cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3122713.v1
title: Bilateral retinal hemorrhages following finger pressure against the soft palate (الترفيع) in recessive <i>CRB1</i>-related retinopathy

description: <i>Purpose</i>: To report two siblings with <i>CRB1</i>-related retinopathy who developed retinal hemorrhages following village traditional treatment of upward finger pressure against the soft palate (). <i>Methods</i>: A retrospective case series. <i>Results</i>: Two sisters were clinically diagnosed and genetically confirmed to have recessive <i>CRB1</i>-related retinal dystrophy. The family did not accept the condition as non-treatable and took both sisters for a traditional village therapy, consisting of several sessions of intense upward index finger pressure by the healer against the soft palate for each child. When examined following this therapy, both sisters had bilateral pre-retinal hemorrhages which were not present before the intervention and resolved without sequelae over the next several months. <i>Conclusions</i>: The traditional village therapy may have compromised retinal venous outflow and/or provoked a Valsalva phenomenon, leading to the bilateral retinal hemorrhages. The fact that this occurred bilaterally and in both sisters supports the concept of relative vessel wall incompetence as part of <i>CRB1</i>-related retinopathy.
DOI: 10.6084/m9.figshare.3122695
title: Aligning physical learning spaces with the curriculum: AMEE Guide No. 107

description: This Guide explores emerging issues on the alignment of learning spaces with the changing curriculum in medical education. As technology and new teaching methods have altered the nature of learning in medical education, it is necessary to re-think how physical learning spaces are aligned with the curriculum. The better alignment of learning spaces with the curriculum depends on more directly engaged leadership from faculty and the community of medical education for briefing the requirements for the design of all kinds of learning spaces. However, there is a lack of precedent and well-established processes as to how new kinds of learning spaces should be programmed. Such programmes are essential aspects of optimizing the intended experience of the curriculum. Faculty and the learning community need better tools and instruments to support their leadership role in briefing and programming. A Guide to critical concepts for exploring the alignment of curriculum and learning spaces is provided. The idea of a networked learning landscape is introduced as a way of assessing and evaluating the alignment of physical spaces to the emerging curriculum. The concept is used to explore how technology has widened the range of spaces and places in which learning happens as well as enabling new styles of learning. The networked learning landscaped is explored through four different scales within which learning is accommodated: the classroom, the building, the campus, and the city. High-level guidance on the process of briefing for the networked learning landscape is provided, to take into account the wider scale of learning spaces and the impact of technology. Key to a successful measurement process is argued to be the involvement of relevant academic stakeholders who can identify the strategic direction and purpose for the design of the learning environments in relation to the emerging demands of the curriculum.
DOI: 10.6084/m9.figshare.3122734.v1
title: SCSdata

description: We validated the French version of the Self-Compassion Scale (SCS) on a community sample. Convergent validity was tested with happiness (Bonh), satisfaction with life (LS), depression (BDI), mindfulness (PLC) and affect (PANAS).<br>
DOI: 10.6084/m9.figshare.3122752.v2
title: Effect of detection heterogeneity on N-mixture models

description: These datasets have compiled results from multiple model runs. They do not contain the raw simulated abundance data from each model run. See the Veech et al. (2016) paper in Methods in Ecology and Evolution for more details.
DOI: 10.6084/m9.figshare.3122692
title: Aureolysin of <i>Staphylococcus warneri</i> M accelerates its proteolytic cascade, and participates in biofilm formation

description: The aureolysin (Aur) gene of <i>S. warneri</i> M (<i>aurWM</i>) was cloned and sequenced. Analyses of the <i>aurWM</i>-inactivated mutant (<i>S. warneri</i> Mau) suggested that AurWM was probably associated with efficient processing of the PROM protease (homolog of V8/SspA serine protease), whereas considerable amount of mature-PROC protease (homolog of SspB cysteine protease) accumulated without AurWM. Additionally, AurWM appeared to affect biofilm formation in an uncertain suppressive way.
DOI: 10.6084/m9.figshare.3122692.v1
title: Aureolysin of <i>Staphylococcus warneri</i> M accelerates its proteolytic cascade, and participates in biofilm formation

