cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3504026
title: Molecular properties in the Tamm–Dancoff approximation: indirect nuclear spin–spin coupling constants

description: The Tamm–Dancoff approximation (TDA) can be applied to the computation of excitation energies using time-dependent Hartree–Fock (TD-HF) and time-dependent density-functional theory (TD-DFT). In addition to simplifying the resulting response equations, the TDA has been shown to significantly improve the calculation of triplet excitation energies in these theories, largely overcoming issues associated with triplet instabilities of the underlying reference wave functions. Here, we examine the application of the TDA to the calculation of another response property involving triplet perturbations, namely the indirect nuclear spin–spin coupling constant. Particular attention is paid to the accuracy of the triplet spin–dipole and Fermi-contact components. The application of the TDA in HF calculations leads to vastly improved results. For DFT calculations, the TDA delivers improved stability with respect to geometrical variations but does not deliver higher accuracy close to equilibrium geometries. These observations are rationalised in terms of the ground- and excited-state potential energy surfaces and, in particular, the severity of the triplet instabilities associated with each method. A notable feature of the DFT results within the TDA is their similarity across a wide range of different functionals. The uniformity of the TDA results suggests that some conventional evaluations may exploit error cancellations between approximations in the functional forms and those arising from triplet instabilities. The importance of an accurate treatment of correlation for evaluating spin–spin coupling constants is highlighted by this comparison.
DOI: 10.6084/m9.figshare.3504026.v1
title: Molecular properties in the Tamm–Dancoff approximation: indirect nuclear spin–spin coupling constants

description: The Tamm–Dancoff approximation (TDA) can be applied to the computation of excitation energies using time-dependent Hartree–Fock (TD-HF) and time-dependent density-functional theory (TD-DFT). In addition to simplifying the resulting response equations, the TDA has been shown to significantly improve the calculation of triplet excitation energies in these theories, largely overcoming issues associated with triplet instabilities of the underlying reference wave functions. Here, we examine the application of the TDA to the calculation of another response property involving triplet perturbations, namely the indirect nuclear spin–spin coupling constant. Particular attention is paid to the accuracy of the triplet spin–dipole and Fermi-contact components. The application of the TDA in HF calculations leads to vastly improved results. For DFT calculations, the TDA delivers improved stability with respect to geometrical variations but does not deliver higher accuracy close to equilibrium geometries. These observations are rationalised in terms of the ground- and excited-state potential energy surfaces and, in particular, the severity of the triplet instabilities associated with each method. A notable feature of the DFT results within the TDA is their similarity across a wide range of different functionals. The uniformity of the TDA results suggests that some conventional evaluations may exploit error cancellations between approximations in the functional forms and those arising from triplet instabilities. The importance of an accurate treatment of correlation for evaluating spin–spin coupling constants is highlighted by this comparison.
DOI: 10.6084/m9.figshare.3503972
title: Experimental Data

description: Experimental data used in the following research paper, which presents a minimally invasive wearable muscle sensing device consisting of jogging leggings, with embroidered surface EMG electrodes. Muscle activity from the quadriceps group is collected during running trials on multiple surfaces. <br><br>R. B. Ribas Manero, J. Grewal, B. Michael, A. Shafti, K. Althoefer, J. Ll. Ribas Fernandez, M. J. Howard. "Wearable Embroidered Muscle Activity Sensing Device for the Human Upper Leg." EMBC (2016), In Press.<br><br>
DOI: 10.6084/m9.figshare.3503972.v1
title: Experimental Data

description: Experimental data used in the following research paper, which presents a minimally invasive wearable muscle sensing device consisting of jogging leggings, with embroidered surface EMG electrodes. Muscle activity from the quadriceps group is collected during running trials on multiple surfaces. <br><br>R. B. Ribas Manero, J. Grewal, B. Michael, A. Shafti, K. Althoefer, J. Ll. Ribas Fernandez, M. J. Howard. "Wearable Embroidered Muscle Activity Sensing Device for the Human Upper Leg." EMBC (2016), In Press.<br><br>
DOI: 10.6084/m9.figshare.3503933
title: Tomographic modelling of H 1743-322

description: Results of fitting a tomographic model to the ~4s quasi periodic oscillation (QPO) in XMM-Newton and NuSTAR data from the black hole X-ray binary system H 1743-322. This is an animated version of Fig 3 in Ingram et al (2016). The most intensely illuminated patches of the disc rotate about the disc surface, causing the iron line to rock from red to blue shifted during a QPO cycle.
DOI: 10.6084/m9.figshare.3503912
title: Supplementary Material for: Muscle MRI of the Upper Extremity in the Myotonic Dystrophy Type 1

