cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4481182
title: Simulating a Chemically-Fueled Molecular Motor with Nonequilibrium Molecular Dynamics

description: This .zip file contains the code, simulation scripts and settings, and figure generation scripts for our manuscript "Simulating a Chemically-Fueled Molecular Motor with Nonequilibrium Molecular Dynamics." More detailed descriptions are found in the 0README.txt files within the .zip folder. Manuscript link: https://arxiv.org/abs/2102.06298 Manuscript abstract: Most computer simulations of molecular dynamics take place under equilibrium conditions—in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are introduced to those simulations to probe one type of nonequilibrium response to external forces. Catalysts and molecular motors, however, function based on the nonequilibrium dynamics induced by a chemical reaction's thermodynamic driving force. In this scenario, simulations require chemostats capable of preserving the chemical concentrations of the nonequilibrium steady state. We develop such a dynamic scheme and use it to observe cycles of a new particle-based classical model of a catenane-like molecular motor. Molecular motors are frequently modeled with detailed-balance-breaking Markov models, and we explicitly construct such a picture by coarse graining the microscopic dynamics of our simulations in order to extract rates. This work identifies inter-particle interactions that tune those rates to create a functional motor, thereby yielding a computational playground to investigate the interplay between directional bias, current generation, and coupling strength in molecular information ratchets.
DOI: 10.5281/zenodo.4481181
title: Simulating a Chemically-Fueled Molecular Motor with Nonequilibrium Molecular Dynamics

description: This .zip file contains the code, simulation scripts and settings, and figure generation scripts for our manuscript "Simulating a Chemically-Fueled Molecular Motor with Nonequilibrium Molecular Dynamics." More detailed descriptions are found in the 0README.txt files within the .zip folder. Manuscript link: https://arxiv.org/abs/2102.06298 Manuscript abstract: Most computer simulations of molecular dynamics take place under equilibrium conditions—in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are introduced to those simulations to probe one type of nonequilibrium response to external forces. Catalysts and molecular motors, however, function based on the nonequilibrium dynamics induced by a chemical reaction's thermodynamic driving force. In this scenario, simulations require chemostats capable of preserving the chemical concentrations of the nonequilibrium steady state. We develop such a dynamic scheme and use it to observe cycles of a new particle-based classical model of a catenane-like molecular motor. Molecular motors are frequently modeled with detailed-balance-breaking Markov models, and we explicitly construct such a picture by coarse graining the microscopic dynamics of our simulations in order to extract rates. This work identifies inter-particle interactions that tune those rates to create a functional motor, thereby yielding a computational playground to investigate the interplay between directional bias, current generation, and coupling strength in molecular information ratchets.
DOI: 10.6073/pasta/f9238657d3716bfbda9de413b3b39e79
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 5 meteorological station: 5-minute summary wind and air temperature data: 2013 - ongoing

description: This data package contains 5-minute air temperature and wind summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-5 met station. Average air temperature, wind speed, and wind direction are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. This is a subset of baseline weather data collected at the 15 Jornada Basin LTER CSIS study blocks, New Mexico. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. The met station variables measured include air temperature, precipitation, relative humidity, wind direction, wind speed. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively . This is an ONGOING dataset.
DOI: 10.6073/pasta/aa06fe5204f346c07776653516aeb419
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 5 meteorological station: 1-hour summary data: 2017 - ongoing

description: This data package contains hourly air temperature, relative humidity, wind speed, wind direction, and precipitation summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-5 met station. Air temperature, relative humidity, wind speed, wind direction, and precipitation are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively . This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.19111055
title: FDTD simulation data for Optical Diffraction Tomography