description: The aureolysin (Aur) gene of <i>S. warneri</i> M (<i>aurWM</i>) was cloned and sequenced. Analyses of the <i>aurWM</i>-inactivated mutant (<i>S. warneri</i> Mau) suggested that AurWM was probably associated with efficient processing of the PROM protease (homolog of V8/SspA serine protease), whereas considerable amount of mature-PROC protease (homolog of SspB cysteine protease) accumulated without AurWM. Additionally, AurWM appeared to affect biofilm formation in an uncertain suppressive way.
DOI: 10.6084/m9.figshare.3122695.v1
title: Aligning physical learning spaces with the curriculum: AMEE Guide No. 107

description: This Guide explores emerging issues on the alignment of learning spaces with the changing curriculum in medical education. As technology and new teaching methods have altered the nature of learning in medical education, it is necessary to re-think how physical learning spaces are aligned with the curriculum. The better alignment of learning spaces with the curriculum depends on more directly engaged leadership from faculty and the community of medical education for briefing the requirements for the design of all kinds of learning spaces. However, there is a lack of precedent and well-established processes as to how new kinds of learning spaces should be programmed. Such programmes are essential aspects of optimizing the intended experience of the curriculum. Faculty and the learning community need better tools and instruments to support their leadership role in briefing and programming. A Guide to critical concepts for exploring the alignment of curriculum and learning spaces is provided. The idea of a networked learning landscape is introduced as a way of assessing and evaluating the alignment of physical spaces to the emerging curriculum. The concept is used to explore how technology has widened the range of spaces and places in which learning happens as well as enabling new styles of learning. The networked learning landscaped is explored through four different scales within which learning is accommodated: the classroom, the building, the campus, and the city. High-level guidance on the process of briefing for the networked learning landscape is provided, to take into account the wider scale of learning spaces and the impact of technology. Key to a successful measurement process is argued to be the involvement of relevant academic stakeholders who can identify the strategic direction and purpose for the design of the learning environments in relation to the emerging demands of the curriculum.
DOI: 10.6084/m9.figshare.3122752.v1
title: master_output_negbinom (Oct 2015).xlsx

description: These datasets have compiled results from multiple model runs. They do not contain the raw simulated abundance data from each model run. See the Veech et al. (2016) paper in Methods in Ecology and Evolution for more details.
DOI: 10.6084/m9.figshare.3122674
title: A critical investigation of proposed electrostatic corrections to quantum mechanical volumes: the importance of variation and the irrelevance of imbalance

description: The crystal density of neutral and ionic molecular crystals is remarkably well approximated by the enclosed volume of molecular surfaces, where these surfaces are defined as regions of constant and small electron density. Several workers have proposed that estimates may be improved if one includes quantities extracted from the electrostatic potential on the surface of the molecule. The variation of the potential and the imbalance of positive and negative values have been considered to be of importance. In this study we demonstrate that whereas variation is important for improving crystal density predictions, imbalance is not. We present a density functional theory study on a set of 44 neutral molecular crystals. Ten-fold cross-validations were performed on models that incorporate variation, imbalance and combinations of both. Geometries were optimised using B3LYP and basis sets of type 6-31G(d). Electron densities and electrostatic potentials were computed with B3LYP and M05. Regardless of functional, models that correct for variation yield a relative decrease of 15%–18% in root-mean-square error of prediction. This correction appears to sharpen the error distribution about zero. Models based on imbalance yield no improvement, and we argue that it plays an insignificant role.
DOI: 10.6084/m9.figshare.3122734.v2
title: SCS: Self-CompassionScale, validation of the French version

description: We validated the French version of the Self-Compassion Scale (SCS) on a community sample. Convergent validity was tested with happiness (Bonh), satisfaction with life (LS), depression (BDI), mindfulness (PLC) and affect (PANAS).<br>
DOI: 10.6084/m9.figshare.3122674.v1
title: A critical investigation of proposed electrostatic corrections to quantum mechanical volumes: the importance of variation and the irrelevance of imbalance

