cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/h8y867fkry.1
title: Early stages in Ab1-42 spontaneous aggregation: an unbiased dataset from coarse-grained molecular dynamics simulations.

description: Soluble oligomers of AB-1-42 are widely recognized as crucial targets for the design of inhibitors for potential therapeutic intervention against Alzheimer´s disease. However, the intrinsically disordered character of this polypeptide poses serious difficulties for the experimental determination of conserved structural motifs. Indeed, initial aggregation steps are extremely challenging for state-of-the-art experimental techniques. Although molecular dynamics simulations harbor the potential to capture such initial association events, unbiased exploration of the conformational landscape available to unstructured dimers implies a significant computational cost.
Here, we provide a dataset of configurations of Aβ1-42 dimers obtained by coarse-grained molecular dynamics (MD) simulations using the SIRAH force field. Trajectories are provided in standard gromacs format and can be easily converted to fully atomistic representations for visualization and analysis using molecular visualization/analysis software. The dataset contains MD trajectories of Aβ1-42  that undergo spontaneous and unbiased dimerization. We provide the time series of 25 replicates simulated for 10 microseconds under room conditions and physiological salt concentration. These multiple aggregation events provide valuable information not only on new binding pockets formed by the dimeric interface but also monomeric hot spots that can be targeted by small molecules on high-throughput docking campaigns. Alternatively, Aβ1-42 dimers could be used as aggregation seeds in studies of Aβ secondary nucleation.
DOI: 10.17632/h8y867fkry.2
title: Early stages in Ab1-42 spontaneous aggregation: an unbiased dataset from coarse-grained molecular dynamics simulations.

description: Soluble oligomers of Aβ-1-42 are widely recognized as crucial targets for the design of inhibitors for potential therapeutic intervention against Alzheimer´s disease. However, the intrinsically disordered character of this polypeptide poses serious difficulties for the experimental determination of conserved structural motifs. Indeed, initial aggregation steps are extremely challenging for state-of-the-art experimental techniques. Although molecular dynamics simulations harbor the potential to capture such initial association events, unbiased exploration of the conformational landscape available to unstructured dimers implies a significant computational cost.
Here, we provide a dataset of configurations of Aβ1-42 dimers obtained by coarse-grained molecular dynamics (MD) simulations using the SIRAH force field. Trajectories are provided in standard gromacs format and can be easily converted to fully atomistic representations for visualization and analysis using molecular visualization/analysis software. The dataset contains MD trajectories of Aβ1-42  that undergo spontaneous and unbiased dimerization. We provide the time series of 25 replicates simulated for 10 microseconds under room conditions and physiological salt concentration. These multiple aggregation events provide valuable information not only on new binding pockets formed by the dimeric interface but also monomeric hot spots that can be targeted by small molecules on high-throughput docking campaigns. Alternatively, Aβ1-42 dimers could be used as aggregation seeds in studies of Aβ secondary nucleation.
DOI: 10.6084/m9.figshare.22840976
title: Supplementary Material for: Differential unmet needs and experience of restorative dental care in trajectories of dental caries experience: a birth cohort study.

