cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11438991.v2
title: Source Data of figure 4c for "Reconfigurable symmetry-broken laser in a symmetricmicrocavity"

description: 1. This "Source Data" folder provides the corresponding experimental data files for figure 4c in the main text, including the figure, the raw data, the processed data, a source file of the figure, etc.<br>2. The "Source Data\raw data" folder includes the experimental results for the output intensity of chiral Raman laser under different linear coupling strengths of the Raman mode, namely the splitting of the doublet. The file name indicates the corresponding linear coupling strength, for example, the "2g_6.7584" file stands for the results with the mode splitting of 6.7584 MHz.<br>The file folder ("2g_***") is loaded with the repeated measurements under the same linear coupling strength. Each data file (data****.txt) contains two collection channels as the binary format from an oscilloscope: the first channel records the output intensity of the counter-clockwise Raman laser and the Raman mode transmission spectrum simultaneously, and the second channel records the output intensity of the clockwise Raman laser.<br>The specific data is the signal on the oscilloscope with the unit of volt, where 100 mV corresponds to the power of 17.379 microwatts for the Raman laser signal. Besides, the signal of the first (second) channel has an offset being 2.8 mV (31.5 mV).<br>3. The dependence of the chiral threshold power of the Raman laser on the Raman mode splitting can be extracted from the raw data and is shown in the "processed data.xlsx", as well as a modified standard deviation in each case. Here the standard deviation is obtained by considering the deviation from the mean value with a small distribution in the threshold region in each measurement. <br><br>
DOI: 10.6084/m9.figshare.11438976.v1
title: Exploring 2D-QSAR for prediction of beta-secretase 1 (BACE1) inhibitory activity against Alzheimer’s disease

description: We have developed a robust quantitative structure–activity relationship (QSAR) model employing a dataset of 98 heterocycle compounds to identify structural features responsible for BACE1 (beta-secretase 1) enzyme inhibition. We have used only 2D descriptors for model development purpose thus avoiding the conformational complications arising due to 3D geometry considerations. Following the strict Organization for Economic Co-operation and Development (OECD) guidelines, we have developed models using stepwise regression analysis followed by the best subset selection, while the final model was developed by partial least squares regression technique. The model was validated using various internationally accepted stringent validation parameters. From the insights obtained from the developed model, we have concluded that heteroatoms (nitrogen, oxygen, etc.) present within to an aromatic nucleus and the structural features such as hydrophobic, ring aromatic and hydrogen bond acceptor/donor are responsible for the enhancement of the BACE1 enzyme inhibitory activity. Moreover, we have performed the pharmacophore modelling to unveil the structural requirements for the inhibitory activity against the BACE1 enzyme. Furthermore, molecular docking studies were carried out to understand the molecular interactions involved in binding, and the results are then correlated with the requisite structural features obtained from the QSAR and pharmacophore models.
DOI: 10.6084/m9.figshare.11438991.v1
title: Source Data of figure 4c for "Reconfigurable symmetry-broken laser in a symmetricmicrocavity"

description: 1. This "Source Data" folder provides the corresponding experimental data files for figure 4c in the main text, including the figure, the raw data, the processed data, a source file of the figure, etc.<br>2. The "Source Data\raw data" folder includes the experimental results for the output intensity of chiral Raman laser under different linear coupling strengths of the Raman mode, namely the splitting of the doublet. The file name indicates the corresponding linear coupling strength, for example, the "2g_6.7584" file stands for the results with the mode splitting of 6.7584 MHz.<br>The file folder ("2g_***") is loaded with the repeated measurements under the same linear coupling strength. Each data file (data****.txt) contains two collection channels as the binary format from an oscilloscope: the first channel records the output intensity of the counter-clockwise Raman laser and the Raman mode transmission spectrum simultaneously, and the second channel records the output intensity of the clockwise Raman laser.<br>The specific data is the signal on the oscilloscope with the unit of volt, where 100 mV corresponds to the power of 17.379 microwatts for the Raman laser signal. Besides, the signal of the first (second) channel has an offset being 2.8 mV (31.5 mV).<br>3. The dependence of the chiral threshold power of the Raman laser on the Raman mode splitting can be extracted from the raw data and is shown in the "processed data.xlsx", as well as a modified standard deviation in each case. Here the standard deviation is obtained by considering the deviation from the mean value with a small distribution in the threshold region in each measurement. <br><br>
DOI: 10.6084/m9.figshare.11438895
title: A novel 4-dimensional live-cell imaging system to study leukocyte-endothelial dynamics in ANCA-associated vasculitis