description: This dataset contains 2D and 3D complex field sinograms for optical diffraction tomography created with finite-difference time domain simulations using Meep (http://ab-initio.mit.edu/wiki/index.php?title=Meep). The entire complex electric field data from the simulations would have amounted to &gt;2TB of data which is not easy to share and also contain a lot of redundant and uninteresting (for tomography at least) information. Most of these data were used in the ODTbrain paper (https://dx.doi.org/10.1186/s12859-015-0764-0). <br> <b>Data Structure</b> Each dataset is an HDF5 file (https://www.hdfgroup.org) that contains the simulation structure (the cell phantom), a background field (simulation without phantom), and a field for each rotational position of the phantom (sinogram). The fields are slices through the complex electrical field in the original simulation volume behind the phantom at the end of the simulation (supposedly steady state). The slice position is written as the HDF5 attribute “extraction focus distance [px]”. The slice position is important for the reconstruction, because the fields must be numerically refocused to the center of the simulation volume before reconstruction. The perfectly matched layer (PML) has already been cropped from the fields. Alongside each field, the source code of the Meep simulation and the standard-output of the compiled simulation are stored. You can also find the simulation templates in the ODTbrain repository at https://github.com/RI-imaging/ODTbrain/tree/master/misc. I recommend you to explore the files using HDFView (https://www.hdfgroup.org/downloads/hdfview/). <br> <b>Naming Scheme</b> I adopted the naming scheme of the original simulations. - The first part of the file name determines the dimension of the simulation. The larger “phantom_3d” files contain the 3D simulation sinograms. - “A” is the total number of angles for which simulations were performed. - “R” is the resolution (number of pixels per wavelength). - “T” is the total number of simulation steps performed. - “Nmed” is the refractive index (RI) of the medium surrounding the cell phantom. - “Ncyt” is the RI of the phantom’s cytoplasm. - “Nnuc” is the RI of the phantom’s nucleus. - “Nleo” is the RI of the phantom’s nucleolus. The final part of the file name indicates to which type of study the simulation belongs: - “angles”: varying the total number of acquisition angles - “step-count”: varying the total number of time steps - “refractive-index”: varying the internal RI values of the cell phantom - “size”: varying the size of the phantom <br> <b>Getting Started</b> I added two Python scripts “recon_2d.py” and “recon_3d.py” (tested with Python 3.9 on Ubuntu 22.04) that will allow you to obtain RI reconstructions from the 2D and 3D sinograms. For this to work, you will have to install the Python libraries imported in those scripts. Note that for the 3D data you can also use the graphical tool CellReel (https://github.com/RI-imaging/CellReel).<br>
DOI: 10.6084/m9.figshare.12515560
title: Long-term evolution and short-term adaptation of microbiota strains and sub-strains

description: Long-term evolution and short-term adaptation of microbiota strains and sub-strains<br>Catherine Mooser1,2,9, Bahtiyar Yilmaz1,2,9, Irene Keller1,3,9, Lars Bosshard3,8, Jakob Zimmermann1,2, Tobias Fuhrer4, Mercedes Gomez de Agüero1,2, Heidi Tschanz-Lischer1,3, Hai Li1,2, Julien P. Limenitakis1,2, Wolf-Dietrich Hardt5, Kathy D. McCoy1,2, Bärbel Stecher6,7, Laurent Excoffier3,8, Uwe Sauer4, Stephanie C. Ganal-Vonarburg1,2, Andrew J. Macpherson1,2,*<br>SUMMARYStable animal models are essential to reproducibly investigate mechanisms of host-microbial mutualism. Isobiotic mice, with an identical stable microbiota composition, potentially allow models of host-microbial mutualism to be studied over time and between different laboratories. To understand how microbiota evolution occurs in these models, we carried out a 6-year experiment in mice colonized with 12 representative fully-sequenced taxa. External introduction of new taxa was strictly avoided to distinguish microbiota evolution without confounding immigrant microbes. Increased non-synonymous to synonymous mutation fixation rates (dN/dS &gt; 1) indicated positive selection in multiple taxa, particularly for genes annotated for nutrient acquisition or replication. Microbial sub-strains that had evolved within a single taxon were able to stably coexist, consistent with niche partitioning of ecotypes in the complex intestinal environment. Dietary shifts triggered rapid transcriptional adaptation to macronutrient and micronutrient changes in individual taxa and alterations in taxa biomass. The proportions of different sub-strains were also rapidly altered after dietary shift. This indicates that microbial taxa adapt to changes in the intestinal environment by long-term genomic positive selection and short-term effects of transcriptional reprogramming and adjustments in sub-strain proportions.<br><br><br>
DOI: 10.6084/m9.figshare.12515560.v1
title: Long-term evolution and short-term adaptation of microbiota strains and sub-strains