description: Dental caries is a chronic and cumulative disease but little has been reported on the continuity of the disease and its treatment through life. Group-based multi-trajectory modelling was used to identify developmental trajectories of untreated carious tooth surfaces (DS), restored tooth surfaces (FS), and teeth extracted due to caries (MT) from ages 9 to 45 years in a New Zealand longitudinal birth cohort, the Dunedin Multidisciplinary Health and Development Study (n=975). Associations between early life risk factors and trajectory group membership were examined by specifying the probability of group membership according to a multinomial logit model. Six trajectory groups were identified and labelled: ‘low caries rate’; ‘moderate caries rate, maintained’; ‘moderate caries rate, unmaintained’; ‘high caries rate, restored’; ‘high caries rate, tooth loss’; and ‘high caries rate, untreated caries’. The two moderate-caries-rate groups differed in count of FS. The three high-caries-rate groups differed in the relative proportion of accumulated DS, FS, and MT. Early childhood risk factors associated with less favourable trajectories included higher dmfs scores at age 5, lack of exposure to community water fluoridation during the first five years of life, lower childhood IQ, and low childhood socioeconomic status. Parent self-ratings of their own or their child’s oral health as ‘poor’ were associated with less favourable caries experience trajectories. Children who had clinical signs of dental caries together with a parent rating of child’s oral health as poor were more likely to follow a less favourable caries trajectory. Higher deciduous dentition caries experience at age 5 years was associated with less favourable caries trajectories, as were children whose parents gave ‘poor’ ratings of their own or their child’s oral health. These findings highlight the considerable intergenerational continuity in dental caries risk and experience from early childhood to midlife. Subjective measures of child oral health are informative and might aid as predictors of adult caries experience in cases where childhood dental clinical data were not available.
DOI: 10.6084/m9.figshare.22840976.v1
title: Supplementary Material for: Differential unmet needs and experience of restorative dental care in trajectories of dental caries experience: a birth cohort study.

description: Dental caries is a chronic and cumulative disease but little has been reported on the continuity of the disease and its treatment through life. Group-based multi-trajectory modelling was used to identify developmental trajectories of untreated carious tooth surfaces (DS), restored tooth surfaces (FS), and teeth extracted due to caries (MT) from ages 9 to 45 years in a New Zealand longitudinal birth cohort, the Dunedin Multidisciplinary Health and Development Study (n=975). Associations between early life risk factors and trajectory group membership were examined by specifying the probability of group membership according to a multinomial logit model. Six trajectory groups were identified and labelled: ‘low caries rate’; ‘moderate caries rate, maintained’; ‘moderate caries rate, unmaintained’; ‘high caries rate, restored’; ‘high caries rate, tooth loss’; and ‘high caries rate, untreated caries’. The two moderate-caries-rate groups differed in count of FS. The three high-caries-rate groups differed in the relative proportion of accumulated DS, FS, and MT. Early childhood risk factors associated with less favourable trajectories included higher dmfs scores at age 5, lack of exposure to community water fluoridation during the first five years of life, lower childhood IQ, and low childhood socioeconomic status. Parent self-ratings of their own or their child’s oral health as ‘poor’ were associated with less favourable caries experience trajectories. Children who had clinical signs of dental caries together with a parent rating of child’s oral health as poor were more likely to follow a less favourable caries trajectory. Higher deciduous dentition caries experience at age 5 years was associated with less favourable caries trajectories, as were children whose parents gave ‘poor’ ratings of their own or their child’s oral health. These findings highlight the considerable intergenerational continuity in dental caries risk and experience from early childhood to midlife. Subjective measures of child oral health are informative and might aid as predictors of adult caries experience in cases where childhood dental clinical data were not available.
DOI: 10.6084/m9.figshare.22841024
title: Supplementary Material for: Differential unmet needs and experience of restorative dental care in trajectories of dental caries experience: a birth cohort study.

description: Dental caries is a chronic and cumulative disease but little has been reported on the continuity of the disease and its treatment through life. Group-based multi-trajectory modelling was used to identify developmental trajectories of untreated carious tooth surfaces (DS), restored tooth surfaces (FS), and teeth extracted due to caries (MT) from ages 9 to 45 years in a New Zealand longitudinal birth cohort, the Dunedin Multidisciplinary Health and Development Study (n=975). Associations between early life risk factors and trajectory group membership were examined by specifying the probability of group membership according to a multinomial logit model. Six trajectory groups were identified and labelled: ‘low caries rate’; ‘moderate caries rate, maintained’; ‘moderate caries rate, unmaintained’; ‘high caries rate, restored’; ‘high caries rate, tooth loss’; and ‘high caries rate, untreated caries’. The two moderate-caries-rate groups differed in count of FS. The three high-caries-rate groups differed in the relative proportion of accumulated DS, FS, and MT. Early childhood risk factors associated with less favourable trajectories included higher dmfs scores at age 5, lack of exposure to community water fluoridation during the first five years of life, lower childhood IQ, and low childhood socioeconomic status. Parent self-ratings of their own or their child’s oral health as ‘poor’ were associated with less favourable caries experience trajectories. Children who had clinical signs of dental caries together with a parent rating of child’s oral health as poor were more likely to follow a less favourable caries trajectory. Higher deciduous dentition caries experience at age 5 years was associated with less favourable caries trajectories, as were children whose parents gave ‘poor’ ratings of their own or their child’s oral health. These findings highlight the considerable intergenerational continuity in dental caries risk and experience from early childhood to midlife. Subjective measures of child oral health are informative and might aid as predictors of adult caries experience in cases where childhood dental clinical data were not available.
DOI: 10.6084/m9.figshare.22841024.v1
title: Supplementary Material for: Differential unmet needs and experience of restorative dental care in trajectories of dental caries experience: a birth cohort study.

