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162 results for “truncating”
Truncated RNA-Seq ENCODE Dataset. Chr 22 only
<p>Truncated from ENCSR754WLW: https://www.encodeproject.org/experiments/ENCSR754WLW/</p>
ITC data set of nanobody (Nb33) binding to PaaR2 repressor truncates from Escherichia coli O157:H7
<p>Raw isothermal titration calorimetry data set from the published article De Bruyn, P., Prolič-Kalinšek, M., Vandervelde, A., Malfait, M., Sterckx, Y. G. J., Sobott, F., Hadži, S., Pardon, E., Steyaert, J., & Loris, R. (2021). Nanobody-aided crystallization of the transcription regulator PaaR2 from Escherichia coli O157:H7. <em>Acta crystallographica. Section F, Structural biology communications</em>, <em>77</em>(Pt 10), 374–384. https://doi.org/10.1107/S2053230X21009006.</p> <p>Titrations were measured at different temperatures (5-37 °C, indicated in the file name). Concentrations are listed in each itc data file. Buffer is 10 m<em>M</em> NaH<sub>2</sub>PO<sub>4</sub>, 10 m<em>M</em> Na<sub>2</sub>HPO<sub>4</sub>, 150 m<em>M</em> NaCl, 0.01% Triton X-100, pH 7.5.</p>
Exploring the Impact of Physiological C-Terminal Truncation on α-Synuclein Conformations to Unveil Mechanisms Regulating Pathological Aggregation
<p><span>Emerging evidence suggests that <a name="_Hlk179101300"></a>physiological C-terminal truncation of α-synuclein (αS) plays a critical role in regulating <a name="_Hlk178755669"></a>liquid–liquid phase separation and promoting amyloid aggregation, processes implicated in neurodegenerative diseases such as Parkinson’s disease (PD). However, the molecular mechanisms through which C-terminal truncation influences αS conformation and modulates its aggregation remain poorly understood. In this study, we investigated the impact of C-terminal truncation on αS conformational dynamics by comparing full-length αS<sub>1-140</sub> with truncated αS<sub>1-103</sub> monomers using atomistic discrete molecular dynamics (DMD) simulations. Our findings revealed that both αS<sub>1-140</sub> and αS<sub>1-103</sub> primarily adopted helical conformations around residues 7–32, while residues 35-95, located in the second half of the N-terminal and NAC domains, predominantly formed a dynamic β-sheet core. The C-terminus of αS<sub>1-140</sub> was largely unstructured and dynamically wrapped around the β-sheet core. While residues 1-95 exhibited similar secondary structure propensities in both αS<sub>1-140</sub> and αS<sub>1-103</sub>, the dynamic capping by the C-terminus in αS<sub>1-140</sub> slightly enhanced β-sheet formation around residues 35-95. In contrast, key aggregation-driving regions (residues 2-9, 36-42, 45-57, and 68-78) were dynamically shielded by the C-terminus in αS<sub>1-140</sub>, reducing their exposure and potentially preventing inter-peptide interactions that drive aggregation. C-terminal truncation, on the other hand, increased the exposed surface area of these aggregation-prone regions, thereby enhancing inter-peptide interactions, phase separation, and amyloid aggregation. Overall, our simulations provide valuable insights into the conformational effects of C-terminal truncation on αS and its role in promoting pathological aggregation.</span></p>
Outcome Following Truncation of Asparaginase
ClinicalTrials.gov study NCT03987542. IPD Sharing: NO. Countries: 1. Publications: 1.
Moderate Intensity Training in Patients With Truncating Genetic Variants in TTN.
ClinicalTrials.gov study NCT05180188. IPD Sharing: NO. Countries: 1. Publications: 35.