description: <i>Background:</i> The purpose of this study was to explore the relation between muscle MRI findings and weakness of the upper extremity muscles in patients with myotonic dystrophy type 1 (DM1). <i>Methods:</i> Nineteen DM1 patients from 15 families were enrolled in this study. Muscle weakness was evaluated using the modified Medical Research Council scale. Subjects also underwent a genetic study and muscle MRI of the upper extremities. <i>Results:</i> In patients with DM1, the flexor digitorum profundus (FDP), flexor pollicis longus, flexor digitorum superficialis (FDS), extensor pollicis, abductor pollicis longus (APL), lateral head of triceps brachii and infraspinatus (INF) muscles were frequently and severely affected. Muscle strength was significantly correlated with the severity of muscle MRI findings in the FDP, short head of biceps brachii (SBB), and medial head of triceps brachii muscles. Disease duration was correlated significantly with MRI findings in the FDP, FDS, long head of biceps brachii, INF, APL, and SBB muscles. Unexpectedly, the degree of trinucleotide expansion of myotonin protein kinase was not correlated with muscle MRI findings. <i>Conclusion:</i>Muscle MRI of the upper extremity is useful to detect affected muscles in DM1 patients.
DOI: 10.6084/m9.figshare.3503885.v1
title: OCTET Statistical Analysis Plan

description: <b>Scientific title</b> Obsessive Compulsive Treatment Efficacy Trial (OCTET) <b>Acronym</b> OCTET<b>ISRCTN Registration</b>ISRCTN73535163 DOI 10.1186/ISRCTN73535163 <b>Study hypothesis</b> 1. Identify and confirm estimated recruitment rates for an obsessive compulsive disorder (OCD) treatment trial via an internal pilot phase aimed at evaluating recruitment rates and primary outcome point<br> 2. Proceed seamlessly to a full RCT (if recruitment is successful in the pilot phase) to determine:<br> 2.1. The clinical and cost-effectiveness of two self-managed CBT interventions (cCBT and bibliotherapy) compared to a CBT waiting list in the management of OCD patients in the short term at 3- and 6-month follow-up<br> 2.2. The clinical and cost-effectiveness of self-managed therapies plus conventional CBT compared to waiting list plus conventional CBT at 12-month follow-up <br> 3. Determine patient compliance and patient and health professional acceptability of the two self-managed therapy packages (cCBT & GSH)<br> <br> More details can be found at http://www.nets.nihr.ac.uk/projects/hta/098101<br> Protocol can be found at http://www.nets.nihr.ac.uk/__data/assets/pdf_file/0006/54699/PRO-09-81-01.pd
DOI: 10.6084/m9.figshare.3503873
title: Tools and methods in genomic data analysis: TGAC - Repositive Preliminary Survey Results

description: In this survey, we aimed to get a better understanding of the current software tools used by bioinformaticians and data scientists working in the field of genomics, as well as the scientific questions asked when analysing variant data.Additionally, we were interested in the survey participants’ genomic data search and access habits and whether our recipients behave similarly to or differently from those surveyed in Van Schaik et al., 2014.We sent out a short web questionnaire generated with typeform via e-mail to a selected user-base including nine questions in total.The preliminary results presented are derived from 16 business professionals and researchers working in genomics, with their work field ranging from biology and bioinformatics to data science and software development.
DOI: 10.6084/m9.figshare.3503873.v1
title: TGAC - Repositive Preliminary Survey Results

description: In this survey, we aimed to get a better understanding of the current software tools used by bioinformaticians and data scientists working in the field of genomics, as well as the scientific questions asked when analysing variant data.Additionally, we were interested in the survey participants’ genomic data search and access habits and whether our recipients behave similarly to or differently from those surveyed in Van Schaik et al., 2014.We sent out a short web questionnaire generated with typeform via e-mail to a selected user-base including nine questions in total.The preliminary results presented are derived from 16 business professionals and researchers working in genomics, with their work field ranging from biology and bioinformatics to data science and software development.
DOI: 10.6084/m9.figshare.3503873.v3
title: Tools and methods in genomic data analysis: TGAC - Repositive Preliminary Survey Results