description: Dental caries is a chronic and cumulative disease but little has been reported on the continuity of the disease and its treatment through life. Group-based multi-trajectory modelling was used to identify developmental trajectories of untreated carious tooth surfaces (DS), restored tooth surfaces (FS), and teeth extracted due to caries (MT) from ages 9 to 45 years in a New Zealand longitudinal birth cohort, the Dunedin Multidisciplinary Health and Development Study (n=975). Associations between early life risk factors and trajectory group membership were examined by specifying the probability of group membership according to a multinomial logit model. Six trajectory groups were identified and labelled: ‘low caries rate’; ‘moderate caries rate, maintained’; ‘moderate caries rate, unmaintained’; ‘high caries rate, restored’; ‘high caries rate, tooth loss’; and ‘high caries rate, untreated caries’. The two moderate-caries-rate groups differed in count of FS. The three high-caries-rate groups differed in the relative proportion of accumulated DS, FS, and MT. Early childhood risk factors associated with less favourable trajectories included higher dmfs scores at age 5, lack of exposure to community water fluoridation during the first five years of life, lower childhood IQ, and low childhood socioeconomic status. Parent self-ratings of their own or their child’s oral health as ‘poor’ were associated with less favourable caries experience trajectories. Children who had clinical signs of dental caries together with a parent rating of child’s oral health as poor were more likely to follow a less favourable caries trajectory. Higher deciduous dentition caries experience at age 5 years was associated with less favourable caries trajectories, as were children whose parents gave ‘poor’ ratings of their own or their child’s oral health. These findings highlight the considerable intergenerational continuity in dental caries risk and experience from early childhood to midlife. Subjective measures of child oral health are informative and might aid as predictors of adult caries experience in cases where childhood dental clinical data were not available.
DOI: 10.6084/m9.figshare.22841117
title: validation_dataset_disgust

description: This data was the pre-registered subjective disgust validation dataset, details see Gan et al. 2023 BioRxiv.
DOI: 10.34740/kaggle/dsv/5698598
title: BIOINFOXF_datasets
DOI: 10.34740/kaggle/dsv/5698617
title: BIOINFOXF_datasets
DOI: 10.6084/m9.figshare.21543333
title: Syphilis_Genomic_Epi_England_2022-23

description: Genomic and epidemiological analysis of Treponema pallidum genomes from UK (English) patients, 2012-2018.
DOI: 10.6073/pasta/e87910d2313e269c3e2124b85dc03011
title: The dual invasion of Amur honeysuckle and Emerald Ash Borer Shifts Fungal Driven Decomposition in Midwestern Forests

