Find research datasets worth reusing

opencc-by-4.0Nov 2023View details →

Fine-scale Quantification of Absorbed Photosynthetically Active Radiation (APAR) in Plantation Forests with 3D Radiative Transfer Modeling and LiDAR Data

In recent years, LiDAR technology has gained widespread attention for its ability to provide precise 3D vertical structural data for various objects, particularly forests. In our dataset, we utilized LiDAR data to reconstruct intricately detailed three-dimensional representations of specific larch forest landscapes. These detailed forest structural models enable us to drive three-dimensional radiative transfer models, analyze the radiation budget of the forest canopy, and gain valuable insights into fine-scale forest management strategies. This is the research work we conducted by combining the aforementioned 3D forest scenes with the 3D RTM LESS. If you use our data, please cite our article. You can access our publication via DOI: 10.34133/plantphenomics.0166. We welcome researchers interested in a wide range of fields, such as vegetation ecological applications, to communicate with us by combining 3D vegetation modeling.

opencc-by-4.0Dec 2023View details →

Critical Domains for NACC2-NTRK2 Fusion Protein Activation

Critical Domains for NACC2-NTRK2 Fusion Protein Activation.  Authors: Wei Yang, April N. Meyer, Zian Jiang, Xuan Jiang, and Daniel J. Donoghue. This dataset contains annotated raw images of immunoblots to accompany article, as well as files showing quantitation presented in various figures. Abstract: Neurotrophic receptor tyrosine kinases (NTRKs) belong to the receptor tyrosine kinase (RTK) family. NTRKs are responsible for the activation of multiple downstream signaling pathways that regulate cell growth, proliferation, differentiation, and apoptosis. NTRK-associated mutations often result in oncogenesis and lead to aberrant activation of downstream signaling pathways including MAPK, JAK/STAT, and PLCγ. This study characterizes the NACC2-NTRK2 oncogenic fusion protein that leads to pilocytic astrocytoma and pediatric glioblastoma. This fusion joins the BTB domain (Broad-complex, Tramtrack, and Bric-a-brac) domain of NACC2 (Nucleus Accumbens-associated protein 2) with the transmembrane helix and tyrosine kinase domain of NTRK2. We focus on identifying critical domains for the biological activity of the fusion protein. Mutations were introduced in the charged pocket of the BTB domain or in the monomer core, based on a structural comparison of the NACC2 BTB domain with that of PLZF, another BTB-containing protein. Mutations were also introduced into the NTRK2-derived portion to allow comparison of two different breakpoints that have been clinically reported. We show that activation of the NTRK2 kinase domain relies on multimerization of the BTB domain in NACC2-NTRK2. Mutations which disrupt BTB-mediated multimerization significantly reduce kinase activity and downstream signaling. The ability of these mutations to abrogate biological activity suggests that BTB domain inhibition could be a potential treatment for NACC2-NTRK2-induced cancers. Removal of the transmembrane helix leads to enhanced stability of the fusion protein and increased activity of the NACC2-NTRK2 fusion, suggesting a mechanism for the oncogenicity of a distinct NACC2-NTRK2 isoform observed in pediatric glioblastoma.

opencc-by-4.0Sep 2023View details →

Hop Flower Supercritical Carbon Dioxide Extracts Coupled with Carriers with Solubilizing Properties—Antioxidant Activity and Neuroprotective Potential

