cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22004003
title: Supplementary Material for: Case report: prenatal recurrent microcephaly and corpus callosum abnormalities in a Chinese family with novel biallelic SASS6 mutations

description: Introduction: Primary microcephaly (MCPH) is not an uncommon disorder with multiple etiologies. There is a growing number of MCPH-related genes discovered due to the extensive application of whole-exome sequencing (WES) in clinical and research settings. Biallelic mutations in the SASS6 gene cause an extremely rare MCPH, type 14. To date, only two families with SASS6 gene-related microcephaly have been reported. Case description: We report a case of recurrent congenital microcephaly in a Chinese family. The two affected fetuses presented with microcephaly early in the second trimester with agenesis of the corpus callosum. In the first affected fetus, trio WES detected two compound heterozygous candidate variants c.1139T&gt;C(p.L380P) and c.1223C&gt;G (p.T408S) in the SASS6 gene. Another affected fetus also inherited both variants, while the normal child carried neither variant through Sanger sequencing analysis. Both variants were classified as a variant of uncertain significance according to the current American College of Medical Genetics and Genomics guidelines. Conclusion: We reported novel biallelic variants in the SASS6 gene, encoding the SAS6 centriolar assembly protein, associated with prenatal onset of autosomal recessive microcephaly. We postulate that the pathomechanism of the compound heterozygous variants in close proximity could potentiate the overall coiled instability leading to the phenotypic features of our case.
DOI: 10.6084/m9.figshare.22004003.v1
title: Supplementary Material for: Case report: prenatal recurrent microcephaly and corpus callosum abnormalities in a Chinese family with novel biallelic SASS6 mutations

description: Introduction: Primary microcephaly (MCPH) is not an uncommon disorder with multiple etiologies. There is a growing number of MCPH-related genes discovered due to the extensive application of whole-exome sequencing (WES) in clinical and research settings. Biallelic mutations in the SASS6 gene cause an extremely rare MCPH, type 14. To date, only two families with SASS6 gene-related microcephaly have been reported. Case description: We report a case of recurrent congenital microcephaly in a Chinese family. The two affected fetuses presented with microcephaly early in the second trimester with agenesis of the corpus callosum. In the first affected fetus, trio WES detected two compound heterozygous candidate variants c.1139T&gt;C(p.L380P) and c.1223C&gt;G (p.T408S) in the SASS6 gene. Another affected fetus also inherited both variants, while the normal child carried neither variant through Sanger sequencing analysis. Both variants were classified as a variant of uncertain significance according to the current American College of Medical Genetics and Genomics guidelines. Conclusion: We reported novel biallelic variants in the SASS6 gene, encoding the SAS6 centriolar assembly protein, associated with prenatal onset of autosomal recessive microcephaly. We postulate that the pathomechanism of the compound heterozygous variants in close proximity could potentiate the overall coiled instability leading to the phenotypic features of our case.
DOI: 10.15151/esrf-es-1018258616
title: FInnish National Protein Crystallography Consortium

description: The Finnish BAG encompasses 24 groups active in crystallography in Finland. The projects vary widely and include membrane proteins and protein complexes, other proteins involved in disease and antibiotics and drug development and discovery (endoplasmic regulation and protein secretion, ADP-ribosylation and several oncogenic proteins including kinases, biocatalysis) and several pathogen proteins and various enzyme targets and e.g. studies on phytochrome photoreceptors and complexes involved in actin dynamics regulation. Overall the BAG serves the national needs for highly variable projects, with different biological and biotechnological applications. Several project will benefit from microfocus beam lines and tunable wavelength options for phasing, others benefit from quick robust screening by MASSIF. Biology lab is needed for SAXS experiments.
DOI: 10.15151/esrf-es-1018273163
title: BAG Barcelona