description: In this survey, we aimed to get a better understanding of the current software tools used by bioinformaticians and data scientists working in the field of genomics, as well as the scientific questions asked when analysing variant data.Additionally, we were interested in the survey participants’ genomic data search and access habits and whether our recipients behave similarly to or differently from those surveyed in Van Schaik et al., 2014.We sent out a short web questionnaire generated with typeform via e-mail to a selected user-base including nine questions in total.The preliminary results presented are derived from 16 business professionals and researchers working in genomics, with their work field ranging from biology and bioinformatics to data science and software development.
DOI: 10.6084/m9.figshare.3503873.v2
title: Tools and methods in genomic data analysis. TGAC - Repositive Preliminary Survey Results

description: In this survey, we aimed to get a better understanding of the current software tools used by bioinformaticians and data scientists working in the field of genomics, as well as the scientific questions asked when analysing variant data.Additionally, we were interested in the survey participants’ genomic data search and access habits and whether our recipients behave similarly to or differently from those surveyed in Van Schaik et al., 2014.We sent out a short web questionnaire generated with typeform via e-mail to a selected user-base including nine questions in total.The preliminary results presented are derived from 16 business professionals and researchers working in genomics, with their work field ranging from biology and bioinformatics to data science and software development.
DOI: 10.6084/m9.figshare.3503870
title: Stanley Gadfield Aglionby Burrowes WWI Misc scans

description: Additional photos found with photos taken by Trooper Stanley Gadfield Aglionby Burrowes during his service with the Mounted Rifles in Palestine. Some photo are after his return to New Zealand, and some look to be in Newtown Wellington, pre-deployment. <br>
DOI: 10.6084/m9.figshare.3503870.v1
title: Stanley Gadfield Aglionby Burrowes WWI Misc scans

description: Additional photos found with photos taken by Trooper Stanley Gadfield Aglionby Burrowes during his service with the Mounted Rifles in Palestine. Some photo are after his return to New Zealand, and some look to be in Newtown Wellington, pre-deployment. <br>
DOI: 10.6084/m9.figshare.3503639
title: meteorological data over Guanzhong Plain

description: meteorological data over Guanzhong Plain
DOI: 10.6084/m9.figshare.3503639.v1
title: meteorological data over Guanzhong Plain

description: meteorological data over Guanzhong Plain
DOI: 10.6084/m9.figshare.3503618
title: Test_Data

description: Test data set for MetaGen
DOI: 10.6084/m9.figshare.3503618.v2
title: Test_Data

description: Test data set for MetaGen
DOI: 10.6084/m9.figshare.3503618.v1
title: Test_Data

description: Test data set for MetaGen
DOI: 10.6084/m9.figshare.3503576
title: Slides: How open science helps researchers succeed

description: Slides based on eLife article:<br>McKiernan, E. C., Bourne, P. E., Brown, C. T., Buck, S., Kenall, A., Lin, J., McDougall, D., Nosek, B. A., Ram, K., Soderberg, C. K., Spies, J. R., Thaney, K., Updegrove, A., Woo, K. H., & Yarkoni, T. How open science helps researchers succeed. <i>eLife</i> 2016;10.7554/eLife.16800
DOI: 10.6084/m9.figshare.3503576.v1
title: Slides: How open science helps researchers succeed

description: Slides based on eLife article:<br>McKiernan, E. C., Bourne, P. E., Brown, C. T., Buck, S., Kenall, A., Lin, J., McDougall, D., Nosek, B. A., Ram, K., Soderberg, C. K., Spies, J. R., Thaney, K., Updegrove, A., Woo, K. H., & Yarkoni, T. How open science helps researchers succeed. <i>eLife</i> 2016;10.7554/eLife.16800<br>
DOI: 10.6084/m9.figshare.3503576.v3
title: Slides: How open science helps researchers succeed

description: Slides based on eLife article:<br>McKiernan, E. C., Bourne, P. E., Brown, C. T., Buck, S., Kenall, A., Lin, J., McDougall, D., Nosek, B. A., Ram, K., Soderberg, C. K., Spies, J. R., Thaney, K., Updegrove, A., Woo, K. H., & Yarkoni, T. How open science helps researchers succeed. <i>eLife</i> 2016;10.7554/eLife.16800
DOI: 10.6084/m9.figshare.3503576.v2
title: Slides: How open science helps researchers succeed

description: Slides based on eLife article:<br>McKiernan, E. C., Bourne, P. E., Brown, C. T., Buck, S., Kenall, A., Lin, J., McDougall, D., Nosek, B. A., Ram, K., Soderberg, C. K., Spies, J. R., Thaney, K., Updegrove, A., Woo, K. H., & Yarkoni, T. How open science helps researchers succeed. <i>eLife</i> 2016;10.7554/eLife.16800
DOI: 10.6084/m9.figshare.3503567
title: Spectroscopic and DNA interaction studies on mixed ligand copper(II) complexes of dicyanamide with ethylenediamine or 1,3-diaminopropane

