Find research datasets worth reusing

opencc-by-4.0Apr 2024View details →

DATASET OF "Evolutionary Pathways to Thin-Coated Seeds in Crops: Insights from Allometric Scaling" by Milla et al.

<table> <tbody> <tr> <td>This database is composed of four spreadsheets:</td> </tr> <tr> <td>data</td> <td>Unpublished data used in the manuscript. Data that was published earlier is not included to avoid duplicates, but reference to their source is given in the other two spreadsheets</td> </tr> <tr> <td>species_in_sources</td> <td>Key to the sources of data for the project, for each species, and each observation within species</td> </tr> <tr> <td>list_of_sources</td> <td>Key to sources plus full reference of each key</td> </tr> <tr> <td>list_accessions</td> <td>list of accessions identities for each crop and domestication status</td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td>Meaning of colums in each spreadsheet</td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td>data:</td> <td> </td> </tr> <tr> <td>id_data</td> <td>id of row in this spreadsheet</td> </tr> <tr> <td>id_sources</td> <td>id of row in the species_in_sources spreadsheet</td> </tr> <tr> <td>species</td> <td>Botanical name of the species</td> </tr> <tr> <td>family</td> <td>Family adscription of the species</td> </tr> <tr> <td>genus</td> <td>genus</td> </tr> <tr> <td>species_epith</td> <td>species epithet</td> </tr> <tr> <td>cultivar_subsp_type</td> <td>for domesticated genotypes, cultivar, subspecies, or type</td> </tr> <tr> <td>accesion_id</td> <td>accesion id from seedbanks</td> </tr> <tr> <td>crop</td> <td>for domesticated genotypes and their direct wild progenitors: common name of the crop</td> </tr> <tr> <td>dom_status_c_w</td> <td>whether an entry comes from a domesticated or a wild genotype or species</td> </tr> <tr> <td>dom_status_im_lr_wp_wnowp</td> <td>domestication status of the entry, either an improved cultivar of a crop (im), a landrace (lr), a wild progenitor (wp) or a wild species not closely related to any crop (wnowp)</td> </tr> <tr> <td>seed_mass_mg</td> <td>seed mass, in mg</td> </tr> <tr> <td>seed_coat_mass_mg</td> <td>seed coat mass, in mg</td> </tr> <tr> <td>kernel_mass_mg</td> <td>kernel mass, in mg</td> </tr> <tr> <td>key_to_source</td> <td>code to link with the references listed in the list_of_sources spreadsheet</td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td>species_in_sources:</td> <td> </td> </tr> <tr> <td>id_sources</td> <td>see above for data spreadsheet</td> </tr> <tr> <td>species</td> <td>see above for data spreadsheet</td> </tr> <tr> <td>family</td> <td>see above for data spreadsheet</td> </tr> <tr> <td>genus</td> <td>see above for data spreadsheet</td> </tr> <tr> <td>species_epith</td> <td>see above for data spreadsheet</td> </tr> <tr> <td>cultivar_subsp_type</td> <td>see above for data spreadsheet</td> </tr> <tr> <td>accesion_id</td> <td>see above for data spreadsheet</td> </tr> <tr> <td>crop</td> <td>see above for data spreadsheet</td> </tr> <tr> <td>dom_status_c_w</td> <td>see above for data spreadsheet</td> </tr> <tr> <td>dom_status_im_lr_wp_wnowp</td> <td>see above for data spreadsheet</td> </tr> <tr> <td>key_to_source</td> <td>see above for data spreadsheet</td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td>list_of_sources:</td> <td> </td> </tr> <tr> <td>key_to_source</td> <td>code to link with the references</td> </tr> <tr> <td>source</td> <td>full reference</td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td>list_accessions:</td> <td>see "data" sheet</td> </tr> </tbody> </table>

opencc-by-4.0Apr 2024View details →

Supplement Tables of Recombinant Klotho protein protects pulmonary alveolar epithelial cells against sepsis-induced apoptosis by inhibiting the Bcl-2/Bax/caspase-3 pathway

This is Supplement Tables of Recombinant Klotho protein protects pulmonary  alveolar epithelial cells against sepsis-induced apoptosis  by inhibiting the Bcl-2/Bax/caspase-3 pathway.