description: The crystal density of neutral and ionic molecular crystals is remarkably well approximated by the enclosed volume of molecular surfaces, where these surfaces are defined as regions of constant and small electron density. Several workers have proposed that estimates may be improved if one includes quantities extracted from the electrostatic potential on the surface of the molecule. The variation of the potential and the imbalance of positive and negative values have been considered to be of importance. In this study we demonstrate that whereas variation is important for improving crystal density predictions, imbalance is not. We present a density functional theory study on a set of 44 neutral molecular crystals. Ten-fold cross-validations were performed on models that incorporate variation, imbalance and combinations of both. Geometries were optimised using B3LYP and basis sets of type 6-31G(d). Electron densities and electrostatic potentials were computed with B3LYP and M05. Regardless of functional, models that correct for variation yield a relative decrease of 15%–18% in root-mean-square error of prediction. This correction appears to sharpen the error distribution about zero. Models based on imbalance yield no improvement, and we argue that it plays an insignificant role.
DOI: 10.6084/m9.figshare.3122659
title: Folk's theory Article: Implementation Sciences

description: Documents reviewed for the programme theory development of the adherence club intervention for the management of patients on long-term antiretroviral therapy
DOI: 10.6084/m9.figshare.3122659.v1
title: Folk's theory Article: Implementation Sciences

description: Documents reviewed for the programme theory development of the adherence club intervention for the management of patients on long-term antiretroviral therapy
DOI: 10.6084/m9.figshare.3122515
title: Stories (PhD thesis Kandylaki K.D.)

description: These stories were the material I created for my PhD thesis project and I would like to make available for further research. The stories are in German language, 40 stories in total, which consist of 20 original and 20 twin stories. Along with the audio files (wav format) of the experimental stories I have uploaded audio files of two practice stories and their transcription, the pdf transcription of the experimental stories and the files I used to construct and control the stories.<br><br>Please feel free to contact me for enquires on the architecture of the stories and on possible collaborations using this material. I am curious to see these stories from a new perspective.<br>
DOI: 10.6084/m9.figshare.3122251
title: Data from: Parallel NMR Spectroscopy With Simultaneous Detection of 1H and 19F Nuclei

description: NMR instruments equipped with multiple receivers can significantly increase the information content in experiments by recording multiple free induction decays (FID-s) from several nuclear species in a single pass. This in turn reduces the number of experiments required to solve a particular analytical or structure elucidation problem. We present a comprehensive series of such experiments that involve multi-receiver detection of two of the most sensitive NMR nuclei – <sup>1</sup>H and <sup>19</sup>F. The experiment designs are categorized into three main groups – (i) interleaved experiments, (ii) parallel acquisition experiments and (iii) sequential acquisition experiments. The interleaved experiments are based on independent pulse programs that are typically dealing with more or less isolated spin systems and avoid perturbing spin system(s) that are recovering while the experiment involving the active spin system is conducted. The parallel acquisition experiments are based on simultaneous observation of the free induction decays (FID-s) of several spin systems in parallel. The multi-dimensional experiments of this type usually involve joint coherence transfer pathways and one or more joint frequency domains. Finally, the sequential acquisition experiments involve direct observation of one or more FID-s within the pulse sequence and otherwise are similar to the parallel acquisition experiments. Several examples of each type of multi-receive H/F experiments involving the most popular NMR pulse sequences including COSY, TOCSY, DOSY, HOESY, HETCOR, HSQC, HMQC, HMBC and T<sub>1</sub> measurement by inversion recovery method are presented and discussed. Furthermore, we demonstrate that efficiency of such experiments can be further improved by combining the multi-receiver methodology with the modern approaches of fast methods, such as relaxation optimization, non-uniform sampling, Hadamard encoding, computer-optimized folding and ultra-fast NMR by spatial encoding. We believe that the multi-receiver technology is set to become a routine way of multiplying the efficiency and throughput in high-resolution NMR spectroscopy.
DOI: 10.6084/m9.figshare.3122254
title: Supplementary Datasets for "mdRNA-Seq analysis of marine microbial communities from the northern Red Sea"