Article, Dataset for article   <h1>Hop Flower Supercritical Carbon Dioxide Extracts Coupled with Carriers with Solubilizing Properties—Antioxidant Activity and Neuroprotective Potential</h1>   <h2>Abstract</h2> <div>Lupuli flos shows many biological activities like antioxidant potential, extended by a targeted effect on selected enzymes, the expression of which is characteristic for neurodegenerative changes within the nervous system. Lupuli flos extracts (LFE) were prepared by supercritical carbon dioxide (scCO2) extraction with various pressure and temperature parameters. The antioxidant, chelating activity, and inhibition of acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and tyrosinase by extracts were studied. The extracts containing ethanol were used as references. The most beneficial neuroprotective effects were shown by the extract obtained under 5000 PSI and 50 °C. The neuroprotective effect of active compounds is limited by poor solubility; therefore, carriers with solubilizing properties were used for scCO2 extracts, combined with post-scCO2 ethanol extract. Hydroxypropyl-β-cyclodextrin (HP-β-CD) in combination with magnesium aluminometasilicate (Neusilin US2) in the ratio 1:0.5 improved dissolution profiles to the greatest extent, while the apparent permeability coefficients of these compounds determined using the parallel artificial membrane permeability assay in the gastrointestinal (PAMPA GIT) model were increased the most by only HP-β-CD.</div> <div> <div> <div>Keywords: </div> <a href="https://www.mdpi.com/search?q=neuroprotection">neuroprotection</a>; <a href="https://www.mdpi.com/search?q=hop+strobile">hop strobile</a>; <a href="https://www.mdpi.com/search?q=inhibition+of+enzymes">inhibition of enzymes</a>; <a href="https://www.mdpi.com/search?q=xanthohumol">xanthohumol</a></div> </div>

opencc-by-4.0Jul 2023View details →

Determining Antioxidant Activity of Cannabis Leaves Extracts from Different Varieties—Unveiling Nature's Treasure Trove

Article, Dataset for article   <h1>Determining Antioxidant Activity of Cannabis Leaves Extracts from Different Varieties—Unveiling Nature’s Treasure Trove</h1>   <h2>Abstract</h2> <div>Cannabis leaves contain a diverse range of antioxidants, including cannabinoids, flavonoids, and phenolic compounds, which offer significant health benefits. Utilising cannabis leaves as a source of antioxidants presents a cost-effective approach because they are typically discarded during the cultivation of cannabis plants for their seeds or fibres. Therefore, this presented study aimed to assess the antioxidant activity of the leaves of selected hemp cultivars, such as Białobrzeska, Tygra, and Henola, based on the results obtained with the 2,2′-Azino-bis(3-ethylbenzthiazoline-6-sulfonic acid, ferric reducing antioxidant power, cupric reducing antioxidant capacity, and 2,2-Diphenyl-1-picrylhydrazyl assays. The cannabinoid profile was analysed for the antioxidant activity to the contents of cannabidiol (CBD), cannabigerol (CBG), Δ9-tetrahydrocannabinol (Δ9-THC), and cannabichromene (CBC), determined based on chromatographic assays. The following variables were tested: the impact of various extractants (methanol, ethanol, and isopropanol), and their mixtures (50:50, v/v, as well as extraction methods (maceration and ultra-sound-assisted extraction) significant in obtaining hemp extracts characterised by different cannabinoid profiles. The results revealed that the selection of extractant and extraction conditions significantly influenced the active compounds’ extraction efficiency and antioxidant activity. Among the tested conditions, ultrasound-assisted extraction using methanol yielded the highest cannabinoid profile: CBD = 184.51 ± 5.61; CBG = 6.10 ± 0.21; Δ9-THC = 0.51 ± 0.01; and CBC = 0.71 ± 0.01 μg/g antioxidant potential in Białobrzeska leaf extracts.</div> <div> <div> <div>Keywords: </div> <a href="https://www.mdpi.com/search?q=Cannabis+sativa">Cannabis sativa</a>; <a href="https://www.mdpi.com/search?q=antioxidant">antioxidant</a>; <a href="https://www.mdpi.com/search?q=cannabidiol">cannabidiol</a>; <a href="https://www.mdpi.com/search?q=cannabigerol">cannabigerol</a>; <a href="https://www.mdpi.com/search?q=oxidative+stress">oxidative stress</a></div> </div>

Dataset (Russian companies' activity information)

Indicators characterizing the activities of Russian companies and macroeconomic indicators related to the effectiveness of working capital management