opencc-zeroApr 2024View details →

Data from: Major group-B enterovirus populations deleted in the noncoding 5' region of genomic RNA modulate activation of the type I interferon pathway in cardiomyocytes and induce myocarditis

Major 5'-terminally deleted (5'TD) RNA forms of group-B coxsackievirus (CVB-5'TD) has been associated with myocarditis in both mice and humans. Although it is known that interferon-β (IFN-β) signaling is critical for an efficient innate immune response against CVB-induced myocarditis, the link between CVB-5'TD RNA forms and type I IFN signaling in cardiomyocytes remains to be explored. In a mouse model of CVB3/28-induced myocarditis, major early-emerging forms of CVB-5'TD RNA have been characterized as replicative viral populations that impair IFN-β production in the heart. Synthetic CVB3/28 RNA forms mimicking each of these major 5'TD virus populations were transfected in mice and have been shown to modulate innate immune responses in the heart and to induce myocarditis in mice. Remarkably, transfection of synthetic viral RNA with deletions in the secondary structures of the 5'-terminal CVB3 RNA domain I, modifying stem-loops "b", "c" or "d", were found to impair IFN-β production in human cardiomyocytes. In addition, the activation of innate immune response by Poly(I:C), was found to restore IFN-β production and to reduce the burden of CVB-5'TD RNA-forms in cardiac tissues, thereby reducing the mortality rate of infected mice. Overall, our results indicate that major early-emerging CVB3 populations deleted in the domain I of genomic RNA, in the 5' noncoding region, modulate the activation of the type I IFN pathway in cardiomyocytes and induce myocarditis in mice. These findings shed new light on the role of replicative CVB-5'TD RNA forms as key pathophysiological factors in CVB-induced human myocarditis.

OEtiBCh structures at 10 different levels of theory, full reaction pathways

The archive contains full reaction pathway of MeCl reduction by OEtiBCh at 10 different levels of theory as xyz coordinates.

Hydrogen Modelling Pathways - Training Case

This training material includes the baseline energy system model and the techno-economic data needed to create a simplified hydrogen supply-demand chain using MUIO (Modelling User Interface for OSeMOSYS).

opencc-by-4.0Dec 2024View details →

DNA large fragment deleting by compact, sequence-motif-free and specific TaqTth-hpRNA assisted with the microhomology-mediated end joining pathway

A DNA editing tool TaqTth-hpRNA was developed in this study, composed of a compact recombinant TaqTth nuclease (832 aa) and a simple hairpin-RNA guiding probe (hpRNA). In vitro biochemical studies showed the TaqTth-hpRNA efficiently cleaves artificially synthesized ssDNA without stringent sequence motif like PAM. It can also cleave the genomic DNA of E. coli with ~80% efficiency. The TaqTth-hpRNA cleavage of genomic DNA in mammalian cells generated products with large fragment deletions mediated by the microhomology-mediated end joining (MMEJ) pathway. In addition, the cleavage was sensitive to mismatches in targeted regions, which was applied to specific damage of the APPlon mutation in Alzheimer’s disease without disrupting the APPwt locus. It is worth mentioning that the APPlon sequence has only one base difference from that of APPwt. The characteristics of small size, no PAM requirement, high specificity, and large deletion products make the TaqTth-hpRNA a potential therapeutic strategy for treating autosomal dominant disorders in the future.

opencc-by-4.0Sep 2024View details →

Multiple extracellular polymeric substances pathways expressed by Accumulibacter and the flanking community during aerobic granule formation and after influent modification

Aerobic granular sludge is a biological wastewater treatment process in which a microbial community forms a granular biofilm. The role of Candidatus Accumulibacter in the production of a biofilm matrix, composed of extracellular polymeric substances, was studied in a sequencing batch reactor enriched with polyphosphate-accumulating organisms. The metabolisms of the microbial populations were investigated using de novo metatranscriptomics analysis. Finally, the effect of decreasing the influent phosphate concentration on the granule stability and microbial activity was investigated. A few weeks after the reactor start-up, the microbial community was dominated by Accumulibacter with up to nine species active in parallel. However, the most active species differed according to sampling time. Decreasing drastically the influent phosphate concentration led to a dominance of the glycogen-accumulating organism Propionivibrio, with some Accumulibacter species still abundant. De novo metatranscriptomics analysis indicated a high diversity of potential extracellular substances produced mainly by Accumulibacter, Azonexus, Candidatus Contendobacter, and Propionivibrio. Moreover, the results suggest that Azonexus, Contendobacter and Propionivibrio recycle the neuraminic acids produced by Accumulibacter. Changes in the microbial community did not cause the granules to disintegrate, indicating that a Propionivibrio-dominated community can maintain stable granules.