description: Neutrophils, monocytes and the endothelium are critical to ANCA-associated vasculitis (AAV) pathogenesis. This study aimed to develop a 4-dimensional (4D) live-cell imaging system that would enable investigation of spatial and temporal dynamics of these cells in health and disease. We further aimed to validate this system using autologous donor serum from AAV patients and polyclonal ANCA IgG, as well as exploring its potential in the pre-clinical testing of putative therapeutic compounds. Neutrophils and monocytes were isolated from peripheral venous blood of AAV patients or healthy controls and co-incubated on an endothelial monolayer in the presence of autologous serum. Alternatively, polyclonal ANCA IgG was used, following TNF-α priming, and imaged in 4-dimensions for 3 h using a spinning disc confocal microscope. Volocity 6.3<sup>®</sup> analysis software was used for quantification of leukocyte dynamics. The use of autologous serum resulted in increased neutrophil degranulation (<i>p</i> = .002), transmigration (<i>p</i> = .0096) and monocyte transcellular transmigration (<i>p</i> = .0013) in AAV patients. Polyclonal MPO-ANCA IgG induced neutrophil degranulation (<i>p</i> p in vitro system that allows accurate quantification of multiple neutrophil- and monocyte-endothelial interactions in AAV in a single assay. This system has the potential to highlight dynamics key to pathophysiology of disease, as well investigating the impact of potential therapeutics on these functions.
DOI: 10.6084/m9.figshare.11438895.v1
title: A novel 4-dimensional live-cell imaging system to study leukocyte-endothelial dynamics in ANCA-associated vasculitis

description: Neutrophils, monocytes and the endothelium are critical to ANCA-associated vasculitis (AAV) pathogenesis. This study aimed to develop a 4-dimensional (4D) live-cell imaging system that would enable investigation of spatial and temporal dynamics of these cells in health and disease. We further aimed to validate this system using autologous donor serum from AAV patients and polyclonal ANCA IgG, as well as exploring its potential in the pre-clinical testing of putative therapeutic compounds. Neutrophils and monocytes were isolated from peripheral venous blood of AAV patients or healthy controls and co-incubated on an endothelial monolayer in the presence of autologous serum. Alternatively, polyclonal ANCA IgG was used, following TNF-α priming, and imaged in 4-dimensions for 3 h using a spinning disc confocal microscope. Volocity 6.3<sup>®</sup> analysis software was used for quantification of leukocyte dynamics. The use of autologous serum resulted in increased neutrophil degranulation (<i>p</i> = .002), transmigration (<i>p</i> = .0096) and monocyte transcellular transmigration (<i>p</i> = .0013) in AAV patients. Polyclonal MPO-ANCA IgG induced neutrophil degranulation (<i>p</i> p in vitro system that allows accurate quantification of multiple neutrophil- and monocyte-endothelial interactions in AAV in a single assay. This system has the potential to highlight dynamics key to pathophysiology of disease, as well investigating the impact of potential therapeutics on these functions.
DOI: 10.6084/m9.figshare.11438772
title: Comprehensive plans as tools for enhancing coastal community resilience