description: Mixed ligand copper(II) complexes of dicyanamide with different polyamines, <i>viz.</i> ethylenediamine (<b>1</b>) and 1,3-diaminopropane (<b>2</b>), have been synthesized and characterized. The crystal structure of complex <b>1</b> contains a five-coordinated copper in a distorted square-pyramidal environment and forms 1D zig-zag polymeric chain via the bridging ligand dicyanamide. Hydrogen bonding contributes supramolecular architecture in the crystal. Electronic spectral studies suggest the distorted square-pyramidal structure of the complexes. The interaction of the copper(II) complexes with calf-thymus DNA reveals nonintercalative binding mode. The two complexes have antimicrobial activity against the bacteria (<i>viz. Salmonella paratyphi</i>), which is responsible for paratyphoid fever.
DOI: 10.6084/m9.figshare.3503567.v2
title: Spectroscopic and DNA interaction studies on mixed ligand copper(II) complexes of dicyanamide with ethylenediamine or 1,3-diaminopropane

description: Mixed ligand copper(II) complexes of dicyanamide with different polyamines, <i>viz.</i> ethylenediamine (<b>1</b>) and 1,3-diaminopropane (<b>2</b>), have been synthesized and characterized. The crystal structure of complex <b>1</b> contains a five-coordinated copper in a distorted square-pyramidal environment and forms 1D zig-zag polymeric chain via the bridging ligand dicyanamide. Hydrogen bonding contributes supramolecular architecture in the crystal. Electronic spectral studies suggest the distorted square-pyramidal structure of the complexes. The interaction of the copper(II) complexes with calf-thymus DNA reveals nonintercalative binding mode. The two complexes have antimicrobial activity against the bacteria (<i>viz. Salmonella paratyphi</i>), which is responsible for paratyphoid fever.
DOI: 10.6084/m9.figshare.3503567.v1
title: Spectroscopic and DNA Interaction Studies on Mixed Ligand Copper(II) Complexes of Dicyanamide with ethylenediamine or 1,3-diaminopropane

description: Mixed ligand copper(II) complexes of dicyanamide with different polyamines <i>viz</i>. ethylenediamine (<b>1</b>) and 1,3-diaminopropane (<b>2</b>) have been synthesized and characterized. The crystal structure of complex (<b>1</b>) contains a five coordinated copper in a distorted square pyramidal environment and forms 1D zig-zag polymeric chain via the bridging ligand dicyanamide. Hydrogen bonding contributes supramolecular architecture in the crystal. Electronic spectral studies suggest the distorted square pyramidal structure of the complexes. The interaction of the copper(II) complexes with Calf Thymus(CT)-DNA reveals non-intercalative binding mode. The two complexes have antimicrobial activity against the bacteria (<i>viz. salmonella paratyphi</i>) which is responsible for paratyphoid fever.
DOI: 10.6084/m9.figshare.3503528
title: Pace of Landscape Change and Pediment Development in the Northeastern Sonoran Desert, United States

description: Pediments of the Sonoran Desert in the United States have intrigued physical geographers and geomorphologists for nearly a century. These gently sloping bedrock landforms are a staple of the desert landscape that millions visit each year. Despite the long-lived scientific curiosity, an understanding of the processes operating on the pediment has remained elusive. In this study we revisit the extensive history of pediment research. We then apply geospatial, field, and laboratory cosmogenic <sup>10</sup>Be nuclide dating and back-scattered electron microscopy methods to assess the pace and processes of landscape change on pediment systems abutting the Salt River in Arizona. Our study focuses on the Usery pediments linked to base-level fluctuations (river terraces) of the Salt River. Relict pediment surfaces were reconstructed with dGPS data and kriging methodologies utilized in ArcGIS—based on preserved evidence of ancient pediment surfaces. <sup>10</sup>Be ages of Salt River terraces established a chronology of incision events, where calculating the volume between the reconstructed relict pediment and modern surface topography established minimum erosion rates (∼41 mm/ka to ∼415 mm/ka). Pediment area and length appear to have a positive correlation to erosion rate and development of planar pediment surfaces. Field and laboratory observations reveal that pediment systems adjust and stabilize at each Salt River terrace. Relief reduction across the pediment begins with pediment channel incision via headward erosion. Next, tributary drainage capture begins and collapses interfluves. Lateral stream erosion promotes planation where the porosity of decayed granite along channel banks exceeds the bedrock underneath ephemeral channels.
DOI: 10.6084/m9.figshare.3503480
title: Synthesis, Crystal Structure, and Properties of a New Zinc(II) Coordination Polymer With Mixed 4,4′-biphenyldisulfonic Acid and N-Donor Ligands