opencc-by-4.0Feb 2024View details →

A data repository for the study of Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes

This repository contains data associated with the study: "Alpha-synuclein Aggregates Trigger Anti-Viral Immune Pathways and RNA Editing in Human Astrocytes" Published as a bioRxiv preprint: <a href="https://doi.org/10.1101/2024.02.26.582055">DOI: 10.1101/2024.02.26.582055</a>

Characterizing Metabolic Alterations in Early-stage chronic kidney disease (CKD) patients: A Pathway for Improved Diagnosis and Personalized Treatment.

The raw NMR data that I have uploaded contains the final concentration results that have been used for this study.

Additional data repository for the study of Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes

Zip file 1: astrocytes calcium data measured using Fura 2 Zip file2: astrocytes ROS measured using DHE (Dihydroethidium) Zip file 3: astrocytes cell death measured using Sytox green

opencc-by-4.0Aug 2023View details →

Developmental pyrethroid exposure disrupts molecular pathways for MAP kinase and circadian rhythms in mouse brain

Neurodevelopmental disorders (NDDs) are a category of pervasive disorders of the developing nervous system with few or no recognized biomarkers. A significant portion of the risk for NDDs, including attention deficit hyperactivity disorder (ADHD), is contributed by the environment, and exposure to pyrethroid pesticides during pregnancy has been identified as a potential risk factor for NDD in the unborn child. We recently showed that low-dose developmental exposure to the pyrethroid pesticide deltamethrin in mice causes male-biased changes to ADHD- and NDD-relevant behaviors as well as the striatal dopamine system. Here, we used an integrated multiomics approach to determine the broadest possible set of biological changes in the mouse brain caused by developmental pyrethroid exposure (DPE). Using a litter-based, split-sample design, we exposed mouse dams during pregnancy and lactation to deltamethrin (3 mg/kg or vehicle every 3 days) at a concentration well below the EPA-determined benchmark dose used for regulatory guidance. We raised male offspring to adulthood, euthanized them, and pulverized and divided whole brain samples for split-sample transcriptomics, kinomics and multiomics integration. Transcriptome analysis revealed alterations to multiple canonical clock genes, and kinome analysis revealed changes in the activity of multiple kinases involved in synaptic plasticity, including the mitogen-activated protein (MAP) kinase ERK. Multiomics integration revealed a dysregulated protein-protein interaction network containing primary clusters for MAP kinase cascades, regulation of apoptosis, and synaptic function. These results demonstrate that DPE causes a multi-modal biophenotype in the brain relevant to ADHD and identifies new potential mechanisms of action.

opencc-by-4.0Jul 2024View details →

LRRK2 mediates haloperidol-induced changes in striatal indirect pathway circuits

Haloperidol is used to manage psychotic symptoms in several neurological disorders through mechanisms that involve antagonism of dopamine D2Rs that are highly expressed in the striatum. Significant side effects of haloperidol, known as extrapyramidal symptoms, lead to motor deficits similar to those seen in Parkinson's disease and present a major challenge in clinical settings. The underlying molecular mechanisms responsible for these side effects remain poorly understood. Parkinson's disease associated LRRK2 kinase has a critical role in striatal physiology and a known link to D2R signaling. Here, we systematically explore convergent signaling of haloperidol and LRRK2 through pharmacological or genetic inhibition of LRRK2 kinase, as well as knock-in mouse models expressing pathogenic mutant LRRK2 with increased kinase activity. Behavioral assays show that LRRK2 kinase inhibition ameliorates haloperidol-induced motor changes in mice. A combination of electrophysiological and anatomical approaches reveals that LRRK2 kinase inhibition interferes with haloperidol-induced changes, specifically in striatal neurons of the indirect pathway. Proteomic studies and targeted intracellular pathway analyses demonstrate that haloperidol induces a similar pattern of intracellular signaling as increased LRRK2 kinase activity. Our study suggests that LRRK2 kinase plays a key role in striatal D2R signaling underlying the undesirable motor side effects of haloperidol. This work opens up new therapeutic avenues for dopamine-related disorders, such as psychosis, also furthering our understanding of Parkinson's disease pathophysiology.