description: Planning for change is critical to ensuring resilient coastal communities. In Maine, USA, the comprehensive planning process provides a platform for communities to articulate policies that address social, economic, and environmental issues. While comprehensive plans were initially required of municipalities to address urban sprawl over thirty years ago, a broad range of challenges face coastal communities today. Here, we report on an assessment of 30 comprehensive plans from coastal communities across the state. We analyzed the degree to which plans incorporate principles of social-ecological resilience. Our results reveal significant variability across comprehensive plans, with some communities addressing key indicators of resilience and others engaging with them in a limited way. By more explicitly incorporating principles of social-ecological resilience, the next-generation of comprehensive plans can be repurposed to serve as tools for communities to implement strategies that build adaptive capacity as they face unprecedented challenges and plan for a changing world.
DOI: 10.6084/m9.figshare.11438772.v1
title: Comprehensive plans as tools for enhancing coastal community resilience

description: Planning for change is critical to ensuring resilient coastal communities. In Maine, USA, the comprehensive planning process provides a platform for communities to articulate policies that address social, economic, and environmental issues. While comprehensive plans were initially required of municipalities to address urban sprawl over thirty years ago, a broad range of challenges face coastal communities today. Here, we report on an assessment of 30 comprehensive plans from coastal communities across the state. We analyzed the degree to which plans incorporate principles of social-ecological resilience. Our results reveal significant variability across comprehensive plans, with some communities addressing key indicators of resilience and others engaging with them in a limited way. By more explicitly incorporating principles of social-ecological resilience, the next-generation of comprehensive plans can be repurposed to serve as tools for communities to implement strategies that build adaptive capacity as they face unprecedented challenges and plan for a changing world.
DOI: 10.6084/m9.figshare.11438490
title: sokaiincdatsuraku

description: program data
DOI: 10.6084/m9.figshare.11438490.v1
title: sokaiincdatsuraku

description: program data
DOI: 10.6084/m9.figshare.11437224
title: Reconstructor: a computer program that uses three-valued logics to represent lack of information in empirical scientific contexts

description: In this article, I develop three conceptual innovations within the area of formal metatheory, and present a computer program, called Reconstructor, that implements those developments. The first development consists in a methodology for testing formal reconstructions of scientific theories, which involves checking both whether translations of paradigmatically successful applications into models satisfy the formalisation of the laws, and also whether unsuccessful applications do not. I show how Reconstructor can help carry this out, since it allows the end-user to specify a formal language, input axioms and models formulated in that language, and then ask if the models satisfy the axioms. The second innovation is the introduction of incomplete models (for which the denotation of some terms is missing) into scientific metatheory, in order to represent cases of missing information. I specify the paracomplete semantics built into Reconstructor to deal with sentences where denotation failures occur. The third development consists in a new way of explicating the structuralist notion of a determination method, by equating them with algorithms. This allows determination methods to be loaded into Reconstructor and then executed within a model to find out the value of a previously non-denoting term (i.e. it allows the formal reconstruction to make predictions). This, in turn, can help test the reconstruction in a different way. Finally, I conclude with some suggestions about additional uses the program may have.
DOI: 10.6084/m9.figshare.11437233
title: Supplementary Table 1. Primer sets for real-time RT-PCR analysis of gene expression

description: Supplementary Table 1. Primer sets for real-time RT-PCR analysis of gene expression<br>
DOI: 10.6084/m9.figshare.11437233.v1
title: Supplementary Table 1. Primer sets for real-time RT-PCR analysis of gene expression

description: Supplementary Table 1. Primer sets for real-time RT-PCR analysis of gene expression<br>
DOI: 10.6084/m9.figshare.11437224.v1
title: Reconstructor: a computer program that uses three-valued logics to represent lack of information in empirical scientific contexts