description: BAG Barcelona has a long tradition of accessing the ESRF. It is constituted by 10 groups that belong to the Institute of Molecular Biology Barcelona from the Spanish Research Council (IBMB-CSIC), the Institute for Research in Biomedicine (IRB), and the Research Institute from Hospital Santa Creu i Sant Pau (HSCSP-IR). The main subjects of research are protein/DBA complexes, molecular machines, compounds of viruses, molecular mechanisms of proteases, and other enzymes. Recently, a new group (E. Marcos) interested in de-novo designed protein scaffolds has joined the BAG. Our Scientific results strongly rely on the high-quality data and excellent performance and support of ESRF macromolecular crystallography beamlines.
DOI: 10.15151/esrf-es-1018398714
title: Structural Biology of Macromolecules and Macromolecular complexes from India

description: Structural biology research groups located in India constitute the INDIA-BAG and will utilize MX & SAXS to study different biological macromolecules. The non-proprietary agreement signed between ESRF and the Department of Biotechnology (DBT) enables studies that provide fundamental mechanistic insight regarding different biological processes. A brief description of over 50 research groups is provided in the global summary and a summary of their research contributions involving data collected at ESRF is provided in the 2 year BAG report. The ESRF-India partnership is supported by a single grant provided to the RCB by the DBT. Please note that a report listing no. of shifts utilized, details of users and the research output from these visits has to be sent to the DBT to obtain release of funds to pay ESRF membership dues. Consequently, all the structural biologists from India are grouped in a single BAG to enable monitoring of progress to collect the required statistics.
DOI: 10.15151/esrf-es-1018419442
title: The Israeli BAG

description: The BAG is quite large with 24 principal investigators covering almost all groups in Israel. The scientific topics are diverse and so different that depicting them in a short Abstract is extremely difficult. In this context BAG members are studying the parameters that govern protein assemblage, structural impacts of signaling processes in different cascades. There are several projects that are directed towards molecular recognition with implementation towards drug design. In addition, we still have the ribosome project and the design of unique antibiotics with specific functional interactions from the mycinamycins family and their resistance related mechanism compared with other macrolides and the photosystem and how it converts light into energy. Since Covid-19 is still a relevant topic as are other viral infections BAG members are and have been involved in the understanding of the infection process and the means to hinder it.
DOI: 10.15151/esrf-es-1026152185
title: Analysis of heart morphology in zebrafish mutants with targeted inactivation of the dio2 gene.

description: Genetic inactivation of the type II deiodinase gene (dio2) involved in thyroid signaling results in hypothyroidism and is associated with developmental defects in zebrafish. Observation of the heart region in this mutant contrasts strongly with that of a wild-type animal, suggesting a cardiac hypertrophy, a hypothesis supported by gene expression and immunological data. To better characterize the morphological differences induced in zebrafish organs, in particular the heart, our aim is to use X-ray phase contrast technology on whole zebrafish to image body with sufficient resolution to obtain a good view of the morphology of the heart in dio2 mutants compared to wild type sibling fishes. Our goal is 1) to observe the heart in an in situ context and measure the volume, shape and position of the heart in these animals, 2) to determine the precise topography (e.g. barycenter analysis) of the organs relative to each other to assess the effects of the mutation on the whole animal.
DOI: 10.15151/esrf-es-1025992627
title: Metal-Support Interactions on Iridium-based Catalysts for electrochemical Water Electrolysis probed by operando QuickXAS

description: Our goal is to provide deeper insights into the MSI of Ir NPs deposited on highly graphitized C and TiO2 during OER conditions and to correlate this information with the resulting catalytic activities. Operando electrochemical QuickXAS studies enable us to identify dynamic behavior of the nature of Ir oxide species and its electronic and geometric interactions (oxidation state, local environment) on two different support materials (MSI) as a function of the applied potential (before, during and after OER). In a two-step synthetic route, Ir NPs will be prepared by a colloidal approach and then immobilized either on the carbon or TiO2 support material. From XAS data recorded at Ir LII/LIII-edges, linear combination fit and EXAFS analysis will be carried out to understand the potential-resolved dynamic behavior of the chemical state of the Ir NPs (2-4 nm) and the nature of catalytically active oxide phase before, during and after the OER.
DOI: 10.15151/esrf-es-1025992995
title: Structure and dynamics of supercooled suspensions composed of fractal colloids