DESIGN, SYNTHESIS AND STUDY OF BIOLOGICAL ACTIVITY OF PEPTIDES WITH NEUROPROTECTIVE PROPERTIES

The main purpose of this project is to search for novel compounds that will protect neurons against oxidative stress (6-hydroxydopamine, 6-OHDA) and glucocorticoids (corticosterone, CORT) in a human neuroblastoma cell line (SH-SY5Y) and elucidate the mechanism by which attenuated the physiological changes induced by these neurotoxins. We will explore whether this protective role of tested compounds will be involved also in the regulation of apoptosis, maintaining oxidoreductive balance, and stabilization of mitochondrial membrane potential. Furthermore, the involvement of the BDNF/TrkB-ERK-CREB/mTOR signalling pathway in neuronal survival will be examined.

opencc-by-4.0Dec 2021View details →

Fig. 1 Screening flow, testing 1600 FDA compounds against S in Assessment of FDA-approved drugs against StrongyloideS rAtti in vitro and in vivo to identify potentially active drugs against strongyloidiasis

Fig. 1 Screening flow, testing 1600 FDA compounds against S. ratti

opencc-zeroApr 2024View details →

Data from: Seamounts generate efficient active transport loops to nourish the twilight ecosystem

Seamounts are ecological oases nurturing abundant fisheries resources and epibenthic megafauna in the vast oligotrophic ocean. Despite their significance, the formation mechanisms underlying these seamount ecological oases remain uncertain. To shed light on this phenomenon, this study conducted interdisciplinary in-situ observations focusing on a shallow seamount in the oligotrophic ocean. In this dataset, we report high-resolution hydrographic and biochemical observational data from both sectional observations and time-series stations observations.

Towards intelligent living facades: On electrical activity of ordinary moss \emph{Brachythecium rutabulum}

Electrical recordings of of ordinary moss \emph{Brachythecium rutabulum}. Data for the paper Towards intelligent living facades: On electrical activity of ordinary moss \emph{Brachythecium rutabulum}

opencc-zeroApr 2024View details →

Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity

Isocitrate Dehydrogenase 1 (IDH1) is the most commonly mutated metabolic gene across human cancers. Mutant IDH1 (mIDH1) generates the oncometabolite (R)-2-hydroxyglutarate, disrupting enzymes involved in epigenetics and other processes. A hallmark of IDH1-mutant solid tumors is T cell exclusion, whereas mIDH1 inhibition in preclinical models restores anti-tumor immunity. Here, we define a cell-autonomous mechanism of mIDH1-driven immune evasion. IDH1-mutant solid tumors show striking, selective hypermethylation and silencing of the cytoplasmic dsDNA sensor, CGAS, compromising innate immune signaling. mIDH1 inhibition restores DNA demethylation, derepressing CGAS and transposable element (TE) subclasses. dsDNA produced by TE-reverse transcriptase activates cGAS, triggering viral mimicry and stimulating anti-tumor immunity. Thus, we demonstrate that mIDH1 epigenetically suppresses innate immunity and link endogenous reverse transcriptase activity to the mechanism of action of an FDA-approved oncology drug.

opencc-zeroApr 2024View details →

Data for: Multimodal convergence in the pedunculopontine tegmental nucleus: motor, sensory, and theta-frequency inputs influence the activity of single neurons

The pedunculopontine tegmental nucleus of the brainstem (PPTg) has extensive interconnections and neuronal-behavioural correlates. It is implicated in movement control and sensorimotor integration. We investigated whether single neuron activity in freely moving rats is correlated with components of skilled forelimb movement and whether individual neurons respond to both motor and sensory events. We found that individual PPTg neurons showed changes in firing rate at different times during the reach. This type of temporally specific modulation is like activity seen elsewhere in voluntary movement control circuits, such as the motor cortex, and suggests that PPTg neural activity is related to different specific events occurring during the reach. In particular, many neuronal modulations were time-locked to the end of the extension phase of the reach, when fine distal movements related to food grasping occur, indicating strong engagement of PPTg in this phase of skilled individual forelimb movements. In addition, some neurons showed brief periods of apparent oscillatory firing in the theta range at specific phases of the reach-to-grasp movement. When movement-related neurons were tested with tone stimuli, many also responded to this auditory input, allowing for sensorimotor integration at the cellular level. Together, these data extend the concept of the PPTg as an integrative structure in the generation of complex movements, by showing that this function extends to the highly coordinated control of the forelimb during skilled reach to grasp movement and that sensory and motor-related information converges on a single neuron, allowing for direct integration at the cellular level.