description: In this article, I develop three conceptual innovations within the area of formal metatheory, and present a computer program, called Reconstructor, that implements those developments. The first development consists in a methodology for testing formal reconstructions of scientific theories, which involves checking both whether translations of paradigmatically successful applications into models satisfy the formalisation of the laws, and also whether unsuccessful applications do not. I show how Reconstructor can help carry this out, since it allows the end-user to specify a formal language, input axioms and models formulated in that language, and then ask if the models satisfy the axioms. The second innovation is the introduction of incomplete models (for which the denotation of some terms is missing) into scientific metatheory, in order to represent cases of missing information. I specify the paracomplete semantics built into Reconstructor to deal with sentences where denotation failures occur. The third development consists in a new way of explicating the structuralist notion of a determination method, by equating them with algorithms. This allows determination methods to be loaded into Reconstructor and then executed within a model to find out the value of a previously non-denoting term (i.e. it allows the formal reconstruction to make predictions). This, in turn, can help test the reconstruction in a different way. Finally, I conclude with some suggestions about additional uses the program may have.
DOI: 10.6084/m9.figshare.11437023
title: MOESM6 of MiRNA-disease interaction prediction based on kernel neighborhood similarity and multi-network bidirectional propagation

description: Additional file 6. The candidate miRNAs of 579 diseases were sequenced according to the predicted score using the data set extracted from the new version of HMDB.
DOI: 10.6084/m9.figshare.11437023.v1
title: MOESM6 of MiRNA-disease interaction prediction based on kernel neighborhood similarity and multi-network bidirectional propagation

description: Additional file 6. The candidate miRNAs of 579 diseases were sequenced according to the predicted score using the data set extracted from the new version of HMDB.
DOI: 10.6084/m9.figshare.11437017
title: MOESM7 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 7. Plasmid map for pQP347.
DOI: 10.6084/m9.figshare.11437017.v1
title: MOESM7 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 7. Plasmid map for pQP347.
DOI: 10.6084/m9.figshare.11437005
title: MOESM4 of MiRNA-disease interaction prediction based on kernel neighborhood similarity and multi-network bidirectional propagation

description: Additional file 4. The prediction scores of 199 new diseases and candidate mirnas sorted by score were obtained using the data set extracted from the old version HMDB.
DOI: 10.6084/m9.figshare.11437008
title: MOESM6 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 6. Plasmid map for pQP346.
DOI: 10.6084/m9.figshare.11437005.v1
title: MOESM4 of MiRNA-disease interaction prediction based on kernel neighborhood similarity and multi-network bidirectional propagation

description: Additional file 4. The prediction scores of 199 new diseases and candidate mirnas sorted by score were obtained using the data set extracted from the old version HMDB.
DOI: 10.6084/m9.figshare.11437008.v1
title: MOESM6 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 6. Plasmid map for pQP346.
DOI: 10.6084/m9.figshare.11436999
title: MOESM5 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 5. Plasmid map for pQP345.
DOI: 10.6084/m9.figshare.11436999.v1
title: MOESM5 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 5. Plasmid map for pQP345.
DOI: 10.6084/m9.figshare.11436993
title: MOESM4 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 4. Plasmid map for pQP344.
DOI: 10.6084/m9.figshare.11436993.v1
title: MOESM4 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 4. Plasmid map for pQP344.
DOI: 10.6084/m9.figshare.11436981
title: MOESM3 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 3. Plasmid map for pQP348.
DOI: 10.6084/m9.figshare.11436981.v1
title: MOESM3 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 3. Plasmid map for pQP348.
DOI: 10.6084/m9.figshare.11436969
title: MOESM2 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 2. Plasmid map for pJE1553.
DOI: 10.6084/m9.figshare.11436969.v1
title: MOESM2 of Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose

description: Additional file 2. Plasmid map for pJE1553.
DOI: 10.6084/m9.figshare.11436960
title: MOESM2 of A qualitative study of older adultsâ€™ perspectives on initiating exercise and mindfulness practice

description: Additional file 2. Raw data from the focus groups classified by groups.
DOI: 10.6084/m9.figshare.11436960.v1
title: MOESM2 of A qualitative study of older adultsâ€™ perspectives on initiating exercise and mindfulness practice

