cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26182/gcwd-v284
title: Maximising crops and minimising weeds with smart phase farming
DOI: 10.6084/m9.figshare.22116218
title: Supplementary Material for: Genetic alterations of esophageal squamous cell carcinoma in Korean patients

description: Introduction: Esophageal squamous cell carcinoma (ESCC) is one of the deadliest cancers in Korea, although its incidence is lower in Korea than in China and Japan. There are no data on genetic alterations associated with ESCC in Korea. Our study is the first report of the mutational landscape of ESCC in a Korean cohort. Methods: We performed whole exome sequencing analysis of 43 ESCC tumor samples and germline DNA from normal esophageal mucosa or whole blood. Using electronic medical records, the patients’ clinical characteristics were reviewed carefully. Results: We found a mutually exclusive mutation pattern in NFE2L2–ZNF750 gene pairs. Non-silent variants of KMT2D (MLL2) were associated with a poor prognosis. An analysis to identify potentially druggable genes revealed NOTCH1 as a potential therapeutic target. We observed a high frequency of C:G → T:A transitions regardless of smoking history. In our cohort, deconstruction of the mutation signature revealed enrichment of COSMIC single base substitution (SBS) 13, SBS 39, SBS 2, SBS 40, and SBS 1. Conclusion: We did not find a Korean-specific signature of genetic alterations, but our data suggest that KMT2D is a molecular prognostic marker. Further studies need to examine the role of KMT2D in ESCC prognosis due to our small sample size.
DOI: 10.6084/m9.figshare.22116218.v1
title: Supplementary Material for: Genetic alterations of esophageal squamous cell carcinoma in Korean patients

description: Introduction: Esophageal squamous cell carcinoma (ESCC) is one of the deadliest cancers in Korea, although its incidence is lower in Korea than in China and Japan. There are no data on genetic alterations associated with ESCC in Korea. Our study is the first report of the mutational landscape of ESCC in a Korean cohort. Methods: We performed whole exome sequencing analysis of 43 ESCC tumor samples and germline DNA from normal esophageal mucosa or whole blood. Using electronic medical records, the patients’ clinical characteristics were reviewed carefully. Results: We found a mutually exclusive mutation pattern in NFE2L2–ZNF750 gene pairs. Non-silent variants of KMT2D (MLL2) were associated with a poor prognosis. An analysis to identify potentially druggable genes revealed NOTCH1 as a potential therapeutic target. We observed a high frequency of C:G → T:A transitions regardless of smoking history. In our cohort, deconstruction of the mutation signature revealed enrichment of COSMIC single base substitution (SBS) 13, SBS 39, SBS 2, SBS 40, and SBS 1. Conclusion: We did not find a Korean-specific signature of genetic alterations, but our data suggest that KMT2D is a molecular prognostic marker. Further studies need to examine the role of KMT2D in ESCC prognosis due to our small sample size.
DOI: 10.5281/zenodo.7344432
title: Teleseismic P records and ambient noise cross-correlations from a dense ocean-bottom seismometer array at Hyuga-nada

description: <strong>Telesesimic P and ambient noise cross-correlation dataset from a dense OBS array at Hyuganada, SW Japan. </strong> The dataset are used in a manuscript titled 'Fluid reservoir in the Hyuga-nada accretionary prism near the Kyushu-Palau ridge: insights from a passive seismic array', which is submitted to the Journal of Geophysical Research: Solid Earth.
DOI: 10.5281/zenodo.7648150
title: Teleseismic P records and ambient noise cross-correlations from a dense ocean-bottom seismometer array at Hyuga-nada

description: <strong>Telesesimic P and ambient noise cross-correlation dataset from a dense OBS array at Hyuganada, SW Japan. </strong> The dataset are used in a manuscript titled 'Shallow low-velocity layer in the Hyuga-nada accretionary prism and its hydrological implications: insights from a passive seismic array', which is submitted to the Journal of Geophysical Research: Solid Earth. It also contains necessary data for reproducing inversion analysis performed in the manuscript. <em>Teleseismic_P.tar.gz</em>: contains teleseismic P wave forms in SAC format <em>Noise_cross_corr.tar.gz</em>: contains ambient noise cross-correlation functions in SAC format <em>Reproduce.tar.gz</em>: dataset for reproducing inversion analysis. <pre><code class="language-bash"># Example shell script for reproduce inversion results HDA01 cd Reproduce/INV/HDA01 mpirun -np 20 joint_inv joint_inv.in</code></pre> The SEIS_FILO software (https://doi.org/10.5281/zenodo.6330840) is required for this reproduction.
DOI: 10.5281/zenodo.7344431
title: Teleseismic P records and ambient noise cross-correlations from a dense ocean-bottom seismometer array at Hyuga-nada