Supplementary File 8; The full data set derived from formal quantitative surveys of land cover types and activities of humans, livestock and wildlife (Section 2.3) that were used for the analyses described in sections 2.4, 2.5 and 2.7

Open the record for dataset details and reuse information.

Evolution of retinal degeneration and prediction of disease activity in relapsing and progressive multiple sclerosis

Retinal optical coherence tomography has been identified as biomarker for disease progression in relapsing-remitting multiple sclerosis (RRMS), while the dynamics of retinal atrophy in progressive MS are less clear. We investigated retinal layer thickness changes in RRMS, primary and secondary progressive MS (PPMS, SPMS), and their prognostic value for disease activity. Here, we analyzed 2651 OCT measurements of 195 RRMS, 87 SPMS, 125 PPMS patients, and 98 controls from five German MS centers after quality control. Peripapillary and macular retinal nerve fiber layer (pRNFL, mRNFL) thickness predicted future relapses in all MS and RRMS patients while mRNFL and ganglion cell-inner plexiform layer (GCIPL) thickness predicted future MRI activity in RRMS (mRNFL, GCIPL) and PPMS (GCIPL). mRNFL thickness predicted future disability progression in PPMS. However, thickness change rates were subject to considerable amounts of measurement variability. In conclusion, retinal degeneration, most pronounced of pRNFL and GCIPL, occurs in all subtypes. Using the current state of technology, longitudinal assessments of retinal thickness may not be suitable on a single patient level.

Pylake example: Active calibration bead-bead coupling data

A dataset acquired on a LUMICKS C-Trap used to demonstrate coupling between beads in active calibration. The dataset contains dual trap data with 2.1 micron beads captured in each trap. Files starting with bead1, bead2, bead3 are different bead pairs, while bead4, bead4b and bead4c contain technical replicates for a fourth bead.

The role of Cornulin (CRNN) in the progression of cutaneous squamous cell carcinoma involving AKT activation in SCL-1

Cutaneous squamous cell carcinoma (cSCC) is a prevalent type of skin cancer that has been on the rise in recent times, particularly among older individuals. Cornulin (CRNN) is increasingly recognized as an oncogene involved in developing various types of tumors. However, the precise contribution to cSCC remains unclear. Our study observed a significant increase in CRNN expression in cSCC samples compared to healthy skin. CRNN expression in the SCL-1 cell line derived from cSCC was reduced, leading to a halt in cell growth during the transition from the G1 phase to the S phase. This reduction inhibits cell division, promotes cell death, and decreases cell invasion and migration. CRNN overexpression has been found to enhance cell growth and prevent cells from undergoing natural cell death, and the cancer-promoting effects of CRNN are linked to AKT activation. Using a mouse xenograft model, we demonstrated that the inhibition of CRNN led to a decline in cSCC tumor growth in a living organism, providing evidence of CRNN’s involvement in cSCC occurrence and development. This study establishes a foundation for evaluating the effectiveness of CRNN in treating cSCC, enabling further investigation in this area

opencc-by-nc-nd-4.0May 2024View details →

Replication data for: "Effectiveness of iso-inertial resistance training on eccentric and concentric power, physical performance, and risk of falls in physically active middle-older adults: a randomised controlled trial"

Replication data for: "Effectiveness of iso-inertial resistance training on eccentric and concentric power, physical performance, and risk of falls in physically active middle-older adults: a randomised controlled trial" This folder contains 4 files: 1) Database that contains the values for concentric and eccentric power measured with both iso-inertial and gravitational systems (Dataset_power.xlsx) 2) Database that contains the values for the Short Physical Performance Battery (SPPB) and Get Up and Go (GUG) test (Dataset_SPPB_GUG.xlsx) 3) R Software script used to analyse file 1 (Iso-inertial analysis_power.R)   4) R Software script used to analyse file 2 (Iso-inertial analysis_SPPB_GUG.R)

opencc-zeroMay 2024View details →

Data from: Scaling of leaf area with biomass in trees reconsidered: Constant metabolically active sapwood volume per unit leaf area with height growth