Data from: Diversification and convergence of aposematic phenotypes: truncated receptors and cellular arrangements mediate rapid evolution of coloration in harlequin poison frogs
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Data from: Dead before detection: addressing the effects of left truncation on survival estimation and ecological inference for neonates
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Age-specific habitat preference, carrying capacity, and landscape structure determine the response of population spatial variability to fishing-driven age truncation
<p>1. Understanding the mechanisms underlying spatial variability of exploited fish is critical for the sustainable management of fish stocks. Empirical studies suggest that size-selective fishing can elevate fish population spatial variability (i.e., more heterogeneous distribution) through age truncation, making the population less resilient to changing environment. However, species differ in how their spatial variability respond to age truncation and the underlying mechanisms remain unclear.</p> <p>2. We hypothesize that age-specific habitat preference, together with environmental carrying capacity and landscape structure, determines the response of population spatial variability to fishing-induced age truncation. To test these hypotheses, we design an individual-based model of an age-structured fish population on a two-dimensional landscape under size-selective fishing. Individual fish reproduces and survives, and moves between habitats according to age-specific habitat preference and density-dependent habitat selection.</p> <p>3. Population spatial variability elevates with increasing age truncation and the response is stronger for populations with stronger age-specific habitat preference. On a gradient landscape, reducing carrying capacity elevates the relative importance of density-dependence in habitat selection, which weakens the response of spatial variability to age truncation for populations with strong age-specific habitat preference. On a fragmented landscape, both populations with strong and weak age-specific habitat preferences are restricted at local optimal habitats, and reducing carrying capacity weakens the responses of spatial variability to age truncation for both populations.</p> <p>4. Synthesis and applications. We demonstrate that to track and predict the changes in population spatial variability under exploitation, it is essential to consider the interactive effects of age-specific habitat preference, carrying capacity, and landscape structure. To improve spatial management in fisheries, it is crucial to enhance empirical and theoretical developments in the methodology to quantify age-specific habitat preference of marine fish, and to understand how climatic change influences carrying capacity and landscape continuity.</p>
Route to chaos and resonant triads interaction in a truncated Rotating Nonlinear shallow–water model
<p>A five-mode Galerkin truncated rotating shallow-water model</p>
Data from: The truncated bell: an enigmatic but pervasive elevational diversity pattern in Middle American ants
Studies on elevation gradients in Panama and Costa Rica have shown that leaf-litter ants exhibit a mid-elevation peak in diversity. This diversity pattern has been observed in other groups and regions, but uncertainty remains as to just how pervasive it is and what might explain it. Here we examine the robustness of the mid-elevation peak in ant diversity across the entire Middle American corridor, from Veracruz, Mexico, to Costa Rica. We sampled 56 sites distributed throughout Middle America. All were in closed-canopy evergreen wet forest, spanning 11° latitude, from near sea level to 2600 m elevation. Ants were extracted from 100 litter samples from each site and identified to genus or species. Model selection was performed on richness and diversity variables to test if ant diversity best fits a linear model or one allowing for a mid-elevation peak. Linear models were also used to examine the relationships among diversity measures and temperature, precipitation, and seasonality. Species richness measures and diversity indices that incorporate relative abundance show a similar relationship to elevation throughout the region: a truncated bell curve with a mode near 400 m. A cubic relationship is statistically favored over quadratic or linear. Temperature is a significant correlate with diversity, but does not predict a bell-curve. Precipitation and precipitation seasonality fail to explain much of the variability, and no combination of environmental variables predicts a bell curve. Potential causes of the truncated bell curve include lowland biotic attrition, mid-point attractors, and ecotonal transitions from lowland to montane communities. Analysis of 17 subclades within ants mostly showed the same truncated curve but six clades were anomalous. Distinctive behavioral or historical features potentially explain their patterns.
Datasets for "Truncated log-concave Sampling for Convex Bodies with Reflective Hamiltonian Monte Carlo"
<p>See README.txt for instructions. </p>
A Study of Carboplatin, Pemetrexed Plus Placebo vs Carboplatin, Pemetrexed Plus 1 or 2 Truncated Courses of Demcizumab in Subjects With Non-Squamous Non-Small Cell Lung Cancer
ClinicalTrials.gov study NCT02259582. IPD Sharing: Not stated. Countries: 5. Publications: 0.
Study of Gemcitabine, Abraxane® Plus Placebo Versus Gemcitabine, Abraxane® Plus 1 or 2 Truncated Courses of Demcizumab in Subjects With 1st-Line Metastatic Pancreatic Ductal Adenocarcinoma
ClinicalTrials.gov study NCT02289898. IPD Sharing: Not stated. Countries: 6. Publications: 0.
Age-specific habitat preference, carrying capacity, and landscape structure determine the response of population spatial variability to fishing-driven age truncation
Open the record for dataset details and reuse information.
Data from: The truncated bell: an enigmatic but pervasive elevational diversity pattern in Middle American ants
Open the record for dataset details and reuse information.
Neutralization of truncated procalcitonin by antibody treatment protects vascular barrier integrity during systemic inflammation
GEO Series GSE245013. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Cistromic re-programming by truncating GATA3 mutations promotes mesenchymal transformation in vitro, but not mammary tumour formation in mice
GEO Series GSE122849. Homo sapiens. 34 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
A novel IRES identified in DMD results in a functional N-truncated dystrophin, providing a potential route to therapy for patients with 5’ mutations.
GEO Series GSE56148. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing; Other.
MAU2 and NIPBL variants in Cornelia de Lange syndrome reveal MAU2-independent loading of cohesin and uncover protective mechanisms against early truncating mutations in NIPBL
GEO Series GSE122299. Homo sapiens. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Multi-locus imprinting disturbances in a family harboring a ZFP57 truncation
GEO Series GSE149568. Homo sapiens. 6 samples. Type: Methylation profiling by genome tiling array; Methylation profiling by SNP array.
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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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.