description: Midwestern forests are currently impacted by two prominent invaders, the Emerald Ash Borer (EAB), Agrilus planipennis and Amur honeysuckle, Lonicera maackii. The loss of ash (Fraxinus spp.) trees due to EAB invasion can further facilitate honeysuckle invasion, driving changes in the composition of forest leaf litter. To evaluate the extent to which these changes alter ecosystem function, we conducted litter bag and culture-based decomposition experiments using leaf litter from sugar maple (Acer saccharum), oak (Quercus spp.), black ash (Fraxinus nigra), green ash (Fraxinus pennsylvanica), spicebush (Lindera benzoin), and Amur honeysuckle (Lonicera maackii). To further understand the mechanism driving differences in decay rates, we inoculated six species of decomposing fungi separately onto both single species and multispecies (half honeysuckle and half native species) leaf litter and measured decomposition rate, fungal growth and enzymatic activity in laboratory-based cultures. Honeysuckle leaf litter decomposed faster, had increased fungal growth, and had higher activity for carbon degrading enzymes compared to native species leaf litter. Furthermore, multispecies mixtures followed the same patterns as honeysuckle, suggesting that the addition of honeysuckle to leaf litter will accelerate ecosystem functions related to carbon breakdown. Consequently, forests that experience the invasion of honeysuckle and EAB induced loss of ash are likely to have faster decomposition, potentially resulting in an influx of available nutrients.
DOI: 10.5517/ccdc.csd.cc2460ds
title: CCDC 1971984: Experimental Crystal Structure Determination

description: Related Article: Daijiao Zhuang, Shixuan Jiang, Youzhi Wang, Xiajun Wang, Siwei Shen, Rulong Yan|2023|Org.Lett.|25|3007|doi:10.1021/acs.orglett.3c00790
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.cc24c3zm
title: CCDC 1976900: Experimental Crystal Structure Determination

description: Related Article: Ming Bao, Xiongda Xie, Jingjing Huang, Michael P. Doyle, Zhi Ren, Haibo Yue, Xinfang Xu|2023|Chem.-Eur.J.|29|e202300140|doi:10.1002/chem.202300140
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.cc28rwrp
title: CCDC 2108333: Experimental Crystal Structure Determination

description: Related Article: Walter Kuba, Barbara Sohr, Patrick Keppel, Dennis Svatunek, Viktoria Humhal, Berthold Stöger, Marion Goldeck, Jonathan C. T. Carlson, Hannes Mikula|2023|Chem.-Eur.J.|29|e202203069|doi:10.1002/chem.202203069
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.cc296msy
title: CCDC 2121540: Experimental Crystal Structure Determination

description: Related Article: Guo-Zhang Huang, Peng-Xu Lu, Meng-Meng Zeng, Wei Deng, Kai-Ping Xie, Zhen-Xing Wang, Jun-Liang Liu, Yan-Cong Chen, Ming-Liang Tong|2023|J.Mater.Chem.C|11|5611|doi:10.1039/D3TC00343D
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: 10.34740/kaggle/dsv/5698664
title: BIOINFOXF_datasets
DOI: 10.6084/m9.figshare.22836635
title: Supplemental Material: Bulldoze and rebuild: Modifying cratonic lithosphere via removal and replacement induced by continental subduction

description: We provide the results of anisotropy of magnetic susceptibility, zircon U-Pb dating results and Hf isotopic composition for the Yunshan unit in the Jiaodong Peninsula, east of North China craton (NCC). According to these data, we recognized the presence of crustal material from South China block (SCB) in the NCC. Combined with previous geological and geophysical data, our new data show that the NCC lithosphere has been “bulldozed and rebuilt” by the subducted SCB in the Middle-Late Triassic. This model has further implications for craton modification or destruction related to continental collision.
DOI: 10.6084/m9.figshare.22836635.v1
title: Supplemental Material: Bulldoze and rebuild: Modifying cratonic lithosphere via removal and replacement induced by continental subduction

description: We provide the results of anisotropy of magnetic susceptibility, zircon U-Pb dating results and Hf isotopic composition for the Yunshan unit in the Jiaodong Peninsula, east of North China craton (NCC). According to these data, we recognized the presence of crustal material from South China block (SCB) in the NCC. Combined with previous geological and geophysical data, our new data show that the NCC lithosphere has been “bulldozed and rebuilt” by the subducted SCB in the Middle-Late Triassic. This model has further implications for craton modification or destruction related to continental collision.
DOI: 10.25430/researchdata.cab.unipd.it.00000891
title: Structural Evolution of a Crustal-Scale Seismogenic Fault in a Magmatic Arc: The Bolfin Fault Zone (Atacama Fault System)