description: The glass transition is an out of equilibrium transition from the fluid to a disordered solid obtained at very high volume fractions. The glass transition is a dynamical arrested transition where colloids are trapped within the cage formed by their neighbors. The absence of rearrangement on long time scales leads to the solid behavior of the suspension. This transition has been well studied for hard-sphere colloids. Here, we aim to study this transition for fractal colloids, namely fumed silica dispersed in a good solvent. Preliminary results show that this system presents two originalities compared to hard-sphere colloidal systems. As the volume fraction is increased, the system viscosity diverges at low volume fraction, 30% and the colloids interpenetrate each other. Using SAXS and XPCS, we will systematically explore the structure and dynamics of fumed silica dispersion as a function of their volume fraction. We aim to unravel the role of interpenetration in glass forming liquids.
DOI: 10.15151/esrf-es-1025993716
title: Detailing the Mbar pressure-temperature phase diagram of BaZrO3 perovskite

description: Information on the structural stability of cubic ABO3 perovskite still lacks systematic detailing. BaZrO3 is a key material for several applications in broad fields due to its unusual properties; however, its structural stability under pressure still raises great doubts. This topic is considered a challenge, especially when related to the possible phase transition also at low temperature. The lack of detailed structural data along with the small amount of previous studies on the phase transitions of BaZrO3 makes this topic an interesting to be explored. Therefore, we propose here to study the phase transition under pressure Pm-3m to I4/mcm in BaZrO3 perovskite and to probe its pressure-temperature phase diagram, considering runs at low temperature (10-300K) and high-pressure (0-1.2 Mbar). This will provide information on crystal structure stability of BaZrO3 perovskite.
DOI: 10.15151/esrf-es-1036370999
title: 165 Ma Polychelidan lobster organs from La Voulte (France)

description: Polychelidan lobsters are decapod crustaceans that used to be abundant until Late Jurassic in many environments and are now restricted to deep-sea environment. Fossil specimens found in La Voulte-sur-Rhône (Callovian, 165 Ma) are often preserved in nodules and preserve organs that can be studied almost as well as on fresh species. The goal of this project is to study how their anatomy compares to their extant relatives and other crustaceans to assess the impact of 165 Ma of evolution and an environmental shift on organs morphology, as well as to provide new characters to place polychelidans within decapod crustaceans, their phylogenetic position still being a matter of debates.
DOI: 10.34740/kaggle/dsv/4939768
title: Malaysia General Election (PRU15) Dataset
DOI: 10.6084/m9.figshare.22003049.v1
title: Long Read Samples used for lasTEq

description: Long-read TE quantifications in 6 samples. Two HCT116 samples exist generated by our own lab and by SG-NEx study. <br> 1. long_read_TE_quantification_SG-NEx_K562: TE TPM counts in SG-NEx K562(sample id: ERR6053079) 2. long_read_TE_quantification_SG-NEx_HepG2: TE TPM counts in SG-NEx HepG2(sample id: ERR6053063) 3. long_read_TE_quantification_SG-NEx_A549: TE TPM counts in SG-NEx A549(sample id: ERR6053016) 4. long_read_TE_quantification_SG-NEx_MCF-7: TE TPM counts in SG-NEx MCF-7(sample id: ERR6053093) 5. long_read_TE_quantification_own_HCT116: TE TPM counts in own HCT116(GEO: ) 6. long_read_TE_quantification_SG-NEx_HCT116: TE TPM counts in SG-NEx HCT116(sample id: ERR6053040)
DOI: 10.5281/zenodo.7601907
title: 71e84b62-8ba8-4681-9ca8-a121e755f84a

description: These data sets are one of the workflows in manabuishii/yevis-getting-started.
DOI: 10.5281/zenodo.7601906
title: 71e84b62-8ba8-4681-9ca8-a121e755f84a

description: These data sets are one of the workflows in manabuishii/yevis-getting-started.
DOI: 10.5281/zenodo.7601883
title: A crowd clustering prediction and captioning technique for public health emergencies

description: Data set used to implement the project <strong>A crowd clustering prediction and captioning technique for public health emergencies crowd clustering prediction and captioning technique for public health emergencies</strong>
DOI: 10.5281/zenodo.7601882
title: A crowd clustering prediction and captioning technique for public health emergencies

