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opencc-by-3.0-usDec 2022View details →

Structural diversity as a reliable and novel predictor for ecosystem productivity

Data and code for LaRue et al. (2023) Structural diversity as a reliable and novel  predictor for ecosystem productivity. Frontiers in Ecology and the Environment: Accepted.

opencc-by-4.0Dec 2021View details →

Integrative genetic analyses illuminates ALS heritability and identifies novel risk genes

Amyotrophic lateral sclerosis (ALS), the major adult onset motor neuron disease, has substantial heritability, in part shared with fronto-temporal dementia (FTD). We show here that ALS heritability is enriched in splicing variants and in binding sites of 6 RNA binding proteins including TDP-43 and FUS. A discovery and replication transcriptome wide association study (TWAS) identified 6 loci associated with ALS, 3 in known ALS loci (C9ORF72, SCFD1, SLC9A8) and 3 novel loci including NUP50 encoding for the nucleopore basket protein NUP50 In our meta-analysis of TWAS cohorts, NUP50 common variant was associated with ALS and to decreased expression of NUP50 in the central nervous system. Independently, we further show association of rare variants in NUP50 with ALS risk (P = 3.71.10-03; odds ratio  = 3.29; 95%CI, 1.37 to 7.87) in a cohort of 9,390 ALS/FTD patients and 4,594 controls. Cells from one patient carrying a NUP50 frameshift mutation displayed a decreased levels of NUP50. Loss of NUP50 leads to neuronal death in cultured neurons, and motor defects in Drosophila and zebrafish models. Thus, our study identifies alterations in splicing in neurons as a critical pathogenic process in ALS, uncovers several new loci potentially contributing to ALS, and provides genetic evidence linking nuclear pore defects to ALS.

opencc-by-4.0Dec 2022View details →

A Novel Curated Scholarly Graph Connecting Textual and Data Publications

This dataset contains an open and curated scholarly graph we built as a training and test set for data discovery, data connection, author disambiguation, and link prediction tasks. This graph represents the European Marine Science community included in the OpenAIRE Graph. The nodes of the graph we release represent publications, datasets, software, and authors respectively; edges interconnecting research products always have the publication as source, and the dataset/software as target. In addition, edges are labeled with semantics that outline whether the publication is referencing, citing, documenting, or supplementing the related outcome. To curate and enrich nodes metadata and edges semantics, we relied on the information extracted from the PDF of the publications and the datasets/software webpages respectively. We curated the authors so to remove duplicated nodes representing the same person.  The resource we release counts 4,047 publications, 5,488 datasets, 22 software, 21,561 authors, and 9,692 edges connect publications to datasets/software. This graph is in the curated_MES folder. We provide this resource as: <ol> <li>a property graph: we provide the dump that can be imported in neo4j</li> <li>5 jsonl files containing publications, datasets, software, authors, and relationships respectively. Each line of a jsonl file contains a JSON object representing a node and contains the metadata of that node (or a relationship).</li> </ol> We provide two additional scholarly graphs: <ul> <li>The curated MES graph with the removed edges. During the curation we removed some edges since they were labeled with an inconsistent or imprecise semantics. This graph includes the same nodes and edges as the previous one, and, in addition, it contains the edges removed during the curation pipeline; these edges are marked as Removed. This graph is in the curated_MES_with_removed_semantics folder.  </li> <li>The original MES community of OpenAIRE. It represents the MES community extracted from the OpenAIRE Research Graph. This graph has not been curated, and the metadata and semantics are those of the OpenAIRE Research Graph. This graph is in the original_MES_community folder.</li> </ul>

opencc-by-4.0Dec 2022View details →

Dataset related to the article "LITHOTRIPSY OF CALCIFIED AORTIC VALVE LEAFLETS BY A NOVEL ULTRASOUND TRANSCATHETER-BASED DEVICE"

This record contains raw data related to the article “LITHOTRIPSY OF CALCIFIED AORTIC VALVE LEAFLETS BY A NOVEL ULTRASOUND TRANSCATHETER-BASED DEVICE” The increasing incidence of calcific aortic valve disease necessitates the elaboration of new strategies to retard the progression of the pathology with an innovative solution. While the increasing diffusion of the transcatheter aortic valve replacements (TAVRs) allows a mini-invasive approach to aortic valve substitution as an alternative to conventional surgical replacement (SAVR) in an always larger patient population, TAVR implantation still has contraindications for young patients. In addition, it is liable to undergo calcification with the consequent necessity of re-intervention with conventional valve surgery or repeated implantation in the so-called TAVR-in-TAVR procedure. Inspired by applications for non-cardiac pathologies or for vascular decalcification before stenting (i.e., coronary lithotripsy), in the present study, we show the feasibility of human valve treatment with a mini-invasive device tailored to deliver shockwaves to the calcific leaflets. We provide evidence of efficient calcium deposit ruptures in human calcified leaflets treated ex vivo and the safety of the treatment in pigs. The use of this device could be helpful to perform shockwaves valvuloplasty as an option to retard TAVR/SAVR, or as a pretreatment to facilitate prosthesis implantation and minimize the occurrence of paravalvular leak.