description: How major crustal-scale seismogenic faults nucleate and evolve in crystalline basements represents a long-standing, but poorly understood, issue in structural geology and fault mechanics. Here, we address the spatio-temporal evolution of the Bolfin Fault Zone (BFZ), a &gt;40-km-long exhumed seismogenic splay fault of the 1000-km-long strike-slip Atacama Fault System. The BFZ has a sinuous fault trace across the Mesozoic magmatic arc of the Coastal Cordillera (Northern Chile) and formed during the oblique subduction of the Aluk plate beneath the South American plate. Seismic faulting occurred at 5–7 km depth and ≤ 300°C in a fluid-rich environment as recorded by extensive propylitic alteration and epidote-chlorite veining. Ancient (125–118 Ma) seismicity is attested by the widespread occurrence of pseudotachylytes. Field geologic surveys indicate nucleation of the BFZ on precursory geometrical anisotropies represented by magmatic foliation of plutons (northern and central segments) and andesitic dyke swarms (southern segment) within the heterogeneous crystalline basement. Seismic faulting exploited the segments of precursory anisotropies that were optimal to favorably oriented with respect to the long-term far-stress field associated with the oblique ancient subduction. The large-scale sinuous geometry of the BFZ resulted from the hard linkage of these anisotropy-pinned segments during fault growth.
DOI: 10.18716/dch/a.00000014
title: Prominence related structures in Austronesian symmetrical voice languages

description: This project investigates whether there is evidence for widely attested prominence relations relevant at the syntax-semantics interface (e.g. agentive arguments tend to be more prominent than non-agentive ones) in western Austronesian symmetrical voice languages. These languages challenge the concept of prominence because they exhibit two (or more) equally marked constructions to express transitive eventualities. The project looks at the discourse factors governing these voice alternations, at linear ordering constraints, and at the alternation between the dynamic and the potentive paradigm.
DOI: 10.5281/zenodo.7473190
title: A Gas Chromatography – Ion Mobility Spectrometry dataset for colorectal cancer diagnostic of 56 urine samples corresponding to 29 subjects.

description: This is a .zip file which includes a dataset. The dataset includes 2 folders: one called Urines and a second one called Analytical Standards. The Urines folder includes a set of urine measures done with a GC-IMS FlavourSpec® instrument from G.A.S. Dortmund (Dortmund, Germany) in format .mea. The samples were incubated for 15 minutes at 60ºC, the flow rate of the drift gas was 200 ml/min, and the carrier gas was 11 ml/min. Both the dirft and carrier gas were Nitrogen 5.0. Finally, the GC and IMS temperature were set at 60ºC and the measurement time lasted 33 minutes. Besides the urines, there are included a set of measures performed everyday as analytical standard control of the equipment. There is also one csv file that contains all the samples annotations. Finally, it is also included one excel file with the drift and retention times of some reference’s peaks present in all the samples. The annotation file includes information about the subject: Class: Negativo/CRC. It is the diagnostic (Control/CRC) Sex: M/F (Male/Female) Volume: volume in mL of urine analyzed Fasting: Yes/No/NA. It indicates if the subject was in fasting conditions when the urine was collected Age: age of the subject Kg: Weight in kilograms cm: Height in centimeters BMI: Body Mass Index Smooking: Smoking habit Diseases: other diseases The analytical standard folder includes the measures of a mixture of 6 ketones (2-butanone, 2-pentanone, 2-hexanone, 2-heptanone, 2-ocatanone and 2-nonanone). This mixture is used as quality control of the equipment and are measured every day in the same conditions as the urines. The study protocol was approved by the Ethics Committee of Hospital de Reus (study approval no. 074/2018).
DOI: 10.17638/datacat.liverpool.ac.uk/2236
title: Epidemiological connectivity between humans and animals across an urban landscape
DOI: 10.34740/kaggle/dsv/5698772
title: COVID Vaccination in World (updated daily)