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Dataset results
30 results for “quality loss”
The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens
<p>Nonsense-mediated mRNA decay (NMD) is important for both RNA quality control and gene regulation. NMD targets aberrant mRNA transcripts for decay and also directly influences the abundance of specific, non-aberrant transcripts in a wide range of eukaryotes. In animals, the PIK kinase, SMG1, plays an essential role in NMD, by phosphorylating the core NMD effector, UPF1. Despite being absent from the genome of the model plant, <em>Arabidopsis thaliana</em>, SMG1 is ubiquitous throughout the plant kingdom. Here we utilize RNA-seq to reveal the full range of processes involving <em>SMG1</em> in plants. In NMD-compromised, <em>smg1</em> mutant moss, 30% of multi-isoform genes produce NMD targeted transcript isoforms. Taking a machine learning approach, we show that an exon-exon junction downstream of a stop codon acts as the major feature to target transcripts to NMD and that retained intron isoforms are underrepresented among NMD targets. Furthermore, we show that <em>SMG1</em> is involved in other quality control pathways, affecting DNA repair and the unfolded protein response, in addition to its role in mRNA quality control. <em>smg1</em> plants have increased susceptibility to DNA damage, but increased tolerance to unfolded protein inducing agents. The involvement of SMG1 in RNA, DNA and protein quality control has major implications for the study of these processes in plants.</p>
Supporting data for the manuscript "Protein quality assessment with graph convolution guided by a loss function designed for high quality decoys"
<p>This dataset provides the predictions of the protein quality<br> assessment method Q_epsilon with respect to CASP13 and CASP14, as well<br> as a snapshot of the github repository providing the code for the<br> method.<br> The format of the file is as follows: The first column represents the<br> target and decoy names in the format <target name>_<decoy name>. The<br> second column is the true GDTTS, and the third column represents the<br> predicted GDTTS by Q_epsilon.</p>
Permafrost thaw causes large carbon loss in boreal peatlands while changes to peat quality are limited
<p>Rapid, ongoing permafrost thaw of peatlands in the discontinuous permafrost zone is exposing a globally significant store of soil carbon (C) to microbial processes. Mineralisation and release of this peat C to the atmosphere as greenhouse gases is a potentially important feedback to climate change. Here we investigated the effects of permafrost thaw on peat C at a peatland complex in western Canada. We collected 15 complete peat cores (between 2.7 abd 4.5 m deep) along four chronosequences, from elevated permafrost plateaus to saturated thermokarst bogs that thawed up to 600 years ago. The peat cores were analysed for peat C storage and peat quality, as indicated by decomposition proxies (FTIR and C/N ratios) and potential decomposability using a 200-day aerobic incubation. Our results suggest net C loss following thaw, with average total peat C stocks decreasing by ~19.3 +/- 7.2 kg C m<sup>-2</sup> over <600 years (~13% loss). Average post-thaw accumulation of new peat at the surface over the same period was ~13.1 +/- 2.5 kg C m<sup>-2</sup>. We estimate ~19% (+/- 5.8%) of deep peat (>40 cm below surface) C is lost following thaw (average 26 +/- 7.9 kg C m<sup>-2</sup> over <600 years). Our FTIR analysis shows peat below the thaw transition in thermokarst bogs is slightly more decomposed than peat of a similar type and age in permafrost plateaus, but we found no significant changes to the quality or lability of deeper peat across the chronosequences. Our incubation results also showed no increase in C mineralisation of deep peat across the chronosequences. While these limited changes in peat quality in deeper peat following permafrost thaw highlight uncertainty in the exact mechanisms and processes for C loss, our analysis of peat C stocks shows large C losses following permafrost thaw in peatlands in western Canada.</p>
Fitness, Hearing and Quality of Life in Older Adults With Hearing Loss. Walk, Talk and Listen for Your Life
ClinicalTrials.gov study NCT02662192. IPD Sharing: NO. Countries: 1. Publications: 2.
Permafrost thaw causes large carbon loss in boreal peatlands while changes to peat quality are limited
Open the record for dataset details and reuse information.