description: <strong>Telesesimic P and ambient noise cross-correlation dataset from a dense OBS array at Hyuganada, SW Japan. </strong> The dataset are used in a manuscript titled 'Shallow low-velocity layer in the Hyuga-nada accretionary prism and its hydrological implications: insights from a passive seismic array', which is submitted to the Journal of Geophysical Research: Solid Earth. It also contains necessary data for reproducing inversion analysis performed in the manuscript. <em>Teleseismic_P.tar.gz</em>: contains teleseismic P wave forms in SAC format <em>Noise_cross_corr.tar.gz</em>: contains ambient noise cross-correlation functions in SAC format <em>Reproduce.tar.gz</em>: dataset for reproducing inversion analysis. <pre><code class="language-bash"># Example shell script for reproduce inversion results HDA01 cd Reproduce/INV/HDA01 mpirun -np 20 joint_inv joint_inv.in</code></pre> The SEIS_FILO software (https://doi.org/10.5281/zenodo.6330840) is required for this reproduction.
DOI: 10.6084/m9.figshare.22115492
title: Social media improves farmers’ knowledge of invasive alien species: the case study of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae)

description: Supplementary file 1 and 2
DOI: 10.6084/m9.figshare.22115492.v1
title: Social media improves farmers’ knowledge of invasive alien species: the case study of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae)

description: Supplementary file 1 and 2
DOI: 10.25345/c5hx1614q
title: MassIVE MSV000091310 - Transcriptomics and proteomics of gastrocnemius muscle biopsies in peripheral artery disease
title: Peripheral artery disease (PAD) is associated with lower extremity muscle pathology and mobility loss, with few effective treatments. In this study, in-depth transcriptomic and proteomic analyses were performed on gastrocnemius muscle from 31 people with PAD without diabetes or chronic limb-threatening ischemia and 29 age- and sex-matched non-PAD controls. Analyses of transcripts and proteins suggest activation of stress-response mechanisms in PAD muscle, including inflammation, fibrosis, apoptosis, angiogenesis, unfolded protein response, nerve and muscle repair. The stoichiometric proportions of mitochondrial respiratory proteins but not their corresponding transcripts were aberrant in PAD compared to non-PAD, and mitochondrial respiratory protein abundance was significantly associated with mitochondrial respiratory activity in non-PAD but not in PAD muscle; suggesting that in PAD muscle, respiratory proteins are not assembled into functional units, likely contributing to the abnormal mitochondrial activity in PAD. The levels of rate-limiting glycolytic enzymes, such as exokinase and pyruvate kinase, were lower in muscle of people with PAD compared to non-PAD participants. This study points to novel mechanisms underlying muscle damage in PAD that, If confirmed, may serve as targets for disease modification.
DOI: 10.6084/m9.figshare.22110584.v1
title: Supplementary information.xlsx

description: Traditional Chinese medicine (TCM) has a wide range of clinical applications and good efficacy. However, due to the inherent multi-level, multi-linked, and multi-dimensional non-linear synergistic action characteristics, explaining the mechanism of action (MOA) of TCM in the treatment of diseases still faces great challenges. Therefore, a systematic and applicable research strategy that suits the therapeutic characteristics of TCM is urgently needed. Liu <em>et al.</em> proposed the Quality marker (Q-marker) opinion to monitor and evaluate the qualities of TCM products, which has significantly promoted the development of TCM in recent years. In this study, a Q-marker screening strategy for TCM formula which emphasizes efficacy and biological activities was proposed. In principle, we have integrated absorption, distribution, metabolism, and excretion (ADME) studies, systems biology, and experimental verification in the Q-marker screening workflow. Qianghuo Shengshi decoction (QHSSD) in treating rheumatoid arthritis (RA) was taken as an example to screen Q-markers. As a result, five Q-markers with significant<em> in vitro</em> anti-inflammatory effects were screened out from 159 compounds in QHSSD for treating RA, including notopterol, isoliquiritin, imperatorin, cimifugin, and glycyrrhizic acid. Moreover, much instructive information on pharmacological mechanisms was obtained through the integrated analysis of network pharmacology and metabolomics, such as the main targets and pathways that QHSSD plays important roles in the treatment of RA, which provided a research foundation for the further in-depth study of QHSSD. In conclusion, this work illustrates that the strategy is feasible and offers a practical reference model for the systematic research of TCM formula
DOI: 10.6084/m9.figshare.21799793.v6
title: Precision Oncology-Based Targeting of Signaling Pathways Toward a Holistic Approach to Cancer Therapeutics