opencc-by-4.0Jan 2023View details →

A Novel Architecture for room temperature microwave optomechanical experiments

The dataset contains cavity optomechanical measurements of the Si3N4 membrane at room temperature. These datasets correspond to different techniques to extract single photon coupling rate  g0. The files with the name starting with fig_2 are about the characterization of the microwave cavity (S21) and Si3N4 membrane (noise spectrum). The file names with initials as fig_3 is contains data of noise spectrum when Si3N4 membrane is driven by white noise using piezoelectric transducer. It is the file names with initials as fig_4 that are about the optically induced transparency/absorption, while the file names with initials as fig_5 are about the driven nonlinear Si3N4 membrane.

opencc-by-4.0Nov 2022View details →

YbiB: a Novel Interactor of the GTPase ObgE

This dataset contains the raw data that lie at the basis of the results discussed in the paper entitled "YbiB: a Novel Interactor of the GTPase ObgE".  The accompanying README.txt file describes the specific data that can be found in the different raw data files.

Experimental heatwaves and warming induce distinctive community responses through their interactions with a novel species

This repository provides the data for the manuscript "experimental heatwaves and warming induce distinctive community responses through their interactions with a novel species" As the climate warms, species shift their distributions at different rates, re-organising ecological communities. The resulting novel interactions will shape the local community’s response to ongoing climate change. The distinction between extreme events and a rising mean temperature in driving range expansion of the neighbouring species has not been examined empirically, nor has the resulting ecological impact propagating through multi-trophic networks been addressed. In this study, we recreated a high-elevation host-parasitoid community comprising Drosophila species and their associated parasitoid species from the Australian Wet Tropics, and subjected them to either heatwaves or warming in combination with the introduction of a low-elevation-specific Drosophila species. This dataset contains three groups of measurements: 1. Single-generation reproductive success of each species at various sampling times (about every 3 weeks) throughout the initiation and maintenance of the community. 2. Population size of each species before the community was terminated. 3. One-day reproductive success of each species before, during, and after the last heatwave event.

dataset related to article "A NOVEL BIO-INSPIRED STRATEGY TO PREVENT AMYLOIDOGENESIS AND SYNAPTIC DAMAGE IN ALZHEIMER'S DISEASE"

Levels of Abeta40, Abeta42 and aggregated Abeta results obtained from plaque count densitometric analysis of ctf and synaptic proteins levels of antibodies against Abeta42 and Abeta1-6

datset related to article "THE NOVEL I213S MUTATION IN PSEN1 GENE IS LOCATED IN A HOTSPOT CODON ASSOCIATED WITH FAMILIAL EARLY-ONSET ALZHEIMER'S DISEASE"

Electropherogram of the proband psen1 exon 7 ngs analysis of causal and risk genes associated to dementia

Dataset related to article: "Congenital insensitivity to pain a novel mutation affecting a U12-type intron causes multiple aberrant splicing of SCN9A"

raw data related to article reported at title

A novel R744 multi-temperature cycle for refrigerated transport applications with low-temperature ejector: experimental ejector characterization and thermodynamic cycle assessment - Ejector experimental data

Experimental data obtained during the characterization of a R744 ejector in low-temperature suction operating conditions. The complete description of the experimental setup and of the R744 cooling unit concept designed to employ the tested ejector, as well as the discussion on the experimental data, are available in: Fabris, F.,  Pardiñas, Á. Á., Marinetti, S., Rossetti, A., Hafner, A., Minetto, S. (2023). A novel R744 multi-temperature cycle for refrigerated transport applications with low-temperature ejector: experimental ejector characterization and thermodynamic cycle assessment. International Journal of Refrigeration.

Fig. 2. A in Novel data support validity of Phoxinus chrysoprasius (Pallas, 1814) (Actinopterygii, Leuciscidae)

Fig. 2. A haplotype network based on cytochrome oxidase I (CO1) fragment using 112 previously published GenBank sequences and representing 20 genetic clades numbered as in Palandačić et al. (2017, 2020), of which 12 are considered valid species including P. chrysoprasius (Pallas, 1814) and Kuban' Phoxinus (an available species name not known). The lines carry the number of mutational steps (shown in red).

Fig. 1 in Novel data support validity of Phoxinus chrysoprasius (Pallas, 1814) (Actinopterygii, Leuciscidae)

Fig. 1. Map of the localities of Phoxinus Agassiz, 1835 in river drainages of the northern and north-eastern coasts of the Black Sea and the Caspian Sea based on numerous published sources (references available in Supp. file 1) and public museum collections (Museum of Zoology, National Museum of Natural History, Kyiv, Ukraine; Natural History Museum, Vienna, Austria; Zoological Research Museum Alexander Koenig, Bonn, Germany). Coloured circles and numbers correspond to genetically examined individuals of clades specified in Palandačić et al. (2017, 2020): yellow circle = P. marsilii, Clade 9; black circles = 'Baltic Phoxinus', Clade 17; grey circles = P. colchicus, Clade 18; purple circle = 'Kuban Phoxinus', Clade 19; pink circle = 'Crimean Phoxinus', Clade 20.

