revealed that the majority of the cases where the algorithms failed can be attributed to problems of independent semantic shift (homoplasy), to morphological processes in lexical change, and to wrong reconstructions in the independently created test sets that we employed.
DOI: 10.6084/m9.figshare.6580349
title: Deposit for "Communal breeding affects offspring behaviours associated with a competitive social environment"

description: "Communal breeding affects offspring behaviours associated with a competitive social environment"<br>Please find in this deposit the raw data as well as the acompanied R-codes<br><br><br>
DOI: 10.6084/m9.figshare.6580349.v1
title: Deposit for "Communal breeding affects offspring behaviours associated with a competitive social environment"

description: "Communal breeding affects offspring behaviours associated with a competitive social environment"<br>Please find in this deposit the raw data as well as the acompanied R-codes<br><br><br>
DOI: 10.6084/m9.figshare.6580223
title: Trajectory Change Blindness data (online and lab)

description: These data are obtained using a JavaScript implementation of a 'flicker' change blindness paradigm. Each trial shows some rectangles moving across the screen, and after 700ms a change occurs whereby one of the rectangles alters either its orientation or trajectory. On some of these trials the change occurs visibly, in others the change occurs while the screen is blank. On some trials there are 2 rectangles, and on the others there are 6. The participant stops the motion of the display when they are ready, and then identifies the changed rectangle.<br>Trial types: <br>0: 2 rectangles, orientation change, masked<br>1: 6 rectangles, orientation change, masked2: 2 rectangles, trajectory change, masked3: 6 rectangles, trajectory change, masked4: 2 rectangles, orientation change, unmasked5: 6 rectangles, orientation change, unmasked6: 2 rectangles, trajectory change, unmasked7: 6 rectangles, trajectory change, unmasked<br>The analysis_paper.Rmd file contains R code for generating the analysis_paper.html file, which displays the output of analyses reported in the paper.<br>
DOI: 10.6084/m9.figshare.6580187
title: Growth data of Lactobacillus crispatus on glycogen

description: Growth data of <i>Lactobacillus crispatus</i> on glycogen. Both xls file and GraphPad Prism 7 file. Belonging to http://www.reblab.org/ongoing-experiments-log/carbohydrate-active-enzymes-in-lactobacillus-crispatus-a-possible-link-between-the-pullulanase-gene-and-growth-on-glycogen/
DOI: 10.6084/m9.figshare.6580187.v1
title: Growth data of Lactobacillus crispatus on glycogen

description: Growth data of Lactobacillus crispatus on glycogen. Both xls file and GraphPad Prism 7 file. Belonging to http://www.reblab.org/ongoing-experiments-log/carbohydrate-active-enzymes-in-lactobacillus-crispatus-a-possible-link-between-the-pullulanase-gene-and-growth-on-glycogen/
DOI: 10.6084/m9.figshare.6579248
title: DiLisi_phylogenetic-features-july2017

description: The full data matrix with descriptions of the 172 characters as well as their values for all 23 dialects used in the phylogenetic analysis in Section 5.1. of the article 'Armenian prosody in typology and diachrony'. This paper examines the relationship between typology and historical linguistics through a case study from the history of Armenian, where two different stress systems are found in the modern language. The first is a penult system with no associated secondary stress ([... σ́σ]ω). The other, the so-called hammock pattern, has primary stress on the final syllable and secondary stress on the initial syllable of the prosodic word ([σ̀ ... σ́]ω). Although penult stress patterns are by far more typologically common than the hammock pattern in the world’s languages, I will argue that the hammock pattern must be reconstructed for the period of shared innovation, the Proto-Armenian period.
DOI: 10.6084/m9.figshare.6579248.v1
title: DiLisi_phylogenetic-features-july2017

description: The full data matrix with descriptions of the 172 characters as well as their values for all 23 dialects used in the phylogenetic analysis in Section 5.1. of the article 'Armenian prosody in typology and diachrony'. This paper examines the relationship between typology and historical linguistics through a case study from the history of Armenian, where two different stress systems are found in the modern language. The first is a penult system with no associated secondary stress ([... σ́σ]ω). The other, the so-called hammock pattern, has primary stress on the final syllable and secondary stress on the initial syllable of the prosodic word ([σ̀ ... σ́]ω). Although penult stress patterns are by far more typologically common than the hammock pattern in the world’s languages, I will argue that the hammock pattern must be reconstructed for the period of shared innovation, the Proto-Armenian period.
DOI: 10.6084/m9.figshare.6575552
title: 3D printed sensor base for five PCB 208C01 force sensors, designed for toe pressings experiments

description: This contains a 3D printable sensor based for five PCB 208C01 piezoelectric force sensors. It is designed to be used in toe pressing experiments. Further details can be found on the linked thingiverse page. There are three different sizes (for different size feet). The forward-back location of the sensors can be changed by sliding them backwards or forwards. It can be used for left or right foot by turning it upside down. <br>
DOI: 10.6084/m9.figshare.6575438
title: Models and trajectories of GLUTAMINE SYNTHETASE with palmitoyl-coenzyme A

description: These are the models and molecular dynamics trajectories obtained for the paper Role of glutamine synthetase in angiogenesis beyond glutamine synthesis [G. Eelen et al. Nature 2018 vol. 561 (7721) pp. 63-69].<br>The PDB files (human.pdb and bacterial.pdb) contain representative structures extracted from the molecular dynamics simulations of the S. Typhimurium (bacterial.pdb) and Human Glutamine Synthetase (human.pdb). For the latter, models of the two most relevant binding modes of Palmitoyl-CoA are included in the file.<br><br>The trajectories included are the FINAL 450 ns of 2 fully atomistic molecular dynamics simulations of Glutamine Synthetase (GS) performed with GROMACS and the Amber ff14SB force field. The Human_GS.x is the trajectory of human GS (reference PDB 2OJW) with Palmitoyl-CoA. In this trajecory the palmitate tail points upwards (which was the most interesting orientation found). "Bacterial_GS" is the bacterial GS trajectory (reference starting PDB 1FPY) with Palmitoyl-CoA - palmitate tail points downwards. The trajectories are in GROMACS trr format and have been saved every 200ps.<b> </b>Water molecules and the initial 50 ns (relaxation) are not included in the files.