description: The mutational changes occurring in the regulatory genes responsible for the maintenance of optimal cell growth and proliferation gradually lead to cancer progression and metastasis. Furthermore, patients with the same cancer types often respond differently to different cancer therapies, indicating the need for a patient-specific treatment regimen for the disease. Precision oncology is the new field of cancer research that relies on genetic profiling of individual tumors to identify targetable alterations for custom-tailored personalized treatment of the disease. It is to rely upon the genomic study of cancer cells to get a clear picture of the prognosis and pathways involved in disease progression and to look for the means to selectively target them for a cure. This article intends to briefly explain the foundations and frontiers of precision oncology in the context of technological advances being made in this direction to assess its scope and importance in the realization of a proper cure for cancer.
DOI: 10.5519/qd.y0qhjda6
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (311 records)
DOI: 10.34740/kaggle/dsv/5013791
title: Article and Customer Embeddings for H&MFashion
DOI: 10.6084/m9.figshare.22116311
title: Experiment data

description: Data collected through experiments
DOI: 10.6084/m9.figshare.22116311.v1
title: Experiment data

description: Data collected through experiments
DOI: 10.6084/m9.figshare.22110584.v2
title: Supplementary information and raw data of LC-MS.xlsx

description: Traditional Chinese medicine (TCM) has a wide range of clinical applications and good efficacy. However, due to the inherent multi-level, multi-linked, and multi-dimensional non-linear synergistic action characteristics, explaining the mechanism of action (MOA) of TCM in the treatment of diseases still faces great challenges. Therefore, a systematic and applicable research strategy that suits the therapeutic characteristics of TCM is urgently needed. Liu <em>et al.</em> proposed the Quality marker (Q-marker) opinion to monitor and evaluate the qualities of TCM products, which has significantly promoted the development of TCM in recent years. In this study, a Q-marker screening strategy for TCM formula which emphasizes efficacy and biological activities was proposed. In principle, we have integrated absorption, distribution, metabolism, and excretion (ADME) studies, systems biology, and experimental verification in the Q-marker screening workflow. Qianghuo Shengshi decoction (QHSSD) in treating rheumatoid arthritis (RA) was taken as an example to screen Q-markers. As a result, five Q-markers with significant<em> in vitro</em> anti-inflammatory effects were screened out from 159 compounds in QHSSD for treating RA, including notopterol, isoliquiritin, imperatorin, cimifugin, and glycyrrhizic acid. Moreover, much instructive information on pharmacological mechanisms was obtained through the integrated analysis of network pharmacology and metabolomics, such as the main targets and pathways that QHSSD plays important roles in the treatment of RA, which provided a research foundation for the further in-depth study of QHSSD. In conclusion, this work illustrates that the strategy is feasible and offers a practical reference model for the systematic research of TCM formula
DOI: 10.6084/m9.figshare.22110584
title: MS raw data of metabolomics.xlsx

description: MS raw data of metabolomics
DOI: 10.6084/m9.figshare.22110584.v3
title: Raw data of mass spectrometry for metabolomics.xlsx

description: Raw data of mass spectrometry for metabolomics
DOI: 10.15151/esrf-es-1018399371
title: PROTEINS RELATED TO PATHOGENESIS OF DISEASES, VIRAL PROTEINS, CELL DIVISION, SIGNALLING AND CHROMATIN PROCESSES

description: Our BAG is composed of eight PIs at six different institutions in Italy and Austria. We focus on a large variety of human, bacterial, viral and synthetic protein targets and address diverse biological contexts by combining structural biology with biochemistry, biophysics, cellular and in vivo investigations.
DOI: 10.15151/esrf-es-1026152954
title: Universities of St. Andrews, Dundee, Glasgow, and Aberdeen