description: Long-term evolution and short-term adaptation of microbiota strains and sub-strains<br>Catherine Mooser1,2,9, Bahtiyar Yilmaz1,2,9, Irene Keller1,3,9, Lars Bosshard3,8, Jakob Zimmermann1,2, Tobias Fuhrer4, Mercedes Gomez de Agüero1,2, Heidi Tschanz-Lischer1,3, Hai Li1,2, Julien P. Limenitakis1,2, Wolf-Dietrich Hardt5, Kathy D. McCoy1,2, Bärbel Stecher6,7, Laurent Excoffier3,8, Uwe Sauer4, Stephanie C. Ganal-Vonarburg1,2, Andrew J. Macpherson1,2,*<br>SUMMARYStable animal models are essential to reproducibly investigate mechanisms of host-microbial mutualism. Isobiotic mice, with an identical stable microbiota composition, potentially allow models of host-microbial mutualism to be studied over time and between different laboratories. To understand how microbiota evolution occurs in these models, we carried out a 6-year experiment in mice colonized with 12 representative fully-sequenced taxa. External introduction of new taxa was strictly avoided to distinguish microbiota evolution without confounding immigrant microbes. Increased non-synonymous to synonymous mutation fixation rates (dN/dS &gt; 1) indicated positive selection in multiple taxa, particularly for genes annotated for nutrient acquisition or replication. Microbial sub-strains that had evolved within a single taxon were able to stably coexist, consistent with niche partitioning of ecotypes in the complex intestinal environment. Dietary shifts triggered rapid transcriptional adaptation to macronutrient and micronutrient changes in individual taxa and alterations in taxa biomass. The proportions of different sub-strains were also rapidly altered after dietary shift. This indicates that microbial taxa adapt to changes in the intestinal environment by long-term genomic positive selection and short-term effects of transcriptional reprogramming and adjustments in sub-strain proportions.<br><br><br>
DOI: 10.6073/pasta/7ee27effcc31133e478a3bfcd07a07da
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 5 meteorological station: 30-minute soil volumetric water content data: 2013 - ongoing

description: 30-minute Soil Moisture data at 10 cm at CSIS Block-5. Collection of soil volumetric water content data at Jornada LTER Cross-scale Interactions Study (CSIS) blocks, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Soil volumetric water content is measured at 10 cm depth at 3 locations at each of the 4 plots per block. The locations in each plot are under bare soil, under perennial grass, and under shrub. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are recorded every 30 minutes at an automated meteorological station installed at Jornada LTER CSIS Block-5 site. This is an ONGOING dataset.
DOI: 10.6073/pasta/675850b4aeabdeeccaf137891b7a50e5
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 5 meteorological station: Daily average soil volumetric water content data: 2013 - ongoing

description: Daily Average of 30-minute Soil Volumetric Water Content data at 10 cm at CSIS Block-5. Collection of soil water content data at Jornada LTER Cross-scale Interactions Study (CSIS) blocks, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Soil volumetric water content is measured every 30 minutes at 10 cm depth at 3 locations at each of the 4 plots per block and averaged for the daily value. The locations in each plot are under bare soil, under perennial grass, and under shrub. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are recorded at an automated meteorological station installed at Jornada LTER CSIS Block-5 site. This is an ONGOING dataset.
DOI: 10.6073/pasta/338d7ddd7b92f05c8f350f9b9f18d669
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 5 meteorological station: Daily summary data: 2013 - ongoing