description: A new zinc(II) coordination polymer, namely [Zn(bipy)<sub>2</sub>(H<sub>2</sub>O)<sub>4</sub>]<i><sub>n</sub></i>·<i>n</i>(dsba) (1), has been synthesized by the mixed 4,4′-biphenyldisulfonic acid (H<sub>2</sub>dsba) and 4,4′-bipyridine (bipy) ligands with Zinc(II) salt under the common solution evaporation method. The results of the X-ray crystal diffraction analysis show that complex 1 belongs to the monoclinic system with <i>P2<sub>1</sub>/c</i> space group. The unit cell constants of complex 1 are <i>a</i> = 9.2579 Å, <i>b</i> = 12.2016 Å, <i>c</i> = 14.447 Å, α = γ = 90˚, β = 93.476˚. Complex 1 exhibits a three-dimensional supramolecular network based on the discrete structure by utilizing various H-bonded interactions. In addition, the properties of complex 1, such as the elemental analysis, FT-IR spectroscopy, X-ray powder diffraction, and fluorescence spectroscopy were also characterized and are discussed in detailed.
DOI: 10.6084/m9.figshare.3503480.v1
title: Synthesis, Crystal Structure, and Properties of a New Zinc(II) Coordination Polymer With Mixed 4,4′-biphenyldisulfonic Acid and N-Donor Ligands

description: A new zinc(II) coordination polymer, namely [Zn(bipy)<sub>2</sub>(H<sub>2</sub>O)<sub>4</sub>]<i><sub>n</sub></i>·<i>n</i>(dsba) (1), has been synthesized by the mixed 4,4′-biphenyldisulfonic acid (H<sub>2</sub>dsba) and 4,4′-bipyridine (bipy) ligands with Zinc(II) salt under the common solution evaporation method. The results of the X-ray crystal diffraction analysis show that complex 1 belongs to the monoclinic system with <i>P2<sub>1</sub>/c</i> space group. The unit cell constants of complex 1 are <i>a</i> = 9.2579 Å, <i>b</i> = 12.2016 Å, <i>c</i> = 14.447 Å, α = γ = 90˚, β = 93.476˚. Complex 1 exhibits a three-dimensional supramolecular network based on the discrete structure by utilizing various H-bonded interactions. In addition, the properties of complex 1, such as the elemental analysis, FT-IR spectroscopy, X-ray powder diffraction, and fluorescence spectroscopy were also characterized and are discussed in detailed.
DOI: 10.6084/m9.figshare.3503477
title: Impaired autophagy in macrophages promotes inflammatory eye disease

description: Autophagy is critical for maintaining cellular homeostasis. Organs such as the eye and brain are immunologically privileged. Here, we demonstrate that autophagy is essential for maintaining ocular immune privilege. Deletion of multiple autophagy genes in macrophages leads to an inflammation-mediated eye disease called uveitis that can cause blindness. Loss of autophagy activates inflammasome-mediated IL1B secretion that increases disease severity. Inhibition of caspase activity by gene deletion or pharmacological means completely reverses the disease phenotype. Of interest, experimental uveitis was also increased in a model of Crohn disease, a systemic autoimmune disease in which patients often develop uveitis, offering a potential mechanistic link between macrophage autophagy and systemic disease. These findings directly implicate the homeostatic process of autophagy in blinding eye disease and identify novel pathways for therapeutic intervention in uveitis.
DOI: 10.6084/m9.figshare.3503477.v2
title: Impaired autophagy in macrophages promotes inflammatory eye disease

description: Autophagy is critical for maintaining cellular homeostasis. Organs such as the eye and brain are immunologically privileged. Here, we demonstrate that autophagy is essential for maintaining ocular immune privilege. Deletion of multiple autophagy genes in macrophages leads to an inflammation-mediated eye disease called uveitis that can cause blindness. Loss of autophagy activates inflammasome-mediated IL1B secretion that increases disease severity. Inhibition of caspase activity by gene deletion or pharmacological means completely reverses the disease phenotype. Of interest, experimental uveitis was also increased in a model of Crohn disease, a systemic autoimmune disease in which patients often develop uveitis, offering a potential mechanistic link between macrophage autophagy and systemic disease. These findings directly implicate the homeostatic process of autophagy in blinding eye disease and identify novel pathways for therapeutic intervention in uveitis.