description: This file set contains supplementary datasets for paper "Hou, S.<i> et al.</i> mdRNA-Seq analysis of marine microbial communities from the northern Red Sea. Sci. Rep. 6, 35470; doi: 10.1038/srep35470 (2016)." Please refer to this paper for more information.<b>File Description:</b> <b>Supplemental Dataset S1: </b>Genome wide graphical overview of the mapped reads and coverage for the genome of <i>Synechococcus</i> CC9605. <b></b><b>Supplemental Dataset S2: </b>Genome wide graphical overview of the mapped reads and coverage for the genome of <i>Candidatus </i>Pelagibacter sp. HTCC7211. <b>Supplemental Dataset S3:</b> Visualization of the details of mapped reads and annotated TSSs on the basis of 17 chromosomes, mitochondrial and chloroplast genomes of <i>Micromonas </i>sp. RCC299. <b>Supplemental Dataset S</b><b>4:</b> Visualization of the details of mapped reads and annotated TSSs on the basis of 149 environmental contigs belonging to the <i>Euryarchaeota</i>. <b>Supplemental Dataset S</b><b>5:</b> Alignment of archaeal RNase P RNA sequences including eight euryarchaeal sequences from the Red Sea metatranscriptome. <b>Supplemental Dataset S6:</b> Visualization of the details of mapped reads and annotated TSSs on the basis of 52 environmental contigs belonging to the <i>Thaumarchaeota</i>.<br><br><b>How to cite this dataset:</b><br>If you find this dataset useful to your research, please consider to cite the main paper: Hou, S. <i>et al</i>. <b>mdRNA-Seq analysis of marine microbial communities from the northern </b><b>Red Sea</b>. <i>Sci. Rep.</i> <b>6</b>, 35470; doi: 10.1038/srep35470 (2016).<br><br><br>
DOI: 10.6084/m9.figshare.3122212
title: Key impacts of climate engineering on biodiversity and ecosystems, with priorities for future research

description: Climate change has significant implications for biodiversity and ecosystems. With slow progress towards reducing greenhouse gas emissions, climate engineering (or ‘geoengineering’) is receiving increasing attention for its potential to limit anthropogenic climate change and its damaging effects. Proposed techniques, such as ocean fertilization for carbon dioxide removal or stratospheric sulfate injections to reduce incoming solar radiation, would significantly alter atmospheric, terrestrial and marine environments, yet potential side-effects of their implementation for ecosystems and biodiversity have received little attention. A literature review was carried out to identify details of the potential ecological effects of climate engineering techniques. A group of biodiversity and environmental change researchers then employed a modified Delphi expert consultation technique to evaluate this evidence and prioritize the effects based on the relative importance of, and scientific understanding about, their biodiversity and ecosystem consequences. The key issues and knowledge gaps are used to shape a discussion of the biodiversity and ecosystem implications of climate engineering, including novel climatic conditions, alterations to marine systems and substantial terrestrial habitat change. This review highlights several current research priorities in which the climate engineering context is crucial to consider, as well as identifying some novel topics for ecological investigation.
DOI: 10.6084/m9.figshare.3122251.v1
title: Data from: Parallel NMR Spectroscopy With Simultaneous Detection of 1H and 19F Nuclei

description: NMR instruments equipped with multiple receivers can significantly increase the information content in experiments by recording multiple free induction decays (FID-s) from several nuclear species in a single pass. This in turn reduces the number of experiments required to solve a particular analytical or structure elucidation problem. We present a comprehensive series of such experiments that involve multi-receiver detection of two of the most sensitive NMR nuclei – <sup>1</sup>H and <sup>19</sup>F. The experiment designs are categorized into three main groups – (i) interleaved experiments, (ii) parallel acquisition experiments and (iii) sequential acquisition experiments. The interleaved experiments are based on independent pulse programs that are typically dealing with more or less isolated spin systems and avoid perturbing spin system(s) that are recovering while the experiment involving the active spin system is conducted. The parallel acquisition experiments are based on simultaneous observation of the free induction decays (FID-s) of several spin systems in parallel. The multi-dimensional experiments of this type usually involve joint coherence transfer pathways and one or more joint frequency domains. Finally, the sequential acquisition experiments involve direct observation of one or more FID-s within the pulse sequence and otherwise are similar to the parallel acquisition experiments. Several examples of each type of multi-receive H/F experiments involving the most popular NMR pulse sequences including COSY, TOCSY, DOSY, HOESY, HETCOR, HSQC, HMQC, HMBC and T<sub>1</sub> measurement by inversion recovery method are presented and discussed. Furthermore, we demonstrate that efficiency of such experiments can be further improved by combining the multi-receiver methodology with the modern approaches of fast methods, such as relaxation optimization, non-uniform sampling, Hadamard encoding, computer-optimized folding and ultra-fast NMR by spatial encoding. We believe that the multi-receiver technology is set to become a routine way of multiplying the efficiency and throughput in high-resolution NMR spectroscopy.
DOI: 10.6084/m9.figshare.3122212.v1
title: Key impacts of climate engineering on biodiversity and ecosystems, with priorities for future research