description: Data set used to implement the project <strong>A crowd clustering prediction and captioning technique for public health emergencies crowd clustering prediction and captioning technique for public health emergencies</strong>
DOI: 10.34740/kaggle/dsv/4940204
title: IMDB Movies - All Categories
DOI: 10.6084/m9.figshare.22003922
title: The potential for synthesized invasive plant biochar with hydroxyapatite to mitigate allelopathy of Solidago canadensis

description: Few studies tried to explore the mitigation effect and underlying mechanisms of biochar and their complex for negative allelopathy from invasive plants, which may provide a new way in the invasive plant management. Herein, an invasive plant (<em>Solidago canadensis</em>)-derived biochar (IBC) and its composite with hydroxyapatite (HAP/IBC) were synthesized by high temperature pyrolysis, and characterized by SEM, EDS, XRD, FTIR, and XPS. Then, both the batch adsorption and pot experiments were conducted to compare the removal effects of kaempferol-3-<em>O</em>-<em>β</em>-<em>D</em>-glucoside (C21H20O11, kaempf), an allelochemical from <em>S. canadensis, </em>on IBC and HAP/IBC, respectively. HAP/IBC showed a stronger affinity for kaempf than IBC due to its higher specific surface area, more functional groups (P-O, P-O-P, PO43-), stronger crystallization [Ca3(PO4)2]. The maximum kaempf adsorption capacity on HAP/IBC was 7 times higher than on IBC (10.482 mg/g &gt; 1.709 mg/g) via π-π interactions, functional groups, and metal complexation. The kaempf adsorption process could be fitted best by both pseudo-second-order kinetic and Langmuir isotherm models. Furthermore, HAP/IBC addition into soils could enhance and even recover the germination rate and/or seedling growth of tomato inhibited by negative allelopathy from the invasive<em> S. canadensis</em>. These results indicate that the composite of HAP/IBC could more effectively mitigate the allelopathy from <em>S. canadensis</em> than IBC, which may be a potential efficient approach to control the invasive plant and improve soils.
DOI: 10.6084/m9.figshare.22003922.v1
title: The potential for synthesized invasive plant biochar with hydroxyapatite to mitigate allelopathy of Solidago canadensis

description: Few studies tried to explore the mitigation effect and underlying mechanisms of biochar and their complex for negative allelopathy from invasive plants, which may provide a new way in the invasive plant management. Herein, an invasive plant (<em>Solidago canadensis</em>)-derived biochar (IBC) and its composite with hydroxyapatite (HAP/IBC) were synthesized by high temperature pyrolysis, and characterized by SEM, EDS, XRD, FTIR, and XPS. Then, both the batch adsorption and pot experiments were conducted to compare the removal effects of kaempferol-3-<em>O</em>-<em>β</em>-<em>D</em>-glucoside (C21H20O11, kaempf), an allelochemical from <em>S. canadensis, </em>on IBC and HAP/IBC, respectively. HAP/IBC showed a stronger affinity for kaempf than IBC due to its higher specific surface area, more functional groups (P-O, P-O-P, PO43-), stronger crystallization [Ca3(PO4)2]. The maximum kaempf adsorption capacity on HAP/IBC was 7 times higher than on IBC (10.482 mg/g &gt; 1.709 mg/g) via π-π interactions, functional groups, and metal complexation. The kaempf adsorption process could be fitted best by both pseudo-second-order kinetic and Langmuir isotherm models. Furthermore, HAP/IBC addition into soils could enhance and even recover the germination rate and/or seedling growth of tomato inhibited by negative allelopathy from the invasive<em> S. canadensis</em>. These results indicate that the composite of HAP/IBC could more effectively mitigate the allelopathy from <em>S. canadensis</em> than IBC, which may be a potential efficient approach to control the invasive plant and improve soils.
DOI: 10.34740/kaggle/dsv/4940234
title: IMDB Movies - All Categories
DOI: 10.12751/g-node.thlt1j
title: Dataset - Marmoset retinal ganglion cell responses to saccadic grating shifts and supporting stimuli