description: This data package contains hourly air temperature, relative humidity, wind speed, wind direction, and precipitation summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-5 met station. Air temperature, relative humidity, wind speed, wind direction, and precipitation are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. The met station variables measured include air temperature, precipitation, relative humidity, wind direction, wind speed. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively . This is an ONGOING dataset.
DOI: 10.6073/pasta/580837994426db4afec380fc0761731e
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 6 meteorological station: 30-minute summary data: 2017 - ongoing

description: This data package contains 30-minute air temperature, relative humidity, and wind summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-1 met station. Average air temperature, relative humidity, wind speed, wind direction, and precipitation are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. The met station variables measured include air temperature, precipitation, relative humidity, wind direction, wind speed. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively. This is an ONGOING dataset.
DOI: 10.5281/zenodo.5950827
title: Dispersal probabilities and geography input for BioGeoBEARS

description: Dispersal probabilities by assigned geographical time-slice and range data for use in BioGeoBEARS ancestral range reconstruction of Caribbean <em>Micrathena. </em>
DOI: 10.5281/zenodo.5553437
title: Dispersal probabilities and geography input for BioGeoBEARS

description: Dispersal probabilities by assigned geographical time-slice and range data for use in BioGeoBEARS ancestral range reconstruction of Caribbean <em>Micrathena. </em>
DOI: 10.5281/zenodo.5949376
title: Replication package for: Privatization and Productivity in China

description: This replication package contains the data and the code to generate the results reported in "Privatization and Productivity in China" by Yuyu Chen, Mitsuru Igami, Masayuki Sawada, and Mo Xiao, published in The RAND Journal of Economics (Winter 2021), volume 52, issue 4, pages 884–916.
DOI: 10.5281/zenodo.5949375
title: Replication package for: Privatization and Productivity in China

description: This replication package contains the data and the code to generate the results reported in "Privatization and Productivity in China" by Yuyu Chen, Mitsuru Igami, Masayuki Sawada, and Mo Xiao, published in The RAND Journal of Economics (Winter 2021), volume 52, issue 4, pages 884–916.
DOI: 10.6073/pasta/0d65ec8a4a7712a1901452884ad0085f
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 6 meteorological station: 5-minute summary wind and air temperature data: 2013 - ongoing

description: This data package contains 5-minute air temperature and wind summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-6 met station. Average air temperature, wind speed, and wind direction are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. This is a subset of baseline weather data collected at the 15 Jornada Basin LTER CSIS study blocks, New Mexico. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. The met station variables measured include air temperature, precipitation, relative humidity, wind direction, wind speed. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively . This is an ONGOING dataset.
DOI: 10.6073/pasta/871e6129ec25c91a681dd5265e06df0a
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 6 meteorological station: 1-hour summary data: 2017 - ongoing

description: This data package contains hourly air temperature, relative humidity, wind speed, wind direction, and precipitation summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-6 met station. Air temperature, relative humidity, wind speed, wind direction, and precipitation are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively . This is an ONGOING dataset.
DOI: 10.5517/ccdc.csd.cc24q6jm
title: CCDC 1987550: Experimental Crystal Structure Determination

description: Related Article: Angshuman Roy Choudhury|2020|CSD Communication|||
DOI: 10.25505/fiz.icsd.cc24qmj1
title: CSD 1987953: Experimental Crystal Structure Determination

description: Related Article: Javier Gonzalez-Platas, Sinhue Lopez-Moreno, Enrico Bandiello, Marco Bettinelli, Daniel Errandonea|2020|Inorg.Chem.|59|6623|doi:10.1021/acs.inorgchem.0c00772
DOI: 10.25505/fiz.icsd.cc24qmk2
title: CSD 1987954: Experimental Crystal Structure Determination