description: The Dundee/St Andrews/Glasgow/Aberdeen BAG research interests fall into two broad areas. Firstly, we use structural information to understand mechanisms of fundamental biological processes, protein engineering, enzymes, and biological chemistry. Secondly, we utilize structural insights to guide target selection and development of lead compounds for drug development. Fundamental insights obtained into biological processes are often closely coupled to target identification and development of tools, reagents, or inhibitors, which feed into a range of biomedical applications. Our research relies heavily on high quality, reliable and tunable synchrotron radiation, along with state-of-the-art optics, detectors, sample changers, and computation, to support determination of new structures, as well as collect high resolution diffraction data to provide the level of accuracy important in structure-guided drug design.
DOI: 10.15151/esrf-es-1031244062
title: BAG STRASBOURG-NANCY-DIJON

description: The members of the BAG are working on different projects, including proteins, nucleic acids and nucleic acid-protein complexes. The teams from Nancy work on structure-function relationship of glutathione transferases and RNA-protein complexes. A team from Dijon works on proteins involved in genetic disorders. The IBMC study RNAP proteins and tRNA precursors with partners in relation with the evolution of translation machinery and with human pathologies, ribozymes and RNA-protein complexes involved in the mitochondrial import. IGBMC (Strasbourg-Illkirch) teams are focused on nuclear receptors and complexes involving nuclear receptors and co-activators or co-repressors, transcription factor complexes, RNA polymerases, epigenetic molecular targets or cancer related proteins as well as large protein-nucleic acids complexes such as ribosomes.
DOI: 10.15151/esrf-es-1031244204
title: Berlin-Karlsruhe - Macromolecular Crystallography BAG - Structural Biology of light responsive, signal transducing and metalloproteins

description: The project aims to investigate structure-function relationships in different groups of soluble and membrane proteins, most of which are involved in signal transduction or energy conversion. We investigate the signalling mechanisms of phytochromes by focusing on the structures of the intermediates of the photocycle and by analysing domain movements or by introducing unnatural amino acids. We analyse the structures of different G protein-coupled receptors (GPCRs; e.g. melanocortin-4 receptor and rhodopsin), either alone or in complex with their cognate G-proteins, to understand their signalling mechanisms. In our work on the biocatalytic splitting of molecular hydrogen into protons and electrons, we analyse the membrane-bound and soluble [NiFe] hydrogenases, proteins of the remarkably small subgroup of hydrogenases that are active under aerobic conditions. Other research areas include mechanosensitive channels, microbial rhodopsins, cytomegalovirus proteins and DNA photolyases.
DOI: 10.15151/esrf-es-1014668852
title: Structural Biology BAG - Portugal

description: The Portuguese MX BAG includes 13 PIs from three different institutions. Our research interests include soluble and membrane proteins of biomedical interest from humans or pathogenic organisms, several of which can be drug targets. Focus is also given to structural enzymology, aimed at the elucidation of reaction mechanisms, active sites, and inhibition tolerance in proteins with potential biotechnology applications. In several cases, complementary structural biology approaches are being used, combining MX with SAXS and, more recently, CryoEM.
DOI: 10.15151/esrf-es-1078473037
title: Propagation phase contrast tomography of paraffin-embedded samples before nanotomography

description: Pre-characterization of mounted samples to extract relevant samples for nanotomography
DOI: 10.15151/esrf-es-1034440029
title: A SAXS Study on the Nanostructure of Novel Collagen-Stimulating Peptide Amphiphiles

description: As part of our research programme on self-assembling peptide amphiphiles (PAs) we will investigate the temperature- and pH- dependent self-assembly behaviour of a novel series of PAs based on C16-KTTKS (MatrixylTM) containing the collagen-stimulating KTTKS sequence. BioSAXS will be used to probe the self-assembled structure in aqueous solution, via analysis of form factor in dilute solution. This builds on our earlier research on this system, but the new compounds contain novel lipid chains and PEG spacers desgined to both influence the molecular packing and the bioactivity.
DOI: 10.15151/esrf-es-1030813041
title: Atomic Structure of Colloidal Semi Conducting Nanoplatelets with High Energy X-ray Scattering