description: Dataset accompanying the manuscript by Krüppel et al. 2023: Diversity of Ganglion Cell Responses to Saccade-like Image Shifts in the Primate Retina.
description: IsSupplementTo: Krüppel S, Khani MH, Karamanlis D, Erol YC, Zapp SJ, Mietsch M, Protti DA, Rozenblit F, Gollisch T (2023), Diversity of Ganglion Cell Responses to Saccade-like Image Shifts in the Primate Retina.
DOI: 10.25381/cput.21989078
title: ANAEROBIC TREATMENT OF TANNERY EFFLUENTS FOR RESOURCE RECOVERY IN A CIRCULAR BIOECONOMY

description: The datasets presented are for a number of inter-related studies that focussed on the optimisation of the anaerobic treatment of ostrich and bovine tannery wastewater for resource recovery to promote a circular bioeconomy and net positive tannery operations. The studies: https://doi.org/10.1016/j.jclepro.2023.135872; https://doi.org/10.1016/j.psep.2021.12.027; and https://doi.org/10.3390/en14092491 investigated the characteristics of different tannery effluent streams, their anaerobic mono/co-digestion, process kinetics, treatment in a biological integrated system (IBS) and suitability of the recovered resources for recycling and/or reuse. <br> The full-scale application of the IBS at a local medium-sized tannery treating 2258 m<sup>3</sup>/day of bovine tannery wastewater demonstrated the feasibility of producing a floating sulfur biofilm with 33% elementary sulfur (S<sup>0</sup>), 3420 m<sup>3 </sup>of CH<sub>4</sub>, and 31 tonnes of biofertiliser. The sale of recovered resources and potential savings from 72% reduction in electricity demand and 62% in sludge disposal had a potential revenue of US$5559. The integrated system has a payback period of about 5 years and an internal rate of return of about 18%.
DOI: 10.5281/zenodo.7600209
title: Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters, data part 5

description: Part 5 of data for the article Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters.
DOI: 10.5281/zenodo.7600208
title: Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters, data part 5

description: Part 5 of data for the article Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters.
DOI: 10.6084/m9.figshare.21973785
title: Supplement from Export of ice-nucleating particles from watersheds: results from the Amazon and Tocantins river plumes

description: Numerical data shown in Figure 2 of the manuscript.
DOI: 10.6084/m9.figshare.21973785.v2
title: Supplement from Export of ice-nucleating particles from watersheds: results from the Amazon and Tocantins river plumes

description: Numerical data shown in Figure 2 of the manuscript.
DOI: 10.6084/m9.figshare.21973785.v1
title: Supplement from Export of ice nucleating particles from watersheds: results from the Amazon and Tocantins River Plumes

description: Numerical data shown in Figure 2 of the manuscript.
DOI: 10.5517/ccdc.csd.cc2b9bqq
title: CCDC 2153933: Experimental Crystal Structure Determination

description: Related Article: Ya-Jie Wang, Xu-Yang Wang, Hong Xu, Wei-Wei Ren, Rui Pang, Li Yang, Wen-Chao Tong, Qian-You Wang, Shuang-Quan Zang|2022|Chem.Eng.Journal|455|140587|doi:10.1016/j.cej.2022.140587
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2b9brr
title: CCDC 2153934: Experimental Crystal Structure Determination

description: Related Article: Ya-Jie Wang, Xu-Yang Wang, Hong Xu, Wei-Wei Ren, Rui Pang, Li Yang, Wen-Chao Tong, Qian-You Wang, Shuang-Quan Zang|2022|Chem.Eng.Journal|455|140587|doi:10.1016/j.cej.2022.140587
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2b9c01
title: CCDC 2153942: Experimental Crystal Structure Determination

description: Related Article: Ya-Jie Wang, Xu-Yang Wang, Hong Xu, Wei-Wei Ren, Rui Pang, Li Yang, Wen-Chao Tong, Qian-You Wang, Shuang-Quan Zang|2022|Chem.Eng.Journal|455|140587|doi:10.1016/j.cej.2022.140587
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bzn55
title: CCDC 2174407: Experimental Crystal Structure Determination

description: Related Article: M. Carmen Torralba, Carla I. Nieto, Rosa M. Claramunt, José Elguero|2023|Cryst.Growth Des.|23|1145|doi:10.1021/acs.cgd.2c01271
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.