opencc-by-2.0Nov 2021View details →

Advancing the Adverse Outcome Pathway (AOP) in Radiation Research: An International Horizon-Style Exercise

Over the past few decades, the chemical and ecotoxicology fields have been using the Adverse Outcome Pathway (AOP) framework to advance research and regulation. This framework offers an effective means to organize biological data into key events in the progression to an adverse outcome of interest to regulatory decision-making. The AOP framework is gaining traction within the radiation risk assessment community as the framework provides a linkage between experimentally derived biological data at different levels of biological organization with disease progression. It is envisioned that the AOP framework can strengthen the weight of evidence, decrease the uncertainty in radiation risk assessment, and enhance the understanding of radiation-induced effects at low doses and low dose rates. However, to advance the AOP framework within the field of radiation, uptake from the research community, policy makers, regulators and other stakeholders (e.g., industry) will be required. To explore the diversity of opinions and ideas on incorporating the AOP framework in research and regulation, an international horizon-style exercise is being undertaken by the Nuclear Energy Agency’s High-Level Group on Low Dose Research (HLG-LDR) Radiation/Chemical (Rad/Chem) AOP joint topical group.  This exercise will identify the most important open questions regarding the use of the AOP framework in radiation research and regulation. The vision of the topical group is to demonstrate AOPs as an essential tool to characterize the knowledge domain, define evidence gaps, and ultimately, inform research directions based on knowledge from both the chemical and the radiation research communities. The first phase of the horizon-style exercise, the candidate question solicitation, is now complete with input from around the globe. Currently, a dedicated steering committee is sorting the collected questions with the intent to identifying key areas where radiation AOPs can support and identify challenges to its implementation in regulatory decision-making.  Completion of this phase of the exercise will identify the most important questions for inclusion in an international survey. The survey will permit survey respondents to highlight priority questions specific to individual interests. The outcome of the international survey will guide future initiatives of the Rad/Chem AOP joint topical group, inform focused workshop topics, and ultimately facilitate the integration of the AOP framework into radiation risk assessment and radiation protection.

opencc-by-4.0Nov 2021View details →

Cost reductions in renewables can substantially erode the value of carbon capture and storage in mitigation pathways: supporting data

This provides supporting data for the paper, Cost reductions in renewables can substantially erode the value of carbon capture and storage in mitigation pathways, published in One Earth. The full paper can be accessed at the following DOI: https://doi.org/10.1016/j.oneear.2021.10.024, published on the 19th November 2021.

opencc-by-4.0Nov 2021View details →

Fluorescence lifetime imaging of pH along the secretory pathway

Many cellular processes are dependent on correct pH levels, and this is especially important for the secretory pathway. Defects in pH homeostasis in distinct organelles cause a wide range of diseases, including disorders of glycosylation and lysosomal storage diseases. Ratiometric imaging of the pH-sensitive mutant of green fluorescent protein (GFP), pHLuorin, has allowed for targeted pH measurements in various organelles, but the required sequential image acquisition is intrinsically slow and therefore the temporal resolution unsuitable to follow the rapid transit of cargo between organelles. We therefore applied fluorescence lifetime imaging microscopy (FLIM) to measure intraorganellar pH with just a single excitation wavelength. We first validated this method by confirming the pH in multiple compartments along the secretory pathway. Then, we analyze the dynamic pH changes within cells treated with Brefeldin A, a COPI coat inhibitor. Finally, we followed the pH changes of newly-synthesized molecules of the inflammatory cytokine tumor necrosis factor (TNF)-α while it was in transit from the endoplasmic reticulum via the Golgi to the plasma membrane. The toolbox we present here can be applied to measure intracellular pH with high spatial and temporal resolution, and can be used to assess organellar pH in disease models.

