On the generation of periodic discrete structures with identical two-point correlation.
Ontology highlight
ABSTRACT:
SUBMITTER: Fernandez M
PROVIDER: S-EPMC7655758 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Until relatively recently the immunoglobulin molecule was viewed as composed of two independent domains comprised of the variable (V) and constant (C) regions. However, recent work has established that the C region mediates allosteric changes in the V region that can influence specificity and affinity. To further explore cross-domain interrelationship in murine IgG structure we carried out solution small angle X-ray scattering (SAXS) measurements for four V region identical IgG isotypes. SAXS analysis revealed elongated Y-shaped structures in solution with significantly different, isotype-dependent domain orientations. To further explore local C region effects on the V region, the IgG? Fab crystal structure from the same family was determined to 2.45 Å resolution. The IgG? Fab crystal structure differs from a closely related previously solved IgG1 Fab revealing significant structural differences, which may account for isotype-related specificity differences in V region identical Abs. Among the four murine isotypes, IgG? was the most different in solution with regards to overall structure as well as aggregate formation in solution suggesting that the greater apparent affinity of this isotype resulted from polyvalent complexes with enhanced avidity. Our results provide additional evidence that Ig V and C domains influence each other structurally and suggest that V region structure can have significant effects on overall Ig structure.
| S-EPMC3864969 | biostudies-literature
Project description:The time-resolved analysis of periodically excited luminescence decays by the phasor method in the presence of time-gating or binning is revisited. Analytical expressions for discrete configurations of square gates are derived, and the locus of the phasors of such modified periodic single-exponential decays is compared to the canonical universal semicircle. The effects of instrument response function offset, decay truncation, and gate shape are also discussed. Finally, modified expressions for the phase and modulus lifetimes are provided for some simple cases. A discussion of a modified phasor calibration approach is presented, and an illustration of the new concepts with examples from the literature concludes this work.
| S-EPMC7990508 | biostudies-literature
Project description:ObjectivePeriodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome is the most common periodic fever syndrome in children; by definition, episodes occur every 2 to 8 weeks. However, in a subset of our patients, we noticed a higher frequency of attacks, of less than 2 weeks, which we refer to as extreme PFAPA (ePFAPA). This group consisted of patients who were extreme upon presentation of PFAPA, and those who became extreme after initiation of abortive corticosteroid treatment. We aimed to characterize demographic and clinical features of ePFAPA, including the two groups, and to compare them to patients with non-extreme PFAPA (nPFAPA).Study designThe medical records of 365 patients with PFAPA who attended Schneider Children's Medical Center of Israel from March 2014 to April 2021 were reviewed. Patients with concomitant familial Mediterranean fever were excluded. Characteristics of the ePFAPA (including subgroups) and nPFAPA groups were compared using Wilcoxon rank sum, Pearson's chi-squared, and Fisher's exact tests.ResultsForty-seven patients (12.9%) were identified as having ePFAPA. Among patients with ePFAPA, compared to patients with nPFAPA, the median (interquartile range) age at disease onset was earlier: 1.5 years (0.7-2.5) vs. 2.5 years (1.5-4.0), P < 0.001; and diagnosis was younger: 2.6 years (2.0-3.6) vs. 4.5 years (3.0-6.2), P < 0.001. A higher proportion of patients with ePFAPA than nPFAPA were treated with colchicine prophylaxis (53% vs. 19%, P < 0.001), but symptoms and signs during flares did not differ significantly between these groups. Demographic and clinical characteristics were similar between patients with ePFAPA from presentation of PFAPA (22, 47% of those with ePFAPA) and ePFAPA from after corticosteroid treatment.ConclusionAbout half the patients categorized with ePFAPA syndrome already had extreme features upon presentation. Patients with ePFAPA compared to nPFAPA presented and were diagnosed at an earlier age.
| S-EPMC10474755 | biostudies-literature
Project description:Control of periodic sequential flows of multisolutions is invaluable in a variety of technology and science applications, but it requires complex and expensive external controllers. Here, we present microfluidic systems that autonomously regulate periodic sequential flows without any user instructions or dynamic external controllers. The systems consist of astable and monostable actuators that mimic the functions of analog electronic circuits. With a constant water head pressure of the input solution acting as the sole driving force, these systems generate periodic sequential flows in a predetermined and sophisticated manner. We validate our technology with the applications that have been previously addressed only by dynamic external controllers: dynamic staining of cell nuclei and playing a touchscreen piano. Our approach provides a useful and effective alternative to dynamic external controllers.
| S-EPMC6474772 | biostudies-literature
Project description:We study the properties of almost periodic solutions for a general discrete system of plankton allelopathy with feedback controls and establish a theorem on the uniformly asymptotic stability of almost periodic solutions.