description: Climate change has significant implications for biodiversity and ecosystems. With slow progress towards reducing greenhouse gas emissions, climate engineering (or ‘geoengineering’) is receiving increasing attention for its potential to limit anthropogenic climate change and its damaging effects. Proposed techniques, such as ocean fertilization for carbon dioxide removal or stratospheric sulfate injections to reduce incoming solar radiation, would significantly alter atmospheric, terrestrial and marine environments, yet potential side-effects of their implementation for ecosystems and biodiversity have received little attention. A literature review was carried out to identify details of the potential ecological effects of climate engineering techniques. A group of biodiversity and environmental change researchers then employed a modified Delphi expert consultation technique to evaluate this evidence and prioritize the effects based on the relative importance of, and scientific understanding about, their biodiversity and ecosystem consequences. The key issues and knowledge gaps are used to shape a discussion of the biodiversity and ecosystem implications of climate engineering, including novel climatic conditions, alterations to marine systems and substantial terrestrial habitat change. This review highlights several current research priorities in which the climate engineering context is crucial to consider, as well as identifying some novel topics for ecological investigation.
DOI: 10.6084/m9.figshare.3122254.v1
title: Supplementary Datasets for "mdRNA-Seq analysis of marine microbial communities from the northern Red Sea"

description: This file set contains supplementary datasets for paper "Hou, S.<i> et al.</i> mdRNA-Seq analysis of marine microbial communities from the northern Red Sea. Sci. Rep. 6, 35470; doi: 10.1038/srep35470 (2016)." Please refer to this paper for more information.<b>File Description:</b> <b>Supplemental Dataset S1: </b>Genome wide graphical overview of the mapped reads and coverage for the genome of <i>Synechococcus</i> CC9605. <b></b><b>Supplemental Dataset S2: </b>Genome wide graphical overview of the mapped reads and coverage for the genome of <i>Candidatus </i>Pelagibacter sp. HTCC7211. <b>Supplemental Dataset S3:</b> Visualization of the details of mapped reads and annotated TSSs on the basis of 17 chromosomes, mitochondrial and chloroplast genomes of <i>Micromonas </i>sp. RCC299. <b>Supplemental Dataset S</b><b>4:</b> Visualization of the details of mapped reads and annotated TSSs on the basis of 149 environmental contigs belonging to the <i>Euryarchaeota</i>. <b>Supplemental Dataset S</b><b>5:</b> Alignment of archaeal RNase P RNA sequences including eight euryarchaeal sequences from the Red Sea metatranscriptome. <b>Supplemental Dataset S6:</b> Visualization of the details of mapped reads and annotated TSSs on the basis of 52 environmental contigs belonging to the <i>Thaumarchaeota</i>.<br><br><b>How to cite this dataset:</b><br>If you find this dataset useful to your research, please consider to cite the main paper: Hou, S. <i>et al</i>. <b>mdRNA-Seq analysis of marine microbial communities from the northern </b><b>Red Sea</b>. <i>Sci. Rep.</i> <b>6</b>, 35470; doi: 10.1038/srep35470 (2016).<br><br><br>
DOI: 10.6084/m9.figshare.3122170
title: SMILES to CID mappings for the MMV Pathogen Box

description: MMV Pathogen Box SMILES to PubChem CID mapping (see blogpost in link)<br>
DOI: 10.6084/m9.figshare.3122173
title: Goodreads Social Reviews for Book Impact Assessment: A Multidisciplinary Study

description: Appendixes for an articles submitted to Journal of the Association for Information Science and Technology entitled: Goodreads Social Reviews for Book Impact Assessment: A Multidisciplinary Study