opencc-zeroDec 2021View details →

Task-induced modulations of neuronal activity along the auditory pathway

Sensory processing varies depending on behavioral context. Here, we ask how task-engagement modulates neurons in the auditory system. We train mice in a simple tone-detection task, and compare their neuronal activity during passive hearing and active listening. Electrophysiological extracellular recordings in the inferior colliculus, medial geniculate body, primary auditory cortex and anterior auditory field reveals widespread modulations across all regions and cortical layers, and in both putative regular and fast-spiking cortical neurons. Clustering analysis unveils ten distinct modulation patterns that can either enhance or suppress neuronal activity. Task-engagement changes the tone-onset response in most neurons. Such modulations first emerge in subcortical areas, ruling out cortical feedback as the only mechanism underlying subcortical modulations. Half the neurons additionally display late modulations associated with licking, arousal or reward. Our results reveal the presence of functionally distinct subclasses of neurons, differentially sensitive to specific task-related variables but anatomically distributed along the auditory pathway.

opencc-zeroJan 2022View details →

Grazing changes the direction of direct effect of shrubs on nematode communities but suppresses indirect effects through microbial pathways

It is well established that dominant plants shape belowground communities, which in turn influence ecosystem functioning. Similarly, herbivores affect belowground communities through physical disturbance and redistribution of organic inputs, but also through their interactions with the plants themselves. However, we know little about how grazing moderates effects of dominant plants on belowground organisms. We established a three-year removal experiment in a grazed and an ungrazed alpine meadow on the Qinghai-Tibet plateau to explore how grazing mediates the effects of the dominant shrub, Dosiphora fruticosa, on nematode communities. We applied structural equation modelling to assess how grazing moderates the effects of D. fruticosa on nematode communities both directly and indirectly via changes in soil physicochemical properties, root biomass and microbial communities. We found that 1) grazing changed the direction of the direct effect of shrub on nematode communities as indicated by the shift from a negative to a positive path coefficient; 2) shrub affected nematode richness mainly through microbial richness. Accordingly, nematode community composition was more closely related to microbial community composition in the ungrazed alpine meadow, while edaphic properties were stronger predictors of nematode community composition responses to shrubs in the grazed meadow; and 3) grazing suppressed the indirect effects of shrub on nematode communities via microbial communities. Our study shows that grazing plays an important role in regulating dominant plant's effects on belowground community composition and interactions in alpine meadows.

opencc-zeroJan 2022View details →

Data from: Neural pathways of autonomic reflexes in familial autonomic ganglionopathy

Objective: We determined the molecular basis of a new monogenetic recessive disorder that results in familial neurogenic orthostatic hypotension (nOH) with impaired sympathetic (SNS) and parasympathetic (PNS) activity. Methods: Two adult siblings from one family (I-4, I-5) and an another subject from a second family (II-3) presented with severe nOH, poor compensatory increase in heart rate, small non-reactive pupils and constipation. All three affected members had low norepinephrine levels and diffuse autonomic failure. Results: Whole exome sequencing of DNAs from subjects (I-4, I-5) showed compound heterozygosity for c.907_908delCT (p.L303Dfs*115) /c.688G>A (p.D230N) pathologic variants in the acetylcholine receptor, neuronal nicotinic, alpha 3 subunit (CHRNA3) gene. The II-3 from the second family was homozygous for the same frameshift(fs) variant (p.L303Dfs*115// p.L303Dfs*115). The CHRNA3 is a subunit of nicotinic acetylcholine receptors (nAChRs) that regulate SNS and PNS activity through fast synaptic transmission in the autonomic ganglia. The fs variant is obviously pathogenic and the p.D230N variant is predicted to be damaging (SIFT)/probably damaging (PolyPhen2). The p.D230N variant lies on the interface between CHRNA3 and other nAChR subunits based on structural modeling and is predicted to destabilize the nAChR pentameric complex. Conclusions: We report a novel genetic disease that affected three individuals from two unrelated families who presented with nOH and diffuse autonomic failure. These subjects had rare pathologic variants in the CHRNA3 gene that co-segregate with and are predicted to be the likely cause of their SNS and PNS failure.

opencc-by-4.0Jan 2022View details →

Datasets of the paper "Sustainable development pathways for Chinese cities: an assessment of the advanced inclusive wealth index"

这是《中国城市可持续发展路径:先进包容性财富指数评估 》一文的数据集和代码,该论文涵盖了中国 10 个城市用于计算包容性财富的所有指标的数据。“calculatorADJUST.m”是matlab代码,“data_city_2010.xlsx”和“data_city_2019.xlsx”分别是2010年和2019年的普惠财富数据。