| S-EPMC3921949 | biostudies-other
Project description:In this work, it is reported for the first time the use of a network of periodic optical resonant nanopillars for sensing vapors of volatile organic components. In particular, this work evaluates the presence of methanol, ethanol, isopropanol, acetic acid, propionic acid, and toluene vapors at different working distances between the transducer and the surface of the sample in the liquid state, obtaining the sensing curve response of each one of them. In addition, it studies the thin film of liquid condensed onto the nanopillar surface, estimating their corresponding thickness value by means of numerical photonic simulations and their correlation with the corresponding vapor pressure of different specimens.
| S-EPMC7558036 | biostudies-literature
Project description:Many systems of interacting elements can be conceptualized as networks, where network nodes represent the elements and network ties represent interactions between the elements. In systems where the underlying network evolves, it is useful to determine the points in time where the network structure changes significantly as these may correspond to functional change points. We propose a method for detecting change points in correlation networks that, unlike previous change point detection methods designed for time series data, requires minimal distributional assumptions. We investigate the difficulty of change point detection near the boundaries of the time series in correlation networks and study the power of our method and competing methods through simulation. We also show the generalizable nature of the method by applying it to stock price data as well as fMRI data.
| S-EPMC4703970 | biostudies-literature
Project description:Hydroxynitrile lyases (HNLs) catalyze the cleavage of cyanohydrins to yield hydrocyanic acid (HCN) and the respective carbonyl compound and are key enzymes in the process of cyanogenesis in plants. In organic syntheses, HNLs are used as biocatalysts for the formation of enantiopure cyanohydrins. We determined the structure of the recently identified, R-selective HNL from Arabidopsis thaliana (AtHNL) at a crystallographic resolution of 2.5 Å. The structure exhibits an α/β-hydrolase fold, very similar to the homologous, but S-selective, HNL from Hevea brasiliensis (HbHNL). The similarities also extend to the active sites of these enzymes, with a Ser-His-Asp catalytic triad present in all three cases. In order to elucidate the mode of substrate binding and to understand the unexpected opposite enantioselectivity of AtHNL, complexes of the enzyme with both (R)- and (S)-mandelonitrile were modeled using molecular docking simulations. Compared to the complex of HbHNL with (S)-mandelonitrile, the calculations produced an approximate mirror image binding mode of the substrate with the phenyl rings located at very similar positions, but with the cyano groups pointing in opposite directions. A catalytic mechanism for AtHNL is proposed, in which His236 from the catalytic triad acts as a general base and the emerging negative charge on the cyano group is stabilized by main-chain amide groups and an α-helix dipole very similar to α/β-hydrolases. This mechanistic proposal is additionally supported by mutagenesis studies.
| S-EPMC3444685 | biostudies-literature
Project description:This SuperSeries is composed of the following subset Series: GSE29772: CNV analysis for Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations GSE29773: Gene Expression Data for Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations Refer to individual Series
2011-07-25 | E-GEOD-29774 | biostudies-arrayexpress
Project description:High-dimensional biological data collection across heterogeneous groups of samples has become increasingly common, creating high demand for dimensionality reduction techniques that capture underlying structure of the data. Discovering low-dimensional embeddings that describe the separation of any underlying discrete latent structure in data is an important motivation for applying these techniques since these latent classes can represent important sources of unwanted variability, such as batch effects, or interesting sources of signal such as unknown cell types. The features that define this discrete latent structure are often hard to identify in high-dimensional data. Principal component analysis (PCA) is one of the most widely used methods as an unsupervised step for dimensionality reduction. This reduction technique finds linear transformations of the data which explain total variance. When the goal is detecting discrete structure, PCA is applied with the assumption that classes will be separated in directions of maximum variance. However, PCA will fail to accurately find discrete latent structure if this assumption does not hold. Visualization techniques, such as t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP), attempt to mitigate these problems with PCA by creating a low-dimensional space where similar objects are modeled by nearby points in the low-dimensional embedding and dissimilar objects are modeled by distant points with high probability. However, since t-SNE and UMAP are computationally expensive, often a PCA reduction is done before applying them which makes it sensitive to PCAs downfalls. Also, tSNE is limited to only two or three dimensions as a visualization tool, which may not be adequate for retaining discriminatory information. The linear transformations of PCA are preferable to non-linear transformations provided by methods like t-SNE and UMAP for interpretable feature weights. Here, we propose iterative discriminant analysis (iDA), a dimensionality reduction technique designed to mitigate these limitations. iDA produces an embedding that carries discriminatory information which optimally separates latent clusters using linear transformations that permit post hoc analysis to determine features that define these latent structures.
| S-EPMC9748550 | biostudies-literature