description: Related Article: Javier Gonzalez-Platas, Sinhue Lopez-Moreno, Enrico Bandiello, Marco Bettinelli, Daniel Errandonea|2020|Inorg.Chem.|59|6623|doi:10.1021/acs.inorgchem.0c00772
DOI: 10.25505/fiz.icsd.cc24qml3
title: CSD 1987955: Experimental Crystal Structure Determination

description: Related Article: Javier Gonzalez-Platas, Sinhue Lopez-Moreno, Enrico Bandiello, Marco Bettinelli, Daniel Errandonea|2020|Inorg.Chem.|59|6623|doi:10.1021/acs.inorgchem.0c00772
DOI: 10.25505/fiz.icsd.cc24qmm4
title: CSD 1987956: Experimental Crystal Structure Determination

description: Related Article: Javier Gonzalez-Platas, Sinhue Lopez-Moreno, Enrico Bandiello, Marco Bettinelli, Daniel Errandonea|2020|Inorg.Chem.|59|6623|doi:10.1021/acs.inorgchem.0c00772
DOI: 10.25505/fiz.icsd.cc24qmn5
title: CSD 1987957: Experimental Crystal Structure Determination

description: Related Article: Javier Gonzalez-Platas, Sinhue Lopez-Moreno, Enrico Bandiello, Marco Bettinelli, Daniel Errandonea|2020|Inorg.Chem.|59|6623|doi:10.1021/acs.inorgchem.0c00772
DOI: 10.25505/fiz.icsd.cc24qmp6
title: CSD 1987958: Experimental Crystal Structure Determination

description: Related Article: Javier Gonzalez-Platas, Sinhue Lopez-Moreno, Enrico Bandiello, Marco Bettinelli, Daniel Errandonea|2020|Inorg.Chem.|59|6623|doi:10.1021/acs.inorgchem.0c00772
DOI: 10.25505/fiz.icsd.cc24qmq7
title: CSD 1987959: Experimental Crystal Structure Determination

description: Related Article: Javier Gonzalez-Platas, Sinhue Lopez-Moreno, Enrico Bandiello, Marco Bettinelli, Daniel Errandonea|2020|Inorg.Chem.|59|6623|doi:10.1021/acs.inorgchem.0c00772
DOI: 10.25505/fiz.icsd.cc24qmr8
title: CSD 1987960: Experimental Crystal Structure Determination

description: Related Article: Javier Gonzalez-Platas, Sinhue Lopez-Moreno, Enrico Bandiello, Marco Bettinelli, Daniel Errandonea|2020|Inorg.Chem.|59|6623|doi:10.1021/acs.inorgchem.0c00772
DOI: 10.25505/fiz.icsd.cc24qms9
title: CSD 1987961: Experimental Crystal Structure Determination

description: Related Article: Javier Gonzalez-Platas, Sinhue Lopez-Moreno, Enrico Bandiello, Marco Bettinelli, Daniel Errandonea|2020|Inorg.Chem.|59|6623|doi:10.1021/acs.inorgchem.0c00772
DOI: 10.25505/fiz.icsd.cc24qmtb
title: CSD 1987962: Experimental Crystal Structure Determination

description: Related Article: Javier Gonzalez-Platas, Sinhue Lopez-Moreno, Enrico Bandiello, Marco Bettinelli, Daniel Errandonea|2020|Inorg.Chem.|59|6623|doi:10.1021/acs.inorgchem.0c00772
DOI: 10.25505/fiz.icsd.cc24qmvc
title: CSD 1987963: Experimental Crystal Structure Determination

description: Related Article: Javier Gonzalez-Platas, Sinhue Lopez-Moreno, Enrico Bandiello, Marco Bettinelli, Daniel Errandonea|2020|Inorg.Chem.|59|6623|doi:10.1021/acs.inorgchem.0c00772