Fig. 4 in Novel data support validity of Phoxinus chrysoprasius (Pallas, 1814) (Actinopterygii, Leuciscidae)

Fig. 4. DFA based on 11 counts, two coded characters, and 55 relative measurements, for males and females separately (A) and for females only (B). Numbers of samples or clades as in Fig. 3. Abbreviations: f = females; m = males. DFA statistics values: A. Wilks' Lambda 0.00000, approx. F (156.189) = 11.390, p <0.0000. B. Wilks' Lambda 0.00002, approx. F (48.48) = 36.279, p <0.0000 (perfect discrimination).

Fig. 3 in Novel data support validity of Phoxinus chrysoprasius (Pallas, 1814) (Actinopterygii, Leuciscidae)

Fig. 3. DFA based on 11 counts and 2 coded characters as in Supp. file 4. Clade 5 = 5a, Danubian tributaries in Bulgaria (Nishava, Beli Vit, and Palakaria samples and P. csikii Hankó, 1922 from type locality). Clade 14 = non-Danubian rivers of the Black Sea coast in Bulgaria (14a, Izvorska, Veleka, Karaagach and Kamchiya) and Turkey (14b, Gönen and Sapanca). Clade 9 = P. marsilii Heckel, 1836. Clade 20 = Crimea, Salhir. DFA statistics values: Wilks' Lambda 0.16694, approx. F (45.1345) = 14.709, p <0.0000 (perfect discrimination).

Fig. 5. A in Novel data support validity of Phoxinus chrysoprasius (Pallas, 1814) (Actinopterygii, Leuciscidae)

Fig. 5. A. Neotype of Phoxinus chrysoprasius (Pallas, 1814), ♂ (ZFMK 93640-59). B. ♀ (ZFMK 93640- 59), 87.2 mm SL, same locality and date as the neotype.

opencc-zeroMar 2023View details →

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Genetic variation in mouse islet Ca2+ oscillations reveals novel regulators of islet function

Insufficient insulin secretion to meet metabolic demand results in diabetes. The intracellular flux of Ca2+ into β-cells triggers insulin release. Since genetics strongly influences variation in islet secretory responses, we surveyed islet Ca2+ dynamics in eight genetically diverse mouse strains. We found high strain variation in response to four conditions: 1) 8 mM glucose; 2) 8 mM glucose plus amino acids; 3) 8 mM glucose, amino acids, plus 10nM GIP; and 4) 2 mM glucose. These stimuli interrogate β-cell function, α-cell to β-cell signaling, and incretin responses. We then correlated components of the Ca2+ waveforms to islet protein abundances in the same strains used for the Ca2+ measurements. To focus on proteins relevant to human islet function, we identified human orthologues of correlated mouse proteins that are proximal to glycemic-associated SNPs in human GWAS. Several orthologues have previously been shown to regulate insulin secretion (e.g. ABCC8, PCSK1, and GCK), supporting our mouse-to-human integration as a discovery platform. By integrating these data, we nominated novel regulators of islet Ca2+ oscillations and insulin secretion with potential relevance for human islet function. We also provide a resource for identifying appropriate mouse strains in which to study these regulators.

opencc-by-4.0Jul 2021View details →

FIGURE 3 in Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.

FIGURE 3. Summary of nuclear–plastid phylogenomic incongruence based on PACo analysis across different taxonomic levels between clades of Epidendroideae based on nuclear and plastid ML trees. Conflicting positions between orchid (A) genera, (B) subtribes, and (C) tribes. Association of terminals found to be incongruent and placed with robust support in nuclear and plastid trees are highlighted in bold and red. Pie diagrams at nodes represent quartet support values. Likelihood bootstrap support (LBS) percentages at nodes are 100 unless shown otherwise (LBS <85 are highlighted in red). Photos: Representatives of three strongly conflicting groups in the orchid family (Epidendreae: Pleurothallis perryi.; Catasetinae: Cycnoches guttulatum with its potential orchid bee pollinator (Euglossa aff. cybelia); Angraecinae: Angraecum rutenbergianum). Photo credits: O. A. Pérez-Escobar.

opencc-by-4.0Jul 2021View details →

FIGURE 1 in Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.

FIGURE 1. Split network of Orchidaceae computed from uncorrected p-distances and a supermatrix of 292 low-copy nuclear genes and 75 species. Splits are color-coded by orchid subfamily (see legend). Box on left: Taxonomic representativeness of orchid genera, tribes and subtribes sampled by nuclear gene datasets in this study. (Inset): Iconic representatives of different tribes in the orchid family (Vanilloideae: Vanilla inodora, Cleistes rosea; Cypripedioideae: Paphiopediluminsigne; Orchidoideae-Cranichideae:Ludisia discolor, Disa uniflora; Orchidoideae-Orchideae:Disa uniflora; Malaxidae: Dendrobium nobile; Epidendreae: Pleurothallis perryi and Scaphosepalum verrucosum; Cymbidieae: Zygopetalum crinitum and Maxillaria pereziana; Vandeae: Angraecum rutenbergianum). Photo credits: O. A. Pérez-Escobar and Sebastian Vieira.