Hypoallometric (slope<1) scaling between metabolic rate and body mass is often regarded as near-universal across organisms. However, there are compelling reasons to question hypoallometric scaling in woody plants, where metabolic rate=leaf area. This leaf area must provide carbon to the metabolically active sapwood volume (VMASW). Within populations of a species, variants in which VMASW increases per unit leaf area with height growth (e.g. ⅔ or ¾ scaling) would have proportionally less carbon for growth and reproduction as they grow taller. Therefore, selection should favor individuals in which, as they grow taller, leaf area scales isometrically with shoot VMASW (slope=1). Using tetrazolium staining, we measured total VMASW and total leaf area (LAtot) across 22 individuals of Ricinus communis and confirmed that leaf area scales isometrically with VMASW, and that VMASW is much smaller than total sapwood volume. With the potential of the LAtot-VMASW relationship to shape factors as diverse as the crown area-stem diameter relationship, conduit diameter scaling, reproductive output, and drought-induced mortality, our work suggests that the notion that sapwood increases per unit leaf area with height growth requires revision.

Dataset for "Formal Single Atom Editing of the Glycosylated Natural Product Fidaxomicin Improves Acid Stability and Retains Antibiotic Activity"

ZIP File: Characterisation data (such as e.g. NMR, IR, MS spectra) NMR raw data, .mnova files DP4+ data (final conformer coordinate files, result tables) DFT simulation data (coordinate files, results table) PDF file: Supporting information for Formal Single Atom Editing of the Glycosylated Natural Product Fidaxomicin Improves Acid Stability and Retains Antibiotic Activity

Automatic State Interaction for Large Localized Active Spaces for Multimetallic Systmes

The localized active space self consistent field (LASSCF) method factorizes a complete active space (CAS) wave function into an antisymmetrized product of localized active space wave function fragments. Correlation between fragments is then reintroduced through LAS state interaction (LASSI), in which the Hamiltonian is diagonalized in a model space of LAS states. However, the optimal procedure for defining the LAS fragments and LASSI model space is unknown. We here present an automated framework to explore systematically convergent sets of model spaces, which we call LASSI[$r$,$\nmax$]. This method requires the user to select only $r$, the number of electron hops from one fragment to another and $\nmax$, the number of fragment basis functions per Hilbert space, which converges to CASCI in the limit of $r,\nmax\to\infty$. Numerical tests of this method on the tri-metal complexes [Fe(III)Al(III)Fe(II)($\mu_3$-O)]$^{6+}$ and [Fe(III)$_2$Fe(II)($\mu_3$-O)]$^{6+}$ show efficient convergence to the CASCI limit with 4-10 orders of magnitude fewer states.

Global Urban Activity Changes from COVID-19 Physical Distancing Restrictions Dataset: TRacking Anomalous COVID-19 induced changEs in NightTime Lights (TRACE-NTL)

We use satellite-derived (NASA Black Marble) nighttime lights to identify, quantify, and map daily changes in human activity that are atypical for each urban area, globally, from the beginning of the pandemic until two years after its onset. The dataset TRACE-NTL consists of global daily urban disruption and recovery metrics as a response to COVID-19. TRACE-NTL: ├───ancillary ├───data └───metrics     ├───disruption     │   ├───change_segment     │   ├───city_uncertainty     │   ├───daily_change     │   └───daily_qa_flags     └───recovery <a title="Dataset description" href="https://github.com/srijac/covid-19_Nightlights">https://github.com/srijac/covid-19_Nightlights</a> Accompanying paper: Accompanying paper: Chakraborty, S., Stokes, E.C. & Alexander, O. Global urban activity changes from COVID-19 physical distancing restrictions. Sci Data 12, 98 (2025). https://doi.org/10.1038/s41597-025-04398-x