description: Ultrathin semi-conducting colloidal nanoplatelets have outstanding optical properties which gather increasing scrutiny from various communities. Their thickness being very small (around 1 nm), their shape strongly depends on the organic ligand monolayer coated at their surface which can cause surface stress and deformation. We aim at getting an atomic resolution of the structure of the crystalline core depending on the ligand structure using high energy X-ray diffraction in order to better understand the ligand induced deformation. Ultimately this new fundamental understanding of ligand induced shape morphing will lead to the predictive design of original shapes.
DOI: 10.15151/esrf-es-1030392887
title: Development of cellulosic based composites with typical three-layer orthotropic cartilage organization by combined ultrafiltration, ultrasou

description: The aim of this project is to develop multilayered cellulosic-based composites with structural organization pertaining to cartilage tissue engineering. Recently, frontal ultrafiltration (FU) under ultrasounds (US) processing applied on nanocrystal celluloses (CNCs) aqueous suspensions, have allowed to achieve the three orthotropic structured layers representatives of the multizonal material cartilage. In-situ SAXS revealed a parallel orientation of the CNCs near the membrane surface, an intermediate isotropic layer and a vertical orientation layer of the CNCs near the ultrasonic vibrating blade. The goal of this proposal is firstly, to freeze this structural organization thanks to the mixing of CNCS with UV cured polymer and in-situ photopolymerization applied at the end of the builded multilayered organization, secondly bring an understanding of the organization mechanism induces during FU/US/UVcuring processing from nanometric to micrometric length scales by in-situ SAXS and USAXS.
DOI: 10.15151/esrf-es-1030394505
title: Effect of hydration on the structure of spiders cuticular hair sensilla

description: Cuticular hair sensilla serve as mechano sensors (touch and flow-sensing) in many animals. They are some of the most sensitive sensilla known in the animal kingdom. The hair-like structures appear simple, but show striking sensitivity, specificity and mechanical robustness. It is unknown how architecture, composition (chitin-protein), and their hydration state contribute to the hairs function. Flowing up on our proposal SC 5187 we suggest to extend our study of the hair sensilla of the spider, Cupiennius salei to include the effect of water on the chitin-protein structure. To do so we plan to perform SAXS/XRD/XRF scans on fully hydrated samples (intact hairs and cross sections). With this we will be able to elucidate the effects of water on the structure of the hair sensilla. This work will pave the way for understanding the structure-properties-function relationships in arthropod sensors and will serve as archetype for bioinspired materials with embedded sensory functions.
DOI: 10.15151/esrf-es-1030394765
title: X-Ray diffraction study of the Kitaev candidate Na2IrO3 under uniaxial strain

description: Kitaev systems have attracted a lot of attention this last decade as they have been theoretically predicted to exhibit a very exotic and intriguing quantum phase of matter called a quantum spin liquid phase, where no magnetic order occurs but rather a strong quantum entanglement between particles, usually characterized by fractionalized excitations. Some strong spin-orbital entangled Jeff = 1/2 honeycomb systems such as Na2IrO3 exhibit such Kitaev interactions. However they have been shown to magnetically order due to other interactions driving those systems away from the pure Kitaev case. These interactions are strongly believed to arise from the distortions of the Ir-O-Ir angles away from 90°. Here we propose to perform a high precision diffraction experiment on NaIr2O3 under uniaxial strain to probe how the atomic positions and those angles are affected.
DOI: 10.15151/esrf-es-1029994945
title: Local structure study of orbital order-disorder transition in ACrF3 and ACuF3 (A = Ag, Na, K, Rb, Cs and NH4) fluoroperovskites

description: ACrF3 and ACuF3 (A = Ag, Na, K, Rb, Cs and NH4) have Jahn-Teller active electron configurations and as a consequence, the crystal structures are distorted. The crystal structure is triclinic form small A-site cations (Ag and Na) and tetragonal for large A-site cations (K, Rb, Cs and NH4). Upon heating, the orbital ordering melts into a distordered state with higher symmetry. The proposed experiment aims to study the local structure in ACrF3 and ACuF3 over the order-disorder transition by pair distribution functions (PDFs) and x-ray absorption spectroscopy (XAS). The experiment will address the nature of the transition and give insight to electronic and magnetic isotropy present in the compounds.