Stronger effect of litter quality than microorganisms on leaf and root litter C and N loss at different decomposition stages following a subtropical land use change
<p>Litter decomposition contributes largely to global carbon (C) and nitrogen (N) cycling, and it is strongly determined by litter quality and microbial community composition in ways that are poorly understood. Here, we conducted a 2-year field litter decomposition experiment by collecting leaf and root litter of crops (from cropland), shrubs (from shrubland), and wood (from woodland) and placing samples for decomposition in woodland soil in central China to investigate the effects of litter quality and microbial community composition on C and N loss of leaf and root litter of three species under different decomposition stages. Our results showed that the leaf litter C and N losses of shrubs were significantly higher than those of crops and wood, whereas the root litter C and N losses of crops were significantly higher than those of shrubs and wood. Generally, the leaf litter C and N losses of the three species were higher on average than those of fine root litter under the whole decomposition period. For the C loss of the three species, litter lignin and phosphorus as well as initial litter quality were predominant drivers of root litter decomposition, while litter lignin, cellulose, and hemicellulose concentrations were dominant for leaf litter decomposition. For N loss, litter stoichiometry and litter quality directly governed leaf and root litter N loss, and the initial litter quality largely regulated N loss at the late decomposition stage. Unexpectedly, the effect of microbial community composition on litter C and N loss was relatively weak and only exhibited an effect on litter C and N loss during the early stage of decomposition. Thus, our results revealed the huge disparity in C and N loss of plant species and litter types at different decomposition stages, which should be considered jointly when evaluating their roles in plant-soil feedbacks under global land use change.</p>
Effects of Lifestyle-modification Induced Weight Loss on Sexual and Urinary Function, and Quality of Life in Obese Men
ClinicalTrials.gov study NCT01554735. IPD Sharing: Not stated. Countries: 1. Publications: 1.
An Enhanced Protein (Dairy) Weight Loss Intervention for Dynapenic Obesity: Impact on Muscle Quality and Composition
ClinicalTrials.gov study NCT02437643. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Assessment of Advanced Glaucomatous Visual Field Loss and Its Impact on Visual Exploration, Activities of Daily Living (ADL) and Quality of Life (QoL)
ClinicalTrials.gov study NCT01372319. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Evaluation of Impact of Disease and Visual Disability on Quality of Life and Loss of Independence of Patients Living in France With Leber's Hereditary Optic Neuropathy (LHON) Through Qualitative and Q
ClinicalTrials.gov study NCT05555784. IPD Sharing: NO. Countries: 1. Publications: 5.
Effect of Sarcopenic Obesity on Weight Loss Outcomes and Quality of Life After Laparoscopic Sleeve Gastrectomy
ClinicalTrials.gov study NCT05826210. IPD Sharing: Not stated. Countries: 1. Publications: 16.
Assessment of Homonymous Visual Loss and Its Impact on Visual Exploration, Activities of Daily Living (ADL) and Quality of Life (QoL)
ClinicalTrials.gov study NCT01372332. IPD Sharing: Not stated. Countries: 1. Publications: 3.
High Quality Protein for Assisting With Weight Loss
ClinicalTrials.gov study NCT03085511. IPD Sharing: NO. Countries: 1. Publications: 3.
Mass loss and nutrient release during the decomposition of sixteen types of plant litter with contrasting quality under three precipitation regimes
Open the record for dataset details and reuse information.
Stronger effect of litter quality than microorganisms on leaf and root litter C and N loss at different decomposition stages following a subtropical land use change
Open the record for dataset details and reuse information.
Loss of function of chromatin remodeler OsCLSY4 led to RdDM-mediated mis-expression of endosperm-specific genes effecting grain qualities
GEO Series GSE290279. Oryza sativa. 17 samples. Type: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Loss of function of chromatin remodeler OsCLSY4 led to RdDM-mediated mis-expression of endosperm-specific genes effecting grain qualities [Bisulfite_sequencing]
GEO Series GSE289152. Oryza sativa. 1 samples. Type: Methylation profiling by high throughput sequencing.
Loss of function of chromatin remodeler OsCLSY4 led to RdDM-mediated mis-expression of endosperm-specific genes effecting grain qualities [RNA-Seq]
GEO Series GSE289150. Oryza sativa. 6 samples. Type: Expression profiling by high throughput sequencing.
Group Education & Lifestyle Modification's Impact on Weight Loss & Quality Life of Patients with OA
ClinicalTrials.gov study NCT04439019. IPD Sharing: NO. Countries: 1. Publications: 0.
The Effect of Telephone and Video Counseling on Weight Loss and Quality of Life
ClinicalTrials.gov study NCT05276544. IPD Sharing: NO. Countries: 1. Publications: 0.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.