description: Additional file 2. Raw data from the focus groups classified by groups.
DOI: 10.6084/m9.figshare.11436957
title: MOESM1 of Evaluation of the genetic diversity of fibre quality traits in upland cotton (Gossypium hirsutum L.) inferred from phenotypic variations

description: Additional file 1: Table S1. List of 719 upland accessions used in this study. Table S2. Correlation coefficients among the 40 phenotypic traits using 719 upland cotton.
DOI: 10.6084/m9.figshare.11436957.v1
title: MOESM1 of Evaluation of the genetic diversity of fibre quality traits in upland cotton (Gossypium hirsutum L.) inferred from phenotypic variations

description: Additional file 1: Table S1. List of 719 upland accessions used in this study. Table S2. Correlation coefficients among the 40 phenotypic traits using 719 upland cotton.
DOI: 10.6084/m9.figshare.11436879
title: dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes

description: This file contains the datasets of phosphorylation sites in prokaryotes.
DOI: 10.6084/m9.figshare.11436522
title: spot4_14725_BW91_SM250.zip

description: radio channel measurement of 144-element uniform cylindrical antenna array at 1.4725GHz
DOI: 10.6084/m9.figshare.11436522.v1
title: spot4_14725_BW91_SM250.zip

description: radio channel measurement of 144-element uniform cylindrical antenna array at 1.4725GHz
DOI: 10.6084/m9.figshare.11435850
title: 6-days breakfast skipping_data

description: core body temperature, expression of clock genes, heart rate variability, and melatonin
DOI: 10.6084/m9.figshare.11435568
title: Proteome database of Serratia marcescens strain SMO3

description: Originally an environmental microorganism common in soil and water, <i>Serratia marcescens</i> is increasingly recognized as an opportunistic human pathogen, especially in hospital acquired infections. Typical infection sites include catheter, urinary tract and wounds, which speaks for the Gram-negative facultative anaerobic bacterium’s preference for damp conditions. But, the defining attribute of the bacterium is its red colouration due to a tripyrrole pigment, prodigiosin. Overall, <i>S. marcescens</i> remains a less well characterized human pathogen, which opens up much room for research both from the fundamental biology and clinical perspectives. This work sought to shed some light on fundamental aspects of the bacterium through parsing the UniProt proteome file of <i>S. marcescens</i> strain SMO3 using an in-house MATLAB software. Through this exercise, a proteome database comprising protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence was constructed. This provides the necessary starting point for either genome editing approaches in designing specific mutants useful for characterising functions of particular genes, or in understanding the interactions of different pathways in mediating pathogenesis using a systems biology approach. Altogether, the presented proteome database should find use in a variety of basic microbiological and clinical research seeking to unveil the secrets of this human pathogen. <br><br>
DOI: 10.6084/m9.figshare.11435568.v1
title: Proteome database of Serratia marcescens strain SMO3

description: Originally an environmental microorganism common in soil and water, <i>Serratia marcescens</i> is increasingly recognized as an opportunistic human pathogen, especially in hospital acquired infections. Typical infection sites include catheter, urinary tract and wounds, which speaks for the Gram-negative facultative anaerobic bacterium’s preference for damp conditions. But, the defining attribute of the bacterium is its red colouration due to a tripyrrole pigment, prodigiosin. Overall, <i>S. marcescens</i> remains a less well characterized human pathogen, which opens up much room for research both from the fundamental biology and clinical perspectives. This work sought to shed some light on fundamental aspects of the bacterium through parsing the UniProt proteome file of <i>S. marcescens</i> strain SMO3 using an in-house MATLAB software. Through this exercise, a proteome database comprising protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence was constructed. This provides the necessary starting point for either genome editing approaches in designing specific mutants useful for characterising functions of particular genes, or in understanding the interactions of different pathways in mediating pathogenesis using a systems biology approach. Altogether, the presented proteome database should find use in a variety of basic microbiological and clinical research seeking to unveil the secrets of this human pathogen. <br><br>